From bac2fa921a4790787d2804967276f43c23af7495 Mon Sep 17 00:00:00 2001 From: pescobar Date: Thu, 25 Jun 2015 17:44:36 +0200 Subject: [PATCH 0001/1603] NLopt easyconfig --- .../n/NLopt/NLopt-2.4.2-goolf-1.4.10.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/n/NLopt/NLopt-2.4.2-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/n/NLopt/NLopt-2.4.2-goolf-1.4.10.eb b/easybuild/easyconfigs/n/NLopt/NLopt-2.4.2-goolf-1.4.10.eb new file mode 100644 index 0000000000..abf5bbc277 --- /dev/null +++ b/easybuild/easyconfigs/n/NLopt/NLopt-2.4.2-goolf-1.4.10.eb @@ -0,0 +1,26 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = 'ConfigureMake' + +name = 'NLopt' +version = '2.4.2' + +homepage = 'http://ab-initio.mit.edu/wiki/index.php/NLopt' +description = """ NLopt is a free/open-source library for nonlinear optimization, + providing a common interface for a number of different free optimization routines + available online as well as original implementations of various other algorithms. """ + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['http://ab-initio.mit.edu/nlopt/'] +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': ["lib/libnlopt.a", "include/nlopt.h"], + 'dirs': [""], +} + +moduleclass = 'numlib' -- GitLab From e8425f623546f2fcb3614a86a09c6602aa6ddb06 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 17 Feb 2016 17:53:38 +0100 Subject: [PATCH 0002/1603] Use Style test from framework to check easyconfigs --- test/easyconfigs/styletests.py | 70 ++++++++++++++++++++++++++++++++++ test/easyconfigs/suite.py | 4 +- 2 files changed, 72 insertions(+), 2 deletions(-) create mode 100644 test/easyconfigs/styletests.py diff --git a/test/easyconfigs/styletests.py b/test/easyconfigs/styletests.py new file mode 100644 index 0000000000..ca82ff8b0a --- /dev/null +++ b/test/easyconfigs/styletests.py @@ -0,0 +1,70 @@ +## +# Copyright 2016 Ghent University +# +# This file is part of EasyBuild, +# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en), +# with support of Ghent University (http://ugent.be/hpc), +# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en), +# the Hercules foundation (http://www.herculesstichting.be/in_English) +# and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en). +# +# http://github.com/hpcugent/easybuild +# +# EasyBuild is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation v2. +# +# EasyBuild is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with EasyBuild. If not, see . +## +""" +Style tests for easyconfig files. Uses pep8. + +@author: Ward Poelmans (Ghent University) +""" + +import glob +import sys +from unittest import TestCase, TestLoader, main +from vsc.utils import fancylogger + +from easybuild.framework.easyconfig.tools import get_paths_for +from easybuild.framework.easyconfig.style import style_conformance + +try: + import pep8 +except ImportError: + pass + + +class StyleTest(TestCase): + log = fancylogger.getLogger("StyleTest", fname=False) + + def test_style_conformance(self): + """Check the easyconfigs for style""" + if 'pep8' not in sys.modules: + print "Skipping style checks (no pep8 available)" + return + + # all available easyconfig files + easyconfigs_path = get_paths_for("easyconfigs")[0] + specs = glob.glob('%s/*/*/*.eb' % easyconfigs_path) + specs = sorted(specs) + + result = style_conformance(specs) + + self.assertEqual(result, 0, "Found code style errors (and/or warnings).") + + +def suite(): + """Return all style tests for easyconfigs.""" + return TestLoader().loadTestsFromTestCase(StyleTest) + + +if __name__ == '__main__': + main() diff --git a/test/easyconfigs/suite.py b/test/easyconfigs/suite.py index 6afbd6ffb1..43542cb1f8 100644 --- a/test/easyconfigs/suite.py +++ b/test/easyconfigs/suite.py @@ -30,7 +30,6 @@ Usage: "python -m easybuild.easyconfigs.test.suite.py" or "./easybuild/easyconfi @author: Toon Willems (Ghent University) @author: Kenneth Hoste (Ghent University) """ -import glob import os import shutil import sys @@ -41,6 +40,7 @@ from vsc.utils import fancylogger import easybuild.tools.build_log # initialize EasyBuild logging, so we disable it import test.easyconfigs.easyconfigs as e +import test.easyconfigs.styletests as s # disable all logging to significantly speed up tests fancylogger.disableDefaultHandlers() @@ -52,7 +52,7 @@ os.environ['EASYBUILD_DEPRECATED'] = '10000' os.environ['EASYBUILD_TMP_LOGDIR'] = tempfile.mkdtemp(prefix='easyconfigs_test_') # call suite() for each module and then run them all -SUITE = unittest.TestSuite([x.suite() for x in [e]]) +SUITE = unittest.TestSuite([x.suite() for x in [e, s]) # uses XMLTestRunner if possible, so we can output an XML file that can be supplied to Jenkins xml_msg = "" -- GitLab From 803a9868379be9487627c86b9de5c058b1e85ec9 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Mon, 18 Apr 2016 14:22:01 +1200 Subject: [PATCH 0003/1603] New EasyConfig for PGI 16.1 with GCC 4.9.2 --- .../p/PGI/PGI-16.1-GCC-4.9.2-2.25.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/p/PGI/PGI-16.1-GCC-4.9.2-2.25.eb diff --git a/easybuild/easyconfigs/p/PGI/PGI-16.1-GCC-4.9.2-2.25.eb b/easybuild/easyconfigs/p/PGI/PGI-16.1-GCC-4.9.2-2.25.eb new file mode 100644 index 0000000000..5972e15b28 --- /dev/null +++ b/easybuild/easyconfigs/p/PGI/PGI-16.1-GCC-4.9.2-2.25.eb @@ -0,0 +1,25 @@ +name = 'PGI' +version = '16.1' + +homepage = 'http://www.pgroup.com/' +description = "C, C++ and Fortran compilers from The Portland Group - PGI" + +toolchain = {'name': 'dummy', 'version': ''} + +sources = ['pgicdk-%(version_major)s%(version_minor)s.tar.gz'] +checksums = ['442c044b9690a84b6600cd6919480bcb'] + +gccver = '4.9.2' +binutilsver = '2.25' +versionsuffix = '-GCC-%s-%s' % (gccver, binutilsver) + +dependencies = [ + ('GCCcore', gccver), + ('binutils', binutilsver, '', ('GCCcore', gccver)), + ('numactl', '2.0.11', '', ('GCCcore', gccver)), +] + +# license file +license_file = HOME + '/licenses/pgi/license.dat' + +moduleclass = 'compiler' -- GitLab From 77829e78309a5abee41e99ae3738435badc19f77 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Tue, 19 Apr 2016 10:56:27 +1200 Subject: [PATCH 0004/1603] Look for the PGI licence file in the home directory of the installing user --- easybuild/easyconfigs/p/PGI/PGI-16.1-GCC-4.9.2-2.25.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PGI/PGI-16.1-GCC-4.9.2-2.25.eb b/easybuild/easyconfigs/p/PGI/PGI-16.1-GCC-4.9.2-2.25.eb index 5972e15b28..eedfe32fda 100644 --- a/easybuild/easyconfigs/p/PGI/PGI-16.1-GCC-4.9.2-2.25.eb +++ b/easybuild/easyconfigs/p/PGI/PGI-16.1-GCC-4.9.2-2.25.eb @@ -20,6 +20,7 @@ dependencies = [ ] # license file -license_file = HOME + '/licenses/pgi/license.dat' +import os +license_file = os.path.join(os.getenv('HOME'), "licenses", "pgi", "license.dat") moduleclass = 'compiler' -- GitLab From 564feda22e5efaa132254a5fd1f9fb1019970bd7 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Mon, 2 May 2016 16:56:03 +1200 Subject: [PATCH 0005/1603] Use HOME constant instead of env var --- easybuild/easyconfigs/p/PGI/PGI-16.1-GCC-4.9.2-2.25.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PGI/PGI-16.1-GCC-4.9.2-2.25.eb b/easybuild/easyconfigs/p/PGI/PGI-16.1-GCC-4.9.2-2.25.eb index eedfe32fda..7f076bfe4d 100644 --- a/easybuild/easyconfigs/p/PGI/PGI-16.1-GCC-4.9.2-2.25.eb +++ b/easybuild/easyconfigs/p/PGI/PGI-16.1-GCC-4.9.2-2.25.eb @@ -21,6 +21,6 @@ dependencies = [ # license file import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "pgi", "license.dat") +license_file = os.path.join(HOME, "licenses", "pgi", "license.dat") moduleclass = 'compiler' -- GitLab From 81decb13f423645cc345b6edcfae06d1de383dbc Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Tue, 17 May 2016 14:08:53 +1200 Subject: [PATCH 0006/1603] Put license_file path in canonical EB form --- easybuild/easyconfigs/p/PGI/PGI-16.1-GCC-4.9.2-2.25.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/PGI/PGI-16.1-GCC-4.9.2-2.25.eb b/easybuild/easyconfigs/p/PGI/PGI-16.1-GCC-4.9.2-2.25.eb index 7f076bfe4d..5972e15b28 100644 --- a/easybuild/easyconfigs/p/PGI/PGI-16.1-GCC-4.9.2-2.25.eb +++ b/easybuild/easyconfigs/p/PGI/PGI-16.1-GCC-4.9.2-2.25.eb @@ -20,7 +20,6 @@ dependencies = [ ] # license file -import os -license_file = os.path.join(HOME, "licenses", "pgi", "license.dat") +license_file = HOME + '/licenses/pgi/license.dat' moduleclass = 'compiler' -- GitLab From ce0a4a3b314dbdf5855dc236c3a65046359eb08f Mon Sep 17 00:00:00 2001 From: Xavier Besseron Date: Sun, 5 Jun 2016 22:58:56 +0200 Subject: [PATCH 0007/1603] add easyconfig Valgrind-3.11.0-intel-2016a.eb --- .../v/Valgrind/Valgrind-3.11.0-intel-2016a.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/v/Valgrind/Valgrind-3.11.0-intel-2016a.eb diff --git a/easybuild/easyconfigs/v/Valgrind/Valgrind-3.11.0-intel-2016a.eb b/easybuild/easyconfigs/v/Valgrind/Valgrind-3.11.0-intel-2016a.eb new file mode 100644 index 0000000000..ec140b0ac3 --- /dev/null +++ b/easybuild/easyconfigs/v/Valgrind/Valgrind-3.11.0-intel-2016a.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'Valgrind' +version = '3.11.0' + +homepage = 'http://valgrind.org/downloads/' +description = "Valgrind: Debugging and profiling tools" + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://valgrind.org/downloads/'] + +toolchain = {'name': 'intel', 'version': '2016a'} + +configopts = ' --with-mpicc="$MPICC"' + +binaries = [ + 'callgrind_annotate', 'callgrind_control', 'cg_annotate', 'cg_diff', + 'cg_merge', 'ms_print', 'valgrind', 'valgrind-listener', 'vgdb' +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in binaries] + + ['lib/valgrind/libmpiwrap-amd64-linux.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'debugger' -- GitLab From a8328c3b2e010c31888b1edcf6076d413a5cb3d4 Mon Sep 17 00:00:00 2001 From: jhein32 Date: Fri, 10 Jun 2016 15:21:38 +0200 Subject: [PATCH 0008/1603] Create NAMD-2.11-intel-2016a-mpi.eb --- .../n/NAMD/NAMD-2.11-intel-2016a-mpi.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/n/NAMD/NAMD-2.11-intel-2016a-mpi.eb diff --git a/easybuild/easyconfigs/n/NAMD/NAMD-2.11-intel-2016a-mpi.eb b/easybuild/easyconfigs/n/NAMD/NAMD-2.11-intel-2016a-mpi.eb new file mode 100644 index 0000000000..bd27d52f00 --- /dev/null +++ b/easybuild/easyconfigs/n/NAMD/NAMD-2.11-intel-2016a-mpi.eb @@ -0,0 +1,28 @@ +name = 'NAMD' +version = '2.11' +versionsuffix = '-mpi' + +homepage = 'http://www.ks.uiuc.edu/Research/namd/' +description = """NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'opt': True, 'pic': True, 'usempi': True} + +runtest = False + +parallel = 12 + +sources = ['NAMD_%(version)s_Source.tar.gz'] + +dependencies = [ + ('Tcl', '8.6.4'), + ('FFTW', '3.3.4'), +] + +charm_arch = 'mpi-linux-x86_64' + +namd_cfg_opts = " --with-tcl --tcl-prefix $EBROOTTCL " + +prebuildopts = 'echo "TCLLIB=-L\$(TCLDIR)/lib -ltcl8.6 -ldl -lpthread" >> Make.config && ' + +moduleclass = 'chem' -- GitLab From 46c9e87b624824295e678071def0de1b2f262ee3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 10 Jun 2016 18:53:26 +0200 Subject: [PATCH 0009/1603] style fixes for NAMD 2.11 easyconfig --- .../easyconfigs/n/NAMD/NAMD-2.11-intel-2016a-mpi.eb | 11 +++++------ 1 file changed, 5 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/n/NAMD/NAMD-2.11-intel-2016a-mpi.eb b/easybuild/easyconfigs/n/NAMD/NAMD-2.11-intel-2016a-mpi.eb index bd27d52f00..8e28254ee8 100644 --- a/easybuild/easyconfigs/n/NAMD/NAMD-2.11-intel-2016a-mpi.eb +++ b/easybuild/easyconfigs/n/NAMD/NAMD-2.11-intel-2016a-mpi.eb @@ -3,14 +3,11 @@ version = '2.11' versionsuffix = '-mpi' homepage = 'http://www.ks.uiuc.edu/Research/namd/' -description = """NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.""" +description = """NAMD is a parallel molecular dynamics code designed for high-performance simulation of + large biomolecular systems.""" toolchain = {'name': 'intel', 'version': '2016a'} -toolchainopts = {'opt': True, 'pic': True, 'usempi': True} - -runtest = False - -parallel = 12 +toolchainopts = {'pic': True, 'usempi': True} sources = ['NAMD_%(version)s_Source.tar.gz'] @@ -19,6 +16,8 @@ dependencies = [ ('FFTW', '3.3.4'), ] +runtest = False + charm_arch = 'mpi-linux-x86_64' namd_cfg_opts = " --with-tcl --tcl-prefix $EBROOTTCL " -- GitLab From 09c31673c23660033fdebecdcf71c35a30ca7401 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Wed, 22 Jun 2016 12:13:18 +1200 Subject: [PATCH 0010/1603] First attempt at a CGAL easyconfig --- .../CGAL-4.8.1-foss-2015a-Python-2.7.11.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/c/CGAL/CGAL-4.8.1-foss-2015a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.8.1-foss-2015a-Python-2.7.11.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.8.1-foss-2015a-Python-2.7.11.eb new file mode 100644 index 0000000000..3e83eb1dbe --- /dev/null +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.8.1-foss-2015a-Python-2.7.11.eb @@ -0,0 +1,33 @@ +name = 'CGAL' +version = '4.8.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.cgal.org/' +description = """The goal of the CGAL Open Source Project is to provide easy access to efficient + and reliable geometric algorithms in the form of a C++ library.""" + +toolchain = {'name': 'foss', 'version': '2015a'} +toolchainopts = {'strict': True} + +# note: source URL needs to be updated for a new version (checksums too)! +source_urls = ['https://github.com/%(name)s/%(namelower)s/releases/download/releases%2F%(name)s-%(version)s'] +sources = [SOURCE_TAR_XZ] +checksums = ['1cbcb3f251822766ed3d744f923c782d'] + +dependencies = [ + ('Python', '2.7.11'), + ('Boost', '1.60.0', versionsuffix), + ('MPFR', '3.1.2'), + ('Qt5', '5.6.0'), + ('libGLU', '9.0.0', '-Mesa-11.2.1'), +] + +configopts = "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " +configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT +configopts += "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT + +builddependencies = [ + ('CMake', '3.4.1'), +] + +moduleclass = 'numlib' -- GitLab From 0d54283d911a55ea99dd8e28ba9f0f105b63ab5b Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Wed, 29 Jun 2016 17:46:09 +1200 Subject: [PATCH 0011/1603] No dependency on Python; simplified CGAL without GUI for OSGEO stack --- .../CGAL-4.8.1-foss-2015a-Python-2.7.11.eb | 33 ---------------- .../c/CGAL/CGAL-4.8.1-foss-2015a.eb | 38 +++++++++++++++++++ 2 files changed, 38 insertions(+), 33 deletions(-) delete mode 100644 easybuild/easyconfigs/c/CGAL/CGAL-4.8.1-foss-2015a-Python-2.7.11.eb create mode 100644 easybuild/easyconfigs/c/CGAL/CGAL-4.8.1-foss-2015a.eb diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.8.1-foss-2015a-Python-2.7.11.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.8.1-foss-2015a-Python-2.7.11.eb deleted file mode 100644 index 3e83eb1dbe..0000000000 --- a/easybuild/easyconfigs/c/CGAL/CGAL-4.8.1-foss-2015a-Python-2.7.11.eb +++ /dev/null @@ -1,33 +0,0 @@ -name = 'CGAL' -version = '4.8.1' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'http://www.cgal.org/' -description = """The goal of the CGAL Open Source Project is to provide easy access to efficient - and reliable geometric algorithms in the form of a C++ library.""" - -toolchain = {'name': 'foss', 'version': '2015a'} -toolchainopts = {'strict': True} - -# note: source URL needs to be updated for a new version (checksums too)! -source_urls = ['https://github.com/%(name)s/%(namelower)s/releases/download/releases%2F%(name)s-%(version)s'] -sources = [SOURCE_TAR_XZ] -checksums = ['1cbcb3f251822766ed3d744f923c782d'] - -dependencies = [ - ('Python', '2.7.11'), - ('Boost', '1.60.0', versionsuffix), - ('MPFR', '3.1.2'), - ('Qt5', '5.6.0'), - ('libGLU', '9.0.0', '-Mesa-11.2.1'), -] - -configopts = "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " -configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT -configopts += "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT - -builddependencies = [ - ('CMake', '3.4.1'), -] - -moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.8.1-foss-2015a.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.8.1-foss-2015a.eb new file mode 100644 index 0000000000..f8ab683344 --- /dev/null +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.8.1-foss-2015a.eb @@ -0,0 +1,38 @@ +name = 'CGAL' +version = '4.8.1' +gmpver = '6.0.0a' + +homepage = 'http://www.cgal.org/' +description = """The goal of the CGAL Open Source Project is to provide easy access to efficient + and reliable geometric algorithms in the form of a C++ library.""" + +toolchain = {'name': 'foss', 'version': '2015a'} +toolchainopts = {'strict': True} + +# note: source URL needs to be updated for a new version (checksums too)! +source_urls = ['https://github.com/%(name)s/%(namelower)s/releases/download/releases%2F%(name)s-%(version)s'] +sources = [SOURCE_TAR_XZ] +checksums = ['1cbcb3f251822766ed3d744f923c782d'] + +dependencies = [ + ('Boost', '1.60.0'), + ('GMP', gmpver), + ('MPFR', '3.1.2', '-GMP-%s' % gmpver), +] + +configopts = "-DCMAKE_VERBOSE_MAKEFILE=ON " +configopts += "-DBoost_INCLUDE_DIR=$EBROOTBOOST/include " +configopts += "-DBoost_LIBRARY_DIRS=$EBROOTBOOST/lib " +configopts += "-DBoost_SYSTEM_LIBRARY=$EBROOTBOOST/libboost_system.%s " % SHLIB_EXT +configopts += "-DBoost_THREAD_LIBRARY=$EBROOTBOOST/libboost_thread.%s " % SHLIB_EXT +configopts += "-DMPFR_INCLUDE_DIR=$EBROOTMPFR/include " +configopts += "-DMPFR_LIBRARIES=$EBROOTMPFR/lib/libmpfr.%s " % SHLIB_EXT +configopts += "-DGMP_INCLUDE_DIR=$EBROOTGMP/include " +configopts += "-DGMP_LIBRARIES=$EBROOTGMP/lib/libgmp.%s " % SHLIB_EXT +configopts += "-DGMP_LIBRARIES_DIR=$EBROOTGMP/lib " + +builddependencies = [ + ('CMake', '3.4.1'), +] + +moduleclass = 'numlib' -- GitLab From a5b2984c569ffdebc1a7d7cb886b439631334e46 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Tue, 13 Sep 2016 11:25:38 +0200 Subject: [PATCH 0012/1603] add easyconfig MultiQC-0.7-goolf-1.7.20.eb --- .../m/MultiQC/MultiQC-0.7-goolf-1.7.20.eb | 79 +++++++++++++++++++ 1 file changed, 79 insertions(+) create mode 100644 easybuild/easyconfigs/m/MultiQC/MultiQC-0.7-goolf-1.7.20.eb diff --git a/easybuild/easyconfigs/m/MultiQC/MultiQC-0.7-goolf-1.7.20.eb b/easybuild/easyconfigs/m/MultiQC/MultiQC-0.7-goolf-1.7.20.eb new file mode 100644 index 0000000000..1d864fa9f0 --- /dev/null +++ b/easybuild/easyconfigs/m/MultiQC/MultiQC-0.7-goolf-1.7.20.eb @@ -0,0 +1,79 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'Bundle' + +name = 'MultiQC' +version = '0.7' + +homepage = 'http://multiqc.info/' +description = """Aggregate results from bioinformatics analyses across many samples into a single report""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} +toolchainopts = {'optarch': False, 'pic': False} + +parallel = 1 + +dependencies = [ + ('Python', '2.7.11'), + ('matplotlib', '1.5.1', '-Python-%(pyver)s'), + ('numpy', '1.10.1', '-Python-%(pyver)s'), +] + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' +exts_filter = ("python -c 'import %(ext_name)s'", '') + +exts_list = [ + ('six', '1.10.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), + ('pyparsing', '2.1.9', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], + }), + ('pytz', '2016.6.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pytz/'], + }), + ('cycler', '0.10.0', { + 'source_urls': ['https://pypi.python.org/packages/source/c/cycler/'], + }), + ('python-dateutil', '2.5.3', { + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], + 'modulename': 'dateutil', + }), + ('MarkupSafe', '0.23', { + 'source_urls': ['https://pypi.python.org/packages/source/m/markupsafe'], + }), + ('click', '6.6', { + 'source_urls': ['https://pypi.python.org/packages/source/c/click/'], + }), + ('PyYAML', '3.12', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyyaml'], + 'modulename': 'yaml', + }), + ('simplejson', '3.8.2', { + 'source_urls': ['https://pypi.python.org/packages/source/s/simplejson/'], + }), + ('Jinja2', '2.8', { + 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2/'], + }), + ('multiqc', version, { + #'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/m/multiqc/'], + }), +] + +modextrapaths = { + 'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages'], + 'LD_LIBRARY_PATH': ['lib/python%(pyshortver)s/site-packages'] +} + +sanity_check_paths = { + 'files': [], + #'dirs': ['lib/python%s/site-packages/pysam-%s-py%s-linux-x86_64.egg' % (pyshortver, version, pyshortver)] + 'dirs': ['.'] +} + +moduleclass = 'bio' -- GitLab From 4d84d1c074fd1ce8e38af2ffb9df37698abb7bd2 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Tue, 13 Sep 2016 11:34:56 +0200 Subject: [PATCH 0013/1603] added missing deps --- ...lotlib-1.5.1-goolf-1.7.20-Python-2.7.11.eb | 45 +++++++++++++++++++ ...numpy-1.10.1-goolf-1.7.20-Python-2.7.11.eb | 23 ++++++++++ 2 files changed, 68 insertions(+) create mode 100644 easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-goolf-1.7.20-Python-2.7.11.eb create mode 100644 easybuild/easyconfigs/n/numpy/numpy-1.10.1-goolf-1.7.20-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-goolf-1.7.20-Python-2.7.11.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-goolf-1.7.20-Python-2.7.11.eb new file mode 100644 index 0000000000..506dad104c --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-goolf-1.7.20-Python-2.7.11.eb @@ -0,0 +1,45 @@ +easyblock = 'Bundle' + +name = 'matplotlib' +version = '1.5.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://matplotlib.org' +description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of + hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python + and ipython shell, web application servers, and six graphical user interface toolkits.""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' + +dependencies = [ + ('Python', '2.7.11'), + ('freetype', '2.5.5'), + ('libpng', '1.6.18'), +] + +exts_list = [ + ('Cycler', '0.9.0', { + 'modulename': 'cycler', + 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], + 'source_tmpl': 'cycler-%(version)s.tar.gz', + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], + 'patches': ['matplotlib-1.5.1_fix-Tcl-Tk-libdir.patch'], + }), +] + +# specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module +full_sanity_check = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/n/numpy/numpy-1.10.1-goolf-1.7.20-Python-2.7.11.eb b/easybuild/easyconfigs/n/numpy/numpy-1.10.1-goolf-1.7.20-Python-2.7.11.eb new file mode 100644 index 0000000000..b4a5ec30e9 --- /dev/null +++ b/easybuild/easyconfigs/n/numpy/numpy-1.10.1-goolf-1.7.20-Python-2.7.11.eb @@ -0,0 +1,23 @@ +name = 'numpy' +version = '1.10.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.numpy.org' +description = """NumPy is the fundamental package for scientific computing with Python. It contains among other things: + a powerful N-dimensional array object, sophisticated (broadcasting) functions, tools for integrating C/C++ and Fortran + code, useful linear algebra, Fourier transform, and random number capabilities. Besides its obvious scientific uses, + NumPy can also be used as an efficient multi-dimensional container of generic data. Arbitrary data-types can be + defined. This allows NumPy to seamlessly and speedily integrate with a wide variety of databases.""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_GZ] + +#patches = ['numpy-1.8.0-mkl.patch'] + +dependencies = [ + ('Python', '2.7.11'), +] + +moduleclass = 'math' -- GitLab From 1692d120c89603830a89dac9eb2348d6d1d0f2bf Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Tue, 13 Sep 2016 11:43:45 +0200 Subject: [PATCH 0014/1603] added sanity checking --- easybuild/easyconfigs/m/MultiQC/MultiQC-0.7-goolf-1.7.20.eb | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/m/MultiQC/MultiQC-0.7-goolf-1.7.20.eb b/easybuild/easyconfigs/m/MultiQC/MultiQC-0.7-goolf-1.7.20.eb index 1d864fa9f0..7c5179be13 100644 --- a/easybuild/easyconfigs/m/MultiQC/MultiQC-0.7-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/m/MultiQC/MultiQC-0.7-goolf-1.7.20.eb @@ -71,9 +71,8 @@ modextrapaths = { } sanity_check_paths = { - 'files': [], - #'dirs': ['lib/python%s/site-packages/pysam-%s-py%s-linux-x86_64.egg' % (pyshortver, version, pyshortver)] - 'dirs': ['.'] + 'files': ['bin/multiqc'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/multiqc-%(version)s-py%(pyshortver)s.egg'] } moduleclass = 'bio' -- GitLab From ad9690f939d7cb1df29891addb2e6ab2bd943116 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Tue, 13 Sep 2016 11:57:10 +0200 Subject: [PATCH 0015/1603] added missing deps --- .../f/freetype/freetype-2.5.5-goolf-1.7.20.eb | 21 +++++++++++++++++++ .../l/libpng/libpng-1.6.18-goolf-1.7.20.eb | 19 +++++++++++++++++ 2 files changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/f/freetype/freetype-2.5.5-goolf-1.7.20.eb create mode 100644 easybuild/easyconfigs/l/libpng/libpng-1.6.18-goolf-1.7.20.eb diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.5.5-goolf-1.7.20.eb b/easybuild/easyconfigs/f/freetype/freetype-2.5.5-goolf-1.7.20.eb new file mode 100644 index 0000000000..c3aab419f3 --- /dev/null +++ b/easybuild/easyconfigs/f/freetype/freetype-2.5.5-goolf-1.7.20.eb @@ -0,0 +1,21 @@ +name = 'freetype' +version = '2.5.5' + +homepage = 'http://freetype.org' +description = """FreeType 2 is a software font engine that is designed to be small, efficient, highly customizable, and + portable while capable of producing high-quality output (glyph images). It can be used in graphics libraries, display + servers, font conversion tools, text image generation tools, and many other products as well.""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +source_urls = [GNU_SAVANNAH_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [('libpng', '1.6.18')] + +sanity_check_paths = { + 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], + 'dirs': ['include/freetype2'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.18-goolf-1.7.20.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.18-goolf-1.7.20.eb new file mode 100644 index 0000000000..a083925f91 --- /dev/null +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.18-goolf-1.7.20.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'libpng' +version = '1.6.18' + +homepage = 'http://www.libpng.org/pub/png/libpng.html' +description = "libpng is the official PNG reference library" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('zlib', '1.2.8')] + +configopts = "--with-pic" + +moduleclass = 'lib' -- GitLab From 8ade81939c72f037ae59f9f4e7f1f2d16d478740 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Wed, 14 Sep 2016 08:58:56 +0200 Subject: [PATCH 0016/1603] remove toolchainopts --- easybuild/easyconfigs/m/MultiQC/MultiQC-0.7-goolf-1.7.20.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MultiQC/MultiQC-0.7-goolf-1.7.20.eb b/easybuild/easyconfigs/m/MultiQC/MultiQC-0.7-goolf-1.7.20.eb index 7c5179be13..3c54d448e9 100644 --- a/easybuild/easyconfigs/m/MultiQC/MultiQC-0.7-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/m/MultiQC/MultiQC-0.7-goolf-1.7.20.eb @@ -12,7 +12,6 @@ homepage = 'http://multiqc.info/' description = """Aggregate results from bioinformatics analyses across many samples into a single report""" toolchain = {'name': 'goolf', 'version': '1.7.20'} -toolchainopts = {'optarch': False, 'pic': False} parallel = 1 -- GitLab From 516ee8e6c960b2723c9dbb4d86465de772ce7c52 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Wed, 14 Sep 2016 09:00:14 +0200 Subject: [PATCH 0017/1603] remove numpy dep --- easybuild/easyconfigs/m/MultiQC/MultiQC-0.7-goolf-1.7.20.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MultiQC/MultiQC-0.7-goolf-1.7.20.eb b/easybuild/easyconfigs/m/MultiQC/MultiQC-0.7-goolf-1.7.20.eb index 3c54d448e9..f2c87048d9 100644 --- a/easybuild/easyconfigs/m/MultiQC/MultiQC-0.7-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/m/MultiQC/MultiQC-0.7-goolf-1.7.20.eb @@ -18,7 +18,7 @@ parallel = 1 dependencies = [ ('Python', '2.7.11'), ('matplotlib', '1.5.1', '-Python-%(pyver)s'), - ('numpy', '1.10.1', '-Python-%(pyver)s'), + # numpy dependency provided by python module ] # this is a bundle of Python packages -- GitLab From 7680debb5c3e01b70ca6fe8e1fd8bfc2572248c8 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Wed, 14 Sep 2016 09:00:43 +0200 Subject: [PATCH 0018/1603] added version suffix --- easybuild/easyconfigs/m/MultiQC/MultiQC-0.7-goolf-1.7.20.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/m/MultiQC/MultiQC-0.7-goolf-1.7.20.eb b/easybuild/easyconfigs/m/MultiQC/MultiQC-0.7-goolf-1.7.20.eb index f2c87048d9..14c2e7f378 100644 --- a/easybuild/easyconfigs/m/MultiQC/MultiQC-0.7-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/m/MultiQC/MultiQC-0.7-goolf-1.7.20.eb @@ -7,6 +7,7 @@ easyblock = 'Bundle' name = 'MultiQC' version = '0.7' +versionsuffix = '-Python-%(pyver)s' homepage = 'http://multiqc.info/' description = """Aggregate results from bioinformatics analyses across many samples into a single report""" -- GitLab From 264450f3c354dc0d322b16b8e4eaa1348b3288ce Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Wed, 14 Sep 2016 09:23:45 +0200 Subject: [PATCH 0019/1603] file renamed to add suffix --- ...-goolf-1.7.20.eb => MultiQC-0.7-goolf-1.7.20-Python-2.7.11.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/m/MultiQC/{MultiQC-0.7-goolf-1.7.20.eb => MultiQC-0.7-goolf-1.7.20-Python-2.7.11.eb} (100%) diff --git a/easybuild/easyconfigs/m/MultiQC/MultiQC-0.7-goolf-1.7.20.eb b/easybuild/easyconfigs/m/MultiQC/MultiQC-0.7-goolf-1.7.20-Python-2.7.11.eb similarity index 100% rename from easybuild/easyconfigs/m/MultiQC/MultiQC-0.7-goolf-1.7.20.eb rename to easybuild/easyconfigs/m/MultiQC/MultiQC-0.7-goolf-1.7.20-Python-2.7.11.eb -- GitLab From 7c1c632123eea66191c8bb8a4a75218f8621dadf Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Wed, 14 Sep 2016 15:24:30 +0200 Subject: [PATCH 0020/1603] updated dependencies --- .../f/freetype/freetype-2.6.2-goolf-1.7.20.eb | 21 +++++++++++++++++++ .../l/libpng/libpng-1.6.21-goolf-1.7.20.eb | 19 +++++++++++++++++ ...lotlib-1.5.1-goolf-1.7.20-Python-2.7.11.eb | 4 ++-- 3 files changed, 42 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/f/freetype/freetype-2.6.2-goolf-1.7.20.eb create mode 100644 easybuild/easyconfigs/l/libpng/libpng-1.6.21-goolf-1.7.20.eb diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.6.2-goolf-1.7.20.eb b/easybuild/easyconfigs/f/freetype/freetype-2.6.2-goolf-1.7.20.eb new file mode 100644 index 0000000000..76cd412cf3 --- /dev/null +++ b/easybuild/easyconfigs/f/freetype/freetype-2.6.2-goolf-1.7.20.eb @@ -0,0 +1,21 @@ +name = 'freetype' +version = '2.6.2' + +homepage = 'http://freetype.org' +description = """FreeType 2 is a software font engine that is designed to be small, efficient, highly customizable, and + portable while capable of producing high-quality output (glyph images). It can be used in graphics libraries, display + servers, font conversion tools, text image generation tools, and many other products as well.""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +source_urls = [GNU_SAVANNAH_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [('libpng', '1.6.21')] + +sanity_check_paths = { + 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], + 'dirs': ['include/freetype2'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.21-goolf-1.7.20.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.21-goolf-1.7.20.eb new file mode 100644 index 0000000000..cb4fbebab2 --- /dev/null +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.21-goolf-1.7.20.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'libpng' +version = '1.6.21' + +homepage = 'http://www.libpng.org/pub/png/libpng.html' +description = "libpng is the official PNG reference library" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('zlib', '1.2.8')] + +configopts = "--with-pic" + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-goolf-1.7.20-Python-2.7.11.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-goolf-1.7.20-Python-2.7.11.eb index 506dad104c..697a58300b 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-goolf-1.7.20-Python-2.7.11.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-goolf-1.7.20-Python-2.7.11.eb @@ -16,8 +16,8 @@ exts_defaultclass = 'PythonPackage' dependencies = [ ('Python', '2.7.11'), - ('freetype', '2.5.5'), - ('libpng', '1.6.18'), + ('freetype', '2.6.2'), + ('libpng', '1.6.21'), ] exts_list = [ -- GitLab From 19ece4eea21398f809056a138dbb6bc14abc5eca Mon Sep 17 00:00:00 2001 From: Fokke Dijkstra Date: Tue, 11 Oct 2016 15:07:45 +0200 Subject: [PATCH 0021/1603] Caffe rc3 built using the foss 2016a toolchain. --- ...6a-CUDA-7.5.18-Python-2.7.11-foss-2016a.eb | 58 +++++++++++++++++++ 1 file changed, 58 insertions(+) create mode 100644 easybuild/easyconfigs/c/Caffe/Caffe-rc3-foss-2016a-CUDA-7.5.18-Python-2.7.11-foss-2016a.eb diff --git a/easybuild/easyconfigs/c/Caffe/Caffe-rc3-foss-2016a-CUDA-7.5.18-Python-2.7.11-foss-2016a.eb b/easybuild/easyconfigs/c/Caffe/Caffe-rc3-foss-2016a-CUDA-7.5.18-Python-2.7.11-foss-2016a.eb new file mode 100644 index 0000000000..9a164bb75c --- /dev/null +++ b/easybuild/easyconfigs/c/Caffe/Caffe-rc3-foss-2016a-CUDA-7.5.18-Python-2.7.11-foss-2016a.eb @@ -0,0 +1,58 @@ +easyblock = 'CMakeMake' + +name = 'Caffe' +version = 'rc3' + +cudaversion = '7.5.18' +versionsuffix = '-CUDA-%s-Python-%%(pyver)s' % cudaversion + +homepage = 'https://github.com/BVLC/caffe' +description = """ +Caffe is a deep learning framework made with expression, speed, +and modularity in mind. It is developed by the Berkeley Vision +and Learning Center (BVLC) and community contributors. +""" +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': False, 'pic': True} + +sources = ['%(version)s.tar.gz'] +source_urls = ['https://github.com/BVLC/caffe/archive/'] + +builddependencies = [ + ('CMake', '3.4.3'), +] + +protobuf_ver = '3.0.2' + +dependencies = [ + ('glog', '0.3.4'), + ('gflags', '2.1.2'), + ('OpenCV', '3.1.0'), + ('CUDA', cudaversion, '', True), + ('cuDNN', '4.0', '', True), + ('LMDB', '0.9.18'), + ('LevelDB', '1.18'), + ('snappy', '1.1.3'), + ('protobuf', protobuf_ver), + ('protobuf-python', protobuf_ver, '-Python-%(pyver)s'), + ('HDF5', '1.8.16', '-serial'), + ('Boost', '1.61.0', '-Python-%(pyver)s'), + ('Python', '2.7.11'), + ('scikit-image', '0.12.3', '-Python-%(pyver)s') +] + +configopts = '-DBLAS=open' + +modextrapaths = {'PYTHONPATH': ['python'] } + +sanity_check_paths = { + 'files': ['bin/caffe'] + + ['lib/%s' % x for x in ['libcaffe.so','libproto.a']] + + ['python/caffe/_caffe.so'] + + ['include/caffe/proto/caffe.pb.h'], + 'dirs': [], +} + +sanity_check_commands = [('python', "-c 'import caffe'")] + +moduleclass = 'devel' -- GitLab From 0ea09aa90e2af9b75352003f330c838a7a52c1fc Mon Sep 17 00:00:00 2001 From: Fokke Dijkstra Date: Tue, 11 Oct 2016 15:23:33 +0200 Subject: [PATCH 0022/1603] Fixed filename, which accidentally included foss-2016a twice. --- ...2016a.eb => Caffe-rc3-foss-2016a-CUDA-7.5.18-Python-2.7.11.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/c/Caffe/{Caffe-rc3-foss-2016a-CUDA-7.5.18-Python-2.7.11-foss-2016a.eb => Caffe-rc3-foss-2016a-CUDA-7.5.18-Python-2.7.11.eb} (100%) diff --git a/easybuild/easyconfigs/c/Caffe/Caffe-rc3-foss-2016a-CUDA-7.5.18-Python-2.7.11-foss-2016a.eb b/easybuild/easyconfigs/c/Caffe/Caffe-rc3-foss-2016a-CUDA-7.5.18-Python-2.7.11.eb similarity index 100% rename from easybuild/easyconfigs/c/Caffe/Caffe-rc3-foss-2016a-CUDA-7.5.18-Python-2.7.11-foss-2016a.eb rename to easybuild/easyconfigs/c/Caffe/Caffe-rc3-foss-2016a-CUDA-7.5.18-Python-2.7.11.eb -- GitLab From 83b5973dbc3450bf8155a6c68f734fa3ddbcb7fb Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 30 Nov 2016 16:31:35 +0100 Subject: [PATCH 0023/1603] Update to use framework style tests --- test/easyconfigs/styletests.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/test/easyconfigs/styletests.py b/test/easyconfigs/styletests.py index ca82ff8b0a..c8c17769f4 100644 --- a/test/easyconfigs/styletests.py +++ b/test/easyconfigs/styletests.py @@ -34,7 +34,7 @@ from unittest import TestCase, TestLoader, main from vsc.utils import fancylogger from easybuild.framework.easyconfig.tools import get_paths_for -from easybuild.framework.easyconfig.style import style_conformance +from easybuild.framework.easyconfig.style import check_easyconfigs_style try: import pep8 @@ -56,7 +56,7 @@ class StyleTest(TestCase): specs = glob.glob('%s/*/*/*.eb' % easyconfigs_path) specs = sorted(specs) - result = style_conformance(specs) + result = check_easyconfigs_style(specs) self.assertEqual(result, 0, "Found code style errors (and/or warnings).") -- GitLab From 7867bfe87d684124c7752a50c7b7588ef5b834f4 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 30 Nov 2016 16:46:24 +0100 Subject: [PATCH 0024/1603] Fix typo --- test/easyconfigs/suite.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test/easyconfigs/suite.py b/test/easyconfigs/suite.py index 921df252ae..56d7f05b41 100644 --- a/test/easyconfigs/suite.py +++ b/test/easyconfigs/suite.py @@ -52,7 +52,7 @@ os.environ['EASYBUILD_DEPRECATED'] = '10000' os.environ['EASYBUILD_TMP_LOGDIR'] = tempfile.mkdtemp(prefix='easyconfigs_test_') # call suite() for each module and then run them all -SUITE = unittest.TestSuite([x.suite() for x in [e, s]) +SUITE = unittest.TestSuite([x.suite() for x in [e, s]]) # uses XMLTestRunner if possible, so we can output an XML file that can be supplied to Jenkins xml_msg = "" -- GitLab From eb68480a8ce0e2c922be2966a61b0f0db76453fd Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 30 Nov 2016 16:56:47 +0100 Subject: [PATCH 0025/1603] Install pep8 in travis --- .travis.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.travis.yml b/.travis.yml index 13ca5c0612..4a9b0a0109 100644 --- a/.travis.yml +++ b/.travis.yml @@ -24,7 +24,7 @@ install: # pydot (dep for python-graph-dot) 1.2.0 and more recent doesn't work with Python 2.6 - if [ "x$TRAVIS_PYTHON_VERSION" == 'x2.6' ]; then pip install pydot==1.1.0; else pip install pydot; fi # required for test_dep_graph - - pip install python-graph-core python-graph-dot + - pip install pep8 python-graph-core python-graph-dot # install easybuild-framework/easybuild-easyblocks (and dependencies) # use 'develop' branch of framework/easyblocks, except when testing 'master' - if [ "x$TRAVIS_BRANCH" = 'xmaster' ]; then BRANCH=master; else BRANCH=develop; fi -- GitLab From f523bc200ebdb8d1f30cd81ee0f7a37f8c339c3f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 30 Nov 2016 19:13:33 +0100 Subject: [PATCH 0026/1603] include count of easyconfigs that fail style check in error message --- test/easyconfigs/styletests.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test/easyconfigs/styletests.py b/test/easyconfigs/styletests.py index c8c17769f4..2ea259071e 100644 --- a/test/easyconfigs/styletests.py +++ b/test/easyconfigs/styletests.py @@ -58,7 +58,7 @@ class StyleTest(TestCase): result = check_easyconfigs_style(specs) - self.assertEqual(result, 0, "Found code style errors (and/or warnings).") + self.assertEqual(result, 0, "Found code style errors (and/or warnings): %s" % result) def suite(): -- GitLab From 95a8a8ebeb6e358b8ce4ce24a8e6903e5f2421d7 Mon Sep 17 00:00:00 2001 From: edo Date: Thu, 22 Dec 2016 12:58:28 +0100 Subject: [PATCH 0027/1603] adding easyconfigs: libpciaccess-0.13.4-foss-2016a.eb --- .../l/libpciaccess/libpciaccess-0.13.4-foss-2016a.eb | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-foss-2016a.eb b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-foss-2016a.eb index c39482e40c..0baaea5ccf 100644 --- a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-foss-2016a.eb @@ -6,7 +6,7 @@ version = '0.13.4' homepage = 'http://cgit.freedesktop.org/xorg/lib/libpciaccess/' description = """Generic PCI access library.""" -source_urls = ['http://cgit.freedesktop.org/xorg/lib/libpciaccess/snapshot'] +source_urls = ['https://www.x.org/releases/individual/lib/'] sources = [SOURCE_TAR_GZ] toolchain = {'name': 'foss', 'version': '2016a'} @@ -16,8 +16,6 @@ builddependencies = [ ('xorg-macros', '1.19.0'), ] -preconfigopts = "env ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " - sanity_check_paths = { 'files': ['include/pciaccess.h', 'lib/libpciaccess.a'], 'dirs': ['lib/pkgconfig'], -- GitLab From 175e23dc49bf0d75743200410f8d726937f306ad Mon Sep 17 00:00:00 2001 From: edo Date: Tue, 10 Jan 2017 17:27:23 +0100 Subject: [PATCH 0028/1603] adding easyconfigs: OpenFOAM-4.0-foss-2016b.eb --- .../o/OpenFOAM/OpenFOAM-4.0-foss-2016b.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.0-foss-2016b.eb diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.0-foss-2016b.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.0-foss-2016b.eb new file mode 100644 index 0000000000..bf8451bef3 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.0-foss-2016b.eb @@ -0,0 +1,38 @@ +name = 'OpenFOAM' +version = '4.0' + +homepage = 'http://www.openfoam.com/' +description = """OpenFOAM is a free, open source CFD software package. + OpenFOAM has an extensive range of features to solve anything from complex fluid flows + involving chemical reactions, turbulence and heat transfer, + to solid dynamics and electromagnetics.""" + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'cstd': 'c++11'} + +source_urls = ['https://github.com/OpenFOAM/OpenFOAM-%(version_major)s.x/archive'] +sources = ['version-%(version)s.tar.gz'] + +checksums = ['294b520811aae87241f3a78423f05952'] + +patches = ['OpenFOAM-%(version)s-cleanup.patch'] + +dependencies = [ + ('libreadline', '6.3'), + ('ncurses', '6.0'), + # OpenFOAM requires 64 bit METIS using 32 bit indexes (array indexes) + ('METIS', '5.1.0'), + #('METIS', '5.1.0', '-32bitIDX'), + ('SCOTCH', '6.0.4'), + #('Boost', '1.61.0'), + ('CGAL', '4.8.1'), + ('ParaView', '5.1.2', '-mpi'), +] + +builddependencies = [ + ('Bison', '3.0.4'), + ('CMake', '3.6.1'), + ('flex', '2.6.0'), +] + +moduleclass = 'cae' -- GitLab From f45bd6199b3798c3e71822f0dd8a39f9fc37bcc9 Mon Sep 17 00:00:00 2001 From: edo Date: Tue, 10 Jan 2017 17:41:04 +0100 Subject: [PATCH 0029/1603] Missing dep. --- .../c/CGAL/CGAL-4.8.1-foss-2016b.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/c/CGAL/CGAL-4.8.1-foss-2016b.eb diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.8.1-foss-2016b.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.8.1-foss-2016b.eb new file mode 100644 index 0000000000..20c45dda38 --- /dev/null +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.8.1-foss-2016b.eb @@ -0,0 +1,34 @@ +name = 'CGAL' +version = '4.8.1' + +homepage = 'http://www.cgal.org/' +description = """The goal of the CGAL Open Source Project is to provide easy access to efficient + and reliable geometric algorithms in the form of a C++ library.""" + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'strict': True} + +source_urls = ['https://github.com/CGAL/cgal/releases/download/releases%2FCGAL-%(version)s'] +sources = [SOURCE_TAR_XZ] + +dependencies = [ + ('zlib', '1.2.8'), + ('Boost', '1.61.0'), + ('MPFR', '3.1.4'), + ('GMP', '6.1.1'), + ('libGLU', '9.0.0'), + ('Qt5', '5.7.0'), +] + +builddependencies = [ + ('CMake', '3.6.1'), + ('Eigen', '3.2.9'), +] + +configopts = "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " +configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT +configopts += "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT +configopts += "-DWITH_ZLIB=ON -DWITH_MPFR=ON -DWITH_OpenGL=ON -DWITH_Eigen3=ON " +configopts += "-DWITH_GMPXX=ON -DWITH_LAPACK=ON -DWITH_BLAS=ON " + +moduleclass = 'numlib' -- GitLab From ffd9e45bc0efcbb849de538cfec749b3bc9979c1 Mon Sep 17 00:00:00 2001 From: edo Date: Tue, 10 Jan 2017 17:50:57 +0100 Subject: [PATCH 0030/1603] Missing dep. --- .../m/MPFR/MPFR-3.1.4-foss-2016b.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/m/MPFR/MPFR-3.1.4-foss-2016b.eb diff --git a/easybuild/easyconfigs/m/MPFR/MPFR-3.1.4-foss-2016b.eb b/easybuild/easyconfigs/m/MPFR/MPFR-3.1.4-foss-2016b.eb new file mode 100644 index 0000000000..d0abf27110 --- /dev/null +++ b/easybuild/easyconfigs/m/MPFR/MPFR-3.1.4-foss-2016b.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'MPFR' +version = '3.1.4' + +homepage = 'http://www.mpfr.org' +description = """The MPFR library is a C library for multiple-precision + floating-point computations with correct rounding.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['http://www.mpfr.org/mpfr-%(version)s/'] +sources = [SOURCELOWER_TAR_BZ2] + +patches = ['MPFR_ictce_remove-deprecated-mp.patch'] + +dependencies = [('GMP', '6.1.1')] + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libmpfr.%s' % SHLIB_EXT, 'include/mpfr.h'], + 'dirs': [] +} + +moduleclass = 'math' -- GitLab From 8ecbcdc8d31f3058a3dca8daa4122933479d7696 Mon Sep 17 00:00:00 2001 From: edo Date: Tue, 10 Jan 2017 17:53:02 +0100 Subject: [PATCH 0031/1603] Missing dep. --- .../easyconfigs/q/Qt5/Qt5-5.7.0-foss-2016b.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/q/Qt5/Qt5-5.7.0-foss-2016b.eb diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.7.0-foss-2016b.eb b/easybuild/easyconfigs/q/Qt5/Qt5-5.7.0-foss-2016b.eb new file mode 100644 index 0000000000..66c30f53b8 --- /dev/null +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.7.0-foss-2016b.eb @@ -0,0 +1,33 @@ +easyblock = 'EB_Qt' + +name = 'Qt5' +version = '5.7.0' + +homepage = 'http://qt.io/' +description = "Qt is a comprehensive cross-platform C++ application framework." + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = [ + 'http://download.qt.io/official_releases/qt/%(version_major_minor)s/%(version)s/single/', + 'http://download.qt.io/archive/qt/%(version_major_minor)s/%(version)s/single/' +] +sources = ['qt-everywhere-opensource-src-%(version)s.tar.xz'] + +patches = ['%(name)s-%(version)s-workaround-icpc-bug.patch'] + +builddependencies = [ + ('pkg-config', '0.29.1'), +] + +# qtgamepad needs recent kernel/libevdev (fails on RHEL 6.x) +configopts = '-skip qtgamepad' + +dependencies = [ + ('GLib', '2.49.5'), + ('libpng', '1.6.24'), + ('X11', '20160819'), + ('libGLU', '9.0.0'), +] + +moduleclass = 'devel' -- GitLab From a1158ee3b38aaa61221ad610324a0b35a60831c1 Mon Sep 17 00:00:00 2001 From: edo Date: Tue, 10 Jan 2017 17:54:24 +0100 Subject: [PATCH 0032/1603] Missing dep. --- .../easyconfigs/e/Eigen/Eigen-3.2.9-foss-2016b.eb | 13 +++++++++++++ 1 file changed, 13 insertions(+) create mode 100644 easybuild/easyconfigs/e/Eigen/Eigen-3.2.9-foss-2016b.eb diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.9-foss-2016b.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.9-foss-2016b.eb new file mode 100644 index 0000000000..2e997dc434 --- /dev/null +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.9-foss-2016b.eb @@ -0,0 +1,13 @@ +name = 'Eigen' +version = '3.2.9' + +homepage = 'http://eigen.tuxfamily.org/index.php?title=Main_Page' +description = """Eigen is a C++ template library for linear algebra: + matrices, vectors, numerical solvers, and related algorithms.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['http://bitbucket.org/%(namelower)s/%(namelower)s/get'] +sources = ['%(version)s.tar.bz2'] + +moduleclass = 'math' -- GitLab From 2a44ed6074b21315d39c1617b7fb511b91674c8a Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Fri, 13 Jan 2017 09:52:39 +1300 Subject: [PATCH 0033/1603] EasyConfigs for Perl 5.22.0 with the foss-2015a toolchain --- .../p/Perl/Perl-5.22.0-foss-2015a-mt.eb | 904 ++++++++++++++++++ .../p/Perl/Perl-5.22.0-foss-2015a.eb | 903 +++++++++++++++++ 2 files changed, 1807 insertions(+) create mode 100644 easybuild/easyconfigs/p/Perl/Perl-5.22.0-foss-2015a-mt.eb create mode 100644 easybuild/easyconfigs/p/Perl/Perl-5.22.0-foss-2015a.eb diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.22.0-foss-2015a-mt.eb b/easybuild/easyconfigs/p/Perl/Perl-5.22.0-foss-2015a-mt.eb new file mode 100644 index 0000000000..43dbd48785 --- /dev/null +++ b/easybuild/easyconfigs/p/Perl/Perl-5.22.0-foss-2015a-mt.eb @@ -0,0 +1,904 @@ +name = 'Perl' +version = '5.22.0' +use_perl_threads = True +versionsuffix = '-mt' + +homepage = 'http://www.perl.org/' +description = """Larry Wall's Practical Extraction and Report Language""" + +toolchain = {'name': 'foss', 'version': '2015a'} +toolchainopts = {'optarch': True, 'pic': True} + +dependencies = [ + ('DB', '6.0.30'), # for DB_File module + ('SQLite', '3.8.9'), # for DBD::SQLite module + ('expat', '2.1.0'), # for XML::Parser I think + ('libxml2', '2.9.2'), # for XML::LibXML + ] + +#builddependencies = [('SAMtools', '0.1.20')] # NOT A LATER VERSION. For Bio::DB::Sam to static link to. + +source_urls = ['http://www.cpan.org/src/5.0'] +sources = [SOURCELOWER_TAR_GZ] +#runtest = 'test' + +exts_list = [ + ('Module::Build', '0.4210', { # std module but recent BioPerl needs a recent version for some reason + 'source_tmpl': 'Module-Build-0.4210.tar.gz', + 'source_urls': ['http://www.cpan.org/modules/by-module/Module/LEONT/'], + }), + ('ExtUtils::MakeMaker', '7.04', { + 'source_tmpl': 'ExtUtils-MakeMaker-7.04.tar.gz', + 'source_urls': ['http://www.cpan.org/modules/by-module/ExtUtils/BINGOS/'], + }), + ('local::lib', '2.000011', { + 'source_tmpl': 'local-lib-2.000011.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/E/ET/ETHER/'], + }), + ('IO::String', '1.08', { + 'source_tmpl': 'IO-String-1.08.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS/'], + }), + ('Data::Stag', '0.14', { + 'source_tmpl': 'Data-Stag-0.14.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/C/CM/CMUNGALL/'], + }), + ('DB_File', '1.835', { + 'source_urls': ['http://www.cpan.org/modules/by-module/DB_File/PMQS/'], + }), + ('DBI', '1.633', { + 'source_urls': ['http://www.cpan.org/modules/by-module/DBI/TIMB/'], + }), + ('Sub::Uplevel', '0.25', { + 'source_tmpl': 'Sub-Uplevel-0.25.tar.gz', + 'source_urls': ['http://www.cpan.org/modules/by-module/Sub/DAGOLDEN/'], + }), + ('Tree::DAG_Node', '1.26', { + 'source_tmpl': 'Tree-DAG_Node-1.26.tgz', + 'source_urls': ['http://www.cpan.org/modules/by-module/Tree/RSAVAGE/'], + }), + ('Try::Tiny', '0.22', { + 'source_tmpl': 'Try-Tiny-0.22.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/D/DO/DOY/'], + }), + ('Devel::StackTrace', '2.00', { + 'source_tmpl': 'Devel-StackTrace-2.00.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DR/DROLSKY/'], + }), + ('Class::Data::Inheritable', '0.08', { + 'source_tmpl': 'Class-Data-Inheritable-0.08.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/T/TM/TMTM/'], + }), + ('Exception::Class', '1.39', { + 'source_tmpl': 'Exception-Class-1.39.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DR/DROLSKY/'], + }), + ('Test::Fatal', '0.014', { + 'source_tmpl': 'Test-Fatal-0.014.tar.gz', + 'source_urls': ['http://www.cpan.org/modules/by-module/Test/RJBS/'], + }), + ('Test::NoWarnings', '1.04', { + 'source_tmpl': 'Test-NoWarnings-1.04.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AD/ADAMK/'], + }), + ('Test::Deep', '0.117', { + 'source_tmpl': 'Test-Deep-0.117.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS/'], + }), + ('Algorithm::Diff', '1.15', { + 'source_tmpl': 'Algorithm-Diff-1.15.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/N/NE/NEDKONZ/'], + }), + ('Text::Diff', '1.41', { + 'source_tmpl': 'Text-Diff-1.41.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/O/OV/OVID/'], + }), + ('Test::Differences', '0.61', { + 'source_tmpl': 'Test-Differences-0.61.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/O/OV/OVID/'], + }), + ('Test::Exception', '0.32', { + 'source_tmpl': 'Test-Exception-0.32.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AD/ADIE/'], + }), + ('Test::Warn', '0.30', { + 'source_tmpl': 'Test-Warn-0.30.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/C/CH/CHORNY/'], + }), + ('Test::Requires', '0.08', { + 'source_tmpl': 'Test-Requires-0.08.tar.gz', + 'source_urls': ['http://www.cpan.org/modules/by-module/Test/TOKUHIROM/'], + }), + ('Test::Tester', '0.109', { + 'source_tmpl': 'Test-Tester-0.109.tar.gz', + 'source_urls': ['http://www.cpan.org/modules/by-module/Test/FDALY/'], + }), + ('File::Slurp::Tiny', '0.003', { + 'source_tmpl': 'File-Slurp-Tiny-0.003.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('Params::Util', '1.07', { + 'source_tmpl': 'Params-Util-1.07.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AD/ADAMK/'], + }), + ('Sub::Install', '0.928', { + 'source_tmpl': 'Sub-Install-0.928.tar.gz', + 'source_urls': ['http://www.cpan.org/modules/by-module/Sub/RJBS/'], + }), + ('Data::OptList', '0.109', { + 'source_tmpl': 'Data-OptList-0.109.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS/'], + }), + ('Sub::Exporter', '0.987', { + 'source_tmpl': 'Sub-Exporter-0.987.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS/'], + }), + ('Capture::Tiny', '0.30', { + 'source_tmpl': 'Capture-Tiny-0.30.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN/'], + }), + ('Test::Output', '1.03', { + 'source_tmpl': 'Test-Output-1.03.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/B/BD/BDFOY/'], + }), + ('Module::Runtime', '0.014', { + 'source_tmpl': 'Module-Runtime-0.014.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/Z/ZE/ZEFRAM/'], + }), + ('Module::Implementation', '0.09', { + 'source_tmpl': 'Module-Implementation-0.09.tar.gz', + 'source_urls': ['http://www.cpan.org/modules/by-module/Module/DROLSKY/'], + }), + ('List::MoreUtils', '0.413', { + 'source_tmpl': 'List-MoreUtils-0.413.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RE/REHSACK/'], + }), + ('Package::DeprecationManager', '0.14', { + 'source_tmpl': 'Package-DeprecationManager-0.14.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DR/DROLSKY/'], + }), + ('Dist::CheckConflicts', '0.11', { + 'source_tmpl': 'Dist-CheckConflicts-0.11.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DO/DOY/'], + }), + ('Package::Stash', '0.37', { + 'source_tmpl': 'Package-Stash-0.37.tar.gz', + 'source_urls': ['http://www.cpan.org/modules/by-module/Package/DOY/'], + }), + ('Class::Load', '0.23', { + 'source_tmpl': 'Class-Load-0.23.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/E/ET/ETHER/'], + }), + ('TAP::Harness::Env', '3.35', { + 'source_tmpl': 'Test-Harness-3.35.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/L/LE/LEONT/'], + }), + ('ExtUtils::Helpers', '0.022', { + 'source_tmpl': 'ExtUtils-Helpers-0.022.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('ExtUtils::Config', '0.008', { + 'source_tmpl': 'ExtUtils-Config-0.008.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('ExtUtils::InstallPaths', '0.011', { + 'source_tmpl': 'ExtUtils-InstallPaths-0.011.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('Module::Build::Tiny', '0.039', { + 'source_tmpl': 'Module-Build-Tiny-0.039.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/L/LE/LEONT/'], + }), + ('MRO::Compat', '0.12', { + 'source_tmpl': 'MRO-Compat-0.12.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/B/BO/BOBTFISH/'], + }), + ('Sub::Name', '0.05', { + 'source_tmpl': 'Sub-Name-0.05.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/F/FL/FLORA/'], + }), + ('Eval::Closure', '0.13', { + 'source_tmpl': 'Eval-Closure-0.13.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DO/DOY/'], + }), + ('Sub::Exporter::Progressive', '0.001011', { + 'source_tmpl': 'Sub-Exporter-Progressive-0.001011.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/F/FR/FREW/'], + }), + ('Devel::GlobalDestruction', '0.13', { + 'source_tmpl': 'Devel-GlobalDestruction-0.13.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/H/HA/HAARG/'], + }), + ('boolean', '0.45', { + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/I/IN/INGY/'], + }), + ('Tie::IxHash', '1.23', { + 'source_tmpl': 'Tie-IxHash-1.23.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/C/CH/CHORNY/'], + }), + ('Moose', '2.1405', { + 'source_urls': ['http://www.cpan.org/modules/by-module/MooseX/ETHER/'], + }), + ('Package::Stash::XS', '0.28', { + 'source_tmpl': 'Package-Stash-XS-0.28.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DO/DOY/'], + }), + ('Params::Validate', '1.20', { + 'source_tmpl': 'Params-Validate-1.20.tar.gz', + 'source_urls': ['http://www.cpan.org/modules/by-module/Params/DROLSKY/'], + }), + ('Class::Load::XS', '0.09', { + 'source_tmpl': 'Class-Load-XS-0.09.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/E/ET/ETHER/'], + }), + + # For uoa00001, Zendesk #9076 + ('Math::CDF', '0.1', { + 'source_tmpl': 'Math-CDF-0.1.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/C/CA/CALLAHAN/'], + }), + + ('DateTime::Locale', '0.46', { + 'source_tmpl': 'DateTime-Locale-0.46.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DR/DROLSKY/'], + }), + ('Class::Singleton', '1.4', { + 'source_tmpl': 'Class-Singleton-1.4.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AB/ABW/'], + }), + ('DateTime::TimeZone', '1.92', { + 'source_tmpl': 'DateTime-TimeZone-1.92.tar.gz', + 'source_urls': ['http://www.cpan.org/modules/by-module/DateTime/DROLSKY/'], + }), + ('Test::Warnings', '0.021', { + 'source_tmpl': 'Test-Warnings-0.021.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/E/ET/ETHER/'], + }), + ('Data::Types', '0.09', { + 'source_tmpl': 'Data-Types-0.09.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DW/DWHEELER/'], + }), + ('Exporter::Tiny', '0.042', { + 'source_tmpl': 'Exporter-Tiny-0.042.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/T/TO/TOBYINK/'], + }), + + ('List::AllUtils', '0.09', { + 'source_tmpl': 'List-AllUtils-0.09.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DR/DROLSKY/'], + }), + ('DateTime', '1.20', { + 'source_urls': ['http://www.cpan.org/modules/by-module/DateTime/DROLSKY/'], + }), + ('DateTime::Tiny', '1.04', { + 'source_tmpl': 'DateTime-Tiny-1.04.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AD/ADAMK/'], + }), + ('File::Slurp', '9999.19', { + 'source_tmpl': 'File-Slurp-9999.19.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/U/UR/URI/'], + }), + ('HTTP::Date', '6.02', { + 'source_tmpl': 'HTTP-Date-6.02.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS/'], + }), + ('IO::HTML', '1.001', { + 'source_tmpl': 'IO-HTML-1.001.tar.gz', + 'source_urls': ['http://www.cpan.org/modules/by-module/IO/CJM/'], + }), + ('LWP::MediaTypes', '6.02', { + 'source_tmpl': 'LWP-MediaTypes-6.02.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS/'], + }), + ('URI', '1.69', { + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/E/ET/ETHER/'], + }), + ('Encode::Locale', '1.05', { + 'source_tmpl': 'Encode-Locale-1.05.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS/'], + }), + ('HTTP::Request', '6.06', { + 'source_tmpl': 'HTTP-Message-6.06.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS/'], + }), + ('HTML::Tagset', '3.20', { + 'source_tmpl': 'HTML-Tagset-3.20.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/P/PE/PETDANCE/'], + }), + ('HTML::Entities', '3.71', { + 'source_tmpl': 'HTML-Parser-3.71.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS/'], + }), + ('File::Listing', '6.04', { + 'source_tmpl': 'File-Listing-6.04.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/G/GA/GAAS/'], + }), + ('AnyEvent', '7.09', { + 'source_urls': ['http://cpan.metacpan.org/authors/id/M/ML/MLEHMANN/'], + }), + ('Devel::CheckCompiler', '0.06', { + 'source_tmpl': 'Devel-CheckCompiler-0.06.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/S/SY/SYOHEX'], + }), + ('File::Copy::Recursive', '0.38', { + 'source_tmpl': 'File-Copy-Recursive-0.38.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DM/DMUEY/'], + }), + ('Cwd::Guard', '0.04', { + 'source_tmpl': 'Cwd-Guard-0.04.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/K/KA/KAZEBURO'], + }), + ('Module::Build::XSUtil', '0.16', { + 'source_tmpl': 'Module-Build-XSUtil-0.16.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/H/HI/HIDEAKIO/'], + }), + ('LWP', '6.13', { + 'source_tmpl': 'libwww-perl-6.13.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/E/ET/ETHER/'], + }), + ('Fennec::Lite', '0.004', { + 'source_tmpl': 'Fennec-Lite-0.004.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/E/EX/EXODIST/'], + }), + ('aliased', '0.31', { + 'source_urls': ['http://cpan.metacpan.org/authors/id/O/OV/OVID/'], + }), + ('Meta::Builder', '0.003', { + 'source_tmpl': 'Meta-Builder-0.003.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/E/EX/EXODIST/'], + }), + ('Exporter::Declare', '0.114', { + 'source_tmpl': 'Exporter-Declare-0.114.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/E/EX/EXODIST/'], + }), + ('Mock::Quick', '1.108', { + 'source_tmpl': 'Mock-Quick-1.108.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/E/EX/EXODIST/'], + }), + ('Test::Exception::LessClever', '0.006', { + 'source_tmpl': 'Test-Exception-LessClever-0.006.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/E/EX/EXODIST/'], + }), + ('Test::LeakTrace', '0.15', { + 'source_tmpl': 'Test-LeakTrace-0.15.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GF/GFUJI/'], + }), + ('Mouse', '2.4.2', { + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GF/GFUJI/'], + }), + ('XML::NamespaceSupport', '1.11', { + 'source_tmpl': 'XML-NamespaceSupport-1.11.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/P/PE/PERIGRIN/'], + }), + ('XML::SAX::Base', '1.08', { + 'source_tmpl': 'XML-SAX-Base-1.08.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GR/GRANTM/'], + }), + ('XML::SAX', '0.99', { + 'source_tmpl': 'XML-SAX-0.99.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GR/GRANTM/'], + }), + ('XML::LibXML', '2.0121', { + 'source_tmpl': 'XML-LibXML-2.0121.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/S/SH/SHLOMIF/'], + }), + ('Clone', '0.38', { + 'source_tmpl': 'Clone-0.38.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GARU'], + }), + ('Config::General', '2.58', { + 'source_tmpl': 'Config-General-2.58.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/T/TL/TLINDEN'], + }), + ('Test::Simple', '0.98', { + 'source_tmpl': 'Test-Simple-0.98_05.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/M/MS/MSCHWERN'], + }), + ('Font::TTF', '1.05', { + 'source_tmpl': 'Font-TTF-1.05.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/M/MH/MHOSKEN'], + }), + ('IO::Tty', '1.12', { + 'source_tmpl': 'IO-Tty-1.12.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/T/TO/TODDR'], + }), + ('Math::Bezier', '0.01', { + 'source_tmpl': 'Math-Bezier-0.01.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AB/ABW'], + }), + ('IPC::Run', '0.94', { + 'source_tmpl': 'IPC-Run-0.94.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/T/TO/TODDR'], + }), + ('Math::Round', '0.07', { + 'source_tmpl': 'Math-Round-0.07.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GR/GROMMEL'], + }), + ('B::LintSubs', '0.06', { + 'source_tmpl': 'B-LintSubs-0.06.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/P/PE/PEVANS'], + }), + ('Math::VecStat', '0.08', { + 'source_tmpl': 'Math-VecStat-0.08.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AS/ASPINELLI'], + }), + ('Test::Most', '0.34', { + 'source_tmpl': 'Test-Most-0.34.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/O/OV/OVID/'], + }), + ('Readonly', '1.04', { + 'source_tmpl': 'Readonly-1.04.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/S/SA/SANKO/'], + }), + ('Regexp::Common', '2013031301', { + 'source_tmpl': 'Regexp-Common-2013031301.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AB/ABIGAIL'], + }), + ('Want', '0.26', { + 'source_tmpl': 'Want-0.26.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/R/RO/ROBIN/'], + }), + ('DBD::SQLite', '1.48', { + 'source_tmpl': 'DBD-SQLite-1.48.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/I/IS/ISHIGAKI/'], + }), + ('Set::IntSpan', '1.19', { + 'source_tmpl': 'Set-IntSpan-1.19.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/S/SW/SWMCD'], + }), + ('forks', '0.36', { + 'source_tmpl': 'forks-0.36.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/R/RY/RYBSKEJ/'], + }), + ('File::Which', '1.09', { + 'source_tmpl': 'File-Which-1.09.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/A/AD/ADAMK/'], + }), + ('Perl::Unsafe::Signals', '', { + 'source_tmpl': 'Perl-Unsafe-Signals-0.02.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/R/RG/RGARCIA/'], + }), + ('Bit::Vector', '7.4', { + 'source_tmpl': 'Bit-Vector-7.4.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/S/ST/STBEY/'], + }), + ('Parse::RecDescent', '1.967009', { + 'source_tmpl': 'Parse-RecDescent-1.967009.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/J/JT/JTBRAUN/'], + }), + ('Inline', '0.80', { + 'source_tmpl': 'Inline-0.80.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/I/IN/INGY/'], + }), + ('File::ShareDir::Install', '0.10', { + 'source_tmpl': 'File-ShareDir-Install-0.10.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/G/GW/GWYN/'], + }), + ('Inline::C', '0.76', { + 'source_tmpl': 'Inline-C-0.76.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/I/IN/INGY/'], + }), + ('IO::All', '0.85', { + 'source_tmpl': 'IO-All-0.85.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/F/FR/FREW/'], + }), + ('IO::Prompt', '0.997002', { + 'source_tmpl': 'IO-Prompt-0.997002.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/D/DC/DCONWAY/'], + }), + ('Getopt::Long', '2.47', { + 'source_tmpl': 'Getopt-Long-2.47.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/J/JV/JV/'], + }), + ('AppConfig', '1.66', { + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AB/ABW/'], + }), + ('Archive::Extract', '0.76', { + 'source_tmpl': 'Archive-Extract-0.76.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/B/BI/BINGOS/'], + }), + ('Archive::Tar', '2.08', { + 'source_tmpl': 'Archive-Tar-2.08.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/B/BI/BINGOS/'], + }), + ('Archive::Zip', '1.57', { + 'source_tmpl': 'Archive-Zip-1.57.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/P/PH/PHRED/'], + }), + ('Authen::SASL', '2.16', { + 'source_tmpl': 'Authen-SASL-2.16.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GB/GBARR/'], + }), + ('B::Lint', '1.20', { + 'source_tmpl': 'B-Lint-1.20.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS/'], + }), + # BioPerl bundle was here + ('Class::Accessor', '0.34', { + 'source_tmpl': 'Class-Accessor-0.34.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/K/KA/KASEI/'], + }), + ('Class::DBI', '3.0.17', { + 'source_tmpl': 'Class-DBI-v3.0.17.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/T/TM/TMTM/'], + }), + ('Class::Inspector', '1.28', { + 'source_tmpl': 'Class-Inspector-1.28.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AD/ADAMK/'], + }), + ('Class::ISA', '0.36', { + 'source_tmpl': 'Class-ISA-0.36.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/S/SM/SMUELLER/'], + }), + ('Class::Trigger', '0.14', { + 'source_tmpl': 'Class-Trigger-0.14.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA/'], + }), + ('CPANPLUS', '0.9154', { + 'source_urls': ['http://cpan.metacpan.org/authors/id/B/BI/BINGOS/'], + }), + ('Data::Grove', '0.08', { + 'source_tmpl': 'libxml-perl-0.08.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/K/KM/KMACLEOD/'], + }), + ('Data::UUID', '1.220', { + 'source_tmpl': 'Data-UUID-1.220.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS/'], + }), + ('Date::Language', '2.30', { + 'source_tmpl': 'TimeDate-2.30.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GB/GBARR/'], + }), + ('Date::Handler', '1.2', { + 'source_tmpl': 'Date-Handler-1.2.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/B/BB/BBEAUSEJ/'], + }), + ('SQL::Statement', '1.407', { + 'source_tmpl': 'SQL-Statement-1.407.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RE/REHSACK/'], + }), + ('Module::Pluggable', '5.1', { + 'source_tmpl': 'Module-Pluggable-5.1.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/S/SI/SIMONW/'], + }), + ('Digest::HMAC', '1.03', { + 'source_tmpl': 'Digest-HMAC-1.03.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS/'], + }), + ('Digest::SHA1', '2.13', { + 'source_tmpl': 'Digest-SHA1-2.13.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS/'], + }), + ('Email::Date::Format', '1.005', { + 'source_tmpl': 'Email-Date-Format-1.005.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS/'], + }), + ('Error', '0.17024', { + 'source_urls': ['http://cpan.metacpan.org/authors/id/S/SH/SHLOMIF/'], + }), + ('Expect', '1.21', { + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RG/RGIERSIG/'], + }), + ('File::CheckTree', '4.42', { + 'source_tmpl': 'File-CheckTree-4.42.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS/'], + }), + ('FreezeThaw', '0.5001', { + 'source_urls': ['http://cpan.metacpan.org/authors/id/I/IL/ILYAZ/modules/'], + }), + ('Git', '0.41', { + 'source_tmpl': 'Git-0.41.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/M/MS/MSOUTH/'], + }), + ('GO::Utils', '0.15', { + 'source_tmpl': 'go-perl-0.15.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/C/CM/CMUNGALL/'], + }), + ('GO', '0.04', { + 'source_tmpl': 'go-db-perl-0.04.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/S/SJ/SJCARBON/'], + }), + ('HTML::Form', '6.03', { + 'source_tmpl': 'HTML-Form-6.03.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS/'], + }), + ('HTTP::Cookies', '6.01', { + 'source_tmpl': 'HTTP-Cookies-6.01.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS/'], + }), + ('HTTP::Daemon', '6.01', { + 'source_tmpl': 'HTTP-Daemon-6.01.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS/'], + }), + ('HTTP::Negotiate', '6.01', { + 'source_tmpl': 'HTTP-Negotiate-6.01.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS/'], + }), + ('IO::Stringy', '2.111', { + 'source_tmpl': 'IO-stringy-2.111.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DS/DSKOLL/'], + }), + ('IO::Socket::SSL', '2.016', { + 'source_tmpl': 'IO-Socket-SSL-2.016.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/S/SU/SULLR/'], + }), + ('JSON', '2.90', { + 'source_urls': ['http://cpan.metacpan.org/authors/id/M/MA/MAKAMAKA/'], + }), + ('Log::Message', '0.08', { + 'source_tmpl': 'Log-Message-0.08.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/B/BI/BINGOS/'], + }), + ('Log::Message::Simple', '0.10', { + 'source_tmpl': 'Log-Message-Simple-0.10.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/B/BI/BINGOS/'], + }), + ('Mail::Util', '2.14', { + 'source_tmpl': 'MailTools-2.14.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/M/MA/MARKOV/'], + }), + ('MIME::Types', '2.11', { + 'source_tmpl': 'MIME-Types-2.11.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/M/MA/MARKOV/'], + }), + ('MIME::Lite', '3.030', { + 'source_tmpl': 'MIME-Lite-3.030.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS/'], + }), + ('Net::HTTP', '6.06', { + 'source_tmpl': 'Net-HTTP-6.06.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS/'], + }), + ('Net::SMTP::SSL', '1.01', { + 'source_tmpl': 'Net-SMTP-SSL-1.01.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/C/CW/CWEST/'], + }), + ('Object::Accessor', '0.48', { + 'source_tmpl': 'Object-Accessor-0.48.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/B/BI/BINGOS/'], + }), + ('Pod::LaTeX', '0.61', { + 'source_tmpl': 'Pod-LaTeX-0.61.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/T/TJ/TJENNESS/'], + }), + ('Pod::Plainer', '1.04', { + 'source_tmpl': 'Pod-Plainer-1.04.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RM/RMBARKER/'], + }), + ('Pod::POM', '0.29', { + 'source_tmpl': 'Pod-POM-0.29.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AN/ANDREWF/'], + }), + ('Shell', '0.72', { + 'source_urls': ['http://cpan.metacpan.org/authors/id/F/FE/FERREIRA/'], + }), + ('Statistics::Descriptive', '3.0609', { + 'source_tmpl': 'Statistics-Descriptive-3.0609.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/S/SH/SHLOMIF/'], + }), + ('Switch', '2.17', { + 'source_urls': ['http://cpan.metacpan.org/authors/id/C/CH/CHORNY/'], + }), + ('Template', '2.26', { + 'source_tmpl': 'Template-Toolkit-2.26.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AB/ABW/'], + }), + ('Term::UI', '0.46', { + 'source_tmpl': 'Term-UI-0.46.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/B/BI/BINGOS/'], + }), + ('Text::Iconv', '1.7', { + 'source_tmpl': 'Text-Iconv-1.7.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/M/MP/MPIOTR/'], + }), + ('Text::Soundex', '3.04', { + 'source_tmpl': 'Text-Soundex-3.04.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS/'], + }), + ('Time::Piece', '1.30', { + 'source_tmpl': 'Time-Piece-1.30.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS/'], + }), + ('Time::Piece::MySQL', '0.06', { + 'source_tmpl': 'Time-Piece-MySQL-0.06.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/K/KA/KASEI/'], + }), + ('UNIVERSAL::moniker', '0.08', { + 'source_tmpl': 'UNIVERSAL-moniker-0.08.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/K/KA/KASEI/'], + }), + ('version', '0.9912', { + 'source_urls': ['http://cpan.metacpan.org/authors/id/J/JP/JPEACOCK/'], + }), + ('WWW::RobotRules', '6.02', { + 'source_tmpl': 'WWW-RobotRules-6.02.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS/'], + }), + ('XML::SAX::Writer', '0.56', { + 'source_tmpl': 'XML-SAX-Writer-0.56.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/P/PE/PERIGRIN/'], + }), + ('XML::Simple', '2.20', { + 'source_tmpl': 'XML-Simple-2.20.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GR/GRANTM/'], + }), + ('XML::XPath', '1.13', { + 'source_tmpl': 'XML-XPath-1.13.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/M/MS/MSERGEANT/'], + }), + ('DBD::AnyData', '0.110', { + 'source_tmpl': 'DBD-AnyData-0.110.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RE/REHSACK/'], + }), + ('Ima::DBI', '0.35', { + 'source_tmpl': 'Ima-DBI-0.35.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/P/PE/PERRIN/'], + }), + ('DBIx::ContextualFetch', '1.03', { + 'source_tmpl': 'DBIx-ContextualFetch-1.03.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/T/TM/TMTM/'], + }), + ('DBIx::Simple', '1.35', { + 'source_tmpl': 'DBIx-Simple-1.35.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/J/JU/JUERD/'], + }), + ('Term::ReadKey', '2.32', { + 'source_tmpl': 'TermReadKey-2.32.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/J/JS/JSTOWE/'], + 'patches': ['TermReadKey-2.32.patch'], + }), + ('Moo', '2.000001', { + 'source_tmpl': 'Moo-2.000001.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/H/HA/HAARG/'], + }), + ('strictures', '2.000001', { + 'source_tmpl': 'strictures-2.000001.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/H/HA/HAARG/'], + }), + ('File::Find::Rule::Perl', '1.13', { + 'source_tmpl': 'File-Find-Rule-Perl-1.13.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AD/ADAMK/'], + }), + ('Test::Version', '1.002004', { + 'source_tmpl': 'Test-Version-1.002004.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/X/XE/XENO/'], + }), + ('Test::Harness', '3.35', { + 'source_tmpl': 'Test-Harness-3.35.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/L/LE/LEONT/'], + }), + ('Import::Into', '1.002004', { + 'source_tmpl': 'Import-Into-1.002004.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/E/ET/ETHER/'], + }), + ('File::Find::Rule', '0.33', { + 'source_tmpl': 'File-Find-Rule-0.33.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RC/RCLAMP/'], + }), + ('Data::Section::Simple', '0.07', { + 'source_tmpl': 'Data-Section-Simple-0.07.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA/'], + }), + ('Text::Glob', '0.09', { + 'source_tmpl': 'Text-Glob-0.09.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RC/RCLAMP/'], + }), + ('Number::Compare', '0.03', { + 'source_tmpl': 'Number-Compare-0.03.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RC/RCLAMP/'], + }), + ('IPC::Run3', '0.048', { + 'source_tmpl': 'IPC-Run3-0.048.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS/'], + }), + ('Set::Array', '0.30', { + 'source_tmpl': 'Set-Array-0.30.tgz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RS/RSAVAGE/'], + }), + ('Bundle::BioPerl', '2.1.9', { + 'source_tmpl': 'Bundle-BioPerl-2.1.9.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS/'], + }), + + ('Algorithm::Munkres', '0.08', { + 'source_tmpl': 'Algorithm-Munkres-0.08.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/T/TP/TPEDERSE/'], + }), +# Lots of deps: Carp, Types::Standard etc. +# ('Array::Compare', '2.11', { +# 'source_tmpl': 'Array-Compare-2.11.tar.gz', +# 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DA/DAVECROSS/'], +# }), + ('Graph', '0.96', { + 'source_urls': ['http://cpan.metacpan.org/authors/id/J/JH/JHI/'], + }), + ('Set::Scalar', '1.29', { + 'source_tmpl': 'Set-Scalar-1.29.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DA/DAVIDO/'], + }), + + ('CGI', '4.21', { + 'source_tmpl': 'CGI-4.21.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/L/LE/LEEJO/'], + }), + ('Bio::Phylo', '0.58', { + 'source_tmpl': 'Bio-Phylo-0.58.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RV/RVOSA/'], + }), +# ('GD', '2.56', { +# 'source_urls': 'http://cpan.metacpan.org/authors/id/L/LD/LDS/'], +# }), + ('SVG', '2.64', { + 'source_urls': ['http://cpan.metacpan.org/authors/id/S/SZ/SZABGAB/'], + }), + ('XML::DOM', '1.44', { + 'source_tmpl': 'XML-DOM-1.44.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/T/TJ/TJMATHER/'], + }), + ('XML::DOM::XPath', '0.14', { + 'source_tmpl': 'XML-DOM-XPath-0.14.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/M/MI/MIROD/'], + }), + ('XML::Parser::PerlSAX', '0.08', { + 'source_tmpl': 'libxml-perl-0.08.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/K/KM/KMACLEOD/'], + }), + ('XML::Parser', '2.44', { + 'source_tmpl': 'XML-Parser-2.44.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/T/TO/TODDR/'], + }), + ('XML::Twig', '3.49', { + 'source_tmpl': 'XML-Twig-3.49.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/M/MI/MIROD/'], + }), + ('XML::Writer', '0.625', { + 'source_tmpl': 'XML-Writer-0.625.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/J/JO/JOSEPHW/'], + }), + ('XML::DOM', '1.44', { + 'source_tmpl': 'XML-DOM-1.44.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/T/TJ/TJMATHER/'], + }), + ('Spreadsheet::ParseExcel', '0.65', { + 'source_tmpl': 'Spreadsheet-ParseExcel-0.65.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DO/DOUGW/'], + }), + ('XML::DOM::XPath', '0.14', { + 'source_tmpl': 'XML-DOM-XPath-0.14.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/M/MI/MIROD/'], + }), + ('Convert::Binary::C', '0.77', { + 'source_tmpl': 'Convert-Binary-C-0.77.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/M/MH/MHX/'], + }), + ('Sys::SigAction.pm', '0.21', { + 'source_tmpl': 'Sys-SigAction-0.21.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/L/LB/LBAXTER/'], + }), + ('Acme::Damn', '0.06', { + 'source_tmpl': 'Acme-Damn-0.06.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/I/IB/IBB/'], + }), + ('Set::IntervalTree', '0.10', { + 'source_tmpl': 'Set-IntervalTree-0.10.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/B/BE/BENBOOTH/'], + }), + +# Trouble finding libbam.a and bam/bam.h - try Alien::Samtools next +# ('Bio::DB::Sam', '1.41', { +# 'source_tmpl': 'Bio-SamTools-1.41.tar.gz', +# 'source_urls': ['http://cpan.metacpan.org/authors/id/L/LD/LDS/'], +# 'patches': ['Perl-Bio-SamTools.patch'], +# }), + ('HTML::TableExtract', '2.13', { + 'source_tmpl': 'HTML-TableExtract-2.13.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/M/MS/MSISK/'], + }), + + ('Bio::Perl', '1.6.924', { + 'source_tmpl': 'BioPerl-1.6.924.tar.gz', + 'source_urls': ['http://www.cpan.org/modules/by-module/Bio/CJFIELDS/'], + }), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.22.0-foss-2015a.eb b/easybuild/easyconfigs/p/Perl/Perl-5.22.0-foss-2015a.eb new file mode 100644 index 0000000000..dc4e724075 --- /dev/null +++ b/easybuild/easyconfigs/p/Perl/Perl-5.22.0-foss-2015a.eb @@ -0,0 +1,903 @@ +name = 'Perl' +version = '5.22.0' +use_perl_threads = False + +homepage = 'http://www.perl.org/' +description = """Larry Wall's Practical Extraction and Report Language""" + +toolchain = {'name': 'foss', 'version': '2015a'} +toolchainopts = {'optarch': True, 'pic': True} + +dependencies = [ + ('DB', '6.0.30'), # for DB_File module + ('SQLite', '3.8.9'), # for DBD::SQLite module + ('expat', '2.1.0'), # for XML::Parser I think + ('libxml2', '2.9.2'), # for XML::LibXML + ] + +#builddependencies = [('SAMtools', '0.1.20')] # NOT A LATER VERSION. For Bio::DB::Sam to static link to. + +source_urls = ['http://www.cpan.org/src/5.0'] +sources = [SOURCELOWER_TAR_GZ] +#runtest = 'test' + +exts_list = [ + ('Module::Build', '0.4210', { # std module but recent BioPerl needs a recent version for some reason + 'source_tmpl': 'Module-Build-0.4210.tar.gz', + 'source_urls': ['http://www.cpan.org/modules/by-module/Module/LEONT/'], + }), + ('ExtUtils::MakeMaker', '7.04', { + 'source_tmpl': 'ExtUtils-MakeMaker-7.04.tar.gz', + 'source_urls': ['http://www.cpan.org/modules/by-module/ExtUtils/BINGOS/'], + }), + ('local::lib', '2.000011', { + 'source_tmpl': 'local-lib-2.000011.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/E/ET/ETHER/'], + }), + ('IO::String', '1.08', { + 'source_tmpl': 'IO-String-1.08.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS/'], + }), + ('Data::Stag', '0.14', { + 'source_tmpl': 'Data-Stag-0.14.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/C/CM/CMUNGALL/'], + }), + ('DB_File', '1.835', { + 'source_urls': ['http://www.cpan.org/modules/by-module/DB_File/PMQS/'], + }), + ('DBI', '1.633', { + 'source_urls': ['http://www.cpan.org/modules/by-module/DBI/TIMB/'], + }), + ('Sub::Uplevel', '0.25', { + 'source_tmpl': 'Sub-Uplevel-0.25.tar.gz', + 'source_urls': ['http://www.cpan.org/modules/by-module/Sub/DAGOLDEN/'], + }), + ('Tree::DAG_Node', '1.26', { + 'source_tmpl': 'Tree-DAG_Node-1.26.tgz', + 'source_urls': ['http://www.cpan.org/modules/by-module/Tree/RSAVAGE/'], + }), + ('Try::Tiny', '0.22', { + 'source_tmpl': 'Try-Tiny-0.22.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/D/DO/DOY/'], + }), + ('Devel::StackTrace', '2.00', { + 'source_tmpl': 'Devel-StackTrace-2.00.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DR/DROLSKY/'], + }), + ('Class::Data::Inheritable', '0.08', { + 'source_tmpl': 'Class-Data-Inheritable-0.08.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/T/TM/TMTM/'], + }), + ('Exception::Class', '1.39', { + 'source_tmpl': 'Exception-Class-1.39.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DR/DROLSKY/'], + }), + ('Test::Fatal', '0.014', { + 'source_tmpl': 'Test-Fatal-0.014.tar.gz', + 'source_urls': ['http://www.cpan.org/modules/by-module/Test/RJBS/'], + }), + ('Test::NoWarnings', '1.04', { + 'source_tmpl': 'Test-NoWarnings-1.04.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AD/ADAMK/'], + }), + ('Test::Deep', '0.117', { + 'source_tmpl': 'Test-Deep-0.117.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS/'], + }), + ('Algorithm::Diff', '1.15', { + 'source_tmpl': 'Algorithm-Diff-1.15.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/N/NE/NEDKONZ/'], + }), + ('Text::Diff', '1.41', { + 'source_tmpl': 'Text-Diff-1.41.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/O/OV/OVID/'], + }), + ('Test::Differences', '0.61', { + 'source_tmpl': 'Test-Differences-0.61.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/O/OV/OVID/'], + }), + ('Test::Exception', '0.32', { + 'source_tmpl': 'Test-Exception-0.32.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AD/ADIE/'], + }), + ('Test::Warn', '0.30', { + 'source_tmpl': 'Test-Warn-0.30.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/C/CH/CHORNY/'], + }), + ('Test::Requires', '0.08', { + 'source_tmpl': 'Test-Requires-0.08.tar.gz', + 'source_urls': ['http://www.cpan.org/modules/by-module/Test/TOKUHIROM/'], + }), + ('Test::Tester', '0.109', { + 'source_tmpl': 'Test-Tester-0.109.tar.gz', + 'source_urls': ['http://www.cpan.org/modules/by-module/Test/FDALY/'], + }), + ('File::Slurp::Tiny', '0.003', { + 'source_tmpl': 'File-Slurp-Tiny-0.003.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('Params::Util', '1.07', { + 'source_tmpl': 'Params-Util-1.07.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AD/ADAMK/'], + }), + ('Sub::Install', '0.928', { + 'source_tmpl': 'Sub-Install-0.928.tar.gz', + 'source_urls': ['http://www.cpan.org/modules/by-module/Sub/RJBS/'], + }), + ('Data::OptList', '0.109', { + 'source_tmpl': 'Data-OptList-0.109.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS/'], + }), + ('Sub::Exporter', '0.987', { + 'source_tmpl': 'Sub-Exporter-0.987.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS/'], + }), + ('Capture::Tiny', '0.30', { + 'source_tmpl': 'Capture-Tiny-0.30.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN/'], + }), + ('Test::Output', '1.03', { + 'source_tmpl': 'Test-Output-1.03.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/B/BD/BDFOY/'], + }), + ('Module::Runtime', '0.014', { + 'source_tmpl': 'Module-Runtime-0.014.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/Z/ZE/ZEFRAM/'], + }), + ('Module::Implementation', '0.09', { + 'source_tmpl': 'Module-Implementation-0.09.tar.gz', + 'source_urls': ['http://www.cpan.org/modules/by-module/Module/DROLSKY/'], + }), + ('List::MoreUtils', '0.413', { + 'source_tmpl': 'List-MoreUtils-0.413.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RE/REHSACK/'], + }), + ('Package::DeprecationManager', '0.14', { + 'source_tmpl': 'Package-DeprecationManager-0.14.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DR/DROLSKY/'], + }), + ('Dist::CheckConflicts', '0.11', { + 'source_tmpl': 'Dist-CheckConflicts-0.11.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DO/DOY/'], + }), + ('Package::Stash', '0.37', { + 'source_tmpl': 'Package-Stash-0.37.tar.gz', + 'source_urls': ['http://www.cpan.org/modules/by-module/Package/DOY/'], + }), + ('Class::Load', '0.23', { + 'source_tmpl': 'Class-Load-0.23.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/E/ET/ETHER/'], + }), + ('TAP::Harness::Env', '3.35', { + 'source_tmpl': 'Test-Harness-3.35.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/L/LE/LEONT/'], + }), + ('ExtUtils::Helpers', '0.022', { + 'source_tmpl': 'ExtUtils-Helpers-0.022.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('ExtUtils::Config', '0.008', { + 'source_tmpl': 'ExtUtils-Config-0.008.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('ExtUtils::InstallPaths', '0.011', { + 'source_tmpl': 'ExtUtils-InstallPaths-0.011.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('Module::Build::Tiny', '0.039', { + 'source_tmpl': 'Module-Build-Tiny-0.039.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/L/LE/LEONT/'], + }), + ('MRO::Compat', '0.12', { + 'source_tmpl': 'MRO-Compat-0.12.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/B/BO/BOBTFISH/'], + }), + ('Sub::Name', '0.05', { + 'source_tmpl': 'Sub-Name-0.05.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/F/FL/FLORA/'], + }), + ('Eval::Closure', '0.13', { + 'source_tmpl': 'Eval-Closure-0.13.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DO/DOY/'], + }), + ('Sub::Exporter::Progressive', '0.001011', { + 'source_tmpl': 'Sub-Exporter-Progressive-0.001011.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/F/FR/FREW/'], + }), + ('Devel::GlobalDestruction', '0.13', { + 'source_tmpl': 'Devel-GlobalDestruction-0.13.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/H/HA/HAARG/'], + }), + ('boolean', '0.45', { + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/I/IN/INGY/'], + }), + ('Tie::IxHash', '1.23', { + 'source_tmpl': 'Tie-IxHash-1.23.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/C/CH/CHORNY/'], + }), + ('Moose', '2.1405', { + 'source_urls': ['http://www.cpan.org/modules/by-module/MooseX/ETHER/'], + }), + ('Package::Stash::XS', '0.28', { + 'source_tmpl': 'Package-Stash-XS-0.28.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DO/DOY/'], + }), + ('Params::Validate', '1.20', { + 'source_tmpl': 'Params-Validate-1.20.tar.gz', + 'source_urls': ['http://www.cpan.org/modules/by-module/Params/DROLSKY/'], + }), + ('Class::Load::XS', '0.09', { + 'source_tmpl': 'Class-Load-XS-0.09.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/E/ET/ETHER/'], + }), + + # For uoa00001, Zendesk #9076 + ('Math::CDF', '0.1', { + 'source_tmpl': 'Math-CDF-0.1.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/C/CA/CALLAHAN/'], + }), + + ('DateTime::Locale', '0.46', { + 'source_tmpl': 'DateTime-Locale-0.46.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DR/DROLSKY/'], + }), + ('Class::Singleton', '1.4', { + 'source_tmpl': 'Class-Singleton-1.4.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AB/ABW/'], + }), + ('DateTime::TimeZone', '1.92', { + 'source_tmpl': 'DateTime-TimeZone-1.92.tar.gz', + 'source_urls': ['http://www.cpan.org/modules/by-module/DateTime/DROLSKY/'], + }), + ('Test::Warnings', '0.021', { + 'source_tmpl': 'Test-Warnings-0.021.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/E/ET/ETHER/'], + }), + ('Data::Types', '0.09', { + 'source_tmpl': 'Data-Types-0.09.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DW/DWHEELER/'], + }), + ('Exporter::Tiny', '0.042', { + 'source_tmpl': 'Exporter-Tiny-0.042.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/T/TO/TOBYINK/'], + }), + + ('List::AllUtils', '0.09', { + 'source_tmpl': 'List-AllUtils-0.09.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DR/DROLSKY/'], + }), + ('DateTime', '1.20', { + 'source_urls': ['http://www.cpan.org/modules/by-module/DateTime/DROLSKY/'], + }), + ('DateTime::Tiny', '1.04', { + 'source_tmpl': 'DateTime-Tiny-1.04.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AD/ADAMK/'], + }), + ('File::Slurp', '9999.19', { + 'source_tmpl': 'File-Slurp-9999.19.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/U/UR/URI/'], + }), + ('HTTP::Date', '6.02', { + 'source_tmpl': 'HTTP-Date-6.02.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS/'], + }), + ('IO::HTML', '1.001', { + 'source_tmpl': 'IO-HTML-1.001.tar.gz', + 'source_urls': ['http://www.cpan.org/modules/by-module/IO/CJM/'], + }), + ('LWP::MediaTypes', '6.02', { + 'source_tmpl': 'LWP-MediaTypes-6.02.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS/'], + }), + ('URI', '1.69', { + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/E/ET/ETHER/'], + }), + ('Encode::Locale', '1.05', { + 'source_tmpl': 'Encode-Locale-1.05.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS/'], + }), + ('HTTP::Request', '6.06', { + 'source_tmpl': 'HTTP-Message-6.06.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS/'], + }), + ('HTML::Tagset', '3.20', { + 'source_tmpl': 'HTML-Tagset-3.20.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/P/PE/PETDANCE/'], + }), + ('HTML::Entities', '3.71', { + 'source_tmpl': 'HTML-Parser-3.71.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS/'], + }), + ('File::Listing', '6.04', { + 'source_tmpl': 'File-Listing-6.04.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/G/GA/GAAS/'], + }), + ('AnyEvent', '7.09', { + 'source_urls': ['http://cpan.metacpan.org/authors/id/M/ML/MLEHMANN/'], + }), + ('Devel::CheckCompiler', '0.06', { + 'source_tmpl': 'Devel-CheckCompiler-0.06.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/S/SY/SYOHEX'], + }), + ('File::Copy::Recursive', '0.38', { + 'source_tmpl': 'File-Copy-Recursive-0.38.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DM/DMUEY/'], + }), + ('Cwd::Guard', '0.04', { + 'source_tmpl': 'Cwd-Guard-0.04.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/K/KA/KAZEBURO'], + }), + ('Module::Build::XSUtil', '0.16', { + 'source_tmpl': 'Module-Build-XSUtil-0.16.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/H/HI/HIDEAKIO/'], + }), + ('LWP', '6.13', { + 'source_tmpl': 'libwww-perl-6.13.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/E/ET/ETHER/'], + }), + ('Fennec::Lite', '0.004', { + 'source_tmpl': 'Fennec-Lite-0.004.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/E/EX/EXODIST/'], + }), + ('aliased', '0.31', { + 'source_urls': ['http://cpan.metacpan.org/authors/id/O/OV/OVID/'], + }), + ('Meta::Builder', '0.003', { + 'source_tmpl': 'Meta-Builder-0.003.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/E/EX/EXODIST/'], + }), + ('Exporter::Declare', '0.114', { + 'source_tmpl': 'Exporter-Declare-0.114.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/E/EX/EXODIST/'], + }), + ('Mock::Quick', '1.108', { + 'source_tmpl': 'Mock-Quick-1.108.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/E/EX/EXODIST/'], + }), + ('Test::Exception::LessClever', '0.006', { + 'source_tmpl': 'Test-Exception-LessClever-0.006.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/E/EX/EXODIST/'], + }), + ('Test::LeakTrace', '0.15', { + 'source_tmpl': 'Test-LeakTrace-0.15.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GF/GFUJI/'], + }), + ('Mouse', '2.4.2', { + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GF/GFUJI/'], + }), + ('XML::NamespaceSupport', '1.11', { + 'source_tmpl': 'XML-NamespaceSupport-1.11.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/P/PE/PERIGRIN/'], + }), + ('XML::SAX::Base', '1.08', { + 'source_tmpl': 'XML-SAX-Base-1.08.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GR/GRANTM/'], + }), + ('XML::SAX', '0.99', { + 'source_tmpl': 'XML-SAX-0.99.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GR/GRANTM/'], + }), + ('XML::LibXML', '2.0121', { + 'source_tmpl': 'XML-LibXML-2.0121.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/S/SH/SHLOMIF/'], + }), + ('Clone', '0.38', { + 'source_tmpl': 'Clone-0.38.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GARU'], + }), + ('Config::General', '2.58', { + 'source_tmpl': 'Config-General-2.58.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/T/TL/TLINDEN'], + }), + ('Test::Simple', '0.98', { + 'source_tmpl': 'Test-Simple-0.98_05.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/M/MS/MSCHWERN'], + }), + ('Font::TTF', '1.05', { + 'source_tmpl': 'Font-TTF-1.05.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/M/MH/MHOSKEN'], + }), + ('IO::Tty', '1.12', { + 'source_tmpl': 'IO-Tty-1.12.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/T/TO/TODDR'], + }), + ('Math::Bezier', '0.01', { + 'source_tmpl': 'Math-Bezier-0.01.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AB/ABW'], + }), + ('IPC::Run', '0.94', { + 'source_tmpl': 'IPC-Run-0.94.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/T/TO/TODDR'], + }), + ('Math::Round', '0.07', { + 'source_tmpl': 'Math-Round-0.07.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GR/GROMMEL'], + }), + ('B::LintSubs', '0.06', { + 'source_tmpl': 'B-LintSubs-0.06.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/P/PE/PEVANS'], + }), + ('Math::VecStat', '0.08', { + 'source_tmpl': 'Math-VecStat-0.08.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AS/ASPINELLI'], + }), + ('Test::Most', '0.34', { + 'source_tmpl': 'Test-Most-0.34.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/O/OV/OVID/'], + }), + ('Readonly', '1.04', { + 'source_tmpl': 'Readonly-1.04.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/S/SA/SANKO/'], + }), + ('Regexp::Common', '2013031301', { + 'source_tmpl': 'Regexp-Common-2013031301.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AB/ABIGAIL'], + }), + ('Want', '0.26', { + 'source_tmpl': 'Want-0.26.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/R/RO/ROBIN/'], + }), + ('DBD::SQLite', '1.48', { + 'source_tmpl': 'DBD-SQLite-1.48.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/I/IS/ISHIGAKI/'], + }), + ('Set::IntSpan', '1.19', { + 'source_tmpl': 'Set-IntSpan-1.19.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/S/SW/SWMCD'], + }), + ('forks', '0.36', { + 'source_tmpl': 'forks-0.36.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/R/RY/RYBSKEJ/'], + }), + ('File::Which', '1.09', { + 'source_tmpl': 'File-Which-1.09.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/A/AD/ADAMK/'], + }), + ('Perl::Unsafe::Signals', '', { + 'source_tmpl': 'Perl-Unsafe-Signals-0.02.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/R/RG/RGARCIA/'], + }), + ('Bit::Vector', '7.4', { + 'source_tmpl': 'Bit-Vector-7.4.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/S/ST/STBEY/'], + }), + ('Parse::RecDescent', '1.967009', { + 'source_tmpl': 'Parse-RecDescent-1.967009.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/J/JT/JTBRAUN/'], + }), + ('Inline', '0.80', { + 'source_tmpl': 'Inline-0.80.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/I/IN/INGY/'], + }), + ('File::ShareDir::Install', '0.10', { + 'source_tmpl': 'File-ShareDir-Install-0.10.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/G/GW/GWYN/'], + }), + ('Inline::C', '0.76', { + 'source_tmpl': 'Inline-C-0.76.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/I/IN/INGY/'], + }), + ('IO::All', '0.85', { + 'source_tmpl': 'IO-All-0.85.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/F/FR/FREW/'], + }), + ('IO::Prompt', '0.997002', { + 'source_tmpl': 'IO-Prompt-0.997002.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/D/DC/DCONWAY/'], + }), + ('Getopt::Long', '2.47', { + 'source_tmpl': 'Getopt-Long-2.47.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/J/JV/JV/'], + }), + ('AppConfig', '1.66', { + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AB/ABW/'], + }), + ('Archive::Extract', '0.76', { + 'source_tmpl': 'Archive-Extract-0.76.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/B/BI/BINGOS/'], + }), + ('Archive::Tar', '2.08', { + 'source_tmpl': 'Archive-Tar-2.08.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/B/BI/BINGOS/'], + }), + ('Archive::Zip', '1.57', { + 'source_tmpl': 'Archive-Zip-1.57.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/P/PH/PHRED/'], + }), + ('Authen::SASL', '2.16', { + 'source_tmpl': 'Authen-SASL-2.16.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GB/GBARR/'], + }), + ('B::Lint', '1.20', { + 'source_tmpl': 'B-Lint-1.20.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS/'], + }), + # BioPerl bundle was here + ('Class::Accessor', '0.34', { + 'source_tmpl': 'Class-Accessor-0.34.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/K/KA/KASEI/'], + }), + ('Class::DBI', '3.0.17', { + 'source_tmpl': 'Class-DBI-v3.0.17.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/T/TM/TMTM/'], + }), + ('Class::Inspector', '1.28', { + 'source_tmpl': 'Class-Inspector-1.28.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AD/ADAMK/'], + }), + ('Class::ISA', '0.36', { + 'source_tmpl': 'Class-ISA-0.36.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/S/SM/SMUELLER/'], + }), + ('Class::Trigger', '0.14', { + 'source_tmpl': 'Class-Trigger-0.14.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA/'], + }), + ('CPANPLUS', '0.9154', { + 'source_urls': ['http://cpan.metacpan.org/authors/id/B/BI/BINGOS/'], + }), + ('Data::Grove', '0.08', { + 'source_tmpl': 'libxml-perl-0.08.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/K/KM/KMACLEOD/'], + }), + ('Data::UUID', '1.220', { + 'source_tmpl': 'Data-UUID-1.220.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS/'], + }), + ('Date::Language', '2.30', { + 'source_tmpl': 'TimeDate-2.30.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GB/GBARR/'], + }), + ('Date::Handler', '1.2', { + 'source_tmpl': 'Date-Handler-1.2.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/B/BB/BBEAUSEJ/'], + }), + ('SQL::Statement', '1.407', { + 'source_tmpl': 'SQL-Statement-1.407.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RE/REHSACK/'], + }), + ('Module::Pluggable', '5.1', { + 'source_tmpl': 'Module-Pluggable-5.1.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/S/SI/SIMONW/'], + }), + ('Digest::HMAC', '1.03', { + 'source_tmpl': 'Digest-HMAC-1.03.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS/'], + }), + ('Digest::SHA1', '2.13', { + 'source_tmpl': 'Digest-SHA1-2.13.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS/'], + }), + ('Email::Date::Format', '1.005', { + 'source_tmpl': 'Email-Date-Format-1.005.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS/'], + }), + ('Error', '0.17024', { + 'source_urls': ['http://cpan.metacpan.org/authors/id/S/SH/SHLOMIF/'], + }), + ('Expect', '1.21', { + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RG/RGIERSIG/'], + }), + ('File::CheckTree', '4.42', { + 'source_tmpl': 'File-CheckTree-4.42.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS/'], + }), + ('FreezeThaw', '0.5001', { + 'source_urls': ['http://cpan.metacpan.org/authors/id/I/IL/ILYAZ/modules/'], + }), + ('Git', '0.41', { + 'source_tmpl': 'Git-0.41.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/M/MS/MSOUTH/'], + }), + ('GO::Utils', '0.15', { + 'source_tmpl': 'go-perl-0.15.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/C/CM/CMUNGALL/'], + }), + ('GO', '0.04', { + 'source_tmpl': 'go-db-perl-0.04.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/S/SJ/SJCARBON/'], + }), + ('HTML::Form', '6.03', { + 'source_tmpl': 'HTML-Form-6.03.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS/'], + }), + ('HTTP::Cookies', '6.01', { + 'source_tmpl': 'HTTP-Cookies-6.01.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS/'], + }), + ('HTTP::Daemon', '6.01', { + 'source_tmpl': 'HTTP-Daemon-6.01.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS/'], + }), + ('HTTP::Negotiate', '6.01', { + 'source_tmpl': 'HTTP-Negotiate-6.01.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS/'], + }), + ('IO::Stringy', '2.111', { + 'source_tmpl': 'IO-stringy-2.111.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DS/DSKOLL/'], + }), + ('IO::Socket::SSL', '2.016', { + 'source_tmpl': 'IO-Socket-SSL-2.016.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/S/SU/SULLR/'], + }), + ('JSON', '2.90', { + 'source_urls': ['http://cpan.metacpan.org/authors/id/M/MA/MAKAMAKA/'], + }), + ('Log::Message', '0.08', { + 'source_tmpl': 'Log-Message-0.08.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/B/BI/BINGOS/'], + }), + ('Log::Message::Simple', '0.10', { + 'source_tmpl': 'Log-Message-Simple-0.10.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/B/BI/BINGOS/'], + }), + ('Mail::Util', '2.14', { + 'source_tmpl': 'MailTools-2.14.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/M/MA/MARKOV/'], + }), + ('MIME::Types', '2.11', { + 'source_tmpl': 'MIME-Types-2.11.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/M/MA/MARKOV/'], + }), + ('MIME::Lite', '3.030', { + 'source_tmpl': 'MIME-Lite-3.030.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS/'], + }), + ('Net::HTTP', '6.06', { + 'source_tmpl': 'Net-HTTP-6.06.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS/'], + }), + ('Net::SMTP::SSL', '1.01', { + 'source_tmpl': 'Net-SMTP-SSL-1.01.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/C/CW/CWEST/'], + }), + ('Object::Accessor', '0.48', { + 'source_tmpl': 'Object-Accessor-0.48.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/B/BI/BINGOS/'], + }), + ('Pod::LaTeX', '0.61', { + 'source_tmpl': 'Pod-LaTeX-0.61.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/T/TJ/TJENNESS/'], + }), + ('Pod::Plainer', '1.04', { + 'source_tmpl': 'Pod-Plainer-1.04.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RM/RMBARKER/'], + }), + ('Pod::POM', '0.29', { + 'source_tmpl': 'Pod-POM-0.29.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AN/ANDREWF/'], + }), + ('Shell', '0.72', { + 'source_urls': ['http://cpan.metacpan.org/authors/id/F/FE/FERREIRA/'], + }), + ('Statistics::Descriptive', '3.0609', { + 'source_tmpl': 'Statistics-Descriptive-3.0609.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/S/SH/SHLOMIF/'], + }), + ('Switch', '2.17', { + 'source_urls': ['http://cpan.metacpan.org/authors/id/C/CH/CHORNY/'], + }), + ('Template', '2.26', { + 'source_tmpl': 'Template-Toolkit-2.26.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AB/ABW/'], + }), + ('Term::UI', '0.46', { + 'source_tmpl': 'Term-UI-0.46.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/B/BI/BINGOS/'], + }), + ('Text::Iconv', '1.7', { + 'source_tmpl': 'Text-Iconv-1.7.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/M/MP/MPIOTR/'], + }), + ('Text::Soundex', '3.04', { + 'source_tmpl': 'Text-Soundex-3.04.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS/'], + }), + ('Time::Piece', '1.30', { + 'source_tmpl': 'Time-Piece-1.30.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS/'], + }), + ('Time::Piece::MySQL', '0.06', { + 'source_tmpl': 'Time-Piece-MySQL-0.06.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/K/KA/KASEI/'], + }), + ('UNIVERSAL::moniker', '0.08', { + 'source_tmpl': 'UNIVERSAL-moniker-0.08.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/K/KA/KASEI/'], + }), + ('version', '0.9912', { + 'source_urls': ['http://cpan.metacpan.org/authors/id/J/JP/JPEACOCK/'], + }), + ('WWW::RobotRules', '6.02', { + 'source_tmpl': 'WWW-RobotRules-6.02.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS/'], + }), + ('XML::SAX::Writer', '0.56', { + 'source_tmpl': 'XML-SAX-Writer-0.56.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/P/PE/PERIGRIN/'], + }), + ('XML::Simple', '2.20', { + 'source_tmpl': 'XML-Simple-2.20.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GR/GRANTM/'], + }), + ('XML::XPath', '1.13', { + 'source_tmpl': 'XML-XPath-1.13.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/M/MS/MSERGEANT/'], + }), + ('DBD::AnyData', '0.110', { + 'source_tmpl': 'DBD-AnyData-0.110.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RE/REHSACK/'], + }), + ('Ima::DBI', '0.35', { + 'source_tmpl': 'Ima-DBI-0.35.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/P/PE/PERRIN/'], + }), + ('DBIx::ContextualFetch', '1.03', { + 'source_tmpl': 'DBIx-ContextualFetch-1.03.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/T/TM/TMTM/'], + }), + ('DBIx::Simple', '1.35', { + 'source_tmpl': 'DBIx-Simple-1.35.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/J/JU/JUERD/'], + }), + ('Term::ReadKey', '2.32', { + 'source_tmpl': 'TermReadKey-2.32.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/J/JS/JSTOWE/'], + 'patches': ['TermReadKey-2.32.patch'], + }), + ('Moo', '2.000001', { + 'source_tmpl': 'Moo-2.000001.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/H/HA/HAARG/'], + }), + ('strictures', '2.000001', { + 'source_tmpl': 'strictures-2.000001.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/H/HA/HAARG/'], + }), + ('File::Find::Rule::Perl', '1.13', { + 'source_tmpl': 'File-Find-Rule-Perl-1.13.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AD/ADAMK/'], + }), + ('Test::Version', '1.002004', { + 'source_tmpl': 'Test-Version-1.002004.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/X/XE/XENO/'], + }), + ('Test::Harness', '3.35', { + 'source_tmpl': 'Test-Harness-3.35.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/L/LE/LEONT/'], + }), + ('Import::Into', '1.002004', { + 'source_tmpl': 'Import-Into-1.002004.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/E/ET/ETHER/'], + }), + ('File::Find::Rule', '0.33', { + 'source_tmpl': 'File-Find-Rule-0.33.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RC/RCLAMP/'], + }), + ('Data::Section::Simple', '0.07', { + 'source_tmpl': 'Data-Section-Simple-0.07.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA/'], + }), + ('Text::Glob', '0.09', { + 'source_tmpl': 'Text-Glob-0.09.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RC/RCLAMP/'], + }), + ('Number::Compare', '0.03', { + 'source_tmpl': 'Number-Compare-0.03.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RC/RCLAMP/'], + }), + ('IPC::Run3', '0.048', { + 'source_tmpl': 'IPC-Run3-0.048.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS/'], + }), + ('Set::Array', '0.30', { + 'source_tmpl': 'Set-Array-0.30.tgz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RS/RSAVAGE/'], + }), + ('Bundle::BioPerl', '2.1.9', { + 'source_tmpl': 'Bundle-BioPerl-2.1.9.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS/'], + }), + + ('Algorithm::Munkres', '0.08', { + 'source_tmpl': 'Algorithm-Munkres-0.08.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/T/TP/TPEDERSE/'], + }), +# Lots of deps: Carp, Types::Standard etc. +# ('Array::Compare', '2.11', { +# 'source_tmpl': 'Array-Compare-2.11.tar.gz', +# 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DA/DAVECROSS/'], +# }), + ('Graph', '0.96', { + 'source_urls': ['http://cpan.metacpan.org/authors/id/J/JH/JHI/'], + }), + ('Set::Scalar', '1.29', { + 'source_tmpl': 'Set-Scalar-1.29.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DA/DAVIDO/'], + }), + + ('CGI', '4.21', { + 'source_tmpl': 'CGI-4.21.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/L/LE/LEEJO/'], + }), + ('Bio::Phylo', '0.58', { + 'source_tmpl': 'Bio-Phylo-0.58.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RV/RVOSA/'], + }), +# ('GD', '2.56', { +# 'source_urls': 'http://cpan.metacpan.org/authors/id/L/LD/LDS/'], +# }), + ('SVG', '2.64', { + 'source_urls': ['http://cpan.metacpan.org/authors/id/S/SZ/SZABGAB/'], + }), + ('XML::DOM', '1.44', { + 'source_tmpl': 'XML-DOM-1.44.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/T/TJ/TJMATHER/'], + }), + ('XML::DOM::XPath', '0.14', { + 'source_tmpl': 'XML-DOM-XPath-0.14.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/M/MI/MIROD/'], + }), + ('XML::Parser::PerlSAX', '0.08', { + 'source_tmpl': 'libxml-perl-0.08.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/K/KM/KMACLEOD/'], + }), + ('XML::Parser', '2.44', { + 'source_tmpl': 'XML-Parser-2.44.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/T/TO/TODDR/'], + }), + ('XML::Twig', '3.49', { + 'source_tmpl': 'XML-Twig-3.49.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/M/MI/MIROD/'], + }), + ('XML::Writer', '0.625', { + 'source_tmpl': 'XML-Writer-0.625.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/J/JO/JOSEPHW/'], + }), + ('XML::DOM', '1.44', { + 'source_tmpl': 'XML-DOM-1.44.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/T/TJ/TJMATHER/'], + }), + ('Spreadsheet::ParseExcel', '0.65', { + 'source_tmpl': 'Spreadsheet-ParseExcel-0.65.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DO/DOUGW/'], + }), + ('XML::DOM::XPath', '0.14', { + 'source_tmpl': 'XML-DOM-XPath-0.14.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/M/MI/MIROD/'], + }), + ('Convert::Binary::C', '0.77', { + 'source_tmpl': 'Convert-Binary-C-0.77.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/M/MH/MHX/'], + }), + ('Sys::SigAction.pm', '0.21', { + 'source_tmpl': 'Sys-SigAction-0.21.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/L/LB/LBAXTER/'], + }), + ('Acme::Damn', '0.06', { + 'source_tmpl': 'Acme-Damn-0.06.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/I/IB/IBB/'], + }), + ('Set::IntervalTree', '0.10', { + 'source_tmpl': 'Set-IntervalTree-0.10.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/B/BE/BENBOOTH/'], + }), + +# Trouble finding libbam.a and bam/bam.h - try Alien::Samtools next +# ('Bio::DB::Sam', '1.41', { +# 'source_tmpl': 'Bio-SamTools-1.41.tar.gz', +# 'source_urls': ['http://cpan.metacpan.org/authors/id/L/LD/LDS/'], +# 'patches': ['Perl-Bio-SamTools.patch'], +# }), + ('HTML::TableExtract', '2.13', { + 'source_tmpl': 'HTML-TableExtract-2.13.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/M/MS/MSISK/'], + }), + + ('Bio::Perl', '1.6.924', { + 'source_tmpl': 'BioPerl-1.6.924.tar.gz', + 'source_urls': ['http://www.cpan.org/modules/by-module/Bio/CJFIELDS/'], + }), +] + +moduleclass = 'lang' -- GitLab From 15166547d968dd415bcd4ee7ff3afd3c4c87801b Mon Sep 17 00:00:00 2001 From: iotaka Date: Fri, 13 Jan 2017 08:34:02 +0100 Subject: [PATCH 0034/1603] Update Eigen-3.2.9-foss-2016b.eb --- easybuild/easyconfigs/e/Eigen/Eigen-3.2.9-foss-2016b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.9-foss-2016b.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.9-foss-2016b.eb index 2e997dc434..ce9863f2a8 100644 --- a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.9-foss-2016b.eb +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.9-foss-2016b.eb @@ -10,4 +10,4 @@ toolchain = {'name': 'foss', 'version': '2016b'} source_urls = ['http://bitbucket.org/%(namelower)s/%(namelower)s/get'] sources = ['%(version)s.tar.bz2'] -moduleclass = 'math' +moduleclass = 'math' -- GitLab From dc32386174c298a197a322b054861cc680465e9b Mon Sep 17 00:00:00 2001 From: iotaka Date: Fri, 13 Jan 2017 08:34:36 +0100 Subject: [PATCH 0035/1603] Update MPFR-3.1.4-foss-2016b.eb --- easybuild/easyconfigs/m/MPFR/MPFR-3.1.4-foss-2016b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MPFR/MPFR-3.1.4-foss-2016b.eb b/easybuild/easyconfigs/m/MPFR/MPFR-3.1.4-foss-2016b.eb index d0abf27110..d9a98da483 100644 --- a/easybuild/easyconfigs/m/MPFR/MPFR-3.1.4-foss-2016b.eb +++ b/easybuild/easyconfigs/m/MPFR/MPFR-3.1.4-foss-2016b.eb @@ -23,4 +23,4 @@ sanity_check_paths = { 'dirs': [] } -moduleclass = 'math' +moduleclass = 'math' -- GitLab From 8f00294c539073d806560da454b5c50866c9bd0e Mon Sep 17 00:00:00 2001 From: iotaka Date: Fri, 13 Jan 2017 08:35:05 +0100 Subject: [PATCH 0036/1603] Update Qt5-5.7.0-foss-2016b.eb --- easybuild/easyconfigs/q/Qt5/Qt5-5.7.0-foss-2016b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.7.0-foss-2016b.eb b/easybuild/easyconfigs/q/Qt5/Qt5-5.7.0-foss-2016b.eb index 66c30f53b8..22b14d640f 100644 --- a/easybuild/easyconfigs/q/Qt5/Qt5-5.7.0-foss-2016b.eb +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.7.0-foss-2016b.eb @@ -30,4 +30,4 @@ dependencies = [ ('libGLU', '9.0.0'), ] -moduleclass = 'devel' +moduleclass = 'devel' -- GitLab From 335d827a10dea245843c2417a102742267739caa Mon Sep 17 00:00:00 2001 From: iotaka Date: Fri, 13 Jan 2017 08:35:49 +0100 Subject: [PATCH 0037/1603] Update OpenFOAM-4.0-foss-2016b.eb --- easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.0-foss-2016b.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.0-foss-2016b.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.0-foss-2016b.eb index bf8451bef3..4f9d282dad 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.0-foss-2016b.eb +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.0-foss-2016b.eb @@ -1,7 +1,7 @@ name = 'OpenFOAM' version = '4.0' -homepage = 'http://www.openfoam.com/' +homepage = 'http://www.openfoam.org/' description = """OpenFOAM is a free, open source CFD software package. OpenFOAM has an extensive range of features to solve anything from complex fluid flows involving chemical reactions, turbulence and heat transfer, @@ -24,7 +24,6 @@ dependencies = [ ('METIS', '5.1.0'), #('METIS', '5.1.0', '-32bitIDX'), ('SCOTCH', '6.0.4'), - #('Boost', '1.61.0'), ('CGAL', '4.8.1'), ('ParaView', '5.1.2', '-mpi'), ] -- GitLab From 9c776b363b36183ecb03badc02d0237d47b49bc0 Mon Sep 17 00:00:00 2001 From: iotaka Date: Fri, 13 Jan 2017 08:37:20 +0100 Subject: [PATCH 0038/1603] Update CGAL-4.8.1-foss-2016b.eb --- easybuild/easyconfigs/c/CGAL/CGAL-4.8.1-foss-2016b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.8.1-foss-2016b.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.8.1-foss-2016b.eb index 20c45dda38..44d057e3a2 100644 --- a/easybuild/easyconfigs/c/CGAL/CGAL-4.8.1-foss-2016b.eb +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.8.1-foss-2016b.eb @@ -17,7 +17,7 @@ dependencies = [ ('MPFR', '3.1.4'), ('GMP', '6.1.1'), ('libGLU', '9.0.0'), - ('Qt5', '5.7.0'), + ('Qt', '4.8.7'), ] builddependencies = [ -- GitLab From 4229c6053dfea2329c61f5e83c035753155de94d Mon Sep 17 00:00:00 2001 From: iotaka Date: Fri, 13 Jan 2017 08:50:19 +0100 Subject: [PATCH 0039/1603] Update Qt5-5.7.0-foss-2016b.eb --- easybuild/easyconfigs/q/Qt5/Qt5-5.7.0-foss-2016b.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.7.0-foss-2016b.eb b/easybuild/easyconfigs/q/Qt5/Qt5-5.7.0-foss-2016b.eb index 22b14d640f..aed1d16c64 100644 --- a/easybuild/easyconfigs/q/Qt5/Qt5-5.7.0-foss-2016b.eb +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.7.0-foss-2016b.eb @@ -14,8 +14,6 @@ source_urls = [ ] sources = ['qt-everywhere-opensource-src-%(version)s.tar.xz'] -patches = ['%(name)s-%(version)s-workaround-icpc-bug.patch'] - builddependencies = [ ('pkg-config', '0.29.1'), ] -- GitLab From 6f5b48e3b6be222884ce59fb87e880b594b3500f Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Thu, 2 Feb 2017 17:24:20 +0100 Subject: [PATCH 0040/1603] adding easyconfigs: PyTables-3.2.2-foss-2016b-Python-2.7.12.eb, numexpr-2.6.1-foss-2016b-Python-2.7.12.eb --- .../numexpr-2.6.1-foss-2016b-Python-2.7.12.eb | 27 +++++++++++++ ...PyTables-3.2.2-foss-2016b-Python-2.7.12.eb | 38 +++++++++++++++++++ 2 files changed, 65 insertions(+) create mode 100644 easybuild/easyconfigs/n/numexpr/numexpr-2.6.1-foss-2016b-Python-2.7.12.eb create mode 100644 easybuild/easyconfigs/p/PyTables/PyTables-3.2.2-foss-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/n/numexpr/numexpr-2.6.1-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/n/numexpr/numexpr-2.6.1-foss-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..1cddd58e1d --- /dev/null +++ b/easybuild/easyconfigs/n/numexpr/numexpr-2.6.1-foss-2016b-Python-2.7.12.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'numexpr' +version = '2.6.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://code.google.com/p/numexpr/' +description = """The numexpr package evaluates multiple-operator array expressions many times faster than NumPy can. + It accepts the expression as a string, analyzes it, rewrites it more efficiently, and compiles it on the fly into + code for its internal virtual machine (VM). Due to its integrated just-in-time (JIT) compiler, it does not require a + compiler at runtime.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['https://github.com/pydata/numexpr/archive/'] +sources = ['v%(version)s.tar.gz'] + +dependencies = [ + ('Python', '2.7.12'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/PyTables/PyTables-3.2.2-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/PyTables/PyTables-3.2.2-foss-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..836640b941 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTables/PyTables-3.2.2-foss-2016b-Python-2.7.12.eb @@ -0,0 +1,38 @@ +easyblock = 'PythonPackage' + +name = 'PyTables' +version = '3.2.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.pytables.org' +description = """PyTables is a package for managing hierarchical datasets and designed to efficiently and easily cope + with extremely large amounts of data. PyTables is built on top of the HDF5 library, using the Python language and the + NumPy package. It features an object-oriented interface that, combined with C extensions for the performance-critical + parts of the code (generated using Cython), makes it a fast, yet extremely easy to use tool for interactively browse, + process and search very large amounts of data. One important feature of PyTables is that it optimizes memory and disk + resources so that data takes much less space (specially if on-flight compression is used) than other solutions such as + relational or object oriented databases.""" + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/PyTables/PyTables/archive/'] +sources = ['v.%(version)s.tar.gz'] + +patches = ['pyTables-%(version)s-fix-libs.patch'] + +dependencies = [ + ('Python', '2.7.12'), + ('numpy', '1.11.1', versionsuffix), + ('numexpr', '2.6.1', versionsuffix), + ('HDF5', '1.8.17'), +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['pt2to3', 'ptdump', 'ptrepack']], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +options = {'modulename': 'tables'} + +moduleclass = 'data' -- GitLab From 5fcb829872dfb476fdd3c7fc0a2ef897b43a65bc Mon Sep 17 00:00:00 2001 From: Maxime Boissonneault Date: Thu, 2 Feb 2017 14:53:34 +0000 Subject: [PATCH 0041/1603] Added MCR 2013b, 2014b, 2015b, 2016b with Java 1.8.0_121 as dependency --- easybuild/easyconfigs/m/MCR/MCR-R2013b.eb | 18 ++++++++++++++++++ easybuild/easyconfigs/m/MCR/MCR-R2014b.eb | 18 ++++++++++++++++++ easybuild/easyconfigs/m/MCR/MCR-R2015b.eb | 18 ++++++++++++++++++ easybuild/easyconfigs/m/MCR/MCR-R2016b.eb | 18 ++++++++++++++++++ 4 files changed, 72 insertions(+) create mode 100644 easybuild/easyconfigs/m/MCR/MCR-R2013b.eb create mode 100644 easybuild/easyconfigs/m/MCR/MCR-R2014b.eb create mode 100644 easybuild/easyconfigs/m/MCR/MCR-R2015b.eb create mode 100644 easybuild/easyconfigs/m/MCR/MCR-R2016b.eb diff --git a/easybuild/easyconfigs/m/MCR/MCR-R2013b.eb b/easybuild/easyconfigs/m/MCR/MCR-R2013b.eb new file mode 100644 index 0000000000..ea139590d9 --- /dev/null +++ b/easybuild/easyconfigs/m/MCR/MCR-R2013b.eb @@ -0,0 +1,18 @@ +name = 'MCR' +version = 'R2013b' + +homepage = 'http://www.mathworks.com/products/compiler/mcr/' +description = """The MATLAB Runtime is a standalone set of shared libraries + that enables the execution of compiled MATLAB applications + or components on computers that do not have MATLAB installed.""" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = [ + 'http://www.mathworks.com/supportfiles/MCR_Runtime/%(version)s/', +] +sources = ['%(name)s_%(version)s_glnxa64_installer.zip'] + +dependencies = [('Java', '1.8.0_121')] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/MCR/MCR-R2014b.eb b/easybuild/easyconfigs/m/MCR/MCR-R2014b.eb new file mode 100644 index 0000000000..1aaf919350 --- /dev/null +++ b/easybuild/easyconfigs/m/MCR/MCR-R2014b.eb @@ -0,0 +1,18 @@ +name = 'MCR' +version = 'R2014b' + +homepage = 'http://www.mathworks.com/products/compiler/mcr/' +description = """The MATLAB Runtime is a standalone set of shared libraries + that enables the execution of compiled MATLAB applications + or components on computers that do not have MATLAB installed.""" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = [ + 'http://www.mathworks.com/supportfiles/downloads/%(version)s/deployment_files/%(version)s/installers/glnxa64/', +] +sources = ['%(name)s_%(version)s_glnxa64_installer.zip'] + +dependencies = [('Java', '1.8.0_121')] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/MCR/MCR-R2015b.eb b/easybuild/easyconfigs/m/MCR/MCR-R2015b.eb new file mode 100644 index 0000000000..02cf05532e --- /dev/null +++ b/easybuild/easyconfigs/m/MCR/MCR-R2015b.eb @@ -0,0 +1,18 @@ +name = 'MCR' +version = 'R2015b' + +homepage = 'http://www.mathworks.com/products/compiler/mcr/' +description = """The MATLAB Runtime is a standalone set of shared libraries + that enables the execution of compiled MATLAB applications + or components on computers that do not have MATLAB installed.""" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = [ + 'http://www.mathworks.com/supportfiles/downloads/%(version)s/deployment_files/%(version)s/installers/glnxa64/', +] +sources = ['%(name)s_%(version)s_glnxa64_installer.zip'] + +dependencies = [('Java', '1.8.0_121')] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/MCR/MCR-R2016b.eb b/easybuild/easyconfigs/m/MCR/MCR-R2016b.eb new file mode 100644 index 0000000000..78ab492fb8 --- /dev/null +++ b/easybuild/easyconfigs/m/MCR/MCR-R2016b.eb @@ -0,0 +1,18 @@ +name = 'MCR' +version = 'R2016b' + +homepage = 'http://www.mathworks.com/products/compiler/mcr/' +description = """The MATLAB Runtime is a standalone set of shared libraries + that enables the execution of compiled MATLAB applications + or components on computers that do not have MATLAB installed.""" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = [ + 'http://www.mathworks.com/supportfiles/downloads/%(version)s/deployment_files/%(version)s/installers/glnxa64/', +] +sources = ['%(name)s_%(version)s_glnxa64_installer.zip'] + +dependencies = [('Java', '1.8.0_121')] + +moduleclass = 'math' -- GitLab From 2247e3141717a397e142124699e715c75eb94f4d Mon Sep 17 00:00:00 2001 From: Maxime Boissonneault Date: Thu, 2 Feb 2017 14:16:51 +0000 Subject: [PATCH 0042/1603] Added Java 1.8.0_121, which is the latest version --- easybuild/easyconfigs/j/Java/Java-1.8.0_121.eb | 15 +++++++++++++++ 1 file changed, 15 insertions(+) create mode 100644 easybuild/easyconfigs/j/Java/Java-1.8.0_121.eb diff --git a/easybuild/easyconfigs/j/Java/Java-1.8.0_121.eb b/easybuild/easyconfigs/j/Java/Java-1.8.0_121.eb new file mode 100644 index 0000000000..f95da7cf07 --- /dev/null +++ b/easybuild/easyconfigs/j/Java/Java-1.8.0_121.eb @@ -0,0 +1,15 @@ +name = 'Java' +version = '1.8.0_121' + +homepage = 'http://java.com/' +description = """Java Platform, Standard Edition (Java SE) lets you develop and deploy + Java applications on desktops and servers.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +# download the tar.gz directly from http://www.oracle.com/technetwork/java/javase/downloads/index.html +(vp, vs) = version.split('_') +altver = '%su%s' % (vp.split('.')[1], vs) +sources = ['jdk-%s-linux-x64.tar.gz' % altver] + +moduleclass = 'lang' -- GitLab From bfecb9916c49d2f19d942dcb4d5a9d6153fac0ba Mon Sep 17 00:00:00 2001 From: Masao Fujinaga Date: Fri, 3 Feb 2017 16:40:02 +0000 Subject: [PATCH 0043/1603] Allow intel 2017 to compile --- .../b/Bowtie/Bowtie-1.1.2-iimkl-2017a.eb | 20 +++++++++++++++++++ easybuild/easyconfigs/b/Bowtie/void2int.patch | 13 ++++++++++++ 2 files changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2-iimkl-2017a.eb create mode 100644 easybuild/easyconfigs/b/Bowtie/void2int.patch diff --git a/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2-iimkl-2017a.eb b/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2-iimkl-2017a.eb new file mode 100644 index 0000000000..500679eb6f --- /dev/null +++ b/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2-iimkl-2017a.eb @@ -0,0 +1,20 @@ +# Modified from existing version by: +# Robert Schmidt +# Ottawa Hospital Research Institute - Bioinformatics Team +name = 'Bowtie' +version = '1.1.2' + +homepage = 'http://bowtie-bio.sourceforge.net/index.shtml' +description = """Bowtie is an ultrafast, memory-efficient short read aligner. +It aligns short DNA sequences (reads) to the human genome. +""" + +toolchain = {'name': 'iimkl', 'version': '2017a'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = ['%(namelower)s-%(version)s-src.zip'] +source_urls = ['http://download.sourceforge.net/bowtie-bio/'] + +patches = ['int64typedef.patch','void2int.patch'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/Bowtie/void2int.patch b/easybuild/easyconfigs/b/Bowtie/void2int.patch new file mode 100644 index 0000000000..80b76591d4 --- /dev/null +++ b/easybuild/easyconfigs/b/Bowtie/void2int.patch @@ -0,0 +1,13 @@ +--- processor_support.h.orig 2017-02-02 21:48:42.436432756 +0000 ++++ processor_support.h 2017-02-02 21:48:54.419309743 +0000 +@@ -44,8 +44,8 @@ + + try { + #if ( defined(USING_INTEL_COMPILER) || defined(USING_MSC_COMPILER) ) +- __cpuid((void *) ®s,0); // test if __cpuid() works, if not catch the exception +- __cpuid((void *) ®s,0x1); // POPCNT bit is bit 23 in ECX ++ __cpuid((int *) ®s,0); // test if __cpuid() works, if not catch the exception ++ __cpuid((int *) ®s,0x1); // POPCNT bit is bit 23 in ECX + #elif defined(USING_GCC_COMPILER) + __get_cpuid(0x1, ®s.EAX, ®s.EBX, ®s.ECX, ®s.EDX); + #else -- GitLab From cfcada98291a92ba8989119892999eb990644080 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Sun, 5 Feb 2017 23:04:31 +0100 Subject: [PATCH 0044/1603] adding easyconfigs: Armadillo-7.600.2-foss-2016b-Python-2.7.12.eb, arpack-ng-3.4.0-foss-2016b.eb --- ...adillo-7.600.2-foss-2016b-Python-2.7.12.eb | 23 +++++++++++++++++ .../a/arpack-ng/arpack-ng-3.4.0-foss-2016b.eb | 25 +++++++++++++++++++ 2 files changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/a/Armadillo/Armadillo-7.600.2-foss-2016b-Python-2.7.12.eb create mode 100644 easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.4.0-foss-2016b.eb diff --git a/easybuild/easyconfigs/a/Armadillo/Armadillo-7.600.2-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/a/Armadillo/Armadillo-7.600.2-foss-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..8f548fef7d --- /dev/null +++ b/easybuild/easyconfigs/a/Armadillo/Armadillo-7.600.2-foss-2016b-Python-2.7.12.eb @@ -0,0 +1,23 @@ +name = 'Armadillo' +version = '7.600.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://arma.sourceforge.net/' +description = """Armadillo is an open-source C++ linear algebra library (matrix maths) aiming towards + a good balance between speed and ease of use. Integer, floating point and complex numbers are supported, + as well as a subset of trigonometric and statistics functions.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +sources = [SOURCELOWER_TAR_XZ] +source_urls = ['http://sourceforge.net/projects/arma/files'] + +dependencies = [ + ('Boost', '1.61.0', versionsuffix), + ('arpack-ng', '3.4.0'), + ('Python', '2.7.12'), +] + +builddependencies = [('CMake', '3.6.2')] + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.4.0-foss-2016b.eb b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.4.0-foss-2016b.eb new file mode 100644 index 0000000000..9320f188ec --- /dev/null +++ b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.4.0-foss-2016b.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'arpack-ng' +version = '3.4.0' + +homepage = 'http://forge.scilab.org/index.php/p/arpack-ng/' +description = """ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems.""" + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'opt': True, 'pic': True, 'usempi': True} + +source_urls = ['https://github.com/opencollab/arpack-ng/archive/'] +sources = ['%(version)s.tar.gz'] + +builddependencies = [('Autotools', '20150215')] + +preconfigopts = "sh bootstrap && " +configopts = '--with-pic --with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK"' + +sanity_check_paths = { + 'files': ["lib/libarpack.a", "lib/libarpack.so"], + 'dirs': [] +} + +moduleclass = 'numlib' -- GitLab From eddb755218b40bd824e560f71a8579c0316a8fc7 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Sun, 5 Feb 2017 23:46:40 +0100 Subject: [PATCH 0045/1603] adding easyconfigs: protobuf-python-3.2.0-foss-2016b-Python-2.7.12.eb, protobuf-python-3.2.0-foss-2016b-Python-3.5.2.eb, protobuf-3.2.0-foss-2016b.eb, Tensorflow-0.12.1-foss-2016b-Python-2.7.12.eb, Tensorflow-0.12.1-foss-2016b-Python-3.5.2.eb --- ...f-python-3.2.0-foss-2016b-Python-2.7.12.eb | 29 +++++++++++++++ ...uf-python-3.2.0-foss-2016b-Python-3.5.2.eb | 29 +++++++++++++++ .../p/protobuf/protobuf-3.2.0-foss-2016b.eb | 23 ++++++++++++ ...sorflow-0.12.1-foss-2016b-Python-2.7.12.eb | 35 +++++++++++++++++++ ...nsorflow-0.12.1-foss-2016b-Python-3.5.2.eb | 35 +++++++++++++++++++ 5 files changed, 151 insertions(+) create mode 100644 easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.2.0-foss-2016b-Python-2.7.12.eb create mode 100644 easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.2.0-foss-2016b-Python-3.5.2.eb create mode 100755 easybuild/easyconfigs/p/protobuf/protobuf-3.2.0-foss-2016b.eb create mode 100755 easybuild/easyconfigs/t/Tensorflow/Tensorflow-0.12.1-foss-2016b-Python-2.7.12.eb create mode 100755 easybuild/easyconfigs/t/Tensorflow/Tensorflow-0.12.1-foss-2016b-Python-3.5.2.eb diff --git a/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.2.0-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.2.0-foss-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..25a3d48ede --- /dev/null +++ b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.2.0-foss-2016b-Python-2.7.12.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'protobuf-python' +version = '3.2.0' +versionsuffix= '-Python-%(pyver)s' + +homepage = 'https://github.com/google/protobuf/' +description = """Python Protocol Buffers runtime library.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['https://github.com/google/protobuf/archive/v%(version)s'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.12'), + ('protobuf', version) +] + +start_dir = 'python' + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +options = {'modulename': 'google.protobuf' } + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.2.0-foss-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.2.0-foss-2016b-Python-3.5.2.eb new file mode 100644 index 0000000000..a88f02f65a --- /dev/null +++ b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.2.0-foss-2016b-Python-3.5.2.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'protobuf-python' +version = '3.2.0' +versionsuffix= '-Python-%(pyver)s' + +homepage = 'https://github.com/google/protobuf/' +description = """Python Protocol Buffers runtime library.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['https://github.com/google/protobuf/archive/v%(version)s'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '3.5.2'), + ('protobuf', version) +] + +start_dir = 'python' + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +options = {'modulename': 'google.protobuf' } + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/protobuf/protobuf-3.2.0-foss-2016b.eb b/easybuild/easyconfigs/p/protobuf/protobuf-3.2.0-foss-2016b.eb new file mode 100755 index 0000000000..f6b756484f --- /dev/null +++ b/easybuild/easyconfigs/p/protobuf/protobuf-3.2.0-foss-2016b.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'protobuf' +version = '3.2.0' + +homepage = 'https://github.com/google/protobuf/' +description = """Google Protocol Buffers""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['https://github.com/google/protobuf/archive/v%(version)s/'] +sources = [SOURCE_TAR_GZ] + +builddependencies = [('Autotools', '20150215')] + +preconfigopts = "./autogen.sh && " + +sanity_check_paths = { + 'files': ['bin/protoc', 'lib/libprotobuf.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/t/Tensorflow/Tensorflow-0.12.1-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/t/Tensorflow/Tensorflow-0.12.1-foss-2016b-Python-2.7.12.eb new file mode 100755 index 0000000000..b94ca618c9 --- /dev/null +++ b/easybuild/easyconfigs/t/Tensorflow/Tensorflow-0.12.1-foss-2016b-Python-2.7.12.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonPackage' + +name = 'Tensorflow' +version = '0.12.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://www.tensorflow.org/' +description = "An open-source software library for Machine Intelligence" + +toolchain = {'name': 'foss', 'version': '2016b'} + +pymaj = '2' +pymin = '7' +pymajmin = pymaj + pymin + +source_urls = ['https://pypi.python.org/packages/7e/c6/837f4e249aae5c86a632eaaa9779e601eca1487772f8ad75c347bf9e813f/'] +sources = [ + 'tensorflow-%%(version)s-cp%(pymajmin)s-cp%(pymajmin)smu-manylinux1_x86_64.whl' % {'pymajmin': pymajmin}, +] +checksums = ['c98fd26b79a97cc490c942bbafed5462'] + +dependencies = [ + ('Python', '%s.%s.12' % (pymaj, pymin)), + ('protobuf-python', '3.2.0', versionsuffix), +] + +use_pip = True +unpack_sources = False + +sanity_check_paths = { + 'files': ['bin/tensorboard'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/Tensorflow/Tensorflow-0.12.1-foss-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/t/Tensorflow/Tensorflow-0.12.1-foss-2016b-Python-3.5.2.eb new file mode 100755 index 0000000000..d8b2947422 --- /dev/null +++ b/easybuild/easyconfigs/t/Tensorflow/Tensorflow-0.12.1-foss-2016b-Python-3.5.2.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonPackage' + +name = 'Tensorflow' +version = '0.12.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://www.tensorflow.org/' +description = "An open-source software library for Machine Intelligence" + +toolchain = {'name': 'foss', 'version': '2016b'} + +pymaj = '3' +pymin = '5' +pymajmin = pymaj + pymin + +source_urls = ['https://pypi.python.org/packages/e5/5c/56e6522fdcd6f8739dcbc4de62e8b0040e141785bb42e5b53a83b0ba3e58/'] +sources = [ + 'tensorflow-%%(version)s-cp%(pymajmin)s-cp%(pymajmin)sm-manylinux1_x86_64.whl' % {'pymajmin': pymajmin}, +] +checksums = ['c6e3ba8579754f37d37be26e863f9d95'] + +dependencies = [ + ('Python', '%s.%s.2' % (pymaj, pymin)), + ('protobuf-python', '3.2.0', versionsuffix), +] + +use_pip = True +unpack_sources = False + +sanity_check_paths = { + 'files': ['bin/tensorboard'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'lib' -- GitLab From 92797f67325c275d17e41b0927a882b744761024 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Mon, 6 Feb 2017 10:29:09 +0100 Subject: [PATCH 0046/1603] adding easyconfigs: DIAMOND-0.8.35-goolf-1.7.20.eb --- .../d/DIAMOND/DIAMOND-0.8.35-goolf-1.7.20.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/d/DIAMOND/DIAMOND-0.8.35-goolf-1.7.20.eb diff --git a/easybuild/easyconfigs/d/DIAMOND/DIAMOND-0.8.35-goolf-1.7.20.eb b/easybuild/easyconfigs/d/DIAMOND/DIAMOND-0.8.35-goolf-1.7.20.eb new file mode 100644 index 0000000000..19f96d592f --- /dev/null +++ b/easybuild/easyconfigs/d/DIAMOND/DIAMOND-0.8.35-goolf-1.7.20.eb @@ -0,0 +1,32 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = "CMakeMake" + +name = 'DIAMOND' +version = '0.8.35' + +homepage = 'https://github.com/bbuchfink/diamond' +description = """Accelerated BLAST compatible local sequence aligner""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +source_urls = ['https://github.com/bbuchfink/diamond/archive/'] +sources = ['v%(version)s.tar.gz'] + +separate_build_dir = True + +builddependencies = [('CMake', '3.4.3')] + +dependencies = [ + ('zlib', '1.2.8'), +] + +sanity_check_paths = { + 'files': ['bin/diamond'], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From 511de25f91be78fdd24e8e7fe913e3b4dce1c4c6 Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Wed, 8 Feb 2017 13:41:32 +0100 Subject: [PATCH 0047/1603] Add patch to work around build failures with GCC 6 --- .../pkg-config-0.29.1-foss-2017a.eb | 30 +++++++++++++++++++ .../pkg-config/pkg-config-0.29.1_gcc-6.patch | 22 ++++++++++++++ 2 files changed, 52 insertions(+) create mode 100644 easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1-foss-2017a.eb create mode 100644 easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1_gcc-6.patch diff --git a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1-foss-2017a.eb b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1-foss-2017a.eb new file mode 100644 index 0000000000..b3ddd790cb --- /dev/null +++ b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1-foss-2017a.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'pkg-config' +version = '0.29.1' + +homepage = 'http://www.freedesktop.org/wiki/Software/pkg-config/' +description = """pkg-config is a helper tool used when compiling applications and libraries. It helps you insert the + correct compiler options on the command line so an application can use + gcc -o test test.c `pkg-config --libs --cflags glib-2.0` + for instance, rather than hard-coding values on where to find glib (or other libraries).""" + +toolchain = {'name': 'foss', 'version': '2017a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['https://pkg-config.freedesktop.org/releases/'] +patches = [ + 'pkg-config-%(version)s_gcc-6.patch', +] + +# don't use PAX, it might break. +tar_config_opts = True + +configopts = " --with-internal-glib" + +sanity_check_paths = { + 'files': ['bin/pkg-config'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1_gcc-6.patch b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1_gcc-6.patch new file mode 100644 index 0000000000..a83002f30d --- /dev/null +++ b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1_gcc-6.patch @@ -0,0 +1,22 @@ +Work around for build failures with GCC 6 backported from upstream glib. +See https://bugzilla.gnome.org/761550 for details. + +diff -Nrup pkg-config-0.29.1.orig/glib/glib/gdate.c pkg-config-0.29.1/glib/glib/gdate.c +--- pkg-config-0.29.1.orig/glib/glib/gdate.c 2016-01-24 22:51:38.000000000 +0100 ++++ pkg-config-0.29.1/glib/glib/gdate.c 2017-02-07 17:34:54.372617599 +0100 +@@ -2439,6 +2439,9 @@ win32_strftime_helper (const GDate * + * + * Returns: number of characters written to the buffer, or 0 the buffer was too small + */ ++#pragma GCC diagnostic push ++#pragma GCC diagnostic ignored "-Wformat-nonliteral" ++ + gsize + g_date_strftime (gchar *s, + gsize slen, +@@ -2549,3 +2552,5 @@ g_date_strftime (gchar *s, + return retval; + #endif + } ++ ++#pragma GCC diagnostic pop -- GitLab From c3def62161b75ed733478aadd83675e4bfbcf79b Mon Sep 17 00:00:00 2001 From: Yann Sagon Date: Wed, 8 Feb 2017 14:27:48 +0100 Subject: [PATCH 0048/1603] smoldyn --- .../s/Smoldyn/Smoldyn-2.48-foss-2016a.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/s/Smoldyn/Smoldyn-2.48-foss-2016a.eb diff --git a/easybuild/easyconfigs/s/Smoldyn/Smoldyn-2.48-foss-2016a.eb b/easybuild/easyconfigs/s/Smoldyn/Smoldyn-2.48-foss-2016a.eb new file mode 100644 index 0000000000..71310f26f2 --- /dev/null +++ b/easybuild/easyconfigs/s/Smoldyn/Smoldyn-2.48-foss-2016a.eb @@ -0,0 +1,39 @@ +easyblock = 'CMakeMake' + +name = 'Smoldyn' +version = '2.48' + +homepage = 'http://www.smoldyn.org/' +description = """ +Smoldyn is a computer program for cell-scale biochemical simulations. It simulates each molecule of interest individually to capture natural stochasticity and to yield nanometer-scale spatial resolution. It treats other molecules implicitly, enabling it to simulate hundreds of thousands of molecules over several minutes of real time. Simulated molecules diffuse, react, are confined by surfaces, and bind to membranes much as they would in a real biological system. +""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://www.smoldyn.org/'] +sources = ['smoldyn-%(version)s.tgz'] + +builddependencies = [ + ('CMake', '3.4.3'), + ('LibTIFF','4.0.6'), + ('zlib', '1.2.8'), + ('freeglut', '3.0.0'), + ('libXmu', '1.1.2'), + ('libXi', '1.7.6') +] + +dependencies = [ + ('LibTIFF','4.0.6'), + ('zlib', '1.2.8'), + ('freeglut', '3.0.0'), + ('libXmu', '1.1.2'), + ('libXi', '1.7.6') +] + + +sanity_check_paths = { + 'files': ["bin/smoldyn"], + 'dirs': [] +} + +moduleclass = 'bio' -- GitLab From 9943419d1751374d5dce9fb3c799dbc0b17b59ab Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Thu, 9 Feb 2017 10:17:10 +0100 Subject: [PATCH 0049/1603] Add Bison and gettext as build dependencies --- easybuild/easyconfigs/x/X11/X11-20160819-foss-2015a.eb | 2 ++ easybuild/easyconfigs/x/X11/X11-20160819-foss-2016b.eb | 2 ++ easybuild/easyconfigs/x/X11/X11-20160819-intel-2016b.eb | 2 ++ 3 files changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/x/X11/X11-20160819-foss-2015a.eb b/easybuild/easyconfigs/x/X11/X11-20160819-foss-2015a.eb index ca30f6a696..94c5bfdb69 100644 --- a/easybuild/easyconfigs/x/X11/X11-20160819-foss-2015a.eb +++ b/easybuild/easyconfigs/x/X11/X11-20160819-foss-2015a.eb @@ -18,6 +18,8 @@ source_urls = [ builddependencies = [ ('Autotools', '20150215'), + ('Bison', '3.0.4'), + ('gettext', '0.19.4'), ('pkg-config', '0.29.1'), ] dependencies = [ diff --git a/easybuild/easyconfigs/x/X11/X11-20160819-foss-2016b.eb b/easybuild/easyconfigs/x/X11/X11-20160819-foss-2016b.eb index c44e65c206..fbaa5cf2db 100644 --- a/easybuild/easyconfigs/x/X11/X11-20160819-foss-2016b.eb +++ b/easybuild/easyconfigs/x/X11/X11-20160819-foss-2016b.eb @@ -18,6 +18,8 @@ source_urls = [ builddependencies = [ ('Autotools', '20150215'), + ('Bison', '3.0.4'), + ('gettext', '0.19.8'), ('pkg-config', '0.29.1'), ] dependencies = [ diff --git a/easybuild/easyconfigs/x/X11/X11-20160819-intel-2016b.eb b/easybuild/easyconfigs/x/X11/X11-20160819-intel-2016b.eb index 556bda9f6e..586cdcf5d6 100644 --- a/easybuild/easyconfigs/x/X11/X11-20160819-intel-2016b.eb +++ b/easybuild/easyconfigs/x/X11/X11-20160819-intel-2016b.eb @@ -18,6 +18,8 @@ source_urls = [ builddependencies = [ ('Autotools', '20150215'), + ('Bison', '3.0.4'), + ('gettext', '0.19.8'), ('pkg-config', '0.29.1'), ] dependencies = [ -- GitLab From 1e581b8020df5f7d38333ea148b710d93f38d61f Mon Sep 17 00:00:00 2001 From: RvDijk Date: Thu, 9 Feb 2017 11:38:22 +0100 Subject: [PATCH 0050/1603] Emacs with foss2016a --- .../e/Emacs/Emacs-25.1-foss-2016a.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/e/Emacs/Emacs-25.1-foss-2016a.eb diff --git a/easybuild/easyconfigs/e/Emacs/Emacs-25.1-foss-2016a.eb b/easybuild/easyconfigs/e/Emacs/Emacs-25.1-foss-2016a.eb new file mode 100644 index 0000000000..3b50903d7f --- /dev/null +++ b/easybuild/easyconfigs/e/Emacs/Emacs-25.1-foss-2016a.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'Emacs' +version = '25.1' + +homepage = 'http://www.gnu.org/software/emacs/' +description = """GNU Emacs is an extensible, customizable text editor—and more. + At its core is an interpreter for Emacs Lisp, a dialect of the Lisp programming language + with extensions to support text editing.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +osdependencies = [ + ('ncurses'), +] + +dependencies = [ + ('zlib', '1.2.8'), + ('libpng', '1.6.23'), + ('libjpeg-turbo', '1.5.0'), + ('ncurses', '6.0'), +] + +configopts = '--with-gif=no --with-tiff=no --with-x-toolkit=no --with-xpm=no ' + +sanity_check_paths = { + 'files': ["bin/emacs", "bin/emacs-%(version)s", "bin/emacsclient", "bin/etags"], + 'dirs': [] +} + +moduleclass = 'tools' -- GitLab From 97c566f492c41b47976aedb88f1ffe5ad77c38d3 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Thu, 9 Feb 2017 12:51:50 +0100 Subject: [PATCH 0051/1603] rm builddep --- easybuild/easyconfigs/e/Emacs/Emacs-25.1-foss-2016a.eb | 4 ---- 1 file changed, 4 deletions(-) diff --git a/easybuild/easyconfigs/e/Emacs/Emacs-25.1-foss-2016a.eb b/easybuild/easyconfigs/e/Emacs/Emacs-25.1-foss-2016a.eb index 3b50903d7f..bc3043a68b 100644 --- a/easybuild/easyconfigs/e/Emacs/Emacs-25.1-foss-2016a.eb +++ b/easybuild/easyconfigs/e/Emacs/Emacs-25.1-foss-2016a.eb @@ -13,10 +13,6 @@ toolchain = {'name': 'foss', 'version': '2016a'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] -osdependencies = [ - ('ncurses'), -] - dependencies = [ ('zlib', '1.2.8'), ('libpng', '1.6.23'), -- GitLab From 3b9db641f233dbf157d15c2aa51f79d20846ca0b Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Thu, 9 Feb 2017 13:29:58 +0100 Subject: [PATCH 0052/1603] libdrm: clean up dependencies --- easybuild/easyconfigs/l/libdrm/libdrm-2.4.70-foss-2016b.eb | 2 -- easybuild/easyconfigs/l/libdrm/libdrm-2.4.70-intel-2016b.eb | 2 -- 2 files changed, 4 deletions(-) diff --git a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.70-foss-2016b.eb b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.70-foss-2016b.eb index bd2875fe53..5d9e8ac938 100644 --- a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.70-foss-2016b.eb +++ b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.70-foss-2016b.eb @@ -13,8 +13,6 @@ toolchain = {'name': 'foss', 'version': '2016b'} dependencies = [ ('X11', '20160819'), - ('libpthread-stubs', '0.3'), - ('libpciaccess', '0.13.4'), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.70-intel-2016b.eb b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.70-intel-2016b.eb index 1f6c3d5a42..9fb07a2954 100644 --- a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.70-intel-2016b.eb +++ b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.70-intel-2016b.eb @@ -13,8 +13,6 @@ toolchain = {'name': 'intel', 'version': '2016b'} dependencies = [ ('X11', '20160819'), - ('libpthread-stubs', '0.3'), - ('libpciaccess', '0.13.4'), ] sanity_check_paths = { -- GitLab From bcfcb50c38b30a3cb613d1d3c97cc061d8a5db29 Mon Sep 17 00:00:00 2001 From: Robert Schmidt Date: Thu, 9 Feb 2017 12:52:18 +0000 Subject: [PATCH 0053/1603] update for non cray --- easybuild/easyconfigs/b/Bazel/Bazel-0.4.4.eb | 30 +++++++++++++++++++ .../easyconfigs/j/Java/Java-1.8.0_121.eb | 15 ++++++++++ 2 files changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bazel/Bazel-0.4.4.eb create mode 100644 easybuild/easyconfigs/j/Java/Java-1.8.0_121.eb diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-0.4.4.eb b/easybuild/easyconfigs/b/Bazel/Bazel-0.4.4.eb new file mode 100644 index 0000000000..81fd376a8e --- /dev/null +++ b/easybuild/easyconfigs/b/Bazel/Bazel-0.4.4.eb @@ -0,0 +1,30 @@ +# @author: Robert Schmidt (OHRI) +# @author: Guilherme Peretti-Pezzi (CSCS) + +easyblock = "CmdCp" + +name = 'Bazel' +version = '0.4.4' + +homepage = 'http://bazel.io/' +description = """Bazel is a build tool that builds code quickly and reliably. +It is used to build the majority of Google's software.""" + +toolchain = {'name': 'dummy', 'version': ''} + +dependencies = [ + ('Java', '1.8.0_121'), +] + +sources = ['%(namelower)s-%(version)s-dist.zip'] +source_urls = ['https://github.com/bazelbuild/bazel/releases/download/%(version)s'] +cmds_map = [('.*', "JAVA_VERSION=1.8 CC=gcc CXX=g++ ./compile.sh")] + +files_to_copy = [(['output/bazel'], 'bin')] + +sanity_check_paths={ + 'files': ['bin/bazel'], + 'dirs': ['bin'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/j/Java/Java-1.8.0_121.eb b/easybuild/easyconfigs/j/Java/Java-1.8.0_121.eb new file mode 100644 index 0000000000..2782d792e8 --- /dev/null +++ b/easybuild/easyconfigs/j/Java/Java-1.8.0_121.eb @@ -0,0 +1,15 @@ +name = 'Java' +version = "1.8.0_121" + +homepage = 'http://java.com/' +description = """Java Platform, Standard Edition (Java SE) lets you develop and deploy + Java applications on desktops and servers.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +# download the tar.gz directly from http://www.oracle.com/technetwork/java/javase/downloads/index.html +(vp, vs) = version.split('_') +altver = '%su%s' % (vp.split('.')[1], vs) +sources = ['jdk-%s-linux-x64.tar.gz' % altver] + +moduleclass = 'lang' -- GitLab From 3f6c9e9493b7048cc08631e07b673f8686efdf62 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Thu, 9 Feb 2017 14:43:37 +0100 Subject: [PATCH 0054/1603] adding easyconfigs: GMP-6.1.2-foss-2016b.eb --- .../easyconfigs/g/GMP/GMP-6.1.2-foss-2016b.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/g/GMP/GMP-6.1.2-foss-2016b.eb diff --git a/easybuild/easyconfigs/g/GMP/GMP-6.1.2-foss-2016b.eb b/easybuild/easyconfigs/g/GMP/GMP-6.1.2-foss-2016b.eb new file mode 100644 index 0000000000..8f949a1a92 --- /dev/null +++ b/easybuild/easyconfigs/g/GMP/GMP-6.1.2-foss-2016b.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'GMP' +version = '6.1.2' + +homepage = 'http://gmplib.org/' +description = """GMP is a free library for arbitrary precision arithmetic, +operating on signed integers, rational numbers, and floating point numbers. """ + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'pic': True, 'precise': True} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://ftp.gnu.org/gnu/gmp'] + +builddependencies = [ + ('Autotools', '20150215'), +] + +# enable C++ interface +configopts = '--enable-cxx' + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libgmp.%s' % SHLIB_EXT, 'include/gmp.h'], + 'dirs': [], +} + +moduleclass = 'math' -- GitLab From a7ea9016be0d7c6c077f075513fbd31f27e4835d Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Fri, 10 Feb 2017 11:09:29 +0100 Subject: [PATCH 0055/1603] {vis}[intel/2016b] Ghostscript 9.20 use external freetype, libpng, jpeg, and zlib (REVIEW) --- .../easyconfigs/g/Ghostscript/Ghostscript-9.20-intel-2016b.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.20-intel-2016b.eb b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.20-intel-2016b.eb index 2238d98b96..d3f76e106a 100644 --- a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.20-intel-2016b.eb +++ b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.20-intel-2016b.eb @@ -24,6 +24,9 @@ dependencies = [ ('LibTIFF', '4.0.6'), ] +#Do not use local copies of zlib, jpeg, freetype, and png +preconfigopts = "mv zlib zlib.no && mv jpeg jpeg.no && mv freetype freetype.no && mv libpng libpng.no &&" + configopts = "--with-system-libtiff --enable-dynamic" moduleclass = 'tools' -- GitLab From ee0a56a7b7adb71c4e776ea17e9a17446e6fa064 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Fri, 10 Feb 2017 11:38:17 +0100 Subject: [PATCH 0056/1603] {vis}[foss/2016b] graphviz 0.5.1 w/ Python 2.7.12 (REVIEW) --- .../c/Clang/Clang-3.8.1-foss-2016b.eb | 49 ++++++++++++++ .../c/cairo/cairo-1.14.6-foss-2016b.eb | 40 +++++++++++ ...GObject-Introspection-1.49.1-foss-2016b.eb | 47 +++++++++++++ .../Ghostscript-9.20-foss-2016b.eb | 32 +++++++++ .../g/Graphviz/Graphviz-2.38.0-foss-2016b.eb | 67 +++++++++++++++++++ ...graphviz-0.5.1-foss-2016b-Python-2.7.12.eb | 25 +++++++ .../h/HarfBuzz/HarfBuzz-1.3.1-foss-2016b.eb | 34 ++++++++++ .../p/Pango/Pango-1.40.3-foss-2016b.eb | 31 +++++++++ .../p/pixman/pixman-0.34.0-foss-2016b.eb | 20 ++++++ 9 files changed, 345 insertions(+) create mode 100644 easybuild/easyconfigs/c/Clang/Clang-3.8.1-foss-2016b.eb create mode 100644 easybuild/easyconfigs/c/cairo/cairo-1.14.6-foss-2016b.eb create mode 100644 easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.49.1-foss-2016b.eb create mode 100644 easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.20-foss-2016b.eb create mode 100644 easybuild/easyconfigs/g/Graphviz/Graphviz-2.38.0-foss-2016b.eb create mode 100644 easybuild/easyconfigs/g/graphviz/graphviz-0.5.1-foss-2016b-Python-2.7.12.eb create mode 100644 easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.3.1-foss-2016b.eb create mode 100644 easybuild/easyconfigs/p/Pango/Pango-1.40.3-foss-2016b.eb create mode 100644 easybuild/easyconfigs/p/pixman/pixman-0.34.0-foss-2016b.eb diff --git a/easybuild/easyconfigs/c/Clang/Clang-3.8.1-foss-2016b.eb b/easybuild/easyconfigs/c/Clang/Clang-3.8.1-foss-2016b.eb new file mode 100644 index 0000000000..bc4ee73735 --- /dev/null +++ b/easybuild/easyconfigs/c/Clang/Clang-3.8.1-foss-2016b.eb @@ -0,0 +1,49 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2013-2015 Dmitri Gribenko, Ward Poelmans +# Authors:: Dmitri Gribenko +# Authors:: Ward Poelmans +# License:: GPLv2 or later, MIT, three-clause BSD. +# $Id$ +## + +name = "Clang" +version = "3.8.1" + +homepage = "http://clang.llvm.org/" +description = """C, C++, Objective-C compiler, based on LLVM. Does not + include C++ standard library -- use libstdc++ from GCC.""" + +# Clang also depends on libstdc++ during runtime, but this dependency is +# already specified as the toolchain. +toolchain = {'name': 'foss', 'version': '2016b'} +# Do not set optarch to True: it will cause the build to fail +toolchainopts = {'optarch': False} + +source_urls = ["http://llvm.org/releases/%(version)s"] +sources = [ + "llvm-%(version)s.src.tar.xz", + "cfe-%(version)s.src.tar.xz", + "compiler-rt-%(version)s.src.tar.xz", + "polly-%(version)s.src.tar.xz", + "openmp-%(version)s.src.tar.xz", +] + +dependencies = [ + ('GMP', '6.1.1'), +] + +builddependencies = [ + ('CMake', '3.6.1'), + ('Python', '2.7.12'), + ('libxml2', '2.9.4'), +] + +assertions = True + +usepolly = True + +build_targets = ['X86'] + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/c/cairo/cairo-1.14.6-foss-2016b.eb b/easybuild/easyconfigs/c/cairo/cairo-1.14.6-foss-2016b.eb new file mode 100644 index 0000000000..39aaca6d60 --- /dev/null +++ b/easybuild/easyconfigs/c/cairo/cairo-1.14.6-foss-2016b.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'cairo' +version = '1.14.6' + +homepage = 'http://cairographics.org' +description = """Cairo is a 2D graphics library with support for multiple output devices. + Currently supported output targets include the X Window System (via both Xlib and XCB), Quartz, Win32, image buffers, + PostScript, PDF, and SVG file output. Experimental backends include OpenGL, BeOS, OS/2, and DirectFB""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['http://cairographics.org/releases/'] +sources = [SOURCE_TAR_XZ] + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libpng', '1.6.24'), + ('freetype', '2.6.5'), + ('pixman', '0.34.0'), + ('expat', '2.2.0'), + ('GLib', '2.49.5'), + ('X11', '20160819'), +] + +# disable symbol lookup, which requires -lbfd, to avoid link issues with (non-PIC) libiberty.a provided by GCC +configopts = "--enable-symbol-lookup=no --enable-gobject=yes --enable-svg=yes --enable-tee=yes --enable-xlib-xcb " + +sanity_check_paths = { + 'files': ['bin/cairo-trace', 'lib/cairo/libcairo-trace.so', 'lib/cairo/libcairo-trace.a', + 'lib/libcairo.a', 'lib/libcairo-gobject.a', 'lib/libcairo-script-interpreter.a', + 'lib/libcairo-gobject.so', 'lib/libcairo-script-interpreter.so', 'lib/libcairo.so'] + + ['include/cairo/cairo%s.h' % x for x in ['', '-deprecated', '-features', '-ft', '-gobject', '-pdf', '-ps', + '-script', '-script-interpreter', '-svg', '-version', '-xcb', + '-xlib', '-xlib-xrender']], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.49.1-foss-2016b.eb b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.49.1-foss-2016b.eb new file mode 100644 index 0000000000..76281fb06e --- /dev/null +++ b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.49.1-foss-2016b.eb @@ -0,0 +1,47 @@ +easyblock = 'ConfigureMake' + +name = 'GObject-Introspection' +version = '1.49.1' + +homepage = 'https://wiki.gnome.org/GObjectIntrospection/' +description = """GObject introspection is a middleware layer between C libraries + (using GObject) and language bindings. The C library can be scanned at + compile time and generate a metadata file, in addition to the actual + native C library. Then at runtime, language bindings can read this + metadata and automatically provide bindings to call into the C library.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('Python', '2.7.12'), + ('GLib', '2.49.5'), + ('libffi', '3.2.1'), +] + +builddependencies = [ + ('Autotools', '20150215'), + ('flex', '2.6.0'), + ('Bison', '3.0.4'), + ('cairo', '1.14.6'), +] + +preconfigopts = "env GI_SCANNER_DISABLE_CACHE=true " + +# avoid using hard-coded path to 'python' in shebang of scripts +buildopts = "PYTHON=python" + +modextrapaths = { + 'GI_TYPELIB_PATH': 'share', + 'XDG_DATA_DIRS': 'share', +} + +sanity_check_paths = { + 'files': ['bin/g-ir-%s' % x for x in ['annotation-tool', 'compiler', 'generate', 'scanner']] + + ['lib/libgirepository-1.0.%s' % x for x in ['so', 'a']], + 'dirs': ['include', 'share'] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.20-foss-2016b.eb b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.20-foss-2016b.eb new file mode 100644 index 0000000000..7305497c37 --- /dev/null +++ b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.20-foss-2016b.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'Ghostscript' +version = '9.20' + +homepage = 'http://ghostscript.com' +description = """Ghostscript is a versatile processor for PostScript data with the ability to render PostScript to + different targets. It used to be part of the cups printing stack, but is no longer used for that.""" + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'pic': True} + +source_urls = ["https://github.com/ArtifexSoftware/ghostpdl-downloads/releases/download/gs%(version_major)s%(version_minor)s/"] +sources = ['ghostscript-%(version)s.tar.gz'] + +dependencies = [ + ('zlib', '1.2.8'), + ('libpng', '1.6.24'), + ('freetype', '2.6.5'), + ('libjpeg-turbo', '1.5.0'), + ('expat', '2.2.0'), + ('GLib', '2.49.5'), + ('cairo', '1.14.6'), + ('LibTIFF', '4.0.6'), +] + +#Do not use local copies of zlib, jpeg, freetype, and png +preconfigopts = "mv zlib zlib.no && mv jpeg jpeg.no && mv freetype freetype.no && mv libpng libpng.no &&" + +configopts = "--with-system-libtiff --enable-dynamic" + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/g/Graphviz/Graphviz-2.38.0-foss-2016b.eb b/easybuild/easyconfigs/g/Graphviz/Graphviz-2.38.0-foss-2016b.eb new file mode 100644 index 0000000000..0454227509 --- /dev/null +++ b/easybuild/easyconfigs/g/Graphviz/Graphviz-2.38.0-foss-2016b.eb @@ -0,0 +1,67 @@ +easyblock = 'ConfigureMake' + +name = 'Graphviz' +version = '2.38.0' + +homepage = 'http://www.graphviz.org/' +description = """Graphviz is open source graph visualization software. Graph visualization + is a way of representing structural information as diagrams of + abstract graphs and networks. It has important applications in networking, + bioinformatics, software engineering, database and web design, machine learning, + and in visual interfaces for other technical domains.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['http://www.graphviz.org/pub/graphviz/stable/SOURCES/'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('cairo', '1.14.6'), + ('expat', '2.2.0'), + ('freetype', '2.6.5'), + ('Ghostscript', '9.20'), + ('GTS', '0.7.6'), + ('Java', '1.8.0_92', '', True), + ('libpng', '1.6.24'), + ('Pango', '1.40.3'), + ('Perl', '5.24.0'), + ('Qt', '4.8.7'), + ('Tcl', '8.6.5'), + ('zlib', '1.2.8'), +] + +builddependencies = [ + ('M4', '1.4.17'), + ('SWIG', '3.0.10', '-Python-2.7.12'), +] + +#patches = [ +# 'Graphviz-2.38.0_icc_vmalloc.patch', +# 'Graphviz-2.38.0_icc_sfio.patch', +#] + +preconfigopts = "sed -i 's/install-data-hook$//g' tclpkg/Makefile.in && " +configopts = '--enable-guile=no --enable-lua=no --enable-ocaml=no ' +configopts += '--enable-r=no --enable-ruby=no ' + +prebuildopts = 'qmake -o cmd/gvedit/qMakefile cmd/gvedit/gvedit.pro && ' + +sanity_check_paths = { + 'files': ['bin/cluster', 'bin/dot', 'bin/gvmap', + 'lib/libcdt.%s' % SHLIB_EXT, 'lib/libgvc.%s' % SHLIB_EXT, 'lib/libxdot.%s' % SHLIB_EXT], + 'dirs': ['include', 'lib/graphviz'] +} + +sanity_check_commands = [ + ("test ! -d $EBROOTTCL/lib/*/graphviz", ''), + ("test ! -d $EBROOTTCL/lib64/*/graphviz", ''), +] + +modextrapaths = { + 'PYTHONPATH': 'lib/graphviz/python', + 'CLASSPATH': 'lib/graphviz/java/org/graphviz', + 'LD_LIBRARY_PATH': 'lib/graphviz/java', + 'TCLLIBPATH': 'lib/graphviz/tcl', +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/graphviz/graphviz-0.5.1-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/g/graphviz/graphviz-0.5.1-foss-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..7290bfdd17 --- /dev/null +++ b/easybuild/easyconfigs/g/graphviz/graphviz-0.5.1-foss-2016b-Python-2.7.12.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'graphviz' +version = '0.5.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pypi.python.org/pypi/graphviz' +description = """Simple Python interface for Graphviz""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_ZIP] + +dependencies = [ + ('Python', '2.7.12'), + ('Graphviz', '2.38.0'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.3.1-foss-2016b.eb b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.3.1-foss-2016b.eb new file mode 100644 index 0000000000..28916e2a3a --- /dev/null +++ b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.3.1-foss-2016b.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'HarfBuzz' +version = '1.3.1' + +homepage = 'http://www.freedesktop.org/wiki/Software/HarfBuzz' +description = """HarfBuzz is an OpenType text shaping engine.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['http://www.freedesktop.org/software/harfbuzz/release/'] +sources = [SOURCELOWER_TAR_BZ2] + +dependencies = [ + ('GLib', '2.49.5'), + ('cairo', '1.14.6'), + ('freetype', '2.6.5'), +] + +builddependencies = [('GObject-Introspection', '1.49.1')] + +configopts = "--enable-introspection=yes --with-gobject=yes --enable-static --enable-shared --with-cairo " + +modextrapaths = { + 'GI_TYPELIB_PATH': 'share', + 'XDG_DATA_DIRS': 'share', +} + +sanity_check_paths = { + 'files': ['lib/libharfbuzz.%s' % SHLIB_EXT, 'bin/hb-view'], + 'dirs': [] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.40.3-foss-2016b.eb b/easybuild/easyconfigs/p/Pango/Pango-1.40.3-foss-2016b.eb new file mode 100644 index 0000000000..d9bd112b39 --- /dev/null +++ b/easybuild/easyconfigs/p/Pango/Pango-1.40.3-foss-2016b.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'Pango' +version = '1.40.3' + +homepage = 'http://www.pango.org/' +description = """Pango is a library for laying out and rendering of text, with an emphasis on internationalization. +Pango can be used anywhere that text layout is needed, though most of the work on Pango so far has been done in the +context of the GTK+ widget toolkit. Pango forms the core of text and font handling for GTK+-2.x.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('X11', '20160819'), + ('GLib', '2.49.5'), + ('cairo', '1.14.6'), + ('HarfBuzz', '1.3.1'), +] + +builddependencies = [('GObject-Introspection', '1.49.1')] + +configopts = "--disable-silent-rules --enable-introspection=yes --enable-static --enable-shared " + +modextrapaths = { + 'XDG_DATA_DIRS': 'share', +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/pixman/pixman-0.34.0-foss-2016b.eb b/easybuild/easyconfigs/p/pixman/pixman-0.34.0-foss-2016b.eb new file mode 100644 index 0000000000..9306c63805 --- /dev/null +++ b/easybuild/easyconfigs/p/pixman/pixman-0.34.0-foss-2016b.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = "pixman" +version = '0.34.0' + +homepage = 'http://www.pixman.org/' +description = """Pixman is a low-level software library for pixel manipulation, providing features such as image +compositing and trapezoid rasterization. Important users of pixman are the cairo graphics library and the X server.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['http://cairographics.org/releases/'] +sources = [SOURCE_TAR_GZ] + +sanity_check_paths = { + 'files': ['lib/libpixman-1.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'vis' -- GitLab From 9c3f6772c903d996b6589cfc3c8f24e6c5022af2 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Fri, 10 Feb 2017 12:52:48 +0100 Subject: [PATCH 0057/1603] {vis}[foss/2016b] OpenCV 3.1.0 (REVIEW) --- .../a/ATK/ATK-2.22.0-foss-2016b.eb | 34 ++++++++++ .../f/FFmpeg/FFmpeg-3.1.3-foss-2016b.eb | 32 +++++++++ .../g/GTK+/GTK+-2.24.31-foss-2016b.eb | 25 +++++++ .../Gdk-Pixbuf-2.36.0-foss-2016b.eb | 34 ++++++++++ .../j/JasPer/JasPer-1.900.1-foss-2016b.eb | 21 ++++++ .../o/OpenCV/OpenCV-3.1.0-foss-2016b.eb | 65 +++++++++++++++++++ .../x/x264/x264-20160614-foss-2016b.eb | 27 ++++++++ .../y/Yasm/Yasm-1.3.0-foss-2016b.eb | 31 +++++++++ 8 files changed, 269 insertions(+) create mode 100644 easybuild/easyconfigs/a/ATK/ATK-2.22.0-foss-2016b.eb create mode 100644 easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.1.3-foss-2016b.eb create mode 100644 easybuild/easyconfigs/g/GTK+/GTK+-2.24.31-foss-2016b.eb create mode 100644 easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.36.0-foss-2016b.eb create mode 100644 easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-foss-2016b.eb create mode 100644 easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016b.eb create mode 100644 easybuild/easyconfigs/x/x264/x264-20160614-foss-2016b.eb create mode 100644 easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-foss-2016b.eb diff --git a/easybuild/easyconfigs/a/ATK/ATK-2.22.0-foss-2016b.eb b/easybuild/easyconfigs/a/ATK/ATK-2.22.0-foss-2016b.eb new file mode 100644 index 0000000000..357880d140 --- /dev/null +++ b/easybuild/easyconfigs/a/ATK/ATK-2.22.0-foss-2016b.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'ATK' +version = '2.22.0' + +homepage = 'https://developer.gnome.org/ATK/stable/' +description = """ + ATK provides the set of accessibility interfaces that are implemented by other + toolkits and applications. Using the ATK interfaces, accessibility tools have + full access to view and control running applications. +""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('GLib', '2.49.5'), + ('GObject-Introspection', '1.49.1') +] + +configopts = "--enable-introspection=yes" + +modextrapaths = { + 'XDG_DATA_DIRS': 'share', +} + +sanity_check_paths = { + 'files': ['lib/libatk-1.0.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.1.3-foss-2016b.eb b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.1.3-foss-2016b.eb new file mode 100644 index 0000000000..235a728b8c --- /dev/null +++ b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.1.3-foss-2016b.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'FFmpeg' +version = '3.1.3' + +homepage = 'https://www.ffmpeg.org/' +description = """A complete, cross-platform solution to record, convert and stream audio and video.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://ffmpeg.org/releases/'] + +dependencies = [ + ('NASM', '2.12.02'), + ('zlib', '1.2.8'), + ('bzip2', '1.0.6'), + ('x264', '20160614'), + ('X11', '20160819'), +] + +configopts = '--enable-pic --enable-shared --enable-gpl --enable-version3 --enable-nonfree --cc="$CC" --cxx="$CXX" ' +configopts += '--enable-libx264' + +sanity_check_paths = { + 'files': ['bin/ff%s' % x for x in ['mpeg', 'probe', 'server']] + + ['lib/lib%s.%s' % (x, y) for x in ['avdevice', 'avfilter', 'avformat', 'avcodec', 'postproc', + 'swresample', 'swscale', 'avutil'] for y in [SHLIB_EXT, 'a']], + 'dirs': ['include'] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GTK+/GTK+-2.24.31-foss-2016b.eb b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.31-foss-2016b.eb new file mode 100644 index 0000000000..c33f283106 --- /dev/null +++ b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.31-foss-2016b.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'GTK+' +version = '2.24.31' + +homepage = 'https://developer.gnome.org/gtk+/stable/' +description = """ + The GTK+ 2 package contains libraries used for creating graphical user interfaces for applications. +""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('ATK', '2.22.0'), + ('Gdk-Pixbuf', '2.36.0'), + ('Pango', '1.40.3'), + ('GObject-Introspection', '1.49.1'), +] + +configopts = "--disable-silent-rules --disable-glibtest --enable-introspection=yes --disable-visibility " + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.36.0-foss-2016b.eb b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.36.0-foss-2016b.eb new file mode 100644 index 0000000000..0ffa31b3f4 --- /dev/null +++ b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.36.0-foss-2016b.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'Gdk-Pixbuf' +version = '2.36.0' + +homepage = 'https://developer.gnome.org/gdk-pixbuf/stable/' +description = """ + The Gdk Pixbuf is a toolkit for image loading and pixel buffer manipulation. + It is used by GTK+ 2 and GTK+ 3 to load and manipulate images. In the past it + was distributed as part of GTK+ 2 but it was split off into a separate package + in preparation for the change to GTK+ 3. +""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('GLib', '2.49.5'), + ('libjpeg-turbo', '1.5.0'), + ('libpng', '1.6.24'), + ('LibTIFF', '4.0.6'), + ('GObject-Introspection', '1.49.1') +] + +configopts = "--disable-maintainer-mode --enable-debug=no --enable-introspection=yes " +configopts += "--disable-Bsymbolic --without-gdiplus --enable-shared --enable-static" + +modextrapaths = { + 'XDG_DATA_DIRS': 'share', +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-foss-2016b.eb b/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-foss-2016b.eb new file mode 100644 index 0000000000..57b073f549 --- /dev/null +++ b/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-foss-2016b.eb @@ -0,0 +1,21 @@ +easyblock = 'ConfigureMake' + +name = 'JasPer' +version = '1.900.1' + +homepage = 'http://www.ece.uvic.ca/~frodo/jasper/' +description = """The JasPer Project is an open-source initiative to provide a free + software-based reference implementation of the codec specified in the JPEG-2000 Part-1 standard.""" + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_ZIP] +source_urls = ['http://www.ece.uvic.ca/~frodo/jasper/software/'] + +sanity_check_paths = { + 'files': ["bin/jasper", "lib/libjasper.a"], + 'dirs': ["include"], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016b.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016b.eb new file mode 100644 index 0000000000..df0dfae353 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016b.eb @@ -0,0 +1,65 @@ +easyblock = 'CMakeMake' + +name = 'OpenCV' +version = '3.1.0' + +homepage = 'http://opencv.org/' +description = """OpenCV (Open Source Computer Vision Library) is an open source computer vision + and machine learning software library. OpenCV was built to provide + a common infrastructure for computer vision applications and to accelerate + the use of machine perception in the commercial products.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['https://github.com/Itseez/opencv/archive/'] +sources = ['%(version)s.zip'] + +builddependencies = [ + ('CMake', '3.5.2'), +] + +dependencies = [ + ('Python', '2.7.12'), + ('zlib', '1.2.8'), + ('FFmpeg', '3.1.3'), + ('libjpeg-turbo', '1.5.0'), + ('libpng', '1.6.24'), + ('LibTIFF', '4.0.6'), + ('JasPer', '1.900.1'), + ('Java', '1.8.0_92', '', True), + ('ant', '1.9.7', '-Java-%(javaver)s', True), + ('GLib', '2.49.5'), + ('GTK+', '2.24.31'), +] + +configopts = '-DCMAKE_BUILD_TYPE=RELEASE ' +configopts += '-DBUILD_PYTHON_SUPPORT=ON ' +configopts += '-DPYTHON_PACKAGES_PATH=%(installdir)s/lib/python%(pyshortver)s/site-packages ' +configopts += '-DBUILD_NEW_PYTHON_SUPPORT=ON ' +configopts += '-DZLIB_LIBRARY=$EBROOTZLIB/lib/libz.%s ' % SHLIB_EXT +configopts += '-DZLIB_INCLUDE_DIR=$EBROOTZLIB/include ' +configopts += '-DTIFF_LIBRARY=$EBROOTLIBTIFF/lib/libtiff.%s ' % SHLIB_EXT +configopts += '-DTIFF_INCLUDE_DIR=$EBROOTLIBTIFF/include ' +configopts += '-DPNG_LIBRARY=$EBROOTLIBPNG/lib/libpng.%s ' % SHLIB_EXT +configopts += '-DPNG_INCLUDE_DIR=$EBROOTLIBPNG/include ' +configopts += '-DJPEG_LIBRARY=$EBROOTLIBJPEGMINTURBO/lib/libjpeg.%s ' % SHLIB_EXT +configopts += '-DJPEG_INCLUDE_DIR=$EBROOTLIBJPEGMINTURBO/include ' +configopts += '-DJASPER_LIBRARY=$EBROOTJASPER/lib/libjasper.a ' +configopts += '-DJASPER_INCLUDE_DIR=$EBROOTJASPER/include ' +configopts += '-DWITH_IPP=ON ' +configopts += '-DENABLE_SSE=ON -DENABLE_SSE2=ON -DENABLE_SSE3=ON ' +configopts += '-DWITH_CUDA=OFF ' + +sanity_check_paths = { + 'files': ['lib/libopencv_core.%s' % SHLIB_EXT ] + + ['lib/python%%(pyshortver)s/site-packages/cv2.%s' % SHLIB_EXT ] + + ['bin/opencv_%s' % x for x in ['annotation', 'createsamples', 'traincascade']], + 'dirs': ['include'] +} + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', + 'CLASSPATH': 'share/OpenCV/java', +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/x/x264/x264-20160614-foss-2016b.eb b/easybuild/easyconfigs/x/x264/x264-20160614-foss-2016b.eb new file mode 100644 index 0000000000..b44af67ba6 --- /dev/null +++ b/easybuild/easyconfigs/x/x264/x264-20160614-foss-2016b.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'x264' +version = '20160614' + +homepage = 'http://www.videolan.org/developers/x264.html' +description = """x264 is a free software library and application for encoding video streams into the H.264/MPEG-4 + AVC compression format, and is released under the terms of the GNU GPL.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = [ + 'https://download.videolan.org/pub/videolan/x264/snapshots/', + 'ftp://ftp.videolan.org/pub/videolan/x264/snapshots/', +] +sources = ['x264-snapshot-%(version)s-2245-stable.tar.bz2'] + +dependencies = [('Yasm', '1.3.0')] + +configopts = " --enable-shared --enable-static " + +sanity_check_paths = { + 'files': ['bin/x264', 'include/x264_config.h', 'include/x264.h', 'lib/libx264.a', 'lib/libx264.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-foss-2016b.eb b/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-foss-2016b.eb new file mode 100644 index 0000000000..d40e39150a --- /dev/null +++ b/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-foss-2016b.eb @@ -0,0 +1,31 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-90.html +## + +easyblock = 'ConfigureMake' + +name = 'Yasm' +version = '1.3.0' + +homepage = 'http://www.tortall.net/projects/yasm/' +description = """Yasm: Complete rewrite of the NASM assembler with BSD license""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.tortall.net/projects/yasm/releases/'] + +sanity_check_paths = { + 'files': ['bin/yasm'], + 'dirs': [], +} + +moduleclass = 'lang' -- GitLab From 8b9c836ff987d76b17964b7001ece60d513c98f9 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Fri, 10 Feb 2017 17:11:57 +0100 Subject: [PATCH 0058/1603] Add missing numpy dep --- .../numpy-1.11.1-foss-2016b-Python-2.7.12.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100755 easybuild/easyconfigs/n/numpy/numpy-1.11.1-foss-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/n/numpy/numpy-1.11.1-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/n/numpy/numpy-1.11.1-foss-2016b-Python-2.7.12.eb new file mode 100755 index 0000000000..23d10a78e7 --- /dev/null +++ b/easybuild/easyconfigs/n/numpy/numpy-1.11.1-foss-2016b-Python-2.7.12.eb @@ -0,0 +1,25 @@ +name = 'numpy' +version = '1.11.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.numpy.org' +description = """NumPy is the fundamental package for scientific computing with Python. It contains among other things: + a powerful N-dimensional array object, sophisticated (broadcasting) functions, tools for integrating C/C++ and Fortran + code, useful linear algebra, Fourier transform, and random number capabilities. Besides its obvious scientific uses, + NumPy can also be used as an efficient multi-dimensional container of generic data. Arbitrary data-types can be + defined. This allows NumPy to seamlessly and speedily integrate with a wide variety of databases.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_GZ] + +patches = [ + 'numpy-1.8.0-mkl.patch', +] + +dependencies = [ + ('Python', '2.7.12'), +] + +moduleclass = 'math' -- GitLab From 1932c3467cfc0b1758decc73685ce2643f69ce3c Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Mon, 13 Feb 2017 13:42:55 +0100 Subject: [PATCH 0059/1603] adding easyconfigs: disambiguate-1.0.0-goolf-1.7.20-Python-2.7.11.eb --- ...iguate-1.0.0-goolf-1.7.20-Python-2.7.11.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/d/disambiguate/disambiguate-1.0.0-goolf-1.7.20-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/d/disambiguate/disambiguate-1.0.0-goolf-1.7.20-Python-2.7.11.eb b/easybuild/easyconfigs/d/disambiguate/disambiguate-1.0.0-goolf-1.7.20-Python-2.7.11.eb new file mode 100644 index 0000000000..08032c986d --- /dev/null +++ b/easybuild/easyconfigs/d/disambiguate/disambiguate-1.0.0-goolf-1.7.20-Python-2.7.11.eb @@ -0,0 +1,40 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = "PythonPackage" + +name = 'disambiguate' +version = '1.0.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = "https://github.com/AstraZeneca-NGS/disambiguate" +description = "Disambiguation algorithm for reads aligned to human and mouse genomes using Tophat or BWA mem" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +source_urls = ["https://github.com/AstraZeneca-NGS/disambiguate/archive/"] +sources = ["v%(version)s.tar.gz"] + +dependencies = [ + ('Python', '2.7.11'), + ('BamTools', '2.4.0'), + ('zlib', '1.2.8'), + ('Pysam', '0.9.0', versionsuffix), +] + +# this application provides a python implementation and a C++ implementation +# in the postinstallcmds we compile the C++ version +postinstallcmds = ['$CXX -I$EBROOTBAMTOOLS/include -I./ -L$EBROOTBAMTOOLS/lib -o disambiguate dismain.cpp -lz -lbamtools', + 'cp disambiguate %(installdir)s/bin/'] + +# workaround to avoid the import sanity check +options = {'modulename': 'os'} + +sanity_check_paths = { + 'files': ['bin/disambiguate.py', 'bin/disambiguate'], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From 042334c87be6f297150acc7507478ba63cfa9967 Mon Sep 17 00:00:00 2001 From: Fokke Dijkstra Date: Mon, 13 Feb 2017 14:44:03 +0100 Subject: [PATCH 0060/1603] Small formatting change. --- .../c/Caffe/Caffe-rc3-foss-2016a-CUDA-7.5.18-Python-2.7.11.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/c/Caffe/Caffe-rc3-foss-2016a-CUDA-7.5.18-Python-2.7.11.eb b/easybuild/easyconfigs/c/Caffe/Caffe-rc3-foss-2016a-CUDA-7.5.18-Python-2.7.11.eb index 9a164bb75c..184119ac43 100644 --- a/easybuild/easyconfigs/c/Caffe/Caffe-rc3-foss-2016a-CUDA-7.5.18-Python-2.7.11.eb +++ b/easybuild/easyconfigs/c/Caffe/Caffe-rc3-foss-2016a-CUDA-7.5.18-Python-2.7.11.eb @@ -12,6 +12,7 @@ Caffe is a deep learning framework made with expression, speed, and modularity in mind. It is developed by the Berkeley Vision and Learning Center (BVLC) and community contributors. """ + toolchain = {'name': 'foss', 'version': '2016a'} toolchainopts = {'optarch': False, 'pic': True} -- GitLab From 1c7a87a90015a6afb50d6e963021d0888f8661eb Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Mon, 13 Feb 2017 14:49:40 +0100 Subject: [PATCH 0061/1603] added bamtools dependency --- .../b/BamTools/BamTools-2.4.0-goolf-1.7.20.eb | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) create mode 100644 easybuild/easyconfigs/b/BamTools/BamTools-2.4.0-goolf-1.7.20.eb diff --git a/easybuild/easyconfigs/b/BamTools/BamTools-2.4.0-goolf-1.7.20.eb b/easybuild/easyconfigs/b/BamTools/BamTools-2.4.0-goolf-1.7.20.eb new file mode 100644 index 0000000000..d0e6af59d8 --- /dev/null +++ b/easybuild/easyconfigs/b/BamTools/BamTools-2.4.0-goolf-1.7.20.eb @@ -0,0 +1,16 @@ +name = 'BamTools' +version = '2.4.0' + +homepage = 'https://github.com/pezmaster31/bamtools' +description = """BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files.""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +sources = ['v%(version)s.tar.gz'] +source_urls = ['https://github.com/pezmaster31/bamtools/archive'] + +builddependencies = [('CMake', '2.8.12')] + +files_to_copy = ["bin", "lib", "include", "docs", "LICENSE", "README"] + +moduleclass = 'bio' -- GitLab From 694507e94d1d49292f1bf6e584f90a7a81952e37 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Mon, 13 Feb 2017 16:08:55 +0100 Subject: [PATCH 0062/1603] {vis}[mixed] OpenCV 3.1.0 fix ippicv source download and library install (REVIEW) --- .../o/OpenCV/OpenCV-3.1.0-foss-2016a.eb | 17 +++++++++++++++-- .../o/OpenCV/OpenCV-3.1.0-intel-2016a.eb | 16 ++++++++++++++-- .../o/OpenCV/OpenCV-3.1.0-intel-2016b.eb | 17 +++++++++++++++-- 3 files changed, 44 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016a.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016a.eb index f835d278f9..c3490d5f5f 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016a.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016a.eb @@ -11,8 +11,16 @@ description = """OpenCV (Open Source Computer Vision Library) is an open source toolchain = {'name': 'foss', 'version': '2016a'} -source_urls = ['https://github.com/Itseez/opencv/archive/'] -sources = ['%(version)s.zip'] +source_urls = [ + 'https://github.com/Itseez/opencv/archive/', + #The Hash is version dependent! see 3rdparty/ippicv/downloader.cmake + 'https://raw.githubusercontent.com/Itseez/opencv_3rdparty/81a676001ca8075ada498583e4166079e5744668/ippicv', +] + +sources = [ + '%(version)s.zip', + ('ippicv_linux_20151201.tgz', 'cp %s %(builddir)s'), +] builddependencies = [ ('CMake', '3.5.2'), @@ -34,6 +42,9 @@ dependencies = [ ('GST-plugins-base', '1.6.4'), ] +#The destination directory is "linux-" see 3rdparty/ippicv/downloader.cmake +preconfigopts = 'mkdir -p {0} && cp -a ../*.tgz {0}. &&'.format("3rdparty/ippicv/downloads/linux-808b791a6eac9ed78d32a7666804320e/") + configopts = '-DCMAKE_BUILD_TYPE=RELEASE ' configopts += '-DBUILD_PYTHON_SUPPORT=ON ' configopts += '-DPYTHON_PACKAGES_PATH=%(installdir)s/lib/python%(pyshortver)s/site-packages ' @@ -52,6 +63,8 @@ configopts += '-DWITH_IPP=ON ' configopts += '-DENABLE_SSE=ON -DENABLE_SSE2=ON -DENABLE_SSE3=ON ' configopts += '-DWITH_CUDA=OFF ' +postinstallcmds = ["cp 3rdparty/ippicv/unpack/ippicv_lnx/lib/intel64/libippicv.* %(installdir)s/lib"] + sanity_check_paths = { 'files': ['lib/libopencv_core.%s' % SHLIB_EXT ] + ['lib/python%%(pyshortver)s/site-packages/cv2.%s' % SHLIB_EXT ] + diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016a.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016a.eb index b12504dd19..f247b850d9 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016a.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016a.eb @@ -11,8 +11,16 @@ description = """OpenCV (Open Source Computer Vision Library) is an open source toolchain = {'name': 'intel', 'version': '2016a'} -source_urls = ['https://github.com/Itseez/opencv/archive/'] -sources = ['%(version)s.zip'] +source_urls = [ + 'https://github.com/Itseez/opencv/archive/', + #The Hash is version dependent! see 3rdparty/ippicv/downloader.cmake + 'https://raw.githubusercontent.com/Itseez/opencv_3rdparty/81a676001ca8075ada498583e4166079e5744668/ippicv', +] + +sources = [ + '%(version)s.zip', + ('ippicv_linux_20151201.tgz', 'cp %s %(builddir)s'), +] patches = ['OpenCV-%(version)s_with_IPP.patch'] @@ -35,6 +43,8 @@ dependencies = [ ] preconfigopts = 'export IPPROOT=$EBROOTICC/ipp && ' +#The destination directory is "linux-" see 3rdparty/ippicv/downloader.cmake +preconfigopts += 'mkdir -p {0} && cp -a ../*.tgz {0}. &&'.format("3rdparty/ippicv/downloads/linux-808b791a6eac9ed78d32a7666804320e/") configopts = '-DCMAKE_BUILD_TYPE=RELEASE ' configopts += '-DBUILD_PYTHON_SUPPORT=ON ' @@ -54,6 +64,8 @@ configopts += '-DWITH_IPP=ON ' configopts += '-DENABLE_SSE=ON -DENABLE_SSE2=ON -DENABLE_SSE3=ON ' configopts += '-DWITH_CUDA=OFF ' +postinstallcmds = ["cp 3rdparty/ippicv/unpack/ippicv_lnx/lib/intel64/libippicv.* %(installdir)s/lib"] + sanity_check_paths = { 'files': ['lib/libopencv_core.%s' % SHLIB_EXT ] + ['lib/python%%(pyshortver)s/site-packages/cv2.%s' % SHLIB_EXT ] + diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016b.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016b.eb index 896ae67a98..b38d822003 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016b.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016b.eb @@ -11,8 +11,16 @@ description = """OpenCV (Open Source Computer Vision Library) is an open source toolchain = {'name': 'intel', 'version': '2016b'} -source_urls = ['https://github.com/Itseez/opencv/archive/'] -sources = ['%(version)s.zip'] +source_urls = [ + 'https://github.com/Itseez/opencv/archive/', + #The Hash is version dependent! see 3rdparty/ippicv/downloader.cmake + 'https://raw.githubusercontent.com/Itseez/opencv_3rdparty/81a676001ca8075ada498583e4166079e5744668/ippicv', +] + +sources = [ + '%(version)s.zip', + ('ippicv_linux_20151201.tgz', 'cp %s %(builddir)s'), +] patches = ['OpenCV-%(version)s_with_IPP.patch'] @@ -36,6 +44,9 @@ dependencies = [ preconfigopts = 'export IPPROOT=$EBROOTICC/ipp && ' +#The destination directory is "linux-" see 3rdparty/ippicv/downloader.cmake +preconfigopts += 'mkdir -p {0} && cp -a ../*.tgz {0}. &&'.format("3rdparty/ippicv/downloads/linux-808b791a6eac9ed78d32a7666804320e/") + configopts = '-DCMAKE_BUILD_TYPE=RELEASE ' configopts += '-DBUILD_PYTHON_SUPPORT=ON ' configopts += '-DPYTHON_PACKAGES_PATH=%(installdir)s/lib/python%(pyshortver)s/site-packages ' @@ -54,6 +65,8 @@ configopts += '-DWITH_IPP=ON ' configopts += '-DENABLE_SSE=ON -DENABLE_SSE2=ON -DENABLE_SSE3=ON ' configopts += '-DWITH_CUDA=OFF ' +postinstallcmds = ["cp 3rdparty/ippicv/unpack/ippicv_lnx/lib/intel64/libippicv.* %(installdir)s/lib"] + sanity_check_paths = { 'files': ['lib/libopencv_core.%s' % SHLIB_EXT ] + ['lib/python%%(pyshortver)s/site-packages/cv2.%s' % SHLIB_EXT ] + -- GitLab From 161806e5c689355cdf17dc83f6dcf795800943e1 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Mon, 13 Feb 2017 16:12:52 +0100 Subject: [PATCH 0063/1603] fix ippicv source download and library installation --- .../o/OpenCV/OpenCV-3.1.0-foss-2016b.eb | 17 +++++++++++++++-- 1 file changed, 15 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016b.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016b.eb index df0dfae353..261f39024d 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016b.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016b.eb @@ -11,8 +11,16 @@ description = """OpenCV (Open Source Computer Vision Library) is an open source toolchain = {'name': 'foss', 'version': '2016b'} -source_urls = ['https://github.com/Itseez/opencv/archive/'] -sources = ['%(version)s.zip'] +source_urls = [ + 'https://github.com/Itseez/opencv/archive/', + #The Hash is version dependent! see 3rdparty/ippicv/downloader.cmake + 'https://raw.githubusercontent.com/Itseez/opencv_3rdparty/81a676001ca8075ada498583e4166079e5744668/ippicv', +] + +sources = [ + '%(version)s.zip', + ('ippicv_linux_20151201.tgz', 'cp %s %(builddir)s'), +] builddependencies = [ ('CMake', '3.5.2'), @@ -32,6 +40,9 @@ dependencies = [ ('GTK+', '2.24.31'), ] +#The destination directory is "linux-" see 3rdparty/ippicv/downloader.cmake +preconfigopts = 'mkdir -p {0} && cp -a ../*.tgz {0}. &&'.format("3rdparty/ippicv/downloads/linux-808b791a6eac9ed78d32a7666804320e/") + configopts = '-DCMAKE_BUILD_TYPE=RELEASE ' configopts += '-DBUILD_PYTHON_SUPPORT=ON ' configopts += '-DPYTHON_PACKAGES_PATH=%(installdir)s/lib/python%(pyshortver)s/site-packages ' @@ -50,6 +61,8 @@ configopts += '-DWITH_IPP=ON ' configopts += '-DENABLE_SSE=ON -DENABLE_SSE2=ON -DENABLE_SSE3=ON ' configopts += '-DWITH_CUDA=OFF ' +postinstallcmds = ["cp 3rdparty/ippicv/unpack/ippicv_lnx/lib/intel64/libippicv.* %(installdir)s/lib"] + sanity_check_paths = { 'files': ['lib/libopencv_core.%s' % SHLIB_EXT ] + ['lib/python%%(pyshortver)s/site-packages/cv2.%s' % SHLIB_EXT ] + -- GitLab From 9c14d4917e06d1fa78aaab60791e75378faf7b94 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 14 Feb 2017 12:40:41 +0200 Subject: [PATCH 0064/1603] adding easyconfigs: likwid-4.2.0-GCCcore-6.3.0.eb --- .../l/likwid/likwid-4.2.0-GCCcore-6.3.0.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/l/likwid/likwid-4.2.0-GCCcore-6.3.0.eb diff --git a/easybuild/easyconfigs/l/likwid/likwid-4.2.0-GCCcore-6.3.0.eb b/easybuild/easyconfigs/l/likwid/likwid-4.2.0-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..a5b92f3bfe --- /dev/null +++ b/easybuild/easyconfigs/l/likwid/likwid-4.2.0-GCCcore-6.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'likwid' +version = '4.2.0' + +homepage = 'http://code.google.com/p/likwid/' +description = """Likwid stands for Like I knew what I am doing. This project contributes easy to use + command line tools for Linux to support programmers in developing high performance multi threaded programs.""" + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/RRZE-HPC/likwid/archive/'] +sources = ['%(version)s.tar.gz'] + +patches = ['likwid-%(version)s-config-mk.patch'] + +builddependencies = [('binutils', '2.27')] + +skipsteps = ['configure'] +buildopts = 'CC="$CC" CFLAGS="$CFLAGS -std=c99" PREFIX=%(installdir)s' +installopts = 'PREFIX=%(installdir)s' + +sanity_check_paths = { + 'files': ["bin/likwid-memsweeper", "bin/likwid-mpirun", "bin/likwid-perfctr", + "bin/likwid-perfscope", "bin/likwid-pin", "bin/likwid-powermeter", "bin/likwid-topology", + "lib/liblikwidpin.%s" % SHLIB_EXT, "lib/liblikwid.%s" % SHLIB_EXT], + 'dirs': ["man/man1"] +} + +maxparallel = 1 + +moduleclass = 'devel' -- GitLab From 17ab69aa0e6c3c836826fed76a7c0e13a93224b1 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 14 Feb 2017 13:40:56 +0200 Subject: [PATCH 0065/1603] Adding the missing patch file --- .../l/likwid/likwid-4.2.0-config-mk.patch | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/l/likwid/likwid-4.2.0-config-mk.patch diff --git a/easybuild/easyconfigs/l/likwid/likwid-4.2.0-config-mk.patch b/easybuild/easyconfigs/l/likwid/likwid-4.2.0-config-mk.patch new file mode 100644 index 0000000000..735ec88bea --- /dev/null +++ b/easybuild/easyconfigs/l/likwid/likwid-4.2.0-config-mk.patch @@ -0,0 +1,43 @@ +# Patches the build system +# Ward Poelmans +diff -ur likwid-likwid-4.1.0.orig/config.mk likwid-likwid-4.1.0/config.mk +--- likwid-likwid-4.1.0.orig/config.mk 2016-05-19 13:16:28.000000000 +0200 ++++ likwid-likwid-4.1.0/config.mk 2016-05-19 13:46:33.345284562 +0200 +@@ -9,7 +9,7 @@ + COLOR = BLUE#NO SPACE + + # Path were to install likwid +-PREFIX = /usr/local#NO SPACE ++#PREFIX = /usr/local#NO SPACE + + ################################################################# + # Common users do not need to change values below this comment! # +@@ -33,7 +33,7 @@ + # chown installed tools to this user/group + # if you change anything here, make sure that the user/group can access + # the MSR devices and (on Intel) the PCI devices. +-INSTALL_CHOWN = -g root -o root ++INSTALL_CHOWN = + + # For the daemon based secure msr/pci access configure + # the absolute path to the msr daemon executable. +@@ -44,7 +44,7 @@ + # Build the accessDaemon. Have a look in the WIKI for details. + BUILDDAEMON = true#NO SPACE + #Build the setFrequencies tool +-BUILDFREQ = true#NO SPACE ++BUILDFREQ = false#NO SPACE + + # Set the default mode for MSR access. + # This can usually be overriden on the commandline. +@@ -71,8 +71,8 @@ + # a proper config file at CFG_FILE_PATH) + MAX_NUM_THREADS = 263 + MAX_NUM_NODES = 64 +-CFG_FILE_PATH = /etc/likwid.cfg +-TOPO_FILE_PATH = /etc/likwid_topo.cfg ++CFG_FILE_PATH = $(PREFIX)/etc/likwid.cfg ++TOPO_FILE_PATH = $(PREFIX)/etc/likwid_topo.cfg + + # Versioning Information + VERSION = 4 -- GitLab From d4ca88d5d12880c6f4efce64141d1df222854385 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Feb 2017 15:24:11 +0100 Subject: [PATCH 0066/1603] adding easyconfigs: Cantera-2.3.0-intel-2016b-Python-2.7.12.eb --- ...Cantera-2.3.0-intel-2016b-Python-2.7.12.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/c/Cantera/Cantera-2.3.0-intel-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/c/Cantera/Cantera-2.3.0-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/c/Cantera/Cantera-2.3.0-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..1347cddcd9 --- /dev/null +++ b/easybuild/easyconfigs/c/Cantera/Cantera-2.3.0-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,44 @@ +easyblock = 'SCons' + +name = 'Cantera' +version = '2.3.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/Cantera/cantera' +description = """Chemical kinetics, thermodynamics, and transport tool suite""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['https://github.com/Cantera/cantera/archive/'] +sources = ['v%(version)s.tar.gz'] + +dependencies = [ + ('Python', '2.7.12'), + ('Boost', '1.63.0', versionsuffix), + ('SUNDIALS', '2.7.0'), + ('Eigen', '3.3.2'), + ('fmt', '3.0.1'), + ('googletest', '1.8.0'), +] +builddependencies = [ + ('SCons', '2.5.1', versionsuffix), + ('3to2', '1.1.1', versionsuffix), +] + +common_opts = 'env_vars=all CC="$CC" CXX="$CXX" blas_lapack_libs=mkl_rt blas_lapack_dir=$BLAS_LAPACK_LIB_DIR' +common_opts += ' sundials_include=$EBROOTSUNDIALS/include sundials_libdir=$EBROOTSUNDIALS/lib' +buildopts = 'build ' + common_opts +runtest = 'test ' + common_opts +buildopts = 'install ' + common_opts +prefix_arg = 'prefix=' + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +sanity_check_paths = { + 'files': ['bin/mixmaster'], + 'dirs': ['include/cantera', 'lib/pkgconfig', 'lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [('python', "-c 'import cantera'")] + +moduleclass = 'chem' -- GitLab From 2d323b10300b35261d5c2492b3e83d9d2123f01c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Feb 2017 15:25:24 +0100 Subject: [PATCH 0067/1603] adding easyconfigs: OrthoMCL-2.0.9-intel-2016b-Perl-5.24.0.eb --- .../m/MCL/MCL-14.137-intel-2016b.eb | 21 +++++++++++ .../OrthoMCL-2.0.9-intel-2016b-Perl-5.24.0.eb | 36 +++++++++++++++++++ 2 files changed, 57 insertions(+) create mode 100644 easybuild/easyconfigs/m/MCL/MCL-14.137-intel-2016b.eb create mode 100644 easybuild/easyconfigs/o/OrthoMCL/OrthoMCL-2.0.9-intel-2016b-Perl-5.24.0.eb diff --git a/easybuild/easyconfigs/m/MCL/MCL-14.137-intel-2016b.eb b/easybuild/easyconfigs/m/MCL/MCL-14.137-intel-2016b.eb new file mode 100644 index 0000000000..11b922bce7 --- /dev/null +++ b/easybuild/easyconfigs/m/MCL/MCL-14.137-intel-2016b.eb @@ -0,0 +1,21 @@ +easyblock = 'ConfigureMake' + +name = 'MCL' +version = '14.137' + +homepage = 'http://micans.org/mcl/' +description = """The MCL algorithm is short for the Markov Cluster Algorithm, a fast +and scalable unsupervised cluster algorithm for graphs (also known as networks) based +on simulation of (stochastic) flow in graphs. """ + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['http://micans.org/%(namelower)s/src/'] +sources = ['%(namelower)s-%(version_major)s-%(version_minor)s.tar.gz'] + +sanity_check_paths = { + 'files': ['bin/mcl'], + 'dirs': ['share'] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/o/OrthoMCL/OrthoMCL-2.0.9-intel-2016b-Perl-5.24.0.eb b/easybuild/easyconfigs/o/OrthoMCL/OrthoMCL-2.0.9-intel-2016b-Perl-5.24.0.eb new file mode 100644 index 0000000000..c6b49af363 --- /dev/null +++ b/easybuild/easyconfigs/o/OrthoMCL/OrthoMCL-2.0.9-intel-2016b-Perl-5.24.0.eb @@ -0,0 +1,36 @@ +easyblock = 'Tarball' + +name = 'OrthoMCL' +version = '2.0.9' +versionsuffix = '-Perl-%(perlver)s' + +homepage = 'http://orthomcl.org/' +description = """OrthoMCL is a genome-scale algorithm for grouping orthologous protein sequences.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +sources = ['%(name)sSoftware-v%(version)s.tar.gz'] +source_urls = ['http://orthomcl.org/common/downloads/software/v%(version_major_minor)s/'] + +patches = ['orthomcl_fix-perl-hashbang.patch'] + +dependencies = [ + # a Perl installation providing the DBI module is required + ('Perl', '5.24.0'), + ('MCL', '14.137'), +] + +sanity_check_paths = { + 'files': ['bin/orthomcl%s' % bin for bin in ['AdjustFasta', 'BlastParser', 'DropSchema', 'DumpPairsFiles', + 'ExtractProteinIdsFromGroupsFile', 'ExtractProteinPairsFromGroupsFile', + 'FilterFasta', 'InstallSchema', 'LoadBlast', 'MclToGroups', 'Pairs', + 'ReduceFasta', 'ReduceGroups', 'RemoveIdenticalGroups', 'Singletons', + 'SortGroupMembersByScore', 'SortGroupsFile']], + 'dirs': ['lib/perl/OrthoMCLEngine'], +} + +modextrapaths = {'PERL5LIB': 'lib/perl'} + +sanity_check_commands = [('perl', '-e "use OrthoMCLEngine::Main::Base"')] + +moduleclass = 'bio' -- GitLab From 79058145b43f9220323e5a2a9f4284b478d94e27 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Feb 2017 15:28:20 +0100 Subject: [PATCH 0068/1603] fix software name for OrthomCL --- .../OrthoMCL-2.0.8-goolf-1.4.10-Perl-5.16.3.eb} | 14 ++++++-------- .../OrthoMCL-2.0.8-ictce-5.3.0-Perl-5.16.3.eb} | 14 ++++++-------- .../orthomcl_fix-perl-hashbang.patch | 0 3 files changed, 12 insertions(+), 16 deletions(-) rename easybuild/easyconfigs/o/{orthomcl/orthomcl-2.0.8-goolf-1.4.10-Perl-5.16.3.eb => OrthoMCL/OrthoMCL-2.0.8-goolf-1.4.10-Perl-5.16.3.eb} (83%) rename easybuild/easyconfigs/o/{orthomcl/orthomcl-2.0.8-ictce-5.3.0-Perl-5.16.3.eb => OrthoMCL/OrthoMCL-2.0.8-ictce-5.3.0-Perl-5.16.3.eb} (83%) rename easybuild/easyconfigs/o/{orthomcl => OrthoMCL}/orthomcl_fix-perl-hashbang.patch (100%) diff --git a/easybuild/easyconfigs/o/orthomcl/orthomcl-2.0.8-goolf-1.4.10-Perl-5.16.3.eb b/easybuild/easyconfigs/o/OrthoMCL/OrthoMCL-2.0.8-goolf-1.4.10-Perl-5.16.3.eb similarity index 83% rename from easybuild/easyconfigs/o/orthomcl/orthomcl-2.0.8-goolf-1.4.10-Perl-5.16.3.eb rename to easybuild/easyconfigs/o/OrthoMCL/OrthoMCL-2.0.8-goolf-1.4.10-Perl-5.16.3.eb index 2cbfe2886f..5b8fd1b338 100644 --- a/easybuild/easyconfigs/o/orthomcl/orthomcl-2.0.8-goolf-1.4.10-Perl-5.16.3.eb +++ b/easybuild/easyconfigs/o/OrthoMCL/OrthoMCL-2.0.8-goolf-1.4.10-Perl-5.16.3.eb @@ -1,7 +1,8 @@ -easyblock = "Tarball" +easyblock = 'Tarball' -name = 'orthomcl' +name = 'OrthoMCL' version = '2.0.8' +versionsuffix = '-Perl-%(perlver)s' homepage = 'http://orthomcl.org/' description = """OrthoMCL is a genome-scale algorithm for grouping orthologous protein sequences.""" @@ -9,16 +10,13 @@ description = """OrthoMCL is a genome-scale algorithm for grouping orthologous p toolchain = {'name': 'goolf', 'version': '1.4.10'} sources = ['%(name)sSoftware-v%(version)s.tar.gz'] -source_urls = ['http://orthomcl.org/common/downloads/software/v%s/' % '.'.join(version.split('.')[:2])] +source_urls = ['http://orthomcl.org/common/downloads/software/v%(version_major_minor)s/'] patches = ['orthomcl_fix-perl-hashbang.patch'] -# a Perl installation providing the DBI module is required -perl = 'Perl' -perlver = '5.16.3' -versionsuffix = '-%s-%s' % (perl, perlver) dependencies = [ - (perl, perlver), + # a Perl installation providing the DBI module is required + ('Perl', '5.16.3'), ('MCL', '12.135'), ] diff --git a/easybuild/easyconfigs/o/orthomcl/orthomcl-2.0.8-ictce-5.3.0-Perl-5.16.3.eb b/easybuild/easyconfigs/o/OrthoMCL/OrthoMCL-2.0.8-ictce-5.3.0-Perl-5.16.3.eb similarity index 83% rename from easybuild/easyconfigs/o/orthomcl/orthomcl-2.0.8-ictce-5.3.0-Perl-5.16.3.eb rename to easybuild/easyconfigs/o/OrthoMCL/OrthoMCL-2.0.8-ictce-5.3.0-Perl-5.16.3.eb index 2fe0311606..238ebe881b 100644 --- a/easybuild/easyconfigs/o/orthomcl/orthomcl-2.0.8-ictce-5.3.0-Perl-5.16.3.eb +++ b/easybuild/easyconfigs/o/OrthoMCL/OrthoMCL-2.0.8-ictce-5.3.0-Perl-5.16.3.eb @@ -1,7 +1,8 @@ -easyblock = "Tarball" +easyblock = 'Tarball' -name = 'orthomcl' +name = 'OrthoMCL' version = '2.0.8' +versionsuffix = '-Perl-%(perlver)s' homepage = 'http://orthomcl.org/' description = """OrthoMCL is a genome-scale algorithm for grouping orthologous protein sequences.""" @@ -9,16 +10,13 @@ description = """OrthoMCL is a genome-scale algorithm for grouping orthologous p toolchain = {'name': 'ictce', 'version': '5.3.0'} sources = ['%(name)sSoftware-v%(version)s.tar.gz'] -source_urls = ['http://orthomcl.org/common/downloads/software/v%s/' % '.'.join(version.split('.')[:2])] +source_urls = ['http://orthomcl.org/common/downloads/software/v%(version_major_minor)s/'] patches = ['orthomcl_fix-perl-hashbang.patch'] -# a Perl installation providing the DBI module is required -perl = 'Perl' -perlver = '5.16.3' -versionsuffix = '-%s-%s' % (perl, perlver) dependencies = [ - (perl, perlver), + # a Perl installation providing the DBI module is required + ('Perl', '5.16.3'), ('MCL', '12.135'), ] diff --git a/easybuild/easyconfigs/o/orthomcl/orthomcl_fix-perl-hashbang.patch b/easybuild/easyconfigs/o/OrthoMCL/orthomcl_fix-perl-hashbang.patch similarity index 100% rename from easybuild/easyconfigs/o/orthomcl/orthomcl_fix-perl-hashbang.patch rename to easybuild/easyconfigs/o/OrthoMCL/orthomcl_fix-perl-hashbang.patch -- GitLab From e657761ef99ebeb760d351404dd867448cba4a11 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Feb 2017 19:10:59 +0100 Subject: [PATCH 0069/1603] fix sources spec --- .../o/OrthoMCL/OrthoMCL-2.0.8-goolf-1.4.10-Perl-5.16.3.eb | 2 +- .../o/OrthoMCL/OrthoMCL-2.0.8-ictce-5.3.0-Perl-5.16.3.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/o/OrthoMCL/OrthoMCL-2.0.8-goolf-1.4.10-Perl-5.16.3.eb b/easybuild/easyconfigs/o/OrthoMCL/OrthoMCL-2.0.8-goolf-1.4.10-Perl-5.16.3.eb index 5b8fd1b338..b0f832c53a 100644 --- a/easybuild/easyconfigs/o/OrthoMCL/OrthoMCL-2.0.8-goolf-1.4.10-Perl-5.16.3.eb +++ b/easybuild/easyconfigs/o/OrthoMCL/OrthoMCL-2.0.8-goolf-1.4.10-Perl-5.16.3.eb @@ -9,7 +9,7 @@ description = """OrthoMCL is a genome-scale algorithm for grouping orthologous p toolchain = {'name': 'goolf', 'version': '1.4.10'} -sources = ['%(name)sSoftware-v%(version)s.tar.gz'] +sources = ['%(namelower)sSoftware-v%(version)s.tar.gz'] source_urls = ['http://orthomcl.org/common/downloads/software/v%(version_major_minor)s/'] patches = ['orthomcl_fix-perl-hashbang.patch'] diff --git a/easybuild/easyconfigs/o/OrthoMCL/OrthoMCL-2.0.8-ictce-5.3.0-Perl-5.16.3.eb b/easybuild/easyconfigs/o/OrthoMCL/OrthoMCL-2.0.8-ictce-5.3.0-Perl-5.16.3.eb index 238ebe881b..2f54ba6ec5 100644 --- a/easybuild/easyconfigs/o/OrthoMCL/OrthoMCL-2.0.8-ictce-5.3.0-Perl-5.16.3.eb +++ b/easybuild/easyconfigs/o/OrthoMCL/OrthoMCL-2.0.8-ictce-5.3.0-Perl-5.16.3.eb @@ -9,7 +9,7 @@ description = """OrthoMCL is a genome-scale algorithm for grouping orthologous p toolchain = {'name': 'ictce', 'version': '5.3.0'} -sources = ['%(name)sSoftware-v%(version)s.tar.gz'] +sources = ['%(namelower)sSoftware-v%(version)s.tar.gz'] source_urls = ['http://orthomcl.org/common/downloads/software/v%(version_major_minor)s/'] patches = ['orthomcl_fix-perl-hashbang.patch'] -- GitLab From f410c5f9d8a9506ea039409a066d860ec5cb8e7f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Feb 2017 19:11:57 +0100 Subject: [PATCH 0070/1603] fix sources spec in OrthoMCL easyconfig --- .../o/OrthoMCL/OrthoMCL-2.0.9-intel-2016b-Perl-5.24.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OrthoMCL/OrthoMCL-2.0.9-intel-2016b-Perl-5.24.0.eb b/easybuild/easyconfigs/o/OrthoMCL/OrthoMCL-2.0.9-intel-2016b-Perl-5.24.0.eb index c6b49af363..31aa43dbba 100644 --- a/easybuild/easyconfigs/o/OrthoMCL/OrthoMCL-2.0.9-intel-2016b-Perl-5.24.0.eb +++ b/easybuild/easyconfigs/o/OrthoMCL/OrthoMCL-2.0.9-intel-2016b-Perl-5.24.0.eb @@ -9,7 +9,7 @@ description = """OrthoMCL is a genome-scale algorithm for grouping orthologous p toolchain = {'name': 'intel', 'version': '2016b'} -sources = ['%(name)sSoftware-v%(version)s.tar.gz'] +sources = ['%(namelower)sSoftware-v%(version)s.tar.gz'] source_urls = ['http://orthomcl.org/common/downloads/software/v%(version_major_minor)s/'] patches = ['orthomcl_fix-perl-hashbang.patch'] -- GitLab From 867434e5a6957fcc9685beaa3b4f59ed60d3733a Mon Sep 17 00:00:00 2001 From: RvDijk Date: Wed, 15 Feb 2017 11:01:55 +0100 Subject: [PATCH 0071/1603] DMTCP 2.5.0 with foss 2016a --- .../d/DMTCP/DMTCP-2.5.0-foss-2016a.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/d/DMTCP/DMTCP-2.5.0-foss-2016a.eb diff --git a/easybuild/easyconfigs/d/DMTCP/DMTCP-2.5.0-foss-2016a.eb b/easybuild/easyconfigs/d/DMTCP/DMTCP-2.5.0-foss-2016a.eb new file mode 100644 index 0000000000..3f64420e2e --- /dev/null +++ b/easybuild/easyconfigs/d/DMTCP/DMTCP-2.5.0-foss-2016a.eb @@ -0,0 +1,27 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Ravi Tripathi +# Email: ravi89@uab.edu + +easyblock = 'ConfigureMake' + +name = 'DMTCP' +version = '2.5.0' + +homepage = "http://dmtcp.sourceforge.net/index.html" +description = """DMTCP (Distributed MultiThreaded Checkpointing) +transparently checkpoints a single-host or distributed computation +in user-space -- with no modifications to user code or to the O/S.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['https://github.com/dmtcp/dmtcp/archive/'] +sources = ['%(version)s.tar.gz'] + +sanity_check_paths = { + 'files': ['bin/dmtcp_command', 'bin/dmtcp_discover_rm', 'bin/dmtcp_nocheckpoint', 'bin/dmtcp_srun_helper', + 'bin/dmtcp_sshd', 'bin/dmtcp_coordinator', 'bin/dmtcp_launch', 'bin/dmtcp_restart', 'bin/dmtcp_ssh'], + 'dirs': [], +} + +moduleclass = 'tools' + -- GitLab From b1f42dea4affc87dda18850e35a79f63dca4d1dc Mon Sep 17 00:00:00 2001 From: RvDijk Date: Wed, 15 Feb 2017 11:09:29 +0100 Subject: [PATCH 0072/1603] Stacks 1.44 with foss-2016a --- .../s/Stacks/Stacks-1.44-foss-2016a.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/s/Stacks/Stacks-1.44-foss-2016a.eb diff --git a/easybuild/easyconfigs/s/Stacks/Stacks-1.44-foss-2016a.eb b/easybuild/easyconfigs/s/Stacks/Stacks-1.44-foss-2016a.eb new file mode 100644 index 0000000000..6ef7429937 --- /dev/null +++ b/easybuild/easyconfigs/s/Stacks/Stacks-1.44-foss-2016a.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'Stacks' +version = '1.44' + +homepage = 'http://creskolab.uoregon.edu/stacks/' +description = """Stacks is a software pipeline for building loci from short-read sequences, such as those generated on + the Illumina platform. Stacks was developed to work with restriction enzyme-based data, such as RAD-seq, for the purpose + of building genetic maps and conducting population genomics and phylogeography. +""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://catchenlab.life.illinois.edu/stacks/source/'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('zlib', '1.2.8'), + ('SAMtools', '1.3.1'), + ('sparsehash', '2.0.2'), +] + +sanity_check_paths = { + 'files': [ + 'bin/%s' % binfile for binfile in [ + 'clone_filter', 'denovo_map.pl', 'exec_velvet.pl', 'genotypes', 'index_radtags.pl', 'load_radtags.pl', + 'populations', 'process_shortreads', 'ref_map.pl', 'sstacks', 'ustacks', 'cstacks', 'estacks', + 'export_sql.pl', 'hstacks', 'kmer_filter', 'load_sequences.pl', 'process_radtags', 'pstacks', + 'sort_read_pairs.pl', 'stacks_export_notify.pl', + ] + ], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From 873bad384198bf5bd300d11b4297db759e803b03 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Wed, 15 Feb 2017 11:11:02 +0100 Subject: [PATCH 0073/1603] Vim 8.0 with foss 2016a --- .../v/Vim/Vim-8.0-foss-2016a-Python-2.7.11.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/v/Vim/Vim-8.0-foss-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/v/Vim/Vim-8.0-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/v/Vim/Vim-8.0-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..1caa37ba7a --- /dev/null +++ b/easybuild/easyconfigs/v/Vim/Vim-8.0-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,35 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = 'ConfigureMake' + +name = 'Vim' +version = '8.0' + +homepage = 'http://www.vim.org' +description = """ Vim is an advanced text editor that seeks to provide the power + of the de-facto Unix editor 'Vi', with a more complete feature set. """ + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://ftp.vim.org/pub/vim/unix/'] +sources = [SOURCELOWER_TAR_BZ2] + +# this dependencies are required for --enable-pythoninterp=yes and --enable-perlinterp=yes to work +# check enabled features running "vim --version" after compilation +dependencies = [ + ('Python', '2.7.11'), + ('Perl', '5.22.1', '-bare') + ] +#osdependencies = ['python','perl-devel'] + +configopts = '--with-features=huge --enable-pythoninterp=yes --enable-perlinterp=yes' + +sanity_check_paths = { + 'files': ['bin/vim','bin/vimdiff'], + 'dirs': [], +} + +moduleclass = 'tools' -- GitLab From a1c0fe373c8123e1474daef7a0857ba72818617d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 15 Feb 2017 13:08:30 +0100 Subject: [PATCH 0074/1603] adding easyconfigs: PEAR-0.9.8-intel-2016b.eb --- .../p/PEAR/PEAR-0.9.8-intel-2016b.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/p/PEAR/PEAR-0.9.8-intel-2016b.eb diff --git a/easybuild/easyconfigs/p/PEAR/PEAR-0.9.8-intel-2016b.eb b/easybuild/easyconfigs/p/PEAR/PEAR-0.9.8-intel-2016b.eb new file mode 100644 index 0000000000..33e09a2ad6 --- /dev/null +++ b/easybuild/easyconfigs/p/PEAR/PEAR-0.9.8-intel-2016b.eb @@ -0,0 +1,31 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild + +easyblock = 'ConfigureMake' + +name = 'PEAR' +version = '0.9.8' + +homepage = 'http://sco.h-its.org/exelixis/web/software/pear/' +description = """PEAR is an ultrafast, memory-efficient and highly accurate pair-end read merger. + It is fully parallelized and can run with as low as just a few kilobytes of memory.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['http://sco.h-its.org/exelixis/web/software/pear/files/'] +sources = ['%(namelower)s-%(version)s.tar.gz'] + +checksums = ['1ab079a2cea61aee816012966b7ccacd'] + +dependencies = [ + ('zlib', '1.2.8'), + ('bzip2', '1.0.6'), +] + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/pear'], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From bac77786fe50b626ed263a3adcaa8734bdda36a4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 15 Feb 2017 14:26:36 +0100 Subject: [PATCH 0075/1603] add easyconfigs for Boost & SCons (build) deps of Cantera --- .../Boost-1.63.0-intel-2016b-Python-2.7.12.eb | 23 ++++++++++++++++++ .../SCons-2.5.1-intel-2016b-Python-2.7.12.eb | 24 +++++++++++++++++++ 2 files changed, 47 insertions(+) create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.63.0-intel-2016b-Python-2.7.12.eb create mode 100644 easybuild/easyconfigs/s/SCons/SCons-2.5.1-intel-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.63.0-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/b/Boost/Boost-1.63.0-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..b110a50dba --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.63.0-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,23 @@ +name = 'Boost' +version = '1.63.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.boost.org/' +description = "Boost provides free peer-reviewed portable C++ source libraries." + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'usempi': True, 'pic': True} + +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] +source_urls = ['https://sourceforge.net/projects/%(namelower)s/files/%(namelower)s/%(version)s'] + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('Python', '2.7.12'), +] + +# also build boost_mpi +boost_mpi = True + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/SCons/SCons-2.5.1-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/s/SCons/SCons-2.5.1-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..6df761e722 --- /dev/null +++ b/easybuild/easyconfigs/s/SCons/SCons-2.5.1-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'SCons' +version = '2.5.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.scons.org/' +description = "SCons is a software construction tool." + +toolchain = {'name': 'intel', 'version': '2016b'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] + +dependencies = [('Python', '2.7.12')] + +sanity_check_paths = { + 'files': ['bin/scons', 'bin/scons-time', 'bin/sconsign'], + 'dirs': ['lib/%(namelower)s-%(version)s/%(name)s'], +} + +options = {'modulename': False} + +moduleclass = 'devel' -- GitLab From b90a1547abec7a46929257ad7197cd48d11497cd Mon Sep 17 00:00:00 2001 From: Yann Sagon Date: Wed, 15 Feb 2017 15:50:27 +0100 Subject: [PATCH 0076/1603] platanus-1.2.4-foss-2017a --- .../p/Platanus/Platanus-1.2.4-foss-2017a.eb | 25 +++++++++++++++++++ .../p/Platanus/Platanus_new_gcc.patch | 9 +++++++ 2 files changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/p/Platanus/Platanus-1.2.4-foss-2017a.eb create mode 100644 easybuild/easyconfigs/p/Platanus/Platanus_new_gcc.patch diff --git a/easybuild/easyconfigs/p/Platanus/Platanus-1.2.4-foss-2017a.eb b/easybuild/easyconfigs/p/Platanus/Platanus-1.2.4-foss-2017a.eb new file mode 100644 index 0000000000..d09524d53c --- /dev/null +++ b/easybuild/easyconfigs/p/Platanus/Platanus-1.2.4-foss-2017a.eb @@ -0,0 +1,25 @@ +easyblock = 'MakeCp' + +name = 'Platanus' +version = '1.2.4' + +homepage = 'http://platanus.bio.titech.ac.jp/' +description = """PLATform for Assembling NUcleotide Sequences""" + +toolchain = {'name': 'foss', 'version': '2017a'} +toolchainopts = {'openmp': True} + +source_urls = ['http://platanus.bio.titech.ac.jp/?ddownload=150'] +sources = ['%(name)s_v%(version)s.tar.gz'] + +# fix Makefile to support newer gcc version +patches = ['Platanus_new_gcc.patch'] + +files_to_copy = [(["platanus"],'bin'), "README", "LICENSE"] + +sanity_check_paths = { + 'files': ["bin/platanus"], + 'dirs': [""], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/Platanus/Platanus_new_gcc.patch b/easybuild/easyconfigs/p/Platanus/Platanus_new_gcc.patch new file mode 100644 index 0000000000..531c797148 --- /dev/null +++ b/easybuild/easyconfigs/p/Platanus/Platanus_new_gcc.patch @@ -0,0 +1,9 @@ +--- Makefile.o 2015-06-03 07:39:00.000000000 +0200 ++++ Makefile 2017-02-15 15:33:18.000000000 +0100 +@@ -1,5 +1,5 @@ + CXX = g++ +-CXXFLAGS = -std=c++0x -O3 -funroll-loops -Wall -fopenmp -finline-limit-50000 -lm -Dnullptr=0 ++CXXFLAGS = -std=c++0x -O3 -funroll-loops -Wall -fopenmp -finline-limit-50000 -lm -Dnullptr=0 -fpermissive + + + PRG = platanus -- GitLab From c261e36bb0a467bd6d270faf48f9304f729b568a Mon Sep 17 00:00:00 2001 From: Robert Schmidt Date: Wed, 15 Feb 2017 16:23:29 +0000 Subject: [PATCH 0077/1603] updating with review feedback --- easybuild/easyconfigs/b/Bazel/Bazel-0.4.4.eb | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-0.4.4.eb b/easybuild/easyconfigs/b/Bazel/Bazel-0.4.4.eb index 81fd376a8e..2c824e618b 100644 --- a/easybuild/easyconfigs/b/Bazel/Bazel-0.4.4.eb +++ b/easybuild/easyconfigs/b/Bazel/Bazel-0.4.4.eb @@ -12,19 +12,20 @@ It is used to build the majority of Google's software.""" toolchain = {'name': 'dummy', 'version': ''} +sources = ['%(namelower)s-%(version)s-dist.zip'] +source_urls = ['https://github.com/bazelbuild/bazel/releases/download/%(version)s'] + dependencies = [ ('Java', '1.8.0_121'), ] -sources = ['%(namelower)s-%(version)s-dist.zip'] -source_urls = ['https://github.com/bazelbuild/bazel/releases/download/%(version)s'] -cmds_map = [('.*', "JAVA_VERSION=1.8 CC=gcc CXX=g++ ./compile.sh")] +cmds_map = [('.*', "JAVA_VERSION=%(javashortver)s CC=gcc CXX=g++ ./compile.sh")] files_to_copy = [(['output/bazel'], 'bin')] sanity_check_paths={ - 'files': ['bin/bazel'], - 'dirs': ['bin'], + 'dirs': ['bin'], + 'files': ['bin/bazel'] } moduleclass = 'devel' -- GitLab From e076db3cc515038c54c49ecd3dc4a6543c4783f6 Mon Sep 17 00:00:00 2001 From: Robert Schmidt Date: Wed, 15 Feb 2017 19:11:34 +0000 Subject: [PATCH 0078/1603] update per review --- easybuild/easyconfigs/b/Bazel/Bazel-0.4.4.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-0.4.4.eb b/easybuild/easyconfigs/b/Bazel/Bazel-0.4.4.eb index 2c824e618b..dd70600323 100644 --- a/easybuild/easyconfigs/b/Bazel/Bazel-0.4.4.eb +++ b/easybuild/easyconfigs/b/Bazel/Bazel-0.4.4.eb @@ -19,13 +19,13 @@ dependencies = [ ('Java', '1.8.0_121'), ] -cmds_map = [('.*', "JAVA_VERSION=%(javashortver)s CC=gcc CXX=g++ ./compile.sh")] +cmds_map = [('.*', "./compile.sh")] files_to_copy = [(['output/bazel'], 'bin')] sanity_check_paths={ - 'dirs': ['bin'], - 'files': ['bin/bazel'] + 'files': ['bin/bazel'], + 'dirs': [], } moduleclass = 'devel' -- GitLab From 1331efc4299668ef27b7ebbb87bbd217b7b39825 Mon Sep 17 00:00:00 2001 From: Maxime Boissonneault Date: Wed, 15 Feb 2017 21:44:17 +0000 Subject: [PATCH 0079/1603] modified source url for MCR R2013a and b --- easybuild/easyconfigs/m/MCR/MCR-R2013a.eb | 2 +- easybuild/easyconfigs/m/MCR/MCR-R2013b.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/MCR/MCR-R2013a.eb b/easybuild/easyconfigs/m/MCR/MCR-R2013a.eb index caffaedaa3..2df01756bc 100644 --- a/easybuild/easyconfigs/m/MCR/MCR-R2013a.eb +++ b/easybuild/easyconfigs/m/MCR/MCR-R2013a.eb @@ -9,7 +9,7 @@ description = """The MATLAB Runtime is a standalone set of shared libraries toolchain = {'name': 'dummy', 'version': ''} source_urls = [ - 'http://www.mathworks.com/supportfiles/MCR_Runtime/%(version)s/', + 'http://www.mathworks.com/supportfiles/downloads/%(version)s/deployment_files/%(version)s/installers/glnxa64/', ] sources = ['%(name)s_%(version)s_glnxa64_installer.zip'] diff --git a/easybuild/easyconfigs/m/MCR/MCR-R2013b.eb b/easybuild/easyconfigs/m/MCR/MCR-R2013b.eb index ea139590d9..4d025dab9a 100644 --- a/easybuild/easyconfigs/m/MCR/MCR-R2013b.eb +++ b/easybuild/easyconfigs/m/MCR/MCR-R2013b.eb @@ -9,7 +9,7 @@ description = """The MATLAB Runtime is a standalone set of shared libraries toolchain = {'name': 'dummy', 'version': ''} source_urls = [ - 'http://www.mathworks.com/supportfiles/MCR_Runtime/%(version)s/', + 'http://www.mathworks.com/supportfiles/downloads/%(version)s/deployment_files/%(version)s/installers/glnxa64/', ] sources = ['%(name)s_%(version)s_glnxa64_installer.zip'] -- GitLab From d30b6d06cff6eef14665c45a9c14229aa1cd7b39 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Thu, 16 Feb 2017 08:28:51 +0100 Subject: [PATCH 0080/1603] added RNAz for GCC 5 and above GCC changed the default C standard from gnu89 to gnu11, RNAz needs gnu89 --- .../easyconfigs/r/RNAz/RNAz-2.1-foss-2016b.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/r/RNAz/RNAz-2.1-foss-2016b.eb diff --git a/easybuild/easyconfigs/r/RNAz/RNAz-2.1-foss-2016b.eb b/easybuild/easyconfigs/r/RNAz/RNAz-2.1-foss-2016b.eb new file mode 100644 index 0000000000..bdf32dd367 --- /dev/null +++ b/easybuild/easyconfigs/r/RNAz/RNAz-2.1-foss-2016b.eb @@ -0,0 +1,25 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild + +easyblock = 'ConfigureMake' + +name = 'RNAz' +version = '2.1' + +homepage = 'http://www.tbi.univie.ac.at/~wash/RNAz/' +description = """RNAz is a program for predicting structurally conserved and +thermodynamically stable RNA secondary structures in multiple sequence alignments.""" + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'optarch': True, 'pic': True} + +buildopts = 'CFLAGS="-std=gnu89 $CFLAGS"' + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://www.tbi.univie.ac.at/~wash/%s' % name] + +sanity_check_paths = { + 'files': ['bin/RNAz'], + 'dirs': [] +} + +moduleclass = 'bio' -- GitLab From 972efb3ff93db5861f76d3ff71e79e7cc73143f6 Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Thu, 16 Feb 2017 09:34:36 +0100 Subject: [PATCH 0081/1603] Add configurations for GCCcore-6.3.0 and intel-2017a --- .../pkg-config-0.29.1-GCCcore-6.3.0.eb | 30 +++++++++++++++++++ .../pkg-config-0.29.1-intel-2017a.eb | 27 +++++++++++++++++ 2 files changed, 57 insertions(+) create mode 100644 easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1-GCCcore-6.3.0.eb create mode 100644 easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1-intel-2017a.eb diff --git a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1-GCCcore-6.3.0.eb b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..5cd807b0de --- /dev/null +++ b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1-GCCcore-6.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'pkg-config' +version = '0.29.1' + +homepage = 'http://www.freedesktop.org/wiki/Software/pkg-config/' +description = """pkg-config is a helper tool used when compiling applications and libraries. It helps you insert the + correct compiler options on the command line so an application can use + gcc -o test test.c `pkg-config --libs --cflags glib-2.0` + for instance, rather than hard-coding values on where to find glib (or other libraries).""" + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['https://pkg-config.freedesktop.org/releases/'] +patches = [ + 'pkg-config-%(version)s_gcc-6.patch', +] + +# don't use PAX, it might break. +tar_config_opts = True + +configopts = " --with-internal-glib" + +sanity_check_paths = { + 'files': ['bin/pkg-config'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1-intel-2017a.eb b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1-intel-2017a.eb new file mode 100644 index 0000000000..25371013eb --- /dev/null +++ b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1-intel-2017a.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'pkg-config' +version = '0.29.1' + +homepage = 'http://www.freedesktop.org/wiki/Software/pkg-config/' +description = """pkg-config is a helper tool used when compiling applications and libraries. It helps you insert the + correct compiler options on the command line so an application can use + gcc -o test test.c `pkg-config --libs --cflags glib-2.0` + for instance, rather than hard-coding values on where to find glib (or other libraries).""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['https://pkg-config.freedesktop.org/releases/'] + +# don't use PAX, it might break. +tar_config_opts = True + +configopts = " --with-internal-glib" + +sanity_check_paths = { + 'files': ['bin/pkg-config'], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From 201cc133fb10dfb11c9d5b7e6877535c8d8180dd Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Thu, 16 Feb 2017 09:48:32 +0100 Subject: [PATCH 0082/1603] Add missing builddep on binutils --- .../p/pkg-config/pkg-config-0.29.1-GCCcore-6.3.0.eb | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1-GCCcore-6.3.0.eb b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1-GCCcore-6.3.0.eb index 5cd807b0de..dadba07804 100644 --- a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1-GCCcore-6.3.0.eb @@ -17,6 +17,11 @@ patches = [ 'pkg-config-%(version)s_gcc-6.patch', ] +builddependencies = [ + # use same binutils version that was used when building GCCcore toolchain + ('binutils', '2.27', '', True), +] + # don't use PAX, it might break. tar_config_opts = True -- GitLab From a9ec4e655b47953fbb7bc916dfebca9d120361e5 Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Thu, 16 Feb 2017 10:55:29 +0100 Subject: [PATCH 0083/1603] Updated X11 bundle and dependencies for GCCcore-6.3.0: - Bumped components to the latest available versions - Added libXfont2 --- .../a/Autoconf/Autoconf-2.69-GCCcore-6.3.0.eb | 29 ++++ .../a/Automake/Automake-1.15-GCCcore-6.3.0.eb | 36 +++++ .../Autotools-20150215-GCCcore-6.3.0.eb | 18 +++ .../b/bzip2/bzip2-1.0.6-GCCcore-6.3.0.eb | 18 +++ .../e/expat/expat-2.2.0-GCCcore-6.3.0.eb | 19 +++ .../fontconfig-2.12.1-GCCcore-6.3.0.eb | 25 ++++ .../freetype/freetype-2.7.1-GCCcore-6.3.0.eb | 29 ++++ .../gettext/gettext-0.19.8.1-GCCcore-6.3.0.eb | 26 ++++ .../easyconfigs/g/gettext/gettext-0.19.8.1.eb | 25 ++++ .../l/libpng/libpng-1.6.28-GCCcore-6.3.0.eb | 29 ++++ .../l/libtool/libtool-2.4.6-GCCcore-6.3.0.eb | 20 +++ .../l/libxml2/libxml2-2.9.4-GCCcore-6.3.0.eb | 26 ++++ .../n/ncurses/ncurses-6.0-GCCcore-6.3.0.eb | 39 +++++ .../x/X11/X11-20170129-GCCcore-6.3.0.eb | 136 ++++++++++++++++++ .../x/XZ/XZ-5.2.3-GCCcore-6.3.0.eb | 28 ++++ 15 files changed, 503 insertions(+) create mode 100644 easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-6.3.0.eb create mode 100644 easybuild/easyconfigs/a/Automake/Automake-1.15-GCCcore-6.3.0.eb create mode 100644 easybuild/easyconfigs/a/Autotools/Autotools-20150215-GCCcore-6.3.0.eb create mode 100644 easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCCcore-6.3.0.eb create mode 100644 easybuild/easyconfigs/e/expat/expat-2.2.0-GCCcore-6.3.0.eb create mode 100644 easybuild/easyconfigs/f/fontconfig/fontconfig-2.12.1-GCCcore-6.3.0.eb create mode 100644 easybuild/easyconfigs/f/freetype/freetype-2.7.1-GCCcore-6.3.0.eb create mode 100644 easybuild/easyconfigs/g/gettext/gettext-0.19.8.1-GCCcore-6.3.0.eb create mode 100644 easybuild/easyconfigs/g/gettext/gettext-0.19.8.1.eb create mode 100644 easybuild/easyconfigs/l/libpng/libpng-1.6.28-GCCcore-6.3.0.eb create mode 100644 easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-6.3.0.eb create mode 100644 easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-GCCcore-6.3.0.eb create mode 100644 easybuild/easyconfigs/n/ncurses/ncurses-6.0-GCCcore-6.3.0.eb create mode 100644 easybuild/easyconfigs/x/X11/X11-20170129-GCCcore-6.3.0.eb create mode 100644 easybuild/easyconfigs/x/XZ/XZ-5.2.3-GCCcore-6.3.0.eb diff --git a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-6.3.0.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..84aebc0f8f --- /dev/null +++ b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-6.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'Autoconf' +version = '2.69' + +homepage = 'http://www.gnu.org/software/autoconf/' +description = """Autoconf is an extensible package of M4 macros that produce shell scripts + to automatically configure software source code packages. These scripts can adapt the + packages to many kinds of UNIX-like systems without manual user intervention. Autoconf + creates a configuration script for a package from a template file that lists the + operating system features that the package can use, in the form of M4 macro calls.""" + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('M4', '1.4.18')] + +# use same binutils version that was used when building GCCcore toolchain +builddependencies = [('binutils', '2.27', '', True)] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["autoconf", "autoheader", "autom4te", "autoreconf", "autoscan", + "autoupdate", "ifnames"]], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.15-GCCcore-6.3.0.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..304170650f --- /dev/null +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15-GCCcore-6.3.0.eb @@ -0,0 +1,36 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## + +easyblock = 'ConfigureMake' + +name = 'Automake' +version = "1.15" + +homepage = 'http://www.gnu.org/software/automake/automake.html' +description = "Automake: GNU Standards-compliant Makefile generator" + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('Autoconf', '2.69')] + +# use same binutils version that was used when building GCCcore toolchain +builddependencies = [('binutils', '2.27', '', True)] + +sanity_check_paths = { + 'files': ['bin/automake', 'bin/aclocal'], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/a/Autotools/Autotools-20150215-GCCcore-6.3.0.eb b/easybuild/easyconfigs/a/Autotools/Autotools-20150215-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..9e2d66a8e2 --- /dev/null +++ b/easybuild/easyconfigs/a/Autotools/Autotools-20150215-GCCcore-6.3.0.eb @@ -0,0 +1,18 @@ +easyblock = 'Bundle' + +name = 'Autotools' +version = '20150215' # date of the most recent change + +homepage = 'http://autotools.io' +description = """This bundle collect the standard GNU build tools: Autoconf, Automake and libtool""" + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} + +dependencies = [ + ('Autoconf', '2.69'), # 20120424 + ('Automake', '1.15'), # 20150105 + ('libtool', '2.4.6'), # 20150215 +] +# Pure bundle -- no need to specify 'binutils' used when building GCCcore toolchain as build dependency + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCCcore-6.3.0.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..5ec3bbe0cb --- /dev/null +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCCcore-6.3.0.eb @@ -0,0 +1,18 @@ +name = 'bzip2' +version = '1.0.6' + +homepage = 'http://www.bzip.org/' +description = """bzip2 is a freely available, patent free, high-quality data compressor. It typically + compresses files to within 10% to 15% of the best available techniques (the PPM family of statistical + compressors), whilst being around twice as fast at compression and six times faster at decompression.""" + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} +toolchainopts = {'pic': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://www.bzip.org/%(version)s'] + +# use same binutils version that was used when building GCCcore toolchain +builddependencies = [('binutils', '2.27', '', True)] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/e/expat/expat-2.2.0-GCCcore-6.3.0.eb b/easybuild/easyconfigs/e/expat/expat-2.2.0-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..a67bb4fc20 --- /dev/null +++ b/easybuild/easyconfigs/e/expat/expat-2.2.0-GCCcore-6.3.0.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'expat' +version = '2.2.0' + +homepage = 'http://expat.sourceforge.net/' +description = """Expat is an XML parser library written in C. It is a stream-oriented parser in which an application + registers handlers for things the parser might find in the XML document (like start tags)""" + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = [SOURCEFORGE_SOURCE] + +# use same binutils version that was used when building GCCcore toolchain +builddependencies = [('binutils', '2.27', '', True)] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/f/fontconfig/fontconfig-2.12.1-GCCcore-6.3.0.eb b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.12.1-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..2cdc8b58de --- /dev/null +++ b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.12.1-GCCcore-6.3.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'fontconfig' +version = '2.12.1' + +homepage = 'http://www.freedesktop.org/software/fontconfig' +description = """Fontconfig is a library designed to provide system-wide font configuration, customization and +application access.""" + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} + +source_urls = ['http://www.freedesktop.org/software/fontconfig/release/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('expat', '2.2.0'), + ('freetype', '2.7.1'), +] + +# use same binutils version that was used when building GCCcore toolchain +builddependencies = [('binutils', '2.27', '', True)] + +configopts = '--disable-docs ' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.7.1-GCCcore-6.3.0.eb b/easybuild/easyconfigs/f/freetype/freetype-2.7.1-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..2892f7ffb0 --- /dev/null +++ b/easybuild/easyconfigs/f/freetype/freetype-2.7.1-GCCcore-6.3.0.eb @@ -0,0 +1,29 @@ +name = 'freetype' +version = '2.7.1' + +homepage = 'http://freetype.org' +description = """FreeType 2 is a software font engine that is designed to be small, efficient, highly customizable, and + portable while capable of producing high-quality output (glyph images). It can be used in graphics libraries, display + servers, font conversion tools, text image generation tools, and many other products as well.""" + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} + +source_urls = [GNU_SAVANNAH_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('bzip2', '1.0.6'), + ('libpng', '1.6.28'), + ('zlib', '1.2.11'), +] + +# use same binutils version that was used when building GCCcore toolchain +builddependencies = [('binutils', '2.27', '', True)] + +sanity_check_paths = { + 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, + 'lib/pkgconfig/freetype2.pc'], + 'dirs': ['include/freetype2'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.8.1-GCCcore-6.3.0.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.8.1-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..6e2d7b23a6 --- /dev/null +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.8.1-GCCcore-6.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'gettext' +version = '0.19.8.1' + +homepage = 'http://www.gnu.org/software/gettext/' +description = """GNU `gettext' is an important step for the GNU Translation Project, as it is an asset on which we may +build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools +and documentation""" + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} + +sources = [SOURCE_TAR_GZ] +source_urls = [GNU_SOURCE] + +dependencies = [ + ('libxml2', '2.9.4'), + ('ncurses', '6.0'), +] + +# use same binutils version that was used when building GCCcore toolchain +builddependencies = [('binutils', '2.27', '', True)] + +configopts = '--without-emacs --with-libxml2-prefix=$EBROOTLIBXML2' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.8.1.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.8.1.eb new file mode 100644 index 0000000000..f1e80cfb3b --- /dev/null +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.8.1.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'gettext' +version = '0.19.8.1' + +homepage = 'http://www.gnu.org/software/gettext/' +description = """GNU `gettext' is an important step for the GNU Translation Project, as it is an asset on which we may +build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools +and documentation""" + +# This is a basic stripped down version of gettext without any +# dependencies on other packages used as initial builddep for XZ +# It is the first step in the cyclic dependency chain of +# XZ -> libxml2 -> gettext -> XZ + +toolchain = {'name': 'dummy', 'version': ''} + +sources = [SOURCE_TAR_GZ] +source_urls = [GNU_SOURCE] + +dependencies = [('ncurses', '6.0')] + +configopts = '--without-emacs --with-included-libxml --without-xz --without-bzip2' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.28-GCCcore-6.3.0.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.28-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..7aca3fe451 --- /dev/null +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.28-GCCcore-6.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'libpng' +version = '1.6.28' + +homepage = 'http://www.libpng.org/pub/png/libpng.html' +description = "libpng is the official PNG reference library" + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('zlib', '1.2.11')] + +# use same binutils version that was used when building GCCcore toolchain +builddependencies = [('binutils', '2.27', '', True)] + +configopts = "--with-pic" + +majminver = ''.join(version.split('.')[:2]) +sanity_check_paths = { + 'files': ['include/pngconf.h', 'include/png.h', 'include/pnglibconf.h', 'lib/libpng.a', + 'lib/libpng.%s' % SHLIB_EXT, 'lib/libpng%s.a' % majminver, 'lib/libpng%s.%s' % (majminver, SHLIB_EXT)], + 'dirs': ['bin', 'include/libpng%s' % majminver, 'share/man'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-6.3.0.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..9e72961b6b --- /dev/null +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-6.3.0.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'libtool' +version = '2.4.6' + +homepage = 'http://www.gnu.org/software/libtool' +description = """GNU libtool is a generic library support script. Libtool hides the complexity of using shared libraries + behind a consistent, portable interface.""" + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +dependencies = [('M4', '1.4.18')] + +# use same binutils version that was used when building GCCcore toolchain +builddependencies = [('binutils', '2.27', '', True)] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-GCCcore-6.3.0.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..b71554c4df --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-GCCcore-6.3.0.eb @@ -0,0 +1,26 @@ +name = 'libxml2' +version = '2.9.4' + +homepage = 'http://xmlsoft.org/' +description = """Libxml2 is the XML C parser and +toolchain developed for the Gnome project + (but usable outside of the Gnome platform).""" + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} +toolchainopts = {'pic': True} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('zlib', '1.2.11'), + ('XZ', '5.2.3'), +] + +# use same binutils version that was used when building GCCcore toolchain +builddependencies = [('binutils', '2.27', '', True)] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.0-GCCcore-6.3.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..097f0bd4af --- /dev/null +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-GCCcore-6.3.0.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'ncurses' +version = '6.0' + +homepage = 'http://www.gnu.org/software/ncurses/' +description = """The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, + and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and + function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.""" + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} +toolchainopts = {'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] + +patches = ['ncurses-%(version)s_gcc-5.patch'] + +# use same binutils version that was used when building GCCcore toolchain +builddependencies = [('binutils', '2.27')] + +configopts = [ + # default build + '--with-shared --enable-overwrite', + # the UTF-8 enabled version (ncursesw) + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses%(version_major)s-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.%s' % (x, y, SHLIB_EXT) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/X11/X11-20170129-GCCcore-6.3.0.eb b/easybuild/easyconfigs/x/X11/X11-20170129-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..2e89d51b91 --- /dev/null +++ b/easybuild/easyconfigs/x/X11/X11-20170129-GCCcore-6.3.0.eb @@ -0,0 +1,136 @@ +easyblock = 'Bundle' + +name = 'X11' +version = '20170129' + +homepage = 'https://www.x.org' +description = "The X Window System (X11) is a windowing system for bitmap displays" + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} + +source_urls = [ + XORG_LIB_SOURCE, + XORG_PROTO_SOURCE, + 'http://xcb.freedesktop.org/dist/', + 'http://xkbcommon.org/download/', + 'http://cgit.freedesktop.org/xorg/util/macros/snapshot', +] + +dependencies = [ + ('bzip2', '1.0.6'), + ('fontconfig', '2.12.1'), + ('freetype', '2.7.1'), + ('zlib', '1.2.11'), +] +builddependencies = [ + ('Autotools', '20150215'), + ('Bison', '3.0.4'), + ('gettext', '0.19.8.1'), + ('pkg-config', '0.29.1'), + # use same binutils version that was used when building GCCcore toolchain + ('binutils', '2.27', '', True), +] + +default_easyblock = 'ConfigureMake' + +common_specs = { + 'sources': [SOURCE_TAR_GZ], + 'start_dir': '%(name)s-%(version)s', +} +components = [ + ('xorg-macros', '1.19.1', { # 2017-01-29 + 'sources': ['util-macros-%(version)s.tar.gz'], + 'start_dir': 'util-macros-%(version)s', + }), + ('libpthread-stubs', '0.3', common_specs), # 2009-10-14 + ('bigreqsproto', '1.1.2', common_specs), # 2012-03-23 + ('compositeproto', '0.4.2', common_specs), # 2010-10-30 + ('damageproto', '1.2.1', common_specs), # 2010-10-30 + ('dmxproto', '2.3.1', common_specs), # 2011-01-06 + ('dri2proto', '2.8', common_specs), # 2012-07-11 + ('dri3proto', '1.0', common_specs), # 2013-11-01 + ('fixesproto', '5.0', common_specs), # 2011-03-08 + ('fontsproto', '2.1.3', common_specs), # 2014-04-14 + ('glproto', '1.4.17', common_specs), # 2013-12-10 + ('inputproto', '2.3.2', common_specs), # 2016-04-04 + ('kbproto', '1.0.7', common_specs), # 2015-05-01 + ('presentproto', '1.1', common_specs), # 2017-01-26 + ('randrproto', '1.5.0', common_specs), # 2015-05-17 + ('recordproto', '1.14.2', common_specs), # 2012-03-23 + ('renderproto', '0.11.1', common_specs), # 2010-08-10 + ('resourceproto', '1.2.0', common_specs), # 2011-05-28 + ('scrnsaverproto', '1.2.2', common_specs), # 2012-03-23 + ('videoproto', '2.3.3', common_specs), # 2016-03-11 + ('xcmiscproto', '1.2.2', common_specs), # 2012-03-23 + ('xextproto', '7.3.0', common_specs), # 2013-12-27 + ('xf86bigfontproto', '1.2.0', common_specs), # 2009-08-27 + ('xf86dgaproto', '2.1', common_specs), # 2009-10-01 + ('xf86driproto', '2.1.1', common_specs), # 2011-01-06 + ('xf86vidmodeproto', '2.3.1', common_specs), # 2011-01-06 + ('xineramaproto', '1.2.1', common_specs), # 2011-01-06 + ('xproto', '7.0.31', common_specs), # 2016-09-23 + ('libXau', '1.0.8', common_specs), # 2013-05-24 + ('libXdmcp', '1.1.2', common_specs), # 2015-03-21 + ('xcb-proto', '1.12', common_specs), # 2016-05-18 + ('libxcb', '1.12', common_specs), # 2016-05-18 + ('xtrans', '1.3.5', common_specs), # 2014-09-22 + ('libxkbcommon', '0.7.1', { # 2017-01-18 + 'sources': ['libxkbcommon-%(version)s.tar.xz'], + 'start_dir': 'libxkbcommon-%(version)s', + }), + ('libX11', '1.6.4', common_specs), # 2016-10-04 + ('libXext', '1.3.3', common_specs), # 2014-07-24 + ('libFS', '1.0.7', common_specs), # 2015-05-01 + ('libICE', '1.0.9', common_specs), # 2014-06-07 + ('libSM', '1.2.2', common_specs), # 2013-09-08 + ('libXScrnSaver', '1.2.2', common_specs), # 2012-03-08 + ('libXt', '1.1.5', common_specs), # 2015-05-01 + ('libXmu', '1.1.2', common_specs), # 2013-09-08 + ('libXpm', '3.5.12', common_specs), # 2016-12-15 + ('libXaw', '1.0.13', common_specs), # 2015-05-01 + ('libXfixes', '5.0.3', common_specs), # 2016-10-04 + ('libXcomposite', '0.4.4', common_specs), # 2013-01-03 + ('libXrender', '0.9.10', common_specs), # 2016-10-04 + ('libXcursor', '1.1.14', common_specs), # 2013-05-30 + ('libXdamage', '1.1.4', common_specs), # 2013-01-03 + ('libfontenc', '1.1.3', common_specs), # 2015-05-01 + ('libXfont', '1.5.2', common_specs), # 2016-08-31 + ('libXfont2', '2.0.1', common_specs), # 2015-12-11 + ('libXft', '2.3.2', common_specs), # 2014-06-06 + ('libXi', '1.7.9', common_specs), # 2017-01-23 + ('libXinerama', '1.1.3', common_specs), # 2013-05-31 + ('libXrandr', '1.5.1', common_specs), # 2016-10-04 + ('libXres', '1.0.7', common_specs), # 2013-05-31 + ('libXtst', '1.2.3', common_specs), # 2016-10-04 + ('libXv', '1.0.11', common_specs), # 2016-10-04 + ('libXvMC', '1.0.10', common_specs), # 2016-10-04 + ('libXxf86dga', '1.1.4', common_specs), # 2013-05-31 + ('libXxf86vm', '1.1.4', common_specs), # 2015-02-24 + ('libdmx', '1.1.3', common_specs), # 2013-05-28 + ('libpciaccess', '0.13.4', common_specs), # 2015-05-01 + ('libxkbfile', '1.0.9', common_specs), # 2015-05-01 + ('libxshmfence', '1.2', common_specs), # 2015-01-02 + ('xcb-util', '0.4.0', common_specs), # 2014-10-15 + ('xcb-util-image', '0.4.0', common_specs), # 2014-10-15 + ('xcb-util-keysyms', '0.4.0', common_specs), # 2014-10-01 + ('xcb-util-renderutil', '0.3.9', common_specs), # 2014-06-13 + ('xcb-util-wm', '0.4.1', common_specs), # 2014-02-19 + ('xcb-util-cursor', '0.1.3', common_specs), # 2016-05-12 +] + +# Python is required for xcb-proto +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] +pyshortver = '.'.join(SYS_PYTHON_VERSION.split('.')[0:2]) + +preconfigopts = "if [ ! -f configure ]; then ./autogen.sh; fi && " + +# specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module +full_sanity_check = True + +sanity_check_paths = { + 'files': ['include/X11/Xlib.h', 'include/X11/Xutil.h'], + 'dirs': ['include/GL', 'include/X11', 'include/X11/extensions', 'lib', + 'lib/python%s/site-packages/xcbgen' % pyshortver, 'lib/pkgconfig', 'share/pkgconfig'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.3-GCCcore-6.3.0.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.3-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..0e517cfb0f --- /dev/null +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.3-GCCcore-6.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'XZ' +version = '5.2.3' + +homepage = 'http://tukaani.org/xz/' +description = "xz: XZ utilities" + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://tukaani.org/xz/'] + +builddependencies = [ + ('gettext', '0.19.8.1', '', True), + # use same binutils version that was used when building GCCcore toolchain + ('binutils', '2.27', '', True), +] + +# may become useful in non-x86 archs +# configopts = ' --disable-assembler ' + +sanity_check_paths = { + 'files': ["bin/xz", "bin/lzmainfo"], + 'dirs': [] +} + +moduleclass = 'tools' -- GitLab From ee6c56245332a6367a33663e56f3f6eae904d981 Mon Sep 17 00:00:00 2001 From: Basil Neff Date: Thu, 16 Feb 2017 11:10:05 +0100 Subject: [PATCH 0084/1603] Change backticks in the gettext description to build RPM Packages with fpm. EasyBuild fails to create RPM packages with backticks in the description. The backticks are not escaped by EasyBuild or fpm. --- easybuild/easyconfigs/g/gettext/gettext-0.18.2-foss-2015b.eb | 2 +- easybuild/easyconfigs/g/gettext/gettext-0.18.2-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/g/gettext/gettext-0.18.2-goolf-1.5.14.eb | 2 +- easybuild/easyconfigs/g/gettext/gettext-0.18.2-ictce-5.2.0.eb | 2 +- easybuild/easyconfigs/g/gettext/gettext-0.18.2-ictce-5.3.0.eb | 2 +- easybuild/easyconfigs/g/gettext/gettext-0.18.2.eb | 2 +- easybuild/easyconfigs/g/gettext/gettext-0.19.2-goolf-1.5.14.eb | 2 +- easybuild/easyconfigs/g/gettext/gettext-0.19.2-goolf-1.7.20.eb | 2 +- easybuild/easyconfigs/g/gettext/gettext-0.19.2-intel-2014.06.eb | 2 +- easybuild/easyconfigs/g/gettext/gettext-0.19.2-intel-2014b.eb | 2 +- easybuild/easyconfigs/g/gettext/gettext-0.19.2-intel-2015a.eb | 2 +- easybuild/easyconfigs/g/gettext/gettext-0.19.2-intel-2015b.eb | 2 +- easybuild/easyconfigs/g/gettext/gettext-0.19.4-GCC-4.9.2.eb | 2 +- easybuild/easyconfigs/g/gettext/gettext-0.19.4-foss-2015a.eb | 2 +- easybuild/easyconfigs/g/gettext/gettext-0.19.4-intel-2015a.eb | 2 +- easybuild/easyconfigs/g/gettext/gettext-0.19.4.eb | 2 +- .../easyconfigs/g/gettext/gettext-0.19.6-GNU-4.9.3-2.25.eb | 2 +- easybuild/easyconfigs/g/gettext/gettext-0.19.6-foss-2016a.eb | 2 +- easybuild/easyconfigs/g/gettext/gettext-0.19.6-gimkl-2.11.5.eb | 2 +- easybuild/easyconfigs/g/gettext/gettext-0.19.6-intel-2015b.eb | 2 +- easybuild/easyconfigs/g/gettext/gettext-0.19.6-intel-2016a.eb | 2 +- easybuild/easyconfigs/g/gettext/gettext-0.19.6.eb | 2 +- easybuild/easyconfigs/g/gettext/gettext-0.19.7-foss-2015b.eb | 2 +- easybuild/easyconfigs/g/gettext/gettext-0.19.7-foss-2016a.eb | 2 +- easybuild/easyconfigs/g/gettext/gettext-0.19.7-intel-2016a.eb | 2 +- easybuild/easyconfigs/g/gettext/gettext-0.19.7.eb | 2 +- easybuild/easyconfigs/g/gettext/gettext-0.19.8-GCCcore-4.9.3.eb | 2 +- easybuild/easyconfigs/g/gettext/gettext-0.19.8-foss-2016.04.eb | 2 +- easybuild/easyconfigs/g/gettext/gettext-0.19.8-foss-2016b.eb | 2 +- easybuild/easyconfigs/g/gettext/gettext-0.19.8-intel-2016b.eb | 2 +- easybuild/easyconfigs/g/gettext/gettext-0.19.8.eb | 2 +- 31 files changed, 31 insertions(+), 31 deletions(-) diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.18.2-foss-2015b.eb b/easybuild/easyconfigs/g/gettext/gettext-0.18.2-foss-2015b.eb index e7d30bfac7..400996e08a 100644 --- a/easybuild/easyconfigs/g/gettext/gettext-0.18.2-foss-2015b.eb +++ b/easybuild/easyconfigs/g/gettext/gettext-0.18.2-foss-2015b.eb @@ -4,7 +4,7 @@ name = 'gettext' version = '0.18.2' homepage = 'http://www.gnu.org/software/gettext/' -description = """GNU `gettext' is an important step for the GNU Translation Project, as it is an asset on which we may +description = """GNU 'gettext' is an important step for the GNU Translation Project, as it is an asset on which we may build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools and documentation""" diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.18.2-goolf-1.4.10.eb b/easybuild/easyconfigs/g/gettext/gettext-0.18.2-goolf-1.4.10.eb index 686c6f9d40..645bdc29be 100644 --- a/easybuild/easyconfigs/g/gettext/gettext-0.18.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/g/gettext/gettext-0.18.2-goolf-1.4.10.eb @@ -4,7 +4,7 @@ name = 'gettext' version = '0.18.2' homepage = 'http://www.gnu.org/software/gettext/' -description = """GNU `gettext' is an important step for the GNU Translation Project, as it is an asset on which we may +description = """GNU 'gettext' is an important step for the GNU Translation Project, as it is an asset on which we may build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools and documentation""" diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.18.2-goolf-1.5.14.eb b/easybuild/easyconfigs/g/gettext/gettext-0.18.2-goolf-1.5.14.eb index adf041c9d3..ccaa5c1d29 100644 --- a/easybuild/easyconfigs/g/gettext/gettext-0.18.2-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/g/gettext/gettext-0.18.2-goolf-1.5.14.eb @@ -4,7 +4,7 @@ name = 'gettext' version = '0.18.2' homepage = 'http://www.gnu.org/software/gettext/' -description = """GNU `gettext' is an important step for the GNU Translation Project, as it is an asset on which we may +description = """GNU 'gettext' is an important step for the GNU Translation Project, as it is an asset on which we may build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools and documentation""" diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.18.2-ictce-5.2.0.eb b/easybuild/easyconfigs/g/gettext/gettext-0.18.2-ictce-5.2.0.eb index 5479e98f23..b9f046449c 100644 --- a/easybuild/easyconfigs/g/gettext/gettext-0.18.2-ictce-5.2.0.eb +++ b/easybuild/easyconfigs/g/gettext/gettext-0.18.2-ictce-5.2.0.eb @@ -4,7 +4,7 @@ name = 'gettext' version = '0.18.2' homepage = 'http://www.gnu.org/software/gettext/' -description = """GNU `gettext' is an important step for the GNU Translation Project, as it is an asset on which we may +description = """GNU 'gettext' is an important step for the GNU Translation Project, as it is an asset on which we may build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools and documentation""" diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.18.2-ictce-5.3.0.eb b/easybuild/easyconfigs/g/gettext/gettext-0.18.2-ictce-5.3.0.eb index 21f6d06397..54b916db8e 100644 --- a/easybuild/easyconfigs/g/gettext/gettext-0.18.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/g/gettext/gettext-0.18.2-ictce-5.3.0.eb @@ -4,7 +4,7 @@ name = 'gettext' version = '0.18.2' homepage = 'http://www.gnu.org/software/gettext/' -description = """GNU `gettext' is an important step for the GNU Translation Project, as it is an asset on which we may +description = """GNU 'gettext' is an important step for the GNU Translation Project, as it is an asset on which we may build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools and documentation""" diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.18.2.eb b/easybuild/easyconfigs/g/gettext/gettext-0.18.2.eb index 68b4d25ce9..000ef4aa2d 100644 --- a/easybuild/easyconfigs/g/gettext/gettext-0.18.2.eb +++ b/easybuild/easyconfigs/g/gettext/gettext-0.18.2.eb @@ -4,7 +4,7 @@ name = 'gettext' version = '0.18.2' homepage = 'http://www.gnu.org/software/gettext/' -description = """GNU `gettext' is an important step for the GNU Translation Project, as it is an asset on which we may +description = """GNU 'gettext' is an important step for the GNU Translation Project, as it is an asset on which we may build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools and documentation""" diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.2-goolf-1.5.14.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.2-goolf-1.5.14.eb index a1a642076c..eeeccb35d4 100644 --- a/easybuild/easyconfigs/g/gettext/gettext-0.19.2-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.2-goolf-1.5.14.eb @@ -4,7 +4,7 @@ name = 'gettext' version = '0.19.2' homepage = 'http://www.gnu.org/software/gettext/' -description = """GNU `gettext' is an important step for the GNU Translation Project, as it is an asset on which we may +description = """GNU 'gettext' is an important step for the GNU Translation Project, as it is an asset on which we may build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools and documentation""" diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.2-goolf-1.7.20.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.2-goolf-1.7.20.eb index b9b28dda44..827716cf97 100644 --- a/easybuild/easyconfigs/g/gettext/gettext-0.19.2-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.2-goolf-1.7.20.eb @@ -4,7 +4,7 @@ name = 'gettext' version = '0.19.2' homepage = 'http://www.gnu.org/software/gettext/' -description = """GNU `gettext' is an important step for the GNU Translation Project, as it is an asset on which we may +description = """GNU 'gettext' is an important step for the GNU Translation Project, as it is an asset on which we may build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools and documentation""" diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.2-intel-2014.06.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.2-intel-2014.06.eb index 238843b206..450a973ebb 100644 --- a/easybuild/easyconfigs/g/gettext/gettext-0.19.2-intel-2014.06.eb +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.2-intel-2014.06.eb @@ -4,7 +4,7 @@ name = 'gettext' version = '0.19.2' homepage = 'http://www.gnu.org/software/gettext/' -description = """GNU `gettext' is an important step for the GNU Translation Project, as it is an asset on which we may +description = """GNU 'gettext' is an important step for the GNU Translation Project, as it is an asset on which we may build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools and documentation""" diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.2-intel-2014b.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.2-intel-2014b.eb index a0c6e92339..43c9195057 100644 --- a/easybuild/easyconfigs/g/gettext/gettext-0.19.2-intel-2014b.eb +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.2-intel-2014b.eb @@ -4,7 +4,7 @@ name = 'gettext' version = '0.19.2' homepage = 'http://www.gnu.org/software/gettext/' -description = """GNU `gettext' is an important step for the GNU Translation Project, as it is an asset on which we may +description = """GNU 'gettext' is an important step for the GNU Translation Project, as it is an asset on which we may build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools and documentation""" diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.2-intel-2015a.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.2-intel-2015a.eb index c49302820d..57381cdd38 100644 --- a/easybuild/easyconfigs/g/gettext/gettext-0.19.2-intel-2015a.eb +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.2-intel-2015a.eb @@ -4,7 +4,7 @@ name = 'gettext' version = '0.19.2' homepage = 'http://www.gnu.org/software/gettext/' -description = """GNU `gettext' is an important step for the GNU Translation Project, as it is an asset on which we may +description = """GNU 'gettext' is an important step for the GNU Translation Project, as it is an asset on which we may build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools and documentation""" diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.2-intel-2015b.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.2-intel-2015b.eb index 2d3d1e0547..1a7da10440 100644 --- a/easybuild/easyconfigs/g/gettext/gettext-0.19.2-intel-2015b.eb +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.2-intel-2015b.eb @@ -4,7 +4,7 @@ name = 'gettext' version = '0.19.2' homepage = 'http://www.gnu.org/software/gettext/' -description = """GNU `gettext' is an important step for the GNU Translation Project, as it is an asset on which we may +description = """GNU 'gettext' is an important step for the GNU Translation Project, as it is an asset on which we may build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools and documentation""" diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.4-GCC-4.9.2.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.4-GCC-4.9.2.eb index 7e8ff4e184..27ab692a93 100644 --- a/easybuild/easyconfigs/g/gettext/gettext-0.19.4-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.4-GCC-4.9.2.eb @@ -4,7 +4,7 @@ name = 'gettext' version = '0.19.4' homepage = 'http://www.gnu.org/software/gettext/' -description = """GNU `gettext' is an important step for the GNU Translation Project, as it is an asset on which we may +description = """GNU 'gettext' is an important step for the GNU Translation Project, as it is an asset on which we may build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools and documentation""" diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.4-foss-2015a.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.4-foss-2015a.eb index 51c244d3ef..e435d00102 100644 --- a/easybuild/easyconfigs/g/gettext/gettext-0.19.4-foss-2015a.eb +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.4-foss-2015a.eb @@ -4,7 +4,7 @@ name = 'gettext' version = '0.19.4' homepage = 'http://www.gnu.org/software/gettext/' -description = """GNU `gettext' is an important step for the GNU Translation Project, as it is an asset on which we may +description = """GNU 'gettext' is an important step for the GNU Translation Project, as it is an asset on which we may build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools and documentation""" diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.4-intel-2015a.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.4-intel-2015a.eb index 0dbf6fce3a..246fbea3c6 100644 --- a/easybuild/easyconfigs/g/gettext/gettext-0.19.4-intel-2015a.eb +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.4-intel-2015a.eb @@ -4,7 +4,7 @@ name = 'gettext' version = '0.19.4' homepage = 'http://www.gnu.org/software/gettext/' -description = """GNU `gettext' is an important step for the GNU Translation Project, as it is an asset on which we may +description = """GNU 'gettext' is an important step for the GNU Translation Project, as it is an asset on which we may build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools and documentation""" diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.4.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.4.eb index ed81b95755..11ed30961c 100644 --- a/easybuild/easyconfigs/g/gettext/gettext-0.19.4.eb +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.4.eb @@ -4,7 +4,7 @@ name = 'gettext' version = '0.19.4' homepage = 'http://www.gnu.org/software/gettext/' -description = """GNU `gettext' is an important step for the GNU Translation Project, as it is an asset on which we may +description = """GNU 'gettext' is an important step for the GNU Translation Project, as it is an asset on which we may build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools and documentation""" diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.6-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.6-GNU-4.9.3-2.25.eb index 90c8e2d47d..4ff92c775d 100644 --- a/easybuild/easyconfigs/g/gettext/gettext-0.19.6-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.6-GNU-4.9.3-2.25.eb @@ -4,7 +4,7 @@ name = 'gettext' version = '0.19.6' homepage = 'http://www.gnu.org/software/gettext/' -description = """GNU `gettext' is an important step for the GNU Translation Project, as it is an asset on which we may +description = """GNU 'gettext' is an important step for the GNU Translation Project, as it is an asset on which we may build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools and documentation""" diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.6-foss-2016a.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.6-foss-2016a.eb index 1fdb744032..ac6519ed4a 100644 --- a/easybuild/easyconfigs/g/gettext/gettext-0.19.6-foss-2016a.eb +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.6-foss-2016a.eb @@ -4,7 +4,7 @@ name = 'gettext' version = '0.19.6' homepage = 'http://www.gnu.org/software/gettext/' -description = """GNU `gettext' is an important step for the GNU Translation Project, as it is an asset on which we may +description = """GNU 'gettext' is an important step for the GNU Translation Project, as it is an asset on which we may build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools and documentation""" diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.6-gimkl-2.11.5.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.6-gimkl-2.11.5.eb index 4aed92d350..859ba0f08f 100644 --- a/easybuild/easyconfigs/g/gettext/gettext-0.19.6-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.6-gimkl-2.11.5.eb @@ -4,7 +4,7 @@ name = 'gettext' version = '0.19.6' homepage = 'http://www.gnu.org/software/gettext/' -description = """GNU `gettext' is an important step for the GNU Translation Project, as it is an asset on which we may +description = """GNU 'gettext' is an important step for the GNU Translation Project, as it is an asset on which we may build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools and documentation""" diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.6-intel-2015b.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.6-intel-2015b.eb index a9b8c4c455..802790cb29 100644 --- a/easybuild/easyconfigs/g/gettext/gettext-0.19.6-intel-2015b.eb +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.6-intel-2015b.eb @@ -4,7 +4,7 @@ name = 'gettext' version = '0.19.6' homepage = 'http://www.gnu.org/software/gettext/' -description = """GNU `gettext' is an important step for the GNU Translation Project, as it is an asset on which we may +description = """GNU 'gettext' is an important step for the GNU Translation Project, as it is an asset on which we may build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools and documentation""" diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.6-intel-2016a.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.6-intel-2016a.eb index d58aad1970..220b284a16 100644 --- a/easybuild/easyconfigs/g/gettext/gettext-0.19.6-intel-2016a.eb +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.6-intel-2016a.eb @@ -4,7 +4,7 @@ name = 'gettext' version = '0.19.6' homepage = 'http://www.gnu.org/software/gettext/' -description = """GNU `gettext' is an important step for the GNU Translation Project, as it is an asset on which we may +description = """GNU 'gettext' is an important step for the GNU Translation Project, as it is an asset on which we may build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools and documentation""" diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.6.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.6.eb index ce355420b2..902bd2a236 100644 --- a/easybuild/easyconfigs/g/gettext/gettext-0.19.6.eb +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.6.eb @@ -4,7 +4,7 @@ name = 'gettext' version = '0.19.6' homepage = 'http://www.gnu.org/software/gettext/' -description = """GNU `gettext' is an important step for the GNU Translation Project, as it is an asset on which we may +description = """GNU 'gettext' is an important step for the GNU Translation Project, as it is an asset on which we may build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools and documentation""" diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.7-foss-2015b.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.7-foss-2015b.eb index 690872c686..79d7c0db22 100644 --- a/easybuild/easyconfigs/g/gettext/gettext-0.19.7-foss-2015b.eb +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.7-foss-2015b.eb @@ -4,7 +4,7 @@ name = 'gettext' version = '0.19.7' homepage = 'http://www.gnu.org/software/gettext/' -description = """GNU `gettext' is an important step for the GNU Translation Project, as it is an asset on which we may +description = """GNU 'gettext' is an important step for the GNU Translation Project, as it is an asset on which we may build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools and documentation""" diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.7-foss-2016a.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.7-foss-2016a.eb index 4580e48c6a..a61ec3269b 100644 --- a/easybuild/easyconfigs/g/gettext/gettext-0.19.7-foss-2016a.eb +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.7-foss-2016a.eb @@ -4,7 +4,7 @@ name = 'gettext' version = '0.19.7' homepage = 'http://www.gnu.org/software/gettext/' -description = """GNU `gettext' is an important step for the GNU Translation Project, as it is an asset on which we may +description = """GNU 'gettext' is an important step for the GNU Translation Project, as it is an asset on which we may build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools and documentation""" diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.7-intel-2016a.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.7-intel-2016a.eb index 4f86721ed0..57cdaad01b 100644 --- a/easybuild/easyconfigs/g/gettext/gettext-0.19.7-intel-2016a.eb +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.7-intel-2016a.eb @@ -4,7 +4,7 @@ name = 'gettext' version = '0.19.7' homepage = 'http://www.gnu.org/software/gettext/' -description = """GNU `gettext' is an important step for the GNU Translation Project, as it is an asset on which we may +description = """GNU 'gettext' is an important step for the GNU Translation Project, as it is an asset on which we may build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools and documentation""" diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.7.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.7.eb index 578b07b38d..8e1eda7fc9 100644 --- a/easybuild/easyconfigs/g/gettext/gettext-0.19.7.eb +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.7.eb @@ -4,7 +4,7 @@ name = 'gettext' version = '0.19.7' homepage = 'http://www.gnu.org/software/gettext/' -description = """GNU `gettext' is an important step for the GNU Translation Project, as it is an asset on which we may +description = """GNU 'gettext' is an important step for the GNU Translation Project, as it is an asset on which we may build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools and documentation""" diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.8-GCCcore-4.9.3.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.8-GCCcore-4.9.3.eb index 8e1b03ad2a..13b1f6601b 100644 --- a/easybuild/easyconfigs/g/gettext/gettext-0.19.8-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.8-GCCcore-4.9.3.eb @@ -4,7 +4,7 @@ name = 'gettext' version = '0.19.8' homepage = 'http://www.gnu.org/software/gettext/' -description = """GNU `gettext' is an important step for the GNU Translation Project, as it is an asset on which we may +description = """GNU 'gettext' is an important step for the GNU Translation Project, as it is an asset on which we may build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools and documentation""" diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.8-foss-2016.04.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.8-foss-2016.04.eb index 47b250264e..8f8b64bb6f 100644 --- a/easybuild/easyconfigs/g/gettext/gettext-0.19.8-foss-2016.04.eb +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.8-foss-2016.04.eb @@ -4,7 +4,7 @@ name = 'gettext' version = '0.19.8' homepage = 'http://www.gnu.org/software/gettext/' -description = """GNU `gettext' is an important step for the GNU Translation Project, as it is an asset on which we may +description = """GNU 'gettext' is an important step for the GNU Translation Project, as it is an asset on which we may build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools and documentation""" diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.8-foss-2016b.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.8-foss-2016b.eb index 91c8cacd60..bcee20f66b 100644 --- a/easybuild/easyconfigs/g/gettext/gettext-0.19.8-foss-2016b.eb +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.8-foss-2016b.eb @@ -4,7 +4,7 @@ name = 'gettext' version = '0.19.8' homepage = 'http://www.gnu.org/software/gettext/' -description = """GNU `gettext' is an important step for the GNU Translation Project, as it is an asset on which we may +description = """GNU 'gettext' is an important step for the GNU Translation Project, as it is an asset on which we may build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools and documentation""" diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.8-intel-2016b.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.8-intel-2016b.eb index 6df1b22caa..8671de264d 100644 --- a/easybuild/easyconfigs/g/gettext/gettext-0.19.8-intel-2016b.eb +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.8-intel-2016b.eb @@ -4,7 +4,7 @@ name = 'gettext' version = '0.19.8' homepage = 'http://www.gnu.org/software/gettext/' -description = """GNU `gettext' is an important step for the GNU Translation Project, as it is an asset on which we may +description = """GNU 'gettext' is an important step for the GNU Translation Project, as it is an asset on which we may build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools and documentation""" diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.8.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.8.eb index 45caa1fde8..dd9bbb81e0 100644 --- a/easybuild/easyconfigs/g/gettext/gettext-0.19.8.eb +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.8.eb @@ -4,7 +4,7 @@ name = 'gettext' version = '0.19.8' homepage = 'http://www.gnu.org/software/gettext/' -description = """GNU `gettext' is an important step for the GNU Translation Project, as it is an asset on which we may +description = """GNU 'gettext' is an important step for the GNU Translation Project, as it is an asset on which we may build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools and documentation""" -- GitLab From e1553722814b3068881671e50a3d0ae2dd4a5227 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 16 Feb 2017 11:14:19 +0100 Subject: [PATCH 0085/1603] stick to old source URL for MCR R2013a --- easybuild/easyconfigs/m/MCR/MCR-R2013a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MCR/MCR-R2013a.eb b/easybuild/easyconfigs/m/MCR/MCR-R2013a.eb index 2df01756bc..caffaedaa3 100644 --- a/easybuild/easyconfigs/m/MCR/MCR-R2013a.eb +++ b/easybuild/easyconfigs/m/MCR/MCR-R2013a.eb @@ -9,7 +9,7 @@ description = """The MATLAB Runtime is a standalone set of shared libraries toolchain = {'name': 'dummy', 'version': ''} source_urls = [ - 'http://www.mathworks.com/supportfiles/downloads/%(version)s/deployment_files/%(version)s/installers/glnxa64/', + 'http://www.mathworks.com/supportfiles/MCR_Runtime/%(version)s/', ] sources = ['%(name)s_%(version)s_glnxa64_installer.zip'] -- GitLab From e8a9ba660567279d75ccf08f1be320d6663e12a2 Mon Sep 17 00:00:00 2001 From: Yann Sagon Date: Thu, 16 Feb 2017 11:26:35 +0100 Subject: [PATCH 0086/1603] removed patch, controlling CXXFLAGS in the eb file --- .../easyconfigs/p/Platanus/Platanus-1.2.4-foss-2017a.eb | 7 +++---- easybuild/easyconfigs/p/Platanus/Platanus_new_gcc.patch | 9 --------- 2 files changed, 3 insertions(+), 13 deletions(-) delete mode 100644 easybuild/easyconfigs/p/Platanus/Platanus_new_gcc.patch diff --git a/easybuild/easyconfigs/p/Platanus/Platanus-1.2.4-foss-2017a.eb b/easybuild/easyconfigs/p/Platanus/Platanus-1.2.4-foss-2017a.eb index d09524d53c..47debc3391 100644 --- a/easybuild/easyconfigs/p/Platanus/Platanus-1.2.4-foss-2017a.eb +++ b/easybuild/easyconfigs/p/Platanus/Platanus-1.2.4-foss-2017a.eb @@ -7,14 +7,13 @@ homepage = 'http://platanus.bio.titech.ac.jp/' description = """PLATform for Assembling NUcleotide Sequences""" toolchain = {'name': 'foss', 'version': '2017a'} -toolchainopts = {'openmp': True} +toolchainopts = {'openmp': True, 'cstd': 'c++0x'} + +buildopts = 'CXXFLAGS="$CXXFLAGS -Dnullptr=0 -lm -fpermissive"' source_urls = ['http://platanus.bio.titech.ac.jp/?ddownload=150'] sources = ['%(name)s_v%(version)s.tar.gz'] -# fix Makefile to support newer gcc version -patches = ['Platanus_new_gcc.patch'] - files_to_copy = [(["platanus"],'bin'), "README", "LICENSE"] sanity_check_paths = { diff --git a/easybuild/easyconfigs/p/Platanus/Platanus_new_gcc.patch b/easybuild/easyconfigs/p/Platanus/Platanus_new_gcc.patch deleted file mode 100644 index 531c797148..0000000000 --- a/easybuild/easyconfigs/p/Platanus/Platanus_new_gcc.patch +++ /dev/null @@ -1,9 +0,0 @@ ---- Makefile.o 2015-06-03 07:39:00.000000000 +0200 -+++ Makefile 2017-02-15 15:33:18.000000000 +0100 -@@ -1,5 +1,5 @@ - CXX = g++ --CXXFLAGS = -std=c++0x -O3 -funroll-loops -Wall -fopenmp -finline-limit-50000 -lm -Dnullptr=0 -+CXXFLAGS = -std=c++0x -O3 -funroll-loops -Wall -fopenmp -finline-limit-50000 -lm -Dnullptr=0 -fpermissive - - - PRG = platanus -- GitLab From 1e74088992605614a2b9dbf4a745c4776e6fac39 Mon Sep 17 00:00:00 2001 From: Yann Sagon Date: Thu, 16 Feb 2017 11:37:08 +0100 Subject: [PATCH 0087/1603] sickle 1.33 foss 2017a --- .../s/sickle/sickle-1.33-foss-2017a.eb | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/s/sickle/sickle-1.33-foss-2017a.eb diff --git a/easybuild/easyconfigs/s/sickle/sickle-1.33-foss-2017a.eb b/easybuild/easyconfigs/s/sickle/sickle-1.33-foss-2017a.eb new file mode 100644 index 0000000000..aad6c785a5 --- /dev/null +++ b/easybuild/easyconfigs/s/sickle/sickle-1.33-foss-2017a.eb @@ -0,0 +1,21 @@ +easyblock = 'MakeCp' + +name = "sickle" +version = "1.33" + +homepage = 'https://github.com/najoshi/sickle' +description = """ Windowed Adaptive Trimming for fastq files using quality """ + +toolchain = {'name': 'foss', 'version': '2017a'} + +source_urls = ['https://github.com/najoshi/sickle/archive/'] +sources = ['v%(version)s.tar.gz'] + +files_to_copy = [(['sickle'], 'bin'), "README.md", "test"] + +sanity_check_paths = { + 'files': ['bin/sickle'], + 'dirs': [] +} + +moduleclass = 'bio' -- GitLab From 949f36606ae1a3b5566b26e45041854c23f17bd3 Mon Sep 17 00:00:00 2001 From: Yann Sagon Date: Thu, 16 Feb 2017 11:45:30 +0100 Subject: [PATCH 0088/1603] removed buildependencies --- .../easyconfigs/s/Smoldyn/Smoldyn-2.48-foss-2016a.eb | 9 --------- 1 file changed, 9 deletions(-) diff --git a/easybuild/easyconfigs/s/Smoldyn/Smoldyn-2.48-foss-2016a.eb b/easybuild/easyconfigs/s/Smoldyn/Smoldyn-2.48-foss-2016a.eb index 71310f26f2..7f6179784c 100644 --- a/easybuild/easyconfigs/s/Smoldyn/Smoldyn-2.48-foss-2016a.eb +++ b/easybuild/easyconfigs/s/Smoldyn/Smoldyn-2.48-foss-2016a.eb @@ -13,15 +13,6 @@ toolchain = {'name': 'foss', 'version': '2016a'} source_urls = ['http://www.smoldyn.org/'] sources = ['smoldyn-%(version)s.tgz'] -builddependencies = [ - ('CMake', '3.4.3'), - ('LibTIFF','4.0.6'), - ('zlib', '1.2.8'), - ('freeglut', '3.0.0'), - ('libXmu', '1.1.2'), - ('libXi', '1.7.6') -] - dependencies = [ ('LibTIFF','4.0.6'), ('zlib', '1.2.8'), -- GitLab From 51343da1acd9adf8c70f11d3f93c03b86c4b62d4 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 16 Feb 2017 13:30:33 +0200 Subject: [PATCH 0089/1603] Adding patch to install libelpatest. --- .../e/ELPA/ELPA-2016.05.004-intel-2017a.eb | 63 +++++++++++++++++++ .../e/ELPA/install_libelpatest.patch | 11 ++++ 2 files changed, 74 insertions(+) create mode 100644 easybuild/easyconfigs/e/ELPA/ELPA-2016.05.004-intel-2017a.eb create mode 100644 easybuild/easyconfigs/e/ELPA/install_libelpatest.patch diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2016.05.004-intel-2017a.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2016.05.004-intel-2017a.eb new file mode 100644 index 0000000000..fe3eecd918 --- /dev/null +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2016.05.004-intel-2017a.eb @@ -0,0 +1,63 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Authors:: Inge Gutheil , Alan O'Cais +# License:: MIT/GPL +# $Id$ +# +## + +easyblock = 'ConfigureMake' + +name = 'ELPA' +version = '2016.05.004' + +homepage = 'http://elpa.rzg.mpg.de' +description = """Eigenvalue SoLvers for Petaflop-Applications .""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'usempi': True} + +source_urls = ['http://elpa.mpcdf.mpg.de/html/Releases/%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] + +patches = [ + 'install_libelpatest.patch', +] + +builddependencies = [ + ('Autotools', '20150215'), +] + +preconfigopts = 'autoreconf && ' + +common_configopts = 'FCFLAGS="-I$EBROOTIMKL/mkl/include/intel64/lp64 $FCFLAGS" ' +common_configopts += 'LIBS="$LIBSCALAPACK" ' + +configopts = [ + common_configopts + '--enable-openmp ', + common_configopts, # Default version last, so we can get the normal config.h/config-f90.h installed afterwards. +] + +buildopts = ' V=1 ' + +postinstallcmds = [ + 'cp config.h config-f90.h %(installdir)s/share/doc/elpa/examples', +] + +sanity_check_paths = { + 'files': [ + 'lib/libelpa.a', 'lib/libelpa.%s' % SHLIB_EXT, + 'lib/libelpa_openmp.a', 'lib/libelpa_openmp.%s' % SHLIB_EXT, + 'lib/libelpatest.a', 'lib/libelpatest.%s' % SHLIB_EXT, + 'lib/libelpatest_openmp.a', 'lib/libelpatest_openmp.%s' % SHLIB_EXT, + 'share/doc/elpa/examples/config.h', + 'share/doc/elpa/examples/config-f90.h', + ], + 'dirs': [ + 'bin', 'include/elpa-%(version)s/elpa', + 'include/elpa-%(version)s/modules', 'lib/pkgconfig', + ], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/e/ELPA/install_libelpatest.patch b/easybuild/easyconfigs/e/ELPA/install_libelpatest.patch new file mode 100644 index 0000000000..2c8f6390ed --- /dev/null +++ b/easybuild/easyconfigs/e/ELPA/install_libelpatest.patch @@ -0,0 +1,11 @@ +--- Makefile.am.orig 2017-02-16 10:32:55.789545672 +0100 ++++ Makefile.am 2017-02-16 10:33:15.213234461 +0100 +@@ -255,7 +255,7 @@ + build_lib = libelpatest@SUFFIX@.la libelpa@SUFFIX@.la + + # library with shared sources for the test files +-noinst_LTLIBRARIES += libelpatest@SUFFIX@.la ++lib_LTLIBRARIES += libelpatest@SUFFIX@.la + libelpatest@SUFFIX@_la_FCFLAGS = $(AM_FCFLAGS) @FC_MODOUT@private_modules @FC_MODINC@private_modules + libelpatest@SUFFIX@_la_SOURCES = \ + test/shared/util.F90 \ -- GitLab From 59be6a908dfd1ba7cd0778e5096573de5ba8472c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Thu, 16 Feb 2017 13:34:40 +0100 Subject: [PATCH 0090/1603] added requested changes used toolchain option cstd instead of buildopts removed toolchain option optarch changed name template --- easybuild/easyconfigs/r/RNAz/RNAz-2.1-foss-2016b.eb | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/r/RNAz/RNAz-2.1-foss-2016b.eb b/easybuild/easyconfigs/r/RNAz/RNAz-2.1-foss-2016b.eb index bdf32dd367..4ff67a0efb 100644 --- a/easybuild/easyconfigs/r/RNAz/RNAz-2.1-foss-2016b.eb +++ b/easybuild/easyconfigs/r/RNAz/RNAz-2.1-foss-2016b.eb @@ -10,12 +10,10 @@ description = """RNAz is a program for predicting structurally conserved and thermodynamically stable RNA secondary structures in multiple sequence alignments.""" toolchain = {'name': 'foss', 'version': '2016b'} -toolchainopts = {'optarch': True, 'pic': True} - -buildopts = 'CFLAGS="-std=gnu89 $CFLAGS"' +toolchainopts = {'cstd': 'gnu89', 'pic': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://www.tbi.univie.ac.at/~wash/%s' % name] +source_urls = ['http://www.tbi.univie.ac.at/~wash/%(name)s'] sanity_check_paths = { 'files': ['bin/RNAz'], -- GitLab From 055afec64649e52a63df8d499f1d82e7ab720789 Mon Sep 17 00:00:00 2001 From: Yann Sagon Date: Thu, 16 Feb 2017 14:29:53 +0100 Subject: [PATCH 0091/1603] requested changes --- .../s/Smoldyn/Smoldyn-2.48-foss-2016a.eb | 21 ++++++++++++------- 1 file changed, 14 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/s/Smoldyn/Smoldyn-2.48-foss-2016a.eb b/easybuild/easyconfigs/s/Smoldyn/Smoldyn-2.48-foss-2016a.eb index 7f6179784c..fc06a65970 100644 --- a/easybuild/easyconfigs/s/Smoldyn/Smoldyn-2.48-foss-2016a.eb +++ b/easybuild/easyconfigs/s/Smoldyn/Smoldyn-2.48-foss-2016a.eb @@ -4,8 +4,11 @@ name = 'Smoldyn' version = '2.48' homepage = 'http://www.smoldyn.org/' -description = """ -Smoldyn is a computer program for cell-scale biochemical simulations. It simulates each molecule of interest individually to capture natural stochasticity and to yield nanometer-scale spatial resolution. It treats other molecules implicitly, enabling it to simulate hundreds of thousands of molecules over several minutes of real time. Simulated molecules diffuse, react, are confined by surfaces, and bind to membranes much as they would in a real biological system. +description = """Smoldyn is a computer program for cell-scale biochemical simulations. It simulates each molecule of +interest individually to capture natural stochasticity and to yield nanometer-scale spatial resolution. It treats +other molecules implicitly, enabling it to simulate hundreds of thousands of molecules over several minutes of real +time. Simulated molecules diffuse, react, are confined by surfaces, and bind to membranes much as they would in a real +biological system. """ toolchain = {'name': 'foss', 'version': '2016a'} @@ -13,12 +16,16 @@ toolchain = {'name': 'foss', 'version': '2016a'} source_urls = ['http://www.smoldyn.org/'] sources = ['smoldyn-%(version)s.tgz'] +builddependencies = [ + ('CMake', '3.4.3') +] + dependencies = [ - ('LibTIFF','4.0.6'), - ('zlib', '1.2.8'), - ('freeglut', '3.0.0'), - ('libXmu', '1.1.2'), - ('libXi', '1.7.6') + ('LibTIFF','4.0.6'), + ('zlib', '1.2.8'), + ('freeglut', '3.0.0'), + ('libXmu', '1.1.2'), + ('libXi', '1.7.6') ] -- GitLab From e81eab07bf42f6f4cdab2184e9625c49ff01d264 Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Thu, 16 Feb 2017 14:32:30 +0100 Subject: [PATCH 0092/1603] Removed backticks in gettest description --- .../easyconfigs/g/gettext/gettext-0.19.8.1-GCCcore-6.3.0.eb | 2 +- easybuild/easyconfigs/g/gettext/gettext-0.19.8.1.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.8.1-GCCcore-6.3.0.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.8.1-GCCcore-6.3.0.eb index 6e2d7b23a6..c366761771 100644 --- a/easybuild/easyconfigs/g/gettext/gettext-0.19.8.1-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.8.1-GCCcore-6.3.0.eb @@ -4,7 +4,7 @@ name = 'gettext' version = '0.19.8.1' homepage = 'http://www.gnu.org/software/gettext/' -description = """GNU `gettext' is an important step for the GNU Translation Project, as it is an asset on which we may +description = """GNU 'gettext' is an important step for the GNU Translation Project, as it is an asset on which we may build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools and documentation""" diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.8.1.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.8.1.eb index f1e80cfb3b..ee5718ec11 100644 --- a/easybuild/easyconfigs/g/gettext/gettext-0.19.8.1.eb +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.8.1.eb @@ -4,7 +4,7 @@ name = 'gettext' version = '0.19.8.1' homepage = 'http://www.gnu.org/software/gettext/' -description = """GNU `gettext' is an important step for the GNU Translation Project, as it is an asset on which we may +description = """GNU 'gettext' is an important step for the GNU Translation Project, as it is an asset on which we may build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools and documentation""" -- GitLab From c247db112687dc657a726cce723e2f43ae70377a Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 16 Feb 2017 17:11:38 +0200 Subject: [PATCH 0093/1603] Rename the patchfile to match the version of ELPA. --- .../e/ELPA/ELPA-2016.05.004-intel-2017a.eb | 2 +- .../ELPA-2016.05.004_install-libelpatest.patch | 16 ++++++++++++++++ 2 files changed, 17 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/e/ELPA/ELPA-2016.05.004_install-libelpatest.patch diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2016.05.004-intel-2017a.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2016.05.004-intel-2017a.eb index fe3eecd918..2c6c725788 100644 --- a/easybuild/easyconfigs/e/ELPA/ELPA-2016.05.004-intel-2017a.eb +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2016.05.004-intel-2017a.eb @@ -22,7 +22,7 @@ source_urls = ['http://elpa.mpcdf.mpg.de/html/Releases/%(version)s/'] sources = [SOURCELOWER_TAR_GZ] patches = [ - 'install_libelpatest.patch', + '%(name)s-%(version)s_install-libelpatest.patch', ] builddependencies = [ diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2016.05.004_install-libelpatest.patch b/easybuild/easyconfigs/e/ELPA/ELPA-2016.05.004_install-libelpatest.patch new file mode 100644 index 0000000000..61ac356266 --- /dev/null +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2016.05.004_install-libelpatest.patch @@ -0,0 +1,16 @@ +Change the Makefile.am so that libelpatest gets installed too. +This makes it easier to build the examples. + +Åke Sandgren, HPC2N +diff -ru elpa-2016.05.004.orig/Makefile.am elpa-2016.05.004/Makefile.am +--- elpa-2016.05.004.orig/Makefile.am 2016-10-25 07:13:46.000000000 +0200 ++++ elpa-2016.05.004/Makefile.am 2017-02-16 16:04:40.976781413 +0100 +@@ -255,7 +255,7 @@ + build_lib = libelpatest@SUFFIX@.la libelpa@SUFFIX@.la + + # library with shared sources for the test files +-noinst_LTLIBRARIES += libelpatest@SUFFIX@.la ++lib_LTLIBRARIES += libelpatest@SUFFIX@.la + libelpatest@SUFFIX@_la_FCFLAGS = $(AM_FCFLAGS) @FC_MODOUT@private_modules @FC_MODINC@private_modules + libelpatest@SUFFIX@_la_SOURCES = \ + test/shared/util.F90 \ -- GitLab From 0bd80f7045b1aad79ff905593f5f452c4ea7e417 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 16 Feb 2017 16:13:21 +0100 Subject: [PATCH 0094/1603] Delete the old non-version specific patch file. --- .../easyconfigs/e/ELPA/install_libelpatest.patch | 11 ----------- 1 file changed, 11 deletions(-) delete mode 100644 easybuild/easyconfigs/e/ELPA/install_libelpatest.patch diff --git a/easybuild/easyconfigs/e/ELPA/install_libelpatest.patch b/easybuild/easyconfigs/e/ELPA/install_libelpatest.patch deleted file mode 100644 index 2c8f6390ed..0000000000 --- a/easybuild/easyconfigs/e/ELPA/install_libelpatest.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- Makefile.am.orig 2017-02-16 10:32:55.789545672 +0100 -+++ Makefile.am 2017-02-16 10:33:15.213234461 +0100 -@@ -255,7 +255,7 @@ - build_lib = libelpatest@SUFFIX@.la libelpa@SUFFIX@.la - - # library with shared sources for the test files --noinst_LTLIBRARIES += libelpatest@SUFFIX@.la -+lib_LTLIBRARIES += libelpatest@SUFFIX@.la - libelpatest@SUFFIX@_la_FCFLAGS = $(AM_FCFLAGS) @FC_MODOUT@private_modules @FC_MODINC@private_modules - libelpatest@SUFFIX@_la_SOURCES = \ - test/shared/util.F90 \ -- GitLab From 485e058298063893104af9fe5c873cee6628fb14 Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Thu, 16 Feb 2017 20:06:01 +0100 Subject: [PATCH 0095/1603] Remove duplicate sources specification --- easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.2-GCC-6.3.0-2.27.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.2-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.2-GCC-6.3.0-2.27.eb index 2e2eda32d4..c13ef6b657 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.2-GCC-6.3.0-2.27.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.2-GCC-6.3.0-2.27.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'GCC', 'version': '6.3.0-2.27'} source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] -sources = ['openmpi-%(version)s.tar.gz'] + checksums = ['886698becc5bea8c151c0af2074b8392'] dependencies = [('hwloc', '1.11.5')] -- GitLab From e3d01adc1cf95181b1c90f62d8b6f1395ee7686f Mon Sep 17 00:00:00 2001 From: RvDijk Date: Fri, 17 Feb 2017 11:00:39 +0100 Subject: [PATCH 0096/1603] Make Travis happy --- .../easyconfigs/v/Vim/Vim-8.0-foss-2016a-Python-2.7.11.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/v/Vim/Vim-8.0-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/v/Vim/Vim-8.0-foss-2016a-Python-2.7.11.eb index 1caa37ba7a..69dae180f9 100644 --- a/easybuild/easyconfigs/v/Vim/Vim-8.0-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/v/Vim/Vim-8.0-foss-2016a-Python-2.7.11.eb @@ -7,6 +7,7 @@ easyblock = 'ConfigureMake' name = 'Vim' version = '8.0' +versionsuffix = '-Python-%(pyver)s' homepage = 'http://www.vim.org' description = """ Vim is an advanced text editor that seeks to provide the power @@ -22,7 +23,7 @@ sources = [SOURCELOWER_TAR_BZ2] dependencies = [ ('Python', '2.7.11'), ('Perl', '5.22.1', '-bare') - ] +] #osdependencies = ['python','perl-devel'] configopts = '--with-features=huge --enable-pythoninterp=yes --enable-perlinterp=yes' -- GitLab From bab557a4492ce1cc551b85cc34f879ee4e4ad37f Mon Sep 17 00:00:00 2001 From: RvDijk Date: Sun, 19 Feb 2017 19:13:22 +0100 Subject: [PATCH 0097/1603] no comments, space behind ',' --- .../easyconfigs/v/Vim/Vim-8.0-foss-2016a-Python-2.7.11.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/v/Vim/Vim-8.0-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/v/Vim/Vim-8.0-foss-2016a-Python-2.7.11.eb index 69dae180f9..674a6d44d5 100644 --- a/easybuild/easyconfigs/v/Vim/Vim-8.0-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/v/Vim/Vim-8.0-foss-2016a-Python-2.7.11.eb @@ -24,12 +24,11 @@ dependencies = [ ('Python', '2.7.11'), ('Perl', '5.22.1', '-bare') ] -#osdependencies = ['python','perl-devel'] configopts = '--with-features=huge --enable-pythoninterp=yes --enable-perlinterp=yes' sanity_check_paths = { - 'files': ['bin/vim','bin/vimdiff'], + 'files': ['bin/vim', 'bin/vimdiff'], 'dirs': [], } -- GitLab From 970453d4200d390d1cc7c4eed4d2f3edb7d09c34 Mon Sep 17 00:00:00 2001 From: Sergey Paramonov Date: Sun, 19 Feb 2017 23:37:56 -0500 Subject: [PATCH 0098/1603] Create Lmod-7.3.eb Lmod 7.3 --- easybuild/easyconfigs/l/Lmod/Lmod-7.3.eb | 28 ++++++++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/l/Lmod/Lmod-7.3.eb diff --git a/easybuild/easyconfigs/l/Lmod/Lmod-7.3.eb b/easybuild/easyconfigs/l/Lmod/Lmod-7.3.eb new file mode 100644 index 0000000000..d56882eb94 --- /dev/null +++ b/easybuild/easyconfigs/l/Lmod/Lmod-7.3.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = "Lmod" +version = "7.3" + +homepage = "http://sourceforge.net/projects/lmod/" +description = """Lmod is a Lua based module system. Modules allow for dynamic modification + of a user's environment under Unix systems. See www.tacc.utexas.edu/tacc-projects/lmod + for a complete description. Lmod is a new implementation that easily handles the MODULEPATH + Hierarchical problem. It is drop-in replacement for TCL/C modules and reads TCL modulefiles directly.""" + +toolchain = {'name': 'dummy', 'version': ''} + +sources = ['%(version)s.tar.gz'] +source_urls = [ + 'https://github.com/TACC/Lmod/archive', + 'http://sourceforge.net/projects/lmod/files/', + 'http://sourceforge.net/projects/lmod/files/Testing' +] + +dependencies = [("Lua", "5.1.4-8")] + +sanity_check_paths = { + 'files': ["lmod/%(version)s/libexec/lmod", "lmod/%(version)s/init/profile"], + 'dirs': [] +} + +moduleclass = "tools" -- GitLab From 1b5f840316fa864453146d2b77c726f7bf58c097 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 20 Feb 2017 12:02:29 +0100 Subject: [PATCH 0099/1603] adding easyconfigs: StringTie-1.3.3-intel-2017a.eb --- .../StringTie/StringTie-1.3.3-intel-2017a.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/s/StringTie/StringTie-1.3.3-intel-2017a.eb diff --git a/easybuild/easyconfigs/s/StringTie/StringTie-1.3.3-intel-2017a.eb b/easybuild/easyconfigs/s/StringTie/StringTie-1.3.3-intel-2017a.eb new file mode 100644 index 0000000000..aa49a6e1bd --- /dev/null +++ b/easybuild/easyconfigs/s/StringTie/StringTie-1.3.3-intel-2017a.eb @@ -0,0 +1,26 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'MakeCp' + +name = 'StringTie' +version = '1.3.3' + +homepage = 'http://ccb.jhu.edu/software/stringtie/' +description = """StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['http://ccb.jhu.edu/software/stringtie/dl/'] +sources = [SOURCELOWER_TAR_GZ] + +files_to_copy = [(['stringtie'], 'bin'), 'README', 'LICENSE'] + +sanity_check_paths = { + 'files': ['bin/stringtie'], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From 58a3f10c6d41e8f7a233c700f03ad81ed5c901fa Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 20 Feb 2017 13:03:50 +0100 Subject: [PATCH 0100/1603] adding easyconfigs: OpenSSL-1.1.0e-intel-2016a.eb --- .../o/OpenSSL/OpenSSL-1.1.0e-intel-2016a.eb | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.1.0e-intel-2016a.eb diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.1.0e-intel-2016a.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.1.0e-intel-2016a.eb new file mode 100644 index 0000000000..297ae5a79e --- /dev/null +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.1.0e-intel-2016a.eb @@ -0,0 +1,19 @@ +name = 'OpenSSL' +version = '1.1.0e' + +homepage = 'http://www.openssl.org/' +description = """The OpenSSL Project is a collaborative effort to develop a robust, commercial-grade, full-featured, + and Open Source toolchain implementing the Secure Sockets Layer (SSL v2/v3) and Transport Layer Security (TLS v1) + protocols as well as a full-strength general purpose cryptography library. """ + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.openssl.org/source/'] + +dependencies = [('zlib', '1.2.8')] + +runtest = 'test' + +moduleclass = 'system' -- GitLab From fecb6bc94694e55a96bba372d9c7dd0c6635f76e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 20 Feb 2017 13:08:42 +0100 Subject: [PATCH 0101/1603] adding easyconfigs: Pysam-0.10.0-intel-2016b-Python-2.7.12.eb --- .../c/cURL/cURL-7.52.1-intel-2016b.eb | 31 ++++++++++++++++ .../Pysam-0.10.0-intel-2016b-Python-2.7.12.eb | 36 +++++++++++++++++++ 2 files changed, 67 insertions(+) create mode 100644 easybuild/easyconfigs/c/cURL/cURL-7.52.1-intel-2016b.eb create mode 100644 easybuild/easyconfigs/p/Pysam/Pysam-0.10.0-intel-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.52.1-intel-2016b.eb b/easybuild/easyconfigs/c/cURL/cURL-7.52.1-intel-2016b.eb new file mode 100644 index 0000000000..669ee4f2be --- /dev/null +++ b/easybuild/easyconfigs/c/cURL/cURL-7.52.1-intel-2016b.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'cURL' +version = '7.52.1' + +homepage = 'http://curl.haxx.se' +description = """libcurl is a free and easy-to-use client-side URL transfer library, + supporting DICT, FILE, FTP, FTPS, Gopher, HTTP, HTTPS, IMAP, IMAPS, LDAP, LDAPS, + POP3, POP3S, RTMP, RTSP, SCP, SFTP, SMTP, SMTPS, Telnet and TFTP. libcurl supports + SSL certificates, HTTP POST, HTTP PUT, FTP uploading, HTTP form based upload, + proxies, cookies, user+password authentication (Basic, Digest, NTLM, Negotiate, + Kerberos), file transfer resume, http proxy tunneling and more.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://curl.haxx.se/download/'] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# dependencies = [('OpenSSL', '1.1.0e')] +# configopts = "--with-ssl=$EBROOTOPENSSL" + +modextravars = {'CURL_INCLUDES': '%(installdir)s/include'} + +sanity_check_paths = { + 'files': ['bin/curl', 'lib/libcurl.a', 'lib/libcurl.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/Pysam/Pysam-0.10.0-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/Pysam/Pysam-0.10.0-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..624f14ed18 --- /dev/null +++ b/easybuild/easyconfigs/p/Pysam/Pysam-0.10.0-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,36 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# 0.9.1.4: +# Modified by: Adam Huffman +# The Francis Crick Institute + +easyblock = 'PythonPackage' + +name = 'Pysam' +version = '0.10.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/pysam-developers/pysam' +description = """Pysam is a python module for reading and manipulating Samfiles. + It's a lightweight wrapper of the samtools C-API. Pysam also includes an interface for tabix.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['https://github.com/pysam-developers/pysam/archive/'] +sources = ['v%(version)s.tar.gz'] + +dependencies = [ + ('Python', '2.7.12'), + ('ncurses', '6.0'), + ('zlib', '1.2.8'), + ('cURL', '7.52.1'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'bio' -- GitLab From 1a94fbc1ae2bcdf0846d3770f45a6040a26bac32 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 20 Feb 2017 13:13:13 +0100 Subject: [PATCH 0102/1603] fix toolchain spec to intel/2016b for OpenSSL 1.1.0e easyconfig --- ...nSSL-1.1.0e-intel-2016a.eb => OpenSSL-1.1.0e-intel-2016b.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/o/OpenSSL/{OpenSSL-1.1.0e-intel-2016a.eb => OpenSSL-1.1.0e-intel-2016b.eb} (92%) diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.1.0e-intel-2016a.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.1.0e-intel-2016b.eb similarity index 92% rename from easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.1.0e-intel-2016a.eb rename to easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.1.0e-intel-2016b.eb index 297ae5a79e..81a9ed4ca3 100644 --- a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.1.0e-intel-2016a.eb +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.1.0e-intel-2016b.eb @@ -6,7 +6,7 @@ description = """The OpenSSL Project is a collaborative effort to develop a robu and Open Source toolchain implementing the Secure Sockets Layer (SSL v2/v3) and Transport Layer Security (TLS v1) protocols as well as a full-strength general purpose cryptography library. """ -toolchain = {'name': 'intel', 'version': '2016a'} +toolchain = {'name': 'intel', 'version': '2016b'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] -- GitLab From 0058215568b776b205473bae2b5e26fc2a10790a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 20 Feb 2017 14:52:44 +0100 Subject: [PATCH 0103/1603] remove numpy 1.11.1 easyconfig using Python 2.7.12 since Python installation already includes numpy 1.11.1 --- .../numpy-1.11.1-foss-2016b-Python-2.7.12.eb | 25 ------------------- ...PyTables-3.2.2-foss-2016b-Python-2.7.12.eb | 1 - 2 files changed, 26 deletions(-) delete mode 100755 easybuild/easyconfigs/n/numpy/numpy-1.11.1-foss-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/n/numpy/numpy-1.11.1-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/n/numpy/numpy-1.11.1-foss-2016b-Python-2.7.12.eb deleted file mode 100755 index 23d10a78e7..0000000000 --- a/easybuild/easyconfigs/n/numpy/numpy-1.11.1-foss-2016b-Python-2.7.12.eb +++ /dev/null @@ -1,25 +0,0 @@ -name = 'numpy' -version = '1.11.1' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'http://www.numpy.org' -description = """NumPy is the fundamental package for scientific computing with Python. It contains among other things: - a powerful N-dimensional array object, sophisticated (broadcasting) functions, tools for integrating C/C++ and Fortran - code, useful linear algebra, Fourier transform, and random number capabilities. Besides its obvious scientific uses, - NumPy can also be used as an efficient multi-dimensional container of generic data. Arbitrary data-types can be - defined. This allows NumPy to seamlessly and speedily integrate with a wide variety of databases.""" - -toolchain = {'name': 'foss', 'version': '2016b'} - -source_urls = [SOURCEFORGE_SOURCE] -sources = [SOURCE_TAR_GZ] - -patches = [ - 'numpy-1.8.0-mkl.patch', -] - -dependencies = [ - ('Python', '2.7.12'), -] - -moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/PyTables/PyTables-3.2.2-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/PyTables/PyTables-3.2.2-foss-2016b-Python-2.7.12.eb index 836640b941..fbfabfe34d 100644 --- a/easybuild/easyconfigs/p/PyTables/PyTables-3.2.2-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/p/PyTables/PyTables-3.2.2-foss-2016b-Python-2.7.12.eb @@ -23,7 +23,6 @@ patches = ['pyTables-%(version)s-fix-libs.patch'] dependencies = [ ('Python', '2.7.12'), - ('numpy', '1.11.1', versionsuffix), ('numexpr', '2.6.1', versionsuffix), ('HDF5', '1.8.17'), ] -- GitLab From 9c423e6dcf5e01b5d218859ad432f6fa9d037a33 Mon Sep 17 00:00:00 2001 From: Fokke Dijkstra Date: Mon, 20 Feb 2017 15:13:35 +0100 Subject: [PATCH 0104/1603] Removed setting of optarch to disabled, which was used during debugging. --- .../c/Caffe/Caffe-rc3-foss-2016a-CUDA-7.5.18-Python-2.7.11.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/Caffe/Caffe-rc3-foss-2016a-CUDA-7.5.18-Python-2.7.11.eb b/easybuild/easyconfigs/c/Caffe/Caffe-rc3-foss-2016a-CUDA-7.5.18-Python-2.7.11.eb index 184119ac43..ef1b4dd449 100644 --- a/easybuild/easyconfigs/c/Caffe/Caffe-rc3-foss-2016a-CUDA-7.5.18-Python-2.7.11.eb +++ b/easybuild/easyconfigs/c/Caffe/Caffe-rc3-foss-2016a-CUDA-7.5.18-Python-2.7.11.eb @@ -14,7 +14,7 @@ and Learning Center (BVLC) and community contributors. """ toolchain = {'name': 'foss', 'version': '2016a'} -toolchainopts = {'optarch': False, 'pic': True} +toolchainopts = {'optarch': True, 'pic': True} sources = ['%(version)s.tar.gz'] source_urls = ['https://github.com/BVLC/caffe/archive/'] -- GitLab From 0c61800c9ea6bef57ee64a528744990e2e1163b9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 20 Feb 2017 16:14:32 +0100 Subject: [PATCH 0105/1603] fix definition of buildopts/installopts in Cantera easyconfig --- .../c/Cantera/Cantera-2.2.1-intel-2016b-Python-2.7.12.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/Cantera/Cantera-2.2.1-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/c/Cantera/Cantera-2.2.1-intel-2016b-Python-2.7.12.eb index df2115bf2e..6ba32558a2 100644 --- a/easybuild/easyconfigs/c/Cantera/Cantera-2.2.1-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/c/Cantera/Cantera-2.2.1-intel-2016b-Python-2.7.12.eb @@ -26,7 +26,7 @@ common_opts = 'env_vars=all CC="$CC" CXX="$CXX" blas_lapack_libs=mkl_rt blas_lap common_opts += ' sundials_include=$EBROOTSUNDIALS/include sundials_libdir=$EBROOTSUNDIALS/lib' buildopts = 'build ' + common_opts runtest = 'test ' + common_opts -buildopts = 'install ' + common_opts +installopts = 'install ' + common_opts prefix_arg = 'prefix=' modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} -- GitLab From b6b0b3109f6ad009ea0a387602461e56a0f3e348 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 20 Feb 2017 16:16:24 +0100 Subject: [PATCH 0106/1603] fix buildopts/installopts in Cantera easyconfig + add patches to fix/skip broken tests --- ...Cantera-2.3.0-intel-2016b-Python-2.7.12.eb | 8 +- .../c/Cantera/Cantera-2.3.0_fix-bug-416.patch | 138 ++++++++++++++++++ .../Cantera-2.3.0_skip-broken-tests.patch | 25 ++++ 3 files changed, 170 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/c/Cantera/Cantera-2.3.0_fix-bug-416.patch create mode 100644 easybuild/easyconfigs/c/Cantera/Cantera-2.3.0_skip-broken-tests.patch diff --git a/easybuild/easyconfigs/c/Cantera/Cantera-2.3.0-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/c/Cantera/Cantera-2.3.0-intel-2016b-Python-2.7.12.eb index 1347cddcd9..594203f790 100644 --- a/easybuild/easyconfigs/c/Cantera/Cantera-2.3.0-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/c/Cantera/Cantera-2.3.0-intel-2016b-Python-2.7.12.eb @@ -8,10 +8,16 @@ homepage = 'https://github.com/Cantera/cantera' description = """Chemical kinetics, thermodynamics, and transport tool suite""" toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'strict': True} source_urls = ['https://github.com/Cantera/cantera/archive/'] sources = ['v%(version)s.tar.gz'] +patches = [ + 'Cantera-%(version)s_fix-bug-416.patch', + 'Cantera-%(version)s_skip-broken-tests.patch', +] + dependencies = [ ('Python', '2.7.12'), ('Boost', '1.63.0', versionsuffix), @@ -29,7 +35,7 @@ common_opts = 'env_vars=all CC="$CC" CXX="$CXX" blas_lapack_libs=mkl_rt blas_lap common_opts += ' sundials_include=$EBROOTSUNDIALS/include sundials_libdir=$EBROOTSUNDIALS/lib' buildopts = 'build ' + common_opts runtest = 'test ' + common_opts -buildopts = 'install ' + common_opts +installopts = 'install ' + common_opts prefix_arg = 'prefix=' modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} diff --git a/easybuild/easyconfigs/c/Cantera/Cantera-2.3.0_fix-bug-416.patch b/easybuild/easyconfigs/c/Cantera/Cantera-2.3.0_fix-bug-416.patch new file mode 100644 index 0000000000..74efe309f7 --- /dev/null +++ b/easybuild/easyconfigs/c/Cantera/Cantera-2.3.0_fix-bug-416.patch @@ -0,0 +1,138 @@ +backport of fix for broken tests, see https://github.com/Cantera/cantera/issues/416 and https://github.com/Cantera/cantera/pull/430 + +From 0a1257daed71fdd621ac25bcdeea911d84036bfd Mon Sep 17 00:00:00 2001 +From: Ray Speth +Date: Mon, 13 Feb 2017 17:35:35 -0500 +Subject: [PATCH] Stream input to ctml_writer to avoid command line length + limits + +Resolves #416. +--- + src/base/ct2ctml.cpp | 84 ++++++++++------------------------------------------ + 1 file changed, 15 insertions(+), 69 deletions(-) + +diff --git a/src/base/ct2ctml.cpp b/src/base/ct2ctml.cpp +index f04e58f..687fcba 100644 +--- a/src/base/ct2ctml.cpp ++++ b/src/base/ct2ctml.cpp +@@ -18,8 +18,6 @@ + + #ifdef _WIN32 + #include +-#else +-#include + #endif + + using namespace std; +@@ -82,14 +80,6 @@ void ct2ctml(const char* file, const int debug) + static std::string call_ctml_writer(const std::string& text, bool isfile) + { + std::string file, arg; +- bool temp_file_created = false; +- std::string temp_cti_file_name = std::tmpnam(nullptr); +- +- if (temp_cti_file_name.find('\\') == 0) { +- // Some versions of MinGW give paths in the root directory. Using the +- // current directory is more likely to succeed. +- temp_cti_file_name = "." + temp_cti_file_name; +- } + + if (isfile) { + file = text; +@@ -99,44 +89,6 @@ static std::string call_ctml_writer(const std::string& text, bool isfile) + arg = "text=r'''" + text + "'''"; + } + +- // If the user wants to convert a mechanism using a text passed via the +- // source="""...""" +- // argument in python, then we have to make sure that it is short enough +- // to fit in the command line when routed to python as: +- // python -c ... +- // statement downstream in the code +- +- // So, check the max size of a string that can be passed on the command line +- // This is OS Specific. *nix systems have the sysconf() function that tells +- // us the largest argument we can pass. Since such a function does not exist +- // for Windows, we set a safe limit of 32 kB +- +-#ifdef _WIN32 +- long int max_argv_size = 32768; +-#else +- long int max_argv_size = sysconf(_SC_ARG_MAX); +-#endif +- +- if (text.size() > static_cast(max_argv_size) - 500) { +- // If the file is too big to be passed as a command line argument later +- // in the file, then create a temporary file and execute this function +- // as though an input file was specified as the source. +- // We assume the text passed + 500 chars = total size of argv +- +- ofstream temp_cti_file(temp_cti_file_name); +- +- if (temp_cti_file) { +- temp_cti_file << text; +- file = temp_cti_file_name; +- arg = "r'" + file + "'"; +- temp_file_created = true; +- } else { +- // If we are here, then a temp file could not be created +- throw CanteraError("call_ctml_writer", "Very long source argument. " +- "Error creating temporary file '{}'", temp_cti_file_name); +- } +- } +- + #ifdef HAS_NO_PYTHON + //! Section to bomb out if python is not present in the computation + //! environment. +@@ -151,21 +103,23 @@ static std::string call_ctml_writer(const std::string& text, bool isfile) + exec_stream_t python; + python.set_wait_timeout(exec_stream_t::s_all, 1800000); // 30 minutes + stringstream output_stream, error_stream; +- std::vector args; +- args.push_back("-c"); ++ python.start(pypath(), ""); ++ ostream& pyin = python.in(); + +- args.push_back( +- "from __future__ import print_function\n" +- "import sys\n" +- "try:\n" +- " from cantera import ctml_writer\n" +- "except ImportError:\n" +- " print('sys.path: ' + repr(sys.path) + '\\n', file=sys.stderr)\n" +- " raise\n" +- "ctml_writer.convert(" + arg + ", outName='STDOUT')\n" +- "sys.exit(0)\n"); ++ pyin << "from __future__ import print_function\n" ++ "if True:\n" ++ " import sys\n" ++ " try:\n" ++ " from cantera import ctml_writer\n" ++ " except ImportError:\n" ++ " print('sys.path: ' + repr(sys.path) + '\\n', file=sys.stderr)\n" ++ " raise\n" ++ " ctml_writer.convert("; ++ pyin << arg << ", outName='STDOUT')\n"; ++ pyin << " sys.exit(0)\n\n"; ++ pyin << "sys.exit(7)\n"; + +- python.start(pypath(), args.begin(), args.end()); ++ python.close_in(); + std::string line; + + while (python.out().good()) { +@@ -221,14 +175,6 @@ static std::string call_ctml_writer(const std::string& text, bool isfile) + writelog(message.str()); + } + +- if (temp_file_created) { +- // A temp file was created and has to be removed +- bool status = std::remove(temp_cti_file_name.c_str()); +- if (status) { +- writelog("WARNING: Error removing tmp file {}\n", temp_cti_file_name); +- } +- } +- + return python_output; + } + diff --git a/easybuild/easyconfigs/c/Cantera/Cantera-2.3.0_skip-broken-tests.patch b/easybuild/easyconfigs/c/Cantera/Cantera-2.3.0_skip-broken-tests.patch new file mode 100644 index 0000000000..d3b26cf18f --- /dev/null +++ b/easybuild/easyconfigs/c/Cantera/Cantera-2.3.0_skip-broken-tests.patch @@ -0,0 +1,25 @@ +skip broken test, fails due to strict floating-point value comparison +see https://github.com/Cantera/cantera/issues/433 + +author: Kenneth Hoste (HPC-UGent) + +--- test/kinetics/kineticsFromScratch.cpp.orig 2017-02-15 16:32:24.518921570 +0100 ++++ test/kinetics/kineticsFromScratch.cpp 2017-02-15 16:32:38.509147212 +0100 +@@ -453,7 +453,7 @@ + } + }; + +-TEST_F(KineticsAddSpecies, add_species_sequential) ++/*TEST_F(KineticsAddSpecies, add_species_sequential) + { + ASSERT_EQ((size_t) 0, kin.nReactions()); + +@@ -480,7 +480,7 @@ + p.addSpecies(species["HO2"]); + kin.addReaction(reactions[4]); + check_rates(5, "O:0.01, H2:0.1, H:0.02, OH:0.03, O2:0.4, AR:0.3, H2O2:0.03, HO2:0.01"); +-} ++}*/ + + TEST_F(KineticsAddSpecies, add_species_err_first) + { -- GitLab From a7cb22ec88506b3657bbd7301146e86f3da462ef Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Mon, 20 Feb 2017 16:24:46 +0100 Subject: [PATCH 0107/1603] comment removed --- .../easyconfigs/g/Graphviz/Graphviz-2.38.0-foss-2016b.eb | 5 ----- 1 file changed, 5 deletions(-) diff --git a/easybuild/easyconfigs/g/Graphviz/Graphviz-2.38.0-foss-2016b.eb b/easybuild/easyconfigs/g/Graphviz/Graphviz-2.38.0-foss-2016b.eb index 0454227509..ef9c393d1a 100644 --- a/easybuild/easyconfigs/g/Graphviz/Graphviz-2.38.0-foss-2016b.eb +++ b/easybuild/easyconfigs/g/Graphviz/Graphviz-2.38.0-foss-2016b.eb @@ -35,11 +35,6 @@ builddependencies = [ ('SWIG', '3.0.10', '-Python-2.7.12'), ] -#patches = [ -# 'Graphviz-2.38.0_icc_vmalloc.patch', -# 'Graphviz-2.38.0_icc_sfio.patch', -#] - preconfigopts = "sed -i 's/install-data-hook$//g' tclpkg/Makefile.in && " configopts = '--enable-guile=no --enable-lua=no --enable-ocaml=no ' configopts += '--enable-r=no --enable-ruby=no ' -- GitLab From 488878acc274064fc674e9c66a166982e19ace76 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 20 Feb 2017 16:38:31 +0100 Subject: [PATCH 0108/1603] adding easyconfigs: CMake-3.7.2-intel-2016b.eb --- .../c/CMake/CMake-3.7.2-intel-2016b.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.7.2-intel-2016b.eb diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.7.2-intel-2016b.eb b/easybuild/easyconfigs/c/CMake/CMake-3.7.2-intel-2016b.eb new file mode 100644 index 0000000000..2c33988a54 --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.7.2-intel-2016b.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.7.2' + +homepage = 'http://www.cmake.org' +description = """CMake, the cross-platform, open-source build system. + CMake is a family of tools designed to build, test and package software.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = '-- -DCMAKE_USE_OPENSSL=1' + +dependencies = [ + ('ncurses', '6.0'), + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + #('OpenSSL', '1.0.2j'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From 9c059fcd9caf2012c038c6ff4a5ed575e02762a0 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Mon, 20 Feb 2017 16:43:53 +0100 Subject: [PATCH 0109/1603] style changes and sanity check added --- easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016a.eb | 4 +++- easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016a.eb | 4 +++- easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016b.eb | 4 +++- 3 files changed, 9 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016a.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016a.eb index c3490d5f5f..5b1245248a 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016a.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016a.eb @@ -43,7 +43,8 @@ dependencies = [ ] #The destination directory is "linux-" see 3rdparty/ippicv/downloader.cmake -preconfigopts = 'mkdir -p {0} && cp -a ../*.tgz {0}. &&'.format("3rdparty/ippicv/downloads/linux-808b791a6eac9ed78d32a7666804320e/") +ippicv_dir = '3rdparty/ippicv/downloads/linux-808b791a6eac9ed78d32a7666804320e/' +preconfigopts = "mkdir -p %s && cp -a ../*.tgz %s && " % (ippicv_dir, ippicv_dir) configopts = '-DCMAKE_BUILD_TYPE=RELEASE ' configopts += '-DBUILD_PYTHON_SUPPORT=ON ' @@ -68,6 +69,7 @@ postinstallcmds = ["cp 3rdparty/ippicv/unpack/ippicv_lnx/lib/intel64/libippicv.* sanity_check_paths = { 'files': ['lib/libopencv_core.%s' % SHLIB_EXT ] + ['lib/python%%(pyshortver)s/site-packages/cv2.%s' % SHLIB_EXT ] + + ['lib/libippicv.a'] + ['bin/opencv_%s' % x for x in ['annotation', 'createsamples', 'traincascade']], 'dirs': ['include'] } diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016a.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016a.eb index f247b850d9..bd5181fa1c 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016a.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016a.eb @@ -44,7 +44,8 @@ dependencies = [ preconfigopts = 'export IPPROOT=$EBROOTICC/ipp && ' #The destination directory is "linux-" see 3rdparty/ippicv/downloader.cmake -preconfigopts += 'mkdir -p {0} && cp -a ../*.tgz {0}. &&'.format("3rdparty/ippicv/downloads/linux-808b791a6eac9ed78d32a7666804320e/") +ippicv_dir = '3rdparty/ippicv/downloads/linux-808b791a6eac9ed78d32a7666804320e/' +preconfigopts = "mkdir -p %s && cp -a ../*.tgz %s && " % (ippicv_dir, ippicv_dir) configopts = '-DCMAKE_BUILD_TYPE=RELEASE ' configopts += '-DBUILD_PYTHON_SUPPORT=ON ' @@ -69,6 +70,7 @@ postinstallcmds = ["cp 3rdparty/ippicv/unpack/ippicv_lnx/lib/intel64/libippicv.* sanity_check_paths = { 'files': ['lib/libopencv_core.%s' % SHLIB_EXT ] + ['lib/python%%(pyshortver)s/site-packages/cv2.%s' % SHLIB_EXT ] + + ['lib/libippicv.a'] + ['bin/opencv_%s' % x for x in ['annotation', 'createsamples', 'traincascade']], 'dirs': ['include'] } diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016b.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016b.eb index b38d822003..e7f6df5043 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016b.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016b.eb @@ -45,7 +45,8 @@ dependencies = [ preconfigopts = 'export IPPROOT=$EBROOTICC/ipp && ' #The destination directory is "linux-" see 3rdparty/ippicv/downloader.cmake -preconfigopts += 'mkdir -p {0} && cp -a ../*.tgz {0}. &&'.format("3rdparty/ippicv/downloads/linux-808b791a6eac9ed78d32a7666804320e/") +ippicv_dir = '3rdparty/ippicv/downloads/linux-808b791a6eac9ed78d32a7666804320e/' +preconfigopts = "mkdir -p %s && cp -a ../*.tgz %s && " % (ippicv_dir, ippicv_dir) configopts = '-DCMAKE_BUILD_TYPE=RELEASE ' configopts += '-DBUILD_PYTHON_SUPPORT=ON ' @@ -70,6 +71,7 @@ postinstallcmds = ["cp 3rdparty/ippicv/unpack/ippicv_lnx/lib/intel64/libippicv.* sanity_check_paths = { 'files': ['lib/libopencv_core.%s' % SHLIB_EXT ] + ['lib/python%%(pyshortver)s/site-packages/cv2.%s' % SHLIB_EXT ] + + ['lib/libippicv.a'] + ['bin/opencv_%s' % x for x in ['annotation', 'createsamples', 'traincascade']], 'dirs': ['include'] } -- GitLab From 3f4f319516313cd0929d18752d148e428851a0c8 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Mon, 20 Feb 2017 16:47:12 +0100 Subject: [PATCH 0110/1603] style changes and sanity check added --- easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016b.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016b.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016b.eb index 261f39024d..7d801b065b 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016b.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016b.eb @@ -41,7 +41,8 @@ dependencies = [ ] #The destination directory is "linux-" see 3rdparty/ippicv/downloader.cmake -preconfigopts = 'mkdir -p {0} && cp -a ../*.tgz {0}. &&'.format("3rdparty/ippicv/downloads/linux-808b791a6eac9ed78d32a7666804320e/") +ppicv_dir = '3rdparty/ippicv/downloads/linux-808b791a6eac9ed78d32a7666804320e/' +preconfigopts = "mkdir -p %s && cp -a ../*.tgz %s && " % (ippicv_dir, ippicv_dir) configopts = '-DCMAKE_BUILD_TYPE=RELEASE ' configopts += '-DBUILD_PYTHON_SUPPORT=ON ' @@ -66,6 +67,7 @@ postinstallcmds = ["cp 3rdparty/ippicv/unpack/ippicv_lnx/lib/intel64/libippicv.* sanity_check_paths = { 'files': ['lib/libopencv_core.%s' % SHLIB_EXT ] + ['lib/python%%(pyshortver)s/site-packages/cv2.%s' % SHLIB_EXT ] + + ['lib/libippicv.a'] + ['bin/opencv_%s' % x for x in ['annotation', 'createsamples', 'traincascade']], 'dirs': ['include'] } -- GitLab From e5f70be0bf3385ce2a84f2d4f81460c2ea6a856a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 20 Feb 2017 16:58:51 +0100 Subject: [PATCH 0111/1603] adding easyconfigs: Armadillo-7.800.0-intel-2016b-Python-2.7.12.eb --- ...dillo-7.800.0-intel-2016b-Python-2.7.12.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/a/Armadillo/Armadillo-7.800.0-intel-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/a/Armadillo/Armadillo-7.800.0-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/a/Armadillo/Armadillo-7.800.0-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..509aa4c19a --- /dev/null +++ b/easybuild/easyconfigs/a/Armadillo/Armadillo-7.800.0-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,23 @@ +name = 'Armadillo' +version = '7.800.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://arma.sourceforge.net/' +description = """Armadillo is an open-source C++ linear algebra library (matrix maths) aiming towards + a good balance between speed and ease of use. Integer, floating point and complex numbers are supported, + as well as a subset of trigonometric and statistics functions.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +sources = [SOURCELOWER_TAR_XZ] +source_urls = ['http://sourceforge.net/projects/arma/files'] + +dependencies = [ + ('Boost', '1.63.0', versionsuffix), + ('arpack-ng', '3.4.0'), + ('Python', '2.7.12'), +] + +builddependencies = [('CMake', '3.7.2')] + +moduleclass = 'numlib' -- GitLab From e883359e8f8a008c4a46f0347a9b7c44b2a825cb Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 20 Feb 2017 17:02:22 +0100 Subject: [PATCH 0112/1603] use http rather than ftp source URLs in CFITSIO easyconfigs --- easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.300-ictce-5.5.0.eb | 2 +- easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.34-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.34-ictce-5.3.0.eb | 2 +- easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.34-ictce-5.5.0.eb | 2 +- easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.350-ictce-5.5.0.eb | 2 +- easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.37-intel-2015a.eb | 2 +- easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.38-foss-2016a.eb | 2 +- easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.38-intel-2016a.eb | 2 +- 8 files changed, 8 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.300-ictce-5.5.0.eb b/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.300-ictce-5.5.0.eb index 8c90ec640b..df0d72298b 100755 --- a/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.300-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.300-ictce-5.5.0.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'ictce', 'version': '5.5.0'} toolchainopts = {'pic': True} srcversion = version.replace('.', '') -source_urls = ['ftp://heasarc.gsfc.nasa.gov/software/fitsio/c/'] +source_urls = ['http://heasarc.gsfc.nasa.gov/FTP/software/fitsio/c/'] sources = ['%%(namelower)s%s.tar.gz' % srcversion] sanity_check_paths = { diff --git a/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.34-goolf-1.4.10.eb b/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.34-goolf-1.4.10.eb index 9a156bffea..79b1be118d 100644 --- a/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.34-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.34-goolf-1.4.10.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'optarch': True, 'pic': True} srcversion = '%s0' % version.replace('.', '') -source_urls = ['ftp://heasarc.gsfc.nasa.gov/software/fitsio/c/'] +source_urls = ['http://heasarc.gsfc.nasa.gov/FTP/software/fitsio/c/'] sources = ['%%(namelower)s%s.tar.gz' % srcversion] sanity_check_paths = { diff --git a/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.34-ictce-5.3.0.eb b/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.34-ictce-5.3.0.eb index bf8fb571c8..a6a8529f92 100644 --- a/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.34-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.34-ictce-5.3.0.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'optarch': True, 'pic': True} srcversion = '%s0' % version.replace('.', '') -source_urls = ['ftp://heasarc.gsfc.nasa.gov/software/fitsio/c/'] +source_urls = ['http://heasarc.gsfc.nasa.gov/FTP/software/fitsio/c/'] sources = ['%%(namelower)s%s.tar.gz' % srcversion] sanity_check_paths = { diff --git a/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.34-ictce-5.5.0.eb b/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.34-ictce-5.5.0.eb index acdf7bfb8d..b205f7fd1f 100644 --- a/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.34-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.34-ictce-5.5.0.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'ictce', 'version': '5.5.0'} toolchainopts = {'optarch': True, 'pic': True} srcversion = '%s0' % version.replace('.', '') -source_urls = ['ftp://heasarc.gsfc.nasa.gov/software/fitsio/c/'] +source_urls = ['http://heasarc.gsfc.nasa.gov/FTP/software/fitsio/c/'] sources = ['%%(namelower)s%s.tar.gz' % srcversion] sanity_check_paths = { diff --git a/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.350-ictce-5.5.0.eb b/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.350-ictce-5.5.0.eb index 177bb20dcc..32bbb18488 100644 --- a/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.350-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.350-ictce-5.5.0.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'ictce', 'version': '5.5.0'} toolchainopts = {'optarch': True, 'pic': True} srcversion = '%s' % version.replace('.', '') -source_urls = ['ftp://heasarc.gsfc.nasa.gov/software/fitsio/c/'] +source_urls = ['http://heasarc.gsfc.nasa.gov/FTP/software/fitsio/c/'] sources = ['%%(namelower)s%s.tar.gz' % srcversion] sanity_check_paths = { diff --git a/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.37-intel-2015a.eb b/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.37-intel-2015a.eb index 08e0bf1795..32720c1e1c 100644 --- a/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.37-intel-2015a.eb +++ b/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.37-intel-2015a.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'intel', 'version': '2015a'} toolchainopts = {'optarch': True, 'pic': True} srcversion = '%s0' % version.replace('.', '') -source_urls = ['ftp://heasarc.gsfc.nasa.gov/software/fitsio/c/'] +source_urls = ['http://heasarc.gsfc.nasa.gov/FTP/software/fitsio/c/'] sources = ['%%(namelower)s%s.tar.gz' % srcversion] sanity_check_paths = { diff --git a/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.38-foss-2016a.eb b/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.38-foss-2016a.eb index 654a6284e8..4ea772d549 100644 --- a/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.38-foss-2016a.eb +++ b/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.38-foss-2016a.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'foss', 'version': '2016a'} toolchainopts = {'optarch': True, 'pic': True} srcversion = '%s0' % version.replace('.', '') -source_urls = ['ftp://heasarc.gsfc.nasa.gov/software/fitsio/c/'] +source_urls = ['http://heasarc.gsfc.nasa.gov/FTP/software/fitsio/c/'] sources = ['%%(namelower)s%s.tar.gz' % srcversion] sanity_check_paths = { diff --git a/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.38-intel-2016a.eb b/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.38-intel-2016a.eb index 6291c97147..d7830dc633 100644 --- a/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.38-intel-2016a.eb +++ b/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.38-intel-2016a.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'intel', 'version': '2016a'} toolchainopts = {'optarch': True, 'pic': True} srcversion = '%s0' % version.replace('.', '') -source_urls = ['ftp://heasarc.gsfc.nasa.gov/software/fitsio/c/'] +source_urls = ['http://heasarc.gsfc.nasa.gov/FTP/software/fitsio/c/'] sources = ['%%(namelower)s%s.tar.gz' % srcversion] sanity_check_paths = { -- GitLab From f3d0f859cfb5f742029a92697b56d5a930d5d58f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 20 Feb 2017 17:46:00 +0100 Subject: [PATCH 0113/1603] adding easyconfigs: ROOT-v6.06.02-intel-2016b-Python-2.7.12.eb, PCRE-8.40-intel-2016b.eb, CFITSIO-3.41-intel-2016b.eb --- .../c/CFITSIO/CFITSIO-3.41-intel-2016b.eb | 22 ++++++++ .../p/PCRE/PCRE-8.40-intel-2016b.eb | 20 +++++++ ...ROOT-v6.06.02-intel-2016b-Python-2.7.12.eb | 55 +++++++++++++++++++ 3 files changed, 97 insertions(+) create mode 100644 easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.41-intel-2016b.eb create mode 100644 easybuild/easyconfigs/p/PCRE/PCRE-8.40-intel-2016b.eb create mode 100644 easybuild/easyconfigs/r/ROOT/ROOT-v6.06.02-intel-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.41-intel-2016b.eb b/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.41-intel-2016b.eb new file mode 100644 index 0000000000..382c9e2061 --- /dev/null +++ b/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.41-intel-2016b.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'CFITSIO' +version = '3.41' + +homepage = 'http://heasarc.gsfc.nasa.gov/fitsio/' +description = """CFITSIO is a library of C and Fortran subroutines for reading and writing data files in +FITS (Flexible Image Transport System) data format.""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'pic': True} + +srcversion = '%s0' % version.replace('.', '') +source_urls = ['http://heasarc.gsfc.nasa.gov/FTP/software/fitsio/c/'] +sources = ['%%(namelower)s%s.tar.gz' % srcversion] + +sanity_check_paths = { + 'files': ['lib/libcfitsio.a'], + 'dirs': ['include'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PCRE/PCRE-8.40-intel-2016b.eb b/easybuild/easyconfigs/p/PCRE/PCRE-8.40-intel-2016b.eb new file mode 100644 index 0000000000..136a1027bb --- /dev/null +++ b/easybuild/easyconfigs/p/PCRE/PCRE-8.40-intel-2016b.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'PCRE' +version = '8.40' + +homepage = 'http://www.pcre.org/' +description = """ + The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax + and semantics as Perl 5. +""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +configopts = "--with-pic --disable-cpp --enable-utf --enable-unicode-properties" + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-v6.06.02-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/r/ROOT/ROOT-v6.06.02-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..2ddf7531c8 --- /dev/null +++ b/easybuild/easyconfigs/r/ROOT/ROOT-v6.06.02-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,55 @@ +name = 'ROOT' +version = 'v6.06.02' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://root.cern.ch/drupal/' +description = """The ROOT system provides a set of OO frameworks with all the functionality + needed to handle and analyze large amounts of data in a very efficient way.""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'pic': True} + +sources = ['%(namelower)s_%(version)s.source.tar.gz'] +source_urls = ['ftp://root.cern.ch/root/'] +patches = [ + 'configure_FftwFromMkl_28.patch', + 'ROOT-v5_recent-ifort.patch', + 'ROOT-v5.34.26_libX.patch', +] + +dependencies = [ + ('GSL', '2.3'), + ('libxml2', '2.9.4'), + ('PCRE', '8.40'), + ('CFITSIO', '3.41'), + ('freetype', '2.6.5'), + ('Python', '2.7.12'), + ('zlib', '1.2.8'), + ('X11', '20160819'), + ('Mesa', '12.0.2'), + ('libGLU', '9.0.0'), + ('GL2PS', '1.3.9'), +] + +# use external ZLIB +preconfigopts = 'env ZLIB=$EBROOTZLIB ' + +# architecture +arch = 'linuxx8664icc' + +# disable features +configopts = ' --disable-xrootd --disable-mysql --disable-krb5 --disable-odbc ' +configopts += ' --disable-oracle --disable-pgsql --disable-qt --disable-sqlite' +# enable features +configopts += ' --enable-unuran --enable-table --enable-explicitlink --enable-minuit2 --enable-roofit' +configopts += ' --with-gsl-incdir=$EBROOTGSL/include/gsl --with-gsl-libdir=$EBROOTGSL/lib' +configopts += ' --with-fftw3-incdir=$MKLROOT/mkl/include/fftw --with-fftw3-libdir=$MKLROOT/mkl/lib/intel64' +configopts += ' --with-xml-incdir=$EBROOTLIBXML2/include/libxml2/libxml --with-xml-libdir=$EBROOTLIBXML2/lib' +configopts += ' --with-python-libdir=$EBROOTPYTHON/lib' +configopts += ' --with-cfitsio-incdir=$EBROOTCFITSIO/include --with-cfitsio-libdir=$EBROOTCFITSIO/lib' +configopts += ' --with-opengl-incdir=$EBROOTMESA/include --with-opengl-libdir=$EBROOTMESA/lib' +configopts += ' --with-x11-libdir=$EBROOTX11/lib --with-xext-libdir=$EBROOTLIBX11/lib' +configopts += ' --with-xft-libdir=$EBROOTX11/lib' +configopts += ' --with-xpm-incdir=$EBROOTX11/include --with-xpm-libdir=$EBROOTX11/lib' + +moduleclass = 'data' -- GitLab From 42b679976f9cfacadddedc7fe079b4674ed701b5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 20 Feb 2017 18:21:08 +0100 Subject: [PATCH 0114/1603] adding easyconfigs: OrthoMCL-1.4-intel-2016b-Perl-5.24.0.eb --- .../BioPerl-1.7.1-intel-2016b-Perl-5.24.0.eb | 28 +++++++++++++++ .../m/MCL/MCL-02.063-intel-2016b.eb | 23 ++++++++++++ .../OrthoMCL-1.4-intel-2016b-Perl-5.24.0.eb | 35 +++++++++++++++++++ 3 files changed, 86 insertions(+) create mode 100644 easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.1-intel-2016b-Perl-5.24.0.eb create mode 100644 easybuild/easyconfigs/m/MCL/MCL-02.063-intel-2016b.eb create mode 100644 easybuild/easyconfigs/o/OrthoMCL/OrthoMCL-1.4-intel-2016b-Perl-5.24.0.eb diff --git a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.1-intel-2016b-Perl-5.24.0.eb b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.1-intel-2016b-Perl-5.24.0.eb new file mode 100644 index 0000000000..d5d219aba4 --- /dev/null +++ b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.1-intel-2016b-Perl-5.24.0.eb @@ -0,0 +1,28 @@ +# easybuild easyconfig +# +# John Dey jfdey@fredhutch.org +# +# Fred Hutchinson Cancer Research Center + +easyblock = 'PerlModule' + +name = 'BioPerl' +version = '1.7.1' +versionsuffix = '-Perl-%(perlver)s' + +homepage = 'http://www.bioperl.org/' +description = """Bioperl is the product of a community effort to produce Perl code which is useful in biology. + Examples include Sequence objects, Alignment objects and database searching objects.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['https://github.com/bioperl/bioperl-live/archive/'] +sources = ['release-%s.zip' % version.replace('.', '-')] + +dependencies = [ + ('Perl', '5.24.0'), +] + +options = {'modulename': 'Bio::Perl'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MCL/MCL-02.063-intel-2016b.eb b/easybuild/easyconfigs/m/MCL/MCL-02.063-intel-2016b.eb new file mode 100644 index 0000000000..7cdcdee529 --- /dev/null +++ b/easybuild/easyconfigs/m/MCL/MCL-02.063-intel-2016b.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'MCL' +version = '02.063' + +homepage = 'http://micans.org/mcl/' +description = """The MCL algorithm is short for the Markov Cluster Algorithm, a fast +and scalable unsupervised cluster algorithm for graphs (also known as networks) based +on simulation of (stochastic) flow in graphs. """ + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['http://orthomcl.org/common/downloads/software/unsupported/v1.4/'] +sources = ['%(namelower)s-%(version_major)s-%(version_minor)s.tar.gz'] + +preconfigopts = "rm config.cache && " + +sanity_check_paths = { + 'files': ['bin/mcl'], + 'dirs': ['share'] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/o/OrthoMCL/OrthoMCL-1.4-intel-2016b-Perl-5.24.0.eb b/easybuild/easyconfigs/o/OrthoMCL/OrthoMCL-1.4-intel-2016b-Perl-5.24.0.eb new file mode 100644 index 0000000000..6820502e94 --- /dev/null +++ b/easybuild/easyconfigs/o/OrthoMCL/OrthoMCL-1.4-intel-2016b-Perl-5.24.0.eb @@ -0,0 +1,35 @@ +easyblock = 'Tarball' + +name = 'OrthoMCL' +version = '1.4' +versionsuffix = '-Perl-%(perlver)s' + +homepage = 'http://orthomcl.org/' +description = """OrthoMCL is a genome-scale algorithm for grouping orthologous protein sequences.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +mcl_majver = '02' +mcl_minver = '063' +sources = ['ORTHOMCL_V%%(version)s_mcl-%s-%s.tar' % (mcl_majver, mcl_minver)] +source_urls = ['http://orthomcl.org/common/downloads/software/unsupported/v%(version)s'] + +dependencies = [ + # a Perl installation providing the DBI module is required + ('Perl', '5.24.0'), + ('MCL', '%s.%s' % (mcl_majver, mcl_minver)), + ('BioPerl', '1.7.1', versionsuffix), +] + +start_dir = 'ORTHOMCLV%(version)s' + +sanity_check_paths = { + 'files': ['orthomcl_module.pm', 'orthomcl.pl', 'README'], + 'dirs': ['sample_data'], +} + +modextrapaths = {'PERL5LIB': ''} + +sanity_check_commands = [('perl', '-e "use orthomcl_module;"')] + +moduleclass = 'bio' -- GitLab From 63f002eaf7b16555acb0b4f49c61c148850393ea Mon Sep 17 00:00:00 2001 From: Maxime Boissonneault Date: Tue, 21 Feb 2017 15:22:14 +0000 Subject: [PATCH 0115/1603] added eb recipe for igraph --- .../igraph-0.7.1-fix-aclocal-version.patch | 43 +++ .../i/igraph/igraph-0.7.1-intel-2016a.eb | 31 +++ .../igraph-0.7.1-no-lapack-no-blas.patch | 259 ++++++++++++++++++ 3 files changed, 333 insertions(+) create mode 100644 easybuild/easyconfigs/i/igraph/igraph-0.7.1-fix-aclocal-version.patch create mode 100644 easybuild/easyconfigs/i/igraph/igraph-0.7.1-intel-2016a.eb create mode 100644 easybuild/easyconfigs/i/igraph/igraph-0.7.1-no-lapack-no-blas.patch diff --git a/easybuild/easyconfigs/i/igraph/igraph-0.7.1-fix-aclocal-version.patch b/easybuild/easyconfigs/i/igraph/igraph-0.7.1-fix-aclocal-version.patch new file mode 100644 index 0000000000..fc7ded594f --- /dev/null +++ b/easybuild/easyconfigs/i/igraph/igraph-0.7.1-fix-aclocal-version.patch @@ -0,0 +1,43 @@ +diff -ru igraph-0.7.1.orig/aclocal.m4 igraph-0.7.1/aclocal.m4 +--- igraph-0.7.1.orig/aclocal.m4 2014-04-22 17:54:54.000000000 +0000 ++++ igraph-0.7.1/aclocal.m4 2017-02-21 15:10:50.062279982 +0000 +@@ -1,4 +1,4 @@ +-# generated automatically by aclocal 1.14 -*- Autoconf -*- ++# generated automatically by aclocal 1.15 -*- Autoconf -*- + + # Copyright (C) 1996-2013 Free Software Foundation, Inc. + +@@ -8619,10 +8619,10 @@ + # generated from the m4 files accompanying Automake X.Y. + # (This private macro should not be called outside this file.) + AC_DEFUN([AM_AUTOMAKE_VERSION], +-[am__api_version='1.14' ++[am__api_version='1.15' + dnl Some users find AM_AUTOMAKE_VERSION and mistake it for a way to + dnl require some minimum version. Point them to the right macro. +-m4_if([$1], [1.14], [], ++m4_if([$1], [1.15], [], + [AC_FATAL([Do not call $0, use AM_INIT_AUTOMAKE([$1]).])])dnl + ]) + +@@ -8638,7 +8638,7 @@ + # Call AM_AUTOMAKE_VERSION and AM_AUTOMAKE_VERSION so they can be traced. + # This function is AC_REQUIREd by AM_INIT_AUTOMAKE. + AC_DEFUN([AM_SET_CURRENT_AUTOMAKE_VERSION], +-[AM_AUTOMAKE_VERSION([1.14])dnl ++[AM_AUTOMAKE_VERSION([1.15])dnl + m4_ifndef([AC_AUTOCONF_VERSION], + [m4_copy([m4_PACKAGE_VERSION], [AC_AUTOCONF_VERSION])])dnl + _AM_AUTOCONF_VERSION(m4_defn([AC_AUTOCONF_VERSION]))]) +diff -ru igraph-0.7.1.orig/configure igraph-0.7.1/configure +--- igraph-0.7.1.orig/configure 2014-04-22 17:55:00.000000000 +0000 ++++ igraph-0.7.1/configure 2017-02-21 15:10:50.082279777 +0000 +@@ -2532,7 +2532,7 @@ + + + +-am__api_version='1.14' ++am__api_version='1.15' + + ac_aux_dir= + for ac_dir in "$srcdir" "$srcdir/.." "$srcdir/../.."; do diff --git a/easybuild/easyconfigs/i/igraph/igraph-0.7.1-intel-2016a.eb b/easybuild/easyconfigs/i/igraph/igraph-0.7.1-intel-2016a.eb new file mode 100644 index 0000000000..53b27e3fc2 --- /dev/null +++ b/easybuild/easyconfigs/i/igraph/igraph-0.7.1-intel-2016a.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'igraph' +version = '0.7.1' + +homepage = 'http://igraph.org' +description = """igraph is a collection of network analysis tools with the emphasis on +efficiency, portability and ease of use. igraph is open source and free. igraph can be +programmed in R, Python and C/C++.""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'pic': True} + +sources = ['igraph-%(version)s.tar.gz'] +source_urls = ['https://github.com/igraph/igraph/releases/download/%(version)s'] + +# Fix llapack and llblas when compiling with MKL +# Fix aclocal which is hard-coded to version 1.14 +patches = ['igraph-0.7.1-no-lapack-no-blas.patch', 'igraph-0.7.1-fix-aclocal-version.patch'] + +# link against MKL rather than blas/lapack +preconfigopts = "env LDFLAGS='-lmkl_intel_lp64 -lmkl_core -lmkl_sequential -lpthread -lm'" +configopts = "--with-external-blas=yes --with-external-lapack=yes" + +sanity_check_paths = { + 'files': ['lib/libigraph.so', 'lib/libigraph.la', 'lib/pkgconfig/igraph.pc'] + + ['include/igraph/%s' % x for x in ['igraph_version.h', 'igraph_types.h', 'igraph_constants.h']], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/i/igraph/igraph-0.7.1-no-lapack-no-blas.patch b/easybuild/easyconfigs/i/igraph/igraph-0.7.1-no-lapack-no-blas.patch new file mode 100644 index 0000000000..70635982cf --- /dev/null +++ b/easybuild/easyconfigs/i/igraph/igraph-0.7.1-no-lapack-no-blas.patch @@ -0,0 +1,259 @@ +diff -ru igraph-0.7.1.orig/configure igraph-0.7.1/configure +--- igraph-0.7.1.orig/configure 2014-04-22 17:55:00.000000000 +0000 ++++ igraph-0.7.1/configure 2017-02-21 15:00:00.398921297 +0000 +@@ -17266,13 +17266,13 @@ + fi + + if test "$internal_blas" = "no"; then +- { $as_echo "$as_me:${as_lineno-$LINENO}: checking for daxpy_ in -lblas" >&5 +-$as_echo_n "checking for daxpy_ in -lblas... " >&6; } ++ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for daxpy_ in " >&5 ++$as_echo_n "checking for daxpy_ in ... " >&6; } + if ${ac_cv_lib_blas_daxpy_+:} false; then : + $as_echo_n "(cached) " >&6 + else + ac_check_lib_save_LIBS=$LIBS +-LIBS="-lblas $LIBS" ++LIBS=" $LIBS" + cat confdefs.h - <<_ACEOF >conftest.$ac_ext + /* end confdefs.h. */ + +@@ -17307,16 +17307,16 @@ + #define HAVE_LIBBLAS 1 + _ACEOF + +- LIBS="-lblas $LIBS" ++ LIBS=" $LIBS" + + else +- { $as_echo "$as_me:${as_lineno-$LINENO}: checking for daxpy in -lblas" >&5 +-$as_echo_n "checking for daxpy in -lblas... " >&6; } ++ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for daxpy in " >&5 ++$as_echo_n "checking for daxpy in ... " >&6; } + if ${ac_cv_lib_blas_daxpy+:} false; then : + $as_echo_n "(cached) " >&6 + else + ac_check_lib_save_LIBS=$LIBS +-LIBS="-lblas $LIBS" ++LIBS=" $LIBS" + cat confdefs.h - <<_ACEOF >conftest.$ac_ext + /* end confdefs.h. */ + +@@ -17351,16 +17351,16 @@ + #define HAVE_LIBBLAS 1 + _ACEOF + +- LIBS="-lblas $LIBS" ++ LIBS=" $LIBS" + + else +- { $as_echo "$as_me:${as_lineno-$LINENO}: checking for DAXPY_ in -lblas" >&5 +-$as_echo_n "checking for DAXPY_ in -lblas... " >&6; } ++ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for DAXPY_ in " >&5 ++$as_echo_n "checking for DAXPY_ in ... " >&6; } + if ${ac_cv_lib_blas_DAXPY_+:} false; then : + $as_echo_n "(cached) " >&6 + else + ac_check_lib_save_LIBS=$LIBS +-LIBS="-lblas $LIBS" ++LIBS=" $LIBS" + cat confdefs.h - <<_ACEOF >conftest.$ac_ext + /* end confdefs.h. */ + +@@ -17395,16 +17395,16 @@ + #define HAVE_LIBBLAS 1 + _ACEOF + +- LIBS="-lblas $LIBS" ++ LIBS=" $LIBS" + + else +- { $as_echo "$as_me:${as_lineno-$LINENO}: checking for DAXPY in -lblas" >&5 +-$as_echo_n "checking for DAXPY in -lblas... " >&6; } ++ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for DAXPY in " >&5 ++$as_echo_n "checking for DAXPY in ... " >&6; } + if ${ac_cv_lib_blas_DAXPY+:} false; then : + $as_echo_n "(cached) " >&6 + else + ac_check_lib_save_LIBS=$LIBS +-LIBS="-lblas $LIBS" ++LIBS=" $LIBS" + cat confdefs.h - <<_ACEOF >conftest.$ac_ext + /* end confdefs.h. */ + +@@ -17439,7 +17439,7 @@ + #define HAVE_LIBBLAS 1 + _ACEOF + +- LIBS="-lblas $LIBS" ++ LIBS=" $LIBS" + + else + { $as_echo "$as_me:${as_lineno-$LINENO}: result: not found" >&5 +@@ -17452,8 +17452,8 @@ + + fi + +- LDFLAGS="${LDFLAGS} -lblas" +- PKGCONFIG_LIBS_PRIVATE="${PKGCONFIG_LIBS_PRIVATE} -lblas" ++ LDFLAGS="${LDFLAGS} " ++ PKGCONFIG_LIBS_PRIVATE="${PKGCONFIG_LIBS_PRIVATE} " + else + + $as_echo "#define INTERNAL_BLAS 1" >>confdefs.h +@@ -17461,13 +17461,13 @@ + fi + + if test "$internal_lapack" = "no"; then +- { $as_echo "$as_me:${as_lineno-$LINENO}: checking for dlarnv_ in -llapack" >&5 +-$as_echo_n "checking for dlarnv_ in -llapack... " >&6; } ++ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for dlarnv_ in " >&5 ++$as_echo_n "checking for dlarnv_ in ... " >&6; } + if ${ac_cv_lib_lapack_dlarnv_+:} false; then : + $as_echo_n "(cached) " >&6 + else + ac_check_lib_save_LIBS=$LIBS +-LIBS="-llapack $LIBS" ++LIBS=" $LIBS" + cat confdefs.h - <<_ACEOF >conftest.$ac_ext + /* end confdefs.h. */ + +@@ -17502,16 +17502,16 @@ + #define HAVE_LIBLAPACK 1 + _ACEOF + +- LIBS="-llapack $LIBS" ++ LIBS=" $LIBS" + + else +- { $as_echo "$as_me:${as_lineno-$LINENO}: checking for dlarnv in -llapack" >&5 +-$as_echo_n "checking for dlarnv in -llapack... " >&6; } ++ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for dlarnv in " >&5 ++$as_echo_n "checking for dlarnv in ... " >&6; } + if ${ac_cv_lib_lapack_dlarnv+:} false; then : + $as_echo_n "(cached) " >&6 + else + ac_check_lib_save_LIBS=$LIBS +-LIBS="-llapack $LIBS" ++LIBS=" $LIBS" + cat confdefs.h - <<_ACEOF >conftest.$ac_ext + /* end confdefs.h. */ + +@@ -17546,16 +17546,16 @@ + #define HAVE_LIBLAPACK 1 + _ACEOF + +- LIBS="-llapack $LIBS" ++ LIBS=" $LIBS" + + else +- { $as_echo "$as_me:${as_lineno-$LINENO}: checking for DLARNV_ in -llapack" >&5 +-$as_echo_n "checking for DLARNV_ in -llapack... " >&6; } ++ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for DLARNV_ in " >&5 ++$as_echo_n "checking for DLARNV_ in ... " >&6; } + if ${ac_cv_lib_lapack_DLARNV_+:} false; then : + $as_echo_n "(cached) " >&6 + else + ac_check_lib_save_LIBS=$LIBS +-LIBS="-llapack $LIBS" ++LIBS=" $LIBS" + cat confdefs.h - <<_ACEOF >conftest.$ac_ext + /* end confdefs.h. */ + +@@ -17590,16 +17590,16 @@ + #define HAVE_LIBLAPACK 1 + _ACEOF + +- LIBS="-llapack $LIBS" ++ LIBS=" $LIBS" + + else +- { $as_echo "$as_me:${as_lineno-$LINENO}: checking for DLARNV in -llapack" >&5 +-$as_echo_n "checking for DLARNV in -llapack... " >&6; } ++ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for DLARNV in " >&5 ++$as_echo_n "checking for DLARNV in ... " >&6; } + if ${ac_cv_lib_lapack_DLARNV+:} false; then : + $as_echo_n "(cached) " >&6 + else + ac_check_lib_save_LIBS=$LIBS +-LIBS="-llapack $LIBS" ++LIBS=" $LIBS" + cat confdefs.h - <<_ACEOF >conftest.$ac_ext + /* end confdefs.h. */ + +@@ -17634,7 +17634,7 @@ + #define HAVE_LIBLAPACK 1 + _ACEOF + +- LIBS="-llapack $LIBS" ++ LIBS=" $LIBS" + + else + { $as_echo "$as_me:${as_lineno-$LINENO}: result: not found" >&5 +@@ -17647,8 +17647,8 @@ + + fi + +- LDFLAGS="${LDFLAGS} -llapack" +- PKGCONFIG_LIBS_PRIVATE="${PKGCONFIG_LIBS_PRIVATE} -llapack" ++ LDFLAGS="${LDFLAGS} " ++ PKGCONFIG_LIBS_PRIVATE="${PKGCONFIG_LIBS_PRIVATE} " + else + + $as_echo "#define INTERNAL_LAPACK 1" >>confdefs.h +diff -ru igraph-0.7.1.orig/configure.ac igraph-0.7.1/configure.ac +--- igraph-0.7.1.orig/configure.ac 2014-04-22 13:01:17.000000000 +0000 ++++ igraph-0.7.1/configure.ac 2017-02-21 15:00:00.398921297 +0000 +@@ -235,9 +235,9 @@ + AC_CHECK_LIB([blas], [daxpy], [], + AC_CHECK_LIB([blas], [DAXPY_], [], + AC_CHECK_LIB([blas], [DAXPY], [], +- [AC_MSG_RESULT(not found, trying to use -lblas anyway.)])))) +- LDFLAGS="${LDFLAGS} -lblas" +- PKGCONFIG_LIBS_PRIVATE="${PKGCONFIG_LIBS_PRIVATE} -lblas" ++ [AC_MSG_RESULT(not found, trying to use anyway.)])))) ++ LDFLAGS="${LDFLAGS} " ++ PKGCONFIG_LIBS_PRIVATE="${PKGCONFIG_LIBS_PRIVATE} " + else + AC_DEFINE([INTERNAL_BLAS], [1], [Define to 1 if you use the internal BLAS library]) + fi +@@ -247,9 +247,9 @@ + AC_CHECK_LIB([lapack], [dlarnv], [], + AC_CHECK_LIB([lapack], [DLARNV_], [], + AC_CHECK_LIB([lapack], [DLARNV], [], +- [AC_MSG_RESULT(not found, trying to use -llapack anyway.)])))) +- LDFLAGS="${LDFLAGS} -llapack" +- PKGCONFIG_LIBS_PRIVATE="${PKGCONFIG_LIBS_PRIVATE} -llapack" ++ [AC_MSG_RESULT(not found, trying to use anyway.)])))) ++ LDFLAGS="${LDFLAGS} " ++ PKGCONFIG_LIBS_PRIVATE="${PKGCONFIG_LIBS_PRIVATE} " + else + AC_DEFINE([INTERNAL_LAPACK], [1], [Define to 1 if you use the internal LAPACK library]) + fi +diff -ru igraph-0.7.1.orig/tests/testsuite igraph-0.7.1/tests/testsuite +--- igraph-0.7.1.orig/tests/testsuite 2014-04-22 17:55:15.000000000 +0000 ++++ igraph-0.7.1/tests/testsuite 2017-02-21 15:00:00.417921103 +0000 +@@ -3793,9 +3793,9 @@ + + + { set +x +-$as_echo "$at_srcdir/types.at:136: \$CC \${abs_top_srcdir}/examples/simple/igraph_sparsemat2.c -I\${abs_top_srcdir}/include -I\${abs_top_srcdir}/src -I\${abs_top_builddir}/include -I\${abs_top_builddir} -L\${abs_top_builddir}/src/.libs -ligraph -lm -lblas -o itest" ++$as_echo "$at_srcdir/types.at:136: \$CC \${abs_top_srcdir}/examples/simple/igraph_sparsemat2.c -I\${abs_top_srcdir}/include -I\${abs_top_srcdir}/src -I\${abs_top_builddir}/include -I\${abs_top_builddir} -L\${abs_top_builddir}/src/.libs -ligraph -lm -o itest" + at_fn_check_prepare_notrace 'a ${...} parameter expansion' "types.at:136" +-( $at_check_trace; $CC ${abs_top_srcdir}/examples/simple/igraph_sparsemat2.c -I${abs_top_srcdir}/include -I${abs_top_srcdir}/src -I${abs_top_builddir}/include -I${abs_top_builddir} -L${abs_top_builddir}/src/.libs -ligraph -lm -lblas -o itest ++( $at_check_trace; $CC ${abs_top_srcdir}/examples/simple/igraph_sparsemat2.c -I${abs_top_srcdir}/include -I${abs_top_srcdir}/src -I${abs_top_builddir}/include -I${abs_top_builddir} -L${abs_top_builddir}/src/.libs -ligraph -lm -o itest + ) >>"$at_stdout" 2>>"$at_stderr" 5>&- + at_status=$? at_failed=false + $at_check_filter +diff -ru igraph-0.7.1.orig/tests/types.at igraph-0.7.1/tests/types.at +--- igraph-0.7.1.orig/tests/types.at 2014-04-15 13:00:46.000000000 +0000 ++++ igraph-0.7.1/tests/types.at 2017-02-21 15:00:00.417921103 +0000 +@@ -133,7 +133,7 @@ + AT_SETUP([Sparse matrix, multiplications (igraph_sparsemat_t): ]) + AT_KEYWORDS([sparse matrix igraph_sparsemat_t]) + AT_COMPILE_CHECK([simple/igraph_sparsemat2.c], [simple/igraph_sparsemat2.out], +- [], [INTERNAL], [-lblas]) ++ [], [INTERNAL], []) + AT_CLEANUP + + AT_SETUP([Sparse matrix, indexing (igraph_sparsemat_t): ]) -- GitLab From 0731bdbd8e8fee86ea385140bf383a8c52e238e8 Mon Sep 17 00:00:00 2001 From: Maxime Boissonneault Date: Tue, 21 Feb 2017 16:10:35 +0000 Subject: [PATCH 0116/1603] fixed naming convention of the easyconfig file --- .../{igraph-0.7.1-intel-2016a.eb => igraph-0.7.1-intel-2016b.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/i/igraph/{igraph-0.7.1-intel-2016a.eb => igraph-0.7.1-intel-2016b.eb} (100%) diff --git a/easybuild/easyconfigs/i/igraph/igraph-0.7.1-intel-2016a.eb b/easybuild/easyconfigs/i/igraph/igraph-0.7.1-intel-2016b.eb similarity index 100% rename from easybuild/easyconfigs/i/igraph/igraph-0.7.1-intel-2016a.eb rename to easybuild/easyconfigs/i/igraph/igraph-0.7.1-intel-2016b.eb -- GitLab From 5d951ce558039bed7e9cb0b4f74c29aaf268492b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 21 Feb 2017 20:23:57 +0100 Subject: [PATCH 0117/1603] more style fixes in easyconfigs --- .../a/ALPS/ALPS-2.3.0-foss-2016b-Python-2.7.12.eb | 2 +- .../a/ALPS/ALPS-2.3.0-foss-2016b-Python-3.5.2.eb | 2 +- .../b/BayesAss/BayesAss-3.0.4-foss-2016a.eb | 4 ++-- .../b/Bazel/Bazel-0.3.0-CrayGNU-2016.03.eb | 2 +- easybuild/easyconfigs/b/Bazel/Bazel-0.4.4.eb | 2 +- .../Boost-1.60.0-CrayGNU-2016.03-Python-2.7.11.eb | 2 +- ...fe-rc3-foss-2016a-CUDA-7.5.18-Python-2.7.11.eb | 2 +- .../Commet-20150415-foss-2016a-Python-2.7.11.eb | 2 +- .../c/CrossTalkZ/CrossTalkZ-1.4-foss-2016a.eb | 2 +- .../easyconfigs/g/GSL/GSL-2.1-CrayGNU-2015.11.eb | 2 +- .../g/gtest/gtest-1.7.0-CrayGNU-2015.11.eb | 2 +- easybuild/easyconfigs/i/IMB/IMB-4.1-foss-2016a.eb | 2 +- .../i/IOzone/IOzone-3.434-foss-2016a.eb | 8 ++++---- .../Kraken-0.10.5-beta-foss-2016a-Perl-5.22.1.eb | 2 +- .../Kraken-0.10.5-beta-foss-2016b-Perl-5.24.0.eb | 2 +- .../l/LevelDB/LevelDB-1.18-foss-2016a.eb | 2 +- .../l/Libint/Libint-1.1.4-CrayGNU-2015.06.eb | 2 +- .../l/Libint/Libint-1.1.4-CrayGNU-2015.11.eb | 2 +- .../easyconfigs/l/Loki/Loki-0.1.7-foss-2016a.eb | 2 +- .../easyconfigs/l/Loki/Loki-0.1.7-foss-2016b.eb | 2 +- .../easyconfigs/l/Loki/Loki-0.1.7-intel-2016a.eb | 2 +- .../easyconfigs/l/Loki/Loki-0.1.7-intel-2016b.eb | 2 +- .../l/libpsortb/libpsortb-1.0-foss-2016a.eb | 4 ++-- ...0.67-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb | 2 +- ....67-goolf-1.5.16-Java-1.7.0_79-Python-2.7.9.eb | 2 +- .../m/MIGRATE-N/MIGRATE-N-4.2.8-foss-2016a.eb | 2 +- .../MPJ-Express-0.44-foss-2016a-Java-1.8.0_92.eb | 2 +- ...MPJ-Express-0.44-goolf-1.4.10-Java-1.7.0_75.eb | 2 +- .../m/MaCH/MaCH-1.0.18.c-goolf-1.4.10.eb | 2 +- .../m/MaCH/MaCH-1.0.18.c-ictce-6.2.5.eb | 2 +- .../easyconfigs/m/Mesa/Mesa-11.1.2-foss-2016a.eb | 4 ++-- .../m/Mesa/Mesa-11.1.2-gimkl-2.11.5.eb | 4 ++-- .../easyconfigs/m/Mesa/Mesa-11.1.2-intel-2016a.eb | 4 ++-- .../easyconfigs/m/Mesa/Mesa-11.2.1-foss-2016a.eb | 4 ++-- .../easyconfigs/m/Mesa/Mesa-11.2.1-intel-2016a.eb | 4 ++-- .../easyconfigs/m/Mesa/Mesa-12.0.2-foss-2016b.eb | 2 +- .../easyconfigs/m/Mesa/Mesa-12.0.2-intel-2016b.eb | 2 +- .../m/Metal/Metal-2011-03-25-foss-2016a.eb | 4 ++-- .../m/Minimac2/Minimac2-2014.9.15-goolf-1.7.20.eb | 2 +- .../m/magma/magma-2.0.0-CrayGNU-2015.11.eb | 2 +- .../numpy-1.9.2-intel-2016b-Python-2.7.12.eb | 2 +- .../OBITools-1.2.9-foss-2016a-Python-2.7.11.eb | 4 ++-- .../p/PARI-GP/PARI-GP-2.7.6-foss-2016a.eb | 7 +++---- .../PGDSpider/PGDSpider-2.1.0.3-Java-1.7.0_80.eb | 2 +- .../PLAST/PLAST-2.3.1-foss-2016a-Java-1.8.0_92.eb | 4 ++-- .../PSORTb/PSORTb-3.0.4-foss-2016a-Perl-5.22.1.eb | 8 ++++---- .../p/Paraver/Paraver-4.4.5-GCC-4.7.3.eb | 2 +- .../p/Paraver/Paraver-4.5.6-foss-2015a.eb | 2 +- ...2.0-foss-2016a-Python-2.7.11-freetype-2.6.3.eb | 2 +- .../p/Platanus/Platanus-1.2.4-goolf-1.7.20.eb | 6 +++--- .../easyconfigs/p/ProbABEL/ProbABEL-0.5.0.eb | 2 +- .../PyGTS/PyGTS-0.3.1-foss-2016a-Python-2.7.11.eb | 4 ++-- .../PyGTS/PyGTS-0.3.1-foss-2016b-Python-2.7.12.eb | 4 ++-- .../PyGTS-0.3.1-intel-2016a-Python-2.7.11.eb | 4 ++-- .../PyGTS-0.3.1-intel-2016b-Python-2.7.12.eb | 4 ++-- .../p/Python/Python-2.7.12-GCCcore-4.9.3-bare.eb | 2 +- .../p/pftoolsV3/pftoolsV3-20160324-foss-2016a.eb | 2 +- ...tobuf-python-3.0.2-foss-2016a-Python-2.7.11.eb | 2 +- ...otobuf-python-3.0.2-foss-2016a-Python-3.5.1.eb | 2 +- ...tobuf-python-3.2.0-foss-2016b-Python-2.7.12.eb | 2 +- ...otobuf-python-3.2.0-foss-2016b-Python-3.5.2.eb | 2 +- ...obuf-python-3.2.0-intel-2016b-Python-2.7.12.eb | 2 +- ...tobuf-python-3.2.0-intel-2016b-Python-3.5.2.eb | 2 +- .../pyGIMLi-20160803-foss-2016a-Python-3.5.1.eb | 2 +- .../easyconfigs/r/Rust/Rust-1.12.0-foss-2016b.eb | 2 +- .../easyconfigs/r/Rust/Rust-1.12.1-foss-2016b.eb | 2 +- .../easyconfigs/s/SHORE/SHORE-0.9.3-foss-2016a.eb | 6 +++--- .../s/SUMACLUST/SUMACLUST-1.0.20-foss-2016a.eb | 4 ++-- .../s/SUMATRA/SUMATRA-1.0.20-foss-2016a.eb | 4 ++-- .../s/Saxon-HE/Saxon-HE-9.7.0.4-Java-1.7.0_79.eb | 2 +- .../s/Smoldyn/Smoldyn-2.48-foss-2016a.eb | 2 +- .../s/SortMeRNA/SortMeRNA-2.1-foss-2016a.eb | 15 ++++++--------- .../Sphinx-1.4.8-foss-2016a-Python-2.7.11.eb | 2 +- .../Sphinx-1.4.8-foss-2016a-Python-3.5.1.eb | 2 +- .../s/Stacks/Stacks-1.03-goolf-1.4.10.eb | 4 ++-- .../s/Stacks/Stacks-1.03-ictce-5.3.0.eb | 4 ++-- .../s/Stacks/Stacks-1.40-foss-2016a.eb | 4 ++-- .../s/Stacks/Stacks-1.42-foss-2016a.eb | 4 ++-- .../s/Stacks/Stacks-1.44-foss-2016a.eb | 4 ++-- .../s/StringTie/StringTie-1.2.2-goolf-1.4.10.eb | 2 +- .../s/StringTie/StringTie-1.3.0-intel-2016b.eb | 2 +- .../s/StringTie/StringTie-1.3.3-intel-2017a.eb | 2 +- .../easyconfigs/s/Szip/Szip-2.1-iomkl-2016.07.eb | 2 +- .../scipy-0.16.0-intel-2016b-Python-2.7.12.eb | 2 +- .../s/segemehl/segemehl-0.2.0-goolf-1.4.10.eb | 12 ++++++------ .../stemming-1.0-ictce-5.5.0-Python-2.7.6.eb | 2 +- .../s/sympy/sympy-1.0-foss-2016a-Python-2.7.11.eb | 2 +- .../sympy/sympy-1.0-intel-2016a-Python-2.7.11.eb | 2 +- .../easyconfigs/t/TAU/TAU-2.22.2-goolf-1.5.14.eb | 4 ++-- .../t/Trinity/Trinity-2.1.1-intel-2015b.eb | 2 +- .../t/Trinity/Trinity-2.2.0-foss-2016a.eb | 2 +- .../USPEX-9.4.4-intel-2016b-Python-2.7.12.eb | 3 +-- .../xcb-util-image-0.4.0-intel-2015b.eb | 2 +- .../z/ZeroMQ/ZeroMQ-4.2.0-foss-2016b.eb | 2 +- .../z/ZeroMQ/ZeroMQ-4.2.0-intel-2016b.eb | 2 +- 95 files changed, 139 insertions(+), 144 deletions(-) diff --git a/easybuild/easyconfigs/a/ALPS/ALPS-2.3.0-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/a/ALPS/ALPS-2.3.0-foss-2016b-Python-2.7.12.eb index 12d87fd3a6..56456bbd62 100644 --- a/easybuild/easyconfigs/a/ALPS/ALPS-2.3.0-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/a/ALPS/ALPS-2.3.0-foss-2016b-Python-2.7.12.eb @@ -32,7 +32,7 @@ modextrapaths = { 'PYTHONPATH': ['lib/'] } -sanity_check_paths={ +sanity_check_paths = { 'files': ['lib/libalps.%s' % SHLIB_EXT], 'dirs': ['include/alps', 'bin/', 'share/'], } diff --git a/easybuild/easyconfigs/a/ALPS/ALPS-2.3.0-foss-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/a/ALPS/ALPS-2.3.0-foss-2016b-Python-3.5.2.eb index 33dbe5c739..f21285e25b 100644 --- a/easybuild/easyconfigs/a/ALPS/ALPS-2.3.0-foss-2016b-Python-3.5.2.eb +++ b/easybuild/easyconfigs/a/ALPS/ALPS-2.3.0-foss-2016b-Python-3.5.2.eb @@ -32,7 +32,7 @@ modextrapaths = { 'PYTHONPATH': ['lib/'] } -sanity_check_paths={ +sanity_check_paths = { 'files': ['lib/libalps.%s' % SHLIB_EXT], 'dirs': ['include/alps', 'bin/', 'share/'], } diff --git a/easybuild/easyconfigs/b/BayesAss/BayesAss-3.0.4-foss-2016a.eb b/easybuild/easyconfigs/b/BayesAss/BayesAss-3.0.4-foss-2016a.eb index 0dc4a540af..20f57806c7 100644 --- a/easybuild/easyconfigs/b/BayesAss/BayesAss-3.0.4-foss-2016a.eb +++ b/easybuild/easyconfigs/b/BayesAss/BayesAss-3.0.4-foss-2016a.eb @@ -8,13 +8,13 @@ description = """ BayesAss: Bayesian Inference of Recent Migration Using Multilocus Genotypes """ -toolchain = {'name': 'foss','version': '2016a'} +toolchain = {'name': 'foss', 'version': '2016a'} sources = ['BA3-%(version)s.tar.gz'] source_urls = ['http://downloads.sourceforge.net/project/bayesass/BA3/%(version)s/src/'] dependencies = [ - ('GSL','2.1') + ('GSL', '2.1') ] runtest = 'check' diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-0.3.0-CrayGNU-2016.03.eb b/easybuild/easyconfigs/b/Bazel/Bazel-0.3.0-CrayGNU-2016.03.eb index 2490a42529..b13a4f1946 100644 --- a/easybuild/easyconfigs/b/Bazel/Bazel-0.3.0-CrayGNU-2016.03.eb +++ b/easybuild/easyconfigs/b/Bazel/Bazel-0.3.0-CrayGNU-2016.03.eb @@ -22,7 +22,7 @@ cmds_map = [('.*', "JAVA_VERSION=1.8 CC=gcc CXX=g++ ./compile.sh")] files_to_copy = [(['output/bazel'], 'bin')] -sanity_check_paths={ +sanity_check_paths = { 'files': ['bin/bazel'], 'dirs': ['bin'], } diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-0.4.4.eb b/easybuild/easyconfigs/b/Bazel/Bazel-0.4.4.eb index dd70600323..5bfa2535aa 100644 --- a/easybuild/easyconfigs/b/Bazel/Bazel-0.4.4.eb +++ b/easybuild/easyconfigs/b/Bazel/Bazel-0.4.4.eb @@ -23,7 +23,7 @@ cmds_map = [('.*', "./compile.sh")] files_to_copy = [(['output/bazel'], 'bin')] -sanity_check_paths={ +sanity_check_paths = { 'files': ['bin/bazel'], 'dirs': [], } diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.60.0-CrayGNU-2016.03-Python-2.7.11.eb b/easybuild/easyconfigs/b/Boost/Boost-1.60.0-CrayGNU-2016.03-Python-2.7.11.eb index 18a7a4b744..b906f81abf 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.60.0-CrayGNU-2016.03-Python-2.7.11.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.60.0-CrayGNU-2016.03-Python-2.7.11.eb @@ -25,6 +25,6 @@ dependencies = [ # also build boost_mpi boost_mpi = True -osdependencies = [('zlib-devel','zlib1g-dev')] +osdependencies = [('zlib-devel', 'zlib1g-dev')] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/c/Caffe/Caffe-rc3-foss-2016a-CUDA-7.5.18-Python-2.7.11.eb b/easybuild/easyconfigs/c/Caffe/Caffe-rc3-foss-2016a-CUDA-7.5.18-Python-2.7.11.eb index ef1b4dd449..e1484d4027 100644 --- a/easybuild/easyconfigs/c/Caffe/Caffe-rc3-foss-2016a-CUDA-7.5.18-Python-2.7.11.eb +++ b/easybuild/easyconfigs/c/Caffe/Caffe-rc3-foss-2016a-CUDA-7.5.18-Python-2.7.11.eb @@ -48,7 +48,7 @@ modextrapaths = {'PYTHONPATH': ['python'] } sanity_check_paths = { 'files': ['bin/caffe'] + - ['lib/%s' % x for x in ['libcaffe.so','libproto.a']] + + ['lib/%s' % x for x in ['libcaffe.so', 'libproto.a']] + ['python/caffe/_caffe.so'] + ['include/caffe/proto/caffe.pb.h'], 'dirs': [], diff --git a/easybuild/easyconfigs/c/Commet/Commet-20150415-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/c/Commet/Commet-20150415-foss-2016a-Python-2.7.11.eb index 549296f08e..a2bd44831e 100644 --- a/easybuild/easyconfigs/c/Commet/Commet-20150415-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/c/Commet/Commet-20150415-foss-2016a-Python-2.7.11.eb @@ -21,7 +21,7 @@ dependencies = [ ('Python', '2.7.11'), ] -files_to_copy = ["bin","doc","include","ABCDE_bench",(["Commet.py"],'bin')] +files_to_copy = ['bin', 'doc', 'include', 'ABCDE_bench', (['Commet.py'], 'bin')] sanity_check_paths = { 'files': ['bin/%s' % binfile for binfile in ['Commet.py', 'bvop', 'compare_reads', diff --git a/easybuild/easyconfigs/c/CrossTalkZ/CrossTalkZ-1.4-foss-2016a.eb b/easybuild/easyconfigs/c/CrossTalkZ/CrossTalkZ-1.4-foss-2016a.eb index 2facea57d9..e56c03bf3f 100644 --- a/easybuild/easyconfigs/c/CrossTalkZ/CrossTalkZ-1.4-foss-2016a.eb +++ b/easybuild/easyconfigs/c/CrossTalkZ/CrossTalkZ-1.4-foss-2016a.eb @@ -19,7 +19,7 @@ sources = ['%(name)s_%(version)s.tgz'] dependencies = [('Boost', '1.60.0')] -builddependencies = [('CMake', '3.4.3',)] +builddependencies = [('CMake', '3.4.3')] start_dir = 'src' diff --git a/easybuild/easyconfigs/g/GSL/GSL-2.1-CrayGNU-2015.11.eb b/easybuild/easyconfigs/g/GSL/GSL-2.1-CrayGNU-2015.11.eb index 378ea5f63e..634f2c0cf8 100644 --- a/easybuild/easyconfigs/g/GSL/GSL-2.1-CrayGNU-2015.11.eb +++ b/easybuild/easyconfigs/g/GSL/GSL-2.1-CrayGNU-2015.11.eb @@ -16,7 +16,7 @@ sources = [SOURCELOWER_TAR_GZ] configopts = "--with-pic" -sanity_check_paths={ +sanity_check_paths = { 'files': ['lib/libgsl.so', 'lib/libgsl.a'], 'dirs': ['include'], } diff --git a/easybuild/easyconfigs/g/gtest/gtest-1.7.0-CrayGNU-2015.11.eb b/easybuild/easyconfigs/g/gtest/gtest-1.7.0-CrayGNU-2015.11.eb index 3ebc1003fc..0d6323dcef 100644 --- a/easybuild/easyconfigs/g/gtest/gtest-1.7.0-CrayGNU-2015.11.eb +++ b/easybuild/easyconfigs/g/gtest/gtest-1.7.0-CrayGNU-2015.11.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'CrayGNU', 'version': '2015.11'} sources = [SOURCE_ZIP] source_urls = ['https://googletest.googlecode.com/files'] -sanity_check_paths={ +sanity_check_paths = { 'files': ['CMakeLists.txt', ], 'dirs': ['include', 'src'], } diff --git a/easybuild/easyconfigs/i/IMB/IMB-4.1-foss-2016a.eb b/easybuild/easyconfigs/i/IMB/IMB-4.1-foss-2016a.eb index 09fb675534..f6d0b1f028 100644 --- a/easybuild/easyconfigs/i/IMB/IMB-4.1-foss-2016a.eb +++ b/easybuild/easyconfigs/i/IMB/IMB-4.1-foss-2016a.eb @@ -24,7 +24,7 @@ files_to_copy = [(['src/IMB-*'], 'bin'), (['doc/IMB_Users_Guide.pdf'], 'doc')] sanity_check_paths = { 'files': ['bin/%s' % binfile for binfile in ['IMB-RMA', 'IMB-EXT', 'IMB-NBC', 'IMB-MPI1']], - 'dirs': ['bin','doc'] + 'dirs': ['bin', 'doc'] } moduleclass = 'perf' diff --git a/easybuild/easyconfigs/i/IOzone/IOzone-3.434-foss-2016a.eb b/easybuild/easyconfigs/i/IOzone/IOzone-3.434-foss-2016a.eb index 8bd48f9c2e..9e03233c20 100644 --- a/easybuild/easyconfigs/i/IOzone/IOzone-3.434-foss-2016a.eb +++ b/easybuild/easyconfigs/i/IOzone/IOzone-3.434-foss-2016a.eb @@ -19,17 +19,17 @@ buildopts = 'linux-AMD64' files_to_copy = [ (['src/current/iozone'], 'bin'), - (['src/current/%s' % docfile for docfile in ['gengnuplot.sh','report.pl','Changes.txt']],'share/doc'), - (['src/current/%s' % docfile for docfile in ['gengnuplot.sh','Generate_Graphs','gnu3d.dem']],'share'), + (['src/current/%s' % docfile for docfile in ['gengnuplot.sh', 'report.pl', 'Changes.txt']], 'share/doc'), + (['src/current/%s' % docfile for docfile in ['gengnuplot.sh', 'Generate_Graphs', 'gnu3d.dem']], 'share'), (['docs/iozone.1'], 'share/man/man1'), - (['docs/%s' % docfile for docfile in ['IOzone_msword_98.doc','IOzone_msword_98.pdf','Iozone_ps.gz','Run_rules.doc']], + (['docs/%s' % docfile for docfile in ['IOzone_msword_98.doc', 'IOzone_msword_98.pdf', 'Iozone_ps.gz', 'Run_rules.doc']], 'share/doc'), ] sanity_check_paths = { 'files': ['bin/iozone'], - 'dirs': ['bin','share/doc','share/man'] + 'dirs': ['bin', 'share/doc', 'share/man'] } moduleclass = 'tools' diff --git a/easybuild/easyconfigs/k/Kraken/Kraken-0.10.5-beta-foss-2016a-Perl-5.22.1.eb b/easybuild/easyconfigs/k/Kraken/Kraken-0.10.5-beta-foss-2016a-Perl-5.22.1.eb index 4bb09cbfe2..9a8c7fce6d 100644 --- a/easybuild/easyconfigs/k/Kraken/Kraken-0.10.5-beta-foss-2016a-Perl-5.22.1.eb +++ b/easybuild/easyconfigs/k/Kraken/Kraken-0.10.5-beta-foss-2016a-Perl-5.22.1.eb @@ -2,7 +2,7 @@ easyblock = 'PackedBinary' name = 'Kraken' version = '0.10.5-beta' -versionsuffix='-Perl-%(perlver)s' +versionsuffix ='-Perl-%(perlver)s' homepage = 'http://ccb.jhu.edu/software/kraken/' description = """Kraken is a system for assigning taxonomic labels to short DNA sequences, diff --git a/easybuild/easyconfigs/k/Kraken/Kraken-0.10.5-beta-foss-2016b-Perl-5.24.0.eb b/easybuild/easyconfigs/k/Kraken/Kraken-0.10.5-beta-foss-2016b-Perl-5.24.0.eb index 8814a7c92c..fc353606af 100644 --- a/easybuild/easyconfigs/k/Kraken/Kraken-0.10.5-beta-foss-2016b-Perl-5.24.0.eb +++ b/easybuild/easyconfigs/k/Kraken/Kraken-0.10.5-beta-foss-2016b-Perl-5.24.0.eb @@ -2,7 +2,7 @@ easyblock = 'PackedBinary' name = 'Kraken' version = '0.10.5-beta' -versionsuffix='-Perl-%(perlver)s' +versionsuffix ='-Perl-%(perlver)s' homepage = 'http://ccb.jhu.edu/software/kraken/' description = """Kraken is a system for assigning taxonomic labels to short DNA sequences, diff --git a/easybuild/easyconfigs/l/LevelDB/LevelDB-1.18-foss-2016a.eb b/easybuild/easyconfigs/l/LevelDB/LevelDB-1.18-foss-2016a.eb index f3fb0f0115..c5eee2ec3d 100644 --- a/easybuild/easyconfigs/l/LevelDB/LevelDB-1.18-foss-2016a.eb +++ b/easybuild/easyconfigs/l/LevelDB/LevelDB-1.18-foss-2016a.eb @@ -26,7 +26,7 @@ postinstallcmds=[ sanity_check_paths = { - 'files': ['include/leveldb/cache.h','include/leveldb/table.h', + 'files': ['include/leveldb/cache.h', 'include/leveldb/table.h', 'lib/libleveldb.a', 'lib/libleveldb.%s' % SHLIB_EXT], 'dirs': [], } diff --git a/easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-2015.06.eb b/easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-2015.06.eb index 173c7dbd1e..534b88561a 100644 --- a/easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-2015.06.eb +++ b/easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-2015.06.eb @@ -18,7 +18,7 @@ sanity_check_paths = { ['include/libint/hrr_header.h', 'include/libint/vrr_header.h'] + ['lib/lib%s.a' % x for x in ['deriv', 'int', 'r12']] + ['lib/lib%s.so' % x for x in ['deriv', 'int', 'r12']], - 'dirs':[], + 'dirs': [], } moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-2015.11.eb b/easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-2015.11.eb index ef47d32bbf..deb2164941 100644 --- a/easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-2015.11.eb +++ b/easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-2015.11.eb @@ -18,7 +18,7 @@ sanity_check_paths = { ['include/libint/hrr_header.h', 'include/libint/vrr_header.h'] + ['lib/lib%s.a' % x for x in ['deriv', 'int', 'r12']] + ['lib/lib%s.so' % x for x in ['deriv', 'int', 'r12']], - 'dirs':[], + 'dirs': [], } moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/Loki/Loki-0.1.7-foss-2016a.eb b/easybuild/easyconfigs/l/Loki/Loki-0.1.7-foss-2016a.eb index 07ee053893..9297cefc7a 100644 --- a/easybuild/easyconfigs/l/Loki/Loki-0.1.7-foss-2016a.eb +++ b/easybuild/easyconfigs/l/Loki/Loki-0.1.7-foss-2016a.eb @@ -16,7 +16,7 @@ skipsteps = ['configure'] installopts = "prefix=%(installdir)s" -sanity_check_paths={ +sanity_check_paths = { 'files': ['lib/libloki.a', 'lib/libloki.%s' % SHLIB_EXT, 'lib/libloki.%s.%%(version)s' % SHLIB_EXT], 'dirs': ['include/loki'], } diff --git a/easybuild/easyconfigs/l/Loki/Loki-0.1.7-foss-2016b.eb b/easybuild/easyconfigs/l/Loki/Loki-0.1.7-foss-2016b.eb index 63a5c28598..9301b8c32d 100644 --- a/easybuild/easyconfigs/l/Loki/Loki-0.1.7-foss-2016b.eb +++ b/easybuild/easyconfigs/l/Loki/Loki-0.1.7-foss-2016b.eb @@ -16,7 +16,7 @@ skipsteps = ['configure'] installopts = "prefix=%(installdir)s" -sanity_check_paths={ +sanity_check_paths = { 'files': ['lib/libloki.a', 'lib/libloki.%s' % SHLIB_EXT, 'lib/libloki.%s.%%(version)s' % SHLIB_EXT], 'dirs': ['include/loki'], } diff --git a/easybuild/easyconfigs/l/Loki/Loki-0.1.7-intel-2016a.eb b/easybuild/easyconfigs/l/Loki/Loki-0.1.7-intel-2016a.eb index 353bbfd940..fb4f7b4645 100644 --- a/easybuild/easyconfigs/l/Loki/Loki-0.1.7-intel-2016a.eb +++ b/easybuild/easyconfigs/l/Loki/Loki-0.1.7-intel-2016a.eb @@ -16,7 +16,7 @@ skipsteps = ['configure'] installopts = "prefix=%(installdir)s" -sanity_check_paths={ +sanity_check_paths = { 'files': ['lib/libloki.a', 'lib/libloki.%s' % SHLIB_EXT, 'lib/libloki.%s.%%(version)s' % SHLIB_EXT], 'dirs': ['include/loki'], } diff --git a/easybuild/easyconfigs/l/Loki/Loki-0.1.7-intel-2016b.eb b/easybuild/easyconfigs/l/Loki/Loki-0.1.7-intel-2016b.eb index a25e47aac4..a61396897c 100644 --- a/easybuild/easyconfigs/l/Loki/Loki-0.1.7-intel-2016b.eb +++ b/easybuild/easyconfigs/l/Loki/Loki-0.1.7-intel-2016b.eb @@ -16,7 +16,7 @@ skipsteps = ['configure'] installopts = "prefix=%(installdir)s" -sanity_check_paths={ +sanity_check_paths = { 'files': ['lib/libloki.a', 'lib/libloki.%s' % SHLIB_EXT, 'lib/libloki.%s.%%(version)s' % SHLIB_EXT], 'dirs': ['include/loki'], } diff --git a/easybuild/easyconfigs/l/libpsortb/libpsortb-1.0-foss-2016a.eb b/easybuild/easyconfigs/l/libpsortb/libpsortb-1.0-foss-2016a.eb index 41eb85171a..49ee159605 100644 --- a/easybuild/easyconfigs/l/libpsortb/libpsortb-1.0-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libpsortb/libpsortb-1.0-foss-2016a.eb @@ -13,8 +13,8 @@ source_urls = ['http://www.psort.org/download/'] sources = [SOURCELOWER_TAR_GZ] sanity_check_paths = { - 'files': ['lib64/libhmmer.so','lib64/libsvmloc.so'], + 'files': ['lib64/libhmmer.so', 'lib64/libsvmloc.so'], 'dirs': [], } -moduleclass = 'bio' \ No newline at end of file +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MDSplus/MDSplus-7.0.67-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb b/easybuild/easyconfigs/m/MDSplus/MDSplus-7.0.67-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb index de510f4adc..9b8ad14bb5 100644 --- a/easybuild/easyconfigs/m/MDSplus/MDSplus-7.0.67-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb +++ b/easybuild/easyconfigs/m/MDSplus/MDSplus-7.0.67-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb @@ -11,7 +11,7 @@ description = """MDSplus is a set of software tools for data acquisition and sto toolchain = {'name': 'foss', 'version': '2016a'} source_urls = ['https://github.com/%(name)s/%(namelower)s/archive'] -sources = ['stable_release-%s.zip' % version.replace('.','-')] +sources = ['stable_release-%s.zip' % version.replace('.', '-')] dependencies = [ ('Java', '1.7.0_79', '', True), diff --git a/easybuild/easyconfigs/m/MDSplus/MDSplus-7.0.67-goolf-1.5.16-Java-1.7.0_79-Python-2.7.9.eb b/easybuild/easyconfigs/m/MDSplus/MDSplus-7.0.67-goolf-1.5.16-Java-1.7.0_79-Python-2.7.9.eb index 25d836f8e5..9296449814 100644 --- a/easybuild/easyconfigs/m/MDSplus/MDSplus-7.0.67-goolf-1.5.16-Java-1.7.0_79-Python-2.7.9.eb +++ b/easybuild/easyconfigs/m/MDSplus/MDSplus-7.0.67-goolf-1.5.16-Java-1.7.0_79-Python-2.7.9.eb @@ -11,7 +11,7 @@ description = """MDSplus is a set of software tools for data acquisition and sto toolchain = {'name': 'goolf', 'version': '1.5.16'} source_urls = ['https://github.com/%(name)s/%(namelower)s/archive'] -sources = ['stable_release-%s.zip' % version.replace('.','-')] +sources = ['stable_release-%s.zip' % version.replace('.', '-')] dependencies = [ ('Java', '1.7.0_79', '', True), diff --git a/easybuild/easyconfigs/m/MIGRATE-N/MIGRATE-N-4.2.8-foss-2016a.eb b/easybuild/easyconfigs/m/MIGRATE-N/MIGRATE-N-4.2.8-foss-2016a.eb index b6f05aeb5d..25e6d72da5 100644 --- a/easybuild/easyconfigs/m/MIGRATE-N/MIGRATE-N-4.2.8-foss-2016a.eb +++ b/easybuild/easyconfigs/m/MIGRATE-N/MIGRATE-N-4.2.8-foss-2016a.eb @@ -35,7 +35,7 @@ prebuildopts = 'make mpis && make clean && ' start_dir = 'src' sanity_check_paths = { - 'files': ['bin/%s' % x for x in ['migrate-n','migrate-n-mpi']], + 'files': ['bin/%s' % x for x in ['migrate-n', 'migrate-n-mpi']], 'dirs': ['man'], } diff --git a/easybuild/easyconfigs/m/MPJ-Express/MPJ-Express-0.44-foss-2016a-Java-1.8.0_92.eb b/easybuild/easyconfigs/m/MPJ-Express/MPJ-Express-0.44-foss-2016a-Java-1.8.0_92.eb index c8deee658d..3bb9c9fb71 100644 --- a/easybuild/easyconfigs/m/MPJ-Express/MPJ-Express-0.44-foss-2016a-Java-1.8.0_92.eb +++ b/easybuild/easyconfigs/m/MPJ-Express/MPJ-Express-0.44-foss-2016a-Java-1.8.0_92.eb @@ -16,7 +16,7 @@ description = """MPJ Express is an open source Java message passing library that toolchain = {'name': 'foss', 'version': '2016a'} source_urls = ['https://sourceforge.net/projects/mpjexpress/files/releases/'] -sources = ['mpj-v%s.tar.gz' % (version.replace('.','_'))] +sources = ['mpj-v%s.tar.gz' % (version.replace('.', '_'))] builddependencies = [('CMake', '3.5.2')] diff --git a/easybuild/easyconfigs/m/MPJ-Express/MPJ-Express-0.44-goolf-1.4.10-Java-1.7.0_75.eb b/easybuild/easyconfigs/m/MPJ-Express/MPJ-Express-0.44-goolf-1.4.10-Java-1.7.0_75.eb index 273c10ebde..8c2cfb12b9 100644 --- a/easybuild/easyconfigs/m/MPJ-Express/MPJ-Express-0.44-goolf-1.4.10-Java-1.7.0_75.eb +++ b/easybuild/easyconfigs/m/MPJ-Express/MPJ-Express-0.44-goolf-1.4.10-Java-1.7.0_75.eb @@ -15,7 +15,7 @@ description = """MPJ Express is an open source Java message passing library that toolchain = {'name': 'goolf', 'version': '1.4.10'} source_urls = ['https://sourceforge.net/projects/mpjexpress/files/releases/'] -sources = ['mpj-v%s.tar.gz' % (version.replace('.','_'))] +sources = ['mpj-v%s.tar.gz' % (version.replace('.', '_'))] java = 'Java' javaver = '1.7.0_75' diff --git a/easybuild/easyconfigs/m/MaCH/MaCH-1.0.18.c-goolf-1.4.10.eb b/easybuild/easyconfigs/m/MaCH/MaCH-1.0.18.c-goolf-1.4.10.eb index 3c30407be2..b454981b04 100644 --- a/easybuild/easyconfigs/m/MaCH/MaCH-1.0.18.c-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/m/MaCH/MaCH-1.0.18.c-goolf-1.4.10.eb @@ -16,7 +16,7 @@ description = """ MaCH 1.0 is a Markov Chain based haplotyper. It can resolve lo toolchain = {'name': 'goolf', 'version': '1.4.10'} source_urls = ['http://www.sph.umich.edu/csg/abecasis/MaCH/download/'] -sources = ['%s.%s.source.tgz' % (name.lower(), version.replace(".c",""))] +sources = ['%s.%s.source.tgz' % (name.lower(), version.replace('.c', ''))] dependencies = [('zlib', '1.2.8')] diff --git a/easybuild/easyconfigs/m/MaCH/MaCH-1.0.18.c-ictce-6.2.5.eb b/easybuild/easyconfigs/m/MaCH/MaCH-1.0.18.c-ictce-6.2.5.eb index 250398115a..e008b133f5 100644 --- a/easybuild/easyconfigs/m/MaCH/MaCH-1.0.18.c-ictce-6.2.5.eb +++ b/easybuild/easyconfigs/m/MaCH/MaCH-1.0.18.c-ictce-6.2.5.eb @@ -16,7 +16,7 @@ description = """ MaCH 1.0 is a Markov Chain based haplotyper. It can resolve lo toolchain = {'name': 'ictce', 'version': '6.2.5'} source_urls = ['http://www.sph.umich.edu/csg/abecasis/MaCH/download/'] -sources = ['%s.%s.source.tgz' % (name.lower(), version.replace(".c",""))] +sources = ['%s.%s.source.tgz' % (name.lower(), version.replace('.c', ''))] dependencies = [('zlib', '1.2.8')] diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-foss-2016a.eb b/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-foss-2016a.eb index fb2151e5df..231d3ed99e 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-foss-2016a.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-foss-2016a.eb @@ -32,7 +32,7 @@ builddependencies = [ dependencies = [ ('libxml2', '2.9.3'), ('libdrm', '2.4.67'), - ('libX11', '1.6.3',), + ('libX11', '1.6.3'), ('libXext', '1.3.3'), ('libXfixes', '5.0.1'), ('libXdamage', '1.1.4'), @@ -57,7 +57,7 @@ prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm:$CPATH" ' sanity_check_paths = { 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libOSMesa.%s' % SHLIB_EXT, 'lib/libGLESv1_CM.%s' % SHLIB_EXT, - 'lib/libGLESv2.%s' %SHLIB_EXT, 'include/GL/glext.h', 'include/GL/gl_mangle.h', 'include/GL/glx.h', + 'lib/libGLESv2.%s' % SHLIB_EXT, 'include/GL/glext.h', 'include/GL/gl_mangle.h', 'include/GL/glx.h', 'include/GL/osmesa.h', 'include/GL/wglext.h', 'include/GL/gl.h', 'include/GL/glxext.h', 'include/GL/glx_mangle.h', 'include/GLES/gl.h', 'include/GLES2/gl2.h', 'include/GLES3/gl3.h'], 'dirs': [] diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-gimkl-2.11.5.eb b/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-gimkl-2.11.5.eb index 171b47710c..7b54c5a0b7 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-gimkl-2.11.5.eb @@ -32,7 +32,7 @@ builddependencies = [ dependencies = [ ('libxml2', '2.9.3'), ('libdrm', '2.4.67'), - ('libX11', '1.6.3',), + ('libX11', '1.6.3'), ('libXext', '1.3.3'), ('libXfixes', '5.0.1'), ('libXdamage', '1.1.4'), @@ -57,7 +57,7 @@ prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm:$CPATH" ' sanity_check_paths = { 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libOSMesa.%s' % SHLIB_EXT, 'lib/libGLESv1_CM.%s' % SHLIB_EXT, - 'lib/libGLESv2.%s' %SHLIB_EXT, 'include/GL/glext.h', 'include/GL/gl_mangle.h', 'include/GL/glx.h', + 'lib/libGLESv2.%s' % SHLIB_EXT, 'include/GL/glext.h', 'include/GL/gl_mangle.h', 'include/GL/glx.h', 'include/GL/osmesa.h', 'include/GL/wglext.h', 'include/GL/gl.h', 'include/GL/glxext.h', 'include/GL/glx_mangle.h', 'include/GLES/gl.h', 'include/GLES2/gl2.h', 'include/GLES3/gl3.h'], 'dirs': [] diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-intel-2016a.eb b/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-intel-2016a.eb index 3282ad740c..ecd0aaeeb3 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-intel-2016a.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-intel-2016a.eb @@ -32,7 +32,7 @@ builddependencies = [ dependencies = [ ('libxml2', '2.9.3'), ('libdrm', '2.4.67'), - ('libX11', '1.6.3',), + ('libX11', '1.6.3'), ('libXext', '1.3.3'), ('libXfixes', '5.0.1'), ('libXdamage', '1.1.4'), @@ -57,7 +57,7 @@ prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm:$CPATH" ' sanity_check_paths = { 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libOSMesa.%s' % SHLIB_EXT, 'lib/libGLESv1_CM.%s' % SHLIB_EXT, - 'lib/libGLESv2.%s' %SHLIB_EXT, 'include/GL/glext.h', 'include/GL/gl_mangle.h', 'include/GL/glx.h', + 'lib/libGLESv2.%s' % SHLIB_EXT, 'include/GL/glext.h', 'include/GL/gl_mangle.h', 'include/GL/glx.h', 'include/GL/osmesa.h', 'include/GL/wglext.h', 'include/GL/gl.h', 'include/GL/glxext.h', 'include/GL/glx_mangle.h', 'include/GLES/gl.h', 'include/GLES2/gl2.h', 'include/GLES3/gl3.h'], 'dirs': [] diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-11.2.1-foss-2016a.eb b/easybuild/easyconfigs/m/Mesa/Mesa-11.2.1-foss-2016a.eb index a919f2eab9..18bebf34fd 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-11.2.1-foss-2016a.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-11.2.1-foss-2016a.eb @@ -32,7 +32,7 @@ builddependencies = [ dependencies = [ ('libxml2', '2.9.3'), ('libdrm', '2.4.68'), - ('libX11', '1.6.3',), + ('libX11', '1.6.3'), ('libXext', '1.3.3'), ('libXfixes', '5.0.1'), ('libXdamage', '1.1.4'), @@ -57,7 +57,7 @@ prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm:$CPATH" ' sanity_check_paths = { 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libOSMesa.%s' % SHLIB_EXT, 'lib/libGLESv1_CM.%s' % SHLIB_EXT, - 'lib/libGLESv2.%s' %SHLIB_EXT, 'include/GL/glext.h', 'include/GL/gl_mangle.h', 'include/GL/glx.h', + 'lib/libGLESv2.%s' % SHLIB_EXT, 'include/GL/glext.h', 'include/GL/gl_mangle.h', 'include/GL/glx.h', 'include/GL/osmesa.h', 'include/GL/wglext.h', 'include/GL/gl.h', 'include/GL/glxext.h', 'include/GL/glx_mangle.h', 'include/GLES/gl.h', 'include/GLES2/gl2.h', 'include/GLES3/gl3.h'], 'dirs': [] diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-11.2.1-intel-2016a.eb b/easybuild/easyconfigs/m/Mesa/Mesa-11.2.1-intel-2016a.eb index 54f7d8a513..09f90b3879 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-11.2.1-intel-2016a.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-11.2.1-intel-2016a.eb @@ -32,7 +32,7 @@ builddependencies = [ dependencies = [ ('libxml2', '2.9.3'), ('libdrm', '2.4.68'), - ('libX11', '1.6.3',), + ('libX11', '1.6.3'), ('libXext', '1.3.3'), ('libXfixes', '5.0.1'), ('libXdamage', '1.1.4'), @@ -57,7 +57,7 @@ prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm:$CPATH" ' sanity_check_paths = { 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libOSMesa.%s' % SHLIB_EXT, 'lib/libGLESv1_CM.%s' % SHLIB_EXT, - 'lib/libGLESv2.%s' %SHLIB_EXT, 'include/GL/glext.h', 'include/GL/gl_mangle.h', 'include/GL/glx.h', + 'lib/libGLESv2.%s' % SHLIB_EXT, 'include/GL/glext.h', 'include/GL/gl_mangle.h', 'include/GL/glx.h', 'include/GL/osmesa.h', 'include/GL/wglext.h', 'include/GL/gl.h', 'include/GL/glxext.h', 'include/GL/glx_mangle.h', 'include/GLES/gl.h', 'include/GLES2/gl2.h', 'include/GLES3/gl3.h'], 'dirs': [] diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-12.0.2-foss-2016b.eb b/easybuild/easyconfigs/m/Mesa/Mesa-12.0.2-foss-2016b.eb index 8152b5bb38..b8a0ae2d3f 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-12.0.2-foss-2016b.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-12.0.2-foss-2016b.eb @@ -50,7 +50,7 @@ configopts += " --with-osmesa-bits=32 --enable-texture-float --enable-llvm-share sanity_check_paths = { 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libOSMesa.%s' % SHLIB_EXT, 'lib/libGLESv1_CM.%s' % SHLIB_EXT, - 'lib/libGLESv2.%s' %SHLIB_EXT, 'include/GL/glext.h', 'include/GL/gl_mangle.h', 'include/GL/glx.h', + 'lib/libGLESv2.%s' % SHLIB_EXT, 'include/GL/glext.h', 'include/GL/gl_mangle.h', 'include/GL/glx.h', 'include/GL/osmesa.h', 'include/GL/wglext.h', 'include/GL/gl.h', 'include/GL/glxext.h', 'include/GL/glx_mangle.h', 'include/GLES/gl.h', 'include/GLES2/gl2.h', 'include/GLES3/gl3.h'], 'dirs': [] diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-12.0.2-intel-2016b.eb b/easybuild/easyconfigs/m/Mesa/Mesa-12.0.2-intel-2016b.eb index 90fd4b0810..d9578ef42b 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-12.0.2-intel-2016b.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-12.0.2-intel-2016b.eb @@ -50,7 +50,7 @@ configopts += " --with-osmesa-bits=32 --enable-texture-float --enable-llvm-share sanity_check_paths = { 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libOSMesa.%s' % SHLIB_EXT, 'lib/libGLESv1_CM.%s' % SHLIB_EXT, - 'lib/libGLESv2.%s' %SHLIB_EXT, 'include/GL/glext.h', 'include/GL/gl_mangle.h', 'include/GL/glx.h', + 'lib/libGLESv2.%s' % SHLIB_EXT, 'include/GL/glext.h', 'include/GL/gl_mangle.h', 'include/GL/glx.h', 'include/GL/osmesa.h', 'include/GL/wglext.h', 'include/GL/gl.h', 'include/GL/glxext.h', 'include/GL/glx_mangle.h', 'include/GLES/gl.h', 'include/GLES2/gl2.h', 'include/GLES3/gl3.h'], 'dirs': [] diff --git a/easybuild/easyconfigs/m/Metal/Metal-2011-03-25-foss-2016a.eb b/easybuild/easyconfigs/m/Metal/Metal-2011-03-25-foss-2016a.eb index 6f7d234353..04f7962ec3 100644 --- a/easybuild/easyconfigs/m/Metal/Metal-2011-03-25-foss-2016a.eb +++ b/easybuild/easyconfigs/m/Metal/Metal-2011-03-25-foss-2016a.eb @@ -16,11 +16,11 @@ source_urls = ['http://csg.sph.umich.edu/abecasis/Metal/download/'] toolchain = {'name': 'foss', 'version': '2016a'} toolchainopts = {'pic': True} -patches=['Metal-%(version)s_Makefile.patch'] +patches = ['Metal-%(version)s_Makefile.patch'] skipsteps=['configure'] -buildopts='all' +buildopts = 'all' installopts = 'INSTALLDIR=%(installdir)s/bin' diff --git a/easybuild/easyconfigs/m/Minimac2/Minimac2-2014.9.15-goolf-1.7.20.eb b/easybuild/easyconfigs/m/Minimac2/Minimac2-2014.9.15-goolf-1.7.20.eb index 79a432c81f..50e766c0ce 100644 --- a/easybuild/easyconfigs/m/Minimac2/Minimac2-2014.9.15-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/m/Minimac2/Minimac2-2014.9.15-goolf-1.7.20.eb @@ -3,7 +3,7 @@ # sciCORE - University of Basel # SIB Swiss Institute of Bioinformatics -easyblock='MakeCp' +easyblock = 'MakeCp' name = 'Minimac2' version = '2014.9.15' diff --git a/easybuild/easyconfigs/m/magma/magma-2.0.0-CrayGNU-2015.11.eb b/easybuild/easyconfigs/m/magma/magma-2.0.0-CrayGNU-2015.11.eb index fdd34a04e1..ba77602cd4 100644 --- a/easybuild/easyconfigs/m/magma/magma-2.0.0-CrayGNU-2015.11.eb +++ b/easybuild/easyconfigs/m/magma/magma-2.0.0-CrayGNU-2015.11.eb @@ -21,7 +21,7 @@ skipsteps = ['configure'] preinstallopts = "export EBINSTALLPREFIX=%(installdir)s && " -sanity_check_paths={ +sanity_check_paths = { 'files': ['lib/libmagma.so', 'lib/libmagma.a'], 'dirs': ['include'], } diff --git a/easybuild/easyconfigs/n/numpy/numpy-1.9.2-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/n/numpy/numpy-1.9.2-intel-2016b-Python-2.7.12.eb index b0f7a1aaf1..4cb1525158 100644 --- a/easybuild/easyconfigs/n/numpy/numpy-1.9.2-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/n/numpy/numpy-1.9.2-intel-2016b-Python-2.7.12.eb @@ -20,7 +20,7 @@ dependencies = [ ('Python', '2.7.12'), ] -# need to use pip rather than regular 'setup.py install,' +# need to use pip rather than regular 'setup.py install' # to ensure that this numpy wins over the one in the Python installation; # using easy_install does not work... use_pip = True diff --git a/easybuild/easyconfigs/o/OBITools/OBITools-1.2.9-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/o/OBITools/OBITools-1.2.9-foss-2016a-Python-2.7.11.eb index d30d6266ab..fbe8f5cfab 100644 --- a/easybuild/easyconfigs/o/OBITools/OBITools-1.2.9-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/o/OBITools/OBITools-1.2.9-foss-2016a-Python-2.7.11.eb @@ -27,8 +27,8 @@ dependencies = [ options = {'modulename': 'obitools'} sanity_check_paths = { - 'files': ["bin/%s" % binfile for binfile in ['ali2consensus','ecotag','obiaddtaxids','obicount','obistat']], - 'dirs': ['bin','lib/python%(pyshortver)s/site-packages/obitools'], + 'files': ['bin/%s' % binfile for binfile in ['ali2consensus', 'ecotag', 'obiaddtaxids', 'obicount', 'obistat']], + 'dirs': ['bin', 'lib/python%(pyshortver)s/site-packages/obitools'], } moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/PARI-GP/PARI-GP-2.7.6-foss-2016a.eb b/easybuild/easyconfigs/p/PARI-GP/PARI-GP-2.7.6-foss-2016a.eb index b46c6bff0d..c67cbf7de9 100644 --- a/easybuild/easyconfigs/p/PARI-GP/PARI-GP-2.7.6-foss-2016a.eb +++ b/easybuild/easyconfigs/p/PARI-GP/PARI-GP-2.7.6-foss-2016a.eb @@ -25,10 +25,9 @@ dependencies = [ ] sanity_check_paths = { - 'files': - ["bin/%s" % binfile for binfile in ['gp','gp-2.7','gphelp','tex2mail']] + - [ "include/pari/%s" % incfile for incfile in ['pari.h','genpari.h']], - 'dirs': ["bin","include"] + 'files': ['bin/%s' % binfile for binfile in ['gp', 'gp-2.7', 'gphelp', 'tex2mail']] + + ['include/pari/%s' % incfile for incfile in ['pari.h', 'genpari.h']], + 'dirs': ['bin', 'include'] } moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/PGDSpider/PGDSpider-2.1.0.3-Java-1.7.0_80.eb b/easybuild/easyconfigs/p/PGDSpider/PGDSpider-2.1.0.3-Java-1.7.0_80.eb index 89ae4df712..32e6adc9b7 100644 --- a/easybuild/easyconfigs/p/PGDSpider/PGDSpider-2.1.0.3-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/p/PGDSpider/PGDSpider-2.1.0.3-Java-1.7.0_80.eb @@ -3,7 +3,7 @@ # sciCORE - University of Basel # SIB Swiss Institute of Bioinformatics -easyblock='Tarball' +easyblock = 'Tarball' name = "PGDSpider" version = "2.1.0.3" diff --git a/easybuild/easyconfigs/p/PLAST/PLAST-2.3.1-foss-2016a-Java-1.8.0_92.eb b/easybuild/easyconfigs/p/PLAST/PLAST-2.3.1-foss-2016a-Java-1.8.0_92.eb index bb22d3db40..61cae6188e 100644 --- a/easybuild/easyconfigs/p/PLAST/PLAST-2.3.1-foss-2016a-Java-1.8.0_92.eb +++ b/easybuild/easyconfigs/p/PLAST/PLAST-2.3.1-foss-2016a-Java-1.8.0_92.eb @@ -10,7 +10,7 @@ description = """PLAST is a parallel alignment search tool for comparing large p toolchain = {'name': 'foss', 'version': '2016a'} source_urls = ['https://github.com/PLAST-software/plast-library/releases/download/v%(version)s/'] -sources=['%(namelower)s_source_v%(version)s.tar.gz'] +sources = ['%(namelower)s_source_v%(version)s.tar.gz'] builddependencies = [ ('CMake', '3.5.2'), @@ -26,4 +26,4 @@ sanity_check_paths = { 'dirs': ['include', 'include/algo', 'include/alignment', 'include/misc'], } -moduleclass = 'bio' \ No newline at end of file +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/PSORTb/PSORTb-3.0.4-foss-2016a-Perl-5.22.1.eb b/easybuild/easyconfigs/p/PSORTb/PSORTb-3.0.4-foss-2016a-Perl-5.22.1.eb index 79449c632c..b5baf3a55c 100644 --- a/easybuild/easyconfigs/p/PSORTb/PSORTb-3.0.4-foss-2016a-Perl-5.22.1.eb +++ b/easybuild/easyconfigs/p/PSORTb/PSORTb-3.0.4-foss-2016a-Perl-5.22.1.eb @@ -18,10 +18,10 @@ patches = [ dependencies = [ ('Perl', '5.22.1'), - ('libpsortb','1.0'), - ('BioPerl','1.6.924','-Perl-5.22.1'), - ('BLAST','2.2.26', '-Linux_x86_64', True), - ('pftoolsV3','20160324'), + ('libpsortb', '1.0'), + ('BioPerl', '1.6.924', '-Perl-5.22.1'), + ('BLAST', '2.2.26', '-Linux_x86_64', True), + ('pftoolsV3', '20160324'), ] options = {'modulename': 'Bio::Tools::PSort'} diff --git a/easybuild/easyconfigs/p/Paraver/Paraver-4.4.5-GCC-4.7.3.eb b/easybuild/easyconfigs/p/Paraver/Paraver-4.4.5-GCC-4.7.3.eb index 298d4bf94a..aabbb0dc24 100644 --- a/easybuild/easyconfigs/p/Paraver/Paraver-4.4.5-GCC-4.7.3.eb +++ b/easybuild/easyconfigs/p/Paraver/Paraver-4.4.5-GCC-4.7.3.eb @@ -24,6 +24,6 @@ dependencies = [ # http://www.bsc.es/computer-sciences/performance-tools/downloads # Requires input of email address for download -sources = ['%(namelower)s-' + "sources" +'-%(version)s.tar.bz2'] +sources = ['%(namelower)s-' + "sources" + '-%(version)s.tar.bz2'] moduleclass = 'perf' diff --git a/easybuild/easyconfigs/p/Paraver/Paraver-4.5.6-foss-2015a.eb b/easybuild/easyconfigs/p/Paraver/Paraver-4.5.6-foss-2015a.eb index 646562570d..f5a5940d0d 100644 --- a/easybuild/easyconfigs/p/Paraver/Paraver-4.5.6-foss-2015a.eb +++ b/easybuild/easyconfigs/p/Paraver/Paraver-4.5.6-foss-2015a.eb @@ -27,6 +27,6 @@ dependencies = [ # http://www.bsc.es/computer-sciences/performance-tools/downloads # Requires input of email address for download -sources = ['%(namelower)s-' + "sources" +'-%(version)s.tar.gz'] +sources = ['%(namelower)s-' + "sources" + '-%(version)s.tar.gz'] moduleclass = 'perf' diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-3.2.0-foss-2016a-Python-2.7.11-freetype-2.6.3.eb b/easybuild/easyconfigs/p/Pillow/Pillow-3.2.0-foss-2016a-Python-2.7.11-freetype-2.6.3.eb index 16cea8d33b..c3b096e84c 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-3.2.0-foss-2016a-Python-2.7.11-freetype-2.6.3.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-3.2.0-foss-2016a-Python-2.7.11-freetype-2.6.3.eb @@ -18,7 +18,7 @@ versionsuffix += '-freetype-%s' % freetype_ver dependencies = [ ('Python', '2.7.11'), - ('libjpeg-turbo', '1.4.2','-NASM-2.12.01'), + ('libjpeg-turbo', '1.4.2', '-NASM-2.12.01'), ('libpng', '1.6.21'), ('zlib', '1.2.8'), ('LibTIFF', '4.0.6'), diff --git a/easybuild/easyconfigs/p/Platanus/Platanus-1.2.4-goolf-1.7.20.eb b/easybuild/easyconfigs/p/Platanus/Platanus-1.2.4-goolf-1.7.20.eb index 9f312bdd69..7dffcdb458 100644 --- a/easybuild/easyconfigs/p/Platanus/Platanus-1.2.4-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/p/Platanus/Platanus-1.2.4-goolf-1.7.20.eb @@ -20,11 +20,11 @@ sources = ['%(name)s_v%(version)s.tar.gz'] buildopts = 'CXX="$CXX"' -files_to_copy = [(["platanus"],'bin'), "README", "LICENSE"] +files_to_copy = [(['platanus'], 'bin'), 'README', 'LICENSE'] sanity_check_paths = { - 'files': ["bin/platanus"], - 'dirs': [""], + 'files': ['bin/platanus'], + 'dirs': [], } moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/ProbABEL/ProbABEL-0.5.0.eb b/easybuild/easyconfigs/p/ProbABEL/ProbABEL-0.5.0.eb index 379bdbc80d..4c23222ada 100644 --- a/easybuild/easyconfigs/p/ProbABEL/ProbABEL-0.5.0.eb +++ b/easybuild/easyconfigs/p/ProbABEL/ProbABEL-0.5.0.eb @@ -21,7 +21,7 @@ configopts = '--disable-latex-doc' postinstallcmds = ["mv %(installdir)s/etc/probabel_config.cfg.example %(installdir)s/etc/probabel_config.cfg"] sanity_check_paths = { - 'files': ['bin/probabel', 'bin/pacoxph', 'bin/palinear', 'bin/palogist','etc/probabel_config.cfg'], + 'files': ['bin/probabel', 'bin/pacoxph', 'bin/palinear', 'bin/palogist', 'etc/probabel_config.cfg'], 'dirs': ['share'], } diff --git a/easybuild/easyconfigs/p/PyGTS/PyGTS-0.3.1-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/PyGTS/PyGTS-0.3.1-foss-2016a-Python-2.7.11.eb index 1438b0e86a..13ffa9e09b 100644 --- a/easybuild/easyconfigs/p/PyGTS/PyGTS-0.3.1-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/PyGTS/PyGTS-0.3.1-foss-2016a-Python-2.7.11.eb @@ -17,14 +17,14 @@ sources = [SOURCELOWER_TAR_GZ] dependencies = [ ('Python', '2.7.11'), ('GLib', '2.48.0'), - ('GTS' ,'0.7.6'), + ('GTS', '0.7.6'), ] options = {'modulename': 'gts'} sanity_check_paths = { 'files': ['lib/python%%(pyshortver)s/site-packages/gts/_gts.%s' % SHLIB_EXT], - 'dirs':[], + 'dirs': [], } moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/PyGTS/PyGTS-0.3.1-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/PyGTS/PyGTS-0.3.1-foss-2016b-Python-2.7.12.eb index 372e050018..57753b92f3 100644 --- a/easybuild/easyconfigs/p/PyGTS/PyGTS-0.3.1-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/p/PyGTS/PyGTS-0.3.1-foss-2016b-Python-2.7.12.eb @@ -17,14 +17,14 @@ sources = [SOURCELOWER_TAR_GZ] dependencies = [ ('Python', '2.7.12'), ('GLib', '2.49.5'), - ('GTS' ,'0.7.6'), + ('GTS', '0.7.6'), ] options = {'modulename': 'gts'} sanity_check_paths = { 'files': ['lib/python%%(pyshortver)s/site-packages/gts/_gts.%s' % SHLIB_EXT], - 'dirs':[], + 'dirs': [], } moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/PyGTS/PyGTS-0.3.1-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/PyGTS/PyGTS-0.3.1-intel-2016a-Python-2.7.11.eb index 7383e08e64..4f0ee83679 100644 --- a/easybuild/easyconfigs/p/PyGTS/PyGTS-0.3.1-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/PyGTS/PyGTS-0.3.1-intel-2016a-Python-2.7.11.eb @@ -17,14 +17,14 @@ sources = [SOURCELOWER_TAR_GZ] dependencies = [ ('Python', '2.7.11'), ('GLib', '2.48.0'), - ('GTS' ,'0.7.6'), + ('GTS', '0.7.6'), ] options = {'modulename': 'gts'} sanity_check_paths = { 'files': ['lib/python%%(pyshortver)s/site-packages/gts/_gts.%s' % SHLIB_EXT], - 'dirs':[], + 'dirs': [], } moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/PyGTS/PyGTS-0.3.1-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/PyGTS/PyGTS-0.3.1-intel-2016b-Python-2.7.12.eb index b961fbd0a4..56f61040cd 100644 --- a/easybuild/easyconfigs/p/PyGTS/PyGTS-0.3.1-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/p/PyGTS/PyGTS-0.3.1-intel-2016b-Python-2.7.12.eb @@ -17,14 +17,14 @@ sources = [SOURCELOWER_TAR_GZ] dependencies = [ ('Python', '2.7.12'), ('GLib', '2.49.5'), - ('GTS' ,'0.7.6'), + ('GTS', '0.7.6'), ] options = {'modulename': 'gts'} sanity_check_paths = { 'files': ['lib/python%%(pyshortver)s/site-packages/gts/_gts.%s' % SHLIB_EXT], - 'dirs':[], + 'dirs': [], } moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.12-GCCcore-4.9.3-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.12-GCCcore-4.9.3-bare.eb index 62cd674cc5..dcac389893 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.12-GCCcore-4.9.3-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.12-GCCcore-4.9.3-bare.eb @@ -32,6 +32,6 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] #hidden = True # bare installation: only known module deps for GCCcore tools included -exts_list =[] +exts_list = [] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/pftoolsV3/pftoolsV3-20160324-foss-2016a.eb b/easybuild/easyconfigs/p/pftoolsV3/pftoolsV3-20160324-foss-2016a.eb index 8d5302dd6c..f72f7b4c0e 100644 --- a/easybuild/easyconfigs/p/pftoolsV3/pftoolsV3-20160324-foss-2016a.eb +++ b/easybuild/easyconfigs/p/pftoolsV3/pftoolsV3-20160324-foss-2016a.eb @@ -1,4 +1,4 @@ -easyblock='ConfigureMake' +easyblock = 'ConfigureMake' name = 'pftoolsV3' version = '20160324' diff --git a/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.0.2-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.0.2-foss-2016a-Python-2.7.11.eb index 3deb45334a..986362ad06 100644 --- a/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.0.2-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.0.2-foss-2016a-Python-2.7.11.eb @@ -2,7 +2,7 @@ easyblock = 'PythonPackage' name = 'protobuf-python' version = '3.0.2' -versionsuffix= '-Python-%(pyver)s' +versionsuffix = '-Python-%(pyver)s' homepage = 'https://github.com/google/protobuf/' description = """Python Protocol Buffers runtime library.""" diff --git a/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.0.2-foss-2016a-Python-3.5.1.eb b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.0.2-foss-2016a-Python-3.5.1.eb index 64b04ec53c..fbb897d434 100644 --- a/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.0.2-foss-2016a-Python-3.5.1.eb +++ b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.0.2-foss-2016a-Python-3.5.1.eb @@ -2,7 +2,7 @@ easyblock = 'PythonPackage' name = 'protobuf-python' version = '3.0.2' -versionsuffix= '-Python-%(pyver)s' +versionsuffix = '-Python-%(pyver)s' homepage = 'https://github.com/google/protobuf/' description = """Python Protocol Buffers runtime library.""" diff --git a/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.2.0-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.2.0-foss-2016b-Python-2.7.12.eb index 25a3d48ede..8512c8ff8b 100644 --- a/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.2.0-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.2.0-foss-2016b-Python-2.7.12.eb @@ -2,7 +2,7 @@ easyblock = 'PythonPackage' name = 'protobuf-python' version = '3.2.0' -versionsuffix= '-Python-%(pyver)s' +versionsuffix = '-Python-%(pyver)s' homepage = 'https://github.com/google/protobuf/' description = """Python Protocol Buffers runtime library.""" diff --git a/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.2.0-foss-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.2.0-foss-2016b-Python-3.5.2.eb index a88f02f65a..c25cad0fae 100644 --- a/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.2.0-foss-2016b-Python-3.5.2.eb +++ b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.2.0-foss-2016b-Python-3.5.2.eb @@ -2,7 +2,7 @@ easyblock = 'PythonPackage' name = 'protobuf-python' version = '3.2.0' -versionsuffix= '-Python-%(pyver)s' +versionsuffix = '-Python-%(pyver)s' homepage = 'https://github.com/google/protobuf/' description = """Python Protocol Buffers runtime library.""" diff --git a/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.2.0-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.2.0-intel-2016b-Python-2.7.12.eb index 136b95fa55..2dd5db9c4e 100755 --- a/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.2.0-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.2.0-intel-2016b-Python-2.7.12.eb @@ -2,7 +2,7 @@ easyblock = 'PythonPackage' name = 'protobuf-python' version = '3.2.0' -versionsuffix= '-Python-%(pyver)s' +versionsuffix = '-Python-%(pyver)s' homepage = 'https://github.com/google/protobuf/' description = """Python Protocol Buffers runtime library.""" diff --git a/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.2.0-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.2.0-intel-2016b-Python-3.5.2.eb index 89a06c0e60..fa54b7dce0 100644 --- a/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.2.0-intel-2016b-Python-3.5.2.eb +++ b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.2.0-intel-2016b-Python-3.5.2.eb @@ -2,7 +2,7 @@ easyblock = 'PythonPackage' name = 'protobuf-python' version = '3.2.0' -versionsuffix= '-Python-%(pyver)s' +versionsuffix = '-Python-%(pyver)s' homepage = 'https://github.com/google/protobuf/' description = """Python Protocol Buffers runtime library.""" diff --git a/easybuild/easyconfigs/p/pyGIMLi/pyGIMLi-20160803-foss-2016a-Python-3.5.1.eb b/easybuild/easyconfigs/p/pyGIMLi/pyGIMLi-20160803-foss-2016a-Python-3.5.1.eb index bf649cda81..3b3bd56fa2 100644 --- a/easybuild/easyconfigs/p/pyGIMLi/pyGIMLi-20160803-foss-2016a-Python-3.5.1.eb +++ b/easybuild/easyconfigs/p/pyGIMLi/pyGIMLi-20160803-foss-2016a-Python-3.5.1.eb @@ -58,7 +58,7 @@ installopts += '&& cp ../easybuild_obj/bin/* %(installdir)s/bin' sanity_check_paths = { 'files': ['bin/%s' % x for x in ['bms2vtk', 'dc1dinv', 'dc1dsmooth', 'fdem1dinv', 'fdem1dsmooth', 'harmfit', 'invlinearmat', 'mrs1dblock', 'mrs1dsmooth', - 'mt1dinv', 'mt1dsmooth', 'polyfit', 'ttinv', 'ttmod']]+ + 'mt1dinv', 'mt1dsmooth', 'polyfit', 'ttinv', 'ttmod']] + ['lib/libgimli.%s' % SHLIB_EXT, 'lib/python%(pyshortver)s/site-packages/pygimli.h'], 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'], } diff --git a/easybuild/easyconfigs/r/Rust/Rust-1.12.0-foss-2016b.eb b/easybuild/easyconfigs/r/Rust/Rust-1.12.0-foss-2016b.eb index de615e7620..04ee893a0e 100644 --- a/easybuild/easyconfigs/r/Rust/Rust-1.12.0-foss-2016b.eb +++ b/easybuild/easyconfigs/r/Rust/Rust-1.12.0-foss-2016b.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'foss', 'version': '2016b'} source_urls = ['https://static.rust-lang.org/dist/'] sources = ['rustc-%(version)s-src.tar.gz'] -builddependencies = [('Python', '2.7.12'), ('CMake','3.6.2')] +builddependencies = [('Python', '2.7.12'), ('CMake', '3.6.2')] sanity_check_paths = { 'files': ['bin/rustc', 'bin/rustdoc'], diff --git a/easybuild/easyconfigs/r/Rust/Rust-1.12.1-foss-2016b.eb b/easybuild/easyconfigs/r/Rust/Rust-1.12.1-foss-2016b.eb index a06ae54597..ed54478e03 100644 --- a/easybuild/easyconfigs/r/Rust/Rust-1.12.1-foss-2016b.eb +++ b/easybuild/easyconfigs/r/Rust/Rust-1.12.1-foss-2016b.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'foss', 'version': '2016b'} source_urls = ['https://static.rust-lang.org/dist/'] sources = ['rustc-%(version)s-src.tar.gz'] -builddependencies = [('Python', '2.7.12'), ('CMake','3.6.2')] +builddependencies = [('Python', '2.7.12'), ('CMake', '3.6.2')] sanity_check_paths = { 'files': ['bin/rustc', 'bin/rustdoc'], diff --git a/easybuild/easyconfigs/s/SHORE/SHORE-0.9.3-foss-2016a.eb b/easybuild/easyconfigs/s/SHORE/SHORE-0.9.3-foss-2016a.eb index 756efd9115..189d1b413d 100644 --- a/easybuild/easyconfigs/s/SHORE/SHORE-0.9.3-foss-2016a.eb +++ b/easybuild/easyconfigs/s/SHORE/SHORE-0.9.3-foss-2016a.eb @@ -15,9 +15,9 @@ sources = [SOURCELOWER_TAR_GZ] configopts = '--with-mpi' dependencies = [ - ('XZ','5.2.2'), - ('zlib','1.2.8'), - ('GSL','1.16'), # GSL 2.1 does not work. + ('XZ', '5.2.2'), + ('zlib', '1.2.8'), + ('GSL', '1.16'), # GSL 2.1 does not work. ('Boost', '1.61.0'), ] diff --git a/easybuild/easyconfigs/s/SUMACLUST/SUMACLUST-1.0.20-foss-2016a.eb b/easybuild/easyconfigs/s/SUMACLUST/SUMACLUST-1.0.20-foss-2016a.eb index 15d6744935..a2a47d4c1e 100644 --- a/easybuild/easyconfigs/s/SUMACLUST/SUMACLUST-1.0.20-foss-2016a.eb +++ b/easybuild/easyconfigs/s/SUMACLUST/SUMACLUST-1.0.20-foss-2016a.eb @@ -13,11 +13,11 @@ description = """SUMATRA and SUMACLUST: fast and exact comparison and clustering toolchain = {'name': 'foss', 'version': '2016a'} source_urls = ['https://git.metabarcoding.org/obitools/sumaclust/uploads/69f757c42f2cd45212c587e87c75a00f/'] -sources=['%(namelower)s_v%(version)s.tar.gz'] +sources = ['%(namelower)s_v%(version)s.tar.gz'] prebuildopts = 'make clean &&' -files_to_copy = [(['sumaclust'],'bin'),'sumaclust_user_manual.pdf'] +files_to_copy = [(['sumaclust'], 'bin'), 'sumaclust_user_manual.pdf'] sanity_check_paths = { 'files': ['bin/sumaclust', 'sumaclust_user_manual.pdf'], diff --git a/easybuild/easyconfigs/s/SUMATRA/SUMATRA-1.0.20-foss-2016a.eb b/easybuild/easyconfigs/s/SUMATRA/SUMATRA-1.0.20-foss-2016a.eb index 6ad5e46d49..b96f631d9c 100644 --- a/easybuild/easyconfigs/s/SUMATRA/SUMATRA-1.0.20-foss-2016a.eb +++ b/easybuild/easyconfigs/s/SUMATRA/SUMATRA-1.0.20-foss-2016a.eb @@ -13,11 +13,11 @@ description = """SUMATRA and SUMACLUST: fast and exact comparison and clustering toolchain = {'name': 'foss', 'version': '2016a'} source_urls = ['https://git.metabarcoding.org/obitools/sumatra/uploads/251020bbbd6c6595cb9fce6077e29952/'] -sources=['%(namelower)s_v%(version)s.tar.gz'] +sources = ['%(namelower)s_v%(version)s.tar.gz'] prebuildopts = 'make clean &&' -files_to_copy = [(['sumatra'],'bin'),'sumatra_user_manual.pdf'] +files_to_copy = [(['sumatra'], 'bin'), 'sumatra_user_manual.pdf'] sanity_check_paths = { 'files': ['bin/sumatra', 'sumatra_user_manual.pdf'], diff --git a/easybuild/easyconfigs/s/Saxon-HE/Saxon-HE-9.7.0.4-Java-1.7.0_79.eb b/easybuild/easyconfigs/s/Saxon-HE/Saxon-HE-9.7.0.4-Java-1.7.0_79.eb index d38576ab53..031be8f553 100644 --- a/easybuild/easyconfigs/s/Saxon-HE/Saxon-HE-9.7.0.4-Java-1.7.0_79.eb +++ b/easybuild/easyconfigs/s/Saxon-HE/Saxon-HE-9.7.0.4-Java-1.7.0_79.eb @@ -9,7 +9,7 @@ description = """Open Source SAXON XSLT processor developed by Saxonica Limited. toolchain = {'name': 'dummy', 'version': ''} -sources = ['SaxonHE%sJ.zip' % version.replace(".","-")] +sources = ['SaxonHE%sJ.zip' % version.replace('.', '-')] source_urls = ['https://sourceforge.net/projects/saxon/files/Saxon-HE/%(version_major_minor)s' , 'download'] dependencies = [('Java', '1.7.0_79')] diff --git a/easybuild/easyconfigs/s/Smoldyn/Smoldyn-2.48-foss-2016a.eb b/easybuild/easyconfigs/s/Smoldyn/Smoldyn-2.48-foss-2016a.eb index fc06a65970..0d3233c817 100644 --- a/easybuild/easyconfigs/s/Smoldyn/Smoldyn-2.48-foss-2016a.eb +++ b/easybuild/easyconfigs/s/Smoldyn/Smoldyn-2.48-foss-2016a.eb @@ -21,7 +21,7 @@ builddependencies = [ ] dependencies = [ - ('LibTIFF','4.0.6'), + ('LibTIFF', '4.0.6'), ('zlib', '1.2.8'), ('freeglut', '3.0.0'), ('libXmu', '1.1.2'), diff --git a/easybuild/easyconfigs/s/SortMeRNA/SortMeRNA-2.1-foss-2016a.eb b/easybuild/easyconfigs/s/SortMeRNA/SortMeRNA-2.1-foss-2016a.eb index f15b6559ac..6af29bdb8b 100644 --- a/easybuild/easyconfigs/s/SortMeRNA/SortMeRNA-2.1-foss-2016a.eb +++ b/easybuild/easyconfigs/s/SortMeRNA/SortMeRNA-2.1-foss-2016a.eb @@ -14,10 +14,8 @@ easyblock = 'ConfigureMake' name = 'SortMeRNA' version = '2.1' -homepage = 'http://bioinfo.lifl.fr/RNA/sortmerna/' -description = """ -SortMeRNA is a biological sequence analysis tool for filtering, mapping and OTU-picking NGS reads. -""" +homepage = 'http://bioinfo.lifl.fr/RNA/sortmerna/' +description = "SortMeRNA is a biological sequence analysis tool for filtering, mapping and OTU-picking NGS reads." toolchain = {'name': 'foss', 'version': '2016a'} toolchainopts = {'optarch': True, 'pic': True} @@ -26,12 +24,11 @@ source_urls = ['https://github.com/biocore/sortmerna/archive/'] sources = ['%(version)s.tar.gz'] # Patch for double includes of header files in Makefile.in -patches=['SortMeRNA-%(version)s_Makefile.in.patch'] - -sanity_check_paths={ - 'files': ['bin/indexdb_rna','bin/sortmerna'], - 'dirs': ['include','sortmerna'] +patches = ['SortMeRNA-%(version)s_Makefile.in.patch'] +sanity_check_paths = { + 'files': ['bin/indexdb_rna', 'bin/sortmerna'], + 'dirs': ['include', 'sortmerna'] } moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/Sphinx/Sphinx-1.4.8-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/s/Sphinx/Sphinx-1.4.8-foss-2016a-Python-2.7.11.eb index e8b9b26666..656bb0f55e 100644 --- a/easybuild/easyconfigs/s/Sphinx/Sphinx-1.4.8-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/s/Sphinx/Sphinx-1.4.8-foss-2016a-Python-2.7.11.eb @@ -47,7 +47,7 @@ exts_list = [ }), (name, version, { 'source_urls': ['https://pypi.python.org/packages/source/S/Sphinx/'], - 'patches': ['Sphinx-%s-pdflatex_failing_tests.patch' %version], + 'patches': ['Sphinx-%s-pdflatex_failing_tests.patch' % version], }), # sphinx_rtd_theme depends on Sphinx, and should be there to make the tests work ('sphinx_rtd_theme', '0.1.10a0', { diff --git a/easybuild/easyconfigs/s/Sphinx/Sphinx-1.4.8-foss-2016a-Python-3.5.1.eb b/easybuild/easyconfigs/s/Sphinx/Sphinx-1.4.8-foss-2016a-Python-3.5.1.eb index a58b6b19e0..26cda8da07 100644 --- a/easybuild/easyconfigs/s/Sphinx/Sphinx-1.4.8-foss-2016a-Python-3.5.1.eb +++ b/easybuild/easyconfigs/s/Sphinx/Sphinx-1.4.8-foss-2016a-Python-3.5.1.eb @@ -47,7 +47,7 @@ exts_list = [ }), (name, version, { 'source_urls': ['https://pypi.python.org/packages/source/S/Sphinx/'], - 'patches': ['Sphinx-%s-pdflatex_failing_tests.patch' %version], + 'patches': ['Sphinx-%s-pdflatex_failing_tests.patch' % version], }), # sphinx_rtd_theme depends on Sphinx, and should be there to make the tests work ('sphinx_rtd_theme', '0.1.10a0', { diff --git a/easybuild/easyconfigs/s/Stacks/Stacks-1.03-goolf-1.4.10.eb b/easybuild/easyconfigs/s/Stacks/Stacks-1.03-goolf-1.4.10.eb index a99ef374cd..5590d0a6b0 100644 --- a/easybuild/easyconfigs/s/Stacks/Stacks-1.03-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/s/Stacks/Stacks-1.03-goolf-1.4.10.eb @@ -5,8 +5,8 @@ version = '1.03' homepage = 'http://creskolab.uoregon.edu/stacks/' description = """Stacks is a software pipeline for building loci from short-read sequences, such as those generated on - the Illumina platform. Stacks was developed to work with restriction enzyme-based data, such as RAD-seq, for the purpose - of building genetic maps and conducting population genomics and phylogeography. + the Illumina platform. Stacks was developed to work with restriction enzyme-based data, such as RAD-seq, + for the purpose of building genetic maps and conducting population genomics and phylogeography. """ toolchain = {'name': 'goolf', 'version': '1.4.10'} diff --git a/easybuild/easyconfigs/s/Stacks/Stacks-1.03-ictce-5.3.0.eb b/easybuild/easyconfigs/s/Stacks/Stacks-1.03-ictce-5.3.0.eb index a9bfd6bbb4..005b7b2b57 100644 --- a/easybuild/easyconfigs/s/Stacks/Stacks-1.03-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/s/Stacks/Stacks-1.03-ictce-5.3.0.eb @@ -5,8 +5,8 @@ version = '1.03' homepage = 'http://creskolab.uoregon.edu/stacks/' description = """Stacks is a software pipeline for building loci from short-read sequences, such as those generated on - the Illumina platform. Stacks was developed to work with restriction enzyme-based data, such as RAD-seq, for the purpose - of building genetic maps and conducting population genomics and phylogeography. + the Illumina platform. Stacks was developed to work with restriction enzyme-based data, such as RAD-seq, + for the purpose of building genetic maps and conducting population genomics and phylogeography. """ toolchain = {'name': 'ictce', 'version': '5.3.0'} diff --git a/easybuild/easyconfigs/s/Stacks/Stacks-1.40-foss-2016a.eb b/easybuild/easyconfigs/s/Stacks/Stacks-1.40-foss-2016a.eb index 189d7f6db0..197e799318 100644 --- a/easybuild/easyconfigs/s/Stacks/Stacks-1.40-foss-2016a.eb +++ b/easybuild/easyconfigs/s/Stacks/Stacks-1.40-foss-2016a.eb @@ -5,8 +5,8 @@ version = '1.40' homepage = 'http://creskolab.uoregon.edu/stacks/' description = """Stacks is a software pipeline for building loci from short-read sequences, such as those generated on - the Illumina platform. Stacks was developed to work with restriction enzyme-based data, such as RAD-seq, for the purpose - of building genetic maps and conducting population genomics and phylogeography. + the Illumina platform. Stacks was developed to work with restriction enzyme-based data, such as RAD-seq, + for the purpose of building genetic maps and conducting population genomics and phylogeography. """ toolchain = {'name': 'foss', 'version': '2016a'} diff --git a/easybuild/easyconfigs/s/Stacks/Stacks-1.42-foss-2016a.eb b/easybuild/easyconfigs/s/Stacks/Stacks-1.42-foss-2016a.eb index 6d5d6358c8..e042becab7 100644 --- a/easybuild/easyconfigs/s/Stacks/Stacks-1.42-foss-2016a.eb +++ b/easybuild/easyconfigs/s/Stacks/Stacks-1.42-foss-2016a.eb @@ -5,8 +5,8 @@ version = '1.42' homepage = 'http://creskolab.uoregon.edu/stacks/' description = """Stacks is a software pipeline for building loci from short-read sequences, such as those generated on - the Illumina platform. Stacks was developed to work with restriction enzyme-based data, such as RAD-seq, for the purpose - of building genetic maps and conducting population genomics and phylogeography. + the Illumina platform. Stacks was developed to work with restriction enzyme-based data, such as RAD-seq, + for the purpose of building genetic maps and conducting population genomics and phylogeography. """ toolchain = {'name': 'foss', 'version': '2016a'} diff --git a/easybuild/easyconfigs/s/Stacks/Stacks-1.44-foss-2016a.eb b/easybuild/easyconfigs/s/Stacks/Stacks-1.44-foss-2016a.eb index 6ef7429937..1df7d789c0 100644 --- a/easybuild/easyconfigs/s/Stacks/Stacks-1.44-foss-2016a.eb +++ b/easybuild/easyconfigs/s/Stacks/Stacks-1.44-foss-2016a.eb @@ -5,8 +5,8 @@ version = '1.44' homepage = 'http://creskolab.uoregon.edu/stacks/' description = """Stacks is a software pipeline for building loci from short-read sequences, such as those generated on - the Illumina platform. Stacks was developed to work with restriction enzyme-based data, such as RAD-seq, for the purpose - of building genetic maps and conducting population genomics and phylogeography. + the Illumina platform. Stacks was developed to work with restriction enzyme-based data, such as RAD-seq, + for the purpose of building genetic maps and conducting population genomics and phylogeography. """ toolchain = {'name': 'foss', 'version': '2016a'} diff --git a/easybuild/easyconfigs/s/StringTie/StringTie-1.2.2-goolf-1.4.10.eb b/easybuild/easyconfigs/s/StringTie/StringTie-1.2.2-goolf-1.4.10.eb index 70ca06ed76..f2c6a5db74 100644 --- a/easybuild/easyconfigs/s/StringTie/StringTie-1.2.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/s/StringTie/StringTie-1.2.2-goolf-1.4.10.eb @@ -17,7 +17,7 @@ source_urls = ['http://ccb.jhu.edu/software/stringtie/dl/'] sources = [SOURCELOWER_TAR_GZ] files_to_copy = [(['stringtie'], 'bin'), 'README', 'LICENSE'] - + sanity_check_paths = { 'files': ['bin/stringtie'], 'dirs': [], diff --git a/easybuild/easyconfigs/s/StringTie/StringTie-1.3.0-intel-2016b.eb b/easybuild/easyconfigs/s/StringTie/StringTie-1.3.0-intel-2016b.eb index 424d2b7aeb..69634c30e6 100644 --- a/easybuild/easyconfigs/s/StringTie/StringTie-1.3.0-intel-2016b.eb +++ b/easybuild/easyconfigs/s/StringTie/StringTie-1.3.0-intel-2016b.eb @@ -17,7 +17,7 @@ source_urls = ['http://ccb.jhu.edu/software/stringtie/dl/'] sources = [SOURCELOWER_TAR_GZ] files_to_copy = [(['stringtie'], 'bin'), 'README', 'LICENSE'] - + sanity_check_paths = { 'files': ['bin/stringtie'], 'dirs': [], diff --git a/easybuild/easyconfigs/s/StringTie/StringTie-1.3.3-intel-2017a.eb b/easybuild/easyconfigs/s/StringTie/StringTie-1.3.3-intel-2017a.eb index aa49a6e1bd..2476496f2d 100644 --- a/easybuild/easyconfigs/s/StringTie/StringTie-1.3.3-intel-2017a.eb +++ b/easybuild/easyconfigs/s/StringTie/StringTie-1.3.3-intel-2017a.eb @@ -17,7 +17,7 @@ source_urls = ['http://ccb.jhu.edu/software/stringtie/dl/'] sources = [SOURCELOWER_TAR_GZ] files_to_copy = [(['stringtie'], 'bin'), 'README', 'LICENSE'] - + sanity_check_paths = { 'files': ['bin/stringtie'], 'dirs': [], diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1-iomkl-2016.07.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1-iomkl-2016.07.eb index 512dbbe733..6f12c299b1 100644 --- a/easybuild/easyconfigs/s/Szip/Szip-2.1-iomkl-2016.07.eb +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1-iomkl-2016.07.eb @@ -15,7 +15,7 @@ sources = [SOURCELOWER_TAR_GZ] configopts = "--with-pic" sanity_check_paths = { - 'files': ["lib/libsz.a", "lib/libsz.%s" %SHLIB_EXT] + + 'files': ["lib/libsz.a", "lib/libsz.%s" % SHLIB_EXT] + ["include/%s" % x for x in ["ricehdf.h", "szip_adpt.h", "szlib.h"]], 'dirs': [], } diff --git a/easybuild/easyconfigs/s/scipy/scipy-0.16.0-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/s/scipy/scipy-0.16.0-intel-2016b-Python-2.7.12.eb index a6ab83c9a7..1d1ef64120 100644 --- a/easybuild/easyconfigs/s/scipy/scipy-0.16.0-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/s/scipy/scipy-0.16.0-intel-2016b-Python-2.7.12.eb @@ -21,7 +21,7 @@ dependencies = [ # recompile patch Cython source file prebuildopts = "cython scipy/linalg/_decomp_update.pyx && " -# need to use pip rather than regular 'setup.py install,' +# need to use pip rather than regular 'setup.py install' # to ensure that this scipy wins over the one in the Python installation; # using easy_install does not work... use_pip = True diff --git a/easybuild/easyconfigs/s/segemehl/segemehl-0.2.0-goolf-1.4.10.eb b/easybuild/easyconfigs/s/segemehl/segemehl-0.2.0-goolf-1.4.10.eb index 39c950b357..a9245a0b76 100644 --- a/easybuild/easyconfigs/s/segemehl/segemehl-0.2.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/s/segemehl/segemehl-0.2.0-goolf-1.4.10.eb @@ -5,8 +5,8 @@ easyblock = 'MakeCp' -name = "segemehl" -version = "0.2.0" +name = 'segemehl' +version = '0.2.0' homepage = 'http://www.bioinf.uni-leipzig.de/Software/segemehl/' description = """ segemehl is a software to map short sequencer reads to reference genomes. @@ -20,7 +20,7 @@ description = """ segemehl is a software to map short sequencer reads to referen toolchain = {'name': 'goolf', 'version': '1.4.10'} source_urls = ['http://www.bioinf.uni-leipzig.de/Software/segemehl/'] -sources = ['%s_%s.tar.gz' % (name, version.replace('.','_'))] +sources = ['%s_%s.tar.gz' % (name, version.replace('.', '_'))] parallel = 1 @@ -29,11 +29,11 @@ dependencies = [ ('zlib', '1.2.8'), ] -files_to_copy = [(["lack.x", "segemehl.x", "testrealign.x"], "bin")] +files_to_copy = [(['lack.x', 'segemehl.x', 'testrealign.x'], 'bin')] sanity_check_paths = { - 'files': ["bin/%s" % x for x in ["lack.x" , "segemehl.x", "testrealign.x"]], - 'dirs': ["."] + 'files': ['bin/%s' % x for x in ['lack.x', 'segemehl.x', 'testrealign.x']], + 'dirs': [] } moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/stemming/stemming-1.0-ictce-5.5.0-Python-2.7.6.eb b/easybuild/easyconfigs/s/stemming/stemming-1.0-ictce-5.5.0-Python-2.7.6.eb index 241a1d5fbf..7c1426364f 100644 --- a/easybuild/easyconfigs/s/stemming/stemming-1.0-ictce-5.5.0-Python-2.7.6.eb +++ b/easybuild/easyconfigs/s/stemming/stemming-1.0-ictce-5.5.0-Python-2.7.6.eb @@ -4,7 +4,7 @@ name = "stemming" version = "1.0" homepage = "https://pypi.python.org/pypi/stemming/" -description = """Python implementations of the Porter, Porter2, Paice-Husk, and Lovins stemming algorithms for English.""" +description = "Python implementations of the Porter, Porter2, Paice-Husk, and Lovins stemming algorithms for English." toolchain = {'name': 'ictce', 'version': '5.5.0'} diff --git a/easybuild/easyconfigs/s/sympy/sympy-1.0-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/s/sympy/sympy-1.0-foss-2016a-Python-2.7.11.eb index 6ab91f87e3..1ee4a4a0bc 100644 --- a/easybuild/easyconfigs/s/sympy/sympy-1.0-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/s/sympy/sympy-1.0-foss-2016a-Python-2.7.11.eb @@ -15,7 +15,7 @@ toolchain = {'name': 'foss', 'version': '2016a'} source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] -#Patch to fix tests +# patch to fix tests patches = ['sympy-1.0_tests-unicode.patch'] dependencies = [ diff --git a/easybuild/easyconfigs/s/sympy/sympy-1.0-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/s/sympy/sympy-1.0-intel-2016a-Python-2.7.11.eb index 09140f6d09..1c13652bc7 100644 --- a/easybuild/easyconfigs/s/sympy/sympy-1.0-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/s/sympy/sympy-1.0-intel-2016a-Python-2.7.11.eb @@ -15,7 +15,7 @@ toolchain = {'name': 'intel', 'version': '2016a'} source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] -#Patch to fix tests +# patch to fix tests patches = ['sympy-1.0_tests-unicode.patch'] dependencies = [ diff --git a/easybuild/easyconfigs/t/TAU/TAU-2.22.2-goolf-1.5.14.eb b/easybuild/easyconfigs/t/TAU/TAU-2.22.2-goolf-1.5.14.eb index 2f2888a832..72a246892c 100644 --- a/easybuild/easyconfigs/t/TAU/TAU-2.22.2-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/t/TAU/TAU-2.22.2-goolf-1.5.14.eb @@ -25,8 +25,8 @@ dependencies = [ ('PDT', '3.19'), ('Score-P', '1.2.1'), # obsolete backends, use Score-P instead - #('Scalasca', '1.4.3'), - #('VampirTrace', '5.14.4'), + # ('Scalasca', '1.4.3'), + # ('VampirTrace', '5.14.4'), ] # scalasca and vampirtrace backends are deprecated diff --git a/easybuild/easyconfigs/t/Trinity/Trinity-2.1.1-intel-2015b.eb b/easybuild/easyconfigs/t/Trinity/Trinity-2.1.1-intel-2015b.eb index 5f116c4b08..71643e32bd 100644 --- a/easybuild/easyconfigs/t/Trinity/Trinity-2.1.1-intel-2015b.eb +++ b/easybuild/easyconfigs/t/Trinity/Trinity-2.1.1-intel-2015b.eb @@ -29,7 +29,7 @@ dependencies = [ ('ant', '1.9.6', '-%s-%s' % (java, javaver), True), ('Bowtie', '1.1.2'), ('Bowtie2', '2.2.6'), - ('ncurses', '5.9',), + ('ncurses', '5.9'), ('zlib', '1.2.8'), ('Perl', '5.20.3'), ] diff --git a/easybuild/easyconfigs/t/Trinity/Trinity-2.2.0-foss-2016a.eb b/easybuild/easyconfigs/t/Trinity/Trinity-2.2.0-foss-2016a.eb index 58018d9335..181142b3db 100644 --- a/easybuild/easyconfigs/t/Trinity/Trinity-2.2.0-foss-2016a.eb +++ b/easybuild/easyconfigs/t/Trinity/Trinity-2.2.0-foss-2016a.eb @@ -30,7 +30,7 @@ dependencies = [ ('ant', '1.9.7', '-Java-%(javaver)s', True), ('Bowtie', '1.1.2'), ('Bowtie2', '2.2.8'), - ('ncurses', '6.0',), + ('ncurses', '6.0'), ('zlib', '1.2.8'), ('Perl', '5.22.1'), ] diff --git a/easybuild/easyconfigs/u/USPEX/USPEX-9.4.4-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/u/USPEX/USPEX-9.4.4-intel-2016b-Python-2.7.12.eb index ae04827ae1..ce865ad5b9 100644 --- a/easybuild/easyconfigs/u/USPEX/USPEX-9.4.4-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/u/USPEX/USPEX-9.4.4-intel-2016b-Python-2.7.12.eb @@ -22,9 +22,8 @@ USPEX can also be used for finding low-energy metastable phases, as well as stab toolchain = {'name': 'intel', 'version': '2016b'} +# you have to register before download via http://uspex-team.org/uspex/downloads sources = ['%(name)s-%(version)s.tar.gz'] -#You have to register before download -#source_urls = ['http://uspex-team.org/uspex/downloads'] dependencies = [ ('Python', '2.7.12'), diff --git a/easybuild/easyconfigs/x/xcb-util-image/xcb-util-image-0.4.0-intel-2015b.eb b/easybuild/easyconfigs/x/xcb-util-image/xcb-util-image-0.4.0-intel-2015b.eb index 933c8b66d8..3b7e3d4f5d 100644 --- a/easybuild/easyconfigs/x/xcb-util-image/xcb-util-image-0.4.0-intel-2015b.eb +++ b/easybuild/easyconfigs/x/xcb-util-image/xcb-util-image-0.4.0-intel-2015b.eb @@ -12,7 +12,7 @@ source_urls = ['http://xcb.freedesktop.org/dist/'] sources = [SOURCELOWER_TAR_GZ] dependencies = [ - ('xcb-util', '0.4.0',), + ('xcb-util', '0.4.0'), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.2.0-foss-2016b.eb b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.2.0-foss-2016b.eb index 2e2077d599..f85c7f00dd 100644 --- a/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.2.0-foss-2016b.eb +++ b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.2.0-foss-2016b.eb @@ -15,7 +15,7 @@ toolchain = {'name': 'foss', 'version': '2016b'} source_urls = ['https://github.com/zeromq/libzmq/releases/download/v%(version)s/'] sources = [SOURCELOWER_TAR_GZ] -checksums=['1fb2595d2a905a9e820c976a1d8348bc'] +checksums = ['1fb2595d2a905a9e820c976a1d8348bc'] # --with-pgm will use shipped OpenPGM (in foreign subdir) configopts = '--with-pic --with-system-pgm ' diff --git a/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.2.0-intel-2016b.eb b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.2.0-intel-2016b.eb index b5d9aa81e3..4c59674a12 100644 --- a/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.2.0-intel-2016b.eb +++ b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.2.0-intel-2016b.eb @@ -15,7 +15,7 @@ toolchain = {'name': 'intel', 'version': '2016b'} source_urls = ['https://github.com/zeromq/libzmq/releases/download/v%(version)s/'] sources = [SOURCELOWER_TAR_GZ] -checksums=['1fb2595d2a905a9e820c976a1d8348bc'] +checksums = ['1fb2595d2a905a9e820c976a1d8348bc'] # --with-pgm will use shipped OpenPGM (in foreign subdir) configopts = '--with-pic --with-system-pgm ' -- GitLab From 87b347871ec03bfdb8474f406965cb522ebf9dfa Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 21 Feb 2017 21:08:32 +0100 Subject: [PATCH 0118/1603] more style fixes in easyconfigs --- .../s/SHORE/SHORE-0.9.3-foss-2016a.eb | 8 +++---- .../SLEPc-3.3-p1-goolf-1.4.10-Python-2.7.3.eb | 8 +++---- .../SLEPc-3.3-p1-ictce-5.3.0-Python-2.7.3.eb | 9 ++++---- .../SLEPc-3.5.3-intel-2015a-Python-2.7.9.eb | 8 +++---- .../SLEPc-3.6.2-intel-2015b-Python-2.7.11.eb | 8 +++---- .../s/SPRNG/SPRNG-2.0a-goolf-1.4.10.eb | 3 ++- .../s/SPRNG/SPRNG-2.0a-ictce-5.3.0.eb | 3 ++- .../s/SPRNG/SPRNG-2.0a-ictce-5.5.0.eb | 3 ++- .../s/SPRNG/SPRNG-2.0b-foss-2016a.eb | 3 ++- .../s/SPRNG/SPRNG-2.0b-goolf-1.4.10.eb | 3 ++- .../s/SPRNG/SPRNG-2.0b-ictce-5.3.0.eb | 3 ++- .../s/SPRNG/SPRNG-2.0b-ictce-5.5.0.eb | 3 ++- .../s/SQLite/SQLite-3.14.1-GCCcore-4.9.3.eb | 3 ++- .../SQLite/SQLite-3.8.10.2-GCC-4.9.3-2.25.eb | 3 ++- .../s/SQLite/SQLite-3.8.10.2-foss-2015a.eb | 3 ++- .../s/SQLite/SQLite-3.8.10.2-foss-2015b.eb | 3 ++- .../s/SQLite/SQLite-3.8.10.2-gimkl-2.11.5.eb | 3 ++- .../s/SQLite/SQLite-3.8.10.2-goolf-1.4.10.eb | 3 ++- .../s/SQLite/SQLite-3.8.10.2-goolf-1.7.20.eb | 3 ++- .../s/SQLite/SQLite-3.8.10.2-intel-2015a.eb | 3 ++- .../s/SQLite/SQLite-3.8.10.2-intel-2015b.eb | 3 ++- .../s/SQLite/SQLite-3.8.4.1-goolf-1.4.10.eb | 2 +- .../s/SQLite/SQLite-3.9.2-CrayGNU-2015.11.eb | 3 ++- .../s/SQLite/SQLite-3.9.2-CrayGNU-2016.03.eb | 3 ++- .../s/SQLite/SQLite-3.9.2-foss-2016a.eb | 3 ++- .../s/SQLite/SQLite-3.9.2-gimkl-2.11.5.eb | 3 ++- .../s/SQLite/SQLite-3.9.2-goolf-1.7.20.eb | 3 ++- .../s/SQLite/SQLite-3.9.2-intel-2015b.eb | 3 ++- .../SQLite-3.9.2-intel-2016.02-GCC-4.9.eb | 3 ++- .../s/SQLite/SQLite-3.9.2-intel-2016a.eb | 3 ++- .../s/SQLite/SQLite-3.9.2-iomkl-2016.07.eb | 3 ++- ...Lite-3.9.2-iomkl-2016.09-GCC-4.9.3-2.25.eb | 3 ++- ...R-Fusion-0.6.0-goolf-1.4.10-Perl-5.16.3.eb | 10 ++++----- .../s/STAR/STAR-2.5.0a-GNU-4.9.3-2.25.eb | 7 +++---- .../s/STAR/STAR-2.5.0a-goolf-1.4.10.eb | 7 +++---- .../s/STAR/STAR-2.5.1b-foss-2015b.eb | 9 ++++---- .../s/STAR/STAR-2.5.1b-goolf-1.4.10.eb | 9 ++++---- .../s/STAR/STAR-2.5.2a-foss-2016a.eb | 21 +++++++++---------- .../s/STAR/STAR-2.5.2a-goolf-1.7.20.eb | 21 +++++++++---------- .../s/SUMATRA/SUMATRA-1.0.20-foss-2016a.eb | 2 +- .../Saxon-HE-9.7.0.4-Java-1.7.0_79.eb | 2 +- .../s/SeqPrep/SeqPrep-1.2-goolf-1.7.20.eb | 2 +- .../s/Serf/Serf-1.3.8-foss-2015a.eb | 4 ++-- 43 files changed, 117 insertions(+), 98 deletions(-) diff --git a/easybuild/easyconfigs/s/SHORE/SHORE-0.9.3-foss-2016a.eb b/easybuild/easyconfigs/s/SHORE/SHORE-0.9.3-foss-2016a.eb index 189d1b413d..4078e01a54 100644 --- a/easybuild/easyconfigs/s/SHORE/SHORE-0.9.3-foss-2016a.eb +++ b/easybuild/easyconfigs/s/SHORE/SHORE-0.9.3-foss-2016a.eb @@ -15,10 +15,10 @@ sources = [SOURCELOWER_TAR_GZ] configopts = '--with-mpi' dependencies = [ - ('XZ', '5.2.2'), - ('zlib', '1.2.8'), - ('GSL', '1.16'), # GSL 2.1 does not work. - ('Boost', '1.61.0'), + ('XZ', '5.2.2'), + ('zlib', '1.2.8'), + ('GSL', '1.16'), # GSL 2.1 does not work. + ('Boost', '1.61.0'), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/s/SLEPc/SLEPc-3.3-p1-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/s/SLEPc/SLEPc-3.3-p1-goolf-1.4.10-Python-2.7.3.eb index 3c14ae7d6c..e137f85d4d 100644 --- a/easybuild/easyconfigs/s/SLEPc/SLEPc-3.3-p1-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/s/SLEPc/SLEPc-3.3-p1-goolf-1.4.10-Python-2.7.3.eb @@ -3,10 +3,10 @@ version = "3.3-p1" versionsuffix = '-Python-2.7.3' homepage = 'http://www.grycap.upv.es/slepc/' -description = """SLEPc (Scalable Library for Eigenvalue Problem Computations) is a software library for the solution of -large scale sparse eigenvalue problems on parallel computers. It is an extension of PETSc and can be used for either standard or -generalized eigenproblems, with real or complex arithmetic. It can also be used for computing a partial SVD of a large, sparse, -rectangular matrix, and to solve quadratic eigenvalue problems.""" +description = """SLEPc (Scalable Library for Eigenvalue Problem Computations) is a software library for the solution + of large scale sparse eigenvalue problems on parallel computers. It is an extension of PETSc and can be used for + either standard or generalized eigenproblems, with real or complex arithmetic. It can also be used for computing a + partial SVD of a large, sparse, rectangular matrix, and to solve quadratic eigenvalue problems.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'usempi': True} diff --git a/easybuild/easyconfigs/s/SLEPc/SLEPc-3.3-p1-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/s/SLEPc/SLEPc-3.3-p1-ictce-5.3.0-Python-2.7.3.eb index 1b4c48aa91..e3ec9ea769 100644 --- a/easybuild/easyconfigs/s/SLEPc/SLEPc-3.3-p1-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/s/SLEPc/SLEPc-3.3-p1-ictce-5.3.0-Python-2.7.3.eb @@ -3,11 +3,10 @@ version = "3.3-p1" versionsuffix = '-Python-2.7.3' homepage = 'http://www.grycap.upv.es/slepc/' -description = """SLEPc (Scalable Library for Eigenvalue Problem Computations) is a software library for the solution of - large scale sparse eigenvalue problems on parallel computers. It is an extension of PETSc and can be used for either standard or - generalized eigenproblems, with real or complex arithmetic. It can also be used for computing a partial SVD of a large, sparse, - rectangular matrix, and to solve quadratic eigenvalue problems.""" - +description = """SLEPc (Scalable Library for Eigenvalue Problem Computations) is a software library for the solution + of large scale sparse eigenvalue problems on parallel computers. It is an extension of PETSc and can be used for + either standard or generalized eigenproblems, with real or complex arithmetic. It can also be used for computing a + partial SVD of a large, sparse, rectangular matrix, and to solve quadratic eigenvalue problems.""" toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'usempi': True} diff --git a/easybuild/easyconfigs/s/SLEPc/SLEPc-3.5.3-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/s/SLEPc/SLEPc-3.5.3-intel-2015a-Python-2.7.9.eb index 0f01678e28..fd3e7c3888 100644 --- a/easybuild/easyconfigs/s/SLEPc/SLEPc-3.5.3-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/s/SLEPc/SLEPc-3.5.3-intel-2015a-Python-2.7.9.eb @@ -3,10 +3,10 @@ version = '3.5.3' versionsuffix = '-Python-2.7.9' homepage = 'http://www.grycap.upv.es/slepc/' -description = """SLEPc (Scalable Library for Eigenvalue Problem Computations) is a software library for the solution of - large scale sparse eigenvalue problems on parallel computers. It is an extension of PETSc and can be used for either - standard or generalized eigenproblems, with real or complex arithmetic. It can also be used for computing a partial - SVD of a large, sparse, rectangular matrix, and to solve quadratic eigenvalue problems.""" +description = """SLEPc (Scalable Library for Eigenvalue Problem Computations) is a software library for the solution + of large scale sparse eigenvalue problems on parallel computers. It is an extension of PETSc and can be used for + either standard or generalized eigenproblems, with real or complex arithmetic. It can also be used for computing a + partial SVD of a large, sparse, rectangular matrix, and to solve quadratic eigenvalue problems.""" toolchain = {'name': 'intel', 'version': '2015a'} toolchainopts = {'usempi': True} diff --git a/easybuild/easyconfigs/s/SLEPc/SLEPc-3.6.2-intel-2015b-Python-2.7.11.eb b/easybuild/easyconfigs/s/SLEPc/SLEPc-3.6.2-intel-2015b-Python-2.7.11.eb index 775feb3837..351ac62d2c 100644 --- a/easybuild/easyconfigs/s/SLEPc/SLEPc-3.6.2-intel-2015b-Python-2.7.11.eb +++ b/easybuild/easyconfigs/s/SLEPc/SLEPc-3.6.2-intel-2015b-Python-2.7.11.eb @@ -3,10 +3,10 @@ version = '3.6.2' versionsuffix = '-Python-2.7.11' homepage = 'http://www.grycap.upv.es/slepc/' -description = """SLEPc (Scalable Library for Eigenvalue Problem Computations) is a software library for the solution of - large scale sparse eigenvalue problems on parallel computers. It is an extension of PETSc and can be used for either - standard or generalized eigenproblems, with real or complex arithmetic. It can also be used for computing a partial - SVD of a large, sparse, rectangular matrix, and to solve quadratic eigenvalue problems.""" +description = """SLEPc (Scalable Library for Eigenvalue Problem Computations) is a software library for the solution + of large scale sparse eigenvalue problems on parallel computers. It is an extension of PETSc and can be used for + either standard or generalized eigenproblems, with real or complex arithmetic. It can also be used for computing a + partial SVD of a large, sparse, rectangular matrix, and to solve quadratic eigenvalue problems.""" toolchain = {'name': 'intel', 'version': '2015b'} toolchainopts = {'usempi': True} diff --git a/easybuild/easyconfigs/s/SPRNG/SPRNG-2.0a-goolf-1.4.10.eb b/easybuild/easyconfigs/s/SPRNG/SPRNG-2.0a-goolf-1.4.10.eb index 762b8d9995..4a20471e6d 100644 --- a/easybuild/easyconfigs/s/SPRNG/SPRNG-2.0a-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/s/SPRNG/SPRNG-2.0a-goolf-1.4.10.eb @@ -16,7 +16,8 @@ patches = ['SPRNG-2.0_fix-metropolis-test.patch'] dependencies = [('GMP', '5.1.3')] -buildopts = 'PLAT=INTEL MPIDEF="-DSPRNG_MPI" CC="$CC" F77="$F77" PMLCGDEF="-DUSE_PMLCG" GMPLIB="-L$EBROOTGMP/lib -lgmp" FFXN="-DAdd_"' +buildopts = 'PLAT=INTEL MPIDEF="-DSPRNG_MPI" CC="$CC" F77="$F77" PMLCGDEF="-DUSE_PMLCG" ' +buildopts += 'GMPLIB="-L$EBROOTGMP/lib -lgmp" FFXN="-DAdd_"' # does not support parallel build parallel = 1 diff --git a/easybuild/easyconfigs/s/SPRNG/SPRNG-2.0a-ictce-5.3.0.eb b/easybuild/easyconfigs/s/SPRNG/SPRNG-2.0a-ictce-5.3.0.eb index 3d66a9ad8c..9464d99616 100644 --- a/easybuild/easyconfigs/s/SPRNG/SPRNG-2.0a-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/s/SPRNG/SPRNG-2.0a-ictce-5.3.0.eb @@ -16,7 +16,8 @@ patches = ['SPRNG-2.0_fix-metropolis-test.patch'] dependencies = [('GMP', '5.1.3')] -buildopts = 'PLAT=INTEL MPIDEF="-DSPRNG_MPI" CC="$CC" F77="$F77" PMLCGDEF="-DUSE_PMLCG" GMPLIB="-L$EBROOTGMP/lib -lgmp" FFXN="-DAdd_"' +buildopts = 'PLAT=INTEL MPIDEF="-DSPRNG_MPI" CC="$CC" F77="$F77" PMLCGDEF="-DUSE_PMLCG" ' +buildopts += 'GMPLIB="-L$EBROOTGMP/lib -lgmp" FFXN="-DAdd_"' # does not support parallel build parallel = 1 diff --git a/easybuild/easyconfigs/s/SPRNG/SPRNG-2.0a-ictce-5.5.0.eb b/easybuild/easyconfigs/s/SPRNG/SPRNG-2.0a-ictce-5.5.0.eb index 0b67d316a2..380060ff3b 100644 --- a/easybuild/easyconfigs/s/SPRNG/SPRNG-2.0a-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/s/SPRNG/SPRNG-2.0a-ictce-5.5.0.eb @@ -16,7 +16,8 @@ patches = ['SPRNG-2.0_fix-metropolis-test.patch'] dependencies = [('GMP', '5.1.3')] -buildopts = 'PLAT=INTEL MPIDEF="-DSPRNG_MPI" CC="$CC" F77="$F77" PMLCGDEF="-DUSE_PMLCG" GMPLIB="-L$EBROOTGMP/lib -lgmp" FFXN="-DAdd_"' +buildopts = 'PLAT=INTEL MPIDEF="-DSPRNG_MPI" CC="$CC" F77="$F77" PMLCGDEF="-DUSE_PMLCG" ' +buildopts += 'GMPLIB="-L$EBROOTGMP/lib -lgmp" FFXN="-DAdd_"' # does not support parallel build parallel = 1 diff --git a/easybuild/easyconfigs/s/SPRNG/SPRNG-2.0b-foss-2016a.eb b/easybuild/easyconfigs/s/SPRNG/SPRNG-2.0b-foss-2016a.eb index 59be5269fa..59c5938c90 100644 --- a/easybuild/easyconfigs/s/SPRNG/SPRNG-2.0b-foss-2016a.eb +++ b/easybuild/easyconfigs/s/SPRNG/SPRNG-2.0b-foss-2016a.eb @@ -16,7 +16,8 @@ patches = ['SPRNG-2.0_fix-metropolis-test.patch'] dependencies = [('GMP', '6.1.0')] -buildopts = 'PLAT=INTEL MPIDEF="-DSPRNG_MPI" CC="$CC" F77="$F77" PMLCGDEF="-DUSE_PMLCG" GMPLIB="-L$EBROOTGMP/lib -lgmp" FFXN="-DAdd_"' +buildopts = 'PLAT=INTEL MPIDEF="-DSPRNG_MPI" CC="$CC" F77="$F77" PMLCGDEF="-DUSE_PMLCG" ' +buildopts += 'GMPLIB="-L$EBROOTGMP/lib -lgmp" FFXN="-DAdd_"' # does not support parallel build parallel = 1 diff --git a/easybuild/easyconfigs/s/SPRNG/SPRNG-2.0b-goolf-1.4.10.eb b/easybuild/easyconfigs/s/SPRNG/SPRNG-2.0b-goolf-1.4.10.eb index 4df722877b..36cdd512d2 100644 --- a/easybuild/easyconfigs/s/SPRNG/SPRNG-2.0b-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/s/SPRNG/SPRNG-2.0b-goolf-1.4.10.eb @@ -16,7 +16,8 @@ patches = ['SPRNG-2.0_fix-metropolis-test.patch'] dependencies = [('GMP', '5.1.3')] -buildopts = 'PLAT=INTEL MPIDEF="-DSPRNG_MPI" CC="$CC" F77="$F77" PMLCGDEF="-DUSE_PMLCG" GMPLIB="-L$EBROOTGMP/lib -lgmp" FFXN="-DAdd_"' +buildopts = 'PLAT=INTEL MPIDEF="-DSPRNG_MPI" CC="$CC" F77="$F77" PMLCGDEF="-DUSE_PMLCG" ' +buildopts += 'GMPLIB="-L$EBROOTGMP/lib -lgmp" FFXN="-DAdd_"' # does not support parallel build parallel = 1 diff --git a/easybuild/easyconfigs/s/SPRNG/SPRNG-2.0b-ictce-5.3.0.eb b/easybuild/easyconfigs/s/SPRNG/SPRNG-2.0b-ictce-5.3.0.eb index ba3405a6f5..44b9de5758 100644 --- a/easybuild/easyconfigs/s/SPRNG/SPRNG-2.0b-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/s/SPRNG/SPRNG-2.0b-ictce-5.3.0.eb @@ -16,7 +16,8 @@ patches = ['SPRNG-2.0_fix-metropolis-test.patch'] dependencies = [('GMP', '5.1.3')] -buildopts = 'PLAT=INTEL MPIDEF="-DSPRNG_MPI" CC="$CC" F77="$F77" PMLCGDEF="-DUSE_PMLCG" GMPLIB="-L$EBROOTGMP/lib -lgmp" FFXN="-DAdd_"' +buildopts = 'PLAT=INTEL MPIDEF="-DSPRNG_MPI" CC="$CC" F77="$F77" PMLCGDEF="-DUSE_PMLCG" ' +buildopts += 'GMPLIB="-L$EBROOTGMP/lib -lgmp" FFXN="-DAdd_"' # does not support parallel build parallel = 1 diff --git a/easybuild/easyconfigs/s/SPRNG/SPRNG-2.0b-ictce-5.5.0.eb b/easybuild/easyconfigs/s/SPRNG/SPRNG-2.0b-ictce-5.5.0.eb index 435de49323..def70b5b62 100644 --- a/easybuild/easyconfigs/s/SPRNG/SPRNG-2.0b-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/s/SPRNG/SPRNG-2.0b-ictce-5.5.0.eb @@ -16,7 +16,8 @@ patches = ['SPRNG-2.0_fix-metropolis-test.patch'] dependencies = [('GMP', '5.1.3')] -buildopts = 'PLAT=INTEL MPIDEF="-DSPRNG_MPI" CC="$CC" F77="$F77" PMLCGDEF="-DUSE_PMLCG" GMPLIB="-L$EBROOTGMP/lib -lgmp" FFXN="-DAdd_"' +buildopts = 'PLAT=INTEL MPIDEF="-DSPRNG_MPI" CC="$CC" F77="$F77" PMLCGDEF="-DUSE_PMLCG" ' +buildopts += 'GMPLIB="-L$EBROOTGMP/lib -lgmp" FFXN="-DAdd_"' # does not support parallel build parallel = 1 diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.14.1-GCCcore-4.9.3.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.14.1-GCCcore-4.9.3.eb index d38cf61101..cb84023340 100644 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.14.1-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.14.1-GCCcore-4.9.3.eb @@ -37,7 +37,8 @@ dependencies = [ parallel = 1 sanity_check_paths = { - 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', 'lib/libsqlite3.a', 'lib/libsqlite3.%s' % SHLIB_EXT], + 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', 'lib/libsqlite3.a', + 'lib/libsqlite3.%s' % SHLIB_EXT], 'dirs': ['lib/pkgconfig'], } diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-GCC-4.9.3-2.25.eb index 62c6f7b8b2..15a228e4cf 100644 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-GCC-4.9.3-2.25.eb @@ -33,7 +33,8 @@ dependencies = [ parallel = 1 sanity_check_paths = { - 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', 'lib/libsqlite3.a', 'lib/libsqlite3.%s' % SHLIB_EXT], + 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', 'lib/libsqlite3.a', + 'lib/libsqlite3.%s' % SHLIB_EXT], 'dirs': ['lib/pkgconfig'], } diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-foss-2015a.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-foss-2015a.eb index 06b2583e36..0e3d5b0943 100644 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-foss-2015a.eb +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-foss-2015a.eb @@ -33,7 +33,8 @@ dependencies = [ parallel = 1 sanity_check_paths = { - 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', 'lib/libsqlite3.a', 'lib/libsqlite3.%s' % SHLIB_EXT], + 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', 'lib/libsqlite3.a', + 'lib/libsqlite3.%s' % SHLIB_EXT], 'dirs': ['lib/pkgconfig'], } diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-foss-2015b.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-foss-2015b.eb index 5708afcd84..3cdb5e9a31 100644 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-foss-2015b.eb +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-foss-2015b.eb @@ -33,7 +33,8 @@ dependencies = [ parallel = 1 sanity_check_paths = { - 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', 'lib/libsqlite3.a', 'lib/libsqlite3.%s' % SHLIB_EXT], + 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', 'lib/libsqlite3.a', + 'lib/libsqlite3.%s' % SHLIB_EXT], 'dirs': ['lib/pkgconfig'], } diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-gimkl-2.11.5.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-gimkl-2.11.5.eb index 11fc55a1b6..c9bee3d1d5 100644 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-gimkl-2.11.5.eb @@ -33,7 +33,8 @@ dependencies = [ parallel = 1 sanity_check_paths = { - 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', 'lib/libsqlite3.a', 'lib/libsqlite3.%s' % SHLIB_EXT], + 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', 'lib/libsqlite3.a', + 'lib/libsqlite3.%s' % SHLIB_EXT], 'dirs': ['lib/pkgconfig'], } diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-goolf-1.4.10.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-goolf-1.4.10.eb index 6a41f5863c..2b1f98a6ac 100644 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-goolf-1.4.10.eb @@ -33,7 +33,8 @@ dependencies = [ parallel = 1 sanity_check_paths = { - 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', 'lib/libsqlite3.a', 'lib/libsqlite3.%s' % SHLIB_EXT], + 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', 'lib/libsqlite3.a', + 'lib/libsqlite3.%s' % SHLIB_EXT], 'dirs': ['lib/pkgconfig'], } diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-goolf-1.7.20.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-goolf-1.7.20.eb index e06537d494..86716967ff 100644 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-goolf-1.7.20.eb @@ -33,7 +33,8 @@ dependencies = [ parallel = 1 sanity_check_paths = { - 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', 'lib/libsqlite3.a', 'lib/libsqlite3.%s' % SHLIB_EXT], + 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', 'lib/libsqlite3.a', + 'lib/libsqlite3.%s' % SHLIB_EXT], 'dirs': ['lib/pkgconfig'], } diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-intel-2015a.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-intel-2015a.eb index 17d369e530..70270519d3 100644 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-intel-2015a.eb +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-intel-2015a.eb @@ -33,7 +33,8 @@ dependencies = [ parallel = 1 sanity_check_paths = { - 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', 'lib/libsqlite3.a', 'lib/libsqlite3.%s' % SHLIB_EXT], + 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', 'lib/libsqlite3.a', + 'lib/libsqlite3.%s' % SHLIB_EXT], 'dirs': ['lib/pkgconfig'], } diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-intel-2015b.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-intel-2015b.eb index 26439e2d65..5c38e72b1a 100644 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-intel-2015b.eb +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-intel-2015b.eb @@ -33,7 +33,8 @@ dependencies = [ parallel = 1 sanity_check_paths = { - 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', 'lib/libsqlite3.a', 'lib/libsqlite3.%s' % SHLIB_EXT], + 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', 'lib/libsqlite3.a', + 'lib/libsqlite3.%s' % SHLIB_EXT], 'dirs': ['lib/pkgconfig'], } diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.4.1-goolf-1.4.10.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.4.1-goolf-1.4.10.eb index 5d1c89464a..0a07713fbb 100644 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.4.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.4.1-goolf-1.4.10.eb @@ -19,7 +19,7 @@ description = "SQLite: SQL Database Engine in a C Library" # eg. http://www.hwaci.com/sw/sqlite/2013/sqlite-autoconf-3080100.tar.gz source_urls = ['http://www.hwaci.com/sw/sqlite/2014'] -sources = ['sqlite-autoconf-%s0%s0%s0%s.tar.gz' % tuple(version.split('.'))] # very weird way to calculate your filename +sources = ['sqlite-autoconf-%s0%s0%s0%s.tar.gz' % tuple(version.split('.'))] toolchain = {'name': 'goolf', 'version': '1.4.10'} diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-CrayGNU-2015.11.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-CrayGNU-2015.11.eb index 429cfc37d8..408f74829a 100644 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-CrayGNU-2015.11.eb +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-CrayGNU-2015.11.eb @@ -33,7 +33,8 @@ dependencies = [ parallel = 1 sanity_check_paths = { - 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', 'lib/libsqlite3.a', 'lib/libsqlite3.%s' % SHLIB_EXT], + 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', 'lib/libsqlite3.a', + 'lib/libsqlite3.%s' % SHLIB_EXT], 'dirs': ['lib/pkgconfig'], } diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-CrayGNU-2016.03.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-CrayGNU-2016.03.eb index 51941069b6..5c92bc8136 100644 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-CrayGNU-2016.03.eb +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-CrayGNU-2016.03.eb @@ -33,7 +33,8 @@ dependencies = [ parallel = 1 sanity_check_paths = { - 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', 'lib/libsqlite3.a', 'lib/libsqlite3.%s' % SHLIB_EXT], + 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', 'lib/libsqlite3.a', + 'lib/libsqlite3.%s' % SHLIB_EXT], 'dirs': ['lib/pkgconfig'], } diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-foss-2016a.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-foss-2016a.eb index 47bee4f624..8902612f46 100644 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-foss-2016a.eb +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-foss-2016a.eb @@ -33,7 +33,8 @@ dependencies = [ parallel = 1 sanity_check_paths = { - 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', 'lib/libsqlite3.a', 'lib/libsqlite3.%s' % SHLIB_EXT], + 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', 'lib/libsqlite3.a', + 'lib/libsqlite3.%s' % SHLIB_EXT], 'dirs': ['lib/pkgconfig'], } diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-gimkl-2.11.5.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-gimkl-2.11.5.eb index 8d257ce664..4b9cea2422 100644 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-gimkl-2.11.5.eb @@ -33,7 +33,8 @@ dependencies = [ parallel = 1 sanity_check_paths = { - 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', 'lib/libsqlite3.a', 'lib/libsqlite3.%s' % SHLIB_EXT], + 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', 'lib/libsqlite3.a', + 'lib/libsqlite3.%s' % SHLIB_EXT], 'dirs': ['lib/pkgconfig'], } diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-goolf-1.7.20.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-goolf-1.7.20.eb index c1e564bfd6..d75861cbb6 100644 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-goolf-1.7.20.eb @@ -33,7 +33,8 @@ dependencies = [ parallel = 1 sanity_check_paths = { - 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', 'lib/libsqlite3.a', 'lib/libsqlite3.%s' % SHLIB_EXT], + 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', 'lib/libsqlite3.a', + 'lib/libsqlite3.%s' % SHLIB_EXT], 'dirs': ['lib/pkgconfig'], } diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-intel-2015b.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-intel-2015b.eb index 79c1231084..177a74a0fb 100644 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-intel-2015b.eb +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-intel-2015b.eb @@ -33,7 +33,8 @@ dependencies = [ parallel = 1 sanity_check_paths = { - 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', 'lib/libsqlite3.a', 'lib/libsqlite3.%s' % SHLIB_EXT], + 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', 'lib/libsqlite3.a', + 'lib/libsqlite3.%s' % SHLIB_EXT], 'dirs': ['lib/pkgconfig'], } diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-intel-2016.02-GCC-4.9.eb index 3555a7ac4c..885ab346a9 100644 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-intel-2016.02-GCC-4.9.eb @@ -33,7 +33,8 @@ dependencies = [ parallel = 1 sanity_check_paths = { - 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', 'lib/libsqlite3.a', 'lib/libsqlite3.%s' % SHLIB_EXT], + 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', 'lib/libsqlite3.a', + 'lib/libsqlite3.%s' % SHLIB_EXT], 'dirs': ['lib/pkgconfig'], } diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-intel-2016a.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-intel-2016a.eb index a35ea6d281..46583c5246 100644 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-intel-2016a.eb +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-intel-2016a.eb @@ -33,7 +33,8 @@ dependencies = [ parallel = 1 sanity_check_paths = { - 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', 'lib/libsqlite3.a', 'lib/libsqlite3.%s' % SHLIB_EXT], + 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', 'lib/libsqlite3.a', + 'lib/libsqlite3.%s' % SHLIB_EXT], 'dirs': ['lib/pkgconfig'], } diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-iomkl-2016.07.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-iomkl-2016.07.eb index 4eb223b17f..c1a72bbbe4 100644 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-iomkl-2016.07.eb +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-iomkl-2016.07.eb @@ -33,7 +33,8 @@ dependencies = [ parallel = 1 sanity_check_paths = { - 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', 'lib/libsqlite3.a', 'lib/libsqlite3.%s' % SHLIB_EXT], + 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', 'lib/libsqlite3.a', + 'lib/libsqlite3.%s' % SHLIB_EXT], 'dirs': ['lib/pkgconfig'], } diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-iomkl-2016.09-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-iomkl-2016.09-GCC-4.9.3-2.25.eb index e099c4dd67..68f9f01974 100644 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-iomkl-2016.09-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-iomkl-2016.09-GCC-4.9.3-2.25.eb @@ -33,7 +33,8 @@ dependencies = [ parallel = 1 sanity_check_paths = { - 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', 'lib/libsqlite3.a', 'lib/libsqlite3.%s' % SHLIB_EXT], + 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', 'lib/libsqlite3.a', + 'lib/libsqlite3.%s' % SHLIB_EXT], 'dirs': ['lib/pkgconfig'], } diff --git a/easybuild/easyconfigs/s/STAR-Fusion/STAR-Fusion-0.6.0-goolf-1.4.10-Perl-5.16.3.eb b/easybuild/easyconfigs/s/STAR-Fusion/STAR-Fusion-0.6.0-goolf-1.4.10-Perl-5.16.3.eb index 58fcb58c2d..c87beb9409 100644 --- a/easybuild/easyconfigs/s/STAR-Fusion/STAR-Fusion-0.6.0-goolf-1.4.10-Perl-5.16.3.eb +++ b/easybuild/easyconfigs/s/STAR-Fusion/STAR-Fusion-0.6.0-goolf-1.4.10-Perl-5.16.3.eb @@ -30,17 +30,17 @@ exts_filter = ("perldoc -lm %(ext_name)s ", "") exts_list = [ ('Set::IntervalTree', '0.10', { - 'source_tmpl': 'Set-IntervalTree-0.10.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BE/BENBOOTH/'], + 'source_tmpl': 'Set-IntervalTree-0.10.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BE/BENBOOTH/'], }), ('DB_File', '1.835', { - 'source_tmpl': 'DB_File-1.835.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PM/PMQS/'], + 'source_tmpl': 'DB_File-1.835.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PM/PMQS/'], }), ] modextrapaths = { - 'PATH': "", # add installation dir to PATH + 'PATH': "", # add installation dir to PATH 'PERL5LIB': 'lib/perl5/site_perl/%(perlver)s/' } diff --git a/easybuild/easyconfigs/s/STAR/STAR-2.5.0a-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/s/STAR/STAR-2.5.0a-GNU-4.9.3-2.25.eb index b6190397ee..bc379c42eb 100644 --- a/easybuild/easyconfigs/s/STAR/STAR-2.5.0a-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/s/STAR/STAR-2.5.0a-GNU-4.9.3-2.25.eb @@ -9,8 +9,7 @@ name = 'STAR' version = '2.5.0a' homepage = 'https://github.com/alexdobin/STAR' -description = """ STAR aligns RNA-seq reads to a reference genome using - uncompressed suffix arrays. """ +description = "STAR aligns RNA-seq reads to a reference genome using uncompressed suffix arrays." toolchain = {'name': 'GNU', 'version': '4.9.3-2.25'} toolchainopts = {'openmp': True} @@ -19,7 +18,7 @@ source_urls = ['https://github.com/alexdobin/STAR/archive/'] sources = ['%(name)s_%(version)s.tar.gz'] dependencies = [ - ('zlib', '1.2.8'), + ('zlib', '1.2.8'), ] start_dir = 'source' @@ -29,7 +28,7 @@ buildopts = ' STAR && make STARlong' parallel = 1 files_to_copy = [(["source/STAR", "source/STARlong"], "bin"), "CHANGES.md", "doc", "extras", "LICENSE", "README.md", "RELEASEnotes.md"] - + sanity_check_paths = { 'files': ["bin/STAR", "bin/STARlong"], 'dirs': [], diff --git a/easybuild/easyconfigs/s/STAR/STAR-2.5.0a-goolf-1.4.10.eb b/easybuild/easyconfigs/s/STAR/STAR-2.5.0a-goolf-1.4.10.eb index ee25be84dd..9bf855263a 100644 --- a/easybuild/easyconfigs/s/STAR/STAR-2.5.0a-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/s/STAR/STAR-2.5.0a-goolf-1.4.10.eb @@ -9,8 +9,7 @@ name = 'STAR' version = '2.5.0a' homepage = 'https://github.com/alexdobin/STAR' -description = """ STAR aligns RNA-seq reads to a reference genome using - uncompressed suffix arrays. """ +description = "STAR aligns RNA-seq reads to a reference genome using uncompressed suffix arrays." toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'openmp': True} @@ -19,7 +18,7 @@ source_urls = ['https://github.com/alexdobin/STAR/archive/'] sources = ['%(name)s_%(version)s.tar.gz'] dependencies = [ - ('zlib', '1.2.8'), + ('zlib', '1.2.8'), ] start_dir = 'source' @@ -29,7 +28,7 @@ buildopts = ' STAR && make STARlong' parallel = 1 files_to_copy = [(["source/STAR", "source/STARlong"], "bin"), "CHANGES.md", "doc", "extras", "LICENSE", "README.md", "RELEASEnotes.md"] - + sanity_check_paths = { 'files': ["bin/STAR", "bin/STARlong"], 'dirs': [], diff --git a/easybuild/easyconfigs/s/STAR/STAR-2.5.1b-foss-2015b.eb b/easybuild/easyconfigs/s/STAR/STAR-2.5.1b-foss-2015b.eb index 406fea6072..947c48d129 100644 --- a/easybuild/easyconfigs/s/STAR/STAR-2.5.1b-foss-2015b.eb +++ b/easybuild/easyconfigs/s/STAR/STAR-2.5.1b-foss-2015b.eb @@ -8,11 +8,10 @@ easyblock = 'MakeCp' name = 'STAR' -version = '2.5.1b' +version = '2.5.1b' homepage = 'https://github.com/alexdobin/STAR' -description = """ STAR aligns RNA-seq reads to a reference genome using - uncompressed suffix arrays. """ +description = "STAR aligns RNA-seq reads to a reference genome using uncompressed suffix arrays." toolchain = {'name': 'foss', 'version': '2015b'} toolchainopts = {'openmp': True} @@ -21,7 +20,7 @@ source_urls = ['https://github.com/alexdobin/STAR/archive/'] sources = ['%(version)s.tar.gz'] dependencies = [ - ('zlib', '1.2.8'), + ('zlib', '1.2.8'), ] start_dir = 'source' @@ -31,7 +30,7 @@ buildopts = ' STAR && make STARlong' parallel = 1 files_to_copy = [(["source/STAR", "source/STARlong"], "bin"), "CHANGES.md", "doc", "extras", "LICENSE", "README.md", "RELEASEnotes.md"] - + sanity_check_paths = { 'files': ["bin/STAR", "bin/STARlong"], 'dirs': [], diff --git a/easybuild/easyconfigs/s/STAR/STAR-2.5.1b-goolf-1.4.10.eb b/easybuild/easyconfigs/s/STAR/STAR-2.5.1b-goolf-1.4.10.eb index b04986c691..c67472aaa1 100644 --- a/easybuild/easyconfigs/s/STAR/STAR-2.5.1b-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/s/STAR/STAR-2.5.1b-goolf-1.4.10.eb @@ -6,11 +6,10 @@ easyblock = 'MakeCp' name = 'STAR' -version = '2.5.1b' +version = '2.5.1b' homepage = 'https://github.com/alexdobin/STAR' -description = """ STAR aligns RNA-seq reads to a reference genome using - uncompressed suffix arrays. """ +description = "STAR aligns RNA-seq reads to a reference genome using uncompressed suffix arrays." toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'openmp': True} @@ -19,7 +18,7 @@ source_urls = ['https://github.com/alexdobin/STAR/archive/'] sources = ['%(version)s.tar.gz'] dependencies = [ - ('zlib', '1.2.8'), + ('zlib', '1.2.8'), ] start_dir = 'source' @@ -29,7 +28,7 @@ buildopts = ' STAR && make STARlong' parallel = 1 files_to_copy = [(["source/STAR", "source/STARlong"], "bin"), "CHANGES.md", "doc", "extras", "LICENSE", "README.md", "RELEASEnotes.md"] - + sanity_check_paths = { 'files': ["bin/STAR", "bin/STARlong"], 'dirs': [], diff --git a/easybuild/easyconfigs/s/STAR/STAR-2.5.2a-foss-2016a.eb b/easybuild/easyconfigs/s/STAR/STAR-2.5.2a-foss-2016a.eb index 769bc0a35c..b5f453b8c8 100644 --- a/easybuild/easyconfigs/s/STAR/STAR-2.5.2a-foss-2016a.eb +++ b/easybuild/easyconfigs/s/STAR/STAR-2.5.2a-foss-2016a.eb @@ -9,11 +9,10 @@ easyblock = 'MakeCp' name = 'STAR' -version = '2.5.2a' +version = '2.5.2a' homepage = 'https://github.com/alexdobin/STAR' -description = """ STAR aligns RNA-seq reads to a reference genome using - uncompressed suffix arrays. """ +description = "STAR aligns RNA-seq reads to a reference genome using uncompressed suffix arrays." toolchain = {'name': 'foss', 'version': '2016a'} toolchainopts = {'openmp': True} @@ -22,7 +21,7 @@ source_urls = ['https://github.com/alexdobin/STAR/archive/'] sources = ['%(version)s.tar.gz'] dependencies = [ - ('zlib', '1.2.8'), + ('zlib', '1.2.8'), ] start_dir = 'source' @@ -32,15 +31,15 @@ buildopts = ' STAR && make STARlong' parallel = 1 files_to_copy = [ - (["source/STAR", "source/STARlong"], "bin"), - "CHANGES.md", - "doc", - "extras", - "LICENSE", - "README.md", + (["source/STAR", "source/STARlong"], "bin"), + "CHANGES.md", + "doc", + "extras", + "LICENSE", + "README.md", "RELEASEnotes.md" ] - + sanity_check_paths = { 'files': ["bin/STAR", "bin/STARlong"], 'dirs': [], diff --git a/easybuild/easyconfigs/s/STAR/STAR-2.5.2a-goolf-1.7.20.eb b/easybuild/easyconfigs/s/STAR/STAR-2.5.2a-goolf-1.7.20.eb index fd35161f48..545af822d8 100644 --- a/easybuild/easyconfigs/s/STAR/STAR-2.5.2a-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/s/STAR/STAR-2.5.2a-goolf-1.7.20.eb @@ -6,11 +6,10 @@ easyblock = 'MakeCp' name = 'STAR' -version = '2.5.2a' +version = '2.5.2a' homepage = 'https://github.com/alexdobin/STAR' -description = """ STAR aligns RNA-seq reads to a reference genome using - uncompressed suffix arrays. """ +description = "STAR aligns RNA-seq reads to a reference genome using uncompressed suffix arrays." toolchain = {'name': 'goolf', 'version': '1.7.20'} toolchainopts = {'openmp': True} @@ -19,7 +18,7 @@ source_urls = ['https://github.com/alexdobin/STAR/archive/'] sources = ['%(version)s.tar.gz'] dependencies = [ - ('zlib', '1.2.8'), + ('zlib', '1.2.8'), ] start_dir = 'source' @@ -29,15 +28,15 @@ buildopts = ' STAR && make STARlong' parallel = 1 files_to_copy = [ - (["source/STAR", "source/STARlong"], "bin"), - "CHANGES.md", - "doc", - "extras", - "LICENSE", - "README.md", + (["source/STAR", "source/STARlong"], "bin"), + "CHANGES.md", + "doc", + "extras", + "LICENSE", + "README.md", "RELEASEnotes.md" ] - + sanity_check_paths = { 'files': ["bin/STAR", "bin/STARlong"], 'dirs': [], diff --git a/easybuild/easyconfigs/s/SUMATRA/SUMATRA-1.0.20-foss-2016a.eb b/easybuild/easyconfigs/s/SUMATRA/SUMATRA-1.0.20-foss-2016a.eb index b96f631d9c..352f9013ea 100644 --- a/easybuild/easyconfigs/s/SUMATRA/SUMATRA-1.0.20-foss-2016a.eb +++ b/easybuild/easyconfigs/s/SUMATRA/SUMATRA-1.0.20-foss-2016a.eb @@ -7,7 +7,7 @@ easyblock = 'MakeCp' name = 'SUMATRA' version = '1.0.20' -homepage = "http://metabarcoding.org/sumatra" +homepage = 'http://metabarcoding.org/sumatra' description = """SUMATRA and SUMACLUST: fast and exact comparison and clustering of sequences.""" toolchain = {'name': 'foss', 'version': '2016a'} diff --git a/easybuild/easyconfigs/s/Saxon-HE/Saxon-HE-9.7.0.4-Java-1.7.0_79.eb b/easybuild/easyconfigs/s/Saxon-HE/Saxon-HE-9.7.0.4-Java-1.7.0_79.eb index 031be8f553..2de8d75b11 100644 --- a/easybuild/easyconfigs/s/Saxon-HE/Saxon-HE-9.7.0.4-Java-1.7.0_79.eb +++ b/easybuild/easyconfigs/s/Saxon-HE/Saxon-HE-9.7.0.4-Java-1.7.0_79.eb @@ -10,7 +10,7 @@ description = """Open Source SAXON XSLT processor developed by Saxonica Limited. toolchain = {'name': 'dummy', 'version': ''} sources = ['SaxonHE%sJ.zip' % version.replace('.', '-')] -source_urls = ['https://sourceforge.net/projects/saxon/files/Saxon-HE/%(version_major_minor)s' , 'download'] +source_urls = ['https://sourceforge.net/projects/saxon/files/Saxon-HE/%(version_major_minor)s', 'download'] dependencies = [('Java', '1.7.0_79')] diff --git a/easybuild/easyconfigs/s/SeqPrep/SeqPrep-1.2-goolf-1.7.20.eb b/easybuild/easyconfigs/s/SeqPrep/SeqPrep-1.2-goolf-1.7.20.eb index 29459a5481..86ba1ed78f 100644 --- a/easybuild/easyconfigs/s/SeqPrep/SeqPrep-1.2-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/s/SeqPrep/SeqPrep-1.2-goolf-1.7.20.eb @@ -23,7 +23,7 @@ dependencies = [ files_to_copy = [(['SeqPrep'], 'bin'), ] parallel = 1 - + sanity_check_paths = { 'files': ['bin/SeqPrep'], 'dirs': [], diff --git a/easybuild/easyconfigs/s/Serf/Serf-1.3.8-foss-2015a.eb b/easybuild/easyconfigs/s/Serf/Serf-1.3.8-foss-2015a.eb index 987ce669c8..dd4add0a50 100644 --- a/easybuild/easyconfigs/s/Serf/Serf-1.3.8-foss-2015a.eb +++ b/easybuild/easyconfigs/s/Serf/Serf-1.3.8-foss-2015a.eb @@ -21,8 +21,8 @@ builddependencies = [('SCons', '2.3.6', '-Python-2.7.9')] dependencies = [ ('APR', '1.5.2'), ('APR-util', '1.5.4'), - # ('OpenSSL', '1.0.1p'), # OS dependency should be preferred if the os version is more recent then this version, it's - # nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1p'), # OS dependency should be preferred if the os version is more recent then this version, it's + # nice to have an up to date openssl for security reasons ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] -- GitLab From c49c34991d67d6c086933324d4c1533ae7063f73 Mon Sep 17 00:00:00 2001 From: Robert Date: Wed, 22 Feb 2017 11:09:07 +1030 Subject: [PATCH 0119/1603] meRanTK-1.1.1b added --- .../easyconfigs/m/meRanTK/meRanTK-1.1.1b.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/m/meRanTK/meRanTK-1.1.1b.eb diff --git a/easybuild/easyconfigs/m/meRanTK/meRanTK-1.1.1b.eb b/easybuild/easyconfigs/m/meRanTK/meRanTK-1.1.1b.eb new file mode 100644 index 0000000000..25c303ad85 --- /dev/null +++ b/easybuild/easyconfigs/m/meRanTK/meRanTK-1.1.1b.eb @@ -0,0 +1,37 @@ +## +# This is a contribution from Phoenix HPC Service, The University of Adelaide, Australia +# Homepage: https://www.adelaide.edu.au/phoenix/ +# +# Copyright:: adelaide.edu.au/phoenix +# Authors:: Robert Qiao , Exequiel Manuel Sepulveda Escobedo +# License:: +# +# Notes:: +## + +name = 'meRanTK' +version = '1.1.1b' + +easyblock = 'BinariesTarball' +homepage = 'http://www.icbi.at/index.html' +description = """meRanTK is a versatile high performance toolkit for complete analysis of methylated RNA data.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['http://www.icbi.at/software/meRanTK/downloads'] +sources = ['%s/meRanTK-%s.zip' %(version,version,)] + +dependencies = [ +] + +sanity_check_paths = { + 'files':['bin/meRanAnnotate'], + 'files':['bin/meRanCall'], + 'files':['bin/meRanCompare'], + 'files':['bin/meRanGs'], + 'files':['bin/meRanGt'], + 'files':['bin/meRanT'], + 'dirs':[], +} + +moduleclass = 'bio' -- GitLab From 3403881a052f5c7f80732205b069295dae319e9e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 22 Feb 2017 09:44:06 +0100 Subject: [PATCH 0120/1603] fix broken test in Cantera 2.3.0 rather than skipping it --- ...Cantera-2.3.0-intel-2016b-Python-2.7.12.eb | 2 +- .../Cantera-2.3.0_fix-test-reprod.patch | 31 +++++++++++++++++++ .../Cantera-2.3.0_skip-broken-tests.patch | 25 --------------- 3 files changed, 32 insertions(+), 26 deletions(-) create mode 100644 easybuild/easyconfigs/c/Cantera/Cantera-2.3.0_fix-test-reprod.patch delete mode 100644 easybuild/easyconfigs/c/Cantera/Cantera-2.3.0_skip-broken-tests.patch diff --git a/easybuild/easyconfigs/c/Cantera/Cantera-2.3.0-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/c/Cantera/Cantera-2.3.0-intel-2016b-Python-2.7.12.eb index 594203f790..62c745b353 100644 --- a/easybuild/easyconfigs/c/Cantera/Cantera-2.3.0-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/c/Cantera/Cantera-2.3.0-intel-2016b-Python-2.7.12.eb @@ -15,7 +15,7 @@ sources = ['v%(version)s.tar.gz'] patches = [ 'Cantera-%(version)s_fix-bug-416.patch', - 'Cantera-%(version)s_skip-broken-tests.patch', + 'Cantera-%(version)s_fix-test-reprod.patch', ] dependencies = [ diff --git a/easybuild/easyconfigs/c/Cantera/Cantera-2.3.0_fix-test-reprod.patch b/easybuild/easyconfigs/c/Cantera/Cantera-2.3.0_fix-test-reprod.patch new file mode 100644 index 0000000000..83dde312f8 --- /dev/null +++ b/easybuild/easyconfigs/c/Cantera/Cantera-2.3.0_fix-test-reprod.patch @@ -0,0 +1,31 @@ +see https://github.com/Cantera/cantera/issues/433 and https://github.com/Cantera/cantera/commit/11a0727d5ca6172fcb3596dbc11e7f7b1cc2e806 + +From 11a0727d5ca6172fcb3596dbc11e7f7b1cc2e806 Mon Sep 17 00:00:00 2001 +From: Ray Speth +Date: Tue, 21 Feb 2017 20:29:37 -0500 +Subject: [PATCH] [Test] Fix reproducibility of values used in + add_species_sequential test + +Exact floating point equality can be assured only in the case where the species +are added in the same order, since this affects summations involved in +calculating the mixture molecular weight. This resulted in test failures with +certain versions of the Intel compiler. + +Resolves #433. +--- + test/data/kineticsfromscratch.cti | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/test/data/kineticsfromscratch.cti b/test/data/kineticsfromscratch.cti +index eaba17b..25983cf 100644 +--- a/test/data/kineticsfromscratch.cti ++++ b/test/data/kineticsfromscratch.cti +@@ -2,7 +2,7 @@ units(length='m', time='s', quantity='kmol', act_energy='cal/mol') + + ideal_gas(name = "ohmech", + elements = " O H Ar ", +- species = """ h2o2: H2 H O O2 OH H2O HO2 H2O2 AR""", ++ species = """ h2o2: AR O H2 H OH O2 H2O H2O2 HO2""", + reactions = "all", + transport = "None", + initial_state = state(temperature = 300.0, diff --git a/easybuild/easyconfigs/c/Cantera/Cantera-2.3.0_skip-broken-tests.patch b/easybuild/easyconfigs/c/Cantera/Cantera-2.3.0_skip-broken-tests.patch deleted file mode 100644 index d3b26cf18f..0000000000 --- a/easybuild/easyconfigs/c/Cantera/Cantera-2.3.0_skip-broken-tests.patch +++ /dev/null @@ -1,25 +0,0 @@ -skip broken test, fails due to strict floating-point value comparison -see https://github.com/Cantera/cantera/issues/433 - -author: Kenneth Hoste (HPC-UGent) - ---- test/kinetics/kineticsFromScratch.cpp.orig 2017-02-15 16:32:24.518921570 +0100 -+++ test/kinetics/kineticsFromScratch.cpp 2017-02-15 16:32:38.509147212 +0100 -@@ -453,7 +453,7 @@ - } - }; - --TEST_F(KineticsAddSpecies, add_species_sequential) -+/*TEST_F(KineticsAddSpecies, add_species_sequential) - { - ASSERT_EQ((size_t) 0, kin.nReactions()); - -@@ -480,7 +480,7 @@ - p.addSpecies(species["HO2"]); - kin.addReaction(reactions[4]); - check_rates(5, "O:0.01, H2:0.1, H:0.02, OH:0.03, O2:0.4, AR:0.3, H2O2:0.03, HO2:0.01"); --} -+}*/ - - TEST_F(KineticsAddSpecies, add_species_err_first) - { -- GitLab From c37616e94582207c44ea75ea166b7e4f96b664ae Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 22 Feb 2017 10:34:28 +0100 Subject: [PATCH 0121/1603] adding easyconfigs: meshio-1.7.1-intel-2016b-Python-2.7.12.eb --- .../meshio-1.7.1-intel-2016b-Python-2.7.12.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/m/meshio/meshio-1.7.1-intel-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/m/meshio/meshio-1.7.1-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/m/meshio/meshio-1.7.1-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..d41f8720e8 --- /dev/null +++ b/easybuild/easyconfigs/m/meshio/meshio-1.7.1-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,39 @@ +easyblock = 'PythonPackage' + +name = 'meshio' +version = '1.7.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/nschloe/meshio' +description = "meshio is a tool for reading/writing various mesh formats representing unstructured meshes" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.12'), # includes numpy + ('h5py', '2.6.0', versionsuffix + '-HDF5-1.8.18'), + ('VTK', '6.3.0', versionsuffix), +] + +exts_defaultclass = 'PythonPackage' +exts_list = [ + ('appdirs', '1.4.0', { + 'source_urls': ['https://pypi.python.org/packages/source/a/appdirs'], + }), + ('requests', '2.13.0', { + 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], + }), + ('pipdated', '0.1.4', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pipdated'], + }), +] + +sanity_check_paths = { + 'files': ['bin/meshio-convert'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'cae' -- GitLab From f1d9415b25a98b2b6668a260f91f83978a1a38fc Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 22 Feb 2017 11:17:47 +0100 Subject: [PATCH 0122/1603] add patch for XZ 5.2.2 to include 5.1.2alpha symbols required by 'rpm' command on CentOS 7.x --- .../x/XZ/XZ-5.2.2-GCC-5.4.0-2.26.eb | 2 ++ .../x/XZ/XZ-5.2.2-GCCcore-4.9.3.eb | 2 ++ .../easyconfigs/x/XZ/XZ-5.2.2-foss-2015a.eb | 2 ++ .../easyconfigs/x/XZ/XZ-5.2.2-foss-2016.04.eb | 2 ++ .../XZ/XZ-5.2.2-foss-2016a-gettext-0.19.7.eb | 2 ++ .../easyconfigs/x/XZ/XZ-5.2.2-foss-2016a.eb | 2 ++ .../easyconfigs/x/XZ/XZ-5.2.2-foss-2016b.eb | 2 ++ .../easyconfigs/x/XZ/XZ-5.2.2-goolf-1.4.10.eb | 2 ++ .../easyconfigs/x/XZ/XZ-5.2.2-ictce-5.3.0.eb | 2 ++ .../XZ/XZ-5.2.2-intel-2016a-gettext-0.19.7.eb | 2 ++ .../easyconfigs/x/XZ/XZ-5.2.2-intel-2016a.eb | 2 ++ .../easyconfigs/x/XZ/XZ-5.2.2-intel-2016b.eb | 2 ++ .../x/XZ/XZ-5.2.2_compat-libs.patch | 27 +++++++++++++++++++ 13 files changed, 51 insertions(+) create mode 100644 easybuild/easyconfigs/x/XZ/XZ-5.2.2_compat-libs.patch diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-GCC-5.4.0-2.26.eb index 96695c9d5c..6c49a4458b 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-GCC-5.4.0-2.26.eb @@ -11,6 +11,8 @@ toolchain = {'name': 'GCC', 'version': '5.4.0-2.26'} sources = [SOURCELOWER_TAR_BZ2] source_urls = ['http://tukaani.org/xz/'] +patches = ['XZ-%(version)s_compat-libs.patch'] + builddependencies = [ ('Autotools', '20150215'), ('gettext', '0.19.8', '', True), diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-GCCcore-4.9.3.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-GCCcore-4.9.3.eb index f08ddf7da4..001a737c6e 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-GCCcore-4.9.3.eb @@ -11,6 +11,8 @@ toolchain = {'name': 'GCCcore', 'version': '4.9.3'} sources = [SOURCELOWER_TAR_BZ2] source_urls = ['http://tukaani.org/xz/'] +patches = ['XZ-%(version)s_compat-libs.patch'] + builddependencies = [ ('Autotools', '20150215'), ('gettext', '0.19.8', '', True), diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2015a.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2015a.eb index d4f3584da4..f5d80fe9e5 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2015a.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2015a.eb @@ -11,6 +11,8 @@ toolchain = {'name': 'foss', 'version': '2015a'} sources = [SOURCELOWER_TAR_BZ2] source_urls = ['http://tukaani.org/xz/'] +patches = ['XZ-%(version)s_compat-libs.patch'] + builddependencies = [ ('Autotools', '20150215'), ('gettext', '0.19.4', '', True), diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016.04.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016.04.eb index 90393732b9..08aad5d870 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016.04.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016.04.eb @@ -11,6 +11,8 @@ toolchain = {'name': 'foss', 'version': '2016.04'} sources = [SOURCELOWER_TAR_BZ2] source_urls = ['http://tukaani.org/xz/'] +patches = ['XZ-%(version)s_compat-libs.patch'] + builddependencies = [ ('Autotools', '20150215'), ('gettext', '0.19.8', '', True), diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016a-gettext-0.19.7.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016a-gettext-0.19.7.eb index 52273a7c6b..deb8d13a10 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016a-gettext-0.19.7.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016a-gettext-0.19.7.eb @@ -11,6 +11,8 @@ toolchain = {'name': 'foss', 'version': '2016a'} sources = [SOURCELOWER_TAR_BZ2] source_urls = ['http://tukaani.org/xz/'] +patches = ['XZ-%(version)s_compat-libs.patch'] + gettext_ver = '0.19.7' versionsuffix = '-gettext-%s' % gettext_ver diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016a.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016a.eb index 8985ebbf18..a0c7f313e0 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016a.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016a.eb @@ -11,6 +11,8 @@ toolchain = {'name': 'foss', 'version': '2016a'} sources = [SOURCELOWER_TAR_BZ2] source_urls = ['http://tukaani.org/xz/'] +patches = ['XZ-%(version)s_compat-libs.patch'] + builddependencies = [ ('Autotools', '20150215'), ('gettext', '0.19.6', '', True), diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016b.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016b.eb index aaea1f659f..e891d5536a 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016b.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016b.eb @@ -11,6 +11,8 @@ toolchain = {'name': 'foss', 'version': '2016b'} sources = [SOURCELOWER_TAR_BZ2] source_urls = ['http://tukaani.org/xz/'] +patches = ['XZ-%(version)s_compat-libs.patch'] + builddependencies = [ ('Autotools', '20150215'), ('gettext', '0.19.8', '', True), diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-goolf-1.4.10.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-goolf-1.4.10.eb index 1b63e65341..4c118e934f 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-goolf-1.4.10.eb @@ -11,6 +11,8 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} sources = [SOURCELOWER_TAR_BZ2] source_urls = ['http://tukaani.org/xz/'] +patches = ['XZ-%(version)s_compat-libs.patch'] + builddependencies = [ ('Autotools', '20150215', '', ('GCC', '4.7.2')), ('gettext', '0.18.2', '', True), diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-ictce-5.3.0.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-ictce-5.3.0.eb index 2cb7040caf..43117900f6 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-ictce-5.3.0.eb @@ -11,6 +11,8 @@ toolchain = {'name': 'ictce', 'version': '5.3.0'} sources = [SOURCELOWER_TAR_BZ2] source_urls = ['http://tukaani.org/xz/'] +patches = ['XZ-%(version)s_compat-libs.patch'] + builddependencies = [ ('Autotools', '20150215'), ('gettext', '0.18.2', '', True), diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-intel-2016a-gettext-0.19.7.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-intel-2016a-gettext-0.19.7.eb index 9822949071..0e6f109230 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-intel-2016a-gettext-0.19.7.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-intel-2016a-gettext-0.19.7.eb @@ -11,6 +11,8 @@ toolchain = {'name': 'intel', 'version': '2016a'} sources = [SOURCELOWER_TAR_BZ2] source_urls = ['http://tukaani.org/xz/'] +patches = ['XZ-%(version)s_compat-libs.patch'] + gettext_ver = '0.19.7' versionsuffix = '-gettext-%s' % gettext_ver diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-intel-2016a.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-intel-2016a.eb index bcd46743d2..fdf1453ac4 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-intel-2016a.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-intel-2016a.eb @@ -11,6 +11,8 @@ toolchain = {'name': 'intel', 'version': '2016a'} sources = [SOURCELOWER_TAR_BZ2] source_urls = ['http://tukaani.org/xz/'] +patches = ['XZ-%(version)s_compat-libs.patch'] + builddependencies = [ ('Autotools', '20150215'), ('gettext', '0.19.6', '', True), diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-intel-2016b.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-intel-2016b.eb index 95304a848d..85431b3d6e 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-intel-2016b.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-intel-2016b.eb @@ -11,6 +11,8 @@ toolchain = {'name': 'intel', 'version': '2016b'} sources = [SOURCELOWER_TAR_BZ2] source_urls = ['http://tukaani.org/xz/'] +patches = ['XZ-%(version)s_compat-libs.patch'] + builddependencies = [ ('Autotools', '20150215'), ('gettext', '0.19.8', '', True), diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.2_compat-libs.patch b/easybuild/easyconfigs/x/XZ/XZ-5.2.2_compat-libs.patch new file mode 100644 index 0000000000..3090e4e0ea --- /dev/null +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.2_compat-libs.patch @@ -0,0 +1,27 @@ +include two 5.1.2aplha symbols that were included in XZ 5.1.2alpha which are required by the 'rpm' command on CentOS 7.x +see also https://github.com/hpcugent/easybuild-easyconfigs/issues/4036 +original patch: xz-5.2.2-compat-libs.patch, cfr. https://git.centos.org/patch/rpms!xz.git/3f035cee1da9f864609885e5ef2a1be77cd37eee + +--- src/liblzma/liblzma.map.orig 2015-09-29 12:57:36.000000000 +0200 ++++ src/liblzma/liblzma.map 2017-02-22 11:10:33.432868185 +0100 +@@ -95,7 +95,13 @@ + lzma_vli_size; + }; + +-XZ_5.2 { ++XZ_5.1.2alpha { ++global: ++ lzma_stream_encoder_mt; ++ lzma_stream_encoder_mt_memusage; ++} XZ_5.0; ++ ++XZ_5.2.2 { + global: + lzma_block_uncomp_encode; + lzma_cputhreads; +@@ -105,4 +111,4 @@ + + local: + *; +-} XZ_5.0; ++} XZ_5.1.2alpha; -- GitLab From 20aeb9694bf980ddff62a92f4dee8e4c83abec20 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Wed, 22 Feb 2017 12:46:14 +0100 Subject: [PATCH 0123/1603] adding easyconfigs: stress-1.0.4-goolf-1.7.20.eb --- .../s/stress/stress-1.0.4-goolf-1.7.20.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/s/stress/stress-1.0.4-goolf-1.7.20.eb diff --git a/easybuild/easyconfigs/s/stress/stress-1.0.4-goolf-1.7.20.eb b/easybuild/easyconfigs/s/stress/stress-1.0.4-goolf-1.7.20.eb new file mode 100644 index 0000000000..e91ebd2437 --- /dev/null +++ b/easybuild/easyconfigs/s/stress/stress-1.0.4-goolf-1.7.20.eb @@ -0,0 +1,30 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'ConfigureMake' + +name = 'stress' +version = '1.0.4' + +homepage = 'http://people.seas.harvard.edu/~apw/stress/' +description = """stress is a deliberately simple workload generator for POSIX systems. + It imposes a configurable amount of CPU, memory, I/O, and disk stress on the system. + It is written in C, and is free software licensed under the GPLv2.""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +source_urls = ['http://people.seas.harvard.edu/~apw/stress/'] +sources = [SOURCELOWER_TAR_GZ] + +parallel = 1 + +runtest = "check" + +sanity_check_paths = { + 'files': ['bin/stress'], + 'dirs': [] +} + +moduleclass = 'tools' -- GitLab From 21638aa97e214095a6737e9ce6bad388d60d7c99 Mon Sep 17 00:00:00 2001 From: Maxime Boissonneault Date: Wed, 22 Feb 2017 13:44:49 +0000 Subject: [PATCH 0124/1603] fixed patch descriptions, added EB autotools --- .../i/igraph/igraph-0.7.1-intel-2016b.eb | 14 +++++++++++--- 1 file changed, 11 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/i/igraph/igraph-0.7.1-intel-2016b.eb b/easybuild/easyconfigs/i/igraph/igraph-0.7.1-intel-2016b.eb index 53b27e3fc2..68c14b0bae 100644 --- a/easybuild/easyconfigs/i/igraph/igraph-0.7.1-intel-2016b.eb +++ b/easybuild/easyconfigs/i/igraph/igraph-0.7.1-intel-2016b.eb @@ -14,9 +14,17 @@ toolchainopts = {'pic': True} sources = ['igraph-%(version)s.tar.gz'] source_urls = ['https://github.com/igraph/igraph/releases/download/%(version)s'] -# Fix llapack and llblas when compiling with MKL -# Fix aclocal which is hard-coded to version 1.14 -patches = ['igraph-0.7.1-no-lapack-no-blas.patch', 'igraph-0.7.1-fix-aclocal-version.patch'] +builddependencies = [('Autotools', '20150215')] + +patches = [ + # Author: Maxime Boissonneault + # Remove explicit linking on -llapack and -llblas, which are not found when linking against MKL + 'igraph-%(version)s-no-lapack-no-blas.patch', + + # Author: Maxime Boissonneault + # Fix explicit version of aclocal (specified 1.14). Replaced with version 1.15 which corresponds to the 20150215 Autotools + 'igraph-%(version)s-fix-aclocal-version.patch' + ] # link against MKL rather than blas/lapack preconfigopts = "env LDFLAGS='-lmkl_intel_lp64 -lmkl_core -lmkl_sequential -lpthread -lm'" -- GitLab From fd948a94153527552aaf7a620f48b6b3b7606de7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 22 Feb 2017 15:06:26 +0100 Subject: [PATCH 0125/1603] adding easyconfigs: CGAL-4.9-intel-2016b-Python-2.7.12.eb, Qt5-5.8.0-intel-2016b.eb, Eigen-3.3.3-intel-2016b.eb --- .../CGAL-4.9-intel-2016b-Python-2.7.12.eb | 36 +++++++++++++++++++ .../e/Eigen/Eigen-3.3.3-intel-2016b.eb | 13 +++++++ .../q/Qt5/Qt5-5.8.0-intel-2016b.eb | 33 +++++++++++++++++ 3 files changed, 82 insertions(+) create mode 100644 easybuild/easyconfigs/c/CGAL/CGAL-4.9-intel-2016b-Python-2.7.12.eb create mode 100644 easybuild/easyconfigs/e/Eigen/Eigen-3.3.3-intel-2016b.eb create mode 100644 easybuild/easyconfigs/q/Qt5/Qt5-5.8.0-intel-2016b.eb diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.9-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.9-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..1e392edbad --- /dev/null +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.9-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,36 @@ +name = 'CGAL' +version = '4.9' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.cgal.org/' +description = """The goal of the CGAL Open Source Project is to provide easy access to efficient + and reliable geometric algorithms in the form of a C++ library.""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'strict': True} + +source_urls = ['https://github.com/CGAL/cgal/releases/download/releases%2FCGAL-%(version)s'] +sources = [SOURCE_TAR_XZ] + +dependencies = [ + ('zlib', '1.2.8'), + ('Python', '2.7.12'), + ('Boost', '1.63.0', versionsuffix), + ('MPFR', '3.1.4'), + ('GMP', '6.1.1'), + ('libGLU', '9.0.0'), + ('Qt5', '5.8.0'), +] + +builddependencies = [ + ('CMake', '3.7.2'), + ('Eigen', '3.3.3'), +] + +configopts = "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " +configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT +configopts += "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT +configopts += "-DWITH_ZLIB=ON -DWITH_MPFR=ON -DWITH_OpenGL=ON -DWITH_Eigen3=ON " +configopts += "-DWITH_GMPXX=ON -DWITH_LAPACK=ON -DWITH_BLAS=ON " + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.3.3-intel-2016b.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.3.3-intel-2016b.eb new file mode 100644 index 0000000000..fdeb038ac8 --- /dev/null +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.3.3-intel-2016b.eb @@ -0,0 +1,13 @@ +name = 'Eigen' +version = '3.3.3' + +homepage = 'http://eigen.tuxfamily.org/index.php?title=Main_Page' +description = """Eigen is a C++ template library for linear algebra: + matrices, vectors, numerical solvers, and related algorithms.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['http://bitbucket.org/%(namelower)s/%(namelower)s/get'] +sources = ['%(version)s.tar.bz2'] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.8.0-intel-2016b.eb b/easybuild/easyconfigs/q/Qt5/Qt5-5.8.0-intel-2016b.eb new file mode 100644 index 0000000000..a05afd5096 --- /dev/null +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.8.0-intel-2016b.eb @@ -0,0 +1,33 @@ +easyblock = 'EB_Qt' + +name = 'Qt5' +version = '5.8.0' + +homepage = 'http://qt.io/' +description = "Qt is a comprehensive cross-platform C++ application framework." + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = [ + 'http://download.qt.io/official_releases/qt/%(version_major_minor)s/%(version)s/single/', + 'http://download.qt.io/archive/qt/%(version_major_minor)s/%(version)s/single/' +] +sources = ['qt-everywhere-opensource-src-%(version)s.tar.xz'] + +patches = ['Qt5-5.7.1_fix-nan-inf.patch'] + +builddependencies = [ + ('pkg-config', '0.29.1'), +] + +# qtgamepad needs recent kernel/libevdev (fails on RHEL 6.x) +configopts = '-skip qtgamepad' + +dependencies = [ + ('GLib', '2.49.5'), + ('libpng', '1.6.24'), + ('X11', '20160819'), + ('libGLU', '9.0.0'), +] + +moduleclass = 'devel' -- GitLab From 025436aa2f38dd73c5b65a23d304108a04699be6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 22 Feb 2017 15:38:04 +0100 Subject: [PATCH 0126/1603] also update $PATH in OrthoMCL 1.4 easyconfig --- .../o/OrthoMCL/OrthoMCL-1.4-intel-2016b-Perl-5.24.0.eb | 10 ++++++++-- 1 file changed, 8 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/o/OrthoMCL/OrthoMCL-1.4-intel-2016b-Perl-5.24.0.eb b/easybuild/easyconfigs/o/OrthoMCL/OrthoMCL-1.4-intel-2016b-Perl-5.24.0.eb index 6820502e94..55f6dee9e2 100644 --- a/easybuild/easyconfigs/o/OrthoMCL/OrthoMCL-1.4-intel-2016b-Perl-5.24.0.eb +++ b/easybuild/easyconfigs/o/OrthoMCL/OrthoMCL-1.4-intel-2016b-Perl-5.24.0.eb @@ -28,8 +28,14 @@ sanity_check_paths = { 'dirs': ['sample_data'], } -modextrapaths = {'PERL5LIB': ''} +modextrapaths = { + 'PATH': '', + 'PERL5LIB': '', +} -sanity_check_commands = [('perl', '-e "use orthomcl_module;"')] +sanity_check_commands = [ + "orthomcl.pl --help 2>&1 | grep Usage", + "perl -e 'use orthomcl_module;'", +] moduleclass = 'bio' -- GitLab From 8eb3821e5f0dd65e74a6bdb6d9d8db6d4b28ea71 Mon Sep 17 00:00:00 2001 From: Masao Fujinaga Date: Wed, 22 Feb 2017 16:27:20 +0000 Subject: [PATCH 0127/1603] Changed to intel,2017a toolchain --- .../b/Bowtie/Bowtie-1.1.2-intel-2017a.eb | 20 +++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2-intel-2017a.eb diff --git a/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2-intel-2017a.eb b/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2-intel-2017a.eb new file mode 100644 index 0000000000..e573ab735a --- /dev/null +++ b/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2-intel-2017a.eb @@ -0,0 +1,20 @@ +# Modified from existing version by: +# Robert Schmidt +# Ottawa Hospital Research Institute - Bioinformatics Team +name = 'Bowtie' +version = '1.1.2' + +homepage = 'http://bowtie-bio.sourceforge.net/index.shtml' +description = """Bowtie is an ultrafast, memory-efficient short read aligner. +It aligns short DNA sequences (reads) to the human genome. +""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = ['%(namelower)s-%(version)s-src.zip'] +source_urls = ['http://download.sourceforge.net/bowtie-bio/'] + +patches = ['int64typedef.patch','void2int.patch'] + +moduleclass = 'bio' -- GitLab From 29d274f5ae6614213f1f0fb1db0d873782922e78 Mon Sep 17 00:00:00 2001 From: Masao Fujinaga Date: Wed, 22 Feb 2017 17:07:17 +0000 Subject: [PATCH 0128/1603] delete Bowtie-1.1.2-iimkl-2017a.eb --- .../b/Bowtie/Bowtie-1.1.2-iimkl-2017a.eb | 20 ------------------- 1 file changed, 20 deletions(-) delete mode 100644 easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2-iimkl-2017a.eb diff --git a/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2-iimkl-2017a.eb b/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2-iimkl-2017a.eb deleted file mode 100644 index 500679eb6f..0000000000 --- a/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2-iimkl-2017a.eb +++ /dev/null @@ -1,20 +0,0 @@ -# Modified from existing version by: -# Robert Schmidt -# Ottawa Hospital Research Institute - Bioinformatics Team -name = 'Bowtie' -version = '1.1.2' - -homepage = 'http://bowtie-bio.sourceforge.net/index.shtml' -description = """Bowtie is an ultrafast, memory-efficient short read aligner. -It aligns short DNA sequences (reads) to the human genome. -""" - -toolchain = {'name': 'iimkl', 'version': '2017a'} -toolchainopts = {'optarch': True, 'pic': True} - -sources = ['%(namelower)s-%(version)s-src.zip'] -source_urls = ['http://download.sourceforge.net/bowtie-bio/'] - -patches = ['int64typedef.patch','void2int.patch'] - -moduleclass = 'bio' -- GitLab From 8566fc7e05fb81386d3b2684d19ee4d523197b3f Mon Sep 17 00:00:00 2001 From: Masao Fujinaga Date: Wed, 22 Feb 2017 17:22:28 +0000 Subject: [PATCH 0129/1603] Added comments to void2int.patch --- easybuild/easyconfigs/b/Bowtie/void2int.patch | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/b/Bowtie/void2int.patch b/easybuild/easyconfigs/b/Bowtie/void2int.patch index 80b76591d4..b2b7d467a3 100644 --- a/easybuild/easyconfigs/b/Bowtie/void2int.patch +++ b/easybuild/easyconfigs/b/Bowtie/void2int.patch @@ -1,3 +1,6 @@ +#The latest Intel compiler (2016,2017) complains about the incompatibility of "void *" argument +#being incompatible with parameter of type "int *" +#M. Fujinaga (fujinaga@ualberta.ca) --- processor_support.h.orig 2017-02-02 21:48:42.436432756 +0000 +++ processor_support.h 2017-02-02 21:48:54.419309743 +0000 @@ -44,8 +44,8 @@ -- GitLab From 646b59d0a5b6ad6be3619c1b2c8f519a7f7cff7f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 22 Feb 2017 18:51:23 +0100 Subject: [PATCH 0130/1603] fix hardcoded paths in OrthoMCL 1.4 installation --- .../OrthoMCL-1.4-intel-2016b-Perl-5.24.0.eb | 18 ++++++++++++++---- 1 file changed, 14 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/o/OrthoMCL/OrthoMCL-1.4-intel-2016b-Perl-5.24.0.eb b/easybuild/easyconfigs/o/OrthoMCL/OrthoMCL-1.4-intel-2016b-Perl-5.24.0.eb index 55f6dee9e2..8cdb56fbdb 100644 --- a/easybuild/easyconfigs/o/OrthoMCL/OrthoMCL-1.4-intel-2016b-Perl-5.24.0.eb +++ b/easybuild/easyconfigs/o/OrthoMCL/OrthoMCL-1.4-intel-2016b-Perl-5.24.0.eb @@ -19,20 +19,30 @@ dependencies = [ ('Perl', '5.24.0'), ('MCL', '%s.%s' % (mcl_majver, mcl_minver)), ('BioPerl', '1.7.1', versionsuffix), + ('BLAST', '2.2.26', '-Linux_x86_64', True), ] start_dir = 'ORTHOMCLV%(version)s' -sanity_check_paths = { - 'files': ['orthomcl_module.pm', 'orthomcl.pl', 'README'], - 'dirs': ['sample_data'], -} +# fix hardcoded paths +postinstallcmds = [ + 'sed -i"" "s@/usr/bin/perl@$EBROOTPERL/bin/perl@g" %(installdir)s/orthomcl.pl', + 'sed -i"" "s@\\"/.*blastall\\";@\\"$EBROOTBLAST/bin/blastall\\";@g" %(installdir)s/orthomcl_module.pm', + 'sed -i"" "s@\\"/.*formatdb\\";@\\"$EBROOTBLAST/bin/formatdb\\";@g" %(installdir)s/orthomcl_module.pm', + 'sed -i"" "s@\\"/.*mcl\\";@\\"$EBROOTMCL/bin/mcl\\";@g" %(installdir)s/orthomcl_module.pm', + 'sed -i"" "s@\\"/.*ORTHOMCL.*%(version)s/\\";@\\"\\$ENV{\'PWD\'}/\\";@g" %(installdir)s/orthomcl_module.pm', +] modextrapaths = { 'PATH': '', 'PERL5LIB': '', } +sanity_check_paths = { + 'files': ['orthomcl_module.pm', 'orthomcl.pl', 'README'], + 'dirs': ['sample_data'], +} + sanity_check_commands = [ "orthomcl.pl --help 2>&1 | grep Usage", "perl -e 'use orthomcl_module;'", -- GitLab From 45166cf524156762318bcb5e1742c503bc032662 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 22 Feb 2017 19:07:17 +0100 Subject: [PATCH 0131/1603] adding easyconfigs: matplotlib-2.0.0-intel-2016b-Python-2.7.12.eb --- .../f/freetype/freetype-2.7.1-intel-2016b.eb | 26 +++++++++++ .../l/libpng/libpng-1.6.27-intel-2016b.eb | 26 +++++++++++ ...plotlib-2.0.0-intel-2016b-Python-2.7.12.eb | 44 +++++++++++++++++++ 3 files changed, 96 insertions(+) create mode 100644 easybuild/easyconfigs/f/freetype/freetype-2.7.1-intel-2016b.eb create mode 100644 easybuild/easyconfigs/l/libpng/libpng-1.6.27-intel-2016b.eb create mode 100644 easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.0-intel-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.7.1-intel-2016b.eb b/easybuild/easyconfigs/f/freetype/freetype-2.7.1-intel-2016b.eb new file mode 100644 index 0000000000..d3a160563e --- /dev/null +++ b/easybuild/easyconfigs/f/freetype/freetype-2.7.1-intel-2016b.eb @@ -0,0 +1,26 @@ +name = 'freetype' +version = '2.7.1' + +homepage = 'http://freetype.org' +description = """FreeType 2 is a software font engine that is designed to be small, efficient, highly customizable, and + portable while capable of producing high-quality output (glyph images). It can be used in graphics libraries, display + servers, font conversion tools, text image generation tools, and many other products as well.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = [GNU_SAVANNAH_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('libpng', '1.6.27'), + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), +] + +sanity_check_paths = { + 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, + 'lib/pkgconfig/freetype2.pc'], + 'dirs': ['include/freetype2'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.27-intel-2016b.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.27-intel-2016b.eb new file mode 100644 index 0000000000..e0204f6881 --- /dev/null +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.27-intel-2016b.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'libpng' +version = '1.6.27' + +homepage = 'http://www.libpng.org/pub/png/libpng.html' +description = "libpng is the official PNG reference library" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('zlib', '1.2.8')] + +configopts = "--with-pic" + +majminver = ''.join(version.split('.')[:2]) +sanity_check_paths = { + 'files': ['include/pngconf.h', 'include/png.h', 'include/pnglibconf.h', 'lib/libpng.a', + 'lib/libpng.%s' % SHLIB_EXT, 'lib/libpng%s.a' % majminver, 'lib/libpng%s.%s' % (majminver, SHLIB_EXT)], + 'dirs': ['bin', 'include/libpng%s' % majminver, 'share/man'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.0-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.0-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..def79919ce --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.0-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,44 @@ +easyblock = 'Bundle' + +name = 'matplotlib' +version = '2.0.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://matplotlib.org' +description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of + hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python + and ipython shell, web application servers, and six graphical user interface toolkits.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' + +dependencies = [ + ('Python', '2.7.12'), + ('freetype', '2.7.1'), + ('libpng', '1.6.27'), +] + +exts_list = [ + ('Cycler', '0.10.0', { + 'modulename': 'cycler', + 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], + 'source_tmpl': 'cycler-%(version)s.tar.gz', + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], + }), +] + +# specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module +full_sanity_check = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +moduleclass = 'vis' -- GitLab From e068d3f6eef6a902f63a06ec7485472d1b1347e4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 22 Feb 2017 19:12:06 +0100 Subject: [PATCH 0132/1603] adding easyconfigs: IPython-5.2.2-intel-2016b-Python-2.7.12.eb --- ...IPython-5.2.2-intel-2016b-Python-2.7.12.eb | 151 ++++++++++++++++++ .../path.py-10.1-intel-2016b-Python-2.7.12.eb | 30 ++++ ...oolkit-1.0.13-intel-2016b-Python-2.7.12.eb | 30 ++++ 3 files changed, 211 insertions(+) create mode 100644 easybuild/easyconfigs/i/IPython/IPython-5.2.2-intel-2016b-Python-2.7.12.eb create mode 100644 easybuild/easyconfigs/p/path.py/path.py-10.1-intel-2016b-Python-2.7.12.eb create mode 100644 easybuild/easyconfigs/p/prompt-toolkit/prompt-toolkit-1.0.13-intel-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/i/IPython/IPython-5.2.2-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/i/IPython/IPython-5.2.2-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..bc8f42751d --- /dev/null +++ b/easybuild/easyconfigs/i/IPython/IPython-5.2.2-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,151 @@ +easyblock = 'Bundle' + +name = 'IPython' +version = '5.2.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://ipython.org/index.html' +description = """IPython provides a rich architecture for interactive computing with: + Powerful interactive shells (terminal and Qt-based). + A browser-based notebook with support for code, text, mathematical expressions, inline plots and other rich media. + Support for interactive data visualization and use of GUI toolkits. + Flexible, embeddable interpreters to load into your own projects. + Easy to use, high performance tools for parallel computing.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +dependencies = [ + ('Python', '2.7.12'), + ('PyZMQ', '16.0.2', '%s-zmq4' % versionsuffix), + ('testpath', '0.3', versionsuffix), + # required by 'nbconvert', but causes problems w.r.t. 'backports' module... + # see https://github.com/hpcugent/easybuild-easyconfigs/issues/3825 + #('entrypoints', '0.2.2', versionsuffix), + ('path.py', '10.1', versionsuffix), + ('prompt-toolkit', '1.0.13', versionsuffix), +] + +# this is a bundle of Python packages +# XXX: the wheel packages (testpath, entrypoints, path.py, prompt-toolkit) have +# to be included as dependencies because bundling wheels does not work +exts_defaultclass = 'PythonPackage' +exts_filter = ("python -c 'import %(ext_name)s'", '') + +exts_list = [ + ('nose', '1.3.7', { + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], + }), + ('requests', '2.13.0', { + 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], + }), + ('nbformat', '4.3.0', { + 'source_urls': ['https://pypi.python.org/packages/source/n/nbformat/'], + }), + ('Pygments', '2.2.0', { + 'source_urls': ['https://pypi.python.org/packages/source/P/Pygments/'], + 'modulename': 'pygments', + }), + ('singledispatch', '3.4.0.3', { + 'source_urls': ['https://pypi.python.org/packages/source/s/singledispatch/'], + }), + ('certifi', '2017.1.23', { + 'source_urls': ['https://pypi.python.org/packages/source/c/certifi/'], + }), + ('backports_abc', '0.5', { + 'source_urls': ['https://pypi.python.org/packages/source/b/backports_abc/'], + }), + ('tornado', '4.4.2', { + 'source_urls': ['https://pypi.python.org/packages/source/t/tornado/'], + }), + ('MarkupSafe', '0.23', { + 'source_urls': ['https://pypi.python.org/packages/source/M/MarkupSafe/'], + 'modulename': 'markupsafe', + }), + ('Jinja2', '2.9.5', { + 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2/'], + 'modulename': 'jinja2', + }), + ('jupyter_client', '5.0.0', { + 'source_urls': ['https://pypi.python.org/packages/source/j/jupyter_client/'], + }), + ('functools32', '3.2.3-2', { + 'source_urls': ['https://pypi.python.org/packages/source/f/functools32/'], + }), + ('jsonschema', '2.6.0', { + 'source_urls': ['https://pypi.python.org/packages/source/j/jsonschema/'], + }), + ('mistune', '0.7.3', { + 'source_urls': ['https://pypi.python.org/packages/source/m/mistune/'], + }), + ('ptyprocess', '0.5.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/ptyprocess/'], + }), + ('terminado', '0.6', { + 'source_urls': ['https://pypi.python.org/packages/source/t/terminado/'], + }), + ('simplegeneric', '0.8.1', { + 'source_urls': ['https://pypi.python.org/packages/source/s/simplegeneric/'], + 'source_tmpl': 'simplegeneric-%(version)s.zip', + }), + ('ipython_genutils', '0.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/i/ipython_genutils/'], + }), + ('pathlib2', '2.2.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pathlib2/'], + }), + ('pickleshare', '0.7.4', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pickleshare/'], + }), + ('traitlets', '4.3.1', { + 'source_urls': ['https://pypi.python.org/packages/source/t/traitlets/'], + }), + ('notebook', '4.4.1', { + 'source_urls': ['https://pypi.python.org/packages/source/n/notebook/'], + }), + ('jupyter_core', '4.3.0', { + 'source_urls': ['https://pypi.python.org/packages/source/j/jupyter_core/'], + }), + ('ipykernel', '4.5.2', { + 'source_urls': ['https://pypi.python.org/packages/source/i/ipykernel/'], + }), + ('pexpect', '4.2.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pexpect/'], + }), + # disabled because entrypoints on which this depends pull in configparser, which causes problems + # see https://github.com/hpcugent/easybuild-easyconfigs/issues/3825 + #('nbconvert', '5.1.1', { + # 'source_urls': ['https://pypi.python.org/packages/source/n/nbconvert/'], + #}), + ('backports.shutil_get_terminal_size', '1.0.0', { + 'source_urls': ['https://pypi.python.org/packages/source/b/backports.shutil_get_terminal_size/'], + }), + ('decorator', '4.0.11', { + 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], + }), + ('ipython', version, { + 'source_urls': ['https://pypi.python.org/packages/source/i/ipython/'], + 'modulename': 'IPython', + }), + ('ipywidgets', '5.2.2', { + 'source_urls': ['https://pypi.python.org/packages/source/i/ipywidgets/'], + }), + ('widgetsnbextension', '1.2.6', { + 'source_urls': ['https://pypi.python.org/packages/source/w/widgetsnbextension/'], + }), +] + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +sanity_check_paths = { + 'files': ['bin/ipython'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/IPython'], +} + +sanity_check_commands = [ + ('ipython -h', ''), + ('ipython notebook --help', ''), + ('iptest', ''), + ('iptest2', ''), +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/path.py/path.py-10.1-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/path.py/path.py-10.1-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..d128f00a07 --- /dev/null +++ b/easybuild/easyconfigs/p/path.py/path.py-10.1-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'path.py' +version = '10.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/jaraco/path.py' +description = """path.py is a Python library implementing path objects as first-class entities, + allowing common operations on files to be invoked on those path objects directly.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = [PYPI_SOURCE] +sources = ['path.py-%(version)s-py2.py3-none-any.whl'] + +dependencies = [ + ('Python', '2.7.12'), +] + +use_pip = True +unpack_sources = False + +sanity_check_paths = { + 'files': ['lib/python%(pyshortver)s/site-packages/path.py'], + 'dirs': [], +} + +options = {'modulename': 'path'} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/prompt-toolkit/prompt-toolkit-1.0.13-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/prompt-toolkit/prompt-toolkit-1.0.13-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..0dc0fbea27 --- /dev/null +++ b/easybuild/easyconfigs/p/prompt-toolkit/prompt-toolkit-1.0.13-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'prompt-toolkit' +version = '1.0.13' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/jonathanslenders/python-prompt-toolkit' +description = """prompt_toolkit is a Python library for building powerful interactive command lines and terminal applications.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = [PYPI_SOURCE] +sources = ['prompt_toolkit-%(version)s-py2-none-any.whl'] + +dependencies = [ + ('Python', '2.7.12'), + ('wcwidth', '0.1.7', versionsuffix), +] + +use_pip = True +unpack_sources = False + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/prompt_toolkit'], +} + +options = {'modulename': 'prompt_toolkit'} + +moduleclass = 'lib' -- GitLab From 7ab0d656dd4fd3170d0b197481127c1d36f2c4a2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 22 Feb 2017 19:13:07 +0100 Subject: [PATCH 0133/1603] adding easyconfigs: VTK-7.1.0-intel-2016b-Python-2.7.12.eb --- .../VTK-7.1.0-intel-2016b-Python-2.7.12.eb | 58 +++++++++++++++++++ 1 file changed, 58 insertions(+) create mode 100644 easybuild/easyconfigs/v/VTK/VTK-7.1.0-intel-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/v/VTK/VTK-7.1.0-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/v/VTK/VTK-7.1.0-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..ff2f4a0f63 --- /dev/null +++ b/easybuild/easyconfigs/v/VTK/VTK-7.1.0-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,58 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-97.html +## + +easyblock = 'CMakeMake' + +name = 'VTK' +version = '7.1.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.vtk.org' +description = """The Visualization Toolkit (VTK) is an open-source, freely available software system for + 3D computer graphics, image processing and visualization. VTK consists of a C++ class library and several + interpreted interface layers including Tcl/Tk, Java, and Python. VTK supports a wide variety of visualization + algorithms including: scalar, vector, tensor, texture, and volumetric methods; and advanced modeling techniques + such as: implicit modeling, polygon reduction, mesh smoothing, cutting, contouring, and Delaunay triangulation.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['http://www.vtk.org/files/release/%(version_major_minor)s'] +sources = [ + SOURCE_TAR_GZ, + '%(name)sData-%(version)s.tar.gz', +] + +builddependencies = [('CMake', '3.7.2')] + +dependencies = [ + ('Python', '2.7.12'), + ('libGLU', '9.0.0'), +] + +configopts = "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT +configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT +configopts += "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include -DVTK_WRAP_PYTHON=ON " +configopts += "-DPYTHON_LIBRARY=$EBROOTPYTHON/lib/libpython%%(pyshortver)s.%s " % SHLIB_EXT +configopts += " -DPYTHON_INCLUDE_DIR=$EBROOTPYTHON/include/python%(pyshortver)s " +preinstallopts = "mkdir -p %(installdir)s/lib/python%(pyshortver)s/site-packages/ && " +preinstallopts += "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +sanity_check_paths = { + 'files': ['bin/vtk%s-%%(version_major_minor)s' % x for x in ['EncodeString', 'HashSource']], + 'dirs': ['lib/python%(pyshortver)s/site-packages/', 'include/vtk-%(version_major_minor)s'], +} + +sanity_check_commands = [('python', "-c 'import %(namelower)s'")] + +moduleclass = 'vis' -- GitLab From 4b9994f8d76853810b7b36a486c27c2dd76704e1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 22 Feb 2017 19:15:10 +0100 Subject: [PATCH 0134/1603] adding easyconfigs: Yade-2017.01a-intel-2016b-Python-2.7.12.eb, libQGLViewer-2.6.4-intel-2016b.eb, minieigen-0.5.3-intel-2016b-Python-2.7.12-Boost-1.63.0.eb --- .../libQGLViewer-2.6.4-intel-2016b.eb | 20 ++++++ ...-intel-2016b-Python-2.7.12-Boost-1.63.0.eb | 27 ++++++++ ...Yade-2017.01a-intel-2016b-Python-2.7.12.eb | 61 +++++++++++++++++++ 3 files changed, 108 insertions(+) create mode 100644 easybuild/easyconfigs/l/libQGLViewer/libQGLViewer-2.6.4-intel-2016b.eb create mode 100644 easybuild/easyconfigs/m/minieigen/minieigen-0.5.3-intel-2016b-Python-2.7.12-Boost-1.63.0.eb create mode 100644 easybuild/easyconfigs/y/Yade/Yade-2017.01a-intel-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/l/libQGLViewer/libQGLViewer-2.6.4-intel-2016b.eb b/easybuild/easyconfigs/l/libQGLViewer/libQGLViewer-2.6.4-intel-2016b.eb new file mode 100644 index 0000000000..b66d7bd768 --- /dev/null +++ b/easybuild/easyconfigs/l/libQGLViewer/libQGLViewer-2.6.4-intel-2016b.eb @@ -0,0 +1,20 @@ +name = 'libQGLViewer' +version = '2.6.4' + +homepage = 'http://libqglviewer.com/' +description = "libQGLViewer is a C++ library based on Qt that eases the creation of OpenGL 3D viewers." + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['http://www.libqglviewer.com/src/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('libGLU', '9.0.0'), +] + +builddependencies = [('Qt', '4.8.7')] + +start_dir = '%(builddir)s/libQGLViewer-%(version)s/QGLViewer' + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/minieigen/minieigen-0.5.3-intel-2016b-Python-2.7.12-Boost-1.63.0.eb b/easybuild/easyconfigs/m/minieigen/minieigen-0.5.3-intel-2016b-Python-2.7.12-Boost-1.63.0.eb new file mode 100644 index 0000000000..4226d4a6e1 --- /dev/null +++ b/easybuild/easyconfigs/m/minieigen/minieigen-0.5.3-intel-2016b-Python-2.7.12-Boost-1.63.0.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'minieigen' +version = '0.5.3' +boostver = '1.63.0' +versionsuffix = '-Python-%%(pyver)s-Boost-%s' % boostver + +homepage = 'https://launchpad.net/minieigen/' +description = """A small wrapper for core parts of EIgen, c++ library for linear algebra.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +sources = [SOURCE_TAR_GZ] +source_urls = [PYPI_SOURCE] + +dependencies = [ + ('Boost', boostver, '-Python-%(pyver)s'), + ('Eigen', '3.3.3'), + ('Python', '2.7.12'), +] + +sanity_check_paths = { + 'files': ['lib/python%%(pyshortver)s/site-packages/minieigen.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/y/Yade/Yade-2017.01a-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/y/Yade/Yade-2017.01a-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..5f79b0294c --- /dev/null +++ b/easybuild/easyconfigs/y/Yade/Yade-2017.01a-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,61 @@ +easyblock = 'CMakeMake' + +name = 'Yade' +version = '2017.01a' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://yade-dem.org/doc/' +description = """ Yade is an extensible open-source framework for discrete numerical models, + focused on Discrete Element Method. The computation parts are written in c++ using flexible object model, + allowing independent implementation of new alogrithms and interfaces. + Python is used for rapid and concise scene construction, simulation control, postprocessing and debugging. """ + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['https://launchpad.net/yade/trunk/yade-1.00.0/+download/'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('Boost', '1.63.0', versionsuffix), + ('CGAL', '4.9', versionsuffix), + ('GDB', '7.11.1', versionsuffix), + ('GL2PS', '1.3.9'), + ('GTS', '0.7.6'), + ('IPython', '5.2.2', versionsuffix), + ('libQGLViewer', '2.6.4'), + ('Loki', '0.1.7'), + ('matplotlib', '1.5.2', versionsuffix), + ('minieigen', '0.5.3', versionsuffix + '-Boost-1.63.0'), + ('PyGTS', '0.3.1', versionsuffix), + ('Python', '2.7.12'), + ('Qt5', '5.8.0'), + ('SQLite', '3.13.0'), + ('VTK', '7.1.0', versionsuffix), + ('zlib', '1.2.8'), +] + +builddependencies = [ + ('CMake', '3.7.2'), + ('Eigen', '3.3.3'), +] + +separate_build_dir = True + +configopts = '-DENABLE_GUI=OFF -DENABLE_LINSOLV=OFF -DENABLE_PFVFLOW=OFF ' +configopts += '-DCGAL_INCLUDE_DIR=$EBROOTCGAL/include ' +configopts += '-DGMP_INCLUDE_DIR=$EBROOTGMP/include -DGMP_LIBRARIES=$EBROOTGMP/lib -DGMPXX_LIBRARIES=$EBROOTGMP/lib ' + +modextrapaths = { + 'LD_LIBRARY_PATH': ['lib64/lib64/yade-%(version)s', 'lib/x86_64-linux-gnu/yade-%(version)s'], + 'LIBRARY_PATH': ['lib64/lib64/yade-%(version)s', 'lib/x86_64-linux-gnu/yade-%(version)s'], + 'PYTHONPATH': ['lib/x86_64-linux-gnu/yade-%(version)s/py', 'lib64/yade-%(version)s/py'], +} + +sanity_check_paths = { + 'files': ['bin/yade-%(version)s', 'bin/yade-%(version)s-batch', + ('lib/x86_64-linux-gnu/yade-%%(version)s/libyade.%s' % SHLIB_EXT, + 'lib64/yade-%%(version)s/libyade.%s' % SHLIB_EXT)], + 'dirs': [('lib/x86_64-linux-gnu/yade-%(version)s/py/yade', 'lib64/yade-%(version)s/py/yade')], +} + +moduleclass = 'devel' -- GitLab From dfe6c82f37987b616023f96006e0daec02f9aa83 Mon Sep 17 00:00:00 2001 From: Masao Fujinaga Date: Wed, 22 Feb 2017 18:41:24 +0000 Subject: [PATCH 0135/1603] Stylistic changes --- easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2-intel-2017a.eb | 7 +++++-- .../Bowtie/{void2int.patch => Bowtie-1.1.2_void2int.patch} | 0 2 files changed, 5 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/b/Bowtie/{void2int.patch => Bowtie-1.1.2_void2int.patch} (100%) diff --git a/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2-intel-2017a.eb b/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2-intel-2017a.eb index e573ab735a..db4bf02c9f 100644 --- a/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2-intel-2017a.eb +++ b/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2-intel-2017a.eb @@ -10,11 +10,14 @@ It aligns short DNA sequences (reads) to the human genome. """ toolchain = {'name': 'intel', 'version': '2017a'} -toolchainopts = {'optarch': True, 'pic': True} +toolchainopts = {'pic': True} sources = ['%(namelower)s-%(version)s-src.zip'] source_urls = ['http://download.sourceforge.net/bowtie-bio/'] -patches = ['int64typedef.patch','void2int.patch'] +patches = [ + 'int64typedef.patch', + 'void2int.patch' +] moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/Bowtie/void2int.patch b/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2_void2int.patch similarity index 100% rename from easybuild/easyconfigs/b/Bowtie/void2int.patch rename to easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2_void2int.patch -- GitLab From 1a3cdba55d30d08a8a83ffbc4c2c28af55589525 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 22 Feb 2017 19:43:12 +0100 Subject: [PATCH 0136/1603] bump VTK to 7.1.0 in meshio easyconfig for compatibility with Yade 2017.01a --- .../m/meshio/meshio-1.7.1-intel-2016b-Python-2.7.12.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/meshio/meshio-1.7.1-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/m/meshio/meshio-1.7.1-intel-2016b-Python-2.7.12.eb index d41f8720e8..cda151feb8 100644 --- a/easybuild/easyconfigs/m/meshio/meshio-1.7.1-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/m/meshio/meshio-1.7.1-intel-2016b-Python-2.7.12.eb @@ -15,7 +15,7 @@ sources = [SOURCE_TAR_GZ] dependencies = [ ('Python', '2.7.12'), # includes numpy ('h5py', '2.6.0', versionsuffix + '-HDF5-1.8.18'), - ('VTK', '6.3.0', versionsuffix), + ('VTK', '7.1.0', versionsuffix), ] exts_defaultclass = 'PythonPackage' -- GitLab From 4ac20d4004c8e89e3659ce635ac7a8275231c4e9 Mon Sep 17 00:00:00 2001 From: Masao Fujinaga Date: Wed, 22 Feb 2017 19:01:17 +0000 Subject: [PATCH 0137/1603] Correct patch file name in easyconfig --- easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2-intel-2017a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2-intel-2017a.eb b/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2-intel-2017a.eb index db4bf02c9f..2f5b9aef33 100644 --- a/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2-intel-2017a.eb +++ b/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2-intel-2017a.eb @@ -17,7 +17,7 @@ source_urls = ['http://download.sourceforge.net/bowtie-bio/'] patches = [ 'int64typedef.patch', - 'void2int.patch' + 'Bowtie-%(version)_void2int.patch' ] moduleclass = 'bio' -- GitLab From 764c127d8474caf90fd492d65653aed6b910fe94 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 22 Feb 2017 20:02:33 +0100 Subject: [PATCH 0138/1603] fix remarks --- .../easyconfigs/s/STAR/STAR-2.5.0a-GNU-4.9.3-2.25.eb | 5 ++++- easybuild/easyconfigs/s/STAR/STAR-2.5.0a-goolf-1.4.10.eb | 5 ++++- easybuild/easyconfigs/s/STAR/STAR-2.5.1b-foss-2015b.eb | 5 ++++- easybuild/easyconfigs/s/STAR/STAR-2.5.1b-goolf-1.4.10.eb | 5 ++++- easybuild/easyconfigs/s/STAR/STAR-2.5.2a-foss-2016a.eb | 9 ++------- easybuild/easyconfigs/s/STAR/STAR-2.5.2a-goolf-1.7.20.eb | 9 ++------- easybuild/easyconfigs/s/Serf/Serf-1.3.8-foss-2015a.eb | 5 +++-- 7 files changed, 23 insertions(+), 20 deletions(-) diff --git a/easybuild/easyconfigs/s/STAR/STAR-2.5.0a-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/s/STAR/STAR-2.5.0a-GNU-4.9.3-2.25.eb index bc379c42eb..04188b3f1a 100644 --- a/easybuild/easyconfigs/s/STAR/STAR-2.5.0a-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/s/STAR/STAR-2.5.0a-GNU-4.9.3-2.25.eb @@ -27,7 +27,10 @@ buildopts = ' STAR && make STARlong' parallel = 1 -files_to_copy = [(["source/STAR", "source/STARlong"], "bin"), "CHANGES.md", "doc", "extras", "LICENSE", "README.md", "RELEASEnotes.md"] +files_to_copy = [ + (['source/STAR', 'source/STARlong'], 'bin'), + 'CHANGES.md', 'doc', 'extras', 'LICENSE', 'README.md', 'RELEASEnotes.md', +] sanity_check_paths = { 'files': ["bin/STAR", "bin/STARlong"], diff --git a/easybuild/easyconfigs/s/STAR/STAR-2.5.0a-goolf-1.4.10.eb b/easybuild/easyconfigs/s/STAR/STAR-2.5.0a-goolf-1.4.10.eb index 9bf855263a..457ab933f7 100644 --- a/easybuild/easyconfigs/s/STAR/STAR-2.5.0a-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/s/STAR/STAR-2.5.0a-goolf-1.4.10.eb @@ -27,7 +27,10 @@ buildopts = ' STAR && make STARlong' parallel = 1 -files_to_copy = [(["source/STAR", "source/STARlong"], "bin"), "CHANGES.md", "doc", "extras", "LICENSE", "README.md", "RELEASEnotes.md"] +files_to_copy = [ + (['source/STAR', 'source/STARlong'], 'bin'), + 'CHANGES.md', 'doc', 'extras', 'LICENSE', 'README.md', 'RELEASEnotes.md', +] sanity_check_paths = { 'files': ["bin/STAR", "bin/STARlong"], diff --git a/easybuild/easyconfigs/s/STAR/STAR-2.5.1b-foss-2015b.eb b/easybuild/easyconfigs/s/STAR/STAR-2.5.1b-foss-2015b.eb index 947c48d129..b4f28e006e 100644 --- a/easybuild/easyconfigs/s/STAR/STAR-2.5.1b-foss-2015b.eb +++ b/easybuild/easyconfigs/s/STAR/STAR-2.5.1b-foss-2015b.eb @@ -29,7 +29,10 @@ buildopts = ' STAR && make STARlong' parallel = 1 -files_to_copy = [(["source/STAR", "source/STARlong"], "bin"), "CHANGES.md", "doc", "extras", "LICENSE", "README.md", "RELEASEnotes.md"] +files_to_copy = [ + (['source/STAR', 'source/STARlong'], 'bin'), + 'CHANGES.md', 'doc', 'extras', 'LICENSE', 'README.md', 'RELEASEnotes.md', +] sanity_check_paths = { 'files': ["bin/STAR", "bin/STARlong"], diff --git a/easybuild/easyconfigs/s/STAR/STAR-2.5.1b-goolf-1.4.10.eb b/easybuild/easyconfigs/s/STAR/STAR-2.5.1b-goolf-1.4.10.eb index c67472aaa1..acf5436cbe 100644 --- a/easybuild/easyconfigs/s/STAR/STAR-2.5.1b-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/s/STAR/STAR-2.5.1b-goolf-1.4.10.eb @@ -27,7 +27,10 @@ buildopts = ' STAR && make STARlong' parallel = 1 -files_to_copy = [(["source/STAR", "source/STARlong"], "bin"), "CHANGES.md", "doc", "extras", "LICENSE", "README.md", "RELEASEnotes.md"] +files_to_copy = [ + (['source/STAR', 'source/STARlong'], 'bin'), + 'CHANGES.md', 'doc', 'extras', 'LICENSE', 'README.md', 'RELEASEnotes.md', +] sanity_check_paths = { 'files': ["bin/STAR", "bin/STARlong"], diff --git a/easybuild/easyconfigs/s/STAR/STAR-2.5.2a-foss-2016a.eb b/easybuild/easyconfigs/s/STAR/STAR-2.5.2a-foss-2016a.eb index b5f453b8c8..43cc47b2aa 100644 --- a/easybuild/easyconfigs/s/STAR/STAR-2.5.2a-foss-2016a.eb +++ b/easybuild/easyconfigs/s/STAR/STAR-2.5.2a-foss-2016a.eb @@ -31,13 +31,8 @@ buildopts = ' STAR && make STARlong' parallel = 1 files_to_copy = [ - (["source/STAR", "source/STARlong"], "bin"), - "CHANGES.md", - "doc", - "extras", - "LICENSE", - "README.md", - "RELEASEnotes.md" + (['source/STAR', 'source/STARlong'], 'bin'), + 'CHANGES.md', 'doc', 'extras', 'LICENSE', 'README.md', 'RELEASEnotes.md', ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/s/STAR/STAR-2.5.2a-goolf-1.7.20.eb b/easybuild/easyconfigs/s/STAR/STAR-2.5.2a-goolf-1.7.20.eb index 545af822d8..d8c6f0be04 100644 --- a/easybuild/easyconfigs/s/STAR/STAR-2.5.2a-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/s/STAR/STAR-2.5.2a-goolf-1.7.20.eb @@ -28,13 +28,8 @@ buildopts = ' STAR && make STARlong' parallel = 1 files_to_copy = [ - (["source/STAR", "source/STARlong"], "bin"), - "CHANGES.md", - "doc", - "extras", - "LICENSE", - "README.md", - "RELEASEnotes.md" + (['source/STAR', 'source/STARlong'], 'bin'), + 'CHANGES.md', 'doc', 'extras', 'LICENSE', 'README.md', 'RELEASEnotes.md', ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/s/Serf/Serf-1.3.8-foss-2015a.eb b/easybuild/easyconfigs/s/Serf/Serf-1.3.8-foss-2015a.eb index dd4add0a50..2852bb52f5 100644 --- a/easybuild/easyconfigs/s/Serf/Serf-1.3.8-foss-2015a.eb +++ b/easybuild/easyconfigs/s/Serf/Serf-1.3.8-foss-2015a.eb @@ -21,8 +21,9 @@ builddependencies = [('SCons', '2.3.6', '-Python-2.7.9')] dependencies = [ ('APR', '1.5.2'), ('APR-util', '1.5.4'), - # ('OpenSSL', '1.0.1p'), # OS dependency should be preferred if the os version is more recent then this version, it's - # nice to have an up to date openssl for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it is nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1p'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] -- GitLab From 11f27f266a4522fccc531926731e2b381ac4f235 Mon Sep 17 00:00:00 2001 From: Masao Fujinaga Date: Wed, 22 Feb 2017 19:07:01 +0000 Subject: [PATCH 0139/1603] second correction of easyconfig --- easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2-intel-2017a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2-intel-2017a.eb b/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2-intel-2017a.eb index 2f5b9aef33..a59e6f69ac 100644 --- a/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2-intel-2017a.eb +++ b/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2-intel-2017a.eb @@ -17,7 +17,7 @@ source_urls = ['http://download.sourceforge.net/bowtie-bio/'] patches = [ 'int64typedef.patch', - 'Bowtie-%(version)_void2int.patch' + 'Bowtie-%(version)s_void2int.patch' ] moduleclass = 'bio' -- GitLab From 7800a4e5451a7ebaed4e93fa4dd64415f2ea7142 Mon Sep 17 00:00:00 2001 From: Maxime Boissonneault Date: Wed, 22 Feb 2017 20:03:38 +0000 Subject: [PATCH 0140/1603] Added comments in the patch --- .../i/igraph/igraph-0.7.1-fix-aclocal-version.patch | 6 ++++++ .../i/igraph/igraph-0.7.1-no-lapack-no-blas.patch | 5 +++++ 2 files changed, 11 insertions(+) diff --git a/easybuild/easyconfigs/i/igraph/igraph-0.7.1-fix-aclocal-version.patch b/easybuild/easyconfigs/i/igraph/igraph-0.7.1-fix-aclocal-version.patch index fc7ded594f..81b9d69187 100644 --- a/easybuild/easyconfigs/i/igraph/igraph-0.7.1-fix-aclocal-version.patch +++ b/easybuild/easyconfigs/i/igraph/igraph-0.7.1-fix-aclocal-version.patch @@ -1,3 +1,9 @@ +Change the version of autoconf which is required to configure from 1.14 to 1.15 + +From: Maxime Boissonneault +Date: Wed, 22 Feb 2017 + + diff -ru igraph-0.7.1.orig/aclocal.m4 igraph-0.7.1/aclocal.m4 --- igraph-0.7.1.orig/aclocal.m4 2014-04-22 17:54:54.000000000 +0000 +++ igraph-0.7.1/aclocal.m4 2017-02-21 15:10:50.062279982 +0000 diff --git a/easybuild/easyconfigs/i/igraph/igraph-0.7.1-no-lapack-no-blas.patch b/easybuild/easyconfigs/i/igraph/igraph-0.7.1-no-lapack-no-blas.patch index 70635982cf..339e68cee3 100644 --- a/easybuild/easyconfigs/i/igraph/igraph-0.7.1-no-lapack-no-blas.patch +++ b/easybuild/easyconfigs/i/igraph/igraph-0.7.1-no-lapack-no-blas.patch @@ -1,3 +1,8 @@ +Removes explicit linking of libblas and liblapack for when linking with MKL + +From: Maxime Boissonneault +Date: Wed, 22 Feb 2017 + diff -ru igraph-0.7.1.orig/configure igraph-0.7.1/configure --- igraph-0.7.1.orig/configure 2014-04-22 17:55:00.000000000 +0000 +++ igraph-0.7.1/configure 2017-02-21 15:00:00.398921297 +0000 -- GitLab From eb544d54e03bef5fc962f1c76c127517e7765a00 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 22 Feb 2017 21:29:48 +0100 Subject: [PATCH 0141/1603] clean up trailing whitespace --- .../a/ant/ant-1.10.0-Java-1.8.0_112.eb | 2 +- .../a/ant/ant-1.9.7-Java-1.8.0_92.eb | 2 +- ...ommet-20150415-foss-2016a-Python-2.7.11.eb | 22 +++++----- ...cutadapt-1.9.1-foss-2016a-Python-2.7.11.eb | 2 +- .../GMAP-GSNAP-2015-12-31.v2-foss-2015b.eb | 2 +- .../GMAP-GSNAP-2016-05-01-foss-2016a.eb | 2 +- .../GMAP-GSNAP-2016-11-07-foss-2016b.eb | 2 +- .../g/GP2C/GP2C-0.0.9pl5-foss-2016a.eb | 4 +- .../easyconfigs/g/gompi/gompi-2016.09.eb | 36 +++++++-------- .../g/grabix/grabix-0.1.6-goolf-1.7.20.eb | 6 +-- .../h/hwloc/hwloc-1.11.4-GCC-6.2.0-2.27.eb | 44 +++++++++---------- .../h/hwloc/hwloc-1.11.4-gcccuda-2016.10.eb | 44 +++++++++---------- .../h/hwloc/hwloc-1.11.5-GCC-6.3.0-2.27.eb | 44 +++++++++---------- .../i/IOR/IOR-3.0.1-foss-2016a-mpiio.eb | 8 ++-- .../Mawk/Mawk-1.3.4-goolf-1.4.10-20150503.eb | 4 +- .../m/Mono/Mono-2.10.6-intel-2016b.eb | 2 +- .../m/Mono/Mono-4.6.2.7-intel-2016b.eb | 2 +- easybuild/easyconfigs/m/Mono/Mono-4.6.2.7.eb | 2 +- .../networkx-1.11-foss-2016a-Python-2.7.11.eb | 2 +- .../networkx-1.11-foss-2016a-Python-3.5.1.eb | 2 +- .../numactl/numactl-2.0.11-GCC-6.2.0-2.27.eb | 40 ++++++++--------- .../numactl/numactl-2.0.11-GCC-6.3.0-2.27.eb | 40 ++++++++--------- .../p/PARI-GP/PARI-GP-2.7.6-foss-2016a.eb | 2 +- .../PLAST-2.3.1-foss-2016a-Java-1.8.0_92.eb | 2 +- .../p/Platanus/Platanus-1.2.4-goolf-1.7.20.eb | 2 +- .../SUMACLUST/SUMACLUST-1.0.20-foss-2016a.eb | 6 +-- 26 files changed, 163 insertions(+), 163 deletions(-) diff --git a/easybuild/easyconfigs/a/ant/ant-1.10.0-Java-1.8.0_112.eb b/easybuild/easyconfigs/a/ant/ant-1.10.0-Java-1.8.0_112.eb index cf1f192a70..2d88d28b75 100644 --- a/easybuild/easyconfigs/a/ant/ant-1.10.0-Java-1.8.0_112.eb +++ b/easybuild/easyconfigs/a/ant/ant-1.10.0-Java-1.8.0_112.eb @@ -1,6 +1,6 @@ name = 'ant' version = '1.10.0' -versionsuffix = '-Java-%(javaver)s' +versionsuffix = '-Java-%(javaver)s' homepage = 'http://ant.apache.org/' description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files diff --git a/easybuild/easyconfigs/a/ant/ant-1.9.7-Java-1.8.0_92.eb b/easybuild/easyconfigs/a/ant/ant-1.9.7-Java-1.8.0_92.eb index 186bcfb543..175bb2628a 100644 --- a/easybuild/easyconfigs/a/ant/ant-1.9.7-Java-1.8.0_92.eb +++ b/easybuild/easyconfigs/a/ant/ant-1.9.7-Java-1.8.0_92.eb @@ -1,6 +1,6 @@ name = 'ant' version = '1.9.7' -versionsuffix = '-Java-%(javaver)s' +versionsuffix = '-Java-%(javaver)s' homepage = 'http://ant.apache.org/' description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files diff --git a/easybuild/easyconfigs/c/Commet/Commet-20150415-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/c/Commet/Commet-20150415-foss-2016a-Python-2.7.11.eb index a2bd44831e..3abe5c93c9 100644 --- a/easybuild/easyconfigs/c/Commet/Commet-20150415-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/c/Commet/Commet-20150415-foss-2016a-Python-2.7.11.eb @@ -1,27 +1,27 @@ -easyblock = 'MakeCp' +easyblock = 'MakeCp' -name = 'Commet' -version = '20150415' +name = 'Commet' +version = '20150415' commit = '4ef0705' -versionsuffix = '-Python-%(pyver)s' +versionsuffix = '-Python-%(pyver)s' -homepage = 'https://colibread.inria.fr/software/commet/' +homepage = 'https://colibread.inria.fr/software/commet/' description = """ COMMET ("COmpare Multiple METagenomes") provides a global similarity overview between all datasets of - a large metagenomic project. -""" + a large metagenomic project. +""" toolchain = {'name': 'foss', 'version': '2016a'} source_urls = ['https://github.com/pierrepeterlongo/commet/archive'] sources = ['%s.tar.gz' % commit] -checksums = ['19cba09ca7a92eaed75ed6af820d9451'] +checksums = ['19cba09ca7a92eaed75ed6af820d9451'] dependencies = [ - ('Python', '2.7.11'), -] + ('Python', '2.7.11'), +] -files_to_copy = ['bin', 'doc', 'include', 'ABCDE_bench', (['Commet.py'], 'bin')] +files_to_copy = ['bin', 'doc', 'include', 'ABCDE_bench', (['Commet.py'], 'bin')] sanity_check_paths = { 'files': ['bin/%s' % binfile for binfile in ['Commet.py', 'bvop', 'compare_reads', diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.9.1-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.9.1-foss-2016a-Python-2.7.11.eb index 5c57e5846c..99d5dfa45c 100644 --- a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.9.1-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.9.1-foss-2016a-Python-2.7.11.eb @@ -9,7 +9,7 @@ easyblock = "PythonPackage" name = 'cutadapt' version = '1.9.1' -versionsuffix = '-Python-%(pyver)s' +versionsuffix = '-Python-%(pyver)s' homepage = 'http://opensource.scilifelab.se/projects/cutadapt/' description = """ Cutadapt finds and removes adapter sequences, primers, poly-A tails and diff --git a/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2015-12-31.v2-foss-2015b.eb b/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2015-12-31.v2-foss-2015b.eb index db19b2803a..5440f25394 100644 --- a/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2015-12-31.v2-foss-2015b.eb +++ b/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2015-12-31.v2-foss-2015b.eb @@ -3,7 +3,7 @@ # Swiss Institute of Bioinformatics # Biozentrum - University of Basel -easyblock = 'ConfigureMake' +easyblock = 'ConfigureMake' name = 'GMAP-GSNAP' version = "2015-12-31.v2" diff --git a/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2016-05-01-foss-2016a.eb b/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2016-05-01-foss-2016a.eb index 84e054bf9c..5e9cfedc47 100644 --- a/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2016-05-01-foss-2016a.eb +++ b/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2016-05-01-foss-2016a.eb @@ -3,7 +3,7 @@ # Swiss Institute of Bioinformatics # Biozentrum - University of Basel -easyblock = 'ConfigureMake' +easyblock = 'ConfigureMake' name = 'GMAP-GSNAP' version = '2016-05-01' diff --git a/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2016-11-07-foss-2016b.eb b/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2016-11-07-foss-2016b.eb index a8ca27958e..00035603e7 100644 --- a/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2016-11-07-foss-2016b.eb +++ b/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2016-11-07-foss-2016b.eb @@ -6,7 +6,7 @@ # Adam Huffman # The Francis Crick Institute -easyblock = 'ConfigureMake' +easyblock = 'ConfigureMake' name = 'GMAP-GSNAP' version = '2016-11-07' diff --git a/easybuild/easyconfigs/g/GP2C/GP2C-0.0.9pl5-foss-2016a.eb b/easybuild/easyconfigs/g/GP2C/GP2C-0.0.9pl5-foss-2016a.eb index e78f2ba765..f302d9f398 100644 --- a/easybuild/easyconfigs/g/GP2C/GP2C-0.0.9pl5-foss-2016a.eb +++ b/easybuild/easyconfigs/g/GP2C/GP2C-0.0.9pl5-foss-2016a.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'GP2C' version = '0.0.9pl5' -homepage = 'http://pari.math.u-bordeaux.fr/pub/pari/manuals/gp2c/gp2c.html' +homepage = 'http://pari.math.u-bordeaux.fr/pub/pari/manuals/gp2c/gp2c.html' description = """The gp2c compiler is a package for translating GP routines into the C programming language, so that they can be compiled and used with the PARI system or the GP calculator. """ @@ -17,7 +17,7 @@ dependencies = [ ('PARI-GP', '2.7.6'), ] -configopts = '--with-paricfg=$EBROOTPARIMINGP/lib/pari/pari.cfg' +configopts = '--with-paricfg=$EBROOTPARIMINGP/lib/pari/pari.cfg' runtest = 'check' diff --git a/easybuild/easyconfigs/g/gompi/gompi-2016.09.eb b/easybuild/easyconfigs/g/gompi/gompi-2016.09.eb index b4350de73a..d4b83fb9a0 100644 --- a/easybuild/easyconfigs/g/gompi/gompi-2016.09.eb +++ b/easybuild/easyconfigs/g/gompi/gompi-2016.09.eb @@ -1,20 +1,20 @@ -easyblock = "Toolchain" +easyblock = "Toolchain" + +name = 'gompi' +version = '2016.09' + +homepage = '(none)' +description = """GNU Compiler Collection (GCC) based compiler toolchain, +including OpenMPI for MPI support.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +gccver = '6.2.0-2.27' + +# compiler toolchain dependencies +dependencies = [ + ('GCC', gccver), # includes both GCC and binutils + ('OpenMPI', '2.0.1', '', ('GCC', gccver)), +] -name = 'gompi' -version = '2016.09' - -homepage = '(none)' -description = """GNU Compiler Collection (GCC) based compiler toolchain, -including OpenMPI for MPI support.""" - -toolchain = {'name': 'dummy', 'version': 'dummy'} - -gccver = '6.2.0-2.27' - -# compiler toolchain dependencies -dependencies = [ - ('GCC', gccver), # includes both GCC and binutils - ('OpenMPI', '2.0.1', '', ('GCC', gccver)), -] - moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/g/grabix/grabix-0.1.6-goolf-1.7.20.eb b/easybuild/easyconfigs/g/grabix/grabix-0.1.6-goolf-1.7.20.eb index fc1bd33358..1bf0222ad3 100644 --- a/easybuild/easyconfigs/g/grabix/grabix-0.1.6-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/g/grabix/grabix-0.1.6-goolf-1.7.20.eb @@ -6,7 +6,7 @@ easyblock = 'MakeCp' name = 'grabix' -version = '0.1.6' +version = '0.1.6' homepage = 'https://github.com/arq5x/grabix' description = """a wee tool for random access into BGZF files""" @@ -17,13 +17,13 @@ source_urls = ['https://github.com/arq5x/grabix/archive/'] sources = ['%(version)s.tar.gz'] dependencies = [ - ('zlib', '1.2.8'), + ('zlib', '1.2.8'), ] parallel = 1 files_to_copy = [(["grabix"], "bin"), "README.md", "tests", "test.sh"] - + sanity_check_paths = { 'files': ["bin/grabix"], 'dirs': [], diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.4-GCC-6.2.0-2.27.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.4-GCC-6.2.0-2.27.eb index 35ced3699b..071326cd0d 100644 --- a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.4-GCC-6.2.0-2.27.eb +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.4-GCC-6.2.0-2.27.eb @@ -1,23 +1,23 @@ -easyblock = 'ConfigureMake' - -name = 'hwloc' -version = '1.11.4' - -homepage = 'http://www.open-mpi.org/projects/hwloc/' -description = """The Portable Hardware Locality (hwloc) software package provides a portable abstraction -(across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including -NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various -system attributes such as cache and memory information as well as the locality of I/O devices such as -network interfaces, InfiniBand HCAs or GPUs. It primarily aims at helping applications with gathering -information about modern computing hardware so as to exploit it accordingly and efficiently.""" - -toolchain = {'name': 'GCC', 'version': '6.2.0-2.27'} - -source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] -sources = [SOURCE_TAR_GZ] - -dependencies = [('numactl', '2.0.11')] - -configopts = "--enable-libnuma=$EBROOTNUMACTL" - +easyblock = 'ConfigureMake' + +name = 'hwloc' +version = '1.11.4' + +homepage = 'http://www.open-mpi.org/projects/hwloc/' +description = """The Portable Hardware Locality (hwloc) software package provides a portable abstraction +(across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including +NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various +system attributes such as cache and memory information as well as the locality of I/O devices such as +network interfaces, InfiniBand HCAs or GPUs. It primarily aims at helping applications with gathering +information about modern computing hardware so as to exploit it accordingly and efficiently.""" + +toolchain = {'name': 'GCC', 'version': '6.2.0-2.27'} + +source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [('numactl', '2.0.11')] + +configopts = "--enable-libnuma=$EBROOTNUMACTL" + moduleclass = 'system' diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.4-gcccuda-2016.10.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.4-gcccuda-2016.10.eb index a83862d853..ed51d67326 100644 --- a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.4-gcccuda-2016.10.eb +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.4-gcccuda-2016.10.eb @@ -1,23 +1,23 @@ -easyblock = 'ConfigureMake' - -name = 'hwloc' -version = '1.11.4' - -homepage = 'http://www.open-mpi.org/projects/hwloc/' -description = """The Portable Hardware Locality (hwloc) software package provides a portable abstraction -(across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including -NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various -system attributes such as cache and memory information as well as the locality of I/O devices such as -network interfaces, InfiniBand HCAs or GPUs. It primarily aims at helping applications with gathering -information about modern computing hardware so as to exploit it accordingly and efficiently.""" - -toolchain = {'name': 'gcccuda', 'version': '2016.10'} - -source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] -sources = [SOURCE_TAR_GZ] - -dependencies = [('numactl', '2.0.11')] - -configopts = "--enable-libnuma=$EBROOTNUMACTL" - +easyblock = 'ConfigureMake' + +name = 'hwloc' +version = '1.11.4' + +homepage = 'http://www.open-mpi.org/projects/hwloc/' +description = """The Portable Hardware Locality (hwloc) software package provides a portable abstraction +(across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including +NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various +system attributes such as cache and memory information as well as the locality of I/O devices such as +network interfaces, InfiniBand HCAs or GPUs. It primarily aims at helping applications with gathering +information about modern computing hardware so as to exploit it accordingly and efficiently.""" + +toolchain = {'name': 'gcccuda', 'version': '2016.10'} + +source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [('numactl', '2.0.11')] + +configopts = "--enable-libnuma=$EBROOTNUMACTL" + moduleclass = 'system' diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.5-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.5-GCC-6.3.0-2.27.eb index b130fe6456..1aeec6a116 100644 --- a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.5-GCC-6.3.0-2.27.eb +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.5-GCC-6.3.0-2.27.eb @@ -1,23 +1,23 @@ -easyblock = 'ConfigureMake' - -name = 'hwloc' -version = '1.11.5' - -homepage = 'http://www.open-mpi.org/projects/hwloc/' -description = """The Portable Hardware Locality (hwloc) software package provides a portable abstraction -(across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including -NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various -system attributes such as cache and memory information as well as the locality of I/O devices such as -network interfaces, InfiniBand HCAs or GPUs. It primarily aims at helping applications with gathering -information about modern computing hardware so as to exploit it accordingly and efficiently.""" - -toolchain = {'name': 'GCC', 'version': '6.3.0-2.27'} - -source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] -sources = [SOURCE_TAR_GZ] - -dependencies = [('numactl', '2.0.11')] - -configopts = "--enable-libnuma=$EBROOTNUMACTL" - +easyblock = 'ConfigureMake' + +name = 'hwloc' +version = '1.11.5' + +homepage = 'http://www.open-mpi.org/projects/hwloc/' +description = """The Portable Hardware Locality (hwloc) software package provides a portable abstraction +(across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including +NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various +system attributes such as cache and memory information as well as the locality of I/O devices such as +network interfaces, InfiniBand HCAs or GPUs. It primarily aims at helping applications with gathering +information about modern computing hardware so as to exploit it accordingly and efficiently.""" + +toolchain = {'name': 'GCC', 'version': '6.3.0-2.27'} + +source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [('numactl', '2.0.11')] + +configopts = "--enable-libnuma=$EBROOTNUMACTL" + moduleclass = 'system' diff --git a/easybuild/easyconfigs/i/IOR/IOR-3.0.1-foss-2016a-mpiio.eb b/easybuild/easyconfigs/i/IOR/IOR-3.0.1-foss-2016a-mpiio.eb index 521eb6e805..1c64db33bd 100644 --- a/easybuild/easyconfigs/i/IOR/IOR-3.0.1-foss-2016a-mpiio.eb +++ b/easybuild/easyconfigs/i/IOR/IOR-3.0.1-foss-2016a-mpiio.eb @@ -6,10 +6,10 @@ easyblock = 'ConfigureMake' name = "IOR" -version = "3.0.1" +version = "3.0.1" versionsuffix = "-mpiio" -homepage = 'https://github.com/chaos/ior' +homepage = 'https://github.com/chaos/ior' description = """ The IOR software is used for benchmarking parallel file systems using POSIX, MPIIO, or HDF5 interfaces. """ @@ -18,7 +18,7 @@ toolchain = {'name': 'foss', 'version': '2016a' } source_urls = [('https://github.com/chaos/ior/archive/')] sources = ['%(version)s.tar.gz'] -# configure opts listed below +# configure opts listed below # --with-PACKAGE[=ARG] use PACKAGE [ARG=yes] # --without-PACKAGE do not use PACKAGE (same as --with-PACKAGE=no) # --with-lustre support configurable Lustre striping values [default=check] @@ -26,7 +26,7 @@ sources = ['%(version)s.tar.gz'] # --with-mpiio support IO with MPI-IO backend [default=yes] # --with-hdf5 support IO with HDF5 backend [default=no] # --with-ncmpi support IO with NCMPI backend [default=no] -preconfigopts = "./bootstrap &&" +preconfigopts = "./bootstrap &&" sanity_check_paths = { 'files': ["bin/ior"], diff --git a/easybuild/easyconfigs/m/Mawk/Mawk-1.3.4-goolf-1.4.10-20150503.eb b/easybuild/easyconfigs/m/Mawk/Mawk-1.3.4-goolf-1.4.10-20150503.eb index 7235621e5d..5b5a91c678 100644 --- a/easybuild/easyconfigs/m/Mawk/Mawk-1.3.4-goolf-1.4.10-20150503.eb +++ b/easybuild/easyconfigs/m/Mawk/Mawk-1.3.4-goolf-1.4.10-20150503.eb @@ -1,13 +1,13 @@ # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # Author: Pablo Escobar Lopez # sciCORE - University of Basel -# SIB Swiss Institute of Bioinformatics +# SIB Swiss Institute of Bioinformatics easyblock = 'ConfigureMake' name = 'Mawk' version = '1.3.4' -versionsuffix = '-20150503' +versionsuffix = '-20150503' homepage = 'http://invisible-island.net/mawk/' description = """mawk is an interpreter for the AWK Programming Language.""" diff --git a/easybuild/easyconfigs/m/Mono/Mono-2.10.6-intel-2016b.eb b/easybuild/easyconfigs/m/Mono/Mono-2.10.6-intel-2016b.eb index 365455df1b..e8b59e1494 100644 --- a/easybuild/easyconfigs/m/Mono/Mono-2.10.6-intel-2016b.eb +++ b/easybuild/easyconfigs/m/Mono/Mono-2.10.6-intel-2016b.eb @@ -1,7 +1,7 @@ name = 'Mono' version = '2.10.6' -homepage = 'http://mono-framework.com' +homepage = 'http://mono-framework.com' description = """An open source, cross-platform, implementation of C# and the CLR that is binary compatible with Microsoft.NET.""" diff --git a/easybuild/easyconfigs/m/Mono/Mono-4.6.2.7-intel-2016b.eb b/easybuild/easyconfigs/m/Mono/Mono-4.6.2.7-intel-2016b.eb index 4b58a5cd71..11e5afa9ee 100644 --- a/easybuild/easyconfigs/m/Mono/Mono-4.6.2.7-intel-2016b.eb +++ b/easybuild/easyconfigs/m/Mono/Mono-4.6.2.7-intel-2016b.eb @@ -1,7 +1,7 @@ name = 'Mono' version = '4.6.2.7' -homepage = 'http://mono-framework.com' +homepage = 'http://mono-framework.com' description = """An open source, cross-platform, implementation of C# and the CLR that is binary compatible with Microsoft.NET.""" diff --git a/easybuild/easyconfigs/m/Mono/Mono-4.6.2.7.eb b/easybuild/easyconfigs/m/Mono/Mono-4.6.2.7.eb index ea1fdc2813..5d4a7d1a7d 100644 --- a/easybuild/easyconfigs/m/Mono/Mono-4.6.2.7.eb +++ b/easybuild/easyconfigs/m/Mono/Mono-4.6.2.7.eb @@ -1,7 +1,7 @@ name = 'Mono' version = '4.6.2.7' -homepage = 'http://mono-framework.com' +homepage = 'http://mono-framework.com' description = """An open source, cross-platform, implementation of C# and the CLR that is binary compatible with Microsoft.NET.""" diff --git a/easybuild/easyconfigs/n/networkx/networkx-1.11-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/n/networkx/networkx-1.11-foss-2016a-Python-2.7.11.eb index 8dde76eb25..afc809e585 100644 --- a/easybuild/easyconfigs/n/networkx/networkx-1.11-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/n/networkx/networkx-1.11-foss-2016a-Python-2.7.11.eb @@ -2,7 +2,7 @@ easyblock = 'PythonPackage' name = 'networkx' version = '1.11' -versionsuffix = '-Python-%(pyver)s' +versionsuffix = '-Python-%(pyver)s' homepage = 'https://pypi.python.org/pypi/networkx' description = """NetworkX is a Python package for the creation, manipulation, and study of the structure, dynamics, diff --git a/easybuild/easyconfigs/n/networkx/networkx-1.11-foss-2016a-Python-3.5.1.eb b/easybuild/easyconfigs/n/networkx/networkx-1.11-foss-2016a-Python-3.5.1.eb index 488dd6f650..162c58702c 100644 --- a/easybuild/easyconfigs/n/networkx/networkx-1.11-foss-2016a-Python-3.5.1.eb +++ b/easybuild/easyconfigs/n/networkx/networkx-1.11-foss-2016a-Python-3.5.1.eb @@ -2,7 +2,7 @@ easyblock = 'PythonPackage' name = 'networkx' version = '1.11' -versionsuffix = '-Python-%(pyver)s' +versionsuffix = '-Python-%(pyver)s' homepage = 'https://pypi.python.org/pypi/networkx' description = """NetworkX is a Python package for the creation, manipulation, and study of the structure, dynamics, diff --git a/easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCC-6.2.0-2.27.eb b/easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCC-6.2.0-2.27.eb index 7d6ccf3999..01a8bfdf0f 100644 --- a/easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCC-6.2.0-2.27.eb +++ b/easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCC-6.2.0-2.27.eb @@ -1,23 +1,23 @@ -easyblock = 'ConfigureMake' - -name = 'numactl' -version = '2.0.11' - -homepage = 'http://oss.sgi.com/projects/libnuma/' -description = """The numactl program allows you to run your application program on specific cpu's and memory nodes. -It does this by supplying a NUMA memory policy to the operating system before running your program. -The libnuma library provides convenient ways for you to add NUMA memory policies into your own program.""" - +easyblock = 'ConfigureMake' + +name = 'numactl' +version = '2.0.11' + +homepage = 'http://oss.sgi.com/projects/libnuma/' +description = """The numactl program allows you to run your application program on specific cpu's and memory nodes. +It does this by supplying a NUMA memory policy to the operating system before running your program. +The libnuma library provides convenient ways for you to add NUMA memory policies into your own program.""" + toolchain = {'name': 'GCC', 'version': '6.2.0-2.27'} -source_urls = ['ftp://oss.sgi.com/www/projects/libnuma/download/'] -sources = [SOURCE_TAR_GZ] - -checksums = ['d3bc88b7ddb9f06d60898f4816ae9127'] - -sanity_check_paths = { - 'files': ['bin/numactl', 'bin/numastat', 'lib/libnuma.%s' % SHLIB_EXT, 'lib/libnuma.a'], - 'dirs': ['share/man', 'include'] -} - +source_urls = ['ftp://oss.sgi.com/www/projects/libnuma/download/'] +sources = [SOURCE_TAR_GZ] + +checksums = ['d3bc88b7ddb9f06d60898f4816ae9127'] + +sanity_check_paths = { + 'files': ['bin/numactl', 'bin/numastat', 'lib/libnuma.%s' % SHLIB_EXT, 'lib/libnuma.a'], + 'dirs': ['share/man', 'include'] +} + moduleclass = 'tools' diff --git a/easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCC-6.3.0-2.27.eb index ee922f3337..7fe4d082b3 100644 --- a/easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCC-6.3.0-2.27.eb +++ b/easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCC-6.3.0-2.27.eb @@ -1,23 +1,23 @@ -easyblock = 'ConfigureMake' - -name = 'numactl' -version = '2.0.11' - -homepage = 'http://oss.sgi.com/projects/libnuma/' -description = """The numactl program allows you to run your application program on specific cpu's and memory nodes. -It does this by supplying a NUMA memory policy to the operating system before running your program. -The libnuma library provides convenient ways for you to add NUMA memory policies into your own program.""" - +easyblock = 'ConfigureMake' + +name = 'numactl' +version = '2.0.11' + +homepage = 'http://oss.sgi.com/projects/libnuma/' +description = """The numactl program allows you to run your application program on specific cpu's and memory nodes. +It does this by supplying a NUMA memory policy to the operating system before running your program. +The libnuma library provides convenient ways for you to add NUMA memory policies into your own program.""" + toolchain = {'name': 'GCC', 'version': '6.3.0-2.27'} -source_urls = ['ftp://oss.sgi.com/www/projects/libnuma/download/'] -sources = [SOURCE_TAR_GZ] - -checksums = ['d3bc88b7ddb9f06d60898f4816ae9127'] - -sanity_check_paths = { - 'files': ['bin/numactl', 'bin/numastat', 'lib/libnuma.%s' % SHLIB_EXT, 'lib/libnuma.a'], - 'dirs': ['share/man', 'include'] -} - +source_urls = ['ftp://oss.sgi.com/www/projects/libnuma/download/'] +sources = [SOURCE_TAR_GZ] + +checksums = ['d3bc88b7ddb9f06d60898f4816ae9127'] + +sanity_check_paths = { + 'files': ['bin/numactl', 'bin/numastat', 'lib/libnuma.%s' % SHLIB_EXT, 'lib/libnuma.a'], + 'dirs': ['share/man', 'include'] +} + moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/PARI-GP/PARI-GP-2.7.6-foss-2016a.eb b/easybuild/easyconfigs/p/PARI-GP/PARI-GP-2.7.6-foss-2016a.eb index c67cbf7de9..807e673a1f 100644 --- a/easybuild/easyconfigs/p/PARI-GP/PARI-GP-2.7.6-foss-2016a.eb +++ b/easybuild/easyconfigs/p/PARI-GP/PARI-GP-2.7.6-foss-2016a.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'PARI-GP' version = '2.7.6' -homepage = 'http://pari.math.u-bordeaux.fr' +homepage = 'http://pari.math.u-bordeaux.fr' description = """PARI/GP is a widely used computer algebra system designed for fast computations in number theory (factorizations, algebraic number theory, elliptic curves...), but also contains a large number of other useful functions to compute with mathematical entities such as matrices, polynomials, power series, algebraic numbers etc., diff --git a/easybuild/easyconfigs/p/PLAST/PLAST-2.3.1-foss-2016a-Java-1.8.0_92.eb b/easybuild/easyconfigs/p/PLAST/PLAST-2.3.1-foss-2016a-Java-1.8.0_92.eb index 61cae6188e..6d4327f5c0 100644 --- a/easybuild/easyconfigs/p/PLAST/PLAST-2.3.1-foss-2016a-Java-1.8.0_92.eb +++ b/easybuild/easyconfigs/p/PLAST/PLAST-2.3.1-foss-2016a-Java-1.8.0_92.eb @@ -4,7 +4,7 @@ name = 'PLAST' version = '2.3.1' versionsuffix = '-Java-%(javaver)s' -homepage = "http://www.irisa.fr/symbiose/projects/plast/" +homepage = "http://www.irisa.fr/symbiose/projects/plast/" description = """PLAST is a parallel alignment search tool for comparing large protein banks""" toolchain = {'name': 'foss', 'version': '2016a'} diff --git a/easybuild/easyconfigs/p/Platanus/Platanus-1.2.4-goolf-1.7.20.eb b/easybuild/easyconfigs/p/Platanus/Platanus-1.2.4-goolf-1.7.20.eb index 7dffcdb458..fb465f5c89 100644 --- a/easybuild/easyconfigs/p/Platanus/Platanus-1.2.4-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/p/Platanus/Platanus-1.2.4-goolf-1.7.20.eb @@ -6,7 +6,7 @@ easyblock = 'MakeCp' name = 'Platanus' -version = '1.2.4' +version = '1.2.4' homepage = 'http://platanus.bio.titech.ac.jp/' description = """PLATform for Assembling NUcleotide Sequences""" diff --git a/easybuild/easyconfigs/s/SUMACLUST/SUMACLUST-1.0.20-foss-2016a.eb b/easybuild/easyconfigs/s/SUMACLUST/SUMACLUST-1.0.20-foss-2016a.eb index a2a47d4c1e..bbf5a698d9 100644 --- a/easybuild/easyconfigs/s/SUMACLUST/SUMACLUST-1.0.20-foss-2016a.eb +++ b/easybuild/easyconfigs/s/SUMACLUST/SUMACLUST-1.0.20-foss-2016a.eb @@ -1,13 +1,13 @@ # Author: Pablo Escobar Lopez; Wiktor Jurkowski # Swiss Institute of Bioinformatics (SIB), Biozentrum - University of Basel -# Babraham Institute, UK +# Babraham Institute, UK easyblock = 'MakeCp' name = 'SUMACLUST' version = '1.0.20' -homepage = "http://metabarcoding.org/sumatra" +homepage = "http://metabarcoding.org/sumatra" description = """SUMATRA and SUMACLUST: fast and exact comparison and clustering of sequences.""" toolchain = {'name': 'foss', 'version': '2016a'} @@ -15,7 +15,7 @@ toolchain = {'name': 'foss', 'version': '2016a'} source_urls = ['https://git.metabarcoding.org/obitools/sumaclust/uploads/69f757c42f2cd45212c587e87c75a00f/'] sources = ['%(namelower)s_v%(version)s.tar.gz'] -prebuildopts = 'make clean &&' +prebuildopts = 'make clean &&' files_to_copy = [(['sumaclust'], 'bin'), 'sumaclust_user_manual.pdf'] -- GitLab From 5e41c7e7ff395d5f331dfcfda505bc47d13f8df8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 22 Feb 2017 21:35:28 +0100 Subject: [PATCH 0142/1603] remove whitespace from blank lines --- easybuild/easyconfigs/a/angsd/angsd-0.910-foss-2016a.eb | 2 +- .../easyconfigs/b/BayeScEnv/BayeScEnv-1.1-foss-2016a.eb | 4 ++-- .../easyconfigs/b/BayeScEnv/BayeScEnv-1.1-goolf-1.4.10.eb | 4 ++-- .../easyconfigs/b/BayeScan/BayeScan-2.1-foss-2016a.eb | 6 +++--- .../easyconfigs/b/BayeScan/BayeScan-2.1-goolf-1.4.10.eb | 8 ++++---- .../easyconfigs/c/ctffind/ctffind-4.0.17-intel-2015b.eb | 4 ++-- ...fastQValidator-0.1.1a-20151214-goolf-1.7.20-aadc6f9.eb | 8 ++++---- .../g/GEOS/GEOS-3.5.0-foss-2015a-Python-2.7.11.eb | 2 +- .../MOSAIK/MOSAIK-2.2.28-goolf-1.4.10-20140425-24cf06.eb | 6 +++--- .../m/MOSAIK/MOSAIK-2.2.28-ictce-6.2.5-20140425-24cf06.eb | 6 +++--- easybuild/easyconfigs/p/psmc/psmc-0.6.5-foss-2016a.eb | 4 ++-- .../QuantumESPRESSO-5.4.0-foss-2016b-hybrid.eb | 8 ++++---- .../easyconfigs/r/rainbow/rainbow-2.0.4-goolf-1.4.10.eb | 6 +++--- 13 files changed, 34 insertions(+), 34 deletions(-) diff --git a/easybuild/easyconfigs/a/angsd/angsd-0.910-foss-2016a.eb b/easybuild/easyconfigs/a/angsd/angsd-0.910-foss-2016a.eb index c9d9db6e85..39352e91cb 100644 --- a/easybuild/easyconfigs/a/angsd/angsd-0.910-foss-2016a.eb +++ b/easybuild/easyconfigs/a/angsd/angsd-0.910-foss-2016a.eb @@ -5,7 +5,7 @@ version = '0.910' homepage = 'http://www.popgen.dk/angsd' description = """Program for analysing NGS data.""" - + toolchain = {'name': 'foss', 'version': '2016a'} source_urls = ['https://github.com/ANGSD/angsd/archive/'] diff --git a/easybuild/easyconfigs/b/BayeScEnv/BayeScEnv-1.1-foss-2016a.eb b/easybuild/easyconfigs/b/BayeScEnv/BayeScEnv-1.1-foss-2016a.eb index cd1dd2595a..25707a1810 100644 --- a/easybuild/easyconfigs/b/BayeScEnv/BayeScEnv-1.1-foss-2016a.eb +++ b/easybuild/easyconfigs/b/BayeScEnv/BayeScEnv-1.1-foss-2016a.eb @@ -1,7 +1,7 @@ # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # Author: Pablo Escobar Lopez # sciCORE - University of Basel -# SIB Swiss Institute of Bioinformatics +# SIB Swiss Institute of Bioinformatics easyblock = 'MakeCp' @@ -23,7 +23,7 @@ start_dir = 'source' files_to_copy = [(['source/bayescenv'], 'bin'), 'test', 'COPYING', 'README.md', 'ChangeLog'] parallel = 1 - + sanity_check_paths = { 'files': ['bin/bayescenv'], 'dirs': [], diff --git a/easybuild/easyconfigs/b/BayeScEnv/BayeScEnv-1.1-goolf-1.4.10.eb b/easybuild/easyconfigs/b/BayeScEnv/BayeScEnv-1.1-goolf-1.4.10.eb index 7a976185d2..25b2cd8bb7 100644 --- a/easybuild/easyconfigs/b/BayeScEnv/BayeScEnv-1.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/BayeScEnv/BayeScEnv-1.1-goolf-1.4.10.eb @@ -1,7 +1,7 @@ # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # Author: Pablo Escobar Lopez # sciCORE - University of Basel -# SIB Swiss Institute of Bioinformatics +# SIB Swiss Institute of Bioinformatics easyblock = 'MakeCp' @@ -22,7 +22,7 @@ start_dir = 'source' files_to_copy = [(['source/bayescenv'], 'bin'), 'test', 'COPYING', 'README.md', 'ChangeLog'] parallel = 1 - + sanity_check_paths = { 'files': ['bin/bayescenv'], 'dirs': [], diff --git a/easybuild/easyconfigs/b/BayeScan/BayeScan-2.1-foss-2016a.eb b/easybuild/easyconfigs/b/BayeScan/BayeScan-2.1-foss-2016a.eb index c4932d3953..ebd814c54e 100644 --- a/easybuild/easyconfigs/b/BayeScan/BayeScan-2.1-foss-2016a.eb +++ b/easybuild/easyconfigs/b/BayeScan/BayeScan-2.1-foss-2016a.eb @@ -1,7 +1,7 @@ # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # Author: Pablo Escobar Lopez # sciCORE - University of Basel -# SIB Swiss Institute of Bioinformatics +# SIB Swiss Institute of Bioinformatics easyblock = 'MakeCp' @@ -9,7 +9,7 @@ name = 'BayeScan' version = '2.1' homepage = 'http://cmpg.unibe.ch/software/BayeScan/' -description = """BayeScan aims at identifying candidate loci under natural selection from genetic data, +description = """BayeScan aims at identifying candidate loci under natural selection from genetic data, using differences in allele frequencies between populations.""" toolchain = {'name': 'foss', 'version': '2016a'} @@ -30,7 +30,7 @@ files_to_copy = [ ] parallel = 1 - + sanity_check_paths = { 'files': ['bin/bayescan_%(version)s'], 'dirs': [], diff --git a/easybuild/easyconfigs/b/BayeScan/BayeScan-2.1-goolf-1.4.10.eb b/easybuild/easyconfigs/b/BayeScan/BayeScan-2.1-goolf-1.4.10.eb index 3745f65f5f..de8bcce297 100644 --- a/easybuild/easyconfigs/b/BayeScan/BayeScan-2.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/BayeScan/BayeScan-2.1-goolf-1.4.10.eb @@ -1,7 +1,7 @@ # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # Author: Pablo Escobar Lopez # sciCORE - University of Basel -# SIB Swiss Institute of Bioinformatics +# SIB Swiss Institute of Bioinformatics easyblock = 'MakeCp' @@ -9,10 +9,10 @@ name = 'BayeScan' version = '2.1' homepage = 'http://cmpg.unibe.ch/software/BayeScan/' -description = """BayeScan aims at identifying candidate loci under natural selection from genetic data, +description = """BayeScan aims at identifying candidate loci under natural selection from genetic data, using differences in allele frequencies between populations.""" -# BayeScan makefile is hardcoded to use g++. In case you want to use a non-gcc toolchain you will need to patch the makefile +# BayeScan makefile is hardcoded to use g++. In case you want to use a non-gcc toolchain you will need to patch the makefile toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'openmp': True} @@ -31,7 +31,7 @@ files_to_copy = [ 'R functions'] parallel = 1 - + sanity_check_paths = { 'files': ['bin/bayescan_%(version)s'], 'dirs': [], diff --git a/easybuild/easyconfigs/c/ctffind/ctffind-4.0.17-intel-2015b.eb b/easybuild/easyconfigs/c/ctffind/ctffind-4.0.17-intel-2015b.eb index 7a15e698bd..8c2ecba76b 100644 --- a/easybuild/easyconfigs/c/ctffind/ctffind-4.0.17-intel-2015b.eb +++ b/easybuild/easyconfigs/c/ctffind/ctffind-4.0.17-intel-2015b.eb @@ -1,7 +1,7 @@ # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # Author: Pablo Escobar Lopez # sciCORE - University of Basel -# SIB Swiss Institute of Bioinformatics +# SIB Swiss Institute of Bioinformatics easyblock = 'MakeCp' @@ -27,7 +27,7 @@ prebuildopts += ' ../configure --enable-static --disable-debug --enable-optimisa files_to_copy = [(['build/ctffind'], 'bin'), 'doc', 'scripts'] parallel = 1 - + sanity_check_paths = { 'files': ['bin/ctffind'], 'dirs': [], diff --git a/easybuild/easyconfigs/f/fastQValidator/fastQValidator-0.1.1a-20151214-goolf-1.7.20-aadc6f9.eb b/easybuild/easyconfigs/f/fastQValidator/fastQValidator-0.1.1a-20151214-goolf-1.7.20-aadc6f9.eb index 7eeaa4c1a4..f9d3b4a7b5 100644 --- a/easybuild/easyconfigs/f/fastQValidator/fastQValidator-0.1.1a-20151214-goolf-1.7.20-aadc6f9.eb +++ b/easybuild/easyconfigs/f/fastQValidator/fastQValidator-0.1.1a-20151214-goolf-1.7.20-aadc6f9.eb @@ -1,7 +1,7 @@ # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # Author: Pablo Escobar Lopez # sciCORE - University of Basel -# SIB Swiss Institute of Bioinformatics +# SIB Swiss Institute of Bioinformatics easyblock = 'MakeCp' @@ -20,12 +20,12 @@ toolchain = {'name': 'goolf', 'version': '1.7.20'} # using latest release tags doesn't work # https://github.com/statgen/fastQValidator/issues/9 source_urls = [ - 'https://github.com/statgen/fastQValidator/archive/', + 'https://github.com/statgen/fastQValidator/archive/', 'https://github.com/statgen/libStatGen/archive/' ] sources = [ - '%s.tar.gz' % fastqvalidator_git_commit, + '%s.tar.gz' % fastqvalidator_git_commit, '%s.tar.gz' % libstatgen_git_commit ] @@ -46,7 +46,7 @@ buildopts = ' LIB_PATH_GENERAL=../libStatGen ' files_to_copy = [(['bin/fastQValidator'], 'bin')] parallel = 1 - + sanity_check_paths = { 'files': ['bin/fastQValidator'], 'dirs': [], diff --git a/easybuild/easyconfigs/g/GEOS/GEOS-3.5.0-foss-2015a-Python-2.7.11.eb b/easybuild/easyconfigs/g/GEOS/GEOS-3.5.0-foss-2015a-Python-2.7.11.eb index 3053b75ee0..acdde9dd04 100644 --- a/easybuild/easyconfigs/g/GEOS/GEOS-3.5.0-foss-2015a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/g/GEOS/GEOS-3.5.0-foss-2015a-Python-2.7.11.eb @@ -18,7 +18,7 @@ versionsuffix = '-Python-%s' % pyver dependencies = [('Python', pyver)] builddependencies = [('SWIG', '3.0.8', versionsuffix)] - + configopts = '--enable-python' modextrapaths = {'PYTHONPATH': 'lib/python%s/site-packages' % pyshortver} diff --git a/easybuild/easyconfigs/m/MOSAIK/MOSAIK-2.2.28-goolf-1.4.10-20140425-24cf06.eb b/easybuild/easyconfigs/m/MOSAIK/MOSAIK-2.2.28-goolf-1.4.10-20140425-24cf06.eb index 5b23296323..4a0d2c666a 100644 --- a/easybuild/easyconfigs/m/MOSAIK/MOSAIK-2.2.28-goolf-1.4.10-20140425-24cf06.eb +++ b/easybuild/easyconfigs/m/MOSAIK/MOSAIK-2.2.28-goolf-1.4.10-20140425-24cf06.eb @@ -1,7 +1,7 @@ # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # Author: Pablo Escobar Lopez # sciCORE - University of Basel -# SIB Swiss Institute of Bioinformatics +# SIB Swiss Institute of Bioinformatics easyblock = 'MakeCp' @@ -11,7 +11,7 @@ git_commit_id = '24cf06' #first six digits of the commit id we will download fro versionsuffix = '-20140425-%s' % git_commit_id homepage = 'https://code.google.com/p/mosaik-aligner/' -description = """ MOSAIK is a reference-guided aligner for next-generation +description = """ MOSAIK is a reference-guided aligner for next-generation sequencing technologies """ toolchain = {'name': 'goolf', 'version': '1.4.10'} @@ -28,7 +28,7 @@ start_dir = "src" buildopts = ' BIN_DIR="./bin" OBJ_DIR="./obj"' files_to_copy = ["bin", "../README", "demo"] - + sanity_check_paths = { 'files': ["bin/%s" % x for x in ["MosaikAligner", "MosaikBuild", "MosaikJump", "MosaikText"]], 'dirs': [], diff --git a/easybuild/easyconfigs/m/MOSAIK/MOSAIK-2.2.28-ictce-6.2.5-20140425-24cf06.eb b/easybuild/easyconfigs/m/MOSAIK/MOSAIK-2.2.28-ictce-6.2.5-20140425-24cf06.eb index 77047640bf..06031fc9f0 100644 --- a/easybuild/easyconfigs/m/MOSAIK/MOSAIK-2.2.28-ictce-6.2.5-20140425-24cf06.eb +++ b/easybuild/easyconfigs/m/MOSAIK/MOSAIK-2.2.28-ictce-6.2.5-20140425-24cf06.eb @@ -1,7 +1,7 @@ # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # Author: Pablo Escobar Lopez # sciCORE - University of Basel -# SIB Swiss Institute of Bioinformatics +# SIB Swiss Institute of Bioinformatics easyblock = 'MakeCp' @@ -11,7 +11,7 @@ git_commit_id = '24cf06' #first six digits of the commit id we will download fro versionsuffix = '-20140425-%s' % git_commit_id homepage = 'https://code.google.com/p/mosaik-aligner/' -description = """ MOSAIK is a reference-guided aligner for next-generation +description = """ MOSAIK is a reference-guided aligner for next-generation sequencing technologies """ toolchain = {'name': 'ictce', 'version': '6.2.5'} @@ -28,7 +28,7 @@ start_dir = "src" buildopts = ' BIN_DIR="./bin" OBJ_DIR="./obj"' files_to_copy = ["bin", "../README", "demo"] - + sanity_check_paths = { 'files': ["bin/%s" % x for x in ["MosaikAligner", "MosaikBuild", "MosaikJump", "MosaikText"]], 'dirs': [], diff --git a/easybuild/easyconfigs/p/psmc/psmc-0.6.5-foss-2016a.eb b/easybuild/easyconfigs/p/psmc/psmc-0.6.5-foss-2016a.eb index 59517cb978..86cd994610 100644 --- a/easybuild/easyconfigs/p/psmc/psmc-0.6.5-foss-2016a.eb +++ b/easybuild/easyconfigs/p/psmc/psmc-0.6.5-foss-2016a.eb @@ -6,7 +6,7 @@ version = '0.6.5' homepage = 'https://github.com/lh3/psmc' description = """This software package infers population size history from a diploid sequence using the Pairwise Sequentially Markovian Coalescent (PSMC) model.""" - + toolchain = {'name': 'foss', 'version': '2016a'} source_urls = ['https://github.com/lh3/psmc/archive/'] @@ -16,7 +16,7 @@ buildopts = '&& cd utils && make' utils = [ 'avg.pl', 'calD', 'cntcpg', 'ctime_plot.pl', 'dec2ctime.pl', 'decode2bed.pl', 'fq2psmcfa', 'history2ms.pl', - 'ms2psmcfa.pl', 'mutDiff', 'pcnt_bezier.lua', 'psmc2history.pl', 'psmc_plot.pl', 'psmc_trunc.pl', 'splitfa', + 'ms2psmcfa.pl', 'mutDiff', 'pcnt_bezier.lua', 'psmc2history.pl', 'psmc_plot.pl', 'psmc_trunc.pl', 'splitfa', ] files_to_copy = [ diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.4.0-foss-2016b-hybrid.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.4.0-foss-2016b-hybrid.eb index 57849d2efa..b1b7c57728 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.4.0-foss-2016b-hybrid.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.4.0-foss-2016b-hybrid.eb @@ -11,7 +11,7 @@ description = """Quantum ESPRESSO is an integrated suite of computer codes toolchain = {'name': 'foss', 'version': '2016b'} toolchainopts = {'usempi': True, 'openmp': True} -# this list was determined from QE 5.4.0 version release +# this list was determined from QE 5.4.0 version release sources = [ # Common source 'espresso-%(version)s.tar.gz', @@ -32,7 +32,7 @@ source_urls = [ 'http://www.qe-forge.org/gf/download/frsrelease/211/968/', # espresso-5.4.0.tar.gz # These will not be used because of the 404 signal not found from the previous link. 'http://www.qe-forge.org/gf/download/frsrelease/211/961/', # PWgui-5.4.0.tar.gz - 'http://www.qe-forge.org/gf/download/frsrelease/211/956/', # tddfpt-5.4.0.tar.gz + 'http://www.qe-forge.org/gf/download/frsrelease/211/956/', # tddfpt-5.4.0.tar.gz 'http://www.qe-forge.org/gf/download/frsrelease/211/954/', # atomic-5.4.0.tar.gz 'http://www.qe-forge.org/gf/download/frsrelease/211/959/', # neb-5.4.0.tar.gz 'http://www.qe-forge.org/gf/download/frsrelease/211/962/', # PHonon-5.4.0.tar.gz @@ -46,8 +46,8 @@ source_urls = [ # Hybrid option exists only for backward compatibility, use toolchain option openmp instead. hybrid = True # Patch file to avoid the CPP problem generated by different OSes -patches = ['QuantumESPRESSO-5.4.0_fix-f90rule-gfortran.patch'] - +patches = ['QuantumESPRESSO-5.4.0_fix-f90rule-gfortran.patch'] + # packages included in 5.4.0 version of QE. We met errors when try to include gipaw, yambo and someother packages. buildopts = 'all tddfpt neb xspectra ph ' diff --git a/easybuild/easyconfigs/r/rainbow/rainbow-2.0.4-goolf-1.4.10.eb b/easybuild/easyconfigs/r/rainbow/rainbow-2.0.4-goolf-1.4.10.eb index e5d10e8061..ebe8bfa5d5 100644 --- a/easybuild/easyconfigs/r/rainbow/rainbow-2.0.4-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/r/rainbow/rainbow-2.0.4-goolf-1.4.10.eb @@ -1,7 +1,7 @@ # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # Author: Pablo Escobar Lopez # sciCORE - University of Basel -# SIB Swiss Institute of Bioinformatics +# SIB Swiss Institute of Bioinformatics easyblock = 'MakeCp' @@ -18,11 +18,11 @@ sources = ['%(name)s_%(version)s.tar.gz'] buildopts = ' CC=$CC' -files_to_copy = [(['rainbow', 'ezmsim', 'rbasm', 'select_sec_rbcontig.pl', +files_to_copy = [(['rainbow', 'ezmsim', 'rbasm', 'select_sec_rbcontig.pl', 'select_best_rbcontig_plus_read1.pl', 'select_sec_rbcontig.pl', 'select_all_rbcontig.pl'], 'bin')] parallel = 1 - + sanity_check_paths = { 'files': ['bin/rainbow', 'bin/ezmsim', 'bin/rbasm'], 'dirs': [], -- GitLab From c69a2ada4ad62775620a7eee897e439ae28e0954 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 22 Feb 2017 21:45:13 +0100 Subject: [PATCH 0143/1603] include two spaces before inline comment --- .../cclib-1.5-foss-2016b-Python-3.5.2.eb | 2 +- .../e/ELPA/ELPA-2016.05.004-intel-2017a.eb | 2 +- .../easyconfigs/g/GCC/GCC-4.8.1-CLooG.eb | 2 +- .../g/GCC/GCC-4.8.2-CLooG-multilib.eb | 2 +- .../easyconfigs/g/GCC/GCC-4.8.2-CLooG.eb | 2 +- .../g/GCC/GCC-4.8.3-CLooG-multilib.eb | 2 +- .../g/GCC/GCC-4.8.4-CLooG-multilib.eb | 2 +- .../easyconfigs/g/GCC/GCC-4.8.4-CLooG.eb | 2 +- .../g/GCC/GCC-4.9.0-CLooG-multilib.eb | 2 +- .../easyconfigs/g/GCC/GCC-4.9.0-CLooG.eb | 2 +- .../g/GCC/GCC-4.9.1-CLooG-multilib.eb | 2 +- .../easyconfigs/g/GCC/GCC-4.9.1-CLooG.eb | 2 +- .../g/GCC/GCC-4.9.2-CLooG-multilib.eb | 2 +- .../easyconfigs/g/GCC/GCC-4.9.2-CLooG.eb | 2 +- .../g/GCC/GCC-5.1.0-binutils-2.25.eb | 2 +- easybuild/easyconfigs/g/GCC/GCC-5.1.0.eb | 2 +- easybuild/easyconfigs/g/GCC/GCC-5.2.0.eb | 2 +- easybuild/easyconfigs/g/GCC/GCC-5.3.0.eb | 2 +- .../easyconfigs/g/GCCcore/GCCcore-5.3.0.eb | 2 +- .../easyconfigs/g/GCCcore/GCCcore-5.4.0.eb | 2 +- .../easyconfigs/g/GCCcore/GCCcore-6.1.0.eb | 2 +- .../easyconfigs/g/GCCcore/GCCcore-6.2.0.eb | 2 +- .../easyconfigs/g/GCCcore/GCCcore-6.3.0.eb | 2 +- .../i/intelcuda/intelcuda-2016.10.eb | 2 +- ...AIK-2.2.28-goolf-1.4.10-20140425-24cf06.eb | 2 +- ...SAIK-2.2.28-ictce-6.2.5-20140425-24cf06.eb | 2 +- ...J-Express-0.44-foss-2016a-Java-1.8.0_92.eb | 2 +- ...Express-0.44-goolf-1.4.10-Java-1.7.0_75.eb | 2 +- .../OpenMPI-1.10.2-PGI-16.3-GCC-4.9.3-2.25.eb | 2 +- .../OpenMPI-1.10.2-PGI-16.4-GCC-5.3.0-2.26.eb | 2 +- .../OpenMPI-1.10.4-PGI-16.7-GCC-5.4.0-2.26.eb | 2 +- .../PRINSEQ-0.20.4-foss-2015b-Perl-5.20.3.eb | 6 ++--- ...PRINSEQ-0.20.4-goolf-1.4.10-Perl-5.16.3.eb | 6 ++--- .../PostgreSQL-9.3.5-intel-2014b.eb | 2 +- ...tgreSQL-9.4.7-intel-2016a-Python-2.7.11.eb | 2 +- ...tgreSQL-9.5.2-intel-2016a-Python-2.7.11.eb | 2 +- ...tgreSQL-9.6.0-intel-2016b-Python-2.7.12.eb | 2 +- ...gres-XL-9.5r1-intel-2016a-Python-2.7.11.eb | 2 +- .../p/Python/Python-2.7.9-CrayGNU-2015.06.eb | 2 +- .../p/Python/Python-2.7.9-CrayGNU-2015.11.eb | 2 +- ...QuantumESPRESSO-5.4.0-foss-2016b-hybrid.eb | 22 +++++++++---------- .../easyconfigs/r/R/R-3.2.3-foss-2015b.eb | 2 +- .../easyconfigs/r/R/R-3.2.3-foss-2016a.eb | 2 +- .../easyconfigs/r/R/R-3.2.3-foss-2016b.eb | 2 +- .../r/R/R-3.2.3-intel-2016a-libX11-1.6.3.eb | 6 ++--- .../easyconfigs/r/R/R-3.2.3-intel-2016a.eb | 2 +- .../easyconfigs/r/R/R-3.3.1-foss-2016a.eb | 2 +- .../easyconfigs/r/R/R-3.3.1-foss-2016b.eb | 2 +- .../easyconfigs/r/R/R-3.3.1-intel-2016b.eb | 2 +- .../easyconfigs/r/Reads2snp/Reads2snp-2.0.eb | 2 +- 50 files changed, 66 insertions(+), 66 deletions(-) diff --git a/easybuild/easyconfigs/c/cclib/cclib-1.5-foss-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/c/cclib/cclib-1.5-foss-2016b-Python-3.5.2.eb index 78196b3b89..fe63f8a29c 100644 --- a/easybuild/easyconfigs/c/cclib/cclib-1.5-foss-2016b-Python-3.5.2.eb +++ b/easybuild/easyconfigs/c/cclib/cclib-1.5-foss-2016b-Python-3.5.2.eb @@ -15,7 +15,7 @@ source_urls = ['https://github.com/cclib/cclib/releases/download/v%(version)s/'] sources = ['%(name)s-%(version)s.post1.tar.gz'] dependencies = [ - ('Python', '3.5.2'), # This contains numpy as extension needed for cclib + ('Python', '3.5.2'), # This contains numpy as extension needed for cclib ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2016.05.004-intel-2017a.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2016.05.004-intel-2017a.eb index 2c6c725788..4851fc5541 100644 --- a/easybuild/easyconfigs/e/ELPA/ELPA-2016.05.004-intel-2017a.eb +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2016.05.004-intel-2017a.eb @@ -36,7 +36,7 @@ common_configopts += 'LIBS="$LIBSCALAPACK" ' configopts = [ common_configopts + '--enable-openmp ', - common_configopts, # Default version last, so we can get the normal config.h/config-f90.h installed afterwards. + common_configopts, # Default version last, so we can get the normal config.h/config-f90.h installed afterwards. ] buildopts = ' V=1 ' diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.8.1-CLooG.eb b/easybuild/easyconfigs/g/GCC/GCC-4.8.1-CLooG.eb index 041898fae9..618d553031 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.8.1-CLooG.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.8.1-CLooG.eb @@ -16,7 +16,7 @@ source_urls = [ 'http://www.bastoul.net/cloog/pages/download/', # CLooG official 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies 'http://gcc.cybermirror.org/infrastructure/', # HTTP mirror for GCC dependencies - 'http://isl.gforge.inria.fr/', # original HTTP source for ISL + 'http://isl.gforge.inria.fr/', # original HTTP source for ISL ] sources = [ SOURCELOWER_TAR_GZ, diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.8.2-CLooG-multilib.eb b/easybuild/easyconfigs/g/GCC/GCC-4.8.2-CLooG-multilib.eb index 91e4497eaa..6d29040095 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.8.2-CLooG-multilib.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.8.2-CLooG-multilib.eb @@ -16,7 +16,7 @@ source_urls = [ 'http://www.bastoul.net/cloog/pages/download/', # CLooG official 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies 'http://gcc.cybermirror.org/infrastructure/', # HTTP mirror for GCC dependencies - 'http://isl.gforge.inria.fr/', # original HTTP source for ISL + 'http://isl.gforge.inria.fr/', # original HTTP source for ISL ] sources = [ SOURCELOWER_TAR_GZ, diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.8.2-CLooG.eb b/easybuild/easyconfigs/g/GCC/GCC-4.8.2-CLooG.eb index d6ce9a89a0..9a60bde46d 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.8.2-CLooG.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.8.2-CLooG.eb @@ -16,7 +16,7 @@ source_urls = [ 'http://www.bastoul.net/cloog/pages/download/', # CLooG official 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies 'http://gcc.cybermirror.org/infrastructure/', # HTTP mirror for GCC dependencies - 'http://isl.gforge.inria.fr/', # original HTTP source for ISL + 'http://isl.gforge.inria.fr/', # original HTTP source for ISL ] sources = [ SOURCELOWER_TAR_GZ, diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.8.3-CLooG-multilib.eb b/easybuild/easyconfigs/g/GCC/GCC-4.8.3-CLooG-multilib.eb index a5d4cd082d..54f482d906 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.8.3-CLooG-multilib.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.8.3-CLooG-multilib.eb @@ -16,7 +16,7 @@ source_urls = [ 'http://www.bastoul.net/cloog/pages/download/', # CLooG official 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies 'http://gcc.cybermirror.org/infrastructure/', # HTTP mirror for GCC dependencies - 'http://isl.gforge.inria.fr/', # original HTTP source for ISL + 'http://isl.gforge.inria.fr/', # original HTTP source for ISL ] sources = [ SOURCELOWER_TAR_GZ, diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.8.4-CLooG-multilib.eb b/easybuild/easyconfigs/g/GCC/GCC-4.8.4-CLooG-multilib.eb index 1d2159779b..89f13931a3 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.8.4-CLooG-multilib.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.8.4-CLooG-multilib.eb @@ -16,7 +16,7 @@ source_urls = [ 'http://www.bastoul.net/cloog/pages/download/', # CLooG official 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies 'http://gcc.cybermirror.org/infrastructure/', # HTTP mirror for GCC dependencies - 'http://isl.gforge.inria.fr/', # original HTTP source for ISL + 'http://isl.gforge.inria.fr/', # original HTTP source for ISL ] sources = [ SOURCELOWER_TAR_GZ, diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.8.4-CLooG.eb b/easybuild/easyconfigs/g/GCC/GCC-4.8.4-CLooG.eb index bcc4336300..1fee24d2ad 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.8.4-CLooG.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.8.4-CLooG.eb @@ -16,7 +16,7 @@ source_urls = [ 'http://www.bastoul.net/cloog/pages/download/', # CLooG official 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies 'http://gcc.cybermirror.org/infrastructure/', # HTTP mirror for GCC dependencies - 'http://isl.gforge.inria.fr/', # original HTTP source for ISL + 'http://isl.gforge.inria.fr/', # original HTTP source for ISL ] sources = [ SOURCELOWER_TAR_GZ, diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.9.0-CLooG-multilib.eb b/easybuild/easyconfigs/g/GCC/GCC-4.9.0-CLooG-multilib.eb index 1293532d23..c0cd444cef 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.9.0-CLooG-multilib.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.9.0-CLooG-multilib.eb @@ -18,7 +18,7 @@ source_urls = [ 'http://www.bastoul.net/cloog/pages/download/', # CLooG official 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies 'http://gcc.cybermirror.org/infrastructure/', # HTTP mirror for GCC dependencies - 'http://isl.gforge.inria.fr/', # original HTTP source for ISL + 'http://isl.gforge.inria.fr/', # original HTTP source for ISL ] sources = [ SOURCELOWER_TAR_BZ2, diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.9.0-CLooG.eb b/easybuild/easyconfigs/g/GCC/GCC-4.9.0-CLooG.eb index 82341a9a29..7a4b755a4c 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.9.0-CLooG.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.9.0-CLooG.eb @@ -18,7 +18,7 @@ source_urls = [ 'http://www.bastoul.net/cloog/pages/download/', # CLooG official 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies 'http://gcc.cybermirror.org/infrastructure/', # HTTP mirror for GCC dependencies - 'http://isl.gforge.inria.fr/', # original HTTP source for ISL + 'http://isl.gforge.inria.fr/', # original HTTP source for ISL ] sources = [ SOURCELOWER_TAR_BZ2, diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.9.1-CLooG-multilib.eb b/easybuild/easyconfigs/g/GCC/GCC-4.9.1-CLooG-multilib.eb index 7f03450a91..bd08517bfa 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.9.1-CLooG-multilib.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.9.1-CLooG-multilib.eb @@ -18,7 +18,7 @@ source_urls = [ 'http://www.bastoul.net/cloog/pages/download/', # CLooG official 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies 'http://gcc.cybermirror.org/infrastructure/', # HTTP mirror for GCC dependencies - 'http://isl.gforge.inria.fr/', # original HTTP source for ISL + 'http://isl.gforge.inria.fr/', # original HTTP source for ISL ] sources = [ SOURCELOWER_TAR_BZ2, diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.9.1-CLooG.eb b/easybuild/easyconfigs/g/GCC/GCC-4.9.1-CLooG.eb index 163de21ca1..5cb7dc788a 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.9.1-CLooG.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.9.1-CLooG.eb @@ -18,7 +18,7 @@ source_urls = [ 'http://www.bastoul.net/cloog/pages/download/', # CLooG official 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies 'http://gcc.cybermirror.org/infrastructure/', # HTTP mirror for GCC dependencies - 'http://isl.gforge.inria.fr/', # original HTTP source for ISL + 'http://isl.gforge.inria.fr/', # original HTTP source for ISL ] sources = [ SOURCELOWER_TAR_BZ2, diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.9.2-CLooG-multilib.eb b/easybuild/easyconfigs/g/GCC/GCC-4.9.2-CLooG-multilib.eb index 323622921d..4b52dcc343 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.9.2-CLooG-multilib.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.9.2-CLooG-multilib.eb @@ -18,7 +18,7 @@ source_urls = [ 'http://www.bastoul.net/cloog/pages/download/', # CLooG official 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies 'http://gcc.cybermirror.org/infrastructure/', # HTTP mirror for GCC dependencies - 'http://isl.gforge.inria.fr/', # original HTTP source for ISL + 'http://isl.gforge.inria.fr/', # original HTTP source for ISL ] sources = [ SOURCELOWER_TAR_BZ2, diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.9.2-CLooG.eb b/easybuild/easyconfigs/g/GCC/GCC-4.9.2-CLooG.eb index b5769a1078..1ec5100100 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.9.2-CLooG.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.9.2-CLooG.eb @@ -18,7 +18,7 @@ source_urls = [ 'http://www.bastoul.net/cloog/pages/download/', # CLooG official 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies 'http://gcc.cybermirror.org/infrastructure/', # HTTP mirror for GCC dependencies - 'http://isl.gforge.inria.fr/', # original HTTP source for ISL + 'http://isl.gforge.inria.fr/', # original HTTP source for ISL ] sources = [ SOURCELOWER_TAR_BZ2, diff --git a/easybuild/easyconfigs/g/GCC/GCC-5.1.0-binutils-2.25.eb b/easybuild/easyconfigs/g/GCC/GCC-5.1.0-binutils-2.25.eb index 4820fd1026..897ca9088c 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-5.1.0-binutils-2.25.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-5.1.0-binutils-2.25.eb @@ -19,7 +19,7 @@ source_urls = [ 'http://www.multiprecision.org/mpc/download', # MPC official 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies 'http://gcc.cybermirror.org/infrastructure/', # HTTP mirror for GCC dependencies - 'http://isl.gforge.inria.fr/', # original HTTP source for ISL + 'http://isl.gforge.inria.fr/', # original HTTP source for ISL ] sources = [ diff --git a/easybuild/easyconfigs/g/GCC/GCC-5.1.0.eb b/easybuild/easyconfigs/g/GCC/GCC-5.1.0.eb index f182579664..88c83fce42 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-5.1.0.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-5.1.0.eb @@ -16,7 +16,7 @@ source_urls = [ 'http://www.multiprecision.org/mpc/download', # MPC official 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies 'http://gcc.cybermirror.org/infrastructure/', # HTTP mirror for GCC dependencies - 'http://isl.gforge.inria.fr/', # original HTTP source for ISL + 'http://isl.gforge.inria.fr/', # original HTTP source for ISL ] sources = [ diff --git a/easybuild/easyconfigs/g/GCC/GCC-5.2.0.eb b/easybuild/easyconfigs/g/GCC/GCC-5.2.0.eb index 47b8d2c23b..4052ab789b 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-5.2.0.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-5.2.0.eb @@ -16,7 +16,7 @@ source_urls = [ 'http://www.multiprecision.org/mpc/download', # MPC official 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies 'http://gcc.cybermirror.org/infrastructure/', # HTTP mirror for GCC dependencies - 'http://isl.gforge.inria.fr/', # original HTTP source for ISL + 'http://isl.gforge.inria.fr/', # original HTTP source for ISL ] sources = [ diff --git a/easybuild/easyconfigs/g/GCC/GCC-5.3.0.eb b/easybuild/easyconfigs/g/GCC/GCC-5.3.0.eb index 3aa9d513bb..30c9cc61c0 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-5.3.0.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-5.3.0.eb @@ -16,7 +16,7 @@ source_urls = [ 'http://www.multiprecision.org/mpc/download', # MPC official 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies 'http://gcc.cybermirror.org/infrastructure/', # HTTP mirror for GCC dependencies - 'http://isl.gforge.inria.fr/', # original HTTP source for ISL + 'http://isl.gforge.inria.fr/', # original HTTP source for ISL ] sources = [ diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-5.3.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-5.3.0.eb index 4998bcfaba..508f91d3f8 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-5.3.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-5.3.0.eb @@ -18,7 +18,7 @@ source_urls = [ 'http://www.multiprecision.org/mpc/download', # MPC official 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies 'http://gcc.cybermirror.org/infrastructure/', # HTTP mirror for GCC dependencies - 'http://isl.gforge.inria.fr/', # original HTTP source for ISL + 'http://isl.gforge.inria.fr/', # original HTTP source for ISL ] sources = [ diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-5.4.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-5.4.0.eb index 2a3fe7ab85..1a5cf8b884 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-5.4.0.eb @@ -18,7 +18,7 @@ source_urls = [ 'http://www.multiprecision.org/mpc/download', # MPC official 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies 'http://gcc.cybermirror.org/infrastructure/', # HTTP mirror for GCC dependencies - 'http://isl.gforge.inria.fr/', # original HTTP source for ISL + 'http://isl.gforge.inria.fr/', # original HTTP source for ISL ] sources = [ diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-6.1.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-6.1.0.eb index 603dbd6cc5..a645d60588 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-6.1.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-6.1.0.eb @@ -19,7 +19,7 @@ source_urls = [ 'http://gcc.cybermirror.org/infrastructure/', # HTTP mirror for GCC dependencies 'http://ftpmirror.gnu.org/gcc/gcc-%(version)s', # GCC auto-resolving HTTP mirror 'https://ftp.gnu.org/gnu/gcc/gcc-%(version)s/', # Alternative GCC - 'http://isl.gforge.inria.fr/', # original HTTP source for ISL + 'http://isl.gforge.inria.fr/', # original HTTP source for ISL ] sources = [ diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-6.2.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-6.2.0.eb index 5b1200a09b..a460408c19 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-6.2.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-6.2.0.eb @@ -18,7 +18,7 @@ source_urls = [ 'http://www.multiprecision.org/mpc/download', # MPC official 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies 'http://gcc.cybermirror.org/infrastructure/', # HTTP mirror for GCC dependencies - 'http://isl.gforge.inria.fr/', # original HTTP source for ISL + 'http://isl.gforge.inria.fr/', # original HTTP source for ISL ] sources = [ diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-6.3.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-6.3.0.eb index 725e558810..a581540c04 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-6.3.0.eb @@ -18,7 +18,7 @@ source_urls = [ 'http://www.multiprecision.org/mpc/download', # MPC official 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies 'http://gcc.cybermirror.org/infrastructure/', # HTTP mirror for GCC dependencies - 'http://isl.gforge.inria.fr/', # original HTTP source for ISL + 'http://isl.gforge.inria.fr/', # original HTTP source for ISL ] sources = [ diff --git a/easybuild/easyconfigs/i/intelcuda/intelcuda-2016.10.eb b/easybuild/easyconfigs/i/intelcuda/intelcuda-2016.10.eb index ac6a734e6e..82121910a8 100644 --- a/easybuild/easyconfigs/i/intelcuda/intelcuda-2016.10.eb +++ b/easybuild/easyconfigs/i/intelcuda/intelcuda-2016.10.eb @@ -16,7 +16,7 @@ gccsuff = '-GCC-%s-%s' % (gccver, binutilsver) comp = (comp_name, '%s%s' % (comp_ver, gccsuff)) dependencies = [ - comp, # part of iimpic + comp, # part of iimpic ('CUDA', '8.0.44', '', comp), ('icc', comp_ver, gccsuff), ('ifort', comp_ver, gccsuff), diff --git a/easybuild/easyconfigs/m/MOSAIK/MOSAIK-2.2.28-goolf-1.4.10-20140425-24cf06.eb b/easybuild/easyconfigs/m/MOSAIK/MOSAIK-2.2.28-goolf-1.4.10-20140425-24cf06.eb index 4a0d2c666a..a98288f900 100644 --- a/easybuild/easyconfigs/m/MOSAIK/MOSAIK-2.2.28-goolf-1.4.10-20140425-24cf06.eb +++ b/easybuild/easyconfigs/m/MOSAIK/MOSAIK-2.2.28-goolf-1.4.10-20140425-24cf06.eb @@ -7,7 +7,7 @@ easyblock = 'MakeCp' name = 'MOSAIK' version = '2.2.28' -git_commit_id = '24cf06' #first six digits of the commit id we will download from github +git_commit_id = '24cf06' # first six digits of the commit id we will download from github versionsuffix = '-20140425-%s' % git_commit_id homepage = 'https://code.google.com/p/mosaik-aligner/' diff --git a/easybuild/easyconfigs/m/MOSAIK/MOSAIK-2.2.28-ictce-6.2.5-20140425-24cf06.eb b/easybuild/easyconfigs/m/MOSAIK/MOSAIK-2.2.28-ictce-6.2.5-20140425-24cf06.eb index 06031fc9f0..3ce4130b75 100644 --- a/easybuild/easyconfigs/m/MOSAIK/MOSAIK-2.2.28-ictce-6.2.5-20140425-24cf06.eb +++ b/easybuild/easyconfigs/m/MOSAIK/MOSAIK-2.2.28-ictce-6.2.5-20140425-24cf06.eb @@ -7,7 +7,7 @@ easyblock = 'MakeCp' name = 'MOSAIK' version = '2.2.28' -git_commit_id = '24cf06' #first six digits of the commit id we will download from github +git_commit_id = '24cf06' # first six digits of the commit id we will download from github versionsuffix = '-20140425-%s' % git_commit_id homepage = 'https://code.google.com/p/mosaik-aligner/' diff --git a/easybuild/easyconfigs/m/MPJ-Express/MPJ-Express-0.44-foss-2016a-Java-1.8.0_92.eb b/easybuild/easyconfigs/m/MPJ-Express/MPJ-Express-0.44-foss-2016a-Java-1.8.0_92.eb index 3bb9c9fb71..21ae128381 100644 --- a/easybuild/easyconfigs/m/MPJ-Express/MPJ-Express-0.44-foss-2016a-Java-1.8.0_92.eb +++ b/easybuild/easyconfigs/m/MPJ-Express/MPJ-Express-0.44-foss-2016a-Java-1.8.0_92.eb @@ -36,7 +36,7 @@ modextrapaths = { } modextravars = { - 'MPJ_HOME': '$root', # MPJ_HOME points to install directory + 'MPJ_HOME': '$root', # MPJ_HOME points to install directory } sanity_check_paths = { diff --git a/easybuild/easyconfigs/m/MPJ-Express/MPJ-Express-0.44-goolf-1.4.10-Java-1.7.0_75.eb b/easybuild/easyconfigs/m/MPJ-Express/MPJ-Express-0.44-goolf-1.4.10-Java-1.7.0_75.eb index 8c2cfb12b9..41195e5042 100644 --- a/easybuild/easyconfigs/m/MPJ-Express/MPJ-Express-0.44-goolf-1.4.10-Java-1.7.0_75.eb +++ b/easybuild/easyconfigs/m/MPJ-Express/MPJ-Express-0.44-goolf-1.4.10-Java-1.7.0_75.eb @@ -39,7 +39,7 @@ modextrapaths = { } modextravars = { - 'MPJ_HOME': '$root', # MPJ_HOME points to install directory + 'MPJ_HOME': '$root', # MPJ_HOME points to install directory } sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-PGI-16.3-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-PGI-16.3-GCC-4.9.3-2.25.eb index 3dfb0c023b..26ff9690ec 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-PGI-16.3-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-PGI-16.3-GCC-4.9.3-2.25.eb @@ -15,7 +15,7 @@ configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading -configopts += '--with-cxxrtlib="-lgcc_s -lstdc++"' # for vt-mpi-unify +configopts += '--with-cxxrtlib="-lgcc_s -lstdc++"' # for vt-mpi-unify dependencies = [('hwloc', '1.11.3')] diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-PGI-16.4-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-PGI-16.4-GCC-5.3.0-2.26.eb index 274fb15e1f..64e4eca3c7 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-PGI-16.4-GCC-5.3.0-2.26.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-PGI-16.4-GCC-5.3.0-2.26.eb @@ -15,7 +15,7 @@ configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading -configopts += '--with-cxxrtlib="-lgcc_s -lstdc++"' # for vt-mpi-unify +configopts += '--with-cxxrtlib="-lgcc_s -lstdc++"' # for vt-mpi-unify dependencies = [('hwloc', '1.11.3')] diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.4-PGI-16.7-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.4-PGI-16.7-GCC-5.4.0-2.26.eb index fd6bb36c38..f7b06dcb04 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.4-PGI-16.7-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.4-PGI-16.7-GCC-5.4.0-2.26.eb @@ -17,7 +17,7 @@ configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading -configopts += '--with-cxxrtlib="-lgcc_s -lstdc++"' # for vt-mpi-unify +configopts += '--with-cxxrtlib="-lgcc_s -lstdc++"' # for vt-mpi-unify dependencies = [('hwloc', '1.11.4')] diff --git a/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-foss-2015b-Perl-5.20.3.eb b/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-foss-2015b-Perl-5.20.3.eb index 1d36878e90..c76887ac30 100644 --- a/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-foss-2015b-Perl-5.20.3.eb +++ b/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-foss-2015b-Perl-5.20.3.eb @@ -101,13 +101,13 @@ exts_list = [ sanity_check_commands = [('perl', '%(installdir)s/prinseq-graphs.pl')] modextrapaths = { - 'PATH': "", # add installation dir to PATH + 'PATH': "", # add installation dir to PATH 'PERL5LIB': 'lib/perl5/site_perl/%s/' % (perlver) } postinstallcmds = [ - "sed -i -e 's|/usr/bin/perl|/usr/bin/env\ perl|' %(installdir)s/*.pl", # fix shebang line - "chmod +x %(installdir)s/*.pl" # add execution permission + "sed -i -e 's|/usr/bin/perl|/usr/bin/env\ perl|' %(installdir)s/*.pl", # fix shebang line + "chmod +x %(installdir)s/*.pl" # add execution permission ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-goolf-1.4.10-Perl-5.16.3.eb b/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-goolf-1.4.10-Perl-5.16.3.eb index fc0341658f..4dc47a8df2 100644 --- a/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-goolf-1.4.10-Perl-5.16.3.eb +++ b/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-goolf-1.4.10-Perl-5.16.3.eb @@ -99,13 +99,13 @@ exts_list = [ sanity_check_commands = [('perl', '%(installdir)s/prinseq-graphs.pl')] modextrapaths = { - 'PATH': "", # add installation dir to PATH + 'PATH': "", # add installation dir to PATH 'PERL5LIB': 'lib/perl5/site_perl/%s/' % (perlver) } postinstallcmds = [ - "sed -i -e 's|/usr/bin/perl|/usr/bin/env\ perl|' %(installdir)s/*.pl", # fix shebang line - "chmod +x %(installdir)s/*.pl" # add execution permission + "sed -i -e 's|/usr/bin/perl|/usr/bin/env\ perl|' %(installdir)s/*.pl", # fix shebang line + "chmod +x %(installdir)s/*.pl" # add execution permission ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.3.5-intel-2014b.eb b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.3.5-intel-2014b.eb index 815c947eac..b694510474 100644 --- a/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.3.5-intel-2014b.eb +++ b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.3.5-intel-2014b.eb @@ -27,7 +27,7 @@ dependencies = [ (java, javaver, '', True), ('libreadline', '6.3'), ('zlib', '1.2.8'), - # ('OpenSSL', '1.0.1i'), # OS dependency should be preferred for security reasons + # ('OpenSSL', '1.0.1i'), # OS dependency should be preferred for security reasons ] builddependencies = [ diff --git a/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.4.7-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.4.7-intel-2016a-Python-2.7.11.eb index 9afa456cae..a7d2b6c4a0 100644 --- a/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.4.7-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.4.7-intel-2016a-Python-2.7.11.eb @@ -25,7 +25,7 @@ dependencies = [ ('libreadline', '6.3'), ('zlib', '1.2.8'), ('Python', '2.7.11'), - # ('OpenSSL', '1.0.1i'), # OS dependency should be preferred for security reasons + # ('OpenSSL', '1.0.1i'), # OS dependency should be preferred for security reasons ] builddependencies = [ diff --git a/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.5.2-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.5.2-intel-2016a-Python-2.7.11.eb index fca7dea11c..46e78c9224 100644 --- a/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.5.2-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.5.2-intel-2016a-Python-2.7.11.eb @@ -25,7 +25,7 @@ dependencies = [ ('libreadline', '6.3'), ('zlib', '1.2.8'), ('Python', '2.7.11'), - # ('OpenSSL', '1.0.1i'), # OS dependency should be preferred for security reasons + # ('OpenSSL', '1.0.1i'), # OS dependency should be preferred for security reasons ] builddependencies = [ diff --git a/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.6.0-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.6.0-intel-2016b-Python-2.7.12.eb index a1b0d0ba13..8f8750717c 100644 --- a/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.6.0-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.6.0-intel-2016b-Python-2.7.12.eb @@ -25,7 +25,7 @@ dependencies = [ ('libreadline', '6.3'), ('zlib', '1.2.8'), ('Python', '2.7.12'), - # ('OpenSSL', '1.0.1i'), # OS dependency should be preferred for security reasons + # ('OpenSSL', '1.0.1i'), # OS dependency should be preferred for security reasons ] builddependencies = [ diff --git a/easybuild/easyconfigs/p/Postgres-XL/Postgres-XL-9.5r1-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/Postgres-XL/Postgres-XL-9.5r1-intel-2016a-Python-2.7.11.eb index 01c5da8a48..8261dc989e 100644 --- a/easybuild/easyconfigs/p/Postgres-XL/Postgres-XL-9.5r1-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/Postgres-XL/Postgres-XL-9.5r1-intel-2016a-Python-2.7.11.eb @@ -19,7 +19,7 @@ dependencies = [ ('libreadline', '6.3'), ('zlib', '1.2.8'), ('Python', '2.7.11'), - # ('OpenSSL', '1.0.1i'), # OS dependency should be preferred for security reasons + # ('OpenSSL', '1.0.1i'), # OS dependency should be preferred for security reasons ] builddependencies = [ diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.06.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.06.eb index 2c98486b92..a0d5fb01e5 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.06.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.06.eb @@ -42,7 +42,7 @@ exts_list = [ ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], 'patches': [ - 'numpy-1.8.0-mkl.patch', # % numpyversion, + 'numpy-1.8.0-mkl.patch', ], }), ('scipy', scipyversion, { diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.11.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.11.eb index 23449c0834..eb90e5f158 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.11.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.11.eb @@ -42,7 +42,7 @@ exts_list = [ ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], 'patches': [ - 'numpy-1.8.0-mkl.patch', # % numpyversion, + 'numpy-1.8.0-mkl.patch', ], }), ('scipy', scipyversion, { diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.4.0-foss-2016b-hybrid.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.4.0-foss-2016b-hybrid.eb index b1b7c57728..09b026a284 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.4.0-foss-2016b-hybrid.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.4.0-foss-2016b-hybrid.eb @@ -29,18 +29,18 @@ sources = [ ] source_urls = [ 'http://files.qe-forge.org/index.php?file=', # Almost all - 'http://www.qe-forge.org/gf/download/frsrelease/211/968/', # espresso-5.4.0.tar.gz + 'http://www.qe-forge.org/gf/download/frsrelease/211/968/', # espresso-5.4.0.tar.gz # These will not be used because of the 404 signal not found from the previous link. - 'http://www.qe-forge.org/gf/download/frsrelease/211/961/', # PWgui-5.4.0.tar.gz - 'http://www.qe-forge.org/gf/download/frsrelease/211/956/', # tddfpt-5.4.0.tar.gz - 'http://www.qe-forge.org/gf/download/frsrelease/211/954/', # atomic-5.4.0.tar.gz - 'http://www.qe-forge.org/gf/download/frsrelease/211/959/', # neb-5.4.0.tar.gz - 'http://www.qe-forge.org/gf/download/frsrelease/211/962/', # PHonon-5.4.0.tar.gz - 'http://www.qe-forge.org/gf/download/frsrelease/211/960/', # pwcond-5.4.0.tar.gz - 'http://www.qe-forge.org/gf/download/frsrelease/211/958/', # xspectra-5.4.0.tar.gz - 'http://www.qe-forge.org/gf/download/frsrelease/211/969/', # EPW-5.4.0.tar.gz - 'http://www.qe-forge.org/gf/download/frsrelease/211/963/', # test-suite-5.4.0.tar.gz - 'http://www.qe-forge.org/gf/download/frsrelease/211/957/', # GWW-5.4.0.tar.gz + 'http://www.qe-forge.org/gf/download/frsrelease/211/961/', # PWgui-5.4.0.tar.gz + 'http://www.qe-forge.org/gf/download/frsrelease/211/956/', # tddfpt-5.4.0.tar.gz + 'http://www.qe-forge.org/gf/download/frsrelease/211/954/', # atomic-5.4.0.tar.gz + 'http://www.qe-forge.org/gf/download/frsrelease/211/959/', # neb-5.4.0.tar.gz + 'http://www.qe-forge.org/gf/download/frsrelease/211/962/', # PHonon-5.4.0.tar.gz + 'http://www.qe-forge.org/gf/download/frsrelease/211/960/', # pwcond-5.4.0.tar.gz + 'http://www.qe-forge.org/gf/download/frsrelease/211/958/', # xspectra-5.4.0.tar.gz + 'http://www.qe-forge.org/gf/download/frsrelease/211/969/', # EPW-5.4.0.tar.gz + 'http://www.qe-forge.org/gf/download/frsrelease/211/963/', # test-suite-5.4.0.tar.gz + 'http://www.qe-forge.org/gf/download/frsrelease/211/957/', # GWW-5.4.0.tar.gz ] # Hybrid option exists only for backward compatibility, use toolchain option openmp instead. diff --git a/easybuild/easyconfigs/r/R/R-3.2.3-foss-2015b.eb b/easybuild/easyconfigs/r/R/R-3.2.3-foss-2015b.eb index b54b0f68e9..95846046fc 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.3-foss-2015b.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.3-foss-2015b.eb @@ -25,7 +25,7 @@ dependencies = [ ('cURL', '7.45.0'), # for RCurl ('libxml2', '2.9.2'), # for XML ('GDAL', '2.0.1'), # for rgdal - ('PROJ', '4.8.0'), # for rgdal + ('PROJ', '4.8.0'), # for rgdal ('GMP', '6.0.0a', '', ('GNU', '4.9.3-2.25')), # for igraph ] diff --git a/easybuild/easyconfigs/r/R/R-3.2.3-foss-2016a.eb b/easybuild/easyconfigs/r/R/R-3.2.3-foss-2016a.eb index 580f74438d..1389b272dd 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.3-foss-2016a.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.3-foss-2016a.eb @@ -25,7 +25,7 @@ dependencies = [ ('cURL', '7.47.0'), # for RCurl ('libxml2', '2.9.3'), # for XML ('GDAL', '2.0.2'), # for rgdal - ('PROJ', '4.9.2'), # for rgdal + ('PROJ', '4.9.2'), # for rgdal ('GMP', '6.1.0'), # for igraph ] diff --git a/easybuild/easyconfigs/r/R/R-3.2.3-foss-2016b.eb b/easybuild/easyconfigs/r/R/R-3.2.3-foss-2016b.eb index 004c178582..0acfcbd0b3 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.3-foss-2016b.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.3-foss-2016b.eb @@ -25,7 +25,7 @@ dependencies = [ ('cURL', '7.49.1'), # for RCurl ('libxml2', '2.9.4'), # for XML ('GDAL', '2.1.0'), # for rgdal - ('PROJ', '4.9.2'), # for rgdal + ('PROJ', '4.9.2'), # for rgdal ('GMP', '6.1.1'), # for igraph ] diff --git a/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a-libX11-1.6.3.eb b/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a-libX11-1.6.3.eb index 1a886a00c9..39a19900bb 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a-libX11-1.6.3.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a-libX11-1.6.3.eb @@ -28,15 +28,15 @@ dependencies = [ ('ncurses', '6.0'), ('libpng', '1.6.21'), # for plotting in R ('libjpeg-turbo', '1.4.2'), # for plottting in R - ('LibTIFF', '4.0.6'), # for plotting in R - ('cairo', '1.14.6'), # for plotting in R + ('LibTIFF', '4.0.6'), # for plotting in R + ('cairo', '1.14.6'), # for plotting in R ('Java', '1.8.0_72', '', True), # Java bindings are built if Java is found, might as well provide it ('Tcl', '8.6.4'), # for tcltk ('Tk', '8.6.4', versionsuffix), # for tcltk ('cURL', '7.47.0'), # for RCurl ('libxml2', '2.9.3'), # for XML ('GDAL', '2.0.2'), # for rgdal - ('PROJ', '4.9.2'), # for rgdal + ('PROJ', '4.9.2'), # for rgdal ('GMP', '6.1.0'), # for igraph ] diff --git a/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a.eb b/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a.eb index 7baa761be0..ad907eaa04 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a.eb @@ -25,7 +25,7 @@ dependencies = [ ('cURL', '7.47.0'), # for RCurl ('libxml2', '2.9.3'), # for XML ('GDAL', '2.0.2'), # for rgdal - ('PROJ', '4.9.2'), # for rgdal + ('PROJ', '4.9.2'), # for rgdal ('GMP', '6.1.0'), # for igraph ] diff --git a/easybuild/easyconfigs/r/R/R-3.3.1-foss-2016a.eb b/easybuild/easyconfigs/r/R/R-3.3.1-foss-2016a.eb index 7ed2007d87..7c7e501aad 100644 --- a/easybuild/easyconfigs/r/R/R-3.3.1-foss-2016a.eb +++ b/easybuild/easyconfigs/r/R/R-3.3.1-foss-2016a.eb @@ -31,7 +31,7 @@ dependencies = [ ('cURL', '7.49.1'), # for RCurl ('libxml2', '2.9.4'), # for XML ('GDAL', '2.1.0'), # for rgdal - ('PROJ', '4.9.2'), # for rgdal + ('PROJ', '4.9.2'), # for rgdal ('GMP', '6.1.1'), # for igraph # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons diff --git a/easybuild/easyconfigs/r/R/R-3.3.1-foss-2016b.eb b/easybuild/easyconfigs/r/R/R-3.3.1-foss-2016b.eb index e6d46c62ea..9380aadc9b 100644 --- a/easybuild/easyconfigs/r/R/R-3.3.1-foss-2016b.eb +++ b/easybuild/easyconfigs/r/R/R-3.3.1-foss-2016b.eb @@ -31,7 +31,7 @@ dependencies = [ ('cURL', '7.49.1'), # for RCurl ('libxml2', '2.9.4'), # for XML ('GDAL', '2.1.0'), # for rgdal - ('PROJ', '4.9.2'), # for rgdal + ('PROJ', '4.9.2'), # for rgdal ('GMP', '6.1.1'), # for igraph # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons diff --git a/easybuild/easyconfigs/r/R/R-3.3.1-intel-2016b.eb b/easybuild/easyconfigs/r/R/R-3.3.1-intel-2016b.eb index 09f5b0a4c6..88223934d1 100644 --- a/easybuild/easyconfigs/r/R/R-3.3.1-intel-2016b.eb +++ b/easybuild/easyconfigs/r/R/R-3.3.1-intel-2016b.eb @@ -31,7 +31,7 @@ dependencies = [ ('cURL', '7.49.1'), # for RCurl ('libxml2', '2.9.4'), # for XML ('GDAL', '2.1.0'), # for rgdal - ('PROJ', '4.9.2'), # for rgdal + ('PROJ', '4.9.2'), # for rgdal ('GMP', '6.1.1'), # for igraph # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons diff --git a/easybuild/easyconfigs/r/Reads2snp/Reads2snp-2.0.eb b/easybuild/easyconfigs/r/Reads2snp/Reads2snp-2.0.eb index 506890dce2..462568a58d 100644 --- a/easybuild/easyconfigs/r/Reads2snp/Reads2snp-2.0.eb +++ b/easybuild/easyconfigs/r/Reads2snp/Reads2snp-2.0.eb @@ -25,7 +25,7 @@ sanity_check_paths = { } modextrapaths = { - 'PATH': "", # add the installation dir to PATH + 'PATH': "", # add the installation dir to PATH } moduleclass = 'bio' -- GitLab From 465017c088b49dcbf976764f7fe42a80326b9149 Mon Sep 17 00:00:00 2001 From: Maxime Boissonneault Date: Wed, 22 Feb 2017 21:34:48 +0000 Subject: [PATCH 0144/1603] removed comments from the recipe --- easybuild/easyconfigs/i/igraph/igraph-0.7.1-intel-2016b.eb | 5 ----- 1 file changed, 5 deletions(-) diff --git a/easybuild/easyconfigs/i/igraph/igraph-0.7.1-intel-2016b.eb b/easybuild/easyconfigs/i/igraph/igraph-0.7.1-intel-2016b.eb index 68c14b0bae..ddf779e0e0 100644 --- a/easybuild/easyconfigs/i/igraph/igraph-0.7.1-intel-2016b.eb +++ b/easybuild/easyconfigs/i/igraph/igraph-0.7.1-intel-2016b.eb @@ -17,12 +17,7 @@ source_urls = ['https://github.com/igraph/igraph/releases/download/%(version)s'] builddependencies = [('Autotools', '20150215')] patches = [ - # Author: Maxime Boissonneault - # Remove explicit linking on -llapack and -llblas, which are not found when linking against MKL 'igraph-%(version)s-no-lapack-no-blas.patch', - - # Author: Maxime Boissonneault - # Fix explicit version of aclocal (specified 1.14). Replaced with version 1.15 which corresponds to the 20150215 Autotools 'igraph-%(version)s-fix-aclocal-version.patch' ] -- GitLab From f134c4ca7dcb46bb0eedae01d0fe4c05115e013e Mon Sep 17 00:00:00 2001 From: Robert Qiao Date: Thu, 23 Feb 2017 10:06:10 +1030 Subject: [PATCH 0145/1603] error corrected --- .../easyconfigs/m/meRanTK/meRanTK-1.1.1b.eb | 20 ++++++------------- 1 file changed, 6 insertions(+), 14 deletions(-) diff --git a/easybuild/easyconfigs/m/meRanTK/meRanTK-1.1.1b.eb b/easybuild/easyconfigs/m/meRanTK/meRanTK-1.1.1b.eb index 25c303ad85..2075adf0b4 100644 --- a/easybuild/easyconfigs/m/meRanTK/meRanTK-1.1.1b.eb +++ b/easybuild/easyconfigs/m/meRanTK/meRanTK-1.1.1b.eb @@ -3,35 +3,27 @@ # Homepage: https://www.adelaide.edu.au/phoenix/ # # Copyright:: adelaide.edu.au/phoenix -# Authors:: Robert Qiao , Exequiel Manuel Sepulveda Escobedo +# Authors:: Robert Qiao , Exe Escobedo # License:: # # Notes:: ## +easyblock = 'BinariesTarball' + name = 'meRanTK' version = '1.1.1b' -easyblock = 'BinariesTarball' homepage = 'http://www.icbi.at/index.html' description = """meRanTK is a versatile high performance toolkit for complete analysis of methylated RNA data.""" toolchain = {'name': 'dummy', 'version': 'dummy'} -source_urls = ['http://www.icbi.at/software/meRanTK/downloads'] -sources = ['%s/meRanTK-%s.zip' %(version,version,)] - -dependencies = [ -] +source_urls = ['http://www.icbi.at/software/meRanTK/downloads/%(version)s/'] +sources = ['meRanTK-%(version)s.zip'] sanity_check_paths = { - 'files':['bin/meRanAnnotate'], - 'files':['bin/meRanCall'], - 'files':['bin/meRanCompare'], - 'files':['bin/meRanGs'], - 'files':['bin/meRanGt'], - 'files':['bin/meRanT'], - 'dirs':[], + 'files': ['bin/meRan%s' % x for x in ['Annotate', 'Call', 'Compare', 'Gs', 'Gt', 'T']], } moduleclass = 'bio' -- GitLab From 1b573a83426da3b37a07896b9bbdbdc5cdcea9dc Mon Sep 17 00:00:00 2001 From: Robert Date: Thu, 23 Feb 2017 14:58:00 +1030 Subject: [PATCH 0146/1603] Style fixed --- easybuild/easyconfigs/m/meRanTK/meRanTK-1.1.1b.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/meRanTK/meRanTK-1.1.1b.eb b/easybuild/easyconfigs/m/meRanTK/meRanTK-1.1.1b.eb index 2075adf0b4..0d549f7977 100644 --- a/easybuild/easyconfigs/m/meRanTK/meRanTK-1.1.1b.eb +++ b/easybuild/easyconfigs/m/meRanTK/meRanTK-1.1.1b.eb @@ -23,7 +23,8 @@ source_urls = ['http://www.icbi.at/software/meRanTK/downloads/%(version)s/'] sources = ['meRanTK-%(version)s.zip'] sanity_check_paths = { - 'files': ['bin/meRan%s' % x for x in ['Annotate', 'Call', 'Compare', 'Gs', 'Gt', 'T']], + 'files': ['bin/meRan%s' % x for x in ['Annotate', 'Call', 'Compare', 'Gs', 'Gt', 'T']], + 'dirs': [], } moduleclass = 'bio' -- GitLab From 637f19f50c5b6cf5e59b6e83d016a7634c60e52e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 23 Feb 2017 09:14:15 +0100 Subject: [PATCH 0147/1603] prefer OpenSSL as OS dep in easyconfig for Python 2.7.11 w/ iomkl/2016.07 --- .../easyconfigs/p/Python/Python-2.7.11-iomkl-2016.07.eb | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-iomkl-2016.07.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-iomkl-2016.07.eb index c445811709..ceffc4847a 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-iomkl-2016.07.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-iomkl-2016.07.eb @@ -23,14 +23,14 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '6.0'), ('SQLite', '3.9.2'), - #('Tk', '8.6.4', '-no-X11'), # this requires a full X11 stack ('Tk', '8.6.4'), # this requires a full X11 stack ('GMP', '6.1.0'), - ('OpenSSL', '1.0.2h'), # OS dependency should be preferred if the os version is more recent then this version, it's -# nice to have an up to date openssl for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.2h'), ] -#osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! # package versions updated May 28th 2015 -- GitLab From 5b23bc5e4ac2d1e0c0fcfef2211f17e4b3e846d2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 23 Feb 2017 09:20:47 +0100 Subject: [PATCH 0148/1603] comments should start with '# ' --- easybuild/easyconfigs/a/ASHS/ASHS-rev103_20140612.eb | 4 ++-- .../a/Allinea/Allinea-6.1.1-Ubuntu-14.04-x86_64.eb | 6 +++--- .../easyconfigs/b/Bowtie2/Bowtie2-2.0.5-goolf-1.4.10.eb | 2 +- .../easyconfigs/b/Bowtie2/Bowtie2-2.0.6-goolf-1.4.10.eb | 2 +- .../easyconfigs/b/Bowtie2/Bowtie2-2.1.0-goolf-1.4.10.eb | 2 +- .../easyconfigs/b/Bowtie2/Bowtie2-2.2.0-goolf-1.4.10.eb | 2 +- .../easyconfigs/b/Bowtie2/Bowtie2-2.2.2-goolf-1.4.10.eb | 2 +- .../easyconfigs/b/Bowtie2/Bowtie2-2.2.4-goolf-1.4.10.eb | 2 +- .../easyconfigs/b/Bowtie2/Bowtie2-2.2.5-goolf-1.7.20.eb | 2 +- .../easyconfigs/b/Bowtie2/Bowtie2-2.2.5-intel-2015a.eb | 2 +- .../easyconfigs/b/Bowtie2/Bowtie2-2.2.6-foss-2015b.eb | 2 +- .../easyconfigs/b/Bowtie2/Bowtie2-2.2.6-intel-2015b.eb | 2 +- .../easyconfigs/b/Bowtie2/Bowtie2-2.2.7-foss-2015b.eb | 2 +- .../easyconfigs/b/Bowtie2/Bowtie2-2.2.8-foss-2015b.eb | 2 +- .../easyconfigs/b/Bowtie2/Bowtie2-2.2.8-foss-2016a.eb | 2 +- .../easyconfigs/b/Bowtie2/Bowtie2-2.2.9-foss-2016a.eb | 2 +- .../easyconfigs/b/Bowtie2/Bowtie2-2.2.9-goolf-1.7.20.eb | 2 +- easybuild/easyconfigs/c/CMake/CMake-3.2.3-foss-2015a.eb | 2 +- easybuild/easyconfigs/c/CMake/CMake-3.2.3-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/c/CMake/CMake-3.2.3-intel-2015a.eb | 2 +- easybuild/easyconfigs/c/CMake/CMake-3.2.3-intel-2015b.eb | 2 +- easybuild/easyconfigs/c/CMake/CMake-3.3.1-intel-2015a.eb | 2 +- .../easyconfigs/c/CMake/CMake-3.3.2-GNU-4.9.3-2.25.eb | 2 +- easybuild/easyconfigs/c/CMake/CMake-3.3.2-gimkl-2.11.5.eb | 2 +- easybuild/easyconfigs/c/CMake/CMake-3.3.2-intel-2015b.eb | 2 +- easybuild/easyconfigs/c/CMake/CMake-3.4.0-intel-2015b.eb | 2 +- .../easyconfigs/c/CMake/CMake-3.4.1-GCCcore-4.9.3.eb | 2 +- easybuild/easyconfigs/c/CMake/CMake-3.4.1-foss-2015b.eb | 2 +- easybuild/easyconfigs/c/CMake/CMake-3.4.1-foss-2016a.eb | 2 +- easybuild/easyconfigs/c/CMake/CMake-3.4.1-intel-2015b.eb | 2 +- .../c/CMake/CMake-3.4.1-intel-2016.02-GCC-4.9.eb | 2 +- easybuild/easyconfigs/c/CMake/CMake-3.4.1-intel-2016a.eb | 2 +- .../easyconfigs/c/CMake/CMake-3.4.1-iomkl-2016.07.eb | 2 +- .../c/CMake/CMake-3.4.1-iomkl-2016.09-GCC-4.9.3-2.25.eb | 2 +- easybuild/easyconfigs/c/CMake/CMake-3.4.3-foss-2016a.eb | 2 +- easybuild/easyconfigs/c/CMake/CMake-3.4.3-foss-2016b.eb | 2 +- easybuild/easyconfigs/c/CMake/CMake-3.4.3-gimkl-2.11.5.eb | 2 +- easybuild/easyconfigs/c/CMake/CMake-3.4.3-goolf-1.7.20.eb | 2 +- easybuild/easyconfigs/c/CMake/CMake-3.4.3-ictce-7.3.5.eb | 2 +- easybuild/easyconfigs/c/CMake/CMake-3.4.3-intel-2016a.eb | 2 +- easybuild/easyconfigs/c/CMake/CMake-3.5.1-intel-2016a.eb | 2 +- .../easyconfigs/c/CMake/CMake-3.5.2-GCC-4.9.3-2.25.eb | 2 +- easybuild/easyconfigs/c/CMake/CMake-3.5.2-foss-2016a.eb | 2 +- easybuild/easyconfigs/c/CMake/CMake-3.5.2-foss-2016b.eb | 2 +- easybuild/easyconfigs/c/CMake/CMake-3.5.2-goolf-1.7.20.eb | 2 +- easybuild/easyconfigs/c/CMake/CMake-3.5.2-intel-2016a.eb | 2 +- easybuild/easyconfigs/c/CMake/CMake-3.5.2-intel-2016b.eb | 2 +- .../easyconfigs/c/CMake/CMake-3.6.1-GCC-5.4.0-2.26.eb | 2 +- .../easyconfigs/c/CMake/CMake-3.6.1-GCCcore-4.9.3.eb | 2 +- easybuild/easyconfigs/c/CMake/CMake-3.6.1-foss-2016b.eb | 2 +- easybuild/easyconfigs/c/CMake/CMake-3.6.1-intel-2016b.eb | 2 +- .../easyconfigs/c/CMake/CMake-3.6.2-GCCcore-5.4.0.eb | 2 +- easybuild/easyconfigs/c/CMake/CMake-3.6.2-foss-2016b.eb | 2 +- easybuild/easyconfigs/c/CMake/CMake-3.6.2-intel-2016b.eb | 2 +- .../easyconfigs/c/CMake/CMake-3.7.1-GCCcore-5.4.0.eb | 2 +- .../easyconfigs/c/CMake/CMake-3.7.1-GCCcore-6.2.0.eb | 2 +- easybuild/easyconfigs/c/CMake/CMake-3.7.1-foss-2016b.eb | 2 +- easybuild/easyconfigs/c/CMake/CMake-3.7.1-intel-2016b.eb | 2 +- easybuild/easyconfigs/c/CMake/CMake-3.7.2-intel-2016b.eb | 2 +- .../c/CP2K/CP2K-3.0-CrayGNU-2015.11-cuda-7.0.eb | 2 +- easybuild/easyconfigs/c/CP2K/CP2K-3.0-CrayGNU-2015.11.eb | 2 +- .../CUDA-7.5.18-iccifort-2015.3.187-GNU-4.9.3-2.25.eb | 2 -- .../CUDA-7.5.18-iccifort-2016.3.210-GCC-4.9.3-2.25.eb | 2 -- .../DBD-mysql/DBD-mysql-4.032-intel-2016a-Perl-5.22.2.eb | 2 +- .../DBD-mysql/DBD-mysql-4.033-intel-2016b-Perl-5.24.0.eb | 2 +- ...-library-20130406-045632_pre-release-3_Linux-x86_64.eb | 2 +- .../g/GMAP-GSNAP/GMAP-GSNAP-2014-01-21-goolf-1.4.10.eb | 2 +- .../g/GMAP-GSNAP/GMAP-GSNAP-2014-06-10-goolf-1.4.10.eb | 2 +- .../g/GMAP-GSNAP/GMAP-GSNAP-2015-12-31.v2-foss-2015b.eb | 2 +- .../g/GMAP-GSNAP/GMAP-GSNAP-2016-05-01-foss-2016a.eb | 2 +- .../g/GMAP-GSNAP/GMAP-GSNAP-2016-11-07-foss-2016b.eb | 2 +- .../g/Ghostscript/Ghostscript-9.20-foss-2016b.eb | 2 +- .../g/Ghostscript/Ghostscript-9.20-intel-2016b.eb | 2 +- .../gencore_variant_detection-1.0.eb | 2 +- .../h/hanythingondemand/hanythingondemand-3.0.0-cli.eb | 8 ++++---- .../h/hanythingondemand/hanythingondemand-3.0.1-cli.eb | 8 ++++---- .../h/hanythingondemand/hanythingondemand-3.0.2-cli.eb | 8 ++++---- .../h/hanythingondemand/hanythingondemand-3.0.3-cli.eb | 8 ++++---- .../h/hanythingondemand/hanythingondemand-3.0.4-cli.eb | 8 ++++---- .../h/hanythingondemand/hanythingondemand-3.1.0-cli.eb | 8 ++++---- .../h/hanythingondemand/hanythingondemand-3.1.1-cli.eb | 8 ++++---- .../h/hanythingondemand/hanythingondemand-3.1.2-cli.eb | 8 ++++---- .../h/hanythingondemand/hanythingondemand-3.1.3-cli.eb | 8 ++++---- .../h/hanythingondemand/hanythingondemand-3.1.4-cli.eb | 8 ++++---- .../h/hanythingondemand/hanythingondemand-3.2.0-cli.eb | 8 ++++---- easybuild/easyconfigs/i/I-TASSER/I-TASSER-4.0.eb | 2 +- easybuild/easyconfigs/i/I-TASSER/I-TASSER-4.2.eb | 2 +- .../i/IPython/IPython-5.1.0-foss-2016b-Python-2.7.12.eb | 6 +++--- .../i/IPython/IPython-5.1.0-intel-2016b-Python-2.7.12.eb | 6 +++--- .../k/Kraken/Kraken-0.10.5-beta-foss-2016a-Perl-5.22.1.eb | 2 +- .../k/Kraken/Kraken-0.10.5-beta-foss-2016b-Perl-5.24.0.eb | 2 +- easybuild/easyconfigs/l/LeadIT/LeadIT-2.1.9.eb | 2 +- easybuild/easyconfigs/l/libxc/libxc-2.0.1-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/l/libxc/libxc-2.0.1-ictce-5.3.0.eb | 2 +- easybuild/easyconfigs/l/libxc/libxc-2.0.1-ictce-5.5.0.eb | 2 +- easybuild/easyconfigs/l/libxc/libxc-2.0.1-intel-2014b.eb | 2 +- easybuild/easyconfigs/l/libxc/libxc-2.0.2-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/l/libxc/libxc-2.0.2-ictce-5.3.0.eb | 2 +- easybuild/easyconfigs/l/libxc/libxc-2.0.3-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/l/libxc/libxc-2.2.0-intel-2014b.eb | 2 +- .../easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-2015.06.eb | 2 +- .../easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-2015.11.eb | 2 +- easybuild/easyconfigs/l/libxc/libxc-2.2.1-intel-2015a.eb | 2 +- .../easyconfigs/l/libxc/libxc-2.2.2-CrayGNU-2015.11.eb | 2 +- easybuild/easyconfigs/l/libxc/libxc-2.2.2-foss-2015b.eb | 2 +- easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015a.eb | 2 +- easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015b.eb | 2 +- easybuild/easyconfigs/l/libxc/libxc-2.2.3-foss-2016b.eb | 2 +- easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016a.eb | 2 +- easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016b.eb | 2 +- easybuild/easyconfigs/l/libxc/libxc-3.0.0-intel-2016a.eb | 2 +- easybuild/easyconfigs/l/libxc/libxc-3.0.0-intel-2016b.eb | 2 +- .../l/libxcb/libxcb-1.10-foss-2014b-Python-2.7.8.eb | 2 -- .../m/Mesa/Mesa-10.4.5-intel-2015a-Python-2.7.9.eb | 4 ++-- .../m/Mesa/Mesa-10.5.5-intel-2015a-Python-2.7.10.eb | 4 ++-- .../m/Mesa/Mesa-11.0.2-intel-2015b-Python-2.7.10.eb | 4 ++-- .../m/Mesa/Mesa-11.0.8-intel-2015b-Python-2.7.11.eb | 4 ++-- easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-foss-2016a.eb | 4 ++-- easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-gimkl-2.11.5.eb | 4 ++-- easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-intel-2016a.eb | 4 ++-- easybuild/easyconfigs/m/Mesa/Mesa-11.2.1-foss-2016a.eb | 4 ++-- easybuild/easyconfigs/m/Mesa/Mesa-11.2.1-intel-2016a.eb | 4 ++-- .../m/Molpro/Molpro-mpp-2010.1.23.Linux_x86_64.eb | 2 +- .../m/Molpro/Molpro-mpp-2015.1.0.linux_x86_64_intel.eb | 2 +- .../m/Molpro/Molpro-mpp-2015.1.10.linux_x86_64_openmp.eb | 2 +- .../m/Molpro/Molpro-mpp-2015.1.3.linux_x86_64_openmp.eb | 2 +- .../o/OpenBLAS/OpenBLAS-0.2.12-GCC-4.9.2-LAPACK-3.5.0.eb | 2 +- .../o/OpenBLAS/OpenBLAS-0.2.13-GCC-4.8.4-LAPACK-3.5.0.eb | 2 +- .../o/OpenBLAS/OpenBLAS-0.2.13-GCC-4.9.2-LAPACK-3.5.0.eb | 2 +- .../OpenBLAS/OpenBLAS-0.2.13-gompi-1.5.16-LAPACK-3.5.0.eb | 2 +- .../OpenBLAS-0.2.14-GNU-4.9.2-2.25-LAPACK-3.5.0.eb | 2 +- .../OpenBLAS-0.2.14-GNU-4.9.3-2.25-LAPACK-3.5.0.eb | 2 +- .../OpenBLAS-0.2.15-GCC-4.9.3-2.25-LAPACK-3.6.0.eb | 2 +- .../OpenBLAS-0.2.18-GCC-4.9.4-2.25-LAPACK-3.6.0.eb | 2 +- .../OpenBLAS-0.2.18-GCC-5.3.0-2.26-LAPACK-3.6.0.eb | 2 +- .../OpenBLAS-0.2.18-GCC-5.4.0-2.26-LAPACK-3.6.0.eb | 2 +- .../OpenBLAS-0.2.18-GCC-5.4.0-2.26-LAPACK-3.6.1.eb | 2 +- .../OpenBLAS-0.2.19-GCC-6.3.0-2.27-LAPACK-3.7.0.eb | 2 +- .../OpenBLAS/OpenBLAS-0.2.6-gompi-1.4.10-LAPACK-3.4.2.eb | 2 +- .../o/OpenBLAS/OpenBLAS-0.2.6-ictce-5.3.0-LAPACK-3.4.2.eb | 2 +- .../OpenBLAS/OpenBLAS-0.2.8-gompi-1.5.14-LAPACK-3.5.0.eb | 2 +- .../OpenBLAS/OpenBLAS-0.2.8-gompi-1.6.10-LAPACK-3.4.2.eb | 2 +- .../o/OpenBLAS/OpenBLAS-0.2.8-ictce-5.3.0-LAPACK-3.4.2.eb | 2 +- .../o/OpenBLAS/OpenBLAS-0.2.9-GCC-4.8.3-LAPACK-3.5.0.eb | 2 +- easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016a.eb | 4 ++-- .../easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016a.eb | 4 ++-- .../easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016b.eb | 4 ++-- .../p/PSI4/PSI4-1.0-intel-2016a-Python-2.7.11.eb | 4 ++-- .../ParaView-4.3.1-intel-2015a-Python-2.7.10-mpi.eb | 2 +- .../ParaView/ParaView-4.3.1-intel-2015a-Python-2.7.10.eb | 2 +- .../easyconfigs/p/Python/Python-2.7.11-goolf-1.7.20.eb | 1 - .../Python/Python-2.7.11-iomkl-2016.09-GCC-4.9.3-2.25.eb | 3 +-- .../p/Python/Python-2.7.12-GCCcore-4.9.3-bare.eb | 2 +- .../easyconfigs/p/Python/Python-2.7.9-GCC-4.8.4-bare.eb | 5 +++-- .../easyconfigs/p/Python/Python-2.7.9-goolf-1.7.20.eb | 5 +++-- .../easyconfigs/p/Python/Python-3.5.2-foss-2016.04.eb | 2 +- .../pyGIMLi/pyGIMLi-20160803-foss-2016a-Python-2.7.11.eb | 4 ++-- .../p/pyGIMLi/pyGIMLi-20160803-foss-2016a-Python-3.5.1.eb | 4 ++-- easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb | 2 +- easybuild/easyconfigs/r/ROOT/ROOT-v5.34.18-ictce-5.5.0.eb | 2 +- 160 files changed, 215 insertions(+), 221 deletions(-) diff --git a/easybuild/easyconfigs/a/ASHS/ASHS-rev103_20140612.eb b/easybuild/easyconfigs/a/ASHS/ASHS-rev103_20140612.eb index 1e7fda13a1..bfa52a0b28 100644 --- a/easybuild/easyconfigs/a/ASHS/ASHS-rev103_20140612.eb +++ b/easybuild/easyconfigs/a/ASHS/ASHS-rev103_20140612.eb @@ -12,8 +12,8 @@ description = """ Automatic Segmentation of Hippocampal Subfields (ASHS) """ toolchain = {'name': 'dummy', 'version': 'dummy'} -#You need to create an account to download the source -#from https://www.nitrc.org/frs/?group_id=370 +# You need to create an account to download the source +# from https://www.nitrc.org/frs/?group_id=370 sources = ['ashs_Linux64_%(version)s.tgz'] checksums= ["07fea2883b856af8797b200212b72e71"] diff --git a/easybuild/easyconfigs/a/Allinea/Allinea-6.1.1-Ubuntu-14.04-x86_64.eb b/easybuild/easyconfigs/a/Allinea/Allinea-6.1.1-Ubuntu-14.04-x86_64.eb index 9a71b607be..5f9521e1fe 100644 --- a/easybuild/easyconfigs/a/Allinea/Allinea-6.1.1-Ubuntu-14.04-x86_64.eb +++ b/easybuild/easyconfigs/a/Allinea/Allinea-6.1.1-Ubuntu-14.04-x86_64.eb @@ -11,13 +11,13 @@ source_urls = ['http://content.allinea.com/downloads/'] sources = ['%(namelower)s-forge-%(version)s.tar'] # Example of templates usage -#templates = [ +# templates = [ # 'kebnekaise.qtf', # 'kebnekaise-gpu.qtf', -#] +# ] # Example of sysconfig usage -#sysconfig = 'system.config.hpc2n' +# sysconfig = 'system.config.hpc2n' # license file license_file = HOME + '/licenses/allinea/license.lic' diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.5-goolf-1.4.10.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.5-goolf-1.4.10.eb index 361932b89c..9469af37f5 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.5-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.5-goolf-1.4.10.eb @@ -30,6 +30,6 @@ sanity_check_paths = { } # to add scripts folder to $PATH just uncomment this line -#modextrapaths = {'PATH': 'scripts'} +# modextrapaths = {'PATH': 'scripts'} moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.6-goolf-1.4.10.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.6-goolf-1.4.10.eb index 02e855be5b..264b5296c0 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.6-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.6-goolf-1.4.10.eb @@ -30,6 +30,6 @@ sanity_check_paths = { } # to add scripts folder to $PATH just uncomment this line -#modextrapaths = {'PATH': 'scripts'} +# modextrapaths = {'PATH': 'scripts'} moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.1.0-goolf-1.4.10.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.1.0-goolf-1.4.10.eb index 2877853840..f3e4ae2e16 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.1.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.1.0-goolf-1.4.10.eb @@ -30,6 +30,6 @@ sanity_check_paths = { } # to add scripts folder to $PATH just uncomment this line -#modextrapaths = {'PATH': 'scripts'} +# modextrapaths = {'PATH': 'scripts'} moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.0-goolf-1.4.10.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.0-goolf-1.4.10.eb index 58e8cf38d8..3ccec7b3ec 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.0-goolf-1.4.10.eb @@ -31,6 +31,6 @@ sanity_check_paths = { } # to add scripts folder to $PATH just uncomment this line -#modextrapaths = {'PATH': 'scripts'} +# modextrapaths = {'PATH': 'scripts'} moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.2-goolf-1.4.10.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.2-goolf-1.4.10.eb index da15149173..37790b2b2b 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.2-goolf-1.4.10.eb @@ -31,6 +31,6 @@ sanity_check_paths = { } # to add script folder to path just uncomment this line -#modextrapaths = {'PATH': 'scripts'} +# modextrapaths = {'PATH': 'scripts'} moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.4-goolf-1.4.10.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.4-goolf-1.4.10.eb index d2d24de2f8..48fab89b05 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.4-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.4-goolf-1.4.10.eb @@ -33,6 +33,6 @@ sanity_check_paths = { } # to add script folder to path just uncomment this line -#modextrapaths = {'PATH': 'scripts'} +# modextrapaths = {'PATH': 'scripts'} moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.5-goolf-1.7.20.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.5-goolf-1.7.20.eb index 3f05bda0e8..3f2240e2f4 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.5-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.5-goolf-1.7.20.eb @@ -33,6 +33,6 @@ sanity_check_paths = { } # to add script folder to path just uncomment this line -#modextrapaths = {'PATH': 'scripts'} +# modextrapaths = {'PATH': 'scripts'} moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.5-intel-2015a.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.5-intel-2015a.eb index d7856c8fa2..0bb8d3c531 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.5-intel-2015a.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.5-intel-2015a.eb @@ -33,6 +33,6 @@ sanity_check_paths = { } # to add script folder to path just uncomment this line -#modextrapaths = {'PATH': 'scripts'} +# modextrapaths = {'PATH': 'scripts'} moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.6-foss-2015b.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.6-foss-2015b.eb index a342fa3e4d..ab7844bff7 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.6-foss-2015b.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.6-foss-2015b.eb @@ -33,6 +33,6 @@ sanity_check_paths = { } # to add script folder to path just uncomment this line -#modextrapaths = {'PATH': 'scripts'} +# modextrapaths = {'PATH': 'scripts'} moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.6-intel-2015b.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.6-intel-2015b.eb index 3901df0ef7..9167bcb56a 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.6-intel-2015b.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.6-intel-2015b.eb @@ -33,6 +33,6 @@ sanity_check_paths = { } # to add script folder to path just uncomment this line -#modextrapaths = {'PATH': 'scripts'} +# modextrapaths = {'PATH': 'scripts'} moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.7-foss-2015b.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.7-foss-2015b.eb index f74362241f..063d865aaf 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.7-foss-2015b.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.7-foss-2015b.eb @@ -35,6 +35,6 @@ sanity_check_paths = { } # to add script folder to path just uncomment this line -#modextrapaths = {'PATH': 'scripts'} +# modextrapaths = {'PATH': 'scripts'} moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.8-foss-2015b.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.8-foss-2015b.eb index 29bf068b6a..7309705748 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.8-foss-2015b.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.8-foss-2015b.eb @@ -35,6 +35,6 @@ sanity_check_paths = { } # to add script folder to path just uncomment this line -#modextrapaths = {'PATH': 'scripts'} +# modextrapaths = {'PATH': 'scripts'} moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.8-foss-2016a.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.8-foss-2016a.eb index e48888855e..4a280ff234 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.8-foss-2016a.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.8-foss-2016a.eb @@ -35,6 +35,6 @@ sanity_check_paths = { } # to add script folder to path just uncomment this line -#modextrapaths = {'PATH': 'scripts'} +# modextrapaths = {'PATH': 'scripts'} moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9-foss-2016a.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9-foss-2016a.eb index 63080d8ef9..7f469a05ee 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9-foss-2016a.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9-foss-2016a.eb @@ -35,6 +35,6 @@ sanity_check_paths = { } # to add script folder to path just uncomment this line -#modextrapaths = {'PATH': 'scripts'} +# modextrapaths = {'PATH': 'scripts'} moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9-goolf-1.7.20.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9-goolf-1.7.20.eb index ab9ee385d7..c03250720b 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9-goolf-1.7.20.eb @@ -35,6 +35,6 @@ sanity_check_paths = { } # to add script folder to path just uncomment this line -#modextrapaths = {'PATH': 'scripts'} +# modextrapaths = {'PATH': 'scripts'} moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.2.3-foss-2015a.eb b/easybuild/easyconfigs/c/CMake/CMake-3.2.3-foss-2015a.eb index e6f905f409..b5f1d052ce 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.2.3-foss-2015a.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.2.3-foss-2015a.eb @@ -18,7 +18,7 @@ dependencies = [ ('ncurses', '5.9'), # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons - #('OpenSSL', '1.0.1k'), + # ('OpenSSL', '1.0.1k'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.2.3-goolf-1.4.10.eb b/easybuild/easyconfigs/c/CMake/CMake-3.2.3-goolf-1.4.10.eb index 130d3553bd..bbe947dc70 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.2.3-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.2.3-goolf-1.4.10.eb @@ -18,7 +18,7 @@ dependencies = [ ('ncurses', '5.9'), # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons - #('OpenSSL', '1.0.1k'), + # ('OpenSSL', '1.0.1k'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.2.3-intel-2015a.eb b/easybuild/easyconfigs/c/CMake/CMake-3.2.3-intel-2015a.eb index 5e1447f0f0..e4ebb6e711 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.2.3-intel-2015a.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.2.3-intel-2015a.eb @@ -18,7 +18,7 @@ dependencies = [ ('ncurses', '5.9'), # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons - #('OpenSSL', '1.0.1k'), + # ('OpenSSL', '1.0.1k'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.2.3-intel-2015b.eb b/easybuild/easyconfigs/c/CMake/CMake-3.2.3-intel-2015b.eb index 135315981b..c20cd926c3 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.2.3-intel-2015b.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.2.3-intel-2015b.eb @@ -18,7 +18,7 @@ dependencies = [ ('ncurses', '5.9'), # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons - #('OpenSSL', '1.0.1k'), + # ('OpenSSL', '1.0.1k'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.3.1-intel-2015a.eb b/easybuild/easyconfigs/c/CMake/CMake-3.3.1-intel-2015a.eb index b8e7064fcc..86657cbc54 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.3.1-intel-2015a.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.3.1-intel-2015a.eb @@ -18,7 +18,7 @@ dependencies = [ ('ncurses', '5.9'), # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons - #('OpenSSL', '1.0.1p'), + # ('OpenSSL', '1.0.1p'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.3.2-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/c/CMake/CMake-3.3.2-GNU-4.9.3-2.25.eb index 86f4ad5681..b454e2d862 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.3.2-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.3.2-GNU-4.9.3-2.25.eb @@ -18,7 +18,7 @@ dependencies = [ ('ncurses', '5.9'), # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons - #('OpenSSL', '1.0.1p'), + # ('OpenSSL', '1.0.1p'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.3.2-gimkl-2.11.5.eb b/easybuild/easyconfigs/c/CMake/CMake-3.3.2-gimkl-2.11.5.eb index 635df8455b..a7b9c8e81a 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.3.2-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.3.2-gimkl-2.11.5.eb @@ -18,7 +18,7 @@ dependencies = [ ('ncurses', '5.9'), # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons - #('OpenSSL', '1.0.1p'), + # ('OpenSSL', '1.0.1p'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.3.2-intel-2015b.eb b/easybuild/easyconfigs/c/CMake/CMake-3.3.2-intel-2015b.eb index ba3ca2e1aa..4e830d782c 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.3.2-intel-2015b.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.3.2-intel-2015b.eb @@ -18,7 +18,7 @@ dependencies = [ ('ncurses', '5.9'), # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons - #('OpenSSL', '1.0.1p'), + # ('OpenSSL', '1.0.1p'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.4.0-intel-2015b.eb b/easybuild/easyconfigs/c/CMake/CMake-3.4.0-intel-2015b.eb index 21bbc29383..d1f1daadea 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.4.0-intel-2015b.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.4.0-intel-2015b.eb @@ -18,7 +18,7 @@ dependencies = [ ('ncurses', '5.9'), # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons - #('OpenSSL', '1.0.1p'), + # ('OpenSSL', '1.0.1p'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.4.1-GCCcore-4.9.3.eb b/easybuild/easyconfigs/c/CMake/CMake-3.4.1-GCCcore-4.9.3.eb index 1a599467bd..48abe1a308 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.4.1-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.4.1-GCCcore-4.9.3.eb @@ -20,7 +20,7 @@ dependencies = [ ('ncurses', '6.0'), # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons - #('OpenSSL', '1.0.1p'), + # ('OpenSSL', '1.0.1p'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.4.1-foss-2015b.eb b/easybuild/easyconfigs/c/CMake/CMake-3.4.1-foss-2015b.eb index 5702e9976d..0302fdf415 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.4.1-foss-2015b.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.4.1-foss-2015b.eb @@ -18,7 +18,7 @@ dependencies = [ ('ncurses', '5.9'), # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons - #('OpenSSL', '1.0.1p'), + # ('OpenSSL', '1.0.1p'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.4.1-foss-2016a.eb b/easybuild/easyconfigs/c/CMake/CMake-3.4.1-foss-2016a.eb index 87dc8ebec4..d1277a5a59 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.4.1-foss-2016a.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.4.1-foss-2016a.eb @@ -18,7 +18,7 @@ dependencies = [ ('ncurses', '6.0'), # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons - #('OpenSSL', '1.0.1p'), + # ('OpenSSL', '1.0.1p'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.4.1-intel-2015b.eb b/easybuild/easyconfigs/c/CMake/CMake-3.4.1-intel-2015b.eb index 638514df1f..e56455fcc7 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.4.1-intel-2015b.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.4.1-intel-2015b.eb @@ -18,7 +18,7 @@ dependencies = [ ('ncurses', '5.9'), # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons - #('OpenSSL', '1.0.1p'), + # ('OpenSSL', '1.0.1p'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.4.1-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/c/CMake/CMake-3.4.1-intel-2016.02-GCC-4.9.eb index df5823de42..fe1b6c58f6 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.4.1-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.4.1-intel-2016.02-GCC-4.9.eb @@ -18,7 +18,7 @@ dependencies = [ ('ncurses', '6.0'), # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons - #('OpenSSL', '1.0.1p'), + # ('OpenSSL', '1.0.1p'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.4.1-intel-2016a.eb b/easybuild/easyconfigs/c/CMake/CMake-3.4.1-intel-2016a.eb index db841bbaef..1b59bc2fe5 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.4.1-intel-2016a.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.4.1-intel-2016a.eb @@ -18,7 +18,7 @@ dependencies = [ ('ncurses', '6.0'), # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons - #('OpenSSL', '1.0.1p'), + # ('OpenSSL', '1.0.1p'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.4.1-iomkl-2016.07.eb b/easybuild/easyconfigs/c/CMake/CMake-3.4.1-iomkl-2016.07.eb index 0204c038c7..3888217474 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.4.1-iomkl-2016.07.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.4.1-iomkl-2016.07.eb @@ -18,7 +18,7 @@ dependencies = [ ('ncurses', '6.0'), # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons - #('OpenSSL', '1.0.1p'), + # ('OpenSSL', '1.0.1p'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.4.1-iomkl-2016.09-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/c/CMake/CMake-3.4.1-iomkl-2016.09-GCC-4.9.3-2.25.eb index 36a239c230..d031a47e1d 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.4.1-iomkl-2016.09-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.4.1-iomkl-2016.09-GCC-4.9.3-2.25.eb @@ -18,7 +18,7 @@ dependencies = [ ('ncurses', '6.0'), # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons - #('OpenSSL', '1.0.1p'), + # ('OpenSSL', '1.0.1p'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.4.3-foss-2016a.eb b/easybuild/easyconfigs/c/CMake/CMake-3.4.3-foss-2016a.eb index e6beb92bee..1b238fe9f8 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.4.3-foss-2016a.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.4.3-foss-2016a.eb @@ -18,7 +18,7 @@ dependencies = [ ('ncurses', '6.0'), # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons - #('OpenSSL', '1.0.1p'), + # ('OpenSSL', '1.0.1p'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.4.3-foss-2016b.eb b/easybuild/easyconfigs/c/CMake/CMake-3.4.3-foss-2016b.eb index cfb29da8c6..f96062a9f5 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.4.3-foss-2016b.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.4.3-foss-2016b.eb @@ -18,7 +18,7 @@ dependencies = [ ('ncurses', '6.0'), # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons - #('OpenSSL', '1.0.1p'), + # ('OpenSSL', '1.0.1p'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.4.3-gimkl-2.11.5.eb b/easybuild/easyconfigs/c/CMake/CMake-3.4.3-gimkl-2.11.5.eb index f5527c16d6..19d8dce097 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.4.3-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.4.3-gimkl-2.11.5.eb @@ -18,7 +18,7 @@ dependencies = [ ('ncurses', '5.9'), # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons - #('OpenSSL', '1.0.1p'), + # ('OpenSSL', '1.0.1p'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.4.3-goolf-1.7.20.eb b/easybuild/easyconfigs/c/CMake/CMake-3.4.3-goolf-1.7.20.eb index 383be7ac07..3b0f2cdbc8 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.4.3-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.4.3-goolf-1.7.20.eb @@ -18,7 +18,7 @@ dependencies = [ ('ncurses', '5.9'), # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons - #('OpenSSL', '1.0.1p'), + # ('OpenSSL', '1.0.1p'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.4.3-ictce-7.3.5.eb b/easybuild/easyconfigs/c/CMake/CMake-3.4.3-ictce-7.3.5.eb index 7deb175b91..591130db85 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.4.3-ictce-7.3.5.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.4.3-ictce-7.3.5.eb @@ -18,7 +18,7 @@ dependencies = [ ('ncurses', '5.9'), # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons - #('OpenSSL', '1.0.1k'), + # ('OpenSSL', '1.0.1k'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.4.3-intel-2016a.eb b/easybuild/easyconfigs/c/CMake/CMake-3.4.3-intel-2016a.eb index 31b70f1b8a..a1da8e92c6 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.4.3-intel-2016a.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.4.3-intel-2016a.eb @@ -18,7 +18,7 @@ dependencies = [ ('ncurses', '6.0'), # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons - #('OpenSSL', '1.0.1p'), + # ('OpenSSL', '1.0.1p'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.5.1-intel-2016a.eb b/easybuild/easyconfigs/c/CMake/CMake-3.5.1-intel-2016a.eb index a70441375c..b649d19572 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.5.1-intel-2016a.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.5.1-intel-2016a.eb @@ -18,7 +18,7 @@ dependencies = [ ('ncurses', '6.0'), # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons - #('OpenSSL', '1.0.1s'), + # ('OpenSSL', '1.0.1s'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.5.2-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/c/CMake/CMake-3.5.2-GCC-4.9.3-2.25.eb index 619aaa3ab8..d09d0de5fa 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.5.2-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.5.2-GCC-4.9.3-2.25.eb @@ -18,7 +18,7 @@ dependencies = [ ('ncurses', '6.0', '', ('GCCcore', '4.9.3')), # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons - #('OpenSSL', '1.0.1s'), + # ('OpenSSL', '1.0.1s'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.5.2-foss-2016a.eb b/easybuild/easyconfigs/c/CMake/CMake-3.5.2-foss-2016a.eb index 9075c094fb..46fe821879 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.5.2-foss-2016a.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.5.2-foss-2016a.eb @@ -18,7 +18,7 @@ dependencies = [ ('ncurses', '6.0'), # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons - #('OpenSSL', '1.0.1s'), + # ('OpenSSL', '1.0.1s'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.5.2-foss-2016b.eb b/easybuild/easyconfigs/c/CMake/CMake-3.5.2-foss-2016b.eb index 42e9b3b3bd..1c577d44b5 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.5.2-foss-2016b.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.5.2-foss-2016b.eb @@ -18,7 +18,7 @@ dependencies = [ ('ncurses', '6.0'), # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons - #('OpenSSL', '1.0.1s'), + # ('OpenSSL', '1.0.1s'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.5.2-goolf-1.7.20.eb b/easybuild/easyconfigs/c/CMake/CMake-3.5.2-goolf-1.7.20.eb index 1f3daa3224..4634580e57 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.5.2-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.5.2-goolf-1.7.20.eb @@ -18,7 +18,7 @@ dependencies = [ ('ncurses', '5.9'), # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons - #('OpenSSL', '1.0.1s'), + # ('OpenSSL', '1.0.1s'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.5.2-intel-2016a.eb b/easybuild/easyconfigs/c/CMake/CMake-3.5.2-intel-2016a.eb index 6d07f31ebd..7df8000a04 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.5.2-intel-2016a.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.5.2-intel-2016a.eb @@ -18,7 +18,7 @@ dependencies = [ ('ncurses', '6.0'), # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons - #('OpenSSL', '1.0.1s'), + # ('OpenSSL', '1.0.1s'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.5.2-intel-2016b.eb b/easybuild/easyconfigs/c/CMake/CMake-3.5.2-intel-2016b.eb index b68274e5b4..b3ea9ff87e 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.5.2-intel-2016b.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.5.2-intel-2016b.eb @@ -18,7 +18,7 @@ dependencies = [ ('ncurses', '6.0'), # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons - #('OpenSSL', '1.0.1s'), + # ('OpenSSL', '1.0.1s'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.6.1-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/c/CMake/CMake-3.6.1-GCC-5.4.0-2.26.eb index 97b2282312..0fcaa0288c 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.6.1-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.6.1-GCC-5.4.0-2.26.eb @@ -18,7 +18,7 @@ dependencies = [ ('ncurses', '6.0'), # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons - #('OpenSSL', '1.0.1s'), + # ('OpenSSL', '1.0.1s'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.6.1-GCCcore-4.9.3.eb b/easybuild/easyconfigs/c/CMake/CMake-3.6.1-GCCcore-4.9.3.eb index d5ca429e05..8955a08ffe 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.6.1-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.6.1-GCCcore-4.9.3.eb @@ -22,7 +22,7 @@ dependencies = [ ('ncurses', '6.0'), # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons - #('OpenSSL', '1.0.1p'), + # ('OpenSSL', '1.0.1p'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.6.1-foss-2016b.eb b/easybuild/easyconfigs/c/CMake/CMake-3.6.1-foss-2016b.eb index c1386c78f8..bdffe9630d 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.6.1-foss-2016b.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.6.1-foss-2016b.eb @@ -18,7 +18,7 @@ dependencies = [ ('ncurses', '6.0'), # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons - #('OpenSSL', '1.0.1s'), + # ('OpenSSL', '1.0.1s'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.6.1-intel-2016b.eb b/easybuild/easyconfigs/c/CMake/CMake-3.6.1-intel-2016b.eb index 40d915d152..f6bb9a5e3d 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.6.1-intel-2016b.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.6.1-intel-2016b.eb @@ -20,7 +20,7 @@ dependencies = [ ('ncurses', '6.0'), # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons - #('OpenSSL', '1.0.1s'), + # ('OpenSSL', '1.0.1s'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.6.2-GCCcore-5.4.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.6.2-GCCcore-5.4.0.eb index aa63de70da..476a5bdd98 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.6.2-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.6.2-GCCcore-5.4.0.eb @@ -23,7 +23,7 @@ dependencies = [ ('ncurses', '6.0'), # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons - #('OpenSSL', '1.1.0c'), + # ('OpenSSL', '1.1.0c'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.6.2-foss-2016b.eb b/easybuild/easyconfigs/c/CMake/CMake-3.6.2-foss-2016b.eb index adb0724437..31ce4be00a 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.6.2-foss-2016b.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.6.2-foss-2016b.eb @@ -18,7 +18,7 @@ dependencies = [ ('ncurses', '6.0'), # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons - #('OpenSSL', '1.0.2j'), + # ('OpenSSL', '1.0.2j'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.6.2-intel-2016b.eb b/easybuild/easyconfigs/c/CMake/CMake-3.6.2-intel-2016b.eb index b6e496837c..6f2f602755 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.6.2-intel-2016b.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.6.2-intel-2016b.eb @@ -18,7 +18,7 @@ dependencies = [ ('ncurses', '6.0'), # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons - #('OpenSSL', '1.0.2j'), + # ('OpenSSL', '1.0.2j'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.7.1-GCCcore-5.4.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.7.1-GCCcore-5.4.0.eb index 5b3221d0bf..bb9e39dab2 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.7.1-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.7.1-GCCcore-5.4.0.eb @@ -23,7 +23,7 @@ dependencies = [ ('ncurses', '6.0'), # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons - #('OpenSSL', '1.1.0c'), + # ('OpenSSL', '1.1.0c'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.7.1-GCCcore-6.2.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.7.1-GCCcore-6.2.0.eb index b364332ea0..e5028321c6 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.7.1-GCCcore-6.2.0.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.7.1-GCCcore-6.2.0.eb @@ -22,7 +22,7 @@ dependencies = [ ('ncurses', '6.0'), # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons - #('OpenSSL', '1.1.0c'), + # ('OpenSSL', '1.1.0c'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.7.1-foss-2016b.eb b/easybuild/easyconfigs/c/CMake/CMake-3.7.1-foss-2016b.eb index e459f784ef..b93ad04bc3 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.7.1-foss-2016b.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.7.1-foss-2016b.eb @@ -18,7 +18,7 @@ dependencies = [ ('ncurses', '6.0'), # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons - #('OpenSSL', '1.0.2j'), + # ('OpenSSL', '1.0.2j'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.7.1-intel-2016b.eb b/easybuild/easyconfigs/c/CMake/CMake-3.7.1-intel-2016b.eb index 0464c9024d..dec6da7b0d 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.7.1-intel-2016b.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.7.1-intel-2016b.eb @@ -18,7 +18,7 @@ dependencies = [ ('ncurses', '6.0'), # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons - #('OpenSSL', '1.0.2j'), + # ('OpenSSL', '1.0.2j'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.7.2-intel-2016b.eb b/easybuild/easyconfigs/c/CMake/CMake-3.7.2-intel-2016b.eb index 2c33988a54..f118a4b2fb 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.7.2-intel-2016b.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.7.2-intel-2016b.eb @@ -18,7 +18,7 @@ dependencies = [ ('ncurses', '6.0'), # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons - #('OpenSSL', '1.0.2j'), + # ('OpenSSL', '1.0.2j'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-3.0-CrayGNU-2015.11-cuda-7.0.eb b/easybuild/easyconfigs/c/CP2K/CP2K-3.0-CrayGNU-2015.11-cuda-7.0.eb index d34361f252..bf60245a75 100644 --- a/easybuild/easyconfigs/c/CP2K/CP2K-3.0-CrayGNU-2015.11-cuda-7.0.eb +++ b/easybuild/easyconfigs/c/CP2K/CP2K-3.0-CrayGNU-2015.11-cuda-7.0.eb @@ -40,7 +40,7 @@ parallel = 1 # regression test runtest = False # regression test reports failures -#ignore_regtest_fails = True +# ignore_regtest_fails = True # build type type = 'psmp' diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-3.0-CrayGNU-2015.11.eb b/easybuild/easyconfigs/c/CP2K/CP2K-3.0-CrayGNU-2015.11.eb index e7bf9550c7..20bfca4976 100644 --- a/easybuild/easyconfigs/c/CP2K/CP2K-3.0-CrayGNU-2015.11.eb +++ b/easybuild/easyconfigs/c/CP2K/CP2K-3.0-CrayGNU-2015.11.eb @@ -37,7 +37,7 @@ parallel = 1 # regression test runtest = False # regression test reports failures -#ignore_regtest_fails = True +# ignore_regtest_fails = True # build type type = 'psmp' diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-7.5.18-iccifort-2015.3.187-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/c/CUDA/CUDA-7.5.18-iccifort-2015.3.187-GNU-4.9.3-2.25.eb index 50a365b60a..45b63f0380 100644 --- a/easybuild/easyconfigs/c/CUDA/CUDA-7.5.18-iccifort-2015.3.187-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/c/CUDA/CUDA-7.5.18-iccifort-2015.3.187-GNU-4.9.3-2.25.eb @@ -12,8 +12,6 @@ # http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-99.html ## -#easyblock = 'ConfigureMake' - name = 'CUDA' version = '7.5.18' diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-7.5.18-iccifort-2016.3.210-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/c/CUDA/CUDA-7.5.18-iccifort-2016.3.210-GCC-4.9.3-2.25.eb index dc4d389baf..72651d5b54 100644 --- a/easybuild/easyconfigs/c/CUDA/CUDA-7.5.18-iccifort-2016.3.210-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/c/CUDA/CUDA-7.5.18-iccifort-2016.3.210-GCC-4.9.3-2.25.eb @@ -12,8 +12,6 @@ # http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-99.html ## -#easyblock = 'ConfigureMake' - name = 'CUDA' version = '7.5.18' diff --git a/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.032-intel-2016a-Perl-5.22.2.eb b/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.032-intel-2016a-Perl-5.22.2.eb index 6491ebe755..81827042d8 100644 --- a/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.032-intel-2016a-Perl-5.22.2.eb +++ b/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.032-intel-2016a-Perl-5.22.2.eb @@ -18,7 +18,7 @@ dependencies = [ ('zlib', '1.2.8'), # OS dependency should be preferred if the os version is more recent then this version # it's nice to have an up to date openssl for security reasons - #('OpenSSL', '1.0.1q'), + # ('OpenSSL', '1.0.1q'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.033-intel-2016b-Perl-5.24.0.eb b/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.033-intel-2016b-Perl-5.24.0.eb index 0a65c07d0f..d5862a7c5a 100644 --- a/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.033-intel-2016b-Perl-5.24.0.eb +++ b/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.033-intel-2016b-Perl-5.24.0.eb @@ -18,7 +18,7 @@ dependencies = [ ('zlib', '1.2.8'), # OS dependency should be preferred if the os version is more recent then this version # it's nice to have an up to date openssl for security reasons - #('OpenSSL', '1.0.1q'), + # ('OpenSSL', '1.0.1q'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/g/GEM-library/GEM-library-20130406-045632_pre-release-3_Linux-x86_64.eb b/easybuild/easyconfigs/g/GEM-library/GEM-library-20130406-045632_pre-release-3_Linux-x86_64.eb index 009df93cd7..b7ffec63fe 100644 --- a/easybuild/easyconfigs/g/GEM-library/GEM-library-20130406-045632_pre-release-3_Linux-x86_64.eb +++ b/easybuild/easyconfigs/g/GEM-library/GEM-library-20130406-045632_pre-release-3_Linux-x86_64.eb @@ -26,7 +26,7 @@ source_urls = [('http://sourceforge.net/projects/gemlibrary/files/gem-library/Bi # core_i3 is the recommended version by developers. Better performance sources = ['GEM-binaries-Linux-x86_64-core_i3-20130406-045632.tbz2'] # if core_i3 version doesn't work for you, try core_2 version below -#sources = ['GEM-binaries-Linux-x86_64-core_2-20130406-045632.tbz2'] +# sources = ['GEM-binaries-Linux-x86_64-core_2-20130406-045632.tbz2'] # only Linux_x86-64 binaries are provided so we skip build_step. # We just use the MakeCp block to copy each file to the right destination folder (mainly the man files) diff --git a/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2014-01-21-goolf-1.4.10.eb b/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2014-01-21-goolf-1.4.10.eb index 5fbe4acc9a..d00a71f2d8 100644 --- a/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2014-01-21-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2014-01-21-goolf-1.4.10.eb @@ -27,7 +27,7 @@ sources = [SOURCELOWER_TAR_GZ] # you can change the MAX_READLENGTH for GSNAP with something like this. # details in the README http://research-pub.gene.com/gmap/src/README -#configopts = 'MAX_READLENGTH=250' +# configopts = 'MAX_READLENGTH=250' sanity_check_paths = { 'files': ['bin/gmap', 'bin/gsnap'], diff --git a/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2014-06-10-goolf-1.4.10.eb b/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2014-06-10-goolf-1.4.10.eb index 6189b95fa0..3994be6bc4 100644 --- a/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2014-06-10-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2014-06-10-goolf-1.4.10.eb @@ -27,7 +27,7 @@ sources = [SOURCELOWER_TAR_GZ] # you can change the MAX_READLENGTH for GSNAP with something like this. # details in the README http://research-pub.gene.com/gmap/src/README -#configopts = 'MAX_READLENGTH=250' +# configopts = 'MAX_READLENGTH=250' sanity_check_paths = { 'files': ['bin/gmap', 'bin/gsnap'], diff --git a/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2015-12-31.v2-foss-2015b.eb b/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2015-12-31.v2-foss-2015b.eb index 5440f25394..abea13b1ce 100644 --- a/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2015-12-31.v2-foss-2015b.eb +++ b/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2015-12-31.v2-foss-2015b.eb @@ -27,7 +27,7 @@ dependencies = [ # you can change the MAX_READLENGTH for GSNAP with something like this. # details in the README http://research-pub.gene.com/gmap/src/README -#configopts = 'MAX_READLENGTH=250' +# configopts = 'MAX_READLENGTH=250' sanity_check_paths = { 'files': ['bin/gmap', 'bin/gsnap'], diff --git a/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2016-05-01-foss-2016a.eb b/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2016-05-01-foss-2016a.eb index 5e9cfedc47..f2525337c6 100644 --- a/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2016-05-01-foss-2016a.eb +++ b/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2016-05-01-foss-2016a.eb @@ -27,7 +27,7 @@ dependencies = [ # you can change the MAX_READLENGTH for GSNAP with something like this. # details in the README http://research-pub.gene.com/gmap/src/README -#configopts = 'MAX_READLENGTH=250' +# configopts = 'MAX_READLENGTH=250' sanity_check_paths = { 'files': ['bin/gmap', 'bin/gsnap'], diff --git a/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2016-11-07-foss-2016b.eb b/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2016-11-07-foss-2016b.eb index 00035603e7..6b8d559ccc 100644 --- a/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2016-11-07-foss-2016b.eb +++ b/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2016-11-07-foss-2016b.eb @@ -30,7 +30,7 @@ dependencies = [ # you can change the MAX_READLENGTH for GSNAP with something like this. # details in the README http://research-pub.gene.com/gmap/src/README -#configopts = 'MAX_READLENGTH=250' +# configopts = 'MAX_READLENGTH=250' sanity_check_paths = { 'files': ['bin/gmap', 'bin/gsnap'], diff --git a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.20-foss-2016b.eb b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.20-foss-2016b.eb index 7305497c37..c65da40120 100644 --- a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.20-foss-2016b.eb +++ b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.20-foss-2016b.eb @@ -24,7 +24,7 @@ dependencies = [ ('LibTIFF', '4.0.6'), ] -#Do not use local copies of zlib, jpeg, freetype, and png +# Do not use local copies of zlib, jpeg, freetype, and png preconfigopts = "mv zlib zlib.no && mv jpeg jpeg.no && mv freetype freetype.no && mv libpng libpng.no &&" configopts = "--with-system-libtiff --enable-dynamic" diff --git a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.20-intel-2016b.eb b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.20-intel-2016b.eb index d3f76e106a..b89382f6a1 100644 --- a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.20-intel-2016b.eb +++ b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.20-intel-2016b.eb @@ -24,7 +24,7 @@ dependencies = [ ('LibTIFF', '4.0.6'), ] -#Do not use local copies of zlib, jpeg, freetype, and png +# Do not use local copies of zlib, jpeg, freetype, and png preconfigopts = "mv zlib zlib.no && mv jpeg jpeg.no && mv freetype freetype.no && mv libpng libpng.no &&" configopts = "--with-system-libtiff --enable-dynamic" diff --git a/easybuild/easyconfigs/g/gencore_variant_detection/gencore_variant_detection-1.0.eb b/easybuild/easyconfigs/g/gencore_variant_detection/gencore_variant_detection-1.0.eb index b799146d37..f4f2214acc 100644 --- a/easybuild/easyconfigs/g/gencore_variant_detection/gencore_variant_detection-1.0.eb +++ b/easybuild/easyconfigs/g/gencore_variant_detection/gencore_variant_detection-1.0.eb @@ -24,7 +24,7 @@ toolchain = {'name': 'dummy', 'version': ''} builddependencies = [('Anaconda3', '4.0.0')] # Use one of the following - either an environment.yml file or a remote environment definition -#environment_file = '/path/to/conda-environment.yml' +# environment_file = '/path/to/conda-environment.yml' remote_environment = "nyuad-cgsb/%(name)s_%(version)s" sanity_check_paths = { diff --git a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.0.0-cli.eb b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.0.0-cli.eb index 3c591a65e9..f18772cba0 100644 --- a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.0.0-cli.eb +++ b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.0.0-cli.eb @@ -30,11 +30,11 @@ options = {'modulename': 'hod'} modextravars = { # site-specific settings, hence commented out # specify HOD module to use in jobs (*full* HOD installation, not a minimal one) - #'HOD_BATCH_HOD_MODULE': 'hanythingondemand/%(version)s-intel-2015b-Python-2.7.10', - #'HOD_CREATE_HOD_MODULE': 'hanythingondemand/%(version)s-intel-2015b-Python-2.7.10', + # 'HOD_BATCH_HOD_MODULE': 'hanythingondemand/%(version)s-intel-2015b-Python-2.7.10', + # 'HOD_CREATE_HOD_MODULE': 'hanythingondemand/%(version)s-intel-2015b-Python-2.7.10', # specify location on shared 'scratch' filesystem for HOD working directories - #'HOD_BATCH_WORKDIR': '\$VSC_SCRATCH/hod', - #'HOD_CREATE_WORKDIR': '\$VSC_SCRATCH/hod', + # 'HOD_BATCH_WORKDIR': '\$VSC_SCRATCH/hod', + # 'HOD_CREATE_WORKDIR': '\$VSC_SCRATCH/hod', } sanity_check_commands = [('hod', '--help'), ('hod', 'dists')] diff --git a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.0.1-cli.eb b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.0.1-cli.eb index c6c633599b..7d698aa331 100644 --- a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.0.1-cli.eb +++ b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.0.1-cli.eb @@ -30,11 +30,11 @@ options = {'modulename': 'hod'} modextravars = { # site-specific settings, hence commented out # specify HOD module to use in jobs (*full* HOD installation, not a minimal one) - #'HOD_BATCH_HOD_MODULE': 'hanythingondemand/%(version)s-intel-2015b-Python-2.7.10', - #'HOD_CREATE_HOD_MODULE': 'hanythingondemand/%(version)s-intel-2015b-Python-2.7.10', + # 'HOD_BATCH_HOD_MODULE': 'hanythingondemand/%(version)s-intel-2015b-Python-2.7.10', + # 'HOD_CREATE_HOD_MODULE': 'hanythingondemand/%(version)s-intel-2015b-Python-2.7.10', # specify location on shared 'scratch' filesystem for HOD working directories - #'HOD_BATCH_WORKDIR': '\$VSC_SCRATCH/hod', - #'HOD_CREATE_WORKDIR': '\$VSC_SCRATCH/hod', + # 'HOD_BATCH_WORKDIR': '\$VSC_SCRATCH/hod', + # 'HOD_CREATE_WORKDIR': '\$VSC_SCRATCH/hod', } sanity_check_commands = [('hod', '--help'), ('hod', 'dists')] diff --git a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.0.2-cli.eb b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.0.2-cli.eb index a6a417a8dc..79d83ae249 100644 --- a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.0.2-cli.eb +++ b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.0.2-cli.eb @@ -30,11 +30,11 @@ options = {'modulename': 'hod'} modextravars = { # site-specific settings, hence commented out # specify HOD module to use in jobs (*full* HOD installation, not a minimal one) - #'HOD_BATCH_HOD_MODULE': 'hanythingondemand/%(version)s-intel-2015b-Python-2.7.10', - #'HOD_CREATE_HOD_MODULE': 'hanythingondemand/%(version)s-intel-2015b-Python-2.7.10', + # 'HOD_BATCH_HOD_MODULE': 'hanythingondemand/%(version)s-intel-2015b-Python-2.7.10', + # 'HOD_CREATE_HOD_MODULE': 'hanythingondemand/%(version)s-intel-2015b-Python-2.7.10', # specify location on shared 'scratch' filesystem for HOD working directories - #'HOD_BATCH_WORKDIR': '\$VSC_SCRATCH/hod', - #'HOD_CREATE_WORKDIR': '\$VSC_SCRATCH/hod', + # 'HOD_BATCH_WORKDIR': '\$VSC_SCRATCH/hod', + # 'HOD_CREATE_WORKDIR': '\$VSC_SCRATCH/hod', } sanity_check_commands = [('hod', '--help'), ('hod', 'dists')] diff --git a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.0.3-cli.eb b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.0.3-cli.eb index 996a654cea..be5a34157b 100644 --- a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.0.3-cli.eb +++ b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.0.3-cli.eb @@ -30,11 +30,11 @@ options = {'modulename': 'hod'} modextravars = { # site-specific settings, hence commented out # specify HOD module to use in jobs (*full* HOD installation, not a minimal one) - #'HOD_BATCH_HOD_MODULE': 'hanythingondemand/%(version)s-intel-2015b-Python-2.7.10', - #'HOD_CREATE_HOD_MODULE': 'hanythingondemand/%(version)s-intel-2015b-Python-2.7.10', + # 'HOD_BATCH_HOD_MODULE': 'hanythingondemand/%(version)s-intel-2015b-Python-2.7.10', + # 'HOD_CREATE_HOD_MODULE': 'hanythingondemand/%(version)s-intel-2015b-Python-2.7.10', # specify location on shared 'scratch' filesystem for HOD working directories - #'HOD_BATCH_WORKDIR': '\$VSC_SCRATCH/hod', - #'HOD_CREATE_WORKDIR': '\$VSC_SCRATCH/hod', + # 'HOD_BATCH_WORKDIR': '\$VSC_SCRATCH/hod', + # 'HOD_CREATE_WORKDIR': '\$VSC_SCRATCH/hod', } sanity_check_commands = [('hod', '--help'), ('hod', 'dists')] diff --git a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.0.4-cli.eb b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.0.4-cli.eb index 754319d620..e614c725c0 100644 --- a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.0.4-cli.eb +++ b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.0.4-cli.eb @@ -30,11 +30,11 @@ options = {'modulename': 'hod'} modextravars = { # site-specific settings, hence commented out # specify HOD module to use in jobs (*full* HOD installation, not a minimal one) - #'HOD_BATCH_HOD_MODULE': 'hanythingondemand/%(version)s-intel-2015b-Python-2.7.10', - #'HOD_CREATE_HOD_MODULE': 'hanythingondemand/%(version)s-intel-2015b-Python-2.7.10', + # 'HOD_BATCH_HOD_MODULE': 'hanythingondemand/%(version)s-intel-2015b-Python-2.7.10', + # 'HOD_CREATE_HOD_MODULE': 'hanythingondemand/%(version)s-intel-2015b-Python-2.7.10', # specify location on shared 'scratch' filesystem for HOD working directories - #'HOD_BATCH_WORKDIR': '\$VSC_SCRATCH/hod', - #'HOD_CREATE_WORKDIR': '\$VSC_SCRATCH/hod', + # 'HOD_BATCH_WORKDIR': '\$VSC_SCRATCH/hod', + # 'HOD_CREATE_WORKDIR': '\$VSC_SCRATCH/hod', } sanity_check_commands = [('hod', '--help'), ('hod', 'dists')] diff --git a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.0-cli.eb b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.0-cli.eb index 2c68b1bfaa..82c6cbe980 100644 --- a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.0-cli.eb +++ b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.0-cli.eb @@ -30,11 +30,11 @@ options = {'modulename': 'hod'} modextravars = { # site-specific settings, hence commented out # specify HOD module to use in jobs (*full* HOD installation, not a minimal one) - #'HOD_BATCH_HOD_MODULE': 'hanythingondemand/%(version)s-intel-2016a-Python-2.7.11', - #'HOD_CREATE_HOD_MODULE': 'hanythingondemand/%(version)s-intel-2016a-Python-2.7.11', + # 'HOD_BATCH_HOD_MODULE': 'hanythingondemand/%(version)s-intel-2016a-Python-2.7.11', + # 'HOD_CREATE_HOD_MODULE': 'hanythingondemand/%(version)s-intel-2016a-Python-2.7.11', # specify location on shared 'scratch' filesystem for HOD working directories - #'HOD_BATCH_WORKDIR': '\$VSC_SCRATCH/hod', - #'HOD_CREATE_WORKDIR': '\$VSC_SCRATCH/hod', + # 'HOD_BATCH_WORKDIR': '\$VSC_SCRATCH/hod', + # 'HOD_CREATE_WORKDIR': '\$VSC_SCRATCH/hod', } sanity_check_commands = [('hod', '--help'), ('hod', 'dists')] diff --git a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.1-cli.eb b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.1-cli.eb index 3f8a48b472..e91b71bb90 100644 --- a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.1-cli.eb +++ b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.1-cli.eb @@ -30,11 +30,11 @@ options = {'modulename': 'hod'} modextravars = { # site-specific settings, hence commented out # specify HOD module to use in jobs (*full* HOD installation, not a minimal one) - #'HOD_BATCH_HOD_MODULE': 'hanythingondemand/%(version)s-intel-2016a-Python-2.7.11', - #'HOD_CREATE_HOD_MODULE': 'hanythingondemand/%(version)s-intel-2016a-Python-2.7.11', + # 'HOD_BATCH_HOD_MODULE': 'hanythingondemand/%(version)s-intel-2016a-Python-2.7.11', + # 'HOD_CREATE_HOD_MODULE': 'hanythingondemand/%(version)s-intel-2016a-Python-2.7.11', # specify location on shared 'scratch' filesystem for HOD working directories - #'HOD_BATCH_WORKDIR': '\$VSC_SCRATCH/hod', - #'HOD_CREATE_WORKDIR': '\$VSC_SCRATCH/hod', + # 'HOD_BATCH_WORKDIR': '\$VSC_SCRATCH/hod', + # 'HOD_CREATE_WORKDIR': '\$VSC_SCRATCH/hod', } sanity_check_commands = [('hod', '--help'), ('hod', 'dists')] diff --git a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.2-cli.eb b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.2-cli.eb index cb9ae64332..4862029e81 100644 --- a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.2-cli.eb +++ b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.2-cli.eb @@ -30,11 +30,11 @@ options = {'modulename': 'hod'} modextravars = { # site-specific settings, hence commented out # specify HOD module to use in jobs (*full* HOD installation, not a minimal one) - #'HOD_BATCH_HOD_MODULE': 'hanythingondemand/%(version)s-intel-2016a-Python-2.7.11', - #'HOD_CREATE_HOD_MODULE': 'hanythingondemand/%(version)s-intel-2016a-Python-2.7.11', + # 'HOD_BATCH_HOD_MODULE': 'hanythingondemand/%(version)s-intel-2016a-Python-2.7.11', + # 'HOD_CREATE_HOD_MODULE': 'hanythingondemand/%(version)s-intel-2016a-Python-2.7.11', # specify location on shared 'scratch' filesystem for HOD working directories - #'HOD_BATCH_WORKDIR': '\$VSC_SCRATCH/hod', - #'HOD_CREATE_WORKDIR': '\$VSC_SCRATCH/hod', + # 'HOD_BATCH_WORKDIR': '\$VSC_SCRATCH/hod', + # 'HOD_CREATE_WORKDIR': '\$VSC_SCRATCH/hod', } sanity_check_commands = [('hod', '--help'), ('hod', 'dists')] diff --git a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.3-cli.eb b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.3-cli.eb index 4846e39a8e..9e46040159 100644 --- a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.3-cli.eb +++ b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.3-cli.eb @@ -30,11 +30,11 @@ options = {'modulename': 'hod'} modextravars = { # site-specific settings, hence commented out # specify HOD module to use in jobs (*full* HOD installation, not a minimal one) - #'HOD_BATCH_HOD_MODULE': 'hanythingondemand/%(version)s-intel-2016b-Python-2.7.12', - #'HOD_CREATE_HOD_MODULE': 'hanythingondemand/%(version)s-intel-2016b-Python-2.7.12', + # 'HOD_BATCH_HOD_MODULE': 'hanythingondemand/%(version)s-intel-2016b-Python-2.7.12', + # 'HOD_CREATE_HOD_MODULE': 'hanythingondemand/%(version)s-intel-2016b-Python-2.7.12', # specify location on shared 'scratch' filesystem for HOD working directories - #'HOD_BATCH_WORKDIR': '\$VSC_SCRATCH/hod', - #'HOD_CREATE_WORKDIR': '\$VSC_SCRATCH/hod', + # 'HOD_BATCH_WORKDIR': '\$VSC_SCRATCH/hod', + # 'HOD_CREATE_WORKDIR': '\$VSC_SCRATCH/hod', } sanity_check_commands = [('hod', '--help'), ('hod', 'dists')] diff --git a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.4-cli.eb b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.4-cli.eb index 275b2940c7..882a63bafc 100644 --- a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.4-cli.eb +++ b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.4-cli.eb @@ -30,11 +30,11 @@ options = {'modulename': 'hod'} modextravars = { # site-specific settings, hence commented out # specify HOD module to use in jobs (*full* HOD installation, not a minimal one) - #'HOD_BATCH_HOD_MODULE': 'hanythingondemand/%(version)s-intel-2016b-Python-2.7.12', - #'HOD_CREATE_HOD_MODULE': 'hanythingondemand/%(version)s-intel-2016b-Python-2.7.12', + # 'HOD_BATCH_HOD_MODULE': 'hanythingondemand/%(version)s-intel-2016b-Python-2.7.12', + # 'HOD_CREATE_HOD_MODULE': 'hanythingondemand/%(version)s-intel-2016b-Python-2.7.12', # specify location on shared 'scratch' filesystem for HOD working directories - #'HOD_BATCH_WORKDIR': '\$VSC_SCRATCH/hod', - #'HOD_CREATE_WORKDIR': '\$VSC_SCRATCH/hod', + # 'HOD_BATCH_WORKDIR': '\$VSC_SCRATCH/hod', + # 'HOD_CREATE_WORKDIR': '\$VSC_SCRATCH/hod', } sanity_check_commands = [('hod', '--help'), ('hod', 'dists')] diff --git a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.2.0-cli.eb b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.2.0-cli.eb index 7e255dbc21..da0110ba9d 100644 --- a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.2.0-cli.eb +++ b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.2.0-cli.eb @@ -30,11 +30,11 @@ options = {'modulename': 'hod'} modextravars = { # site-specific settings, hence commented out # specify HOD module to use in jobs (*full* HOD installation, not a minimal one) - #'HOD_BATCH_HOD_MODULE': 'hanythingondemand/%(version)s-intel-2016b-Python-2.7.12', - #'HOD_CREATE_HOD_MODULE': 'hanythingondemand/%(version)s-intel-2016b-Python-2.7.12', + # 'HOD_BATCH_HOD_MODULE': 'hanythingondemand/%(version)s-intel-2016b-Python-2.7.12', + # 'HOD_CREATE_HOD_MODULE': 'hanythingondemand/%(version)s-intel-2016b-Python-2.7.12', # specify location on shared 'scratch' filesystem for HOD working directories - #'HOD_BATCH_WORKDIR': '\$VSC_SCRATCH/hod', - #'HOD_CREATE_WORKDIR': '\$VSC_SCRATCH/hod', + # 'HOD_BATCH_WORKDIR': '\$VSC_SCRATCH/hod', + # 'HOD_CREATE_WORKDIR': '\$VSC_SCRATCH/hod', } sanity_check_commands = [('hod', '--help'), ('hod', 'dists')] diff --git a/easybuild/easyconfigs/i/I-TASSER/I-TASSER-4.0.eb b/easybuild/easyconfigs/i/I-TASSER/I-TASSER-4.0.eb index 88b4f2e32e..52f0e797fd 100644 --- a/easybuild/easyconfigs/i/I-TASSER/I-TASSER-4.0.eb +++ b/easybuild/easyconfigs/i/I-TASSER/I-TASSER-4.0.eb @@ -25,6 +25,6 @@ sanity_check_paths = { # You may find it desirable to put this variable in the module file. # The command to do so has been put here (commented out) as a convenience. -#modextravars = { 'IMINTASSERDB' : '/path/to/databases/I-TASSER/%(version)s' } +# modextravars = { 'IMINTASSERDB' : '/path/to/databases/I-TASSER/%(version)s' } moduleclass = 'bio' diff --git a/easybuild/easyconfigs/i/I-TASSER/I-TASSER-4.2.eb b/easybuild/easyconfigs/i/I-TASSER/I-TASSER-4.2.eb index fccdce2d50..681a2da8cf 100644 --- a/easybuild/easyconfigs/i/I-TASSER/I-TASSER-4.2.eb +++ b/easybuild/easyconfigs/i/I-TASSER/I-TASSER-4.2.eb @@ -25,6 +25,6 @@ sanity_check_paths = { # You may find it desirable to put this variable in the module file. # The command to do so has been put here (commented out) as a convenience. -#modextravars = { 'IMINTASSERDB' : '/path/to/databases/I-TASSER/%(version)s' } +# modextravars = { 'IMINTASSERDB' : '/path/to/databases/I-TASSER/%(version)s' } moduleclass = 'bio' diff --git a/easybuild/easyconfigs/i/IPython/IPython-5.1.0-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/i/IPython/IPython-5.1.0-foss-2016b-Python-2.7.12.eb index df95bd6282..15948e83d4 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-5.1.0-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-5.1.0-foss-2016b-Python-2.7.12.eb @@ -20,7 +20,7 @@ dependencies = [ ('testpath', '0.3', versionsuffix), # required by 'nbconvert', but causes problems w.r.t. 'backports' module... # see https://github.com/hpcugent/easybuild-easyconfigs/issues/3825 - #('entrypoints', '0.2.2', versionsuffix), + # ('entrypoints', '0.2.2', versionsuffix), ('path.py', '8.2.1', versionsuffix), ('prompt-toolkit', '1.0.6', versionsuffix), ] @@ -116,9 +116,9 @@ exts_list = [ }), # disabled because entrypoints on which this depends pull in configparser, which causes problems # see https://github.com/hpcugent/easybuild-easyconfigs/issues/3825 - #('nbconvert', '4.2.0', { + # ('nbconvert', '4.2.0', { # 'source_urls': ['https://pypi.python.org/packages/source/n/nbconvert/'], - #}), + # }), ('backports.shutil_get_terminal_size', '1.0.0', { 'source_urls': ['https://pypi.python.org/packages/source/b/backports.shutil_get_terminal_size/'], }), diff --git a/easybuild/easyconfigs/i/IPython/IPython-5.1.0-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/i/IPython/IPython-5.1.0-intel-2016b-Python-2.7.12.eb index d3bbfe47b7..73b84816cd 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-5.1.0-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-5.1.0-intel-2016b-Python-2.7.12.eb @@ -20,7 +20,7 @@ dependencies = [ ('testpath', '0.3', versionsuffix), # required by 'nbconvert', but causes problems w.r.t. 'backports' module... # see https://github.com/hpcugent/easybuild-easyconfigs/issues/3825 - #('entrypoints', '0.2.2', versionsuffix), + # ('entrypoints', '0.2.2', versionsuffix), ('path.py', '8.2.1', versionsuffix), ('prompt-toolkit', '1.0.6', versionsuffix), ] @@ -116,9 +116,9 @@ exts_list = [ }), # disabled because entrypoints on which this depends pull in configparser, which causes problems # see https://github.com/hpcugent/easybuild-easyconfigs/issues/3825 - #('nbconvert', '4.2.0', { + # ('nbconvert', '4.2.0', { # 'source_urls': ['https://pypi.python.org/packages/source/n/nbconvert/'], - #}), + # }), ('backports.shutil_get_terminal_size', '1.0.0', { 'source_urls': ['https://pypi.python.org/packages/source/b/backports.shutil_get_terminal_size/'], }), diff --git a/easybuild/easyconfigs/k/Kraken/Kraken-0.10.5-beta-foss-2016a-Perl-5.22.1.eb b/easybuild/easyconfigs/k/Kraken/Kraken-0.10.5-beta-foss-2016a-Perl-5.22.1.eb index 9a8c7fce6d..bbfde4273f 100644 --- a/easybuild/easyconfigs/k/Kraken/Kraken-0.10.5-beta-foss-2016a-Perl-5.22.1.eb +++ b/easybuild/easyconfigs/k/Kraken/Kraken-0.10.5-beta-foss-2016a-Perl-5.22.1.eb @@ -13,7 +13,7 @@ description = """Kraken is a system for assigning taxonomic labels to short DNA programs. Kraken aims to achieve high sensitivity and high speed by utilizing exact alignments of k-mers and a novel classification algorithm.""" -#Part is compiled with CXX, the rest is in Perl +# Part is compiled with CXX, the rest is in Perl toolchain = {'name': 'foss', 'version': '2016a'} toolchainopts = {'openmp': True} diff --git a/easybuild/easyconfigs/k/Kraken/Kraken-0.10.5-beta-foss-2016b-Perl-5.24.0.eb b/easybuild/easyconfigs/k/Kraken/Kraken-0.10.5-beta-foss-2016b-Perl-5.24.0.eb index fc353606af..a1be8e5709 100644 --- a/easybuild/easyconfigs/k/Kraken/Kraken-0.10.5-beta-foss-2016b-Perl-5.24.0.eb +++ b/easybuild/easyconfigs/k/Kraken/Kraken-0.10.5-beta-foss-2016b-Perl-5.24.0.eb @@ -13,7 +13,7 @@ description = """Kraken is a system for assigning taxonomic labels to short DNA programs. Kraken aims to achieve high sensitivity and high speed by utilizing exact alignments of k-mers and a novel classification algorithm.""" -#Part is compiled with CXX, the rest is in Perl +# Part is compiled with CXX, the rest is in Perl toolchain = {'name': 'foss', 'version': '2016b'} toolchainopts = {'openmp': True} diff --git a/easybuild/easyconfigs/l/LeadIT/LeadIT-2.1.9.eb b/easybuild/easyconfigs/l/LeadIT/LeadIT-2.1.9.eb index 128c5bbc07..27a91f92c0 100644 --- a/easybuild/easyconfigs/l/LeadIT/LeadIT-2.1.9.eb +++ b/easybuild/easyconfigs/l/LeadIT/LeadIT-2.1.9.eb @@ -12,7 +12,7 @@ description = """Visually Informed LeadOpt""" toolchain = {'name': 'dummy', 'version': 'dummy'} -#You need to get the software manually from http://www.biosolveit.de/LeadIT/index.html +# You need to get the software manually from http://www.biosolveit.de/LeadIT/index.html sources = ['leadit-%(version)s-Linux-x64.tar.gz'] checksums = ['363fa557861c4d109fd595ab895df3fd'] diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.0.1-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libxc/libxc-2.0.1-goolf-1.4.10.eb index bd766f2e39..aaf083cf04 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.0.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.0.1-goolf-1.4.10.eb @@ -20,7 +20,7 @@ configopts = 'FC="$F77" FCFLAGS="$FFLAGS" --enable-shared' # a fully working testsuite soon (unless someone wants to volunteer to do # it, of course ) In the meantime, unless the majority of the tests # fail, your build should be fine. -#runtest = 'check' +# runtest = 'check' patches = ['libxc-%(version)s-fix-initialization.patch'] diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.0.1-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libxc/libxc-2.0.1-ictce-5.3.0.eb index f86e8ff9fb..0d7ebaf5fb 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.0.1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.0.1-ictce-5.3.0.eb @@ -20,7 +20,7 @@ configopts = 'FC="$F77" FCFLAGS="$FFLAGS" --enable-shared' # a fully working testsuite soon (unless someone wants to volunteer to do # it, of course ) In the meantime, unless the majority of the tests # fail, your build should be fine. -#runtest = 'check' +# runtest = 'check' patches = ['libxc-%(version)s-fix-initialization.patch'] diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.0.1-ictce-5.5.0.eb b/easybuild/easyconfigs/l/libxc/libxc-2.0.1-ictce-5.5.0.eb index 4c45b545b5..635c9b4d96 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.0.1-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.0.1-ictce-5.5.0.eb @@ -20,7 +20,7 @@ configopts = 'FC="$F77" FCFLAGS="$FFLAGS" FCCPP="$F77 -E" --enable-shared' # a fully working testsuite soon (unless someone wants to volunteer to do # it, of course ) In the meantime, unless the majority of the tests # fail, your build should be fine. -#runtest = 'check' +# runtest = 'check' sanity_check_paths = { 'files': ['lib/libxc.a', 'lib/libxc.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.0.1-intel-2014b.eb b/easybuild/easyconfigs/l/libxc/libxc-2.0.1-intel-2014b.eb index 8276d5a07e..dc228fe31b 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.0.1-intel-2014b.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.0.1-intel-2014b.eb @@ -20,7 +20,7 @@ configopts = 'FC="$F77" FCFLAGS="$FFLAGS" FCCPP="$F77 -E" --enable-shared' # a fully working testsuite soon (unless someone wants to volunteer to do # it, of course ) In the meantime, unless the majority of the tests # fail, your build should be fine. -#runtest = 'check' +# runtest = 'check' sanity_check_paths = { 'files': ['lib/libxc.a', 'lib/libxc.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.0.2-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libxc/libxc-2.0.2-goolf-1.4.10.eb index 0bf711caf0..f440f02af5 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.0.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.0.2-goolf-1.4.10.eb @@ -20,7 +20,7 @@ configopts = 'FC="$F77" FCFLAGS="$FFLAGS" FCCPP="/lib/cpp -ansi" --enable-shared # a fully working testsuite soon (unless someone wants to volunteer to do # it, of course ) In the meantime, unless the majority of the tests # fail, your build should be fine. -#runtest = 'check' +# runtest = 'check' sanity_check_paths = { 'files': ['lib/libxc.a', 'lib/libxc.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.0.2-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libxc/libxc-2.0.2-ictce-5.3.0.eb index e6561d3ed6..df5b0a2ac4 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.0.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.0.2-ictce-5.3.0.eb @@ -20,7 +20,7 @@ configopts = 'FC="$F77" FCFLAGS="$FFLAGS" --enable-shared --enable-fortran' # a fully working testsuite soon (unless someone wants to volunteer to do # it, of course ) In the meantime, unless the majority of the tests # fail, your build should be fine. -#runtest = 'check' +# runtest = 'check' sanity_check_paths = { 'files': ['lib/libxc.a', 'lib/libxc.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.0.3-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libxc/libxc-2.0.3-goolf-1.4.10.eb index c631b87e66..674453ff55 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.0.3-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.0.3-goolf-1.4.10.eb @@ -20,7 +20,7 @@ configopts = 'FC="$F77" FCFLAGS="$FFLAGS" FCCPP="/lib/cpp -ansi" --enable-shared # a fully working testsuite soon (unless someone wants to volunteer to do # it, of course ) In the meantime, unless the majority of the tests # fail, your build should be fine. -#runtest = 'check' +# runtest = 'check' sanity_check_paths = { 'files': ['lib/libxc.a', 'lib/libxc.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.0-intel-2014b.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.0-intel-2014b.eb index 3bee3b3d9c..2ce787f05e 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.2.0-intel-2014b.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.0-intel-2014b.eb @@ -20,7 +20,7 @@ configopts = 'FC="$F77" FCFLAGS="$FFLAGS" --enable-shared' # a fully working testsuite soon (unless someone wants to volunteer to do # it, of course ) In the meantime, unless the majority of the tests # fail, your build should be fine. -#runtest = 'check' +# runtest = 'check' sanity_check_paths = { 'files': ['lib/libxc.a', 'lib/libxc.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-2015.06.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-2015.06.eb index d9d2ff8c6b..d3176a0e56 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-2015.06.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-2015.06.eb @@ -20,7 +20,7 @@ configopts = 'FC="$F77" FCFLAGS="$FFLAGS"' # a fully working testsuite soon (unless someone wants to volunteer to do # it, of course ) In the meantime, unless the majority of the tests # fail, your build should be fine. -#runtest = 'check' +# runtest = 'check' sanity_check_paths = { 'files': ['lib/libxc.a'], diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-2015.11.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-2015.11.eb index 254367cee7..f3870dc3fb 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-2015.11.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-2015.11.eb @@ -20,7 +20,7 @@ configopts = 'FC="$F77" FCFLAGS="$FFLAGS"' # a fully working testsuite soon (unless someone wants to volunteer to do # it, of course ) In the meantime, unless the majority of the tests # fail, your build should be fine. -#runtest = 'check' +# runtest = 'check' sanity_check_paths = { 'files': ['lib/libxc.a'], diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.1-intel-2015a.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.1-intel-2015a.eb index 13f7f941b6..80de4c9f97 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.2.1-intel-2015a.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.1-intel-2015a.eb @@ -20,7 +20,7 @@ configopts = 'FC="$F77" FCFLAGS="$FFLAGS" --enable-shared' # a fully working testsuite soon (unless someone wants to volunteer to do # it, of course ) In the meantime, unless the majority of the tests # fail, your build should be fine. -#runtest = 'check' +# runtest = 'check' sanity_check_paths = { 'files': ['lib/libxc.a', 'lib/libxc.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.2-CrayGNU-2015.11.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.2-CrayGNU-2015.11.eb index ae74d150b0..7a2ba48de6 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.2.2-CrayGNU-2015.11.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.2-CrayGNU-2015.11.eb @@ -21,7 +21,7 @@ configopts = 'FC="$F77" FCFLAGS="$FFLAGS" --enable-shared' # a fully working testsuite soon (unless someone wants to volunteer to do # it, of course ) In the meantime, unless the majority of the tests # fail, your build should be fine. -#runtest = 'check' +# runtest = 'check' sanity_check_paths = { 'files': ['lib/libxc.a', 'lib/libxc.so'], diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.2-foss-2015b.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.2-foss-2015b.eb index b029d7950c..8e7a6d0b88 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.2.2-foss-2015b.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.2-foss-2015b.eb @@ -20,7 +20,7 @@ configopts = 'FC="$F77" FCFLAGS="$FFLAGS" --enable-shared' # a fully working testsuite soon (unless someone wants to volunteer to do # it, of course ) In the meantime, unless the majority of the tests # fail, your build should be fine. -#runtest = 'check' +# runtest = 'check' sanity_check_paths = { 'files': ['lib/libxc.a', 'lib/libxc.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015a.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015a.eb index 7590c8664b..42d53d0949 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015a.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015a.eb @@ -20,7 +20,7 @@ configopts = 'FC="$F77" FCFLAGS="$FFLAGS" --enable-shared' # a fully working testsuite soon (unless someone wants to volunteer to do # it, of course ) In the meantime, unless the majority of the tests # fail, your build should be fine. -#runtest = 'check' +# runtest = 'check' sanity_check_paths = { 'files': ['lib/libxc.a', 'lib/libxc.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015b.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015b.eb index 96aab1d178..2d6dda37b8 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015b.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015b.eb @@ -20,7 +20,7 @@ configopts = 'FC="$F77" FCFLAGS="$FFLAGS" --enable-shared' # a fully working testsuite soon (unless someone wants to volunteer to do # it, of course ) In the meantime, unless the majority of the tests # fail, your build should be fine. -#runtest = 'check' +# runtest = 'check' sanity_check_paths = { 'files': ['lib/libxc.a', 'lib/libxc.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.3-foss-2016b.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.3-foss-2016b.eb index 969028930d..8733225f52 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.2.3-foss-2016b.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.3-foss-2016b.eb @@ -19,7 +19,7 @@ configopts = 'FC="$F77" FCFLAGS="$FFLAGS" --enable-shared --enable-fortran' # a fully working testsuite soon (unless someone wants to volunteer to do # it, of course ) In the meantime, unless the majority of the tests # fail, your build should be fine. -#runtest = 'check' +# runtest = 'check' sanity_check_paths = { 'files': ['lib/libxc%s.%s' % (x,y) for x in ['', 'f90'] for y in ['a', SHLIB_EXT]], diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016a.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016a.eb index 4f8d72a634..40280eac70 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016a.eb @@ -19,7 +19,7 @@ configopts = 'FC="$F77" FCFLAGS="$FFLAGS" --enable-shared --enable-fortran' # a fully working testsuite soon (unless someone wants to volunteer to do # it, of course ) In the meantime, unless the majority of the tests # fail, your build should be fine. -#runtest = 'check' +# runtest = 'check' sanity_check_paths = { 'files': ['lib/libxc%s.%s' % (x,y) for x in ['', 'f90'] for y in ['a', SHLIB_EXT]], diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016b.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016b.eb index a8378f3087..ef6bdb3052 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016b.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016b.eb @@ -19,7 +19,7 @@ configopts = 'FC="$F77" FCFLAGS="$FFLAGS" --enable-shared --enable-fortran' # a fully working testsuite soon (unless someone wants to volunteer to do # it, of course ) In the meantime, unless the majority of the tests # fail, your build should be fine. -#runtest = 'check' +# runtest = 'check' sanity_check_paths = { 'files': ['lib/libxc%s.%s' % (x,y) for x in ['', 'f90'] for y in ['a', SHLIB_EXT]], diff --git a/easybuild/easyconfigs/l/libxc/libxc-3.0.0-intel-2016a.eb b/easybuild/easyconfigs/l/libxc/libxc-3.0.0-intel-2016a.eb index fd83352b30..b63d48a898 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-3.0.0-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-3.0.0-intel-2016a.eb @@ -19,7 +19,7 @@ configopts = 'FC="$F77" FCFLAGS="$FFLAGS" --enable-shared --enable-fortran' # a fully working testsuite soon (unless someone wants to volunteer to do # it, of course ) In the meantime, unless the majority of the tests # fail, your build should be fine. -#runtest = 'check' +# runtest = 'check' sanity_check_paths = { 'files': ['lib/libxc%s.%s' % (x,y) for x in ['', 'f90'] for y in ['a', SHLIB_EXT]], diff --git a/easybuild/easyconfigs/l/libxc/libxc-3.0.0-intel-2016b.eb b/easybuild/easyconfigs/l/libxc/libxc-3.0.0-intel-2016b.eb index 951b7f0605..67f7a66326 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-3.0.0-intel-2016b.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-3.0.0-intel-2016b.eb @@ -19,7 +19,7 @@ configopts = 'FC="$F77" FCFLAGS="$FFLAGS" --enable-shared --enable-fortran' # a fully working testsuite soon (unless someone wants to volunteer to do # it, of course ) In the meantime, unless the majority of the tests # fail, your build should be fine. -#runtest = 'check' +# runtest = 'check' sanity_check_paths = { 'files': ['lib/libxc%s.%s' % (x,y) for x in ['', 'f90'] for y in ['a', SHLIB_EXT]], diff --git a/easybuild/easyconfigs/l/libxcb/libxcb-1.10-foss-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/l/libxcb/libxcb-1.10-foss-2014b-Python-2.7.8.eb index 6921c06b50..58524fdeb0 100644 --- a/easybuild/easyconfigs/l/libxcb/libxcb-1.10-foss-2014b-Python-2.7.8.eb +++ b/easybuild/easyconfigs/l/libxcb/libxcb-1.10-foss-2014b-Python-2.7.8.eb @@ -23,8 +23,6 @@ dependencies = [ ('libpthread-stubs', '0.3'), ] -#preconfigopts = "rm -r aclocal.m4 configure Makefile.in ltmain.sh && ./autogen.sh && " - sanity_check_paths = { 'files': ['lib/libxcb%s.a' % x for x in ['', '-composite', '-damage', '-dpms', '-dri2', '-glx', '-randr', '-record', '-render', '-res', '-screensaver', diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-10.4.5-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/m/Mesa/Mesa-10.4.5-intel-2015a-Python-2.7.9.eb index 3f895315b2..93b02acda8 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-10.4.5-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-10.4.5-intel-2015a-Python-2.7.9.eb @@ -50,14 +50,14 @@ dependencies = [ ] # Use the os provided libudev or the EB provided eudev -#osdependencies = ['libudev'] +# osdependencies = ['libudev'] # GLU is not part anymore of Mesa package! configopts = " --disable-osmesa --disable-gallium-llvm --enable-glx --disable-dri --enable-xlib-glx" configopts += " --disable-driglx-direct --with-gallium-drivers='' --disable-egl""" # package-config files for os dependencies are in an os specific place -#preconfigopts = ' PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' +# preconfigopts = ' PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm:$CPATH" ' diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-10.5.5-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/m/Mesa/Mesa-10.5.5-intel-2015a-Python-2.7.10.eb index 592c4a1182..3ebe66dd51 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-10.5.5-intel-2015a-Python-2.7.10.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-10.5.5-intel-2015a-Python-2.7.10.eb @@ -47,14 +47,14 @@ dependencies = [ ] # Use the os provided libudev or the EB provided eudev -#osdependencies = ['libudev'] +# osdependencies = ['libudev'] # GLU is not part anymore of Mesa package! configopts = " --disable-osmesa --enable-gallium-osmesa --enable-gallium-llvm --enable-glx --disable-dri --enable-xlib-glx" configopts += " --disable-driglx-direct --with-gallium-drivers='swrast' --disable-egl --with-osmesa-bits=32 --enable-texture-float " # package-config files for os dependencies are in an os specific place -#preconfigopts = 'libtoolize && PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' +# preconfigopts = 'libtoolize && PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' preconfigopts = ' libtoolize && ' prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm:$CPATH" ' diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-11.0.2-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/m/Mesa/Mesa-11.0.2-intel-2015b-Python-2.7.10.eb index 2bd0ff0f94..2631598232 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-11.0.2-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-11.0.2-intel-2015b-Python-2.7.10.eb @@ -46,14 +46,14 @@ dependencies = [ ] # Use the os provided libudev or the EB provided eudev -#osdependencies = ['libudev'] +# osdependencies = ['libudev'] # GLU is not part anymore of Mesa package! configopts = " --disable-osmesa --enable-gallium-osmesa --enable-gallium-llvm --enable-glx --disable-dri --enable-xlib-glx" configopts += " --disable-driglx-direct --with-gallium-drivers='swrast' --disable-egl --with-osmesa-bits=32 --enable-texture-float " # package-config files for os dependencies are in an os specific place -#preconfigopts = 'libtoolize && PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' +# preconfigopts = 'libtoolize && PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' preconfigopts = ' libtoolize && ' prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm:$CPATH" ' diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-11.0.8-intel-2015b-Python-2.7.11.eb b/easybuild/easyconfigs/m/Mesa/Mesa-11.0.8-intel-2015b-Python-2.7.11.eb index a22cf02d69..244c4f1427 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-11.0.8-intel-2015b-Python-2.7.11.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-11.0.8-intel-2015b-Python-2.7.11.eb @@ -46,14 +46,14 @@ dependencies = [ ] # Use the os provided libudev or the EB provided eudev -#osdependencies = ['libudev'] +# osdependencies = ['libudev'] # GLU is not part anymore of Mesa package! configopts = " --disable-osmesa --enable-gallium-osmesa --enable-gallium-llvm --enable-glx --disable-dri --enable-xlib-glx" configopts += " --disable-driglx-direct --with-gallium-drivers='swrast' --disable-egl --with-osmesa-bits=32 --enable-texture-float " # package-config files for os dependencies are in an os specific place -#preconfigopts = 'libtoolize && PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' +# preconfigopts = 'libtoolize && PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' preconfigopts = ' libtoolize && ' prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm:$CPATH" ' diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-foss-2016a.eb b/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-foss-2016a.eb index 231d3ed99e..81337fce92 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-foss-2016a.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-foss-2016a.eb @@ -42,7 +42,7 @@ dependencies = [ ] # Use the os provided libudev or the EB provided eudev -#osdependencies = ['libudev'] +# osdependencies = ['libudev'] # GLU is not part anymore of Mesa package! configopts = " --disable-osmesa --enable-gallium-osmesa --enable-gallium-llvm --enable-glx --disable-dri" @@ -50,7 +50,7 @@ configopts += " --enable-xlib-glx --disable-driglx-direct --with-gallium-drivers configopts += " --with-osmesa-bits=32 --enable-texture-float " # package-config files for os dependencies are in an os specific place -#preconfigopts = 'libtoolize && PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' +# preconfigopts = 'libtoolize && PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' preconfigopts = ' libtoolize && ' prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm:$CPATH" ' diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-gimkl-2.11.5.eb b/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-gimkl-2.11.5.eb index 7b54c5a0b7..84db881b8b 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-gimkl-2.11.5.eb @@ -42,7 +42,7 @@ dependencies = [ ] # Use the os provided libudev or the EB provided eudev -#osdependencies = ['libudev'] +# osdependencies = ['libudev'] # GLU is not part anymore of Mesa package! configopts = " --disable-osmesa --enable-gallium-osmesa --enable-gallium-llvm --enable-glx --disable-dri" @@ -50,7 +50,7 @@ configopts += " --enable-xlib-glx --disable-driglx-direct --with-gallium-drivers configopts += " --with-osmesa-bits=32 --enable-texture-float " # package-config files for os dependencies are in an os specific place -#preconfigopts = 'libtoolize && PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' +# preconfigopts = 'libtoolize && PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' preconfigopts = ' libtoolize && ' prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm:$CPATH" ' diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-intel-2016a.eb b/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-intel-2016a.eb index ecd0aaeeb3..9a2892bda4 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-intel-2016a.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-intel-2016a.eb @@ -42,7 +42,7 @@ dependencies = [ ] # Use the os provided libudev or the EB provided eudev -#osdependencies = ['libudev'] +# osdependencies = ['libudev'] # GLU is not part anymore of Mesa package! configopts = " --disable-osmesa --enable-gallium-osmesa --enable-gallium-llvm --enable-glx --disable-dri" @@ -50,7 +50,7 @@ configopts += " --enable-xlib-glx --disable-driglx-direct --with-gallium-drivers configopts += " --with-osmesa-bits=32 --enable-texture-float " # package-config files for os dependencies are in an os specific place -#preconfigopts = 'libtoolize && PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' +# preconfigopts = 'libtoolize && PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' preconfigopts = ' libtoolize && ' prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm:$CPATH" ' diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-11.2.1-foss-2016a.eb b/easybuild/easyconfigs/m/Mesa/Mesa-11.2.1-foss-2016a.eb index 18bebf34fd..8fe85b43fb 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-11.2.1-foss-2016a.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-11.2.1-foss-2016a.eb @@ -42,7 +42,7 @@ dependencies = [ ] # Use the os provided libudev or the EB provided eudev -#osdependencies = ['libudev'] +# osdependencies = ['libudev'] # GLU is not part anymore of Mesa package! configopts = " --disable-osmesa --enable-gallium-osmesa --enable-gallium-llvm --enable-glx --disable-dri" @@ -50,7 +50,7 @@ configopts += " --enable-xlib-glx --disable-driglx-direct --with-gallium-drivers configopts += " --with-osmesa-bits=32 --enable-texture-float " # package-config files for os dependencies are in an os specific place -#preconfigopts = 'libtoolize && PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' +# preconfigopts = 'libtoolize && PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' preconfigopts = ' libtoolize && ' prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm:$CPATH" ' diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-11.2.1-intel-2016a.eb b/easybuild/easyconfigs/m/Mesa/Mesa-11.2.1-intel-2016a.eb index 09f90b3879..c0ae4f1fc2 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-11.2.1-intel-2016a.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-11.2.1-intel-2016a.eb @@ -42,7 +42,7 @@ dependencies = [ ] # Use the os provided libudev or the EB provided eudev -#osdependencies = ['libudev'] +# osdependencies = ['libudev'] # GLU is not part anymore of Mesa package! configopts = " --disable-osmesa --enable-gallium-osmesa --enable-gallium-llvm --enable-glx --disable-dri" @@ -50,7 +50,7 @@ configopts += " --enable-xlib-glx --disable-driglx-direct --with-gallium-drivers configopts += " --with-osmesa-bits=32 --enable-texture-float " # package-config files for os dependencies are in an os specific place -#preconfigopts = 'libtoolize && PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' +# preconfigopts = 'libtoolize && PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' preconfigopts = ' libtoolize && ' prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm:$CPATH" ' diff --git a/easybuild/easyconfigs/m/Molpro/Molpro-mpp-2010.1.23.Linux_x86_64.eb b/easybuild/easyconfigs/m/Molpro/Molpro-mpp-2010.1.23.Linux_x86_64.eb index c80d4d1ee1..51f747c203 100644 --- a/easybuild/easyconfigs/m/Molpro/Molpro-mpp-2010.1.23.Linux_x86_64.eb +++ b/easybuild/easyconfigs/m/Molpro/Molpro-mpp-2010.1.23.Linux_x86_64.eb @@ -15,6 +15,6 @@ precompiled_binaries = True # license file - uncomment if a licence file is supplied by your site and # is valid for all users - the value of license_file may have to be changed -#license_file = HOME + '/licenses/%(name)s/license.lic' +# license_file = HOME + '/licenses/%(name)s/license.lic' moduleclass = 'chem' diff --git a/easybuild/easyconfigs/m/Molpro/Molpro-mpp-2015.1.0.linux_x86_64_intel.eb b/easybuild/easyconfigs/m/Molpro/Molpro-mpp-2015.1.0.linux_x86_64_intel.eb index 251958da52..678309eb8a 100644 --- a/easybuild/easyconfigs/m/Molpro/Molpro-mpp-2015.1.0.linux_x86_64_intel.eb +++ b/easybuild/easyconfigs/m/Molpro/Molpro-mpp-2015.1.0.linux_x86_64_intel.eb @@ -15,6 +15,6 @@ precompiled_binaries = True # license file - uncomment if a licence file is supplied by your site and # is valid for all users - the value of license_file may have to be changed -#license_file = HOME + '/licenses/%(name)s/license.lic' +# license_file = HOME + '/licenses/%(name)s/license.lic' moduleclass = 'chem' diff --git a/easybuild/easyconfigs/m/Molpro/Molpro-mpp-2015.1.10.linux_x86_64_openmp.eb b/easybuild/easyconfigs/m/Molpro/Molpro-mpp-2015.1.10.linux_x86_64_openmp.eb index 22912ecf4a..b2738fff57 100644 --- a/easybuild/easyconfigs/m/Molpro/Molpro-mpp-2015.1.10.linux_x86_64_openmp.eb +++ b/easybuild/easyconfigs/m/Molpro/Molpro-mpp-2015.1.10.linux_x86_64_openmp.eb @@ -15,6 +15,6 @@ precompiled_binaries = True # license file - uncomment if a licence file is supplied by your site and # is valid for all users - the value of license_file may have to be changed -#license_file = HOME + '/licenses/%(name)s/license.lic' +# license_file = HOME + '/licenses/%(name)s/license.lic' moduleclass = 'chem' diff --git a/easybuild/easyconfigs/m/Molpro/Molpro-mpp-2015.1.3.linux_x86_64_openmp.eb b/easybuild/easyconfigs/m/Molpro/Molpro-mpp-2015.1.3.linux_x86_64_openmp.eb index 47852f7b9a..3639fc72f4 100644 --- a/easybuild/easyconfigs/m/Molpro/Molpro-mpp-2015.1.3.linux_x86_64_openmp.eb +++ b/easybuild/easyconfigs/m/Molpro/Molpro-mpp-2015.1.3.linux_x86_64_openmp.eb @@ -15,6 +15,6 @@ precompiled_binaries = True # license file - uncomment if a licence file is supplied by your site and # is valid for all users - the value of license_file may have to be changed -#license_file = HOME + '/licenses/%(name)s/license.lic' +# license_file = HOME + '/licenses/%(name)s/license.lic' moduleclass = 'chem' diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.12-GCC-4.9.2-LAPACK-3.5.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.12-GCC-4.9.2-LAPACK-3.5.0.eb index 3a54e8b3b2..8e7a8e3488 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.12-GCC-4.9.2-LAPACK-3.5.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.12-GCC-4.9.2-LAPACK-3.5.0.eb @@ -39,7 +39,7 @@ buildopts = 'BINARY=64 USE_THREAD=1 CC="$CC" FC="$F77" NO_AFFINITY=1' installopts = "USE_THREAD=1 PREFIX=%(installdir)s" # extensive testing can be enabled by uncommenting the line below -#runtest = 'PATH=.:$PATH lapack-timing' +# runtest = 'PATH=.:$PATH lapack-timing' sanity_check_paths = { 'files': ['include/cblas.h', 'include/f77blas.h', 'include/lapacke_config.h', 'include/lapacke.h', diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.13-GCC-4.8.4-LAPACK-3.5.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.13-GCC-4.8.4-LAPACK-3.5.0.eb index 870b4ca0ec..1aae2d7107 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.13-GCC-4.8.4-LAPACK-3.5.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.13-GCC-4.8.4-LAPACK-3.5.0.eb @@ -39,7 +39,7 @@ buildopts = 'BINARY=64 USE_THREAD=1 CC="$CC" FC="$F77" NO_AFFINITY=1' installopts = "USE_THREAD=1 PREFIX=%(installdir)s" # extensive testing can be enabled by uncommenting the line below -#runtest = 'PATH=.:$PATH lapack-timing' +# runtest = 'PATH=.:$PATH lapack-timing' sanity_check_paths = { 'files': ['include/cblas.h', 'include/f77blas.h', 'include/lapacke_config.h', 'include/lapacke.h', diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.13-GCC-4.9.2-LAPACK-3.5.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.13-GCC-4.9.2-LAPACK-3.5.0.eb index 1291a991d1..1474c30ba6 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.13-GCC-4.9.2-LAPACK-3.5.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.13-GCC-4.9.2-LAPACK-3.5.0.eb @@ -39,7 +39,7 @@ buildopts = 'BINARY=64 USE_THREAD=1 CC="$CC" FC="$F77" NO_AFFINITY=1' installopts = "USE_THREAD=1 PREFIX=%(installdir)s" # extensive testing can be enabled by uncommenting the line below -#runtest = 'PATH=.:$PATH lapack-timing' +# runtest = 'PATH=.:$PATH lapack-timing' sanity_check_paths = { 'files': ['include/cblas.h', 'include/f77blas.h', 'include/lapacke_config.h', 'include/lapacke.h', diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.13-gompi-1.5.16-LAPACK-3.5.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.13-gompi-1.5.16-LAPACK-3.5.0.eb index fe4211f53c..e83941b54c 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.13-gompi-1.5.16-LAPACK-3.5.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.13-gompi-1.5.16-LAPACK-3.5.0.eb @@ -40,7 +40,7 @@ buildopts = 'BINARY=64 ' + threading + ' CC="$CC" FC="$F77"' installopts = threading + " PREFIX=%(installdir)s" # extensive testing can be enabled by uncommenting the line below -#runtest = 'PATH=.:$PATH lapack-timing' +# runtest = 'PATH=.:$PATH lapack-timing' sanity_check_paths = { 'files': ['include/cblas.h', 'include/f77blas.h', 'include/lapacke_config.h', 'include/lapacke.h', diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.14-GNU-4.9.2-2.25-LAPACK-3.5.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.14-GNU-4.9.2-2.25-LAPACK-3.5.0.eb index 23704a985e..9be631f2d3 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.14-GNU-4.9.2-2.25-LAPACK-3.5.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.14-GNU-4.9.2-2.25-LAPACK-3.5.0.eb @@ -39,7 +39,7 @@ buildopts = 'BINARY=64 USE_THREAD=1 CC="$CC" FC="$F77" NO_AFFINITY=1' installopts = "USE_THREAD=1 PREFIX=%(installdir)s" # extensive testing can be enabled by uncommenting the line below -#runtest = 'PATH=.:$PATH lapack-timing' +# runtest = 'PATH=.:$PATH lapack-timing' sanity_check_paths = { 'files': ['include/cblas.h', 'include/f77blas.h', 'include/lapacke_config.h', 'include/lapacke.h', diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.14-GNU-4.9.3-2.25-LAPACK-3.5.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.14-GNU-4.9.3-2.25-LAPACK-3.5.0.eb index b11768a150..d1b44dfae9 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.14-GNU-4.9.3-2.25-LAPACK-3.5.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.14-GNU-4.9.3-2.25-LAPACK-3.5.0.eb @@ -39,7 +39,7 @@ buildopts = 'BINARY=64 USE_THREAD=1 CC="$CC" FC="$F77" NO_AFFINITY=1' installopts = "USE_THREAD=1 PREFIX=%(installdir)s" # extensive testing can be enabled by uncommenting the line below -#runtest = 'PATH=.:$PATH lapack-timing' +# runtest = 'PATH=.:$PATH lapack-timing' sanity_check_paths = { 'files': ['include/cblas.h', 'include/f77blas.h', 'include/lapacke_config.h', 'include/lapacke.h', diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.15-GCC-4.9.3-2.25-LAPACK-3.6.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.15-GCC-4.9.3-2.25-LAPACK-3.6.0.eb index 32dd146e23..1c0d99523c 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.15-GCC-4.9.3-2.25-LAPACK-3.6.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.15-GCC-4.9.3-2.25-LAPACK-3.6.0.eb @@ -39,7 +39,7 @@ buildopts = 'BINARY=64 USE_THREAD=1 CC="$CC" FC="$F77" NO_AFFINITY=1' installopts = "USE_THREAD=1 PREFIX=%(installdir)s" # extensive testing can be enabled by uncommenting the line below -#runtest = 'PATH=.:$PATH lapack-timing' +# runtest = 'PATH=.:$PATH lapack-timing' sanity_check_paths = { 'files': ['include/cblas.h', 'include/f77blas.h', 'include/lapacke_config.h', 'include/lapacke.h', diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-4.9.4-2.25-LAPACK-3.6.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-4.9.4-2.25-LAPACK-3.6.0.eb index abbe566e01..28a8a8d5c5 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-4.9.4-2.25-LAPACK-3.6.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-4.9.4-2.25-LAPACK-3.6.0.eb @@ -43,7 +43,7 @@ buildopts = 'BINARY=64 USE_THREAD=1 CC="$CC" FC="$F77" NO_AFFINITY=1' installopts = "USE_THREAD=1 PREFIX=%(installdir)s" # extensive testing can be enabled by uncommenting the line below -#runtest = 'PATH=.:$PATH lapack-timing' +# runtest = 'PATH=.:$PATH lapack-timing' sanity_check_paths = { 'files': ['include/cblas.h', 'include/f77blas.h', 'include/lapacke_config.h', 'include/lapacke.h', diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-5.3.0-2.26-LAPACK-3.6.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-5.3.0-2.26-LAPACK-3.6.0.eb index 9dd493110f..92f08781e2 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-5.3.0-2.26-LAPACK-3.6.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-5.3.0-2.26-LAPACK-3.6.0.eb @@ -43,7 +43,7 @@ buildopts = 'BINARY=64 USE_THREAD=1 CC="$CC" FC="$F77" NO_AFFINITY=1' installopts = "USE_THREAD=1 PREFIX=%(installdir)s" # extensive testing can be enabled by uncommenting the line below -#runtest = 'PATH=.:$PATH lapack-timing' +# runtest = 'PATH=.:$PATH lapack-timing' sanity_check_paths = { 'files': ['include/cblas.h', 'include/f77blas.h', 'include/lapacke_config.h', 'include/lapacke.h', diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-5.4.0-2.26-LAPACK-3.6.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-5.4.0-2.26-LAPACK-3.6.0.eb index 3879abb7bd..0b62a315f7 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-5.4.0-2.26-LAPACK-3.6.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-5.4.0-2.26-LAPACK-3.6.0.eb @@ -43,7 +43,7 @@ buildopts = 'BINARY=64 USE_THREAD=1 CC="$CC" FC="$F77" NO_AFFINITY=1' installopts = "USE_THREAD=1 PREFIX=%(installdir)s" # extensive testing can be enabled by uncommenting the line below -#runtest = 'PATH=.:$PATH lapack-timing' +# runtest = 'PATH=.:$PATH lapack-timing' sanity_check_paths = { 'files': ['include/cblas.h', 'include/f77blas.h', 'include/lapacke_config.h', 'include/lapacke.h', diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-5.4.0-2.26-LAPACK-3.6.1.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-5.4.0-2.26-LAPACK-3.6.1.eb index 21a2a7c815..85f10c536a 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-5.4.0-2.26-LAPACK-3.6.1.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-5.4.0-2.26-LAPACK-3.6.1.eb @@ -43,7 +43,7 @@ buildopts = 'BINARY=64 USE_THREAD=1 CC="$CC" FC="$F77" NO_AFFINITY=1' installopts = "USE_THREAD=1 PREFIX=%(installdir)s" # extensive testing can be enabled by uncommenting the line below -#runtest = 'PATH=.:$PATH lapack-timing' +# runtest = 'PATH=.:$PATH lapack-timing' sanity_check_paths = { 'files': ['include/cblas.h', 'include/f77blas.h', 'include/lapacke_config.h', 'include/lapacke.h', diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-GCC-6.3.0-2.27-LAPACK-3.7.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-GCC-6.3.0-2.27-LAPACK-3.7.0.eb index ba23eaadbf..143c9edae7 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-GCC-6.3.0-2.27-LAPACK-3.7.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-GCC-6.3.0-2.27-LAPACK-3.7.0.eb @@ -44,7 +44,7 @@ buildopts = 'BINARY=64 USE_THREAD=1 CC="$CC" FC="$F77" NO_AFFINITY=1' installopts = "USE_THREAD=1 PREFIX=%(installdir)s" # extensive testing can be enabled by uncommenting the line below -#runtest = 'PATH=.:$PATH lapack-timing' +# runtest = 'PATH=.:$PATH lapack-timing' sanity_check_paths = { 'files': ['include/cblas.h', 'include/f77blas.h', 'include/lapacke_config.h', 'include/lapacke.h', diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.6-gompi-1.4.10-LAPACK-3.4.2.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.6-gompi-1.4.10-LAPACK-3.4.2.eb index bd9785f7cc..1e915a802f 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.6-gompi-1.4.10-LAPACK-3.4.2.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.6-gompi-1.4.10-LAPACK-3.4.2.eb @@ -41,7 +41,7 @@ buildopts = 'BINARY=64 ' + threading + ' CC="$CC" FC="$F77"' installopts = threading + " PREFIX=%(installdir)s" # extensive testing can be enabled by uncommenting the line below -#runtest = 'PATH=.:$PATH lapack-timing' +# runtest = 'PATH=.:$PATH lapack-timing' sanity_check_paths = { 'files': ['include/cblas.h', 'include/f77blas.h', 'include/lapacke_config.h', 'include/lapacke.h', diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.6-ictce-5.3.0-LAPACK-3.4.2.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.6-ictce-5.3.0-LAPACK-3.4.2.eb index 16af9a1249..30835b6878 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.6-ictce-5.3.0-LAPACK-3.4.2.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.6-ictce-5.3.0-LAPACK-3.4.2.eb @@ -41,7 +41,7 @@ buildopts = 'BINARY=64 ' + threading + ' CC="$CC" FC="$F77"' installopts = threading + " PREFIX=%(installdir)s" # extensive testing can be enabled by uncommenting the line below -#runtest = 'PATH=.:$PATH lapack-timing' +# runtest = 'PATH=.:$PATH lapack-timing' sanity_check_paths = { 'files': ['include/cblas.h', 'include/f77blas.h', 'include/lapacke_config.h', 'include/lapacke.h', diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-gompi-1.5.14-LAPACK-3.5.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-gompi-1.5.14-LAPACK-3.5.0.eb index c183debe56..b1e3b0dad6 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-gompi-1.5.14-LAPACK-3.5.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-gompi-1.5.14-LAPACK-3.5.0.eb @@ -40,7 +40,7 @@ buildopts = 'BINARY=64 ' + threading + ' CC="$CC" FC="$F77"' installopts = threading + " PREFIX=%(installdir)s" # extensive testing can be enabled by uncommenting the line below -#runtest = 'PATH=.:$PATH lapack-timing' +# runtest = 'PATH=.:$PATH lapack-timing' sanity_check_paths = { 'files': ['include/cblas.h', 'include/f77blas.h', 'include/lapacke_config.h', 'include/lapacke.h', diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-gompi-1.6.10-LAPACK-3.4.2.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-gompi-1.6.10-LAPACK-3.4.2.eb index ba2f665b5b..19c2176d82 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-gompi-1.6.10-LAPACK-3.4.2.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-gompi-1.6.10-LAPACK-3.4.2.eb @@ -40,7 +40,7 @@ buildopts = 'BINARY=64 ' + threading + ' CC="$CC" FC="$F77"' installopts = threading + " PREFIX=%(installdir)s" # extensive testing can be enabled by uncommenting the line below -#runtest = 'PATH=.:$PATH lapack-timing' +# runtest = 'PATH=.:$PATH lapack-timing' sanity_check_paths = { 'files': ['include/cblas.h', 'include/f77blas.h', 'include/lapacke_config.h', 'include/lapacke.h', diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-ictce-5.3.0-LAPACK-3.4.2.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-ictce-5.3.0-LAPACK-3.4.2.eb index dbc806f461..d346fc16be 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-ictce-5.3.0-LAPACK-3.4.2.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-ictce-5.3.0-LAPACK-3.4.2.eb @@ -40,7 +40,7 @@ buildopts = 'BINARY=64 ' + threading + ' CC="$CC" FC="$F77"' installopts = threading + " PREFIX=%(installdir)s" # extensive testing can be enabled by uncommenting the line below -#runtest = 'PATH=.:$PATH lapack-timing' +# runtest = 'PATH=.:$PATH lapack-timing' sanity_check_paths = { 'files': ['include/cblas.h', 'include/f77blas.h', 'include/lapacke_config.h', 'include/lapacke.h', diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.9-GCC-4.8.3-LAPACK-3.5.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.9-GCC-4.8.3-LAPACK-3.5.0.eb index d0e54d0995..4cb827eecc 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.9-GCC-4.8.3-LAPACK-3.5.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.9-GCC-4.8.3-LAPACK-3.5.0.eb @@ -39,7 +39,7 @@ buildopts = 'BINARY=64 USE_THREAD=1 CC="$CC" FC="$F77" NO_AFFINITY=1' installopts = "USE_THREAD=1 PREFIX=%(installdir)s" # extensive testing can be enabled by uncommenting the line below -#runtest = 'PATH=.:$PATH lapack-timing' +# runtest = 'PATH=.:$PATH lapack-timing' sanity_check_paths = { 'files': ['include/cblas.h', 'include/f77blas.h', 'include/lapacke_config.h', 'include/lapacke.h', diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016a.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016a.eb index 5b1245248a..fb9d354480 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016a.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016a.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'foss', 'version': '2016a'} source_urls = [ 'https://github.com/Itseez/opencv/archive/', - #The Hash is version dependent! see 3rdparty/ippicv/downloader.cmake + # The Hash is version dependent! see 3rdparty/ippicv/downloader.cmake 'https://raw.githubusercontent.com/Itseez/opencv_3rdparty/81a676001ca8075ada498583e4166079e5744668/ippicv', ] @@ -42,7 +42,7 @@ dependencies = [ ('GST-plugins-base', '1.6.4'), ] -#The destination directory is "linux-" see 3rdparty/ippicv/downloader.cmake +# The destination directory is "linux-" see 3rdparty/ippicv/downloader.cmake ippicv_dir = '3rdparty/ippicv/downloads/linux-808b791a6eac9ed78d32a7666804320e/' preconfigopts = "mkdir -p %s && cp -a ../*.tgz %s && " % (ippicv_dir, ippicv_dir) diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016a.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016a.eb index bd5181fa1c..52aa30e629 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016a.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016a.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'intel', 'version': '2016a'} source_urls = [ 'https://github.com/Itseez/opencv/archive/', - #The Hash is version dependent! see 3rdparty/ippicv/downloader.cmake + # The Hash is version dependent! see 3rdparty/ippicv/downloader.cmake 'https://raw.githubusercontent.com/Itseez/opencv_3rdparty/81a676001ca8075ada498583e4166079e5744668/ippicv', ] @@ -43,7 +43,7 @@ dependencies = [ ] preconfigopts = 'export IPPROOT=$EBROOTICC/ipp && ' -#The destination directory is "linux-" see 3rdparty/ippicv/downloader.cmake +# The destination directory is "linux-" see 3rdparty/ippicv/downloader.cmake ippicv_dir = '3rdparty/ippicv/downloads/linux-808b791a6eac9ed78d32a7666804320e/' preconfigopts = "mkdir -p %s && cp -a ../*.tgz %s && " % (ippicv_dir, ippicv_dir) diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016b.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016b.eb index e7f6df5043..fc8dc13e40 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016b.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016b.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'intel', 'version': '2016b'} source_urls = [ 'https://github.com/Itseez/opencv/archive/', - #The Hash is version dependent! see 3rdparty/ippicv/downloader.cmake + # The Hash is version dependent! see 3rdparty/ippicv/downloader.cmake 'https://raw.githubusercontent.com/Itseez/opencv_3rdparty/81a676001ca8075ada498583e4166079e5744668/ippicv', ] @@ -44,7 +44,7 @@ dependencies = [ preconfigopts = 'export IPPROOT=$EBROOTICC/ipp && ' -#The destination directory is "linux-" see 3rdparty/ippicv/downloader.cmake +# The destination directory is "linux-" see 3rdparty/ippicv/downloader.cmake ippicv_dir = '3rdparty/ippicv/downloads/linux-808b791a6eac9ed78d32a7666804320e/' preconfigopts = "mkdir -p %s && cp -a ../*.tgz %s && " % (ippicv_dir, ippicv_dir) diff --git a/easybuild/easyconfigs/p/PSI4/PSI4-1.0-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/PSI4/PSI4-1.0-intel-2016a-Python-2.7.11.eb index ed0569f101..249aec45bf 100644 --- a/easybuild/easyconfigs/p/PSI4/PSI4-1.0-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/PSI4/PSI4-1.0-intel-2016a-Python-2.7.11.eb @@ -35,10 +35,10 @@ builddependencies = [ configopts = '-DENABLE_MPI=ON -DENABLE_OMP=ON -DENABLE_UNIT_TESTS=ON -DENABLE_CHEMPS2=ON -DENABLE_PLUGINS=ON' # CMake will pick mpiexec by default and this fails with intel MPI -#configopts += ' -DMPIEXEC=$EBROOTIMPI/bin64/mpirun' +# configopts += ' -DMPIEXEC=$EBROOTIMPI/bin64/mpirun' # The tests don't work with MPI (most of them hang or fail) -# ref: https://github.com/psi4/psi4/pull/436#issuecomment-230519769 +# ref: https://github.com/psi4/psi4/pull/436# issuecomment-230519769 runtest = False moduleclass = 'chem' diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-4.3.1-intel-2015a-Python-2.7.10-mpi.eb b/easybuild/easyconfigs/p/ParaView/ParaView-4.3.1-intel-2015a-Python-2.7.10-mpi.eb index c8116fe14f..4a341a8548 100644 --- a/easybuild/easyconfigs/p/ParaView/ParaView-4.3.1-intel-2015a-Python-2.7.10-mpi.eb +++ b/easybuild/easyconfigs/p/ParaView/ParaView-4.3.1-intel-2015a-Python-2.7.10-mpi.eb @@ -39,7 +39,7 @@ configopts = '-DPARAVIEW_INSTALL_DEVELOPMENT_FILES=ON -DVTK_OPENGL_HAS_OSMESA=ON configopts += '-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include -DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.so ' configopts += '-DOSMESA_INCLUDE_DIR=$EBROOTMESA/include -DOSMESA_LIBRARY=$EBROOTMESA/lib/libOSMesa.so ' # Without internet connection turn off testing (uncomment the following line) -#configopts += '-DBUILD_TESTING=OFF ' +# configopts += '-DBUILD_TESTING=OFF ' # Or consult https://gitlab.kitware.com/vtk/vtk/blob/master/Documentation/dev/git/data.md # and download ExternalData to $EASYBUILD_SOURCEPATH and adjust -DExternalData_OBJECT_STORES accordingly # Without internet connection, comment the following two lines (configopts and prebuildopts) diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-4.3.1-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/p/ParaView/ParaView-4.3.1-intel-2015a-Python-2.7.10.eb index 2e184fd801..c862a27b0b 100644 --- a/easybuild/easyconfigs/p/ParaView/ParaView-4.3.1-intel-2015a-Python-2.7.10.eb +++ b/easybuild/easyconfigs/p/ParaView/ParaView-4.3.1-intel-2015a-Python-2.7.10.eb @@ -38,7 +38,7 @@ configopts = '-DPARAVIEW_INSTALL_DEVELOPMENT_FILES=ON -DVTK_OPENGL_HAS_OSMESA=ON configopts += '-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include -DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.so ' configopts += '-DOSMESA_INCLUDE_DIR=$EBROOTMESA/include -DOSMESA_LIBRARY=$EBROOTMESA/lib/libOSMesa.so ' # Without internet connection turn off testing (uncomment the following line) -#configopts += '-DBUILD_TESTING=OFF ' +# configopts += '-DBUILD_TESTING=OFF ' # Or consult https://gitlab.kitware.com/vtk/vtk/blob/master/Documentation/dev/git/data.md # and download ExternalData to $EASYBUILD_SOURCEPATH and adjust -DExternalData_OBJECT_STORES accordingly # Without internet connection, comment the following two lines (configopts and prebuildopts) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-goolf-1.7.20.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-goolf-1.7.20.eb index 974e57d87c..d205929d06 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-goolf-1.7.20.eb @@ -21,7 +21,6 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '5.9'), ('SQLite', '3.9.2'), - #('Tk', '8.6.4', '-no-X11'), # this requires a full X11 stack ('Tk', '8.6.4'), # this requires a full X11 stack ('GMP', '6.1.0'), # ('OpenSSL', '1.0.1q'), # OS dependency should be preferred if the os version is more recent then this version, it's diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-iomkl-2016.09-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-iomkl-2016.09-GCC-4.9.3-2.25.eb index ed40bed006..4127452393 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-iomkl-2016.09-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-iomkl-2016.09-GCC-4.9.3-2.25.eb @@ -21,14 +21,13 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '6.0'), ('SQLite', '3.9.2'), - #('Tk', '8.6.4', '-no-X11'), # this requires a full X11 stack ('Tk', '8.6.4'), # this requires a full X11 stack ('GMP', '6.1.0'), ('OpenSSL', '1.0.2h'), # OS dependency should be preferred if the os version is more recent then this version, it's # nice to have an up to date openssl for security reasons ] -#osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] +# osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! # package versions updated May 28th 2015 diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.12-GCCcore-4.9.3-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.12-GCCcore-4.9.3-bare.eb index dcac389893..571dd12dc1 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.12-GCCcore-4.9.3-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.12-GCCcore-4.9.3-bare.eb @@ -29,7 +29,7 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # We hide this by default since users should not use it in production, high-performance Python should be delivered at # compiler level with a default extension set -#hidden = True +# hidden = True # bare installation: only known module deps for GCCcore tools included exts_list = [] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-GCC-4.8.4-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-GCC-4.8.4-bare.eb index c83dff187b..6f474dc2c1 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-GCC-4.8.4-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-GCC-4.8.4-bare.eb @@ -19,8 +19,9 @@ dependencies = [ ('ncurses', '5.9'), ('SQLite', '3.8.8.1'), ('Tk', '8.6.3', '-no-X11'), # this requires a full X11 stack - #('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's - #nice to have an up to date openssl for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1k'), ] osdependencies = [('openssl-devel', 'libssl-dev')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.7.20.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.7.20.eb index 7bdd55756a..b91c6a4a7d 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.7.20.eb @@ -21,8 +21,9 @@ dependencies = [ ('ncurses', '5.9'), ('SQLite', '3.8.8.1'), ('Tk', '8.6.3', '-no-X11'), # this requires a full X11 stack - #('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's - # nice to have an up to date openssl for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1k'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-3.5.2-foss-2016.04.eb b/easybuild/easyconfigs/p/Python/Python-3.5.2-foss-2016.04.eb index f49b2ff085..3034157afb 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.5.2-foss-2016.04.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.5.2-foss-2016.04.eb @@ -24,7 +24,7 @@ dependencies = [ ('libffi', '3.2.1'), # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons - #('OpenSSL', '1.0.2h'), + # ('OpenSSL', '1.0.2h'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/pyGIMLi/pyGIMLi-20160803-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/pyGIMLi/pyGIMLi-20160803-foss-2016a-Python-2.7.11.eb index 908370bc3a..098af10b8c 100644 --- a/easybuild/easyconfigs/p/pyGIMLi/pyGIMLi-20160803-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/pyGIMLi/pyGIMLi-20160803-foss-2016a-Python-2.7.11.eb @@ -18,8 +18,8 @@ sources = ['%s.tar.gz' % commit_id] patches = ['%(name)s-%(version)s_openblas.patch'] -#pyGIMLi is picky about the version of CastXML/pygccxml/pyplusplus -#Check scripts/buildThirdParty.sh +# pyGIMLi is picky about the version of CastXML/pygccxml/pyplusplus +# Check scripts/buildThirdParty.sh builddependencies = [ ('CMake', '3.4.3'), ('CastXML', '20160617'), diff --git a/easybuild/easyconfigs/p/pyGIMLi/pyGIMLi-20160803-foss-2016a-Python-3.5.1.eb b/easybuild/easyconfigs/p/pyGIMLi/pyGIMLi-20160803-foss-2016a-Python-3.5.1.eb index 3b3bd56fa2..8ab67d6ce0 100644 --- a/easybuild/easyconfigs/p/pyGIMLi/pyGIMLi-20160803-foss-2016a-Python-3.5.1.eb +++ b/easybuild/easyconfigs/p/pyGIMLi/pyGIMLi-20160803-foss-2016a-Python-3.5.1.eb @@ -18,8 +18,8 @@ sources = ['%s.tar.gz' % commit_id] patches = ['%(name)s-%(version)s_openblas.patch'] -#pyGIMLi is picky about the version of CastXML/pygccxml/pyplusplus -#Check scripts/buildThirdParty.sh +# pyGIMLi is picky about the version of CastXML/pygccxml/pyplusplus +# Check scripts/buildThirdParty.sh builddependencies = [ ('CMake', '3.4.3'), ('CastXML', '20160617'), diff --git a/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb b/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb index 499d383ce4..ab47b2f132 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb @@ -54,7 +54,7 @@ exts_list = [ 'utils', # non-standard libraries, should be specified with fixed versions! # Rmpi segfaults (on some systems) when built with goolf/1.7.20? - #('Rmpi', '0.6-5', dict(ext_options.items() + [('patches', ['Rmpi-0.6-5_impi5.patch'])])), + # ('Rmpi', '0.6-5', dict(ext_options.items() + [('patches', ['Rmpi-0.6-5_impi5.patch'])])), ('abind', '1.4-3', ext_options), ('magic', '1.5-6', ext_options), ('geometry', '0.3-5', ext_options), diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.18-ictce-5.5.0.eb b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.18-ictce-5.5.0.eb index cc50539ec7..f0e1274759 100644 --- a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.18-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.18-ictce-5.5.0.eb @@ -24,7 +24,7 @@ dependencies = [ ('libxml2', '2.9.1', '-%s-%s' % (python, pyver)), ('PCRE', '8.12'), ('CFITSIO', '3.34'), - #('graphviz', '2.34.0'), Graphviz is optional, not in EB yet. + # ('graphviz', '2.34.0'), Graphviz is optional, not in EB yet. (python, pyver), ] -- GitLab From 65ef33d28f518a9d63262dc73483420b111e3e31 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 23 Feb 2017 09:46:11 +0100 Subject: [PATCH 0149/1603] fix long lines and space issues --- .../easyconfigs/a/ASHS/ASHS-rev103_20140612.eb | 10 +++++----- .../a/ant/ant-1.10.0-Java-1.8.0_112.eb | 5 +++-- .../a/ant/ant-1.9.7-Java-1.8.0_92.eb | 5 +++-- .../b/BayeScEnv/BayeScEnv-1.1-goolf-1.4.10.eb | 3 ++- .../b/BayeScan/BayeScan-2.1-goolf-1.4.10.eb | 1 - .../Commet-20150415-foss-2016a-Python-2.7.11.eb | 2 +- .../c/ctffind/ctffind-4.0.17-intel-2015b.eb | 3 ++- .../e/ELPA/ELPA-2016.05.004-intel-2017a.eb | 17 +++++------------ ...ator-0.1.1a-20151214-goolf-1.7.20-aadc6f9.eb | 5 +++-- .../g/GP2C/GP2C-0.0.9pl5-foss-2016a.eb | 2 +- .../Ghostscript/Ghostscript-9.20-foss-2016b.eb | 4 +++- .../Ghostscript/Ghostscript-9.20-intel-2016b.eb | 4 +++- easybuild/easyconfigs/g/gompi/gompi-2016.09.eb | 4 ++-- .../i/IOR/IOR-3.0.1-foss-2016a-mpiio.eb | 2 +- .../i/intelcuda/intelcuda-2016.10.eb | 3 ++- ...Kraken-0.10.5-beta-foss-2016a-Perl-5.22.1.eb | 2 +- ...Kraken-0.10.5-beta-foss-2016b-Perl-5.24.0.eb | 2 +- .../l/libxc/libxc-2.2.3-foss-2016b.eb | 2 +- .../l/libxc/libxc-2.2.3-intel-2016a.eb | 2 +- .../l/libxc/libxc-2.2.3-intel-2016b.eb | 2 +- .../l/libxc/libxc-3.0.0-intel-2016a.eb | 2 +- .../l/libxc/libxc-3.0.0-intel-2016b.eb | 2 +- .../Mesa-10.4.5-intel-2015a-Python-2.7.9.eb | 2 +- .../Mesa-10.5.5-intel-2015a-Python-2.7.10.eb | 5 +++-- .../Mesa-11.0.2-intel-2015b-Python-2.7.10.eb | 5 +++-- .../Mesa-11.0.8-intel-2015b-Python-2.7.11.eb | 5 +++-- .../o/OpenCV/OpenCV-3.1.0-foss-2016a.eb | 4 ++-- .../o/OpenCV/OpenCV-3.1.0-intel-2016a.eb | 4 ++-- .../o/OpenCV/OpenCV-3.1.0-intel-2016b.eb | 4 ++-- .../PRINSEQ-0.20.4-foss-2015b-Perl-5.20.3.eb | 12 ++++++------ .../PRINSEQ-0.20.4-goolf-1.4.10-Perl-5.16.3.eb | 12 ++++++------ .../PSI4/PSI4-1.0-intel-2016a-Python-2.7.11.eb | 2 +- .../p/Python/Python-2.5.6-goolf-1.4.10-bare.eb | 3 ++- .../p/Python/Python-2.5.6-ictce-5.2.0-bare.eb | 3 ++- .../p/Python/Python-2.5.6-ictce-5.3.0-bare.eb | 3 ++- .../Python/Python-2.7.10-GCC-4.9.3-2.25-bare.eb | 3 ++- .../Python/Python-2.7.10-GNU-4.9.3-2.25-bare.eb | 3 ++- .../p/Python/Python-2.7.11-CrayGNU-2015.11.eb | 3 ++- .../p/Python/Python-2.7.11-CrayGNU-2016.03.eb | 3 ++- .../p/Python/Python-2.7.11-goolf-1.7.20.eb | 5 +++-- ...ython-2.7.11-iomkl-2016.09-GCC-4.9.3-2.25.eb | 7 ++++--- .../Python/Python-2.7.12-GCCcore-4.9.3-bare.eb | 8 +++++--- .../p/Python/Python-2.7.3-foss-2015b.eb | 3 ++- .../p/Python/Python-2.7.3-goolf-1.4.10.eb | 3 ++- .../p/Python/Python-2.7.3-goolf-1.5.14.eb | 3 ++- .../p/Python/Python-2.7.3-ictce-5.2.0.eb | 3 ++- .../p/Python/Python-2.7.3-ictce-5.3.0.eb | 3 ++- .../p/Python/Python-2.7.3-intel-2015a.eb | 3 ++- .../p/Python/Python-2.7.5-goolf-1.4.10.eb | 3 ++- .../p/Python/Python-2.7.5-ictce-5.3.0.eb | 3 ++- .../p/Python/Python-2.7.5-ictce-5.5.0.eb | 3 ++- .../p/Python/Python-2.7.6-goolf-1.4.10.eb | 3 ++- .../p/Python/Python-2.7.6-ictce-5.5.0.eb | 3 ++- .../p/Python/Python-2.7.8-foss-2014b.eb | 3 ++- .../p/Python/Python-2.7.8-goolf-1.5.14.eb | 3 ++- .../p/Python/Python-2.7.8-ictce-7.1.2.eb | 3 ++- .../p/Python/Python-2.7.8-intel-2014.06.eb | 3 ++- .../p/Python/Python-2.7.8-intel-2014b.eb | 3 ++- .../p/Python/Python-2.7.8-intel-2015a.eb | 3 ++- .../Python/Python-2.7.9-CrayGNU-2015.06-bare.eb | 3 ++- .../p/Python/Python-2.7.9-CrayGNU-2015.06.eb | 8 +++++--- .../Python/Python-2.7.9-CrayGNU-2015.11-bare.eb | 3 ++- .../p/Python/Python-2.7.9-CrayGNU-2015.11.eb | 8 +++++--- .../p/Python/Python-2.7.9-GCC-4.8.4-bare.eb | 3 ++- .../p/Python/Python-2.7.9-GCC-4.9.2-bare.eb | 3 ++- .../p/Python/Python-2.7.9-foss-2015.05.eb | 3 ++- .../p/Python/Python-2.7.9-foss-2015a-bare.eb | 3 ++- .../p/Python/Python-2.7.9-foss-2015a.eb | 3 ++- .../p/Python/Python-2.7.9-foss-2015b.eb | 3 ++- .../p/Python/Python-2.7.9-gompi-1.5.16-bare.eb | 3 ++- .../p/Python/Python-2.7.9-goolf-1.5.14.eb | 3 ++- .../p/Python/Python-2.7.9-goolf-1.5.16.eb | 3 ++- .../p/Python/Python-2.7.9-goolf-1.7.20.eb | 3 ++- .../p/Python/Python-2.7.9-intel-2015a-bare.eb | 3 ++- .../p/Python/Python-2.7.9-intel-2015a.eb | 3 ++- .../p/Python/Python-3.2.3-goolf-1.4.10.eb | 3 ++- .../p/Python/Python-3.2.3-ictce-5.3.0.eb | 3 ++- .../p/Python/Python-3.3.2-goolf-1.4.10.eb | 3 ++- .../p/Python/Python-3.3.2-ictce-5.3.0.eb | 3 ++- .../p/Python/Python-3.4.1-intel-2014b.eb | 3 ++- .../p/Python/Python-3.4.1-intel-2015a.eb | 3 ++- .../p/Python/Python-3.4.3-intel-2015a.eb | 3 ++- .../p/Python/Python-3.5.0-intel-2015b.eb | 3 ++- .../p/Python/Python-3.5.1-foss-2015a.eb | 3 ++- .../p/Python/Python-3.5.1-foss-2016a.eb | 3 ++- .../p/Python/Python-3.5.1-intel-2016a.eb | 3 ++- ...pyGIMLi-20160803-foss-2016a-Python-2.7.11.eb | 2 +- .../QuantumESPRESSO-5.4.0-foss-2016b-hybrid.eb | 11 +++++------ 88 files changed, 198 insertions(+), 137 deletions(-) diff --git a/easybuild/easyconfigs/a/ASHS/ASHS-rev103_20140612.eb b/easybuild/easyconfigs/a/ASHS/ASHS-rev103_20140612.eb index bfa52a0b28..a251f6e6b4 100644 --- a/easybuild/easyconfigs/a/ASHS/ASHS-rev103_20140612.eb +++ b/easybuild/easyconfigs/a/ASHS/ASHS-rev103_20140612.eb @@ -2,7 +2,7 @@ # Author: Ravi Tripathi # Email: ravi89@uab.edu -easyblock = "Tarball" +easyblock = 'Tarball' name = 'ASHS' version = 'rev103_20140612' @@ -16,14 +16,14 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} # from https://www.nitrc.org/frs/?group_id=370 sources = ['ashs_Linux64_%(version)s.tgz'] -checksums= ["07fea2883b856af8797b200212b72e71"] +checksums = ['07fea2883b856af8797b200212b72e71'] modextravars = {'ASHS_ROOT': '%(installdir)s'} sanity_check_paths = { - 'files': ["bin/ashs_main.sh", "bin/ashs_template_qsub.sh", "bin/ashs_train.sh", - "bin/ashs_util_makepdf.sh"], - 'dirs': ["ext"] + 'files': ['bin/ashs_main.sh', 'bin/ashs_template_qsub.sh', 'bin/ashs_train.sh', + 'bin/ashs_util_makepdf.sh'], + 'dirs': ['ext'], } moduleclass = 'bio' diff --git a/easybuild/easyconfigs/a/ant/ant-1.10.0-Java-1.8.0_112.eb b/easybuild/easyconfigs/a/ant/ant-1.10.0-Java-1.8.0_112.eb index 2d88d28b75..d2ebd37189 100644 --- a/easybuild/easyconfigs/a/ant/ant-1.10.0-Java-1.8.0_112.eb +++ b/easybuild/easyconfigs/a/ant/ant-1.10.0-Java-1.8.0_112.eb @@ -3,8 +3,9 @@ version = '1.10.0' versionsuffix = '-Java-%(javaver)s' homepage = 'http://ant.apache.org/' -description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files - as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications.""" +description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in + build files as targets and extension points dependent upon each other. The main known usage of Ant is the build of + Java applications.""" toolchain = {'name': 'dummy', 'version': ''} diff --git a/easybuild/easyconfigs/a/ant/ant-1.9.7-Java-1.8.0_92.eb b/easybuild/easyconfigs/a/ant/ant-1.9.7-Java-1.8.0_92.eb index 175bb2628a..4c6e292088 100644 --- a/easybuild/easyconfigs/a/ant/ant-1.9.7-Java-1.8.0_92.eb +++ b/easybuild/easyconfigs/a/ant/ant-1.9.7-Java-1.8.0_92.eb @@ -3,8 +3,9 @@ version = '1.9.7' versionsuffix = '-Java-%(javaver)s' homepage = 'http://ant.apache.org/' -description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files - as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications.""" +description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in + build files as targets and extension points dependent upon each other. The main known usage of Ant is the build of + Java applications.""" toolchain = {'name': 'dummy', 'version': ''} diff --git a/easybuild/easyconfigs/b/BayeScEnv/BayeScEnv-1.1-goolf-1.4.10.eb b/easybuild/easyconfigs/b/BayeScEnv/BayeScEnv-1.1-goolf-1.4.10.eb index 25b2cd8bb7..a0b996743d 100644 --- a/easybuild/easyconfigs/b/BayeScEnv/BayeScEnv-1.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/BayeScEnv/BayeScEnv-1.1-goolf-1.4.10.eb @@ -9,7 +9,8 @@ name = 'BayeScEnv' version = '1.1' homepage = 'https://github.com/devillemereuil/bayescenv' -description = """BayeScEnv is a Fst-based, genome-scan method that uses environmental variables to detect local adaptation.""" +description = """BayeScEnv is a Fst-based, genome-scan method that uses environmental variables + to detect local adaptation.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'openmp': True} diff --git a/easybuild/easyconfigs/b/BayeScan/BayeScan-2.1-goolf-1.4.10.eb b/easybuild/easyconfigs/b/BayeScan/BayeScan-2.1-goolf-1.4.10.eb index de8bcce297..2902acfde6 100644 --- a/easybuild/easyconfigs/b/BayeScan/BayeScan-2.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/BayeScan/BayeScan-2.1-goolf-1.4.10.eb @@ -12,7 +12,6 @@ homepage = 'http://cmpg.unibe.ch/software/BayeScan/' description = """BayeScan aims at identifying candidate loci under natural selection from genetic data, using differences in allele frequencies between populations.""" -# BayeScan makefile is hardcoded to use g++. In case you want to use a non-gcc toolchain you will need to patch the makefile toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'openmp': True} diff --git a/easybuild/easyconfigs/c/Commet/Commet-20150415-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/c/Commet/Commet-20150415-foss-2016a-Python-2.7.11.eb index 3abe5c93c9..4000cc8571 100644 --- a/easybuild/easyconfigs/c/Commet/Commet-20150415-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/c/Commet/Commet-20150415-foss-2016a-Python-2.7.11.eb @@ -26,7 +26,7 @@ files_to_copy = ['bin', 'doc', 'include', 'ABCDE_bench', (['Commet.py'], 'bin')] sanity_check_paths = { 'files': ['bin/%s' % binfile for binfile in ['Commet.py', 'bvop', 'compare_reads', 'extract_reads', 'filter_reads', 'index_and_search']], - 'dirs' : ['doc', 'include'] + 'dirs': ['doc', 'include'], } moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/ctffind/ctffind-4.0.17-intel-2015b.eb b/easybuild/easyconfigs/c/ctffind/ctffind-4.0.17-intel-2015b.eb index 8c2ecba76b..60152e7602 100644 --- a/easybuild/easyconfigs/c/ctffind/ctffind-4.0.17-intel-2015b.eb +++ b/easybuild/easyconfigs/c/ctffind/ctffind-4.0.17-intel-2015b.eb @@ -22,7 +22,8 @@ dependencies = [('GSL', '1.16')] # when running ./configure in the root folder it fails. # application doesn't provide a 'make install' prebuildopts = 'mkdir build && cd build && ' -prebuildopts += ' ../configure --enable-static --disable-debug --enable-optimisations --enable-openmp FC=${FC} F77=${F77} && ' +prebuildopts += " ../configure --enable-static --disable-debug --enable-optimisations --enable-openmp " +prebuildopts += "FC=${FC} F77=${F77} && " files_to_copy = [(['build/ctffind'], 'bin'), 'doc', 'scripts'] diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2016.05.004-intel-2017a.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2016.05.004-intel-2017a.eb index 4851fc5541..75d318f670 100644 --- a/easybuild/easyconfigs/e/ELPA/ELPA-2016.05.004-intel-2017a.eb +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2016.05.004-intel-2017a.eb @@ -46,18 +46,11 @@ postinstallcmds = [ ] sanity_check_paths = { - 'files': [ - 'lib/libelpa.a', 'lib/libelpa.%s' % SHLIB_EXT, - 'lib/libelpa_openmp.a', 'lib/libelpa_openmp.%s' % SHLIB_EXT, - 'lib/libelpatest.a', 'lib/libelpatest.%s' % SHLIB_EXT, - 'lib/libelpatest_openmp.a', 'lib/libelpatest_openmp.%s' % SHLIB_EXT, - 'share/doc/elpa/examples/config.h', - 'share/doc/elpa/examples/config-f90.h', - ], - 'dirs': [ - 'bin', 'include/elpa-%(version)s/elpa', - 'include/elpa-%(version)s/modules', 'lib/pkgconfig', - ], + 'files': ['lib/libelpa.a', 'lib/libelpa.%s' % SHLIB_EXT, 'lib/libelpa_openmp.a', + 'lib/libelpa_openmp.%s' % SHLIB_EXT, 'lib/libelpatest.a', 'lib/libelpatest.%s' % SHLIB_EXT, + 'lib/libelpatest_openmp.a', 'lib/libelpatest_openmp.%s' % SHLIB_EXT, 'share/doc/elpa/examples/config.h', + 'share/doc/elpa/examples/config-f90.h'], + 'dirs': ['bin', 'include/elpa-%(version)s/elpa', 'include/elpa-%(version)s/modules', 'lib/pkgconfig'], } moduleclass = 'math' diff --git a/easybuild/easyconfigs/f/fastQValidator/fastQValidator-0.1.1a-20151214-goolf-1.7.20-aadc6f9.eb b/easybuild/easyconfigs/f/fastQValidator/fastQValidator-0.1.1a-20151214-goolf-1.7.20-aadc6f9.eb index f9d3b4a7b5..5e8c01ab2d 100644 --- a/easybuild/easyconfigs/f/fastQValidator/fastQValidator-0.1.1a-20151214-goolf-1.7.20-aadc6f9.eb +++ b/easybuild/easyconfigs/f/fastQValidator/fastQValidator-0.1.1a-20151214-goolf-1.7.20-aadc6f9.eb @@ -31,8 +31,9 @@ sources = [ dependencies = [ ('zlib', '1.2.8'), -# ('OpenSSL', '1.0.1q'), # OS dependency should be preferred if the os version is more recent then this version, it's -# nice to have an up to date openssl for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1q'), ] # openssl required by libStatgen diff --git a/easybuild/easyconfigs/g/GP2C/GP2C-0.0.9pl5-foss-2016a.eb b/easybuild/easyconfigs/g/GP2C/GP2C-0.0.9pl5-foss-2016a.eb index f302d9f398..238da5f765 100644 --- a/easybuild/easyconfigs/g/GP2C/GP2C-0.0.9pl5-foss-2016a.eb +++ b/easybuild/easyconfigs/g/GP2C/GP2C-0.0.9pl5-foss-2016a.eb @@ -22,7 +22,7 @@ configopts = '--with-paricfg=$EBROOTPARIMINGP/lib/pari/pari.cfg' runtest = 'check' sanity_check_paths = { - 'files': ['bin/%s' % binfile for binfile in ['gp2c', 'gp2c-run',]], + 'files': ['bin/%s' % binfile for binfile in ['gp2c', 'gp2c-run']], 'dirs': ['bin'] } diff --git a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.20-foss-2016b.eb b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.20-foss-2016b.eb index c65da40120..d7b08e9fef 100644 --- a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.20-foss-2016b.eb +++ b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.20-foss-2016b.eb @@ -10,7 +10,9 @@ description = """Ghostscript is a versatile processor for PostScript data with t toolchain = {'name': 'foss', 'version': '2016b'} toolchainopts = {'pic': True} -source_urls = ["https://github.com/ArtifexSoftware/ghostpdl-downloads/releases/download/gs%(version_major)s%(version_minor)s/"] +source_urls = [ + 'https://github.com/ArtifexSoftware/ghostpdl-downloads/releases/download/gs%(version_major)s%(version_minor)s/', +] sources = ['ghostscript-%(version)s.tar.gz'] dependencies = [ diff --git a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.20-intel-2016b.eb b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.20-intel-2016b.eb index b89382f6a1..eed125d9f6 100644 --- a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.20-intel-2016b.eb +++ b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.20-intel-2016b.eb @@ -10,7 +10,9 @@ description = """Ghostscript is a versatile processor for PostScript data with t toolchain = {'name': 'intel', 'version': '2016b'} toolchainopts = {'pic': True} -source_urls = ["https://github.com/ArtifexSoftware/ghostpdl-downloads/releases/download/gs%(version_major)s%(version_minor)s/"] +source_urls = [ + 'https://github.com/ArtifexSoftware/ghostpdl-downloads/releases/download/gs%(version_major)s%(version_minor)s/', +] sources = ['ghostscript-%(version)s.tar.gz'] dependencies = [ diff --git a/easybuild/easyconfigs/g/gompi/gompi-2016.09.eb b/easybuild/easyconfigs/g/gompi/gompi-2016.09.eb index d4b83fb9a0..7e7b36e603 100644 --- a/easybuild/easyconfigs/g/gompi/gompi-2016.09.eb +++ b/easybuild/easyconfigs/g/gompi/gompi-2016.09.eb @@ -13,8 +13,8 @@ gccver = '6.2.0-2.27' # compiler toolchain dependencies dependencies = [ - ('GCC', gccver), # includes both GCC and binutils - ('OpenMPI', '2.0.1', '', ('GCC', gccver)), + ('GCC', gccver), # includes both GCC and binutils + ('OpenMPI', '2.0.1', '', ('GCC', gccver)), ] moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/IOR/IOR-3.0.1-foss-2016a-mpiio.eb b/easybuild/easyconfigs/i/IOR/IOR-3.0.1-foss-2016a-mpiio.eb index 1c64db33bd..66d029ece5 100644 --- a/easybuild/easyconfigs/i/IOR/IOR-3.0.1-foss-2016a-mpiio.eb +++ b/easybuild/easyconfigs/i/IOR/IOR-3.0.1-foss-2016a-mpiio.eb @@ -13,7 +13,7 @@ homepage = 'https://github.com/chaos/ior' description = """ The IOR software is used for benchmarking parallel file systems using POSIX, MPIIO, or HDF5 interfaces. """ -toolchain = {'name': 'foss', 'version': '2016a' } +toolchain = {'name': 'foss', 'version': '2016a'} source_urls = [('https://github.com/chaos/ior/archive/')] sources = ['%(version)s.tar.gz'] diff --git a/easybuild/easyconfigs/i/intelcuda/intelcuda-2016.10.eb b/easybuild/easyconfigs/i/intelcuda/intelcuda-2016.10.eb index 82121910a8..14c19568ad 100644 --- a/easybuild/easyconfigs/i/intelcuda/intelcuda-2016.10.eb +++ b/easybuild/easyconfigs/i/intelcuda/intelcuda-2016.10.eb @@ -4,7 +4,8 @@ name = 'intelcuda' version = '2016.10' homepage = '(none)' -description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL, with CUDA toolkit""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, + Intel MPI & Intel MKL, with CUDA toolkit""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/k/Kraken/Kraken-0.10.5-beta-foss-2016a-Perl-5.22.1.eb b/easybuild/easyconfigs/k/Kraken/Kraken-0.10.5-beta-foss-2016a-Perl-5.22.1.eb index bbfde4273f..02cc25cfec 100644 --- a/easybuild/easyconfigs/k/Kraken/Kraken-0.10.5-beta-foss-2016a-Perl-5.22.1.eb +++ b/easybuild/easyconfigs/k/Kraken/Kraken-0.10.5-beta-foss-2016a-Perl-5.22.1.eb @@ -2,7 +2,7 @@ easyblock = 'PackedBinary' name = 'Kraken' version = '0.10.5-beta' -versionsuffix ='-Perl-%(perlver)s' +versionsuffix = '-Perl-%(perlver)s' homepage = 'http://ccb.jhu.edu/software/kraken/' description = """Kraken is a system for assigning taxonomic labels to short DNA sequences, diff --git a/easybuild/easyconfigs/k/Kraken/Kraken-0.10.5-beta-foss-2016b-Perl-5.24.0.eb b/easybuild/easyconfigs/k/Kraken/Kraken-0.10.5-beta-foss-2016b-Perl-5.24.0.eb index a1be8e5709..af61c387aa 100644 --- a/easybuild/easyconfigs/k/Kraken/Kraken-0.10.5-beta-foss-2016b-Perl-5.24.0.eb +++ b/easybuild/easyconfigs/k/Kraken/Kraken-0.10.5-beta-foss-2016b-Perl-5.24.0.eb @@ -2,7 +2,7 @@ easyblock = 'PackedBinary' name = 'Kraken' version = '0.10.5-beta' -versionsuffix ='-Perl-%(perlver)s' +versionsuffix = '-Perl-%(perlver)s' homepage = 'http://ccb.jhu.edu/software/kraken/' description = """Kraken is a system for assigning taxonomic labels to short DNA sequences, diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.3-foss-2016b.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.3-foss-2016b.eb index 8733225f52..2ef9de2a2d 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.2.3-foss-2016b.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.3-foss-2016b.eb @@ -22,7 +22,7 @@ configopts = 'FC="$F77" FCFLAGS="$FFLAGS" --enable-shared --enable-fortran' # runtest = 'check' sanity_check_paths = { - 'files': ['lib/libxc%s.%s' % (x,y) for x in ['', 'f90'] for y in ['a', SHLIB_EXT]], + 'files': ['lib/libxc%s.%s' % (x, y) for x in ['', 'f90'] for y in ['a', SHLIB_EXT]], 'dirs': ['include'], } diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016a.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016a.eb index 40280eac70..80e9889a84 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016a.eb @@ -22,7 +22,7 @@ configopts = 'FC="$F77" FCFLAGS="$FFLAGS" --enable-shared --enable-fortran' # runtest = 'check' sanity_check_paths = { - 'files': ['lib/libxc%s.%s' % (x,y) for x in ['', 'f90'] for y in ['a', SHLIB_EXT]], + 'files': ['lib/libxc%s.%s' % (x, y) for x in ['', 'f90'] for y in ['a', SHLIB_EXT]], 'dirs': ['include'], } diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016b.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016b.eb index ef6bdb3052..bd3cb81b7c 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016b.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016b.eb @@ -22,7 +22,7 @@ configopts = 'FC="$F77" FCFLAGS="$FFLAGS" --enable-shared --enable-fortran' # runtest = 'check' sanity_check_paths = { - 'files': ['lib/libxc%s.%s' % (x,y) for x in ['', 'f90'] for y in ['a', SHLIB_EXT]], + 'files': ['lib/libxc%s.%s' % (x, y) for x in ['', 'f90'] for y in ['a', SHLIB_EXT]], 'dirs': ['include'], } diff --git a/easybuild/easyconfigs/l/libxc/libxc-3.0.0-intel-2016a.eb b/easybuild/easyconfigs/l/libxc/libxc-3.0.0-intel-2016a.eb index b63d48a898..9417deb550 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-3.0.0-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-3.0.0-intel-2016a.eb @@ -22,7 +22,7 @@ configopts = 'FC="$F77" FCFLAGS="$FFLAGS" --enable-shared --enable-fortran' # runtest = 'check' sanity_check_paths = { - 'files': ['lib/libxc%s.%s' % (x,y) for x in ['', 'f90'] for y in ['a', SHLIB_EXT]], + 'files': ['lib/libxc%s.%s' % (x, y) for x in ['', 'f90'] for y in ['a', SHLIB_EXT]], 'dirs': ['include'], } diff --git a/easybuild/easyconfigs/l/libxc/libxc-3.0.0-intel-2016b.eb b/easybuild/easyconfigs/l/libxc/libxc-3.0.0-intel-2016b.eb index 67f7a66326..a251dac24c 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-3.0.0-intel-2016b.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-3.0.0-intel-2016b.eb @@ -22,7 +22,7 @@ configopts = 'FC="$F77" FCFLAGS="$FFLAGS" --enable-shared --enable-fortran' # runtest = 'check' sanity_check_paths = { - 'files': ['lib/libxc%s.%s' % (x,y) for x in ['', 'f90'] for y in ['a', SHLIB_EXT]], + 'files': ['lib/libxc%s.%s' % (x, y) for x in ['', 'f90'] for y in ['a', SHLIB_EXT]], 'dirs': ['include'], } diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-10.4.5-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/m/Mesa/Mesa-10.4.5-intel-2015a-Python-2.7.9.eb index 93b02acda8..41d6a64d37 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-10.4.5-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-10.4.5-intel-2015a-Python-2.7.9.eb @@ -54,7 +54,7 @@ dependencies = [ # GLU is not part anymore of Mesa package! configopts = " --disable-osmesa --disable-gallium-llvm --enable-glx --disable-dri --enable-xlib-glx" -configopts += " --disable-driglx-direct --with-gallium-drivers='' --disable-egl""" +configopts += " --disable-driglx-direct --with-gallium-drivers='' --disable-egl" # package-config files for os dependencies are in an os specific place # preconfigopts = ' PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-10.5.5-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/m/Mesa/Mesa-10.5.5-intel-2015a-Python-2.7.10.eb index 3ebe66dd51..8b03ae9140 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-10.5.5-intel-2015a-Python-2.7.10.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-10.5.5-intel-2015a-Python-2.7.10.eb @@ -50,8 +50,9 @@ dependencies = [ # osdependencies = ['libudev'] # GLU is not part anymore of Mesa package! -configopts = " --disable-osmesa --enable-gallium-osmesa --enable-gallium-llvm --enable-glx --disable-dri --enable-xlib-glx" -configopts += " --disable-driglx-direct --with-gallium-drivers='swrast' --disable-egl --with-osmesa-bits=32 --enable-texture-float " +configopts = " --disable-osmesa --enable-gallium-osmesa --enable-gallium-llvm --enable-glx --disable-dri" +configopts += " --enable-xlib-glx --disable-driglx-direct --with-gallium-drivers='swrast' --disable-egl" +configopts += " --with-osmesa-bits=32 --enable-texture-float " # package-config files for os dependencies are in an os specific place # preconfigopts = 'libtoolize && PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-11.0.2-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/m/Mesa/Mesa-11.0.2-intel-2015b-Python-2.7.10.eb index 2631598232..5224023e11 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-11.0.2-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-11.0.2-intel-2015b-Python-2.7.10.eb @@ -49,8 +49,9 @@ dependencies = [ # osdependencies = ['libudev'] # GLU is not part anymore of Mesa package! -configopts = " --disable-osmesa --enable-gallium-osmesa --enable-gallium-llvm --enable-glx --disable-dri --enable-xlib-glx" -configopts += " --disable-driglx-direct --with-gallium-drivers='swrast' --disable-egl --with-osmesa-bits=32 --enable-texture-float " +configopts = " --disable-osmesa --enable-gallium-osmesa --enable-gallium-llvm --enable-glx --disable-dri" +configopts += " --enable-xlib-glx --disable-driglx-direct --with-gallium-drivers='swrast' --disable-egl" +configopts += " --with-osmesa-bits=32 --enable-texture-float " # package-config files for os dependencies are in an os specific place # preconfigopts = 'libtoolize && PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-11.0.8-intel-2015b-Python-2.7.11.eb b/easybuild/easyconfigs/m/Mesa/Mesa-11.0.8-intel-2015b-Python-2.7.11.eb index 244c4f1427..ec21cce29c 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-11.0.8-intel-2015b-Python-2.7.11.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-11.0.8-intel-2015b-Python-2.7.11.eb @@ -49,8 +49,9 @@ dependencies = [ # osdependencies = ['libudev'] # GLU is not part anymore of Mesa package! -configopts = " --disable-osmesa --enable-gallium-osmesa --enable-gallium-llvm --enable-glx --disable-dri --enable-xlib-glx" -configopts += " --disable-driglx-direct --with-gallium-drivers='swrast' --disable-egl --with-osmesa-bits=32 --enable-texture-float " +configopts = " --disable-osmesa --enable-gallium-osmesa --enable-gallium-llvm --enable-glx --disable-dri" +configopts += " --enable-xlib-glx --disable-driglx-direct --with-gallium-drivers='swrast' --disable-egl" +configopts += " --with-osmesa-bits=32 --enable-texture-float " # package-config files for os dependencies are in an os specific place # preconfigopts = 'libtoolize && PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016a.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016a.eb index fb9d354480..141e1f7cdd 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016a.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016a.eb @@ -67,8 +67,8 @@ configopts += '-DWITH_CUDA=OFF ' postinstallcmds = ["cp 3rdparty/ippicv/unpack/ippicv_lnx/lib/intel64/libippicv.* %(installdir)s/lib"] sanity_check_paths = { - 'files': ['lib/libopencv_core.%s' % SHLIB_EXT ] + - ['lib/python%%(pyshortver)s/site-packages/cv2.%s' % SHLIB_EXT ] + + 'files': ['lib/libopencv_core.%s' % SHLIB_EXT] + + ['lib/python%%(pyshortver)s/site-packages/cv2.%s' % SHLIB_EXT] + ['lib/libippicv.a'] + ['bin/opencv_%s' % x for x in ['annotation', 'createsamples', 'traincascade']], 'dirs': ['include'] diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016a.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016a.eb index 52aa30e629..23de8de267 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016a.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016a.eb @@ -68,8 +68,8 @@ configopts += '-DWITH_CUDA=OFF ' postinstallcmds = ["cp 3rdparty/ippicv/unpack/ippicv_lnx/lib/intel64/libippicv.* %(installdir)s/lib"] sanity_check_paths = { - 'files': ['lib/libopencv_core.%s' % SHLIB_EXT ] + - ['lib/python%%(pyshortver)s/site-packages/cv2.%s' % SHLIB_EXT ] + + 'files': ['lib/libopencv_core.%s' % SHLIB_EXT] + + ['lib/python%%(pyshortver)s/site-packages/cv2.%s' % SHLIB_EXT] + ['lib/libippicv.a'] + ['bin/opencv_%s' % x for x in ['annotation', 'createsamples', 'traincascade']], 'dirs': ['include'] diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016b.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016b.eb index fc8dc13e40..0b6f2141a7 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016b.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016b.eb @@ -69,8 +69,8 @@ configopts += '-DWITH_CUDA=OFF ' postinstallcmds = ["cp 3rdparty/ippicv/unpack/ippicv_lnx/lib/intel64/libippicv.* %(installdir)s/lib"] sanity_check_paths = { - 'files': ['lib/libopencv_core.%s' % SHLIB_EXT ] + - ['lib/python%%(pyshortver)s/site-packages/cv2.%s' % SHLIB_EXT ] + + 'files': ['lib/libopencv_core.%s' % SHLIB_EXT] + + ['lib/python%%(pyshortver)s/site-packages/cv2.%s' % SHLIB_EXT] + ['lib/libippicv.a'] + ['bin/opencv_%s' % x for x in ['annotation', 'createsamples', 'traincascade']], 'dirs': ['include'] diff --git a/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-foss-2015b-Perl-5.20.3.eb b/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-foss-2015b-Perl-5.20.3.eb index c76887ac30..261f83dd09 100644 --- a/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-foss-2015b-Perl-5.20.3.eb +++ b/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-foss-2015b-Perl-5.20.3.eb @@ -32,16 +32,16 @@ exts_filter = ("perldoc -lm %(ext_name)s ", "") exts_list = [ ('ExtUtils::Depends', '0.405', { - 'source_tmpl': 'ExtUtils-Depends-0.405.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XA/XAOC/'], + 'source_tmpl': 'ExtUtils-Depends-0.405.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XA/XAOC/'], }), ('ExtUtils::PkgConfig', '1.15', { - 'source_tmpl': 'ExtUtils-PkgConfig-1.15.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XA/XAOC/'], + 'source_tmpl': 'ExtUtils-PkgConfig-1.15.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XA/XAOC/'], }), ('Getopt::Long', '2.48', { - 'source_tmpl': 'Getopt-Long-2.48.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JV/JV/'], + 'source_tmpl': 'Getopt-Long-2.48.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JV/JV/'], }), ('Pod::Usage', '1.68', { 'source_tmpl': 'Pod-Usage-1.68.tar.gz', diff --git a/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-goolf-1.4.10-Perl-5.16.3.eb b/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-goolf-1.4.10-Perl-5.16.3.eb index 4dc47a8df2..f2db549906 100644 --- a/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-goolf-1.4.10-Perl-5.16.3.eb +++ b/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-goolf-1.4.10-Perl-5.16.3.eb @@ -30,16 +30,16 @@ exts_filter = ("perldoc -lm %(ext_name)s ", "") exts_list = [ ('ExtUtils::Depends', '0.405', { - 'source_tmpl': 'ExtUtils-Depends-0.405.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XA/XAOC/'], + 'source_tmpl': 'ExtUtils-Depends-0.405.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XA/XAOC/'], }), ('ExtUtils::PkgConfig', '1.15', { - 'source_tmpl': 'ExtUtils-PkgConfig-1.15.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XA/XAOC/'], + 'source_tmpl': 'ExtUtils-PkgConfig-1.15.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XA/XAOC/'], }), ('Getopt::Long', '2.48', { - 'source_tmpl': 'Getopt-Long-2.48.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JV/JV/'], + 'source_tmpl': 'Getopt-Long-2.48.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JV/JV/'], }), ('Pod::Usage', '1.68', { 'source_tmpl': 'Pod-Usage-1.68.tar.gz', diff --git a/easybuild/easyconfigs/p/PSI4/PSI4-1.0-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/PSI4/PSI4-1.0-intel-2016a-Python-2.7.11.eb index 249aec45bf..57e1bb653a 100644 --- a/easybuild/easyconfigs/p/PSI4/PSI4-1.0-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/PSI4/PSI4-1.0-intel-2016a-Python-2.7.11.eb @@ -29,7 +29,7 @@ dependencies = [ builddependencies = [ ('CMake', '3.5.2'), -# ('Perl', '5.22.1', '-bare'), # for the test suite + # ('Perl', '5.22.1', '-bare'), # for the test suite ] configopts = '-DENABLE_MPI=ON -DENABLE_OMP=ON -DENABLE_UNIT_TESTS=ON -DENABLE_CHEMPS2=ON -DENABLE_PLUGINS=ON' diff --git a/easybuild/easyconfigs/p/Python/Python-2.5.6-goolf-1.4.10-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.5.6-goolf-1.4.10-bare.eb index e815cc69b5..ace4711442 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.5.6-goolf-1.4.10-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.5.6-goolf-1.4.10-bare.eb @@ -3,7 +3,8 @@ version = '2.5.6' versionsuffix = '-bare' homepage = 'http://python.org/' -description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True} diff --git a/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.2.0-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.2.0-bare.eb index 809068de30..b1bdb4f782 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.2.0-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.2.0-bare.eb @@ -3,7 +3,8 @@ version = '2.5.6' versionsuffix = '-bare' homepage = 'http://python.org/' -description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" toolchain = {'name': 'ictce', 'version': '5.2.0'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True} diff --git a/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.3.0-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.3.0-bare.eb index c781bfe8b7..cc84b14111 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.3.0-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.3.0-bare.eb @@ -3,7 +3,8 @@ version = '2.5.6' versionsuffix = '-bare' homepage = 'http://python.org/' -description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True} diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.10-GCC-4.9.3-2.25-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.10-GCC-4.9.3-2.25-bare.eb index fd80fddc40..edaa0f4fa5 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.10-GCC-4.9.3-2.25-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.10-GCC-4.9.3-2.25-bare.eb @@ -3,7 +3,8 @@ version = '2.7.10' versionsuffix = '-bare' homepage = 'http://python.org/' -description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" toolchain = {'name': 'GCC', 'version': '4.9.3-2.25'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True} diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.10-GNU-4.9.3-2.25-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.10-GNU-4.9.3-2.25-bare.eb index 6e9aa1f7c4..ac622805c5 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.10-GNU-4.9.3-2.25-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.10-GNU-4.9.3-2.25-bare.eb @@ -3,7 +3,8 @@ version = '2.7.10' versionsuffix = '-bare' homepage = 'http://python.org/' -description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" toolchain = {'name': 'GNU', 'version': '4.9.3-2.25'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True} diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2015.11.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2015.11.eb index d69b594b08..4289f275f3 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2015.11.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2015.11.eb @@ -5,7 +5,8 @@ name = 'Python' version = "2.7.11" homepage = 'http://python.org/' -description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" toolchain = {'name': 'CrayGNU', 'version': '2015.11'} toolchainopts = {'pic': True} diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2016.03.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2016.03.eb index ab13993dcf..f16c276300 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2016.03.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2016.03.eb @@ -5,7 +5,8 @@ name = 'Python' version = "2.7.11" homepage = 'http://python.org/' -description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" toolchain = {'name': 'CrayGNU', 'version': '2016.03'} toolchainopts = {'pic': True} diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-goolf-1.7.20.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-goolf-1.7.20.eb index d205929d06..500c945db9 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-goolf-1.7.20.eb @@ -23,8 +23,9 @@ dependencies = [ ('SQLite', '3.9.2'), ('Tk', '8.6.4'), # this requires a full X11 stack ('GMP', '6.1.0'), -# ('OpenSSL', '1.0.1q'), # OS dependency should be preferred if the os version is more recent then this version, it's -# nice to have an up to date openssl for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1q'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-iomkl-2016.09-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-iomkl-2016.09-GCC-4.9.3-2.25.eb index 4127452393..42a08985d0 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-iomkl-2016.09-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-iomkl-2016.09-GCC-4.9.3-2.25.eb @@ -23,11 +23,12 @@ dependencies = [ ('SQLite', '3.9.2'), ('Tk', '8.6.4'), # this requires a full X11 stack ('GMP', '6.1.0'), - ('OpenSSL', '1.0.2h'), # OS dependency should be preferred if the os version is more recent then this version, it's -# nice to have an up to date openssl for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.2h'), ] -# osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! # package versions updated May 28th 2015 diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.12-GCCcore-4.9.3-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.12-GCCcore-4.9.3-bare.eb index 571dd12dc1..01b2892c87 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.12-GCCcore-4.9.3-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.12-GCCcore-4.9.3-bare.eb @@ -3,7 +3,8 @@ version = '2.7.12' versionsuffix = '-bare' homepage = 'http://python.org/' -description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" toolchain = {'name': 'GCCcore', 'version': '4.9.3'} toolchainopts = {'pic': True} @@ -21,8 +22,9 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '6.0'), ('SQLite', '3.14.1'), - # ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's - # nice to have an up to date openssl for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1k'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-foss-2015b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-foss-2015b.eb index c93dab2804..bb77d83c1d 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-foss-2015b.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-foss-2015b.eb @@ -2,7 +2,8 @@ name = 'Python' version = '2.7.3' homepage = 'http://python.org/' -description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" toolchain = {'name': 'foss', 'version': '2015b'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True} diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.4.10.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.4.10.eb index 53cdae92ab..0cda45ec7d 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.4.10.eb @@ -2,7 +2,8 @@ name = 'Python' version = '2.7.3' homepage = 'http://python.org/' -description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True} diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.5.14.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.5.14.eb index 4cd83e24d0..4ef1bfeaeb 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.5.14.eb @@ -2,7 +2,8 @@ name = 'Python' version = '2.7.3' homepage = 'http://python.org/' -description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" toolchain = {'name': 'goolf', 'version': '1.5.14'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True} diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.2.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.2.0.eb index 2608210a17..12a347ef6d 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.2.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.2.0.eb @@ -2,7 +2,8 @@ name = 'Python' version = '2.7.3' homepage = 'http://python.org/' -description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" toolchain = {'name': 'ictce', 'version': '5.2.0'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True} diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.3.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.3.0.eb index 4ffdd56f78..6265b2329d 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.3.0.eb @@ -2,7 +2,8 @@ name = 'Python' version = '2.7.3' homepage = 'http://python.org/' -description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True} diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-intel-2015a.eb index 35bbb97553..a22416f124 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-intel-2015a.eb @@ -2,7 +2,8 @@ name = 'Python' version = '2.7.3' homepage = 'http://python.org/' -description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" toolchain = {'name': 'intel', 'version': '2015a'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True} diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.5-goolf-1.4.10.eb b/easybuild/easyconfigs/p/Python/Python-2.7.5-goolf-1.4.10.eb index d2f51e3f22..d9a96be894 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.5-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.5-goolf-1.4.10.eb @@ -2,7 +2,8 @@ name = 'Python' version = '2.7.5' homepage = 'http://python.org/' -description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True} diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.3.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.3.0.eb index c0ac0d38b1..48e0894d30 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.3.0.eb @@ -2,7 +2,8 @@ name = 'Python' version = '2.7.5' homepage = 'http://python.org/' -description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True} diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.5.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.5.0.eb index 513384d5b5..e6e366e13c 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.5.0.eb @@ -2,7 +2,8 @@ name = 'Python' version = '2.7.5' homepage = 'http://python.org/' -description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" toolchain = {'name': 'ictce', 'version': '5.5.0'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True} diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.6-goolf-1.4.10.eb b/easybuild/easyconfigs/p/Python/Python-2.7.6-goolf-1.4.10.eb index 95ff34f3f9..384ccabeee 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.6-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.6-goolf-1.4.10.eb @@ -2,7 +2,8 @@ name = 'Python' version = '2.7.6' homepage = 'http://python.org/' -description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True} diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-5.5.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-5.5.0.eb index 055543dc24..91008ef87d 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-5.5.0.eb @@ -2,7 +2,8 @@ name = 'Python' version = '2.7.6' homepage = 'http://python.org/' -description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" toolchain = {'name': 'ictce', 'version': '5.5.0'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True} diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.8-foss-2014b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.8-foss-2014b.eb index 0409f54975..9f687fe594 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.8-foss-2014b.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.8-foss-2014b.eb @@ -2,7 +2,8 @@ name = 'Python' version = '2.7.8' homepage = 'http://python.org/' -description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" toolchain = {'name': 'foss', 'version': '2014b'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True} diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.8-goolf-1.5.14.eb b/easybuild/easyconfigs/p/Python/Python-2.7.8-goolf-1.5.14.eb index 2a90fee410..5f8e6aeeb0 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.8-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.8-goolf-1.5.14.eb @@ -2,7 +2,8 @@ name = 'Python' version = '2.7.8' homepage = 'http://python.org/' -description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" toolchain = {'name': 'goolf', 'version': '1.5.14'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True} diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.8-ictce-7.1.2.eb b/easybuild/easyconfigs/p/Python/Python-2.7.8-ictce-7.1.2.eb index d975d85c2d..95e0f82630 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.8-ictce-7.1.2.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.8-ictce-7.1.2.eb @@ -2,7 +2,8 @@ name = 'Python' version = '2.7.8' homepage = 'http://python.org/' -description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" toolchain = {'name': 'ictce', 'version': '7.1.2'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True} diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014.06.eb b/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014.06.eb index dca27371ed..18384a6b3c 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014.06.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014.06.eb @@ -2,7 +2,8 @@ name = 'Python' version = '2.7.8' homepage = 'http://python.org/' -description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" toolchain = {'name': 'intel', 'version': '2014.06'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True} diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014b.eb index a7d56bba16..dc5adffe37 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014b.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014b.eb @@ -2,7 +2,8 @@ name = 'Python' version = '2.7.8' homepage = 'http://python.org/' -description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" toolchain = {'name': 'intel', 'version': '2014b'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True} diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2015a.eb index 6b2fccea28..c914576c6c 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2015a.eb @@ -2,7 +2,8 @@ name = 'Python' version = '2.7.8' homepage = 'http://python.org/' -description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" toolchain = {'name': 'intel', 'version': '2015a'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True} diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.06-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.06-bare.eb index 92748077e8..ceb75f485b 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.06-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.06-bare.eb @@ -3,7 +3,8 @@ version = '2.7.9' versionsuffix = '-bare' homepage = 'http://python.org/' -description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" toolchain = {'name': 'CrayGNU', 'version': '2015.06'} toolchainopts = {'pic': True, 'opt': True} diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.06.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.06.eb index a0d5fb01e5..c42116cc9a 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.06.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.06.eb @@ -2,7 +2,8 @@ name = 'Python' version = '2.7.9' homepage = 'http://python.org/' -description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" toolchain = {'name': 'CrayGNU', 'version': '2015.06'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True} @@ -19,8 +20,9 @@ dependencies = [ ('zlib', '1.2.8'), ('libreadline', '6.3'), ('ncurses', '5.9'), -# ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's -# nice to have an up to date openssl for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1k'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel'), 'tk-devel'] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.11-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.11-bare.eb index f7679002a1..46d5881734 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.11-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.11-bare.eb @@ -3,7 +3,8 @@ version = '2.7.9' versionsuffix = '-bare' homepage = 'http://python.org/' -description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" toolchain = {'name': 'CrayGNU', 'version': '2015.11'} toolchainopts = {'pic': True, 'opt': True} diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.11.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.11.eb index eb90e5f158..e020765a41 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.11.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.11.eb @@ -2,7 +2,8 @@ name = 'Python' version = '2.7.9' homepage = 'http://python.org/' -description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" toolchain = {'name': 'CrayGNU', 'version': '2015.11'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True} @@ -19,8 +20,9 @@ dependencies = [ ('zlib', '1.2.8'), ('libreadline', '6.3'), ('ncurses', '5.9'), -# ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's -# nice to have an up to date openssl for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1k'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel'), 'tk-devel'] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-GCC-4.8.4-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-GCC-4.8.4-bare.eb index 6f474dc2c1..7040f073ac 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-GCC-4.8.4-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-GCC-4.8.4-bare.eb @@ -3,7 +3,8 @@ version = '2.7.9' versionsuffix = '-bare' homepage = 'http://python.org/' -description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" toolchain = {'name': 'GCC', 'version': '4.8.4'} toolchainopts = {'pic': True} diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-GCC-4.9.2-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-GCC-4.9.2-bare.eb index a2e4addace..bfaa856129 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-GCC-4.9.2-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-GCC-4.9.2-bare.eb @@ -3,7 +3,8 @@ version = '2.7.9' versionsuffix = '-bare' homepage = 'http://python.org/' -description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" toolchain = {'name': 'GCC', 'version': '4.9.2'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True} diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015.05.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015.05.eb index 5ca1dda84e..6bb38e7647 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015.05.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015.05.eb @@ -2,7 +2,8 @@ name = 'Python' version = '2.7.9' homepage = 'https://python.org/' -description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" toolchain = {'name': 'foss', 'version': '2015.05'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True} diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a-bare.eb index e9063410df..a0543f97f8 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a-bare.eb @@ -3,7 +3,8 @@ version = '2.7.9' versionsuffix = '-bare' homepage = 'http://python.org/' -description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" toolchain = {'name': 'foss', 'version': '2015a'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True} diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a.eb index b636f6b2ef..04c7ab534f 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a.eb @@ -2,7 +2,8 @@ name = 'Python' version = '2.7.9' homepage = 'http://python.org/' -description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" toolchain = {'name': 'foss', 'version': '2015a'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True} diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015b.eb index 82282d02d9..47705d9de9 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015b.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015b.eb @@ -2,7 +2,8 @@ name = 'Python' version = '2.7.9' homepage = 'http://python.org/' -description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" toolchain = {'name': 'foss', 'version': '2015b'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True} diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-gompi-1.5.16-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-gompi-1.5.16-bare.eb index c78274679f..e7e8e929a0 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-gompi-1.5.16-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-gompi-1.5.16-bare.eb @@ -3,7 +3,8 @@ version = '2.7.9' versionsuffix = '-bare' homepage = 'http://python.org/' -description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" toolchain = {'name': 'gompi', 'version': '1.5.16'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True} diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.14.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.14.eb index 987f0852f6..568e58c6d4 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.14.eb @@ -2,7 +2,8 @@ name = 'Python' version = '2.7.9' homepage = 'http://python.org/' -description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" toolchain = {'name': 'goolf', 'version': '1.5.14'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True} diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.16.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.16.eb index 37abf12093..3e3d722c5f 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.16.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.16.eb @@ -2,7 +2,8 @@ name = 'Python' version = '2.7.9' homepage = 'http://python.org/' -description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" toolchain = {'name': 'goolf', 'version': '1.5.16'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True} diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.7.20.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.7.20.eb index b91c6a4a7d..39c33c3855 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.7.20.eb @@ -2,7 +2,8 @@ name = 'Python' version = '2.7.9' homepage = 'https://python.org/' -description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" toolchain = {'name': 'goolf', 'version': '1.7.20'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True} diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a-bare.eb index c672a429fd..0a241766ab 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a-bare.eb @@ -3,7 +3,8 @@ version = '2.7.9' versionsuffix = '-bare' homepage = 'http://python.org/' -description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" toolchain = {'name': 'intel', 'version': '2015a'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True} diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb index 24081c5cf8..bb506a20b0 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb @@ -2,7 +2,8 @@ name = 'Python' version = '2.7.9' homepage = 'http://python.org/' -description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" toolchain = {'name': 'intel', 'version': '2015a'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True} diff --git a/easybuild/easyconfigs/p/Python/Python-3.2.3-goolf-1.4.10.eb b/easybuild/easyconfigs/p/Python/Python-3.2.3-goolf-1.4.10.eb index fc5033662d..e164d75eb8 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.2.3-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.2.3-goolf-1.4.10.eb @@ -2,7 +2,8 @@ name = 'Python' version = '3.2.3' homepage = 'http://python.org/' -description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True} diff --git a/easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-5.3.0.eb b/easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-5.3.0.eb index 1fe945390a..7fc679ddfb 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-5.3.0.eb @@ -2,7 +2,8 @@ name = 'Python' version = '3.2.3' homepage = 'http://python.org/' -description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True} diff --git a/easybuild/easyconfigs/p/Python/Python-3.3.2-goolf-1.4.10.eb b/easybuild/easyconfigs/p/Python/Python-3.3.2-goolf-1.4.10.eb index 0dc65b97ca..5b5ea68742 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.3.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.3.2-goolf-1.4.10.eb @@ -2,7 +2,8 @@ name = 'Python' version = '3.3.2' homepage = 'http://python.org/' -description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True} diff --git a/easybuild/easyconfigs/p/Python/Python-3.3.2-ictce-5.3.0.eb b/easybuild/easyconfigs/p/Python/Python-3.3.2-ictce-5.3.0.eb index 97e6c04ce7..8ba5022eb1 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.3.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.3.2-ictce-5.3.0.eb @@ -2,7 +2,8 @@ name = 'Python' version = '3.3.2' homepage = 'http://python.org/' -description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True} diff --git a/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2014b.eb b/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2014b.eb index ba9c2f40b2..948d875463 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2014b.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2014b.eb @@ -2,7 +2,8 @@ name = 'Python' version = '3.4.1' homepage = 'http://python.org/' -description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" toolchain = {'name': 'intel', 'version': '2014b'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True} diff --git a/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2015a.eb index 910cb21e5c..db1c3e7576 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2015a.eb @@ -2,7 +2,8 @@ name = 'Python' version = '3.4.1' homepage = 'http://python.org/' -description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" toolchain = {'name': 'intel', 'version': '2015a'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True} diff --git a/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb index 8f08cf73e4..3ff51e790b 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb @@ -2,7 +2,8 @@ name = 'Python' version = '3.4.3' homepage = 'http://python.org/' -description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" toolchain = {'name': 'intel', 'version': '2015a'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True} diff --git a/easybuild/easyconfigs/p/Python/Python-3.5.0-intel-2015b.eb b/easybuild/easyconfigs/p/Python/Python-3.5.0-intel-2015b.eb index 825c8e6b10..f46cf60244 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.5.0-intel-2015b.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.5.0-intel-2015b.eb @@ -2,7 +2,8 @@ name = 'Python' version = '3.5.0' homepage = 'http://python.org/' -description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" toolchain = {'name': 'intel', 'version': '2015b'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True} diff --git a/easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2015a.eb b/easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2015a.eb index 68a366030d..a4f85640e5 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2015a.eb @@ -2,7 +2,8 @@ name = 'Python' version = '3.5.1' homepage = 'http://python.org/' -description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" toolchain = {'name': 'foss', 'version': '2015a'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True} diff --git a/easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2016a.eb b/easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2016a.eb index edc992932d..8d085679d5 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2016a.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2016a.eb @@ -2,7 +2,8 @@ name = 'Python' version = '3.5.1' homepage = 'http://python.org/' -description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" toolchain = {'name': 'foss', 'version': '2016a'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True} diff --git a/easybuild/easyconfigs/p/Python/Python-3.5.1-intel-2016a.eb b/easybuild/easyconfigs/p/Python/Python-3.5.1-intel-2016a.eb index 395e40515b..8187598200 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.5.1-intel-2016a.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.5.1-intel-2016a.eb @@ -2,7 +2,8 @@ name = 'Python' version = '3.5.1' homepage = 'http://python.org/' -description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" toolchain = {'name': 'intel', 'version': '2016a'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True} diff --git a/easybuild/easyconfigs/p/pyGIMLi/pyGIMLi-20160803-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/pyGIMLi/pyGIMLi-20160803-foss-2016a-Python-2.7.11.eb index 098af10b8c..3e9cb1c1a3 100644 --- a/easybuild/easyconfigs/p/pyGIMLi/pyGIMLi-20160803-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/pyGIMLi/pyGIMLi-20160803-foss-2016a-Python-2.7.11.eb @@ -58,7 +58,7 @@ installopts += '&& cp ../easybuild_obj/bin/* %(installdir)s/bin' sanity_check_paths = { 'files': ['bin/%s' % x for x in ['bms2vtk', 'dc1dinv', 'dc1dsmooth', 'fdem1dinv', 'fdem1dsmooth', 'harmfit', 'invlinearmat', 'mrs1dblock', 'mrs1dsmooth', - 'mt1dinv', 'mt1dsmooth', 'polyfit', 'ttinv', 'ttmod']]+ + 'mt1dinv', 'mt1dsmooth', 'polyfit', 'ttinv', 'ttmod']] + ['lib/libgimli.%s' % SHLIB_EXT, 'lib/python%(pyshortver)s/site-packages/pygimli.h'], 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'], } diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.4.0-foss-2016b-hybrid.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.4.0-foss-2016b-hybrid.eb index 09b026a284..f15e4b6ae5 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.4.0-foss-2016b-hybrid.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.4.0-foss-2016b-hybrid.eb @@ -21,11 +21,11 @@ sources = [ 'neb-%(version)s.tar.gz', 'PHonon-%(version)s.tar.gz', 'pwcond-%(version)s.tar.gz', - 'xspectra-%(version)s.tar.gz' , - 'PWgui-%(version)s.tar.gz' , - 'EPW-%(version)s.tar.gz' , - 'test-suite-%(version)s.tar.gz' , - 'GWW-%(version)s.tar.gz' , + 'xspectra-%(version)s.tar.gz', + 'PWgui-%(version)s.tar.gz', + 'EPW-%(version)s.tar.gz', + 'test-suite-%(version)s.tar.gz', + 'GWW-%(version)s.tar.gz', ] source_urls = [ 'http://files.qe-forge.org/index.php?file=', # Almost all @@ -55,4 +55,3 @@ buildopts = 'all tddfpt neb xspectra ph ' parallel = 1 moduleclass = 'chem' - -- GitLab From 09eafdcf59c57495cab20f9adf6d8205bc256d6d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 23 Feb 2017 09:52:52 +0100 Subject: [PATCH 0150/1603] fix more minor style issues in Python easyconfigs --- .../p/Python/Python-2.7.10-GCC-4.9.3-2.25-bare.eb | 5 +++-- .../p/Python/Python-2.7.10-GNU-4.9.3-2.25-bare.eb | 5 +++-- easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2015a.eb | 5 +++-- .../p/Python/Python-2.7.9-CrayGNU-2015.06-bare.eb | 5 +++-- .../p/Python/Python-2.7.9-CrayGNU-2015.11-bare.eb | 5 +++-- .../easyconfigs/p/Python/Python-2.7.9-GCC-4.9.2-bare.eb | 5 +++-- .../easyconfigs/p/Python/Python-2.7.9-foss-2015.05.eb | 5 +++-- .../easyconfigs/p/Python/Python-2.7.9-foss-2015a-bare.eb | 5 +++-- easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a.eb | 5 +++-- easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015b.eb | 5 +++-- .../easyconfigs/p/Python/Python-2.7.9-gompi-1.5.16-bare.eb | 5 +++-- .../easyconfigs/p/Python/Python-2.7.9-goolf-1.5.14.eb | 5 +++-- .../easyconfigs/p/Python/Python-2.7.9-goolf-1.5.16.eb | 5 +++-- .../easyconfigs/p/Python/Python-2.7.9-intel-2015a-bare.eb | 5 +++-- easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb | 5 +++-- easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb | 5 +++-- easybuild/easyconfigs/p/Python/Python-3.5.0-intel-2015b.eb | 5 +++-- easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2015a.eb | 5 +++-- easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2016a.eb | 7 ++++--- easybuild/easyconfigs/p/Python/Python-3.5.1-intel-2016a.eb | 7 ++++--- 20 files changed, 62 insertions(+), 42 deletions(-) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.10-GCC-4.9.3-2.25-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.10-GCC-4.9.3-2.25-bare.eb index edaa0f4fa5..492d137f68 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.10-GCC-4.9.3-2.25-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.10-GCC-4.9.3-2.25-bare.eb @@ -20,8 +20,9 @@ dependencies = [ ('ncurses', '6.0', '', ('GCCcore', '4.9.3')), ('SQLite', '3.8.10.2'), ('Tk', '8.6.4', '-no-X11'), # this requires a full X11 stack - # ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's - # nice to have an up to date openssl for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1k'), ] osdependencies = [('openssl-devel', 'libssl-dev')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.10-GNU-4.9.3-2.25-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.10-GNU-4.9.3-2.25-bare.eb index ac622805c5..02428a8c5e 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.10-GNU-4.9.3-2.25-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.10-GNU-4.9.3-2.25-bare.eb @@ -20,8 +20,9 @@ dependencies = [ ('ncurses', '5.9'), ('SQLite', '3.8.10.2'), ('Tk', '8.6.4', '-no-X11'), # this requires a full X11 stack - # ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's - # nice to have an up to date openssl for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1k'), ] osdependencies = [('openssl-devel', 'libssl-dev')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2015a.eb index c914576c6c..a19c3193df 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2015a.eb @@ -23,8 +23,9 @@ dependencies = [ ('zlib', '1.2.8'), ('libreadline', '6.3'), ('ncurses', '5.9'), - # ('OpenSSL', '1.0.1g'), # OS dependency should be preferred if the os version is more recent then this version, it's - # nice to have an up to date openssl for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1g'), ] # order is important! diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.06-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.06-bare.eb index ceb75f485b..b60dac8832 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.06-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.06-bare.eb @@ -18,8 +18,9 @@ dependencies = [ ('zlib', '1.2.8'), ('libreadline', '6.3'), ('ncurses', '5.9'), -# ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's -# nice to have an up to date openssl for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1k'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel'), 'tk-devel'] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.11-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.11-bare.eb index 46d5881734..8249b3b9b9 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.11-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.11-bare.eb @@ -18,8 +18,9 @@ dependencies = [ ('zlib', '1.2.8'), ('libreadline', '6.3'), ('ncurses', '5.9'), -# ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's -# nice to have an up to date openssl for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1k'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel'), 'tk-devel'] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-GCC-4.9.2-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-GCC-4.9.2-bare.eb index bfaa856129..4492ecb9d7 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-GCC-4.9.2-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-GCC-4.9.2-bare.eb @@ -20,8 +20,9 @@ dependencies = [ ('ncurses', '5.9'), ('SQLite', '3.8.8.1'), ('Tk', '8.6.3', '-no-X11'), # this requires a full X11 stack - # ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's - # nice to have an up to date openssl for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1k'), ] osdependencies = [('openssl-devel', 'libssl-dev')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015.05.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015.05.eb index 6bb38e7647..0e5c8bdaf5 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015.05.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015.05.eb @@ -22,8 +22,9 @@ dependencies = [ ('ncurses', '5.9'), ('SQLite', '3.8.8.1'), ('Tk', '8.6.3', '-no-X11'), # this requires a full X11 stack - # ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's - # nice to have an up to date openssl for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1k'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a-bare.eb index a0543f97f8..ed68c4c304 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a-bare.eb @@ -20,8 +20,9 @@ dependencies = [ ('ncurses', '5.9'), ('SQLite', '3.8.8.1'), ('Tk', '8.6.3', '-no-X11'), # this requires a full X11 stack - # ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's - # nice to have an up to date openssl for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1k'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a.eb index 04c7ab534f..50b5d85a22 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a.eb @@ -22,8 +22,9 @@ dependencies = [ ('ncurses', '5.9'), ('SQLite', '3.8.8.1'), ('Tk', '8.6.3', '-no-X11'), # this requires a full X11 stack - # ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's - # nice to have an up to date openssl for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1k'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015b.eb index 47705d9de9..954cb1d6c9 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015b.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015b.eb @@ -22,8 +22,9 @@ dependencies = [ ('ncurses', '5.9'), ('SQLite', '3.8.8.1'), ('Tk', '8.6.3', '-no-X11'), # this requires a full X11 stack -# ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's -# nice to have an up to date openssl for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1k'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-gompi-1.5.16-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-gompi-1.5.16-bare.eb index e7e8e929a0..1ef84a7f5f 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-gompi-1.5.16-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-gompi-1.5.16-bare.eb @@ -19,8 +19,9 @@ dependencies = [ ('ncurses', '5.9'), ('SQLite', '3.8.8.1'), ('Tk', '8.6.3', '-no-X11'), # this requires a full X11 stack - # ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's - # nice to have an up to date openssl for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1k'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.14.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.14.eb index 568e58c6d4..2117038315 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.14.eb @@ -22,8 +22,9 @@ dependencies = [ ('ncurses', '5.9'), ('SQLite', '3.8.8.1'), ('Tk', '8.6.3', '-no-X11'), # this requires a full X11 stack - # ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's - # nice to have an up to date openssl for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1k'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.16.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.16.eb index 3e3d722c5f..de0245d75a 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.16.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.16.eb @@ -22,8 +22,9 @@ dependencies = [ ('ncurses', '5.9'), ('SQLite', '3.8.8.1'), ('Tk', '8.6.3', '-no-X11'), # this requires a full X11 stack -# ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's - # nice to have an up to date openssl for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1k'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a-bare.eb index 0a241766ab..ca9022ba60 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a-bare.eb @@ -20,8 +20,9 @@ dependencies = [ ('ncurses', '5.9'), ('SQLite', '3.8.8.1'), ('Tk', '8.6.3', '-no-X11'), # this requires a full X11 stack - # ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's - # nice to have an up to date openssl for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1k'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb index bb506a20b0..dfd615f248 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb @@ -22,8 +22,9 @@ dependencies = [ ('ncurses', '5.9'), ('SQLite', '3.8.8.1'), ('Tk', '8.6.3', '-no-X11'), # this requires a full X11 stack - # ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's - # nice to have an up to date openssl for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1k'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb index 3ff51e790b..fa4d5db712 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb @@ -20,8 +20,9 @@ dependencies = [ ('zlib', '1.2.8'), ('libreadline', '6.3'), ('ncurses', '5.9'), - # ('OpenSSL', '1.0.1m'), # OS dependency should be preferred if the os version is more recent then this version, it's - # nice to have an up to date openssl for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1m'), ] osdependencies = [('openssl-devel', 'libssl-dev')] diff --git a/easybuild/easyconfigs/p/Python/Python-3.5.0-intel-2015b.eb b/easybuild/easyconfigs/p/Python/Python-3.5.0-intel-2015b.eb index f46cf60244..7f32b2fbd5 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.5.0-intel-2015b.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.5.0-intel-2015b.eb @@ -23,8 +23,9 @@ dependencies = [ ('SQLite', '3.9.2'), ('Tk', '8.6.4', '-no-X11'), # this requires a full X11 stack ('GMP', '6.1.0'), - # ('OpenSSL', '1.0.1p'), # OS dependency should be preferred if the os version is more recent then this version, it's - # nice to have an up to date openssl for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1p'), ] osdependencies = [('openssl-devel', 'libssl-dev')] diff --git a/easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2015a.eb b/easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2015a.eb index a4f85640e5..34b680443b 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2015a.eb @@ -24,8 +24,9 @@ dependencies = [ ('Tk', '8.6.4', '-no-X11'), # this requires a full X11 stack ('GMP', '6.1.0'), ('XZ', '5.2.2'), -# ('OpenSSL', '1.0.1q'), # OS dependency should be preferred if the os version is more recent then this version, it's -# nice to have an up to date openssl for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1q'), ] osdependencies = [('openssl-devel', 'libssl-dev')] diff --git a/easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2016a.eb b/easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2016a.eb index 8d085679d5..f17ad6e258 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2016a.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2016a.eb @@ -24,8 +24,9 @@ dependencies = [ ('Tk', '8.6.4', '-no-X11'), # this requires a full X11 stack ('GMP', '6.1.0'), ('XZ', '5.2.2'), -# ('OpenSSL', '1.0.1q'), # OS dependency should be preferred if the os version is more recent then this version, it's -# nice to have an up to date openssl for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1q'), ] osdependencies = [('openssl-devel', 'libssl-dev')] @@ -99,7 +100,7 @@ exts_list = [ }), ('paramiko', '1.16.0', { 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], - }), + }), ('pyparsing', '2.1.0', { 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], }), diff --git a/easybuild/easyconfigs/p/Python/Python-3.5.1-intel-2016a.eb b/easybuild/easyconfigs/p/Python/Python-3.5.1-intel-2016a.eb index 8187598200..bba87219ba 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.5.1-intel-2016a.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.5.1-intel-2016a.eb @@ -24,8 +24,9 @@ dependencies = [ ('Tk', '8.6.4', '-no-X11'), # this requires a full X11 stack ('GMP', '6.1.0'), ('XZ', '5.2.2'), -# ('OpenSSL', '1.0.1q'), # OS dependency should be preferred if the os version is more recent then this version, it's -# nice to have an up to date openssl for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1q'), ] osdependencies = [('openssl-devel', 'libssl-dev')] @@ -103,7 +104,7 @@ exts_list = [ }), ('paramiko', '1.16.0', { 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], - }), + }), ('pyparsing', '2.1.0', { 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], }), -- GitLab From a87550736263fa0a6f625be0b4dae3f18f9c018c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 23 Feb 2017 11:03:18 +0100 Subject: [PATCH 0151/1603] add sanity check command to Yade easyconfig to make sure that 'import yade' works, include bzip2 as dep --- .../y/Yade/Yade-2017.01a-intel-2016b-Python-2.7.12.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/y/Yade/Yade-2017.01a-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/y/Yade/Yade-2017.01a-intel-2016b-Python-2.7.12.eb index 5f79b0294c..e82ea4a1ae 100644 --- a/easybuild/easyconfigs/y/Yade/Yade-2017.01a-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/y/Yade/Yade-2017.01a-intel-2016b-Python-2.7.12.eb @@ -32,6 +32,7 @@ dependencies = [ ('SQLite', '3.13.0'), ('VTK', '7.1.0', versionsuffix), ('zlib', '1.2.8'), + ('bzip2', '1.0.6'), ] builddependencies = [ @@ -58,4 +59,6 @@ sanity_check_paths = { 'dirs': [('lib/x86_64-linux-gnu/yade-%(version)s/py/yade', 'lib64/yade-%(version)s/py/yade')], } +sanity_check_commands = ["python -c 'import yade'"] + moduleclass = 'devel' -- GitLab From e1923aef1159c638469a084388ff46a67801f6ef Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 23 Feb 2017 11:06:43 +0100 Subject: [PATCH 0152/1603] add sanity check command to Yade easyconfig to make sure that 'import yade' works, include bzip2 as dep --- .../easyconfigs/y/Yade/Yade-1.20.0-foss-2016a-Python-2.7.11.eb | 3 +++ .../y/Yade/Yade-1.20.0-intel-2016a-Python-2.7.11.eb | 3 +++ .../y/Yade/Yade-2016.06a-foss-2016b-Python-2.7.12.eb | 3 +++ .../y/Yade/Yade-2016.06a-intel-2016b-Python-2.7.12.eb | 3 +++ 4 files changed, 12 insertions(+) diff --git a/easybuild/easyconfigs/y/Yade/Yade-1.20.0-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/y/Yade/Yade-1.20.0-foss-2016a-Python-2.7.11.eb index a6e0dada54..eeebc684bc 100644 --- a/easybuild/easyconfigs/y/Yade/Yade-1.20.0-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/y/Yade/Yade-1.20.0-foss-2016a-Python-2.7.11.eb @@ -34,6 +34,7 @@ dependencies = [ ('SQLite', '3.9.2'), ('VTK', '6.3.0', versionsuffix), ('zlib', '1.2.8'), + ('bzip2', '1.0.6'), ] builddependencies = [('CMake', '3.5.2')] @@ -57,4 +58,6 @@ sanity_check_paths = { 'dirs': [('lib/x86_64-linux-gnu/yade-%(version)s/py/yade', 'lib64/yade-%(version)s/py/yade')], } +sanity_check_commands = ["python -c 'import yade'"] + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/y/Yade/Yade-1.20.0-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/y/Yade/Yade-1.20.0-intel-2016a-Python-2.7.11.eb index 4d7005749a..4610fe64fd 100644 --- a/easybuild/easyconfigs/y/Yade/Yade-1.20.0-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/y/Yade/Yade-1.20.0-intel-2016a-Python-2.7.11.eb @@ -34,6 +34,7 @@ dependencies = [ ('SQLite', '3.9.2'), ('VTK', '6.3.0', versionsuffix), ('zlib', '1.2.8'), + ('bzip2', '1.0.6'), ] builddependencies = [('CMake', '3.5.2')] @@ -57,4 +58,6 @@ sanity_check_paths = { 'dirs': [('lib/x86_64-linux-gnu/yade-%(version)s/py/yade', 'lib64/yade-%(version)s/py/yade')], } +sanity_check_commands = ["python -c 'import yade'"] + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/y/Yade/Yade-2016.06a-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/y/Yade/Yade-2016.06a-foss-2016b-Python-2.7.12.eb index 541a3b67c8..64230623c1 100644 --- a/easybuild/easyconfigs/y/Yade/Yade-2016.06a-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/y/Yade/Yade-2016.06a-foss-2016b-Python-2.7.12.eb @@ -34,6 +34,7 @@ dependencies = [ ('SQLite', '3.13.0'), ('VTK', '6.3.0', versionsuffix), ('zlib', '1.2.8'), + ('bzip2', '1.0.6'), ] builddependencies = [ @@ -60,4 +61,6 @@ sanity_check_paths = { 'dirs': [('lib/x86_64-linux-gnu/yade-%(version)s/py/yade', 'lib64/yade-%(version)s/py/yade')], } +sanity_check_commands = ["python -c 'import yade'"] + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/y/Yade/Yade-2016.06a-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/y/Yade/Yade-2016.06a-intel-2016b-Python-2.7.12.eb index 1c86ea984c..5623f2e81c 100644 --- a/easybuild/easyconfigs/y/Yade/Yade-2016.06a-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/y/Yade/Yade-2016.06a-intel-2016b-Python-2.7.12.eb @@ -33,6 +33,7 @@ dependencies = [ ('SQLite', '3.13.0'), ('VTK', '6.3.0', versionsuffix), ('zlib', '1.2.8'), + ('bzip2', '1.0.6'), ] builddependencies = [ @@ -59,4 +60,6 @@ sanity_check_paths = { 'dirs': [('lib/x86_64-linux-gnu/yade-%(version)s/py/yade', 'lib64/yade-%(version)s/py/yade')], } +sanity_check_commands = ["python -c 'import yade'"] + moduleclass = 'devel' -- GitLab From 00c1bb2312d09860ab51e112128e7193bc8a4c38 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 23 Feb 2017 11:33:55 +0100 Subject: [PATCH 0153/1603] add patch for Boost v1.61-1.63 to fix problem with make_array/array_wrapper in boost serialization library --- .../Boost-1.61.0-intel-2016a-Python-2.7.11.eb | 2 ++ .../b/Boost/Boost-1.61.0-intel-2016a.eb | 2 ++ .../Boost-1.61.0-intel-2016b-Python-2.7.12.eb | 2 ++ .../b/Boost/Boost-1.61.0-intel-2016b.eb | 2 ++ .../b/Boost/Boost-1.61_fix-make_array-icpc.patch | 14 ++++++++++++++ .../Boost-1.62.0-intel-2016b-Python-2.7.12.eb | 2 ++ .../Boost-1.63.0-intel-2016b-Python-2.7.12.eb | 2 ++ 7 files changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.61_fix-make_array-icpc.patch diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.61.0-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/b/Boost/Boost-1.61.0-intel-2016a-Python-2.7.11.eb index 822d74b107..0ac767fef8 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.61.0-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.61.0-intel-2016a-Python-2.7.11.eb @@ -11,6 +11,8 @@ toolchainopts = {'pic': True, 'usempi': True} source_urls = [SOURCEFORGE_SOURCE] sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] +patches = ['Boost-1.61_fix-make_array-icpc.patch'] + dependencies = [ ('bzip2', '1.0.6'), ('zlib', '1.2.8'), diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.61.0-intel-2016a.eb b/easybuild/easyconfigs/b/Boost/Boost-1.61.0-intel-2016a.eb index 7840698ed4..526e2b54e1 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.61.0-intel-2016a.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.61.0-intel-2016a.eb @@ -10,6 +10,8 @@ toolchainopts = {'pic': True, 'usempi': True} source_urls = [SOURCEFORGE_SOURCE] sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] +patches = ['Boost-1.61_fix-make_array-icpc.patch'] + dependencies = [ ('bzip2', '1.0.6'), ('zlib', '1.2.8'), diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.61.0-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/b/Boost/Boost-1.61.0-intel-2016b-Python-2.7.12.eb index 015aad2716..918d0a5af6 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.61.0-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.61.0-intel-2016b-Python-2.7.12.eb @@ -11,6 +11,8 @@ toolchainopts = {'pic': True, 'usempi': True} source_urls = [SOURCEFORGE_SOURCE] sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] +patches = ['Boost-1.61_fix-make_array-icpc.patch'] + dependencies = [ ('bzip2', '1.0.6'), ('zlib', '1.2.8'), diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.61.0-intel-2016b.eb b/easybuild/easyconfigs/b/Boost/Boost-1.61.0-intel-2016b.eb index 67f6199614..d76c8ae2bc 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.61.0-intel-2016b.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.61.0-intel-2016b.eb @@ -10,6 +10,8 @@ toolchainopts = {'pic': True, 'usempi': True} source_urls = [SOURCEFORGE_SOURCE] sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] +patches = ['Boost-1.61_fix-make_array-icpc.patch'] + dependencies = [ ('bzip2', '1.0.6'), ('zlib', '1.2.8'), diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.61_fix-make_array-icpc.patch b/easybuild/easyconfigs/b/Boost/Boost-1.61_fix-make_array-icpc.patch new file mode 100644 index 0000000000..f7ffa6aa0d --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.61_fix-make_array-icpc.patch @@ -0,0 +1,14 @@ +fix bug with make_array/array_wrapper introduced in Boost v1.61; cfr.: +* https://svn.boost.org/trac/boost/ticket/12516 +* https://github.com/boostorg/serialization/pull/46 (source of this patch) +--- boost_1_63_0/boost/serialization/array.hpp.orig 2017-02-23 10:38:00.487842679 +0100 ++++ boost_1_63_0/boost/serialization/array.hpp 2017-02-23 10:38:13.918969000 +0100 +@@ -44,7 +44,7 @@ + // note: I would like to make the copy constructor private but this breaks + // make_array. So I try to make make_array a friend - but that doesn't + // build. Need a C++ guru to explain this! +- template ++ template + friend const boost::serialization::array_wrapper make_array( T* t, S s); + + array_wrapper(const array_wrapper & rhs) : diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.62.0-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/b/Boost/Boost-1.62.0-intel-2016b-Python-2.7.12.eb index 8f21675328..f0e124ea49 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.62.0-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.62.0-intel-2016b-Python-2.7.12.eb @@ -11,6 +11,8 @@ toolchainopts = {'pic': True, 'usempi': True} source_urls = [SOURCEFORGE_SOURCE] sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] +patches = ['Boost-1.61_fix-make_array-icpc.patch'] + dependencies = [ ('bzip2', '1.0.6'), ('zlib', '1.2.8'), diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.63.0-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/b/Boost/Boost-1.63.0-intel-2016b-Python-2.7.12.eb index b110a50dba..faed7a8d9c 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.63.0-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.63.0-intel-2016b-Python-2.7.12.eb @@ -11,6 +11,8 @@ toolchainopts = {'usempi': True, 'pic': True} sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] source_urls = ['https://sourceforge.net/projects/%(namelower)s/files/%(namelower)s/%(version)s'] +patches = ['Boost-1.61_fix-make_array-icpc.patch'] + dependencies = [ ('bzip2', '1.0.6'), ('zlib', '1.2.8'), -- GitLab From 71e87c695ad1339b3080fed65744883cd89a37c7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 23 Feb 2017 11:57:19 +0100 Subject: [PATCH 0154/1603] trim spaces --- easybuild/easyconfigs/i/I-TASSER/I-TASSER-4.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/i/I-TASSER/I-TASSER-4.0.eb b/easybuild/easyconfigs/i/I-TASSER/I-TASSER-4.0.eb index 52f0e797fd..56a8573d69 100644 --- a/easybuild/easyconfigs/i/I-TASSER/I-TASSER-4.0.eb +++ b/easybuild/easyconfigs/i/I-TASSER/I-TASSER-4.0.eb @@ -25,6 +25,6 @@ sanity_check_paths = { # You may find it desirable to put this variable in the module file. # The command to do so has been put here (commented out) as a convenience. -# modextravars = { 'IMINTASSERDB' : '/path/to/databases/I-TASSER/%(version)s' } +# modextravars = {'IMINTASSERDB': '/path/to/databases/I-TASSER/%(version)s'} moduleclass = 'bio' -- GitLab From 5e3d994a87ba141c104fef69e57673d596fd18fb Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Thu, 23 Feb 2017 17:19:38 +0100 Subject: [PATCH 0155/1603] Set CMAKE_PREFIX_PATH to ncurses install directory Include ccmake in sanity check --- easybuild/easyconfigs/c/CMake/CMake-3.4.1-GCCcore-4.9.3.eb | 4 ++-- easybuild/easyconfigs/c/CMake/CMake-3.4.1-foss-2016a.eb | 4 ++-- .../easyconfigs/c/CMake/CMake-3.4.1-intel-2016.02-GCC-4.9.eb | 4 ++-- easybuild/easyconfigs/c/CMake/CMake-3.4.1-intel-2016a.eb | 4 ++-- easybuild/easyconfigs/c/CMake/CMake-3.4.1-iomkl-2016.07.eb | 4 ++-- .../c/CMake/CMake-3.4.1-iomkl-2016.09-GCC-4.9.3-2.25.eb | 4 ++-- easybuild/easyconfigs/c/CMake/CMake-3.4.3-foss-2016a.eb | 4 ++-- easybuild/easyconfigs/c/CMake/CMake-3.4.3-foss-2016b.eb | 4 ++-- easybuild/easyconfigs/c/CMake/CMake-3.4.3-intel-2016a.eb | 4 ++-- easybuild/easyconfigs/c/CMake/CMake-3.5.0-CrayGNU-2016.03.eb | 4 +++- easybuild/easyconfigs/c/CMake/CMake-3.5.1-intel-2016a.eb | 4 ++-- easybuild/easyconfigs/c/CMake/CMake-3.5.2-GCC-4.9.3-2.25.eb | 4 ++-- easybuild/easyconfigs/c/CMake/CMake-3.5.2-foss-2016a.eb | 4 ++-- easybuild/easyconfigs/c/CMake/CMake-3.5.2-foss-2016b.eb | 4 ++-- easybuild/easyconfigs/c/CMake/CMake-3.5.2-intel-2016a.eb | 4 ++-- easybuild/easyconfigs/c/CMake/CMake-3.5.2-intel-2016b.eb | 4 ++-- easybuild/easyconfigs/c/CMake/CMake-3.6.1-GCC-5.4.0-2.26.eb | 4 ++-- easybuild/easyconfigs/c/CMake/CMake-3.6.1-GCCcore-4.9.3.eb | 4 ++-- easybuild/easyconfigs/c/CMake/CMake-3.6.1-foss-2016b.eb | 4 ++-- easybuild/easyconfigs/c/CMake/CMake-3.6.1-intel-2016b.eb | 4 ++-- easybuild/easyconfigs/c/CMake/CMake-3.6.2-GCCcore-5.4.0.eb | 4 ++-- easybuild/easyconfigs/c/CMake/CMake-3.6.2-foss-2016b.eb | 4 ++-- easybuild/easyconfigs/c/CMake/CMake-3.6.2-intel-2016b.eb | 4 ++-- easybuild/easyconfigs/c/CMake/CMake-3.7.1-GCCcore-5.4.0.eb | 4 ++-- easybuild/easyconfigs/c/CMake/CMake-3.7.1-GCCcore-6.2.0.eb | 4 ++-- easybuild/easyconfigs/c/CMake/CMake-3.7.1-foss-2016b.eb | 4 ++-- easybuild/easyconfigs/c/CMake/CMake-3.7.1-intel-2016b.eb | 4 ++-- easybuild/easyconfigs/c/CMake/CMake-3.7.2-intel-2016b.eb | 4 ++-- 28 files changed, 57 insertions(+), 55 deletions(-) diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.4.1-GCCcore-4.9.3.eb b/easybuild/easyconfigs/c/CMake/CMake-3.4.1-GCCcore-4.9.3.eb index 1a599467bd..3b95ac0d58 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.4.1-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.4.1-GCCcore-4.9.3.eb @@ -14,7 +14,7 @@ sources = [SOURCELOWER_TAR_GZ] builddependencies = [('binutils', '2.25')] -configopts = '-- -DCMAKE_USE_OPENSSL=1' +configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' dependencies = [ ('ncurses', '6.0'), @@ -26,7 +26,7 @@ dependencies = [ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] sanity_check_paths = { - 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], 'dirs': [], } diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.4.1-foss-2016a.eb b/easybuild/easyconfigs/c/CMake/CMake-3.4.1-foss-2016a.eb index 87dc8ebec4..81d2e3eac3 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.4.1-foss-2016a.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.4.1-foss-2016a.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'foss', 'version': '2016a'} source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] -configopts = '-- -DCMAKE_USE_OPENSSL=1' +configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' dependencies = [ ('ncurses', '6.0'), @@ -24,7 +24,7 @@ dependencies = [ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] sanity_check_paths = { - 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], 'dirs': [], } diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.4.1-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/c/CMake/CMake-3.4.1-intel-2016.02-GCC-4.9.eb index df5823de42..7b3c226f7d 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.4.1-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.4.1-intel-2016.02-GCC-4.9.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] -configopts = '-- -DCMAKE_USE_OPENSSL=1' +configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' dependencies = [ ('ncurses', '6.0'), @@ -24,7 +24,7 @@ dependencies = [ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] sanity_check_paths = { - 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'files': ["bin/%s" % x for x in ['ccmake, 'cmake', 'cpack', 'ctest']], 'dirs': [], } diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.4.1-intel-2016a.eb b/easybuild/easyconfigs/c/CMake/CMake-3.4.1-intel-2016a.eb index db841bbaef..4e67d84e5a 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.4.1-intel-2016a.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.4.1-intel-2016a.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'intel', 'version': '2016a'} source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] -configopts = '-- -DCMAKE_USE_OPENSSL=1' +configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' dependencies = [ ('ncurses', '6.0'), @@ -24,7 +24,7 @@ dependencies = [ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] sanity_check_paths = { - 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], 'dirs': [], } diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.4.1-iomkl-2016.07.eb b/easybuild/easyconfigs/c/CMake/CMake-3.4.1-iomkl-2016.07.eb index 0204c038c7..fe4cdb5cff 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.4.1-iomkl-2016.07.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.4.1-iomkl-2016.07.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'iomkl', 'version': '2016.07'} source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] -configopts = '-- -DCMAKE_USE_OPENSSL=1' +configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' dependencies = [ ('ncurses', '6.0'), @@ -24,7 +24,7 @@ dependencies = [ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] sanity_check_paths = { - 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], 'dirs': [], } diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.4.1-iomkl-2016.09-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/c/CMake/CMake-3.4.1-iomkl-2016.09-GCC-4.9.3-2.25.eb index 36a239c230..5737de5e86 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.4.1-iomkl-2016.09-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.4.1-iomkl-2016.09-GCC-4.9.3-2.25.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'iomkl', 'version': '2016.09-GCC-4.9.3-2.25'} source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] -configopts = '-- -DCMAKE_USE_OPENSSL=1' +configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' dependencies = [ ('ncurses', '6.0'), @@ -24,7 +24,7 @@ dependencies = [ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] sanity_check_paths = { - 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], 'dirs': [], } diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.4.3-foss-2016a.eb b/easybuild/easyconfigs/c/CMake/CMake-3.4.3-foss-2016a.eb index e6beb92bee..6714702dbc 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.4.3-foss-2016a.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.4.3-foss-2016a.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'foss', 'version': '2016a'} source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] -configopts = '-- -DCMAKE_USE_OPENSSL=1' +configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' dependencies = [ ('ncurses', '6.0'), @@ -24,7 +24,7 @@ dependencies = [ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] sanity_check_paths = { - 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], 'dirs': [], } diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.4.3-foss-2016b.eb b/easybuild/easyconfigs/c/CMake/CMake-3.4.3-foss-2016b.eb index cfb29da8c6..a7d7d549c8 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.4.3-foss-2016b.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.4.3-foss-2016b.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'foss', 'version': '2016b'} source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] -configopts = '-- -DCMAKE_USE_OPENSSL=1' +configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' dependencies = [ ('ncurses', '6.0'), @@ -24,7 +24,7 @@ dependencies = [ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] sanity_check_paths = { - 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], 'dirs': [], } diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.4.3-intel-2016a.eb b/easybuild/easyconfigs/c/CMake/CMake-3.4.3-intel-2016a.eb index 31b70f1b8a..de56aab05c 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.4.3-intel-2016a.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.4.3-intel-2016a.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'intel', 'version': '2016a'} source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] -configopts = '-- -DCMAKE_USE_OPENSSL=1' +configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' dependencies = [ ('ncurses', '6.0'), @@ -24,7 +24,7 @@ dependencies = [ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] sanity_check_paths = { - 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], 'dirs': [], } diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.5.0-CrayGNU-2016.03.eb b/easybuild/easyconfigs/c/CMake/CMake-3.5.0-CrayGNU-2016.03.eb index f9e868c77a..38d4964aee 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.5.0-CrayGNU-2016.03.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.5.0-CrayGNU-2016.03.eb @@ -13,10 +13,12 @@ toolchain = {'name': 'CrayGNU', 'version': '2016.03'} source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] +configopts = '-- -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' + dependencies = [('ncurses', '6.0')] sanity_check_paths = { - 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], 'dirs': [], } diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.5.1-intel-2016a.eb b/easybuild/easyconfigs/c/CMake/CMake-3.5.1-intel-2016a.eb index a70441375c..fe0671660a 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.5.1-intel-2016a.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.5.1-intel-2016a.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'intel', 'version': '2016a'} source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] -configopts = '-- -DCMAKE_USE_OPENSSL=1' +configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' dependencies = [ ('ncurses', '6.0'), @@ -24,7 +24,7 @@ dependencies = [ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] sanity_check_paths = { - 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], 'dirs': [], } diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.5.2-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/c/CMake/CMake-3.5.2-GCC-4.9.3-2.25.eb index 619aaa3ab8..1477d6c586 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.5.2-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.5.2-GCC-4.9.3-2.25.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'GCC', 'version': '4.9.3-2.25'} source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] -configopts = '-- -DCMAKE_USE_OPENSSL=1' +configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' dependencies = [ ('ncurses', '6.0', '', ('GCCcore', '4.9.3')), @@ -24,7 +24,7 @@ dependencies = [ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] sanity_check_paths = { - 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], 'dirs': [], } diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.5.2-foss-2016a.eb b/easybuild/easyconfigs/c/CMake/CMake-3.5.2-foss-2016a.eb index 9075c094fb..3c398a1b9c 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.5.2-foss-2016a.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.5.2-foss-2016a.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'foss', 'version': '2016a'} source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] -configopts = '-- -DCMAKE_USE_OPENSSL=1' +configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' dependencies = [ ('ncurses', '6.0'), @@ -24,7 +24,7 @@ dependencies = [ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] sanity_check_paths = { - 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], 'dirs': [], } diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.5.2-foss-2016b.eb b/easybuild/easyconfigs/c/CMake/CMake-3.5.2-foss-2016b.eb index 42e9b3b3bd..d9e89130f0 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.5.2-foss-2016b.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.5.2-foss-2016b.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'foss', 'version': '2016b'} source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] -configopts = '-- -DCMAKE_USE_OPENSSL=1' +configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' dependencies = [ ('ncurses', '6.0'), @@ -24,7 +24,7 @@ dependencies = [ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] sanity_check_paths = { - 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], 'dirs': [], } diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.5.2-intel-2016a.eb b/easybuild/easyconfigs/c/CMake/CMake-3.5.2-intel-2016a.eb index 6d07f31ebd..be6f338d1f 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.5.2-intel-2016a.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.5.2-intel-2016a.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'intel', 'version': '2016a'} source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] -configopts = '-- -DCMAKE_USE_OPENSSL=1' +configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' dependencies = [ ('ncurses', '6.0'), @@ -24,7 +24,7 @@ dependencies = [ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] sanity_check_paths = { - 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], 'dirs': [], } diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.5.2-intel-2016b.eb b/easybuild/easyconfigs/c/CMake/CMake-3.5.2-intel-2016b.eb index b68274e5b4..24f53c01f5 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.5.2-intel-2016b.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.5.2-intel-2016b.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'intel', 'version': '2016b'} source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] -configopts = '-- -DCMAKE_USE_OPENSSL=1' +configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' dependencies = [ ('ncurses', '6.0'), @@ -24,7 +24,7 @@ dependencies = [ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] sanity_check_paths = { - 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], 'dirs': [], } diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.6.1-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/c/CMake/CMake-3.6.1-GCC-5.4.0-2.26.eb index 97b2282312..d495dc07af 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.6.1-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.6.1-GCC-5.4.0-2.26.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'GCC', 'version': '5.4.0-2.26'} source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] -configopts = '-- -DCMAKE_USE_OPENSSL=1' +configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' dependencies = [ ('ncurses', '6.0'), @@ -24,7 +24,7 @@ dependencies = [ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] sanity_check_paths = { - 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], 'dirs': [], } diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.6.1-GCCcore-4.9.3.eb b/easybuild/easyconfigs/c/CMake/CMake-3.6.1-GCCcore-4.9.3.eb index d5ca429e05..26041d2bbc 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.6.1-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.6.1-GCCcore-4.9.3.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'GCCcore', 'version': '4.9.3'} source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] -configopts = '-- -DCMAKE_USE_OPENSSL=1' +configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' builddependencies = [ ('binutils', '2.25'), @@ -28,7 +28,7 @@ dependencies = [ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] sanity_check_paths = { - 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], 'dirs': [], } diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.6.1-foss-2016b.eb b/easybuild/easyconfigs/c/CMake/CMake-3.6.1-foss-2016b.eb index c1386c78f8..520b0309fd 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.6.1-foss-2016b.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.6.1-foss-2016b.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'foss', 'version': '2016b'} source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] -configopts = '-- -DCMAKE_USE_OPENSSL=1' +configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' dependencies = [ ('ncurses', '6.0'), @@ -24,7 +24,7 @@ dependencies = [ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] sanity_check_paths = { - 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], 'dirs': [], } diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.6.1-intel-2016b.eb b/easybuild/easyconfigs/c/CMake/CMake-3.6.1-intel-2016b.eb index 40d915d152..fff0b921eb 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.6.1-intel-2016b.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.6.1-intel-2016b.eb @@ -14,7 +14,7 @@ sources = [SOURCELOWER_TAR_GZ] patches = ['%(name)s-%(version)s-use-gnu11.patch'] -configopts = '-- -DCMAKE_USE_OPENSSL=1' +configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' dependencies = [ ('ncurses', '6.0'), @@ -26,7 +26,7 @@ dependencies = [ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] sanity_check_paths = { - 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], 'dirs': [], } diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.6.2-GCCcore-5.4.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.6.2-GCCcore-5.4.0.eb index aa63de70da..1933c5b5eb 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.6.2-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.6.2-GCCcore-5.4.0.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'GCCcore', 'version': '5.4.0'} source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] -configopts = '-- -DCMAKE_USE_OPENSSL=1' +configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' builddependencies = [ ('binutils', '2.26'), @@ -29,7 +29,7 @@ dependencies = [ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] sanity_check_paths = { - 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], 'dirs': [], } diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.6.2-foss-2016b.eb b/easybuild/easyconfigs/c/CMake/CMake-3.6.2-foss-2016b.eb index adb0724437..4bce1497a6 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.6.2-foss-2016b.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.6.2-foss-2016b.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'foss', 'version': '2016b'} source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] -configopts = '-- -DCMAKE_USE_OPENSSL=1' +configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' dependencies = [ ('ncurses', '6.0'), @@ -24,7 +24,7 @@ dependencies = [ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] sanity_check_paths = { - 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], 'dirs': [], } diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.6.2-intel-2016b.eb b/easybuild/easyconfigs/c/CMake/CMake-3.6.2-intel-2016b.eb index b6e496837c..48141f4592 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.6.2-intel-2016b.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.6.2-intel-2016b.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'intel', 'version': '2016b'} source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] -configopts = '-- -DCMAKE_USE_OPENSSL=1' +configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' dependencies = [ ('ncurses', '6.0'), @@ -24,7 +24,7 @@ dependencies = [ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] sanity_check_paths = { - 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], 'dirs': [], } diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.7.1-GCCcore-5.4.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.7.1-GCCcore-5.4.0.eb index 5b3221d0bf..f932156e58 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.7.1-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.7.1-GCCcore-5.4.0.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'GCCcore', 'version': '5.4.0'} source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] -configopts = '-- -DCMAKE_USE_OPENSSL=1' +configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' builddependencies = [ ('binutils', '2.26'), @@ -29,7 +29,7 @@ dependencies = [ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] sanity_check_paths = { - 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], 'dirs': [], } diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.7.1-GCCcore-6.2.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.7.1-GCCcore-6.2.0.eb index b364332ea0..6c1810956d 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.7.1-GCCcore-6.2.0.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.7.1-GCCcore-6.2.0.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'GCCcore', 'version': '6.2.0'} source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] -configopts = '-- -DCMAKE_USE_OPENSSL=1' +configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' builddependencies = [ ('binutils', '2.27'), @@ -28,7 +28,7 @@ dependencies = [ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] sanity_check_paths = { - 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], 'dirs': [], } diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.7.1-foss-2016b.eb b/easybuild/easyconfigs/c/CMake/CMake-3.7.1-foss-2016b.eb index e459f784ef..db38350c22 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.7.1-foss-2016b.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.7.1-foss-2016b.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'foss', 'version': '2016b'} source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] -configopts = '-- -DCMAKE_USE_OPENSSL=1' +configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' dependencies = [ ('ncurses', '6.0'), @@ -24,7 +24,7 @@ dependencies = [ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] sanity_check_paths = { - 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], 'dirs': [], } diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.7.1-intel-2016b.eb b/easybuild/easyconfigs/c/CMake/CMake-3.7.1-intel-2016b.eb index 0464c9024d..7b760d0e31 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.7.1-intel-2016b.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.7.1-intel-2016b.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'intel', 'version': '2016b'} source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] -configopts = '-- -DCMAKE_USE_OPENSSL=1' +configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' dependencies = [ ('ncurses', '6.0'), @@ -24,7 +24,7 @@ dependencies = [ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] sanity_check_paths = { - 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], 'dirs': [], } diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.7.2-intel-2016b.eb b/easybuild/easyconfigs/c/CMake/CMake-3.7.2-intel-2016b.eb index 2c33988a54..1dc781b04a 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.7.2-intel-2016b.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.7.2-intel-2016b.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'intel', 'version': '2016b'} source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] -configopts = '-- -DCMAKE_USE_OPENSSL=1' +configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' dependencies = [ ('ncurses', '6.0'), @@ -24,7 +24,7 @@ dependencies = [ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] sanity_check_paths = { - 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], 'dirs': [], } -- GitLab From 1f87bce8231854d3f77defafd5c9b76e51af0cc6 Mon Sep 17 00:00:00 2001 From: Maxime Boissonneault Date: Thu, 23 Feb 2017 16:32:27 +0000 Subject: [PATCH 0156/1603] Added an easyconfig with PETSc 3.7.5 and download options rather than relying on existing modules. --- .../PETSc/PETSc-3.7.5-intel-2016a-download.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/p/PETSc/PETSc-3.7.5-intel-2016a-download.eb diff --git a/easybuild/easyconfigs/p/PETSc/PETSc-3.7.5-intel-2016a-download.eb b/easybuild/easyconfigs/p/PETSc/PETSc-3.7.5-intel-2016a-download.eb new file mode 100644 index 0000000000..a59522d52f --- /dev/null +++ b/easybuild/easyconfigs/p/PETSc/PETSc-3.7.5-intel-2016a-download.eb @@ -0,0 +1,41 @@ +name = 'PETSc' +version = '3.7.5' + +homepage = 'http://www.mcs.anl.gov/petsc' +description = """PETSc, pronounced PET-see (the S is silent), is a suite of data structures and routines for the + scalable (parallel) solution of scientific applications modeled by partial differential equations.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'usempi': True, 'pic': True} + +source_urls = ['http://ftp.mcs.anl.gov/pub/petsc/release-snapshots'] +sources = [SOURCELOWER_TAR_GZ] + +shared_libs = 1 +pic = 1 + +downloadinstall = True + +dependencies = [('HDF5','1.8.18')] + +configopts = "" +# compiles PETSc shared +configopts += "--with-mkl_pardiso=1 --with-mkl_pardiso-dir=$MKLROOT " +configopts += "--with-hdf5=1 --with-hdf5-dir=$EBROOTHDF5" + +# external packages that are downloaded +external_packages = ['mumps', 'ptscotch', 'superlu', 'superlu_dist', 'parmetis', 'metis', 'ml', 'suitesparse', 'hypre', 'prometheus'] +# compiles the external dependencies non-shared +external_packages_shared = "no" +for p in external_packages: + configopts += "--download-%s=yes --download-%s-shared=%s " % (p,p,external_packages_shared) +configopts += "--download-triangle=yes" # download-triangle-shared is not supported + +builddependencies = [('CMake', '3.5.2')] + +moduleclass = 'numlib' + +modluafooter = """ +family("petsc") +""" + -- GitLab From 1eef7612f698db9570682e01fa845c88a92ec513 Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Thu, 23 Feb 2017 19:04:49 +0100 Subject: [PATCH 0157/1603] Fix typo --- .../easyconfigs/c/CMake/CMake-3.4.1-intel-2016.02-GCC-4.9.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.4.1-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/c/CMake/CMake-3.4.1-intel-2016.02-GCC-4.9.eb index 7b3c226f7d..85d36d3bbd 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.4.1-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.4.1-intel-2016.02-GCC-4.9.eb @@ -24,7 +24,7 @@ dependencies = [ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] sanity_check_paths = { - 'files': ["bin/%s" % x for x in ['ccmake, 'cmake', 'cpack', 'ctest']], + 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], 'dirs': [], } -- GitLab From 154ccb596730abc6c47f479ce150f1721e6d4dfb Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 23 Feb 2017 20:37:54 +0100 Subject: [PATCH 0158/1603] remove duplicate bzip2 in Yade easyconfig --- .../easyconfigs/y/Yade/Yade-2016.06a-foss-2016b-Python-2.7.12.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/y/Yade/Yade-2016.06a-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/y/Yade/Yade-2016.06a-foss-2016b-Python-2.7.12.eb index 64230623c1..bfb9412cfc 100644 --- a/easybuild/easyconfigs/y/Yade/Yade-2016.06a-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/y/Yade/Yade-2016.06a-foss-2016b-Python-2.7.12.eb @@ -18,7 +18,6 @@ patches = ['Yade-%(version)s_include-signal.patch'] dependencies = [ ('Boost', '1.61.0', versionsuffix), - ('bzip2', '1.0.6'), ('CGAL', '4.8.1', versionsuffix), ('GDB', '7.11.1', versionsuffix), ('GL2PS', '1.3.9'), -- GitLab From 533f365f73661c4fcf0f53d56118556f94b316e3 Mon Sep 17 00:00:00 2001 From: Toon Verstraelen Date: Fri, 24 Feb 2017 04:32:04 +0100 Subject: [PATCH 0159/1603] Switch to lowopt=True for libxc-2.2.* with intel compilers I've noticed that some functionals in LibXC give significantly different results with too much compiler optimization. For example, the energy of a water molecule computed with the TPSS functional changes by 6.5 kJ/mol with lowopt=False. (The problem is in the TPSS correlation functional, somewhere in mgga_c_pkzb.c. I've ruled out numerical integration issues. Similar relative errors appear on every grid point of the tpss_c energy density.) I can only test with libx-2.2.* and intel compilers at the moment. I'll make similar changes for other versions and compilers when the opportunity arises. --- easybuild/easyconfigs/l/libxc/libxc-2.2.0-intel-2014b.eb | 2 +- easybuild/easyconfigs/l/libxc/libxc-2.2.1-intel-2015a.eb | 2 +- easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015a.eb | 2 +- easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015b.eb | 2 +- easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016a.eb | 1 + easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016b.eb | 1 + 6 files changed, 6 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.0-intel-2014b.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.0-intel-2014b.eb index 2ce787f05e..0617eecddd 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.2.0-intel-2014b.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.0-intel-2014b.eb @@ -8,7 +8,7 @@ description = """Libxc is a library of exchange-correlation functionals for dens The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" toolchain = {'name': 'intel', 'version': '2014b'} -toolchainopts = {'opt': True} +toolchainopts = {'opt': False, 'lowopt': True} sources = [SOURCE_TAR_GZ] source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.1-intel-2015a.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.1-intel-2015a.eb index 80de4c9f97..954c4b2503 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.2.1-intel-2015a.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.1-intel-2015a.eb @@ -8,7 +8,7 @@ description = """Libxc is a library of exchange-correlation functionals for dens The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" toolchain = {'name': 'intel', 'version': '2015a'} -toolchainopts = {'opt': True} +toolchainopts = {'opt': False, 'lowopt': True} sources = [SOURCE_TAR_GZ] source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015a.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015a.eb index 42d53d0949..c266e8d3fa 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015a.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015a.eb @@ -8,7 +8,7 @@ description = """Libxc is a library of exchange-correlation functionals for dens The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" toolchain = {'name': 'intel', 'version': '2015a'} -toolchainopts = {'opt': True} +toolchainopts = {'opt': False, 'lowopt': True} sources = [SOURCE_TAR_GZ] source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015b.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015b.eb index 2d6dda37b8..9d234313e3 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015b.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015b.eb @@ -8,7 +8,7 @@ description = """Libxc is a library of exchange-correlation functionals for dens The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" toolchain = {'name': 'intel', 'version': '2015b'} -toolchainopts = {'opt': True} +toolchainopts = {'opt': False, 'lowopt': True} sources = [SOURCE_TAR_GZ] source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016a.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016a.eb index 80e9889a84..e4360c8222 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016a.eb @@ -8,6 +8,7 @@ description = """Libxc is a library of exchange-correlation functionals for dens The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'opt': False, 'lowopt': True} sources = [SOURCE_TAR_GZ] source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016b.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016b.eb index bd3cb81b7c..c15059fd00 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016b.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016b.eb @@ -8,6 +8,7 @@ description = """Libxc is a library of exchange-correlation functionals for dens The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'opt': False, 'lowopt': True} sources = [SOURCE_TAR_GZ] source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] -- GitLab From 0d488e49be4e453e794e5c4636dc9739f884b874 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 24 Feb 2017 09:26:59 +0100 Subject: [PATCH 0160/1603] remove custom sanity_check_paths, since it's identical to that used by the R easyblock --- .../easyconfigs/r/R/R-2.15.2-goolf-1.4.10-bare.eb | 10 ---------- easybuild/easyconfigs/r/R/R-2.15.2-goolf-1.4.10.eb | 10 ---------- easybuild/easyconfigs/r/R/R-2.15.2-ictce-5.3.0-bare.eb | 10 ---------- easybuild/easyconfigs/r/R/R-2.15.2-ictce-5.3.0.eb | 10 ---------- easybuild/easyconfigs/r/R/R-2.15.3-goolf-1.4.10.eb | 10 ---------- easybuild/easyconfigs/r/R/R-2.15.3-ictce-5.3.0.eb | 10 ---------- easybuild/easyconfigs/r/R/R-3.0.1-goolf-1.4.10-bare.eb | 10 ---------- easybuild/easyconfigs/r/R/R-3.0.1-ictce-5.3.0-bare.eb | 10 ---------- easybuild/easyconfigs/r/R/R-3.0.2-goolf-1.4.10.eb | 10 ---------- easybuild/easyconfigs/r/R/R-3.0.2-ictce-5.3.0-bare.eb | 10 ---------- easybuild/easyconfigs/r/R/R-3.0.2-ictce-5.3.0.eb | 10 ---------- easybuild/easyconfigs/r/R/R-3.0.2-ictce-5.5.0.eb | 10 ---------- .../easyconfigs/r/R/R-3.1.1-ictce-6.2.5-bare-mt.eb | 10 ---------- .../easyconfigs/r/R/R-3.1.1-ictce-6.2.5-default-mt.eb | 10 ---------- 14 files changed, 140 deletions(-) diff --git a/easybuild/easyconfigs/r/R/R-2.15.2-goolf-1.4.10-bare.eb b/easybuild/easyconfigs/r/R/R-2.15.2-goolf-1.4.10-bare.eb index b12bc8e75d..fddd66f795 100644 --- a/easybuild/easyconfigs/r/R/R-2.15.2-goolf-1.4.10-bare.eb +++ b/easybuild/easyconfigs/r/R/R-2.15.2-goolf-1.4.10-bare.eb @@ -24,14 +24,4 @@ dependencies = [ exts_list = [] # just to make it explicit this module doesn't include any extensions -sanity_check_paths = { - 'files': ['bin/%s' % x for x in ['R', 'Rscript']] + - ['lib64/R/include/%s' % x for x in ['Rconfig.h', 'Rdefines.h', 'Rembedded.h', - 'R.h', 'Rinterface.h', 'Rinternals.h', - 'Rmath.h', 'Rversion.h', 'S.h']] + - ['lib64/R/modules/%s' % x for x in ['internet.%s' % SHLIB_EXT, 'lapack.%s' % SHLIB_EXT, 'vfonts.%s' % SHLIB_EXT]] + - ['lib64/R/lib/libR.%s' % SHLIB_EXT], - 'dirs': [] -} - moduleclass = 'math' diff --git a/easybuild/easyconfigs/r/R/R-2.15.2-goolf-1.4.10.eb b/easybuild/easyconfigs/r/R/R-2.15.2-goolf-1.4.10.eb index 561a883aa5..41c4f5301f 100644 --- a/easybuild/easyconfigs/r/R/R-2.15.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/r/R/R-2.15.2-goolf-1.4.10.eb @@ -21,16 +21,6 @@ dependencies = [ ('Java', '1.7.0_10', '', True), # Java bindings are built if Java is found, might as well provide it ] -sanity_check_paths = { - 'files': ['bin/%s' % x for x in ['R', 'Rscript']] + - ['lib64/R/include/%s' % x for x in ['Rconfig.h', 'Rdefines.h', 'Rembedded.h', - 'R.h', 'Rinterface.h', 'Rinternals.h', - 'Rmath.h', 'Rversion.h', 'S.h']] + - ['lib64/R/modules/%s' % x for x in ['internet.%s' % SHLIB_EXT, 'lapack.%s' % SHLIB_EXT, 'vfonts.%s' % SHLIB_EXT]] + - ['lib64/R/lib/libR.%s' % SHLIB_EXT], - 'dirs': [] -} - name_tmpl = '%(name)s_%(version)s.tar.gz' ext_options = { 'source_urls': [ diff --git a/easybuild/easyconfigs/r/R/R-2.15.2-ictce-5.3.0-bare.eb b/easybuild/easyconfigs/r/R/R-2.15.2-ictce-5.3.0-bare.eb index d58882331f..69f1781b69 100644 --- a/easybuild/easyconfigs/r/R/R-2.15.2-ictce-5.3.0-bare.eb +++ b/easybuild/easyconfigs/r/R/R-2.15.2-ictce-5.3.0-bare.eb @@ -24,14 +24,4 @@ dependencies = [ exts_list = [] # just to make it explicit this module doesn't include any extensions -sanity_check_paths = { - 'files': ['bin/%s' % x for x in ['R', 'Rscript']] + - ['lib64/R/include/%s' % x for x in ['Rconfig.h', 'Rdefines.h', 'Rembedded.h', - 'R.h', 'Rinterface.h', 'Rinternals.h', - 'Rmath.h', 'Rversion.h', 'S.h']] + - ['lib64/R/modules/%s' % x for x in ['internet.%s' % SHLIB_EXT, 'lapack.%s' % SHLIB_EXT, 'vfonts.%s' % SHLIB_EXT]] + - ['lib64/R/lib/libR.%s' % SHLIB_EXT], - 'dirs': [] -} - moduleclass = 'math' diff --git a/easybuild/easyconfigs/r/R/R-2.15.2-ictce-5.3.0.eb b/easybuild/easyconfigs/r/R/R-2.15.2-ictce-5.3.0.eb index 8ba729ce15..69437c1b5a 100644 --- a/easybuild/easyconfigs/r/R/R-2.15.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/r/R/R-2.15.2-ictce-5.3.0.eb @@ -21,16 +21,6 @@ dependencies = [ ('Java', '1.7.0_10', '', True), # Java bindings are built if Java is found, might as well provide it ] -sanity_check_paths = { - 'files': ['bin/%s' % x for x in ['R', 'Rscript']] + - ['lib64/R/include/%s' % x for x in ['Rconfig.h', 'Rdefines.h', 'Rembedded.h', - 'R.h', 'Rinterface.h', 'Rinternals.h', - 'Rmath.h', 'Rversion.h', 'S.h']] + - ['lib64/R/modules/%s' % x for x in ['internet.%s' % SHLIB_EXT, 'lapack.%s' % SHLIB_EXT, 'vfonts.%s' % SHLIB_EXT]] + - ['lib64/R/lib/libR.%s' % SHLIB_EXT], - 'dirs': [] -} - name_tmpl = '%(name)s_%(version)s.tar.gz' ext_options = { 'source_urls': [ diff --git a/easybuild/easyconfigs/r/R/R-2.15.3-goolf-1.4.10.eb b/easybuild/easyconfigs/r/R/R-2.15.3-goolf-1.4.10.eb index e96756b81d..99f0a85afd 100644 --- a/easybuild/easyconfigs/r/R/R-2.15.3-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/r/R/R-2.15.3-goolf-1.4.10.eb @@ -21,16 +21,6 @@ dependencies = [ ('Java', '1.7.0_15', '', True), # Java bindings are built if Java is found, might as well provide it ] -sanity_check_paths = { - 'files': ['bin/%s' % x for x in ['R', 'Rscript']] + - ['lib64/R/include/%s' % x for x in ['Rconfig.h', 'Rdefines.h', 'Rembedded.h', - 'R.h', 'Rinterface.h', 'Rinternals.h', - 'Rmath.h', 'Rversion.h', 'S.h']] + - ['lib64/R/modules/%s' % x for x in ['internet.%s' % SHLIB_EXT, 'lapack.%s' % SHLIB_EXT, 'vfonts.%s' % SHLIB_EXT]] + - ['lib64/R/lib/libR.%s' % SHLIB_EXT], - 'dirs': [] -} - name_tmpl = '%(name)s_%(version)s.tar.gz' ext_options = { 'source_urls': [ diff --git a/easybuild/easyconfigs/r/R/R-2.15.3-ictce-5.3.0.eb b/easybuild/easyconfigs/r/R/R-2.15.3-ictce-5.3.0.eb index 86f63c2452..b6f9488dc0 100644 --- a/easybuild/easyconfigs/r/R/R-2.15.3-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/r/R/R-2.15.3-ictce-5.3.0.eb @@ -21,16 +21,6 @@ dependencies = [ ('Java', '1.7.0_15', '', True), # Java bindings are built if Java is found, might as well provide it ] -sanity_check_paths = { - 'files': ['bin/%s' % x for x in ['R', 'Rscript']] + - ['lib64/R/include/%s' % x for x in ['Rconfig.h', 'Rdefines.h', 'Rembedded.h', - 'R.h', 'Rinterface.h', 'Rinternals.h', - 'Rmath.h', 'Rversion.h', 'S.h']] + - ['lib64/R/modules/%s' % x for x in ['internet.%s' % SHLIB_EXT, 'lapack.%s' % SHLIB_EXT, 'vfonts.%s' % SHLIB_EXT]] + - ['lib64/R/lib/libR.%s' % SHLIB_EXT], - 'dirs': [] -} - name_tmpl = '%(name)s_%(version)s.tar.gz' ext_options = { 'source_urls': [ diff --git a/easybuild/easyconfigs/r/R/R-3.0.1-goolf-1.4.10-bare.eb b/easybuild/easyconfigs/r/R/R-3.0.1-goolf-1.4.10-bare.eb index a7f037b0a7..6da04393a8 100644 --- a/easybuild/easyconfigs/r/R/R-3.0.1-goolf-1.4.10-bare.eb +++ b/easybuild/easyconfigs/r/R/R-3.0.1-goolf-1.4.10-bare.eb @@ -24,14 +24,4 @@ dependencies = [ exts_list = [] # just to make it explicit this module doesn't include any extensions -sanity_check_paths = { - 'files': ['bin/%s' % x for x in ['R', 'Rscript']] + - ['lib64/R/include/%s' % x for x in ['Rconfig.h', 'Rdefines.h', 'Rembedded.h', - 'R.h', 'Rinterface.h', 'Rinternals.h', - 'Rmath.h', 'Rversion.h', 'S.h']] + - ['lib64/R/modules/%s' % x for x in ['internet.%s' % SHLIB_EXT, 'lapack.%s' % SHLIB_EXT, 'vfonts.%s' % SHLIB_EXT]] + - ['lib64/R/lib/libR.%s' % SHLIB_EXT], - 'dirs': [] -} - moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-3.0.1-ictce-5.3.0-bare.eb b/easybuild/easyconfigs/r/R/R-3.0.1-ictce-5.3.0-bare.eb index c79a8bd4e8..25ba222aa6 100644 --- a/easybuild/easyconfigs/r/R/R-3.0.1-ictce-5.3.0-bare.eb +++ b/easybuild/easyconfigs/r/R/R-3.0.1-ictce-5.3.0-bare.eb @@ -24,14 +24,4 @@ dependencies = [ exts_list = [] # just to make it explicit this module doesn't include any extensions -sanity_check_paths = { - 'files': ['bin/%s' % x for x in ['R', 'Rscript']] + - ['lib64/R/include/%s' % x for x in ['Rconfig.h', 'Rdefines.h', 'Rembedded.h', - 'R.h', 'Rinterface.h', 'Rinternals.h', - 'Rmath.h', 'Rversion.h', 'S.h']] + - ['lib64/R/modules/%s' % x for x in ['internet.%s' % SHLIB_EXT, 'lapack.%s' % SHLIB_EXT, 'vfonts.%s' % SHLIB_EXT]] + - ['lib64/R/lib/libR.%s' % SHLIB_EXT], - 'dirs': [] -} - moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-3.0.2-goolf-1.4.10.eb b/easybuild/easyconfigs/r/R/R-3.0.2-goolf-1.4.10.eb index 3c069b9b81..8abe6d999a 100644 --- a/easybuild/easyconfigs/r/R/R-3.0.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/r/R/R-3.0.2-goolf-1.4.10.eb @@ -21,16 +21,6 @@ dependencies = [ ('Java', '1.7.0_21', '', True), # Java bindings are built if Java is found, might as well provide it ] -sanity_check_paths = { - 'files': ['bin/%s' % x for x in ['R', 'Rscript']] + - ['lib64/R/include/%s' % x for x in ['Rconfig.h', 'Rdefines.h', 'Rembedded.h', - 'R.h', 'Rinterface.h', 'Rinternals.h', - 'Rmath.h', 'Rversion.h', 'S.h']] + - ['lib64/R/modules/%s' % x for x in ['internet.%s' % SHLIB_EXT, 'lapack.%s' % SHLIB_EXT, 'vfonts.%s' % SHLIB_EXT]] + - ['lib64/R/lib/libR.%s' % SHLIB_EXT], - 'dirs': [] -} - name_tmpl = '%(name)s_%(version)s.tar.gz' ext_options = { 'source_urls': [ diff --git a/easybuild/easyconfigs/r/R/R-3.0.2-ictce-5.3.0-bare.eb b/easybuild/easyconfigs/r/R/R-3.0.2-ictce-5.3.0-bare.eb index 8d427ebb5d..d3eaca313f 100644 --- a/easybuild/easyconfigs/r/R/R-3.0.2-ictce-5.3.0-bare.eb +++ b/easybuild/easyconfigs/r/R/R-3.0.2-ictce-5.3.0-bare.eb @@ -23,14 +23,4 @@ dependencies = [ exts_list = [] # just to make it explicit this module doesn't include any extensions -sanity_check_paths = { - 'files': ['bin/%s' % x for x in ['R', 'Rscript']] + - ['lib64/R/include/%s' % x for x in ['Rconfig.h', 'Rdefines.h', 'Rembedded.h', - 'R.h', 'Rinterface.h', 'Rinternals.h', - 'Rmath.h', 'Rversion.h', 'S.h']] + - ['lib64/R/modules/%s' % x for x in ['internet.%s' % SHLIB_EXT, 'lapack.%s' % SHLIB_EXT, 'vfonts.%s' % SHLIB_EXT]] + - ['lib64/R/lib/libR.%s' % SHLIB_EXT], - 'dirs': [] -} - moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-3.0.2-ictce-5.3.0.eb b/easybuild/easyconfigs/r/R/R-3.0.2-ictce-5.3.0.eb index b2aa058997..f34e0f18e6 100644 --- a/easybuild/easyconfigs/r/R/R-3.0.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/r/R/R-3.0.2-ictce-5.3.0.eb @@ -21,16 +21,6 @@ dependencies = [ ('Java', '1.7.0_15', '', True), # Java bindings are built if Java is found, might as well provide it ] -sanity_check_paths = { - 'files': ['bin/%s' % x for x in ['R', 'Rscript']] + - ['lib64/R/include/%s' % x for x in ['Rconfig.h', 'Rdefines.h', 'Rembedded.h', - 'R.h', 'Rinterface.h', 'Rinternals.h', - 'Rmath.h', 'Rversion.h', 'S.h']] + - ['lib64/R/modules/%s' % x for x in ['internet.%s' % SHLIB_EXT, 'lapack.%s' % SHLIB_EXT, 'vfonts.%s' % SHLIB_EXT]] + - ['lib64/R/lib/libR.%s' % SHLIB_EXT], - 'dirs': [] -} - name_tmpl = '%(name)s_%(version)s.tar.gz' ext_options = { 'source_urls': [ diff --git a/easybuild/easyconfigs/r/R/R-3.0.2-ictce-5.5.0.eb b/easybuild/easyconfigs/r/R/R-3.0.2-ictce-5.5.0.eb index ee87a80c86..1572f6e35f 100644 --- a/easybuild/easyconfigs/r/R/R-3.0.2-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/r/R/R-3.0.2-ictce-5.5.0.eb @@ -21,16 +21,6 @@ dependencies = [ ('Java', '1.7.0_15', '', True), # Java bindings are built if Java is found, might as well provide it ] -sanity_check_paths = { - 'files': ['bin/%s' % x for x in ['R', 'Rscript']] + - ['lib64/R/include/%s' % x for x in ['Rconfig.h', 'Rdefines.h', 'Rembedded.h', - 'R.h', 'Rinterface.h', 'Rinternals.h', - 'Rmath.h', 'Rversion.h', 'S.h']] + - ['lib64/R/modules/%s' % x for x in ['internet.%s' % SHLIB_EXT, 'lapack.%s' % SHLIB_EXT, 'vfonts.%s' % SHLIB_EXT]] + - ['lib64/R/lib/libR.%s' % SHLIB_EXT], - 'dirs': [] -} - name_tmpl = '%(name)s_%(version)s.tar.gz' ext_options = { 'source_urls': [ diff --git a/easybuild/easyconfigs/r/R/R-3.1.1-ictce-6.2.5-bare-mt.eb b/easybuild/easyconfigs/r/R/R-3.1.1-ictce-6.2.5-bare-mt.eb index 31222cc1f7..b0d2830c75 100644 --- a/easybuild/easyconfigs/r/R/R-3.1.1-ictce-6.2.5-bare-mt.eb +++ b/easybuild/easyconfigs/r/R/R-3.1.1-ictce-6.2.5-bare-mt.eb @@ -26,14 +26,4 @@ dependencies = [ exts_list = [] # just to make it explicit this module doesn't include any extensions -sanity_check_paths = { - 'files': ['bin/%s' % x for x in ['R', 'Rscript']] + - ['lib64/R/include/%s' % x for x in ['Rconfig.h', 'Rdefines.h', 'Rembedded.h', - 'R.h', 'Rinterface.h', 'Rinternals.h', - 'Rmath.h', 'Rversion.h', 'S.h']] + - ['lib64/R/modules/%s' % x for x in ['internet.%s' % SHLIB_EXT, 'lapack.%s' % SHLIB_EXT, 'vfonts.%s' % SHLIB_EXT]] + - ['lib64/R/lib/libR.%s' % SHLIB_EXT], - 'dirs': [] -} - moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-3.1.1-ictce-6.2.5-default-mt.eb b/easybuild/easyconfigs/r/R/R-3.1.1-ictce-6.2.5-default-mt.eb index 866b40ba81..a2eabbbdcd 100644 --- a/easybuild/easyconfigs/r/R/R-3.1.1-ictce-6.2.5-default-mt.eb +++ b/easybuild/easyconfigs/r/R/R-3.1.1-ictce-6.2.5-default-mt.eb @@ -23,16 +23,6 @@ dependencies = [ ('Java', '1.7.0_60', '', True), # Java bindings are built if Java is found, might as well provide it ] -sanity_check_paths = { - 'files': ['bin/%s' % x for x in ['R', 'Rscript']] + - ['lib64/R/include/%s' % x for x in ['Rconfig.h', 'Rdefines.h', 'Rembedded.h', - 'R.h', 'Rinterface.h', 'Rinternals.h', - 'Rmath.h', 'Rversion.h', 'S.h']] + - ['lib64/R/modules/%s' % x for x in ['internet.%s' % SHLIB_EXT, 'lapack.%s' % SHLIB_EXT, 'vfonts.%s' % SHLIB_EXT]] + - ['lib64/R/lib/libR.%s' % SHLIB_EXT], - 'dirs': [] -} - exts_list = [ # default libraries, only here to sanity check their presence 'base', -- GitLab From 4f3fba3ae7d8c413468784e10b38767e18553240 Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Fri, 24 Feb 2017 11:40:55 +0100 Subject: [PATCH 0161/1603] Apply CMAKE_PREFIX_PATH/ncurses and ccmake tweak to CMake 3.4.0 and up --- easybuild/easyconfigs/c/CMake/CMake-3.4.0-intel-2015b.eb | 4 ++-- easybuild/easyconfigs/c/CMake/CMake-3.4.1-GCC-4.9.2.eb | 4 +++- easybuild/easyconfigs/c/CMake/CMake-3.4.1-foss-2015a.eb | 4 ++-- easybuild/easyconfigs/c/CMake/CMake-3.4.1-foss-2015b.eb | 4 ++-- easybuild/easyconfigs/c/CMake/CMake-3.4.1-intel-2015b.eb | 4 ++-- easybuild/easyconfigs/c/CMake/CMake-3.4.3-gimkl-2.11.5.eb | 4 ++-- easybuild/easyconfigs/c/CMake/CMake-3.4.3-goolf-1.7.20.eb | 4 ++-- easybuild/easyconfigs/c/CMake/CMake-3.4.3-ictce-7.3.5.eb | 4 ++-- easybuild/easyconfigs/c/CMake/CMake-3.5.0-CrayGNU-2015.11.eb | 4 +++- easybuild/easyconfigs/c/CMake/CMake-3.5.2-goolf-1.7.20.eb | 4 ++-- easybuild/easyconfigs/c/CMake/CMake-3.5.2.eb | 4 +++- 11 files changed, 25 insertions(+), 19 deletions(-) diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.4.0-intel-2015b.eb b/easybuild/easyconfigs/c/CMake/CMake-3.4.0-intel-2015b.eb index 21bbc29383..53143ba0a0 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.4.0-intel-2015b.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.4.0-intel-2015b.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'intel', 'version': '2015b'} source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] -configopts = '-- -DCMAKE_USE_OPENSSL=1' +configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' dependencies = [ ('ncurses', '5.9'), @@ -24,7 +24,7 @@ dependencies = [ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] sanity_check_paths = { - 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], 'dirs': [], } diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.4.1-GCC-4.9.2.eb b/easybuild/easyconfigs/c/CMake/CMake-3.4.1-GCC-4.9.2.eb index cb117db322..8b223712cc 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.4.1-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.4.1-GCC-4.9.2.eb @@ -12,10 +12,12 @@ toolchain = {'name': 'GCC', 'version': '4.9.2'} source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] +configopts = '-- -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' + dependencies = [('ncurses', '5.9')] sanity_check_paths = { - 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], 'dirs': [], } diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.4.1-foss-2015a.eb b/easybuild/easyconfigs/c/CMake/CMake-3.4.1-foss-2015a.eb index 4f9c1dcfa2..f268f237cd 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.4.1-foss-2015a.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.4.1-foss-2015a.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'foss', 'version': '2015a'} source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] -configopts = '-- -DCMAKE_USE_OPENSSL=1' +configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' dependencies = [ ('ncurses', '5.9'), @@ -21,7 +21,7 @@ dependencies = [ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] sanity_check_paths = { - 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], 'dirs': [], } diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.4.1-foss-2015b.eb b/easybuild/easyconfigs/c/CMake/CMake-3.4.1-foss-2015b.eb index 5702e9976d..0faaa6fe56 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.4.1-foss-2015b.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.4.1-foss-2015b.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'foss', 'version': '2015b'} source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] -configopts = '-- -DCMAKE_USE_OPENSSL=1' +configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' dependencies = [ ('ncurses', '5.9'), @@ -24,7 +24,7 @@ dependencies = [ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] sanity_check_paths = { - 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], 'dirs': [], } diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.4.1-intel-2015b.eb b/easybuild/easyconfigs/c/CMake/CMake-3.4.1-intel-2015b.eb index 638514df1f..1b0e29c51f 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.4.1-intel-2015b.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.4.1-intel-2015b.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'intel', 'version': '2015b'} source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] -configopts = '-- -DCMAKE_USE_OPENSSL=1' +configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' dependencies = [ ('ncurses', '5.9'), @@ -24,7 +24,7 @@ dependencies = [ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] sanity_check_paths = { - 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], 'dirs': [], } diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.4.3-gimkl-2.11.5.eb b/easybuild/easyconfigs/c/CMake/CMake-3.4.3-gimkl-2.11.5.eb index f5527c16d6..db51b497b9 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.4.3-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.4.3-gimkl-2.11.5.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'gimkl', 'version': '2.11.5'} source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] -configopts = '-- -DCMAKE_USE_OPENSSL=1' +configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' dependencies = [ ('ncurses', '5.9'), @@ -24,7 +24,7 @@ dependencies = [ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] sanity_check_paths = { - 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], 'dirs': [], } diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.4.3-goolf-1.7.20.eb b/easybuild/easyconfigs/c/CMake/CMake-3.4.3-goolf-1.7.20.eb index 383be7ac07..4095a8cf13 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.4.3-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.4.3-goolf-1.7.20.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'goolf', 'version': '1.7.20'} source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] -configopts = '-- -DCMAKE_USE_OPENSSL=1' +configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' dependencies = [ ('ncurses', '5.9'), @@ -24,7 +24,7 @@ dependencies = [ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] sanity_check_paths = { - 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], 'dirs': [], } diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.4.3-ictce-7.3.5.eb b/easybuild/easyconfigs/c/CMake/CMake-3.4.3-ictce-7.3.5.eb index 7deb175b91..9ae7cc86bf 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.4.3-ictce-7.3.5.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.4.3-ictce-7.3.5.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'ictce', 'version': '7.3.5'} source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] -configopts = '-- -DCMAKE_USE_OPENSSL=1' +configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' dependencies = [ ('ncurses', '5.9'), @@ -24,7 +24,7 @@ dependencies = [ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] sanity_check_paths = { - 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], 'dirs': [], } diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.5.0-CrayGNU-2015.11.eb b/easybuild/easyconfigs/c/CMake/CMake-3.5.0-CrayGNU-2015.11.eb index c7cd4a579a..9ffba8c3eb 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.5.0-CrayGNU-2015.11.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.5.0-CrayGNU-2015.11.eb @@ -13,10 +13,12 @@ toolchain = {'name': 'CrayGNU', 'version': '2015.11'} source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] +configopts = '-- -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' + dependencies = [('ncurses', '5.9')] sanity_check_paths = { - 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], 'dirs': [], } diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.5.2-goolf-1.7.20.eb b/easybuild/easyconfigs/c/CMake/CMake-3.5.2-goolf-1.7.20.eb index 1f3daa3224..535e3995e0 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.5.2-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.5.2-goolf-1.7.20.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'goolf', 'version': '1.7.20'} source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] -configopts = '-- -DCMAKE_USE_OPENSSL=1' +configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' dependencies = [ ('ncurses', '5.9'), @@ -24,7 +24,7 @@ dependencies = [ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] sanity_check_paths = { - 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], 'dirs': [], } diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.5.2.eb b/easybuild/easyconfigs/c/CMake/CMake-3.5.2.eb index 412e055df6..701830e871 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.5.2.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.5.2.eb @@ -12,10 +12,12 @@ toolchain = {'name': 'dummy', 'version': ''} source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] +configopts = '-- -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' + dependencies = [('ncurses', '6.0')] sanity_check_paths = { - 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], 'dirs': [], } -- GitLab From 05485fb12247fce13d584bb7c41aaa7ff8e325ba Mon Sep 17 00:00:00 2001 From: Toon Verstraelen Date: Fri, 24 Feb 2017 14:34:17 +0100 Subject: [PATCH 0162/1603] Add comment to EBs to explain low optimization settings --- easybuild/easyconfigs/l/libxc/libxc-2.2.0-intel-2014b.eb | 1 + easybuild/easyconfigs/l/libxc/libxc-2.2.1-intel-2015a.eb | 1 + easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015a.eb | 1 + easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015b.eb | 1 + easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016a.eb | 1 + easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016b.eb | 1 + 6 files changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.0-intel-2014b.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.0-intel-2014b.eb index 0617eecddd..f971a65f6f 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.2.0-intel-2014b.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.0-intel-2014b.eb @@ -8,6 +8,7 @@ description = """Libxc is a library of exchange-correlation functionals for dens The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" toolchain = {'name': 'intel', 'version': '2014b'} +# Results for some functions (e.g. mgga_c_tpss) change with too aggressive optimization settings. toolchainopts = {'opt': False, 'lowopt': True} sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.1-intel-2015a.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.1-intel-2015a.eb index 954c4b2503..6cdc9b59df 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.2.1-intel-2015a.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.1-intel-2015a.eb @@ -8,6 +8,7 @@ description = """Libxc is a library of exchange-correlation functionals for dens The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" toolchain = {'name': 'intel', 'version': '2015a'} +# Results for some functions (e.g. mgga_c_tpss) change with too aggressive optimization settings. toolchainopts = {'opt': False, 'lowopt': True} sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015a.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015a.eb index c266e8d3fa..c926977f8e 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015a.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015a.eb @@ -8,6 +8,7 @@ description = """Libxc is a library of exchange-correlation functionals for dens The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" toolchain = {'name': 'intel', 'version': '2015a'} +# Results for some functions (e.g. mgga_c_tpss) change with too aggressive optimization settings. toolchainopts = {'opt': False, 'lowopt': True} sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015b.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015b.eb index 9d234313e3..9eb91c2953 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015b.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015b.eb @@ -8,6 +8,7 @@ description = """Libxc is a library of exchange-correlation functionals for dens The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" toolchain = {'name': 'intel', 'version': '2015b'} +# Results for some functions (e.g. mgga_c_tpss) change with too aggressive optimization settings. toolchainopts = {'opt': False, 'lowopt': True} sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016a.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016a.eb index e4360c8222..203ac28517 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016a.eb @@ -8,6 +8,7 @@ description = """Libxc is a library of exchange-correlation functionals for dens The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" toolchain = {'name': 'intel', 'version': '2016a'} +# Results for some functions (e.g. mgga_c_tpss) change with too aggressive optimization settings. toolchainopts = {'opt': False, 'lowopt': True} sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016b.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016b.eb index c15059fd00..f83e57a0da 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016b.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016b.eb @@ -8,6 +8,7 @@ description = """Libxc is a library of exchange-correlation functionals for dens The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" toolchain = {'name': 'intel', 'version': '2016b'} +# Results for some functions (e.g. mgga_c_tpss) change with too aggressive optimization settings. toolchainopts = {'opt': False, 'lowopt': True} sources = [SOURCE_TAR_GZ] -- GitLab From 99c191768ac31d851c3a2d75d68c3bad9366d2d7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 24 Feb 2017 17:58:17 +0100 Subject: [PATCH 0163/1603] adding easyconfigs: MEGA-7.0.20-1.eb --- easybuild/easyconfigs/m/MEGA/MEGA-7.0.20-1.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/m/MEGA/MEGA-7.0.20-1.eb diff --git a/easybuild/easyconfigs/m/MEGA/MEGA-7.0.20-1.eb b/easybuild/easyconfigs/m/MEGA/MEGA-7.0.20-1.eb new file mode 100644 index 0000000000..4513c7f7b6 --- /dev/null +++ b/easybuild/easyconfigs/m/MEGA/MEGA-7.0.20-1.eb @@ -0,0 +1,24 @@ +easyblock = 'Tarball' + +name = 'MEGA' +version = '7.0.20-1' + +homepage = 'http://www.megasoftware.net/' +description = """MEGA-CC (Molecular Evolutionary Genetics Analysis Computational Core) is an integrated suite of tools + for statistics-based comparative analysis of molecular sequence data based on evolutionary principles.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +# download requires agreeing with license & filling out a form, see http://www.megasoftware.net/ +sources = ['megacc-%(version)s.x86_64.tar.gz'] + +modextrapaths = { + 'PATH': '', +} + +sanity_check_paths = { + 'files': ['megacc', 'megaproto'], + 'dirs': ['Examples'], +} + +moduleclass = 'bio' -- GitLab From 9161535b5ebb7766dbb2be4122a1790bd8c64c03 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 24 Feb 2017 18:57:57 +0100 Subject: [PATCH 0164/1603] adding easyconfigs: PyTables-3.2.3.1-intel-2016b-Python-2.7.12.eb --- ...ables-3.2.3.1-intel-2016b-Python-2.7.12.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTables/PyTables-3.2.3.1-intel-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/p/PyTables/PyTables-3.2.3.1-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/PyTables/PyTables-3.2.3.1-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..904febe2a2 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTables/PyTables-3.2.3.1-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,39 @@ +easyblock = 'PythonPackage' + +name = 'PyTables' +version = '3.2.3.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.pytables.org' +description = """PyTables is a package for managing hierarchical datasets and designed to efficiently and easily cope + with extremely large amounts of data. PyTables is built on top of the HDF5 library, using the Python language and the + NumPy package. It features an object-oriented interface that, combined with C extensions for the performance-critical + parts of the code (generated using Cython), makes it a fast, yet extremely easy to use tool for interactively browse, + process and search very large amounts of data. One important feature of PyTables is that it optimizes memory and disk + resources so that data takes much less space (specially if on-flight compression is used) than other solutions such as + relational or object oriented databases.""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/PyTables/PyTables/archive/'] +sources = ['v.%(version)s.tar.gz'] + +patches = ['pyTables-3.2.2-fix-libs.patch'] + +dependencies = [ + ('Python', '2.7.12'), + ('numexpr', '2.6.1', versionsuffix), + ('HDF5', '1.8.17'), + ('LZO', '2.09'), + ('Blosc', '1.11.1'), +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['pt2to3', 'ptdump', 'ptrepack']], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +options = {'modulename': 'tables'} + +moduleclass = 'data' -- GitLab From 7e533b72c6d1af1130a16882b38e62ba2bc71ace Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 24 Feb 2017 19:47:32 +0100 Subject: [PATCH 0165/1603] adding easyconfigs: ea-utils-1.04.807-intel-2016b.eb --- .../ea-utils/ea-utils-1.04.807-intel-2016b.eb | 46 +++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/e/ea-utils/ea-utils-1.04.807-intel-2016b.eb diff --git a/easybuild/easyconfigs/e/ea-utils/ea-utils-1.04.807-intel-2016b.eb b/easybuild/easyconfigs/e/ea-utils/ea-utils-1.04.807-intel-2016b.eb new file mode 100644 index 0000000000..79eae70f31 --- /dev/null +++ b/easybuild/easyconfigs/e/ea-utils/ea-utils-1.04.807-intel-2016b.eb @@ -0,0 +1,46 @@ +easyblock = 'MakeCp' + +name = 'ea-utils' +version = '1.04.807' + +homepage = 'http://expressionanalysis.github.io/ea-utils/' +description = """Command-line tools for processing biological sequencing data. +Barcode demultiplexing, adapter trimming, etc. + +Primarily written to support an Illumina based pipeline - +but should work with any FASTQs.""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/ExpressionAnalysis/ea-utils/archive/'] +sources = ['%(version)s.tar.gz'] + +checksums = ['5972b9f712920603b7527f46c0063a09'] + +start_dir = 'clipper' + +prebuildopts = "sed -i 's/$(CFLAGS)/$(CFLAGS) $(LDFLAGS) -I./' Makefile && PREFIX=%(installdir)s " +buildopts = 'fastq-mcf fastq-multx fastq-join fastq-stats fastq-clipper sam-stats varcall' + +builddependencies = [ + ('Perl', '5.24.0'), +] + +dependencies = [ + ('GSL', '2.3'), +] + +files_to_copy = [([ + 'fastq-mcf', 'fastq-multx', 'fastq-join', 'fastq-stats', 'fastq-clipper', + 'sam-stats', 'varcall', 'randomFQ', 'alc', 'determine-phred'], 'bin' +)] + + +sanity_check_paths = { + 'files': ['bin/fastq-mcf', 'bin/fastq-multx', 'bin/fastq-join', 'bin/fastq-stats', + 'bin/fastq-clipper', 'bin/sam-stats', 'bin/varcall'], + 'dirs': [] +} + +moduleclass = 'bio' -- GitLab From 71a4609f70236b90dea63d66161409d7b2dd314d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 25 Feb 2017 08:47:58 +0100 Subject: [PATCH 0166/1603] fix version (& homepage) in ea-utils easyconfigs --- ...16a.eb => ea-utils-1.04.807-foss-2016a.eb} | 20 +++++++++---------- ...16b.eb => ea-utils-1.04.807-foss-2016b.eb} | 18 ++++++++--------- 2 files changed, 17 insertions(+), 21 deletions(-) rename easybuild/easyconfigs/e/ea-utils/{ea-utils-27a4809-foss-2016a.eb => ea-utils-1.04.807-foss-2016a.eb} (64%) rename easybuild/easyconfigs/e/ea-utils/{ea-utils-27a4809-foss-2016b.eb => ea-utils-1.04.807-foss-2016b.eb} (66%) diff --git a/easybuild/easyconfigs/e/ea-utils/ea-utils-27a4809-foss-2016a.eb b/easybuild/easyconfigs/e/ea-utils/ea-utils-1.04.807-foss-2016a.eb similarity index 64% rename from easybuild/easyconfigs/e/ea-utils/ea-utils-27a4809-foss-2016a.eb rename to easybuild/easyconfigs/e/ea-utils/ea-utils-1.04.807-foss-2016a.eb index 7cf3821ef3..498218ede9 100644 --- a/easybuild/easyconfigs/e/ea-utils/ea-utils-27a4809-foss-2016a.eb +++ b/easybuild/easyconfigs/e/ea-utils/ea-utils-1.04.807-foss-2016a.eb @@ -1,9 +1,9 @@ easyblock = 'MakeCp' name = 'ea-utils' -version = '27a4809' +version = '1.04.807' -homepage = 'https://code.google.com/p/ea-utils/' +homepage = 'http://expressionanalysis.github.io/ea-utils/' description = """Command-line tools for processing biological sequencing data. Barcode demultiplexing, adapter trimming, etc. @@ -11,12 +11,12 @@ Primarily written to support an Illumina based pipeline - but should work with any FASTQs.""" toolchain = {'name': 'foss', 'version': '2016a'} -toolchainopts = {'optarch': True, 'pic': True} +toolchainopts = {'pic': True} -source_urls = ['https://github.com/ExpressionAnalysis/%(name)s/tarball/master'] -sources = [SOURCE_TGZ] +source_urls = ['https://github.com/ExpressionAnalysis/ea-utils/archive/'] +sources = ['%(version)s.tar.gz'] -checksums = ['45eef4b040f83abe2c9f51d4a7d18271'] +checksums = ['5972b9f712920603b7527f46c0063a09'] start_dir = 'clipper' @@ -38,11 +38,9 @@ files_to_copy = [([ sanity_check_paths = { - 'files': [ - 'bin/fastq-mcf', 'bin/fastq-multx', 'bin/fastq-join', 'bin/fastq-stats', - 'bin/fastq-clipper', 'bin/sam-stats', 'bin/varcall' - ], + 'files': ['bin/fastq-mcf', 'bin/fastq-multx', 'bin/fastq-join', 'bin/fastq-stats', + 'bin/fastq-clipper', 'bin/sam-stats', 'bin/varcall'], 'dirs': [] } -moduleclass = 'bio' \ No newline at end of file +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/e/ea-utils/ea-utils-27a4809-foss-2016b.eb b/easybuild/easyconfigs/e/ea-utils/ea-utils-1.04.807-foss-2016b.eb similarity index 66% rename from easybuild/easyconfigs/e/ea-utils/ea-utils-27a4809-foss-2016b.eb rename to easybuild/easyconfigs/e/ea-utils/ea-utils-1.04.807-foss-2016b.eb index e8447b7c64..5bd575648e 100644 --- a/easybuild/easyconfigs/e/ea-utils/ea-utils-27a4809-foss-2016b.eb +++ b/easybuild/easyconfigs/e/ea-utils/ea-utils-1.04.807-foss-2016b.eb @@ -1,9 +1,9 @@ easyblock = 'MakeCp' name = 'ea-utils' -version = '27a4809' +version = '1.04.807' -homepage = 'https://code.google.com/p/ea-utils/' +homepage = 'http://expressionanalysis.github.io/ea-utils/' description = """Command-line tools for processing biological sequencing data. Barcode demultiplexing, adapter trimming, etc. @@ -11,12 +11,12 @@ Primarily written to support an Illumina based pipeline - but should work with any FASTQs.""" toolchain = {'name': 'foss', 'version': '2016b'} -toolchainopts = {'optarch': True, 'pic': True} +toolchainopts = {'pic': True} -source_urls = ['https://github.com/ExpressionAnalysis/%(name)s/tarball/master'] -sources = [SOURCE_TGZ] +source_urls = ['https://github.com/ExpressionAnalysis/ea-utils/archive/'] +sources = ['%(version)s.tar.gz'] -checksums = ['45eef4b040f83abe2c9f51d4a7d18271'] +checksums = ['5972b9f712920603b7527f46c0063a09'] start_dir = 'clipper' @@ -38,10 +38,8 @@ files_to_copy = [([ sanity_check_paths = { - 'files': [ - 'bin/fastq-mcf', 'bin/fastq-multx', 'bin/fastq-join', 'bin/fastq-stats', - 'bin/fastq-clipper', 'bin/sam-stats', 'bin/varcall' - ], + 'files': ['bin/fastq-mcf', 'bin/fastq-multx', 'bin/fastq-join', 'bin/fastq-stats', + 'bin/fastq-clipper', 'bin/sam-stats', 'bin/varcall'], 'dirs': [] } -- GitLab From a9f5681fae6e765adb1851e8b1414e6d5f8aecf0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 25 Feb 2017 09:05:26 +0100 Subject: [PATCH 0167/1603] avoid escape double quotes to make tests happy --- .../o/OrthoMCL/OrthoMCL-1.4-intel-2016b-Perl-5.24.0.eb | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/o/OrthoMCL/OrthoMCL-1.4-intel-2016b-Perl-5.24.0.eb b/easybuild/easyconfigs/o/OrthoMCL/OrthoMCL-1.4-intel-2016b-Perl-5.24.0.eb index 8cdb56fbdb..3f9e8e96b8 100644 --- a/easybuild/easyconfigs/o/OrthoMCL/OrthoMCL-1.4-intel-2016b-Perl-5.24.0.eb +++ b/easybuild/easyconfigs/o/OrthoMCL/OrthoMCL-1.4-intel-2016b-Perl-5.24.0.eb @@ -27,10 +27,10 @@ start_dir = 'ORTHOMCLV%(version)s' # fix hardcoded paths postinstallcmds = [ 'sed -i"" "s@/usr/bin/perl@$EBROOTPERL/bin/perl@g" %(installdir)s/orthomcl.pl', - 'sed -i"" "s@\\"/.*blastall\\";@\\"$EBROOTBLAST/bin/blastall\\";@g" %(installdir)s/orthomcl_module.pm', - 'sed -i"" "s@\\"/.*formatdb\\";@\\"$EBROOTBLAST/bin/formatdb\\";@g" %(installdir)s/orthomcl_module.pm', - 'sed -i"" "s@\\"/.*mcl\\";@\\"$EBROOTMCL/bin/mcl\\";@g" %(installdir)s/orthomcl_module.pm', - 'sed -i"" "s@\\"/.*ORTHOMCL.*%(version)s/\\";@\\"\\$ENV{\'PWD\'}/\\";@g" %(installdir)s/orthomcl_module.pm', + 'sed -i"" "s@/.*blastall@$EBROOTBLAST/bin/blastall@g" %(installdir)s/orthomcl_module.pm', + 'sed -i"" "s@/.*formatdb@$EBROOTBLAST/bin/formatdb@g" %(installdir)s/orthomcl_module.pm', + 'sed -i"" "s@/.*\(mcl.;\)@$EBROOTMCL/bin/\\1@g" %(installdir)s/orthomcl_module.pm', + 'sed -i"" "s@/.*ORTHOMCL.*%(version)s/@\\$ENV{\'PWD\'}/@g" %(installdir)s/orthomcl_module.pm', ] modextrapaths = { -- GitLab From e040c832a322df495cd07b6ead1e677372f96d66 Mon Sep 17 00:00:00 2001 From: Toon Verstraelen Date: Sat, 25 Feb 2017 12:53:16 +0100 Subject: [PATCH 0168/1603] Remove redundant toolchainopts (libxc) --- easybuild/easyconfigs/l/libxc/libxc-2.2.0-intel-2014b.eb | 2 +- easybuild/easyconfigs/l/libxc/libxc-2.2.1-intel-2015a.eb | 2 +- easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015a.eb | 2 +- easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015b.eb | 2 +- easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016a.eb | 2 +- easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016b.eb | 2 +- 6 files changed, 6 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.0-intel-2014b.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.0-intel-2014b.eb index f971a65f6f..8c8a06232c 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.2.0-intel-2014b.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.0-intel-2014b.eb @@ -9,7 +9,7 @@ description = """Libxc is a library of exchange-correlation functionals for dens toolchain = {'name': 'intel', 'version': '2014b'} # Results for some functions (e.g. mgga_c_tpss) change with too aggressive optimization settings. -toolchainopts = {'opt': False, 'lowopt': True} +toolchainopts = {'lowopt': True} sources = [SOURCE_TAR_GZ] source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.1-intel-2015a.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.1-intel-2015a.eb index 6cdc9b59df..386fc2d5ba 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.2.1-intel-2015a.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.1-intel-2015a.eb @@ -9,7 +9,7 @@ description = """Libxc is a library of exchange-correlation functionals for dens toolchain = {'name': 'intel', 'version': '2015a'} # Results for some functions (e.g. mgga_c_tpss) change with too aggressive optimization settings. -toolchainopts = {'opt': False, 'lowopt': True} +toolchainopts = {'lowopt': True} sources = [SOURCE_TAR_GZ] source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015a.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015a.eb index c926977f8e..eef2248b2a 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015a.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015a.eb @@ -9,7 +9,7 @@ description = """Libxc is a library of exchange-correlation functionals for dens toolchain = {'name': 'intel', 'version': '2015a'} # Results for some functions (e.g. mgga_c_tpss) change with too aggressive optimization settings. -toolchainopts = {'opt': False, 'lowopt': True} +toolchainopts = {'lowopt': True} sources = [SOURCE_TAR_GZ] source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015b.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015b.eb index 9eb91c2953..658c339764 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015b.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015b.eb @@ -9,7 +9,7 @@ description = """Libxc is a library of exchange-correlation functionals for dens toolchain = {'name': 'intel', 'version': '2015b'} # Results for some functions (e.g. mgga_c_tpss) change with too aggressive optimization settings. -toolchainopts = {'opt': False, 'lowopt': True} +toolchainopts = {'lowopt': True} sources = [SOURCE_TAR_GZ] source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016a.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016a.eb index 203ac28517..4cb658a639 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016a.eb @@ -9,7 +9,7 @@ description = """Libxc is a library of exchange-correlation functionals for dens toolchain = {'name': 'intel', 'version': '2016a'} # Results for some functions (e.g. mgga_c_tpss) change with too aggressive optimization settings. -toolchainopts = {'opt': False, 'lowopt': True} +toolchainopts = {'lowopt': True} sources = [SOURCE_TAR_GZ] source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016b.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016b.eb index f83e57a0da..41bfb6c123 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016b.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016b.eb @@ -9,7 +9,7 @@ description = """Libxc is a library of exchange-correlation functionals for dens toolchain = {'name': 'intel', 'version': '2016b'} # Results for some functions (e.g. mgga_c_tpss) change with too aggressive optimization settings. -toolchainopts = {'opt': False, 'lowopt': True} +toolchainopts = {'lowopt': True} sources = [SOURCE_TAR_GZ] source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] -- GitLab From 3be2942c3f45d3c59b3a320d691b89724f22021d Mon Sep 17 00:00:00 2001 From: Toon Verstraelen Date: Sat, 25 Feb 2017 12:53:43 +0100 Subject: [PATCH 0169/1603] Also use lowopt=True for libxc-3.0.0 --- easybuild/easyconfigs/l/libxc/libxc-3.0.0-intel-2016a.eb | 2 ++ easybuild/easyconfigs/l/libxc/libxc-3.0.0-intel-2016b.eb | 2 ++ 2 files changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/l/libxc/libxc-3.0.0-intel-2016a.eb b/easybuild/easyconfigs/l/libxc/libxc-3.0.0-intel-2016a.eb index 9417deb550..e89a3a0020 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-3.0.0-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-3.0.0-intel-2016a.eb @@ -8,6 +8,8 @@ description = """Libxc is a library of exchange-correlation functionals for dens The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" toolchain = {'name': 'intel', 'version': '2016a'} +# Results for some functions (e.g. mgga_c_tpss) change with too aggressive optimization settings. +toolchainopts = {'lowopt': True} sources = [SOURCE_TAR_GZ] source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] diff --git a/easybuild/easyconfigs/l/libxc/libxc-3.0.0-intel-2016b.eb b/easybuild/easyconfigs/l/libxc/libxc-3.0.0-intel-2016b.eb index a251dac24c..812bf5438b 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-3.0.0-intel-2016b.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-3.0.0-intel-2016b.eb @@ -8,6 +8,8 @@ description = """Libxc is a library of exchange-correlation functionals for dens The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" toolchain = {'name': 'intel', 'version': '2016b'} +# Results for some functions (e.g. mgga_c_tpss) change with too aggressive optimization settings. +toolchainopts = {'lowopt': True} sources = [SOURCE_TAR_GZ] source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] -- GitLab From 9588d0ae3e84fedafce93186a6970e13bacfec07 Mon Sep 17 00:00:00 2001 From: Toon Verstraelen Date: Sat, 25 Feb 2017 13:52:20 +0100 Subject: [PATCH 0170/1603] Apply lowopt=True to all libxc versions + fix typo in comment Consistency across all eb files reduces the risk that this problem gets reintroduced. --- easybuild/easyconfigs/l/libxc/libxc-2.0.1-goolf-1.4.10.eb | 3 ++- easybuild/easyconfigs/l/libxc/libxc-2.0.1-ictce-5.3.0.eb | 3 ++- easybuild/easyconfigs/l/libxc/libxc-2.0.1-ictce-5.5.0.eb | 3 ++- easybuild/easyconfigs/l/libxc/libxc-2.0.1-intel-2014b.eb | 3 ++- easybuild/easyconfigs/l/libxc/libxc-2.0.2-goolf-1.4.10.eb | 3 ++- easybuild/easyconfigs/l/libxc/libxc-2.0.2-ictce-5.3.0.eb | 3 ++- easybuild/easyconfigs/l/libxc/libxc-2.0.3-goolf-1.4.10.eb | 3 ++- easybuild/easyconfigs/l/libxc/libxc-2.2.0-intel-2014b.eb | 2 +- easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-2015.06.eb | 3 ++- easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-2015.11.eb | 3 ++- easybuild/easyconfigs/l/libxc/libxc-2.2.1-intel-2015a.eb | 2 +- easybuild/easyconfigs/l/libxc/libxc-2.2.2-CrayGNU-2015.11.eb | 3 ++- easybuild/easyconfigs/l/libxc/libxc-2.2.2-foss-2015b.eb | 3 ++- easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015a.eb | 2 +- easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015b.eb | 2 +- easybuild/easyconfigs/l/libxc/libxc-2.2.3-foss-2016b.eb | 2 ++ easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016a.eb | 2 +- easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016b.eb | 2 +- easybuild/easyconfigs/l/libxc/libxc-3.0.0-intel-2016a.eb | 2 +- easybuild/easyconfigs/l/libxc/libxc-3.0.0-intel-2016b.eb | 2 +- 20 files changed, 32 insertions(+), 19 deletions(-) diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.0.1-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libxc/libxc-2.0.1-goolf-1.4.10.eb index aaf083cf04..547b2c04e0 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.0.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.0.1-goolf-1.4.10.eb @@ -11,7 +11,8 @@ sources = [SOURCE_TAR_GZ] source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] toolchain = {'name': 'goolf', 'version': '1.4.10'} -toolchainopts = {'opt': True} +# Results for some functionals (e.g. mgga_c_tpss) deviate with too aggressive optimization settings. +toolchainopts = {'lowopt': True} configopts = 'FC="$F77" FCFLAGS="$FFLAGS" --enable-shared' diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.0.1-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libxc/libxc-2.0.1-ictce-5.3.0.eb index 0d7ebaf5fb..ba87bd535c 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.0.1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.0.1-ictce-5.3.0.eb @@ -11,7 +11,8 @@ sources = [SOURCE_TAR_GZ] source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] toolchain = {'name': 'ictce', 'version': '5.3.0'} -toolchainopts = {'opt': True} +# Results for some functionals (e.g. mgga_c_tpss) deviate with too aggressive optimization settings. +toolchainopts = {'lowopt': True} configopts = 'FC="$F77" FCFLAGS="$FFLAGS" --enable-shared' diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.0.1-ictce-5.5.0.eb b/easybuild/easyconfigs/l/libxc/libxc-2.0.1-ictce-5.5.0.eb index 635c9b4d96..e944b72c18 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.0.1-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.0.1-ictce-5.5.0.eb @@ -8,7 +8,8 @@ description = """Libxc is a library of exchange-correlation functionals for dens The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" toolchain = {'name': 'ictce', 'version': '5.5.0'} -toolchainopts = {'opt': True} +# Results for some functionals (e.g. mgga_c_tpss) deviate with too aggressive optimization settings. +toolchainopts = {'lowopt': True} sources = [SOURCE_TAR_GZ] source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.0.1-intel-2014b.eb b/easybuild/easyconfigs/l/libxc/libxc-2.0.1-intel-2014b.eb index dc228fe31b..b9e8982671 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.0.1-intel-2014b.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.0.1-intel-2014b.eb @@ -8,7 +8,8 @@ description = """Libxc is a library of exchange-correlation functionals for dens The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" toolchain = {'name': 'intel', 'version': '2014b'} -toolchainopts = {'opt': True} +# Results for some functionals (e.g. mgga_c_tpss) deviate with too aggressive optimization settings. +toolchainopts = {'lowopt': True} sources = [SOURCE_TAR_GZ] source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.0.2-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libxc/libxc-2.0.2-goolf-1.4.10.eb index f440f02af5..8bd05d53ad 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.0.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.0.2-goolf-1.4.10.eb @@ -11,7 +11,8 @@ sources = [SOURCE_TAR_GZ] source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] toolchain = {'name': 'goolf', 'version': '1.4.10'} -toolchainopts = {'opt': True} +# Results for some functionals (e.g. mgga_c_tpss) deviate with too aggressive optimization settings. +toolchainopts = {'lowopt': True} configopts = 'FC="$F77" FCFLAGS="$FFLAGS" FCCPP="/lib/cpp -ansi" --enable-shared' diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.0.2-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libxc/libxc-2.0.2-ictce-5.3.0.eb index df5b0a2ac4..22e411e0a3 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.0.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.0.2-ictce-5.3.0.eb @@ -11,7 +11,8 @@ sources = [SOURCE_TAR_GZ] source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] toolchain = {'name': 'ictce', 'version': '5.3.0'} -toolchainopts = {'opt': True} +# Results for some functionals (e.g. mgga_c_tpss) deviate with too aggressive optimization settings. +toolchainopts = {'lowopt': True} configopts = 'FC="$F77" FCFLAGS="$FFLAGS" --enable-shared --enable-fortran' diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.0.3-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libxc/libxc-2.0.3-goolf-1.4.10.eb index 674453ff55..51c0a0a535 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.0.3-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.0.3-goolf-1.4.10.eb @@ -11,7 +11,8 @@ sources = [SOURCE_TAR_GZ] source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] toolchain = {'name': 'goolf', 'version': '1.4.10'} -toolchainopts = {'opt': True} +# Results for some functionals (e.g. mgga_c_tpss) deviate with too aggressive optimization settings. +toolchainopts = {'lowopt': True} configopts = 'FC="$F77" FCFLAGS="$FFLAGS" FCCPP="/lib/cpp -ansi" --enable-shared' diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.0-intel-2014b.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.0-intel-2014b.eb index 8c8a06232c..45bb52f70b 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.2.0-intel-2014b.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.0-intel-2014b.eb @@ -8,7 +8,7 @@ description = """Libxc is a library of exchange-correlation functionals for dens The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" toolchain = {'name': 'intel', 'version': '2014b'} -# Results for some functions (e.g. mgga_c_tpss) change with too aggressive optimization settings. +# Results for some functionals (e.g. mgga_c_tpss) deviate with too aggressive optimization settings. toolchainopts = {'lowopt': True} sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-2015.06.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-2015.06.eb index d3176a0e56..39dc38965a 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-2015.06.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-2015.06.eb @@ -8,7 +8,8 @@ description = """Libxc is a library of exchange-correlation functionals for dens The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" toolchain = {'name': 'CrayGNU', 'version': '2015.06'} -toolchainopts = {'opt': True} +# Results for some functionals (e.g. mgga_c_tpss) deviate with too aggressive optimization settings. +toolchainopts = {'lowopt': True} sources = [SOURCE_TAR_GZ] source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-2015.11.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-2015.11.eb index f3870dc3fb..3ce46b5609 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-2015.11.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-2015.11.eb @@ -8,7 +8,8 @@ description = """Libxc is a library of exchange-correlation functionals for dens The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" toolchain = {'name': 'CrayGNU', 'version': '2015.11'} -toolchainopts = {'opt': True} +# Results for some functionals (e.g. mgga_c_tpss) deviate with too aggressive optimization settings. +toolchainopts = {'lowopt': True} sources = [SOURCE_TAR_GZ] source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.1-intel-2015a.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.1-intel-2015a.eb index 386fc2d5ba..3958efb9f5 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.2.1-intel-2015a.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.1-intel-2015a.eb @@ -8,7 +8,7 @@ description = """Libxc is a library of exchange-correlation functionals for dens The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" toolchain = {'name': 'intel', 'version': '2015a'} -# Results for some functions (e.g. mgga_c_tpss) change with too aggressive optimization settings. +# Results for some functionals (e.g. mgga_c_tpss) deviate with too aggressive optimization settings. toolchainopts = {'lowopt': True} sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.2-CrayGNU-2015.11.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.2-CrayGNU-2015.11.eb index 7a2ba48de6..3d0a5a1ed8 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.2.2-CrayGNU-2015.11.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.2-CrayGNU-2015.11.eb @@ -9,7 +9,8 @@ description = """Libxc is a library of exchange-correlation functionals for dens The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" toolchain = {'name': 'CrayGNU', 'version': '2015.11'} -toolchainopts = {'opt': True} +# Results for some functionals (e.g. mgga_c_tpss) deviate with too aggressive optimization settings. +toolchainopts = {'lowopt': True} sources = [SOURCE_TAR_GZ] source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.2-foss-2015b.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.2-foss-2015b.eb index 8e7a6d0b88..5df850f999 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.2.2-foss-2015b.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.2-foss-2015b.eb @@ -8,7 +8,8 @@ description = """Libxc is a library of exchange-correlation functionals for dens The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" toolchain = {'name': 'foss', 'version': '2015b'} -toolchainopts = {'opt': True} +# Results for some functionals (e.g. mgga_c_tpss) deviate with too aggressive optimization settings. +toolchainopts = {'lowopt': True} sources = [SOURCE_TAR_GZ] source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015a.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015a.eb index eef2248b2a..a3e00b811a 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015a.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015a.eb @@ -8,7 +8,7 @@ description = """Libxc is a library of exchange-correlation functionals for dens The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" toolchain = {'name': 'intel', 'version': '2015a'} -# Results for some functions (e.g. mgga_c_tpss) change with too aggressive optimization settings. +# Results for some functionals (e.g. mgga_c_tpss) deviate with too aggressive optimization settings. toolchainopts = {'lowopt': True} sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015b.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015b.eb index 658c339764..3dc273ca2e 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015b.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015b.eb @@ -8,7 +8,7 @@ description = """Libxc is a library of exchange-correlation functionals for dens The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" toolchain = {'name': 'intel', 'version': '2015b'} -# Results for some functions (e.g. mgga_c_tpss) change with too aggressive optimization settings. +# Results for some functionals (e.g. mgga_c_tpss) deviate with too aggressive optimization settings. toolchainopts = {'lowopt': True} sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.3-foss-2016b.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.3-foss-2016b.eb index 2ef9de2a2d..37456a8225 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.2.3-foss-2016b.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.3-foss-2016b.eb @@ -8,6 +8,8 @@ description = """Libxc is a library of exchange-correlation functionals for dens The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" toolchain = {'name': 'foss', 'version': '2016b'} +# Results for some functionals (e.g. mgga_c_tpss) deviate with too aggressive optimization settings. +toolchainopts = {'lowopt': True} sources = [SOURCE_TAR_GZ] source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016a.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016a.eb index 4cb658a639..56fa742d7d 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016a.eb @@ -8,7 +8,7 @@ description = """Libxc is a library of exchange-correlation functionals for dens The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" toolchain = {'name': 'intel', 'version': '2016a'} -# Results for some functions (e.g. mgga_c_tpss) change with too aggressive optimization settings. +# Results for some functionals (e.g. mgga_c_tpss) deviate with too aggressive optimization settings. toolchainopts = {'lowopt': True} sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016b.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016b.eb index 41bfb6c123..0fb5faa09c 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016b.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016b.eb @@ -8,7 +8,7 @@ description = """Libxc is a library of exchange-correlation functionals for dens The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" toolchain = {'name': 'intel', 'version': '2016b'} -# Results for some functions (e.g. mgga_c_tpss) change with too aggressive optimization settings. +# Results for some functionals (e.g. mgga_c_tpss) deviate with too aggressive optimization settings. toolchainopts = {'lowopt': True} sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/l/libxc/libxc-3.0.0-intel-2016a.eb b/easybuild/easyconfigs/l/libxc/libxc-3.0.0-intel-2016a.eb index e89a3a0020..e96102336e 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-3.0.0-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-3.0.0-intel-2016a.eb @@ -8,7 +8,7 @@ description = """Libxc is a library of exchange-correlation functionals for dens The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" toolchain = {'name': 'intel', 'version': '2016a'} -# Results for some functions (e.g. mgga_c_tpss) change with too aggressive optimization settings. +# Results for some functionals (e.g. mgga_c_tpss) deviate with too aggressive optimization settings. toolchainopts = {'lowopt': True} sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/l/libxc/libxc-3.0.0-intel-2016b.eb b/easybuild/easyconfigs/l/libxc/libxc-3.0.0-intel-2016b.eb index 812bf5438b..df3c9b9484 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-3.0.0-intel-2016b.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-3.0.0-intel-2016b.eb @@ -8,7 +8,7 @@ description = """Libxc is a library of exchange-correlation functionals for dens The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" toolchain = {'name': 'intel', 'version': '2016b'} -# Results for some functions (e.g. mgga_c_tpss) change with too aggressive optimization settings. +# Results for some functionals (e.g. mgga_c_tpss) deviate with too aggressive optimization settings. toolchainopts = {'lowopt': True} sources = [SOURCE_TAR_GZ] -- GitLab From f73bd7e2decc3596222e59328b8e7738384ab2eb Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Mon, 27 Feb 2017 16:00:51 +0100 Subject: [PATCH 0171/1603] ppicv->ippicv --- easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016b.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016b.eb index 7d801b065b..0292e9d416 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016b.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016b.eb @@ -41,7 +41,7 @@ dependencies = [ ] #The destination directory is "linux-" see 3rdparty/ippicv/downloader.cmake -ppicv_dir = '3rdparty/ippicv/downloads/linux-808b791a6eac9ed78d32a7666804320e/' +ippicv_dir = '3rdparty/ippicv/downloads/linux-808b791a6eac9ed78d32a7666804320e/' preconfigopts = "mkdir -p %s && cp -a ../*.tgz %s && " % (ippicv_dir, ippicv_dir) configopts = '-DCMAKE_BUILD_TYPE=RELEASE ' -- GitLab From 5ff58b2b990847489c0d7a8d41b7ff2d22680053 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 27 Feb 2017 20:34:03 +0100 Subject: [PATCH 0172/1603] add patch required to make building ea-utils with Intel compilers work --- .../ea-utils/ea-utils-1.04.807-intel-2016b.eb | 4 ++- .../ea-utils-1.04.807_include-unistd.patch | 35 +++++++++++++++++++ 2 files changed, 38 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/e/ea-utils/ea-utils-1.04.807_include-unistd.patch diff --git a/easybuild/easyconfigs/e/ea-utils/ea-utils-1.04.807-intel-2016b.eb b/easybuild/easyconfigs/e/ea-utils/ea-utils-1.04.807-intel-2016b.eb index 79eae70f31..a1c32a3e34 100644 --- a/easybuild/easyconfigs/e/ea-utils/ea-utils-1.04.807-intel-2016b.eb +++ b/easybuild/easyconfigs/e/ea-utils/ea-utils-1.04.807-intel-2016b.eb @@ -18,10 +18,12 @@ sources = ['%(version)s.tar.gz'] checksums = ['5972b9f712920603b7527f46c0063a09'] +patches = ['ea-utils-%(version)s_include-unistd.patch'] + start_dir = 'clipper' prebuildopts = "sed -i 's/$(CFLAGS)/$(CFLAGS) $(LDFLAGS) -I./' Makefile && PREFIX=%(installdir)s " -buildopts = 'fastq-mcf fastq-multx fastq-join fastq-stats fastq-clipper sam-stats varcall' +buildopts = 'CC="$CC" fastq-mcf fastq-multx fastq-join fastq-stats fastq-clipper sam-stats varcall' builddependencies = [ ('Perl', '5.24.0'), diff --git a/easybuild/easyconfigs/e/ea-utils/ea-utils-1.04.807_include-unistd.patch b/easybuild/easyconfigs/e/ea-utils/ea-utils-1.04.807_include-unistd.patch new file mode 100644 index 0000000000..3fb5b110e0 --- /dev/null +++ b/easybuild/easyconfigs/e/ea-utils/ea-utils-1.04.807_include-unistd.patch @@ -0,0 +1,35 @@ +fix for 'identifier "unlink" is undefined' and other similar errors + +author: Kenneth Hoste (HPC-UGent) +--- clipper/sparsehash-2.0.2/src/sparsetable_unittest.cc.orig 2017-02-27 19:11:30.059750601 +0100 ++++ clipper/sparsehash-2.0.2/src/sparsetable_unittest.cc 2017-02-27 19:13:28.438628098 +0100 +@@ -32,7 +32,7 @@ + // Since sparsetable is templatized, it's important that we test every + // function in every class in this file -- not just to see if it + // works, but even if it compiles. +- ++#include + #include + #include + #include +--- clipper/sparsehash-2.0.2/src/hashtable_test.cc.orig 2017-02-27 19:49:55.087723317 +0100 ++++ clipper/sparsehash-2.0.2/src/hashtable_test.cc 2017-02-27 19:50:14.027542195 +0100 +@@ -43,7 +43,7 @@ + // Note that since all these classes are templatized, it's important + // to call every public method on the class: not just to make sure + // they work, but to make sure they even compile. +- ++#include + #include + #include + #include +--- clipper/sparsehash-2.0.2/src/time_hash_map.cc.orig 2017-02-27 20:00:27.821672176 +0100 ++++ clipper/sparsehash-2.0.2/src/time_hash_map.cc 2017-02-27 20:00:57.411387012 +0100 +@@ -54,6 +54,7 @@ + // + // See PERFORMANCE for the output of one example run. + ++#include + #include + #include + #ifdef HAVE_INTTYPES_H -- GitLab From 6ac0bc393ce7afcbd1ea2270c0b8c105f885696f Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Tue, 28 Feb 2017 12:37:06 +0100 Subject: [PATCH 0173/1603] adding easyconfigs: cuDNN-5.1-CUDA-8.0.44.eb --- easybuild/easyconfigs/c/cuDNN/cuDNN-5.1-CUDA-8.0.44.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/cuDNN/cuDNN-5.1-CUDA-8.0.44.eb b/easybuild/easyconfigs/c/cuDNN/cuDNN-5.1-CUDA-8.0.44.eb index 0cbdeea8a4..08976a1f68 100644 --- a/easybuild/easyconfigs/c/cuDNN/cuDNN-5.1-CUDA-8.0.44.eb +++ b/easybuild/easyconfigs/c/cuDNN/cuDNN-5.1-CUDA-8.0.44.eb @@ -24,7 +24,7 @@ sources = ['%(namelower)s-8.0-linux-x64-v%(version)s.tgz'] dependencies = [('CUDA', cuda_version)] checksums = [ - '099ca6a9b21b35e32f3408eff2a1c06d', # cudnn-8.0-linux-x64-v5.1.tgz + '406f4ac7f7ee8aa9e41304c143461a69', # cudnn-8.0-linux-x64-v5.1.tgz, Jan 20 2017 download ] sanity_check_paths = { -- GitLab From 1afbb4489053f466b98d4b4e1e424c14c37eb946 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 28 Feb 2017 13:28:29 +0100 Subject: [PATCH 0174/1603] adding easyconfigs: OOMPA-3.1.2-intel-2016b-R-3.3.1.eb --- .../OOMPA/OOMPA-3.1.2-intel-2016b-R-3.3.1.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/o/OOMPA/OOMPA-3.1.2-intel-2016b-R-3.3.1.eb diff --git a/easybuild/easyconfigs/o/OOMPA/OOMPA-3.1.2-intel-2016b-R-3.3.1.eb b/easybuild/easyconfigs/o/OOMPA/OOMPA-3.1.2-intel-2016b-R-3.3.1.eb new file mode 100644 index 0000000000..1f054c18b4 --- /dev/null +++ b/easybuild/easyconfigs/o/OOMPA/OOMPA-3.1.2-intel-2016b-R-3.3.1.eb @@ -0,0 +1,44 @@ +easyblock = 'Bundle' + +name = 'OOMPA' +version = '3.1.2' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://r-forge.r-project.org/projects/oompa' +description = """OOMPA is a suite of R packages for the analysis of gene expression (RNA), proteomics profiling, + and other high throughput molecular biology data.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +dependencies = [ + ('R', '3.3.1'), + ('R-bundle-Bioconductor', '3.3', versionsuffix), +] + +ext_options = { + 'source_urls': ['http://download.r-forge.r-project.org/src/contrib/'], + 'source_tmpl': '%(name)s_%(version)s.tar.gz', +} + +exts_defaultclass = 'RPackage' +exts_filter = ("R -q --no-save", "library(%(ext_name)s)") + +# !! order of packages is important !! +exts_list = [ + ('oompaBase', '3.1.3', ext_options), + ('oompaData', '3.1.0', ext_options), + ('ClassComparison', '3.1.3', ext_options), + ('ClassDiscovery', '3.3.3', ext_options), + ('Polychrome', '0.8.1', ext_options), + ('PreProcess', '3.1.2', ext_options), + ('TailRank', '3.1.2', ext_options), +] + +modextrapaths = {'R_LIBS': ''} + +sanity_check_paths = { + 'files': [], + 'dirs': [name], +} + +moduleclass = 'lib' -- GitLab From dc8c67ec4f25cbd7821767e0f8392935824a5e4b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 28 Feb 2017 13:38:48 +0100 Subject: [PATCH 0175/1603] fix sanity_check_paths for OOMPA bundle --- .../easyconfigs/o/OOMPA/OOMPA-3.1.2-intel-2016b-R-3.3.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OOMPA/OOMPA-3.1.2-intel-2016b-R-3.3.1.eb b/easybuild/easyconfigs/o/OOMPA/OOMPA-3.1.2-intel-2016b-R-3.3.1.eb index 1f054c18b4..ddc58b8eb3 100644 --- a/easybuild/easyconfigs/o/OOMPA/OOMPA-3.1.2-intel-2016b-R-3.3.1.eb +++ b/easybuild/easyconfigs/o/OOMPA/OOMPA-3.1.2-intel-2016b-R-3.3.1.eb @@ -38,7 +38,7 @@ modextrapaths = {'R_LIBS': ''} sanity_check_paths = { 'files': [], - 'dirs': [name], + 'dirs': ['ClassComparison', 'ClassDiscovery', 'oompaBase', 'oompaData', 'Polychrome', 'PreProcess', 'TailRank'], } moduleclass = 'lib' -- GitLab From 66f753fe7a49f041fb043f7a10a5ca9c601c119d Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Tue, 28 Feb 2017 07:43:35 -0500 Subject: [PATCH 0176/1603] OpenMPI-2.*: remove --with-threads configure option. OpenMPI builds now warn they don't know --with-threads. See OpenMPI commit at https://github.com/open-mpi/ompi/commit/7a55d49ca78bcc157749c04027515f12b026ec33 sed -i 's/--with-threads=posix //' OpenMPI-2*.eb --- easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.0-GCC-5.2.0.eb | 2 +- easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.1-GCC-6.2.0-2.27.eb | 2 +- .../easyconfigs/o/OpenMPI/OpenMPI-2.0.1-gcccuda-2016.10.eb | 2 +- .../OpenMPI/OpenMPI-2.0.1-iccifort-2017.1.132-GCC-5.4.0-2.26.eb | 2 +- easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.2-GCC-6.3.0-2.27.eb | 2 +- 5 files changed, 5 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.0-GCC-5.2.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.0-GCC-5.2.0.eb index 23deffc8f4..e0524fac95 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.0-GCC-5.2.0.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.0-GCC-5.2.0.eb @@ -14,7 +14,7 @@ source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/d dependencies = [('hwloc', '1.11.3')] -configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --with-verbs ' +configopts = '--enable-shared --enable-mpi-thread-multiple --with-verbs ' configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.1-GCC-6.2.0-2.27.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.1-GCC-6.2.0-2.27.eb index aeb2a52e4c..fe84bc7c6d 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.1-GCC-6.2.0-2.27.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.1-GCC-6.2.0-2.27.eb @@ -14,7 +14,7 @@ source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/d dependencies = [('hwloc', '1.11.4')] -configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --with-verbs ' +configopts = '--enable-shared --enable-mpi-thread-multiple --with-verbs ' configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.1-gcccuda-2016.10.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.1-gcccuda-2016.10.eb index 3d626a7c80..109e8a754d 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.1-gcccuda-2016.10.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.1-gcccuda-2016.10.eb @@ -14,7 +14,7 @@ source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/d dependencies = [('hwloc', '1.11.4')] -configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --with-verbs ' +configopts = '--enable-shared --enable-mpi-thread-multiple --with-verbs ' configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support configopts += '--with-cuda=$CUDA_HOME ' # CUDA-aware build; N.B. --disable-dlopen is incompatible diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.1-iccifort-2017.1.132-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.1-iccifort-2017.1.132-GCC-5.4.0-2.26.eb index 7d74bf0639..d395a7e376 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.1-iccifort-2017.1.132-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.1-iccifort-2017.1.132-GCC-5.4.0-2.26.eb @@ -14,7 +14,7 @@ source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/d dependencies = [('hwloc', '1.11.4')] -configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --with-verbs ' +configopts = '--enable-shared --enable-mpi-thread-multiple --with-verbs ' configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.2-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.2-GCC-6.3.0-2.27.eb index c13ef6b657..171f894a0d 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.2-GCC-6.3.0-2.27.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.2-GCC-6.3.0-2.27.eb @@ -15,7 +15,7 @@ checksums = ['886698becc5bea8c151c0af2074b8392'] dependencies = [('hwloc', '1.11.5')] -configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --with-verbs ' +configopts = '--enable-shared --enable-mpi-thread-multiple --with-verbs ' configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading -- GitLab From 78346f0a9a063f7adbdb3361c1eb85017d8514cf Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 28 Feb 2017 14:28:18 +0100 Subject: [PATCH 0177/1603] adding easyconfigs: SpiecEasi-20160830-intel-2016b-R-3.3.1.eb --- .../SpiecEasi-20160830-intel-2016b-R-3.3.1.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/s/SpiecEasi/SpiecEasi-20160830-intel-2016b-R-3.3.1.eb diff --git a/easybuild/easyconfigs/s/SpiecEasi/SpiecEasi-20160830-intel-2016b-R-3.3.1.eb b/easybuild/easyconfigs/s/SpiecEasi/SpiecEasi-20160830-intel-2016b-R-3.3.1.eb new file mode 100644 index 0000000000..4b5fa1bf48 --- /dev/null +++ b/easybuild/easyconfigs/s/SpiecEasi/SpiecEasi-20160830-intel-2016b-R-3.3.1.eb @@ -0,0 +1,26 @@ +easyblock = 'RPackage' + +name = 'SpiecEasi' +version = '20160830' +commit = 'd705428' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://github.com/zdk123/SpiecEasi' +description = "Sparse InversE Covariance estimation for Ecological Association and Statistical Inference" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['https://github.com/zdk123/SpiecEasi/archive/'] +sources = ['%s.tar.gz' % commit] + +dependencies = [ + ('R', '3.3.1'), + ('R-bundle-Bioconductor', '3.3', versionsuffix), +] + +sanity_check_paths = { + 'files': [], + 'dirs': [name], +} + +moduleclass = 'lib' -- GitLab From 91d00909e037c6bfb00ce16fe3a5547e2b750b94 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 28 Feb 2017 15:41:57 +0200 Subject: [PATCH 0178/1603] adding easyconfigs: iomkl-2017a.eb --- ...11.5-iccifort-2017.1.132-GCC-6.3.0-2.27.eb | 27 +++++++++++++ .../i/imkl/imkl-2017.1.132-iompi-2017a.eb | 38 +++++++++++++++++++ easybuild/easyconfigs/i/iomkl/iomkl-2017a.eb | 24 ++++++++++++ easybuild/easyconfigs/i/iompi/iompi-2017a.eb | 21 ++++++++++ .../n/numactl/numactl-2.0.11-GCCcore-6.3.0.eb | 25 ++++++++++++ ....0.2-iccifort-2017.1.132-GCC-6.3.0-2.27.eb | 33 ++++++++++++++++ 6 files changed, 168 insertions(+) create mode 100644 easybuild/easyconfigs/h/hwloc/hwloc-1.11.5-iccifort-2017.1.132-GCC-6.3.0-2.27.eb create mode 100644 easybuild/easyconfigs/i/imkl/imkl-2017.1.132-iompi-2017a.eb create mode 100644 easybuild/easyconfigs/i/iomkl/iomkl-2017a.eb create mode 100644 easybuild/easyconfigs/i/iompi/iompi-2017a.eb create mode 100644 easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCCcore-6.3.0.eb create mode 100644 easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.2-iccifort-2017.1.132-GCC-6.3.0-2.27.eb diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.5-iccifort-2017.1.132-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.5-iccifort-2017.1.132-GCC-6.3.0-2.27.eb new file mode 100644 index 0000000000..51bcdefbaf --- /dev/null +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.5-iccifort-2017.1.132-GCC-6.3.0-2.27.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'hwloc' +version = '1.11.5' + +homepage = 'http://www.open-mpi.org/projects/hwloc/' +description = """The Portable Hardware Locality (hwloc) software package provides a portable abstraction + (across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including + NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various + system attributes such as cache and memory information as well as the locality of I/O devices such as + network interfaces, InfiniBand HCAs or GPUs. It primarily aims at helping applications with gathering + information about modern computing hardware so as to exploit it accordingly and efficiently.""" + +toolchain = {'name': 'iccifort', 'version': '2017.1.132-GCC-6.3.0-2.27'} + +source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] +sources = [SOURCE_TAR_GZ] + +checksums = ['8f5fe6a9be2eb478409ad5e640b2d3ba'] + +dependencies = [ + ('numactl', '2.0.11'), +] + +configopts = "--enable-libnuma=$EBROOTNUMACTL" + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-iompi-2017a.eb b/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-iompi-2017a.eb new file mode 100644 index 0000000000..38909739c9 --- /dev/null +++ b/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-iompi-2017a.eb @@ -0,0 +1,38 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild + +name = 'imkl' +version = '2017.1.132' + +homepage = 'http://software.intel.com/en-us/intel-mkl/' +description = """Intel Math Kernel Library is a library of highly optimized, + extensively threaded math routines for science, engineering, and financial + applications that require maximum performance. Core math functions include + BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.""" + +toolchain = {'name': 'iompi', 'version': '2017a'} + +sources = ['l_mkl_%(version)s.tgz'] +checksums = ['7911c0f777c4cb04225bf4518088939e'] + +dontcreateinstalldir = 'True' + +license_file = HOME + '/licenses/intel/license.lic' + +interfaces = True + +postinstallcmds = [ + # extract the examples + 'tar xvzf %(installdir)s/mkl/examples/examples_cluster_c.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_cluster_f.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_core_c.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_core_f.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_f95.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_mic_c.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_mic_f.tgz -C %(installdir)s/mkl/examples/' +] + +modextravars = { + 'MKL_EXAMPLES': '%(installdir)s/mkl/examples/', +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/iomkl/iomkl-2017a.eb b/easybuild/easyconfigs/i/iomkl/iomkl-2017a.eb new file mode 100644 index 0000000000..442a8f32cc --- /dev/null +++ b/easybuild/easyconfigs/i/iomkl/iomkl-2017a.eb @@ -0,0 +1,24 @@ +easyblock = "Toolchain" + +name = 'iomkl' +version = '2017a' + +homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' +description = """Intel Cluster Toolchain Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MKL & OpenMPI.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +compver = '2017.1.132' +gcc_maj_min = '6.3' +gccver = '%s.0' % gcc_maj_min +binutilsver = '2.27' +gccsuff = '-GCC-%s-%s' % (gccver, binutilsver) + +dependencies = [ + ('icc', compver, gccsuff), + ('ifort', compver, gccsuff), + ('OpenMPI', '2.0.2', '', ('iccifort', '%s%s' % (compver, gccsuff))), + ('imkl', '2017.1.132', '', ('iompi', version)), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/iompi/iompi-2017a.eb b/easybuild/easyconfigs/i/iompi/iompi-2017a.eb new file mode 100644 index 0000000000..6daa72b832 --- /dev/null +++ b/easybuild/easyconfigs/i/iompi/iompi-2017a.eb @@ -0,0 +1,21 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +easyblock = "Toolchain" + +name = 'iompi' +version = '2017a' + +homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' +description = """Intel C/C++ and Fortran compilers, alongside Intel MPI.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +compver = '2017.1.132' +compversuff = '-GCC-6.3.0-2.27' + +dependencies = [ + ('icc', compver, compversuff), + ('ifort', compver, compversuff), + ('OpenMPI', '2.0.2', '', ('iccifort', '%s%s' % (compver, compversuff))), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCCcore-6.3.0.eb b/easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..c6e873dfe1 --- /dev/null +++ b/easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCCcore-6.3.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'numactl' +version = '2.0.11' + +homepage = 'http://oss.sgi.com/projects/libnuma/' +description = """The numactl program allows you to run your application program on specific cpu's and memory nodes. + It does this by supplying a NUMA memory policy to the operating system before running your program. + The libnuma library provides convenient ways for you to add NUMA memory policies into your own program.""" + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} + +source_urls = ['ftp://oss.sgi.com/www/projects/libnuma/download/'] +sources = [SOURCE_TAR_GZ] + +checksums = ['d3bc88b7ddb9f06d60898f4816ae9127'] + +builddependencies = [('binutils', '2.27')] + +sanity_check_paths = { + 'files': ['bin/numactl', 'bin/numastat', 'lib/libnuma.%s' % SHLIB_EXT, 'lib/libnuma.a'], + 'dirs': ['share/man', 'include'] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.2-iccifort-2017.1.132-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.2-iccifort-2017.1.132-GCC-6.3.0-2.27.eb new file mode 100644 index 0000000000..7af5556760 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.2-iccifort-2017.1.132-GCC-6.3.0-2.27.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'OpenMPI' +version = '2.0.2' + +homepage = 'http://www.open-mpi.org/' +description = """The Open MPI Project is an open source MPI-2 implementation.""" + +toolchain = {'name': 'iccifort', 'version': '2017.1.132-GCC-6.3.0-2.27'} + +sources = [SOURCELOWER_TAR_GZ] + +source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads',] + +dependencies = [('hwloc', '1.11.5')] + +configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --with-verbs ' +configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path +configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support +configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading + +# needed for --with-verbs +osdependencies = [('libibverbs-dev', 'libibverbs-devel'),] + +libs = ["mpi_mpifh", "mpi", "ompitrace", "open-pal", "open-rte"] +sanity_check_paths = { + 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] + + ["include/%s.h" % x for x in ["mpi-ext", "mpif-config", "mpif", "mpi", "mpi_portable_platform"]], + 'dirs': [], +} + +moduleclass = 'mpi' -- GitLab From 42ce0387a380bb6e4dee94c7c46b4ed089f45097 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 28 Feb 2017 14:51:56 +0100 Subject: [PATCH 0179/1603] adding easyconfigs: randfold-2.0.1-intel-2016b.eb --- .../r/randfold/randfold-2.0.1-intel-2016b.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/r/randfold/randfold-2.0.1-intel-2016b.eb diff --git a/easybuild/easyconfigs/r/randfold/randfold-2.0.1-intel-2016b.eb b/easybuild/easyconfigs/r/randfold/randfold-2.0.1-intel-2016b.eb new file mode 100644 index 0000000000..e126b5aaec --- /dev/null +++ b/easybuild/easyconfigs/r/randfold/randfold-2.0.1-intel-2016b.eb @@ -0,0 +1,29 @@ +easyblock = 'MakeCp' + +name = 'randfold' +version = '2.0.1' + +homepage = 'http://bioinformatics.psb.ugent.be/software/details/Randfold' +description = "Minimum free energy of folding randomization test software" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['http://bioinformatics.psb.ugent.be/supplementary_data/erbon/nov2003/downloads/'] +sources = [SOURCE_TAR_GZ] + +cleanupoldinstall = False + +prebuildopts = "tar xfvz squid.tar.gz && cd squid-*/ && mkdir -p %(installdir)s && " +prebuildopts += "./configure --prefix=%(installdir)s && make && make install && cd .. && " +prebuildopts += "export CPATH=%(installdir)s/include:$CPATH && export LIBRARY_PATH=%(installdir)s/lib:$LIBRARY_PATH && " + +buildopts = 'CC="$CC" CFLAGS="$CFLAGS"' + +files_to_copy = [(['randfold'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/randfold'], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From 3267d3b1cff1437f05ae5f5452d4f4342a5419e3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 28 Feb 2017 14:56:09 +0100 Subject: [PATCH 0180/1603] clarify installing of included SQUID with comment --- easybuild/easyconfigs/r/randfold/randfold-2.0.1-intel-2016b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/r/randfold/randfold-2.0.1-intel-2016b.eb b/easybuild/easyconfigs/r/randfold/randfold-2.0.1-intel-2016b.eb index e126b5aaec..9858d48447 100644 --- a/easybuild/easyconfigs/r/randfold/randfold-2.0.1-intel-2016b.eb +++ b/easybuild/easyconfigs/r/randfold/randfold-2.0.1-intel-2016b.eb @@ -13,6 +13,7 @@ sources = [SOURCE_TAR_GZ] cleanupoldinstall = False +# also install included SQUID dependency, since it can't be found online anymore... prebuildopts = "tar xfvz squid.tar.gz && cd squid-*/ && mkdir -p %(installdir)s && " prebuildopts += "./configure --prefix=%(installdir)s && make && make install && cd .. && " prebuildopts += "export CPATH=%(installdir)s/include:$CPATH && export LIBRARY_PATH=%(installdir)s/lib:$LIBRARY_PATH && " -- GitLab From 411e66ce8fc8e34be3373f12198d99c0b84f5660 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 28 Feb 2017 16:02:11 +0200 Subject: [PATCH 0181/1603] iompi uses OpenMPI not Intel MPI. Fix description --- easybuild/easyconfigs/i/iompi/iompi-2017a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/i/iompi/iompi-2017a.eb b/easybuild/easyconfigs/i/iompi/iompi-2017a.eb index 6daa72b832..571b319a14 100644 --- a/easybuild/easyconfigs/i/iompi/iompi-2017a.eb +++ b/easybuild/easyconfigs/i/iompi/iompi-2017a.eb @@ -5,7 +5,7 @@ name = 'iompi' version = '2017a' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' -description = """Intel C/C++ and Fortran compilers, alongside Intel MPI.""" +description = """Intel C/C++ and Fortran compilers, alongside Open MPI.""" toolchain = {'name': 'dummy', 'version': 'dummy'} -- GitLab From 63337dd37a65dc82da76f9ed4748b058e6bcd7bf Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 28 Feb 2017 16:03:43 +0200 Subject: [PATCH 0182/1603] OpenMPI droped --with-threads configure option. See PR 4213 --- .../OpenMPI/OpenMPI-2.0.2-iccifort-2017.1.132-GCC-6.3.0-2.27.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.2-iccifort-2017.1.132-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.2-iccifort-2017.1.132-GCC-6.3.0-2.27.eb index 7af5556760..0a89a8a816 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.2-iccifort-2017.1.132-GCC-6.3.0-2.27.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.2-iccifort-2017.1.132-GCC-6.3.0-2.27.eb @@ -14,7 +14,7 @@ source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/d dependencies = [('hwloc', '1.11.5')] -configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --with-verbs ' +configopts = '--enable-shared --enable-mpi-thread-multiple --with-verbs ' configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading -- GitLab From 09869c2c5c361e4900492a81a806d38b9922ea5e Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 28 Feb 2017 16:04:55 +0200 Subject: [PATCH 0183/1603] Reduce variable setting to a minimum --- easybuild/easyconfigs/i/iomkl/iomkl-2017a.eb | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/i/iomkl/iomkl-2017a.eb b/easybuild/easyconfigs/i/iomkl/iomkl-2017a.eb index 442a8f32cc..032f6eb6a2 100644 --- a/easybuild/easyconfigs/i/iomkl/iomkl-2017a.eb +++ b/easybuild/easyconfigs/i/iomkl/iomkl-2017a.eb @@ -9,10 +9,7 @@ description = """Intel Cluster Toolchain Compiler Edition provides Intel C/C++ a toolchain = {'name': 'dummy', 'version': 'dummy'} compver = '2017.1.132' -gcc_maj_min = '6.3' -gccver = '%s.0' % gcc_maj_min -binutilsver = '2.27' -gccsuff = '-GCC-%s-%s' % (gccver, binutilsver) +gccsuff = '-GCC-6.3.0-2.27' dependencies = [ ('icc', compver, gccsuff), -- GitLab From 9285c4116f98be71004dd3f06d564e09df489b43 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 28 Feb 2017 16:07:47 +0200 Subject: [PATCH 0184/1603] Add checksum to OpenMPI config and fix style. --- .../OpenMPI-2.0.2-iccifort-2017.1.132-GCC-6.3.0-2.27.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.2-iccifort-2017.1.132-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.2-iccifort-2017.1.132-GCC-6.3.0-2.27.eb index 0a89a8a816..66e6aa8b1b 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.2-iccifort-2017.1.132-GCC-6.3.0-2.27.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.2-iccifort-2017.1.132-GCC-6.3.0-2.27.eb @@ -8,9 +8,9 @@ description = """The Open MPI Project is an open source MPI-2 implementation.""" toolchain = {'name': 'iccifort', 'version': '2017.1.132-GCC-6.3.0-2.27'} -sources = [SOURCELOWER_TAR_GZ] - source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads',] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['886698becc5bea8c151c0af2074b8392'] dependencies = [('hwloc', '1.11.5')] -- GitLab From 0a5a3aec3cba223f4c5efe9b5200784f8f682cf8 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 28 Feb 2017 16:10:13 +0200 Subject: [PATCH 0185/1603] Add HPL 2.2 as test case. --- .../easyconfigs/h/HPL/HPL-2.2-iomkl-2017a.eb | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.2-iomkl-2017a.eb diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.2-iomkl-2017a.eb b/easybuild/easyconfigs/h/HPL/HPL-2.2-iomkl-2017a.eb new file mode 100644 index 0000000000..77dc4ed21f --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.2-iomkl-2017a.eb @@ -0,0 +1,18 @@ +name = 'HPL' +version = '2.2' + +homepage = 'http://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic + on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the + High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'iomkl', 'version': '2017a'} +toolchainopts = {'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] + +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] + +moduleclass = 'tools' -- GitLab From 8ff202b1373c6545541888371edd6c877c92514b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 28 Feb 2017 15:10:40 +0100 Subject: [PATCH 0186/1603] {bio}[intel/2016b] ViennaRNA v2.2.3 --- .../ViennaRNA/ViennaRNA-2.2.3-intel-2016b.eb | 48 +++++++++++++++++++ .../ViennaRNA-2.2.3_fix-pragma.patch | 41 ++++++++++++++++ 2 files changed, 89 insertions(+) create mode 100644 easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.2.3-intel-2016b.eb create mode 100644 easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.2.3_fix-pragma.patch diff --git a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.2.3-intel-2016b.eb b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.2.3-intel-2016b.eb new file mode 100644 index 0000000000..039ce2f3b3 --- /dev/null +++ b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.2.3-intel-2016b.eb @@ -0,0 +1,48 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Cedric Laczny , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + +easyblock = 'ConfigureMake' + +name = 'ViennaRNA' +version = '2.2.3' + +homepage = 'http://www.tbi.univie.ac.at/~ronny/RNA/vrna2.html' +description = """The Vienna RNA Package consists of a C code library and several +stand-alone programs for the prediction and comparison of RNA secondary structures.""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'pic': True, 'openmp': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://www.tbi.univie.ac.at/~ronny/RNA/packages/source'] + +patches = ['ViennaRNA-%(version)s_fix-pragma.patch'] + +# Prevents the "make install" step from trying to copy to _global_ perl dir and thus make easybuild fail. +configopts = '--without-perl' +# Alternatively, you may want to use the following to copy the perl-module to a "local" directory +# Code NOT yet tested, therefor left here for future recycling +# preconfigopts = 'env PERLPREFIX="/path/where/the/perl/module/shoud/go"' + +buildopts = 'VERBOSE=1 V=1' + +sanity_check_paths = { + 'files': ['bin/RNA%s' % x for x in ['fold', 'eval', 'heat', 'pdist', 'distance', + 'inverse', 'plot', 'subopt', 'Lfold', 'cofold', + 'paln', 'duplex', 'alifold', 'plfold', 'up', + 'aliduplex', 'Lalifold', '2Dfold', 'parconv', + 'PKplex', 'plex', 'snoop', 'forester']] + + ['bin/Kinfold'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.2.3_fix-pragma.patch b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.2.3_fix-pragma.patch new file mode 100644 index 0000000000..b53cab1fff --- /dev/null +++ b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.2.3_fix-pragma.patch @@ -0,0 +1,41 @@ +fix #pragma statements for building with Intel compilers + +author: Kenneth Hoste (HPC-UGent) + +--- ViennaRNA-2.2.3/src/ViennaRNA/plex.c.orig 2017-02-28 14:02:21.733634118 +0100 ++++ ViennaRNA-2.2.3/src/ViennaRNA/plex.c 2017-02-28 14:02:31.303877232 +0100 +@@ -410,7 +410,7 @@ + by = (int**) vrna_alloc(sizeof(int *) * (n3+1)); + inx= (int**) vrna_alloc(sizeof(int *) * (n3+1)); + iny= (int**) vrna_alloc(sizeof(int *) * (n3+1)); +- #pragma omp ++ #pragma omp parallel for + for (i=0; i<=n3; i++){ + c[i] = (int *) vrna_alloc(sizeof(int) * (n4+1)); + in[i] = (int *) vrna_alloc(sizeof(int) * (n4+1)); +--- ViennaRNA-2.2.3/src/Kinfold/cache.c.orig 2017-02-28 14:16:36.074432301 +0100 ++++ ViennaRNA-2.2.3/src/Kinfold/cache.c 2017-02-28 14:16:38.544493318 +0100 +@@ -56,7 +56,6 @@ + 61,59,53,47,43,41,37,31,29,23,17,13,11,7,3,1}; + + /* key must not be longer than 128 */ +-#pragma inline (cache_f) + unsigned cache_f(char *x) { + register char *s; + register int i; +@@ -80,6 +79,7 @@ + int cacheval; + cache_entry *c; + ++ #pragma inline (cache_f) + cacheval=cache_f(x); + if ((c=cachetab[cacheval])) + if (strcmp(c->structure,x)==0) return c; +@@ -92,6 +92,7 @@ + int cacheval; + cache_entry *c; + ++ #pragma inline (cache_f) + cacheval=cache_f(x->structure); + if ((c=cachetab[cacheval])) { + free(c->structure); -- GitLab From 7b0ef57b38446a7307e6ee02a0bc3944954327b4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 28 Feb 2017 15:13:00 +0100 Subject: [PATCH 0187/1603] adding easyconfigs: Bowtie-1.1.2-intel-2016b.eb --- .../b/Bowtie/Bowtie-1.1.2-intel-2016b.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2-intel-2016b.eb diff --git a/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2-intel-2016b.eb b/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2-intel-2016b.eb new file mode 100644 index 0000000000..eeada6c5ac --- /dev/null +++ b/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2-intel-2016b.eb @@ -0,0 +1,23 @@ +# Modified from existing version by: +# Robert Schmidt +# Ottawa Hospital Research Institute - Bioinformatics Team +name = 'Bowtie' +version = '1.1.2' + +homepage = 'http://bowtie-bio.sourceforge.net/index.shtml' +description = """Bowtie is an ultrafast, memory-efficient short read aligner. +It aligns short DNA sequences (reads) to the human genome. +""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'pic': True} + +sources = ['%(namelower)s-%(version)s-src.zip'] +source_urls = ['http://download.sourceforge.net/bowtie-bio/'] + +patches = [ + 'int64typedef.patch', + 'Bowtie-%(version)s_void2int.patch' +] + +moduleclass = 'bio' -- GitLab From f6ba9f30dd604bf161eb9bc3b28c9a772ecd7092 Mon Sep 17 00:00:00 2001 From: Maxime Boissonneault Date: Tue, 28 Feb 2017 15:16:06 +0000 Subject: [PATCH 0188/1603] Added recipe for JasPer 2.0.10. Recent versions use CMake rather than Configure --- .../j/JasPer/JasPer-2.0.10-intel-2016b.eb | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/j/JasPer/JasPer-2.0.10-intel-2016b.eb diff --git a/easybuild/easyconfigs/j/JasPer/JasPer-2.0.10-intel-2016b.eb b/easybuild/easyconfigs/j/JasPer/JasPer-2.0.10-intel-2016b.eb new file mode 100644 index 0000000000..bf07f73dff --- /dev/null +++ b/easybuild/easyconfigs/j/JasPer/JasPer-2.0.10-intel-2016b.eb @@ -0,0 +1,22 @@ +easyblock = 'CMakeMake' + +name = 'JasPer' +version = '2.0.10' + +homepage = 'http://www.ece.uvic.ca/~frodo/jasper/' +description = """The JasPer Project is an open-source initiative to provide a free + software-based reference implementation of the codec specified in the JPEG-2000 Part-1 standard.""" + +separate_build_dir = True +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.ece.uvic.ca/~frodo/jasper/software/'] + +sanity_check_paths = { + 'files': ["bin/jasper", "lib64/libjasper.so"], + 'dirs': ["include"], +} + +moduleclass = 'vis' -- GitLab From c0f7edae47fa7f32c4aef11f36d23b35296b57b8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 28 Feb 2017 17:38:29 +0100 Subject: [PATCH 0189/1603] remove verbose buildopts --- .../easyconfigs/v/ViennaRNA/ViennaRNA-2.2.3-intel-2016b.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.2.3-intel-2016b.eb b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.2.3-intel-2016b.eb index 039ce2f3b3..714f3edc9e 100644 --- a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.2.3-intel-2016b.eb +++ b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.2.3-intel-2016b.eb @@ -33,8 +33,6 @@ configopts = '--without-perl' # Code NOT yet tested, therefor left here for future recycling # preconfigopts = 'env PERLPREFIX="/path/where/the/perl/module/shoud/go"' -buildopts = 'VERBOSE=1 V=1' - sanity_check_paths = { 'files': ['bin/RNA%s' % x for x in ['fold', 'eval', 'heat', 'pdist', 'distance', 'inverse', 'plot', 'subopt', 'Lfold', 'cofold', -- GitLab From c4e9582b13a794b284ae9ffeccbbd3e486bab85c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 28 Feb 2017 18:08:41 +0100 Subject: [PATCH 0190/1603] add PDF::API2 extension to Perl 5.24.0 easyconfigs + sync exts_list --- .../easyconfigs/p/Perl/Perl-5.24.0-GCC-5.4.0-2.26.eb | 4 ++++ easybuild/easyconfigs/p/Perl/Perl-5.24.0-GCCcore-4.9.3.eb | 8 ++++++++ easybuild/easyconfigs/p/Perl/Perl-5.24.0-foss-2016b.eb | 8 ++++++++ easybuild/easyconfigs/p/Perl/Perl-5.24.0-intel-2016b.eb | 8 ++++++++ 4 files changed, 28 insertions(+) diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.24.0-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/p/Perl/Perl-5.24.0-GCC-5.4.0-2.26.eb index 78af957181..f39c5f51b0 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.24.0-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.24.0-GCC-5.4.0-2.26.eb @@ -883,6 +883,10 @@ exts_list = [ 'source_tmpl': 'Text-Template-1.46.tar.gz', 'source_urls': ['http://search.cpan.org/CPAN/authors/id/M/MJ/MJD'], }), + ('PDF::API2', '2.031', { + 'source_tmpl': 'PDF-API2-2.031.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/S/SS/SSIMMS/'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.24.0-GCCcore-4.9.3.eb b/easybuild/easyconfigs/p/Perl/Perl-5.24.0-GCCcore-4.9.3.eb index dc1a3cef69..47164262e3 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.24.0-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.24.0-GCCcore-4.9.3.eb @@ -881,6 +881,14 @@ exts_list = [ 'source_tmpl': 'MailTools-2.18.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARKOV'], }), + ('Text::Template', '1.46', { + 'source_tmpl': 'Text-Template-1.46.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/M/MJ/MJD'], + }), + ('PDF::API2', '2.031', { + 'source_tmpl': 'PDF-API2-2.031.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/S/SS/SSIMMS/'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.24.0-foss-2016b.eb b/easybuild/easyconfigs/p/Perl/Perl-5.24.0-foss-2016b.eb index 77e0aab0f1..3f4c7638c7 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.24.0-foss-2016b.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.24.0-foss-2016b.eb @@ -879,6 +879,14 @@ exts_list = [ 'source_tmpl': 'MailTools-2.18.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARKOV'], }), + ('Text::Template', '1.46', { + 'source_tmpl': 'Text-Template-1.46.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/M/MJ/MJD'], + }), + ('PDF::API2', '2.031', { + 'source_tmpl': 'PDF-API2-2.031.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/S/SS/SSIMMS/'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.24.0-intel-2016b.eb b/easybuild/easyconfigs/p/Perl/Perl-5.24.0-intel-2016b.eb index 087478fa1f..8fd86e040f 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.24.0-intel-2016b.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.24.0-intel-2016b.eb @@ -880,6 +880,14 @@ exts_list = [ 'source_tmpl': 'MailTools-2.18.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARKOV'], }), + ('Text::Template', '1.46', { + 'source_tmpl': 'Text-Template-1.46.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/M/MJ/MJD'], + }), + ('PDF::API2', '2.031', { + 'source_tmpl': 'PDF-API2-2.031.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/S/SS/SSIMMS/'], + }), ] moduleclass = 'lang' -- GitLab From ce9b46c84cf474d3e1c8af7c31a84cf881731cde Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 28 Feb 2017 18:11:47 +0100 Subject: [PATCH 0191/1603] adding easyconfigs: BLASR-2.2-intel-2016b.eb --- .../b/BLASR/BLASR-2.2-intel-2016b.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/b/BLASR/BLASR-2.2-intel-2016b.eb diff --git a/easybuild/easyconfigs/b/BLASR/BLASR-2.2-intel-2016b.eb b/easybuild/easyconfigs/b/BLASR/BLASR-2.2-intel-2016b.eb new file mode 100644 index 0000000000..ea4423904f --- /dev/null +++ b/easybuild/easyconfigs/b/BLASR/BLASR-2.2-intel-2016b.eb @@ -0,0 +1,37 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = 'ConfigureMake' + +name = 'BLASR' +version = '2.2' + +homepage = 'https://github.com/PacificBiosciences/blasr' +description = """ BLASR (Basic Local Alignment with Successive Refinement) rapidly maps + reads to genomes by finding the highest scoring local alignment or set of local alignments + between the read and the genome. Optimized for PacBio's extraordinarily long reads and + taking advantage of rich quality values, BLASR maps reads rapidly with high accuracy. """ + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['https://github.com/PacificBiosciences/blasr/archive/'] +sources = ['smrtanalysis-%(version)s.tar.gz'] + +dependencies = [('HDF5', '1.8.18')] + +skipsteps = ['configure'] + +# the STATIC= option is a workaround. Check details here: +# https://github.com/PacificBiosciences/blasr/issues/4#issuecomment-44142749 +buildopts = ' STATIC= ' + +installopts = ' INSTALL_BIN_DIR=%(installdir)s/bin' + +sanity_check_paths = { + 'files': ["bin/blasr"], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From 907f6bd2d2ff68a363db89ae9888a3f5dd190c34 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 28 Feb 2017 18:13:23 +0100 Subject: [PATCH 0192/1603] adding easyconfigs: networkx-1.1-intel-2016b-Python-2.7.12.eb --- .../networkx-1.1-intel-2016b-Python-2.7.12.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/n/networkx/networkx-1.1-intel-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/n/networkx/networkx-1.1-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/n/networkx/networkx-1.1-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..00b1f15044 --- /dev/null +++ b/easybuild/easyconfigs/n/networkx/networkx-1.1-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'networkx' +version = '1.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pypi.python.org/pypi/networkx' +description = """NetworkX is a Python package for the creation, manipulation, and study of the structure, dynamics, + and functions of complex networks.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.12'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' -- GitLab From 131240ae80a3bad7327bd8aa9d3288e31d182c87 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 28 Feb 2017 18:14:08 +0100 Subject: [PATCH 0193/1603] adding easyconfigs: PBSuite-15.8.24-intel-2016b-Python-2.7.12.eb --- ...Suite-15.8.24-intel-2016b-Python-2.7.12.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/p/PBSuite/PBSuite-15.8.24-intel-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/p/PBSuite/PBSuite-15.8.24-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/PBSuite/PBSuite-15.8.24-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..8626be9af4 --- /dev/null +++ b/easybuild/easyconfigs/p/PBSuite/PBSuite-15.8.24-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,35 @@ +easyblock = 'Tarball' + +name = 'PBSuite' +version = '15.8.24' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://sourceforge.net/p/pb-jelly/wiki/Home/' +description = """PBJelly is a highly automated pipeline that aligns long sequencing reads (such as PacBio RS reads or + long 454 reads in fasta format) to high-confidence draft assembles.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['https://sourceforge.net/projects/pb-jelly/files/latest/download'] +sources = ['%(name)s_%(version)s.tar.gz'] + +dependencies = [ + ('Python', '2.7.12'), + ('networkx', '1.1', versionsuffix), + ('BLASR', '2.2'), +] + +modextrapaths = { + 'PATH': 'bin', + 'PYTHONPATH': '', +} +modextravars = {'SWEETPATH': '%(installdir)s'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['bin', 'pbsuite'], +} + +sanity_check_commands = ["python -c 'import pbsuite'"] + +moduleclass = 'bio' -- GitLab From c859967dea863d871094e07fb7c7f2ba539675c4 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Tue, 28 Feb 2017 18:19:18 +0100 Subject: [PATCH 0194/1603] adding easyconfigs: Python-2.7.13-foss-2016b-bare.eb, Tkinter-2.7.13-foss-2016b-Python-2.7.13-bare.eb --- .../p/Python/Python-2.7.13-foss-2016b-bare.eb | 147 ++++++++++++++++++ ...er-2.7.13-foss-2016b-Python-2.7.13-bare.eb | 30 ++++ 2 files changed, 177 insertions(+) create mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.13-foss-2016b-bare.eb create mode 100755 easybuild/easyconfigs/t/Tkinter/Tkinter-2.7.13-foss-2016b-Python-2.7.13-bare.eb diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.13-foss-2016b-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.13-foss-2016b-bare.eb new file mode 100644 index 0000000000..4c330ffc74 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.13-foss-2016b-bare.eb @@ -0,0 +1,147 @@ +name = 'Python' +version = '2.7.13' +versionsuffix = '-bare' + +homepage = 'http://python.org/' +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively. + + This is a version without Tk or X11.""" + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +# python needs bzip2 to build the bz2 package +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libreadline', '6.3'), + ('ncurses', '6.0'), + ('SQLite', '3.13.0'), + ('GMP', '6.1.2'), + ('libffi', '3.2.1'), + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.2h'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# order is important! +# package versions updated 9th February 2017 +# using easy_update +# the commented out extensions were added by easy_update but broke the build +exts_list = [ + ('six', '1.10.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), + #('packaging', '16.8', { + # 'source_urls': ['https://pypi.python.org/packages/source/p/packaging/'], + #}), + #('pyparsing', '2.1.10', { + # 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], + #}), + #('appdirs', '1.4.0', { + # 'source_urls': ['https://pypi.python.org/packages/source/a/appdirs/'], + #}), + ('setuptools', '32.3.1', { + 'source_tmpl': '%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], + }), + ('pip', '9.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], + }), + ('nose', '1.3.7', { + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], + }), + ('numpy', '1.12.0', { + 'source_tmpl': '%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/n/numpy'], + }), + ('scipy', '0.18.1', { + 'source_urls': ['https://pypi.python.org/packages/source/s/scipy'], + }), + ('blist', '1.3.6', { + 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], + }), + ('mpi4py', '2.0.0', { + 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + }), + ('paycheck', '1.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], + }), + ('pbr', '1.10.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], + }), + ('lockfile', '0.12.2', { + 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], + }), + ('Cython', '0.25.2', { + 'source_urls': ['https://pypi.python.org/packages/source/c/cython/'], + }), + ('dateutil', '2.5.3', { + 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], + }), + ('deap', '1.0.2', { + 'source_tmpl': '%(name)s-%(version)s.post2.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], + }), + ('decorator', '4.0.11', { + 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], + }), + ('arff', '2.1.0', { + 'source_tmpl': 'liac-%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], + }), + ('pycrypto', '2.6.1', { + 'modulename': 'Crypto', + 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + }), + ('ecdsa', '0.13', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), + ('cryptography', '1.7.2', { + 'source_urls': ['https://pypi.python.org/packages/source/c/cryptography/'], + }), + ('pyasn1', '0.2.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyasn1/'], + }), + ('paramiko', '2.1.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], + }), + ('netifaces', '0.10.5', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], + }), + ('netaddr', '0.7.19', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], + }), + ('funcsigs', '1.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/f/funcsigs'], + }), + ('mock', '2.0.0', { + 'source_urls': ['https://pypi.python.org/packages/source/m/mock'], + }), + ('pytz', '2016.10', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pytz'], + }), + ('pandas', '0.19.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], + }), + ('enum34', '1.1.6', { + 'modulename': 'enum', + 'source_urls': ['https://pypi.python.org/packages/source/e/enum34'], + }), + ('bitstring', '3.1.5', { + 'source_tmpl': '%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/b/bitstring'], + }), + ('virtualenv', '15.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/v/virtualenv'], + }), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/t/Tkinter/Tkinter-2.7.13-foss-2016b-Python-2.7.13-bare.eb b/easybuild/easyconfigs/t/Tkinter/Tkinter-2.7.13-foss-2016b-Python-2.7.13-bare.eb new file mode 100755 index 0000000000..4f9e88dceb --- /dev/null +++ b/easybuild/easyconfigs/t/Tkinter/Tkinter-2.7.13-foss-2016b-Python-2.7.13-bare.eb @@ -0,0 +1,30 @@ +easyblock = 'EB_TkinterPython' +# TODO: +# only build the Tkinter parts we want +# using further easyblock customisation + +name = 'Tkinter' +version = '2.7.13' +versionsuffix = '-Python-%(version)s-bare' + +homepage = 'http://python.org/' +description = """Tkinter module, built with the Python buildsystem""" + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.python.org/ftp/python/%(version)s/'] +sources = ['Python-%(version)s.tgz'] + +postinstallcmds = [ ' mv %(installdir)s/lib/python%(pyshortver)s/lib-tk %(installdir)s/lib/ && mv %(installdir)s/lib/python%(pyshortver)s/lib-dynload/_tkinter.so %(installdir)s/lib/ && rm -rf %(installdir)s/lib/python%(pyshortver)s/* && mv %(installdir)s/lib/lib-tk %(installdir)s/lib/python%(pyshortver)s/ && mkdir %(installdir)s/lib/python%(pyshortver)s/lib-dynload && mv %(installdir)s/lib/_tkinter.so %(installdir)s/lib/python%(pyshortver)s/lib-dynload && rm %(installdir)s/bin/python ' ] + +dependencies = [ + ('Python', '2.7.13', '-bare'), + ('Tcl', '8.6.5'), + ('Tk', '8.6.5', '-libX11-1.6.3'), + ('xproto', '7.0.28'), +] + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/lib-dynload:lib/python%(pyshortver)s/lib-tk']} + +moduleclass = 'lang' -- GitLab From 650c707845c54ac8843d0a0b62ef80e2f24976a6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 28 Feb 2017 18:43:33 +0100 Subject: [PATCH 0195/1603] fix check for Szip library in configure script for netCDF 4.1.3 --- .../n/netCDF/netCDF-4.1.3-goolf-1.4.10.eb | 3 +++ .../n/netCDF/netCDF-4.1.3-ictce-5.3.0.eb | 2 ++ .../netCDF-4.1.3_fix-Szip-link-check.patch | 16 ++++++++++++++++ 3 files changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/n/netCDF/netCDF-4.1.3_fix-Szip-link-check.patch diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.1.3-goolf-1.4.10.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.1.3-goolf-1.4.10.eb index 6aa937d650..55b91cb833 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.1.3-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.1.3-goolf-1.4.10.eb @@ -5,6 +5,7 @@ homepage = 'http://www.unidata.ucar.edu/software/netcdf/' description = """NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.""" + toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'pic': True} @@ -14,6 +15,8 @@ source_urls = [ 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', ] +patches = ['netCDF-%(version)s_fix-Szip-link-check.patch'] + dependencies = [('HDF5', '1.8.7')] moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.1.3-ictce-5.3.0.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.1.3-ictce-5.3.0.eb index 36ab674b3d..d130575666 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.1.3-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.1.3-ictce-5.3.0.eb @@ -15,6 +15,8 @@ source_urls = [ 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', ] +patches = ['netCDF-%(version)s_fix-Szip-link-check.patch'] + dependencies = [ ('HDF5', '1.8.9'), ('Doxygen', '1.8.1.1'), diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.1.3_fix-Szip-link-check.patch b/easybuild/easyconfigs/n/netCDF/netCDF-4.1.3_fix-Szip-link-check.patch new file mode 100644 index 0000000000..2e44c10cb4 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.1.3_fix-Szip-link-check.patch @@ -0,0 +1,16 @@ +make configure script look for correct Szip library +see also https://www.unidata.ucar.edu/support/help/MailArchives/netcdf/msg10433.html + +author: Kenneth Hoste (HPC-UGent) + +--- netcdf-4.1.3/configure.orig 2017-02-28 17:55:46.681729087 +0100 ++++ netcdf-4.1.3/configure 2017-02-28 17:55:52.391876458 +0100 +@@ -27142,7 +27142,7 @@ + return 0; + } + _ACEOF +-for ac_lib in '' szip; do ++for ac_lib in '' sz; do + if test -z "$ac_lib"; then + ac_res="none required" + else -- GitLab From 04873c91d34c1c9971889e9505afcfa323c2ea83 Mon Sep 17 00:00:00 2001 From: Maxime Boissonneault Date: Tue, 28 Feb 2017 18:52:19 +0000 Subject: [PATCH 0196/1603] cosmetic change --- easybuild/easyconfigs/j/JasPer/JasPer-2.0.10-intel-2016b.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/j/JasPer/JasPer-2.0.10-intel-2016b.eb b/easybuild/easyconfigs/j/JasPer/JasPer-2.0.10-intel-2016b.eb index bf07f73dff..5bc0738e10 100644 --- a/easybuild/easyconfigs/j/JasPer/JasPer-2.0.10-intel-2016b.eb +++ b/easybuild/easyconfigs/j/JasPer/JasPer-2.0.10-intel-2016b.eb @@ -7,13 +7,14 @@ homepage = 'http://www.ece.uvic.ca/~frodo/jasper/' description = """The JasPer Project is an open-source initiative to provide a free software-based reference implementation of the codec specified in the JPEG-2000 Part-1 standard.""" -separate_build_dir = True toolchain = {'name': 'intel', 'version': '2016b'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.ece.uvic.ca/~frodo/jasper/software/'] +separate_build_dir = True + sanity_check_paths = { 'files': ["bin/jasper", "lib64/libjasper.so"], 'dirs': ["include"], -- GitLab From 98456570308e7a91e4109d0bb18bb26c05bbdf08 Mon Sep 17 00:00:00 2001 From: Maxime Boissonneault Date: Tue, 28 Feb 2017 19:11:27 +0000 Subject: [PATCH 0197/1603] added cmake build dependency --- easybuild/easyconfigs/j/JasPer/JasPer-2.0.10-intel-2016b.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/j/JasPer/JasPer-2.0.10-intel-2016b.eb b/easybuild/easyconfigs/j/JasPer/JasPer-2.0.10-intel-2016b.eb index 5bc0738e10..23bfbfb00d 100644 --- a/easybuild/easyconfigs/j/JasPer/JasPer-2.0.10-intel-2016b.eb +++ b/easybuild/easyconfigs/j/JasPer/JasPer-2.0.10-intel-2016b.eb @@ -13,6 +13,8 @@ toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.ece.uvic.ca/~frodo/jasper/software/'] +builddependencies = [('CMake', '3.6.1')] + separate_build_dir = True sanity_check_paths = { -- GitLab From c341b8bbe3fe8a14a7e181d806548ca1f4b3113b Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 1 Mar 2017 10:15:45 +0800 Subject: [PATCH 0198/1603] fix source_urls --- easybuild/easyconfigs/b/bsoft/bsoft-1.8.8-goolf-1.5.14.eb | 3 ++- .../c/cutadapt/cutadapt-1.5-goolf-1.4.10-Python-2.7.10.eb | 3 ++- easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.5.7-goolf-1.4.10.eb | 3 ++- easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.5.7-ictce-5.3.0.eb | 3 ++- easybuild/easyconfigs/g/GnuTLS/GnuTLS-3.1.8-goolf-1.4.10.eb | 3 ++- .../i/ImageMagick/ImageMagick-6.9.4-8-intel-2016a.eb | 5 +++-- .../i/ImageMagick/ImageMagick-7.0.1-6-intel-2016a.eb | 5 +++-- .../i/ImageMagick/ImageMagick-7.0.1-9-intel-2016a.eb | 5 +++-- .../i/ImageMagick/ImageMagick-7.0.2-9-intel-2016a.eb | 5 +++-- .../i/ImageMagick/ImageMagick-7.0.3-1-intel-2016b.eb | 5 +++-- .../easyconfigs/l/LibTIFF/LibTIFF-4.0.3-intel-2015a.eb | 6 +++++- .../easyconfigs/l/LibTIFF/LibTIFF-4.0.3-intel-2015b.eb | 6 +++++- .../Mercurial/Mercurial-2.3.2-goolf-1.4.10-Python-2.7.3.eb | 3 ++- .../m/Mercurial/Mercurial-2.3.2-ictce-5.3.0-Python-2.7.3.eb | 3 ++- .../Mercurial/Mercurial-2.5.2-goolf-1.4.10-Python-2.7.3.eb | 3 ++- .../m/Mercurial/Mercurial-2.5.2-ictce-5.3.0-Python-2.7.3.eb | 3 ++- .../m/Mercurial/Mercurial-3.2.4-foss-2015a-Python-2.7.9.eb | 3 ++- .../n/netCDF-Fortran/netCDF-Fortran-4.2-ictce-6.1.5.eb | 6 +++++- easybuild/easyconfigs/n/netCDF/netCDF-4.2-ictce-5.4.0.eb | 6 +++++- easybuild/easyconfigs/n/netCDF/netCDF-4.2-intel-2014b.eb | 6 +++++- .../easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-5.4.0.eb | 6 +++++- .../easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-6.1.5.eb | 6 +++++- easybuild/easyconfigs/p/pigz/pigz-2.3.1-goolf-1.4.10.eb | 5 +++-- easybuild/easyconfigs/p/pigz/pigz-2.3.1-ictce-6.2.5.eb | 5 +++-- easybuild/easyconfigs/p/pigz/pigz-2.3.3-foss-2015b.eb | 5 +++-- easybuild/easyconfigs/r/ROOT/ROOT-v5.30.06-goolf-1.4.10.eb | 3 ++- easybuild/easyconfigs/r/ROOT/ROOT-v5.34.01-goolf-1.4.10.eb | 3 ++- easybuild/easyconfigs/r/ROOT/ROOT-v5.34.01-intel-2015a.eb | 4 +++- easybuild/easyconfigs/r/ROOT/ROOT-v5.34.13-ictce-5.5.0.eb | 4 +++- easybuild/easyconfigs/r/ROOT/ROOT-v5.34.18-ictce-5.5.0.eb | 4 +++- easybuild/easyconfigs/r/ROOT/ROOT-v5.34.26-intel-2015a.eb | 4 +++- .../r/ROOT/ROOT-v5.34.34-intel-2015b-Python-2.7.10.eb | 4 +++- .../r/ROOT/ROOT-v5.34.34-intel-2016a-Python-2.7.11.eb | 4 +++- .../r/ROOT/ROOT-v5.34.36-intel-2016a-Python-2.7.11.eb | 4 +++- .../s/Subversion/Subversion-1.8.14-foss-2015a.eb | 2 ++ 35 files changed, 106 insertions(+), 42 deletions(-) mode change 100755 => 100644 easybuild/easyconfigs/r/ROOT/ROOT-v5.30.06-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/b/bsoft/bsoft-1.8.8-goolf-1.5.14.eb b/easybuild/easyconfigs/b/bsoft/bsoft-1.8.8-goolf-1.5.14.eb index 5bba690060..85e23a5ed9 100644 --- a/easybuild/easyconfigs/b/bsoft/bsoft-1.8.8-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/b/bsoft/bsoft-1.8.8-goolf-1.5.14.eb @@ -13,8 +13,9 @@ a resource that can be and has been used in other packages.""" toolchain = {'name': 'goolf', 'version': '1.5.14'} toolchainopts = {'openmp': True} -source_urls = ['http://lsbr.niams.nih.gov/bsoft/'] +source_urls = ['http://lsbr.niams.nih.gov/bsoft/old/'] sources = ['%%(name)s%s.tar' % '_'.join(version.split('.'))] +checksums = ['e97f1fecba89efb5cd35741ce8c6396f'] cmds_map = [('.*', "./bmake omp fftw=$EBROOTFFTW")] files_to_copy = ['bin'] diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.5-goolf-1.4.10-Python-2.7.10.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.5-goolf-1.4.10-Python-2.7.10.eb index 141aedc7d3..2793fdd390 100644 --- a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.5-goolf-1.4.10-Python-2.7.10.eb +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.5-goolf-1.4.10-Python-2.7.10.eb @@ -12,8 +12,9 @@ description = """ cutadapt removes adapter sequences toolchain = {'name': 'goolf', 'version': '1.4.10'} -source_urls = ['http://cutadapt.googlecode.com/files/'] +source_urls = [PYPI_SOURCE] sources = [SOURCELOWER_TAR_GZ] +checksums = ['639b86826778c14c8b1fe512f074b939'] python = 'Python' pyver = '2.7.10' diff --git a/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.5.7-goolf-1.4.10.eb b/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.5.7-goolf-1.4.10.eb index c8367acc34..573a00a185 100644 --- a/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.5.7-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.5.7-goolf-1.4.10.eb @@ -15,8 +15,9 @@ description = """EMBOSS is 'The European Molecular Biology Open Software Suite'. toolchain = {'name': 'goolf', 'version': '1.4.10'} -source_urls = ['ftp://emboss.open-bio.org/pub/EMBOSS/'] +source_urls = ['ftp://emboss.open-bio.org/pub/EMBOSS/old/%(version_major_minor)s.0/'] sources = [SOURCE_TAR_GZ] +checksums = ['6a2cb3f93d5e9415c74ab0f6b1ede5f0'] patches = ['EMBOSS_disable-embossupdate.patch'] diff --git a/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.5.7-ictce-5.3.0.eb b/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.5.7-ictce-5.3.0.eb index 88380bcbab..cfcf1c4b41 100644 --- a/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.5.7-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.5.7-ictce-5.3.0.eb @@ -15,8 +15,9 @@ description = """EMBOSS is 'The European Molecular Biology Open Software Suite'. toolchain = {'name': 'ictce', 'version': '5.3.0'} -source_urls = ['ftp://emboss.open-bio.org/pub/EMBOSS/'] +source_urls = ['ftp://emboss.open-bio.org/pub/EMBOSS/old/%(version_major_minor)s.0/'] sources = [SOURCE_TAR_GZ] +checksums = ['6a2cb3f93d5e9415c74ab0f6b1ede5f0'] patches = ['EMBOSS_disable-embossupdate.patch'] diff --git a/easybuild/easyconfigs/g/GnuTLS/GnuTLS-3.1.8-goolf-1.4.10.eb b/easybuild/easyconfigs/g/GnuTLS/GnuTLS-3.1.8-goolf-1.4.10.eb index 80b639f6e3..72a8492f83 100644 --- a/easybuild/easyconfigs/g/GnuTLS/GnuTLS-3.1.8-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/g/GnuTLS/GnuTLS-3.1.8-goolf-1.4.10.eb @@ -7,8 +7,9 @@ homepage = 'http://www.gnutls.org/' description = "gnutls-3.0.22: GNU Transport Layer Security library" toolchain = {'name': 'goolf', 'version': '1.4.10'} -source_urls = ['ftp://ftp.gnutls.org/pub/gnutls/'] +source_urls = ['ftp://ftp.gnutls.org/gcrypt/gnutls/v%(version_major_minor)s/'] sources = [SOURCELOWER_TAR_XZ] +checksums = ['ffac9e22aba66057d5155ad0e3b62485'] dependencies = [ ('GMP', '5.0.5'), diff --git a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-6.9.4-8-intel-2016a.eb b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-6.9.4-8-intel-2016a.eb index bcbe21baac..9914e312e1 100644 --- a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-6.9.4-8-intel-2016a.eb +++ b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-6.9.4-8-intel-2016a.eb @@ -8,8 +8,9 @@ description = """ImageMagick is a software suite to create, edit, compose, or co toolchain = {'name': 'intel', 'version': '2016a'} -sources = [SOURCE_TAR_XZ] -source_urls = ['http://www.imagemagick.org/download'] +sources = [SOURCE_TAR_GZ] +source_urls = ['https://launchpad.net/imagemagick/main/%(version)s/+download/'] +checksums = ['a347a9d0f9593cf32e7555a51834f340'] dependencies = [ ('bzip2', '1.0.6'), diff --git a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.1-6-intel-2016a.eb b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.1-6-intel-2016a.eb index cc86162eda..ca7cdda8cd 100644 --- a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.1-6-intel-2016a.eb +++ b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.1-6-intel-2016a.eb @@ -8,8 +8,9 @@ description = """ImageMagick is a software suite to create, edit, compose, or co toolchain = {'name': 'intel', 'version': '2016a'} -sources = [SOURCE_TAR_XZ] -source_urls = ['http://www.imagemagick.org/download'] +sources = [SOURCE_TAR_GZ] +source_urls = ['https://launchpad.net/imagemagick/main/%(version)s/+download/'] +checksums = ['e4ad9237f9e04e4d75e06854c55a7944'] dependencies = [ ('bzip2', '1.0.6'), diff --git a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.1-9-intel-2016a.eb b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.1-9-intel-2016a.eb index 7765318123..346c8ee58b 100644 --- a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.1-9-intel-2016a.eb +++ b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.1-9-intel-2016a.eb @@ -8,8 +8,9 @@ description = """ImageMagick is a software suite to create, edit, compose, or co toolchain = {'name': 'intel', 'version': '2016a'} -sources = [SOURCE_TAR_XZ] -source_urls = ['http://www.imagemagick.org/download'] +sources = [SOURCE_TAR_GZ] +source_urls = ['https://launchpad.net/imagemagick/main/%(version)s/+download/'] +checksums = ['b111b2bd932c77217ad97ac8c77009fb'] dependencies = [ ('bzip2', '1.0.6'), diff --git a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.2-9-intel-2016a.eb b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.2-9-intel-2016a.eb index d83125eb93..17c246342c 100644 --- a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.2-9-intel-2016a.eb +++ b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.2-9-intel-2016a.eb @@ -12,8 +12,9 @@ description = """ImageMagick is a software suite to create, edit, compose, or co toolchain = {'name': 'intel', 'version': '2016a'} -sources = [SOURCE_TAR_XZ] -source_urls = ['http://www.imagemagick.org/download'] +sources = [SOURCE_TAR_GZ] +source_urls = ['https://launchpad.net/imagemagick/main/%(version)s/+download/'] +checksums = ['f6a27b7996220a006720bdd82bf131be'] dependencies = [ ('bzip2', '1.0.6'), diff --git a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.3-1-intel-2016b.eb b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.3-1-intel-2016b.eb index f3c4211e84..7e4fd1539e 100644 --- a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.3-1-intel-2016b.eb +++ b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.3-1-intel-2016b.eb @@ -12,8 +12,9 @@ description = """ImageMagick is a software suite to create, edit, compose, or co toolchain = {'name': 'intel', 'version': '2016b'} -sources = [SOURCE_TAR_XZ] -source_urls = ['http://www.imagemagick.org/download'] +sources = [SOURCE_TAR_GZ] +source_urls = ['https://launchpad.net/imagemagick/main/%(version)s/+download/'] +checksums = ['95db9b86ed542cae20634358b4924e10'] dependencies = [ ('bzip2', '1.0.6'), diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-intel-2015a.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-intel-2015a.eb index 5b2c252b76..36759b619b 100644 --- a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-intel-2015a.eb +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-intel-2015a.eb @@ -17,8 +17,12 @@ version = '4.0.3' homepage = 'http://www.remotesensing.org/libtiff/' description = "tiff: Library and tools for reading and writing TIFF data files" -source_urls = ['ftp://ftp.remotesensing.org/pub/libtiff/'] +source_urls = [ + 'http://download.osgeo.org/libtiff/', + 'ftp://ftp.remotesensing.org/pub/libtiff/', +] sources = ['tiff-%(version)s.tar.gz'] +checksums = ['051c1068e6a0627f461948c365290410'] toolchain = {'name': 'intel', 'version': '2015a'} diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-intel-2015b.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-intel-2015b.eb index d18fddfba6..245af77e27 100644 --- a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-intel-2015b.eb +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-intel-2015b.eb @@ -17,8 +17,12 @@ version = '4.0.3' homepage = 'http://www.remotesensing.org/libtiff/' description = "tiff: Library and tools for reading and writing TIFF data files" -source_urls = ['ftp://ftp.remotesensing.org/pub/libtiff/'] +source_urls = [ + 'http://download.osgeo.org/libtiff/', + 'ftp://ftp.remotesensing.org/pub/libtiff/', +] sources = ['tiff-%(version)s.tar.gz'] +checksums = ['051c1068e6a0627f461948c365290410'] toolchain = {'name': 'intel', 'version': '2015b'} diff --git a/easybuild/easyconfigs/m/Mercurial/Mercurial-2.3.2-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/m/Mercurial/Mercurial-2.3.2-goolf-1.4.10-Python-2.7.3.eb index 8175c4c179..e59823b508 100644 --- a/easybuild/easyconfigs/m/Mercurial/Mercurial-2.3.2-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/m/Mercurial/Mercurial-2.3.2-goolf-1.4.10-Python-2.7.3.eb @@ -10,7 +10,8 @@ of any size and offers an easy and intuitive interface. toolchain = {'name': 'goolf', 'version': '1.4.10'} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://mercurial.selenic.com/release/'] +source_urls = ['https://www.mercurial-scm.org/release/'] +checksums = ['6e90450ab3886bc650031e0d9aef367a'] python = "Python" pythonversion = '2.7.3' diff --git a/easybuild/easyconfigs/m/Mercurial/Mercurial-2.3.2-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/m/Mercurial/Mercurial-2.3.2-ictce-5.3.0-Python-2.7.3.eb index f2baa1d123..c992ae6699 100644 --- a/easybuild/easyconfigs/m/Mercurial/Mercurial-2.3.2-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/m/Mercurial/Mercurial-2.3.2-ictce-5.3.0-Python-2.7.3.eb @@ -10,8 +10,9 @@ description = """Mercurial is a free, distributed source control management tool toolchain = {'name': 'ictce', 'version': '5.3.0'} -source_urls = ['http://mercurial.selenic.com/release/'] +source_urls = ['https://www.mercurial-scm.org/release/'] sources = [SOURCELOWER_TAR_GZ] +checksums = ['6e90450ab3886bc650031e0d9aef367a'] python = "Python" pythonversion = '2.7.3' diff --git a/easybuild/easyconfigs/m/Mercurial/Mercurial-2.5.2-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/m/Mercurial/Mercurial-2.5.2-goolf-1.4.10-Python-2.7.3.eb index 43c0bceadf..4021c0012d 100644 --- a/easybuild/easyconfigs/m/Mercurial/Mercurial-2.5.2-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/m/Mercurial/Mercurial-2.5.2-goolf-1.4.10-Python-2.7.3.eb @@ -9,8 +9,9 @@ of any size and offers an easy and intuitive interface. """ toolchain = {'name': 'goolf', 'version': '1.4.10'} -source_urls = ['http://mercurial.selenic.com/release/'] +source_urls = ['https://www.mercurial-scm.org/release/'] sources = [SOURCELOWER_TAR_GZ] +checksums = ['6b467f41a262e2537cf927ed42d0fdda'] python = "Python" pythonversion = '2.7.3' diff --git a/easybuild/easyconfigs/m/Mercurial/Mercurial-2.5.2-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/m/Mercurial/Mercurial-2.5.2-ictce-5.3.0-Python-2.7.3.eb index 47ecebdf53..1db1af42c1 100644 --- a/easybuild/easyconfigs/m/Mercurial/Mercurial-2.5.2-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/m/Mercurial/Mercurial-2.5.2-ictce-5.3.0-Python-2.7.3.eb @@ -9,8 +9,9 @@ description = """Mercurial is a free, distributed source control management tool toolchain = {'name': 'ictce', 'version': '5.3.0'} -source_urls = ['http://mercurial.selenic.com/release/'] +source_urls = ['https://www.mercurial-scm.org/release/'] sources = [SOURCELOWER_TAR_GZ] +checksums = ['6b467f41a262e2537cf927ed42d0fdda'] python = "Python" pythonversion = '2.7.3' diff --git a/easybuild/easyconfigs/m/Mercurial/Mercurial-3.2.4-foss-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/m/Mercurial/Mercurial-3.2.4-foss-2015a-Python-2.7.9.eb index 047324c714..af89a7e145 100644 --- a/easybuild/easyconfigs/m/Mercurial/Mercurial-3.2.4-foss-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/m/Mercurial/Mercurial-3.2.4-foss-2015a-Python-2.7.9.eb @@ -10,8 +10,9 @@ of any size and offers an easy and intuitive interface. toolchain = {'name': 'foss', 'version': '2015a'} -source_urls = ['http://mercurial.selenic.com/release/'] +source_urls = ['https://www.mercurial-scm.org/release/'] sources = [SOURCELOWER_TAR_GZ] +checksums = ['4e9447b538a101138e257d5d774bcbfb'] python = "Python" pythonversion = '2.7.9' diff --git a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-ictce-6.1.5.eb b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-ictce-6.1.5.eb index 87478cf832..8696b556c2 100644 --- a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-ictce-6.1.5.eb +++ b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-ictce-6.1.5.eb @@ -11,7 +11,11 @@ toolchain = {'name': 'ictce', 'version': '6.1.5'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'http://www.unidata.ucar.edu/downloads/netcdf/ftp/', + 'http://www.unidata.ucar.edu/downloads/netcdf/ftp/old/', +] +checksums = ['cc3bf530223e8f4aff93793b9f197bf3'] dependencies = [('netCDF', '4.2.1.1')] diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.2-ictce-5.4.0.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.2-ictce-5.4.0.eb index a0f0b6f197..878ccb62cc 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.2-ictce-5.4.0.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.2-ictce-5.4.0.eb @@ -10,7 +10,11 @@ toolchain = {'name': 'ictce', 'version': '5.4.0'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'http://www.unidata.ucar.edu/downloads/netcdf/ftp/', + 'http://www.unidata.ucar.edu/downloads/netcdf/ftp/old/', +] +checksums = ['e7790bb23d8bc23689f19f5cec81d71e'] configopts = ['--disable-doxygen'] diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.2-intel-2014b.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.2-intel-2014b.eb index fc24bdb27f..72e540c932 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.2-intel-2014b.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.2-intel-2014b.eb @@ -10,7 +10,11 @@ toolchain = {'name': 'intel', 'version': '2014b'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'http://www.unidata.ucar.edu/downloads/netcdf/ftp/', + 'http://www.unidata.ucar.edu/downloads/netcdf/ftp/old/', +] +checksums = ['e7790bb23d8bc23689f19f5cec81d71e'] configopts = ['--disable-doxygen'] diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-5.4.0.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-5.4.0.eb index 49f253f65d..f945f15bca 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-5.4.0.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-5.4.0.eb @@ -10,7 +10,11 @@ toolchain = {'name': 'ictce', 'version': '5.4.0'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'http://www.unidata.ucar.edu/downloads/netcdf/ftp/', + 'http://www.unidata.ucar.edu/downloads/netcdf/ftp/old/', +] +checksums = ['5eebcf19e6ac78a61c73464713cbfafc'] dependencies = [('HDF5', '1.8.10', '-gpfs')] diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-6.1.5.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-6.1.5.eb index 262ebc70b9..b162d589eb 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-6.1.5.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-6.1.5.eb @@ -10,7 +10,11 @@ toolchain = {'name': 'ictce', 'version': '6.1.5'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'http://www.unidata.ucar.edu/downloads/netcdf/ftp/', + 'http://www.unidata.ucar.edu/downloads/netcdf/ftp/old/', +] +checksums = ['5eebcf19e6ac78a61c73464713cbfafc'] dependencies = [('HDF5', '1.8.10', '-gpfs')] diff --git a/easybuild/easyconfigs/p/pigz/pigz-2.3.1-goolf-1.4.10.eb b/easybuild/easyconfigs/p/pigz/pigz-2.3.1-goolf-1.4.10.eb index 292fb226d3..b6ccc91bd2 100644 --- a/easybuild/easyconfigs/p/pigz/pigz-2.3.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/pigz/pigz-2.3.1-goolf-1.4.10.eb @@ -16,8 +16,9 @@ description = """ pigz, which stands for parallel implementation of gzip, is a f toolchain = {'name': 'goolf', 'version': '1.4.10'} -source_urls = ['http://zlib.net/pigz/'] -sources = [SOURCE_TAR_GZ] +source_urls = ['https://github.com/madler/pigz/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['3a41409da23ff093b61e414d602c5650'] # README recommends zlib 1.2.6 or higher dependencies = [('zlib', '1.2.8')] diff --git a/easybuild/easyconfigs/p/pigz/pigz-2.3.1-ictce-6.2.5.eb b/easybuild/easyconfigs/p/pigz/pigz-2.3.1-ictce-6.2.5.eb index 770c70dd5f..e3e7f189b1 100644 --- a/easybuild/easyconfigs/p/pigz/pigz-2.3.1-ictce-6.2.5.eb +++ b/easybuild/easyconfigs/p/pigz/pigz-2.3.1-ictce-6.2.5.eb @@ -16,8 +16,9 @@ description = """ pigz, which stands for parallel implementation of gzip, is a f toolchain = {'name': 'ictce', 'version': '6.2.5'} -source_urls = ['http://zlib.net/pigz/'] -sources = [SOURCE_TAR_GZ] +source_urls = ['https://github.com/madler/pigz/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['3a41409da23ff093b61e414d602c5650'] # README recommends zlib 1.2.6 or higher dependencies = [('zlib', '1.2.8')] diff --git a/easybuild/easyconfigs/p/pigz/pigz-2.3.3-foss-2015b.eb b/easybuild/easyconfigs/p/pigz/pigz-2.3.3-foss-2015b.eb index e95cb85cb9..a50f50774e 100644 --- a/easybuild/easyconfigs/p/pigz/pigz-2.3.3-foss-2015b.eb +++ b/easybuild/easyconfigs/p/pigz/pigz-2.3.3-foss-2015b.eb @@ -16,8 +16,9 @@ description = """ pigz, which stands for parallel implementation of gzip, is a f toolchain = {'name': 'foss', 'version': '2015b'} -source_urls = ['http://zlib.net/pigz/'] -sources = [SOURCE_TAR_GZ] +source_urls = ['https://github.com/madler/pigz/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['fb80e8d31498226c99fe8c8b3d19364d'] # Patch Makefile so zlib provided by EasyBuild is picked up patches = ['pigz-2.3.3_Makefile.patch'] diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-v5.30.06-goolf-1.4.10.eb b/easybuild/easyconfigs/r/ROOT/ROOT-v5.30.06-goolf-1.4.10.eb old mode 100755 new mode 100644 index 9a78780f34..a2bf4ab035 --- a/easybuild/easyconfigs/r/ROOT/ROOT-v5.30.06-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/r/ROOT/ROOT-v5.30.06-goolf-1.4.10.eb @@ -9,7 +9,8 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'pic': True} sources = ['%(namelower)s_%(version)s.source.tar.gz'] -source_urls = ['ftp://root.cern.ch/root/'] +source_urls = ['https://root.cern.ch/download/'] +checksums = ['e60d1a896299d000b6a34f032debc9aa'] python = 'Python' pyver = '2.7.5' diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.01-goolf-1.4.10.eb b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.01-goolf-1.4.10.eb index 4e14ff0190..f56b457e0d 100644 --- a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.01-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.01-goolf-1.4.10.eb @@ -9,7 +9,8 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'pic': True} sources = ['%s_%s.source.tar.gz' % (name.lower(), version)] -source_urls = ['ftp://root.cern.ch/root/'] +source_urls = ['https://root.cern.ch/download/'] +checksums = ['114ea7f18b48ed0b3bb0287f5a6d593f'] python = 'Python' pyver = '2.7.3' diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.01-intel-2015a.eb b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.01-intel-2015a.eb index a65a733278..a263fbc4af 100644 --- a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.01-intel-2015a.eb +++ b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.01-intel-2015a.eb @@ -9,7 +9,9 @@ toolchain = {'name': 'intel', 'version': '2015a'} toolchainopts = {'pic': True} sources = ['%s_%s.source.tar.gz' % (name.lower(), version)] -source_urls = ['ftp://root.cern.ch/root/'] +source_urls = ['https://root.cern.ch/download/'] +checksums = ['114ea7f18b48ed0b3bb0287f5a6d593f'] + patches = [ 'configure_FftwFromMkl_28.patch', 'ROOT-%(version)s_recent-ifort.patch', diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.13-ictce-5.5.0.eb b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.13-ictce-5.5.0.eb index e025c77b02..4f55d64d72 100644 --- a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.13-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.13-ictce-5.5.0.eb @@ -9,7 +9,9 @@ toolchain = {'name': 'ictce', 'version': '5.5.0'} toolchainopts = {'pic': True} sources = ['%(namelower)s_%(version)s.source.tar.gz'] -source_urls = ['ftp://root.cern.ch/root/'] +source_urls = ['https://root.cern.ch/download/'] +checksums = ['3124168ce6b4574b471d6cda4aa40184'] + patches = [ 'configure_FftwFromMkl_28.patch', 'ROOT-v5_recent-ifort.patch', diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.18-ictce-5.5.0.eb b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.18-ictce-5.5.0.eb index f0e1274759..a8ab1f540d 100644 --- a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.18-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.18-ictce-5.5.0.eb @@ -9,7 +9,9 @@ toolchain = {'name': 'ictce', 'version': '5.5.0'} toolchainopts = {'pic': True} sources = ['%(namelower)s_%(version)s.source.tar.gz'] -source_urls = ['ftp://root.cern.ch/root/'] +source_urls = ['https://root.cern.ch/download/'] +checksums = ['2a9ef6a342833cb461020fa0832e78fe'] + patches = [ 'configure_FftwFromMkl_28.patch', 'ROOT-v5_recent-ifort.patch', diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.26-intel-2015a.eb b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.26-intel-2015a.eb index 05baffbd16..5801dbe265 100644 --- a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.26-intel-2015a.eb +++ b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.26-intel-2015a.eb @@ -9,7 +9,9 @@ toolchain = {'name': 'intel', 'version': '2015a'} toolchainopts = {'pic': True} sources = ['%(namelower)s_%(version)s.source.tar.gz'] -source_urls = ['ftp://root.cern.ch/root/'] +source_urls = ['https://root.cern.ch/download/'] +checksums = ['aa90309fa75ab69816dc819f5edd73f5'] + patches = [ 'configure_FftwFromMkl_28.patch', 'ROOT-v5_recent-ifort.patch', diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.34-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.34-intel-2015b-Python-2.7.10.eb index eb76e73818..81b811dc89 100644 --- a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.34-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.34-intel-2015b-Python-2.7.10.eb @@ -9,7 +9,9 @@ toolchain = {'name': 'intel', 'version': '2015b'} toolchainopts = {'pic': True} sources = ['%(namelower)s_%(version)s.source.tar.gz'] -source_urls = ['ftp://root.cern.ch/root/'] +source_urls = ['https://root.cern.ch/download/'] +checksums = ['fd9ee9cfc85cdad3d7c2c41a28796c24'] + patches = [ 'configure_FftwFromMkl_28.patch', ] diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.34-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.34-intel-2016a-Python-2.7.11.eb index fc6f18713c..9dd615415d 100644 --- a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.34-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.34-intel-2016a-Python-2.7.11.eb @@ -10,7 +10,9 @@ toolchain = {'name': 'intel', 'version': '2016a'} toolchainopts = {'pic': True} sources = ['%(namelower)s_%(version)s.source.tar.gz'] -source_urls = ['ftp://root.cern.ch/root/'] +source_urls = ['https://root.cern.ch/download/'] +checksums = ['fd9ee9cfc85cdad3d7c2c41a28796c24'] + patches = [ 'configure_FftwFromMkl_28.patch', 'ROOT-v5_recent-ifort.patch', diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.36-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.36-intel-2016a-Python-2.7.11.eb index 7d1106317b..b51c955db4 100644 --- a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.36-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.36-intel-2016a-Python-2.7.11.eb @@ -10,7 +10,9 @@ toolchain = {'name': 'intel', 'version': '2016a'} toolchainopts = {'pic': True} sources = ['%(namelower)s_%(version)s.source.tar.gz'] -source_urls = ['ftp://root.cern.ch/root/'] +source_urls = ['https://root.cern.ch/download/'] +checksums = ['6a1ad549b3b79b10bbb1f116b49067ee'] + patches = [ 'configure_FftwFromMkl_28.patch', 'ROOT-v5_recent-ifort.patch', diff --git a/easybuild/easyconfigs/s/Subversion/Subversion-1.8.14-foss-2015a.eb b/easybuild/easyconfigs/s/Subversion/Subversion-1.8.14-foss-2015a.eb index be6f1332e2..cf172a3cf0 100644 --- a/easybuild/easyconfigs/s/Subversion/Subversion-1.8.14-foss-2015a.eb +++ b/easybuild/easyconfigs/s/Subversion/Subversion-1.8.14-foss-2015a.eb @@ -12,8 +12,10 @@ source_urls = [ 'http://apache.belnet.be/%(namelower)s', 'http://www.eu.apache.org/dist/%(namelower)s', 'http://www.us.apache.org/dist/%(namelower)s', + 'http://archive.apache.org/dist/%(namelower)s', ] sources = [SOURCELOWER_TAR_BZ2] +checksums = ['fe476ba26d6835eba4393780ea907361'] dependencies = [ ('APR', '1.5.2'), -- GitLab From 17ebe626b0f62265d4275423bddaad96c00bbfb7 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 1 Mar 2017 09:27:13 +0200 Subject: [PATCH 0199/1603] adding easyconfigs: Python-2.7.12-iomkl-2017a.eb --- .../g/GMP/GMP-6.1.1-GCCcore-6.3.0.eb | 31 ++++ .../l/libffi/libffi-3.2.1-GCCcore-6.3.0.eb | 27 ++++ .../libreadline-6.3-GCCcore-6.3.0.eb | 33 +++++ .../p/Python/Python-2.7.12-iomkl-2017a.eb | 133 ++++++++++++++++++ .../s/SQLite/SQLite-3.13.0-GCCcore-6.3.0.eb | 44 ++++++ .../t/Tcl/Tcl-8.6.5-GCCcore-6.3.0.eb | 30 ++++ .../t/Tk/Tk-8.6.5-GCCcore-6.3.0.eb | 30 ++++ .../z/zlib/zlib-1.2.8-GCCcore-6.3.0.eb | 27 ++++ 8 files changed, 355 insertions(+) create mode 100644 easybuild/easyconfigs/g/GMP/GMP-6.1.1-GCCcore-6.3.0.eb create mode 100644 easybuild/easyconfigs/l/libffi/libffi-3.2.1-GCCcore-6.3.0.eb create mode 100644 easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCCcore-6.3.0.eb create mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.12-iomkl-2017a.eb create mode 100644 easybuild/easyconfigs/s/SQLite/SQLite-3.13.0-GCCcore-6.3.0.eb create mode 100644 easybuild/easyconfigs/t/Tcl/Tcl-8.6.5-GCCcore-6.3.0.eb create mode 100644 easybuild/easyconfigs/t/Tk/Tk-8.6.5-GCCcore-6.3.0.eb create mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-6.3.0.eb diff --git a/easybuild/easyconfigs/g/GMP/GMP-6.1.1-GCCcore-6.3.0.eb b/easybuild/easyconfigs/g/GMP/GMP-6.1.1-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..2d442cdea2 --- /dev/null +++ b/easybuild/easyconfigs/g/GMP/GMP-6.1.1-GCCcore-6.3.0.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'GMP' +version = '6.1.1' + +homepage = 'http://gmplib.org/' +description = """GMP is a free library for arbitrary precision arithmetic, +operating on signed integers, rational numbers, and floating point numbers. """ + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} +toolchainopts = {'pic': True, 'precise': True} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://ftp.gnu.org/gnu/gmp'] + +builddependencies = [ + ('binutils', '2.27'), + ('Autotools', '20150215'), +] + +# enable C++ interface +configopts = '--enable-cxx' + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libgmp.%s' % SHLIB_EXT, 'include/gmp.h'], + 'dirs': [], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/l/libffi/libffi-3.2.1-GCCcore-6.3.0.eb b/easybuild/easyconfigs/l/libffi/libffi-3.2.1-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..ab5a66564f --- /dev/null +++ b/easybuild/easyconfigs/l/libffi/libffi-3.2.1-GCCcore-6.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'libffi' +version = '3.2.1' + +homepage = 'http://sourceware.org/libffi/' +description = """The libffi library provides a portable, high level programming interface to various calling +conventions. This allows a programmer to call any function specified by a call interface description at run-time.""" + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} + +source_urls = [ + 'ftp://sourceware.org/pub/libffi/', + 'http://www.mirrorservice.org/sites/sourceware.org/pub/libffi/', +] +sources = [SOURCELOWER_TAR_GZ] + +builddependencies = [ + ('binutils', '2.27'), +] + +sanity_check_paths = { + 'files': [('lib/libffi.%s' % SHLIB_EXT, 'lib64/libffi.%s' % SHLIB_EXT), ('lib/libffi.a', 'lib64/libffi.a')], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCCcore-6.3.0.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..f4f4e99acd --- /dev/null +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCCcore-6.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'libreadline' +version = '6.3' + +homepage = 'http://cnswww.cns.cwru.edu/php/chet/readline/rltop.html' +description = """The GNU Readline library provides a set of functions for use by applications that + allow users to edit command lines as they are typed in. Both Emacs and vi editing modes are available. + The Readline library includes additional functions to maintain a list of previously-entered command lines, + to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands.""" + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} +toolchainopts = {'pic': True} + +sources = ['readline-%(version)s.tar.gz'] +source_urls = ['http://ftp.gnu.org/gnu/readline'] + +patches = ['libreadline-%(version)s-bugfix.patch'] + +builddependencies = [('binutils', '2.27')] +dependencies = [('ncurses', '6.0')] + +# for the termcap symbols, use EB ncurses +preconfigopts = "env LDFLAGS='-lncurses'" + +sanity_check_paths = { + 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.12-iomkl-2017a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.12-iomkl-2017a.eb new file mode 100644 index 0000000000..47c4558b9f --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.12-iomkl-2017a.eb @@ -0,0 +1,133 @@ +name = 'Python' +version = '2.7.12' + +homepage = 'http://python.org/' +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" + +toolchain = {'name': 'iomkl', 'version': '2017a'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +# python needs bzip2 to build the bz2 package +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libreadline', '6.3'), + ('ncurses', '6.0'), + ('SQLite', '3.13.0'), + ('Tk', '8.6.5'), # this requires a full X11 stack + ('GMP', '6.1.1'), + ('libffi', '3.2.1'), + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.2h'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# order is important! +# package versions updated May 28th 2015 +exts_list = [ + ('setuptools', '23.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], + }), + ('pip', '8.1.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], + }), + ('nose', '1.3.7', { + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], + }), + ('numpy', '1.11.1', { + 'source_urls': ['https://pypi.python.org/packages/source/n/numpy'], + 'patches': ['numpy-1.8.0-mkl.patch'], + }), + ('scipy', '0.17.1', { + 'source_urls': ['https://pypi.python.org/packages/source/s/scipy'], + }), + ('blist', '1.3.6', { + 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], + }), + ('mpi4py', '1.3.1', { + 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + }), + ('paycheck', '1.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], + }), + ('pbr', '1.10.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], + }), + ('lockfile', '0.12.2', { + 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], + }), + ('Cython', '0.24', { + 'source_urls': ['https://pypi.python.org/packages/source/c/cython/'], + }), + ('six', '1.10.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), + ('dateutil', '2.5.3', { + 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], + }), + ('deap', '1.0.2', { + 'source_tmpl': '%(name)s-%(version)s.post2.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], + }), + ('decorator', '4.0.10', { + 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], + }), + ('arff', '2.1.0', { + 'source_tmpl': 'liac-%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], + }), + ('pycrypto', '2.6.1', { + 'modulename': 'Crypto', + 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + }), + ('ecdsa', '0.13', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), + ('cryptography', '1.4', { + 'source_urls': ['https://pypi.python.org/packages/source/c/cryptography/'], + }), + ('paramiko', '2.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], + }), + ('pyparsing', '2.1.5', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], + }), + ('netifaces', '0.10.4', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], + }), + ('netaddr', '0.7.18', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], + }), + ('funcsigs', '1.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/f/funcsigs'], + }), + ('mock', '2.0.0', { + 'source_urls': ['https://pypi.python.org/packages/source/m/mock'], + }), + ('pytz', '2016.4', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pytz'], + }), + ('pandas', '0.18.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], + }), + ('enum34', '1.1.6', { + 'modulename': 'enum', + 'source_urls': ['https://pypi.python.org/packages/source/e/enum34'], + }), + ('bitstring', '3.1.5', { + 'source_tmpl': '%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/b/bitstring'], + }), + ('virtualenv', '15.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/v/virtualenv'], + }), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.13.0-GCCcore-6.3.0.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.13.0-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..f7ba78e654 --- /dev/null +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.13.0-GCCcore-6.3.0.eb @@ -0,0 +1,44 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## + +easyblock = 'ConfigureMake' + +name = 'SQLite' +version = '3.13.0' + +homepage = 'http://www.sqlite.org/' +description = 'SQLite: SQL Database Engine in a C Library' + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} + +source_urls = ['http://www.sqlite.org/2016/'] +version_minor_etc = version.split('.')[1:] +version_minor_etc += '0' * (3 - len(version_minor_etc)) +version_str = '%(version_major)s' + ''.join('%02d' % int(x) for x in version_minor_etc) +sources = ['sqlite-autoconf-%s.tar.gz' % version_str] + +builddependencies = [ + ('binutils', '2.27'), +] + +dependencies = [ + ('libreadline', '6.3'), + ('Tcl', '8.6.5'), +] + +sanity_check_paths = { + 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', 'lib/libsqlite3.a', + 'lib/libsqlite3.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.5-GCCcore-6.3.0.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.5-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..3d473ebedb --- /dev/null +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.5-GCCcore-6.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'Tcl' +version = '8.6.5' + +homepage = 'http://www.tcl.tk/' +description = """Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, +suitable for a very wide range of uses, including web and desktop applications, networking, administration, +testing and many more.""" + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +builddependencies = [ + ('binutils', '2.27'), +] + +dependencies = [ + ('zlib', '1.2.8'), +] + +configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' + +runtest = 'test' + +start_dir = 'unix' + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.5-GCCcore-6.3.0.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.5-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..0c78137460 --- /dev/null +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.5-GCCcore-6.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'Tk' +version = '8.6.5' + +homepage = 'http://www.tcl.tk/' +description = """Tk is an open source, cross-platform widget toolchain that provides a library of basic elements for + building a graphical user interface (GUI) in many different programming languages.""" + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +patches = ['Tk-8.6.4_different-prefix-with-tcl.patch'] + +builddependencies = [ + ('binutils', '2.27'), +] + +dependencies = [ + ('Tcl', version), + ('zlib', '1.2.8'), +] + +configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib CFLAGS="-I$EBROOTTCL/include"' + +start_dir = 'unix' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-6.3.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..5c5b309e90 --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-6.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'zlib' +version = '1.2.8' + +homepage = 'http://www.zlib.net/' +description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is, + not covered by any patents -- lossless data-compression library for use on virtually any + computer hardware and operating system.""" + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] + +# use same binutils version that was used when building GCC toolchain +builddependencies = [ + ('binutils', '2.27', '', True) +] + +sanity_check_paths = { + 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' -- GitLab From a9ee6588e0281da234489af8df025bc1ad605b3e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 1 Mar 2017 09:13:45 +0100 Subject: [PATCH 0200/1603] adding easyconfigs: miRDeep2-2.0.0.8-intel-2016b.eb --- .../miRDeep2/miRDeep2-2.0.0.8-intel-2016b.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/m/miRDeep2/miRDeep2-2.0.0.8-intel-2016b.eb diff --git a/easybuild/easyconfigs/m/miRDeep2/miRDeep2-2.0.0.8-intel-2016b.eb b/easybuild/easyconfigs/m/miRDeep2/miRDeep2-2.0.0.8-intel-2016b.eb new file mode 100644 index 0000000000..1a5f00c298 --- /dev/null +++ b/easybuild/easyconfigs/m/miRDeep2/miRDeep2-2.0.0.8-intel-2016b.eb @@ -0,0 +1,29 @@ +easyblock = 'PackedBinary' + +name = 'miRDeep2' +version = '2.0.0.8' +altver = '_'.join(version.split('.')) + +homepage = 'https://www.mdc-berlin.de/8551903/en/' +description = "miRDeep2 is a completely overhauled tool which discovers microRNA genes by analyzing sequenced RNAs" + +source_urls = ['https://www.mdc-berlin.de/45995549/en/research/research_teams/systems_biology_of_gene_regulatory_elements/projects/miRDeep/'] +sources = ['mirdeep%s.zip' % altver] + +toolchain = {'name': 'intel', 'version': '2016b'} + +dependencies = [ + ('Perl', '5.24.0'), # provides PDF::API2 + ('Bowtie', '1.1.2'), + ('ViennaRNA', '2.2.3'), + ('randfold', '2.0.1'), # also provides SQUID +] + +install_cmd = "cp -a mirdeep%s/src %%(installdir)s/bin" % altver + +sanity_check_paths = { + 'files': ['bin/make_html.pl'], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From b61226296efcb1e72e351e595841a25d4a066632 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 1 Mar 2017 09:56:15 +0100 Subject: [PATCH 0201/1603] fix style remarks in miRDeep2 easyconfig --- .../easyconfigs/m/miRDeep2/miRDeep2-2.0.0.8-intel-2016b.eb | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/m/miRDeep2/miRDeep2-2.0.0.8-intel-2016b.eb b/easybuild/easyconfigs/m/miRDeep2/miRDeep2-2.0.0.8-intel-2016b.eb index 1a5f00c298..583f9a91f7 100644 --- a/easybuild/easyconfigs/m/miRDeep2/miRDeep2-2.0.0.8-intel-2016b.eb +++ b/easybuild/easyconfigs/m/miRDeep2/miRDeep2-2.0.0.8-intel-2016b.eb @@ -7,11 +7,12 @@ altver = '_'.join(version.split('.')) homepage = 'https://www.mdc-berlin.de/8551903/en/' description = "miRDeep2 is a completely overhauled tool which discovers microRNA genes by analyzing sequenced RNAs" -source_urls = ['https://www.mdc-berlin.de/45995549/en/research/research_teams/systems_biology_of_gene_regulatory_elements/projects/miRDeep/'] -sources = ['mirdeep%s.zip' % altver] - toolchain = {'name': 'intel', 'version': '2016b'} +source_url_subdir = 'research/research_teams/systems_biology_of_gene_regulatory_elements/projects/miRDeep/' +source_urls = ['https://www.mdc-berlin.de/45995549/en/' + source_url_subdir] +sources = ['mirdeep%s.zip' % altver] + dependencies = [ ('Perl', '5.24.0'), # provides PDF::API2 ('Bowtie', '1.1.2'), -- GitLab From cbaba10168bd2b27c854f848df7fbcbe1d628e88 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 1 Mar 2017 10:18:54 +0100 Subject: [PATCH 0202/1603] fix source spec in PBSuite easyconfig --- .../p/PBSuite/PBSuite-15.8.24-intel-2016b-Python-2.7.12.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PBSuite/PBSuite-15.8.24-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/PBSuite/PBSuite-15.8.24-intel-2016b-Python-2.7.12.eb index 8626be9af4..c6a303fc3e 100644 --- a/easybuild/easyconfigs/p/PBSuite/PBSuite-15.8.24-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/p/PBSuite/PBSuite-15.8.24-intel-2016b-Python-2.7.12.eb @@ -11,7 +11,7 @@ description = """PBJelly is a highly automated pipeline that aligns long sequenc toolchain = {'name': 'intel', 'version': '2016b'} source_urls = ['https://sourceforge.net/projects/pb-jelly/files/latest/download'] -sources = ['%(name)s_%(version)s.tar.gz'] +sources = ['%(name)s_%(version)s.tgz'] dependencies = [ ('Python', '2.7.12'), -- GitLab From 0713ba2281954b4626ad750a98c0a6183a14093e Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 1 Mar 2017 13:21:20 +0200 Subject: [PATCH 0203/1603] adding easyconfigs: NWChem-6.6.revision27746-iomkl-2017a-2015-10-20-Python-2.7.12.eb --- ...46-iomkl-2017a-2015-10-20-Python-2.7.12.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/n/NWChem/NWChem-6.6.revision27746-iomkl-2017a-2015-10-20-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/n/NWChem/NWChem-6.6.revision27746-iomkl-2017a-2015-10-20-Python-2.7.12.eb b/easybuild/easyconfigs/n/NWChem/NWChem-6.6.revision27746-iomkl-2017a-2015-10-20-Python-2.7.12.eb new file mode 100644 index 0000000000..f693ccc152 --- /dev/null +++ b/easybuild/easyconfigs/n/NWChem/NWChem-6.6.revision27746-iomkl-2017a-2015-10-20-Python-2.7.12.eb @@ -0,0 +1,38 @@ +name = 'NWChem' +version = '6.6.revision27746' + +homepage = 'http://www.nwchem-sw.org' +description = """NWChem aims to provide its users with computational chemistry tools that are scalable both in + their ability to treat large scientific computational chemistry problems efficiently, and in their use of available + parallel computing resources from high-performance parallel supercomputers to conventional workstation clusters. + NWChem software can handle: biomolecules, nanostructures, and solid-state; from quantum to classical, and all + combinations; Gaussian basis functions or plane-waves; scaling from one to thousands of processors; properties + and relativity.""" + +toolchain = {'name': 'iomkl', 'version': '2017a'} +toolchainopts = {'i8': True} + +source_urls = ['http://www.nwchem-sw.org/download.php?f='] +verdate = '2015-10-20' +sources = ['Nwchem-%s-src.%s.tar.bz2' % (version, verdate)] + +patches = [ + 'NWChem_fix-date.patch', + 'NWChem-%(version)s-parallelbuild.patch', +] + +python = 'Python' +pyver = '2.7.12' +versionsuffix = '-%s-%s-%s' % (verdate, python, pyver) +dependencies = [(python, pyver)] + +# This easyconfig is using the default for armci_network (OPENIB) and +# thus needs infiniband libraries. +osdependencies = [ + ('libibverbs-dev', 'libibverbs-devel'), + ('libibumad-dev', 'libibumad-devel'), +] + +modules = 'all python' + +moduleclass = 'chem' -- GitLab From 26a826ec08b3b3769ff03ae5179c0c71739a7b39 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 1 Mar 2017 17:54:11 +0200 Subject: [PATCH 0204/1603] Add missing patch file. --- ...Chem-6.6.revision27746-parallelbuild.patch | 80 +++++++++++++++++++ 1 file changed, 80 insertions(+) create mode 100644 easybuild/easyconfigs/n/NWChem/NWChem-6.6.revision27746-parallelbuild.patch diff --git a/easybuild/easyconfigs/n/NWChem/NWChem-6.6.revision27746-parallelbuild.patch b/easybuild/easyconfigs/n/NWChem/NWChem-6.6.revision27746-parallelbuild.patch new file mode 100644 index 0000000000..635f15ee4c --- /dev/null +++ b/easybuild/easyconfigs/n/NWChem/NWChem-6.6.revision27746-parallelbuild.patch @@ -0,0 +1,80 @@ +diff -ru nwchem-6.6.orig/src/config/makefile.h nwchem-6.6/src/config/makefile.h +--- nwchem-6.6.orig/src/config/makefile.h 2015-10-16 02:12:50.000000000 +0200 ++++ nwchem-6.6/src/config/makefile.h 2017-01-12 10:43:00.000000000 +0100 +@@ -958,7 +958,7 @@ + _FC=ifort + #ifort 9.1 + # LINK.f = ifort $(LDFLAGS) +- FOPTIONS += -align -mp1 -w -g -vec-report1 ++ FOPTIONS += -align -mp1 -w -g + ifdef USE_GPROF + FOPTIONS += -qp + endif +@@ -1163,7 +1163,7 @@ + CORE_SUBDIRS_EXTRA = blas lapack + CC = gcc + RANLIB = ranlib +- MAKEFLAGS = -j 1 --no-print-directory ++ MAKEFLAGS = -j 8 --no-print-directory + INSTALL = @echo $@ is built + CPP = gcc -E -nostdinc -undef -P + FCONVERT = (/bin/cp $< /tmp/$$$$.c; \ +@@ -1310,7 +1310,7 @@ + _FC=ifc + endif + ifeq ($(_FC),ifc) +- FOPTIONS = -align -mp1 -w -g -vec-report1 ++ FOPTIONS = -align -mp1 -w -g + ifdef USE_GPROF + FOPTIONS += -qp + endif +@@ -1372,7 +1372,7 @@ + endif + + ifeq ($(CC),icc) +- COPTIONS = -mp1 -w -g -vec-report1 ++ COPTIONS = -mp1 -w -g + COPTIMIZE = -O3 -unroll + ifeq ($(_CPU),i586) + COPTIMIZE += -tpp5 -xi # this are for PentiumII +@@ -1740,7 +1740,7 @@ + # only use EXPLICITF for offload because otherwise we want debugging to be easy + # FOPTIONS += -Qoption,fpp,-P -Qoption,fpp,-c_com=no -allow nofpp_comments + ifdef USE_OPTREPORT +- FOPTIONS += -qopt-report=1 -qopt-report-phase=vec ++ FOPTIONS += -qopt-report=0 -qopt-report-phase=vec + endif + #to avoid compiler crashes on simd directive. e.g .Version 15.0.2.164 Build 20150121 + ifdef USE_NOSIMD +@@ -1748,7 +1748,6 @@ + endif + ifdef USE_OPENMP + FOPTIONS += -qopenmp +- FOPTIONS += -qopt-report-phase=openmp + COPTIONS += -qopenmp + DEFINES+= -DUSE_OPENMP + else +@@ -1759,10 +1758,9 @@ + endif + endif + else +- FOPTIONS += -vec-report6 ++ FOPTIONS += -vec-report0 + ifdef USE_OPENMP + FOPTIONS += -openmp +- FOPTIONS += -openmp-report2 + COPTIONS += -openmp + DEFINES+= -DUSE_OPENMP + endif +@@ -1885,10 +1883,9 @@ + COPTIONS += -qopt-report-phase:openmp + endif + else +- COPTIONS += -vec-report=1 + ifdef USE_OPENMP + COPTIONS += -openmp +- COPTIONS += -openmp-report=2 ++ COPTIONS += -openmp-report=0 + endif + endif + COPTIMIZE = -O3 -- GitLab From 1401b818611d041a21eae310aa329bc03e1b0788 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 1 Mar 2017 20:31:11 +0100 Subject: [PATCH 0205/1603] fx style issues in pscom easyconfigs --- easybuild/easyconfigs/p/pscom/pscom-5.0.43-GCC-4.8.2.eb | 4 ++-- easybuild/easyconfigs/p/pscom/pscom-5.0.44-1-GCC-4.9.2.eb | 4 +++- .../p/pscom/pscom-5.0.44-1-iccifort-2015.1.133.eb | 6 ++++-- easybuild/easyconfigs/p/pscom/pscom-5.0.48-1.eb | 6 ++++-- 4 files changed, 13 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/p/pscom/pscom-5.0.43-GCC-4.8.2.eb b/easybuild/easyconfigs/p/pscom/pscom-5.0.43-GCC-4.8.2.eb index 65a73afe7d..147a4add74 100644 --- a/easybuild/easyconfigs/p/pscom/pscom-5.0.43-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/p/pscom/pscom-5.0.43-GCC-4.8.2.eb @@ -4,8 +4,8 @@ name = 'pscom' version = '5.0.43' homepage = 'http://www.par-tec.com' -description = """ParaStation is a robust and efficient cluster middleware, consisting -of a high-performance communication layer (MPI) and a sophisticated management layer.""" +description = """ParaStation is a robust and efficient cluster middleware, consisting + of a high-performance communication layer (MPI) and a sophisticated management layer.""" toolchain = {'name': 'GCC', 'version': '4.8.2'} diff --git a/easybuild/easyconfigs/p/pscom/pscom-5.0.44-1-GCC-4.9.2.eb b/easybuild/easyconfigs/p/pscom/pscom-5.0.44-1-GCC-4.9.2.eb index b69d0d92dd..0b3259fa6d 100644 --- a/easybuild/easyconfigs/p/pscom/pscom-5.0.44-1-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/p/pscom/pscom-5.0.44-1-GCC-4.9.2.eb @@ -3,7 +3,9 @@ easyblock = 'ConfigureMake' name = 'pscom' version = '5.0.44-1' homepage = 'http://www.par-tec.com' -description = """ParaStation is a robust and efficient cluster middleware, consisting of a high-performance communication layer (MPI) and a sophisticated management layer.""" +description = """ParaStation is a robust and efficient cluster middleware, consisting + of a high-performance communication layer (MPI) and a sophisticated management layer.""" + toolchain = {'name': 'GCC', 'version': '4.9.2'} source_urls = ['https://github.com/ParaStation/%(name)s/archive/'] diff --git a/easybuild/easyconfigs/p/pscom/pscom-5.0.44-1-iccifort-2015.1.133.eb b/easybuild/easyconfigs/p/pscom/pscom-5.0.44-1-iccifort-2015.1.133.eb index 7da1e4a7f7..af331b28c2 100644 --- a/easybuild/easyconfigs/p/pscom/pscom-5.0.44-1-iccifort-2015.1.133.eb +++ b/easybuild/easyconfigs/p/pscom/pscom-5.0.44-1-iccifort-2015.1.133.eb @@ -2,10 +2,12 @@ easyblock = 'ConfigureMake' name = 'pscom' version = '5.0.44-1' + homepage = 'http://www.par-tec.com' -description = """ParaStation is a robust and efficient cluster middleware, consisting of a high-performance communication layer (MPI) and a sophisticated management layer.""" -toolchain = {'name': 'iccifort', 'version': '2015.1.133'} +description = """ParaStation is a robust and efficient cluster middleware, consisting + of a high-performance communication layer (MPI) and a sophisticated management layer.""" +toolchain = {'name': 'iccifort', 'version': '2015.1.133'} source_urls = ['https://github.com/ParaStation/%(name)s/archive/'] sources = ['%(version)s.zip'] diff --git a/easybuild/easyconfigs/p/pscom/pscom-5.0.48-1.eb b/easybuild/easyconfigs/p/pscom/pscom-5.0.48-1.eb index 13b9a47c54..fc283ffce3 100644 --- a/easybuild/easyconfigs/p/pscom/pscom-5.0.48-1.eb +++ b/easybuild/easyconfigs/p/pscom/pscom-5.0.48-1.eb @@ -4,7 +4,8 @@ name = 'pscom' version = '5.0.48-1' homepage = 'http://www.par-tec.com' -description = "ParaStation is a robust and efficient cluster middleware, consisting of a high-performance communication layer (MPI) and a sophisticated management layer." +description = """ParaStation is a robust and efficient cluster middleware, consisting + of a high-performance communication layer (MPI) and a sophisticated management layer.""" toolchain = {'version': '', 'name': 'dummy'} @@ -16,7 +17,8 @@ builddependencies = [ ] sanity_check_paths = { - 'files': ['include/%(name)s.h', ('lib/libpscom.so', 'lib64/libpscom.so'), ('lib/libpscom4mxm.so', 'lib64/libpscom4mxm.so')], + 'files': ['include/pscom.h', ('lib/libpscom.%s' % SHLIB_EXT, 'lib64/libpscom.%s' % SHLIB_EXT), + ('lib/libpscom4mxm.%s' % SHLIB_EXT, 'lib64/libpscom4mxm.%s' % SHLIB_EXT)], 'dirs': [], } -- GitLab From 5357919d46ac26b8e6d0cfe0025c6502725bb75a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 1 Mar 2017 20:32:41 +0100 Subject: [PATCH 0206/1603] fix whitespace issues & long lines --- .../pyplusplus-20160707-foss-2016a-Python-2.7.11.eb | 1 - .../pyplusplus-20160707-foss-2016a-Python-3.5.1.eb | 1 - .../python-dateutil-2.1-goolf-1.4.10-Python-2.7.3.eb | 3 ++- easybuild/easyconfigs/q/Qt/Qt-4.8.6.eb | 8 ++++---- easybuild/easyconfigs/r/RSEM/RSEM-1.2.30-foss-2016a.eb | 4 ++-- easybuild/easyconfigs/r/RSEM/RSEM-1.2.30-intel-2016b.eb | 4 ++-- easybuild/easyconfigs/r/RSEM/RSEM-1.3.0-foss-2016b.eb | 4 ++-- 7 files changed, 12 insertions(+), 13 deletions(-) diff --git a/easybuild/easyconfigs/p/pyplusplus/pyplusplus-20160707-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/pyplusplus/pyplusplus-20160707-foss-2016a-Python-2.7.11.eb index 695617390c..8ebd6c8d2e 100644 --- a/easybuild/easyconfigs/p/pyplusplus/pyplusplus-20160707-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/pyplusplus/pyplusplus-20160707-foss-2016a-Python-2.7.11.eb @@ -32,4 +32,3 @@ sanity_check_paths = { options = {'modulename': '%(name)s'} moduleclass = 'tools' - diff --git a/easybuild/easyconfigs/p/pyplusplus/pyplusplus-20160707-foss-2016a-Python-3.5.1.eb b/easybuild/easyconfigs/p/pyplusplus/pyplusplus-20160707-foss-2016a-Python-3.5.1.eb index 98760a6c19..b72f894f40 100644 --- a/easybuild/easyconfigs/p/pyplusplus/pyplusplus-20160707-foss-2016a-Python-3.5.1.eb +++ b/easybuild/easyconfigs/p/pyplusplus/pyplusplus-20160707-foss-2016a-Python-3.5.1.eb @@ -30,4 +30,3 @@ sanity_check_paths = { options = {'modulename': '%(name)s'} moduleclass = 'tools' - diff --git a/easybuild/easyconfigs/p/python-dateutil/python-dateutil-2.1-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/p/python-dateutil/python-dateutil-2.1-goolf-1.4.10-Python-2.7.3.eb index 9f1bdc61f3..1f3dfbd69d 100644 --- a/easybuild/easyconfigs/p/python-dateutil/python-dateutil-2.1-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/p/python-dateutil/python-dateutil-2.1-goolf-1.4.10-Python-2.7.3.eb @@ -4,7 +4,8 @@ name = "python-dateutil" version = "2.1" homepage = "https://pypi.python.org/pypi/python-dateutil" -description = """The dateutil module provides powerful extensions to the datetime module available in the Python standard library.""" +description = """The dateutil module provides powerful extensions to the datetime module available + in the Python standard library.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.6.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.6.eb index eacf9a8384..48881e75e8 100644 --- a/easybuild/easyconfigs/q/Qt/Qt-4.8.6.eb +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.6.eb @@ -6,11 +6,11 @@ description = "Qt is a comprehensive cross-platform C++ application framework." toolchain = {'name': 'dummy', 'version': 'dummy'} -source_urls = [ 'http://download.qt.io/official_releases/qt/4.8/%(version)s' ] -sources = [ 'qt-everywhere-opensource-src-%(version)s.tar.gz' ] +source_urls = ['http://download.qt.io/official_releases/qt/4.8/%(version)s'] +sources = ['qt-everywhere-opensource-src-%(version)s.tar.gz'] -configopts = ' -opensource -nomake tests -nomake examples -confirm-license -release' -configopts += ' -shared -no-accessibility -no-sql-mysql -no-sql-sqlite -no-webkit' +configopts = ' -opensource -nomake tests -nomake examples -confirm-license -release' +configopts += ' -shared -no-accessibility -no-sql-mysql -no-sql-sqlite -no-webkit' platform = 'linux-g++-64' moduleclass = 'devel' diff --git a/easybuild/easyconfigs/r/RSEM/RSEM-1.2.30-foss-2016a.eb b/easybuild/easyconfigs/r/RSEM/RSEM-1.2.30-foss-2016a.eb index e773ad310a..f091886679 100644 --- a/easybuild/easyconfigs/r/RSEM/RSEM-1.2.30-foss-2016a.eb +++ b/easybuild/easyconfigs/r/RSEM/RSEM-1.2.30-foss-2016a.eb @@ -22,8 +22,8 @@ dependencies = [ ] sanity_check_paths = { - 'files': ['bin/rsem-calculate-expression', 'bin/rsem-plot-model', 'bin/rsem-plot-transcript-wiggles', 'bin/rsem-bam2wig', - 'bin/rsem-generate-data-matrix', 'bin/rsem-run-em', 'bin/convert-sam-for-rsem'], + 'files': ['bin/rsem-calculate-expression', 'bin/rsem-plot-model', 'bin/rsem-plot-transcript-wiggles', + 'bin/rsem-bam2wig', 'bin/rsem-generate-data-matrix', 'bin/rsem-run-em', 'bin/convert-sam-for-rsem'], 'dirs': ['bin/samtools-1.3'], } diff --git a/easybuild/easyconfigs/r/RSEM/RSEM-1.2.30-intel-2016b.eb b/easybuild/easyconfigs/r/RSEM/RSEM-1.2.30-intel-2016b.eb index 5420a22996..85267f0972 100644 --- a/easybuild/easyconfigs/r/RSEM/RSEM-1.2.30-intel-2016b.eb +++ b/easybuild/easyconfigs/r/RSEM/RSEM-1.2.30-intel-2016b.eb @@ -22,8 +22,8 @@ dependencies = [ ] sanity_check_paths = { - 'files': ['bin/rsem-calculate-expression', 'bin/rsem-plot-model', 'bin/rsem-plot-transcript-wiggles', 'bin/rsem-bam2wig', - 'bin/rsem-generate-data-matrix', 'bin/rsem-run-em', 'bin/convert-sam-for-rsem'], + 'files': ['bin/rsem-calculate-expression', 'bin/rsem-plot-model', 'bin/rsem-plot-transcript-wiggles', + 'bin/rsem-bam2wig', 'bin/rsem-generate-data-matrix', 'bin/rsem-run-em', 'bin/convert-sam-for-rsem'], 'dirs': ['bin/samtools-1.3'], } diff --git a/easybuild/easyconfigs/r/RSEM/RSEM-1.3.0-foss-2016b.eb b/easybuild/easyconfigs/r/RSEM/RSEM-1.3.0-foss-2016b.eb index d01f2f9089..e70842c9f5 100644 --- a/easybuild/easyconfigs/r/RSEM/RSEM-1.3.0-foss-2016b.eb +++ b/easybuild/easyconfigs/r/RSEM/RSEM-1.3.0-foss-2016b.eb @@ -24,8 +24,8 @@ dependencies = [ ] sanity_check_paths = { - 'files': ['bin/rsem-calculate-expression', 'bin/rsem-plot-model', 'bin/rsem-plot-transcript-wiggles', 'bin/rsem-bam2wig', - 'bin/rsem-generate-data-matrix', 'bin/rsem-run-em', 'bin/convert-sam-for-rsem'], + 'files': ['bin/rsem-calculate-expression', 'bin/rsem-plot-model', 'bin/rsem-plot-transcript-wiggles', + 'bin/rsem-bam2wig', 'bin/rsem-generate-data-matrix', 'bin/rsem-run-em', 'bin/convert-sam-for-rsem'], 'dirs': ['bin/samtools-1.3'], } -- GitLab From 623dbaebd8e171c358eb6d245bc48c317ce82d3a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 1 Mar 2017 20:35:19 +0100 Subject: [PATCH 0207/1603] fix long lines in RAxML easyconfigs --- .../r/RAxML/RAxML-7.2.6-goolf-1.4.10-hybrid-sse3.eb | 3 ++- .../easyconfigs/r/RAxML/RAxML-7.2.6-goolf-1.4.10-mpi-sse3.eb | 3 ++- .../easyconfigs/r/RAxML/RAxML-7.2.6-goolf-1.4.10-mt-sse3.eb | 3 ++- .../easyconfigs/r/RAxML/RAxML-7.2.6-goolf-1.4.10-seq-sse3.eb | 3 ++- .../easyconfigs/r/RAxML/RAxML-7.2.6-ictce-5.3.0-hybrid-sse3.eb | 3 ++- .../easyconfigs/r/RAxML/RAxML-7.2.6-ictce-5.3.0-mpi-sse3.eb | 3 ++- .../easyconfigs/r/RAxML/RAxML-7.2.6-ictce-5.3.0-mt-sse3.eb | 3 ++- .../easyconfigs/r/RAxML/RAxML-7.2.6-ictce-5.3.0-seq-sse3.eb | 3 ++- .../r/RAxML/RAxML-7.7.5-goolf-1.4.10-hybrid-sse3.eb | 3 ++- .../easyconfigs/r/RAxML/RAxML-7.7.5-goolf-1.4.10-mpi-sse3.eb | 3 ++- .../easyconfigs/r/RAxML/RAxML-7.7.5-goolf-1.4.10-mt-sse3.eb | 3 ++- .../easyconfigs/r/RAxML/RAxML-7.7.5-goolf-1.4.10-seq-sse3.eb | 3 ++- .../easyconfigs/r/RAxML/RAxML-7.7.5-ictce-5.3.0-hybrid-sse3.eb | 3 ++- .../easyconfigs/r/RAxML/RAxML-7.7.5-ictce-5.3.0-mpi-sse3.eb | 3 ++- .../easyconfigs/r/RAxML/RAxML-7.7.5-ictce-5.3.0-mt-sse3.eb | 3 ++- .../easyconfigs/r/RAxML/RAxML-7.7.5-ictce-5.3.0-seq-sse3.eb | 3 ++- 16 files changed, 32 insertions(+), 16 deletions(-) diff --git a/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-goolf-1.4.10-hybrid-sse3.eb b/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-goolf-1.4.10-hybrid-sse3.eb index 985c883441..1eb4b3b846 100644 --- a/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-goolf-1.4.10-hybrid-sse3.eb +++ b/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-goolf-1.4.10-hybrid-sse3.eb @@ -15,7 +15,8 @@ sources = [SOURCE_TAR_BZ2] skipsteps = ['configure', 'install'] -buildopts = '-f Makefile.SSE3.HYBRID.gcc CC="$CC" && mkdir -p %(installdir)s/bin && cp raxmlHPC-HYBRID-SSE3 %(installdir)s/bin' +buildopts = '-f Makefile.SSE3.HYBRID.gcc CC="$CC" && ' +buildopts += "mkdir -p %(installdir)s/bin && cp raxmlHPC-HYBRID-SSE3 %(installdir)s/bin" sanity_check_paths = { 'files': ["bin/raxmlHPC-HYBRID-SSE3"], diff --git a/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-goolf-1.4.10-mpi-sse3.eb b/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-goolf-1.4.10-mpi-sse3.eb index e09f71abf5..7004dce41e 100644 --- a/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-goolf-1.4.10-mpi-sse3.eb +++ b/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-goolf-1.4.10-mpi-sse3.eb @@ -15,7 +15,8 @@ sources = [SOURCE_TAR_BZ2] skipsteps = ['configure', 'install'] -buildopts = '-f Makefile.SSE3.MPI.gcc CC="$CC" && mkdir -p %(installdir)s/bin && cp raxmlHPC-MPI-SSE3 %(installdir)s/bin' +buildopts = '-f Makefile.SSE3.MPI.gcc CC="$CC" && ' +buildopts += "mkdir -p %(installdir)s/bin && cp raxmlHPC-MPI-SSE3 %(installdir)s/bin" sanity_check_paths = { 'files': ["bin/raxmlHPC-MPI-SSE3"], diff --git a/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-goolf-1.4.10-mt-sse3.eb b/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-goolf-1.4.10-mt-sse3.eb index 0fe0530f3a..d7300ce6e9 100644 --- a/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-goolf-1.4.10-mt-sse3.eb +++ b/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-goolf-1.4.10-mt-sse3.eb @@ -14,7 +14,8 @@ sources = [SOURCE_TAR_BZ2] skipsteps = ['configure', 'install'] -buildopts = '-f Makefile.SSE3.PTHREADS.gcc CC="$CC" && mkdir -p %(installdir)s/bin && cp raxmlHPC-PTHREADS-SSE3 %(installdir)s/bin' +buildopts = '-f Makefile.SSE3.PTHREADS.gcc CC="$CC" && ' +buildopts += "mkdir -p %(installdir)s/bin && cp raxmlHPC-PTHREADS-SSE3 %(installdir)s/bin" sanity_check_paths = { 'files': ["bin/raxmlHPC-PTHREADS-SSE3"], diff --git a/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-goolf-1.4.10-seq-sse3.eb b/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-goolf-1.4.10-seq-sse3.eb index af08c5c5e5..ee4a21ba93 100644 --- a/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-goolf-1.4.10-seq-sse3.eb +++ b/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-goolf-1.4.10-seq-sse3.eb @@ -14,7 +14,8 @@ sources = [SOURCE_TAR_BZ2] skipsteps = ['configure', 'install'] -buildopts = '-f Makefile.SSE3.gcc CC="$CC" && mkdir -p %(installdir)s/bin && cp raxmlHPC-SSE3 %(installdir)s/bin' +buildopts = '-f Makefile.SSE3.gcc CC="$CC" && ' +buildopts += "mkdir -p %(installdir)s/bin && cp raxmlHPC-SSE3 %(installdir)s/bin" sanity_check_paths = { 'files': ["bin/raxmlHPC-SSE3"], diff --git a/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-ictce-5.3.0-hybrid-sse3.eb b/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-ictce-5.3.0-hybrid-sse3.eb index 0868a2b38e..fe4066ef14 100644 --- a/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-ictce-5.3.0-hybrid-sse3.eb +++ b/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-ictce-5.3.0-hybrid-sse3.eb @@ -15,7 +15,8 @@ sources = [SOURCE_TAR_BZ2] skipsteps = ['configure', 'install'] -buildopts = '-f Makefile.SSE3.HYBRID.gcc CC="$CC" && mkdir -p %(installdir)s/bin && cp raxmlHPC-HYBRID-SSE3 %(installdir)s/bin' +buildopts = '-f Makefile.SSE3.HYBRID.gcc CC="$CC" && ' +buildopts += "mkdir -p %(installdir)s/bin && cp raxmlHPC-HYBRID-SSE3 %(installdir)s/bin" sanity_check_paths = { 'files': ["bin/raxmlHPC-HYBRID-SSE3"], diff --git a/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-ictce-5.3.0-mpi-sse3.eb b/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-ictce-5.3.0-mpi-sse3.eb index 3a1597463c..fbae2547b2 100644 --- a/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-ictce-5.3.0-mpi-sse3.eb +++ b/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-ictce-5.3.0-mpi-sse3.eb @@ -15,7 +15,8 @@ sources = [SOURCE_TAR_BZ2] skipsteps = ['configure', 'install'] -buildopts = '-f Makefile.SSE3.MPI.gcc CC="$CC" && mkdir -p %(installdir)s/bin && cp raxmlHPC-MPI-SSE3 %(installdir)s/bin' +buildopts = '-f Makefile.SSE3.MPI.gcc CC="$CC" && ' +buildopts += "mkdir -p %(installdir)s/bin && cp raxmlHPC-MPI-SSE3 %(installdir)s/bin" sanity_check_paths = { 'files': ["bin/raxmlHPC-MPI-SSE3"], diff --git a/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-ictce-5.3.0-mt-sse3.eb b/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-ictce-5.3.0-mt-sse3.eb index 153acb7424..c9087e258f 100644 --- a/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-ictce-5.3.0-mt-sse3.eb +++ b/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-ictce-5.3.0-mt-sse3.eb @@ -14,7 +14,8 @@ sources = [SOURCE_TAR_BZ2] skipsteps = ['configure', 'install'] -buildopts = '-f Makefile.SSE3.PTHREADS.gcc CC="$CC" && mkdir -p %(installdir)s/bin && cp raxmlHPC-PTHREADS-SSE3 %(installdir)s/bin' +buildopts = '-f Makefile.SSE3.PTHREADS.gcc CC="$CC" && ' +buildopts += "mkdir -p %(installdir)s/bin && cp raxmlHPC-PTHREADS-SSE3 %(installdir)s/bin" sanity_check_paths = { 'files': ["bin/raxmlHPC-PTHREADS-SSE3"], diff --git a/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-ictce-5.3.0-seq-sse3.eb b/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-ictce-5.3.0-seq-sse3.eb index e7ee2daf46..fdc9f97544 100644 --- a/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-ictce-5.3.0-seq-sse3.eb +++ b/easybuild/easyconfigs/r/RAxML/RAxML-7.2.6-ictce-5.3.0-seq-sse3.eb @@ -14,7 +14,8 @@ sources = [SOURCE_TAR_BZ2] skipsteps = ['configure', 'install'] -buildopts = '-f Makefile.SSE3.gcc CC="$CC" && mkdir -p %(installdir)s/bin && cp raxmlHPC-SSE3 %(installdir)s/bin' +buildopts = '-f Makefile.SSE3.gcc CC="$CC" && ' +buildopts += "mkdir -p %(installdir)s/bin && cp raxmlHPC-SSE3 %(installdir)s/bin" sanity_check_paths = { 'files': ["bin/raxmlHPC-SSE3"], diff --git a/easybuild/easyconfigs/r/RAxML/RAxML-7.7.5-goolf-1.4.10-hybrid-sse3.eb b/easybuild/easyconfigs/r/RAxML/RAxML-7.7.5-goolf-1.4.10-hybrid-sse3.eb index d053b3dc21..1c1435652c 100644 --- a/easybuild/easyconfigs/r/RAxML/RAxML-7.7.5-goolf-1.4.10-hybrid-sse3.eb +++ b/easybuild/easyconfigs/r/RAxML/RAxML-7.7.5-goolf-1.4.10-hybrid-sse3.eb @@ -16,7 +16,8 @@ source_urls = ['https://github.com/stamatak/standard-RAxML/archive/'] skipsteps = ['configure', 'install'] -buildopts = '-f Makefile.SSE3.HYBRID.gcc CC="$CC" && mkdir -p %(installdir)s/bin && cp raxmlHPC-HYBRID-SSE3 %(installdir)s/bin' +buildopts = '-f Makefile.SSE3.HYBRID.gcc CC="$CC" && ' +buildopts += "mkdir -p %(installdir)s/bin && cp raxmlHPC-HYBRID-SSE3 %(installdir)s/bin" sanity_check_paths = { 'files': ["bin/raxmlHPC-HYBRID-SSE3"], diff --git a/easybuild/easyconfigs/r/RAxML/RAxML-7.7.5-goolf-1.4.10-mpi-sse3.eb b/easybuild/easyconfigs/r/RAxML/RAxML-7.7.5-goolf-1.4.10-mpi-sse3.eb index 575001db8d..0ccbb936e8 100644 --- a/easybuild/easyconfigs/r/RAxML/RAxML-7.7.5-goolf-1.4.10-mpi-sse3.eb +++ b/easybuild/easyconfigs/r/RAxML/RAxML-7.7.5-goolf-1.4.10-mpi-sse3.eb @@ -16,7 +16,8 @@ source_urls = ['https://github.com/stamatak/standard-RAxML/archive/'] skipsteps = ['configure', 'install'] -buildopts = '-f Makefile.SSE3.MPI.gcc CC="$CC" && mkdir -p %(installdir)s/bin && cp raxmlHPC-MPI-SSE3 %(installdir)s/bin' +buildopts = '-f Makefile.SSE3.MPI.gcc CC="$CC" && ' +buildopts += "mkdir -p %(installdir)s/bin && cp raxmlHPC-MPI-SSE3 %(installdir)s/bin" sanity_check_paths = { 'files': ["bin/raxmlHPC-MPI-SSE3"], diff --git a/easybuild/easyconfigs/r/RAxML/RAxML-7.7.5-goolf-1.4.10-mt-sse3.eb b/easybuild/easyconfigs/r/RAxML/RAxML-7.7.5-goolf-1.4.10-mt-sse3.eb index a1fec5b741..dc772a459b 100644 --- a/easybuild/easyconfigs/r/RAxML/RAxML-7.7.5-goolf-1.4.10-mt-sse3.eb +++ b/easybuild/easyconfigs/r/RAxML/RAxML-7.7.5-goolf-1.4.10-mt-sse3.eb @@ -15,7 +15,8 @@ source_urls = ['https://github.com/stamatak/standard-RAxML/archive/'] skipsteps = ['configure', 'install'] -buildopts = '-f Makefile.SSE3.PTHREADS.gcc CC="$CC" && mkdir -p %(installdir)s/bin && cp raxmlHPC-PTHREADS-SSE3 %(installdir)s/bin' +buildopts = '-f Makefile.SSE3.PTHREADS.gcc CC="$CC" && ' +buildopts += "mkdir -p %(installdir)s/bin && cp raxmlHPC-PTHREADS-SSE3 %(installdir)s/bin" sanity_check_paths = { 'files': ["bin/raxmlHPC-PTHREADS-SSE3"], diff --git a/easybuild/easyconfigs/r/RAxML/RAxML-7.7.5-goolf-1.4.10-seq-sse3.eb b/easybuild/easyconfigs/r/RAxML/RAxML-7.7.5-goolf-1.4.10-seq-sse3.eb index f253cc9c29..caffbdd4c7 100644 --- a/easybuild/easyconfigs/r/RAxML/RAxML-7.7.5-goolf-1.4.10-seq-sse3.eb +++ b/easybuild/easyconfigs/r/RAxML/RAxML-7.7.5-goolf-1.4.10-seq-sse3.eb @@ -15,7 +15,8 @@ source_urls = ['https://github.com/stamatak/standard-RAxML/archive/'] skipsteps = ['configure', 'install'] -buildopts = '-f Makefile.SSE3.gcc CC="$CC" && mkdir -p %(installdir)s/bin && cp raxmlHPC-SSE3 %(installdir)s/bin' +buildopts = '-f Makefile.SSE3.gcc CC="$CC" && ' +buildopts += "mkdir -p %(installdir)s/bin && cp raxmlHPC-SSE3 %(installdir)s/bin" sanity_check_paths = { 'files': ["bin/raxmlHPC-SSE3"], diff --git a/easybuild/easyconfigs/r/RAxML/RAxML-7.7.5-ictce-5.3.0-hybrid-sse3.eb b/easybuild/easyconfigs/r/RAxML/RAxML-7.7.5-ictce-5.3.0-hybrid-sse3.eb index 7eb0b37f64..05f29e6aa6 100644 --- a/easybuild/easyconfigs/r/RAxML/RAxML-7.7.5-ictce-5.3.0-hybrid-sse3.eb +++ b/easybuild/easyconfigs/r/RAxML/RAxML-7.7.5-ictce-5.3.0-hybrid-sse3.eb @@ -16,7 +16,8 @@ source_urls = ['https://github.com/stamatak/standard-RAxML/archive/'] skipsteps = ['configure', 'install'] -buildopts = '-f Makefile.SSE3.HYBRID.gcc CC="$CC" && mkdir -p %(installdir)s/bin && cp raxmlHPC-HYBRID-SSE3 %(installdir)s/bin' +buildopts = '-f Makefile.SSE3.HYBRID.gcc CC="$CC" && ' +buildopts += "mkdir -p %(installdir)s/bin && cp raxmlHPC-HYBRID-SSE3 %(installdir)s/bin" sanity_check_paths = { 'files': ["bin/raxmlHPC-HYBRID-SSE3"], diff --git a/easybuild/easyconfigs/r/RAxML/RAxML-7.7.5-ictce-5.3.0-mpi-sse3.eb b/easybuild/easyconfigs/r/RAxML/RAxML-7.7.5-ictce-5.3.0-mpi-sse3.eb index 0058765fc5..25dd91ac1d 100644 --- a/easybuild/easyconfigs/r/RAxML/RAxML-7.7.5-ictce-5.3.0-mpi-sse3.eb +++ b/easybuild/easyconfigs/r/RAxML/RAxML-7.7.5-ictce-5.3.0-mpi-sse3.eb @@ -16,7 +16,8 @@ source_urls = ['https://github.com/stamatak/standard-RAxML/archive/'] skipsteps = ['configure', 'install'] -buildopts = '-f Makefile.SSE3.MPI.gcc CC="$CC" && mkdir -p %(installdir)s/bin && cp raxmlHPC-MPI-SSE3 %(installdir)s/bin' +buildopts = '-f Makefile.SSE3.MPI.gcc CC="$CC" && ' +buildopts += "mkdir -p %(installdir)s/bin && cp raxmlHPC-MPI-SSE3 %(installdir)s/bin" sanity_check_paths = { 'files': ["bin/raxmlHPC-MPI-SSE3"], diff --git a/easybuild/easyconfigs/r/RAxML/RAxML-7.7.5-ictce-5.3.0-mt-sse3.eb b/easybuild/easyconfigs/r/RAxML/RAxML-7.7.5-ictce-5.3.0-mt-sse3.eb index 86dab359ac..eef4968327 100644 --- a/easybuild/easyconfigs/r/RAxML/RAxML-7.7.5-ictce-5.3.0-mt-sse3.eb +++ b/easybuild/easyconfigs/r/RAxML/RAxML-7.7.5-ictce-5.3.0-mt-sse3.eb @@ -15,7 +15,8 @@ source_urls = ['https://github.com/stamatak/standard-RAxML/archive/'] skipsteps = ['configure', 'install'] -buildopts = '-f Makefile.SSE3.PTHREADS.gcc CC="$CC" && mkdir -p %(installdir)s/bin && cp raxmlHPC-PTHREADS-SSE3 %(installdir)s/bin' +buildopts = '-f Makefile.SSE3.PTHREADS.gcc CC="$CC" && ' +buildopts += "mkdir -p %(installdir)s/bin && cp raxmlHPC-PTHREADS-SSE3 %(installdir)s/bin" sanity_check_paths = { 'files': ["bin/raxmlHPC-PTHREADS-SSE3"], diff --git a/easybuild/easyconfigs/r/RAxML/RAxML-7.7.5-ictce-5.3.0-seq-sse3.eb b/easybuild/easyconfigs/r/RAxML/RAxML-7.7.5-ictce-5.3.0-seq-sse3.eb index b107d2a11a..89cf1e0f0b 100644 --- a/easybuild/easyconfigs/r/RAxML/RAxML-7.7.5-ictce-5.3.0-seq-sse3.eb +++ b/easybuild/easyconfigs/r/RAxML/RAxML-7.7.5-ictce-5.3.0-seq-sse3.eb @@ -15,7 +15,8 @@ source_urls = ['https://github.com/stamatak/standard-RAxML/archive/'] skipsteps = ['configure', 'install'] -buildopts = '-f Makefile.SSE3.gcc CC="$CC" && mkdir -p %(installdir)s/bin && cp raxmlHPC-SSE3 %(installdir)s/bin' +buildopts = '-f Makefile.SSE3.gcc CC="$CC" && ' +buildopts += "mkdir -p %(installdir)s/bin && cp raxmlHPC-SSE3 %(installdir)s/bin" sanity_check_paths = { 'files': ["bin/raxmlHPC-SSE3"], -- GitLab From 611c237d3dc0b2e4cce6aeee05b9647b156792fe Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 1 Mar 2017 20:57:08 +0100 Subject: [PATCH 0208/1603] trivial whitespace fixes --- easybuild/easyconfigs/c/CUDA/CUDA-8.0.44.eb | 2 +- .../c/Caffe/Caffe-rc3-foss-2016a-CUDA-7.5.18-Python-2.7.11.eb | 2 +- easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.0g-goolf-1.5.14.eb | 2 +- easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.1-intel-2015a.eb | 2 +- easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.2-foss-2015a.eb | 2 +- easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.2-intel-2016b.eb | 2 +- easybuild/easyconfigs/i/I-TASSER/I-TASSER-4.2.eb | 2 +- .../protobuf-python-3.0.2-foss-2016a-Python-2.7.11.eb | 2 +- .../protobuf-python-3.0.2-foss-2016a-Python-3.5.1.eb | 2 +- .../protobuf-python-3.2.0-foss-2016b-Python-2.7.12.eb | 2 +- .../protobuf-python-3.2.0-foss-2016b-Python-3.5.2.eb | 2 +- .../protobuf-python-3.2.0-intel-2016b-Python-2.7.12.eb | 2 +- .../protobuf-python-3.2.0-intel-2016b-Python-3.5.2.eb | 2 +- easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-2015.06.eb | 2 +- easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-2015.11.eb | 2 +- easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-2015.06.eb | 2 +- easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-2015.11.eb | 2 +- easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-2016.03.eb | 2 +- 18 files changed, 18 insertions(+), 18 deletions(-) diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-8.0.44.eb b/easybuild/easyconfigs/c/CUDA/CUDA-8.0.44.eb index 9407a6399e..8a34ad1f5e 100644 --- a/easybuild/easyconfigs/c/CUDA/CUDA-8.0.44.eb +++ b/easybuild/easyconfigs/c/CUDA/CUDA-8.0.44.eb @@ -13,6 +13,6 @@ source_urls = ['https://developer.nvidia.com/compute/cuda/%(version_major_minor) sources = ['%(namelower)s_%(version)s_linux-run'] -modextravars = { 'CUDA_HOME': '%(installdir)s' } +modextravars = {'CUDA_HOME': '%(installdir)s'} moduleclass = 'system' diff --git a/easybuild/easyconfigs/c/Caffe/Caffe-rc3-foss-2016a-CUDA-7.5.18-Python-2.7.11.eb b/easybuild/easyconfigs/c/Caffe/Caffe-rc3-foss-2016a-CUDA-7.5.18-Python-2.7.11.eb index e1484d4027..4a545a7291 100644 --- a/easybuild/easyconfigs/c/Caffe/Caffe-rc3-foss-2016a-CUDA-7.5.18-Python-2.7.11.eb +++ b/easybuild/easyconfigs/c/Caffe/Caffe-rc3-foss-2016a-CUDA-7.5.18-Python-2.7.11.eb @@ -44,7 +44,7 @@ dependencies = [ configopts = '-DBLAS=open' -modextrapaths = {'PYTHONPATH': ['python'] } +modextrapaths = {'PYTHONPATH': ['python']} sanity_check_paths = { 'files': ['bin/caffe'] + diff --git a/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.0g-goolf-1.5.14.eb b/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.0g-goolf-1.5.14.eb index 69c610cd3f..94b4d8c173 100644 --- a/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.0g-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.0g-goolf-1.5.14.eb @@ -17,6 +17,6 @@ builddependencies = [('CMake', '2.8.10.2')] sanity_check_paths = { 'files': ["lib/libfreexl.la"], 'dirs': ["lib"] - } +} moduleclass = 'lib' diff --git a/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.1-intel-2015a.eb b/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.1-intel-2015a.eb index 0401395acc..e2833c7203 100644 --- a/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.1-intel-2015a.eb +++ b/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.1-intel-2015a.eb @@ -17,6 +17,6 @@ builddependencies = [('CMake', '3.2.2')] sanity_check_paths = { 'files': ["lib/libfreexl.la"], 'dirs': ["lib"] - } +} moduleclass = 'lib' diff --git a/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.2-foss-2015a.eb b/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.2-foss-2015a.eb index c38933ad4f..40bff9f910 100644 --- a/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.2-foss-2015a.eb +++ b/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.2-foss-2015a.eb @@ -17,6 +17,6 @@ builddependencies = [('CMake', '3.4.1')] sanity_check_paths = { 'files': ["lib/libfreexl.la"], 'dirs': ["lib"] - } +} moduleclass = 'lib' diff --git a/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.2-intel-2016b.eb b/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.2-intel-2016b.eb index 7b11ad3065..2e9b594a70 100644 --- a/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.2-intel-2016b.eb +++ b/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.2-intel-2016b.eb @@ -17,6 +17,6 @@ builddependencies = [('CMake', '3.7.1')] sanity_check_paths = { 'files': ['lib/libfreexl.a'], 'dirs': [] - } +} moduleclass = 'lib' diff --git a/easybuild/easyconfigs/i/I-TASSER/I-TASSER-4.2.eb b/easybuild/easyconfigs/i/I-TASSER/I-TASSER-4.2.eb index 681a2da8cf..66efa1aea5 100644 --- a/easybuild/easyconfigs/i/I-TASSER/I-TASSER-4.2.eb +++ b/easybuild/easyconfigs/i/I-TASSER/I-TASSER-4.2.eb @@ -25,6 +25,6 @@ sanity_check_paths = { # You may find it desirable to put this variable in the module file. # The command to do so has been put here (commented out) as a convenience. -# modextravars = { 'IMINTASSERDB' : '/path/to/databases/I-TASSER/%(version)s' } +# modextravars = {'IMINTASSERDB': '/path/to/databases/I-TASSER/%(version)s'} moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.0.2-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.0.2-foss-2016a-Python-2.7.11.eb index 986362ad06..3027748d68 100644 --- a/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.0.2-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.0.2-foss-2016a-Python-2.7.11.eb @@ -24,6 +24,6 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages'], } -options = {'modulename': 'google.protobuf' } +options = {'modulename': 'google.protobuf'} moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.0.2-foss-2016a-Python-3.5.1.eb b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.0.2-foss-2016a-Python-3.5.1.eb index fbb897d434..fb8104961b 100644 --- a/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.0.2-foss-2016a-Python-3.5.1.eb +++ b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.0.2-foss-2016a-Python-3.5.1.eb @@ -24,6 +24,6 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages'], } -options = {'modulename': 'google.protobuf' } +options = {'modulename': 'google.protobuf'} moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.2.0-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.2.0-foss-2016b-Python-2.7.12.eb index 8512c8ff8b..1f800a9ecb 100644 --- a/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.2.0-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.2.0-foss-2016b-Python-2.7.12.eb @@ -24,6 +24,6 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages'], } -options = {'modulename': 'google.protobuf' } +options = {'modulename': 'google.protobuf'} moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.2.0-foss-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.2.0-foss-2016b-Python-3.5.2.eb index c25cad0fae..14ca314505 100644 --- a/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.2.0-foss-2016b-Python-3.5.2.eb +++ b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.2.0-foss-2016b-Python-3.5.2.eb @@ -24,6 +24,6 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages'], } -options = {'modulename': 'google.protobuf' } +options = {'modulename': 'google.protobuf'} moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.2.0-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.2.0-intel-2016b-Python-2.7.12.eb index 2dd5db9c4e..fd34141ef9 100755 --- a/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.2.0-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.2.0-intel-2016b-Python-2.7.12.eb @@ -24,6 +24,6 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages'], } -options = {'modulename': 'google.protobuf' } +options = {'modulename': 'google.protobuf'} moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.2.0-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.2.0-intel-2016b-Python-3.5.2.eb index fa54b7dce0..51988758fd 100644 --- a/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.2.0-intel-2016b-Python-3.5.2.eb +++ b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.2.0-intel-2016b-Python-3.5.2.eb @@ -24,6 +24,6 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages'], } -options = {'modulename': 'google.protobuf' } +options = {'modulename': 'google.protobuf'} moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-2015.06.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-2015.06.eb index de900f73b2..01689413cc 100644 --- a/easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-2015.06.eb +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-2015.06.eb @@ -7,7 +7,7 @@ homepage = 'http://www.hdfgroup.org/doc_resource/SZIP/' description = "Szip compression software, providing lossless compression of scientific data" toolchain = {'name': 'CrayGNU', 'version': '2015.06'} -toolchainopts = {'pic': True, } +toolchainopts = {'pic': True} source_urls = ['http://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-2015.11.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-2015.11.eb index 58f5db7a33..2c00792f81 100644 --- a/easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-2015.11.eb +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-2015.11.eb @@ -7,7 +7,7 @@ homepage = 'http://www.hdfgroup.org/doc_resource/SZIP/' description = "Szip compression software, providing lossless compression of scientific data" toolchain = {'name': 'CrayGNU', 'version': '2015.11'} -toolchainopts = {'pic': True, } +toolchainopts = {'pic': True} source_urls = ['http://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-2015.06.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-2015.06.eb index 9daa7bba81..ab2a54c1b6 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-2015.06.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-2015.06.eb @@ -9,7 +9,7 @@ description = """zlib is designed to be a free, general-purpose, legally unencum computer hardware and operating system.""" toolchain = {'name': 'CrayGNU', 'version': '2015.06'} -toolchainopts = {'pic': True, } +toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-2015.11.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-2015.11.eb index ec75812a65..8b079f0d60 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-2015.11.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-2015.11.eb @@ -9,7 +9,7 @@ description = """zlib is designed to be a free, general-purpose, legally unencum computer hardware and operating system.""" toolchain = {'name': 'CrayGNU', 'version': '2015.11'} -toolchainopts = {'pic': True, } +toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-2016.03.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-2016.03.eb index 20e9ee0821..8986e89a6d 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-2016.03.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-2016.03.eb @@ -9,7 +9,7 @@ description = """zlib is designed to be a free, general-purpose, legally unencum computer hardware and operating system.""" toolchain = {'name': 'CrayGNU', 'version': '2016.03'} -toolchainopts = {'pic': True, } +toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] -- GitLab From 6382f6cedc8f53da4f823ca5ed5e545ac5967c0b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 1 Mar 2017 21:06:40 +0100 Subject: [PATCH 0209/1603] sync commented out OpenSSL specs in Python easyconfigs --- .../easyconfigs/p/Python/Python-2.5.6-goolf-1.4.10-bare.eb | 4 +++- .../easyconfigs/p/Python/Python-2.5.6-ictce-5.2.0-bare.eb | 4 +++- .../easyconfigs/p/Python/Python-2.5.6-ictce-5.3.0-bare.eb | 4 +++- easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015a.eb | 5 +++-- easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015b.eb | 5 +++-- easybuild/easyconfigs/p/Python/Python-2.7.10-gimkl-2.11.5.eb | 5 +++-- easybuild/easyconfigs/p/Python/Python-2.7.10-goolf-1.4.10.eb | 5 +++-- easybuild/easyconfigs/p/Python/Python-2.7.10-goolf-1.7.20.eb | 5 +++-- easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015a.eb | 5 +++-- easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015b.eb | 5 +++-- .../p/Python/Python-2.7.11-GCC-4.9.3-2.25-bare.eb | 5 +++-- easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2015a.eb | 5 +++-- easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2016a.eb | 5 +++-- easybuild/easyconfigs/p/Python/Python-2.7.11-gimkl-2.11.5.eb | 5 +++-- easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2015b.eb | 5 +++-- .../p/Python/Python-2.7.11-intel-2016.02-GCC-4.9.eb | 5 +++-- .../p/Python/Python-2.7.11-intel-2016a-libX11-1.6.3.eb | 5 +++-- easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016a.eb | 5 +++-- easybuild/easyconfigs/p/Python/Python-2.7.3-foss-2015b.eb | 4 +++- easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.4.10.eb | 4 +++- easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.5.14.eb | 4 +++- easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.2.0.eb | 4 +++- easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.3.0.eb | 4 +++- easybuild/easyconfigs/p/Python/Python-2.7.3-intel-2015a.eb | 4 +++- easybuild/easyconfigs/p/Python/Python-2.7.5-goolf-1.4.10.eb | 4 +++- easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.3.0.eb | 4 +++- easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.5.0.eb | 4 +++- easybuild/easyconfigs/p/Python/Python-2.7.6-goolf-1.4.10.eb | 4 +++- easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-5.5.0.eb | 4 +++- easybuild/easyconfigs/p/Python/Python-2.7.8-foss-2014b.eb | 4 +++- easybuild/easyconfigs/p/Python/Python-2.7.8-goolf-1.5.14.eb | 4 +++- easybuild/easyconfigs/p/Python/Python-2.7.8-ictce-7.1.2.eb | 4 +++- easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014.06.eb | 4 +++- easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014b.eb | 4 +++- easybuild/easyconfigs/p/Python/Python-3.2.3-goolf-1.4.10.eb | 4 +++- easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-5.3.0.eb | 4 +++- easybuild/easyconfigs/p/Python/Python-3.3.2-goolf-1.4.10.eb | 4 +++- easybuild/easyconfigs/p/Python/Python-3.3.2-ictce-5.3.0.eb | 4 +++- easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2014b.eb | 4 +++- easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2015a.eb | 4 +++- 40 files changed, 120 insertions(+), 55 deletions(-) diff --git a/easybuild/easyconfigs/p/Python/Python-2.5.6-goolf-1.4.10-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.5.6-goolf-1.4.10-bare.eb index ace4711442..bbbadf3e32 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.5.6-goolf-1.4.10-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.5.6-goolf-1.4.10-bare.eb @@ -19,7 +19,9 @@ dependencies = [ ('zlib', '1.2.7'), ('libreadline', '6.2'), ('ncurses', '5.9'), - # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1f'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.2.0-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.2.0-bare.eb index b1bdb4f782..c5675d8144 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.2.0-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.2.0-bare.eb @@ -19,7 +19,9 @@ dependencies = [ ('zlib', '1.2.7'), ('libreadline', '6.2'), ('ncurses', '5.9'), - # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1f'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.3.0-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.3.0-bare.eb index cc84b14111..9cb0c165c6 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.3.0-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.3.0-bare.eb @@ -19,7 +19,9 @@ dependencies = [ ('zlib', '1.2.7'), ('libreadline', '6.2'), ('ncurses', '5.9'), - # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1f'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015a.eb index f325e4238c..0cacb5b908 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015a.eb @@ -23,8 +23,9 @@ dependencies = [ ('SQLite', '3.8.10.2'), ('Tk', '8.6.4', '-no-X11'), # this requires a full X11 stack ('GMP', '6.0.0a', '', ('GCC', '4.9.2')), # required for pycrypto - # ('OpenSSL', '1.0.1m'), # OS dependency should be preferred if the os version is more recent then this version, it's - # nice to have an up to date openssl for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1m'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015b.eb index 1ba18083e7..c4b91910db 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015b.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015b.eb @@ -23,8 +23,9 @@ dependencies = [ ('SQLite', '3.8.10.2'), ('Tk', '8.6.4', '-no-X11'), # this requires a full X11 stack ('GMP', '6.0.0a', '', ('GNU', '4.9.3-2.25')), # required for pycrypto - # ('OpenSSL', '1.0.1m'), # OS dependency should be preferred if the os version is more recent then this version, it's - # nice to have an up to date openssl for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1m'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.10-gimkl-2.11.5.eb b/easybuild/easyconfigs/p/Python/Python-2.7.10-gimkl-2.11.5.eb index e615c89354..6cb74160de 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.10-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.10-gimkl-2.11.5.eb @@ -22,8 +22,9 @@ dependencies = [ ('ncurses', '5.9'), ('SQLite', '3.8.10.2'), ('Tk', '8.6.4', '-no-X11'), # this requires a full X11 stack - # ('OpenSSL', '1.0.1m'), # OS dependency should be preferred if the os version is more recent then this version, it's - # nice to have an up to date openssl for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1m'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.10-goolf-1.4.10.eb b/easybuild/easyconfigs/p/Python/Python-2.7.10-goolf-1.4.10.eb index 7d445cd6ba..2bf2b3c0c7 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.10-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.10-goolf-1.4.10.eb @@ -23,8 +23,9 @@ dependencies = [ ('SQLite', '3.8.10.2'), ('Tk', '8.6.4', '-no-X11'), # this requires a full X11 stack ('GMP', '6.0.0a', '', ('GCC', '4.7.2')), # required for pycrypto - # ('OpenSSL', '1.0.1m'), # OS dependency should be preferred if the os version is more recent then this version, it's - # nice to have an up to date openssl for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1m'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.10-goolf-1.7.20.eb b/easybuild/easyconfigs/p/Python/Python-2.7.10-goolf-1.7.20.eb index 55f10df08f..d616f3a678 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.10-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.10-goolf-1.7.20.eb @@ -23,8 +23,9 @@ dependencies = [ ('SQLite', '3.8.10.2'), ('Tk', '8.6.4', '-no-X11'), # this requires a full X11 stack ('GMP', '6.0.0a', '', ('GCC', '4.8.4')), # required for pycrypto - # ('OpenSSL', '1.0.1m'), # OS dependency should be preferred if the os version is more recent then this version, it's - # nice to have an up to date openssl for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1m'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015a.eb index 017e1ecaae..3bba96e78d 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015a.eb @@ -23,8 +23,9 @@ dependencies = [ ('SQLite', '3.8.10.2'), ('Tk', '8.6.4', '-no-X11'), # this requires a full X11 stack ('GMP', '6.0.0a', '', ('GCC', '4.9.2')), # required for pycrypto - # ('OpenSSL', '1.0.1m'), # OS dependency should be preferred if the os version is more recent then this version, it's - # nice to have an up to date openssl for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1m'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015b.eb index 276aa8a0f3..5578abe094 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015b.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015b.eb @@ -22,8 +22,9 @@ dependencies = [ ('ncurses', '5.9'), ('SQLite', '3.8.10.2'), ('Tk', '8.6.4', '-no-X11'), # this requires a full X11 stack - # ('OpenSSL', '1.0.1m'), # OS dependency should be preferred if the os version is more recent then this version, it's - # nice to have an up to date openssl for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1m'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-GCC-4.9.3-2.25-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-GCC-4.9.3-2.25-bare.eb index 78953148b0..7248257795 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-GCC-4.9.3-2.25-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-GCC-4.9.3-2.25-bare.eb @@ -20,8 +20,9 @@ dependencies = [ ('ncurses', '6.0', '', ('GCCcore', '4.9.3')), ('SQLite', '3.9.2'), ('Tk', '8.6.4', '-no-X11'), # this requires a full X11 stack - # ('OpenSSL', '1.0.1q'), # OS dependency should be preferred if the os version is more recent then this version, it's - # nice to have an up to date openssl for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1q'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2015a.eb index c5fe86070e..7ca3e0d30a 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2015a.eb @@ -23,8 +23,9 @@ dependencies = [ ('SQLite', '3.10.0'), ('Tk', '8.6.4', '-no-X11'), # this requires a full X11 stack ('GMP', '6.1.0'), # required for pycrypto - # ('OpenSSL', '1.0.1q'), # OS dependency should be preferred if the os version is more recent then this version, it's - # nice to have an up to date openssl for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1q'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2016a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2016a.eb index cd19e3b902..90aff56172 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2016a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2016a.eb @@ -23,8 +23,9 @@ dependencies = [ ('SQLite', '3.9.2'), ('Tk', '8.6.4', '-no-X11'), # this requires a full X11 stack ('GMP', '6.1.0'), - # ('OpenSSL', '1.0.1q'), # OS dependency should be preferred if the os version is more recent then this version, it's - # nice to have an up to date openssl for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1q'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-gimkl-2.11.5.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-gimkl-2.11.5.eb index 917a362739..540888954b 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-gimkl-2.11.5.eb @@ -23,8 +23,9 @@ dependencies = [ ('SQLite', '3.9.2'), ('Tk', '8.6.4', '-no-X11'), # this requires a full X11 stack ('GMP', '6.1.0'), - # ('OpenSSL', '1.0.1q'), # OS dependency should be preferred if the os version is more recent then this version, it's - # nice to have an up to date openssl for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1q'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2015b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2015b.eb index fa2f05cdb9..66287172c5 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2015b.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2015b.eb @@ -23,8 +23,9 @@ dependencies = [ ('SQLite', '3.9.2'), ('Tk', '8.6.4', '-no-X11'), # this requires a full X11 stack ('GMP', '6.1.0'), - # ('OpenSSL', '1.0.1q'), # OS dependency should be preferred if the os version is more recent then this version, it's - # nice to have an up to date openssl for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1q'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016.02-GCC-4.9.eb index 914f184b70..49ed840807 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016.02-GCC-4.9.eb @@ -23,8 +23,9 @@ dependencies = [ ('SQLite', '3.9.2'), ('Tk', '8.6.4', '-no-X11'), # this requires a full X11 stack ('GMP', '6.1.0'), - # ('OpenSSL', '1.0.1q'), # OS dependency should be preferred if the os version is more recent then this version, it's - # nice to have an up to date openssl for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1q'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016a-libX11-1.6.3.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016a-libX11-1.6.3.eb index 8b707bfd80..4fa82a32c1 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016a-libX11-1.6.3.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016a-libX11-1.6.3.eb @@ -25,8 +25,9 @@ dependencies = [ ('SQLite', '3.9.2'), ('Tk', '8.6.4', versionsuffix), ('GMP', '6.1.0'), - # ('OpenSSL', '1.0.1q'), # OS dependency should be preferred if the os version is more recent then this version, it's - # nice to have an up to date openssl for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1q'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016a.eb index 711240b058..36a33282cc 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016a.eb @@ -23,8 +23,9 @@ dependencies = [ ('SQLite', '3.9.2'), ('Tk', '8.6.4', '-no-X11'), # this requires a full X11 stack ('GMP', '6.1.0'), - # ('OpenSSL', '1.0.1q'), # OS dependency should be preferred if the os version is more recent then this version, it's - # nice to have an up to date openssl for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1q'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-foss-2015b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-foss-2015b.eb index bb77d83c1d..9cf2d30627 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-foss-2015b.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-foss-2015b.eb @@ -20,7 +20,9 @@ dependencies = [ ('zlib', '1.2.8'), ('libreadline', '6.2'), ('ncurses', '5.9'), - # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1f'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.4.10.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.4.10.eb index 0cda45ec7d..0d7187668b 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.4.10.eb @@ -20,7 +20,9 @@ dependencies = [ ('zlib', '1.2.7'), ('libreadline', '6.2'), ('ncurses', '5.9'), - # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1f'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.5.14.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.5.14.eb index 4ef1bfeaeb..1f04581f6c 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.5.14.eb @@ -20,7 +20,9 @@ dependencies = [ ('zlib', '1.2.7'), ('libreadline', '6.2'), ('ncurses', '5.9'), - # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1f'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.2.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.2.0.eb index 12a347ef6d..d6acb56cd0 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.2.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.2.0.eb @@ -20,7 +20,9 @@ dependencies = [ ('zlib', '1.2.7'), ('libreadline', '6.2'), ('ncurses', '5.9'), - # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1f'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.3.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.3.0.eb index 6265b2329d..0a6a82b9fe 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.3.0.eb @@ -20,7 +20,9 @@ dependencies = [ ('zlib', '1.2.7'), ('libreadline', '6.2'), ('ncurses', '5.9'), - # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1f'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-intel-2015a.eb index a22416f124..78b8331206 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-intel-2015a.eb @@ -20,7 +20,9 @@ dependencies = [ ('zlib', '1.2.8'), ('libreadline', '6.2'), ('ncurses', '5.9'), - # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1f'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.5-goolf-1.4.10.eb b/easybuild/easyconfigs/p/Python/Python-2.7.5-goolf-1.4.10.eb index d9a96be894..8bc486f394 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.5-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.5-goolf-1.4.10.eb @@ -21,7 +21,9 @@ dependencies = [ ('libreadline', '6.2'), ('ncurses', '5.9'), ('SQLite', '3.8.5'), - # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1f'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.3.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.3.0.eb index 48e0894d30..f91d5d9be1 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.3.0.eb @@ -23,7 +23,9 @@ dependencies = [ ('zlib', '1.2.8'), ('libreadline', '6.2'), ('ncurses', '5.9'), - # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1f'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.5.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.5.0.eb index e6e366e13c..1589ad3044 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.5.0.eb @@ -23,7 +23,9 @@ dependencies = [ ('zlib', '1.2.8'), ('libreadline', '6.2'), ('ncurses', '5.9'), - # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1f'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.6-goolf-1.4.10.eb b/easybuild/easyconfigs/p/Python/Python-2.7.6-goolf-1.4.10.eb index 384ccabeee..cc438001ba 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.6-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.6-goolf-1.4.10.eb @@ -20,7 +20,9 @@ dependencies = [ ('zlib', '1.2.7'), ('libreadline', '6.2'), ('ncurses', '5.9'), - # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1f'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-5.5.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-5.5.0.eb index 91008ef87d..8a3b97a885 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-5.5.0.eb @@ -23,7 +23,9 @@ dependencies = [ ('zlib', '1.2.7'), ('libreadline', '6.2'), ('ncurses', '5.9'), - # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1f'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.8-foss-2014b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.8-foss-2014b.eb index 9f687fe594..ff8c4dd1f7 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.8-foss-2014b.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.8-foss-2014b.eb @@ -20,7 +20,9 @@ dependencies = [ ('zlib', '1.2.8'), ('libreadline', '6.3'), ('ncurses', '5.9'), - # ('OpenSSL', '1.0.1g'), # OS dependency should be preferred for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1g'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.8-goolf-1.5.14.eb b/easybuild/easyconfigs/p/Python/Python-2.7.8-goolf-1.5.14.eb index 5f8e6aeeb0..400936afa7 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.8-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.8-goolf-1.5.14.eb @@ -23,7 +23,9 @@ dependencies = [ ('zlib', '1.2.8'), ('libreadline', '6.3'), ('ncurses', '5.9'), - # ('OpenSSL', '1.0.1g'), # OS dependency should be preferred for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1g'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.8-ictce-7.1.2.eb b/easybuild/easyconfigs/p/Python/Python-2.7.8-ictce-7.1.2.eb index 95e0f82630..535df5f445 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.8-ictce-7.1.2.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.8-ictce-7.1.2.eb @@ -26,7 +26,9 @@ dependencies = [ ('zlib', '1.2.8'), ('libreadline', '6.3'), ('ncurses', '5.9'), - # ('OpenSSL', '1.0.1g'), # OS dependency should be preferred for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1g'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014.06.eb b/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014.06.eb index 18384a6b3c..15167c0da9 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014.06.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014.06.eb @@ -23,7 +23,9 @@ dependencies = [ ('zlib', '1.2.8'), ('libreadline', '6.3'), ('ncurses', '5.9'), - # ('OpenSSL', '1.0.1g'), # OS dependency should be preferred for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1g'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014b.eb index dc5adffe37..5da8fad6cd 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014b.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014b.eb @@ -23,7 +23,9 @@ dependencies = [ ('zlib', '1.2.8'), ('libreadline', '6.3'), ('ncurses', '5.9'), - # ('OpenSSL', '1.0.1g'), # OS dependency should be preferred for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1g'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-3.2.3-goolf-1.4.10.eb b/easybuild/easyconfigs/p/Python/Python-3.2.3-goolf-1.4.10.eb index e164d75eb8..530b345146 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.2.3-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.2.3-goolf-1.4.10.eb @@ -20,7 +20,9 @@ dependencies = [ ('zlib', '1.2.7'), ('libreadline', '6.2'), ('ncurses', '5.9'), - # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1f'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-5.3.0.eb b/easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-5.3.0.eb index 7fc679ddfb..1f4aa039b5 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-5.3.0.eb @@ -20,7 +20,9 @@ dependencies = [ ('zlib', '1.2.7'), ('libreadline', '6.2'), ('ncurses', '5.9'), - # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1f'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-3.3.2-goolf-1.4.10.eb b/easybuild/easyconfigs/p/Python/Python-3.3.2-goolf-1.4.10.eb index 5b5ea68742..d79d72ab00 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.3.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.3.2-goolf-1.4.10.eb @@ -20,7 +20,9 @@ dependencies = [ ('zlib', '1.2.8'), ('libreadline', '6.2'), ('ncurses', '5.9'), - # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1f'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-3.3.2-ictce-5.3.0.eb b/easybuild/easyconfigs/p/Python/Python-3.3.2-ictce-5.3.0.eb index 8ba5022eb1..cacde6a179 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.3.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.3.2-ictce-5.3.0.eb @@ -22,7 +22,9 @@ dependencies = [ ('zlib', '1.2.8'), ('libreadline', '6.2'), ('ncurses', '5.9'), - # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1f'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2014b.eb b/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2014b.eb index 948d875463..85a061b4b2 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2014b.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2014b.eb @@ -23,7 +23,9 @@ dependencies = [ ('zlib', '1.2.8'), ('libreadline', '6.3'), ('ncurses', '5.9'), - # ('OpenSSL', '1.0.1g'), # OS dependency should be preferred for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1g'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2015a.eb index db1c3e7576..43f98bbf39 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2015a.eb @@ -23,7 +23,9 @@ dependencies = [ ('zlib', '1.2.8'), ('libreadline', '6.3'), ('ncurses', '5.9'), - # ('OpenSSL', '1.0.1g'), # OS dependency should be preferred for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1g'), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] -- GitLab From 9177dc08613b45e38b6ae052fd1f0ff3cf3d493c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 1 Mar 2017 21:07:08 +0100 Subject: [PATCH 0210/1603] fix more long lines --- .../p/paycheck/paycheck-1.0.2-goolf-1.4.10-Python-2.7.3.eb | 4 +++- .../p/paycheck/paycheck-1.0.2-ictce-5.3.0-Python-2.7.3.eb | 5 +++-- .../p/petsc4py/petsc4py-3.3-goolf-1.4.10-Python-2.7.3.eb | 2 +- .../p/petsc4py/petsc4py-3.3-ictce-5.3.0-Python-2.7.3.eb | 3 +-- .../prompt-toolkit-1.0.13-intel-2016b-Python-2.7.12.eb | 3 ++- .../prompt-toolkit-1.0.3-foss-2016a-Python-2.7.11.eb | 3 ++- .../prompt-toolkit-1.0.3-foss-2016a-Python-3.5.1.eb | 3 ++- .../prompt-toolkit-1.0.6-foss-2016b-Python-2.7.12.eb | 3 ++- .../prompt-toolkit-1.0.6-intel-2016b-Python-2.7.12.eb | 3 ++- .../prompt-toolkit-1.0.6-intel-2016b-Python-3.5.2.eb | 3 ++- 10 files changed, 20 insertions(+), 12 deletions(-) diff --git a/easybuild/easyconfigs/p/paycheck/paycheck-1.0.2-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/p/paycheck/paycheck-1.0.2-goolf-1.4.10-Python-2.7.3.eb index 67abbe4783..ba44c00e4e 100644 --- a/easybuild/easyconfigs/p/paycheck/paycheck-1.0.2-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/p/paycheck/paycheck-1.0.2-goolf-1.4.10-Python-2.7.3.eb @@ -4,7 +4,9 @@ name = 'paycheck' version = '1.0.2' homepage = 'https://pypi.python.org/pypi/paycheck/' -description = """PayCheck is a half-baked implementation of ScalaCheck, which itself is an implementation of QuickCheck for Haskell. PayCheck is useful for defining a specification of what a function should do, rather than testing its results for a given input.""" +description = """PayCheck is a half-baked implementation of ScalaCheck, which itself is an implementation of + QuickCheck for Haskell. PayCheck is useful for defining a specification of what a function should do, + rather than testing its results for a given input.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} diff --git a/easybuild/easyconfigs/p/paycheck/paycheck-1.0.2-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/p/paycheck/paycheck-1.0.2-ictce-5.3.0-Python-2.7.3.eb index 9fdde70731..bead17f746 100644 --- a/easybuild/easyconfigs/p/paycheck/paycheck-1.0.2-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/p/paycheck/paycheck-1.0.2-ictce-5.3.0-Python-2.7.3.eb @@ -4,8 +4,9 @@ name = 'paycheck' version = '1.0.2' homepage = 'https://pypi.python.org/pypi/paycheck/' -description = """PayCheck is a half-baked implementation of ScalaCheck, which itself is an implementation of QuickCheck for Haskell. - PayCheck is useful for defining a specification of what a function should do, rather than testing its results for a given input.""" +description = """PayCheck is a half-baked implementation of ScalaCheck, which itself is an implementation of + QuickCheck for Haskell. PayCheck is useful for defining a specification of what a function should do, + rather than testing its results for a given input.""" toolchain = {'name': 'ictce', 'version': '5.3.0'} diff --git a/easybuild/easyconfigs/p/petsc4py/petsc4py-3.3-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/p/petsc4py/petsc4py-3.3-goolf-1.4.10-Python-2.7.3.eb index 0387cd385f..f2d716e0cd 100644 --- a/easybuild/easyconfigs/p/petsc4py/petsc4py-3.3-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/p/petsc4py/petsc4py-3.3-goolf-1.4.10-Python-2.7.3.eb @@ -4,7 +4,7 @@ name = "petsc4py" version = "3.3" homepage = 'https://code.google.com/p/petsc4py/' -description = """petsc4py are Python bindings for PETSc, the Portable, Extensible Toolchain for Scientific Computation.""" +description = "petsc4py are Python bindings for PETSc, the Portable, Extensible Toolchain for Scientific Computation." toolchain = {'name': 'goolf', 'version': '1.4.10'} diff --git a/easybuild/easyconfigs/p/petsc4py/petsc4py-3.3-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/p/petsc4py/petsc4py-3.3-ictce-5.3.0-Python-2.7.3.eb index 50d6cb2145..d31fcf86b6 100644 --- a/easybuild/easyconfigs/p/petsc4py/petsc4py-3.3-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/p/petsc4py/petsc4py-3.3-ictce-5.3.0-Python-2.7.3.eb @@ -4,8 +4,7 @@ name = "petsc4py" version = "3.3" homepage = 'https://code.google.com/p/petsc4py/' -description = """petsc4py are Python bindings for PETSc, the Portable, Extensible Toolchain for Scientific Computation.""" - +description = "petsc4py are Python bindings for PETSc, the Portable, Extensible Toolchain for Scientific Computation." toolchain = {'name': 'ictce', 'version': '5.3.0'} diff --git a/easybuild/easyconfigs/p/prompt-toolkit/prompt-toolkit-1.0.13-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/prompt-toolkit/prompt-toolkit-1.0.13-intel-2016b-Python-2.7.12.eb index 0dc0fbea27..035c739fdd 100644 --- a/easybuild/easyconfigs/p/prompt-toolkit/prompt-toolkit-1.0.13-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/p/prompt-toolkit/prompt-toolkit-1.0.13-intel-2016b-Python-2.7.12.eb @@ -5,7 +5,8 @@ version = '1.0.13' versionsuffix = '-Python-%(pyver)s' homepage = 'https://github.com/jonathanslenders/python-prompt-toolkit' -description = """prompt_toolkit is a Python library for building powerful interactive command lines and terminal applications.""" +description = """prompt_toolkit is a Python library for building powerful interactive command lines and + terminal applications.""" toolchain = {'name': 'intel', 'version': '2016b'} diff --git a/easybuild/easyconfigs/p/prompt-toolkit/prompt-toolkit-1.0.3-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/prompt-toolkit/prompt-toolkit-1.0.3-foss-2016a-Python-2.7.11.eb index fe4231de3b..4c956fc8b1 100644 --- a/easybuild/easyconfigs/p/prompt-toolkit/prompt-toolkit-1.0.3-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/prompt-toolkit/prompt-toolkit-1.0.3-foss-2016a-Python-2.7.11.eb @@ -5,7 +5,8 @@ version = '1.0.3' versionsuffix = '-Python-%(pyver)s' homepage = 'https://github.com/jonathanslenders/python-prompt-toolkit' -description = """prompt_toolkit is a Python library for building powerful interactive command lines and terminal applications.""" +description = """prompt_toolkit is a Python library for building powerful interactive command lines and + terminal applications.""" toolchain = {'name': 'foss', 'version': '2016a'} diff --git a/easybuild/easyconfigs/p/prompt-toolkit/prompt-toolkit-1.0.3-foss-2016a-Python-3.5.1.eb b/easybuild/easyconfigs/p/prompt-toolkit/prompt-toolkit-1.0.3-foss-2016a-Python-3.5.1.eb index 4b1aefd0e6..83eb4807ee 100644 --- a/easybuild/easyconfigs/p/prompt-toolkit/prompt-toolkit-1.0.3-foss-2016a-Python-3.5.1.eb +++ b/easybuild/easyconfigs/p/prompt-toolkit/prompt-toolkit-1.0.3-foss-2016a-Python-3.5.1.eb @@ -5,7 +5,8 @@ version = '1.0.3' versionsuffix = '-Python-%(pyver)s' homepage = 'https://github.com/jonathanslenders/python-prompt-toolkit' -description = """prompt_toolkit is a Python library for building powerful interactive command lines and terminal applications.""" +description = """prompt_toolkit is a Python library for building powerful interactive command lines and + terminal applications.""" toolchain = {'name': 'foss', 'version': '2016a'} diff --git a/easybuild/easyconfigs/p/prompt-toolkit/prompt-toolkit-1.0.6-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/prompt-toolkit/prompt-toolkit-1.0.6-foss-2016b-Python-2.7.12.eb index e6261f564a..7ba652badd 100644 --- a/easybuild/easyconfigs/p/prompt-toolkit/prompt-toolkit-1.0.6-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/p/prompt-toolkit/prompt-toolkit-1.0.6-foss-2016b-Python-2.7.12.eb @@ -5,7 +5,8 @@ version = '1.0.6' versionsuffix = '-Python-%(pyver)s' homepage = 'https://github.com/jonathanslenders/python-prompt-toolkit' -description = """prompt_toolkit is a Python library for building powerful interactive command lines and terminal applications.""" +description = """prompt_toolkit is a Python library for building powerful interactive command lines and + terminal applications.""" toolchain = {'name': 'foss', 'version': '2016b'} diff --git a/easybuild/easyconfigs/p/prompt-toolkit/prompt-toolkit-1.0.6-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/prompt-toolkit/prompt-toolkit-1.0.6-intel-2016b-Python-2.7.12.eb index a4fd060e9c..dc44707f0f 100644 --- a/easybuild/easyconfigs/p/prompt-toolkit/prompt-toolkit-1.0.6-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/p/prompt-toolkit/prompt-toolkit-1.0.6-intel-2016b-Python-2.7.12.eb @@ -5,7 +5,8 @@ version = '1.0.6' versionsuffix = '-Python-%(pyver)s' homepage = 'https://github.com/jonathanslenders/python-prompt-toolkit' -description = """prompt_toolkit is a Python library for building powerful interactive command lines and terminal applications.""" +description = """prompt_toolkit is a Python library for building powerful interactive command lines and + terminal applications.""" toolchain = {'name': 'intel', 'version': '2016b'} diff --git a/easybuild/easyconfigs/p/prompt-toolkit/prompt-toolkit-1.0.6-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/p/prompt-toolkit/prompt-toolkit-1.0.6-intel-2016b-Python-3.5.2.eb index 6c89475fe0..1e7549ab87 100644 --- a/easybuild/easyconfigs/p/prompt-toolkit/prompt-toolkit-1.0.6-intel-2016b-Python-3.5.2.eb +++ b/easybuild/easyconfigs/p/prompt-toolkit/prompt-toolkit-1.0.6-intel-2016b-Python-3.5.2.eb @@ -5,7 +5,8 @@ version = '1.0.6' versionsuffix = '-Python-%(pyver)s' homepage = 'https://github.com/jonathanslenders/python-prompt-toolkit' -description = """prompt_toolkit is a Python library for building powerful interactive command lines and terminal applications.""" +description = """prompt_toolkit is a Python library for building powerful interactive command lines and + terminal applications.""" toolchain = {'name': 'intel', 'version': '2016b'} -- GitLab From d0561aeac63524671642b317cfbe1135932606d7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 1 Mar 2017 21:16:17 +0100 Subject: [PATCH 0211/1603] fix long lines in ParMETIS easyconfigs --- .../p/ParMETIS/ParMETIS-3.1.1-goolf-1.4.10.eb | 10 +++++----- .../p/ParMETIS/ParMETIS-3.1.1-ictce-5.3.0.eb | 11 +++++------ .../p/ParMETIS/ParMETIS-3.2.0-goolf-1.4.10.eb | 10 +++++----- .../p/ParMETIS/ParMETIS-3.2.0-ictce-6.2.5.eb | 10 +++++----- .../p/ParMETIS/ParMETIS-4.0.2-goolf-1.4.10.eb | 10 +++++----- .../p/ParMETIS/ParMETIS-4.0.2-ictce-5.3.0.eb | 11 +++++------ .../p/ParMETIS/ParMETIS-4.0.3-foss-2016a.eb | 10 +++++----- .../p/ParMETIS/ParMETIS-4.0.3-gimkl-2.11.5.eb | 10 +++++----- .../p/ParMETIS/ParMETIS-4.0.3-goolf-1.4.10.eb | 10 +++++----- .../p/ParMETIS/ParMETIS-4.0.3-ictce-5.5.0.eb | 10 +++++----- .../p/ParMETIS/ParMETIS-4.0.3-intel-2014b.eb | 10 +++++----- .../p/ParMETIS/ParMETIS-4.0.3-intel-2015a.eb | 10 +++++----- .../p/ParMETIS/ParMETIS-4.0.3-intel-2015b.eb | 10 +++++----- .../p/ParMETIS/ParMETIS-4.0.3-intel-2016a.eb | 10 +++++----- 14 files changed, 70 insertions(+), 72 deletions(-) diff --git a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-3.1.1-goolf-1.4.10.eb b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-3.1.1-goolf-1.4.10.eb index 8183de649d..c1a6599161 100644 --- a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-3.1.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-3.1.1-goolf-1.4.10.eb @@ -2,11 +2,11 @@ name = 'ParMETIS' version = '3.1.1' homepage = 'http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview' -description = """ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning unstructured graphs, - meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the functionality provided by METIS and includes - routines that are especially suited for parallel AMR computations and large scale numerical simulations. The algorithms implemented in - ParMETIS are based on the parallel multilevel k-way graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning - schemes.""" +description = """ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning + unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the + functionality provided by METIS and includes routines that are especially suited for parallel AMR computations and + large scale numerical simulations. The algorithms implemented in ParMETIS are based on the parallel multilevel k-way + graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning schemes.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'optarch': True, 'usempi': True, 'pic': True} diff --git a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-3.1.1-ictce-5.3.0.eb b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-3.1.1-ictce-5.3.0.eb index 11db9fe038..f11fa30bf5 100644 --- a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-3.1.1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-3.1.1-ictce-5.3.0.eb @@ -2,12 +2,11 @@ name = 'ParMETIS' version = '3.1.1' homepage = 'http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview' -description = """ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning unstructured graphs, - meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the functionality provided by METIS and includes - routines that are especially suited for parallel AMR computations and large scale numerical simulations. The algorithms implemented in - ParMETIS are based on the parallel multilevel k-way graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning - schemes.""" - +description = """ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning + unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the + functionality provided by METIS and includes routines that are especially suited for parallel AMR computations and + large scale numerical simulations. The algorithms implemented in ParMETIS are based on the parallel multilevel k-way + graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning schemes.""" toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'optarch': True, 'usempi': True, 'pic': True} diff --git a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-3.2.0-goolf-1.4.10.eb b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-3.2.0-goolf-1.4.10.eb index 5223c55c4b..da4fa31fda 100644 --- a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-3.2.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-3.2.0-goolf-1.4.10.eb @@ -2,11 +2,11 @@ name = 'ParMETIS' version = '3.2.0' homepage = 'http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview' -description = """ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning unstructured graphs, - meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the functionality provided by METIS and includes - routines that are especially suited for parallel AMR computations and large scale numerical simulations. The algorithms implemented in - ParMETIS are based on the parallel multilevel k-way graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning - schemes.""" +description = """ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning + unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the + functionality provided by METIS and includes routines that are especially suited for parallel AMR computations and + large scale numerical simulations. The algorithms implemented in ParMETIS are based on the parallel multilevel k-way + graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning schemes.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'optarch': True, 'usempi': True, 'pic': True} diff --git a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-3.2.0-ictce-6.2.5.eb b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-3.2.0-ictce-6.2.5.eb index d331f06b60..0becabf505 100644 --- a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-3.2.0-ictce-6.2.5.eb +++ b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-3.2.0-ictce-6.2.5.eb @@ -2,11 +2,11 @@ name = 'ParMETIS' version = '3.2.0' homepage = 'http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview' -description = """ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning unstructured graphs, - meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the functionality provided by METIS and includes - routines that are especially suited for parallel AMR computations and large scale numerical simulations. The algorithms implemented in - ParMETIS are based on the parallel multilevel k-way graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning - schemes.""" +description = """ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning + unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the + functionality provided by METIS and includes routines that are especially suited for parallel AMR computations and + large scale numerical simulations. The algorithms implemented in ParMETIS are based on the parallel multilevel k-way + graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning schemes.""" toolchain = {'name': 'ictce', 'version': '6.2.5'} toolchainopts = {'optarch': True, 'usempi': True, 'pic': True} diff --git a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.2-goolf-1.4.10.eb b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.2-goolf-1.4.10.eb index f4413be294..36ec81e338 100644 --- a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.2-goolf-1.4.10.eb @@ -2,11 +2,11 @@ name = 'ParMETIS' version = '4.0.2' homepage = 'http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview' -description = """ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning unstructured graphs, - meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the functionality provided by METIS and includes - routines that are especially suited for parallel AMR computations and large scale numerical simulations. The algorithms implemented in - ParMETIS are based on the parallel multilevel k-way graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning - schemes.""" +description = """ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning + unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the + functionality provided by METIS and includes routines that are especially suited for parallel AMR computations and + large scale numerical simulations. The algorithms implemented in ParMETIS are based on the parallel multilevel k-way + graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning schemes.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'optarch': True, 'usempi': True, 'pic': True} diff --git a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.2-ictce-5.3.0.eb b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.2-ictce-5.3.0.eb index a32790b7f1..e92565e46a 100644 --- a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.2-ictce-5.3.0.eb @@ -2,12 +2,11 @@ name = 'ParMETIS' version = '4.0.2' homepage = 'http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview' -description = """ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning unstructured graphs, - meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the functionality provided by METIS and includes - routines that are especially suited for parallel AMR computations and large scale numerical simulations. The algorithms implemented in - ParMETIS are based on the parallel multilevel k-way graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning - schemes.""" - +description = """ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning + unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the + functionality provided by METIS and includes routines that are especially suited for parallel AMR computations and + large scale numerical simulations. The algorithms implemented in ParMETIS are based on the parallel multilevel k-way + graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning schemes.""" toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'optarch': True, 'usempi': True, 'pic': True} diff --git a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-foss-2016a.eb b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-foss-2016a.eb index 6134d068c9..cbbcc0a04a 100644 --- a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-foss-2016a.eb +++ b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-foss-2016a.eb @@ -2,11 +2,11 @@ name = 'ParMETIS' version = '4.0.3' homepage = 'http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview' -description = """ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning unstructured graphs, - meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the functionality provided by METIS and includes - routines that are especially suited for parallel AMR computations and large scale numerical simulations. The algorithms implemented in - ParMETIS are based on the parallel multilevel k-way graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning - schemes.""" +description = """ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning + unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the + functionality provided by METIS and includes routines that are especially suited for parallel AMR computations and + large scale numerical simulations. The algorithms implemented in ParMETIS are based on the parallel multilevel k-way + graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning schemes.""" toolchain = {'name': 'foss', 'version': '2016a'} toolchainopts = {'usempi': True, 'pic': True} diff --git a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-gimkl-2.11.5.eb b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-gimkl-2.11.5.eb index c7f412f769..6ed756b305 100644 --- a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-gimkl-2.11.5.eb @@ -2,11 +2,11 @@ name = 'ParMETIS' version = '4.0.3' homepage = 'http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview' -description = """ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning unstructured graphs, - meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the functionality provided by METIS and includes - routines that are especially suited for parallel AMR computations and large scale numerical simulations. The algorithms implemented in - ParMETIS are based on the parallel multilevel k-way graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning - schemes.""" +description = """ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning + unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the + functionality provided by METIS and includes routines that are especially suited for parallel AMR computations and + large scale numerical simulations. The algorithms implemented in ParMETIS are based on the parallel multilevel k-way + graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning schemes.""" toolchain = {'name': 'gimkl', 'version': '2.11.5'} toolchainopts = {'optarch': True, 'usempi': True, 'pic': True} diff --git a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-goolf-1.4.10.eb b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-goolf-1.4.10.eb index ebbc3db5a2..18b94b4475 100644 --- a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-goolf-1.4.10.eb @@ -2,11 +2,11 @@ name = 'ParMETIS' version = '4.0.3' homepage = 'http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview' -description = """ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning unstructured graphs, - meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the functionality provided by METIS and includes - routines that are especially suited for parallel AMR computations and large scale numerical simulations. The algorithms implemented in - ParMETIS are based on the parallel multilevel k-way graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning - schemes.""" +description = """ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning + unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the + functionality provided by METIS and includes routines that are especially suited for parallel AMR computations and + large scale numerical simulations. The algorithms implemented in ParMETIS are based on the parallel multilevel k-way + graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning schemes.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'optarch': True, 'usempi': True, 'pic': True} diff --git a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-ictce-5.5.0.eb b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-ictce-5.5.0.eb index db08a4e643..07bf0cde29 100644 --- a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-ictce-5.5.0.eb @@ -2,11 +2,11 @@ name = 'ParMETIS' version = '4.0.3' homepage = 'http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview' -description = """ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning unstructured graphs, - meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the functionality provided by METIS and includes - routines that are especially suited for parallel AMR computations and large scale numerical simulations. The algorithms implemented in - ParMETIS are based on the parallel multilevel k-way graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning - schemes.""" +description = """ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning + unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the + functionality provided by METIS and includes routines that are especially suited for parallel AMR computations and + large scale numerical simulations. The algorithms implemented in ParMETIS are based on the parallel multilevel k-way + graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning schemes.""" toolchain = {'name': 'ictce', 'version': '5.5.0'} toolchainopts = {'optarch': True, 'usempi': True, 'pic': True} diff --git a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-intel-2014b.eb b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-intel-2014b.eb index 1521fb5934..f8d63fb067 100644 --- a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-intel-2014b.eb +++ b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-intel-2014b.eb @@ -2,11 +2,11 @@ name = 'ParMETIS' version = '4.0.3' homepage = 'http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview' -description = """ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning unstructured graphs, - meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the functionality provided by METIS and includes - routines that are especially suited for parallel AMR computations and large scale numerical simulations. The algorithms implemented in - ParMETIS are based on the parallel multilevel k-way graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning - schemes.""" +description = """ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning + unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the + functionality provided by METIS and includes routines that are especially suited for parallel AMR computations and + large scale numerical simulations. The algorithms implemented in ParMETIS are based on the parallel multilevel k-way + graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning schemes.""" toolchain = {'name': 'intel', 'version': '2014b'} toolchainopts = {'optarch': True, 'usempi': True, 'pic': True} diff --git a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-intel-2015a.eb b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-intel-2015a.eb index 9212c66919..c2177256c3 100644 --- a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-intel-2015a.eb +++ b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-intel-2015a.eb @@ -2,11 +2,11 @@ name = 'ParMETIS' version = '4.0.3' homepage = 'http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview' -description = """ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning unstructured graphs, - meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the functionality provided by METIS and includes - routines that are especially suited for parallel AMR computations and large scale numerical simulations. The algorithms implemented in - ParMETIS are based on the parallel multilevel k-way graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning - schemes.""" +description = """ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning + unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the + functionality provided by METIS and includes routines that are especially suited for parallel AMR computations and + large scale numerical simulations. The algorithms implemented in ParMETIS are based on the parallel multilevel k-way + graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning schemes.""" toolchain = {'name': 'intel', 'version': '2015a'} toolchainopts = {'optarch': True, 'usempi': True, 'pic': True} diff --git a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-intel-2015b.eb b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-intel-2015b.eb index 3487dd6842..b323ea3886 100644 --- a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-intel-2015b.eb +++ b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-intel-2015b.eb @@ -2,11 +2,11 @@ name = 'ParMETIS' version = '4.0.3' homepage = 'http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview' -description = """ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning unstructured graphs, - meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the functionality provided by METIS and includes - routines that are especially suited for parallel AMR computations and large scale numerical simulations. The algorithms implemented in - ParMETIS are based on the parallel multilevel k-way graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning - schemes.""" +description = """ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning + unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the + functionality provided by METIS and includes routines that are especially suited for parallel AMR computations and + large scale numerical simulations. The algorithms implemented in ParMETIS are based on the parallel multilevel k-way + graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning schemes.""" toolchain = {'name': 'intel', 'version': '2015b'} toolchainopts = {'optarch': True, 'usempi': True, 'pic': True} diff --git a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-intel-2016a.eb b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-intel-2016a.eb index d1d34fb057..ddb7b34451 100644 --- a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-intel-2016a.eb +++ b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-intel-2016a.eb @@ -2,11 +2,11 @@ name = 'ParMETIS' version = '4.0.3' homepage = 'http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview' -description = """ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning unstructured graphs, - meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the functionality provided by METIS and includes - routines that are especially suited for parallel AMR computations and large scale numerical simulations. The algorithms implemented in - ParMETIS are based on the parallel multilevel k-way graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning - schemes.""" +description = """ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning + unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the + functionality provided by METIS and includes routines that are especially suited for parallel AMR computations and + large scale numerical simulations. The algorithms implemented in ParMETIS are based on the parallel multilevel k-way + graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning schemes.""" toolchain = {'name': 'intel', 'version': '2016a'} toolchainopts = {'usempi': True, 'pic': True} -- GitLab From 99a05b9a1f4f368a50b3f7e054a57b733283f151 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 1 Mar 2017 21:35:09 +0100 Subject: [PATCH 0212/1603] fix long lines in PSI easyconfigs --- easybuild/easyconfigs/p/PSI/PSI-4.0b4-ictce-5.3.0-mt.eb | 3 ++- easybuild/easyconfigs/p/PSI/PSI-4.0b4-ictce-5.3.0.eb | 3 ++- easybuild/easyconfigs/p/PSI/PSI-4.0b5-ictce-5.3.0-mt.eb | 3 ++- easybuild/easyconfigs/p/PSI/PSI-4.0b5-ictce-5.3.0.eb | 3 ++- easybuild/easyconfigs/p/PSI/PSI-4.0b5-ictce-5.5.0-mt.eb | 3 ++- easybuild/easyconfigs/p/PSI/PSI-4.0b5-ictce-5.5.0.eb | 3 ++- .../p/PSI/PSI-4.0b5-intel-2015a-mt-maxam7-Python-2.7.10.eb | 3 ++- 7 files changed, 14 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/p/PSI/PSI-4.0b4-ictce-5.3.0-mt.eb b/easybuild/easyconfigs/p/PSI/PSI-4.0b4-ictce-5.3.0-mt.eb index 528a6728be..33bdd4e669 100644 --- a/easybuild/easyconfigs/p/PSI/PSI-4.0b4-ictce-5.3.0-mt.eb +++ b/easybuild/easyconfigs/p/PSI/PSI-4.0b4-ictce-5.3.0-mt.eb @@ -17,7 +17,8 @@ sources = ['%(namelower)s%(version)s.tar.gz'] patches = [ 'PSI-4.0b4-mpi.patch', 'PSI-4.0b4-thread-pool.patch', - 'PSI-%(version)s_python-config.patch', # workaround for broken python-config due to full path to bin/python being used + # workaround for broken python-config due to full path to bin/python being used + 'PSI-%(version)s_python-config.patch', ] python = 'Python' diff --git a/easybuild/easyconfigs/p/PSI/PSI-4.0b4-ictce-5.3.0.eb b/easybuild/easyconfigs/p/PSI/PSI-4.0b4-ictce-5.3.0.eb index 674a15f04b..300abe34c8 100644 --- a/easybuild/easyconfigs/p/PSI/PSI-4.0b4-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/p/PSI/PSI-4.0b4-ictce-5.3.0.eb @@ -15,7 +15,8 @@ sources = ['%(namelower)s%(version)s.tar.gz'] patches = [ 'PSI-4.0b4-mpi.patch', 'PSI-4.0b4-thread-pool.patch', - 'PSI-%(version)s_python-config.patch', # workaround for broken python-config due to full path to bin/python being used + # workaround for broken python-config due to full path to bin/python being used + 'PSI-%(version)s_python-config.patch', ] python = 'Python' diff --git a/easybuild/easyconfigs/p/PSI/PSI-4.0b5-ictce-5.3.0-mt.eb b/easybuild/easyconfigs/p/PSI/PSI-4.0b5-ictce-5.3.0-mt.eb index c680330c40..a35b218f7d 100644 --- a/easybuild/easyconfigs/p/PSI/PSI-4.0b5-ictce-5.3.0-mt.eb +++ b/easybuild/easyconfigs/p/PSI/PSI-4.0b5-ictce-5.3.0-mt.eb @@ -18,7 +18,8 @@ patches = [ 'PSI-4.0b5-failed-test.patch', # the test works but it segfaults on exit 'PSI-4.0b5-thread-pool.patch', 'PSI-4.0b5-new-plugin.patch', - 'PSI-%(version)s_python-config.patch', # workaround for broken python-config due to full path to bin/python being used + # workaround for broken python-config due to full path to bin/python being used + 'PSI-%(version)s_python-config.patch', ] python = 'Python' diff --git a/easybuild/easyconfigs/p/PSI/PSI-4.0b5-ictce-5.3.0.eb b/easybuild/easyconfigs/p/PSI/PSI-4.0b5-ictce-5.3.0.eb index 288d0bd7ab..6444ef03e0 100644 --- a/easybuild/easyconfigs/p/PSI/PSI-4.0b5-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/p/PSI/PSI-4.0b5-ictce-5.3.0.eb @@ -17,7 +17,8 @@ patches = [ 'PSI-4.0b5-failed-test.patch', # the test works but it segfaults on exit 'PSI-4.0b5-thread-pool.patch', 'PSI-4.0b5-new-plugin.patch', - 'PSI-%(version)s_python-config.patch', # workaround for broken python-config due to full path to bin/python being used + # workaround for broken python-config due to full path to bin/python being used + 'PSI-%(version)s_python-config.patch', ] python = 'Python' diff --git a/easybuild/easyconfigs/p/PSI/PSI-4.0b5-ictce-5.5.0-mt.eb b/easybuild/easyconfigs/p/PSI/PSI-4.0b5-ictce-5.5.0-mt.eb index e65fbf7805..d50c1e4431 100644 --- a/easybuild/easyconfigs/p/PSI/PSI-4.0b5-ictce-5.5.0-mt.eb +++ b/easybuild/easyconfigs/p/PSI/PSI-4.0b5-ictce-5.5.0-mt.eb @@ -18,7 +18,8 @@ patches = [ 'PSI-4.0b5-failed-test.patch', # the test works but it segfaults on exit 'PSI-4.0b5-thread-pool.patch', 'PSI-4.0b5-new-plugin.patch', - 'PSI-%(version)s_python-config.patch', # workaround for broken python-config due to full path to bin/python being used + # workaround for broken python-config due to full path to bin/python being used + 'PSI-%(version)s_python-config.patch', ] python = 'Python' diff --git a/easybuild/easyconfigs/p/PSI/PSI-4.0b5-ictce-5.5.0.eb b/easybuild/easyconfigs/p/PSI/PSI-4.0b5-ictce-5.5.0.eb index 7be55fa034..d969aa2c91 100644 --- a/easybuild/easyconfigs/p/PSI/PSI-4.0b5-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/p/PSI/PSI-4.0b5-ictce-5.5.0.eb @@ -17,7 +17,8 @@ patches = [ 'PSI-4.0b5-failed-test.patch', # the test works but it segfaults on exit 'PSI-4.0b5-thread-pool.patch', 'PSI-4.0b5-new-plugin.patch', - 'PSI-%(version)s_python-config.patch', # workaround for broken python-config due to full path to bin/python being used + # workaround for broken python-config due to full path to bin/python being used + 'PSI-%(version)s_python-config.patch', ] python = 'Python' diff --git a/easybuild/easyconfigs/p/PSI/PSI-4.0b5-intel-2015a-mt-maxam7-Python-2.7.10.eb b/easybuild/easyconfigs/p/PSI/PSI-4.0b5-intel-2015a-mt-maxam7-Python-2.7.10.eb index e299f3c676..c3469f5c4d 100644 --- a/easybuild/easyconfigs/p/PSI/PSI-4.0b5-intel-2015a-mt-maxam7-Python-2.7.10.eb +++ b/easybuild/easyconfigs/p/PSI/PSI-4.0b5-intel-2015a-mt-maxam7-Python-2.7.10.eb @@ -19,7 +19,8 @@ patches = [ 'PSI-4.0b5-failed-test.patch', # the test works but it segfaults on exit 'PSI-4.0b5-thread-pool.patch', 'PSI-4.0b5-new-plugin.patch', - 'PSI-%(version)s_python-config.patch', # workaround for broken python-config due to full path to bin/python being used + # workaround for broken python-config due to full path to bin/python being used + 'PSI-%(version)s_python-config.patch', ] python = 'Python' -- GitLab From f4d0a3ef2d2040908622d886f7ed6b717caae073 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 1 Mar 2017 21:35:26 +0100 Subject: [PATCH 0213/1603] minor style fixes in PSORTb and Pasha easyconfigs --- .../p/PSORTb/PSORTb-3.0.4-foss-2016a-Perl-5.22.1.eb | 2 +- easybuild/easyconfigs/p/Pasha/Pasha-1.0.5-ictce-5.3.0.eb | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/p/PSORTb/PSORTb-3.0.4-foss-2016a-Perl-5.22.1.eb b/easybuild/easyconfigs/p/PSORTb/PSORTb-3.0.4-foss-2016a-Perl-5.22.1.eb index b5baf3a55c..99940a8a08 100644 --- a/easybuild/easyconfigs/p/PSORTb/PSORTb-3.0.4-foss-2016a-Perl-5.22.1.eb +++ b/easybuild/easyconfigs/p/PSORTb/PSORTb-3.0.4-foss-2016a-Perl-5.22.1.eb @@ -31,7 +31,7 @@ preconfigopts = "export PSORTROOT=%(installdir)s && " prebuildopts = 'sed -i "s/CC = cc/CC ?= gcc/" bio-tools-psort-modhmm/Makefile && ' postinstallcmds = [ - "cp -r psort/* %(installdir)s/.", + "cp -r psort/* %(installdir)s/.", ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/p/Pasha/Pasha-1.0.5-ictce-5.3.0.eb b/easybuild/easyconfigs/p/Pasha/Pasha-1.0.5-ictce-5.3.0.eb index a72485e97d..161ca2d383 100644 --- a/easybuild/easyconfigs/p/Pasha/Pasha-1.0.5-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/p/Pasha/Pasha-1.0.5-ictce-5.3.0.eb @@ -15,8 +15,8 @@ sources = [SOURCE_TAR_GZ] patches = [ 'intelmpi.patch', - # needed since this still relies on gnu specific includes from libstdc++ which changed in latest version of libstdc++ - # since 1.0.5 pasha tries to use 'backward/' instead of 'ext/' but this might fail on some systems. + # needed since this still relies on gnu specific includes from libstdc++ which changed in latest version + # of libstdc++ since 1.0.5 pasha tries to use 'backward/' instead of 'ext/' but this might fail on some systems. 'old-libstdc++-hash_fun-map-set_pasha-1.0.5.patch', ] -- GitLab From 51157b17a08bfb23ba488cf7144eb84bd73e3146 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 1 Mar 2017 22:21:15 +0100 Subject: [PATCH 0214/1603] moar style fixes in various easyconfigs --- .../c/ConnectomeWorkbench/ConnectomeWorkbench-1.2.2.eb | 2 +- .../m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3-hwloc-chkpt.eb | 2 +- .../easyconfigs/n/NFFT/NFFT-3.3.0-CrayGNU-2015.06.eb | 2 +- .../easyconfigs/n/NFFT/NFFT-3.3.0-CrayGNU-2015.11.eb | 2 +- .../easyconfigs/n/netCDF/netCDF-4.3.2-intel-2015b.eb | 5 +++-- .../o/OBITools/OBITools-1.2.9-foss-2016a-Python-2.7.11.eb | 8 +++----- easybuild/easyconfigs/o/ORCA/ORCA-2_9_1-linux_x86-64.eb | 4 ++-- .../o/ORCA/ORCA-3_0_0-linux_x86-64_openmpi_165.eb | 4 ++-- easybuild/easyconfigs/o/ORCA/ORCA-3_0_2-linux_x86-64.eb | 4 ++-- easybuild/easyconfigs/o/ORCA/ORCA-3_0_3-linux_x86-64.eb | 4 ++-- .../o/Octopus/Octopus-5.0.0-intel-2015b-mpi.eb | 2 +- easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016b.eb | 8 ++++---- .../o/OpenMPI/OpenMPI-1.10.2-GCC-6.1.0-2.27.eb | 4 ++-- .../o/OpenMPI/OpenMPI-1.10.3-GCC-6.1.0-2.27.eb | 4 ++-- .../easyconfigs/o/OpenMPI/OpenMPI-2.0.0-GCC-5.2.0.eb | 4 ++-- .../easyconfigs/o/OpenMPI/OpenMPI-2.0.1-GCC-6.2.0-2.27.eb | 4 ++-- .../o/OpenMPI/OpenMPI-2.0.1-gcccuda-2016.10.eb | 4 ++-- .../OpenMPI-2.0.1-iccifort-2017.1.132-GCC-5.4.0-2.26.eb | 4 ++-- .../easyconfigs/o/OpenMPI/OpenMPI-2.0.2-GCC-6.3.0-2.27.eb | 2 +- .../OpenMPI-2.0.2-iccifort-2017.1.132-GCC-6.3.0-2.27.eb | 4 ++-- .../PCMSolver-20160205-intel-2016a-Python-2.7.11.eb | 3 ++- easybuild/easyconfigs/p/PCRE2/PCRE2-10.21-foss-2016a.eb | 2 +- .../p/PETSc/PETSc-3.3-p2-goolf-1.4.10-Python-2.7.3.eb | 4 ++-- .../p/PETSc/PETSc-3.3-p2-ictce-5.3.0-Python-2.7.3.eb | 5 ++--- .../p/PETSc/PETSc-3.5.1-intel-2014b-Python-2.7.8.eb | 4 ++-- easybuild/easyconfigs/p/PGI/PGI-15.10-GCC-4.9.3-2.25.eb | 3 +-- easybuild/easyconfigs/p/PGI/PGI-15.7-GNU-4.9.2-2.25.eb | 3 +-- easybuild/easyconfigs/p/PGI/PGI-15.7-GNU-4.9.3-2.25.eb | 3 +-- easybuild/easyconfigs/p/PHYLIP/PHYLIP-3.696-foss-2016a.eb | 4 ++-- .../easyconfigs/p/PHYLIP/PHYLIP-3.696-intel-2016a.eb | 4 ++-- .../PSI-4.0b6-20160201-intel-2016a-mt-Python-2.7.11.eb | 2 -- 31 files changed, 54 insertions(+), 60 deletions(-) diff --git a/easybuild/easyconfigs/c/ConnectomeWorkbench/ConnectomeWorkbench-1.2.2.eb b/easybuild/easyconfigs/c/ConnectomeWorkbench/ConnectomeWorkbench-1.2.2.eb index edd7b1aa5d..2db5248504 100644 --- a/easybuild/easyconfigs/c/ConnectomeWorkbench/ConnectomeWorkbench-1.2.2.eb +++ b/easybuild/easyconfigs/c/ConnectomeWorkbench/ConnectomeWorkbench-1.2.2.eb @@ -28,7 +28,7 @@ modextrapaths = { sanity_check_paths = { 'files': ["bin_rh_linux64/wb_import", "bin_rh_linux64/wb_command", - "bin_rh_linux64/wb_view",], + "bin_rh_linux64/wb_view"], 'dirs': ["resources"] } diff --git a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3-hwloc-chkpt.eb b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3-hwloc-chkpt.eb index 0d8dbcbf47..6706bb83e5 100644 --- a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3-hwloc-chkpt.eb +++ b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3-hwloc-chkpt.eb @@ -21,7 +21,7 @@ dependencies = [ builddependencies = [('Bison', '2.5')] -osdependencies = [('libcr-dev', 'blcr-devel'),] +osdependencies = [('libcr-dev', 'blcr-devel')] # enable building of MPE routines withmpe = True diff --git a/easybuild/easyconfigs/n/NFFT/NFFT-3.3.0-CrayGNU-2015.06.eb b/easybuild/easyconfigs/n/NFFT/NFFT-3.3.0-CrayGNU-2015.06.eb index a33090c4b6..81fb2b9ec4 100644 --- a/easybuild/easyconfigs/n/NFFT/NFFT-3.3.0-CrayGNU-2015.06.eb +++ b/easybuild/easyconfigs/n/NFFT/NFFT-3.3.0-CrayGNU-2015.06.eb @@ -14,7 +14,7 @@ source_urls = ['https://www-user.tu-chemnitz.de/~potts/nfft/download/'] sources = [SOURCELOWER_TAR_GZ] dependencies = [ - ('fftw/3.3.4.3', EXTERNAL_MODULE), + ('fftw/3.3.4.3', EXTERNAL_MODULE), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/n/NFFT/NFFT-3.3.0-CrayGNU-2015.11.eb b/easybuild/easyconfigs/n/NFFT/NFFT-3.3.0-CrayGNU-2015.11.eb index c9ebfcb9f5..127aea160a 100644 --- a/easybuild/easyconfigs/n/NFFT/NFFT-3.3.0-CrayGNU-2015.11.eb +++ b/easybuild/easyconfigs/n/NFFT/NFFT-3.3.0-CrayGNU-2015.11.eb @@ -14,7 +14,7 @@ source_urls = ['https://www-user.tu-chemnitz.de/~potts/nfft/download/'] sources = [SOURCELOWER_TAR_GZ] dependencies = [ - ('fftw/3.3.4.5', EXTERNAL_MODULE), + ('fftw/3.3.4.3', EXTERNAL_MODULE), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-intel-2015b.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-intel-2015b.eb index 52365b33f3..126cbec2e8 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-intel-2015b.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-intel-2015b.eb @@ -26,9 +26,10 @@ builddependencies = [ ] # make sure both static and shared libs are built +common_configopts = "-DCURL_LIBRARY=$EBROOTCURL/lib/libcurl.%s -DCURL_INCLUDE_DIR=$EBROOTCURL/include" % SHLIB_EXT configopts = [ - "-DCURL_LIBRARY=$EBROOTCURL/lib/libcurl.%s -DCURL_INCLUDE_DIR=$EBROOTCURL/include -DBUILD_SHARED_LIBS=ON" % SHLIB_EXT, - "-DCURL_LIBRARY=$EBROOTCURL/lib/libcurl.%s -DCURL_INCLUDE_DIR=$EBROOTCURL/include -DBUILD_SHARED_LIBS=OFF" % SHLIB_EXT, + common_configopts + " -DBUILD_SHARED_LIBS=ON", + common_configopts + " -DBUILD_SHARED_LIBS=OFF", ] moduleclass = 'data' diff --git a/easybuild/easyconfigs/o/OBITools/OBITools-1.2.9-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/o/OBITools/OBITools-1.2.9-foss-2016a-Python-2.7.11.eb index fbe8f5cfab..84d9f1db9a 100644 --- a/easybuild/easyconfigs/o/OBITools/OBITools-1.2.9-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/o/OBITools/OBITools-1.2.9-foss-2016a-Python-2.7.11.eb @@ -5,17 +5,15 @@ version = '1.2.9' versionsuffix = '-Python-%(pyver)s' homepage = 'http://www.grenoble.prabi.fr/trac/OBITools' -description = """ The OBITools programs aims to help you to manipulate various data and sequence files in a convenient way using - the Unix command line interface. They follow the standard Unix interface for command line program, allowing to chain a set of - commands using the pipe mecanism. -""" +description = """The OBITools programs aims to help you to manipulate various data and sequence files in a + convenient way using the Unix command line interface. They follow the standard Unix interface for command line + program, allowing to chain a set of commands using the pipe mecanism. """ toolchain = {'name': 'foss', 'version': '2016a'} source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] - dependencies = [ ('Python', '2.7.11'), ('Cython', '0.24.1', versionsuffix), diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-2_9_1-linux_x86-64.eb b/easybuild/easyconfigs/o/ORCA/ORCA-2_9_1-linux_x86-64.eb index a85c46d3f0..95182fb7f6 100644 --- a/easybuild/easyconfigs/o/ORCA/ORCA-2_9_1-linux_x86-64.eb +++ b/easybuild/easyconfigs/o/ORCA/ORCA-2_9_1-linux_x86-64.eb @@ -30,8 +30,8 @@ sanity_check_paths = { } modextravars = { - "SLURM_CPU_BIND" : "none", - "RSH_COMMAND" : "ssh -x", + "SLURM_CPU_BIND": "none", + "RSH_COMMAND": "ssh -x", } moduleclass = 'chem' diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-3_0_0-linux_x86-64_openmpi_165.eb b/easybuild/easyconfigs/o/ORCA/ORCA-3_0_0-linux_x86-64_openmpi_165.eb index 685a061dbd..a2fb635e48 100644 --- a/easybuild/easyconfigs/o/ORCA/ORCA-3_0_0-linux_x86-64_openmpi_165.eb +++ b/easybuild/easyconfigs/o/ORCA/ORCA-3_0_0-linux_x86-64_openmpi_165.eb @@ -32,8 +32,8 @@ sanity_check_paths = { } modextravars = { - "SLURM_CPU_BIND" : "none", - "RSH_COMMAND" : "ssh -x", + "SLURM_CPU_BIND": "none", + "RSH_COMMAND": "ssh -x", } moduleclass = 'chem' diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-3_0_2-linux_x86-64.eb b/easybuild/easyconfigs/o/ORCA/ORCA-3_0_2-linux_x86-64.eb index 7d27755495..9cd49048ac 100644 --- a/easybuild/easyconfigs/o/ORCA/ORCA-3_0_2-linux_x86-64.eb +++ b/easybuild/easyconfigs/o/ORCA/ORCA-3_0_2-linux_x86-64.eb @@ -31,8 +31,8 @@ sanity_check_paths = { } modextravars = { - "SLURM_CPU_BIND" : "none", - "RSH_COMMAND" : "ssh -x", + "SLURM_CPU_BIND": "none", + "RSH_COMMAND": "ssh -x", } moduleclass = 'chem' diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-3_0_3-linux_x86-64.eb b/easybuild/easyconfigs/o/ORCA/ORCA-3_0_3-linux_x86-64.eb index 6a633a98ef..82c2d0b54b 100644 --- a/easybuild/easyconfigs/o/ORCA/ORCA-3_0_3-linux_x86-64.eb +++ b/easybuild/easyconfigs/o/ORCA/ORCA-3_0_3-linux_x86-64.eb @@ -31,8 +31,8 @@ sanity_check_paths = { } modextravars = { - "SLURM_CPU_BIND" : "none", - "RSH_COMMAND" : "ssh -x", + "SLURM_CPU_BIND": "none", + "RSH_COMMAND": "ssh -x", } moduleclass = 'chem' diff --git a/easybuild/easyconfigs/o/Octopus/Octopus-5.0.0-intel-2015b-mpi.eb b/easybuild/easyconfigs/o/Octopus/Octopus-5.0.0-intel-2015b-mpi.eb index e3cd54d745..26fbd9394a 100644 --- a/easybuild/easyconfigs/o/Octopus/Octopus-5.0.0-intel-2015b-mpi.eb +++ b/easybuild/easyconfigs/o/Octopus/Octopus-5.0.0-intel-2015b-mpi.eb @@ -15,7 +15,7 @@ toolchain = {'name': 'intel', 'version': '2015b'} toolchainopts = {'usempi': True, 'opt': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=%(version)s/' ] +source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=%(version)s/'] builddependencies = [ ('Bison', '3.0.4'), diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016b.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016b.eb index 0292e9d416..1495f695f6 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016b.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016b.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'foss', 'version': '2016b'} source_urls = [ 'https://github.com/Itseez/opencv/archive/', - #The Hash is version dependent! see 3rdparty/ippicv/downloader.cmake + # the hash is version dependent! see 3rdparty/ippicv/downloader.cmake 'https://raw.githubusercontent.com/Itseez/opencv_3rdparty/81a676001ca8075ada498583e4166079e5744668/ippicv', ] @@ -40,7 +40,7 @@ dependencies = [ ('GTK+', '2.24.31'), ] -#The destination directory is "linux-" see 3rdparty/ippicv/downloader.cmake +# the destination directory is "linux-" see 3rdparty/ippicv/downloader.cmake ippicv_dir = '3rdparty/ippicv/downloads/linux-808b791a6eac9ed78d32a7666804320e/' preconfigopts = "mkdir -p %s && cp -a ../*.tgz %s && " % (ippicv_dir, ippicv_dir) @@ -65,8 +65,8 @@ configopts += '-DWITH_CUDA=OFF ' postinstallcmds = ["cp 3rdparty/ippicv/unpack/ippicv_lnx/lib/intel64/libippicv.* %(installdir)s/lib"] sanity_check_paths = { - 'files': ['lib/libopencv_core.%s' % SHLIB_EXT ] + - ['lib/python%%(pyshortver)s/site-packages/cv2.%s' % SHLIB_EXT ] + + 'files': ['lib/libopencv_core.%s' % SHLIB_EXT] + + ['lib/python%%(pyshortver)s/site-packages/cv2.%s' % SHLIB_EXT] + ['lib/libippicv.a'] + ['bin/opencv_%s' % x for x in ['annotation', 'createsamples', 'traincascade']], 'dirs': ['include'] diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-GCC-6.1.0-2.27.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-GCC-6.1.0-2.27.eb index ac26d4212f..422607a28b 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-GCC-6.1.0-2.27.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-GCC-6.1.0-2.27.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'GCC', 'version': '6.1.0-2.27'} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads',] +source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] dependencies = [('hwloc', '1.11.3')] @@ -20,7 +20,7 @@ configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading # needed for --with-verbs -osdependencies = [('libibverbs-dev', 'libibverbs-devel'),] +osdependencies = [('libibverbs-dev', 'libibverbs-devel')] libs = ["mpi_cxx", "mpi_mpifh", "mpi", "ompitrace", "open-pal", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.3-GCC-6.1.0-2.27.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.3-GCC-6.1.0-2.27.eb index af22c5f516..ded2f408ed 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.3-GCC-6.1.0-2.27.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.3-GCC-6.1.0-2.27.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'GCC', 'version': '6.1.0-2.27'} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads',] +source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] dependencies = [('hwloc', '1.11.3')] @@ -20,7 +20,7 @@ configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading # needed for --with-verbs -osdependencies = [('libibverbs-dev', 'libibverbs-devel'),] +osdependencies = [('libibverbs-dev', 'libibverbs-devel')] libs = ["mpi_cxx", "mpi_mpifh", "mpi", "ompitrace", "open-pal", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.0-GCC-5.2.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.0-GCC-5.2.0.eb index e0524fac95..ced6423707 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.0-GCC-5.2.0.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.0-GCC-5.2.0.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'GCC', 'version': '5.2.0'} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads',] +source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] dependencies = [('hwloc', '1.11.3')] @@ -20,7 +20,7 @@ configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading # needed for --with-verbs -osdependencies = [('libibverbs-dev', 'libibverbs-devel'),] +osdependencies = [('libibverbs-dev', 'libibverbs-devel')] # VampirTrace is no longer used : https://www.open-mpi.org/community/lists/announce/2016/07/0085.php libs = ["mpi_mpifh", "mpi", "ompitrace", "open-pal", "open-rte"] diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.1-GCC-6.2.0-2.27.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.1-GCC-6.2.0-2.27.eb index fe84bc7c6d..dccf9a16b7 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.1-GCC-6.2.0-2.27.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.1-GCC-6.2.0-2.27.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'GCC', 'version': '6.2.0-2.27'} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads',] +source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] dependencies = [('hwloc', '1.11.4')] @@ -20,7 +20,7 @@ configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading # needed for --with-verbs -osdependencies = [('libibverbs-dev', 'libibverbs-devel'),] +osdependencies = [('libibverbs-dev', 'libibverbs-devel')] libs = ["mpi_mpifh", "mpi", "ompitrace", "open-pal", "open-rte"] sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.1-gcccuda-2016.10.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.1-gcccuda-2016.10.eb index 109e8a754d..bc5a7af11f 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.1-gcccuda-2016.10.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.1-gcccuda-2016.10.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'gcccuda', 'version': '2016.10'} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads',] +source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] dependencies = [('hwloc', '1.11.4')] @@ -20,7 +20,7 @@ configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support configopts += '--with-cuda=$CUDA_HOME ' # CUDA-aware build; N.B. --disable-dlopen is incompatible # needed for --with-verbs -osdependencies = [('libibverbs-dev', 'libibverbs-devel'),] +osdependencies = [('libibverbs-dev', 'libibverbs-devel')] libs = ["mpi_mpifh", "mpi", "ompitrace", "open-pal", "open-rte"] sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.1-iccifort-2017.1.132-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.1-iccifort-2017.1.132-GCC-5.4.0-2.26.eb index d395a7e376..79bff619c0 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.1-iccifort-2017.1.132-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.1-iccifort-2017.1.132-GCC-5.4.0-2.26.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'iccifort', 'version': '2017.1.132-GCC-5.4.0-2.26'} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads',] +source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] dependencies = [('hwloc', '1.11.4')] @@ -20,7 +20,7 @@ configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading # needed for --with-verbs -osdependencies = [('libibverbs-dev', 'libibverbs-devel'),] +osdependencies = [('libibverbs-dev', 'libibverbs-devel')] libs = ["mpi_mpifh", "mpi", "ompitrace", "open-pal", "open-rte"] sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.2-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.2-GCC-6.3.0-2.27.eb index 171f894a0d..3e05777f37 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.2-GCC-6.3.0-2.27.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.2-GCC-6.3.0-2.27.eb @@ -21,7 +21,7 @@ configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading # needed for --with-verbs -osdependencies = [('libibverbs-dev', 'libibverbs-devel'),] +osdependencies = [('libibverbs-dev', 'libibverbs-devel')] libs = ["mpi_mpifh", "mpi", "ompitrace", "open-pal", "open-rte"] sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.2-iccifort-2017.1.132-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.2-iccifort-2017.1.132-GCC-6.3.0-2.27.eb index 66e6aa8b1b..b2aa187ae0 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.2-iccifort-2017.1.132-GCC-6.3.0-2.27.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.2-iccifort-2017.1.132-GCC-6.3.0-2.27.eb @@ -8,7 +8,7 @@ description = """The Open MPI Project is an open source MPI-2 implementation.""" toolchain = {'name': 'iccifort', 'version': '2017.1.132-GCC-6.3.0-2.27'} -source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads',] +source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] checksums = ['886698becc5bea8c151c0af2074b8392'] @@ -20,7 +20,7 @@ configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading # needed for --with-verbs -osdependencies = [('libibverbs-dev', 'libibverbs-devel'),] +osdependencies = [('libibverbs-dev', 'libibverbs-devel')] libs = ["mpi_mpifh", "mpi", "ompitrace", "open-pal", "open-rte"] sanity_check_paths = { diff --git a/easybuild/easyconfigs/p/PCMSolver/PCMSolver-20160205-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/PCMSolver/PCMSolver-20160205-intel-2016a-Python-2.7.11.eb index 861cd9d963..945b858a59 100644 --- a/easybuild/easyconfigs/p/PCMSolver/PCMSolver-20160205-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/PCMSolver/PCMSolver-20160205-intel-2016a-Python-2.7.11.eb @@ -27,7 +27,8 @@ builddependencies = [ ('Eigen', '3.2.7'), ] -configopts = '-DCMAKE_BUILD_TYPE=Release -DEIGEN3_ROOT=$EBROOTEIGEN -DCMAKE_CXX_FLAGS="$LIBLAPACK_MT -DEIGEN_USE_MKL_ALL"' +configopts = "-DCMAKE_BUILD_TYPE=Release -DEIGEN3_ROOT=$EBROOTEIGEN " +configopts += '-DCMAKE_CXX_FLAGS="$LIBLAPACK_MT -DEIGEN_USE_MKL_ALL"' separate_build_dir = True diff --git a/easybuild/easyconfigs/p/PCRE2/PCRE2-10.21-foss-2016a.eb b/easybuild/easyconfigs/p/PCRE2/PCRE2-10.21-foss-2016a.eb index 03cdf3c1c3..12016d01cb 100644 --- a/easybuild/easyconfigs/p/PCRE2/PCRE2-10.21-foss-2016a.eb +++ b/easybuild/easyconfigs/p/PCRE2/PCRE2-10.21-foss-2016a.eb @@ -22,4 +22,4 @@ sanity_check_paths = { 'dirs': [], } -moduleclass = 'devel' \ No newline at end of file +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/PETSc/PETSc-3.3-p2-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/p/PETSc/PETSc-3.3-p2-goolf-1.4.10-Python-2.7.3.eb index 56139c42c1..f00e26a484 100644 --- a/easybuild/easyconfigs/p/PETSc/PETSc-3.3-p2-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/p/PETSc/PETSc-3.3-p2-goolf-1.4.10-Python-2.7.3.eb @@ -3,8 +3,8 @@ version = "3.3-p2" versionsuffix = '-Python-2.7.3' homepage = 'http://www.mcs.anl.gov/petsc' -description = """PETSc, pronounced PET-see (the S is silent), is a suite of data structures and routines for the scalable (parallel) solution -of scientific applications modeled by partial differential equations.""" +description = """PETSc, pronounced PET-see (the S is silent), is a suite of data structures and routines for the + scalable (parallel) solution of scientific applications modeled by partial differential equations.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'usempi': True, 'pic': True} diff --git a/easybuild/easyconfigs/p/PETSc/PETSc-3.3-p2-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/p/PETSc/PETSc-3.3-p2-ictce-5.3.0-Python-2.7.3.eb index 193d113315..deb2a22bc2 100644 --- a/easybuild/easyconfigs/p/PETSc/PETSc-3.3-p2-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/p/PETSc/PETSc-3.3-p2-ictce-5.3.0-Python-2.7.3.eb @@ -3,9 +3,8 @@ version = "3.3-p2" versionsuffix = '-Python-2.7.3' homepage = 'http://www.mcs.anl.gov/petsc' -description = """PETSc, pronounced PET-see (the S is silent), is a suite of data structures and routines for the scalable (parallel) solution - of scientific applications modeled by partial differential equations.""" - +description = """PETSc, pronounced PET-see (the S is silent), is a suite of data structures and routines for the + scalable (parallel) solution of scientific applications modeled by partial differential equations.""" toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'usempi': True, 'pic': True} diff --git a/easybuild/easyconfigs/p/PETSc/PETSc-3.5.1-intel-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/p/PETSc/PETSc-3.5.1-intel-2014b-Python-2.7.8.eb index 72b0ef23a9..15e5de651c 100644 --- a/easybuild/easyconfigs/p/PETSc/PETSc-3.5.1-intel-2014b-Python-2.7.8.eb +++ b/easybuild/easyconfigs/p/PETSc/PETSc-3.5.1-intel-2014b-Python-2.7.8.eb @@ -3,8 +3,8 @@ version = "3.5.1" versionsuffix = '-Python-2.7.8' homepage = 'http://www.mcs.anl.gov/petsc' -description = """PETSc, pronounced PET-see (the S is silent), is a suite of data structures and routines for the scalable (parallel) solution - of scientific applications modeled by partial differential equations.""" +description = """PETSc, pronounced PET-see (the S is silent), is a suite of data structures and routines for the + scalable (parallel) solution of scientific applications modeled by partial differential equations.""" toolchain = {'name': 'intel', 'version': '2014b'} toolchainopts = {'usempi': True, 'pic': True} diff --git a/easybuild/easyconfigs/p/PGI/PGI-15.10-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/p/PGI/PGI-15.10-GCC-4.9.3-2.25.eb index 49864adcd3..099d8a684a 100644 --- a/easybuild/easyconfigs/p/PGI/PGI-15.10-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/p/PGI/PGI-15.10-GCC-4.9.3-2.25.eb @@ -19,7 +19,6 @@ dependencies = [ ] # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "pgi", "license.dat") +license_file = HOME + '/licenses/pgi/license.dat' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/p/PGI/PGI-15.7-GNU-4.9.2-2.25.eb b/easybuild/easyconfigs/p/PGI/PGI-15.7-GNU-4.9.2-2.25.eb index d3260f31f8..4414621a52 100644 --- a/easybuild/easyconfigs/p/PGI/PGI-15.7-GNU-4.9.2-2.25.eb +++ b/easybuild/easyconfigs/p/PGI/PGI-15.7-GNU-4.9.2-2.25.eb @@ -15,7 +15,6 @@ versionsuffix = '-%s-%s' % (gnu, gnuver) dependencies = [(gnu, gnuver)] # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "pgi", "license.dat") +license_file = HOME + '/licenses/pgi/license.dat' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/p/PGI/PGI-15.7-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/p/PGI/PGI-15.7-GNU-4.9.3-2.25.eb index 6589eba972..f9744db69b 100644 --- a/easybuild/easyconfigs/p/PGI/PGI-15.7-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/p/PGI/PGI-15.7-GNU-4.9.3-2.25.eb @@ -15,7 +15,6 @@ versionsuffix = '-%s-%s' % (gnu, gnuver) dependencies = [(gnu, gnuver)] # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "pgi", "license.dat") +license_file = HOME + '/licenses/pgi/license.dat' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/p/PHYLIP/PHYLIP-3.696-foss-2016a.eb b/easybuild/easyconfigs/p/PHYLIP/PHYLIP-3.696-foss-2016a.eb index 90aea78df7..6ded928e61 100644 --- a/easybuild/easyconfigs/p/PHYLIP/PHYLIP-3.696-foss-2016a.eb +++ b/easybuild/easyconfigs/p/PHYLIP/PHYLIP-3.696-foss-2016a.eb @@ -16,8 +16,8 @@ buildopts = '-Csrc -fMakefile.unx all && make -Csrc -fMakefile.unx install' files_to_copy = [(['exe/*'], 'bin'), (['src/libdrawgram.so', 'src/libdrawtree.so'], 'lib')] sanity_check_paths = { - 'files': ['lib/libdrawgram.so', 'lib/libdrawtree.so'], - 'dirs': ['bin'], + 'files': ['lib/libdrawgram.so', 'lib/libdrawtree.so'], + 'dirs': ['bin'], } moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/PHYLIP/PHYLIP-3.696-intel-2016a.eb b/easybuild/easyconfigs/p/PHYLIP/PHYLIP-3.696-intel-2016a.eb index 312062d04f..8fca37e015 100644 --- a/easybuild/easyconfigs/p/PHYLIP/PHYLIP-3.696-intel-2016a.eb +++ b/easybuild/easyconfigs/p/PHYLIP/PHYLIP-3.696-intel-2016a.eb @@ -16,8 +16,8 @@ buildopts = '-Csrc -fMakefile.unx all && make -Csrc -fMakefile.unx install' files_to_copy = [(['exe/*'], 'bin'), (['src/libdrawgram.so', 'src/libdrawtree.so'], 'lib')] sanity_check_paths = { - 'files': ['lib/libdrawgram.so', 'lib/libdrawtree.so'], - 'dirs': ['bin'], + 'files': ['lib/libdrawgram.so', 'lib/libdrawtree.so'], + 'dirs': ['bin'], } moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/PSI/PSI-4.0b6-20160201-intel-2016a-mt-Python-2.7.11.eb b/easybuild/easyconfigs/p/PSI/PSI-4.0b6-20160201-intel-2016a-mt-Python-2.7.11.eb index 3f257ab0c1..ffd93ce336 100644 --- a/easybuild/easyconfigs/p/PSI/PSI-4.0b6-20160201-intel-2016a-mt-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/PSI/PSI-4.0b6-20160201-intel-2016a-mt-Python-2.7.11.eb @@ -42,6 +42,4 @@ configopts += ' -DENABLE_PCMSOLVER=ON -DPCMSOLVER_ROOT=$EBROOTPCMSOLVER' # Execute 4 tests in parallel runtest = 'ARGS="-V -E \'opt10|pubchem1|pubchem2|pywrap-opt-sowreap|sapt4\' -j 4" test' - - moduleclass = 'chem' -- GitLab From 8f5214c969da42a82a783c5782dc13432600647c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 1 Mar 2017 22:27:24 +0100 Subject: [PATCH 0215/1603] fix style fixes in ConnectomeWorkbench easyconfig --- .../c/ConnectomeWorkbench/ConnectomeWorkbench-1.2.2.eb | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/c/ConnectomeWorkbench/ConnectomeWorkbench-1.2.2.eb b/easybuild/easyconfigs/c/ConnectomeWorkbench/ConnectomeWorkbench-1.2.2.eb index 2db5248504..fce250c7cf 100644 --- a/easybuild/easyconfigs/c/ConnectomeWorkbench/ConnectomeWorkbench-1.2.2.eb +++ b/easybuild/easyconfigs/c/ConnectomeWorkbench/ConnectomeWorkbench-1.2.2.eb @@ -21,9 +21,9 @@ source_urls = ['https://ftp.humanconnectome.org/workbench/'] sources = ['workbench-rh_linux64-v%(version)s.zip'] modextrapaths = { - 'PATH': 'bin_rh_linux64', - 'LIBRARY_PATH': 'libs_rh_linux64', - 'LD_LIBRARY_PATH': 'libs_rh_linux64', + 'PATH': 'bin_rh_linux64', + 'LIBRARY_PATH': 'libs_rh_linux64', + 'LD_LIBRARY_PATH': 'libs_rh_linux64', } sanity_check_paths = { @@ -33,4 +33,3 @@ sanity_check_paths = { } moduleclass = 'bio' - -- GitLab From 32a7e256f1753eb22ef21a3eebe466a03106e429 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Thu, 2 Mar 2017 14:04:48 +0800 Subject: [PATCH 0216/1603] prepare release notes for eb311 --- RELEASE_NOTES | 49 +++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 49 insertions(+) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index a240d6d9d8..aa222f795f 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -6,6 +6,55 @@ These release notes can also be consulted at http://easybuild.readthedocs.org/en The latest version of easybuild-easyconfig provides 6,488 easyconfig files, for 1,152 different software packages, 25 different (compiler) toolchains, 13 software bundles and 1 meta-package. +v3.1.1 (March 3rd 2017) +----------------------- + +bugfix release +- added example easyconfig files for 15 new software packages: + - Caffe (#3667), DIAMOND (#4107), fmt (#4131), googletest (#4132), igraph (#4172), MEGA (#4202), meRanTK (#4175), + meshio (#4178), miRDeep2 (#4229), OOMPA (#4211), PBSuite (#4230), randfold (#4217), Smoldyn (#4110), + SpiecEasi (#4215), stress (#4180) +- added additional easyconfigs for various supported software packages, including: + - ATK 2.22.0, Armadillo 7.600.2 + 7.800.0, arpack-ng 3.4.0, BLASR 2.2, Bazel 0.4.4, BioPerl 1.7.1, CFITSIO 3.41, + CGAL 4.9, CMake 3.7.2, Cantera 2.3.0, cURL 7.52.1, DMTCP 2.5.0, Eigen 3.2.10 + 3.3.2 + 3.3.3, Emacs 25.1, + ea-utils 1.04.807, freetype 2.7.1, GMP 6.1.2, Graphviz 2.38.0, gettext 0.19.8.1, IPython 5.2.2, JasPer 2.0.10, + Java 1.8.0_121, Lmod 7.3, libQGLViewer 2.6.4, libpng 1.6.27 + 1.6.28, likwid 4.2.0, MCL 02.063 + 14.137, + MCR R2013b + 2014b + R2015b + R2016b, matplotlib 2.0.0, networkx 1.1, OpenSSL 1.1.0e, OrthoMCL 1.4 + 2.0.9, + PCRE 8.40, PyTables 3.2.3.1, Pysam 0.10.0, path.py 10.1, prompt-toolkit 1.0.13, Qt5 5.8.0, ROOT 6.06.02, + SCons 2.5.1, Stacks 1.44, StringTie 1.3.3, sickle 1.33, VTK 7.1.0, ViennaRNA 2.2.3, Vim 8.0, XZ 5.2.3, + Yade 2017.01a +- added easyconfigs for new 'iomkl/2017a' and 'iompi/2017a' toolchains (#4216) +- various enhancements, including: + - clean up dependencies in libdrm (#4113) + - update X11 bundle and dependencies for GCCcore-6.3.0 (#4147) + - fix style in several easyconfigs (#4174, #4176, #4190) +- various bug fixes, including: + - allow intel 2017 to compile (#4102) + - work around build failure with GCC 6 in pkg-config (#4109) + - add Bison and gettext as build deps for X11 (#4111) + - fix ippicv source download and library install in OpenCV (#4126) + - fix software name for OrthoMCL + modernise OrthoMCL easyconfigs (#4135) + - get rid of backticks in gettext descriptions, causes problems when packaging with FPM (#4146) + - remove duplicate sources specification in OpenMPI (#4150) + - fix definition of buildopts/installopts in Cantera easyconfig (#4164) + - use http rather than ftp source URLs in CFITSIO easyconfigs (#4167) + - fix broken test in Cantera 2.3.0 rather than skipping it (#4177) + - add patch for XZ 5.2.2 to include 5.1.2alpha symbols required by 'rpm' command on CentOS 7.x (#4179) + - update $PATH in OrthoMCL 1.4 easyconfig (#4182) + - bump VTK to 7.1.0 in meshio easyconfig for compatibility with Yade 2017.01a (#4188) + - add patch for Boost v1.61-1.63 to fix problem with make_array/array_wrapper in boost serialization library (#4192) + - add sanity check command to Yade easyconfig to make sure that 'import yade' works, include bzip2 as dep (#4193) + - set CMAKE_PREFIX_PATH to ncurses install directory (#4196) + - switch to lowopt=True for libxc v2.2.* and v3.* (#4199) + - remove custom sanity_check_paths, since it's identical to that used by the R easyblock (#4200) + - fix version (& homepage) in ea-utils easyconfigs (#4205) + - remove --with-threads configure option in OpenMPI-2.* (#4213) + - add PDF::API2 extension to Perl 5.24.0 easyconfigs + sync exts_list (#4221) + - fix check for Szip library in configure script for netCDF 4.1.3 (#4226) +- fix source_urls in several easyconfigs, including: + - bsoft, cutadapt, EMBOSS, GnuTLS, ImageMagick, LibTIFF, Mercurial, netCDF, netCDF-Fortran, pigz, ROOT and Subversion (#4227) + + v3.1.0 (February 3rd 2017) -------------------------- -- GitLab From d6b4285dafcac0f505cfaf93a50910dbe5fe9d54 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 2 Mar 2017 08:45:24 +0200 Subject: [PATCH 0217/1603] Add comment to patch file with author and purpose. --- .../n/NWChem/NWChem-6.6.revision27746-parallelbuild.patch | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/n/NWChem/NWChem-6.6.revision27746-parallelbuild.patch b/easybuild/easyconfigs/n/NWChem/NWChem-6.6.revision27746-parallelbuild.patch index 635f15ee4c..5d07c595e7 100644 --- a/easybuild/easyconfigs/n/NWChem/NWChem-6.6.revision27746-parallelbuild.patch +++ b/easybuild/easyconfigs/n/NWChem/NWChem-6.6.revision27746-parallelbuild.patch @@ -1,3 +1,5 @@ +# corrected parallel builds, no debug info and no vec reports +# B. Hajgato Nov 13 2014 diff -ru nwchem-6.6.orig/src/config/makefile.h nwchem-6.6/src/config/makefile.h --- nwchem-6.6.orig/src/config/makefile.h 2015-10-16 02:12:50.000000000 +0200 +++ nwchem-6.6/src/config/makefile.h 2017-01-12 10:43:00.000000000 +0100 -- GitLab From 8a3f307ee6250f5d70eca2788292014cb1f2c0c9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 2 Mar 2017 09:08:52 +0100 Subject: [PATCH 0218/1603] restore original fftw version in NFFT dep spec --- easybuild/easyconfigs/n/NFFT/NFFT-3.3.0-CrayGNU-2015.11.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/NFFT/NFFT-3.3.0-CrayGNU-2015.11.eb b/easybuild/easyconfigs/n/NFFT/NFFT-3.3.0-CrayGNU-2015.11.eb index 127aea160a..4df5eead7f 100644 --- a/easybuild/easyconfigs/n/NFFT/NFFT-3.3.0-CrayGNU-2015.11.eb +++ b/easybuild/easyconfigs/n/NFFT/NFFT-3.3.0-CrayGNU-2015.11.eb @@ -14,7 +14,7 @@ source_urls = ['https://www-user.tu-chemnitz.de/~potts/nfft/download/'] sources = [SOURCELOWER_TAR_GZ] dependencies = [ - ('fftw/3.3.4.3', EXTERNAL_MODULE), + ('fftw/3.3.4.5', EXTERNAL_MODULE), ] sanity_check_paths = { -- GitLab From b5944e17d62f4cb5a45938768639b2138c9b0f52 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 2 Mar 2017 09:46:45 +0100 Subject: [PATCH 0219/1603] remove single space at the end of OBITools description to make @wpoely86 happy --- .../o/OBITools/OBITools-1.2.9-foss-2016a-Python-2.7.11.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OBITools/OBITools-1.2.9-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/o/OBITools/OBITools-1.2.9-foss-2016a-Python-2.7.11.eb index 84d9f1db9a..82a7c41aa7 100644 --- a/easybuild/easyconfigs/o/OBITools/OBITools-1.2.9-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/o/OBITools/OBITools-1.2.9-foss-2016a-Python-2.7.11.eb @@ -7,7 +7,7 @@ versionsuffix = '-Python-%(pyver)s' homepage = 'http://www.grenoble.prabi.fr/trac/OBITools' description = """The OBITools programs aims to help you to manipulate various data and sequence files in a convenient way using the Unix command line interface. They follow the standard Unix interface for command line - program, allowing to chain a set of commands using the pipe mecanism. """ + program, allowing to chain a set of commands using the pipe mecanism.""" toolchain = {'name': 'foss', 'version': '2016a'} -- GitLab From 05ffcaa5c995fd346fa6b373b604412834c14637 Mon Sep 17 00:00:00 2001 From: Yann Sagon Date: Thu, 2 Mar 2017 11:47:37 +0100 Subject: [PATCH 0220/1603] fix missing PYTHONPATH --- .../r/ROOT/ROOT-v6.08.02-foss-2016a-Python-2.7.11.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-v6.08.02-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/r/ROOT/ROOT-v6.08.02-foss-2016a-Python-2.7.11.eb index 81755cd856..6bb0455477 100644 --- a/easybuild/easyconfigs/r/ROOT/ROOT-v6.08.02-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/r/ROOT/ROOT-v6.08.02-foss-2016a-Python-2.7.11.eb @@ -42,4 +42,6 @@ configopts += '-Doracle=OFF -Dpgsql=OFF -Dqt=OFF -Dsqlite=OFF ' configopts += '-Dcxx14=ON ' configopts += '-Dunuran=ON -Dtable=ON -Dexplicitlink=ON -Dminuit2=ON ' +modextrapaths = {'PYTHONPATH': 'lib/'} + moduleclass = 'data' -- GitLab From 97c578af87d9a9e16dd112cb980d70451d127f0a Mon Sep 17 00:00:00 2001 From: Yann Sagon Date: Thu, 2 Mar 2017 13:35:05 +0100 Subject: [PATCH 0221/1603] rootpy-foss-2016a-python-2.7.11 --- .../rootpy-0.8.0-foss-2016a-Python-2.7.11.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/r/rootpy/rootpy-0.8.0-foss-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/r/rootpy/rootpy-0.8.0-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/r/rootpy/rootpy-0.8.0-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000..a81bc6e8ba --- /dev/null +++ b/easybuild/easyconfigs/r/rootpy/rootpy-0.8.0-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'rootpy' +version = '0.8.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.rootpy.org/' + +description = """The rootpy project is a community-driven initiative aiming to provide a more pythonic interface with +ROOT on top of the existing PyROOT bindings. Given Python’s reflective and dynamic nature, rootpy also aims to +improve ROOT design flaws and supplement existing ROOT functionality. The scientific Python community also offers a +multitude of powerful packages such as SciPy, NumPy, matplotlib, scikit-learn, and PyTables, but a suitable interface +between them and ROOT has been lacking. rootpy provides the interfaces and conversion mechanisms required to liberate +your data and to take advantage of these alternatives if needed.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['https://github.com/rootpy/%(namelower)s/archive/'] +sources = ['%(version)s.tar.gz'] + +dependencies = [ + ('Python', '2.7.11'), + ('ROOT','v6.08.02','-Python-%(pyver)s'), + ('matplotlib', '1.5.1', '-Python-%(pyver)s') +] + +options = {'modulename': 'os'} + +#sanity_check_paths = { +# 'files': ['bin/quast.py'], +# 'dirs': [''], +#} + +moduleclass = 'bio' -- GitLab From 0853a413d724c2ae3d24353a42abaf97d635f6f7 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Luk=C3=A1=C5=A1=20Krup=C4=8D=C3=ADk?= Date: Thu, 2 Mar 2017 16:30:31 +0100 Subject: [PATCH 0222/1603] add tmux-2.3 --- easybuild/easyconfigs/t/tmux/tmux-2.3.eb | 26 ++++++++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/t/tmux/tmux-2.3.eb diff --git a/easybuild/easyconfigs/t/tmux/tmux-2.3.eb b/easybuild/easyconfigs/t/tmux/tmux-2.3.eb new file mode 100644 index 0000000000..d9aa356199 --- /dev/null +++ b/easybuild/easyconfigs/t/tmux/tmux-2.3.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'tmux' +version = '2.3' + +homepage = 'http://tmux.sourceforge.net/' +description = """tmux is a terminal multiplexer. It lets you switch easily +between several programs in one terminal, detach them (they keep running in the background) and reattach them to a different terminal.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['https://github.com/tmux/tmux/releases/download/%(version)s/'] + +dependencies = [ + ('ncurses', '6.0'), + ('libevent', '2.1.8'), +] + +sanity_check_paths = { + 'files': ['bin/tmux'], + 'dirs': [] +} + +moduleclass = 'tools' -- GitLab From 66e53395be9c6c3a6e823fa9066ae6f810fff67c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Luk=C3=A1=C5=A1=20Krup=C4=8D=C3=ADk?= Date: Thu, 2 Mar 2017 16:40:48 +0100 Subject: [PATCH 0223/1603] add libevent-2.1.8.eb --- .../easyconfigs/l/libevent/libevent-2.1.8.eb | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) create mode 100644 easybuild/easyconfigs/l/libevent/libevent-2.1.8.eb diff --git a/easybuild/easyconfigs/l/libevent/libevent-2.1.8.eb b/easybuild/easyconfigs/l/libevent/libevent-2.1.8.eb new file mode 100644 index 0000000000..964ec6943d --- /dev/null +++ b/easybuild/easyconfigs/l/libevent/libevent-2.1.8.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'libevent' +version = '2.1.8' + +homepage = 'http://libevent.org/' +description = """The libevent API provides a mechanism to execute a callback function when a specific + event occurs on a file descriptor or after a timeout has been reached. + Furthermore, libevent also support callbacks due to signals or regular timeouts.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = [ + 'https://github.com/downloads/%(name)s/%(name)s/', + 'https://sourceforge.net/projects/levent/files/%(name)s/%(name)s-%(version_major_minor)s/', +] +sources = ['%(name)s-%(version)s-stable.tar.gz'] + +moduleclass = 'lib' -- GitLab From e61539844a7930b15d93f805c7e1cbd08a8ac3d2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 2 Mar 2017 19:13:20 +0100 Subject: [PATCH 0224/1603] adding easyconfigs: evmix-2.6-intel-2016b-R-3.3.1.eb --- .../e/evmix/evmix-2.6-intel-2016b-R-3.3.1.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/e/evmix/evmix-2.6-intel-2016b-R-3.3.1.eb diff --git a/easybuild/easyconfigs/e/evmix/evmix-2.6-intel-2016b-R-3.3.1.eb b/easybuild/easyconfigs/e/evmix/evmix-2.6-intel-2016b-R-3.3.1.eb new file mode 100644 index 0000000000..9999a81cbc --- /dev/null +++ b/easybuild/easyconfigs/e/evmix/evmix-2.6-intel-2016b-R-3.3.1.eb @@ -0,0 +1,40 @@ +easyblock = 'Bundle' + +name = 'evmix' +version = '2.6' +versionsuffix = '-R-%(rver)s' + +homepage = 'http://cran.r-project.org/web/packages/evmix' +description = """evmix: Extreme Value Mixture Modelling, + Threshold Estimation and Boundary Corrected Kernel Density Estimation""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +dependencies = [ + ('R', '3.3.1'), + ('GSL', '2.3'), +] + +exts_defaultclass = 'RPackage' +exts_list = [ + ('gsl', '1.9-10.3', { + 'source_urls': ['http://cran.r-project.org/src/contrib/'], + 'source_tmpl': '%(name)s_%(version)s.tar.gz', + }), + ('evmix', '2.6', { + 'source_urls': ['http://cran.r-project.org/src/contrib/'], + 'source_tmpl': '%(name)s_%(version)s.tar.gz', + }), +] + +# specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module +full_sanity_check = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['evmix', 'gsl'], +} + +modextrapaths = {'R_LIBS': ['']} + +moduleclass = 'math' -- GitLab From 49d9583a535d924354c98f91e191e05181f49f65 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 2 Mar 2017 19:18:23 +0100 Subject: [PATCH 0225/1603] adding easyconfigs: skewer-0.2.2-intel-2016b.eb --- .../s/skewer/skewer-0.2.2-intel-2016b.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/s/skewer/skewer-0.2.2-intel-2016b.eb diff --git a/easybuild/easyconfigs/s/skewer/skewer-0.2.2-intel-2016b.eb b/easybuild/easyconfigs/s/skewer/skewer-0.2.2-intel-2016b.eb new file mode 100644 index 0000000000..c70dfa11d6 --- /dev/null +++ b/easybuild/easyconfigs/s/skewer/skewer-0.2.2-intel-2016b.eb @@ -0,0 +1,24 @@ +easyblock = 'MakeCp' + +name = 'skewer' +version = '0.2.2' + +homepage = 'https://github.com/relipmoc/skewer' +description = """skewer implements the bit-masked k-difference matching algorithm dedicated to the task of adapter + trimming and it is specially designed for processing next-generation sequencing (NGS) paired-end sequences.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['https://github.com/relipmoc/skewer/archive'] +sources = ['%(version)s.tar.gz'] + +buildopts = 'CXX="$CXX" CXXFLAGS="-c $CXXFLAGS" LDFLAGS="$CXXFLAGS -pthread"' + +files_to_copy = [(['skewer'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/skewer'], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From 6df11f2f4600f8c84f81590c50c447963b08eae5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 3 Mar 2017 09:54:17 +0100 Subject: [PATCH 0226/1603] adding easyconfigs: HPL-2.2-intel-2017.02.eb --- .../h/HPL/HPL-2.2-intel-2017.02.eb | 18 +++++++++ .../i/icc/icc-2017.2.174-GCC-6.3.0-2.27.eb | 33 ++++++++++++++++ .../iccifort-2017.2.174-GCC-6.3.0-2.27.eb | 18 +++++++++ .../ifort/ifort-2017.2.174-GCC-6.3.0-2.27.eb | 36 ++++++++++++++++++ .../i/iimpi/iimpi-2017.02-GCC-6.3.0-2.27.eb | 20 ++++++++++ ...2017.2.174-iimpi-2017.02-GCC-6.3.0-2.27.eb | 38 +++++++++++++++++++ ....174-iccifort-2017.2.174-GCC-6.3.0-2.27.eb | 35 +++++++++++++++++ .../easyconfigs/i/intel/intel-2017.02.eb | 24 ++++++++++++ 8 files changed, 222 insertions(+) create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.2-intel-2017.02.eb create mode 100644 easybuild/easyconfigs/i/icc/icc-2017.2.174-GCC-6.3.0-2.27.eb create mode 100644 easybuild/easyconfigs/i/iccifort/iccifort-2017.2.174-GCC-6.3.0-2.27.eb create mode 100644 easybuild/easyconfigs/i/ifort/ifort-2017.2.174-GCC-6.3.0-2.27.eb create mode 100644 easybuild/easyconfigs/i/iimpi/iimpi-2017.02-GCC-6.3.0-2.27.eb create mode 100644 easybuild/easyconfigs/i/imkl/imkl-2017.2.174-iimpi-2017.02-GCC-6.3.0-2.27.eb create mode 100644 easybuild/easyconfigs/i/impi/impi-2017.2.174-iccifort-2017.2.174-GCC-6.3.0-2.27.eb create mode 100644 easybuild/easyconfigs/i/intel/intel-2017.02.eb diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.2-intel-2017.02.eb b/easybuild/easyconfigs/h/HPL/HPL-2.2-intel-2017.02.eb new file mode 100644 index 0000000000..976ad59fb7 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.2-intel-2017.02.eb @@ -0,0 +1,18 @@ +name = 'HPL' +version = '2.2' + +homepage = 'http://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic + on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the + High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'intel', 'version': '2017.02'} +toolchainopts = {'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] + +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/i/icc/icc-2017.2.174-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/i/icc/icc-2017.2.174-GCC-6.3.0-2.27.eb new file mode 100644 index 0000000000..cd7f8184fe --- /dev/null +++ b/easybuild/easyconfigs/i/icc/icc-2017.2.174-GCC-6.3.0-2.27.eb @@ -0,0 +1,33 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild + +name = 'icc' +version = '2017.2.174' + +homepage = 'http://software.intel.com/en-us/intel-compilers/' +description = "C and C++ compiler from Intel" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition_for_cpp.tgz'] + +checksums = ['1ed9e5176b30ed0f0917a7ea698021ee'] + +gccver = '6.3.0' +binutilsver = '2.27' +versionsuffix = '-GCC-%s-%s' % (gccver, binutilsver) + +dependencies = [ + ('GCCcore', gccver), + ('binutils', binutilsver, '', ('GCCcore', gccver)), +] + +# list of regex for components to install +# full list of components can be obtained from pset/mediaconfig.xml in unpacked sources +# cfr. https://software.intel.com/en-us/articles/intel-composer-xe-2015-silent-installation-guide +components = ['intel-comp', 'intel-ccomp', 'intel-icc', 'intel-openmp', 'intel-ipsc?_', 'intel-gdb(?!.*mic)'] + +dontcreateinstalldir = 'True' + +license_file = HOME + '/licenses/intel/license.lic' + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2017.2.174-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2017.2.174-GCC-6.3.0-2.27.eb new file mode 100644 index 0000000000..a3141d5631 --- /dev/null +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2017.2.174-GCC-6.3.0-2.27.eb @@ -0,0 +1,18 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +easyblock = 'Toolchain' + +name = 'iccifort' +version = '2017.2.174' +versionsuffix = '-GCC-6.3.0-2.27' + +homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' +description = """Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and Intel MKL""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +dependencies = [ + ('icc', version, versionsuffix), + ('ifort', version, versionsuffix), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2017.2.174-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/i/ifort/ifort-2017.2.174-GCC-6.3.0-2.27.eb new file mode 100644 index 0000000000..c4b671b697 --- /dev/null +++ b/easybuild/easyconfigs/i/ifort/ifort-2017.2.174-GCC-6.3.0-2.27.eb @@ -0,0 +1,36 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild + +name = 'ifort' +version = '2017.2.174' + +homepage = 'http://software.intel.com/en-us/intel-compilers/' +description = "Fortran compiler from Intel" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition_for_fortran.tgz'] + +checksums = ['9d5dfa36a36b7c9e877745f3e379248b'] + +# remove dependency on intel-mpi-rt-mic +patches = ['ifort_2017_no_mpi_mic_dependency.patch'] + +gccver = '6.3.0' +binutilsver = '2.27' +versionsuffix = '-GCC-%s-%s' % (gccver, binutilsver) + +dependencies = [ + ('GCCcore', gccver), + ('binutils', binutilsver, '', ('GCCcore', gccver)), +] + +# list of regex for components to install +# full list of components can be obtained from pset/mediaconfig.xml in unpacked sources +# cfr. https://software.intel.com/en-us/articles/intel-composer-xe-2015-silent-installation-guide +components = ['intel-comp', 'intel-fcomp', 'intel-ifort', 'intel-openmp', 'intel-ipsf?_', 'intel-gdb(?!.*mic)'] + +dontcreateinstalldir = 'True' + +license_file = HOME + '/licenses/intel/license.lic' + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-2017.02-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/i/iimpi/iimpi-2017.02-GCC-6.3.0-2.27.eb new file mode 100644 index 0000000000..b0f86b1096 --- /dev/null +++ b/easybuild/easyconfigs/i/iimpi/iimpi-2017.02-GCC-6.3.0-2.27.eb @@ -0,0 +1,20 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +easyblock = "Toolchain" + +name = 'iimpi' +version = '2017.02' +versionsuffix = '-GCC-6.3.0-2.27' + +homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' +description = """Intel C/C++ and Fortran compilers, alongside Intel MPI.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +compver = '2017.2.174' +dependencies = [ + ('icc', compver, versionsuffix), + ('ifort', compver, versionsuffix), + ('impi', compver, '', ('iccifort', '%s%s' % (compver, versionsuffix))), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/imkl/imkl-2017.2.174-iimpi-2017.02-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/i/imkl/imkl-2017.2.174-iimpi-2017.02-GCC-6.3.0-2.27.eb new file mode 100644 index 0000000000..c8801dee34 --- /dev/null +++ b/easybuild/easyconfigs/i/imkl/imkl-2017.2.174-iimpi-2017.02-GCC-6.3.0-2.27.eb @@ -0,0 +1,38 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild + +name = 'imkl' +version = '2017.2.174' + +homepage = 'http://software.intel.com/en-us/intel-mkl/' +description = """Intel Math Kernel Library is a library of highly optimized, + extensively threaded math routines for science, engineering, and financial + applications that require maximum performance. Core math functions include + BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.""" + +toolchain = {'name': 'iimpi', 'version': '2017.02-GCC-6.3.0-2.27'} + +sources = ['l_mkl_%(version)s.tgz'] +checksums = ['ef39a12dcbffe5f4a0ef141b8759208c'] + +dontcreateinstalldir = 'True' + +license_file = HOME + '/licenses/intel/license.lic' + +interfaces = True + +postinstallcmds = [ + # extract the examples + 'tar xvzf %(installdir)s/mkl/examples/examples_cluster_c.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_cluster_f.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_core_c.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_core_f.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_f95.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_mic_f.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_mic_c.tgz -C %(installdir)s/mkl/examples/', +] + +modextravars = { + 'MKL_EXAMPLES': '%(installdir)s/mkl/examples/', +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/impi/impi-2017.2.174-iccifort-2017.2.174-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/i/impi/impi-2017.2.174-iccifort-2017.2.174-GCC-6.3.0-2.27.eb new file mode 100644 index 0000000000..c2e9a1817a --- /dev/null +++ b/easybuild/easyconfigs/i/impi/impi-2017.2.174-iccifort-2017.2.174-GCC-6.3.0-2.27.eb @@ -0,0 +1,35 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild + +name = 'impi' +version = '2017.2.174' + +homepage = 'http://software.intel.com/en-us/intel-mpi-library/' +description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric message + passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for + Linux OS implements the Message Passing Interface, version 2 (MPI-2) specification.""" + +toolchain = {'name': 'iccifort', 'version': '2017.2.174-GCC-6.3.0-2.27'} + +sources = ['l_mpi_%(version)s.tgz'] + +checksums = ['b6c2e62c3fb9b1558ede72ccf72cf1d6'] + +dontcreateinstalldir = 'True' + +components = ['intel-mpi', 'intel-psxe', 'intel-imb'] + +license_file = HOME + '/licenses/intel/license.lic' + +# set up all the mpi commands to default to intel compilers +# set_mpi_wrappers_all = 'True' + +postinstallcmds = [ + 'ln -s %(installdir)s/lib64/libmpi.so %(installdir)s/lib64/libmpich.so', + 'ln -s %(installdir)s/lib64/libmpigc4.so %(installdir)s/lib64/libmpichcxx.so', + 'ln -s %(installdir)s/lib64/libmpigf.so %(installdir)s/lib64/libfmpich.so', + 'ln -s %(installdir)s/lib64/libmpigf.so %(installdir)s/lib64/libmpichf90.so', + 'ln -s %(installdir)s/lib64/libmpi.so %(installdir)s/lib64/libmpl.so', + 'ln -s %(installdir)s/lib64/libmpi.so %(installdir)s/lib64/libopa.so' +] + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/intel/intel-2017.02.eb b/easybuild/easyconfigs/i/intel/intel-2017.02.eb new file mode 100644 index 0000000000..941245b3e6 --- /dev/null +++ b/easybuild/easyconfigs/i/intel/intel-2017.02.eb @@ -0,0 +1,24 @@ +easyblock = 'Toolchain' + +name = 'intel' +version = '2017.02' + +homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +compver = '2017.2.174' +gccver = '6.3.0' +binutilsver = '2.27' +gccsuff = '-GCC-%s-%s' % (gccver, binutilsver) +dependencies = [ + ('GCCcore', gccver), + ('binutils', binutilsver, '-GCCcore-%s' % gccver), + ('icc', compver, gccsuff), + ('ifort', compver, gccsuff), + ('impi', compver, '', ('iccifort', '%s%s' % (compver, gccsuff))), + ('imkl', compver, '', ('iimpi', version + gccsuff)), +] + +moduleclass = 'toolchain' -- GitLab From 6cf55b6fb7840d9db16dc9885bcef520ccd906a2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 3 Mar 2017 10:18:10 +0100 Subject: [PATCH 0227/1603] remove license_file specs in impi/imkl 2017.2.174 easyconfigs --- .../i/imkl/imkl-2017.2.174-iimpi-2017.02-GCC-6.3.0-2.27.eb | 2 -- .../impi/impi-2017.2.174-iccifort-2017.2.174-GCC-6.3.0-2.27.eb | 2 -- 2 files changed, 4 deletions(-) diff --git a/easybuild/easyconfigs/i/imkl/imkl-2017.2.174-iimpi-2017.02-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/i/imkl/imkl-2017.2.174-iimpi-2017.02-GCC-6.3.0-2.27.eb index c8801dee34..62ed829038 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2017.2.174-iimpi-2017.02-GCC-6.3.0-2.27.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2017.2.174-iimpi-2017.02-GCC-6.3.0-2.27.eb @@ -16,8 +16,6 @@ checksums = ['ef39a12dcbffe5f4a0ef141b8759208c'] dontcreateinstalldir = 'True' -license_file = HOME + '/licenses/intel/license.lic' - interfaces = True postinstallcmds = [ diff --git a/easybuild/easyconfigs/i/impi/impi-2017.2.174-iccifort-2017.2.174-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/i/impi/impi-2017.2.174-iccifort-2017.2.174-GCC-6.3.0-2.27.eb index c2e9a1817a..9375fca351 100644 --- a/easybuild/easyconfigs/i/impi/impi-2017.2.174-iccifort-2017.2.174-GCC-6.3.0-2.27.eb +++ b/easybuild/easyconfigs/i/impi/impi-2017.2.174-iccifort-2017.2.174-GCC-6.3.0-2.27.eb @@ -18,8 +18,6 @@ dontcreateinstalldir = 'True' components = ['intel-mpi', 'intel-psxe', 'intel-imb'] -license_file = HOME + '/licenses/intel/license.lic' - # set up all the mpi commands to default to intel compilers # set_mpi_wrappers_all = 'True' -- GitLab From 051a170864a0a07b45d308ce35ef14a1dcb31137 Mon Sep 17 00:00:00 2001 From: Yann Sagon Date: Fri, 3 Mar 2017 11:00:50 +0100 Subject: [PATCH 0228/1603] sanity check fix --- .../r/rootpy/rootpy-0.8.0-foss-2016a-Python-2.7.11.eb | 10 ++++------ 1 file changed, 4 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/r/rootpy/rootpy-0.8.0-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/r/rootpy/rootpy-0.8.0-foss-2016a-Python-2.7.11.eb index a81bc6e8ba..d40917cf4c 100644 --- a/easybuild/easyconfigs/r/rootpy/rootpy-0.8.0-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/r/rootpy/rootpy-0.8.0-foss-2016a-Python-2.7.11.eb @@ -24,11 +24,9 @@ dependencies = [ ('matplotlib', '1.5.1', '-Python-%(pyver)s') ] -options = {'modulename': 'os'} - -#sanity_check_paths = { -# 'files': ['bin/quast.py'], -# 'dirs': [''], -#} +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} moduleclass = 'bio' -- GitLab From ce387d60825aa0b2ff37fe5c1b7e1a110a0a9a7b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Luk=C3=A1=C5=A1=20Krup=C4=8D=C3=ADk?= Date: Fri, 3 Mar 2017 11:40:22 +0100 Subject: [PATCH 0229/1603] @boegel change too long line into tmux, fix sources libevent and added sanity_check_paths to libevent --- easybuild/easyconfigs/l/libevent/libevent-2.1.8.eb | 13 +++++++++++-- easybuild/easyconfigs/t/tmux/tmux-2.3.eb | 3 ++- 2 files changed, 13 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/l/libevent/libevent-2.1.8.eb b/easybuild/easyconfigs/l/libevent/libevent-2.1.8.eb index 964ec6943d..369e68366a 100644 --- a/easybuild/easyconfigs/l/libevent/libevent-2.1.8.eb +++ b/easybuild/easyconfigs/l/libevent/libevent-2.1.8.eb @@ -11,9 +11,18 @@ description = """The libevent API provides a mechanism to execute a callback fun toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = [ - 'https://github.com/downloads/%(name)s/%(name)s/', - 'https://sourceforge.net/projects/levent/files/%(name)s/%(name)s-%(version_major_minor)s/', + 'https://github.com/%(name)s/%(name)s/releases/download/release-%(version)s-stable/', + 'https://downloads.sourceforge.net/project/levent/release-%(version)s-stable/', ] + sources = ['%(name)s-%(version)s-stable.tar.gz'] +checksums = ['f3eeaed018542963b7d2416ef1135ecc'] + +sanity_check_paths = { + 'files': ["bin/event_rpcgen.py"] + + ['include/%s' % x for x in ["evdns.h", "event.h", "evhttp.h", "evrpc.h", "evutil.h"]] + + ['include/event2/%s' % x for x in ['buffer_compat.h', 'bufferevent.h', 'bufferevent_struct.h', 'dns_compat.h', 'dns_struct.h', 'event-config.h', 'event_struct.h', 'http.h', 'keyvalq_struct.h', 'rpc_compat.h', 'rpc_struct.h', 'tag.h', 'util.h', 'bufferevent_compat.h', 'bufferevent_ssl.h', 'buffer.h', 'dns.h', 'event_compat.h', 'event.h', 'http_compat.h', 'http_struct.h', 'listener.h', 'rpc.h', 'tag_compat.h', 'thread.h', 'visibility.h']], + 'dirs': ["lib"] + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/tmux/tmux-2.3.eb b/easybuild/easyconfigs/t/tmux/tmux-2.3.eb index d9aa356199..d8ea21b236 100644 --- a/easybuild/easyconfigs/t/tmux/tmux-2.3.eb +++ b/easybuild/easyconfigs/t/tmux/tmux-2.3.eb @@ -5,7 +5,8 @@ version = '2.3' homepage = 'http://tmux.sourceforge.net/' description = """tmux is a terminal multiplexer. It lets you switch easily -between several programs in one terminal, detach them (they keep running in the background) and reattach them to a different terminal.""" +between several programs in one terminal, detach them (they keep +running in the background) and reattach them to a different terminal.""" toolchain = {'name': 'dummy', 'version': 'dummy'} toolchainopts = {'optarch': True} -- GitLab From 1ad34056480aec11dbfb1667b72b1e37fc15e4dc Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 3 Mar 2017 12:40:44 +0200 Subject: [PATCH 0230/1603] adding easyconfigs: GROMACS-2016.2-foss-2017a.eb --- .../g/GROMACS/GROMACS-2016.2-foss-2017a.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-2016.2-foss-2017a.eb diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.2-foss-2017a.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.2-foss-2017a.eb new file mode 100644 index 0000000000..5a3fc10eef --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.2-foss-2017a.eb @@ -0,0 +1,36 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2016 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, +# Ghent University / The Francis Crick Institute +# Authors:: +# * Wiktor Jurkowski +# * Fotis Georgatos +# * George Tsouloupas +# * Kenneth Hoste +# * Adam Huffman +# License:: MIT/GPL +## + +name = 'GROMACS' +version = '2016.2' + +homepage = 'http://www.gromacs.org' +description = """ +GROMACS is a versatile package to perform molecular dynamics, + i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. + +This is CPU only build, containing both MPI and threadMPI builds. +""" + +toolchain = {'name': 'foss', 'version': '2017a'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = ['ftp://ftp.gromacs.org/pub/gromacs/'] +sources = [SOURCELOWER_TAR_GZ] + +builddependencies = [ + ('CMake', '3.6.2'), +] + +moduleclass = 'bio' -- GitLab From ccda71acf21a6996fdc6d7b5ccc1aafc84614bc1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 3 Mar 2017 11:49:47 +0100 Subject: [PATCH 0231/1603] minor style fixes in NWChem 6.6 easyconfig --- ...vision27746-iomkl-2017a-2015-10-20-Python-2.7.12.eb | 10 ++++------ 1 file changed, 4 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/n/NWChem/NWChem-6.6.revision27746-iomkl-2017a-2015-10-20-Python-2.7.12.eb b/easybuild/easyconfigs/n/NWChem/NWChem-6.6.revision27746-iomkl-2017a-2015-10-20-Python-2.7.12.eb index f693ccc152..27d258eaee 100644 --- a/easybuild/easyconfigs/n/NWChem/NWChem-6.6.revision27746-iomkl-2017a-2015-10-20-Python-2.7.12.eb +++ b/easybuild/easyconfigs/n/NWChem/NWChem-6.6.revision27746-iomkl-2017a-2015-10-20-Python-2.7.12.eb @@ -1,5 +1,7 @@ name = 'NWChem' version = '6.6.revision27746' +verdate = '2015-10-20' +versionsuffix = '-%s-Python-%%(pyver)s' % verdate homepage = 'http://www.nwchem-sw.org' description = """NWChem aims to provide its users with computational chemistry tools that are scalable both in @@ -13,18 +15,14 @@ toolchain = {'name': 'iomkl', 'version': '2017a'} toolchainopts = {'i8': True} source_urls = ['http://www.nwchem-sw.org/download.php?f='] -verdate = '2015-10-20' -sources = ['Nwchem-%s-src.%s.tar.bz2' % (version, verdate)] +sources = ['Nwchem-%%(version)s-src.%s.tar.bz2' % verdate] patches = [ 'NWChem_fix-date.patch', 'NWChem-%(version)s-parallelbuild.patch', ] -python = 'Python' -pyver = '2.7.12' -versionsuffix = '-%s-%s-%s' % (verdate, python, pyver) -dependencies = [(python, pyver)] +dependencies = [('Python', '2.7.12')] # This easyconfig is using the default for armci_network (OPENIB) and # thus needs infiniband libraries. -- GitLab From 3fb14327fb696d1717d7cde894e720db5dbd2de3 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Luk=C3=A1=C5=A1=20Krup=C4=8D=C3=ADk?= Date: Fri, 3 Mar 2017 12:28:54 +0100 Subject: [PATCH 0232/1603] add eb Singularity-2.2.1-GCC-6.3.0-2.27.eb next step chown root:root /apps/all/Singularity/*/etc/singularity/singularity.conf chown root:root /apps/all/Singularity/*/libexec/singularity/sexec-suid chmod +s /apps/all/Singularity/*/libexec/singularity/sexec-suid --- .../Singularity-2.2.1-GCC-6.3.0-2.27.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/s/Singularity/Singularity-2.2.1-GCC-6.3.0-2.27.eb diff --git a/easybuild/easyconfigs/s/Singularity/Singularity-2.2.1-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/s/Singularity/Singularity-2.2.1-GCC-6.3.0-2.27.eb new file mode 100644 index 0000000000..e11fd1f16c --- /dev/null +++ b/easybuild/easyconfigs/s/Singularity/Singularity-2.2.1-GCC-6.3.0-2.27.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'Singularity' +version = '2.2.1' + +homepage = 'http://gmkurtzer.github.io/singularity' +description = """Singularity is a portable application stack packaging and runtime utility.""" + +toolchain = {'name': 'GCC', 'version': '6.3.0-2.27'} + +source_urls = ['https://github.com/gmkurtzer/singularity/archive/'] +sources = ['%(version)s.tar.gz'] + +builddependencies = [('Autotools', '20150215')] + +preconfigopts = './autogen.sh && ' + +sanity_check_paths = { + 'files': ['bin/run-singularity', 'bin/singularity', 'etc/singularity/singularity.conf', 'libexec/singularity/sexec-suid'], + 'dirs': ['etc', '', 'libexec/singularity'], +} + +moduleclass = 'tools' -- GitLab From 68865c34f791fa80abd0ba566daed7de531c3761 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Luk=C3=A1=C5=A1=20Krup=C4=8D=C3=ADk?= Date: Fri, 3 Mar 2017 12:35:36 +0100 Subject: [PATCH 0233/1603] move sanity_check_paths - files -> dirs ... libevents --- easybuild/easyconfigs/l/libevent/libevent-2.1.8.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/l/libevent/libevent-2.1.8.eb b/easybuild/easyconfigs/l/libevent/libevent-2.1.8.eb index 369e68366a..41eaa5ab15 100644 --- a/easybuild/easyconfigs/l/libevent/libevent-2.1.8.eb +++ b/easybuild/easyconfigs/l/libevent/libevent-2.1.8.eb @@ -21,8 +21,8 @@ checksums = ['f3eeaed018542963b7d2416ef1135ecc'] sanity_check_paths = { 'files': ["bin/event_rpcgen.py"] + - ['include/%s' % x for x in ["evdns.h", "event.h", "evhttp.h", "evrpc.h", "evutil.h"]] + - ['include/event2/%s' % x for x in ['buffer_compat.h', 'bufferevent.h', 'bufferevent_struct.h', 'dns_compat.h', 'dns_struct.h', 'event-config.h', 'event_struct.h', 'http.h', 'keyvalq_struct.h', 'rpc_compat.h', 'rpc_struct.h', 'tag.h', 'util.h', 'bufferevent_compat.h', 'bufferevent_ssl.h', 'buffer.h', 'dns.h', 'event_compat.h', 'event.h', 'http_compat.h', 'http_struct.h', 'listener.h', 'rpc.h', 'tag_compat.h', 'thread.h', 'visibility.h']], - 'dirs': ["lib"] + ['include/%s' % x for x in ["evdns.h", "event.h", "evhttp.h", "evrpc.h", "evutil.h"]], + 'dirs': ["lib", "include/event2"] +} moduleclass = 'lib' -- GitLab From 2d1a8eba2da61b56a08904c302d3279ddeeb3408 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Luk=C3=A1=C5=A1=20Krup=C4=8D=C3=ADk?= Date: Fri, 3 Mar 2017 12:55:21 +0100 Subject: [PATCH 0234/1603] remove '', --- .../s/Singularity/Singularity-2.2.1-GCC-6.3.0-2.27.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/Singularity/Singularity-2.2.1-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/s/Singularity/Singularity-2.2.1-GCC-6.3.0-2.27.eb index e11fd1f16c..e1e43de48b 100644 --- a/easybuild/easyconfigs/s/Singularity/Singularity-2.2.1-GCC-6.3.0-2.27.eb +++ b/easybuild/easyconfigs/s/Singularity/Singularity-2.2.1-GCC-6.3.0-2.27.eb @@ -17,7 +17,7 @@ preconfigopts = './autogen.sh && ' sanity_check_paths = { 'files': ['bin/run-singularity', 'bin/singularity', 'etc/singularity/singularity.conf', 'libexec/singularity/sexec-suid'], - 'dirs': ['etc', '', 'libexec/singularity'], + 'dirs': ['etc', 'libexec/singularity'], } moduleclass = 'tools' -- GitLab From 2e04f6c75933547906dadd119c731c43aa3ea456 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 3 Mar 2017 14:04:49 +0200 Subject: [PATCH 0235/1603] adding easyconfigs: PLUMED-2.3.0-foss-2017a.eb --- .../easyconfigs/g/GSL/GSL-2.3-foss-2017a.eb | 25 +++++++++++ .../g/Guile/Guile-1.8.8-foss-2017a.eb | 32 ++++++++++++++ .../libmatheval-1.1.11-foss-2017a.eb | 32 ++++++++++++++ .../libunistring-0.9.6-foss-2017a.eb | 24 +++++++++++ .../p/PLUMED/PLUMED-2.3.0-foss-2017a.eb | 42 +++++++++++++++++++ 5 files changed, 155 insertions(+) create mode 100644 easybuild/easyconfigs/g/GSL/GSL-2.3-foss-2017a.eb create mode 100644 easybuild/easyconfigs/g/Guile/Guile-1.8.8-foss-2017a.eb create mode 100644 easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.11-foss-2017a.eb create mode 100644 easybuild/easyconfigs/l/libunistring/libunistring-0.9.6-foss-2017a.eb create mode 100644 easybuild/easyconfigs/p/PLUMED/PLUMED-2.3.0-foss-2017a.eb diff --git a/easybuild/easyconfigs/g/GSL/GSL-2.3-foss-2017a.eb b/easybuild/easyconfigs/g/GSL/GSL-2.3-foss-2017a.eb new file mode 100644 index 0000000000..66df054b65 --- /dev/null +++ b/easybuild/easyconfigs/g/GSL/GSL-2.3-foss-2017a.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'GSL' +version = '2.3' + +homepage = 'http://www.gnu.org/software/gsl/' +description = """The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. + The library provides a wide range of mathematical routines such as random number generators, special functions + and least-squares fitting.""" + +toolchain = {'name': 'foss', 'version': '2017a'} +toolchainopts = {'unroll': True, 'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +configopts = '--with-pic' + +sanity_check_paths = { + 'files': ['bin/gsl-config', 'lib/libgsl.a', 'lib/libgsl.%s' % SHLIB_EXT, + 'lib/libgslcblas.a', 'lib/libgslcblas.%s' % SHLIB_EXT], + 'dirs': ['include/gsl', 'lib/pkgconfig', 'share'], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/g/Guile/Guile-1.8.8-foss-2017a.eb b/easybuild/easyconfigs/g/Guile/Guile-1.8.8-foss-2017a.eb new file mode 100644 index 0000000000..318524cbae --- /dev/null +++ b/easybuild/easyconfigs/g/Guile/Guile-1.8.8-foss-2017a.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'Guile' +version = '1.8.8' + +homepage = 'http://www.gnu.org/software/guile' +description = """Guile is the GNU Ubiquitous Intelligent Language for Extensions, + the official extension language for the GNU operating system.""" + +toolchain = {'name': 'foss', 'version': '2017a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +dependencies = [ + ('libtool', '2.4.6'), + ('GMP', '6.1.1'), + ('libunistring', '0.9.6'), + ('pkg-config', '0.29.1'), + ('libffi', '3.2.1'), + ('libreadline', '6.3'), +] + +configopts = " --enable-error-on-warning=no" + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["guile", 'guile-config', 'guile-snarf', 'guile-tools']] + + ["lib/libguile.a", "include/libguile.h"], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.11-foss-2017a.eb b/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.11-foss-2017a.eb new file mode 100644 index 0000000000..1d721e0ee3 --- /dev/null +++ b/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.11-foss-2017a.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'libmatheval' +version = '1.1.11' + +homepage = 'http://www.gnu.org/software/libmatheval/' +description = """GNU libmatheval is a library (callable from C and Fortran) to parse + and evaluate symbolic expressions input as text.""" + +toolchain = {'name': 'foss', 'version': '2017a'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +dependencies = [ + ('flex', '2.6.3'), + ('Bison', '3.0.4'), + ('Guile', '1.8.8'), +] + +configopts = '--with-pic ' + +# fix for guile-config being broken because shebang line contains full path to bin/guile +configopts += 'GUILE_CONFIG="$EBROOTGUILE/bin/guile -e main -s $EBROOTGUILE/bin/guile-config"' + +sanity_check_paths = { + 'files': ['lib/libmatheval.a', 'include/matheval.h'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libunistring/libunistring-0.9.6-foss-2017a.eb b/easybuild/easyconfigs/l/libunistring/libunistring-0.9.6-foss-2017a.eb new file mode 100644 index 0000000000..fdee6f5768 --- /dev/null +++ b/easybuild/easyconfigs/l/libunistring/libunistring-0.9.6-foss-2017a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'libunistring' +version = '0.9.6' + +homepage = 'http://www.gnu.org/software/libunistring/' +description = """This library provides functions for manipulating Unicode strings and for manipulating C strings + according to the Unicode standard.""" + +toolchain = {'name': 'foss', 'version': '2017a'} + +sources = [SOURCELOWER_TAR_XZ] +source_urls = [GNU_SOURCE] + +parallel = 1 + +sanity_check_paths = { + 'files': ['lib/libunistring.a', 'lib/libunistring.%s' % SHLIB_EXT] + + ['include/uni%s.h' % x for x in ['case', 'conv', 'ctype', 'lbrk', 'name', 'norm', + 'stdio', 'str', 'types', 'wbrk', 'width']], + 'dirs': ['include/unistring'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.3.0-foss-2017a.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.3.0-foss-2017a.eb new file mode 100644 index 0000000000..1ed42c4139 --- /dev/null +++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.3.0-foss-2017a.eb @@ -0,0 +1,42 @@ +# by Ward Poelmans + +easyblock = 'ConfigureMake' + +name = 'PLUMED' +version = '2.3.0' + +homepage = 'http://www.plumed-code.org' +description = """PLUMED is an open source library for free energy calculations in molecular systems which + works together with some of the most popular molecular dynamics engines. Free energy calculations can be + performed as a function of many order parameters with a particular focus on biological problems, using + state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD. + The software, written in C++, can be easily interfaced with both fortran and C/C++ codes. +""" + +toolchain = {'name': 'foss', 'version': '2017a'} +toolchainopts = {'usempi': 'True'} + +source_urls = ['https://github.com/plumed/plumed2/archive/'] +sources = ['v%(version)s.tar.gz'] + +dependencies = [ + ('zlib', '1.2.8'), + ('GSL', '2.3'), + ('libmatheval', '1.1.11'), +] + +preconfigopts = 'env FC=$MPIF90 LIBS="$LIBLAPACK $LIBS" ' +configopts = ' --exec-prefix=%(installdir)s --enable-gsl' +prebuildopts = 'source sourceme.sh && ' + +sanity_check_paths = { + 'files': ['bin/plumed', 'lib/libplumedKernel.%s' % SHLIB_EXT, 'lib/libplumed.%s' % SHLIB_EXT], + 'dirs': ['lib/plumed'] +} + +modextrapaths = { + 'PLUMED_KERNEL': 'lib/libplumedKernel.%s' % SHLIB_EXT, + 'PLUMED_ROOT': 'lib/plumed', +} + +moduleclass = 'chem' -- GitLab From b025dbb557c46605389c3ff16f68b965d5ec6c79 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 3 Mar 2017 14:18:57 +0200 Subject: [PATCH 0236/1603] Forgot to add dependency, CMake 3.6.2. --- .../c/CMake/CMake-3.6.2-GCCcore-6.3.0.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.6.2-GCCcore-6.3.0.eb diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.6.2-GCCcore-6.3.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.6.2-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..f496787852 --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.6.2-GCCcore-6.3.0.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.6.2' + +homepage = 'http://www.cmake.org' +description = """CMake, the cross-platform, open-source build system. + CMake is a family of tools designed to build, test and package software.""" + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = '-- -DCMAKE_USE_OPENSSL=1' + +builddependencies = [ + ('binutils', '2.27'), +] + + +dependencies = [ + ('ncurses', '6.0'), + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + #('OpenSSL', '1.1.0c'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From 5f471ba1e433fcd3a4e8aa6872b4aabd65e5621e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 3 Mar 2017 14:24:00 +0100 Subject: [PATCH 0237/1603] fix failing tests due to use of \1 in sed expression in OrthoMCL easyconfig --- .../o/OrthoMCL/OrthoMCL-1.4-intel-2016b-Perl-5.24.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OrthoMCL/OrthoMCL-1.4-intel-2016b-Perl-5.24.0.eb b/easybuild/easyconfigs/o/OrthoMCL/OrthoMCL-1.4-intel-2016b-Perl-5.24.0.eb index 3f9e8e96b8..489da9288a 100644 --- a/easybuild/easyconfigs/o/OrthoMCL/OrthoMCL-1.4-intel-2016b-Perl-5.24.0.eb +++ b/easybuild/easyconfigs/o/OrthoMCL/OrthoMCL-1.4-intel-2016b-Perl-5.24.0.eb @@ -29,7 +29,7 @@ postinstallcmds = [ 'sed -i"" "s@/usr/bin/perl@$EBROOTPERL/bin/perl@g" %(installdir)s/orthomcl.pl', 'sed -i"" "s@/.*blastall@$EBROOTBLAST/bin/blastall@g" %(installdir)s/orthomcl_module.pm', 'sed -i"" "s@/.*formatdb@$EBROOTBLAST/bin/formatdb@g" %(installdir)s/orthomcl_module.pm', - 'sed -i"" "s@/.*\(mcl.;\)@$EBROOTMCL/bin/\\1@g" %(installdir)s/orthomcl_module.pm', + 'sed -i"" "s@/.*/mcl@$EBROOTMCL/bin/mcl@g" %(installdir)s/orthomcl_module.pm', 'sed -i"" "s@/.*ORTHOMCL.*%(version)s/@\\$ENV{\'PWD\'}/@g" %(installdir)s/orthomcl_module.pm', ] -- GitLab From 71a84aa705659ffaee36fb39b5b0e66b2c29b855 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 3 Mar 2017 14:45:45 +0100 Subject: [PATCH 0238/1603] adding easyconfigs: CMake-3.7.2-GCCcore-6.3.0.eb --- .../c/CMake/CMake-3.7.2-GCCcore-6.3.0.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.7.2-GCCcore-6.3.0.eb diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.7.2-GCCcore-6.3.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.7.2-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..29e1e466f9 --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.7.2-GCCcore-6.3.0.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.7.2' +homepage = 'http://www.cmake.org' +description = """CMake, the cross-platform, open-source build system. + CMake is a family of tools designed to build, test and package software.""" + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' + +builddependencies = [ + ('binutils', '2.27'), +] + + +dependencies = [ + ('ncurses', '6.0'), + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.1.0c'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From 5852aae17824c13929dbee276eda96b084bd1fa2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 3 Mar 2017 14:58:57 +0100 Subject: [PATCH 0239/1603] adding easyconfigs: binutils-2.28.eb --- .../easyconfigs/b/binutils/binutils-2.28.eb | 19 +++++++++++++ easybuild/easyconfigs/f/flex/flex-2.6.3.eb | 19 +++++++++++++ easybuild/easyconfigs/m/M4/M4-1.4.18.eb | 27 +++++++++++++++++++ easybuild/easyconfigs/z/zlib/zlib-1.2.11.eb | 26 ++++++++++++++++++ 4 files changed, 91 insertions(+) create mode 100644 easybuild/easyconfigs/b/binutils/binutils-2.28.eb create mode 100644 easybuild/easyconfigs/f/flex/flex-2.6.3.eb create mode 100644 easybuild/easyconfigs/m/M4/M4-1.4.18.eb create mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.11.eb diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.28.eb b/easybuild/easyconfigs/b/binutils/binutils-2.28.eb new file mode 100644 index 0000000000..7681d5cc1f --- /dev/null +++ b/easybuild/easyconfigs/b/binutils/binutils-2.28.eb @@ -0,0 +1,19 @@ +name = 'binutils' +version = '2.28' + +homepage = 'http://directory.fsf.org/project/binutils/' +description = "binutils: GNU binary utilities" + +toolchain = {'name': 'dummy', 'version': ''} + +sources = [SOURCE_TAR_GZ] +source_urls = [GNU_SOURCE] + +builddependencies = [ + ('flex', '2.6.3'), + ('Bison', '3.0.4'), + # zlib required, but being linked in statically, so not a runtime dep + ('zlib', '1.2.11'), +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.3.eb b/easybuild/easyconfigs/f/flex/flex-2.6.3.eb new file mode 100644 index 0000000000..de26a2cd74 --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.6.3.eb @@ -0,0 +1,19 @@ +name = 'flex' +version = '2.6.3' + +homepage = 'http://flex.sourceforge.net/' +description = """Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, + sometimes called a tokenizer, is a program which recognizes lexical patterns in text.""" + +toolchain = {'name': 'dummy', 'version': ''} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] + +checksums = ['a5f65570cd9107ec8a8ec88f17b31bb1'] + +dependencies = [('M4', '1.4.18')] +builddependencies = [('Bison', '3.0.4')] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18.eb new file mode 100644 index 0000000000..f186b0ad85 --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'M4' +version = '1.4.18' + +homepage = 'http://www.gnu.org/software/m4/m4.html' +description = """GNU M4 is an implementation of the traditional Unix macro processor. + It is mostly SVR4 compatible although it has some extensions + (for example, handling more than 9 positional parameters to macros). + GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc. +""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +# '-fgnu89-inline' is required to avoid linking errors with older glibc's, +# see https://github.com/hpcugent/easybuild-easyconfigs/issues/529 +configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" + +sanity_check_paths = { + 'files': ["bin/m4"], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.11.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.11.eb new file mode 100644 index 0000000000..b74939ef09 --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.11.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'zlib' +version = '1.2.11' + +homepage = 'http://www.zlib.net/' +description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is, + not covered by any patents -- lossless data-compression library for use on virtually any + computer hardware and operating system.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchainopts = {'pic': True} + +source_urls = ['http://zlib.net/fossils/'] +sources = [SOURCELOWER_TAR_GZ] + +# need to take care of $CFLAGS ourselves with dummy toolchain +# we need to add -fPIC, but should also include -O* option to avoid compiling with -O0 (default for GCC) +buildopts = 'CFLAGS="-O2 -fPIC"' + +sanity_check_paths = { + 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' -- GitLab From 813f5d5f48f966ad2d6304f140cae7dc9d616350 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 3 Mar 2017 15:29:03 +0100 Subject: [PATCH 0240/1603] adding easyconfigs: binutils-2.28-GCCcore-6.3.0.eb --- .../b/binutils/binutils-2.28-GCCcore-6.3.0.eb | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/b/binutils/binutils-2.28-GCCcore-6.3.0.eb diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.28-GCCcore-6.3.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.28-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..de910489db --- /dev/null +++ b/easybuild/easyconfigs/b/binutils/binutils-2.28-GCCcore-6.3.0.eb @@ -0,0 +1,21 @@ +name = 'binutils' +version = '2.28' + +homepage = 'http://directory.fsf.org/project/binutils/' +description = "binutils: GNU binary utilities" + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} + +sources = [SOURCE_TAR_GZ] +source_urls = [GNU_SOURCE] + +builddependencies = [ + ('flex', '2.6.3'), + ('Bison', '3.0.4'), + # zlib required, but being linked in statically, so not a runtime dep + ('zlib', '1.2.11'), + # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils + ('binutils', version, '', True) +] + +moduleclass = 'tools' -- GitLab From 033702853174a9f5f55f0dc776f6d17d269d4730 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 3 Mar 2017 15:33:41 +0100 Subject: [PATCH 0241/1603] enable execution permissions on all Perl scripts in /bin for miRDeep2 --- .../easyconfigs/m/miRDeep2/miRDeep2-2.0.0.8-intel-2016b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/miRDeep2/miRDeep2-2.0.0.8-intel-2016b.eb b/easybuild/easyconfigs/m/miRDeep2/miRDeep2-2.0.0.8-intel-2016b.eb index 583f9a91f7..8a8e1422a7 100644 --- a/easybuild/easyconfigs/m/miRDeep2/miRDeep2-2.0.0.8-intel-2016b.eb +++ b/easybuild/easyconfigs/m/miRDeep2/miRDeep2-2.0.0.8-intel-2016b.eb @@ -20,7 +20,7 @@ dependencies = [ ('randfold', '2.0.1'), # also provides SQUID ] -install_cmd = "cp -a mirdeep%s/src %%(installdir)s/bin" % altver +install_cmd = "chmod a+x mirdeep*/src/*.pl && cp -a mirdeep*/src %(installdir)s/bin" sanity_check_paths = { 'files': ['bin/make_html.pl'], -- GitLab From 4a2d28b655a93c55643153f035b98d982b1ba9f5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 3 Mar 2017 15:57:06 +0100 Subject: [PATCH 0242/1603] fix source_urls for flex, incl. help2man as build dep --- easybuild/easyconfigs/f/flex/flex-2.6.3.eb | 7 +++++-- .../easyconfigs/h/help2man/help2man-1.47.4.eb | 19 +++++++++++++++++++ 2 files changed, 24 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/h/help2man/help2man-1.47.4.eb diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.3.eb b/easybuild/easyconfigs/f/flex/flex-2.6.3.eb index de26a2cd74..568be27f41 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.3.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.3.eb @@ -9,11 +9,14 @@ toolchain = {'name': 'dummy', 'version': ''} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] +source_urls = ['https://github.com/westes/flex/releases/download/v%(version)s/'] checksums = ['a5f65570cd9107ec8a8ec88f17b31bb1'] dependencies = [('M4', '1.4.18')] -builddependencies = [('Bison', '3.0.4')] +builddependencies = [ + ('Bison', '3.0.4'), + ('help2man', '1.47.4'), +] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/h/help2man/help2man-1.47.4.eb b/easybuild/easyconfigs/h/help2man/help2man-1.47.4.eb new file mode 100644 index 0000000000..292de661e9 --- /dev/null +++ b/easybuild/easyconfigs/h/help2man/help2man-1.47.4.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'help2man' +version = '1.47.4' + +homepage = 'https://www.gnu.org/software/help2man/' +description = """help2man produces simple manual pages from the '--help' and '--version' output of other commands.""" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_XZ] + +sanity_check_paths = { + 'files': ['bin/help2man'], + 'dirs': [], +} + +moduleclass = 'tools' -- GitLab From c5582a708e0fdffca7f963810101a93be63047f4 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 3 Mar 2017 17:31:17 +0200 Subject: [PATCH 0243/1603] Updated dependency for Gromacs to CMake 3.7.2. Fixed missing parts in CMake 3.6.2 config. --- easybuild/easyconfigs/c/CMake/CMake-3.6.2-GCCcore-6.3.0.eb | 4 ++-- easybuild/easyconfigs/g/GROMACS/GROMACS-2016.2-foss-2017a.eb | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.6.2-GCCcore-6.3.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.6.2-GCCcore-6.3.0.eb index f496787852..50e2df64aa 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.6.2-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.6.2-GCCcore-6.3.0.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'GCCcore', 'version': '6.3.0'} source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] -configopts = '-- -DCMAKE_USE_OPENSSL=1' +configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' builddependencies = [ ('binutils', '2.27'), @@ -29,7 +29,7 @@ dependencies = [ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] sanity_check_paths = { - 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], 'dirs': [], } diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.2-foss-2017a.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.2-foss-2017a.eb index 5a3fc10eef..8ad8f765c7 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.2-foss-2017a.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.2-foss-2017a.eb @@ -30,7 +30,7 @@ source_urls = ['ftp://ftp.gromacs.org/pub/gromacs/'] sources = [SOURCELOWER_TAR_GZ] builddependencies = [ - ('CMake', '3.6.2'), + ('CMake', '3.7.2'), ] moduleclass = 'bio' -- GitLab From ee8d9018a1381e77be204e32195d29de9268fc3a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 4 Mar 2017 11:40:34 +0100 Subject: [PATCH 0244/1603] complete release notes for v3.1.1 & bump version --- RELEASE_NOTES | 46 ++++++++++++++++++---------------------------- setup.py | 2 +- 2 files changed, 19 insertions(+), 29 deletions(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index aa222f795f..060a0725f1 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -3,53 +3,43 @@ For more detailed information, please see the git log. These release notes can also be consulted at http://easybuild.readthedocs.org/en/latest/Release_notes.html. -The latest version of easybuild-easyconfig provides 6,488 easyconfig files, for 1,152 different software packages, +The latest version of easybuild-easyconfig provides 6,643 easyconfig files, for 1,168 different software packages, 25 different (compiler) toolchains, 13 software bundles and 1 meta-package. -v3.1.1 (March 3rd 2017) +v3.1.1 (March 6th 2017) ----------------------- bugfix release -- added example easyconfig files for 15 new software packages: +- added example easyconfig files for 16 new software packages: - Caffe (#3667), DIAMOND (#4107), fmt (#4131), googletest (#4132), igraph (#4172), MEGA (#4202), meRanTK (#4175), - meshio (#4178), miRDeep2 (#4229), OOMPA (#4211), PBSuite (#4230), randfold (#4217), Smoldyn (#4110), - SpiecEasi (#4215), stress (#4180) + meshio (#4178), miRDeep2 (#4229, #4255), OOMPA (#4211), PBSuite (#4224, #4230), randfold (#4217), skewer (#4246), + Smoldyn (#4110), SpiecEasi (#4215), stress (#4180) - added additional easyconfigs for various supported software packages, including: - - ATK 2.22.0, Armadillo 7.600.2 + 7.800.0, arpack-ng 3.4.0, BLASR 2.2, Bazel 0.4.4, BioPerl 1.7.1, CFITSIO 3.41, - CGAL 4.9, CMake 3.7.2, Cantera 2.3.0, cURL 7.52.1, DMTCP 2.5.0, Eigen 3.2.10 + 3.3.2 + 3.3.3, Emacs 25.1, - ea-utils 1.04.807, freetype 2.7.1, GMP 6.1.2, Graphviz 2.38.0, gettext 0.19.8.1, IPython 5.2.2, JasPer 2.0.10, - Java 1.8.0_121, Lmod 7.3, libQGLViewer 2.6.4, libpng 1.6.27 + 1.6.28, likwid 4.2.0, MCL 02.063 + 14.137, - MCR R2013b + 2014b + R2015b + R2016b, matplotlib 2.0.0, networkx 1.1, OpenSSL 1.1.0e, OrthoMCL 1.4 + 2.0.9, - PCRE 8.40, PyTables 3.2.3.1, Pysam 0.10.0, path.py 10.1, prompt-toolkit 1.0.13, Qt5 5.8.0, ROOT 6.06.02, - SCons 2.5.1, Stacks 1.44, StringTie 1.3.3, sickle 1.33, VTK 7.1.0, ViennaRNA 2.2.3, Vim 8.0, XZ 5.2.3, - Yade 2017.01a -- added easyconfigs for new 'iomkl/2017a' and 'iompi/2017a' toolchains (#4216) + - binutils 2.28, Cantera 2.3.0, CGAL 4.9, GMP 6.1.2, IPython 5.2.2, JasPer 2.0.10, NWChem 6.6, matplotlib 2.0.0, + PCRE 8.40, Qt5 5.8.0, Vim 8.0, X11 bundle v20170129, VTK 7.1.0, Yade 2017.01a +- added new easyconfigs for existing toolchains: + - iomkl/2017a (#4216), intel/2017.02 (#4248) - various enhancements, including: - - clean up dependencies in libdrm (#4113) - - update X11 bundle and dependencies for GCCcore-6.3.0 (#4147) - - fix style in several easyconfigs (#4174, #4176, #4190) + - fix style in several easyconfigs (#4174, #4176, #4190, #4233) + - add sanity check command to Yade easyconfig to make sure that 'import yade' works, include bzip2 as dep (#4193) + - add PDF::API2 extension to Perl 5.24.0 easyconfigs + sync exts_list (#4221) - various bug fixes, including: - - allow intel 2017 to compile (#4102) - - work around build failure with GCC 6 in pkg-config (#4109) - add Bison and gettext as build deps for X11 (#4111) - - fix ippicv source download and library install in OpenCV (#4126) - - fix software name for OrthoMCL + modernise OrthoMCL easyconfigs (#4135) + - clean up dependencies in libdrm (#4113) + - make sure Ghostscript picks up external libraries (#4118) + - fix ippicv source download and library install for OpenCV v3.1.0 (#4126) + - fix software name for OrthoMCL + modernise OrthoMCL easyconfigs (#4134, #4135) - get rid of backticks in gettext descriptions, causes problems when packaging with FPM (#4146) - remove duplicate sources specification in OpenMPI (#4150) - - fix definition of buildopts/installopts in Cantera easyconfig (#4164) + - fix definition of buildopts/installopts in Cantera easyconfig (#4133, #4164, #4177) - use http rather than ftp source URLs in CFITSIO easyconfigs (#4167) - - fix broken test in Cantera 2.3.0 rather than skipping it (#4177) - add patch for XZ 5.2.2 to include 5.1.2alpha symbols required by 'rpm' command on CentOS 7.x (#4179) - - update $PATH in OrthoMCL 1.4 easyconfig (#4182) - - bump VTK to 7.1.0 in meshio easyconfig for compatibility with Yade 2017.01a (#4188) - add patch for Boost v1.61-1.63 to fix problem with make_array/array_wrapper in boost serialization library (#4192) - - add sanity check command to Yade easyconfig to make sure that 'import yade' works, include bzip2 as dep (#4193) - - set CMAKE_PREFIX_PATH to ncurses install directory (#4196) + - set CMAKE_PREFIX_PATH to ncurses install directory in CMake easyconfigs (#4196) - switch to lowopt=True for libxc v2.2.* and v3.* (#4199) - remove custom sanity_check_paths, since it's identical to that used by the R easyblock (#4200) - fix version (& homepage) in ea-utils easyconfigs (#4205) - remove --with-threads configure option in OpenMPI-2.* (#4213) - - add PDF::API2 extension to Perl 5.24.0 easyconfigs + sync exts_list (#4221) - fix check for Szip library in configure script for netCDF 4.1.3 (#4226) - fix source_urls in several easyconfigs, including: - bsoft, cutadapt, EMBOSS, GnuTLS, ImageMagick, LibTIFF, Mercurial, netCDF, netCDF-Fortran, pigz, ROOT and Subversion (#4227) diff --git a/setup.py b/setup.py index a3f5efb8ac..2cd1801e1b 100644 --- a/setup.py +++ b/setup.py @@ -47,7 +47,7 @@ from distutils import log # recent setuptools versions will *TRANSFORM* something like 'X.Y.Zdev' into 'X.Y.Z.dev0', with a warning like # UserWarning: Normalizing '2.4.0dev' to '2.4.0.dev0' # This causes problems further up the dependency chain... -VERSION = '3.1.0' +VERSION = '3.1.1' API_VERSION = VERSION.split('.')[0] EB_VERSION = '.'.join(VERSION.split('.')[0:2]) -- GitLab From 3fd0930568babad34af20192ac18bc32d340de68 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Mon, 6 Mar 2017 16:53:13 +1300 Subject: [PATCH 0245/1603] EasyConfig for ne, the nice editor, with the gimkl 2017a toolchain --- .../easyconfigs/n/ne/ne-3.0.1-gimkl-2017a.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/n/ne/ne-3.0.1-gimkl-2017a.eb diff --git a/easybuild/easyconfigs/n/ne/ne-3.0.1-gimkl-2017a.eb b/easybuild/easyconfigs/n/ne/ne-3.0.1-gimkl-2017a.eb new file mode 100644 index 0000000000..36fd965e66 --- /dev/null +++ b/easybuild/easyconfigs/n/ne/ne-3.0.1-gimkl-2017a.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'ne' +version = '3.0.1' + +homepage = 'http://ne.di.unimi.it/' +description = """ne is a free (GPL'd) text editor based on the POSIX standard +that runs (we hope) on almost any UN*X machine. ne is easy to use for the +beginner, but powerful and fully configurable for the wizard, and most sparing +in its resource usage.""" + +toolchain = {'name': 'gimkl', 'version': '2017a'} + +source_urls = ['http://ne.di.unimi.it/'] +sources = [SOURCELOWER_TAR_GZ] + +skipsteps = ['configure'] +installopts = "PREFIX=%(installdir)s" + +sanity_check_paths = { + 'files': ['bin/ne'], + 'dirs': ['share'], +} + +moduleclass = 'tools' -- GitLab From 5addb445e5dc856d4ebe4970d0ab2488db52ec2f Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Mon, 6 Mar 2017 17:41:10 +1300 Subject: [PATCH 0246/1603] Add explicit ncurses dependency --- easybuild/easyconfigs/n/ne/ne-3.0.1-gimkl-2017a.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/n/ne/ne-3.0.1-gimkl-2017a.eb b/easybuild/easyconfigs/n/ne/ne-3.0.1-gimkl-2017a.eb index 36fd965e66..f6ca385967 100644 --- a/easybuild/easyconfigs/n/ne/ne-3.0.1-gimkl-2017a.eb +++ b/easybuild/easyconfigs/n/ne/ne-3.0.1-gimkl-2017a.eb @@ -14,6 +14,10 @@ toolchain = {'name': 'gimkl', 'version': '2017a'} source_urls = ['http://ne.di.unimi.it/'] sources = [SOURCELOWER_TAR_GZ] +dependencies = [ + ('ncurses', '6.0'), +] + skipsteps = ['configure'] installopts = "PREFIX=%(installdir)s" -- GitLab From 7b15ed20fa7b321bb2ef12657e381d1a1c57bc8a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Luk=C3=A1=C5=A1=20Krup=C4=8D=C3=ADk?= Date: Mon, 6 Mar 2017 08:00:12 +0100 Subject: [PATCH 0247/1603] 'dummy' -> '' --- easybuild/easyconfigs/t/tmux/tmux-2.3.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/tmux/tmux-2.3.eb b/easybuild/easyconfigs/t/tmux/tmux-2.3.eb index d8ea21b236..0423702965 100644 --- a/easybuild/easyconfigs/t/tmux/tmux-2.3.eb +++ b/easybuild/easyconfigs/t/tmux/tmux-2.3.eb @@ -8,7 +8,7 @@ description = """tmux is a terminal multiplexer. It lets you switch easily between several programs in one terminal, detach them (they keep running in the background) and reattach them to a different terminal.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -- GitLab From bb62863e09d4935fe68e96b4055e023014bd2e5f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 6 Mar 2017 11:39:09 +0100 Subject: [PATCH 0248/1603] adding easyconfigs: SPAdes-3.10.1-foss-2016b.eb --- .../s/SPAdes/SPAdes-3.10.1-foss-2016b.eb | 47 +++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 easybuild/easyconfigs/s/SPAdes/SPAdes-3.10.1-foss-2016b.eb diff --git a/easybuild/easyconfigs/s/SPAdes/SPAdes-3.10.1-foss-2016b.eb b/easybuild/easyconfigs/s/SPAdes/SPAdes-3.10.1-foss-2016b.eb new file mode 100644 index 0000000000..c4ecdeaede --- /dev/null +++ b/easybuild/easyconfigs/s/SPAdes/SPAdes-3.10.1-foss-2016b.eb @@ -0,0 +1,47 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# 3.9.0: +# Modified by: +# Adam Huffman +# The Francis Crick Institute + +easyblock = "CMakeMake" + +name = 'SPAdes' +version = '3.10.1' + +homepage = 'http://cab.spbu.ru/software/spades/' +description = """Genome assembler for single-cell and isolates data sets""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['http://cab.spbu.ru/files/release%(version)s'] +sources = [SOURCE_TAR_GZ] + +builddependencies = [ + ('CMake', '3.7.2'), + ('Boost', '1.63.0', '-Python-2.7.12'), +] + +dependencies = [ + ('zlib', '1.2.8'), + ('bzip2', '1.0.6'), +] + +start_dir = 'src' + +separate_build_dir = True + +configopts = ' -DBoost_NO_BOOST_CMAKE=ON' + +sanity_check_commands = [('spades.py', '--test')] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['bwa-spades', 'dipspades', 'dipspades.py', + 'hammer', 'ionhammer', 'spades', 'spades.py']], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From 08689b0d378055ebfe07de920e6a08974761792f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 6 Mar 2017 13:25:09 +0100 Subject: [PATCH 0249/1603] add easyconfig for missing CMake dep --- .../c/CMake/CMake-3.7.2-foss-2016b.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.7.2-foss-2016b.eb diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.7.2-foss-2016b.eb b/easybuild/easyconfigs/c/CMake/CMake-3.7.2-foss-2016b.eb new file mode 100644 index 0000000000..1d41f93b9b --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.7.2-foss-2016b.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.7.2' + +homepage = 'http://www.cmake.org' +description = """CMake, the cross-platform, open-source build system. + CMake is a family of tools designed to build, test and package software.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' + +dependencies = [ + ('ncurses', '6.0'), + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.2j'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From ff49dc26d982489ed1ade8b1e5fd821c2dc239d6 Mon Sep 17 00:00:00 2001 From: Yann Sagon Date: Mon, 6 Mar 2017 14:28:40 +0100 Subject: [PATCH 0250/1603] add sanity check python module --- .../r/ROOT/ROOT-v6.08.02-foss-2016a-Python-2.7.11.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-v6.08.02-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/r/ROOT/ROOT-v6.08.02-foss-2016a-Python-2.7.11.eb index 6bb0455477..902a9ecafd 100644 --- a/easybuild/easyconfigs/r/ROOT/ROOT-v6.08.02-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/r/ROOT/ROOT-v6.08.02-foss-2016a-Python-2.7.11.eb @@ -42,6 +42,8 @@ configopts += '-Doracle=OFF -Dpgsql=OFF -Dqt=OFF -Dsqlite=OFF ' configopts += '-Dcxx14=ON ' configopts += '-Dunuran=ON -Dtable=ON -Dexplicitlink=ON -Dminuit2=ON ' +sanity_check_commands = ["python -c 'import ROOT'"] + modextrapaths = {'PYTHONPATH': 'lib/'} moduleclass = 'data' -- GitLab From de7e657c88579abd4e19329524edce969ff8dce6 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 6 Mar 2017 18:47:52 +0100 Subject: [PATCH 0251/1603] adding easyconfigs: awscli-1.11.56-foss-2016b-Python-2.7.12.eb --- ...awscli-1.11.56-foss-2016b-Python-2.7.12.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/a/awscli/awscli-1.11.56-foss-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/a/awscli/awscli-1.11.56-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/a/awscli/awscli-1.11.56-foss-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..729a10008f --- /dev/null +++ b/easybuild/easyconfigs/a/awscli/awscli-1.11.56-foss-2016b-Python-2.7.12.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'awscli' +version = '1.11.56' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pypi.python.org/pypi/awscli' +description = 'Universal Command Line Environment for AWS' + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.12'), +] + +sanity_check_paths = { + 'files': ['bin/aws'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +moduleclass = 'tools' -- GitLab From adfd421614f445e8fb39495272de39760de504d2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 6 Mar 2017 18:57:47 +0100 Subject: [PATCH 0252/1603] {lang}[intel/2017a] Python v2.7.13 --- .../g/GMP/GMP-6.1.2-GCCcore-6.3.0.eb | 31 ++++ .../libreadline-7.0-GCCcore-6.3.0.eb | 33 +++++ .../p/Python/Python-2.7.13-intel-2017a.eb | 133 ++++++++++++++++++ .../p/Python/numpy-1.12.0-mkl.patch | 55 ++++++++ .../t/Tcl/Tcl-8.6.6-GCCcore-6.3.0.eb | 30 ++++ 5 files changed, 282 insertions(+) create mode 100644 easybuild/easyconfigs/g/GMP/GMP-6.1.2-GCCcore-6.3.0.eb create mode 100644 easybuild/easyconfigs/l/libreadline/libreadline-7.0-GCCcore-6.3.0.eb create mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.13-intel-2017a.eb create mode 100644 easybuild/easyconfigs/p/Python/numpy-1.12.0-mkl.patch create mode 100644 easybuild/easyconfigs/t/Tcl/Tcl-8.6.6-GCCcore-6.3.0.eb diff --git a/easybuild/easyconfigs/g/GMP/GMP-6.1.2-GCCcore-6.3.0.eb b/easybuild/easyconfigs/g/GMP/GMP-6.1.2-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..046f2d1718 --- /dev/null +++ b/easybuild/easyconfigs/g/GMP/GMP-6.1.2-GCCcore-6.3.0.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'GMP' +version = '6.1.2' + +homepage = 'http://gmplib.org/' +description = """GMP is a free library for arbitrary precision arithmetic, +operating on signed integers, rational numbers, and floating point numbers. """ + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} +toolchainopts = {'pic': True, 'precise': True} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://ftp.gnu.org/gnu/gmp'] + +builddependencies = [ + ('binutils', '2.27'), + ('Autotools', '20150215'), +] + +# enable C++ interface +configopts = '--enable-cxx' + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libgmp.%s' % SHLIB_EXT, 'include/gmp.h'], + 'dirs': [], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-7.0-GCCcore-6.3.0.eb b/easybuild/easyconfigs/l/libreadline/libreadline-7.0-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..a64400af8e --- /dev/null +++ b/easybuild/easyconfigs/l/libreadline/libreadline-7.0-GCCcore-6.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'libreadline' +version = '7.0' + +homepage = 'http://cnswww.cns.cwru.edu/php/chet/readline/rltop.html' +description = """The GNU Readline library provides a set of functions for use by applications that + allow users to edit command lines as they are typed in. Both Emacs and vi editing modes are available. + The Readline library includes additional functions to maintain a list of previously-entered command lines, + to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands.""" + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} +toolchainopts = {'pic': True} + +sources = ['readline-%(version)s.tar.gz'] +source_urls = ['http://ftp.gnu.org/gnu/readline'] + +patches = ['libreadline-%(version)s-bugfix.patch'] + +builddependencies = [('binutils', '2.27')] +dependencies = [('ncurses', '6.0')] + +# for the termcap symbols, use EB ncurses +preconfigopts = "env LDFLAGS='-lncurses'" + +sanity_check_paths = { + 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.13-intel-2017a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.13-intel-2017a.eb new file mode 100644 index 0000000000..31e0d3d932 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.13-intel-2017a.eb @@ -0,0 +1,133 @@ +name = 'Python' +version = '2.7.13' + +homepage = 'http://python.org/' +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +# python needs bzip2 to build the bz2 package +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.11'), + ('libreadline', '7.0'), + ('ncurses', '6.0'), + ('SQLite', '3.17.0'), + ('GMP', '6.1.2'), + ('libffi', '3.2.1'), + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.2k'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# order is important! +# package versions updated March 6th 2017 +exts_list = [ + # note: more recent versions of setuptools (v34.x) can not be installed from source anymore, + # see https://github.com/pypa/setuptools/issues/980 + ('setuptools', '33.1.1', { + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], + 'source_tmpl': '%(name)s-%(version)s.zip', + }), + ('pip', '9.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], + }), + ('nose', '1.3.7', { + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], + }), + ('numpy', '1.12.0', { + 'source_urls': ['https://pypi.python.org/packages/source/n/numpy'], + 'source_tmpl': '%(name)s-%(version)s.zip', + 'patches': ['numpy-1.12.0-mkl.patch'], + }), + ('scipy', '0.18.1', { + 'source_urls': ['https://pypi.python.org/packages/source/s/scipy'], + }), + ('blist', '1.3.6', { + 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], + }), + ('mpi4py', '2.0.0', { + 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + }), + ('paycheck', '1.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], + }), + ('pbr', '2.0.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], + }), + ('Cython', '0.25.2', { + 'source_urls': ['https://pypi.python.org/packages/source/c/cython/'], + }), + ('six', '1.10.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), + ('dateutil', '2.6.0', { + 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], + }), + ('deap', '1.0.2', { + 'source_tmpl': '%(name)s-%(version)s.post2.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], + }), + ('decorator', '4.0.11', { + 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], + }), + ('arff', '2.1.0', { + 'source_tmpl': 'liac-%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], + }), + ('pycrypto', '2.6.1', { + 'modulename': 'Crypto', + 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + }), + ('ecdsa', '0.13', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), + ('cryptography', '1.7.2', { + 'source_urls': ['https://pypi.python.org/packages/source/c/cryptography/'], + }), + ('paramiko', '2.1.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], + }), + ('pyparsing', '2.2.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], + }), + ('netifaces', '0.10.5', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], + }), + ('netaddr', '0.7.19', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], + }), + ('funcsigs', '1.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/f/funcsigs'], + }), + ('mock', '2.0.0', { + 'source_urls': ['https://pypi.python.org/packages/source/m/mock'], + }), + ('pytz', '2016.10', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pytz'], + }), + ('pandas', '0.19.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], + }), + ('enum34', '1.1.6', { + 'modulename': 'enum', + 'source_urls': ['https://pypi.python.org/packages/source/e/enum34'], + }), + ('bitstring', '3.1.5', { + 'source_tmpl': '%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/b/bitstring'], + }), + ('virtualenv', '15.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/v/virtualenv'], + }), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/numpy-1.12.0-mkl.patch b/easybuild/easyconfigs/p/Python/numpy-1.12.0-mkl.patch new file mode 100644 index 0000000000..3d09924f96 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/numpy-1.12.0-mkl.patch @@ -0,0 +1,55 @@ +fix issues in numpy distutils pkg w.r.t. detecting BLAS/LAPACK libraries +by Kenneth Hoste (HPC-UGent) +diff -ru numpy-1.12.0.orig/numpy/distutils/fcompiler/__init__.py numpy-1.12.0/numpy/distutils/fcompiler/__init__.py +--- numpy-1.12.0.orig/numpy/distutils/fcompiler/__init__.py 2017-01-15 11:39:18.000000000 +0100 ++++ numpy-1.12.0/numpy/distutils/fcompiler/__init__.py 2017-03-06 17:19:07.262810683 +0100 +@@ -628,7 +628,10 @@ + return options + + def library_option(self, lib): +- return "-l" + lib ++ if lib[0]=='-': ++ return lib ++ else: ++ return "-l" + lib + def library_dir_option(self, dir): + return "-L" + dir + +diff -ru numpy-1.12.0.orig/numpy/distutils/system_info.py numpy-1.12.0/numpy/distutils/system_info.py +--- numpy-1.12.0.orig/numpy/distutils/system_info.py 2017-01-15 11:39:18.000000000 +0100 ++++ numpy-1.12.0/numpy/distutils/system_info.py 2017-03-06 17:25:38.778143748 +0100 +@@ -675,7 +675,7 @@ + if is_string(default): + return [default] + return default +- return [b for b in [a.strip() for a in libs.split(',')] if b] ++ return [b for b in [a.strip().replace(':',',') for a in libs.split(',')] if b] + + def get_libraries(self, key='libraries'): + if hasattr(self, '_lib_names'): +@@ -756,6 +756,9 @@ + # make sure we preserve the order of libs, as it can be important + found_dirs, found_libs = [], [] + for lib in libs: ++ if lib[0] == '-': ++ found_libs.append(lib) ++ continue + for lib_dir in lib_dirs: + found_lib = self._find_lib(lib_dir, lib, exts) + if found_lib: +diff -ru numpy-1.12.0.orig/numpy/distutils/unixccompiler.py numpy-1.12.0/numpy/distutils/unixccompiler.py +--- numpy-1.12.0.orig/numpy/distutils/unixccompiler.py 2016-12-21 16:46:24.000000000 +0100 ++++ numpy-1.12.0/numpy/distutils/unixccompiler.py 2017-03-06 17:19:07.262810683 +0100 +@@ -123,3 +123,12 @@ + + replace_method(UnixCCompiler, 'create_static_lib', + UnixCCompiler_create_static_lib) ++ ++def UnixCCompiler_library_option(self, lib): ++ if lib[0]=='-': ++ return lib ++ else: ++ return "-l" + lib ++ ++replace_method(UnixCCompiler, 'library_option', ++ UnixCCompiler_library_option) diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.6-GCCcore-6.3.0.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.6-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..9dca9f6e5c --- /dev/null +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.6-GCCcore-6.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'Tcl' +version = '8.6.6' + +homepage = 'http://www.tcl.tk/' +description = """Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, +suitable for a very wide range of uses, including web and desktop applications, networking, administration, +testing and many more.""" + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +builddependencies = [ + ('binutils', '2.27'), +] + +dependencies = [ + ('zlib', '1.2.11'), +] + +configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' + +runtest = 'test' + +start_dir = 'unix' + +moduleclass = 'lang' -- GitLab From cf160c44110226e8f37de1d8e3e235af08a0a369 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 7 Mar 2017 08:55:17 +0100 Subject: [PATCH 0253/1603] bump easyconfig files count in release notes --- RELEASE_NOTES | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index 060a0725f1..1c930d74fe 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -3,7 +3,7 @@ For more detailed information, please see the git log. These release notes can also be consulted at http://easybuild.readthedocs.org/en/latest/Release_notes.html. -The latest version of easybuild-easyconfig provides 6,643 easyconfig files, for 1,168 different software packages, +The latest version of easybuild-easyconfig provides 6,647 easyconfig files, for 1,168 different software packages, 25 different (compiler) toolchains, 13 software bundles and 1 meta-package. v3.1.1 (March 6th 2017) -- GitLab From 36877ded32473a03edb33e9d27e99a7f498fc7e0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 7 Mar 2017 08:57:52 +0100 Subject: [PATCH 0254/1603] fix release date for EasyBuild v3.1.1 --- RELEASE_NOTES | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index 1c930d74fe..96a76caa5a 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -6,7 +6,7 @@ These release notes can also be consulted at http://easybuild.readthedocs.org/en The latest version of easybuild-easyconfig provides 6,647 easyconfig files, for 1,168 different software packages, 25 different (compiler) toolchains, 13 software bundles and 1 meta-package. -v3.1.1 (March 6th 2017) +v3.1.1 (March 7th 2017) ----------------------- bugfix release -- GitLab From 533a573a1c8455697a72bd8883503a86c13bf7c0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 7 Mar 2017 15:21:30 +0100 Subject: [PATCH 0255/1603] bump version to 3.2.0.dev0 --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 2cd1801e1b..0683e432c9 100644 --- a/setup.py +++ b/setup.py @@ -47,7 +47,7 @@ from distutils import log # recent setuptools versions will *TRANSFORM* something like 'X.Y.Zdev' into 'X.Y.Z.dev0', with a warning like # UserWarning: Normalizing '2.4.0dev' to '2.4.0.dev0' # This causes problems further up the dependency chain... -VERSION = '3.1.1' +VERSION = '3.2.0.dev0' API_VERSION = VERSION.split('.')[0] EB_VERSION = '.'.join(VERSION.split('.')[0:2]) -- GitLab From fde809e0021a1eb648084501f5b8c547cdd255f4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 7 Mar 2017 16:24:48 +0100 Subject: [PATCH 0256/1603] adding easyconfigs: EasyBuild-3.1.1.eb --- .../e/EasyBuild/EasyBuild-3.1.1.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.1.1.eb diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.1.1.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.1.1.eb new file mode 100644 index 0000000000..2dbc7fa9ba --- /dev/null +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.1.1.eb @@ -0,0 +1,38 @@ +easyblock = 'EB_EasyBuildMeta' + +name = 'EasyBuild' +version = '3.1.1' + +homepage = 'http://hpcugent.github.com/easybuild/' +description = """EasyBuild is a software build and installation framework + written in Python that allows you to install software in a structured, + repeatable and robust way.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = [ + # vsc-install + 'https://pypi.python.org/packages/ef/c7/640c6d791ba452321c0d1371b6626486bb495e0645bb896d33c78a09f810', + # vsc-base + 'https://pypi.python.org/packages/da/90/ee40b1a6a5bfed24139042c737500a9b45db0373a6735e76481fc860fe37', + # easybuild-framework + 'https://pypi.python.org/packages/f2/19/1c79b1ad24f0004e9507f12d4222367611f42ac479abd6315a50a23c52f5', + # easybuild-easyblocks + 'https://pypi.python.org/packages/87/aa/2a19f05c78dd2550f7bd42ef0964b9c51c5626c1e715c2ee0a4f778780b8', + # easybuild-easyconfigs + 'https://pypi.python.org/packages/e6/68/5e977f549bf04b8cd87cdc5179d8b36c1eb971cfe3c43f98053f2dbe9c64', +] +# order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) +sources = [ + 'vsc-install-0.10.25.tar.gz', + 'vsc-base-2.5.7.tar.gz', + 'easybuild-framework-%(version)s.tar.gz', + 'easybuild-easyblocks-%(version)s.tar.gz', + 'easybuild-easyconfigs-%(version)s.tar.gz', +] + +# EasyBuild is a (set of) Python packages, so it depends on Python +# usually, we want to use the system Python, so no actual Python dependency is listed +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +moduleclass = 'tools' -- GitLab From 65002095722c407e0105a5f67bb6950a788793c4 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 8 Mar 2017 11:08:55 +0800 Subject: [PATCH 0257/1603] yet another batch of minor style fixes --- easybuild/easyconfigs/a/ABAQUS/ABAQUS-6.12.1-linux-x86_64.eb | 3 ++- easybuild/easyconfigs/a/ABAQUS/ABAQUS-6.13.5-linux-x86_64.eb | 3 ++- easybuild/easyconfigs/a/ABAQUS/ABAQUS-6.14.1-linux-x86_64.eb | 3 ++- .../a/ALLPATHS-LG/ALLPATHS-LG-46968-goolf-1.4.10.eb | 3 ++- easybuild/easyconfigs/a/Advisor/Advisor-2016_update2.eb | 3 +-- easybuild/easyconfigs/a/Advisor/Advisor-2017_update1.eb | 3 +-- ...-16-iomkl-2016.07-AmberTools-16-patchlevel-5-14-serial.eb | 2 +- .../Amber-16-iomkl-2016.07-AmberTools-16-patchlevel-5-14.eb | 2 +- ...6.09-GCC-4.9.3-2.25-AmberTools-16-patchlevel-5-14-CUDA.eb | 2 +- easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCC-4.7.2.eb | 5 ++++- .../easyconfigs/a/Autoconf/Autoconf-2.69-goolf-1.4.10.eb | 5 ++++- easybuild/easyconfigs/a/ant/ant-1.8.4-Java-1.7.0_10.eb | 5 +++-- easybuild/easyconfigs/a/ant/ant-1.8.4-Java-1.7.0_21.eb | 5 +++-- easybuild/easyconfigs/a/ant/ant-1.9.0-Java-1.7.0_15.eb | 5 +++-- easybuild/easyconfigs/a/ant/ant-1.9.0-Java-1.7.0_21.eb | 5 +++-- easybuild/easyconfigs/a/ant/ant-1.9.3-Java-1.7.0_60.eb | 5 +++-- easybuild/easyconfigs/a/ant/ant-1.9.3-Java-1.7.0_79.eb | 5 +++-- easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.7.0_75.eb | 5 +++-- easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.7.0_79.eb | 5 +++-- easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.7.0_80.eb | 5 +++-- easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.8.0_66.eb | 5 +++-- easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.8.0_72.eb | 5 +++-- easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.8.0_77.eb | 5 +++-- 23 files changed, 57 insertions(+), 37 deletions(-) diff --git a/easybuild/easyconfigs/a/ABAQUS/ABAQUS-6.12.1-linux-x86_64.eb b/easybuild/easyconfigs/a/ABAQUS/ABAQUS-6.12.1-linux-x86_64.eb index 094f648512..1b2933e3ca 100644 --- a/easybuild/easyconfigs/a/ABAQUS/ABAQUS-6.12.1-linux-x86_64.eb +++ b/easybuild/easyconfigs/a/ABAQUS/ABAQUS-6.12.1-linux-x86_64.eb @@ -3,7 +3,8 @@ version = '6.12.1' versionsuffix = '-linux-x86_64' homepage = 'http://www.simulia.com/products/abaqus_fea.html' -description = "Finite Element Analysis software for modeling, visualization and best-in-class implicit and explicit dynamics FEA." +description = """Finite Element Analysis software for modeling, visualization and best-in-class implicit and explicit + dynamics FEA.""" toolchain = {'name': 'dummy', 'version': ''} diff --git a/easybuild/easyconfigs/a/ABAQUS/ABAQUS-6.13.5-linux-x86_64.eb b/easybuild/easyconfigs/a/ABAQUS/ABAQUS-6.13.5-linux-x86_64.eb index f899ce8f01..e7d7f8108e 100644 --- a/easybuild/easyconfigs/a/ABAQUS/ABAQUS-6.13.5-linux-x86_64.eb +++ b/easybuild/easyconfigs/a/ABAQUS/ABAQUS-6.13.5-linux-x86_64.eb @@ -3,7 +3,8 @@ version = '6.13.5' versionsuffix = '-linux-x86_64' homepage = 'http://www.simulia.com/products/abaqus_fea.html' -description = "Finite Element Analysis software for modeling, visualization and best-in-class implicit and explicit dynamics FEA." +description = """Finite Element Analysis software for modeling, visualization and best-in-class implicit and explicit + dynamics FEA.""" toolchain = {'name': 'dummy', 'version': ''} diff --git a/easybuild/easyconfigs/a/ABAQUS/ABAQUS-6.14.1-linux-x86_64.eb b/easybuild/easyconfigs/a/ABAQUS/ABAQUS-6.14.1-linux-x86_64.eb index 2063066a88..77fcbc5c08 100644 --- a/easybuild/easyconfigs/a/ABAQUS/ABAQUS-6.14.1-linux-x86_64.eb +++ b/easybuild/easyconfigs/a/ABAQUS/ABAQUS-6.14.1-linux-x86_64.eb @@ -3,7 +3,8 @@ version = '6.14.1' versionsuffix = '-linux-x86_64' homepage = 'http://www.simulia.com/products/abaqus_fea.html' -description = "Finite Element Analysis software for modeling, visualization and best-in-class implicit and explicit dynamics FEA." +description = """Finite Element Analysis software for modeling, visualization and best-in-class implicit and explicit + dynamics FEA.""" toolchain = {'name': 'dummy', 'version': ''} diff --git a/easybuild/easyconfigs/a/ALLPATHS-LG/ALLPATHS-LG-46968-goolf-1.4.10.eb b/easybuild/easyconfigs/a/ALLPATHS-LG/ALLPATHS-LG-46968-goolf-1.4.10.eb index bde2863301..6fb42921f6 100644 --- a/easybuild/easyconfigs/a/ALLPATHS-LG/ALLPATHS-LG-46968-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/a/ALLPATHS-LG/ALLPATHS-LG-46968-goolf-1.4.10.eb @@ -2,7 +2,8 @@ # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # # Copyright:: Copyright 2012-2013 The Cyprus Institute -# Authors:: Andreas Panteli , Thekla Loizou , George Tsouloupas +# Authors:: Andreas Panteli , Thekla Loizou , +# George Tsouloupas # License:: MIT/GPL # ## diff --git a/easybuild/easyconfigs/a/Advisor/Advisor-2016_update2.eb b/easybuild/easyconfigs/a/Advisor/Advisor-2016_update2.eb index 0e9c615ba9..70205ebf3a 100644 --- a/easybuild/easyconfigs/a/Advisor/Advisor-2016_update2.eb +++ b/easybuild/easyconfigs/a/Advisor/Advisor-2016_update2.eb @@ -15,7 +15,6 @@ sources = ['advisor_xe_%(version)s.tar.gz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'perf' diff --git a/easybuild/easyconfigs/a/Advisor/Advisor-2017_update1.eb b/easybuild/easyconfigs/a/Advisor/Advisor-2017_update1.eb index 22d5bebaad..6e2edca0dc 100644 --- a/easybuild/easyconfigs/a/Advisor/Advisor-2017_update1.eb +++ b/easybuild/easyconfigs/a/Advisor/Advisor-2017_update1.eb @@ -17,7 +17,6 @@ checksums = ['af87b381394be3100507827a3461b3bc'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'perf' diff --git a/easybuild/easyconfigs/a/Amber/Amber-16-iomkl-2016.07-AmberTools-16-patchlevel-5-14-serial.eb b/easybuild/easyconfigs/a/Amber/Amber-16-iomkl-2016.07-AmberTools-16-patchlevel-5-14-serial.eb index 4e451954c3..4e75833d6e 100644 --- a/easybuild/easyconfigs/a/Amber/Amber-16-iomkl-2016.07-AmberTools-16-patchlevel-5-14-serial.eb +++ b/easybuild/easyconfigs/a/Amber/Amber-16-iomkl-2016.07-AmberTools-16-patchlevel-5-14-serial.eb @@ -3,7 +3,7 @@ version = '16' ambertools_ver = '16' # Patch levels from http://ambermd.org/bugfixes16.html and http://ambermd.org/bugfixesat.html patchlevels = (5, 14) # (AmberTools, Amber) -versionsuffix = '-AmberTools-%s-patchlevel-%s-%s-serial' %(ambertools_ver, patchlevels[0], patchlevels[1]) +versionsuffix = '-AmberTools-%s-patchlevel-%s-%s-serial' % (ambertools_ver, patchlevels[0], patchlevels[1]) homepage = 'http://ambermd.org/amber.html' description = """Amber (originally Assisted Model Building with Energy diff --git a/easybuild/easyconfigs/a/Amber/Amber-16-iomkl-2016.07-AmberTools-16-patchlevel-5-14.eb b/easybuild/easyconfigs/a/Amber/Amber-16-iomkl-2016.07-AmberTools-16-patchlevel-5-14.eb index f910ba5400..b2fcc5fada 100644 --- a/easybuild/easyconfigs/a/Amber/Amber-16-iomkl-2016.07-AmberTools-16-patchlevel-5-14.eb +++ b/easybuild/easyconfigs/a/Amber/Amber-16-iomkl-2016.07-AmberTools-16-patchlevel-5-14.eb @@ -3,7 +3,7 @@ version = '16' ambertools_ver = '16' # Patch levels from http://ambermd.org/bugfixes16.html and http://ambermd.org/bugfixesat.html patchlevels = (5, 14) # (AmberTools, Amber) -versionsuffix = '-AmberTools-%s-patchlevel-%s-%s' %(ambertools_ver, patchlevels[0], patchlevels[1]) +versionsuffix = '-AmberTools-%s-patchlevel-%s-%s' % (ambertools_ver, patchlevels[0], patchlevels[1]) homepage = 'http://ambermd.org/amber.html' description = """Amber (originally Assisted Model Building with Energy diff --git a/easybuild/easyconfigs/a/Amber/Amber-16-iomkl-2016.09-GCC-4.9.3-2.25-AmberTools-16-patchlevel-5-14-CUDA.eb b/easybuild/easyconfigs/a/Amber/Amber-16-iomkl-2016.09-GCC-4.9.3-2.25-AmberTools-16-patchlevel-5-14-CUDA.eb index 1b29f57d52..8895c479d8 100644 --- a/easybuild/easyconfigs/a/Amber/Amber-16-iomkl-2016.09-GCC-4.9.3-2.25-AmberTools-16-patchlevel-5-14-CUDA.eb +++ b/easybuild/easyconfigs/a/Amber/Amber-16-iomkl-2016.09-GCC-4.9.3-2.25-AmberTools-16-patchlevel-5-14-CUDA.eb @@ -3,7 +3,7 @@ version = '16' ambertools_ver = '16' # Patch levels from http://ambermd.org/bugfixes16.html and http://ambermd.org/bugfixesat.html patchlevels = (5, 14) # (AmberTools, Amber) -versionsuffix = '-AmberTools-%s-patchlevel-%s-%s-CUDA' %(ambertools_ver, patchlevels[0], patchlevels[1]) +versionsuffix = '-AmberTools-%s-patchlevel-%s-%s-CUDA' % (ambertools_ver, patchlevels[0], patchlevels[1]) homepage = 'http://ambermd.org/amber.html' description = """Amber (originally Assisted Model Building with Energy diff --git a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCC-4.7.2.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCC-4.7.2.eb index 3d86e53a57..552c3eb907 100644 --- a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCC-4.7.2.eb +++ b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCC-4.7.2.eb @@ -4,7 +4,10 @@ name = 'Autoconf' version = '2.69' homepage = 'http://www.gnu.org/software/autoconf/' -description = """Autoconf is an extensible package of M4 macros that produce shell scripts to automatically configure software source code packages. These scripts can adapt the packages to many kinds of UNIX-like systems without manual user intervention. Autoconf creates a configuration script for a package from a template file that lists the operating system features that the package can use, in the form of M4 macro calls.""" +description = """Autoconf is an extensible package of M4 macros that produce shell scripts to automatically configure + software source code packages. These scripts can adapt the packages to many kinds of UNIX-like systems without manual + user intervention. Autoconf creates a configuration script for a package from a template file that lists the operating + system features that the package can use, in the form of M4 macro calls.""" toolchain = {'name': 'GCC', 'version': '4.7.2'} diff --git a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-goolf-1.4.10.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-goolf-1.4.10.eb index 1e344106ca..612bf18994 100644 --- a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-goolf-1.4.10.eb @@ -4,7 +4,10 @@ name = 'Autoconf' version = '2.69' homepage = 'http://www.gnu.org/software/autoconf/' -description = """Autoconf is an extensible package of M4 macros that produce shell scripts to automatically configure software source code packages. These scripts can adapt the packages to many kinds of UNIX-like systems without manual user intervention. Autoconf creates a configuration script for a package from a template file that lists the operating system features that the package can use, in the form of M4 macro calls.""" +description = """Autoconf is an extensible package of M4 macros that produce shell scripts to automatically configure + software source code packages. These scripts can adapt the packages to many kinds of UNIX-like systems without manual + user intervention. Autoconf creates a configuration script for a package from a template file that lists the operating + system features that the package can use, in the form of M4 macro calls.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} diff --git a/easybuild/easyconfigs/a/ant/ant-1.8.4-Java-1.7.0_10.eb b/easybuild/easyconfigs/a/ant/ant-1.8.4-Java-1.7.0_10.eb index 69f6af4aa8..ffe0aa3aaf 100644 --- a/easybuild/easyconfigs/a/ant/ant-1.8.4-Java-1.7.0_10.eb +++ b/easybuild/easyconfigs/a/ant/ant-1.8.4-Java-1.7.0_10.eb @@ -2,8 +2,9 @@ name = 'ant' version = '1.8.4' homepage = 'http://ant.apache.org/' -description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files - as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications.""" +description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in + build files as targets and extension points dependent upon each other. The main known usage of Ant is the build of + Java applications.""" toolchain = {'name': 'dummy', 'version': ''} diff --git a/easybuild/easyconfigs/a/ant/ant-1.8.4-Java-1.7.0_21.eb b/easybuild/easyconfigs/a/ant/ant-1.8.4-Java-1.7.0_21.eb index ed48c65191..f37d535fe6 100644 --- a/easybuild/easyconfigs/a/ant/ant-1.8.4-Java-1.7.0_21.eb +++ b/easybuild/easyconfigs/a/ant/ant-1.8.4-Java-1.7.0_21.eb @@ -2,8 +2,9 @@ name = 'ant' version = '1.8.4' homepage = 'http://ant.apache.org/' -description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files - as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications.""" +description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in + build files as targets and extension points dependent upon each other. The main known usage of Ant is the build of + Java applications.""" toolchain = {'name': 'dummy', 'version': ''} diff --git a/easybuild/easyconfigs/a/ant/ant-1.9.0-Java-1.7.0_15.eb b/easybuild/easyconfigs/a/ant/ant-1.9.0-Java-1.7.0_15.eb index 4e4944c69e..7a79bafbc3 100644 --- a/easybuild/easyconfigs/a/ant/ant-1.9.0-Java-1.7.0_15.eb +++ b/easybuild/easyconfigs/a/ant/ant-1.9.0-Java-1.7.0_15.eb @@ -2,8 +2,9 @@ name = 'ant' version = '1.9.0' homepage = 'http://ant.apache.org/' -description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files - as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications.""" +description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in + build files as targets and extension points dependent upon each other. The main known usage of Ant is the build of + Java applications.""" toolchain = {'name': 'dummy', 'version': ''} diff --git a/easybuild/easyconfigs/a/ant/ant-1.9.0-Java-1.7.0_21.eb b/easybuild/easyconfigs/a/ant/ant-1.9.0-Java-1.7.0_21.eb index b01a6297fc..ab777254e9 100644 --- a/easybuild/easyconfigs/a/ant/ant-1.9.0-Java-1.7.0_21.eb +++ b/easybuild/easyconfigs/a/ant/ant-1.9.0-Java-1.7.0_21.eb @@ -2,8 +2,9 @@ name = 'ant' version = '1.9.0' homepage = 'http://ant.apache.org/' -description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files - as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications.""" +description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in + build files as targets and extension points dependent upon each other. The main known usage of Ant is the build of + Java applications.""" toolchain = {'name': 'dummy', 'version': ''} diff --git a/easybuild/easyconfigs/a/ant/ant-1.9.3-Java-1.7.0_60.eb b/easybuild/easyconfigs/a/ant/ant-1.9.3-Java-1.7.0_60.eb index ad986bd576..03ba48168e 100644 --- a/easybuild/easyconfigs/a/ant/ant-1.9.3-Java-1.7.0_60.eb +++ b/easybuild/easyconfigs/a/ant/ant-1.9.3-Java-1.7.0_60.eb @@ -2,8 +2,9 @@ name = 'ant' version = '1.9.3' homepage = 'http://ant.apache.org/' -description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files - as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications.""" +description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in + build files as targets and extension points dependent upon each other. The main known usage of Ant is the build of + Java applications.""" toolchain = {'name': 'dummy', 'version': ''} diff --git a/easybuild/easyconfigs/a/ant/ant-1.9.3-Java-1.7.0_79.eb b/easybuild/easyconfigs/a/ant/ant-1.9.3-Java-1.7.0_79.eb index e1662e8bf2..986e3e5a6f 100644 --- a/easybuild/easyconfigs/a/ant/ant-1.9.3-Java-1.7.0_79.eb +++ b/easybuild/easyconfigs/a/ant/ant-1.9.3-Java-1.7.0_79.eb @@ -2,8 +2,9 @@ name = 'ant' version = '1.9.3' homepage = 'http://ant.apache.org/' -description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files - as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications.""" +description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in + build files as targets and extension points dependent upon each other. The main known usage of Ant is the build of + Java applications.""" toolchain = {'name': 'dummy', 'version': ''} diff --git a/easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.7.0_75.eb b/easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.7.0_75.eb index 7da7aa32db..6036bb0be8 100644 --- a/easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.7.0_75.eb +++ b/easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.7.0_75.eb @@ -2,8 +2,9 @@ name = 'ant' version = '1.9.6' homepage = 'http://ant.apache.org/' -description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files - as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications.""" +description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in + build files as targets and extension points dependent upon each other. The main known usage of Ant is the build of + Java applications.""" toolchain = {'name': 'dummy', 'version': ''} diff --git a/easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.7.0_79.eb b/easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.7.0_79.eb index 3ee7c5b406..d51a118fba 100644 --- a/easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.7.0_79.eb +++ b/easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.7.0_79.eb @@ -3,8 +3,9 @@ version = '1.9.6' versionsuffix = '-Java-%(javaver)s' homepage = 'http://ant.apache.org/' -description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files - as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications.""" +description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in + build files as targets and extension points dependent upon each other. The main known usage of Ant is the build of + Java applications.""" toolchain = {'name': 'dummy', 'version': ''} diff --git a/easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.7.0_80.eb b/easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.7.0_80.eb index d93ecdb14e..0e7df6fdf1 100644 --- a/easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.7.0_80.eb @@ -3,8 +3,9 @@ version = '1.9.6' versionsuffix = '-Java-%(javaver)s' homepage = 'http://ant.apache.org/' -description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files - as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications.""" +description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in + build files as targets and extension points dependent upon each other. The main known usage of Ant is the build of + Java applications.""" toolchain = {'name': 'dummy', 'version': ''} diff --git a/easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.8.0_66.eb b/easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.8.0_66.eb index b048fcd097..33aa30131b 100644 --- a/easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.8.0_66.eb +++ b/easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.8.0_66.eb @@ -2,8 +2,9 @@ name = 'ant' version = '1.9.6' homepage = 'http://ant.apache.org/' -description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files - as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications.""" +description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in + build files as targets and extension points dependent upon each other. The main known usage of Ant is the build of + Java applications.""" toolchain = {'name': 'dummy', 'version': ''} diff --git a/easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.8.0_72.eb b/easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.8.0_72.eb index 407fa7e1c0..0f10c1689b 100644 --- a/easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.8.0_72.eb +++ b/easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.8.0_72.eb @@ -3,8 +3,9 @@ version = '1.9.6' versionsuffix = '-Java-%(javaver)s' homepage = 'http://ant.apache.org/' -description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files - as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications.""" +description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in + build files as targets and extension points dependent upon each other. The main known usage of Ant is the build of + Java applications.""" toolchain = {'name': 'dummy', 'version': ''} diff --git a/easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.8.0_77.eb b/easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.8.0_77.eb index 08bcaf86cf..f22f0e01b7 100644 --- a/easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.8.0_77.eb +++ b/easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.8.0_77.eb @@ -3,8 +3,9 @@ version = '1.9.6' versionsuffix = '-Java-%(javaver)s' homepage = 'http://ant.apache.org/' -description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files - as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications.""" +description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in + build files as targets and extension points dependent upon each other. The main known usage of Ant is the build of + Java applications.""" toolchain = {'name': 'dummy', 'version': ''} -- GitLab From 645b2a7dc2bad09463a04674595d23417da5a78c Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 8 Mar 2017 11:30:46 +0800 Subject: [PATCH 0258/1603] yet another batch of minor style fixes --- .../b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_66.eb | 2 +- .../b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_74.eb | 2 +- .../b/BBMap/BBMap-36.62-intel-2016b-Java-1.8.0_112.eb | 2 +- .../easyconfigs/b/BCFtools/BCFtools-1.2-foss-2015a.eb | 5 +++-- .../b/BCFtools/BCFtools-1.2-intel-2015a.eb | 3 ++- .../easyconfigs/b/BCFtools/BCFtools-1.3-foss-2016a.eb | 3 ++- .../b/BCFtools/BCFtools-1.3-intel-2016a.eb | 3 ++- .../easyconfigs/b/BEDOPS/BEDOPS-2.4.1-GCC-4.8.4.eb | 6 +++--- easybuild/easyconfigs/b/BLAT/BLAT-3.5-goolf-1.4.10.eb | 3 ++- .../b/BLAT/BLAT-3.5-ictce-5.5.0-libpng-1.6.9.eb | 3 ++- easybuild/easyconfigs/b/BLAT/BLAT-3.5-ictce-5.5.0.eb | 3 ++- .../easyconfigs/b/BWA/BWA-0.7.13-goolf-1.4.10.eb | 3 ++- .../b/BXH_XCEDE_TOOLS/BXH_XCEDE_TOOLS-1.11.1.eb | 1 - .../easyconfigs/b/BayPass/BayPass-2.1-goolf-1.7.20.eb | 11 +++++------ .../b/BayesAss/BayesAss-3.0.4-foss-2016a.eb | 6 ++---- easybuild/easyconfigs/b/Beast/Beast-1.8.4.eb | 2 +- .../BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb | 2 +- .../BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb | 2 +- .../BioPerl/BioPerl-1.6.924-foss-2016a-Perl-5.22.1.eb | 1 - .../Biopython-1.61-goolf-1.4.10-Python-2.7.3.eb | 3 ++- .../Biopython-1.61-ictce-5.3.0-Python-2.7.3.eb | 3 ++- .../Biopython-1.65-foss-2016a-Python-2.7.11.eb | 3 ++- .../Biopython-1.68-foss-2016b-Python-2.7.12.eb | 3 ++- .../Biopython-1.68-intel-2016b-Python-2.7.12.eb | 3 ++- .../Biopython-1.68-intel-2016b-Python-3.5.2.eb | 3 ++- .../Boost-1.60.0-CrayGNU-2016.03-Python-2.7.11.eb | 2 +- .../easyconfigs/b/Bullet/Bullet-2.83.7-foss-2016a.eb | 4 ++-- .../easyconfigs/b/Bullet/Bullet-2.83.7-intel-2016a.eb | 4 ++-- .../b/beagle-lib/beagle-lib-2.1.2-foss-2016a.eb | 9 +++------ .../b/beagle-lib/beagle-lib-2.1.2-goolf-1.7.20.eb | 9 +++------ 30 files changed, 56 insertions(+), 53 deletions(-) diff --git a/easybuild/easyconfigs/b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_66.eb b/easybuild/easyconfigs/b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_66.eb index 76e04042bc..938cb4bc7e 100644 --- a/easybuild/easyconfigs/b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_66.eb +++ b/easybuild/easyconfigs/b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_66.eb @@ -9,7 +9,7 @@ description = """BBMap short read aligner, and other bioinformatic tools.""" toolchain = {'name': 'foss', 'version': '2015b'} source_urls = [SOURCEFORGE_SOURCE] -sources = ['%(name)s_%(version)s.tar.gz' ] +sources = ['%(name)s_%(version)s.tar.gz'] java = 'Java' javaver = '1.8.0_66' diff --git a/easybuild/easyconfigs/b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_74.eb b/easybuild/easyconfigs/b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_74.eb index d1646b7dbe..83c91ab617 100644 --- a/easybuild/easyconfigs/b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_74.eb +++ b/easybuild/easyconfigs/b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_74.eb @@ -9,7 +9,7 @@ description = """BBMap short read aligner, and other bioinformatic tools.""" toolchain = {'name': 'foss', 'version': '2015b'} source_urls = [SOURCEFORGE_SOURCE] -sources = ['%(name)s_%(version)s.tar.gz' ] +sources = ['%(name)s_%(version)s.tar.gz'] java = 'Java' javaver = '1.8.0_74' diff --git a/easybuild/easyconfigs/b/BBMap/BBMap-36.62-intel-2016b-Java-1.8.0_112.eb b/easybuild/easyconfigs/b/BBMap/BBMap-36.62-intel-2016b-Java-1.8.0_112.eb index 7e9be8c9b6..52eabb1bfe 100644 --- a/easybuild/easyconfigs/b/BBMap/BBMap-36.62-intel-2016b-Java-1.8.0_112.eb +++ b/easybuild/easyconfigs/b/BBMap/BBMap-36.62-intel-2016b-Java-1.8.0_112.eb @@ -10,7 +10,7 @@ description = """BBMap short read aligner, and other bioinformatic tools.""" toolchain = {'name': 'intel', 'version': '2016b'} source_urls = [SOURCEFORGE_SOURCE] -sources = ['%(name)s_%(version)s.tar.gz' ] +sources = ['%(name)s_%(version)s.tar.gz'] dependencies = [('Java', '1.8.0_112', '', True)] diff --git a/easybuild/easyconfigs/b/BCFtools/BCFtools-1.2-foss-2015a.eb b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.2-foss-2015a.eb index 2ee4f62216..3ef62f1ae2 100644 --- a/easybuild/easyconfigs/b/BCFtools/BCFtools-1.2-foss-2015a.eb +++ b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.2-foss-2015a.eb @@ -4,8 +4,9 @@ name = 'BCFtools' version = '1.2' homepage = 'http://www.htslib.org/' -description = """Samtools is a suite of programs for interacting with high-throughput sequencing data. - BCFtools - Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence variants""" +description = """Samtools is a suite of programs for interacting with high-throughput sequencing data. + BCFtools - Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence + variants""" toolchain = {'name': 'foss', 'version': '2015a'} toolchainopts = {'optarch': True, 'pic': True} diff --git a/easybuild/easyconfigs/b/BCFtools/BCFtools-1.2-intel-2015a.eb b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.2-intel-2015a.eb index f9319eca14..41baab6d42 100644 --- a/easybuild/easyconfigs/b/BCFtools/BCFtools-1.2-intel-2015a.eb +++ b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.2-intel-2015a.eb @@ -5,7 +5,8 @@ version = '1.2' homepage = 'http://www.htslib.org/' description = """Samtools is a suite of programs for interacting with high-throughput sequencing data. - BCFtools - Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence variants""" + BCFtools - Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence + variants""" toolchain = {'name': 'intel', 'version': '2015a'} toolchainopts = {'optarch': True, 'pic': True} diff --git a/easybuild/easyconfigs/b/BCFtools/BCFtools-1.3-foss-2016a.eb b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.3-foss-2016a.eb index 6d469bdd3b..a0b589e82c 100644 --- a/easybuild/easyconfigs/b/BCFtools/BCFtools-1.3-foss-2016a.eb +++ b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.3-foss-2016a.eb @@ -5,7 +5,8 @@ version = '1.3' homepage = 'http://www.htslib.org/' description = """Samtools is a suite of programs for interacting with high-throughput sequencing data. - BCFtools - Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence variants""" + BCFtools - Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence + variants""" toolchain = {'name': 'foss', 'version': '2016a'} toolchainopts = {'optarch': True, 'pic': True} diff --git a/easybuild/easyconfigs/b/BCFtools/BCFtools-1.3-intel-2016a.eb b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.3-intel-2016a.eb index bd1b04228a..af2dc1fef7 100644 --- a/easybuild/easyconfigs/b/BCFtools/BCFtools-1.3-intel-2016a.eb +++ b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.3-intel-2016a.eb @@ -5,7 +5,8 @@ version = '1.3' homepage = 'http://www.htslib.org/' description = """Samtools is a suite of programs for interacting with high-throughput sequencing data. - BCFtools - Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence variants""" + BCFtools - Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence + variants""" toolchain = {'name': 'intel', 'version': '2016a'} toolchainopts = {'optarch': True, 'pic': True} diff --git a/easybuild/easyconfigs/b/BEDOPS/BEDOPS-2.4.1-GCC-4.8.4.eb b/easybuild/easyconfigs/b/BEDOPS/BEDOPS-2.4.1-GCC-4.8.4.eb index 47aaf73fa3..4ed43caefd 100644 --- a/easybuild/easyconfigs/b/BEDOPS/BEDOPS-2.4.1-GCC-4.8.4.eb +++ b/easybuild/easyconfigs/b/BEDOPS/BEDOPS-2.4.1-GCC-4.8.4.eb @@ -27,9 +27,9 @@ parallel = 1 files_to_copy = ["bin"] sanity_check_paths = { - 'files': ["bin/%s" % x for x in ["bedmap", "bam2bed" , "sort-bed", - "starchcat", "vcf2bed", "wig2bed", - "gtf2bed", "bedops", "wig2bed"]], + 'files': ["bin/%s" % x for x in ["bedmap", "bam2bed", "sort-bed", + "starchcat", "vcf2bed", "wig2bed", + "gtf2bed", "bedops", "wig2bed"]], 'dirs': [] } diff --git a/easybuild/easyconfigs/b/BLAT/BLAT-3.5-goolf-1.4.10.eb b/easybuild/easyconfigs/b/BLAT/BLAT-3.5-goolf-1.4.10.eb index afbf2938b8..eb88b061dd 100644 --- a/easybuild/easyconfigs/b/BLAT/BLAT-3.5-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/BLAT/BLAT-3.5-goolf-1.4.10.eb @@ -11,7 +11,8 @@ name = 'BLAT' version = '3.5' homepage = 'http://genome.ucsc.edu/FAQ/FAQblat.html' -description = "BLAT on DNA is designed to quickly find sequences of 95% and greater similarity of length 25 bases or more." +description = """BLAT on DNA is designed to quickly find sequences of 95% and greater similarity of length 25 bases or + more.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} diff --git a/easybuild/easyconfigs/b/BLAT/BLAT-3.5-ictce-5.5.0-libpng-1.6.9.eb b/easybuild/easyconfigs/b/BLAT/BLAT-3.5-ictce-5.5.0-libpng-1.6.9.eb index e2d58bafb6..0222da1546 100644 --- a/easybuild/easyconfigs/b/BLAT/BLAT-3.5-ictce-5.5.0-libpng-1.6.9.eb +++ b/easybuild/easyconfigs/b/BLAT/BLAT-3.5-ictce-5.5.0-libpng-1.6.9.eb @@ -11,7 +11,8 @@ name = 'BLAT' version = '3.5' homepage = 'http://genome.ucsc.edu/FAQ/FAQblat.html' -description = "BLAT on DNA is designed to quickly find sequences of 95% and greater similarity of length 25 bases or more." +description = """BLAT on DNA is designed to quickly find sequences of 95% and greater similarity of length 25 bases or + more.""" toolchain = {'name': 'ictce', 'version': '5.5.0'} diff --git a/easybuild/easyconfigs/b/BLAT/BLAT-3.5-ictce-5.5.0.eb b/easybuild/easyconfigs/b/BLAT/BLAT-3.5-ictce-5.5.0.eb index 5f6044dcec..955ee61e30 100644 --- a/easybuild/easyconfigs/b/BLAT/BLAT-3.5-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/b/BLAT/BLAT-3.5-ictce-5.5.0.eb @@ -11,7 +11,8 @@ name = 'BLAT' version = '3.5' homepage = 'http://genome.ucsc.edu/FAQ/FAQblat.html' -description = "BLAT on DNA is designed to quickly find sequences of 95% and greater similarity of length 25 bases or more." +description = """BLAT on DNA is designed to quickly find sequences of 95% and greater similarity of length 25 bases or + more.""" toolchain = {'name': 'ictce', 'version': '5.5.0'} diff --git a/easybuild/easyconfigs/b/BWA/BWA-0.7.13-goolf-1.4.10.eb b/easybuild/easyconfigs/b/BWA/BWA-0.7.13-goolf-1.4.10.eb index 9cbb01f191..2dbdeeb980 100644 --- a/easybuild/easyconfigs/b/BWA/BWA-0.7.13-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/BWA/BWA-0.7.13-goolf-1.4.10.eb @@ -2,7 +2,8 @@ # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # # Copyright:: Copyright 2012-2014 Cyprus Institute / CaSToRC, Uni.Lu/LCSB, NTUA -# Authors:: George Tsouloupas , Fotis Georgatos , Daniel Navarro +# Authors:: George Tsouloupas , Fotis Georgatos , +# Daniel Navarro # License:: MIT/GPL # $Id$ # diff --git a/easybuild/easyconfigs/b/BXH_XCEDE_TOOLS/BXH_XCEDE_TOOLS-1.11.1.eb b/easybuild/easyconfigs/b/BXH_XCEDE_TOOLS/BXH_XCEDE_TOOLS-1.11.1.eb index 9cd875e7c6..c0802f9ddd 100644 --- a/easybuild/easyconfigs/b/BXH_XCEDE_TOOLS/BXH_XCEDE_TOOLS-1.11.1.eb +++ b/easybuild/easyconfigs/b/BXH_XCEDE_TOOLS/BXH_XCEDE_TOOLS-1.11.1.eb @@ -25,4 +25,3 @@ sanity_check_paths = { } moduleclass = 'bio' - diff --git a/easybuild/easyconfigs/b/BayPass/BayPass-2.1-goolf-1.7.20.eb b/easybuild/easyconfigs/b/BayPass/BayPass-2.1-goolf-1.7.20.eb index e948c06e11..65f14b74d8 100644 --- a/easybuild/easyconfigs/b/BayPass/BayPass-2.1-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/b/BayPass/BayPass-2.1-goolf-1.7.20.eb @@ -25,12 +25,11 @@ start_dir = 'sources' parallel = 1 -files_to_copy = [(['sources/g_baypass'], 'bin/'), - 'BayPass_manual_2.1.pdf', - 'examples', - 'Licence_CeCILL-B_V1-en.txt', - 'utils' -] +files_to_copy = [(['sources/g_baypass'], 'bin/'), + 'BayPass_manual_2.1.pdf', + 'examples', + 'Licence_CeCILL-B_V1-en.txt', + 'utils'] sanity_check_paths = { 'files': ['bin/g_baypass'], diff --git a/easybuild/easyconfigs/b/BayesAss/BayesAss-3.0.4-foss-2016a.eb b/easybuild/easyconfigs/b/BayesAss/BayesAss-3.0.4-foss-2016a.eb index 20f57806c7..0d36886635 100644 --- a/easybuild/easyconfigs/b/BayesAss/BayesAss-3.0.4-foss-2016a.eb +++ b/easybuild/easyconfigs/b/BayesAss/BayesAss-3.0.4-foss-2016a.eb @@ -4,9 +4,7 @@ name = 'BayesAss' version = '3.0.4' homepage = 'http://www.rannala.org/?page_id=245' -description = """ -BayesAss: Bayesian Inference of Recent Migration Using Multilocus Genotypes -""" +description = "BayesAss: Bayesian Inference of Recent Migration Using Multilocus Genotypes" toolchain = {'name': 'foss', 'version': '2016a'} sources = ['BA3-%(version)s.tar.gz'] @@ -21,7 +19,7 @@ runtest = 'check' sanity_check_paths = { 'files': ['bin/BA3'], - 'dirs' : ['bin', 'include'] + 'dirs': ['bin', 'include'] } moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/Beast/Beast-1.8.4.eb b/easybuild/easyconfigs/b/Beast/Beast-1.8.4.eb index 972161d135..283940594d 100644 --- a/easybuild/easyconfigs/b/Beast/Beast-1.8.4.eb +++ b/easybuild/easyconfigs/b/Beast/Beast-1.8.4.eb @@ -18,7 +18,7 @@ description = """ BEAST is a cross-platform program for Bayesian MCMC analysis o toolchain = {'name': 'dummy', 'version': ''} -source_urls= ['https://github.com/beast-dev/beast-mcmc/releases/download/v%(version)s/'] +source_urls = ['https://github.com/beast-dev/beast-mcmc/releases/download/v%(version)s/'] sources = ['BEASTv%(version)s.tgz'] dependencies = [ diff --git a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb index 5afb842c80..ff35b3fe93 100644 --- a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb @@ -28,7 +28,7 @@ buildopts += 'FFTWINCLUDE="$FFTW_INC_DIR" FFTWLIB="$MKLROOT/lib/intel64/libfftw2 installopts = 'INSTDIR=%(installdir)s' sanity_check_paths = { - 'files': ['bin/'+prog+'.'+flavor+'.x' + 'files': ['bin/' + prog + '.' + flavor + '.x' for prog in ['epsilon', 'sigma', 'kernel', 'absorption'] for flavor in ['real', 'cplx']], 'dirs': [] diff --git a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb index 9d064dae20..0f2dfc0807 100644 --- a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb @@ -28,7 +28,7 @@ buildopts += 'FFTWINCLUDE="$FFTW_INC_DIR" FFTWLIB="$MKLROOT/lib/intel64/libfftw2 installopts = 'INSTDIR=%(installdir)s' sanity_check_paths = { - 'files': ['bin/'+prog+'.'+flavor+'.x' + 'files': ['bin/' + prog + '.' + flavor + '.x' for prog in ['epsilon', 'sigma', 'kernel', 'absorption'] for flavor in ['real', 'cplx']], 'dirs': [] diff --git a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.924-foss-2016a-Perl-5.22.1.eb b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.924-foss-2016a-Perl-5.22.1.eb index 2661f0fe38..c32f54aa1d 100644 --- a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.924-foss-2016a-Perl-5.22.1.eb +++ b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.924-foss-2016a-Perl-5.22.1.eb @@ -37,4 +37,3 @@ modextrapaths = { } moduleclass = 'bio' - diff --git a/easybuild/easyconfigs/b/Biopython/Biopython-1.61-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/b/Biopython/Biopython-1.61-goolf-1.4.10-Python-2.7.3.eb index a3dca17749..26ff0e4f6a 100644 --- a/easybuild/easyconfigs/b/Biopython/Biopython-1.61-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/b/Biopython/Biopython-1.61-goolf-1.4.10-Python-2.7.3.eb @@ -2,7 +2,8 @@ # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # # Copyright:: Copyright 2012-2013 The Cyprus Institute -# Authors:: Andreas Panteli , Thekla Loizou , George Tsouloupas +# Authors:: Andreas Panteli , Thekla Loizou , +# George Tsouloupas # License:: MIT/GPL # ## diff --git a/easybuild/easyconfigs/b/Biopython/Biopython-1.61-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/b/Biopython/Biopython-1.61-ictce-5.3.0-Python-2.7.3.eb index 5efa64f0e0..462ab92f17 100644 --- a/easybuild/easyconfigs/b/Biopython/Biopython-1.61-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/b/Biopython/Biopython-1.61-ictce-5.3.0-Python-2.7.3.eb @@ -2,7 +2,8 @@ # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # # Copyright:: Copyright 2012-2013 The Cyprus Institute -# Authors:: Andreas Panteli , Thekla Loizou , George Tsouloupas +# Authors:: Andreas Panteli , Thekla Loizou , +# George Tsouloupas # License:: MIT/GPL # ## diff --git a/easybuild/easyconfigs/b/Biopython/Biopython-1.65-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/b/Biopython/Biopython-1.65-foss-2016a-Python-2.7.11.eb index a42f248efe..c5aa94f58c 100644 --- a/easybuild/easyconfigs/b/Biopython/Biopython-1.65-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/b/Biopython/Biopython-1.65-foss-2016a-Python-2.7.11.eb @@ -2,7 +2,8 @@ # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # # Copyright:: Copyright 2012-2013 The Cyprus Institute -# Authors:: Andreas Panteli , Thekla Loizou , George Tsouloupas +# Authors:: Andreas Panteli , Thekla Loizou , +# George Tsouloupas # License:: MIT/GPL # ## diff --git a/easybuild/easyconfigs/b/Biopython/Biopython-1.68-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/b/Biopython/Biopython-1.68-foss-2016b-Python-2.7.12.eb index 1c5fd3f356..f5a410bf23 100644 --- a/easybuild/easyconfigs/b/Biopython/Biopython-1.68-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/b/Biopython/Biopython-1.68-foss-2016b-Python-2.7.12.eb @@ -2,7 +2,8 @@ # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # # Copyright:: Copyright 2012-2013 The Cyprus Institute -# Authors:: Andreas Panteli , Thekla Loizou , George Tsouloupas +# Authors:: Andreas Panteli , Thekla Loizou , +# George Tsouloupas # License:: MIT/GPL # ## diff --git a/easybuild/easyconfigs/b/Biopython/Biopython-1.68-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/b/Biopython/Biopython-1.68-intel-2016b-Python-2.7.12.eb index 953304846e..762f84f558 100644 --- a/easybuild/easyconfigs/b/Biopython/Biopython-1.68-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/b/Biopython/Biopython-1.68-intel-2016b-Python-2.7.12.eb @@ -2,7 +2,8 @@ # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # # Copyright:: Copyright 2012-2013 The Cyprus Institute -# Authors:: Andreas Panteli , Thekla Loizou , George Tsouloupas +# Authors:: Andreas Panteli , Thekla Loizou , +# George Tsouloupas # License:: MIT/GPL # ## diff --git a/easybuild/easyconfigs/b/Biopython/Biopython-1.68-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/b/Biopython/Biopython-1.68-intel-2016b-Python-3.5.2.eb index b22f51705c..36d03b946c 100644 --- a/easybuild/easyconfigs/b/Biopython/Biopython-1.68-intel-2016b-Python-3.5.2.eb +++ b/easybuild/easyconfigs/b/Biopython/Biopython-1.68-intel-2016b-Python-3.5.2.eb @@ -2,7 +2,8 @@ # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # # Copyright:: Copyright 2012-2013 The Cyprus Institute -# Authors:: Andreas Panteli , Thekla Loizou , George Tsouloupas +# Authors:: Andreas Panteli , Thekla Loizou , +# George Tsouloupas # License:: MIT/GPL # ## diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.60.0-CrayGNU-2016.03-Python-2.7.11.eb b/easybuild/easyconfigs/b/Boost/Boost-1.60.0-CrayGNU-2016.03-Python-2.7.11.eb index b906f81abf..24c748d95f 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.60.0-CrayGNU-2016.03-Python-2.7.11.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.60.0-CrayGNU-2016.03-Python-2.7.11.eb @@ -18,7 +18,7 @@ pythonversion = '2.7.11' versionsuffix = '-Python-%s' % pythonversion dependencies = [ - ('bzip2', '1.0.6' ), + ('bzip2', '1.0.6'), ('Python', pythonversion), ] diff --git a/easybuild/easyconfigs/b/Bullet/Bullet-2.83.7-foss-2016a.eb b/easybuild/easyconfigs/b/Bullet/Bullet-2.83.7-foss-2016a.eb index 95d2b2fb64..bcb89c1b4e 100644 --- a/easybuild/easyconfigs/b/Bullet/Bullet-2.83.7-foss-2016a.eb +++ b/easybuild/easyconfigs/b/Bullet/Bullet-2.83.7-foss-2016a.eb @@ -19,8 +19,8 @@ builddependencies = [('CMake', '3.5.2')] configopts = "-DBUILD_SHARED_LIBS=ON" sanity_check_paths = { - 'files': ['include/bullet/btBullet%sCommon.h' % x for x in ['Collision', 'Dynamics']] - + ['lib/libBullet%s.%s' % (x,SHLIB_EXT) for x in ['Collision', 'Dynamics']], + 'files': ['include/bullet/btBullet%sCommon.h' % x for x in ['Collision', 'Dynamics']] + + ['lib/libBullet%s.%s' % (x, SHLIB_EXT) for x in ['Collision', 'Dynamics']], 'dirs': [], } diff --git a/easybuild/easyconfigs/b/Bullet/Bullet-2.83.7-intel-2016a.eb b/easybuild/easyconfigs/b/Bullet/Bullet-2.83.7-intel-2016a.eb index d23fa88f57..dce0112a41 100644 --- a/easybuild/easyconfigs/b/Bullet/Bullet-2.83.7-intel-2016a.eb +++ b/easybuild/easyconfigs/b/Bullet/Bullet-2.83.7-intel-2016a.eb @@ -19,8 +19,8 @@ builddependencies = [('CMake', '3.5.2')] configopts = "-DBUILD_SHARED_LIBS=ON" sanity_check_paths = { - 'files': ['include/bullet/btBullet%sCommon.h' % x for x in ['Collision', 'Dynamics']] - + ['lib/libBullet%s.%s' % (x,SHLIB_EXT) for x in ['Collision', 'Dynamics']], + 'files': ['include/bullet/btBullet%sCommon.h' % x for x in ['Collision', 'Dynamics']] + + ['lib/libBullet%s.%s' % (x, SHLIB_EXT) for x in ['Collision', 'Dynamics']], 'dirs': [], } diff --git a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-2.1.2-foss-2016a.eb b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-2.1.2-foss-2016a.eb index 29785ed5e6..49900e2203 100644 --- a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-2.1.2-foss-2016a.eb +++ b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-2.1.2-foss-2016a.eb @@ -2,12 +2,9 @@ easyblock = 'ConfigureMake' name = 'beagle-lib' version = '2.1.2' -homepage= 'https://github.com/beagle-dev/beagle-lib' -description = """ -beagle-lib is a high-performance library that can perform the core -calculations at the heart of most Bayesian and Maximum Likelihood -phylogenetics packages. -""" +homepage = 'https://github.com/beagle-dev/beagle-lib' +description = """beagle-lib is a high-performance library that can perform the core calculations at the heart of most + Bayesian and Maximum Likelihood phylogenetics packages.""" toolchain = {'name': 'foss', 'version': '2016a'} diff --git a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-2.1.2-goolf-1.7.20.eb b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-2.1.2-goolf-1.7.20.eb index ba27dc855d..eb31afb551 100644 --- a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-2.1.2-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-2.1.2-goolf-1.7.20.eb @@ -3,12 +3,9 @@ easyblock = 'ConfigureMake' name = 'beagle-lib' version = '2.1.2' -homepage= 'https://github.com/beagle-dev/beagle-lib' -description = """ -beagle-lib is a high-performance library that can perform the core -calculations at the heart of most Bayesian and Maximum Likelihood -phylogenetics packages. -""" +homepage = 'https://github.com/beagle-dev/beagle-lib' +description = """beagle-lib is a high-performance library that can perform the core calculations at the heart of most + Bayesian and Maximum Likelihood phylogenetics packages.""" toolchain = {'name': 'goolf', 'version': '1.7.20'} -- GitLab From cb34f841946cc8f5be8a95031e763e7c2ddc4c9d Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 8 Mar 2017 14:41:26 +0800 Subject: [PATCH 0259/1603] yet another batch of minor style fixes --- .../easyconfigs/c/CLooG/CLooG-0.18.1-GCC-4.8.2.eb | 14 +++++++------- easybuild/easyconfigs/c/CUDA/CUDA-5.0.35-1.eb | 3 ++- .../easyconfigs/c/CUDA/CUDA-5.0.35-GCC-4.6.4-1.eb | 3 ++- .../CVXOPT-1.1.5-goolf-1.4.10-Python-2.7.3.eb | 5 +++-- .../CVXOPT-1.1.5-ictce-5.3.0-Python-2.7.3.eb | 5 +++-- easybuild/easyconfigs/c/CrayPGI/CrayPGI-2016.04.eb | 9 ++++----- .../Cython-0.16-goolf-1.4.10-Python-2.7.3.eb | 3 ++- .../Cython/Cython-0.16-ictce-5.3.0-Python-2.7.3.eb | 3 ++- .../Cython-0.19.1-goolf-1.4.10-Python-2.7.3.eb | 3 ++- .../Cython-0.19.1-ictce-5.3.0-Python-2.7.3.eb | 3 ++- .../Cython-0.19.2-ictce-5.5.0-Python-2.7.6.eb | 3 ++- .../Cython-0.22-goolf-1.4.10-Python-2.7.3.eb | 3 ++- .../Cython-0.23.4-gimkl-2.11.5-Python-2.7.10.eb | 3 ++- .../Cython-0.24.1-foss-2016a-Python-2.7.11.eb | 3 ++- 14 files changed, 37 insertions(+), 26 deletions(-) diff --git a/easybuild/easyconfigs/c/CLooG/CLooG-0.18.1-GCC-4.8.2.eb b/easybuild/easyconfigs/c/CLooG/CLooG-0.18.1-GCC-4.8.2.eb index fbd1e0f85d..137bbb1603 100644 --- a/easybuild/easyconfigs/c/CLooG/CLooG-0.18.1-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/c/CLooG/CLooG-0.18.1-GCC-4.8.2.eb @@ -4,13 +4,13 @@ name = 'CLooG' version = '0.18.1' homepage = 'http://www.bastoul.net/cloog/index.php' -description = """CLooG is a free software and library to generate code for scanning Z-polyhedra. -That is, it finds a code (e.g. in C, FORTRAN...) that reaches each integral point of one or more parameterized polyhedra. -CLooG has been originally written to solve the code generation problem for optimizing compilers based on the polytope model. -Nevertheless it is used now in various area e.g. to build control automata for high-level synthesis or to find the best -polynomial approximation of a function. CLooG may help in any situation where scanning polyhedra matters. While the user -has full control on generated code quality, CLooG is designed to avoid control overhead and to produce a very effective code. -""" +description = """CLooG is a free software and library to generate code for scanning Z-polyhedra. That is, it finds a + code (e.g. in C, FORTRAN...) that reaches each integral point of one or more parameterized polyhedra. CLooG has been + originally written to solve the code generation problem for optimizing compilers based on the polytope model. + Nevertheless it is used now in various area e.g. to build control automata for high-level synthesis or to find the + best polynomial approximation of a function. CLooG may help in any situation where scanning polyhedra matters. While + the user has full control on generated code quality, CLooG is designed to avoid control overhead and to produce a + very effective code.""" toolchain = {'name': 'GCC', 'version': '4.8.2'} diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-5.0.35-1.eb b/easybuild/easyconfigs/c/CUDA/CUDA-5.0.35-1.eb index 299410b70c..8997152413 100644 --- a/easybuild/easyconfigs/c/CUDA/CUDA-5.0.35-1.eb +++ b/easybuild/easyconfigs/c/CUDA/CUDA-5.0.35-1.eb @@ -36,7 +36,8 @@ elif OS_NAME in ['debian', 'ubuntu']: if OS_VERSION in ['11.10', '10.04']: system = 'ubuntu%s' % OS_VERSION else: - print "Falling back to ubuntu11.10 as default for OS_NAME=%s, OS_VERSION=%s; kindly amend this easyconfig" % (OS_NAME, OS_VERSION) + OS = (OS_NAME, OS_VERSION) + print "Falling back to ubuntu11.10 as default for OS_NAME=%s, OS_VERSION=%s; kindly amend this easyconfig" % OS system = 'ubuntu11.10' elif OS_NAME == "opensuse": system = 'suse12.1' diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-5.0.35-GCC-4.6.4-1.eb b/easybuild/easyconfigs/c/CUDA/CUDA-5.0.35-GCC-4.6.4-1.eb index 9b2a072f8b..194a2991a9 100644 --- a/easybuild/easyconfigs/c/CUDA/CUDA-5.0.35-GCC-4.6.4-1.eb +++ b/easybuild/easyconfigs/c/CUDA/CUDA-5.0.35-GCC-4.6.4-1.eb @@ -36,7 +36,8 @@ elif OS_NAME in ['debian', 'ubuntu']: if OS_VERSION in ['11.10', '10.04']: system = 'ubuntu%s' % OS_VERSION else: - print "Falling back to ubuntu11.10 as default for OS_NAME=%s, OS_VERSION=%s; kindly amend this easyconfig" % (OS_NAME, OS_VERSION) + OS = (OS_NAME, OS_VERSION) + print "Falling back to ubuntu11.10 as default for OS_NAME=%s, OS_VERSION=%s; kindly amend this easyconfig" % OS system = 'ubuntu11.10' elif OS_NAME == "opensuse": system = 'suse12.1' diff --git a/easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.1.5-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.1.5-goolf-1.4.10-Python-2.7.3.eb index 071eb0169f..e06141ece5 100644 --- a/easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.1.5-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.1.5-goolf-1.4.10-Python-2.7.3.eb @@ -5,8 +5,9 @@ version = '1.1.5' homepage = 'http://abel.ee.ucla.edu/cvxopt/' description = """CVXOPT is a free software package for convex optimization based on the Python programming language. -Its main purpose is to make the development of software for convex optimization applications straightforward -by building on Python's extensive standard library and on the strengths of Python as a high-level programming language.""" + Its main purpose is to make the development of software for convex optimization applications straightforward by + building on Python's extensive standard library and on the strengths of Python as a high-level programming language. +""" toolchain = {'name': 'goolf', 'version': '1.4.10'} diff --git a/easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.1.5-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.1.5-ictce-5.3.0-Python-2.7.3.eb index 3e32468f92..795f2f0360 100644 --- a/easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.1.5-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.1.5-ictce-5.3.0-Python-2.7.3.eb @@ -5,8 +5,9 @@ version = '1.1.5' homepage = 'http://abel.ee.ucla.edu/cvxopt/' description = """CVXOPT is a free software package for convex optimization based on the Python programming language. - Its main purpose is to make the development of software for convex optimization applications straightforward - by building on Python's extensive standard library and on the strengths of Python as a high-level programming language.""" + Its main purpose is to make the development of software for convex optimization applications straightforward by + building on Python's extensive standard library and on the strengths of Python as a high-level programming language. +""" toolchain = {'name': 'ictce', 'version': '5.3.0'} diff --git a/easybuild/easyconfigs/c/CrayPGI/CrayPGI-2016.04.eb b/easybuild/easyconfigs/c/CrayPGI/CrayPGI-2016.04.eb index 112a9312bc..8f554a1eb2 100644 --- a/easybuild/easyconfigs/c/CrayPGI/CrayPGI-2016.04.eb +++ b/easybuild/easyconfigs/c/CrayPGI/CrayPGI-2016.04.eb @@ -9,11 +9,10 @@ description = """Toolchain using Cray compiler wrapper, using PrgEnv-pgi module. toolchain = {'name': 'dummy', 'version': 'dummy'} dependencies = [ - # PrgEnv version is not pinned, as Cray recommends to use the latest (default) version - ('PrgEnv-pgi', EXTERNAL_MODULE), - ('pgi/16.3.0' , EXTERNAL_MODULE), - ('cray-mpich/7.3.2', EXTERNAL_MODULE), + # PrgEnv version is not pinned, as Cray recommends to use the latest (default) version + ('PrgEnv-pgi', EXTERNAL_MODULE), + ('pgi/16.3.0', EXTERNAL_MODULE), + ('cray-mpich/7.3.2', EXTERNAL_MODULE), ] moduleclass = 'toolchain' - diff --git a/easybuild/easyconfigs/c/Cython/Cython-0.16-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/c/Cython/Cython-0.16-goolf-1.4.10-Python-2.7.3.eb index fa53744e7c..e22250c990 100644 --- a/easybuild/easyconfigs/c/Cython/Cython-0.16-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/c/Cython/Cython-0.16-goolf-1.4.10-Python-2.7.3.eb @@ -5,7 +5,8 @@ version = '0.16' homepage = 'https://pypi.python.org/pypi/Cython/' description = """The Cython language makes writing C extensions for the Python language as easy as Python itself. - Cython is a source code translator based on the well-known Pyrex, but supports more cutting edge functionality and optimizations.""" + Cython is a source code translator based on the well-known Pyrex, but supports more cutting edge functionality and + optimizations.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} diff --git a/easybuild/easyconfigs/c/Cython/Cython-0.16-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/c/Cython/Cython-0.16-ictce-5.3.0-Python-2.7.3.eb index f2fb277465..33b4c1bc5b 100644 --- a/easybuild/easyconfigs/c/Cython/Cython-0.16-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/c/Cython/Cython-0.16-ictce-5.3.0-Python-2.7.3.eb @@ -5,7 +5,8 @@ version = '0.16' homepage = 'https://pypi.python.org/pypi/Cython/' description = """The Cython language makes writing C extensions for the Python language as easy as Python itself. - Cython is a source code translator based on the well-known Pyrex, but supports more cutting edge functionality and optimizations.""" + Cython is a source code translator based on the well-known Pyrex, but supports more cutting edge functionality and + optimizations.""" toolchain = {'name': 'ictce', 'version': '5.3.0'} diff --git a/easybuild/easyconfigs/c/Cython/Cython-0.19.1-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/c/Cython/Cython-0.19.1-goolf-1.4.10-Python-2.7.3.eb index 0e8ac631d0..ec51d696a0 100644 --- a/easybuild/easyconfigs/c/Cython/Cython-0.19.1-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/c/Cython/Cython-0.19.1-goolf-1.4.10-Python-2.7.3.eb @@ -5,7 +5,8 @@ version = '0.19.1' homepage = 'https://pypi.python.org/pypi/Cython/' description = """The Cython language makes writing C extensions for the Python language as easy as Python itself. - Cython is a source code translator based on the well-known Pyrex, but supports more cutting edge functionality and optimizations.""" + Cython is a source code translator based on the well-known Pyrex, but supports more cutting edge functionality and + optimizations.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} diff --git a/easybuild/easyconfigs/c/Cython/Cython-0.19.1-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/c/Cython/Cython-0.19.1-ictce-5.3.0-Python-2.7.3.eb index 6ba8ee3375..1cdbf2c1fc 100644 --- a/easybuild/easyconfigs/c/Cython/Cython-0.19.1-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/c/Cython/Cython-0.19.1-ictce-5.3.0-Python-2.7.3.eb @@ -5,7 +5,8 @@ version = '0.19.1' homepage = 'https://pypi.python.org/pypi/Cython/' description = """The Cython language makes writing C extensions for the Python language as easy as Python itself. - Cython is a source code translator based on the well-known Pyrex, but supports more cutting edge functionality and optimizations.""" + Cython is a source code translator based on the well-known Pyrex, but supports more cutting edge functionality and + optimizations.""" toolchain = {'name': 'ictce', 'version': '5.3.0'} diff --git a/easybuild/easyconfigs/c/Cython/Cython-0.19.2-ictce-5.5.0-Python-2.7.6.eb b/easybuild/easyconfigs/c/Cython/Cython-0.19.2-ictce-5.5.0-Python-2.7.6.eb index 80955e4cc6..8494b353e5 100644 --- a/easybuild/easyconfigs/c/Cython/Cython-0.19.2-ictce-5.5.0-Python-2.7.6.eb +++ b/easybuild/easyconfigs/c/Cython/Cython-0.19.2-ictce-5.5.0-Python-2.7.6.eb @@ -5,7 +5,8 @@ version = '0.19.2' homepage = 'https://pypi.python.org/pypi/Cython/' description = """The Cython language makes writing C extensions for the Python language as easy as Python itself. - Cython is a source code translator based on the well-known Pyrex, but supports more cutting edge functionality and optimizations.""" + Cython is a source code translator based on the well-known Pyrex, but supports more cutting edge functionality and + optimizations.""" toolchain = {'name': 'ictce', 'version': '5.5.0'} diff --git a/easybuild/easyconfigs/c/Cython/Cython-0.22-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/c/Cython/Cython-0.22-goolf-1.4.10-Python-2.7.3.eb index 1a87b1c99c..769f55ce72 100644 --- a/easybuild/easyconfigs/c/Cython/Cython-0.22-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/c/Cython/Cython-0.22-goolf-1.4.10-Python-2.7.3.eb @@ -5,7 +5,8 @@ version = '0.22' homepage = 'https://pypi.python.org/pypi/Cython/' description = """The Cython language makes writing C extensions for the Python language as easy as Python itself. -Cython is a source code translator based on the well-known Pyrex, but supports more cutting edge functionality and optimizations.""" +Cython is a source code translator based on the well-known Pyrex, but supports more cutting edge functionality and + optimizations.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} diff --git a/easybuild/easyconfigs/c/Cython/Cython-0.23.4-gimkl-2.11.5-Python-2.7.10.eb b/easybuild/easyconfigs/c/Cython/Cython-0.23.4-gimkl-2.11.5-Python-2.7.10.eb index 426fedf887..dd9fc1ad56 100644 --- a/easybuild/easyconfigs/c/Cython/Cython-0.23.4-gimkl-2.11.5-Python-2.7.10.eb +++ b/easybuild/easyconfigs/c/Cython/Cython-0.23.4-gimkl-2.11.5-Python-2.7.10.eb @@ -6,7 +6,8 @@ versionsuffix = '-Python-%(pyver)s' homepage = 'https://pypi.python.org/pypi/Cython/' description = """The Cython language makes writing C extensions for the Python language as easy as Python itself. -Cython is a source code translator based on the well-known Pyrex, but supports more cutting edge functionality and optimizations.""" +Cython is a source code translator based on the well-known Pyrex, but supports more cutting edge functionality and + optimizations.""" toolchain = {'name': 'gimkl', 'version': '2.11.5'} diff --git a/easybuild/easyconfigs/c/Cython/Cython-0.24.1-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/c/Cython/Cython-0.24.1-foss-2016a-Python-2.7.11.eb index a2db0bddbe..0dfcb1056b 100644 --- a/easybuild/easyconfigs/c/Cython/Cython-0.24.1-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/c/Cython/Cython-0.24.1-foss-2016a-Python-2.7.11.eb @@ -6,7 +6,8 @@ versionsuffix = '-Python-%(pyver)s' homepage = 'https://pypi.python.org/pypi/Cython/' description = """The Cython language makes writing C extensions for the Python language as easy as Python itself. -Cython is a source code translator based on the well-known Pyrex, but supports more cutting edge functionality and optimizations.""" + Cython is a source code translator based on the well-known Pyrex, but supports more cutting edge functionality and + optimizations.""" toolchain = {'name': 'foss', 'version': '2016a'} -- GitLab From b2c06bc2d82e3c1e666cff29ade846e11e5eade3 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 8 Mar 2017 14:59:09 +0800 Subject: [PATCH 0260/1603] yet another batch of minor style fixes --- easybuild/easyconfigs/d/DB/DB-6.2.23-foss-2016a.eb | 2 +- .../d/DB_File/DB_File-1.835-foss-2016a-Perl-5.22.1.eb | 1 - easybuild/easyconfigs/d/DBus/DBus-1.10.12-intel-2016b.eb | 3 ++- easybuild/easyconfigs/d/DBus/DBus-1.10.8-foss-2016a.eb | 3 ++- easybuild/easyconfigs/d/DBus/DBus-1.10.8-intel-2016a.eb | 3 ++- easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.1.1-intel-2015a.eb | 3 ++- easybuild/easyconfigs/d/DMTCP/DMTCP-2.4.5.eb | 1 - easybuild/easyconfigs/d/DMTCP/DMTCP-2.5.0-foss-2016a.eb | 1 - easybuild/easyconfigs/d/drFAST/drFAST-1.0.0.0-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/d/drFAST/drFAST-1.0.0.0-ictce-6.2.5.eb | 2 +- 10 files changed, 11 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/d/DB/DB-6.2.23-foss-2016a.eb b/easybuild/easyconfigs/d/DB/DB-6.2.23-foss-2016a.eb index fcf1bd7696..b1a5625761 100644 --- a/easybuild/easyconfigs/d/DB/DB-6.2.23-foss-2016a.eb +++ b/easybuild/easyconfigs/d/DB/DB-6.2.23-foss-2016a.eb @@ -15,4 +15,4 @@ sanity_check_paths = { 'dirs': [], } -moduleclass = 'tools' \ No newline at end of file +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/d/DB_File/DB_File-1.835-foss-2016a-Perl-5.22.1.eb b/easybuild/easyconfigs/d/DB_File/DB_File-1.835-foss-2016a-Perl-5.22.1.eb index 8c069fec94..03f4831ace 100644 --- a/easybuild/easyconfigs/d/DB_File/DB_File-1.835-foss-2016a-Perl-5.22.1.eb +++ b/easybuild/easyconfigs/d/DB_File/DB_File-1.835-foss-2016a-Perl-5.22.1.eb @@ -25,4 +25,3 @@ sanity_check_paths = { } moduleclass = 'data' - diff --git a/easybuild/easyconfigs/d/DBus/DBus-1.10.12-intel-2016b.eb b/easybuild/easyconfigs/d/DBus/DBus-1.10.12-intel-2016b.eb index 7071afdb2c..c041d6e2aa 100644 --- a/easybuild/easyconfigs/d/DBus/DBus-1.10.12-intel-2016b.eb +++ b/easybuild/easyconfigs/d/DBus/DBus-1.10.12-intel-2016b.eb @@ -16,7 +16,8 @@ source_urls = ['http://dbus.freedesktop.org/releases/dbus'] sources = [SOURCELOWER_TAR_GZ] sanity_check_paths = { - 'files': ['bin/dbus-%s' % x for x in ['cleanup-sockets', 'daemon', 'launch', 'monitor', 'run-session', 'send', 'uuidgen']] + + 'files': ['bin/dbus-%s' % x for x in ['cleanup-sockets', 'daemon', 'launch', 'monitor', 'run-session', 'send', + 'uuidgen']] + ['lib/libdbus-1.%s' % x for x in ['a', SHLIB_EXT]], 'dirs': ['include', 'share'] } diff --git a/easybuild/easyconfigs/d/DBus/DBus-1.10.8-foss-2016a.eb b/easybuild/easyconfigs/d/DBus/DBus-1.10.8-foss-2016a.eb index 0940c66fb5..e933c1af39 100644 --- a/easybuild/easyconfigs/d/DBus/DBus-1.10.8-foss-2016a.eb +++ b/easybuild/easyconfigs/d/DBus/DBus-1.10.8-foss-2016a.eb @@ -16,7 +16,8 @@ source_urls = ['http://dbus.freedesktop.org/releases/dbus'] sources = [SOURCELOWER_TAR_GZ] sanity_check_paths = { - 'files': ['bin/dbus-%s' % x for x in ['cleanup-sockets', 'daemon', 'launch', 'monitor', 'run-session', 'send', 'uuidgen']] + + 'files': ['bin/dbus-%s' % x for x in ['cleanup-sockets', 'daemon', 'launch', 'monitor', 'run-session', 'send', + 'uuidgen']] + ['lib/libdbus-1.%s' % x for x in ['a', SHLIB_EXT]], 'dirs': ['include', 'share'] } diff --git a/easybuild/easyconfigs/d/DBus/DBus-1.10.8-intel-2016a.eb b/easybuild/easyconfigs/d/DBus/DBus-1.10.8-intel-2016a.eb index f322881382..74d90eb777 100644 --- a/easybuild/easyconfigs/d/DBus/DBus-1.10.8-intel-2016a.eb +++ b/easybuild/easyconfigs/d/DBus/DBus-1.10.8-intel-2016a.eb @@ -16,7 +16,8 @@ source_urls = ['http://dbus.freedesktop.org/releases/dbus'] sources = [SOURCELOWER_TAR_GZ] sanity_check_paths = { - 'files': ['bin/dbus-%s' % x for x in ['cleanup-sockets', 'daemon', 'launch', 'monitor', 'run-session', 'send', 'uuidgen']] + + 'files': ['bin/dbus-%s' % x for x in ['cleanup-sockets', 'daemon', 'launch', 'monitor', 'run-session', 'send', + 'uuidgen']] + ['lib/libdbus-1.%s' % x for x in ['a', SHLIB_EXT]], 'dirs': ['include', 'share'] } diff --git a/easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.1.1-intel-2015a.eb b/easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.1.1-intel-2015a.eb index 99e680c26d..389f7d8425 100644 --- a/easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.1.1-intel-2015a.eb +++ b/easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.1.1-intel-2015a.eb @@ -4,7 +4,8 @@ name = 'DFT-D3' version = '3.1.1' homepage = 'http://www.thch.uni-bonn.de/tc/index.php?section=downloads&subsection=DFT-D3&lang=english' -description = """DFT-D3 implements a dispersion correction for density functionals, Hartree-Fock and semi-empirical quantum chemical methods.""" +description = """DFT-D3 implements a dispersion correction for density functionals, Hartree-Fock and semi-empirical + quantum chemical methods.""" toolchain = {'name': 'intel', 'version': '2015a'} diff --git a/easybuild/easyconfigs/d/DMTCP/DMTCP-2.4.5.eb b/easybuild/easyconfigs/d/DMTCP/DMTCP-2.4.5.eb index 597de0792e..04e4fd7a51 100644 --- a/easybuild/easyconfigs/d/DMTCP/DMTCP-2.4.5.eb +++ b/easybuild/easyconfigs/d/DMTCP/DMTCP-2.4.5.eb @@ -24,4 +24,3 @@ sanity_check_paths = { } moduleclass = 'tools' - diff --git a/easybuild/easyconfigs/d/DMTCP/DMTCP-2.5.0-foss-2016a.eb b/easybuild/easyconfigs/d/DMTCP/DMTCP-2.5.0-foss-2016a.eb index 3f64420e2e..1687e9b44d 100644 --- a/easybuild/easyconfigs/d/DMTCP/DMTCP-2.5.0-foss-2016a.eb +++ b/easybuild/easyconfigs/d/DMTCP/DMTCP-2.5.0-foss-2016a.eb @@ -24,4 +24,3 @@ sanity_check_paths = { } moduleclass = 'tools' - diff --git a/easybuild/easyconfigs/d/drFAST/drFAST-1.0.0.0-goolf-1.4.10.eb b/easybuild/easyconfigs/d/drFAST/drFAST-1.0.0.0-goolf-1.4.10.eb index ed4f3f692d..3d7e8e50d6 100644 --- a/easybuild/easyconfigs/d/drFAST/drFAST-1.0.0.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/d/drFAST/drFAST-1.0.0.0-goolf-1.4.10.eb @@ -23,7 +23,7 @@ buildopts = ' CC="$CC"' parallel = 1 -files_to_copy = [ (['drfast'], 'bin'), "README.txt" ] +files_to_copy = [(['drfast'], 'bin'), "README.txt"] sanity_check_paths = { 'files': ["bin/drfast", "README.txt"], diff --git a/easybuild/easyconfigs/d/drFAST/drFAST-1.0.0.0-ictce-6.2.5.eb b/easybuild/easyconfigs/d/drFAST/drFAST-1.0.0.0-ictce-6.2.5.eb index 3f01a8dfb9..33794a918d 100644 --- a/easybuild/easyconfigs/d/drFAST/drFAST-1.0.0.0-ictce-6.2.5.eb +++ b/easybuild/easyconfigs/d/drFAST/drFAST-1.0.0.0-ictce-6.2.5.eb @@ -23,7 +23,7 @@ buildopts = ' CC="$CC"' parallel = 1 -files_to_copy = [ (['drfast'], 'bin'), "README.txt" ] +files_to_copy = [(['drfast'], 'bin'), "README.txt"] sanity_check_paths = { 'files': ["bin/drfast", "README.txt"], -- GitLab From 7573dd7036cbb7fd602b4a4c786a4b6c924b0413 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 8 Mar 2017 15:06:39 +0800 Subject: [PATCH 0261/1603] yet another batch of minor style fixes --- .../e/EIGENSOFT/EIGENSOFT-6.1.1-goolf-1.7.20.eb | 12 ++++++------ .../easyconfigs/e/ELPA/ELPA-2013.11-ictce-5.3.0.eb | 3 ++- .../easyconfigs/e/ELPA/ELPA-2013.11-ictce-5.5.0.eb | 3 ++- 3 files changed, 10 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/e/EIGENSOFT/EIGENSOFT-6.1.1-goolf-1.7.20.eb b/easybuild/easyconfigs/e/EIGENSOFT/EIGENSOFT-6.1.1-goolf-1.7.20.eb index 6b962c6687..a429626ec5 100644 --- a/easybuild/easyconfigs/e/EIGENSOFT/EIGENSOFT-6.1.1-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/e/EIGENSOFT/EIGENSOFT-6.1.1-goolf-1.7.20.eb @@ -11,12 +11,12 @@ name = 'EIGENSOFT' version = '6.1.1' homepage = 'http://www.hsph.harvard.edu/alkes-price/software/' -description = """The EIGENSOFT package combines functionality from our population genetics methods (Patterson et al. 2006) - and our EIGENSTRAT stratification correction method (Price et al. 2006). The EIGENSTRAT method uses principal components - analysis to explicitly model ancestry differences between cases and controls along continuous axes of variation; - the resulting correction is specific to a candidate marker’s variation in frequency across ancestral populations, - minimizing spurious associations while maximizing power to detect true associations. The EIGENSOFT package has a built-in - plotting script and supports multiple file formats and quantitative phenotypes.""" +description = """The EIGENSOFT package combines functionality from our population genetics methods (Patterson et al. + 2006) and our EIGENSTRAT stratification correction method (Price et al. 2006). The EIGENSTRAT method uses principal + components analysis to explicitly model ancestry differences between cases and controls along continuous axes of + variation; the resulting correction is specific to a candidate marker’s variation in frequency across ancestral + populations, minimizing spurious associations while maximizing power to detect true associations. The EIGENSOFT + package has a built-in plotting script and supports multiple file formats and quantitative phenotypes.""" toolchain = {'name': 'goolf', 'version': '1.7.20'} diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2013.11-ictce-5.3.0.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2013.11-ictce-5.3.0.eb index 89cd537fc7..5d29ad3201 100644 --- a/easybuild/easyconfigs/e/ELPA/ELPA-2013.11-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2013.11-ictce-5.3.0.eb @@ -23,7 +23,8 @@ sources = ['%(name)s_%(version)s.006_20140312.tar.gz'] patches = ['ELPA_fix-tests.patch'] -configopts = '--with-generic-simple --disable-shared FCFLAGS="-I$EBROOTIMKL/mkl/include/intel64/lp64 $FCFLAGS" LIBS="$LIBSCALAPACK"' +configopts = '--with-generic-simple --disable-shared FCFLAGS="-I$EBROOTIMKL/mkl/include/intel64/lp64 $FCFLAGS" ' +configopts += 'LIBS="$LIBSCALAPACK"' buildopts = ' V=1 LIBS="$LIBSCALAPACK"' start_dir = '%(name)s_%(version)s' diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2013.11-ictce-5.5.0.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2013.11-ictce-5.5.0.eb index bbbc8c56b4..b5d3e358e9 100644 --- a/easybuild/easyconfigs/e/ELPA/ELPA-2013.11-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2013.11-ictce-5.5.0.eb @@ -23,7 +23,8 @@ sources = ['%(name)s_%(version)s.006_20140312.tar.gz'] patches = ['ELPA_fix-tests.patch'] -configopts = '--with-generic-simple --disable-shared FCFLAGS="-I$EBROOTIMKL/mkl/include/intel64/lp64 $FCFLAGS" LIBS="$LIBSCALAPACK"' +configopts = '--with-generic-simple --disable-shared FCFLAGS="-I$EBROOTIMKL/mkl/include/intel64/lp64 $FCFLAGS" ' +configopts += 'LIBS="$LIBSCALAPACK"' buildopts = ' V=1 LIBS="$LIBSCALAPACK"' start_dir = '%(name)s_%(version)s' -- GitLab From b9e4dd100da43895e59db82f464b1e4c11a84ce8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 8 Mar 2017 08:43:10 +0100 Subject: [PATCH 0262/1603] adding easyconfigs: PGI-17.1-GCC-6.3.0-2.27.eb --- .../p/PGI/PGI-17.1-GCC-6.3.0-2.27.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/p/PGI/PGI-17.1-GCC-6.3.0-2.27.eb diff --git a/easybuild/easyconfigs/p/PGI/PGI-17.1-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/p/PGI/PGI-17.1-GCC-6.3.0-2.27.eb new file mode 100644 index 0000000000..6502b349fb --- /dev/null +++ b/easybuild/easyconfigs/p/PGI/PGI-17.1-GCC-6.3.0-2.27.eb @@ -0,0 +1,25 @@ +name = 'PGI' +version = '17.1' + +homepage = 'http://www.pgroup.com/' +description = "C, C++ and Fortran compilers from The Portland Group - PGI" + +toolchain = {'name': 'dummy', 'version': ''} + +sources = ['pgilinux-20%(version_major)s-%(version_major)s%(version_minor)s-x86_64.tar.gz'] +checksums = ['836f536ad8b0aac0234f7528fbd56b62'] + +gccver = '6.3.0' +binutilsver = '2.27' +versionsuffix = '-GCC-%s-%s' % (gccver, binutilsver) + +dependencies = [ + ('GCCcore', gccver), + ('binutils', binutilsver, '', ('GCCcore', gccver)), + ('numactl', '2.0.11', '', ('GCCcore', gccver)), +] + +# license file +license_file = HOME + '/licenses/pgi/license.dat' + +moduleclass = 'compiler' -- GitLab From ebd527a224dce1fa117b30a94a8f5fd5ab75a0fc Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 8 Mar 2017 16:15:51 +0800 Subject: [PATCH 0263/1603] yet another batch of minor style fixes --- easybuild/easyconfigs/f/FASTA/FASTA-36.3.5e-goolf-1.4.10.eb | 3 ++- easybuild/easyconfigs/f/FASTA/FASTA-36.3.5e-ictce-5.3.0.eb | 3 ++- easybuild/easyconfigs/f/FLEUR/FLEUR-0.26e-intel-2016a.eb | 2 +- easybuild/easyconfigs/f/Firefox/Firefox-44.0.2.eb | 6 +++--- .../easyconfigs/f/freetype/freetype-2.4.10-goolf-1.4.10.eb | 3 ++- .../easyconfigs/f/freetype/freetype-2.4.10-ictce-5.3.0.eb | 3 ++- .../easyconfigs/f/freetype/freetype-2.4.11-goolf-1.4.10.eb | 3 ++- .../easyconfigs/f/freetype/freetype-2.4.11-ictce-5.3.0.eb | 3 ++- .../easyconfigs/f/freetype/freetype-2.5.0.1-goolf-1.4.10.eb | 3 ++- .../easyconfigs/f/freetype/freetype-2.5.0.1-ictce-5.3.0.eb | 3 ++- .../easyconfigs/f/freetype/freetype-2.5.0.1-ictce-5.5.0.eb | 3 ++- .../easyconfigs/f/freetype/freetype-2.5.2-ictce-5.5.0.eb | 3 ++- .../easyconfigs/f/freetype/freetype-2.5.3-foss-2014b.eb | 3 ++- .../easyconfigs/f/freetype/freetype-2.5.3-goolf-1.7.20.eb | 3 ++- .../easyconfigs/f/freetype/freetype-2.5.3-intel-2014b.eb | 3 ++- .../easyconfigs/f/freetype/freetype-2.5.5-foss-2015a.eb | 3 ++- .../easyconfigs/f/freetype/freetype-2.5.5-intel-2015a.eb | 3 ++- .../easyconfigs/f/freetype/freetype-2.5.5-intel-2015b.eb | 3 ++- easybuild/easyconfigs/f/freetype/freetype-2.6-foss-2015a.eb | 3 ++- .../easyconfigs/f/freetype/freetype-2.6-goolf-1.7.20.eb | 3 ++- .../easyconfigs/f/freetype/freetype-2.6-intel-2015a.eb | 3 ++- .../f/freetype/freetype-2.6.1-intel-2015b-libpng-1.6.19.eb | 3 ++- .../easyconfigs/f/freetype/freetype-2.6.1-intel-2015b.eb | 3 ++- .../easyconfigs/f/freetype/freetype-2.6.2-foss-2015a.eb | 3 ++- .../easyconfigs/f/freetype/freetype-2.6.2-foss-2015b.eb | 3 ++- 25 files changed, 50 insertions(+), 27 deletions(-) diff --git a/easybuild/easyconfigs/f/FASTA/FASTA-36.3.5e-goolf-1.4.10.eb b/easybuild/easyconfigs/f/FASTA/FASTA-36.3.5e-goolf-1.4.10.eb index c1501d5c82..cb997fa593 100644 --- a/easybuild/easyconfigs/f/FASTA/FASTA-36.3.5e-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/f/FASTA/FASTA-36.3.5e-goolf-1.4.10.eb @@ -2,7 +2,8 @@ # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # # Copyright:: Copyright 2012-2013 The Cyprus Institute -# Authors:: Andreas Panteli , Thekla Loizou , George Tsouloupas +# Authors:: Andreas Panteli , Thekla Loizou , +# George Tsouloupas # License:: MIT/GPL # ## diff --git a/easybuild/easyconfigs/f/FASTA/FASTA-36.3.5e-ictce-5.3.0.eb b/easybuild/easyconfigs/f/FASTA/FASTA-36.3.5e-ictce-5.3.0.eb index 6b9a39e112..31a89c0085 100644 --- a/easybuild/easyconfigs/f/FASTA/FASTA-36.3.5e-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/f/FASTA/FASTA-36.3.5e-ictce-5.3.0.eb @@ -2,7 +2,8 @@ # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # # Copyright:: Copyright 2012-2013 The Cyprus Institute -# Authors:: Andreas Panteli , Thekla Loizou , George Tsouloupas +# Authors:: Andreas Panteli , Thekla Loizou , +# George Tsouloupas # License:: MIT/GPL # ## diff --git a/easybuild/easyconfigs/f/FLEUR/FLEUR-0.26e-intel-2016a.eb b/easybuild/easyconfigs/f/FLEUR/FLEUR-0.26e-intel-2016a.eb index d7d711211d..aee9c310da 100644 --- a/easybuild/easyconfigs/f/FLEUR/FLEUR-0.26e-intel-2016a.eb +++ b/easybuild/easyconfigs/f/FLEUR/FLEUR-0.26e-intel-2016a.eb @@ -19,7 +19,7 @@ dependencies = [ ('zlib', '1.2.8'), ('Szip', '2.1'), ('HDF5', '1.8.16'), -# ('Wannier90', '2.0.1'), # only needed if '#define wann' is added to Imakefile + # ('Wannier90', '2.0.1'), # only needed if '#define wann' is added to Imakefile ] # define hardware platform to be 'parallel intel compiler, 64 bit, use scalapack') diff --git a/easybuild/easyconfigs/f/Firefox/Firefox-44.0.2.eb b/easybuild/easyconfigs/f/Firefox/Firefox-44.0.2.eb index 59de3272db..1788c8a21a 100644 --- a/easybuild/easyconfigs/f/Firefox/Firefox-44.0.2.eb +++ b/easybuild/easyconfigs/f/Firefox/Firefox-44.0.2.eb @@ -9,9 +9,9 @@ name = 'Firefox' version = '44.0.2' homepage = 'https://www.mozilla.org/en-US/firefox/new/' -description = """Firefox is a free, open source Web browser for Windows, Linux and Mac OS X. It is based on the Mozilla code - base and offers customization options and features such as its capability to block pop-up windows, tabbed browsing, privacy - and security measures, smart searching, and RSS live bookmarks.""" +description = """Firefox is a free, open source Web browser for Windows, Linux and Mac OS X. It is based on the + Mozilla code base and offers customization options and features such as its capability to block pop-up windows, + tabbed browsing, privacy and security measures, smart searching, and RSS live bookmarks.""" toolchain = {'name': 'dummy', 'version': ''} diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.4.10-goolf-1.4.10.eb b/easybuild/easyconfigs/f/freetype/freetype-2.4.10-goolf-1.4.10.eb index 09e345ac68..7e51dd88f4 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.4.10-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.4.10-goolf-1.4.10.eb @@ -13,7 +13,8 @@ source_urls = [GNU_SAVANNAH_SOURCE] sources = [SOURCE_TAR_GZ] sanity_check_paths = { - 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], + 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, + 'lib/pkgconfig/freetype2.pc'], 'dirs': ['include/freetype2'], } diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.4.10-ictce-5.3.0.eb b/easybuild/easyconfigs/f/freetype/freetype-2.4.10-ictce-5.3.0.eb index f0c8e977f8..bcf6608413 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.4.10-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.4.10-ictce-5.3.0.eb @@ -12,7 +12,8 @@ source_urls = [GNU_SAVANNAH_SOURCE] sources = [SOURCE_TAR_GZ] sanity_check_paths = { - 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], + 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, + 'lib/pkgconfig/freetype2.pc'], 'dirs': ['include/freetype2'], } diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.4.11-goolf-1.4.10.eb b/easybuild/easyconfigs/f/freetype/freetype-2.4.11-goolf-1.4.10.eb index dafae024b0..916f1302f2 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.4.11-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.4.11-goolf-1.4.10.eb @@ -13,7 +13,8 @@ source_urls = [GNU_SAVANNAH_SOURCE] sources = [SOURCE_TAR_GZ] sanity_check_paths = { - 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], + 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, + 'lib/pkgconfig/freetype2.pc'], 'dirs': ['include/freetype2'], } diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.4.11-ictce-5.3.0.eb b/easybuild/easyconfigs/f/freetype/freetype-2.4.11-ictce-5.3.0.eb index 93ed64ef31..26eaffc5f6 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.4.11-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.4.11-ictce-5.3.0.eb @@ -12,7 +12,8 @@ source_urls = ['http://download.savannah.gnu.org/releases/freetype/'] sources = [SOURCE_TAR_GZ] sanity_check_paths = { - 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], + 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, + 'lib/pkgconfig/freetype2.pc'], 'dirs': ['include/freetype2'], } diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.5.0.1-goolf-1.4.10.eb b/easybuild/easyconfigs/f/freetype/freetype-2.5.0.1-goolf-1.4.10.eb index c7a87aa9ac..cbbe1daafc 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.5.0.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.5.0.1-goolf-1.4.10.eb @@ -14,7 +14,8 @@ sources = [SOURCE_TAR_GZ] dependencies = [('libpng', '1.6.6')] sanity_check_paths = { - 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], + 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, + 'lib/pkgconfig/freetype2.pc'], 'dirs': ['include/freetype2'], } diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.5.0.1-ictce-5.3.0.eb b/easybuild/easyconfigs/f/freetype/freetype-2.5.0.1-ictce-5.3.0.eb index 5fa7fbc89e..a5e70027fa 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.5.0.1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.5.0.1-ictce-5.3.0.eb @@ -14,7 +14,8 @@ sources = [SOURCE_TAR_GZ] dependencies = [('libpng', '1.6.6')] sanity_check_paths = { - 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], + 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, + 'lib/pkgconfig/freetype2.pc'], 'dirs': ['include/freetype2'], } diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.5.0.1-ictce-5.5.0.eb b/easybuild/easyconfigs/f/freetype/freetype-2.5.0.1-ictce-5.5.0.eb index 6af71f85ba..8fa382b0ca 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.5.0.1-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.5.0.1-ictce-5.5.0.eb @@ -14,7 +14,8 @@ sources = [SOURCE_TAR_GZ] dependencies = [('libpng', '1.6.6')] sanity_check_paths = { - 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], + 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, + 'lib/pkgconfig/freetype2.pc'], 'dirs': ['include/freetype2'], } diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.5.2-ictce-5.5.0.eb b/easybuild/easyconfigs/f/freetype/freetype-2.5.2-ictce-5.5.0.eb index 7424371c29..0571a145ad 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.5.2-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.5.2-ictce-5.5.0.eb @@ -14,7 +14,8 @@ sources = [SOURCE_TAR_GZ] dependencies = [('libpng', '1.6.9')] sanity_check_paths = { - 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], + 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, + 'lib/pkgconfig/freetype2.pc'], 'dirs': ['include/freetype2'], } diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.5.3-foss-2014b.eb b/easybuild/easyconfigs/f/freetype/freetype-2.5.3-foss-2014b.eb index 1840f18b99..cea107f292 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.5.3-foss-2014b.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.5.3-foss-2014b.eb @@ -14,7 +14,8 @@ sources = [SOURCE_TAR_GZ] dependencies = [('libpng', '1.6.12')] sanity_check_paths = { - 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], + 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, + 'lib/pkgconfig/freetype2.pc'], 'dirs': ['include/freetype2'], } diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.5.3-goolf-1.7.20.eb b/easybuild/easyconfigs/f/freetype/freetype-2.5.3-goolf-1.7.20.eb index cf4ca6186c..9b0aae30b7 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.5.3-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.5.3-goolf-1.7.20.eb @@ -14,7 +14,8 @@ sources = [SOURCE_TAR_GZ] dependencies = [('libpng', '1.6.12')] sanity_check_paths = { - 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], + 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, + 'lib/pkgconfig/freetype2.pc'], 'dirs': ['include/freetype2'], } diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.5.3-intel-2014b.eb b/easybuild/easyconfigs/f/freetype/freetype-2.5.3-intel-2014b.eb index 68312d108d..45d6dc8e93 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.5.3-intel-2014b.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.5.3-intel-2014b.eb @@ -14,7 +14,8 @@ sources = [SOURCE_TAR_GZ] dependencies = [('libpng', '1.6.12')] sanity_check_paths = { - 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], + 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, + 'lib/pkgconfig/freetype2.pc'], 'dirs': ['include/freetype2'], } diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.5.5-foss-2015a.eb b/easybuild/easyconfigs/f/freetype/freetype-2.5.5-foss-2015a.eb index e9f0fd7c95..c9b6e770b4 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.5.5-foss-2015a.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.5.5-foss-2015a.eb @@ -14,7 +14,8 @@ sources = [SOURCE_TAR_GZ] dependencies = [('libpng', '1.6.16')] sanity_check_paths = { - 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], + 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, + 'lib/pkgconfig/freetype2.pc'], 'dirs': ['include/freetype2'], } diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.5.5-intel-2015a.eb b/easybuild/easyconfigs/f/freetype/freetype-2.5.5-intel-2015a.eb index 5eb7f91b58..07f4f8160c 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.5.5-intel-2015a.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.5.5-intel-2015a.eb @@ -14,7 +14,8 @@ sources = [SOURCE_TAR_GZ] dependencies = [('libpng', '1.6.16')] sanity_check_paths = { - 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], + 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, + 'lib/pkgconfig/freetype2.pc'], 'dirs': ['include/freetype2'], } diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.5.5-intel-2015b.eb b/easybuild/easyconfigs/f/freetype/freetype-2.5.5-intel-2015b.eb index ca24a618dc..44080cb0f8 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.5.5-intel-2015b.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.5.5-intel-2015b.eb @@ -14,7 +14,8 @@ sources = [SOURCE_TAR_GZ] dependencies = [('libpng', '1.6.16')] sanity_check_paths = { - 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], + 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, + 'lib/pkgconfig/freetype2.pc'], 'dirs': ['include/freetype2'], } diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.6-foss-2015a.eb b/easybuild/easyconfigs/f/freetype/freetype-2.6-foss-2015a.eb index 8978812458..7cfa18b2f4 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.6-foss-2015a.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.6-foss-2015a.eb @@ -14,7 +14,8 @@ sources = [SOURCE_TAR_GZ] dependencies = [('libpng', '1.6.17')] sanity_check_paths = { - 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], + 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, + 'lib/pkgconfig/freetype2.pc'], 'dirs': ['include/freetype2'], } diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.6-goolf-1.7.20.eb b/easybuild/easyconfigs/f/freetype/freetype-2.6-goolf-1.7.20.eb index af7228f4f5..78c7fb98d6 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.6-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.6-goolf-1.7.20.eb @@ -14,7 +14,8 @@ sources = [SOURCE_TAR_GZ] dependencies = [('libpng', '1.6.17')] sanity_check_paths = { - 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], + 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, + 'lib/pkgconfig/freetype2.pc'], 'dirs': ['include/freetype2'], } diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.6-intel-2015a.eb b/easybuild/easyconfigs/f/freetype/freetype-2.6-intel-2015a.eb index 316e040e08..4cf88e23a7 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.6-intel-2015a.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.6-intel-2015a.eb @@ -14,7 +14,8 @@ sources = [SOURCE_TAR_GZ] dependencies = [('libpng', '1.6.17')] sanity_check_paths = { - 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], + 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, + 'lib/pkgconfig/freetype2.pc'], 'dirs': ['include/freetype2'], } diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.6.1-intel-2015b-libpng-1.6.19.eb b/easybuild/easyconfigs/f/freetype/freetype-2.6.1-intel-2015b-libpng-1.6.19.eb index 32b12425a8..8405a0ec93 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.6.1-intel-2015b-libpng-1.6.19.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.6.1-intel-2015b-libpng-1.6.19.eb @@ -16,7 +16,8 @@ versionsuffix = '-libpng-%s' % libpngver dependencies = [('libpng', libpngver)] sanity_check_paths = { - 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], + 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, + 'lib/pkgconfig/freetype2.pc'], 'dirs': ['include/freetype2'], } diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.6.1-intel-2015b.eb b/easybuild/easyconfigs/f/freetype/freetype-2.6.1-intel-2015b.eb index 0913227caf..9c9d2b2e08 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.6.1-intel-2015b.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.6.1-intel-2015b.eb @@ -14,7 +14,8 @@ sources = [SOURCE_TAR_GZ] dependencies = [('libpng', '1.6.18')] sanity_check_paths = { - 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], + 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, + 'lib/pkgconfig/freetype2.pc'], 'dirs': ['include/freetype2'], } diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.6.2-foss-2015a.eb b/easybuild/easyconfigs/f/freetype/freetype-2.6.2-foss-2015a.eb index 32c4b9ab5c..bbfd2a2508 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.6.2-foss-2015a.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.6.2-foss-2015a.eb @@ -14,7 +14,8 @@ sources = [SOURCE_TAR_GZ] dependencies = [('libpng', '1.6.20')] sanity_check_paths = { - 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], + 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, + 'lib/pkgconfig/freetype2.pc'], 'dirs': ['include/freetype2'], } diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.6.2-foss-2015b.eb b/easybuild/easyconfigs/f/freetype/freetype-2.6.2-foss-2015b.eb index 54449d2405..912f826139 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.6.2-foss-2015b.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.6.2-foss-2015b.eb @@ -14,7 +14,8 @@ sources = [SOURCE_TAR_GZ] dependencies = [('libpng', '1.6.21')] sanity_check_paths = { - 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], + 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, + 'lib/pkgconfig/freetype2.pc'], 'dirs': ['include/freetype2'], } -- GitLab From 16127fff4d6a6db5774b196d529850bdf34fc427 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 8 Mar 2017 09:21:20 +0100 Subject: [PATCH 0264/1603] revert back to using shipped Boost for SPAdes 3.10.1, since Boost version difference is too big --- easybuild/easyconfigs/s/SPAdes/SPAdes-3.10.1-foss-2016b.eb | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/s/SPAdes/SPAdes-3.10.1-foss-2016b.eb b/easybuild/easyconfigs/s/SPAdes/SPAdes-3.10.1-foss-2016b.eb index c4ecdeaede..6e5c9aeb32 100644 --- a/easybuild/easyconfigs/s/SPAdes/SPAdes-3.10.1-foss-2016b.eb +++ b/easybuild/easyconfigs/s/SPAdes/SPAdes-3.10.1-foss-2016b.eb @@ -20,10 +20,7 @@ toolchain = {'name': 'foss', 'version': '2016b'} source_urls = ['http://cab.spbu.ru/files/release%(version)s'] sources = [SOURCE_TAR_GZ] -builddependencies = [ - ('CMake', '3.7.2'), - ('Boost', '1.63.0', '-Python-2.7.12'), -] +builddependencies = [('CMake', '3.7.2')] dependencies = [ ('zlib', '1.2.8'), -- GitLab From fc7300777ea6b8d9938c626e0f3642a3f7e4119b Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 8 Mar 2017 16:45:11 +0800 Subject: [PATCH 0265/1603] yet another batch of minor style fixes --- easybuild/easyconfigs/g/GATK/GATK-3.3-0-Java-1.7.0_21.eb | 3 ++- easybuild/easyconfigs/g/GATK/GATK-3.3-0-Java-1.7.0_80.eb | 3 ++- easybuild/easyconfigs/g/GATK/GATK-3.3-0-Java-1.8.0_66.eb | 3 ++- easybuild/easyconfigs/g/GATK/GATK-3.5-Java-1.8.0_66.eb | 3 ++- easybuild/easyconfigs/g/GATK/GATK-3.5-Java-1.8.0_74.eb | 3 ++- easybuild/easyconfigs/g/GATK/GATK-3.6-Java-1.8.0_92.eb | 3 ++- easybuild/easyconfigs/g/GATK/GATK-3.7-Java-1.8.0_112.eb | 3 ++- easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.3.eb | 3 ++- easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.0.eb | 3 ++- easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.1.eb | 3 ++- easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.2.eb | 3 ++- easybuild/easyconfigs/g/GLib/GLib-2.48.0-foss-2016a.eb | 3 ++- easybuild/easyconfigs/g/GLib/GLib-2.48.0-intel-2016a.eb | 3 ++- easybuild/easyconfigs/g/GLib/GLib-2.49.5-foss-2016b.eb | 3 ++- easybuild/easyconfigs/g/GLib/GLib-2.49.5-intel-2016b.eb | 3 ++- easybuild/easyconfigs/g/GMP/GMP-6.0.0a-foss-2015b.eb | 1 - .../g/GROMACS/GROMACS-4.6.7-CrayGNU-2015.06-mpi.eb | 4 ++-- .../g/GROMACS/GROMACS-4.6.7-CrayGNU-2015.11-mpi.eb | 4 ++-- .../g/GROMACS/GROMACS-4.6.7-CrayIntel-2015.11-mpi.eb | 4 ++-- .../easyconfigs/g/GROMACS/GROMACS-5.1.2-goolf-1.7.20-mt.eb | 4 ++-- .../easyconfigs/g/Ghostscript/Ghostscript-9.19-intel-2016a.eb | 3 ++- .../easyconfigs/g/Ghostscript/Ghostscript-9.19-intel-2016b.eb | 3 ++- easybuild/easyconfigs/g/Grep/Grep-2.21-GCC-4.9.2.eb | 3 ++- .../g/gensim/gensim-0.13.2-foss-2016a-Python-2.7.11.eb | 2 +- easybuild/easyconfigs/g/git-lfs/git-lfs-1.1.1.eb | 4 ++-- easybuild/easyconfigs/g/gompi/gompi-2016.07.eb | 4 ++-- .../easyconfigs/g/gtkglext/gtkglext-1.2.0-intel-2015b.eb | 3 ++- 27 files changed, 51 insertions(+), 33 deletions(-) diff --git a/easybuild/easyconfigs/g/GATK/GATK-3.3-0-Java-1.7.0_21.eb b/easybuild/easyconfigs/g/GATK/GATK-3.3-0-Java-1.7.0_21.eb index 69dadef3c7..bae4a90d91 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-3.3-0-Java-1.7.0_21.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-3.3-0-Java-1.7.0_21.eb @@ -2,7 +2,8 @@ # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # # Copyright:: Copyright 2012-2013 Cyprus Institute / CaSToRC, University of Luxembourg / LCSB -# Authors:: George Tsouloupas , Fotis Georgatos , Kenneth Hoste (UGent) +# Authors:: George Tsouloupas , Fotis Georgatos , +# Kenneth Hoste (UGent) # License:: MIT/GPL # $Id$ # diff --git a/easybuild/easyconfigs/g/GATK/GATK-3.3-0-Java-1.7.0_80.eb b/easybuild/easyconfigs/g/GATK/GATK-3.3-0-Java-1.7.0_80.eb index c8e83f1af6..88a772e2f8 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-3.3-0-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-3.3-0-Java-1.7.0_80.eb @@ -2,7 +2,8 @@ # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # # Copyright:: Copyright 2012-2013 Cyprus Institute / CaSToRC, University of Luxembourg / LCSB -# Authors:: George Tsouloupas , Fotis Georgatos , Kenneth Hoste (UGent) +# Authors:: George Tsouloupas , Fotis Georgatos , +# Kenneth Hoste (UGent) # License:: MIT/GPL # $Id$ # diff --git a/easybuild/easyconfigs/g/GATK/GATK-3.3-0-Java-1.8.0_66.eb b/easybuild/easyconfigs/g/GATK/GATK-3.3-0-Java-1.8.0_66.eb index e60f317150..d0d5a239b6 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-3.3-0-Java-1.8.0_66.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-3.3-0-Java-1.8.0_66.eb @@ -2,7 +2,8 @@ # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # # Copyright:: Copyright 2012-2013 Cyprus Institute / CaSToRC, University of Luxembourg / LCSB -# Authors:: George Tsouloupas , Fotis Georgatos , Kenneth Hoste (UGent) +# Authors:: George Tsouloupas , Fotis Georgatos , +# Kenneth Hoste (UGent) # License:: MIT/GPL # $Id$ # diff --git a/easybuild/easyconfigs/g/GATK/GATK-3.5-Java-1.8.0_66.eb b/easybuild/easyconfigs/g/GATK/GATK-3.5-Java-1.8.0_66.eb index 47af207c6f..b6d45b10ea 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-3.5-Java-1.8.0_66.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-3.5-Java-1.8.0_66.eb @@ -2,7 +2,8 @@ # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # # Copyright:: Copyright 2012-2013 Cyprus Institute / CaSToRC, University of Luxembourg / LCSB -# Authors:: George Tsouloupas , Fotis Georgatos , Kenneth Hoste (UGent) +# Authors:: George Tsouloupas , Fotis Georgatos , +# Kenneth Hoste (UGent) # License:: MIT/GPL # $Id$ # diff --git a/easybuild/easyconfigs/g/GATK/GATK-3.5-Java-1.8.0_74.eb b/easybuild/easyconfigs/g/GATK/GATK-3.5-Java-1.8.0_74.eb index 9faee44d8b..935f73ec90 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-3.5-Java-1.8.0_74.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-3.5-Java-1.8.0_74.eb @@ -2,7 +2,8 @@ # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # # Copyright:: Copyright 2012-2013 Cyprus Institute / CaSToRC, University of Luxembourg / LCSB -# Authors:: George Tsouloupas , Fotis Georgatos , Kenneth Hoste (UGent) +# Authors:: George Tsouloupas , Fotis Georgatos , +# Kenneth Hoste (UGent) # License:: MIT/GPL # $Id$ # diff --git a/easybuild/easyconfigs/g/GATK/GATK-3.6-Java-1.8.0_92.eb b/easybuild/easyconfigs/g/GATK/GATK-3.6-Java-1.8.0_92.eb index fa068137af..6ed0f40863 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-3.6-Java-1.8.0_92.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-3.6-Java-1.8.0_92.eb @@ -2,7 +2,8 @@ # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # # Copyright:: Copyright 2012-2013 Cyprus Institute / CaSToRC, University of Luxembourg / LCSB -# Authors:: George Tsouloupas , Fotis Georgatos , Kenneth Hoste (UGent) +# Authors:: George Tsouloupas , Fotis Georgatos , +# Kenneth Hoste (UGent) # License:: MIT/GPL # $Id$ # diff --git a/easybuild/easyconfigs/g/GATK/GATK-3.7-Java-1.8.0_112.eb b/easybuild/easyconfigs/g/GATK/GATK-3.7-Java-1.8.0_112.eb index 9d0b198d0f..afc148cb14 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-3.7-Java-1.8.0_112.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-3.7-Java-1.8.0_112.eb @@ -2,7 +2,8 @@ # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # # Copyright:: Copyright 2012-2013 Cyprus Institute / CaSToRC, University of Luxembourg / LCSB -# Authors:: George Tsouloupas , Fotis Georgatos , Kenneth Hoste (UGent) +# Authors:: George Tsouloupas , Fotis Georgatos , +# Kenneth Hoste (UGent) # License:: MIT/GPL # $Id$ # diff --git a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.3.eb b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.3.eb index 4cfb618383..e5810437c4 100644 --- a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.3.eb +++ b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.3.eb @@ -103,7 +103,8 @@ full_sanity_check = True eggname = 'gc3pie-%%(version)s-py%s.egg' % pyver sanity_check_paths = { 'files': ['bin/gc3utils', - ('lib/python%s/site-packages/%s' % (pyver, eggname), 'lib64/python%s/site-packages/%s' % (pyver, eggname))], + ('lib/python%s/site-packages/%s' % (pyver, eggname), + 'lib64/python%s/site-packages/%s' % (pyver, eggname))], 'dirs': [], } diff --git a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.0.eb b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.0.eb index 70eb5b0a10..0a33e2b925 100644 --- a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.0.eb +++ b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.0.eb @@ -103,7 +103,8 @@ full_sanity_check = True eggname = 'gc3pie-%%(version)s-py%s.egg' % pyver sanity_check_paths = { 'files': ['bin/gc3utils', - ('lib/python%s/site-packages/%s' % (pyver, eggname), 'lib64/python%s/site-packages/%s' % (pyver, eggname))], + ('lib/python%s/site-packages/%s' % (pyver, eggname), + 'lib64/python%s/site-packages/%s' % (pyver, eggname))], 'dirs': [], } diff --git a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.1.eb b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.1.eb index 477760c3c0..49772e1a73 100644 --- a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.1.eb +++ b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.1.eb @@ -103,7 +103,8 @@ full_sanity_check = True eggname = 'gc3pie-%%(version)s-py%s.egg' % pyver sanity_check_paths = { 'files': ['bin/gc3utils', - ('lib/python%s/site-packages/%s' % (pyver, eggname), 'lib64/python%s/site-packages/%s' % (pyver, eggname))], + ('lib/python%s/site-packages/%s' % (pyver, eggname), + 'lib64/python%s/site-packages/%s' % (pyver, eggname))], 'dirs': [], } diff --git a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.2.eb b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.2.eb index d952c14671..98f0d96369 100644 --- a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.2.eb +++ b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.2.eb @@ -103,7 +103,8 @@ full_sanity_check = True eggname = 'gc3pie-%%(version)s-py%s.egg' % pyver sanity_check_paths = { 'files': ['bin/gc3utils', - ('lib/python%s/site-packages/%s' % (pyver, eggname), 'lib64/python%s/site-packages/%s' % (pyver, eggname))], + ('lib/python%s/site-packages/%s' % (pyver, eggname), + 'lib64/python%s/site-packages/%s' % (pyver, eggname))], 'dirs': [], } diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.48.0-foss-2016a.eb b/easybuild/easyconfigs/g/GLib/GLib-2.48.0-foss-2016a.eb index 73ce1be6d6..fecad61365 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.48.0-foss-2016a.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.48.0-foss-2016a.eb @@ -21,7 +21,8 @@ dependencies = [ builddependencies = [('Python', '2.7.11')] -configopts = "--disable-maintainer-mode --disable-silent-rules --disable-libelf --enable-static --enable-shared --disable-systemtap" +configopts = "--disable-maintainer-mode --disable-silent-rules --disable-libelf --enable-static --enable-shared " +configopts += "--disable-systemtap" postinstallcmds = ["sed -i -e 's|#!.*python|#!/usr/bin/env python|' %(installdir)s/bin/*"] diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.48.0-intel-2016a.eb b/easybuild/easyconfigs/g/GLib/GLib-2.48.0-intel-2016a.eb index 918c5aec06..b29b2e7ddf 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.48.0-intel-2016a.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.48.0-intel-2016a.eb @@ -21,7 +21,8 @@ dependencies = [ builddependencies = [('Python', '2.7.11')] -configopts = "--disable-maintainer-mode --disable-silent-rules --disable-libelf --enable-static --enable-shared --disable-systemtap" +configopts = "--disable-maintainer-mode --disable-silent-rules --disable-libelf --enable-static --enable-shared " +configopts += "--disable-systemtap" postinstallcmds = ["sed -i -e 's|#!.*python|#!/usr/bin/env python|' %(installdir)s/bin/*"] diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.49.5-foss-2016b.eb b/easybuild/easyconfigs/g/GLib/GLib-2.49.5-foss-2016b.eb index 3e8dd8b2df..ffe44a8cda 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.49.5-foss-2016b.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.49.5-foss-2016b.eb @@ -21,7 +21,8 @@ dependencies = [ builddependencies = [('Python', '2.7.12')] -configopts = "--disable-maintainer-mode --disable-silent-rules --disable-libelf --enable-static --enable-shared --disable-systemtap" +configopts = "--disable-maintainer-mode --disable-silent-rules --disable-libelf --enable-static --enable-shared " +configopts += "--disable-systemtap" postinstallcmds = ["sed -i -e 's|#!.*python|#!/usr/bin/env python|' %(installdir)s/bin/*"] diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.49.5-intel-2016b.eb b/easybuild/easyconfigs/g/GLib/GLib-2.49.5-intel-2016b.eb index cabfe78d32..ba98f92742 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.49.5-intel-2016b.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.49.5-intel-2016b.eb @@ -21,7 +21,8 @@ dependencies = [ builddependencies = [('Python', '2.7.12')] -configopts = "--disable-maintainer-mode --disable-silent-rules --disable-libelf --enable-static --enable-shared --disable-systemtap" +configopts = "--disable-maintainer-mode --disable-silent-rules --disable-libelf --enable-static --enable-shared " +configopts += "--disable-systemtap" postinstallcmds = ["sed -i -e 's|#!.*python|#!/usr/bin/env python|' %(installdir)s/bin/*"] diff --git a/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-foss-2015b.eb b/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-foss-2015b.eb index ab0d6b9ba8..e822e11f35 100644 --- a/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-foss-2015b.eb +++ b/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-foss-2015b.eb @@ -24,4 +24,3 @@ sanity_check_paths = { } moduleclass = 'math' - diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-2015.06-mpi.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-2015.06-mpi.eb index 7fae7e2b3f..adf36de398 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-2015.06-mpi.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-2015.06-mpi.eb @@ -31,11 +31,11 @@ sources = [ 'regressiontests-%(version)s.tar.gz', ] -preconfigopts = "export CMAKE_LIBRARY_PATH=$CMAKE_LIBRARY_PATH:${EBROOTFFTW}/lib && " +preconfigopts = "export CMAKE_LIBRARY_PATH=$CMAKE_LIBRARY_PATH:${EBROOTFFTW}/lib && " preconfigopts += "export CMAKE_INCLUDE_PATH=$CMAKE_INCLUDE_PATH:${EBROOTFFTW}/include && " dependencies = [ - ('fftw/3.3.4.3', EXTERNAL_MODULE), + ('fftw/3.3.4.3', EXTERNAL_MODULE), ] builddependencies = [('CMake', '3.2.2')] diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-2015.11-mpi.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-2015.11-mpi.eb index 83b2732fb5..f52ab6e342 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-2015.11-mpi.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-2015.11-mpi.eb @@ -31,11 +31,11 @@ sources = [ 'regressiontests-%(version)s.tar.gz', ] -preconfigopts = "export CMAKE_LIBRARY_PATH=$CMAKE_LIBRARY_PATH:$EBROOTFFTW/lib && " +preconfigopts = "export CMAKE_LIBRARY_PATH=$CMAKE_LIBRARY_PATH:$EBROOTFFTW/lib && " preconfigopts += "export CMAKE_INCLUDE_PATH=$CMAKE_INCLUDE_PATH:$EBROOTFFTW/include && " dependencies = [ - ('fftw/3.3.4.5', EXTERNAL_MODULE), + ('fftw/3.3.4.5', EXTERNAL_MODULE), ] builddependencies = [('CMake', '3.2.2')] diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayIntel-2015.11-mpi.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayIntel-2015.11-mpi.eb index 350a3d6cfa..3f046b2129 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayIntel-2015.11-mpi.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayIntel-2015.11-mpi.eb @@ -31,11 +31,11 @@ sources = [ 'regressiontests-%(version)s.tar.gz', ] -preconfigopts = "export CMAKE_LIBRARY_PATH=$CMAKE_LIBRARY_PATH:$EBROOTFFTW/lib && " +preconfigopts = "export CMAKE_LIBRARY_PATH=$CMAKE_LIBRARY_PATH:$EBROOTFFTW/lib && " preconfigopts += "export CMAKE_INCLUDE_PATH=$CMAKE_INCLUDE_PATH:$EBROOTFFTW/include && " dependencies = [ - ('fftw/3.3.4.5', EXTERNAL_MODULE), + ('fftw/3.3.4.5', EXTERNAL_MODULE), ] builddependencies = [('CMake', '3.2.2')] diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-5.1.2-goolf-1.7.20-mt.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.1.2-goolf-1.7.20-mt.eb index f8d1e53e32..5f20cd92b4 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-5.1.2-goolf-1.7.20-mt.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.1.2-goolf-1.7.20-mt.eb @@ -28,8 +28,8 @@ source_urls = [ sources = [ SOURCELOWER_TAR_GZ, -# seems to have disappeared? -# 'regressiontests-5.0.2.tar.gz', + # seems to have disappeared? + # 'regressiontests-5.0.2.tar.gz', ] builddependencies = [ diff --git a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.19-intel-2016a.eb b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.19-intel-2016a.eb index fa06ee75b2..dd5cd622b8 100644 --- a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.19-intel-2016a.eb +++ b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.19-intel-2016a.eb @@ -10,7 +10,8 @@ description = """Ghostscript is a versatile processor for PostScript data with t toolchain = {'name': 'intel', 'version': '2016a'} toolchainopts = {'pic': True} -source_urls = ["https://github.com/ArtifexSoftware/ghostpdl-downloads/releases/download/gs%(version_major)s%(version_minor)s/"] +source_subdir = 'gs%(version_major)s%(version_minor)s' +source_urls = ["https://github.com/ArtifexSoftware/ghostpdl-downloads/releases/download/%s/" % source_subdir] sources = ["ghostpdl-%(version)s.tar.bz2"] dependencies = [ diff --git a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.19-intel-2016b.eb b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.19-intel-2016b.eb index 8612f2848b..59430c9acb 100644 --- a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.19-intel-2016b.eb +++ b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.19-intel-2016b.eb @@ -10,7 +10,8 @@ description = """Ghostscript is a versatile processor for PostScript data with t toolchain = {'name': 'intel', 'version': '2016b'} toolchainopts = {'pic': True} -source_urls = ["https://github.com/ArtifexSoftware/ghostpdl-downloads/releases/download/gs%(version_major)s%(version_minor)s/"] +source_subdir = 'gs%(version_major)s%(version_minor)s' +source_urls = ["https://github.com/ArtifexSoftware/ghostpdl-downloads/releases/download/%s/" % source_subdir] sources = ["ghostpdl-%(version)s.tar.bz2"] dependencies = [ diff --git a/easybuild/easyconfigs/g/Grep/Grep-2.21-GCC-4.9.2.eb b/easybuild/easyconfigs/g/Grep/Grep-2.21-GCC-4.9.2.eb index 43c5a459fa..af08c394ee 100644 --- a/easybuild/easyconfigs/g/Grep/Grep-2.21-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/g/Grep/Grep-2.21-GCC-4.9.2.eb @@ -4,7 +4,8 @@ name = 'Grep' version = '2.21' homepage = 'http://www.gnu.org/software/grep/' -description = """The grep command searches one or more input files for lines containing a match to a specified pattern. By default, grep prints the matching lines.""" +description = """The grep command searches one or more input files for lines containing a match to a specified pattern. + By default, grep prints the matching lines.""" toolchain = {'name': 'GCC', 'version': '4.9.2'} diff --git a/easybuild/easyconfigs/g/gensim/gensim-0.13.2-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/g/gensim/gensim-0.13.2-foss-2016a-Python-2.7.11.eb index 991e6da6fa..fe0e24229f 100644 --- a/easybuild/easyconfigs/g/gensim/gensim-0.13.2-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/g/gensim/gensim-0.13.2-foss-2016a-Python-2.7.11.eb @@ -46,4 +46,4 @@ sanity_check_paths = { modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} -moduleclass = 'lib' \ No newline at end of file +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/g/git-lfs/git-lfs-1.1.1.eb b/easybuild/easyconfigs/g/git-lfs/git-lfs-1.1.1.eb index bd4f6deeb9..c16d2b51eb 100755 --- a/easybuild/easyconfigs/g/git-lfs/git-lfs-1.1.1.eb +++ b/easybuild/easyconfigs/g/git-lfs/git-lfs-1.1.1.eb @@ -25,8 +25,8 @@ sanity_check_paths = { # add the installation dir to PATH modextrapaths = { - 'PATH': '', - } + 'PATH': '', +} # remove exec permission for the provided installation script postinstallcmds = ["chmod og-x %(installdir)s/install.sh"] diff --git a/easybuild/easyconfigs/g/gompi/gompi-2016.07.eb b/easybuild/easyconfigs/g/gompi/gompi-2016.07.eb index 5eca4152c8..eec2b277ee 100644 --- a/easybuild/easyconfigs/g/gompi/gompi-2016.07.eb +++ b/easybuild/easyconfigs/g/gompi/gompi-2016.07.eb @@ -15,8 +15,8 @@ gccbinver = '%s-%s' % (gccver, binutilsver) # compiler toolchain dependencies dependencies = [ - ('GCC', gccbinver), # includes both GCC and binutils - ('OpenMPI', '1.10.3', '', ('GCC', gccbinver)), + ('GCC', gccbinver), # includes both GCC and binutils + ('OpenMPI', '1.10.3', '', ('GCC', gccbinver)), ] moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/g/gtkglext/gtkglext-1.2.0-intel-2015b.eb b/easybuild/easyconfigs/g/gtkglext/gtkglext-1.2.0-intel-2015b.eb index a0f2ba3078..2f14396e13 100644 --- a/easybuild/easyconfigs/g/gtkglext/gtkglext-1.2.0-intel-2015b.eb +++ b/easybuild/easyconfigs/g/gtkglext/gtkglext-1.2.0-intel-2015b.eb @@ -21,7 +21,8 @@ dependencies = [ ] sanity_check_paths = { - 'files': ['lib/gtkglext-1.0/include/gdkglext-config.h', 'lib/libgdkglext-x11-1.0.a', 'lib/libgdkglext-x11-1.0.%s' % SHLIB_EXT, + 'files': ['lib/gtkglext-1.0/include/gdkglext-config.h', 'lib/libgdkglext-x11-1.0.a', + 'lib/libgdkglext-x11-1.0.%s' % SHLIB_EXT, 'lib/libgtkglext-x11-1.0.a', 'lib/libgtkglext-x11-1.0.%s' % SHLIB_EXT], 'dirs': ['include/gtkglext-1.0/gdk', 'include/gtkglext-1.0/gtk', 'lib/pkgconfig'], } -- GitLab From 068f2709b301b502210412079179f44b4f9865b5 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 8 Mar 2017 17:02:26 +0800 Subject: [PATCH 0266/1603] yet another style fix --- easybuild/easyconfigs/d/DBus/DBus-1.10.12-intel-2016b.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/d/DBus/DBus-1.10.12-intel-2016b.eb b/easybuild/easyconfigs/d/DBus/DBus-1.10.12-intel-2016b.eb index c041d6e2aa..2a15cb846c 100644 --- a/easybuild/easyconfigs/d/DBus/DBus-1.10.12-intel-2016b.eb +++ b/easybuild/easyconfigs/d/DBus/DBus-1.10.12-intel-2016b.eb @@ -16,8 +16,8 @@ source_urls = ['http://dbus.freedesktop.org/releases/dbus'] sources = [SOURCELOWER_TAR_GZ] sanity_check_paths = { - 'files': ['bin/dbus-%s' % x for x in ['cleanup-sockets', 'daemon', 'launch', 'monitor', 'run-session', 'send', - 'uuidgen']] + + 'files': ['bin/dbus-%s' % x for x in ['cleanup-sockets', 'daemon', 'launch', 'monitor', 'run-session', + 'send', 'uuidgen']] + ['lib/libdbus-1.%s' % x for x in ['a', SHLIB_EXT]], 'dirs': ['include', 'share'] } -- GitLab From c3c6264ef9172d1aab091bb2ba6c0bd42b16ac07 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 8 Mar 2017 17:12:07 +0800 Subject: [PATCH 0267/1603] yet another style fix --- easybuild/easyconfigs/e/ELPA/ELPA-2013.11-ictce-5.3.0.eb | 4 ++-- easybuild/easyconfigs/e/ELPA/ELPA-2013.11-ictce-5.5.0.eb | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2013.11-ictce-5.3.0.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2013.11-ictce-5.3.0.eb index 5d29ad3201..c9a900612f 100644 --- a/easybuild/easyconfigs/e/ELPA/ELPA-2013.11-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2013.11-ictce-5.3.0.eb @@ -23,8 +23,8 @@ sources = ['%(name)s_%(version)s.006_20140312.tar.gz'] patches = ['ELPA_fix-tests.patch'] -configopts = '--with-generic-simple --disable-shared FCFLAGS="-I$EBROOTIMKL/mkl/include/intel64/lp64 $FCFLAGS" ' -configopts += 'LIBS="$LIBSCALAPACK"' +configopts = '--with-generic-simple --disable-shared ' +configopts += 'FCFLAGS="-I$EBROOTIMKL/mkl/include/intel64/lp64 $FCFLAGS" LIBS="$LIBSCALAPACK"' buildopts = ' V=1 LIBS="$LIBSCALAPACK"' start_dir = '%(name)s_%(version)s' diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2013.11-ictce-5.5.0.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2013.11-ictce-5.5.0.eb index b5d3e358e9..9783862078 100644 --- a/easybuild/easyconfigs/e/ELPA/ELPA-2013.11-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2013.11-ictce-5.5.0.eb @@ -23,8 +23,8 @@ sources = ['%(name)s_%(version)s.006_20140312.tar.gz'] patches = ['ELPA_fix-tests.patch'] -configopts = '--with-generic-simple --disable-shared FCFLAGS="-I$EBROOTIMKL/mkl/include/intel64/lp64 $FCFLAGS" ' -configopts += 'LIBS="$LIBSCALAPACK"' +configopts = '--with-generic-simple --disable-shared ' +configopts += 'FCFLAGS="-I$EBROOTIMKL/mkl/include/intel64/lp64 $FCFLAGS" LIBS="$LIBSCALAPACK"' buildopts = ' V=1 LIBS="$LIBSCALAPACK"' start_dir = '%(name)s_%(version)s' -- GitLab From f0ad795a7ccf37af9a466968552f3feee9e98dcb Mon Sep 17 00:00:00 2001 From: HPC core facility CalcUA Date: Wed, 8 Mar 2017 10:26:58 +0100 Subject: [PATCH 0268/1603] Correction: EBROOTLIGJPEGTURBO -> EBROOTLIBJPEGMINTURBO --- .../easyconfigs/g/GDAL/GDAL-1.10.1-intel-2015b-Python-2.7.10.eb | 2 +- .../easyconfigs/g/GDAL/GDAL-2.1.1-intel-2016b-Python-2.7.12.eb | 2 +- .../easyconfigs/g/GDAL/GDAL-2.1.2-intel-2016b-Python-2.7.12.eb | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-1.10.1-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/g/GDAL/GDAL-1.10.1-intel-2015b-Python-2.7.10.eb index 63e63419b2..5eee841793 100644 --- a/easybuild/easyconfigs/g/GDAL/GDAL-1.10.1-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/g/GDAL/GDAL-1.10.1-intel-2015b-Python-2.7.10.eb @@ -37,7 +37,7 @@ dependencies = [ ] configopts = '--with-expat=$EBROOTEXPAT --with-libz=$EBROOTLIBZ --with-hdf5=$EBROOTHDF5 --with-netcdf=$EBROOTNETCDF' -configopts += ' --with-xml2=$EBROOTLIBXML2 --with-geos=$EBROOTGEOS/bin/geos-config --with-jpeg=$EBROOTLIBJPEGTURBO' +configopts += ' --with-xml2=$EBROOTLIBXML2 --with-geos=$EBROOTGEOS/bin/geos-config --with-jpeg=$EBROOTLIBJPEGMINTURBO' configopts += ' --with-png=$EBROOTLIBPNG --with-sqlite3=$EBROOTSQLITE --with-jasper=$EBROOTJASPER' configopts += ' --with-libtiff=$EBROOTLIBTIFF --with-pcre=$EBROOTPCRE --with-python=$EBROOTPYTHON/bin/python' # there is a bug in the build system causing the build with libtool to fail for the moment diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-2.1.1-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/g/GDAL/GDAL-2.1.1-intel-2016b-Python-2.7.12.eb index 6355e7d5d7..6e30f9da8c 100644 --- a/easybuild/easyconfigs/g/GDAL/GDAL-2.1.1-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/g/GDAL/GDAL-2.1.1-intel-2016b-Python-2.7.12.eb @@ -32,7 +32,7 @@ dependencies = [ ] configopts = '--with-expat=$EBROOTEXPAT --with-libz=$EBROOTLIBZ --with-hdf5=$EBROOTHDF5 --with-netcdf=$EBROOTNETCDF' -configopts += ' --with-xml2=$EBROOTLIBXML2 --with-geos=$EBROOTGEOS/bin/geos-config --with-jpeg=$EBROOTLIBJPEGTURBO' +configopts += ' --with-xml2=$EBROOTLIBXML2 --with-geos=$EBROOTGEOS/bin/geos-config --with-jpeg=$EBROOTLIBJPEGMINTURBO' configopts += ' --with-png=$EBROOTLIBPNG --with-sqlite3=$EBROOTSQLITE --with-jasper=$EBROOTJASPER' configopts += ' --with-libtiff=$EBROOTLIBTIFF --with-pcre=$EBROOTPCRE --with-python=$EBROOTPYTHON/bin/python' # there is a bug in the build system causing the build with libtool to fail for the moment diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-2.1.2-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/g/GDAL/GDAL-2.1.2-intel-2016b-Python-2.7.12.eb index 9e5b8f7b62..d2c01232d3 100644 --- a/easybuild/easyconfigs/g/GDAL/GDAL-2.1.2-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/g/GDAL/GDAL-2.1.2-intel-2016b-Python-2.7.12.eb @@ -34,7 +34,7 @@ dependencies = [ ] configopts = '--with-expat=$EBROOTEXPAT --with-libz=$EBROOTLIBZ --with-hdf5=$EBROOTHDF5 --with-netcdf=$EBROOTNETCDF' -configopts += ' --with-xml2=$EBROOTLIBXML2 --with-geos=$EBROOTGEOS/bin/geos-config --with-jpeg=$EBROOTLIBJPEGTURBO' +configopts += ' --with-xml2=$EBROOTLIBXML2 --with-geos=$EBROOTGEOS/bin/geos-config --with-jpeg=$EBROOTLIBJPEGMINTURBO' configopts += ' --with-png=$EBROOTLIBPNG --with-sqlite3=$EBROOTSQLITE --with-jasper=$EBROOTJASPER' configopts += ' --with-libtiff=$EBROOTLIBTIFF --with-pcre=$EBROOTPCRE --with-python=$EBROOTPYTHON/bin/python' # there is a bug in the build system causing the build with libtool to fail for the moment -- GitLab From f2188cf1ad91631353221a858924aae5cbf26719 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 8 Mar 2017 17:32:58 +0800 Subject: [PATCH 0269/1603] yet another style fix --- easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.3.eb | 7 ++----- easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.0.eb | 7 ++----- easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.1.eb | 7 ++----- easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.2.eb | 7 ++----- easybuild/easyconfigs/g/GLib/GLib-2.48.0-foss-2016a.eb | 4 ++-- easybuild/easyconfigs/g/GLib/GLib-2.48.0-intel-2016a.eb | 4 ++-- easybuild/easyconfigs/g/GLib/GLib-2.49.5-foss-2016b.eb | 4 ++-- easybuild/easyconfigs/g/GLib/GLib-2.49.5-intel-2016b.eb | 4 ++-- .../g/Ghostscript/Ghostscript-9.19-intel-2016a.eb | 2 +- .../g/Ghostscript/Ghostscript-9.19-intel-2016b.eb | 2 +- .../easyconfigs/g/gtkglext/gtkglext-1.2.0-intel-2015b.eb | 4 ++-- 11 files changed, 20 insertions(+), 32 deletions(-) diff --git a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.3.eb b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.3.eb index e5810437c4..a4b668c8cb 100644 --- a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.3.eb +++ b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.3.eb @@ -100,12 +100,9 @@ modextrapaths = {'PYTHONPATH': ['lib/python%s/site-packages' % pyver, 'lib64/pyt # specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module full_sanity_check = True -eggname = 'gc3pie-%%(version)s-py%s.egg' % pyver sanity_check_paths = { - 'files': ['bin/gc3utils', - ('lib/python%s/site-packages/%s' % (pyver, eggname), - 'lib64/python%s/site-packages/%s' % (pyver, eggname))], - 'dirs': [], + 'files': ['bin/gc3utils'], + 'dirs': [('lib/python%s/site-packages' % pyver, 'lib64/python%s/site-packages')], } sanity_check_commands = [('gc3utils', 'info --version')] diff --git a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.0.eb b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.0.eb index 0a33e2b925..ec6e1d4b8c 100644 --- a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.0.eb +++ b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.0.eb @@ -100,12 +100,9 @@ modextrapaths = {'PYTHONPATH': ['lib/python%s/site-packages' % pyver, 'lib64/pyt # specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module full_sanity_check = True -eggname = 'gc3pie-%%(version)s-py%s.egg' % pyver sanity_check_paths = { - 'files': ['bin/gc3utils', - ('lib/python%s/site-packages/%s' % (pyver, eggname), - 'lib64/python%s/site-packages/%s' % (pyver, eggname))], - 'dirs': [], + 'files': ['bin/gc3utils'], + 'dirs': [('lib/python%s/site-packages' % pyver, 'lib64/python%s/site-packages')], } sanity_check_commands = [('gc3utils', 'info --version')] diff --git a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.1.eb b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.1.eb index 49772e1a73..33b05c7f1c 100644 --- a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.1.eb +++ b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.1.eb @@ -100,12 +100,9 @@ modextrapaths = {'PYTHONPATH': ['lib/python%s/site-packages' % pyver, 'lib64/pyt # specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module full_sanity_check = True -eggname = 'gc3pie-%%(version)s-py%s.egg' % pyver sanity_check_paths = { - 'files': ['bin/gc3utils', - ('lib/python%s/site-packages/%s' % (pyver, eggname), - 'lib64/python%s/site-packages/%s' % (pyver, eggname))], - 'dirs': [], + 'files': ['bin/gc3utils'], + 'dirs': [('lib/python%s/site-packages' % pyver, 'lib64/python%s/site-packages')], } sanity_check_commands = [('gc3utils', 'info --version')] diff --git a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.2.eb b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.2.eb index 98f0d96369..3d36571118 100644 --- a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.2.eb +++ b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.2.eb @@ -100,12 +100,9 @@ modextrapaths = {'PYTHONPATH': ['lib/python%s/site-packages' % pyver, 'lib64/pyt # specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module full_sanity_check = True -eggname = 'gc3pie-%%(version)s-py%s.egg' % pyver sanity_check_paths = { - 'files': ['bin/gc3utils', - ('lib/python%s/site-packages/%s' % (pyver, eggname), - 'lib64/python%s/site-packages/%s' % (pyver, eggname))], - 'dirs': [], + 'files': ['bin/gc3utils'], + 'dirs': [('lib/python%s/site-packages' % pyver, 'lib64/python%s/site-packages')], } sanity_check_commands = [('gc3utils', 'info --version')] diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.48.0-foss-2016a.eb b/easybuild/easyconfigs/g/GLib/GLib-2.48.0-foss-2016a.eb index fecad61365..02f569f33b 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.48.0-foss-2016a.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.48.0-foss-2016a.eb @@ -21,8 +21,8 @@ dependencies = [ builddependencies = [('Python', '2.7.11')] -configopts = "--disable-maintainer-mode --disable-silent-rules --disable-libelf --enable-static --enable-shared " -configopts += "--disable-systemtap" +configopts = "--disable-maintainer-mode --disable-silent-rules --disable-libelf --disable-systemtap " +configopts += "--enable-static --enable-shared" postinstallcmds = ["sed -i -e 's|#!.*python|#!/usr/bin/env python|' %(installdir)s/bin/*"] diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.48.0-intel-2016a.eb b/easybuild/easyconfigs/g/GLib/GLib-2.48.0-intel-2016a.eb index b29b2e7ddf..08fc164519 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.48.0-intel-2016a.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.48.0-intel-2016a.eb @@ -21,8 +21,8 @@ dependencies = [ builddependencies = [('Python', '2.7.11')] -configopts = "--disable-maintainer-mode --disable-silent-rules --disable-libelf --enable-static --enable-shared " -configopts += "--disable-systemtap" +configopts = "--disable-maintainer-mode --disable-silent-rules --disable-libelf --disable-systemtap " +configopts += "--enable-static --enable-shared" postinstallcmds = ["sed -i -e 's|#!.*python|#!/usr/bin/env python|' %(installdir)s/bin/*"] diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.49.5-foss-2016b.eb b/easybuild/easyconfigs/g/GLib/GLib-2.49.5-foss-2016b.eb index ffe44a8cda..8ed215628a 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.49.5-foss-2016b.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.49.5-foss-2016b.eb @@ -21,8 +21,8 @@ dependencies = [ builddependencies = [('Python', '2.7.12')] -configopts = "--disable-maintainer-mode --disable-silent-rules --disable-libelf --enable-static --enable-shared " -configopts += "--disable-systemtap" +configopts = "--disable-maintainer-mode --disable-silent-rules --disable-libelf --disable-systemtap " +configopts += "--enable-static --enable-shared" postinstallcmds = ["sed -i -e 's|#!.*python|#!/usr/bin/env python|' %(installdir)s/bin/*"] diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.49.5-intel-2016b.eb b/easybuild/easyconfigs/g/GLib/GLib-2.49.5-intel-2016b.eb index ba98f92742..0cfae7ee91 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.49.5-intel-2016b.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.49.5-intel-2016b.eb @@ -21,8 +21,8 @@ dependencies = [ builddependencies = [('Python', '2.7.12')] -configopts = "--disable-maintainer-mode --disable-silent-rules --disable-libelf --enable-static --enable-shared " -configopts += "--disable-systemtap" +configopts = "--disable-maintainer-mode --disable-silent-rules --disable-libelf --disable-systemtap " +configopts += "--enable-static --enable-shared" postinstallcmds = ["sed -i -e 's|#!.*python|#!/usr/bin/env python|' %(installdir)s/bin/*"] diff --git a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.19-intel-2016a.eb b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.19-intel-2016a.eb index dd5cd622b8..9a3a3ea548 100644 --- a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.19-intel-2016a.eb +++ b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.19-intel-2016a.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'intel', 'version': '2016a'} toolchainopts = {'pic': True} source_subdir = 'gs%(version_major)s%(version_minor)s' -source_urls = ["https://github.com/ArtifexSoftware/ghostpdl-downloads/releases/download/%s/" % source_subdir] +source_urls = ["https://github.com/ArtifexSoftware/ghostpdl-downloads/releases/download/" + source_subdir] sources = ["ghostpdl-%(version)s.tar.bz2"] dependencies = [ diff --git a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.19-intel-2016b.eb b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.19-intel-2016b.eb index 59430c9acb..0d5843bdd6 100644 --- a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.19-intel-2016b.eb +++ b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.19-intel-2016b.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'intel', 'version': '2016b'} toolchainopts = {'pic': True} source_subdir = 'gs%(version_major)s%(version_minor)s' -source_urls = ["https://github.com/ArtifexSoftware/ghostpdl-downloads/releases/download/%s/" % source_subdir] +source_urls = ["https://github.com/ArtifexSoftware/ghostpdl-downloads/releases/download/" + source_subdir] sources = ["ghostpdl-%(version)s.tar.bz2"] dependencies = [ diff --git a/easybuild/easyconfigs/g/gtkglext/gtkglext-1.2.0-intel-2015b.eb b/easybuild/easyconfigs/g/gtkglext/gtkglext-1.2.0-intel-2015b.eb index 2f14396e13..8dc32d3aad 100644 --- a/easybuild/easyconfigs/g/gtkglext/gtkglext-1.2.0-intel-2015b.eb +++ b/easybuild/easyconfigs/g/gtkglext/gtkglext-1.2.0-intel-2015b.eb @@ -21,8 +21,8 @@ dependencies = [ ] sanity_check_paths = { - 'files': ['lib/gtkglext-1.0/include/gdkglext-config.h', 'lib/libgdkglext-x11-1.0.a', - 'lib/libgdkglext-x11-1.0.%s' % SHLIB_EXT, + 'files': ['lib/gtkglext-1.0/include/gdkglext-config.h', + 'lib/libgdkglext-x11-1.0.a', 'lib/libgdkglext-x11-1.0.%s' % SHLIB_EXT, 'lib/libgtkglext-x11-1.0.a', 'lib/libgtkglext-x11-1.0.%s' % SHLIB_EXT], 'dirs': ['include/gtkglext-1.0/gdk', 'include/gtkglext-1.0/gtk', 'lib/pkgconfig'], } -- GitLab From 52d921264b76ac2563135e32a93f5df07a4b0be6 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 8 Mar 2017 17:37:23 +0800 Subject: [PATCH 0270/1603] yet another batch of minor style fixes --- easybuild/easyconfigs/h/HDF/HDF-4.2.11-intel-2016a.eb | 3 ++- easybuild/easyconfigs/h/HDF/HDF-4.2.8-ictce-5.3.0.eb | 3 ++- easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-foss-2016a.eb | 2 +- .../HPCBIOS_Debuggers-20130829-goolf-1.4.10.eb | 3 ++- easybuild/easyconfigs/h/HPL/HPL-2.0-foss-2014b.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.0-goolf-1.4.10.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.0-goolf-1.5.16.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.0-ictce-5.3.0.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.0-ictce-6.1.5.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.1-CrayCCE-2015.06.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.1-CrayCCE-2015.11.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2015.06.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2015.11.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2016.03.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2016.04.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2016.06.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-2015.06.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-2015.11.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-2016.06.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2015.05.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2015a.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2015b.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2016.04.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2016.06.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2016a.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2016b.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.1-gimkl-2.11.5.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.1-gmpolf-2016a.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.1-gmvolf-1.7.20.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.1-gmvolf-2016a.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.1-goolf-1.7.20.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.1-ictce-7.1.2.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.1-ictce-7.3.5.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2014.06.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2014.10.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2014.11.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2014b.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2015.02.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2015.08.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2015a.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2015b.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.00.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.01.eb | 6 +++--- .../easyconfigs/h/HPL/HPL-2.1-intel-2016.02-GCC-4.9.eb | 6 +++--- .../easyconfigs/h/HPL/HPL-2.1-intel-2016.02-GCC-5.3.eb | 6 +++--- .../easyconfigs/h/HPL/HPL-2.1-intel-2016.03-GCC-4.9.eb | 6 +++--- .../easyconfigs/h/HPL/HPL-2.1-intel-2016.03-GCC-5.3.eb | 6 +++--- .../easyconfigs/h/HPL/HPL-2.1-intel-2016.03-GCC-5.4.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016a.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016b.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.1-iomkl-2015.01.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.1-iomkl-2015.02.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.1-iomkl-2015.03.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.1-iomkl-2016.07.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.1-pomkl-2016.03.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.1-pomkl-2016.04.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.1-pomkl-2016.09.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.2-foss-2016.07.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.2-foss-2016.09.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.2-foss-2017a.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.2-goolfc-2016.08.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.2-goolfc-2016.10.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.2-intel-2017.00.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.2-intel-2017.01.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.2-intel-2017.02.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.2-intel-2017a.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.2-intelcuda-2016.10.eb | 6 +++--- .../h/HPL/HPL-2.2-iomkl-2016.09-GCC-4.9.3-2.25.eb | 6 +++--- .../h/HPL/HPL-2.2-iomkl-2016.09-GCC-5.4.0-2.26.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.2-iomkl-2017.01.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.2-iomkl-2017a.eb | 6 +++--- easybuild/easyconfigs/h/HPL/HPL-2.2-pomkl-2016.09.eb | 6 +++--- .../easyconfigs/h/Harminv/Harminv-1.3.1-goolf-1.4.10.eb | 7 ++++--- .../easyconfigs/h/Harminv/Harminv-1.3.1-ictce-5.3.0.eb | 7 ++++--- .../easyconfigs/h/Harminv/Harminv-1.4-foss-2016a.eb | 9 +++++---- .../easyconfigs/h/Harminv/Harminv-1.4-intel-2015a.eb | 7 ++++--- easybuild/easyconfigs/h/Hoard/Hoard-3.10-intel-2015a.eb | 2 +- .../h/h5py/h5py-2.0.1-ictce-5.3.0-Python-2.7.3.eb | 5 +++-- .../h/h5py/h5py-2.4.0-intel-2015a-Python-2.7.9-serial.eb | 2 +- .../easyconfigs/h/h5utils/h5utils-1.12.1-ictce-5.3.0.eb | 7 ++++--- .../h/horton/horton-1.0.2-goolf-1.4.10-Python-2.7.3.eb | 3 ++- .../h/horton/horton-1.1.0-goolf-1.4.10-Python-2.7.3.eb | 3 ++- .../h/horton/horton-1.2.0-goolf-1.4.10-Python-2.7.3.eb | 3 ++- .../h/horton/horton-1.2.1-goolf-1.4.10-Python-2.7.3.eb | 3 ++- 84 files changed, 245 insertions(+), 232 deletions(-) diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.11-intel-2016a.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.11-intel-2016a.eb index 28e5e6ad36..e115932f8e 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.11-intel-2016a.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.11-intel-2016a.eb @@ -4,7 +4,8 @@ name = 'HDF' version = '4.2.11' homepage = 'http://www.hdfgroup.org/products/hdf4/' -description = """HDF (also known as HDF4) is a library and multi-object file format for storing and managing data between machines.""" +description = """HDF (also known as HDF4) is a library and multi-object file format for storing and managing data + between machines.""" toolchain = {'name': 'intel', 'version': '2016a'} toolchainopts = {'pic': True} diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.8-ictce-5.3.0.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.8-ictce-5.3.0.eb index fa2a08d015..16556a59b7 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.8-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.8-ictce-5.3.0.eb @@ -4,7 +4,8 @@ name = 'HDF' version = '4.2.8' homepage = 'http://www.hdfgroup.org/products/hdf4/' -description = """HDF (also known as HDF4) is a library and multi-object file format for storing and managing data between machines.""" +description = """HDF (also known as HDF4) is a library and multi-object file format for storing and managing data + between machines.""" toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'opt': True, 'pic': True} diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-foss-2016a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-foss-2016a.eb index b1098f85e1..7250d32fe5 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-foss-2016a.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-foss-2016a.eb @@ -24,4 +24,4 @@ dependencies = [ ('libxml2', '2.9.3') ] -moduleclass = 'data' \ No newline at end of file +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/HPCBIOS_Debuggers/HPCBIOS_Debuggers-20130829-goolf-1.4.10.eb b/easybuild/easyconfigs/h/HPCBIOS_Debuggers/HPCBIOS_Debuggers-20130829-goolf-1.4.10.eb index 76836f3aed..259d3f70b6 100644 --- a/easybuild/easyconfigs/h/HPCBIOS_Debuggers/HPCBIOS_Debuggers-20130829-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/h/HPCBIOS_Debuggers/HPCBIOS_Debuggers-20130829-goolf-1.4.10.eb @@ -16,7 +16,8 @@ name = 'HPCBIOS_Debuggers' version = '20130829' homepage = 'http://hpcbios.readthedocs.org/en/latest/HPCBIOS_06-05.html' -description = """Common Set of Debuggers includes a set of debuggers that can assist HPC users for managing parallel codes.""" +description = """Common Set of Debuggers includes a set of debuggers that can assist HPC users for managing parallel + codes.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.0-foss-2014b.eb b/easybuild/easyconfigs/h/HPL/HPL-2.0-foss-2014b.eb index 576cc9a699..5feb085a79 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.0-foss-2014b.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.0-foss-2014b.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.0' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic -on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the -High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'foss', 'version': '2014b'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.0-goolf-1.4.10.eb b/easybuild/easyconfigs/h/HPL/HPL-2.0-goolf-1.4.10.eb index cf3bd5fd41..0715af27f9 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.0-goolf-1.4.10.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.0' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic -on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the -High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.0-goolf-1.5.16.eb b/easybuild/easyconfigs/h/HPL/HPL-2.0-goolf-1.5.16.eb index d327bfbbab..cd888a1b77 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.0-goolf-1.5.16.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.0-goolf-1.5.16.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.0' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic -on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the -High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'goolf', 'version': '1.5.16'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.0-ictce-5.3.0.eb b/easybuild/easyconfigs/h/HPL/HPL-2.0-ictce-5.3.0.eb index fa3e730343..96f1d5781a 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.0-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.0-ictce-5.3.0.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.0' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.0-ictce-6.1.5.eb b/easybuild/easyconfigs/h/HPL/HPL-2.0-ictce-6.1.5.eb index 91a1cadef9..e3f05fd328 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.0-ictce-6.1.5.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.0-ictce-6.1.5.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.0' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'ictce', 'version': '6.1.5'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayCCE-2015.06.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayCCE-2015.06.eb index 934cc8d3eb..4edf03da45 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayCCE-2015.06.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayCCE-2015.06.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'CrayCCE', 'version': '2015.06'} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayCCE-2015.11.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayCCE-2015.11.eb index 7a8e5a0800..76ee40d652 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayCCE-2015.11.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayCCE-2015.11.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'CrayCCE', 'version': '2015.11'} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2015.06.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2015.06.eb index 4f4dbfc813..2c9f0ea5ba 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2015.06.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2015.06.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'CrayGNU', 'version': '2015.06'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2015.11.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2015.11.eb index 455f495e6e..bff436a5d6 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2015.11.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2015.11.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'CrayGNU', 'version': '2015.11'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2016.03.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2016.03.eb index f64bec348b..b1fe7ccd3c 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2016.03.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2016.03.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'CrayGNU', 'version': '2016.03'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2016.04.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2016.04.eb index 57414cfc79..c7a116c4f3 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2016.04.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2016.04.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'CrayGNU', 'version': '2016.04'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2016.06.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2016.06.eb index b59f7317b1..b9880180b4 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2016.06.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2016.06.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'CrayGNU', 'version': '2016.06'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-2015.06.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-2015.06.eb index 00ee4facc9..4749294d9f 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-2015.06.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-2015.06.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'CrayIntel', 'version': '2015.06'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-2015.11.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-2015.11.eb index 651ae824ba..32ea90665e 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-2015.11.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-2015.11.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'CrayIntel', 'version': '2015.11'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-2016.06.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-2016.06.eb index 9ab9de3734..ab2e745599 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-2016.06.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-2016.06.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'CrayIntel', 'version': '2016.06'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2015.05.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2015.05.eb index 6e7b16eb21..c750f970fb 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2015.05.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2015.05.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'foss', 'version': '2015.05'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2015a.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2015a.eb index 225cb3be6a..97e132a043 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2015a.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2015a.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'foss', 'version': '2015a'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2015b.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2015b.eb index 728ad9cf2e..fe7bda0c23 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2015b.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2015b.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'foss', 'version': '2015b'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2016.04.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2016.04.eb index e65fa73eda..6c486063ce 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2016.04.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2016.04.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'foss', 'version': '2016.04'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2016.06.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2016.06.eb index e44a4ac54d..416d5bc913 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2016.06.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2016.06.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'foss', 'version': '2016.06'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2016a.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2016a.eb index e43e4270dd..df93eaf60f 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2016a.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2016a.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'foss', 'version': '2016a'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2016b.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2016b.eb index 5634e6bd4f..c40112704f 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2016b.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2016b.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'foss', 'version': '2016b'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-gimkl-2.11.5.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-gimkl-2.11.5.eb index 50fef4fac6..5d0475520c 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-gimkl-2.11.5.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'gimkl', 'version': '2.11.5'} toolchainopts = {'optarch': True, 'usempi': True, 'openmp': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-gmpolf-2016a.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-gmpolf-2016a.eb index ae8a971cbf..7513b5c69c 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-gmpolf-2016a.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-gmpolf-2016a.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'gmpolf', 'version': '2016a'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-gmvolf-1.7.20.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-gmvolf-1.7.20.eb index dda08f35b9..7a3660c3cf 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-gmvolf-1.7.20.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-gmvolf-1.7.20.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'gmvolf', 'version': '1.7.20'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-gmvolf-2016a.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-gmvolf-2016a.eb index d581afc6f7..b99e6ef61e 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-gmvolf-2016a.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-gmvolf-2016a.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'gmvolf', 'version': '2016a'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-goolf-1.7.20.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-goolf-1.7.20.eb index fd109a8fed..51de797385 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-goolf-1.7.20.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'goolf', 'version': '1.7.20'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-ictce-7.1.2.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-ictce-7.1.2.eb index 92f6036e1c..036b47fd97 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-ictce-7.1.2.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-ictce-7.1.2.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'ictce', 'version': '7.1.2'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-ictce-7.3.5.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-ictce-7.3.5.eb index 55ab924d7d..7fd7fc7bf8 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-ictce-7.3.5.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-ictce-7.3.5.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'ictce', 'version': '7.3.5'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2014.06.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2014.06.eb index 38c3e337e3..595430c600 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2014.06.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2014.06.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'intel', 'version': '2014.06'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2014.10.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2014.10.eb index 4c3646267b..095ac318fe 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2014.10.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2014.10.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'intel', 'version': '2014.10'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2014.11.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2014.11.eb index 4e8b437981..271e44e3ae 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2014.11.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2014.11.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'intel', 'version': '2014.11'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2014b.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2014b.eb index 07ff11637e..1740a95776 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2014b.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2014b.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'intel', 'version': '2014b'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2015.02.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2015.02.eb index 7597cf43f8..bfca06cd24 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2015.02.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2015.02.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'intel', 'version': '2015.02'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2015.08.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2015.08.eb index 4e727e3fcd..0be6dec3cf 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2015.08.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2015.08.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'intel', 'version': '2015.08'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2015a.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2015a.eb index 97b6ceedd3..774ed3383d 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2015a.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2015a.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'intel', 'version': '2015a'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2015b.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2015b.eb index fa34ec665e..ecdaa77a80 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2015b.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2015b.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'intel', 'version': '2015b'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.00.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.00.eb index 406d3ae039..3f8d9be6d0 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.00.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.00.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'intel', 'version': '2016.00'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.01.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.01.eb index 27b235374a..7fa2f28990 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.01.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.01.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'intel', 'version': '2016.01'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.02-GCC-4.9.eb index 977c7d487d..21af879c00 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.02-GCC-4.9.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.02-GCC-5.3.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.02-GCC-5.3.eb index ffa453cdb4..d6bd01277c 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.02-GCC-5.3.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.02-GCC-5.3.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'intel', 'version': '2016.02-GCC-5.3'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.03-GCC-4.9.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.03-GCC-4.9.eb index f2d54cf671..2c8b3ccfcc 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.03-GCC-4.9.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.03-GCC-4.9.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'intel', 'version': '2016.03-GCC-4.9'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.03-GCC-5.3.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.03-GCC-5.3.eb index 7eaca67c16..eb86100453 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.03-GCC-5.3.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.03-GCC-5.3.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'intel', 'version': '2016.03-GCC-5.3'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.03-GCC-5.4.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.03-GCC-5.4.eb index 660c68898c..3aa6c8de88 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.03-GCC-5.4.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.03-GCC-5.4.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'intel', 'version': '2016.03-GCC-5.4'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016a.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016a.eb index a3af786ca9..2349780aef 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016a.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016a.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'intel', 'version': '2016a'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016b.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016b.eb index 226f45477c..f4cc398833 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016b.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016b.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'intel', 'version': '2016b'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-iomkl-2015.01.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-iomkl-2015.01.eb index e2c8df3cc6..8cc92060d3 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-iomkl-2015.01.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-iomkl-2015.01.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'iomkl', 'version': '2015.01'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-iomkl-2015.02.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-iomkl-2015.02.eb index 28511646d6..645f1e333c 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-iomkl-2015.02.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-iomkl-2015.02.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'iomkl', 'version': '2015.02'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-iomkl-2015.03.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-iomkl-2015.03.eb index 59e1705669..2247657f83 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-iomkl-2015.03.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-iomkl-2015.03.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'iomkl', 'version': '2015.03'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-iomkl-2016.07.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-iomkl-2016.07.eb index 42249afb29..ac09c4d824 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-iomkl-2016.07.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-iomkl-2016.07.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'iomkl', 'version': '2016.07'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-pomkl-2016.03.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-pomkl-2016.03.eb index 9552b4d653..2f6f29630a 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-pomkl-2016.03.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-pomkl-2016.03.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'pomkl', 'version': '2016.03'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-pomkl-2016.04.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-pomkl-2016.04.eb index 4d48990b54..9b006fcd88 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-pomkl-2016.04.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-pomkl-2016.04.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'pomkl', 'version': '2016.04'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-pomkl-2016.09.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-pomkl-2016.09.eb index 112d6aa634..23e9cfc7a8 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-pomkl-2016.09.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-pomkl-2016.09.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.1' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'pomkl', 'version': '2016.09'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.2-foss-2016.07.eb b/easybuild/easyconfigs/h/HPL/HPL-2.2-foss-2016.07.eb index c44018425b..09db015192 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.2-foss-2016.07.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.2-foss-2016.07.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.2' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'foss', 'version': '2016.07'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.2-foss-2016.09.eb b/easybuild/easyconfigs/h/HPL/HPL-2.2-foss-2016.09.eb index be4db4593e..0766c10887 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.2-foss-2016.09.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.2-foss-2016.09.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.2' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'foss', 'version': '2016.09'} toolchainopts = {'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.2-foss-2017a.eb b/easybuild/easyconfigs/h/HPL/HPL-2.2-foss-2017a.eb index e59ac471b9..95e36ebf95 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.2-foss-2017a.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.2-foss-2017a.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.2' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'foss', 'version': '2017a'} toolchainopts = {'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.2-goolfc-2016.08.eb b/easybuild/easyconfigs/h/HPL/HPL-2.2-goolfc-2016.08.eb index d1430d0e3a..c13e143bbf 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.2-goolfc-2016.08.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.2-goolfc-2016.08.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.2' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic -on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the -High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'goolfc', 'version': '2016.08'} toolchainopts = {'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.2-goolfc-2016.10.eb b/easybuild/easyconfigs/h/HPL/HPL-2.2-goolfc-2016.10.eb index fff961832d..069cc730f1 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.2-goolfc-2016.10.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.2-goolfc-2016.10.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.2' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'goolfc', 'version': '2016.10'} toolchainopts = {'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.2-intel-2017.00.eb b/easybuild/easyconfigs/h/HPL/HPL-2.2-intel-2017.00.eb index 48447ddb28..d09d150a57 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.2-intel-2017.00.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.2-intel-2017.00.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.2' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'intel', 'version': '2017.00'} toolchainopts = {'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.2-intel-2017.01.eb b/easybuild/easyconfigs/h/HPL/HPL-2.2-intel-2017.01.eb index 64700f3b27..0db9bffabb 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.2-intel-2017.01.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.2-intel-2017.01.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.2' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'intel', 'version': '2017.01'} toolchainopts = {'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.2-intel-2017.02.eb b/easybuild/easyconfigs/h/HPL/HPL-2.2-intel-2017.02.eb index 976ad59fb7..f53793fe5b 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.2-intel-2017.02.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.2-intel-2017.02.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.2' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'intel', 'version': '2017.02'} toolchainopts = {'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.2-intel-2017a.eb b/easybuild/easyconfigs/h/HPL/HPL-2.2-intel-2017a.eb index 80e701d1a6..6caac90930 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.2-intel-2017a.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.2-intel-2017a.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.2' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'intel', 'version': '2017a'} toolchainopts = {'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.2-intelcuda-2016.10.eb b/easybuild/easyconfigs/h/HPL/HPL-2.2-intelcuda-2016.10.eb index 05f316bde4..b6258c055e 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.2-intelcuda-2016.10.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.2-intelcuda-2016.10.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.2' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'intelcuda', 'version': '2016.10'} toolchainopts = {'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.2-iomkl-2016.09-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/h/HPL/HPL-2.2-iomkl-2016.09-GCC-4.9.3-2.25.eb index 22cd32989a..579a293142 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.2-iomkl-2016.09-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.2-iomkl-2016.09-GCC-4.9.3-2.25.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.2' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'iomkl', 'version': '2016.09-GCC-4.9.3-2.25'} toolchainopts = {'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.2-iomkl-2016.09-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/h/HPL/HPL-2.2-iomkl-2016.09-GCC-5.4.0-2.26.eb index efda5a282c..ed855cdf2a 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.2-iomkl-2016.09-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.2-iomkl-2016.09-GCC-5.4.0-2.26.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.2' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'iomkl', 'version': '2016.09-GCC-5.4.0-2.26'} toolchainopts = {'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.2-iomkl-2017.01.eb b/easybuild/easyconfigs/h/HPL/HPL-2.2-iomkl-2017.01.eb index d890354a7b..37c0a37f5d 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.2-iomkl-2017.01.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.2-iomkl-2017.01.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.2' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'iomkl', 'version': '2017.01'} toolchainopts = {'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.2-iomkl-2017a.eb b/easybuild/easyconfigs/h/HPL/HPL-2.2-iomkl-2017a.eb index 77dc4ed21f..77467edaf2 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.2-iomkl-2017a.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.2-iomkl-2017a.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.2' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'iomkl', 'version': '2017a'} toolchainopts = {'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.2-pomkl-2016.09.eb b/easybuild/easyconfigs/h/HPL/HPL-2.2-pomkl-2016.09.eb index 005a57564c..3ef2663a61 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.2-pomkl-2016.09.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.2-pomkl-2016.09.eb @@ -2,9 +2,9 @@ name = 'HPL' version = '2.2' homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'pomkl', 'version': '2016.09'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/Harminv/Harminv-1.3.1-goolf-1.4.10.eb b/easybuild/easyconfigs/h/Harminv/Harminv-1.3.1-goolf-1.4.10.eb index d46bdf7367..3b8e366300 100644 --- a/easybuild/easyconfigs/h/Harminv/Harminv-1.3.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/h/Harminv/Harminv-1.3.1-goolf-1.4.10.eb @@ -4,9 +4,10 @@ name = 'Harminv' version = '1.3.1' homepage = 'http://ab-initio.mit.edu/wiki/index.php/Harminv' -description = """Harminv is a free program (and accompanying library) to solve the problem of harmonic inversion - given -a discrete-time, finite-length signal that consists of a sum of finitely-many sinusoids (possibly exponentially decaying) -in a given bandwidth, it determines the frequencies, decay constants, amplitudes, and phases of those sinusoids.""" +description = """Harminv is a free program (and accompanying library) to solve the problem of harmonic inversion - + given a discrete-time, finite-length signal that consists of a sum of finitely-many sinusoids (possibly exponentially + decaying) in a given bandwidth, it determines the frequencies, decay constants, amplitudes, and phases of those + sinusoids.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'opt': True, 'unroll': True, 'optarch': True, 'pic': True, 'cstd': 'c99'} diff --git a/easybuild/easyconfigs/h/Harminv/Harminv-1.3.1-ictce-5.3.0.eb b/easybuild/easyconfigs/h/Harminv/Harminv-1.3.1-ictce-5.3.0.eb index 44e47d185b..c2eb89d992 100644 --- a/easybuild/easyconfigs/h/Harminv/Harminv-1.3.1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/h/Harminv/Harminv-1.3.1-ictce-5.3.0.eb @@ -4,9 +4,10 @@ name = 'Harminv' version = '1.3.1' homepage = 'http://ab-initio.mit.edu/wiki/index.php/Harminv' -description = """Harminv is a free program (and accompanying library) to solve the problem of harmonic inversion - given - a discrete-time, finite-length signal that consists of a sum of finitely-many sinusoids (possibly exponentially decaying) - in a given bandwidth, it determines the frequencies, decay constants, amplitudes, and phases of those sinusoids.""" +description = """Harminv is a free program (and accompanying library) to solve the problem of harmonic inversion - + given a discrete-time, finite-length signal that consists of a sum of finitely-many sinusoids (possibly exponentially + decaying) in a given bandwidth, it determines the frequencies, decay constants, amplitudes, and phases of those + sinusoids.""" toolchain = {'name': 'ictce', 'version': '5.3.0'} diff --git a/easybuild/easyconfigs/h/Harminv/Harminv-1.4-foss-2016a.eb b/easybuild/easyconfigs/h/Harminv/Harminv-1.4-foss-2016a.eb index 783b534519..f62ed07a47 100644 --- a/easybuild/easyconfigs/h/Harminv/Harminv-1.4-foss-2016a.eb +++ b/easybuild/easyconfigs/h/Harminv/Harminv-1.4-foss-2016a.eb @@ -4,9 +4,10 @@ name = 'Harminv' version = '1.4' homepage = 'http://ab-initio.mit.edu/wiki/index.php/Harminv' -description = """Harminv is a free program (and accompanying library) to solve the problem of harmonic inversion - given - a discrete-time, finite-length signal that consists of a sum of finitely-many sinusoids (possibly exponentially decaying) - in a given bandwidth, it determines the frequencies, decay constants, amplitudes, and phases of those sinusoids.""" +description = """Harminv is a free program (and accompanying library) to solve the problem of harmonic inversion - + given a discrete-time, finite-length signal that consists of a sum of finitely-many sinusoids (possibly exponentially + decaying) in a given bandwidth, it determines the frequencies, decay constants, amplitudes, and phases of those + sinusoids.""" toolchain = {'name': 'foss', 'version': '2016a'} toolchainopts = {'opt': True, 'unroll': True, 'pic': True, 'cstd': 'c99'} @@ -16,4 +17,4 @@ sources = [SOURCELOWER_TAR_GZ] configopts = "--with-pic --with-blas=openblas --with-lapack=openblas --enable-shared" -moduleclass = 'math' \ No newline at end of file +moduleclass = 'math' diff --git a/easybuild/easyconfigs/h/Harminv/Harminv-1.4-intel-2015a.eb b/easybuild/easyconfigs/h/Harminv/Harminv-1.4-intel-2015a.eb index 8b0afc7b1f..cf92cc3c69 100644 --- a/easybuild/easyconfigs/h/Harminv/Harminv-1.4-intel-2015a.eb +++ b/easybuild/easyconfigs/h/Harminv/Harminv-1.4-intel-2015a.eb @@ -4,9 +4,10 @@ name = 'Harminv' version = '1.4' homepage = 'http://ab-initio.mit.edu/wiki/index.php/Harminv' -description = """Harminv is a free program (and accompanying library) to solve the problem of harmonic inversion - given - a discrete-time, finite-length signal that consists of a sum of finitely-many sinusoids (possibly exponentially decaying) - in a given bandwidth, it determines the frequencies, decay constants, amplitudes, and phases of those sinusoids.""" +description = """Harminv is a free program (and accompanying library) to solve the problem of harmonic inversion - + given a discrete-time, finite-length signal that consists of a sum of finitely-many sinusoids (possibly exponentially + decaying) in a given bandwidth, it determines the frequencies, decay constants, amplitudes, and phases of those + sinusoids.""" toolchain = {'name': 'intel', 'version': '2015a'} toolchainopts = {'opt': True, 'unroll': True, 'optarch': True, 'pic': True, 'cstd': 'c99'} diff --git a/easybuild/easyconfigs/h/Hoard/Hoard-3.10-intel-2015a.eb b/easybuild/easyconfigs/h/Hoard/Hoard-3.10-intel-2015a.eb index 80e0503ba7..5ab80c6f39 100644 --- a/easybuild/easyconfigs/h/Hoard/Hoard-3.10-intel-2015a.eb +++ b/easybuild/easyconfigs/h/Hoard/Hoard-3.10-intel-2015a.eb @@ -4,7 +4,7 @@ name = 'Hoard' version = '3.10' homepage = 'http://www.hoard.org/' -description = """Hoard is a fast, scalable, and memory-efficient memory allocator that can speed up your applications.""" +description = "Hoard is a fast, scalable, and memory-efficient memory allocator that can speed up your applications." toolchain = {'name': 'intel', 'version': '2015a'} diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.0.1-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/h/h5py/h5py-2.0.1-ictce-5.3.0-Python-2.7.3.eb index 17626346c5..1807b63953 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.0.1-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.0.1-ictce-5.3.0-Python-2.7.3.eb @@ -4,8 +4,9 @@ name = 'h5py' version = '2.0.1' homepage = 'http://code.google.com/p/h5py/' -description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, version 5. - HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous amounts of data.""" +description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, + version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of + enormous amounts of data.""" toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'usempi': True} diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.4.0-intel-2015a-Python-2.7.9-serial.eb b/easybuild/easyconfigs/h/h5py/h5py-2.4.0-intel-2015a-Python-2.7.9-serial.eb index 12d6705dfa..d7449726a8 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.4.0-intel-2015a-Python-2.7.9-serial.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.4.0-intel-2015a-Python-2.7.9-serial.eb @@ -29,7 +29,7 @@ dependencies = [ builddependencies = [('pkgconfig', '1.1.0', '-Python-%(pyver)s')] sanity_check_paths = { - 'files': ['lib/python%s/site-packages/%%(name)s-%%(version)s-py%s-linux-x86_64.egg' % (pythonshortver, pythonshortver)], + 'files': ['lib/python%s/site-packages/%%(name)s-%%(version)s-py%s-linux-x86_64.egg' % (2 * (pythonshortver, ))], 'dirs': [], } diff --git a/easybuild/easyconfigs/h/h5utils/h5utils-1.12.1-ictce-5.3.0.eb b/easybuild/easyconfigs/h/h5utils/h5utils-1.12.1-ictce-5.3.0.eb index 09424f6b1b..b789858736 100644 --- a/easybuild/easyconfigs/h/h5utils/h5utils-1.12.1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/h/h5utils/h5utils-1.12.1-ictce-5.3.0.eb @@ -4,9 +4,10 @@ name = 'h5utils' version = '1.12.1' homepage = 'http://ab-initio.mit.edu/wiki/index.php/H5utils' -description = """h5utils is a set of utilities for visualization and conversion of scientific data in the free, portable - HDF5 format. Besides providing a simple tool for batch visualization as PNG images, h5utils also includes programs to - convert HDF5 datasets into the formats required by other free visualization software (e.g. plain text, Vis5d, and VTK).""" +description = """h5utils is a set of utilities for visualization and conversion of scientific data in the free, + portable HDF5 format. Besides providing a simple tool for batch visualization as PNG images, h5utils also includes + programs to convert HDF5 datasets into the formats required by other free visualization software (e.g. plain text, + Vis5d, and VTK).""" source_urls = ['http://ab-initio.mit.edu/h5utils/'] sources = [SOURCELOWER_TAR_GZ] diff --git a/easybuild/easyconfigs/h/horton/horton-1.0.2-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/h/horton/horton-1.0.2-goolf-1.4.10-Python-2.7.3.eb index 944bc27a5e..4ab8e8fc9a 100644 --- a/easybuild/easyconfigs/h/horton/horton-1.0.2-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/h/horton/horton-1.0.2-goolf-1.4.10-Python-2.7.3.eb @@ -28,7 +28,8 @@ dependencies = [ ] # disable tests that require X11 by specifying "backend: agg" in matplotlibrc -runtest = 'export MATPLOTLIBRC=$PWD; echo "backend: agg" > $MATPLOTLIBRC/matplotlibrc; python setup.py build_ext -i; nosetests -v' +runtest = 'export MATPLOTLIBRC=$PWD; echo "backend: agg" > $MATPLOTLIBRC/matplotlibrc; ' +runtest += 'python setup.py build_ext -i; nosetests -v' sanity_check_paths = { 'files': [], diff --git a/easybuild/easyconfigs/h/horton/horton-1.1.0-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/h/horton/horton-1.1.0-goolf-1.4.10-Python-2.7.3.eb index 778a209cab..401ada28ea 100644 --- a/easybuild/easyconfigs/h/horton/horton-1.1.0-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/h/horton/horton-1.1.0-goolf-1.4.10-Python-2.7.3.eb @@ -28,7 +28,8 @@ dependencies = [ ] # disable tests that require X11 by specifying "backend: agg" in matplotlibrc -runtest = 'export MATPLOTLIBRC=$PWD; echo "backend: agg" > $MATPLOTLIBRC/matplotlibrc; python setup.py build_ext -i; nosetests -v' +runtest = 'export MATPLOTLIBRC=$PWD; echo "backend: agg" > $MATPLOTLIBRC/matplotlibrc; ' +runtest += 'python setup.py build_ext -i; nosetests -v' sanity_check_paths = { 'files': [], diff --git a/easybuild/easyconfigs/h/horton/horton-1.2.0-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/h/horton/horton-1.2.0-goolf-1.4.10-Python-2.7.3.eb index 3f0df333bf..067d4ce450 100644 --- a/easybuild/easyconfigs/h/horton/horton-1.2.0-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/h/horton/horton-1.2.0-goolf-1.4.10-Python-2.7.3.eb @@ -28,7 +28,8 @@ dependencies = [ ] # disable tests that require X11 by specifying "backend: agg" in matplotlibrc -runtest = 'export MATPLOTLIBRC=$PWD; echo "backend: agg" > $MATPLOTLIBRC/matplotlibrc; python setup.py build_ext -i; nosetests -v' +runtest = 'export MATPLOTLIBRC=$PWD; echo "backend: agg" > $MATPLOTLIBRC/matplotlibrc; ' +runtest += 'python setup.py build_ext -i; nosetests -v' sanity_check_paths = { 'files': [], diff --git a/easybuild/easyconfigs/h/horton/horton-1.2.1-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/h/horton/horton-1.2.1-goolf-1.4.10-Python-2.7.3.eb index d1f6974e2a..786bdb4f54 100644 --- a/easybuild/easyconfigs/h/horton/horton-1.2.1-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/h/horton/horton-1.2.1-goolf-1.4.10-Python-2.7.3.eb @@ -28,7 +28,8 @@ dependencies = [ ] # disable tests that require X11 by specifying "backend: agg" in matplotlibrc -runtest = 'export MATPLOTLIBRC=$PWD; echo "backend: agg" > $MATPLOTLIBRC/matplotlibrc; python setup.py build_ext -i; nosetests -v' +runtest = 'export MATPLOTLIBRC=$PWD; echo "backend: agg" > $MATPLOTLIBRC/matplotlibrc; ' +runtest += 'python setup.py build_ext -i; nosetests -v' sanity_check_paths = { 'files': [], -- GitLab From 8dba00cbe75ceb7740ef6134c488fba62efc5b7c Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 8 Mar 2017 17:45:35 +0800 Subject: [PATCH 0271/1603] yet another style fix --- easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.3.eb | 2 +- easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.0.eb | 2 +- easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.1.eb | 2 +- easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.2.eb | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.3.eb b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.3.eb index a4b668c8cb..8e387e8194 100644 --- a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.3.eb +++ b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.3.eb @@ -102,7 +102,7 @@ full_sanity_check = True sanity_check_paths = { 'files': ['bin/gc3utils'], - 'dirs': [('lib/python%s/site-packages' % pyver, 'lib64/python%s/site-packages')], + 'dirs': [('lib/python%s/site-packages' % pyver, 'lib64/python%s/site-packages' % pyver)], } sanity_check_commands = [('gc3utils', 'info --version')] diff --git a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.0.eb b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.0.eb index ec6e1d4b8c..3a8e68733e 100644 --- a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.0.eb +++ b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.0.eb @@ -102,7 +102,7 @@ full_sanity_check = True sanity_check_paths = { 'files': ['bin/gc3utils'], - 'dirs': [('lib/python%s/site-packages' % pyver, 'lib64/python%s/site-packages')], + 'dirs': [('lib/python%s/site-packages' % pyver, 'lib64/python%s/site-packages' % pyver)], } sanity_check_commands = [('gc3utils', 'info --version')] diff --git a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.1.eb b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.1.eb index 33b05c7f1c..b9b142b82c 100644 --- a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.1.eb +++ b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.1.eb @@ -102,7 +102,7 @@ full_sanity_check = True sanity_check_paths = { 'files': ['bin/gc3utils'], - 'dirs': [('lib/python%s/site-packages' % pyver, 'lib64/python%s/site-packages')], + 'dirs': [('lib/python%s/site-packages' % pyver, 'lib64/python%s/site-packages' % pyver)], } sanity_check_commands = [('gc3utils', 'info --version')] diff --git a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.2.eb b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.2.eb index 3d36571118..12435392e5 100644 --- a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.2.eb +++ b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.2.eb @@ -102,7 +102,7 @@ full_sanity_check = True sanity_check_paths = { 'files': ['bin/gc3utils'], - 'dirs': [('lib/python%s/site-packages' % pyver, 'lib64/python%s/site-packages')], + 'dirs': [('lib/python%s/site-packages' % pyver, 'lib64/python%s/site-packages' % pyver)], } sanity_check_commands = [('gc3utils', 'info --version')] -- GitLab From e67ec58c9ff764e522fd00ff67a5fcecfb2ca8e9 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 8 Mar 2017 17:51:04 +0800 Subject: [PATCH 0272/1603] yet another style fix --- easybuild/easyconfigs/d/DBus/DBus-1.10.8-foss-2016a.eb | 4 ++-- easybuild/easyconfigs/d/DBus/DBus-1.10.8-intel-2016a.eb | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/d/DBus/DBus-1.10.8-foss-2016a.eb b/easybuild/easyconfigs/d/DBus/DBus-1.10.8-foss-2016a.eb index e933c1af39..7dab289eff 100644 --- a/easybuild/easyconfigs/d/DBus/DBus-1.10.8-foss-2016a.eb +++ b/easybuild/easyconfigs/d/DBus/DBus-1.10.8-foss-2016a.eb @@ -16,8 +16,8 @@ source_urls = ['http://dbus.freedesktop.org/releases/dbus'] sources = [SOURCELOWER_TAR_GZ] sanity_check_paths = { - 'files': ['bin/dbus-%s' % x for x in ['cleanup-sockets', 'daemon', 'launch', 'monitor', 'run-session', 'send', - 'uuidgen']] + + 'files': ['bin/dbus-%s' % x for x in ['cleanup-sockets', 'daemon', 'launch', 'monitor', 'run-session', + 'send', 'uuidgen']] + ['lib/libdbus-1.%s' % x for x in ['a', SHLIB_EXT]], 'dirs': ['include', 'share'] } diff --git a/easybuild/easyconfigs/d/DBus/DBus-1.10.8-intel-2016a.eb b/easybuild/easyconfigs/d/DBus/DBus-1.10.8-intel-2016a.eb index 74d90eb777..e221d7bbc5 100644 --- a/easybuild/easyconfigs/d/DBus/DBus-1.10.8-intel-2016a.eb +++ b/easybuild/easyconfigs/d/DBus/DBus-1.10.8-intel-2016a.eb @@ -16,8 +16,8 @@ source_urls = ['http://dbus.freedesktop.org/releases/dbus'] sources = [SOURCELOWER_TAR_GZ] sanity_check_paths = { - 'files': ['bin/dbus-%s' % x for x in ['cleanup-sockets', 'daemon', 'launch', 'monitor', 'run-session', 'send', - 'uuidgen']] + + 'files': ['bin/dbus-%s' % x for x in ['cleanup-sockets', 'daemon', 'launch', 'monitor', 'run-session', + 'send', 'uuidgen']] + ['lib/libdbus-1.%s' % x for x in ['a', SHLIB_EXT]], 'dirs': ['include', 'share'] } -- GitLab From 64e7a3722e4418e57d89348f065681af55ab9f9b Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Wed, 8 Mar 2017 11:00:24 +0100 Subject: [PATCH 0273/1603] fix to be sure the HDF5 provided by easybuild is used --- easybuild/easyconfigs/b/BLASR/BLASR-2.1-goolf-1.4.10.eb | 3 +++ easybuild/easyconfigs/b/BLASR/BLASR-2.2-intel-2016b.eb | 3 +++ 2 files changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/b/BLASR/BLASR-2.1-goolf-1.4.10.eb b/easybuild/easyconfigs/b/BLASR/BLASR-2.1-goolf-1.4.10.eb index 7b47764f47..1461dc4f22 100644 --- a/easybuild/easyconfigs/b/BLASR/BLASR-2.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/BLASR/BLASR-2.1-goolf-1.4.10.eb @@ -23,6 +23,9 @@ dependencies = [('HDF5', '1.8.11')] skipsteps = ['configure'] +prebuildopts = 'export HDF5LIBDIR=$EBROOTHDF5/lib &&' +prebuildopts += 'export HDF5INCLUDEDIR=$EBROOTHDF5/include &&' + # the STATIC= option is a workaround. Check details here: # https://github.com/PacificBiosciences/blasr/issues/4#issuecomment-44142749 buildopts = ' STATIC= ' diff --git a/easybuild/easyconfigs/b/BLASR/BLASR-2.2-intel-2016b.eb b/easybuild/easyconfigs/b/BLASR/BLASR-2.2-intel-2016b.eb index ea4423904f..d31c4ec289 100644 --- a/easybuild/easyconfigs/b/BLASR/BLASR-2.2-intel-2016b.eb +++ b/easybuild/easyconfigs/b/BLASR/BLASR-2.2-intel-2016b.eb @@ -23,6 +23,9 @@ dependencies = [('HDF5', '1.8.18')] skipsteps = ['configure'] +prebuildopts = 'export HDF5LIBDIR=$EBROOTHDF5/lib &&' +prebuildopts += 'export HDF5INCLUDEDIR=$EBROOTHDF5/include &&' + # the STATIC= option is a workaround. Check details here: # https://github.com/PacificBiosciences/blasr/issues/4#issuecomment-44142749 buildopts = ' STATIC= ' -- GitLab From 515b3bd20aba2f214e9f33d37475e64c53b907ef Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 8 Mar 2017 18:24:06 +0800 Subject: [PATCH 0274/1603] yet another style fix --- .../h/h5py/h5py-2.0.1-ictce-5.3.0-Python-2.7.3.eb | 3 +-- .../h/h5py/h5py-2.4.0-intel-2015a-Python-2.7.9-serial.eb | 5 ++--- 2 files changed, 3 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.0.1-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/h/h5py/h5py-2.0.1-ictce-5.3.0-Python-2.7.3.eb index 1807b63953..72344ad38b 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.0.1-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.0.1-ictce-5.3.0-Python-2.7.3.eb @@ -16,7 +16,6 @@ sources = [SOURCE_TAR_GZ] python = 'Python' pythonver = '2.7.3' -pythonshortver = '.'.join(pythonver.split('.')[0:2]) versionsuffix = '-%s-%s' % (python, pythonver) dependencies = [ @@ -27,7 +26,7 @@ dependencies = [ sanity_check_paths = { 'files': [], - 'dirs': ['lib/python%s/site-packages/%%(name)s' % pythonshortver], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], } moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.4.0-intel-2015a-Python-2.7.9-serial.eb b/easybuild/easyconfigs/h/h5py/h5py-2.4.0-intel-2015a-Python-2.7.9-serial.eb index d7449726a8..56c251d6fa 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.4.0-intel-2015a-Python-2.7.9-serial.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.4.0-intel-2015a-Python-2.7.9-serial.eb @@ -16,7 +16,6 @@ sources = [SOURCE_TAR_GZ] python = 'Python' pythonver = '2.7.9' -pythonshortver = '.'.join(pythonver.split('.')[0:2]) versionsuffix = '-%s-%s-serial' % (python, pythonver) prebuildopts = ' python setup.py configure --hdf5=$EBROOTHDF5 && ' @@ -29,8 +28,8 @@ dependencies = [ builddependencies = [('pkgconfig', '1.1.0', '-Python-%(pyver)s')] sanity_check_paths = { - 'files': ['lib/python%s/site-packages/%%(name)s-%%(version)s-py%s-linux-x86_64.egg' % (2 * (pythonshortver, ))], - 'dirs': [], + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], } moduleclass = 'data' -- GitLab From 2968917cdbfbd864ae1b92aed11f2321f3e049b3 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 8 Mar 2017 18:26:07 +0800 Subject: [PATCH 0275/1603] yet another batch of minor style fixes --- .../easyconfigs/i/IMa2p/IMa2p-20151123-foss-2016a.eb | 2 +- .../easyconfigs/i/IMa2p/IMa2p-20160804-intel-2016b.eb | 2 +- .../easyconfigs/i/IOzone/IOzone-3.434-foss-2016a.eb | 11 +++++------ .../IPython-5.2.2-intel-2016b-Python-2.7.12.eb | 6 +++--- easybuild/easyconfigs/i/ISL/ISL-0.14-GCC-4.9.2.eb | 2 +- .../easyconfigs/i/ISL/ISL-0.15-GCC-4.9.3-2.25.eb | 2 +- .../easyconfigs/i/ISL/ISL-0.15-GNU-4.9.3-2.25.eb | 2 +- easybuild/easyconfigs/i/ISL/ISL-0.15-foss-2016a.eb | 2 +- .../easyconfigs/i/ISL/ISL-0.16-GCC-4.9.3-2.25.eb | 2 +- easybuild/easyconfigs/i/ISL/ISL-0.17-foss-2016a.eb | 2 +- .../easyconfigs/i/Inspector/Inspector-2013_update6.eb | 3 ++- .../Instant-1.0.0-goolf-1.4.10-Python-2.7.3.eb | 4 +++- .../Instant/Instant-1.0.0-ictce-5.3.0-Python-2.7.3.eb | 5 +++-- .../i-PI-1.0-20160213-intel-2016a-Python-2.7.11.eb | 2 +- .../i-cisTarget-20160602-intel-2016a-Python-2.7.11.eb | 2 +- easybuild/easyconfigs/i/icc/icc-11.1.073-32bit.eb | 3 +-- easybuild/easyconfigs/i/icc/icc-11.1.073.eb | 3 +-- easybuild/easyconfigs/i/icc/icc-11.1.075.eb | 3 +-- easybuild/easyconfigs/i/icc/icc-2011.10.319.eb | 3 +-- easybuild/easyconfigs/i/icc/icc-2011.13.367.eb | 3 +-- easybuild/easyconfigs/i/icc/icc-2011.3.174.eb | 3 +-- easybuild/easyconfigs/i/icc/icc-2011.6.233.eb | 3 +-- easybuild/easyconfigs/i/icc/icc-2013.1.117.eb | 3 +-- easybuild/easyconfigs/i/icc/icc-2013.2.146.eb | 3 +-- easybuild/easyconfigs/i/icc/icc-2013.3.163.eb | 3 +-- easybuild/easyconfigs/i/icc/icc-2013.4.183.eb | 3 +-- .../easyconfigs/i/icc/icc-2013.5.192-GCC-4.8.3.eb | 3 +-- easybuild/easyconfigs/i/icc/icc-2013.5.192.eb | 3 +-- easybuild/easyconfigs/i/icc/icc-2013_sp1.0.080.eb | 3 +-- easybuild/easyconfigs/i/icc/icc-2013_sp1.1.106.eb | 3 +-- easybuild/easyconfigs/i/icc/icc-2013_sp1.2.144.eb | 3 +-- easybuild/easyconfigs/i/icc/icc-2013_sp1.3.174.eb | 3 +-- easybuild/easyconfigs/i/icc/icc-2013_sp1.4.211.eb | 3 +-- .../easyconfigs/i/icc/icc-2015.0.090-GCC-4.9.2.eb | 3 +-- easybuild/easyconfigs/i/icc/icc-2015.0.090.eb | 3 +-- .../easyconfigs/i/icc/icc-2015.1.133-GCC-4.9.2.eb | 3 +-- easybuild/easyconfigs/i/icc/icc-2015.1.133.eb | 3 +-- .../easyconfigs/i/icc/icc-2015.2.164-GCC-4.9.2.eb | 3 +-- .../i/icc/icc-2015.3.187-GNU-4.9.3-2.25.eb | 3 +-- easybuild/easyconfigs/i/icc/icc-2015.3.187.eb | 3 +-- .../i/icc/icc-2015.5.223-GCC-4.9.3-2.25.eb | 3 +-- .../i/icc/icc-2016.0.109-GCC-4.9.3-2.25.eb | 3 +-- easybuild/easyconfigs/i/icc/icc-2016.0.109.eb | 3 +-- .../i/icc/icc-2016.1.150-GCC-4.9.3-2.25.eb | 3 +-- .../easyconfigs/i/iccifort/iccifort-2015.0.090.eb | 3 ++- .../easyconfigs/i/iccifort/iccifort-2015.1.133.eb | 3 ++- .../easyconfigs/i/iccifort/iccifort-2015.3.187.eb | 3 ++- .../i/iccifort/iccifort-2016.0.109-GCC-4.9.3-2.25.eb | 3 ++- .../easyconfigs/i/iccifort/iccifort-2016.0.109.eb | 3 ++- .../i/iccifort/iccifort-2016.1.150-GCC-4.9.3-2.25.eb | 3 ++- .../i/iccifort/iccifort-2016.2.181-GCC-4.9.3-2.25.eb | 3 ++- .../i/iccifort/iccifort-2016.2.181-GCC-5.3.0-2.26.eb | 3 ++- .../i/iccifort/iccifort-2016.3.210-GCC-4.9.3-2.25.eb | 3 ++- .../i/iccifort/iccifort-2016.3.210-GCC-5.3.0-2.26.eb | 3 ++- .../i/iccifort/iccifort-2016.3.210-GCC-5.4.0-2.26.eb | 3 ++- .../i/iccifort/iccifort-2017.0.098-GCC-5.4.0-2.26.eb | 3 ++- .../i/iccifort/iccifort-2017.1.132-GCC-5.4.0-2.26.eb | 3 ++- .../i/iccifort/iccifort-2017.1.132-GCC-6.3.0-2.27.eb | 3 ++- .../i/iccifort/iccifort-2017.2.174-GCC-6.3.0-2.27.eb | 3 ++- .../i/iccifortcuda/iccifortcuda-2016.10.eb | 3 ++- .../easyconfigs/i/icmake/icmake-7.23.02-foss-2016a.eb | 8 ++++---- easybuild/easyconfigs/i/ictce/ictce-5.2.0.eb | 3 ++- easybuild/easyconfigs/i/ictce/ictce-5.3.0.eb | 3 ++- easybuild/easyconfigs/i/ictce/ictce-5.4.0.eb | 3 ++- easybuild/easyconfigs/i/ictce/ictce-5.5.0.eb | 3 ++- easybuild/easyconfigs/i/ictce/ictce-6.1.5.eb | 3 ++- easybuild/easyconfigs/i/ictce/ictce-6.2.5.eb | 3 ++- easybuild/easyconfigs/i/ictce/ictce-7.1.2.eb | 3 ++- easybuild/easyconfigs/i/ictce/ictce-7.3.5.eb | 3 ++- easybuild/easyconfigs/i/ifort/ifort-11.1.073-32bit.eb | 3 +-- easybuild/easyconfigs/i/ifort/ifort-11.1.073.eb | 3 +-- easybuild/easyconfigs/i/ifort/ifort-11.1.075.eb | 3 +-- easybuild/easyconfigs/i/ifort/ifort-2011.10.319.eb | 3 +-- easybuild/easyconfigs/i/ifort/ifort-2011.13.367.eb | 3 +-- easybuild/easyconfigs/i/ifort/ifort-2011.3.174.eb | 3 +-- easybuild/easyconfigs/i/ifort/ifort-2011.6.233.eb | 3 +-- easybuild/easyconfigs/i/ifort/ifort-2013.1.117.eb | 3 +-- easybuild/easyconfigs/i/ifort/ifort-2013.2.146.eb | 3 +-- easybuild/easyconfigs/i/ifort/ifort-2013.3.163.eb | 3 +-- easybuild/easyconfigs/i/ifort/ifort-2013.4.183.eb | 3 +-- .../easyconfigs/i/ifort/ifort-2013.5.192-GCC-4.8.3.eb | 3 +-- easybuild/easyconfigs/i/ifort/ifort-2013.5.192.eb | 3 +-- easybuild/easyconfigs/i/ifort/ifort-2013_sp1.0.080.eb | 3 +-- easybuild/easyconfigs/i/ifort/ifort-2013_sp1.1.106.eb | 3 +-- easybuild/easyconfigs/i/ifort/ifort-2013_sp1.2.144.eb | 3 +-- easybuild/easyconfigs/i/ifort/ifort-2013_sp1.3.174.eb | 3 +-- easybuild/easyconfigs/i/ifort/ifort-2013_sp1.4.211.eb | 3 +-- .../easyconfigs/i/ifort/ifort-2015.0.090-GCC-4.9.2.eb | 3 +-- easybuild/easyconfigs/i/ifort/ifort-2015.0.090.eb | 3 +-- .../easyconfigs/i/ifort/ifort-2015.1.133-GCC-4.9.2.eb | 3 +-- easybuild/easyconfigs/i/ifort/ifort-2015.1.133.eb | 3 +-- .../easyconfigs/i/ifort/ifort-2015.2.164-GCC-4.9.2.eb | 3 +-- .../i/ifort/ifort-2015.3.187-GNU-4.9.3-2.25.eb | 3 +-- easybuild/easyconfigs/i/ifort/ifort-2015.3.187.eb | 3 +-- .../i/ifort/ifort-2015.5.223-GCC-4.9.3-2.25.eb | 3 +-- .../i/ifort/ifort-2016.0.109-GCC-4.9.3-2.25.eb | 3 +-- easybuild/easyconfigs/i/ifort/ifort-2016.0.109.eb | 3 +-- .../i/ifort/ifort-2016.1.150-GCC-4.9.3-2.25.eb | 3 +-- .../easyconfigs/i/igraph/igraph-0.7.1-intel-2016b.eb | 6 +++--- easybuild/easyconfigs/i/iimpi/iimpi-7.1.2.eb | 3 ++- easybuild/easyconfigs/i/iimpi/iimpi-7.3.5.eb | 3 ++- easybuild/easyconfigs/i/imkl/imkl-10.2.6.038-32bit.eb | 3 +-- easybuild/easyconfigs/i/imkl/imkl-10.2.6.038.eb | 3 +-- easybuild/easyconfigs/i/imkl/imkl-10.3.10.319.eb | 3 +-- easybuild/easyconfigs/i/imkl/imkl-10.3.12.361.eb | 3 +-- easybuild/easyconfigs/i/imkl/imkl-10.3.6.233.eb | 3 +-- easybuild/easyconfigs/i/imkl/imkl-11.0.1.117.eb | 3 +-- .../easyconfigs/i/imkl/imkl-11.0.2.146-iimpi-5.2.0.eb | 3 +-- easybuild/easyconfigs/i/imkl/imkl-11.0.2.146.eb | 3 +-- .../easyconfigs/i/imkl/imkl-11.0.3.163-iimpi-5.3.0.eb | 3 +-- easybuild/easyconfigs/i/imkl/imkl-11.0.3.163.eb | 3 +-- .../easyconfigs/i/imkl/imkl-11.0.4.183-iimpi-5.4.0.eb | 3 +-- easybuild/easyconfigs/i/imkl/imkl-11.0.4.183.eb | 3 +-- .../i/imkl/imkl-11.0.5.192-iimpi-5.5.0-GCC-4.8.3.eb | 3 +-- .../easyconfigs/i/imkl/imkl-11.0.5.192-iimpi-5.5.0.eb | 3 +-- easybuild/easyconfigs/i/imkl/imkl-11.0.5.192.eb | 3 +-- easybuild/easyconfigs/i/imkl/imkl-11.1.0.080.eb | 3 +-- .../easyconfigs/i/imkl/imkl-11.1.1.106-iimpi-6.1.5.eb | 3 +-- easybuild/easyconfigs/i/imkl/imkl-11.1.1.106.eb | 3 +-- .../i/imkl/imkl-11.1.2.144-2013.5.192-GCC-4.8.3.eb | 3 +-- .../easyconfigs/i/imkl/imkl-11.1.2.144-GCC-4.8.3.eb | 3 +-- .../i/imkl/imkl-11.1.2.144-OpenMPI-1.6.5.eb | 7 +++---- .../i/imkl/imkl-11.1.2.144-iimpi-5.5.3-GCC-4.8.3.eb | 3 +-- .../easyconfigs/i/imkl/imkl-11.1.2.144-iimpi-6.2.5.eb | 3 +-- .../i/imkl/imkl-11.1.2.144-iompi-2015.01.eb | 3 +-- easybuild/easyconfigs/i/imkl/imkl-11.1.2.144.eb | 3 +-- easybuild/easyconfigs/i/imkl/imkl-11.1.3.174.eb | 3 +-- .../i/imkl/imkl-11.2.0.090-iimpi-7.1.2-GCC-4.9.2.eb | 3 +-- .../easyconfigs/i/imkl/imkl-11.2.0.090-iimpi-7.1.2.eb | 3 +-- .../i/imkl/imkl-11.2.1.133-iimpi-7.2.3-GCC-4.9.2.eb | 3 +-- .../i/imkl/imkl-11.2.2.164-iimpi-7.2.5-GCC-4.9.2.eb | 3 +-- .../i/imkl/imkl-11.2.2.164-iompi-2015.02.eb | 3 +-- .../i/imkl/imkl-11.2.3.187-gimpi-2.11.5.eb | 3 +-- .../imkl-11.2.3.187-iimpi-7.3.5-GNU-4.9.3-2.25.eb | 3 +-- .../easyconfigs/i/imkl/imkl-11.2.3.187-iimpi-7.3.5.eb | 3 +-- .../i/imkl/imkl-11.2.3.187-iompi-2015.03.eb | 7 +++---- .../imkl-11.3.0.109-iimpi-2016.00-GCC-4.9.3-2.25.eb | 3 +-- .../imkl-11.3.1.150-iimpi-2016.01-GCC-4.9.3-2.25.eb | 3 +-- .../imkl-11.3.1.150-iimpi-7.5.5-GCC-4.9.3-2.25.eb | 3 +-- .../imkl-11.3.1.150-iimpi-8.1.5-GCC-4.9.3-2.25.eb | 3 +-- easybuild/easyconfigs/i/impi/impi-3.2.2.006.eb | 3 +-- easybuild/easyconfigs/i/impi/impi-4.0.0.028-32bit.eb | 3 +-- easybuild/easyconfigs/i/impi/impi-4.0.0.028.eb | 3 +-- easybuild/easyconfigs/i/impi/impi-4.0.2.003.eb | 3 +-- easybuild/easyconfigs/i/impi/impi-4.1.0.027.eb | 3 +-- .../i/impi/impi-4.1.0.030-iccifort-2013.2.146.eb | 3 +-- .../i/impi/impi-4.1.0.030-iccifort-2013.3.163.eb | 3 +-- .../i/impi/impi-4.1.0.030-iccifort-2013.4.183.eb | 3 +-- easybuild/easyconfigs/i/impi/impi-4.1.0.030.eb | 3 +-- .../impi-4.1.1.036-iccifort-2013.5.192-GCC-4.8.3.eb | 3 +-- .../i/impi/impi-4.1.1.036-iccifort-2013.5.192.eb | 3 +-- easybuild/easyconfigs/i/impi/impi-4.1.1.036.eb | 3 +-- easybuild/easyconfigs/i/impi/impi-4.1.2.040.eb | 3 +-- .../i/impi/impi-4.1.3.045-iccifort-2013_sp1.1.106.eb | 3 +-- easybuild/easyconfigs/i/impi/impi-4.1.3.045.eb | 3 +-- .../easyconfigs/i/impi/impi-4.1.3.049-GCC-4.8.3.eb | 3 +-- .../impi-4.1.3.049-iccifort-2013.5.192-GCC-4.8.3.eb | 3 +-- .../i/impi/impi-4.1.3.049-iccifort-2013_sp1.2.144.eb | 3 +-- easybuild/easyconfigs/i/impi/impi-4.1.3.049.eb | 3 +-- .../impi-5.0.1.035-iccifort-2015.0.090-GCC-4.9.2.eb | 3 +-- .../i/impi/impi-5.0.1.035-iccifort-2015.0.090.eb | 3 +-- .../impi-5.0.2.044-iccifort-2015.1.133-GCC-4.9.2.eb | 3 +-- .../easyconfigs/i/impi/impi-5.0.3.048-GCC-4.9.3.eb | 3 +-- .../impi-5.0.3.048-iccifort-2015.2.164-GCC-4.9.2.eb | 3 +-- ...pi-5.0.3.048-iccifort-2015.3.187-GNU-4.9.3-2.25.eb | 3 +-- .../i/impi/impi-5.0.3.048-iccifort-2015.3.187.eb | 3 +-- .../i/impi/impi-5.1.0.079-iccifort-2015.3.187.eb | 3 +-- ...pi-5.1.1.109-iccifort-2016.0.109-GCC-4.9.3-2.25.eb | 3 +-- ...pi-5.1.2.150-iccifort-2015.5.223-GCC-4.9.3-2.25.eb | 3 +-- ...pi-5.1.2.150-iccifort-2016.1.150-GCC-4.9.3-2.25.eb | 3 +-- easybuild/easyconfigs/i/intel/intel-2014.06.eb | 3 ++- easybuild/easyconfigs/i/intel/intel-2014.10.eb | 3 ++- easybuild/easyconfigs/i/intel/intel-2014.11.eb | 3 ++- easybuild/easyconfigs/i/intel/intel-2014b.eb | 3 ++- easybuild/easyconfigs/i/intel/intel-2015.02.eb | 3 ++- easybuild/easyconfigs/i/intel/intel-2015.08.eb | 3 ++- easybuild/easyconfigs/i/intel/intel-2015a.eb | 3 ++- easybuild/easyconfigs/i/intel/intel-2015b.eb | 3 ++- easybuild/easyconfigs/i/intel/intel-2016.00.eb | 3 ++- easybuild/easyconfigs/i/intel/intel-2016.01.eb | 3 ++- .../easyconfigs/i/intel/intel-2016.02-GCC-4.9.eb | 3 ++- .../easyconfigs/i/intel/intel-2016.02-GCC-5.3.eb | 3 ++- .../easyconfigs/i/intel/intel-2016.03-GCC-4.9.eb | 3 ++- .../easyconfigs/i/intel/intel-2016.03-GCC-5.3.eb | 3 ++- .../easyconfigs/i/intel/intel-2016.03-GCC-5.4.eb | 3 ++- easybuild/easyconfigs/i/intel/intel-2016a.eb | 3 ++- easybuild/easyconfigs/i/intel/intel-2016b.eb | 3 ++- easybuild/easyconfigs/i/intel/intel-2017.00.eb | 3 ++- easybuild/easyconfigs/i/intel/intel-2017.01.eb | 3 ++- easybuild/easyconfigs/i/intel/intel-2017.02.eb | 3 ++- easybuild/easyconfigs/i/intel/intel-2017a.eb | 3 ++- .../intltool-0.51.0-GCCcore-4.9.3-Perl-5.24.0.eb | 2 +- .../intltool-0.51.0-intel-2016a-Perl-5.20.3.eb | 2 +- .../easyconfigs/i/io_lib/io_lib-1.14.8-foss-2016a.eb | 8 ++++---- easybuild/easyconfigs/i/iomkl/iomkl-2015.01.eb | 3 ++- easybuild/easyconfigs/i/iomkl/iomkl-2015.02.eb | 3 ++- easybuild/easyconfigs/i/iomkl/iomkl-2015.03.eb | 3 ++- easybuild/easyconfigs/i/iomkl/iomkl-2016.07.eb | 3 ++- .../i/iomkl/iomkl-2016.09-GCC-4.9.3-2.25.eb | 3 ++- .../i/iomkl/iomkl-2016.09-GCC-5.4.0-2.26.eb | 3 ++- easybuild/easyconfigs/i/iomkl/iomkl-2017.01.eb | 3 ++- easybuild/easyconfigs/i/iomkl/iomkl-2017a.eb | 3 ++- .../i/iompi/iompi-2016.09-GCC-4.9.3-2.25.eb | 1 - .../i/iompi/iompi-2016.09-GCC-5.4.0-2.26.eb | 1 - easybuild/easyconfigs/i/ipp/ipp-7.0.5.233.eb | 3 +-- easybuild/easyconfigs/i/ipp/ipp-8.1.0.144.eb | 3 +-- easybuild/easyconfigs/i/ipp/ipp-9.0.1.150.eb | 3 +-- easybuild/easyconfigs/i/itac/itac-8.0.0.011.eb | 3 +-- easybuild/easyconfigs/i/itac/itac-8.1.4.045.eb | 3 +-- easybuild/easyconfigs/i/itac/itac-9.0.3.051.eb | 3 +-- 210 files changed, 286 insertions(+), 363 deletions(-) diff --git a/easybuild/easyconfigs/i/IMa2p/IMa2p-20151123-foss-2016a.eb b/easybuild/easyconfigs/i/IMa2p/IMa2p-20151123-foss-2016a.eb index 54799f31a3..bfcfa298dc 100644 --- a/easybuild/easyconfigs/i/IMa2p/IMa2p-20151123-foss-2016a.eb +++ b/easybuild/easyconfigs/i/IMa2p/IMa2p-20151123-foss-2016a.eb @@ -1,6 +1,6 @@ easyblock = 'ConfigureMake' -name ='IMa2p' +name = 'IMa2p' version = '20151123' commit = '66e7ac7bc5e4c5bbadbd7de943465afeb4641770' diff --git a/easybuild/easyconfigs/i/IMa2p/IMa2p-20160804-intel-2016b.eb b/easybuild/easyconfigs/i/IMa2p/IMa2p-20160804-intel-2016b.eb index 28cdb8a360..6621f7655d 100644 --- a/easybuild/easyconfigs/i/IMa2p/IMa2p-20160804-intel-2016b.eb +++ b/easybuild/easyconfigs/i/IMa2p/IMa2p-20160804-intel-2016b.eb @@ -1,6 +1,6 @@ easyblock = 'ConfigureMake' -name ='IMa2p' +name = 'IMa2p' version = '20160804' commit = '1ebe5777ed96b878cc81109bede84dc3f7bb5e3b' diff --git a/easybuild/easyconfigs/i/IOzone/IOzone-3.434-foss-2016a.eb b/easybuild/easyconfigs/i/IOzone/IOzone-3.434-foss-2016a.eb index 9e03233c20..6af67462a3 100644 --- a/easybuild/easyconfigs/i/IOzone/IOzone-3.434-foss-2016a.eb +++ b/easybuild/easyconfigs/i/IOzone/IOzone-3.434-foss-2016a.eb @@ -4,10 +4,8 @@ name = 'IOzone' version = '3.434' homepage = 'http://www.iozone.org/' -description = """ -IOzone is a filesystem benchmark tool. The benchmark generates and measures a variety of file operations. Iozone has been ported - to many machines and runs under many operating systems. -""" +description = """IOzone is a filesystem benchmark tool. The benchmark generates and measures a variety of file + operations. Iozone has been ported to many machines and runs under many operating systems.""" toolchain = {'name': 'foss', 'version': '2016a'} @@ -22,8 +20,9 @@ files_to_copy = [ (['src/current/%s' % docfile for docfile in ['gengnuplot.sh', 'report.pl', 'Changes.txt']], 'share/doc'), (['src/current/%s' % docfile for docfile in ['gengnuplot.sh', 'Generate_Graphs', 'gnu3d.dem']], 'share'), (['docs/iozone.1'], 'share/man/man1'), - (['docs/%s' % docfile for docfile in ['IOzone_msword_98.doc', 'IOzone_msword_98.pdf', 'Iozone_ps.gz', 'Run_rules.doc']], - 'share/doc'), + (['docs/%s' % docfile for docfile in ['IOzone_msword_98.doc', 'IOzone_msword_98.pdf', 'Iozone_ps.gz', + 'Run_rules.doc']], + 'share/doc'), ] diff --git a/easybuild/easyconfigs/i/IPython/IPython-5.2.2-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/i/IPython/IPython-5.2.2-intel-2016b-Python-2.7.12.eb index bc8f42751d..89001fc17a 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-5.2.2-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-5.2.2-intel-2016b-Python-2.7.12.eb @@ -20,7 +20,7 @@ dependencies = [ ('testpath', '0.3', versionsuffix), # required by 'nbconvert', but causes problems w.r.t. 'backports' module... # see https://github.com/hpcugent/easybuild-easyconfigs/issues/3825 - #('entrypoints', '0.2.2', versionsuffix), + # ('entrypoints', '0.2.2', versionsuffix), ('path.py', '10.1', versionsuffix), ('prompt-toolkit', '1.0.13', versionsuffix), ] @@ -113,9 +113,9 @@ exts_list = [ }), # disabled because entrypoints on which this depends pull in configparser, which causes problems # see https://github.com/hpcugent/easybuild-easyconfigs/issues/3825 - #('nbconvert', '5.1.1', { + # ('nbconvert', '5.1.1', { # 'source_urls': ['https://pypi.python.org/packages/source/n/nbconvert/'], - #}), + # }), ('backports.shutil_get_terminal_size', '1.0.0', { 'source_urls': ['https://pypi.python.org/packages/source/b/backports.shutil_get_terminal_size/'], }), diff --git a/easybuild/easyconfigs/i/ISL/ISL-0.14-GCC-4.9.2.eb b/easybuild/easyconfigs/i/ISL/ISL-0.14-GCC-4.9.2.eb index a303238f9b..6e5acb74b1 100644 --- a/easybuild/easyconfigs/i/ISL/ISL-0.14-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/i/ISL/ISL-0.14-GCC-4.9.2.eb @@ -4,7 +4,7 @@ name = 'ISL' version = '0.14' homepage = 'http://isl.gforge.inria.fr/' -description = """isl is a library for manipulating sets and relations of integer points bounded by linear constraints.""" +description = "isl is a library for manipulating sets and relations of integer points bounded by linear constraints." toolchain = {'name': 'GCC', 'version': '4.9.2'} diff --git a/easybuild/easyconfigs/i/ISL/ISL-0.15-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/ISL/ISL-0.15-GCC-4.9.3-2.25.eb index e711a7699f..00012d332d 100644 --- a/easybuild/easyconfigs/i/ISL/ISL-0.15-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/ISL/ISL-0.15-GCC-4.9.3-2.25.eb @@ -4,7 +4,7 @@ name = 'ISL' version = '0.15' homepage = 'http://isl.gforge.inria.fr/' -description = """isl is a library for manipulating sets and relations of integer points bounded by linear constraints.""" +description = "isl is a library for manipulating sets and relations of integer points bounded by linear constraints." toolchain = {'name': 'GCC', 'version': '4.9.3-2.25'} diff --git a/easybuild/easyconfigs/i/ISL/ISL-0.15-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/i/ISL/ISL-0.15-GNU-4.9.3-2.25.eb index 5ae9fcabbc..a5f0f5cc5f 100644 --- a/easybuild/easyconfigs/i/ISL/ISL-0.15-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/ISL/ISL-0.15-GNU-4.9.3-2.25.eb @@ -4,7 +4,7 @@ name = 'ISL' version = '0.15' homepage = 'http://isl.gforge.inria.fr/' -description = """isl is a library for manipulating sets and relations of integer points bounded by linear constraints.""" +description = "isl is a library for manipulating sets and relations of integer points bounded by linear constraints." toolchain = {'name': 'GNU', 'version': '4.9.3-2.25'} diff --git a/easybuild/easyconfigs/i/ISL/ISL-0.15-foss-2016a.eb b/easybuild/easyconfigs/i/ISL/ISL-0.15-foss-2016a.eb index bd7c2f7f2a..6fbb191c8b 100644 --- a/easybuild/easyconfigs/i/ISL/ISL-0.15-foss-2016a.eb +++ b/easybuild/easyconfigs/i/ISL/ISL-0.15-foss-2016a.eb @@ -4,7 +4,7 @@ name = 'ISL' version = '0.15' homepage = 'http://isl.gforge.inria.fr/' -description = """isl is a library for manipulating sets and relations of integer points bounded by linear constraints.""" +description = "isl is a library for manipulating sets and relations of integer points bounded by linear constraints." toolchain = {'name': 'foss', 'version': '2016a'} diff --git a/easybuild/easyconfigs/i/ISL/ISL-0.16-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/ISL/ISL-0.16-GCC-4.9.3-2.25.eb index 6b38a91f39..e6211fab28 100644 --- a/easybuild/easyconfigs/i/ISL/ISL-0.16-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/ISL/ISL-0.16-GCC-4.9.3-2.25.eb @@ -4,7 +4,7 @@ name = 'ISL' version = '0.16' homepage = 'http://isl.gforge.inria.fr/' -description = """isl is a library for manipulating sets and relations of integer points bounded by linear constraints.""" +description = "isl is a library for manipulating sets and relations of integer points bounded by linear constraints." toolchain = {'name': 'GCC', 'version': '4.9.3-2.25'} diff --git a/easybuild/easyconfigs/i/ISL/ISL-0.17-foss-2016a.eb b/easybuild/easyconfigs/i/ISL/ISL-0.17-foss-2016a.eb index a7b67d3ddf..23ff5b76f6 100644 --- a/easybuild/easyconfigs/i/ISL/ISL-0.17-foss-2016a.eb +++ b/easybuild/easyconfigs/i/ISL/ISL-0.17-foss-2016a.eb @@ -4,7 +4,7 @@ name = 'ISL' version = '0.17' homepage = 'http://isl.gforge.inria.fr/' -description = """isl is a library for manipulating sets and relations of integer points bounded by linear constraints.""" +description = "isl is a library for manipulating sets and relations of integer points bounded by linear constraints." toolchain = {'name': 'foss', 'version': '2016a'} diff --git a/easybuild/easyconfigs/i/Inspector/Inspector-2013_update6.eb b/easybuild/easyconfigs/i/Inspector/Inspector-2013_update6.eb index 59aa3e7414..ab3458b6cb 100644 --- a/easybuild/easyconfigs/i/Inspector/Inspector-2013_update6.eb +++ b/easybuild/easyconfigs/i/Inspector/Inspector-2013_update6.eb @@ -2,7 +2,8 @@ name = 'Inspector' version = '2013_update6' homepage = 'http://software.intel.com/en-us/intel-inspector-xe' -description = "Intel Inspector XE 2013 is an easy to use memory error checker and thread checker for serial and parallel applications" +description = """Intel Inspector XE 2013 is an easy to use memory error checker and thread checker for serial and + parallel applications""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/Instant/Instant-1.0.0-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/i/Instant/Instant-1.0.0-goolf-1.4.10-Python-2.7.3.eb index 6966353326..5ec986a817 100644 --- a/easybuild/easyconfigs/i/Instant/Instant-1.0.0-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/i/Instant/Instant-1.0.0-goolf-1.4.10-Python-2.7.3.eb @@ -5,7 +5,9 @@ version = '1.0.0' homepage = 'https://launchpad.net/instant' description = """Instant is a Python module that allows for instant inlining of C and C++ code in Python. -It is a small Python module built on top of SWIG and Distutils. It is part of the FEniCS Project (http://fenicsproject.org).""" + It is a small Python module built on top of SWIG and Distutils. It is part of the FEniCS Project + (http://fenicsproject.org).""" + toolchain = {'name': 'goolf', 'version': '1.4.10'} majorversion = "%s.x" % ".".join(version.split('.')[:-1]) diff --git a/easybuild/easyconfigs/i/Instant/Instant-1.0.0-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/i/Instant/Instant-1.0.0-ictce-5.3.0-Python-2.7.3.eb index 4e88df4047..06af631540 100644 --- a/easybuild/easyconfigs/i/Instant/Instant-1.0.0-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/i/Instant/Instant-1.0.0-ictce-5.3.0-Python-2.7.3.eb @@ -4,8 +4,9 @@ name = 'Instant' version = '1.0.0' homepage = 'https://launchpad.net/instant' -description = """Instant is a Python module that allows for instant inlining of C and C++ code in Python. - It is a small Python module built on top of SWIG and Distutils. It is part of the FEniCS Project (http://fenicsproject.org).""" +description = """Instant is a Python module that allows for instant inlining of C and C++ code in Python. + It is a small Python module built on top of SWIG and Distutils. It is part of the FEniCS Project + (http://fenicsproject.org).""" toolchain = {'name': 'ictce', 'version': '5.3.0'} diff --git a/easybuild/easyconfigs/i/i-PI/i-PI-1.0-20160213-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/i/i-PI/i-PI-1.0-20160213-intel-2016a-Python-2.7.11.eb index a0ac2c0885..6b3017a194 100644 --- a/easybuild/easyconfigs/i/i-PI/i-PI-1.0-20160213-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/i/i-PI/i-PI-1.0-20160213-intel-2016a-Python-2.7.11.eb @@ -1,6 +1,6 @@ easyblock = 'PythonPackage' -name ='i-PI' +name = 'i-PI' version = '1.0-20160213' commit = '2a09a6d' versionsuffix = '-Python-%(pyver)s' diff --git a/easybuild/easyconfigs/i/i-cisTarget/i-cisTarget-20160602-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/i/i-cisTarget/i-cisTarget-20160602-intel-2016a-Python-2.7.11.eb index efeb188af2..e0c5f7e40e 100644 --- a/easybuild/easyconfigs/i/i-cisTarget/i-cisTarget-20160602-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/i/i-cisTarget/i-cisTarget-20160602-intel-2016a-Python-2.7.11.eb @@ -14,7 +14,7 @@ toolchain = {'name': 'intel', 'version': '2016a'} exts_defaultclass = 'PythonPackage' exts_list = [ - # airspeed requires this specific version of cachetools + # airspeed requires this specific version of cachetools ('cachetools', '0.8.0', { 'source_urls': ['https://pypi.python.org/packages/source/c/cachetools/'], }), diff --git a/easybuild/easyconfigs/i/icc/icc-11.1.073-32bit.eb b/easybuild/easyconfigs/i/icc/icc-11.1.073-32bit.eb index 25d906e87f..6db65c8a2e 100644 --- a/easybuild/easyconfigs/i/icc/icc-11.1.073-32bit.eb +++ b/easybuild/easyconfigs/i/icc/icc-11.1.073-32bit.eb @@ -15,8 +15,7 @@ patches = ['specified-paths.patch'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' m32 = True diff --git a/easybuild/easyconfigs/i/icc/icc-11.1.073.eb b/easybuild/easyconfigs/i/icc/icc-11.1.073.eb index 270e177a0c..426c8d4726 100644 --- a/easybuild/easyconfigs/i/icc/icc-11.1.073.eb +++ b/easybuild/easyconfigs/i/icc/icc-11.1.073.eb @@ -14,7 +14,6 @@ patches = ['specified-paths.patch'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/icc/icc-11.1.075.eb b/easybuild/easyconfigs/i/icc/icc-11.1.075.eb index 005adc34f3..367d02cc42 100644 --- a/easybuild/easyconfigs/i/icc/icc-11.1.075.eb +++ b/easybuild/easyconfigs/i/icc/icc-11.1.075.eb @@ -14,7 +14,6 @@ patches = ['specified-paths.patch'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/icc/icc-2011.10.319.eb b/easybuild/easyconfigs/i/icc/icc-2011.10.319.eb index e8019bf5f8..df976c997d 100644 --- a/easybuild/easyconfigs/i/icc/icc-2011.10.319.eb +++ b/easybuild/easyconfigs/i/icc/icc-2011.10.319.eb @@ -11,7 +11,6 @@ sources = ['l_ccompxe_intel64_%s.tgz' % version] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/icc/icc-2011.13.367.eb b/easybuild/easyconfigs/i/icc/icc-2011.13.367.eb index 17d0cd2bbe..0e9f729010 100644 --- a/easybuild/easyconfigs/i/icc/icc-2011.13.367.eb +++ b/easybuild/easyconfigs/i/icc/icc-2011.13.367.eb @@ -11,7 +11,6 @@ sources = ['l_ccompxe_%s.tgz' % version] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/icc/icc-2011.3.174.eb b/easybuild/easyconfigs/i/icc/icc-2011.3.174.eb index cf51e4e41b..69a166ec56 100644 --- a/easybuild/easyconfigs/i/icc/icc-2011.3.174.eb +++ b/easybuild/easyconfigs/i/icc/icc-2011.3.174.eb @@ -11,7 +11,6 @@ sources = ['l_ccompxe_intel64_%s.tgz' % version] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/icc/icc-2011.6.233.eb b/easybuild/easyconfigs/i/icc/icc-2011.6.233.eb index 4079daa6ca..5c240e5c11 100644 --- a/easybuild/easyconfigs/i/icc/icc-2011.6.233.eb +++ b/easybuild/easyconfigs/i/icc/icc-2011.6.233.eb @@ -11,7 +11,6 @@ sources = ['l_ccompxe_intel64_%s.tgz' % version] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/icc/icc-2013.1.117.eb b/easybuild/easyconfigs/i/icc/icc-2013.1.117.eb index 818ade63f2..f259138a7e 100644 --- a/easybuild/easyconfigs/i/icc/icc-2013.1.117.eb +++ b/easybuild/easyconfigs/i/icc/icc-2013.1.117.eb @@ -11,7 +11,6 @@ sources = ['l_ccompxe_%s.tgz' % version] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/icc/icc-2013.2.146.eb b/easybuild/easyconfigs/i/icc/icc-2013.2.146.eb index 086b7132e2..c135115579 100644 --- a/easybuild/easyconfigs/i/icc/icc-2013.2.146.eb +++ b/easybuild/easyconfigs/i/icc/icc-2013.2.146.eb @@ -11,7 +11,6 @@ sources = ['l_ccompxe_%s.tgz' % version] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/icc/icc-2013.3.163.eb b/easybuild/easyconfigs/i/icc/icc-2013.3.163.eb index 08d3496656..b9b8d9d6de 100644 --- a/easybuild/easyconfigs/i/icc/icc-2013.3.163.eb +++ b/easybuild/easyconfigs/i/icc/icc-2013.3.163.eb @@ -11,7 +11,6 @@ sources = ['l_ccompxe_%s.tgz' % version] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/icc/icc-2013.4.183.eb b/easybuild/easyconfigs/i/icc/icc-2013.4.183.eb index 8c5cfaeab5..db58351c1b 100644 --- a/easybuild/easyconfigs/i/icc/icc-2013.4.183.eb +++ b/easybuild/easyconfigs/i/icc/icc-2013.4.183.eb @@ -11,7 +11,6 @@ sources = ['l_ccompxe_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/icc/icc-2013.5.192-GCC-4.8.3.eb b/easybuild/easyconfigs/i/icc/icc-2013.5.192-GCC-4.8.3.eb index 446396ee03..a1fab236a7 100644 --- a/easybuild/easyconfigs/i/icc/icc-2013.5.192-GCC-4.8.3.eb +++ b/easybuild/easyconfigs/i/icc/icc-2013.5.192-GCC-4.8.3.eb @@ -17,7 +17,6 @@ dependencies = [(gcc, gccver)] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/icc/icc-2013.5.192.eb b/easybuild/easyconfigs/i/icc/icc-2013.5.192.eb index 3be64f6a79..e42dd9678e 100644 --- a/easybuild/easyconfigs/i/icc/icc-2013.5.192.eb +++ b/easybuild/easyconfigs/i/icc/icc-2013.5.192.eb @@ -11,7 +11,6 @@ sources = ['l_ccompxe_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/icc/icc-2013_sp1.0.080.eb b/easybuild/easyconfigs/i/icc/icc-2013_sp1.0.080.eb index be5072e46d..ace7d02238 100644 --- a/easybuild/easyconfigs/i/icc/icc-2013_sp1.0.080.eb +++ b/easybuild/easyconfigs/i/icc/icc-2013_sp1.0.080.eb @@ -11,7 +11,6 @@ sources = ['l_ccompxe_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/icc/icc-2013_sp1.1.106.eb b/easybuild/easyconfigs/i/icc/icc-2013_sp1.1.106.eb index 2e5244fe91..b62448cecd 100644 --- a/easybuild/easyconfigs/i/icc/icc-2013_sp1.1.106.eb +++ b/easybuild/easyconfigs/i/icc/icc-2013_sp1.1.106.eb @@ -14,5 +14,4 @@ moduleclass = 'compiler' dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' diff --git a/easybuild/easyconfigs/i/icc/icc-2013_sp1.2.144.eb b/easybuild/easyconfigs/i/icc/icc-2013_sp1.2.144.eb index b742c2c7e4..939c072363 100644 --- a/easybuild/easyconfigs/i/icc/icc-2013_sp1.2.144.eb +++ b/easybuild/easyconfigs/i/icc/icc-2013_sp1.2.144.eb @@ -14,5 +14,4 @@ moduleclass = 'compiler' dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' diff --git a/easybuild/easyconfigs/i/icc/icc-2013_sp1.3.174.eb b/easybuild/easyconfigs/i/icc/icc-2013_sp1.3.174.eb index e4c5184bc0..3ebed03a03 100644 --- a/easybuild/easyconfigs/i/icc/icc-2013_sp1.3.174.eb +++ b/easybuild/easyconfigs/i/icc/icc-2013_sp1.3.174.eb @@ -14,5 +14,4 @@ moduleclass = 'compiler' dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' diff --git a/easybuild/easyconfigs/i/icc/icc-2013_sp1.4.211.eb b/easybuild/easyconfigs/i/icc/icc-2013_sp1.4.211.eb index 5850a5593b..26892de20b 100644 --- a/easybuild/easyconfigs/i/icc/icc-2013_sp1.4.211.eb +++ b/easybuild/easyconfigs/i/icc/icc-2013_sp1.4.211.eb @@ -15,5 +15,4 @@ moduleclass = 'compiler' dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' diff --git a/easybuild/easyconfigs/i/icc/icc-2015.0.090-GCC-4.9.2.eb b/easybuild/easyconfigs/i/icc/icc-2015.0.090-GCC-4.9.2.eb index d02dca7d22..e290c96aa6 100644 --- a/easybuild/easyconfigs/i/icc/icc-2015.0.090-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/i/icc/icc-2015.0.090-GCC-4.9.2.eb @@ -17,7 +17,6 @@ dependencies = [(gcc, gccver)] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/icc/icc-2015.0.090.eb b/easybuild/easyconfigs/i/icc/icc-2015.0.090.eb index dba6123fdb..352973960c 100644 --- a/easybuild/easyconfigs/i/icc/icc-2015.0.090.eb +++ b/easybuild/easyconfigs/i/icc/icc-2015.0.090.eb @@ -11,7 +11,6 @@ sources = ['l_ccompxe_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/icc/icc-2015.1.133-GCC-4.9.2.eb b/easybuild/easyconfigs/i/icc/icc-2015.1.133-GCC-4.9.2.eb index 368b594177..13ebafc260 100644 --- a/easybuild/easyconfigs/i/icc/icc-2015.1.133-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/i/icc/icc-2015.1.133-GCC-4.9.2.eb @@ -17,7 +17,6 @@ dependencies = [(gcc, gccver)] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/icc/icc-2015.1.133.eb b/easybuild/easyconfigs/i/icc/icc-2015.1.133.eb index 08a6748331..326875c307 100644 --- a/easybuild/easyconfigs/i/icc/icc-2015.1.133.eb +++ b/easybuild/easyconfigs/i/icc/icc-2015.1.133.eb @@ -11,7 +11,6 @@ sources = ['l_ccompxe_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/icc/icc-2015.2.164-GCC-4.9.2.eb b/easybuild/easyconfigs/i/icc/icc-2015.2.164-GCC-4.9.2.eb index 8439c044f4..dbb4b84039 100644 --- a/easybuild/easyconfigs/i/icc/icc-2015.2.164-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/i/icc/icc-2015.2.164-GCC-4.9.2.eb @@ -17,7 +17,6 @@ dependencies = [(gcc, gccver)] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/icc/icc-2015.3.187-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/i/icc/icc-2015.3.187-GNU-4.9.3-2.25.eb index 37331a1488..ae1d56e8a6 100644 --- a/easybuild/easyconfigs/i/icc/icc-2015.3.187-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/icc/icc-2015.3.187-GNU-4.9.3-2.25.eb @@ -17,7 +17,6 @@ dependencies = [(gnu, gnuver)] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/icc/icc-2015.3.187.eb b/easybuild/easyconfigs/i/icc/icc-2015.3.187.eb index 55dec91be5..833da3c0c7 100644 --- a/easybuild/easyconfigs/i/icc/icc-2015.3.187.eb +++ b/easybuild/easyconfigs/i/icc/icc-2015.3.187.eb @@ -11,7 +11,6 @@ sources = ['l_ccompxe_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/icc/icc-2015.5.223-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/icc/icc-2015.5.223-GCC-4.9.3-2.25.eb index 1ca6568cb7..b9a332e3a0 100644 --- a/easybuild/easyconfigs/i/icc/icc-2015.5.223-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/icc/icc-2015.5.223-GCC-4.9.3-2.25.eb @@ -20,7 +20,6 @@ dependencies = [ dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/icc/icc-2016.0.109-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/icc/icc-2016.0.109-GCC-4.9.3-2.25.eb index 32978c0fbe..f15a97cd30 100644 --- a/easybuild/easyconfigs/i/icc/icc-2016.0.109-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/icc/icc-2016.0.109-GCC-4.9.3-2.25.eb @@ -29,7 +29,6 @@ components = ['intel-comp', 'intel-ccomp', 'intel-icc', 'intel-openmp', 'intel-i dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/icc/icc-2016.0.109.eb b/easybuild/easyconfigs/i/icc/icc-2016.0.109.eb index e56edba4db..18895dbe61 100644 --- a/easybuild/easyconfigs/i/icc/icc-2016.0.109.eb +++ b/easybuild/easyconfigs/i/icc/icc-2016.0.109.eb @@ -20,7 +20,6 @@ components = ['intel-comp', 'intel-ccomp', 'intel-icc', 'intel-openmp', 'intel-i dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/icc/icc-2016.1.150-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/icc/icc-2016.1.150-GCC-4.9.3-2.25.eb index 9d56289dfc..d375c69cbb 100644 --- a/easybuild/easyconfigs/i/icc/icc-2016.1.150-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/icc/icc-2016.1.150-GCC-4.9.3-2.25.eb @@ -29,7 +29,6 @@ components = ['intel-comp', 'intel-ccomp', 'intel-icc', 'intel-openmp', 'intel-i dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2015.0.090.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2015.0.090.eb index 51b0376b09..ebdf9f10ca 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2015.0.090.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2015.0.090.eb @@ -4,7 +4,8 @@ name = 'iccifort' version = '2015.0.090' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' -description = """Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and Intel MKL""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and + Intel MKL""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2015.1.133.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2015.1.133.eb index cb21cd2b6c..06b3d4cc94 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2015.1.133.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2015.1.133.eb @@ -4,7 +4,8 @@ name = 'iccifort' version = '2015.1.133' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' -description = """Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and Intel MKL""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and + Intel MKL""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2015.3.187.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2015.3.187.eb index 8387432380..7029a01c14 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2015.3.187.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2015.3.187.eb @@ -4,7 +4,8 @@ name = 'iccifort' version = '2015.3.187' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' -description = """Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and Intel MKL""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and + Intel MKL""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2016.0.109-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2016.0.109-GCC-4.9.3-2.25.eb index f1a5e6d54b..d51e11b541 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2016.0.109-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2016.0.109-GCC-4.9.3-2.25.eb @@ -6,7 +6,8 @@ version = '2016.0.109' versionsuffix = '-GCC-4.9.3-2.25' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' -description = """Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and Intel MKL""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and + Intel MKL""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2016.0.109.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2016.0.109.eb index a66481f29c..f03bb37944 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2016.0.109.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2016.0.109.eb @@ -5,7 +5,8 @@ name = 'iccifort' version = '2016.0.109' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' -description = """Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and Intel MKL""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and + Intel MKL""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2016.1.150-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2016.1.150-GCC-4.9.3-2.25.eb index 618d381f6e..8bf45db5e6 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2016.1.150-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2016.1.150-GCC-4.9.3-2.25.eb @@ -6,7 +6,8 @@ version = '2016.1.150' versionsuffix = '-GCC-4.9.3-2.25' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' -description = """Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and Intel MKL""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and + Intel MKL""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2016.2.181-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2016.2.181-GCC-4.9.3-2.25.eb index 871fae395a..7fc5fd1e8f 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2016.2.181-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2016.2.181-GCC-4.9.3-2.25.eb @@ -6,7 +6,8 @@ version = '2016.2.181' versionsuffix = '-GCC-4.9.3-2.25' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' -description = """Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and Intel MKL""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and + Intel MKL""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2016.2.181-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2016.2.181-GCC-5.3.0-2.26.eb index e07e4371a2..0b2036c9e0 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2016.2.181-GCC-5.3.0-2.26.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2016.2.181-GCC-5.3.0-2.26.eb @@ -6,7 +6,8 @@ version = '2016.2.181' versionsuffix = '-GCC-5.3.0-2.26' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' -description = """Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and Intel MKL""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and + Intel MKL""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2016.3.210-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2016.3.210-GCC-4.9.3-2.25.eb index 73f4eda01f..f961d74a1f 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2016.3.210-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2016.3.210-GCC-4.9.3-2.25.eb @@ -6,7 +6,8 @@ version = '2016.3.210' versionsuffix = '-GCC-4.9.3-2.25' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' -description = """Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and Intel MKL""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and + Intel MKL""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2016.3.210-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2016.3.210-GCC-5.3.0-2.26.eb index a1f40c75ae..f89991b41e 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2016.3.210-GCC-5.3.0-2.26.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2016.3.210-GCC-5.3.0-2.26.eb @@ -6,7 +6,8 @@ version = '2016.3.210' versionsuffix = '-GCC-5.3.0-2.26' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' -description = """Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and Intel MKL""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and + Intel MKL""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2016.3.210-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2016.3.210-GCC-5.4.0-2.26.eb index 944d7a23b2..52e91145c6 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2016.3.210-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2016.3.210-GCC-5.4.0-2.26.eb @@ -6,7 +6,8 @@ version = '2016.3.210' versionsuffix = '-GCC-5.4.0-2.26' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' -description = """Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and Intel MKL""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and + Intel MKL""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2017.0.098-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2017.0.098-GCC-5.4.0-2.26.eb index 3ed3f947b9..e2ed764a7b 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2017.0.098-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2017.0.098-GCC-5.4.0-2.26.eb @@ -6,7 +6,8 @@ version = '2017.0.098' versionsuffix = '-GCC-5.4.0-2.26' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' -description = """Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and Intel MKL""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and + Intel MKL""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2017.1.132-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2017.1.132-GCC-5.4.0-2.26.eb index 8034a2a1e1..6e347be3a2 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2017.1.132-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2017.1.132-GCC-5.4.0-2.26.eb @@ -6,7 +6,8 @@ version = '2017.1.132' versionsuffix = '-GCC-5.4.0-2.26' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' -description = """Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and Intel MKL""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and + Intel MKL""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2017.1.132-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2017.1.132-GCC-6.3.0-2.27.eb index 11f7aab8ea..ea60f74334 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2017.1.132-GCC-6.3.0-2.27.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2017.1.132-GCC-6.3.0-2.27.eb @@ -6,7 +6,8 @@ version = '2017.1.132' versionsuffix = '-GCC-6.3.0-2.27' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' -description = """Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and Intel MKL""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and + Intel MKL""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2017.2.174-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2017.2.174-GCC-6.3.0-2.27.eb index a3141d5631..d622580adc 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2017.2.174-GCC-6.3.0-2.27.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2017.2.174-GCC-6.3.0-2.27.eb @@ -6,7 +6,8 @@ version = '2017.2.174' versionsuffix = '-GCC-6.3.0-2.27' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' -description = """Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and Intel MKL""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and + Intel MKL""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/iccifortcuda/iccifortcuda-2016.10.eb b/easybuild/easyconfigs/i/iccifortcuda/iccifortcuda-2016.10.eb index 1eeb749c6e..2e8347c1be 100644 --- a/easybuild/easyconfigs/i/iccifortcuda/iccifortcuda-2016.10.eb +++ b/easybuild/easyconfigs/i/iccifortcuda/iccifortcuda-2016.10.eb @@ -4,7 +4,8 @@ name = 'iccifortcuda' version = '2016.10' homepage = '(none)' -description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL, with CUDA toolkit""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & + Intel MKL, with CUDA toolkit""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/icmake/icmake-7.23.02-foss-2016a.eb b/easybuild/easyconfigs/i/icmake/icmake-7.23.02-foss-2016a.eb index ed01c4e744..ecd5b0b755 100644 --- a/easybuild/easyconfigs/i/icmake/icmake-7.23.02-foss-2016a.eb +++ b/easybuild/easyconfigs/i/icmake/icmake-7.23.02-foss-2016a.eb @@ -4,8 +4,8 @@ name = 'icmake' version = '7.23.02' homepage = 'http://icmake.sourceforge.net/' -description = """Icmake is a hybrid between a 'make' utility and a 'shell script' language. Originally, it was written to - provide a useful tool for automatic program maintenance and system administrative tasks on old MS-DOS platforms.""" +description = """Icmake is a hybrid between a 'make' utility and a 'shell script' language. Originally, it was written + to provide a useful tool for automatic program maintenance and system administrative tasks on old MS-DOS platforms.""" toolchain = {'name': 'foss', 'version': '2016a'} toolchainopts = {'pic': True} @@ -18,8 +18,8 @@ install_cmd += './icm_bootstrap %(installdir)s && ./icm_install strip all /' sanity_check_paths = { 'files': [ - 'bin/icmake', 'bin/icmbuild', 'bin/icmstart', 'bin/icmun', - 'lib/icmake/icm-comp', 'lib/icmake/icm-exec', 'lib/icmake/icm-pp' + 'bin/icmake', 'bin/icmbuild', 'bin/icmstart', 'bin/icmun', + 'lib/icmake/icm-comp', 'lib/icmake/icm-exec', 'lib/icmake/icm-pp' ], 'dirs': [] } diff --git a/easybuild/easyconfigs/i/ictce/ictce-5.2.0.eb b/easybuild/easyconfigs/i/ictce/ictce-5.2.0.eb index fc33afb1ef..7f60c5dadb 100644 --- a/easybuild/easyconfigs/i/ictce/ictce-5.2.0.eb +++ b/easybuild/easyconfigs/i/ictce/ictce-5.2.0.eb @@ -4,7 +4,8 @@ name = 'ictce' version = '5.2.0' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' -description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & + Intel MKL.""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/ictce/ictce-5.3.0.eb b/easybuild/easyconfigs/i/ictce/ictce-5.3.0.eb index a6b070f713..0cd535b843 100644 --- a/easybuild/easyconfigs/i/ictce/ictce-5.3.0.eb +++ b/easybuild/easyconfigs/i/ictce/ictce-5.3.0.eb @@ -4,7 +4,8 @@ name = 'ictce' version = '5.3.0' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' -description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & + Intel MKL.""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/ictce/ictce-5.4.0.eb b/easybuild/easyconfigs/i/ictce/ictce-5.4.0.eb index aeb15217ff..feae6d3047 100644 --- a/easybuild/easyconfigs/i/ictce/ictce-5.4.0.eb +++ b/easybuild/easyconfigs/i/ictce/ictce-5.4.0.eb @@ -4,7 +4,8 @@ name = 'ictce' version = '5.4.0' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' -description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & + Intel MKL.""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/ictce/ictce-5.5.0.eb b/easybuild/easyconfigs/i/ictce/ictce-5.5.0.eb index 55b4f558df..7d3a7fe132 100644 --- a/easybuild/easyconfigs/i/ictce/ictce-5.5.0.eb +++ b/easybuild/easyconfigs/i/ictce/ictce-5.5.0.eb @@ -4,7 +4,8 @@ name = 'ictce' version = '5.5.0' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' -description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & + Intel MKL.""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/ictce/ictce-6.1.5.eb b/easybuild/easyconfigs/i/ictce/ictce-6.1.5.eb index e5194b8648..72271c8f07 100644 --- a/easybuild/easyconfigs/i/ictce/ictce-6.1.5.eb +++ b/easybuild/easyconfigs/i/ictce/ictce-6.1.5.eb @@ -4,7 +4,8 @@ name = 'ictce' version = '6.1.5' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' -description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & + Intel MKL.""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/ictce/ictce-6.2.5.eb b/easybuild/easyconfigs/i/ictce/ictce-6.2.5.eb index 41d6ceb53e..fca7778a45 100644 --- a/easybuild/easyconfigs/i/ictce/ictce-6.2.5.eb +++ b/easybuild/easyconfigs/i/ictce/ictce-6.2.5.eb @@ -4,7 +4,8 @@ name = 'ictce' version = '6.2.5' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' -description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & + Intel MKL.""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/ictce/ictce-7.1.2.eb b/easybuild/easyconfigs/i/ictce/ictce-7.1.2.eb index b3dda3d539..d54f7d5724 100644 --- a/easybuild/easyconfigs/i/ictce/ictce-7.1.2.eb +++ b/easybuild/easyconfigs/i/ictce/ictce-7.1.2.eb @@ -4,7 +4,8 @@ name = 'ictce' version = '7.1.2' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' -description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & + Intel MKL.""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/ictce/ictce-7.3.5.eb b/easybuild/easyconfigs/i/ictce/ictce-7.3.5.eb index 6190ed2906..e482585790 100644 --- a/easybuild/easyconfigs/i/ictce/ictce-7.3.5.eb +++ b/easybuild/easyconfigs/i/ictce/ictce-7.3.5.eb @@ -4,7 +4,8 @@ name = 'ictce' version = '7.3.5' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' -description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & + Intel MKL.""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/ifort/ifort-11.1.073-32bit.eb b/easybuild/easyconfigs/i/ifort/ifort-11.1.073-32bit.eb index c4b7144887..640705e6d0 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-11.1.073-32bit.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-11.1.073-32bit.eb @@ -15,8 +15,7 @@ patches = ['specified-paths.patch'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' m32 = True diff --git a/easybuild/easyconfigs/i/ifort/ifort-11.1.073.eb b/easybuild/easyconfigs/i/ifort/ifort-11.1.073.eb index da0e19e8a7..ee69dc8e33 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-11.1.073.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-11.1.073.eb @@ -14,7 +14,6 @@ patches = ['specified-paths.patch'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/ifort/ifort-11.1.075.eb b/easybuild/easyconfigs/i/ifort/ifort-11.1.075.eb index f8534d1717..1372125c7c 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-11.1.075.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-11.1.075.eb @@ -14,7 +14,6 @@ patches = ['specified-paths.patch'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2011.10.319.eb b/easybuild/easyconfigs/i/ifort/ifort-2011.10.319.eb index c0ab005da2..222eeaca4e 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2011.10.319.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2011.10.319.eb @@ -11,7 +11,6 @@ sources = ['l_fcompxe_intel64_%s.tgz' % version] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2011.13.367.eb b/easybuild/easyconfigs/i/ifort/ifort-2011.13.367.eb index 8d6eeaafb4..ef3f60866f 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2011.13.367.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2011.13.367.eb @@ -11,7 +11,6 @@ sources = ['l_fcompxe_%s.tgz' % version] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2011.3.174.eb b/easybuild/easyconfigs/i/ifort/ifort-2011.3.174.eb index 65ff75aa5c..5b08216822 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2011.3.174.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2011.3.174.eb @@ -11,7 +11,6 @@ sources = ['l_fcompxe_intel64_%s.tgz' % version] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2011.6.233.eb b/easybuild/easyconfigs/i/ifort/ifort-2011.6.233.eb index 0749ed0e0c..ad4923d074 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2011.6.233.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2011.6.233.eb @@ -11,7 +11,6 @@ sources = ['l_fcompxe_intel64_%s.tgz' % version] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2013.1.117.eb b/easybuild/easyconfigs/i/ifort/ifort-2013.1.117.eb index 99bf3863c6..43b7969dc4 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2013.1.117.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2013.1.117.eb @@ -11,7 +11,6 @@ sources = ['l_fcompxe_%s.tgz' % version] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2013.2.146.eb b/easybuild/easyconfigs/i/ifort/ifort-2013.2.146.eb index 54b49ddcaf..018ac9b87d 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2013.2.146.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2013.2.146.eb @@ -11,7 +11,6 @@ sources = ['l_fcompxe_%s.tgz' % version] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2013.3.163.eb b/easybuild/easyconfigs/i/ifort/ifort-2013.3.163.eb index 4efd890d23..d84bb054d0 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2013.3.163.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2013.3.163.eb @@ -11,7 +11,6 @@ sources = ['l_fcompxe_%s.tgz' % version] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2013.4.183.eb b/easybuild/easyconfigs/i/ifort/ifort-2013.4.183.eb index 05c638d451..e1ae8632f1 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2013.4.183.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2013.4.183.eb @@ -11,7 +11,6 @@ sources = ['l_fcompxe_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2013.5.192-GCC-4.8.3.eb b/easybuild/easyconfigs/i/ifort/ifort-2013.5.192-GCC-4.8.3.eb index 901fc019cc..0b6f0c22ab 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2013.5.192-GCC-4.8.3.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2013.5.192-GCC-4.8.3.eb @@ -17,7 +17,6 @@ dependencies = [(gcc, gccver)] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2013.5.192.eb b/easybuild/easyconfigs/i/ifort/ifort-2013.5.192.eb index 32705da10f..7b9de4dea5 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2013.5.192.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2013.5.192.eb @@ -11,7 +11,6 @@ sources = ['l_fcompxe_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2013_sp1.0.080.eb b/easybuild/easyconfigs/i/ifort/ifort-2013_sp1.0.080.eb index dc69a4da5e..6402e2f9ac 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2013_sp1.0.080.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2013_sp1.0.080.eb @@ -11,7 +11,6 @@ sources = ['l_fcompxe_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2013_sp1.1.106.eb b/easybuild/easyconfigs/i/ifort/ifort-2013_sp1.1.106.eb index 8d50c3c460..c762cdb26a 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2013_sp1.1.106.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2013_sp1.1.106.eb @@ -14,5 +14,4 @@ moduleclass = 'compiler' dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2013_sp1.2.144.eb b/easybuild/easyconfigs/i/ifort/ifort-2013_sp1.2.144.eb index 058b29e416..f987a0ac44 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2013_sp1.2.144.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2013_sp1.2.144.eb @@ -14,5 +14,4 @@ moduleclass = 'compiler' dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2013_sp1.3.174.eb b/easybuild/easyconfigs/i/ifort/ifort-2013_sp1.3.174.eb index 6a206056e1..a605451b28 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2013_sp1.3.174.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2013_sp1.3.174.eb @@ -14,5 +14,4 @@ moduleclass = 'compiler' dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2013_sp1.4.211.eb b/easybuild/easyconfigs/i/ifort/ifort-2013_sp1.4.211.eb index 4e061aba7c..104d8f2770 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2013_sp1.4.211.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2013_sp1.4.211.eb @@ -15,5 +15,4 @@ moduleclass = 'compiler' dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2015.0.090-GCC-4.9.2.eb b/easybuild/easyconfigs/i/ifort/ifort-2015.0.090-GCC-4.9.2.eb index a94df9884b..420984ed94 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2015.0.090-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2015.0.090-GCC-4.9.2.eb @@ -17,7 +17,6 @@ dependencies = [(gcc, gccver)] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2015.0.090.eb b/easybuild/easyconfigs/i/ifort/ifort-2015.0.090.eb index 62bde3a68e..b312c804d8 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2015.0.090.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2015.0.090.eb @@ -11,7 +11,6 @@ sources = ['l_fcompxe_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2015.1.133-GCC-4.9.2.eb b/easybuild/easyconfigs/i/ifort/ifort-2015.1.133-GCC-4.9.2.eb index 419e0257c0..a775af60a0 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2015.1.133-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2015.1.133-GCC-4.9.2.eb @@ -17,7 +17,6 @@ dependencies = [(gcc, gccver)] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2015.1.133.eb b/easybuild/easyconfigs/i/ifort/ifort-2015.1.133.eb index 02137b7498..c2c4c3e7d1 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2015.1.133.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2015.1.133.eb @@ -11,7 +11,6 @@ sources = ['l_fcompxe_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2015.2.164-GCC-4.9.2.eb b/easybuild/easyconfigs/i/ifort/ifort-2015.2.164-GCC-4.9.2.eb index 5767d1400f..6478030728 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2015.2.164-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2015.2.164-GCC-4.9.2.eb @@ -17,7 +17,6 @@ dependencies = [(gcc, gccver)] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2015.3.187-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/i/ifort/ifort-2015.3.187-GNU-4.9.3-2.25.eb index 0f54df3a82..4a9762b2d0 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2015.3.187-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2015.3.187-GNU-4.9.3-2.25.eb @@ -17,7 +17,6 @@ dependencies = [(gnu, gnuver)] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2015.3.187.eb b/easybuild/easyconfigs/i/ifort/ifort-2015.3.187.eb index 8253a3390b..6e0324f9b5 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2015.3.187.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2015.3.187.eb @@ -11,7 +11,6 @@ sources = ['l_fcompxe_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2015.5.223-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/ifort/ifort-2015.5.223-GCC-4.9.3-2.25.eb index 2fd9b5a946..446656fb7a 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2015.5.223-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2015.5.223-GCC-4.9.3-2.25.eb @@ -20,7 +20,6 @@ dependencies = [ dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2016.0.109-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/ifort/ifort-2016.0.109-GCC-4.9.3-2.25.eb index 9599d68348..a32fd8278a 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2016.0.109-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2016.0.109-GCC-4.9.3-2.25.eb @@ -32,7 +32,6 @@ components = ['intel-comp', 'intel-fcomp', 'intel-ifort', 'intel-openmp', 'intel dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2016.0.109.eb b/easybuild/easyconfigs/i/ifort/ifort-2016.0.109.eb index 657a607db3..b40428eab7 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2016.0.109.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2016.0.109.eb @@ -23,7 +23,6 @@ components = ['intel-comp', 'intel-fcomp', 'intel-ifort', 'intel-openmp', 'intel dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2016.1.150-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/ifort/ifort-2016.1.150-GCC-4.9.3-2.25.eb index 9afeb8bcc9..fdfcf853b6 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2016.1.150-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2016.1.150-GCC-4.9.3-2.25.eb @@ -32,7 +32,6 @@ components = ['intel-comp', 'intel-fcomp', 'intel-ifort', 'intel-openmp', 'intel dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/igraph/igraph-0.7.1-intel-2016b.eb b/easybuild/easyconfigs/i/igraph/igraph-0.7.1-intel-2016b.eb index ddf779e0e0..b0f9d10dbb 100644 --- a/easybuild/easyconfigs/i/igraph/igraph-0.7.1-intel-2016b.eb +++ b/easybuild/easyconfigs/i/igraph/igraph-0.7.1-intel-2016b.eb @@ -17,9 +17,9 @@ source_urls = ['https://github.com/igraph/igraph/releases/download/%(version)s'] builddependencies = [('Autotools', '20150215')] patches = [ - 'igraph-%(version)s-no-lapack-no-blas.patch', - 'igraph-%(version)s-fix-aclocal-version.patch' - ] + 'igraph-%(version)s-no-lapack-no-blas.patch', + 'igraph-%(version)s-fix-aclocal-version.patch' +] # link against MKL rather than blas/lapack preconfigopts = "env LDFLAGS='-lmkl_intel_lp64 -lmkl_core -lmkl_sequential -lpthread -lm'" diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-7.1.2.eb b/easybuild/easyconfigs/i/iimpi/iimpi-7.1.2.eb index d62bc1e82f..8ea51a816a 100644 --- a/easybuild/easyconfigs/i/iimpi/iimpi-7.1.2.eb +++ b/easybuild/easyconfigs/i/iimpi/iimpi-7.1.2.eb @@ -4,7 +4,8 @@ name = 'iimpi' version = '7.1.2' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' -description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & + Intel MKL.""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-7.3.5.eb b/easybuild/easyconfigs/i/iimpi/iimpi-7.3.5.eb index b0fe67cb26..7f36db9539 100644 --- a/easybuild/easyconfigs/i/iimpi/iimpi-7.3.5.eb +++ b/easybuild/easyconfigs/i/iimpi/iimpi-7.3.5.eb @@ -4,7 +4,8 @@ name = 'iimpi' version = '7.3.5' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' -description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & + Intel MKL.""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/imkl/imkl-10.2.6.038-32bit.eb b/easybuild/easyconfigs/i/imkl/imkl-10.2.6.038-32bit.eb index 39b3d7cf7b..f12c8b0a4a 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-10.2.6.038-32bit.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-10.2.6.038-32bit.eb @@ -29,7 +29,6 @@ interfaces = True m32 = True # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/imkl/imkl-10.2.6.038.eb b/easybuild/easyconfigs/i/imkl/imkl-10.2.6.038.eb index b1eb6ee6e3..16e7150410 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-10.2.6.038.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-10.2.6.038.eb @@ -24,7 +24,6 @@ dependencies = [ interfaces = True # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/imkl/imkl-10.3.10.319.eb b/easybuild/easyconfigs/i/imkl/imkl-10.3.10.319.eb index 91c64cfa0d..c3482af83f 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-10.3.10.319.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-10.3.10.319.eb @@ -24,7 +24,6 @@ dontcreateinstalldir = 'True' interfaces = True # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/imkl/imkl-10.3.12.361.eb b/easybuild/easyconfigs/i/imkl/imkl-10.3.12.361.eb index b8769ef805..b9464f9703 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-10.3.12.361.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-10.3.12.361.eb @@ -25,7 +25,6 @@ dontcreateinstalldir = 'True' interfaces = True # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/imkl/imkl-10.3.6.233.eb b/easybuild/easyconfigs/i/imkl/imkl-10.3.6.233.eb index b5b58cc188..23c4595c45 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-10.3.6.233.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-10.3.6.233.eb @@ -23,7 +23,6 @@ dontcreateinstalldir = 'True' interfaces = True # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.0.1.117.eb b/easybuild/easyconfigs/i/imkl/imkl-11.0.1.117.eb index 8adf971a63..11b669be47 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.0.1.117.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.0.1.117.eb @@ -25,7 +25,6 @@ dontcreateinstalldir = 'True' interfaces = True # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.0.2.146-iimpi-5.2.0.eb b/easybuild/easyconfigs/i/imkl/imkl-11.0.2.146-iimpi-5.2.0.eb index c1e7124884..cf9de7a5fc 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.0.2.146-iimpi-5.2.0.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.0.2.146-iimpi-5.2.0.eb @@ -16,7 +16,6 @@ dontcreateinstalldir = 'True' interfaces = True # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.0.2.146.eb b/easybuild/easyconfigs/i/imkl/imkl-11.0.2.146.eb index ccd95b2a7a..beeabe2d96 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.0.2.146.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.0.2.146.eb @@ -25,7 +25,6 @@ dontcreateinstalldir = 'True' interfaces = True # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.0.3.163-iimpi-5.3.0.eb b/easybuild/easyconfigs/i/imkl/imkl-11.0.3.163-iimpi-5.3.0.eb index 74e9065d7c..36091633a7 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.0.3.163-iimpi-5.3.0.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.0.3.163-iimpi-5.3.0.eb @@ -16,7 +16,6 @@ dontcreateinstalldir = 'True' interfaces = True # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.0.3.163.eb b/easybuild/easyconfigs/i/imkl/imkl-11.0.3.163.eb index 8b97b3ff26..cfa4fa1e11 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.0.3.163.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.0.3.163.eb @@ -25,7 +25,6 @@ dontcreateinstalldir = 'True' interfaces = True # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.0.4.183-iimpi-5.4.0.eb b/easybuild/easyconfigs/i/imkl/imkl-11.0.4.183-iimpi-5.4.0.eb index 471f7e9aa6..ce891766f7 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.0.4.183-iimpi-5.4.0.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.0.4.183-iimpi-5.4.0.eb @@ -16,7 +16,6 @@ dontcreateinstalldir = 'True' interfaces = True # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.0.4.183.eb b/easybuild/easyconfigs/i/imkl/imkl-11.0.4.183.eb index 98e5ffd25f..d8ef766bc1 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.0.4.183.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.0.4.183.eb @@ -25,7 +25,6 @@ dontcreateinstalldir = 'True' interfaces = True # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.0.5.192-iimpi-5.5.0-GCC-4.8.3.eb b/easybuild/easyconfigs/i/imkl/imkl-11.0.5.192-iimpi-5.5.0-GCC-4.8.3.eb index e04b151136..5c4db1885b 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.0.5.192-iimpi-5.5.0-GCC-4.8.3.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.0.5.192-iimpi-5.5.0-GCC-4.8.3.eb @@ -16,7 +16,6 @@ dontcreateinstalldir = 'True' interfaces = True # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.0.5.192-iimpi-5.5.0.eb b/easybuild/easyconfigs/i/imkl/imkl-11.0.5.192-iimpi-5.5.0.eb index 0d09ac1d4b..dbddd3cc86 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.0.5.192-iimpi-5.5.0.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.0.5.192-iimpi-5.5.0.eb @@ -16,7 +16,6 @@ dontcreateinstalldir = 'True' interfaces = True # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.0.5.192.eb b/easybuild/easyconfigs/i/imkl/imkl-11.0.5.192.eb index 0fe1b14e46..66e98d5997 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.0.5.192.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.0.5.192.eb @@ -25,7 +25,6 @@ dontcreateinstalldir = 'True' interfaces = True # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.1.0.080.eb b/easybuild/easyconfigs/i/imkl/imkl-11.1.0.080.eb index 7b7f159547..3c52f96be0 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.1.0.080.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.1.0.080.eb @@ -22,8 +22,7 @@ dependencies = [ dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' interfaces = True diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.1.1.106-iimpi-6.1.5.eb b/easybuild/easyconfigs/i/imkl/imkl-11.1.1.106-iimpi-6.1.5.eb index e37a375b7a..5ffe362a58 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.1.1.106-iimpi-6.1.5.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.1.1.106-iimpi-6.1.5.eb @@ -14,8 +14,7 @@ sources = ['l_mkl_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' interfaces = True diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.1.1.106.eb b/easybuild/easyconfigs/i/imkl/imkl-11.1.1.106.eb index cc9f1d89b5..581df89fa9 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.1.1.106.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.1.1.106.eb @@ -22,8 +22,7 @@ dependencies = [ dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' interfaces = True diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144-2013.5.192-GCC-4.8.3.eb b/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144-2013.5.192-GCC-4.8.3.eb index 3b9cb14613..1381ccc44e 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144-2013.5.192-GCC-4.8.3.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144-2013.5.192-GCC-4.8.3.eb @@ -27,7 +27,6 @@ dontcreateinstalldir = 'True' interfaces = True # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144-GCC-4.8.3.eb b/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144-GCC-4.8.3.eb index 4843fd2442..b0b43aa3b0 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144-GCC-4.8.3.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144-GCC-4.8.3.eb @@ -26,7 +26,6 @@ dontcreateinstalldir = 'True' interfaces = True # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144-OpenMPI-1.6.5.eb b/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144-OpenMPI-1.6.5.eb index 3ad520461a..7a0a1e5352 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144-OpenMPI-1.6.5.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144-OpenMPI-1.6.5.eb @@ -3,8 +3,8 @@ version = '11.1.2.144' homepage = 'http://software.intel.com/en-us/intel-mkl/' description = """Intel Math Kernel Library is a library of highly optimized, extensively threaded math routines -for science, engineering, and financial applications that require maximum performance. Core math functions include -BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.""" + for science, engineering, and financial applications that require maximum performance. Core math functions include + BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.""" toolchain = {'name': 'dummy', 'version': ''} @@ -29,7 +29,6 @@ dontcreateinstalldir = 'True' interfaces = True # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144-iimpi-5.5.3-GCC-4.8.3.eb b/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144-iimpi-5.5.3-GCC-4.8.3.eb index 2114374474..846edaec6c 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144-iimpi-5.5.3-GCC-4.8.3.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144-iimpi-5.5.3-GCC-4.8.3.eb @@ -16,7 +16,6 @@ dontcreateinstalldir = 'True' interfaces = True # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144-iimpi-6.2.5.eb b/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144-iimpi-6.2.5.eb index 8854a89598..82e9db5fed 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144-iimpi-6.2.5.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144-iimpi-6.2.5.eb @@ -14,8 +14,7 @@ sources = ['l_mkl_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' interfaces = True diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144-iompi-2015.01.eb b/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144-iompi-2015.01.eb index 2559891bcc..6bbcefb5d7 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144-iompi-2015.01.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144-iompi-2015.01.eb @@ -15,7 +15,6 @@ dontcreateinstalldir = 'True' interfaces = True # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144.eb b/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144.eb index 47e59ba9fc..ddbbf90fd9 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144.eb @@ -22,8 +22,7 @@ dependencies = [ dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' interfaces = True diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.1.3.174.eb b/easybuild/easyconfigs/i/imkl/imkl-11.1.3.174.eb index bd599cfe0d..4b1c8e4141 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.1.3.174.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.1.3.174.eb @@ -22,8 +22,7 @@ dependencies = [ dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' interfaces = True diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.2.0.090-iimpi-7.1.2-GCC-4.9.2.eb b/easybuild/easyconfigs/i/imkl/imkl-11.2.0.090-iimpi-7.1.2-GCC-4.9.2.eb index dcb2085bf3..7028d56135 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.2.0.090-iimpi-7.1.2-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.2.0.090-iimpi-7.1.2-GCC-4.9.2.eb @@ -14,8 +14,7 @@ sources = ['l_mkl_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' interfaces = True diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.2.0.090-iimpi-7.1.2.eb b/easybuild/easyconfigs/i/imkl/imkl-11.2.0.090-iimpi-7.1.2.eb index 3ce046efac..c0c59f1570 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.2.0.090-iimpi-7.1.2.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.2.0.090-iimpi-7.1.2.eb @@ -14,8 +14,7 @@ sources = ['l_mkl_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' interfaces = True diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.2.1.133-iimpi-7.2.3-GCC-4.9.2.eb b/easybuild/easyconfigs/i/imkl/imkl-11.2.1.133-iimpi-7.2.3-GCC-4.9.2.eb index a249ac518b..2ee043da29 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.2.1.133-iimpi-7.2.3-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.2.1.133-iimpi-7.2.3-GCC-4.9.2.eb @@ -14,8 +14,7 @@ sources = ['l_mkl_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' interfaces = True diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.2.2.164-iimpi-7.2.5-GCC-4.9.2.eb b/easybuild/easyconfigs/i/imkl/imkl-11.2.2.164-iimpi-7.2.5-GCC-4.9.2.eb index aadf66c552..490c88a422 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.2.2.164-iimpi-7.2.5-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.2.2.164-iimpi-7.2.5-GCC-4.9.2.eb @@ -14,8 +14,7 @@ sources = ['l_mkl_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' interfaces = True diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.2.2.164-iompi-2015.02.eb b/easybuild/easyconfigs/i/imkl/imkl-11.2.2.164-iompi-2015.02.eb index 82eec3eecb..e1fa90b6ca 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.2.2.164-iompi-2015.02.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.2.2.164-iompi-2015.02.eb @@ -15,7 +15,6 @@ dontcreateinstalldir = 'True' interfaces = True # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.2.3.187-gimpi-2.11.5.eb b/easybuild/easyconfigs/i/imkl/imkl-11.2.3.187-gimpi-2.11.5.eb index ccc021a957..4573f18614 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.2.3.187-gimpi-2.11.5.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.2.3.187-gimpi-2.11.5.eb @@ -14,8 +14,7 @@ sources = ['l_mkl_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' interfaces = True diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.2.3.187-iimpi-7.3.5-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/i/imkl/imkl-11.2.3.187-iimpi-7.3.5-GNU-4.9.3-2.25.eb index b76de536ee..8c6606cc65 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.2.3.187-iimpi-7.3.5-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.2.3.187-iimpi-7.3.5-GNU-4.9.3-2.25.eb @@ -14,8 +14,7 @@ sources = ['l_mkl_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' interfaces = True diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.2.3.187-iimpi-7.3.5.eb b/easybuild/easyconfigs/i/imkl/imkl-11.2.3.187-iimpi-7.3.5.eb index 807b5f2004..1b7dda307a 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.2.3.187-iimpi-7.3.5.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.2.3.187-iimpi-7.3.5.eb @@ -14,8 +14,7 @@ sources = ['l_mkl_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' interfaces = True diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.2.3.187-iompi-2015.03.eb b/easybuild/easyconfigs/i/imkl/imkl-11.2.3.187-iompi-2015.03.eb index 0772c5ff65..5af833e7d6 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.2.3.187-iompi-2015.03.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.2.3.187-iompi-2015.03.eb @@ -3,8 +3,8 @@ version = '11.2.3.187' homepage = 'http://software.intel.com/en-us/intel-mkl/' description = """Intel Math Kernel Library is a library of highly optimized, extensively threaded math routines -for science, engineering, and financial applications that require maximum performance. Core math functions include -BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.""" + for science, engineering, and financial applications that require maximum performance. Core math functions include + BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.""" toolchain = {'name': 'iompi', 'version': '2015.03'} @@ -13,7 +13,6 @@ sources = ['l_mkl_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.0.109-iimpi-2016.00-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.0.109-iimpi-2016.00-GCC-4.9.3-2.25.eb index f295b50925..a928de1ca4 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.3.0.109-iimpi-2016.00-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.0.109-iimpi-2016.00-GCC-4.9.3-2.25.eb @@ -17,8 +17,7 @@ checksums = ['47567e38801efe273b36b5250c759af7'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' interfaces = True diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.1.150-iimpi-2016.01-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.1.150-iimpi-2016.01-GCC-4.9.3-2.25.eb index e40fb8448a..49c3e5d75b 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.3.1.150-iimpi-2016.01-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.1.150-iimpi-2016.01-GCC-4.9.3-2.25.eb @@ -17,8 +17,7 @@ checksums = ['b57ff502b5f97f2f783e4bbda7ce42b3'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' interfaces = True diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.1.150-iimpi-7.5.5-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.1.150-iimpi-7.5.5-GCC-4.9.3-2.25.eb index 53b6037e3f..a1225d2d74 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.3.1.150-iimpi-7.5.5-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.1.150-iimpi-7.5.5-GCC-4.9.3-2.25.eb @@ -14,8 +14,7 @@ sources = ['l_mkl_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' interfaces = True diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.1.150-iimpi-8.1.5-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.1.150-iimpi-8.1.5-GCC-4.9.3-2.25.eb index de96c38b15..c807d796b6 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.3.1.150-iimpi-8.1.5-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.1.150-iimpi-8.1.5-GCC-4.9.3-2.25.eb @@ -14,8 +14,7 @@ sources = ['l_mkl_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' interfaces = True diff --git a/easybuild/easyconfigs/i/impi/impi-3.2.2.006.eb b/easybuild/easyconfigs/i/impi/impi-3.2.2.006.eb index 6a204cb330..f95dd72e44 100644 --- a/easybuild/easyconfigs/i/impi/impi-3.2.2.006.eb +++ b/easybuild/easyconfigs/i/impi/impi-3.2.2.006.eb @@ -13,8 +13,7 @@ sources = ['l_mpi_p_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' # set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) # set_mpi_wrappers_all = 'True' diff --git a/easybuild/easyconfigs/i/impi/impi-4.0.0.028-32bit.eb b/easybuild/easyconfigs/i/impi/impi-4.0.0.028-32bit.eb index 4c78a146fe..028fa649be 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.0.0.028-32bit.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.0.0.028-32bit.eb @@ -14,8 +14,7 @@ sources = ['l_mpi_pu_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' m32 = True diff --git a/easybuild/easyconfigs/i/impi/impi-4.0.0.028.eb b/easybuild/easyconfigs/i/impi/impi-4.0.0.028.eb index c44ccfe556..e460a1a60c 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.0.0.028.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.0.0.028.eb @@ -13,8 +13,7 @@ sources = ['l_mpi_pu_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' # set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) # set_mpi_wrappers_all = 'True' diff --git a/easybuild/easyconfigs/i/impi/impi-4.0.2.003.eb b/easybuild/easyconfigs/i/impi/impi-4.0.2.003.eb index 001ee2403f..7828e8ee3d 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.0.2.003.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.0.2.003.eb @@ -15,8 +15,7 @@ patches = ['impi_4.x_productsdb.patch'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' # set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) # set_mpi_wrappers_all = 'True' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.0.027.eb b/easybuild/easyconfigs/i/impi/impi-4.1.0.027.eb index 6178aa2f65..209842e727 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.0.027.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.0.027.eb @@ -13,8 +13,7 @@ sources = ['l_mpi_p_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' # set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) # set_mpi_wrappers_all = 'True' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.0.030-iccifort-2013.2.146.eb b/easybuild/easyconfigs/i/impi/impi-4.1.0.030-iccifort-2013.2.146.eb index 99cabee972..c4e43d9fa9 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.0.030-iccifort-2013.2.146.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.0.030-iccifort-2013.2.146.eb @@ -13,8 +13,7 @@ sources = ['l_mpi_p_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' # set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) # set_mpi_wrappers_all = 'True' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.0.030-iccifort-2013.3.163.eb b/easybuild/easyconfigs/i/impi/impi-4.1.0.030-iccifort-2013.3.163.eb index c4adbe0ae3..9b5a71ce36 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.0.030-iccifort-2013.3.163.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.0.030-iccifort-2013.3.163.eb @@ -13,8 +13,7 @@ sources = ['l_mpi_p_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' # set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) # set_mpi_wrappers_all = 'True' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.0.030-iccifort-2013.4.183.eb b/easybuild/easyconfigs/i/impi/impi-4.1.0.030-iccifort-2013.4.183.eb index 2121a1a6d9..36a86386a0 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.0.030-iccifort-2013.4.183.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.0.030-iccifort-2013.4.183.eb @@ -13,8 +13,7 @@ sources = ['l_mpi_p_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' # set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) # set_mpi_wrappers_all = 'True' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.0.030.eb b/easybuild/easyconfigs/i/impi/impi-4.1.0.030.eb index 92c9a61b43..3f28cb9676 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.0.030.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.0.030.eb @@ -13,8 +13,7 @@ sources = ['l_mpi_p_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' # set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) # set_mpi_wrappers_all = 'True' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.1.036-iccifort-2013.5.192-GCC-4.8.3.eb b/easybuild/easyconfigs/i/impi/impi-4.1.1.036-iccifort-2013.5.192-GCC-4.8.3.eb index 3cd6a18055..ee1796488d 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.1.036-iccifort-2013.5.192-GCC-4.8.3.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.1.036-iccifort-2013.5.192-GCC-4.8.3.eb @@ -13,8 +13,7 @@ sources = ['l_mpi_p_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' # set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) # set_mpi_wrappers_all = 'True' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.1.036-iccifort-2013.5.192.eb b/easybuild/easyconfigs/i/impi/impi-4.1.1.036-iccifort-2013.5.192.eb index 22f0699649..97573c0075 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.1.036-iccifort-2013.5.192.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.1.036-iccifort-2013.5.192.eb @@ -13,8 +13,7 @@ sources = ['l_mpi_p_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' # set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) # set_mpi_wrappers_all = 'True' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.1.036.eb b/easybuild/easyconfigs/i/impi/impi-4.1.1.036.eb index 922aa79344..5524846083 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.1.036.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.1.036.eb @@ -13,8 +13,7 @@ sources = ['l_mpi_p_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' # set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) # set_mpi_wrappers_all = 'True' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.2.040.eb b/easybuild/easyconfigs/i/impi/impi-4.1.2.040.eb index b7639d24d1..5301684735 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.2.040.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.2.040.eb @@ -13,8 +13,7 @@ sources = ['l_mpi_p_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' # set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) # set_mpi_wrappers_all = 'True' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.3.045-iccifort-2013_sp1.1.106.eb b/easybuild/easyconfigs/i/impi/impi-4.1.3.045-iccifort-2013_sp1.1.106.eb index 21ed19633f..3eef4c39b6 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.3.045-iccifort-2013_sp1.1.106.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.3.045-iccifort-2013_sp1.1.106.eb @@ -13,8 +13,7 @@ sources = ['l_mpi_p_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' # set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) # set_mpi_wrappers_all = 'True' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.3.045.eb b/easybuild/easyconfigs/i/impi/impi-4.1.3.045.eb index da5a2ab9be..de266ab029 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.3.045.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.3.045.eb @@ -13,8 +13,7 @@ sources = ['l_mpi_p_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' # set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) # set_mpi_wrappers_all = 'True' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.3.049-GCC-4.8.3.eb b/easybuild/easyconfigs/i/impi/impi-4.1.3.049-GCC-4.8.3.eb index 9e61812d8f..81b707143d 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.3.049-GCC-4.8.3.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.3.049-GCC-4.8.3.eb @@ -13,8 +13,7 @@ sources = ['l_mpi_p_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' # set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) # set_mpi_wrappers_all = 'True' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.3.049-iccifort-2013.5.192-GCC-4.8.3.eb b/easybuild/easyconfigs/i/impi/impi-4.1.3.049-iccifort-2013.5.192-GCC-4.8.3.eb index 9a3879ee53..91e7ec80d3 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.3.049-iccifort-2013.5.192-GCC-4.8.3.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.3.049-iccifort-2013.5.192-GCC-4.8.3.eb @@ -13,8 +13,7 @@ sources = ['l_mpi_p_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' # set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) # set_mpi_wrappers_all = 'True' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.3.049-iccifort-2013_sp1.2.144.eb b/easybuild/easyconfigs/i/impi/impi-4.1.3.049-iccifort-2013_sp1.2.144.eb index 5e4968df60..3b51024f12 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.3.049-iccifort-2013_sp1.2.144.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.3.049-iccifort-2013_sp1.2.144.eb @@ -13,8 +13,7 @@ sources = ['l_mpi_p_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' # set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) # set_mpi_wrappers_all = 'True' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.3.049.eb b/easybuild/easyconfigs/i/impi/impi-4.1.3.049.eb index 43cd007ba4..7b345a78e7 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.3.049.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.3.049.eb @@ -13,8 +13,7 @@ sources = ['l_mpi_p_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' # set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) # set_mpi_wrappers_all = 'True' diff --git a/easybuild/easyconfigs/i/impi/impi-5.0.1.035-iccifort-2015.0.090-GCC-4.9.2.eb b/easybuild/easyconfigs/i/impi/impi-5.0.1.035-iccifort-2015.0.090-GCC-4.9.2.eb index 28ece27457..154d705ccf 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.0.1.035-iccifort-2015.0.090-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.0.1.035-iccifort-2015.0.090-GCC-4.9.2.eb @@ -13,8 +13,7 @@ sources = ['l_mpi_p_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' # set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) # set_mpi_wrappers_all = 'True' diff --git a/easybuild/easyconfigs/i/impi/impi-5.0.1.035-iccifort-2015.0.090.eb b/easybuild/easyconfigs/i/impi/impi-5.0.1.035-iccifort-2015.0.090.eb index 6f2bcda1cb..952a3f2313 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.0.1.035-iccifort-2015.0.090.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.0.1.035-iccifort-2015.0.090.eb @@ -13,8 +13,7 @@ sources = ['l_mpi_p_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' # set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) # set_mpi_wrappers_all = 'True' diff --git a/easybuild/easyconfigs/i/impi/impi-5.0.2.044-iccifort-2015.1.133-GCC-4.9.2.eb b/easybuild/easyconfigs/i/impi/impi-5.0.2.044-iccifort-2015.1.133-GCC-4.9.2.eb index a9d198b99f..62a9caf2ee 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.0.2.044-iccifort-2015.1.133-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.0.2.044-iccifort-2015.1.133-GCC-4.9.2.eb @@ -13,8 +13,7 @@ sources = ['l_mpi_p_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' # set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) # set_mpi_wrappers_all = 'True' diff --git a/easybuild/easyconfigs/i/impi/impi-5.0.3.048-GCC-4.9.3.eb b/easybuild/easyconfigs/i/impi/impi-5.0.3.048-GCC-4.9.3.eb index 25f7950bae..46722880e7 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.0.3.048-GCC-4.9.3.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.0.3.048-GCC-4.9.3.eb @@ -13,8 +13,7 @@ sources = ['l_mpi_p_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' # set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) # set_mpi_wrappers_all = 'True' diff --git a/easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.2.164-GCC-4.9.2.eb b/easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.2.164-GCC-4.9.2.eb index df72fa53c0..452ab3ddd5 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.2.164-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.2.164-GCC-4.9.2.eb @@ -13,8 +13,7 @@ sources = ['l_mpi_p_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' # set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) # set_mpi_wrappers_all = 'True' diff --git a/easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.3.187-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.3.187-GNU-4.9.3-2.25.eb index 4b32c5dbb2..7de5ce16aa 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.3.187-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.3.187-GNU-4.9.3-2.25.eb @@ -13,8 +13,7 @@ sources = ['l_mpi_p_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' # set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) # set_mpi_wrappers_all = 'True' diff --git a/easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.3.187.eb b/easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.3.187.eb index c247bd8cc6..51baff5e35 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.3.187.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.3.187.eb @@ -13,8 +13,7 @@ sources = ['l_mpi_p_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' # set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) # set_mpi_wrappers_all = 'True' diff --git a/easybuild/easyconfigs/i/impi/impi-5.1.0.079-iccifort-2015.3.187.eb b/easybuild/easyconfigs/i/impi/impi-5.1.0.079-iccifort-2015.3.187.eb index 362bb90b08..51936e972d 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.1.0.079-iccifort-2015.3.187.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.1.0.079-iccifort-2015.3.187.eb @@ -14,8 +14,7 @@ sources = ['l_mpi_p_5.1.0.038.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' # set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) # set_mpi_wrappers_all = 'True' diff --git a/easybuild/easyconfigs/i/impi/impi-5.1.1.109-iccifort-2016.0.109-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/impi/impi-5.1.1.109-iccifort-2016.0.109-GCC-4.9.3-2.25.eb index aafd77aff0..8d146fd342 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.1.1.109-iccifort-2016.0.109-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.1.1.109-iccifort-2016.0.109-GCC-4.9.3-2.25.eb @@ -16,7 +16,6 @@ checksums = ['aa4aaec41526aa5b244e531811877b01'] dontcreateinstalldir = 'True' -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-5.1.2.150-iccifort-2015.5.223-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/impi/impi-5.1.2.150-iccifort-2015.5.223-GCC-4.9.3-2.25.eb index 9e343efe2e..af79fd7190 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.1.2.150-iccifort-2015.5.223-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.1.2.150-iccifort-2015.5.223-GCC-4.9.3-2.25.eb @@ -13,8 +13,7 @@ sources = ['l_mpi_p_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' # set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) # set_mpi_wrappers_all = 'True' diff --git a/easybuild/easyconfigs/i/impi/impi-5.1.2.150-iccifort-2016.1.150-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/impi/impi-5.1.2.150-iccifort-2016.1.150-GCC-4.9.3-2.25.eb index da4a993780..6042d117f6 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.1.2.150-iccifort-2016.1.150-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.1.2.150-iccifort-2016.1.150-GCC-4.9.3-2.25.eb @@ -16,8 +16,7 @@ checksums = ['ec4db8f718c34f09fccf9d1c89454f0a'] dontcreateinstalldir = 'True' -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' # set up all the mpi commands to default to intel compilers # set_mpi_wrappers_all = 'True' diff --git a/easybuild/easyconfigs/i/intel/intel-2014.06.eb b/easybuild/easyconfigs/i/intel/intel-2014.06.eb index 57c2903c57..37318d6737 100644 --- a/easybuild/easyconfigs/i/intel/intel-2014.06.eb +++ b/easybuild/easyconfigs/i/intel/intel-2014.06.eb @@ -4,7 +4,8 @@ name = 'intel' version = '2014.06' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' -description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & + Intel MKL.""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/intel/intel-2014.10.eb b/easybuild/easyconfigs/i/intel/intel-2014.10.eb index d89452f540..42ecc0b6a8 100644 --- a/easybuild/easyconfigs/i/intel/intel-2014.10.eb +++ b/easybuild/easyconfigs/i/intel/intel-2014.10.eb @@ -4,7 +4,8 @@ name = 'intel' version = '2014.10' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' -description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & + Intel MKL.""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/intel/intel-2014.11.eb b/easybuild/easyconfigs/i/intel/intel-2014.11.eb index 1bdbdfe846..82213850c0 100644 --- a/easybuild/easyconfigs/i/intel/intel-2014.11.eb +++ b/easybuild/easyconfigs/i/intel/intel-2014.11.eb @@ -4,7 +4,8 @@ name = 'intel' version = '2014.11' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' -description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & + Intel MKL.""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/intel/intel-2014b.eb b/easybuild/easyconfigs/i/intel/intel-2014b.eb index 9d433db3c4..2cc20c2772 100644 --- a/easybuild/easyconfigs/i/intel/intel-2014b.eb +++ b/easybuild/easyconfigs/i/intel/intel-2014b.eb @@ -4,7 +4,8 @@ name = 'intel' version = '2014b' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' -description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & + Intel MKL.""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/intel/intel-2015.02.eb b/easybuild/easyconfigs/i/intel/intel-2015.02.eb index ab8507944b..a5c22d20a4 100644 --- a/easybuild/easyconfigs/i/intel/intel-2015.02.eb +++ b/easybuild/easyconfigs/i/intel/intel-2015.02.eb @@ -4,7 +4,8 @@ name = 'intel' version = '2015.02' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' -description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & + Intel MKL.""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/intel/intel-2015.08.eb b/easybuild/easyconfigs/i/intel/intel-2015.08.eb index f154fb6c65..fc731e26ee 100644 --- a/easybuild/easyconfigs/i/intel/intel-2015.08.eb +++ b/easybuild/easyconfigs/i/intel/intel-2015.08.eb @@ -4,7 +4,8 @@ name = 'intel' version = '2015.08' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' -description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & + Intel MKL.""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/intel/intel-2015a.eb b/easybuild/easyconfigs/i/intel/intel-2015a.eb index 2cb7f99ce4..702e767c23 100644 --- a/easybuild/easyconfigs/i/intel/intel-2015a.eb +++ b/easybuild/easyconfigs/i/intel/intel-2015a.eb @@ -4,7 +4,8 @@ name = 'intel' version = '2015a' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' -description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & + Intel MKL.""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/intel/intel-2015b.eb b/easybuild/easyconfigs/i/intel/intel-2015b.eb index e0b4b71ab1..dcc37ce659 100644 --- a/easybuild/easyconfigs/i/intel/intel-2015b.eb +++ b/easybuild/easyconfigs/i/intel/intel-2015b.eb @@ -4,7 +4,8 @@ name = 'intel' version = '2015b' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' -description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & + Intel MKL.""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/intel/intel-2016.00.eb b/easybuild/easyconfigs/i/intel/intel-2016.00.eb index 241463337a..2f03a7cc46 100644 --- a/easybuild/easyconfigs/i/intel/intel-2016.00.eb +++ b/easybuild/easyconfigs/i/intel/intel-2016.00.eb @@ -5,7 +5,8 @@ name = 'intel' version = '2016.00' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' -description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & + Intel MKL.""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/intel/intel-2016.01.eb b/easybuild/easyconfigs/i/intel/intel-2016.01.eb index 37f96fa014..7c51ee2938 100644 --- a/easybuild/easyconfigs/i/intel/intel-2016.01.eb +++ b/easybuild/easyconfigs/i/intel/intel-2016.01.eb @@ -5,7 +5,8 @@ name = 'intel' version = '2016.01' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' -description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & + Intel MKL.""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/intel/intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/i/intel/intel-2016.02-GCC-4.9.eb index 41552f25a9..535ba2e732 100644 --- a/easybuild/easyconfigs/i/intel/intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/i/intel/intel-2016.02-GCC-4.9.eb @@ -6,7 +6,8 @@ gcc_maj_min = '4.9' versionsuffix = '-GCC-%s' % gcc_maj_min homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' -description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & + Intel MKL.""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/intel/intel-2016.02-GCC-5.3.eb b/easybuild/easyconfigs/i/intel/intel-2016.02-GCC-5.3.eb index 4d1e0dddac..904f548c97 100644 --- a/easybuild/easyconfigs/i/intel/intel-2016.02-GCC-5.3.eb +++ b/easybuild/easyconfigs/i/intel/intel-2016.02-GCC-5.3.eb @@ -6,7 +6,8 @@ gcc_maj_min = '5.3' versionsuffix = '-GCC-%s' % gcc_maj_min homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' -description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & + Intel MKL.""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/intel/intel-2016.03-GCC-4.9.eb b/easybuild/easyconfigs/i/intel/intel-2016.03-GCC-4.9.eb index aa6be8f54d..c7bc45badd 100644 --- a/easybuild/easyconfigs/i/intel/intel-2016.03-GCC-4.9.eb +++ b/easybuild/easyconfigs/i/intel/intel-2016.03-GCC-4.9.eb @@ -6,7 +6,8 @@ gcc_maj_min = '4.9' versionsuffix = '-GCC-%s' % gcc_maj_min homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' -description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & + Intel MKL.""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/intel/intel-2016.03-GCC-5.3.eb b/easybuild/easyconfigs/i/intel/intel-2016.03-GCC-5.3.eb index 3de185ca63..04c3682224 100644 --- a/easybuild/easyconfigs/i/intel/intel-2016.03-GCC-5.3.eb +++ b/easybuild/easyconfigs/i/intel/intel-2016.03-GCC-5.3.eb @@ -6,7 +6,8 @@ gcc_maj_min = '5.3' versionsuffix = '-GCC-%s' % gcc_maj_min homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' -description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & + Intel MKL.""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/intel/intel-2016.03-GCC-5.4.eb b/easybuild/easyconfigs/i/intel/intel-2016.03-GCC-5.4.eb index 1de4297cce..fd9c783f53 100644 --- a/easybuild/easyconfigs/i/intel/intel-2016.03-GCC-5.4.eb +++ b/easybuild/easyconfigs/i/intel/intel-2016.03-GCC-5.4.eb @@ -6,7 +6,8 @@ gcc_maj_min = '5.4' versionsuffix = '-GCC-%s' % gcc_maj_min homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' -description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & + Intel MKL.""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/intel/intel-2016a.eb b/easybuild/easyconfigs/i/intel/intel-2016a.eb index c858c20f53..5b6fecfd23 100644 --- a/easybuild/easyconfigs/i/intel/intel-2016a.eb +++ b/easybuild/easyconfigs/i/intel/intel-2016a.eb @@ -4,7 +4,8 @@ name = 'intel' version = '2016a' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' -description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & + Intel MKL.""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/intel/intel-2016b.eb b/easybuild/easyconfigs/i/intel/intel-2016b.eb index 92aacd886c..5866da643e 100644 --- a/easybuild/easyconfigs/i/intel/intel-2016b.eb +++ b/easybuild/easyconfigs/i/intel/intel-2016b.eb @@ -4,7 +4,8 @@ name = 'intel' version = '2016b' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' -description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & + Intel MKL.""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/intel/intel-2017.00.eb b/easybuild/easyconfigs/i/intel/intel-2017.00.eb index ad8be63148..a3c48fa4ca 100644 --- a/easybuild/easyconfigs/i/intel/intel-2017.00.eb +++ b/easybuild/easyconfigs/i/intel/intel-2017.00.eb @@ -4,7 +4,8 @@ name = 'intel' version = '2017.00' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' -description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & + Intel MKL.""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/intel/intel-2017.01.eb b/easybuild/easyconfigs/i/intel/intel-2017.01.eb index 9993bc8e47..10392160f1 100644 --- a/easybuild/easyconfigs/i/intel/intel-2017.01.eb +++ b/easybuild/easyconfigs/i/intel/intel-2017.01.eb @@ -4,7 +4,8 @@ name = 'intel' version = '2017.01' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' -description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & + Intel MKL.""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/intel/intel-2017.02.eb b/easybuild/easyconfigs/i/intel/intel-2017.02.eb index 941245b3e6..e39d8da948 100644 --- a/easybuild/easyconfigs/i/intel/intel-2017.02.eb +++ b/easybuild/easyconfigs/i/intel/intel-2017.02.eb @@ -4,7 +4,8 @@ name = 'intel' version = '2017.02' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' -description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & + Intel MKL.""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/intel/intel-2017a.eb b/easybuild/easyconfigs/i/intel/intel-2017a.eb index 4e98f5a7f2..f1760e4271 100644 --- a/easybuild/easyconfigs/i/intel/intel-2017a.eb +++ b/easybuild/easyconfigs/i/intel/intel-2017a.eb @@ -4,7 +4,8 @@ name = 'intel' version = '2017a' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' -description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & + Intel MKL.""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/intltool/intltool-0.51.0-GCCcore-4.9.3-Perl-5.24.0.eb b/easybuild/easyconfigs/i/intltool/intltool-0.51.0-GCCcore-4.9.3-Perl-5.24.0.eb index 0acb163cda..4d7b443901 100644 --- a/easybuild/easyconfigs/i/intltool/intltool-0.51.0-GCCcore-4.9.3-Perl-5.24.0.eb +++ b/easybuild/easyconfigs/i/intltool/intltool-0.51.0-GCCcore-4.9.3-Perl-5.24.0.eb @@ -10,7 +10,7 @@ description = """intltool is a set of tools to centralize translation of toolchain = {'name': 'GCCcore', 'version': '4.9.3'} -source_urls = ['http://launchpad.net/intltool/trunk/%(version)s/+download/'] +source_urls = ['http://launchpad.net/intltool/trunk/%(version)s/+download/'] sources = [SOURCE_TAR_GZ] builddependencies = [ diff --git a/easybuild/easyconfigs/i/intltool/intltool-0.51.0-intel-2016a-Perl-5.20.3.eb b/easybuild/easyconfigs/i/intltool/intltool-0.51.0-intel-2016a-Perl-5.20.3.eb index 8fd4cb48f8..4d3f41da10 100644 --- a/easybuild/easyconfigs/i/intltool/intltool-0.51.0-intel-2016a-Perl-5.20.3.eb +++ b/easybuild/easyconfigs/i/intltool/intltool-0.51.0-intel-2016a-Perl-5.20.3.eb @@ -10,7 +10,7 @@ description = """intltool is a set of tools to centralize translation of toolchain = {'name': 'intel', 'version': '2016a'} -source_urls = ['http://launchpad.net/intltool/trunk/%(version)s/+download/'] +source_urls = ['http://launchpad.net/intltool/trunk/%(version)s/+download/'] sources = [SOURCE_TAR_GZ] dependencies = [ diff --git a/easybuild/easyconfigs/i/io_lib/io_lib-1.14.8-foss-2016a.eb b/easybuild/easyconfigs/i/io_lib/io_lib-1.14.8-foss-2016a.eb index 9d67e52066..74d4ba917e 100644 --- a/easybuild/easyconfigs/i/io_lib/io_lib-1.14.8-foss-2016a.eb +++ b/easybuild/easyconfigs/i/io_lib/io_lib-1.14.8-foss-2016a.eb @@ -4,10 +4,10 @@ name = 'io_lib' version = '1.14.8' homepage = 'http://sourceforge.net/projects/staden/files/io_lib/' -description = """Io_lib is a library of file reading and writing code to provide a general purpose trace file (and Experiment - File) reading interface. The programmer simply calls the (eg) read_reading to create a "Read" C structure with the data loaded - into memory. It has been compiled and tested on a variety of unix systems, MacOS X and MS Windows. -""" +description = """Io_lib is a library of file reading and writing code to provide a general purpose trace file (and + Experiment File) reading interface. The programmer simply calls the (eg) read_reading to create a "Read" C structure + with the data loaded into memory. It has been compiled and tested on a variety of unix systems, MacOS X and MS + Windows.""" toolchain = {'name': 'foss', 'version': '2016a'} diff --git a/easybuild/easyconfigs/i/iomkl/iomkl-2015.01.eb b/easybuild/easyconfigs/i/iomkl/iomkl-2015.01.eb index aa85e82a98..a9a545eec7 100644 --- a/easybuild/easyconfigs/i/iomkl/iomkl-2015.01.eb +++ b/easybuild/easyconfigs/i/iomkl/iomkl-2015.01.eb @@ -4,7 +4,8 @@ name = 'iomkl' version = '2015.01' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' -description = """Intel Cluster Toolchain Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MKL & OpenMPI.""" +description = """Intel Cluster Toolchain Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MKL & + OpenMPI.""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/iomkl/iomkl-2015.02.eb b/easybuild/easyconfigs/i/iomkl/iomkl-2015.02.eb index 544ad6da2e..e17fa43dd2 100644 --- a/easybuild/easyconfigs/i/iomkl/iomkl-2015.02.eb +++ b/easybuild/easyconfigs/i/iomkl/iomkl-2015.02.eb @@ -4,7 +4,8 @@ name = 'iomkl' version = '2015.02' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' -description = """Intel Cluster Toolchain Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MKL & OpenMPI.""" +description = """Intel Cluster Toolchain Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MKL & + OpenMPI.""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/iomkl/iomkl-2015.03.eb b/easybuild/easyconfigs/i/iomkl/iomkl-2015.03.eb index f9059cff3e..93dbfc98f8 100644 --- a/easybuild/easyconfigs/i/iomkl/iomkl-2015.03.eb +++ b/easybuild/easyconfigs/i/iomkl/iomkl-2015.03.eb @@ -4,7 +4,8 @@ name = 'iomkl' version = '2015.03' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' -description = """Intel Cluster Toolchain Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MKL & OpenMPI.""" +description = """Intel Cluster Toolchain Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MKL & + OpenMPI.""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/iomkl/iomkl-2016.07.eb b/easybuild/easyconfigs/i/iomkl/iomkl-2016.07.eb index 54ed73649a..5d1d743242 100644 --- a/easybuild/easyconfigs/i/iomkl/iomkl-2016.07.eb +++ b/easybuild/easyconfigs/i/iomkl/iomkl-2016.07.eb @@ -4,7 +4,8 @@ name = 'iomkl' version = '2016.07' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' -description = """Intel Cluster Toolchain Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MKL & OpenMPI.""" +description = """Intel Cluster Toolchain Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MKL & + OpenMPI.""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/iomkl/iomkl-2016.09-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/iomkl/iomkl-2016.09-GCC-4.9.3-2.25.eb index cf9954cf88..ced0e87585 100644 --- a/easybuild/easyconfigs/i/iomkl/iomkl-2016.09-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/iomkl/iomkl-2016.09-GCC-4.9.3-2.25.eb @@ -4,7 +4,8 @@ name = 'iomkl' version = '2016.09-GCC-4.9.3-2.25' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' -description = """Intel Cluster Toolchain Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MKL & OpenMPI.""" +description = """Intel Cluster Toolchain Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MKL & + OpenMPI.""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/iomkl/iomkl-2016.09-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/iomkl/iomkl-2016.09-GCC-5.4.0-2.26.eb index 6b0377e8e3..f0219ff350 100644 --- a/easybuild/easyconfigs/i/iomkl/iomkl-2016.09-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/iomkl/iomkl-2016.09-GCC-5.4.0-2.26.eb @@ -4,7 +4,8 @@ name = 'iomkl' version = '2016.09-GCC-5.4.0-2.26' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' -description = """Intel Cluster Toolchain Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MKL & OpenMPI.""" +description = """Intel Cluster Toolchain Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MKL & + OpenMPI.""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/iomkl/iomkl-2017.01.eb b/easybuild/easyconfigs/i/iomkl/iomkl-2017.01.eb index 6039ebaad3..9d9e8846e6 100644 --- a/easybuild/easyconfigs/i/iomkl/iomkl-2017.01.eb +++ b/easybuild/easyconfigs/i/iomkl/iomkl-2017.01.eb @@ -4,7 +4,8 @@ name = 'iomkl' version = '2017.01' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' -description = """Intel Cluster Toolchain Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MKL & OpenMPI.""" +description = """Intel Cluster Toolchain Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MKL & + OpenMPI.""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/iomkl/iomkl-2017a.eb b/easybuild/easyconfigs/i/iomkl/iomkl-2017a.eb index 032f6eb6a2..4d75373f4f 100644 --- a/easybuild/easyconfigs/i/iomkl/iomkl-2017a.eb +++ b/easybuild/easyconfigs/i/iomkl/iomkl-2017a.eb @@ -4,7 +4,8 @@ name = 'iomkl' version = '2017a' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' -description = """Intel Cluster Toolchain Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MKL & OpenMPI.""" +description = """Intel Cluster Toolchain Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MKL & + OpenMPI.""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/iompi/iompi-2016.09-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/iompi/iompi-2016.09-GCC-4.9.3-2.25.eb index 3c9854b3e1..9580ff5296 100644 --- a/easybuild/easyconfigs/i/iompi/iompi-2016.09-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/iompi/iompi-2016.09-GCC-4.9.3-2.25.eb @@ -17,4 +17,3 @@ dependencies = [ ] moduleclass = 'toolchain' - diff --git a/easybuild/easyconfigs/i/iompi/iompi-2016.09-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/iompi/iompi-2016.09-GCC-5.4.0-2.26.eb index 6ab1a7b7d5..db8c7fb2af 100644 --- a/easybuild/easyconfigs/i/iompi/iompi-2016.09-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/iompi/iompi-2016.09-GCC-5.4.0-2.26.eb @@ -17,4 +17,3 @@ dependencies = [ ] moduleclass = 'toolchain' - diff --git a/easybuild/easyconfigs/i/ipp/ipp-7.0.5.233.eb b/easybuild/easyconfigs/i/ipp/ipp-7.0.5.233.eb index 1497f12bc7..af01ee3ccc 100644 --- a/easybuild/easyconfigs/i/ipp/ipp-7.0.5.233.eb +++ b/easybuild/easyconfigs/i/ipp/ipp-7.0.5.233.eb @@ -18,5 +18,4 @@ moduleclass = 'perf' dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' diff --git a/easybuild/easyconfigs/i/ipp/ipp-8.1.0.144.eb b/easybuild/easyconfigs/i/ipp/ipp-8.1.0.144.eb index dce7087021..2df68edb57 100644 --- a/easybuild/easyconfigs/i/ipp/ipp-8.1.0.144.eb +++ b/easybuild/easyconfigs/i/ipp/ipp-8.1.0.144.eb @@ -14,7 +14,6 @@ sources = ['l_ipp_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'perf' diff --git a/easybuild/easyconfigs/i/ipp/ipp-9.0.1.150.eb b/easybuild/easyconfigs/i/ipp/ipp-9.0.1.150.eb index c5381d564c..c7f19f61c1 100644 --- a/easybuild/easyconfigs/i/ipp/ipp-9.0.1.150.eb +++ b/easybuild/easyconfigs/i/ipp/ipp-9.0.1.150.eb @@ -14,7 +14,6 @@ sources = ['l_ipp_%(version)s.tgz'] dontcreateinstalldir = 'True' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'perf' diff --git a/easybuild/easyconfigs/i/itac/itac-8.0.0.011.eb b/easybuild/easyconfigs/i/itac/itac-8.0.0.011.eb index b8febc89fc..5e7c707582 100644 --- a/easybuild/easyconfigs/i/itac/itac-8.0.0.011.eb +++ b/easybuild/easyconfigs/i/itac/itac-8.0.0.011.eb @@ -15,7 +15,6 @@ dontcreateinstalldir = 'True' preferredmpi = 'impi4' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'tools' diff --git a/easybuild/easyconfigs/i/itac/itac-8.1.4.045.eb b/easybuild/easyconfigs/i/itac/itac-8.1.4.045.eb index 67482320a6..546ec40361 100644 --- a/easybuild/easyconfigs/i/itac/itac-8.1.4.045.eb +++ b/easybuild/easyconfigs/i/itac/itac-8.1.4.045.eb @@ -15,7 +15,6 @@ dontcreateinstalldir = 'True' preferredmpi = 'impi4' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'tools' diff --git a/easybuild/easyconfigs/i/itac/itac-9.0.3.051.eb b/easybuild/easyconfigs/i/itac/itac-9.0.3.051.eb index 42551d67c6..8922806632 100644 --- a/easybuild/easyconfigs/i/itac/itac-9.0.3.051.eb +++ b/easybuild/easyconfigs/i/itac/itac-9.0.3.051.eb @@ -15,7 +15,6 @@ dontcreateinstalldir = 'True' preferredmpi = 'impi5' # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'tools' -- GitLab From 30861069b7bb9df66f8c347f7ec1010ddcbbf8fe Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 8 Mar 2017 14:26:59 +0100 Subject: [PATCH 0276/1603] adding easyconfigs: fqtrim-0.9.4-intel-2016b.eb --- .../f/fqtrim/fqtrim-0.9.4-intel-2016b.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/f/fqtrim/fqtrim-0.9.4-intel-2016b.eb diff --git a/easybuild/easyconfigs/f/fqtrim/fqtrim-0.9.4-intel-2016b.eb b/easybuild/easyconfigs/f/fqtrim/fqtrim-0.9.4-intel-2016b.eb new file mode 100644 index 0000000000..f57e94703f --- /dev/null +++ b/easybuild/easyconfigs/f/fqtrim/fqtrim-0.9.4-intel-2016b.eb @@ -0,0 +1,25 @@ +easyblock = 'MakeCp' + +name = 'fqtrim' +version = '0.9.4' + +homepage = 'http://ccb.jhu.edu/software/fqtrim/' +description = """fqtrim is a versatile stand-alone utility that can be used to trim adapters, poly-A tails, + terminal unknown bases (Ns) and low quality 3' regions in reads from high-throughput next-generation sequencing + machines.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['http://ccb.jhu.edu/software/fqtrim/dl/'] +sources = [SOURCE_TAR_GZ] + +buildopts = 'release CC="$CXX" LINKER="$CXX" LDFLAGS="$LDFLAGS $CXXFLAGS"' + +files_to_copy = [(['fqtrim'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/fqtrim'], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From ff7cd40c2f0a8da36dee04fb0661c1a3deb211b7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 8 Mar 2017 15:17:27 +0100 Subject: [PATCH 0277/1603] no need to include $CXXFLAGS into LDFLAGS, thanks @wpoely86 --- easybuild/easyconfigs/f/fqtrim/fqtrim-0.9.4-intel-2016b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/fqtrim/fqtrim-0.9.4-intel-2016b.eb b/easybuild/easyconfigs/f/fqtrim/fqtrim-0.9.4-intel-2016b.eb index f57e94703f..4e2183f308 100644 --- a/easybuild/easyconfigs/f/fqtrim/fqtrim-0.9.4-intel-2016b.eb +++ b/easybuild/easyconfigs/f/fqtrim/fqtrim-0.9.4-intel-2016b.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'intel', 'version': '2016b'} source_urls = ['http://ccb.jhu.edu/software/fqtrim/dl/'] sources = [SOURCE_TAR_GZ] -buildopts = 'release CC="$CXX" LINKER="$CXX" LDFLAGS="$LDFLAGS $CXXFLAGS"' +buildopts = 'release CC="$CXX" LINKER="$CXX"' files_to_copy = [(['fqtrim'], 'bin')] -- GitLab From 2fa39e0e47203bebce534d5f36f30a5298d5e0f6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 8 Mar 2017 15:18:18 +0100 Subject: [PATCH 0278/1603] adding easyconfigs: DBG2OLC-20170208-intel-2016b.eb --- .../d/DBG2OLC/DBG2OLC-20170208-intel-2016b.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/d/DBG2OLC/DBG2OLC-20170208-intel-2016b.eb diff --git a/easybuild/easyconfigs/d/DBG2OLC/DBG2OLC-20170208-intel-2016b.eb b/easybuild/easyconfigs/d/DBG2OLC/DBG2OLC-20170208-intel-2016b.eb new file mode 100644 index 0000000000..0f90c41b2a --- /dev/null +++ b/easybuild/easyconfigs/d/DBG2OLC/DBG2OLC-20170208-intel-2016b.eb @@ -0,0 +1,25 @@ +easyblock = 'CmdCp' + +name = 'DBG2OLC' +version = '20170208' +commit = 'b452286' + +homepage = 'https://github.com/yechengxi/DBG2OLC' +description = """DBG2OLC:Efficient Assembly of Large Genomes Using Long Erroneous Reads of the Third Generation + Sequencing Technologies""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['https://github.com/yechengxi/DBG2OLC/archive/'] +sources = ['%s.tar.gz' % commit] + +cmds_map = [('.*', "$CXX $CXXFLAGS -o DBG2OLC *.cpp")] + +files_to_copy = [(['DBG2OLC'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/DBG2OLC'], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From a3c162e9306d788f99d59fd3cfe93c4fee0a4929 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 8 Mar 2017 15:40:56 +0100 Subject: [PATCH 0279/1603] adding easyconfigs: L_RNA_scaffolder-20141124-intel-2016b-Perl-5.24.0.eb --- ...folder-20141124-intel-2016b-Perl-5.24.0.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/l/L_RNA_scaffolder/L_RNA_scaffolder-20141124-intel-2016b-Perl-5.24.0.eb diff --git a/easybuild/easyconfigs/l/L_RNA_scaffolder/L_RNA_scaffolder-20141124-intel-2016b-Perl-5.24.0.eb b/easybuild/easyconfigs/l/L_RNA_scaffolder/L_RNA_scaffolder-20141124-intel-2016b-Perl-5.24.0.eb new file mode 100644 index 0000000000..dd21d5b9af --- /dev/null +++ b/easybuild/easyconfigs/l/L_RNA_scaffolder/L_RNA_scaffolder-20141124-intel-2016b-Perl-5.24.0.eb @@ -0,0 +1,29 @@ +easyblock = 'Tarball' + +name = 'L_RNA_scaffolder' +version = '20141124' +versionsuffix = '-Perl-5.24.0' + +homepage = 'http://www.fishbrowser.org/software/L_RNA_scaffolder/' +description = "L_RNA_scaffolder is a novel scaffolding tool using long trancriptome reads to scaffold genome fragments" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['http://www.fishbrowser.org/software/L_RNA_scaffolder/downloads/'] +sources = ['L_RNA_scaffolder.tar.gz'] +checksums = ['3cc401886c452b1000d434dea776970e'] + +dependencies = [('BioPerl', '1.7.1', versionsuffix)] + +modextrapaths = {'PATH': ''} + +sanity_check_paths = { + 'files': ['calculate-lc', 'calculate-pid', 'convert', 'convert_linker', 'count_connection_frequency', + 'delete_block', 'delete_linker', 'delete_same_fragment', 'exon_length', 'filter_scaffold.pl', + 'find_end_node', 'find_reliable_connection', 'find_start_node', 'form_block', 'form_initial_path.pl', + 'form_path.pl', 'generate_scaffold.pl', 'generate_unscaffold.pl', 'L_RNA_scaffolder.sh', 'link_block', + 'order', 'overlap', 'route.pl', 'search_guider', 'select', 'select_nodes'], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From d789421eeaf1847ca641fdd45ae509c85c2a4b82 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 8 Mar 2017 15:49:35 +0100 Subject: [PATCH 0280/1603] also include $LDFLAGS in compilation command --- easybuild/easyconfigs/d/DBG2OLC/DBG2OLC-20170208-intel-2016b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/DBG2OLC/DBG2OLC-20170208-intel-2016b.eb b/easybuild/easyconfigs/d/DBG2OLC/DBG2OLC-20170208-intel-2016b.eb index 0f90c41b2a..82d644aaff 100644 --- a/easybuild/easyconfigs/d/DBG2OLC/DBG2OLC-20170208-intel-2016b.eb +++ b/easybuild/easyconfigs/d/DBG2OLC/DBG2OLC-20170208-intel-2016b.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'intel', 'version': '2016b'} source_urls = ['https://github.com/yechengxi/DBG2OLC/archive/'] sources = ['%s.tar.gz' % commit] -cmds_map = [('.*', "$CXX $CXXFLAGS -o DBG2OLC *.cpp")] +cmds_map = [('.*', "$CXX $CXXFLAGS $LDFLAGS -o DBG2OLC *.cpp")] files_to_copy = [(['DBG2OLC'], 'bin')] -- GitLab From a9d2e2ae16a0f109e81838f40bc98e395798b2a1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 8 Mar 2017 16:02:14 +0100 Subject: [PATCH 0281/1603] adding easyconfigs: BLAT-3.5-intel-2016b.eb --- .../b/BLAT/BLAT-3.5-intel-2016b.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/b/BLAT/BLAT-3.5-intel-2016b.eb diff --git a/easybuild/easyconfigs/b/BLAT/BLAT-3.5-intel-2016b.eb b/easybuild/easyconfigs/b/BLAT/BLAT-3.5-intel-2016b.eb new file mode 100644 index 0000000000..48a47daaa1 --- /dev/null +++ b/easybuild/easyconfigs/b/BLAT/BLAT-3.5-intel-2016b.eb @@ -0,0 +1,33 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 The Cyprus Institute +# Authors:: Andreas Panteli , Thekla Loizou +# License:: MIT/GPL +# +## + +name = 'BLAT' +version = '3.5' + +homepage = 'http://genome.ucsc.edu/FAQ/FAQblat.html' +description = "BLAT on DNA is designed to quickly find sequences of 95% and greater similarity of length 25 bases or more." + +toolchain = {'name': 'intel', 'version': '2016b'} + +sources = ['%%(namelower)sSrc%s.zip' % ''.join(version.split('.'))] +source_urls = ['http://users.soe.ucsc.edu/~kent/src'] + +dependencies = [('libpng', '1.6.23')] + +buildopts = 'CC="$CC" COPT= L="$LIBS"' + +files_to_copy = ["bin", "blat", "gfClient", "gfServer", "hg", "inc", "jkOwnLib", "lib", "utils", "webBlat"] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['blat', 'faToNib', 'faToTwoBit', 'gfClient', 'gfServer', 'nibFrag', + 'pslPretty', 'pslReps', 'pslSort', 'twoBitInfo', 'twoBitToFa']], + 'dirs': files_to_copy, +} + +moduleclass = 'bio' -- GitLab From 2f20fd4e1aa1e702281a703d7bc114752e1d9b4f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 8 Mar 2017 18:07:11 +0100 Subject: [PATCH 0282/1603] adding easyconfigs: STAR-2.5.2b-intel-2016b.eb --- .../s/STAR/STAR-2.5.2b-intel-2016b.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/s/STAR/STAR-2.5.2b-intel-2016b.eb diff --git a/easybuild/easyconfigs/s/STAR/STAR-2.5.2b-intel-2016b.eb b/easybuild/easyconfigs/s/STAR/STAR-2.5.2b-intel-2016b.eb new file mode 100644 index 0000000000..05c3e56c2f --- /dev/null +++ b/easybuild/easyconfigs/s/STAR/STAR-2.5.2b-intel-2016b.eb @@ -0,0 +1,43 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# Modified by: +# Adam Huffman +# The Francis Crick Institute + +easyblock = 'MakeCp' + +name = 'STAR' +version = '2.5.2b' + +homepage = 'https://github.com/alexdobin/STAR' +description = "STAR aligns RNA-seq reads to a reference genome using uncompressed suffix arrays." + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'openmp': True} + +source_urls = ['https://github.com/alexdobin/STAR/archive/'] +sources = ['%(version)s.tar.gz'] + +dependencies = [ + ('zlib', '1.2.8'), +] + +start_dir = 'source' + +buildopts = ' STAR && make STARlong' + +parallel = 1 + +files_to_copy = [ + (['source/STAR', 'source/STARlong'], 'bin'), + 'CHANGES.md', 'doc', 'extras', 'LICENSE', 'README.md', 'RELEASEnotes.md', +] + +sanity_check_paths = { + 'files': ["bin/STAR", "bin/STARlong"], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From 1dbcd246623116c0cde17cb04e85f87b6cba548d Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Thu, 9 Mar 2017 12:07:23 +0800 Subject: [PATCH 0283/1603] yet another batch of minor style fixes --- .../j/jModelTest/jModelTest-2.1.10r20160303-Java-1.8.0_92.eb | 2 +- .../jModelTest-2.1.9r20160115-goolf-1.4.10-Java-1.7.0_75.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/j/jModelTest/jModelTest-2.1.10r20160303-Java-1.8.0_92.eb b/easybuild/easyconfigs/j/jModelTest/jModelTest-2.1.10r20160303-Java-1.8.0_92.eb index 07eff74434..4dba96087d 100644 --- a/easybuild/easyconfigs/j/jModelTest/jModelTest-2.1.10r20160303-Java-1.8.0_92.eb +++ b/easybuild/easyconfigs/j/jModelTest/jModelTest-2.1.10r20160303-Java-1.8.0_92.eb @@ -10,7 +10,7 @@ version = '2.1.10r20160303' versionsuffix = '-Java-%(javaver)s' homepage = 'https://github.com/ddarriba/jmodeltest2' -description="""jModelTest is a tool to carry out statistical selection of best-fit models of nucleotide substitution.""" +description = "jModelTest is a tool to carry out statistical selection of best-fit models of nucleotide substitution." toolchain = {'name': 'dummy', 'version': ''} diff --git a/easybuild/easyconfigs/j/jModelTest/jModelTest-2.1.9r20160115-goolf-1.4.10-Java-1.7.0_75.eb b/easybuild/easyconfigs/j/jModelTest/jModelTest-2.1.9r20160115-goolf-1.4.10-Java-1.7.0_75.eb index ecf1089f64..37a4b9dd9a 100644 --- a/easybuild/easyconfigs/j/jModelTest/jModelTest-2.1.9r20160115-goolf-1.4.10-Java-1.7.0_75.eb +++ b/easybuild/easyconfigs/j/jModelTest/jModelTest-2.1.9r20160115-goolf-1.4.10-Java-1.7.0_75.eb @@ -9,7 +9,7 @@ name = 'jModelTest' version = '2.1.9r20160115' homepage = 'https://github.com/ddarriba/jmodeltest2' -description="""jModelTest is a tool to carry out statistical selection of best-fit models of nucleotide substitution.""" +description = "jModelTest is a tool to carry out statistical selection of best-fit models of nucleotide substitution." toolchain = {'name': 'goolf', 'version': '1.4.10'} -- GitLab From 86c6bb0e2a0d992ba77efcc6a0577127d18a7b11 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Thu, 9 Mar 2017 12:25:41 +0800 Subject: [PATCH 0284/1603] yet another batch of minor style fixes --- easybuild/easyconfigs/l/LLVM/LLVM-3.7.1-foss-2016a.eb | 4 ++-- .../easyconfigs/l/LevelDB/LevelDB-1.18-foss-2016a.eb | 8 +++----- .../easyconfigs/l/Libint/Libint-1.1.4-intel-2016a.eb | 2 +- easybuild/easyconfigs/l/Libint/Libint-1.1.6-foss-2016b.eb | 2 +- .../easyconfigs/l/Libint/Libint-1.1.6-intel-2016b.eb | 2 +- easybuild/easyconfigs/l/libXi/libXi-1.7.2-goolf-1.4.10.eb | 3 ++- easybuild/easyconfigs/l/libXi/libXi-1.7.2-ictce-5.3.0.eb | 3 ++- easybuild/easyconfigs/l/libXi/libXi-1.7.4-intel-2015a.eb | 3 ++- easybuild/easyconfigs/l/libXi/libXi-1.7.4-intel-2015b.eb | 3 ++- .../l/libXxf86vm/libXxf86vm-1.1.4-foss-2016a.eb | 2 +- .../l/libXxf86vm/libXxf86vm-1.1.4-intel-2016a.eb | 2 +- .../easyconfigs/l/libpng/libpng-1.6.21-intel-2015b.eb | 2 +- .../l/libreadline/libreadline-6.2-goolf-1.7.20.eb | 8 ++++---- .../l/libreadline/libreadline-6.2-ictce-5.4.0.eb | 8 ++++---- .../l/libreadline/libreadline-6.3-CrayGNU-2015.06.eb | 8 ++++---- .../l/libreadline/libreadline-6.3-CrayGNU-2015.11.eb | 8 ++++---- .../l/libreadline/libreadline-6.3-CrayGNU-2016.03.eb | 8 ++++---- .../easyconfigs/l/libsmm/libsmm-20111205-goolf-1.4.10.eb | 5 +++-- .../l/libunistring/libunistring-0.9.3-GCC-4.9.3-2.25.eb | 8 ++++---- .../l/libunistring/libunistring-0.9.3-foss-2015b.eb | 8 ++++---- .../l/libunistring/libunistring-0.9.3-foss-2016a.eb | 8 ++++---- .../l/libunistring/libunistring-0.9.3-intel-2015b.eb | 8 ++++---- 22 files changed, 58 insertions(+), 55 deletions(-) diff --git a/easybuild/easyconfigs/l/LLVM/LLVM-3.7.1-foss-2016a.eb b/easybuild/easyconfigs/l/LLVM/LLVM-3.7.1-foss-2016a.eb index 4228c8e824..59f694676c 100644 --- a/easybuild/easyconfigs/l/LLVM/LLVM-3.7.1-foss-2016a.eb +++ b/easybuild/easyconfigs/l/LLVM/LLVM-3.7.1-foss-2016a.eb @@ -29,8 +29,8 @@ dependencies = [ configopts = '-DBUILD_SHARED_LIBS=ON' sanity_check_paths = { - 'files' : ['bin/llvm-ar'], - 'dirs' : ['include/llvm', 'include/llvm-c'], + 'files': ['bin/llvm-ar'], + 'dirs': ['include/llvm', 'include/llvm-c'], } separate_build_dir = True diff --git a/easybuild/easyconfigs/l/LevelDB/LevelDB-1.18-foss-2016a.eb b/easybuild/easyconfigs/l/LevelDB/LevelDB-1.18-foss-2016a.eb index c5eee2ec3d..daaaa15ecd 100644 --- a/easybuild/easyconfigs/l/LevelDB/LevelDB-1.18-foss-2016a.eb +++ b/easybuild/easyconfigs/l/LevelDB/LevelDB-1.18-foss-2016a.eb @@ -4,10 +4,8 @@ name = 'LevelDB' version = '1.18' homepage = 'https://github.com/google/leveldb' -description = """ -LevelDB is a fast key-value storage library written at Google that provides an -ordered mapping from string keys to string values. -""" +description = """LevelDB is a fast key-value storage library written at Google that provides an + ordered mapping from string keys to string values.""" toolchain = {'name': 'foss', 'version': '2016a'} @@ -19,7 +17,7 @@ files_to_copy = [ (['include/leveldb/*.h'], 'include/leveldb') ] -postinstallcmds=[ +postinstallcmds = [ 'cd %(installdir)s/lib; ln -s libleveldb.so.%(version)s libleveldb.so.%(version_major)s', 'cd %%(installdir)s/lib; ln -s libleveldb.so.%%(version)s libleveldb.%s' % SHLIB_EXT, ] diff --git a/easybuild/easyconfigs/l/Libint/Libint-1.1.4-intel-2016a.eb b/easybuild/easyconfigs/l/Libint/Libint-1.1.4-intel-2016a.eb index 56cf148c48..593afa9ec4 100644 --- a/easybuild/easyconfigs/l/Libint/Libint-1.1.4-intel-2016a.eb +++ b/easybuild/easyconfigs/l/Libint/Libint-1.1.4-intel-2016a.eb @@ -16,7 +16,7 @@ configopts = "--enable-deriv --enable-r12" sanity_check_paths = { 'files': ['include/lib%(x)s/lib%(x)s.h' % {'x': x} for x in ['deriv', 'int', 'r12']] + ['include/libint/hrr_header.h', 'include/libint/vrr_header.h'] + - ['lib/lib%s.%s' % (x,y) for x in ['deriv', 'int', 'r12'] for y in ['a', SHLIB_EXT]], + ['lib/lib%s.%s' % (x, y) for x in ['deriv', 'int', 'r12'] for y in ['a', SHLIB_EXT]], 'dirs': [], } diff --git a/easybuild/easyconfigs/l/Libint/Libint-1.1.6-foss-2016b.eb b/easybuild/easyconfigs/l/Libint/Libint-1.1.6-foss-2016b.eb index 08a7cf496f..928179dc39 100644 --- a/easybuild/easyconfigs/l/Libint/Libint-1.1.6-foss-2016b.eb +++ b/easybuild/easyconfigs/l/Libint/Libint-1.1.6-foss-2016b.eb @@ -20,7 +20,7 @@ configopts = "--enable-deriv --enable-r12" sanity_check_paths = { 'files': ['include/lib%(x)s/lib%(x)s.h' % {'x': x} for x in ['deriv', 'int', 'r12']] + ['include/libint/hrr_header.h', 'include/libint/vrr_header.h'] + - ['lib/lib%s.%s' % (x,y) for x in ['deriv', 'int', 'r12'] for y in ['a', SHLIB_EXT]], + ['lib/lib%s.%s' % (x, y) for x in ['deriv', 'int', 'r12'] for y in ['a', SHLIB_EXT]], 'dirs': [], } diff --git a/easybuild/easyconfigs/l/Libint/Libint-1.1.6-intel-2016b.eb b/easybuild/easyconfigs/l/Libint/Libint-1.1.6-intel-2016b.eb index accf89b9e8..785074f0f9 100644 --- a/easybuild/easyconfigs/l/Libint/Libint-1.1.6-intel-2016b.eb +++ b/easybuild/easyconfigs/l/Libint/Libint-1.1.6-intel-2016b.eb @@ -20,7 +20,7 @@ configopts = "--enable-deriv --enable-r12" sanity_check_paths = { 'files': ['include/lib%(x)s/lib%(x)s.h' % {'x': x} for x in ['deriv', 'int', 'r12']] + ['include/libint/hrr_header.h', 'include/libint/vrr_header.h'] + - ['lib/lib%s.%s' % (x,y) for x in ['deriv', 'int', 'r12'] for y in ['a', SHLIB_EXT]], + ['lib/lib%s.%s' % (x, y) for x in ['deriv', 'int', 'r12'] for y in ['a', SHLIB_EXT]], 'dirs': [], } diff --git a/easybuild/easyconfigs/l/libXi/libXi-1.7.2-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libXi/libXi-1.7.2-goolf-1.4.10.eb index 8b0e336093..b4b7228f14 100644 --- a/easybuild/easyconfigs/l/libXi/libXi-1.7.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/libXi/libXi-1.7.2-goolf-1.4.10.eb @@ -20,7 +20,8 @@ dependencies = [ ] sanity_check_paths = { - 'files': ['include/X11/extensions/XInput.h', 'include/X11/extensions/XInput2.h', 'lib/libXi.%s' % SHLIB_EXT, 'lib/libXi.a'], + 'files': ['include/X11/extensions/XInput.h', 'include/X11/extensions/XInput2.h', + 'lib/libXi.%s' % SHLIB_EXT, 'lib/libXi.a'], 'dirs': [], } diff --git a/easybuild/easyconfigs/l/libXi/libXi-1.7.2-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libXi/libXi-1.7.2-ictce-5.3.0.eb index 0f71868663..bc42f60686 100644 --- a/easybuild/easyconfigs/l/libXi/libXi-1.7.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/l/libXi/libXi-1.7.2-ictce-5.3.0.eb @@ -20,7 +20,8 @@ dependencies = [ ] sanity_check_paths = { - 'files': ['include/X11/extensions/XInput.h', 'include/X11/extensions/XInput2.h', 'lib/libXi.%s' % SHLIB_EXT, 'lib/libXi.a'], + 'files': ['include/X11/extensions/XInput.h', 'include/X11/extensions/XInput2.h', + 'lib/libXi.%s' % SHLIB_EXT, 'lib/libXi.a'], 'dirs': [], } diff --git a/easybuild/easyconfigs/l/libXi/libXi-1.7.4-intel-2015a.eb b/easybuild/easyconfigs/l/libXi/libXi-1.7.4-intel-2015a.eb index 68589245d1..0e45004907 100644 --- a/easybuild/easyconfigs/l/libXi/libXi-1.7.4-intel-2015a.eb +++ b/easybuild/easyconfigs/l/libXi/libXi-1.7.4-intel-2015a.eb @@ -20,7 +20,8 @@ dependencies = [ ] sanity_check_paths = { - 'files': ['include/X11/extensions/XInput.h', 'include/X11/extensions/XInput2.h', 'lib/libXi.%s' % SHLIB_EXT, 'lib/libXi.a'], + 'files': ['include/X11/extensions/XInput.h', 'include/X11/extensions/XInput2.h', + 'lib/libXi.%s' % SHLIB_EXT, 'lib/libXi.a'], 'dirs': [], } diff --git a/easybuild/easyconfigs/l/libXi/libXi-1.7.4-intel-2015b.eb b/easybuild/easyconfigs/l/libXi/libXi-1.7.4-intel-2015b.eb index 60cd626d31..2316d70175 100644 --- a/easybuild/easyconfigs/l/libXi/libXi-1.7.4-intel-2015b.eb +++ b/easybuild/easyconfigs/l/libXi/libXi-1.7.4-intel-2015b.eb @@ -20,7 +20,8 @@ dependencies = [ ] sanity_check_paths = { - 'files': ['include/X11/extensions/XInput.h', 'include/X11/extensions/XInput2.h', 'lib/libXi.%s' % SHLIB_EXT, 'lib/libXi.a'], + 'files': ['include/X11/extensions/XInput.h', 'include/X11/extensions/XInput2.h', + 'lib/libXi.%s' % SHLIB_EXT, 'lib/libXi.a'], 'dirs': [], } diff --git a/easybuild/easyconfigs/l/libXxf86vm/libXxf86vm-1.1.4-foss-2016a.eb b/easybuild/easyconfigs/l/libXxf86vm/libXxf86vm-1.1.4-foss-2016a.eb index ea33d4f180..e34d4affc3 100644 --- a/easybuild/easyconfigs/l/libXxf86vm/libXxf86vm-1.1.4-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libXxf86vm/libXxf86vm-1.1.4-foss-2016a.eb @@ -22,7 +22,7 @@ dependencies = [ ] sanity_check_paths = { - 'files': ['include/X11/extensions/xf86vmode.h']+ + 'files': ['include/X11/extensions/xf86vmode.h'] + ['lib/libXxf86vm.%s' % x for x in ['a', SHLIB_EXT]], 'dirs': [], } diff --git a/easybuild/easyconfigs/l/libXxf86vm/libXxf86vm-1.1.4-intel-2016a.eb b/easybuild/easyconfigs/l/libXxf86vm/libXxf86vm-1.1.4-intel-2016a.eb index 873ae3da80..1fb8f730cc 100644 --- a/easybuild/easyconfigs/l/libXxf86vm/libXxf86vm-1.1.4-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libXxf86vm/libXxf86vm-1.1.4-intel-2016a.eb @@ -22,7 +22,7 @@ dependencies = [ ] sanity_check_paths = { - 'files': ['include/X11/extensions/xf86vmode.h']+ + 'files': ['include/X11/extensions/xf86vmode.h'] + ['lib/libXxf86vm.%s' % x for x in ['a', SHLIB_EXT]], 'dirs': [], } diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.21-intel-2015b.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.21-intel-2015b.eb index b76c98f402..7caa32f2db 100644 --- a/easybuild/easyconfigs/l/libpng/libpng-1.6.21-intel-2015b.eb +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.21-intel-2015b.eb @@ -19,7 +19,7 @@ configopts = "--with-pic" majminver = ''.join(version.split('.')[:2]) sanity_check_paths = { 'files': ['include/pngconf.h', 'include/png.h', 'include/pnglibconf.h', 'lib/libpng.a', - 'lib/libpng.%s' % SHLIB_EXT, 'lib/libpng%s.a' % majminver, 'lib/libpng%s.%s' %(majminver, SHLIB_EXT)], + 'lib/libpng.%s' % SHLIB_EXT, 'lib/libpng%s.a' % majminver, 'lib/libpng%s.%s' % (majminver, SHLIB_EXT)], 'dirs': ['bin', 'include/libpng%s' % majminver, 'share/man'], } diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goolf-1.7.20.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goolf-1.7.20.eb index be707f2f9d..6d2b145e5d 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goolf-1.7.20.eb @@ -21,10 +21,10 @@ dependencies = [('ncurses', '5.9')] preconfigopts = "LDFLAGS='-lncurses'" sanity_check_paths = { - 'files' : ['lib/libreadline.a', 'lib/libhistory.a'] + - ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', - 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], - 'dirs' : [], + 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + 'dirs': [], } moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.4.0.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.4.0.eb index 12e011a8ed..ade9c01fee 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.4.0.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.4.0.eb @@ -21,10 +21,10 @@ dependencies = [('ncurses', '5.9')] preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { - 'files' : ['lib/libreadline.a', 'lib/libhistory.a'] + - ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', - 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], - 'dirs' : [], + 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + 'dirs': [], } moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-2015.06.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-2015.06.eb index 1710b5c8bc..8708402541 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-2015.06.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-2015.06.eb @@ -23,10 +23,10 @@ dependencies = [('ncurses', '5.9')] preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { - 'files' : ['lib/libreadline.a', 'lib/libhistory.a'] + - ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', - 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], - 'dirs' : [], + 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + 'dirs': [], } moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-2015.11.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-2015.11.eb index a4fb8619cb..7bfc1d634c 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-2015.11.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-2015.11.eb @@ -23,10 +23,10 @@ dependencies = [('ncurses', '5.9')] preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { - 'files' : ['lib/libreadline.a', 'lib/libhistory.a'] + - ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', - 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], - 'dirs' : [], + 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + 'dirs': [], } moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-2016.03.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-2016.03.eb index c434630db4..33e6e24615 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-2016.03.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-2016.03.eb @@ -23,10 +23,10 @@ dependencies = [('ncurses', '6.0')] preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { - 'files' : ['lib/libreadline.a', 'lib/libhistory.a'] + - ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', - 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], - 'dirs' : [], + 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + 'dirs': [], } moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libsmm/libsmm-20111205-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libsmm/libsmm-20111205-goolf-1.4.10.eb index d7907d8655..ca93b0d47a 100644 --- a/easybuild/easyconfigs/l/libsmm/libsmm-20111205-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/libsmm/libsmm-20111205-goolf-1.4.10.eb @@ -2,8 +2,9 @@ name = 'libsmm' version = '20111205' homepage = 'http://cp2k.berlios.de/index.html' -description = """libsmm is part of CP2K. It is a library tuned for small size matrix multiplication, - an area where regular BLAS is not so well-tuned. The source can be found in the tools/build_libssm directory of CP2K code.""" +description = """libsmm is part of CP2K. It is a library tuned for small size matrix multiplication, an area where + regular BLAS is not so well-tuned. The source can be found in the tools/build_libssm directory of CP2K code.""" + toolchain = {'name': 'goolf', 'version': '1.4.10'} sources = ['CP2K-%s.tar.gz' % version] diff --git a/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-GCC-4.9.3-2.25.eb index 6d7bea7d3d..5c7a628aaf 100644 --- a/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-GCC-4.9.3-2.25.eb @@ -15,10 +15,10 @@ source_urls = [GNU_SOURCE] parallel = 1 sanity_check_paths = { - 'files' : ['lib/libunistring.a', 'lib/libunistring.%s' % SHLIB_EXT] + - ['include/uni%s.h' % x for x in ['case', 'conv', 'ctype', 'lbrk', 'name', 'norm', - 'stdio', 'str', 'types', 'wbrk', 'width']], - 'dirs' : ['include/unistring'], + 'files': ['lib/libunistring.a', 'lib/libunistring.%s' % SHLIB_EXT] + + ['include/uni%s.h' % x for x in ['case', 'conv', 'ctype', 'lbrk', 'name', 'norm', + 'stdio', 'str', 'types', 'wbrk', 'width']], + 'dirs': ['include/unistring'], } moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-foss-2015b.eb b/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-foss-2015b.eb index 3c6b226b5a..57b9a33b63 100644 --- a/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-foss-2015b.eb +++ b/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-foss-2015b.eb @@ -15,10 +15,10 @@ source_urls = [GNU_SOURCE] parallel = 1 sanity_check_paths = { - 'files' : ['lib/libunistring.a', 'lib/libunistring.%s' % SHLIB_EXT] + - ['include/uni%s.h' % x for x in ['case', 'conv', 'ctype', 'lbrk', 'name', 'norm', - 'stdio', 'str', 'types', 'wbrk', 'width']], - 'dirs' : ['include/unistring'], + 'files': ['lib/libunistring.a', 'lib/libunistring.%s' % SHLIB_EXT] + + ['include/uni%s.h' % x for x in ['case', 'conv', 'ctype', 'lbrk', 'name', 'norm', + 'stdio', 'str', 'types', 'wbrk', 'width']], + 'dirs': ['include/unistring'], } moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-foss-2016a.eb b/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-foss-2016a.eb index 052063704a..25d25c5148 100644 --- a/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-foss-2016a.eb @@ -15,10 +15,10 @@ source_urls = [GNU_SOURCE] parallel = 1 sanity_check_paths = { - 'files' : ['lib/libunistring.a', 'lib/libunistring.%s' % SHLIB_EXT] + - ['include/uni%s.h' % x for x in ['case', 'conv', 'ctype', 'lbrk', 'name', 'norm', - 'stdio', 'str', 'types', 'wbrk', 'width']], - 'dirs' : ['include/unistring'], + 'files': ['lib/libunistring.a', 'lib/libunistring.%s' % SHLIB_EXT] + + ['include/uni%s.h' % x for x in ['case', 'conv', 'ctype', 'lbrk', 'name', 'norm', + 'stdio', 'str', 'types', 'wbrk', 'width']], + 'dirs': ['include/unistring'], } moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-intel-2015b.eb b/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-intel-2015b.eb index 19e0b26c92..bf35428b39 100644 --- a/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-intel-2015b.eb +++ b/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-intel-2015b.eb @@ -17,10 +17,10 @@ patches = ['libunistring_icc_builtin_nan-inf.patch'] parallel = 1 sanity_check_paths = { - 'files' : ['lib/libunistring.a', 'lib/libunistring.%s' % SHLIB_EXT] + - ['include/uni%s.h' % x for x in ['case', 'conv', 'ctype', 'lbrk', 'name', 'norm', - 'stdio', 'str', 'types', 'wbrk', 'width']], - 'dirs' : ['include/unistring'], + 'files': ['lib/libunistring.a', 'lib/libunistring.%s' % SHLIB_EXT] + + ['include/uni%s.h' % x for x in ['case', 'conv', 'ctype', 'lbrk', 'name', 'norm', + 'stdio', 'str', 'types', 'wbrk', 'width']], + 'dirs': ['include/unistring'], } moduleclass = 'lib' -- GitLab From 204a49a722c80e724b395046c744d92ea1076f6b Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Thu, 9 Mar 2017 12:27:35 +0800 Subject: [PATCH 0285/1603] yet another batch of minor style fixes --- .../easyconfigs/m/MVAPICH2/MVAPICH2-1.8.1-GCC-4.7.2.eb | 3 ++- .../easyconfigs/m/MVAPICH2/MVAPICH2-1.9a2-GCC-4.7.2.eb | 3 ++- easybuild/easyconfigs/m/Maq/Maq-0.7.0.eb | 7 +++---- .../m/Mesa/Mesa-7.11.2-goolf-1.4.10-Python-2.7.3.eb | 7 ++++--- .../m/Mesa/Mesa-7.11.2-ictce-5.3.0-Python-2.7.3.eb | 4 ++-- .../m/Mesa/Mesa-7.11.2-ictce-5.5.0-Python-2.7.6.eb | 4 ++-- .../easyconfigs/m/Metal/Metal-2011-03-25-foss-2016a.eb | 9 +++------ .../easyconfigs/m/Minia/Minia-2.0.7-goolf-1.7.20.eb | 1 - .../m/Minimac2/Minimac2-2014.9.15-goolf-1.7.20.eb | 6 ++++-- .../easyconfigs/m/magma/magma-2.0.0-CrayGNU-2015.11.eb | 4 ++-- .../m/molmod/molmod-1.0-goolf-1.4.10-Python-2.7.3.eb | 2 +- .../m/molmod/molmod-1.0-ictce-5.3.0-Python-2.7.3.eb | 2 +- .../m/molmod/molmod-1.0-intel-2015a-Python-2.7.10.eb | 2 +- .../m/molmod/molmod-1.0-intel-2015a-Python-2.7.9.eb | 2 +- .../m/molmod/molmod-1.1-intel-2015b-Python-2.7.10.eb | 2 +- .../m/molmod/molmod-1.1-intel-2016a-Python-2.7.11.eb | 2 +- .../m/molmod/molmod-1.1-intel-2016b-Python-2.7.12.eb | 2 +- easybuild/easyconfigs/m/motif/motif-2.3.5-foss-2016a.eb | 8 ++++---- .../easyconfigs/m/mrFAST/mrFAST-2.6.0.1-goolf-1.4.10.eb | 2 +- .../easyconfigs/m/mrFAST/mrFAST-2.6.0.1-ictce-6.2.5.eb | 2 +- .../m/mrsFAST/mrsFAST-2.6.0.4-goolf-1.4.10.eb | 2 +- .../easyconfigs/m/mrsFAST/mrsFAST-2.6.0.4-ictce-6.2.5.eb | 2 +- 22 files changed, 39 insertions(+), 39 deletions(-) diff --git a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.8.1-GCC-4.7.2.eb b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.8.1-GCC-4.7.2.eb index f289c8d654..c29dfc7a1a 100644 --- a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.8.1-GCC-4.7.2.eb +++ b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.8.1-GCC-4.7.2.eb @@ -2,7 +2,8 @@ name = 'MVAPICH2' version = '1.8.1' homepage = 'http://mvapich.cse.ohio-state.edu/overview/mvapich2/' -description = "This is an MPI-2 implementation (conforming to MPI 2.1 standard) which includes all MPI-1 features. It is based on MPICH2 and MVICH." +description = """This is an MPI-2 implementation (conforming to MPI 2.1 standard) which includes all MPI-1 features. + It is based on MPICH2 and MVICH.""" toolchain = {'name': 'GCC', 'version': '4.7.2'} diff --git a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9a2-GCC-4.7.2.eb b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9a2-GCC-4.7.2.eb index 372dd0b722..777e5a69e1 100644 --- a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9a2-GCC-4.7.2.eb +++ b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9a2-GCC-4.7.2.eb @@ -2,7 +2,8 @@ name = 'MVAPICH2' version = '1.9a2' homepage = 'http://mvapich.cse.ohio-state.edu/overview/mvapich2/' -description = "This is an MPI-2 implementation (conforming to MPI 2.1 standard) which includes all MPI-1 features. It is based on MPICH2 and MVICH." +description = """This is an MPI-2 implementation (conforming to MPI 2.1 standard) which includes all MPI-1 features. + It is based on MPICH2 and MVICH.""" toolchain = {'name': 'GCC', 'version': '4.7.2'} diff --git a/easybuild/easyconfigs/m/Maq/Maq-0.7.0.eb b/easybuild/easyconfigs/m/Maq/Maq-0.7.0.eb index b78da99d83..8357cd6199 100644 --- a/easybuild/easyconfigs/m/Maq/Maq-0.7.0.eb +++ b/easybuild/easyconfigs/m/Maq/Maq-0.7.0.eb @@ -8,16 +8,15 @@ name = 'Maq' version = '0.7.0' homepage = 'http://maq.sourceforge.net/maq-man.shtml' -description = """ Maq is a software that builds mapping -assemblies from short reads generated by the -next-generation sequencing machines. """ +description = """Maq is a software that builds mapping assemblies from short reads generated by the next-generation sequencing + machines.""" toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = ['https://sourceforge.net/projects/maq/files/maq/%(version)s/'] sources = ['maq-%(version)s_x86_64-linux.tar.bz2'] -checksums= ["65edff1529c84783d0a4b9208a91efa9"] +checksums = ["65edff1529c84783d0a4b9208a91efa9"] modextrapaths = {'PATH': ''} diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-goolf-1.4.10-Python-2.7.3.eb index 57483e1d4f..ea99e518c2 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-goolf-1.4.10-Python-2.7.3.eb @@ -5,7 +5,8 @@ version = '7.11.2' homepage = 'http://www.mesa3d.org/' description = """Mesa is an open-source implementation of the OpenGL specification - -a system for rendering interactive 3D graphics.""" + a system for rendering interactive 3D graphics.""" + toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'optarch': True} @@ -37,8 +38,8 @@ osdependencies = [ 'libXfixes-devel', ] -configopts = " --disable-osmesa --enable-glu --disable-gallium-llvm --disable-gallium-gbm --enable-glx --with-driver=xlib" -configopts += " --disable-driglx-direct --with-gallium-drivers='' --without-demos --disable-egl""" +configopts = " --disable-osmesa --enable-glu --disable-gallium-llvm --disable-gallium-gbm --enable-glx " +configopts += " --with-driver=xlib --disable-driglx-direct --with-gallium-drivers='' --without-demos --disable-egl" # package-config files for os dependencies are in an os specific place preconfigopts = ' PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-5.3.0-Python-2.7.3.eb index ac83c1243a..55c990890f 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-5.3.0-Python-2.7.3.eb @@ -39,8 +39,8 @@ osdependencies = [ 'libXfixes-devel', ] -configopts = " --disable-osmesa --enable-glu --disable-gallium-llvm --disable-gallium-gbm --enable-glx --with-driver=xlib" -configopts += " --disable-driglx-direct --with-gallium-drivers='' --without-demos --disable-egl""" +configopts = " --disable-osmesa --enable-glu --disable-gallium-llvm --disable-gallium-gbm --enable-glx " +configopts += " --with-driver=xlib --disable-driglx-direct --with-gallium-drivers='' --without-demos --disable-egl" # package-config files for os dependencies are in an os specific place preconfigopts = ' PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-5.5.0-Python-2.7.6.eb b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-5.5.0-Python-2.7.6.eb index 810e10d3bb..4b5ad07db8 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-5.5.0-Python-2.7.6.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-5.5.0-Python-2.7.6.eb @@ -39,8 +39,8 @@ osdependencies = [ 'libXfixes-devel', ] -configopts = " --disable-osmesa --enable-glu --disable-gallium-llvm --disable-gallium-gbm --enable-glx --with-driver=xlib" -configopts += " --disable-driglx-direct --with-gallium-drivers='' --without-demos --disable-egl""" +configopts = " --disable-osmesa --enable-glu --disable-gallium-llvm --disable-gallium-gbm --enable-glx " +configopts += " --with-driver=xlib --disable-driglx-direct --with-gallium-drivers='' --without-demos --disable-egl" # package-config files for os dependencies are in an os specific place preconfigopts = ' PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' diff --git a/easybuild/easyconfigs/m/Metal/Metal-2011-03-25-foss-2016a.eb b/easybuild/easyconfigs/m/Metal/Metal-2011-03-25-foss-2016a.eb index 04f7962ec3..8c234a753f 100644 --- a/easybuild/easyconfigs/m/Metal/Metal-2011-03-25-foss-2016a.eb +++ b/easybuild/easyconfigs/m/Metal/Metal-2011-03-25-foss-2016a.eb @@ -4,11 +4,8 @@ name = 'Metal' version = '2011-03-25' homepage = 'http://csg.sph.umich.edu/abecasis/Metal/' -description = """ -Metal - Meta Analysis Helper -The METAL software is designed to facilitate meta-analysis of large datasets (such as several whole genome scans) in a - convenient, rapid and memory efficient manner. -""" +description = """Metal - Meta Analysis Helper. The METAL software is designed to facilitate meta-analysis of large + datasets (such as several whole genome scans) in a convenient, rapid and memory efficient manner.""" sources = ['generic-%(namelower)s-%(version)s.tar.gz'] source_urls = ['http://csg.sph.umich.edu/abecasis/Metal/download/'] @@ -18,7 +15,7 @@ toolchainopts = {'pic': True} patches = ['Metal-%(version)s_Makefile.patch'] -skipsteps=['configure'] +skipsteps = ['configure'] buildopts = 'all' diff --git a/easybuild/easyconfigs/m/Minia/Minia-2.0.7-goolf-1.7.20.eb b/easybuild/easyconfigs/m/Minia/Minia-2.0.7-goolf-1.7.20.eb index 8523144221..947de950b4 100644 --- a/easybuild/easyconfigs/m/Minia/Minia-2.0.7-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/m/Minia/Minia-2.0.7-goolf-1.7.20.eb @@ -28,4 +28,3 @@ sanity_check_paths = { } moduleclass = 'bio' - diff --git a/easybuild/easyconfigs/m/Minimac2/Minimac2-2014.9.15-goolf-1.7.20.eb b/easybuild/easyconfigs/m/Minimac2/Minimac2-2014.9.15-goolf-1.7.20.eb index 50e766c0ce..c6a015a815 100644 --- a/easybuild/easyconfigs/m/Minimac2/Minimac2-2014.9.15-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/m/Minimac2/Minimac2-2014.9.15-goolf-1.7.20.eb @@ -24,8 +24,10 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] dependencies = [ ('zlib', '1.2.8'), # This app also depends in openblas -# ('OpenSSL', '1.0.1q'), # OS dependency should be preferred if the os version is more recent then this version, it's -# nice to have an up to date openssl for security reasons + # OS dependency should be preferred if the os version is more recent then this version, it's + # nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1q'), + ] # firt move to folder libStatGen to run make clean && make diff --git a/easybuild/easyconfigs/m/magma/magma-2.0.0-CrayGNU-2015.11.eb b/easybuild/easyconfigs/m/magma/magma-2.0.0-CrayGNU-2015.11.eb index ba77602cd4..4c07b64293 100644 --- a/easybuild/easyconfigs/m/magma/magma-2.0.0-CrayGNU-2015.11.eb +++ b/easybuild/easyconfigs/m/magma/magma-2.0.0-CrayGNU-2015.11.eb @@ -5,7 +5,7 @@ version = '2.0.0' homepage = 'http://icl.cs.utk.edu/magma/' description = """The MAGMA project aims to develop a dense linear algebra library similar to -LAPACK but for heterogeneous/hybrid architectures, starting with current Multicore+GPU systems.""" + LAPACK but for heterogeneous/hybrid architectures, starting with current Multicore+GPU systems.""" toolchain = {'name': 'CrayGNU', 'version': '2015.11'} toolchainopts = {'pic': True} @@ -15,7 +15,7 @@ source_urls = ['http://icl.cs.utk.edu/projectsfiles/magma/downloads/'] patches = [('magma-2.0.0.patch')] -builddependencies = [ ('cudatoolkit/7.0.28-1.0502.10742.5.1', EXTERNAL_MODULE) ] +builddependencies = [('cudatoolkit/7.0.28-1.0502.10742.5.1', EXTERNAL_MODULE)] skipsteps = ['configure'] diff --git a/easybuild/easyconfigs/m/molmod/molmod-1.0-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/m/molmod/molmod-1.0-goolf-1.4.10-Python-2.7.3.eb index 08d2e9759c..73545656c9 100644 --- a/easybuild/easyconfigs/m/molmod/molmod-1.0-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/m/molmod/molmod-1.0-goolf-1.4.10-Python-2.7.3.eb @@ -4,7 +4,7 @@ name = 'molmod' version = '1.0' homepage = 'http://molmod.github.io/molmod/' -description = """MolMod is a Python library with many compoments that are useful to write molecular modeling programs.""" +description = "MolMod is a Python library with many compoments that are useful to write molecular modeling programs." toolchain = {'name': 'goolf', 'version': '1.4.10'} diff --git a/easybuild/easyconfigs/m/molmod/molmod-1.0-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/m/molmod/molmod-1.0-ictce-5.3.0-Python-2.7.3.eb index 221229e3a6..763ccba836 100644 --- a/easybuild/easyconfigs/m/molmod/molmod-1.0-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/m/molmod/molmod-1.0-ictce-5.3.0-Python-2.7.3.eb @@ -4,7 +4,7 @@ name = 'molmod' version = '1.0' homepage = 'http://molmod.github.io/molmod/' -description = """MolMod is a Python library with many compoments that are useful to write molecular modeling programs.""" +description = "MolMod is a Python library with many compoments that are useful to write molecular modeling programs." toolchain = {'name': 'ictce', 'version': '5.3.0'} diff --git a/easybuild/easyconfigs/m/molmod/molmod-1.0-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/m/molmod/molmod-1.0-intel-2015a-Python-2.7.10.eb index 5d19338ab3..dab01e8798 100644 --- a/easybuild/easyconfigs/m/molmod/molmod-1.0-intel-2015a-Python-2.7.10.eb +++ b/easybuild/easyconfigs/m/molmod/molmod-1.0-intel-2015a-Python-2.7.10.eb @@ -4,7 +4,7 @@ name = 'molmod' version = '1.0' homepage = 'http://molmod.github.io/molmod/' -description = """MolMod is a Python library with many compoments that are useful to write molecular modeling programs.""" +description = "MolMod is a Python library with many compoments that are useful to write molecular modeling programs." toolchain = {'name': 'intel', 'version': '2015a'} diff --git a/easybuild/easyconfigs/m/molmod/molmod-1.0-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/m/molmod/molmod-1.0-intel-2015a-Python-2.7.9.eb index b6703cee30..4aa55f0033 100644 --- a/easybuild/easyconfigs/m/molmod/molmod-1.0-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/m/molmod/molmod-1.0-intel-2015a-Python-2.7.9.eb @@ -4,7 +4,7 @@ name = 'molmod' version = '1.0' homepage = 'http://molmod.github.io/molmod/' -description = """MolMod is a Python library with many compoments that are useful to write molecular modeling programs.""" +description = "MolMod is a Python library with many compoments that are useful to write molecular modeling programs." toolchain = {'name': 'intel', 'version': '2015a'} diff --git a/easybuild/easyconfigs/m/molmod/molmod-1.1-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/m/molmod/molmod-1.1-intel-2015b-Python-2.7.10.eb index ee1c589750..eb46a80abe 100644 --- a/easybuild/easyconfigs/m/molmod/molmod-1.1-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/m/molmod/molmod-1.1-intel-2015b-Python-2.7.10.eb @@ -5,7 +5,7 @@ version = '1.1' versionsuffix = '-Python-%(pyver)s' homepage = 'http://molmod.github.io/molmod/' -description = """MolMod is a Python library with many compoments that are useful to write molecular modeling programs.""" +description = "MolMod is a Python library with many compoments that are useful to write molecular modeling programs." toolchain = {'name': 'intel', 'version': '2015b'} diff --git a/easybuild/easyconfigs/m/molmod/molmod-1.1-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/m/molmod/molmod-1.1-intel-2016a-Python-2.7.11.eb index 1673c64e60..62f71cc876 100644 --- a/easybuild/easyconfigs/m/molmod/molmod-1.1-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/m/molmod/molmod-1.1-intel-2016a-Python-2.7.11.eb @@ -5,7 +5,7 @@ version = '1.1' versionsuffix = '-Python-%(pyver)s' homepage = 'http://molmod.github.io/molmod/' -description = """MolMod is a Python library with many compoments that are useful to write molecular modeling programs.""" +description = "MolMod is a Python library with many compoments that are useful to write molecular modeling programs." toolchain = {'name': 'intel', 'version': '2016a'} diff --git a/easybuild/easyconfigs/m/molmod/molmod-1.1-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/m/molmod/molmod-1.1-intel-2016b-Python-2.7.12.eb index 23fd809bd7..1b74bd9124 100644 --- a/easybuild/easyconfigs/m/molmod/molmod-1.1-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/m/molmod/molmod-1.1-intel-2016b-Python-2.7.12.eb @@ -5,7 +5,7 @@ version = '1.1' versionsuffix = '-Python-%(pyver)s' homepage = 'http://molmod.github.io/molmod/' -description = """MolMod is a Python library with many compoments that are useful to write molecular modeling programs.""" +description = "MolMod is a Python library with many compoments that are useful to write molecular modeling programs." toolchain = {'name': 'intel', 'version': '2016b'} diff --git a/easybuild/easyconfigs/m/motif/motif-2.3.5-foss-2016a.eb b/easybuild/easyconfigs/m/motif/motif-2.3.5-foss-2016a.eb index 3a9a7c7e64..91ed160613 100644 --- a/easybuild/easyconfigs/m/motif/motif-2.3.5-foss-2016a.eb +++ b/easybuild/easyconfigs/m/motif/motif-2.3.5-foss-2016a.eb @@ -4,9 +4,9 @@ name = 'motif' version = '2.3.5' homepage = 'http://motif.ics.com/' -description = """Motif refers to both a graphical user interface (GUI) specification and the widget toolkit for building - applications that follow that specification under the X Window System on Unix and other POSIX-compliant systems. - It was the standard toolkit for the Common Desktop Environment and thus for Unix.""" +description = """Motif refers to both a graphical user interface (GUI) specification and the widget toolkit for + building applications that follow that specification under the X Window System on Unix and other POSIX-compliant + systems. It was the standard toolkit for the Common Desktop Environment and thus for Unix.""" toolchain = {'name': 'foss', 'version': '2016a'} # use -O1 to dance around icc segfaulting @@ -42,4 +42,4 @@ sanity_check_paths = { 'dirs': ['include/Mrm', 'include/uil', 'include/X11', 'include/Xm'], } -moduleclass = 'vis' \ No newline at end of file +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/mrFAST/mrFAST-2.6.0.1-goolf-1.4.10.eb b/easybuild/easyconfigs/m/mrFAST/mrFAST-2.6.0.1-goolf-1.4.10.eb index 2b7c9b71bd..fb05915a84 100644 --- a/easybuild/easyconfigs/m/mrFAST/mrFAST-2.6.0.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/m/mrFAST/mrFAST-2.6.0.1-goolf-1.4.10.eb @@ -21,7 +21,7 @@ parallel = 1 buildopts = ' CC="$CC"' -files_to_copy = [ (['mrfast'], 'bin'), "LICENSE" ] +files_to_copy = [(['mrfast'], 'bin'), "LICENSE"] sanity_check_paths = { 'files': ["bin/mrfast"], diff --git a/easybuild/easyconfigs/m/mrFAST/mrFAST-2.6.0.1-ictce-6.2.5.eb b/easybuild/easyconfigs/m/mrFAST/mrFAST-2.6.0.1-ictce-6.2.5.eb index 086efed6cd..1bc0838af6 100644 --- a/easybuild/easyconfigs/m/mrFAST/mrFAST-2.6.0.1-ictce-6.2.5.eb +++ b/easybuild/easyconfigs/m/mrFAST/mrFAST-2.6.0.1-ictce-6.2.5.eb @@ -21,7 +21,7 @@ parallel = 1 buildopts = ' CC="$CC"' -files_to_copy = [ (['mrfast'], 'bin'), "LICENSE" ] +files_to_copy = [(['mrfast'], 'bin'), "LICENSE"] sanity_check_paths = { 'files': ["bin/mrfast"], diff --git a/easybuild/easyconfigs/m/mrsFAST/mrsFAST-2.6.0.4-goolf-1.4.10.eb b/easybuild/easyconfigs/m/mrsFAST/mrsFAST-2.6.0.4-goolf-1.4.10.eb index 7da0c48dde..e58c648eee 100644 --- a/easybuild/easyconfigs/m/mrsFAST/mrsFAST-2.6.0.4-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/m/mrsFAST/mrsFAST-2.6.0.4-goolf-1.4.10.eb @@ -24,7 +24,7 @@ patches = ['mrsFAST-%(version)s-intel-compiler.patch'] parallel = 1 -files_to_copy = [ (['mrsfast'], 'bin'), "Changelog" ] +files_to_copy = [(['mrsfast'], 'bin'), "Changelog"] sanity_check_paths = { 'files': ["bin/mrsfast"], diff --git a/easybuild/easyconfigs/m/mrsFAST/mrsFAST-2.6.0.4-ictce-6.2.5.eb b/easybuild/easyconfigs/m/mrsFAST/mrsFAST-2.6.0.4-ictce-6.2.5.eb index fda1eaa51f..933177a5af 100644 --- a/easybuild/easyconfigs/m/mrsFAST/mrsFAST-2.6.0.4-ictce-6.2.5.eb +++ b/easybuild/easyconfigs/m/mrsFAST/mrsFAST-2.6.0.4-ictce-6.2.5.eb @@ -24,7 +24,7 @@ patches = ['mrsFAST-%(version)s-intel-compiler.patch'] parallel = 1 -files_to_copy = [ (['mrsfast'], 'bin'), "Changelog" ] +files_to_copy = [(['mrsfast'], 'bin'), "Changelog"] sanity_check_paths = { 'files': ["bin/mrsfast"], -- GitLab From 78a9d5a38696a3871b1c9a30cc838f5a3a6a2274 Mon Sep 17 00:00:00 2001 From: Robert Date: Thu, 9 Mar 2017 17:42:47 +1030 Subject: [PATCH 0286/1603] PileOMeth added --- .../p/PileOMeth/PileOMeth-0.1.11.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/p/PileOMeth/PileOMeth-0.1.11.eb diff --git a/easybuild/easyconfigs/p/PileOMeth/PileOMeth-0.1.11.eb b/easybuild/easyconfigs/p/PileOMeth/PileOMeth-0.1.11.eb new file mode 100644 index 0000000000..af4dcdba98 --- /dev/null +++ b/easybuild/easyconfigs/p/PileOMeth/PileOMeth-0.1.11.eb @@ -0,0 +1,40 @@ +## +# This is a contribution from Phoenix HPC Service, The University of Adelaide, Australia +# Homepage: https://www.adelaide.edu.au/phoenix/ +# +# Copyright:: adelaide.edu.au/phoenix +# Authors:: Robert Qiao , Exe Escobedo +# License:: +# +# Notes:: +### + +easyblock = 'MakeCp' + +name = 'PileOMeth' +version = '0.1.11' + +homepage = 'https://github.com/dpryan79/PileOMeth' +description = """PileOMeth processes a coordinate-sorted and indexed BAM or CRAM file containing some form of BS-seq alignments. +PileOMeth extracts per-base methylation metrics from them. +PileOMeth requires an indexed fasta file containing the reference genome as well. +""" +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['%(version)s.zip'] +source_urls = ['https://github.com/dpryan79/PileOMeth/archive/'] + +dependencies = [ + ('HTSlib', '1.2.1', '', ('foss', '2017a')) +] + +files_to_copy = [ + (["PileOMeth"], "bin"), "*.c", "*.h" +] + +sanity_check_paths = { + 'files': ["bin/PileOMeth"], + 'dirs': [] +} + +moduleclass = 'bio' -- GitLab From e1b83120c8d9ac9a9753f21956a8e66d731a0242 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Mar 2017 09:40:33 +0100 Subject: [PATCH 0287/1603] miRDeep2 scripts do a hard check for an (empty) file named 'install_successful' in the install dir... --- .../easyconfigs/m/miRDeep2/miRDeep2-2.0.0.8-intel-2016b.eb | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/miRDeep2/miRDeep2-2.0.0.8-intel-2016b.eb b/easybuild/easyconfigs/m/miRDeep2/miRDeep2-2.0.0.8-intel-2016b.eb index 8a8e1422a7..7f489ba651 100644 --- a/easybuild/easyconfigs/m/miRDeep2/miRDeep2-2.0.0.8-intel-2016b.eb +++ b/easybuild/easyconfigs/m/miRDeep2/miRDeep2-2.0.0.8-intel-2016b.eb @@ -20,10 +20,13 @@ dependencies = [ ('randfold', '2.0.1'), # also provides SQUID ] -install_cmd = "chmod a+x mirdeep*/src/*.pl && cp -a mirdeep*/src %(installdir)s/bin" +install_cmd = "cp -a mirdeep*/src %(installdir)s/bin && chmod a+x %(installdir)s/bin/*.pl && " + +# scripts include a hard check for a file called 'install_successful' in the install directory... +install_cmd += "touch %(installdir)s/install_successful" sanity_check_paths = { - 'files': ['bin/make_html.pl'], + 'files': ['bin/mapper.pl', 'bin/miRDeep2.pl'], 'dirs': [], } -- GitLab From a2c62538a6049740584c8c668082799db24e404f Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Thu, 9 Mar 2017 10:45:09 +0100 Subject: [PATCH 0288/1603] added GFOLD easyconfig for goolf and intel --- .../g/GFOLD/GFOLD-1.1.4-goolf-1.7.20.eb | 34 +++++++++++++++++++ .../g/GFOLD/GFOLD-1.1.4-intel-2016a.eb | 34 +++++++++++++++++++ .../g/GFOLD/gfold-1.1.4-makefile.patch | 18 ++++++++++ 3 files changed, 86 insertions(+) create mode 100644 easybuild/easyconfigs/g/GFOLD/GFOLD-1.1.4-goolf-1.7.20.eb create mode 100644 easybuild/easyconfigs/g/GFOLD/GFOLD-1.1.4-intel-2016a.eb create mode 100644 easybuild/easyconfigs/g/GFOLD/gfold-1.1.4-makefile.patch diff --git a/easybuild/easyconfigs/g/GFOLD/GFOLD-1.1.4-goolf-1.7.20.eb b/easybuild/easyconfigs/g/GFOLD/GFOLD-1.1.4-goolf-1.7.20.eb new file mode 100644 index 0000000000..8d11408e6b --- /dev/null +++ b/easybuild/easyconfigs/g/GFOLD/GFOLD-1.1.4-goolf-1.7.20.eb @@ -0,0 +1,34 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'MakeCp' + +name = 'GFOLD' +version = '1.1.4' + +homepage = 'http://www.tongji.edu.cn/~zhanglab/GFOLD/index.html' +description = 'Generalized fold change for ranking differentially expressed genes from RNA-seq data' + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +source_urls = ['https://bitbucket.org/feeldead/gfold/downloads/'] +sources = ['%(namelower)s.V%(version)s.tar.gz'] + +patches = ['gfold-%(version)s-makefile.patch'] + +dependencies = [ + ('GSL', '1.16'), +] + +files_to_copy = [(['gfold'], 'bin'), 'README', 'doc'] + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/gfold'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GFOLD/GFOLD-1.1.4-intel-2016a.eb b/easybuild/easyconfigs/g/GFOLD/GFOLD-1.1.4-intel-2016a.eb new file mode 100644 index 0000000000..3b289b47ea --- /dev/null +++ b/easybuild/easyconfigs/g/GFOLD/GFOLD-1.1.4-intel-2016a.eb @@ -0,0 +1,34 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'MakeCp' + +name = 'GFOLD' +version = '1.1.4' + +homepage = 'http://www.tongji.edu.cn/~zhanglab/GFOLD/index.html' +description = 'Generalized fold change for ranking differentially expressed genes from RNA-seq data' + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['https://bitbucket.org/feeldead/gfold/downloads/'] +sources = ['%(namelower)s.V%(version)s.tar.gz'] + +patches = ['gfold-%(version)s-makefile.patch'] + +dependencies = [ + ('GSL', '1.16'), +] + +files_to_copy = [(['gfold'], 'bin'), 'README', 'doc'] + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/gfold'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GFOLD/gfold-1.1.4-makefile.patch b/easybuild/easyconfigs/g/GFOLD/gfold-1.1.4-makefile.patch new file mode 100644 index 0000000000..15699d96ba --- /dev/null +++ b/easybuild/easyconfigs/g/GFOLD/gfold-1.1.4-makefile.patch @@ -0,0 +1,18 @@ +fix the hardcoded compiler + +diff -ru gfold.V1.1.4.orig/Makefile gfold.V1.1.4/Makefile +--- gfold.V1.1.4.orig/Makefile 2015-05-24 01:47:13.000000000 +0200 ++++ gfold.V1.1.4/Makefile 2017-03-09 10:32:23.919031000 +0100 +@@ -5,10 +5,10 @@ + all: program + + debug: DataProcessor.hpp GFOLD.hpp Utility.hpp GeneInfo.hpp main.cc +- g++ -Wall -g main.cc -o gfold -lgsl -lgslcblas ++ ${CXX} -Wall -g main.cc -o gfold -lgsl -lgslcblas + + program: DataProcessor.hpp GFOLD.hpp Utility.hpp GeneInfo.hpp main.cc +- g++ -O3 -Wall -g main.cc -o gfold -lgsl -lgslcblas ++ ${CXX} -O3 -Wall -g main.cc -o gfold -lgsl -lgslcblas + + docu: doc/gfold.pod + pod2man doc/gfold.pod > doc/gfold.man -- GitLab From 4f92b9fa68fb297f350a600d382f67e09cb723f5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Mar 2017 11:04:34 +0100 Subject: [PATCH 0289/1603] adding easyconfigs: GDAL-2.1.3-foss-2016b-Python-2.7.12.eb --- .../GDAL-2.1.3-foss-2016b-Python-2.7.12.eb | 54 +++++++++++++++++++ 1 file changed, 54 insertions(+) create mode 100644 easybuild/easyconfigs/g/GDAL/GDAL-2.1.3-foss-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-2.1.3-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/g/GDAL/GDAL-2.1.3-foss-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..0f954c1b05 --- /dev/null +++ b/easybuild/easyconfigs/g/GDAL/GDAL-2.1.3-foss-2016b-Python-2.7.12.eb @@ -0,0 +1,54 @@ +easyblock = 'ConfigureMake' + +name = 'GDAL' +version = '2.1.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.gdal.org/' +description = """GDAL is a translator library for raster geospatial data formats that is released under an X/MIT style + Open Source license by the Open Source Geospatial Foundation. As a library, it presents a single abstract data model + to the calling application for all supported formats. It also comes with a variety of useful commandline utilities for + data translation and processing.""" + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'usempi': True} + +source_urls = ['http://download.osgeo.org/gdal/%(version)s/'] +sources = [SOURCELOWER_TAR_XZ] + +#patches = ['GDAL-2.1.2_fix-vrtsources.patch'] + +dependencies = [ + ('Python', '2.7.12'), + ('netCDF', '4.4.1.1'), + ('expat', '2.2.0'), + ('GEOS', '3.6.1', versionsuffix), + ('SQLite', '3.13.0'), + ('libxml2', '2.9.4'), + ('libpng', '1.6.24'), + ('libjpeg-turbo', '1.5.0'), + ('JasPer', '1.900.1'), + ('LibTIFF', '4.0.6'), + ('zlib', '1.2.8'), + ('cURL', '7.49.1'), + ('PCRE', '8.39'), +] + +configopts = '--with-expat=$EBROOTEXPAT --with-libz=$EBROOTLIBZ --with-hdf5=$EBROOTHDF5 --with-netcdf=$EBROOTNETCDF' +configopts += ' --with-xml2=$EBROOTLIBXML2 --with-geos=$EBROOTGEOS/bin/geos-config --with-jpeg=$EBROOTLIBJPEGMINTURBO' +configopts += ' --with-png=$EBROOTLIBPNG --with-sqlite3=$EBROOTSQLITE --with-jasper=$EBROOTJASPER' +configopts += ' --with-libtiff=$EBROOTLIBTIFF --with-pcre=$EBROOTPCRE --with-python=$EBROOTPYTHON/bin/python' +# there is a bug in the build system causing the build with libtool to fail for the moment +# (static library is also missing because of this) +#configopts += ' --without-libtool' + +#buildopts = 'CXXFLAGS="$CXXFLAGS -fpermissive"' + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +sanity_check_paths = { + 'files': ['lib/libgdal.a', 'lib/libgdal.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include', 'lib/python%(pyshortver)s/site-packages'] +} + +moduleclass = 'data' -- GitLab From b7eee70912a1b3dc6722c933b62449e870a44ffa Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Mar 2017 11:04:52 +0100 Subject: [PATCH 0290/1603] adding easyconfigs: PROJ-4.9.3-foss-2016b.eb --- .../p/PROJ/PROJ-4.9.3-foss-2016b.eb | 57 +++++++++++++++++++ 1 file changed, 57 insertions(+) create mode 100644 easybuild/easyconfigs/p/PROJ/PROJ-4.9.3-foss-2016b.eb diff --git a/easybuild/easyconfigs/p/PROJ/PROJ-4.9.3-foss-2016b.eb b/easybuild/easyconfigs/p/PROJ/PROJ-4.9.3-foss-2016b.eb new file mode 100644 index 0000000000..7c6ed61f58 --- /dev/null +++ b/easybuild/easyconfigs/p/PROJ/PROJ-4.9.3-foss-2016b.eb @@ -0,0 +1,57 @@ +# Built with EasyBuild version 3.1.0 on 2017-03-07_13-55-44 +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2014-2015 The Cyprus Institute +# Authors:: Thekla Loizou +# License:: MIT/GPL +# +## +easyblock = 'ConfigureMake' + +name = 'PROJ' +version = '4.9.3' + +homepage = 'http://trac.osgeo.org/proj/' +description = """Program proj is a standard Unix filter function which converts +geographic longitude and latitude coordinates into cartesian coordinates""" + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['http://download.osgeo.org/proj/'] +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': ['bin/cs2cs', 'bin/geod', 'bin/invgeod', 'bin/invproj', + 'bin/nad2bin', 'bin/proj'], + 'dirs': [], +} + +moduleclass = 'lib' + +# Build statistics +buildstats = [{ + "build_time": 94.84, + "command_line": ["--buildpath='/tmp/vsc40023/easybuild_build'", '--debug', "--github-user='boegel'", "--installpath='/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib'", "--job-backend='PbsPython'", "--packagepath='/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/packages'", "--prefix='/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib'", "--repositorypath='/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/ebfiles_repo'", "--robot='/vscmnt/gent_vulpix/_/user/data/gent/gvo000/gvo00002/vsc40023:/user/data/gent/vsc400/vsc40023/easybuild_easy_installed/lib/python2.7/site-packages/easybuild_easyconfigs-3.1.0-py2.7.egg/easybuild/easyconfigs'", 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"system_python_path": "/usr/bin/python", + "timestamp": 1488891344, + "total_memory": 64303, +}] -- GitLab From 6e355d309317b055b0623b27a22b1a1ff72f6f2f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Mar 2017 11:07:54 +0100 Subject: [PATCH 0291/1603] adding easyconfigs: GEOS-3.6.1-foss-2016b-Python-2.7.12.eb, SWIG-3.0.11-foss-2016b-Python-2.7.12.eb --- .../GEOS-3.6.1-foss-2016b-Python-2.7.12.eb | 55 +++++++++++++++++++ .../SWIG-3.0.11-foss-2016b-Python-2.7.12.eb | 47 ++++++++++++++++ 2 files changed, 102 insertions(+) create mode 100644 easybuild/easyconfigs/g/GEOS/GEOS-3.6.1-foss-2016b-Python-2.7.12.eb create mode 100644 easybuild/easyconfigs/s/SWIG/SWIG-3.0.11-foss-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/g/GEOS/GEOS-3.6.1-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/g/GEOS/GEOS-3.6.1-foss-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..ff17f25dff --- /dev/null +++ b/easybuild/easyconfigs/g/GEOS/GEOS-3.6.1-foss-2016b-Python-2.7.12.eb @@ -0,0 +1,55 @@ +# Built with EasyBuild version 3.1.0 on 2017-03-07_14-08-23 +easyblock = 'ConfigureMake' + +name = 'GEOS' +version = '3.6.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://trac.osgeo.org/geos' +description = """GEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (JTS)""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['http://download.osgeo.org/geos/'] +sources = [SOURCELOWER_TAR_BZ2] + +dependencies = [('Python', '2.7.12')] + +builddependencies = [('SWIG', '3.0.11', versionsuffix)] + +configopts = '--enable-python' + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +sanity_check_paths = { + 'files': ['bin/geos-config', 'lib/libgeos.%s' % SHLIB_EXT, 'lib/libgeos.a', 'include/geos.h'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/geos'], +} + +moduleclass = 'math' + +# Build statistics +buildstats = [{ + "build_time": 431.44, + "command_line": 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b/easybuild/easyconfigs/s/SWIG/SWIG-3.0.11-foss-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..bd7c62c123 --- /dev/null +++ b/easybuild/easyconfigs/s/SWIG/SWIG-3.0.11-foss-2016b-Python-2.7.12.eb @@ -0,0 +1,47 @@ +# Built with EasyBuild version 3.1.0 on 2017-03-07_14-01-11 +name = 'SWIG' +version = '3.0.11' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.swig.org/' +description = """SWIG is a software development tool that connects programs written in C and C++ with + a variety of high-level programming languages.""" + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('Python', '2.7.12'), + ('PCRE', '8.38'), +] + +moduleclass = 'devel' + +# Build statistics +buildstats = [{ + "build_time": 62.35, + "command_line": ["--buildpath='/tmp/vsc40023/easybuild_build'", '--debug', "--github-user='boegel'", 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2.50GHz", + "cpu_speed": 2500.0, + "cpu_vendor": "Intel", + "easybuild-easyblocks_version": "3.1.0", + "easybuild-framework_version": "3.1.0", + "gcc_version": "Using built-in specs.; COLLECT_GCC=/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/software/GCCcore/5.4.0/bin/gcc; COLLECT_LTO_WRAPPER=/user/scratchphanpy/gent/gvo000/gvo00002/vsc40023/easybuild_REGTEST/CO7/haswell-ib/software/GCCcore/5.4.0/bin/../libexec/gcc/x86_64-unknown-linux-gnu/5.4.0/lto-wrapper; Target: x86_64-unknown-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --prefix=/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/software/GCCcore/5.4.0 --with-local-prefix=/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/software/GCCcore/5.4.0 --enable-bootstrap --with-isl=/tmp/vsc40023/easybuild_build/GCCcore/5.4.0/dummy-/gcc-5.4.0/stage2_stuff; Thread model: posix; gcc version 5.4.0 (GCC) ; ", + "glibc_version": "2.17", + "hostname": "node2471.golett.os", + "install_size": 5103738, + "modules_tool": ('Lmod', '/usr/share/lmod/lmod/libexec/lmod', '6.6'), + "os_name": "centos linux", + "os_type": "Linux", + "os_version": "7.3.1611", + "platform_name": "x86_64-unknown-linux", + "python_version": "2.7.5 (default, Nov 6 2016, 00:28:07) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-11)]", + "system_gcc_path": "/tmp/eb-RUaDzP/tmpn3FMec/gcc", + "system_python_path": "/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/software/Python/2.7.12-foss-2016b/bin/python", + "timestamp": 1488891671, + "total_memory": 64303, +}] -- GitLab From 222de2e3bcc8228b30cb935fa60a8e9e27fa2b9f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Mar 2017 11:08:12 +0100 Subject: [PATCH 0292/1603] adding easyconfigs: libspatialindex-1.8.5-foss-2016b.eb --- .../libspatialindex-1.8.5-foss-2016b.eb | 46 +++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/l/libspatialindex/libspatialindex-1.8.5-foss-2016b.eb diff --git a/easybuild/easyconfigs/l/libspatialindex/libspatialindex-1.8.5-foss-2016b.eb b/easybuild/easyconfigs/l/libspatialindex/libspatialindex-1.8.5-foss-2016b.eb new file mode 100644 index 0000000000..33443350fb --- /dev/null +++ b/easybuild/easyconfigs/l/libspatialindex/libspatialindex-1.8.5-foss-2016b.eb @@ -0,0 +1,46 @@ +# Built with EasyBuild version 3.1.0 on 2017-03-07_13-58-08 +easyblock = 'ConfigureMake' + +name = 'libspatialindex' +version = '1.8.5' + +homepage = 'http://libspatialindex.github.io' +description = "C++ implementation of R*-tree, an MVR-tree and a TPR-tree with C API" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['http://download.osgeo.org/libspatialindex/'] +sources = ['spatialindex-src-%(version)s.tar.gz'] + +sanity_check_paths = { + 'files': ['lib/libspatialindex.a', 'lib/libspatialindex.%s' % SHLIB_EXT], + 'dirs': ['include/spatialindex'], +} + +moduleclass = 'lib' + +# Build statistics +buildstats = [{ + "build_time": 143.61, + "command_line": ["--buildpath='/tmp/vsc40023/easybuild_build'", '--debug', "--github-user='boegel'", "--installpath='/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib'", "--job-backend='PbsPython'", "--packagepath='/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/packages'", "--prefix='/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib'", "--repositorypath='/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/ebfiles_repo'", "--robot='/vscmnt/gent_vulpix/_/user/data/gent/gvo000/gvo00002/vsc40023:/user/data/gent/vsc400/vsc40023/easybuild_easy_installed/lib/python2.7/site-packages/easybuild_easyconfigs-3.1.0-py2.7.egg/easybuild/easyconfigs'", "--robot-paths='/vscmnt/gent_vulpix/_/user/data/gent/gvo000/gvo00002/vsc40023:'", "--sourcepath='/user/data/gent/vsc400/vsc40023/EasyBuild/sources:/apps/gent/source:/nfsmuk/apps/gent/source/'", "--try-toolchain='foss,2016b'", "--use-ccache='/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/ccache/CO7/haswell-ib'", 'QGIS.eb'], + "core_count": 24, + "cpu_model": "Intel(R) Xeon(R) CPU E5-2680 v3 @ 2.50GHz", + "cpu_speed": 2500.0, + "cpu_vendor": "Intel", + "easybuild-easyblocks_version": "3.1.0", + "easybuild-framework_version": "3.1.0", + "gcc_version": "Using built-in specs.; COLLECT_GCC=/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/software/GCCcore/5.4.0/bin/gcc; COLLECT_LTO_WRAPPER=/user/scratchphanpy/gent/gvo000/gvo00002/vsc40023/easybuild_REGTEST/CO7/haswell-ib/software/GCCcore/5.4.0/bin/../libexec/gcc/x86_64-unknown-linux-gnu/5.4.0/lto-wrapper; Target: x86_64-unknown-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --prefix=/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/software/GCCcore/5.4.0 --with-local-prefix=/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/software/GCCcore/5.4.0 --enable-bootstrap --with-isl=/tmp/vsc40023/easybuild_build/GCCcore/5.4.0/dummy-/gcc-5.4.0/stage2_stuff; Thread model: posix; gcc version 5.4.0 (GCC) ; ", + "glibc_version": "2.17", + "hostname": "node2471.golett.os", + "install_size": 5693279, + "modules_tool": ('Lmod', '/usr/share/lmod/lmod/libexec/lmod', '6.6'), + "os_name": "centos linux", + "os_type": "Linux", + "os_version": "7.3.1611", + "platform_name": "x86_64-unknown-linux", + "python_version": "2.7.5 (default, Nov 6 2016, 00:28:07) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-11)]", + "system_gcc_path": "/tmp/eb-RUaDzP/tmp07Ujmt/gcc", + "system_python_path": "/usr/bin/python", + "timestamp": 1488891488, + "total_memory": 64303, +}] -- GitLab From 6191d257e6b77b205173a2ef627a9a8f8b81a01d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Mar 2017 11:08:50 +0100 Subject: [PATCH 0293/1603] adding easyconfigs: FreeXL-1.0.2-foss-2016b.eb --- .../f/FreeXL/FreeXL-1.0.2-foss-2016b.eb | 49 +++++++++++++++++++ 1 file changed, 49 insertions(+) create mode 100644 easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.2-foss-2016b.eb diff --git a/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.2-foss-2016b.eb b/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.2-foss-2016b.eb new file mode 100644 index 0000000000..1e91b6e6f0 --- /dev/null +++ b/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.2-foss-2016b.eb @@ -0,0 +1,49 @@ +# Built with EasyBuild version 3.1.0 on 2017-03-07_13-59-03 +easyblock = 'ConfigureMake' + +name = 'FreeXL' +version = '1.0.2' + +homepage = "https://www.gaia-gis.it/fossil/freexl/index" +description = "FreeXL is an open source library to extract valid data from within an Excel (.xls) spreadsheet." + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.gaia-gis.it/gaia-sins/freexl-sources/'] +sources = [SOURCELOWER_TAR_GZ] + +builddependencies = [('CMake', '3.7.1')] + +sanity_check_paths = { + 'files': ['lib/libfreexl.a'], + 'dirs': [] + } + +moduleclass = 'lib' + +# Build statistics +buildstats = [{ + "build_time": 55.18, + "command_line": ["--buildpath='/tmp/vsc40023/easybuild_build'", '--debug', "--github-user='boegel'", "--installpath='/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib'", "--job-backend='PbsPython'", "--packagepath='/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/packages'", "--prefix='/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib'", "--repositorypath='/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/ebfiles_repo'", "--robot='/vscmnt/gent_vulpix/_/user/data/gent/gvo000/gvo00002/vsc40023:/user/data/gent/vsc400/vsc40023/easybuild_easy_installed/lib/python2.7/site-packages/easybuild_easyconfigs-3.1.0-py2.7.egg/easybuild/easyconfigs'", "--robot-paths='/vscmnt/gent_vulpix/_/user/data/gent/gvo000/gvo00002/vsc40023:'", "--sourcepath='/user/data/gent/vsc400/vsc40023/EasyBuild/sources:/apps/gent/source:/nfsmuk/apps/gent/source/'", "--try-toolchain='foss,2016b'", "--use-ccache='/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/ccache/CO7/haswell-ib'", 'QGIS.eb'], + "core_count": 24, + "cpu_model": "Intel(R) Xeon(R) CPU E5-2680 v3 @ 2.50GHz", + "cpu_speed": 2500.0, + "cpu_vendor": "Intel", + "easybuild-easyblocks_version": "3.1.0", + "easybuild-framework_version": "3.1.0", + "gcc_version": "Using built-in specs.; COLLECT_GCC=/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/software/GCCcore/5.4.0/bin/gcc; COLLECT_LTO_WRAPPER=/user/scratchphanpy/gent/gvo000/gvo00002/vsc40023/easybuild_REGTEST/CO7/haswell-ib/software/GCCcore/5.4.0/bin/../libexec/gcc/x86_64-unknown-linux-gnu/5.4.0/lto-wrapper; Target: x86_64-unknown-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --prefix=/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/software/GCCcore/5.4.0 --with-local-prefix=/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/software/GCCcore/5.4.0 --enable-bootstrap --with-isl=/tmp/vsc40023/easybuild_build/GCCcore/5.4.0/dummy-/gcc-5.4.0/stage2_stuff; Thread model: posix; gcc version 5.4.0 (GCC) ; ", + "glibc_version": "2.17", + "hostname": "node2471.golett.os", + "install_size": 205319, + "modules_tool": ('Lmod', '/usr/share/lmod/lmod/libexec/lmod', '6.6'), + "os_name": "centos linux", + "os_type": "Linux", + "os_version": "7.3.1611", + "platform_name": "x86_64-unknown-linux", + "python_version": "2.7.5 (default, Nov 6 2016, 00:28:07) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-11)]", + "system_gcc_path": "/tmp/eb-RUaDzP/tmp6qSQU6/gcc", + "system_python_path": "/usr/bin/python", + "timestamp": 1488891543, + "total_memory": 64303, +}] -- GitLab From 67d6b752d1bfb4e6abe3a7596f966e6a62de5e45 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Mar 2017 11:12:37 +0100 Subject: [PATCH 0294/1603] remove buildstats --- .../p/PROJ/PROJ-4.9.3-foss-2016b.eb | 26 ------------------- 1 file changed, 26 deletions(-) diff --git a/easybuild/easyconfigs/p/PROJ/PROJ-4.9.3-foss-2016b.eb b/easybuild/easyconfigs/p/PROJ/PROJ-4.9.3-foss-2016b.eb index 7c6ed61f58..bd62ff7fdd 100644 --- a/easybuild/easyconfigs/p/PROJ/PROJ-4.9.3-foss-2016b.eb +++ b/easybuild/easyconfigs/p/PROJ/PROJ-4.9.3-foss-2016b.eb @@ -29,29 +29,3 @@ sanity_check_paths = { } moduleclass = 'lib' - -# Build statistics -buildstats = [{ - "build_time": 94.84, - "command_line": ["--buildpath='/tmp/vsc40023/easybuild_build'", '--debug', "--github-user='boegel'", "--installpath='/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib'", "--job-backend='PbsPython'", "--packagepath='/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/packages'", "--prefix='/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib'", "--repositorypath='/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/ebfiles_repo'", "--robot='/vscmnt/gent_vulpix/_/user/data/gent/gvo000/gvo00002/vsc40023:/user/data/gent/vsc400/vsc40023/easybuild_easy_installed/lib/python2.7/site-packages/easybuild_easyconfigs-3.1.0-py2.7.egg/easybuild/easyconfigs'", "--robot-paths='/vscmnt/gent_vulpix/_/user/data/gent/gvo000/gvo00002/vsc40023:'", "--sourcepath='/user/data/gent/vsc400/vsc40023/EasyBuild/sources:/apps/gent/source:/nfsmuk/apps/gent/source/'", "--try-toolchain='foss,2016b'", "--use-ccache='/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/ccache/CO7/haswell-ib'", 'QGIS.eb'], - "core_count": 24, - "cpu_model": "Intel(R) Xeon(R) CPU E5-2680 v3 @ 2.50GHz", - "cpu_speed": 2500.0, - "cpu_vendor": "Intel", - "easybuild-easyblocks_version": "3.1.0", - "easybuild-framework_version": "3.1.0", - "gcc_version": "Using built-in specs.; COLLECT_GCC=/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/software/GCCcore/5.4.0/bin/gcc; COLLECT_LTO_WRAPPER=/user/scratchphanpy/gent/gvo000/gvo00002/vsc40023/easybuild_REGTEST/CO7/haswell-ib/software/GCCcore/5.4.0/bin/../libexec/gcc/x86_64-unknown-linux-gnu/5.4.0/lto-wrapper; Target: x86_64-unknown-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --prefix=/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/software/GCCcore/5.4.0 --with-local-prefix=/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/software/GCCcore/5.4.0 --enable-bootstrap --with-isl=/tmp/vsc40023/easybuild_build/GCCcore/5.4.0/dummy-/gcc-5.4.0/stage2_stuff; Thread model: posix; gcc version 5.4.0 (GCC) ; ", - "glibc_version": "2.17", - "hostname": "node2471.golett.os", - "install_size": 4259625, - "modules_tool": ('Lmod', '/usr/share/lmod/lmod/libexec/lmod', '6.6'), - "os_name": "centos linux", - "os_type": "Linux", - "os_version": "7.3.1611", - "platform_name": "x86_64-unknown-linux", - "python_version": "2.7.5 (default, Nov 6 2016, 00:28:07) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-11)]", - "system_gcc_path": "/tmp/eb-RUaDzP/tmpNuI7H2/gcc", - "system_python_path": "/usr/bin/python", - "timestamp": 1488891344, - "total_memory": 64303, -}] -- GitLab From 8367087c08ef9ae7372e516dc3c7952708051cfa Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Mar 2017 11:13:40 +0100 Subject: [PATCH 0295/1603] remove buildstats --- .../GEOS-3.6.1-foss-2016b-Python-2.7.12.eb | 26 ------------------- .../SWIG-3.0.11-foss-2016b-Python-2.7.12.eb | 26 ------------------- 2 files changed, 52 deletions(-) diff --git a/easybuild/easyconfigs/g/GEOS/GEOS-3.6.1-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/g/GEOS/GEOS-3.6.1-foss-2016b-Python-2.7.12.eb index ff17f25dff..95a33702aa 100644 --- a/easybuild/easyconfigs/g/GEOS/GEOS-3.6.1-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/g/GEOS/GEOS-3.6.1-foss-2016b-Python-2.7.12.eb @@ -27,29 +27,3 @@ sanity_check_paths = { } moduleclass = 'math' - -# Build statistics -buildstats = [{ - "build_time": 431.44, - "command_line": ["--buildpath='/tmp/vsc40023/easybuild_build'", '--debug', "--github-user='boegel'", "--installpath='/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib'", "--job-backend='PbsPython'", "--packagepath='/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/packages'", "--prefix='/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib'", "--repositorypath='/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/ebfiles_repo'", "--robot='/vscmnt/gent_vulpix/_/user/data/gent/gvo000/gvo00002/vsc40023:/user/data/gent/vsc400/vsc40023/easybuild_easy_installed/lib/python2.7/site-packages/easybuild_easyconfigs-3.1.0-py2.7.egg/easybuild/easyconfigs'", "--robot-paths='/vscmnt/gent_vulpix/_/user/data/gent/gvo000/gvo00002/vsc40023:'", "--sourcepath='/user/data/gent/vsc400/vsc40023/EasyBuild/sources:/apps/gent/source:/nfsmuk/apps/gent/source/'", "--try-toolchain='foss,2016b'", "--use-ccache='/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/ccache/CO7/haswell-ib'", 'QGIS.eb'], - "core_count": 24, - "cpu_model": "Intel(R) Xeon(R) CPU E5-2680 v3 @ 2.50GHz", - "cpu_speed": 2500.0, - "cpu_vendor": "Intel", - "easybuild-easyblocks_version": "3.1.0", - "easybuild-framework_version": "3.1.0", - "gcc_version": "Using built-in specs.; COLLECT_GCC=/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/software/GCCcore/5.4.0/bin/gcc; COLLECT_LTO_WRAPPER=/user/scratchphanpy/gent/gvo000/gvo00002/vsc40023/easybuild_REGTEST/CO7/haswell-ib/software/GCCcore/5.4.0/bin/../libexec/gcc/x86_64-unknown-linux-gnu/5.4.0/lto-wrapper; Target: x86_64-unknown-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --prefix=/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/software/GCCcore/5.4.0 --with-local-prefix=/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/software/GCCcore/5.4.0 --enable-bootstrap --with-isl=/tmp/vsc40023/easybuild_build/GCCcore/5.4.0/dummy-/gcc-5.4.0/stage2_stuff; Thread model: posix; gcc version 5.4.0 (GCC) ; ", - "glibc_version": "2.17", - "hostname": "node2471.golett.os", - "install_size": 13415865, - "modules_tool": ('Lmod', '/usr/share/lmod/lmod/libexec/lmod', '6.6'), - "os_name": "centos linux", - "os_type": "Linux", - "os_version": "7.3.1611", - "platform_name": "x86_64-unknown-linux", - "python_version": "2.7.5 (default, Nov 6 2016, 00:28:07) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-11)]", - "system_gcc_path": "/tmp/eb-RUaDzP/tmpb49pQv/gcc", - "system_python_path": "/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/software/Python/2.7.12-foss-2016b/bin/python", - "timestamp": 1488892103, - "total_memory": 64303, -}] diff --git a/easybuild/easyconfigs/s/SWIG/SWIG-3.0.11-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/s/SWIG/SWIG-3.0.11-foss-2016b-Python-2.7.12.eb index bd7c62c123..ef67967e6e 100644 --- a/easybuild/easyconfigs/s/SWIG/SWIG-3.0.11-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/s/SWIG/SWIG-3.0.11-foss-2016b-Python-2.7.12.eb @@ -19,29 +19,3 @@ dependencies = [ ] moduleclass = 'devel' - -# Build statistics -buildstats = [{ - "build_time": 62.35, - "command_line": ["--buildpath='/tmp/vsc40023/easybuild_build'", '--debug', "--github-user='boegel'", "--installpath='/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib'", "--job-backend='PbsPython'", "--packagepath='/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/packages'", "--prefix='/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib'", "--repositorypath='/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/ebfiles_repo'", "--robot='/vscmnt/gent_vulpix/_/user/data/gent/gvo000/gvo00002/vsc40023:/user/data/gent/vsc400/vsc40023/easybuild_easy_installed/lib/python2.7/site-packages/easybuild_easyconfigs-3.1.0-py2.7.egg/easybuild/easyconfigs'", "--robot-paths='/vscmnt/gent_vulpix/_/user/data/gent/gvo000/gvo00002/vsc40023:'", "--sourcepath='/user/data/gent/vsc400/vsc40023/EasyBuild/sources:/apps/gent/source:/nfsmuk/apps/gent/source/'", "--try-toolchain='foss,2016b'", "--use-ccache='/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/ccache/CO7/haswell-ib'", 'QGIS.eb'], - "core_count": 24, - "cpu_model": "Intel(R) Xeon(R) CPU E5-2680 v3 @ 2.50GHz", - "cpu_speed": 2500.0, - "cpu_vendor": "Intel", - "easybuild-easyblocks_version": "3.1.0", - "easybuild-framework_version": "3.1.0", - "gcc_version": "Using built-in specs.; COLLECT_GCC=/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/software/GCCcore/5.4.0/bin/gcc; COLLECT_LTO_WRAPPER=/user/scratchphanpy/gent/gvo000/gvo00002/vsc40023/easybuild_REGTEST/CO7/haswell-ib/software/GCCcore/5.4.0/bin/../libexec/gcc/x86_64-unknown-linux-gnu/5.4.0/lto-wrapper; Target: x86_64-unknown-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --prefix=/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/software/GCCcore/5.4.0 --with-local-prefix=/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/software/GCCcore/5.4.0 --enable-bootstrap --with-isl=/tmp/vsc40023/easybuild_build/GCCcore/5.4.0/dummy-/gcc-5.4.0/stage2_stuff; Thread model: posix; gcc version 5.4.0 (GCC) ; ", - "glibc_version": "2.17", - "hostname": "node2471.golett.os", - "install_size": 5103738, - "modules_tool": ('Lmod', '/usr/share/lmod/lmod/libexec/lmod', '6.6'), - "os_name": "centos linux", - "os_type": "Linux", - "os_version": "7.3.1611", - "platform_name": "x86_64-unknown-linux", - "python_version": "2.7.5 (default, Nov 6 2016, 00:28:07) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-11)]", - "system_gcc_path": "/tmp/eb-RUaDzP/tmpn3FMec/gcc", - "system_python_path": "/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/software/Python/2.7.12-foss-2016b/bin/python", - "timestamp": 1488891671, - "total_memory": 64303, -}] -- GitLab From b5c23e38fc28cceee226e97635e52133ab9ecc3b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Mar 2017 11:13:40 +0100 Subject: [PATCH 0296/1603] remove buildstats --- .../libspatialindex-1.8.5-foss-2016b.eb | 26 ------------------- 1 file changed, 26 deletions(-) diff --git a/easybuild/easyconfigs/l/libspatialindex/libspatialindex-1.8.5-foss-2016b.eb b/easybuild/easyconfigs/l/libspatialindex/libspatialindex-1.8.5-foss-2016b.eb index 33443350fb..6393dbd967 100644 --- a/easybuild/easyconfigs/l/libspatialindex/libspatialindex-1.8.5-foss-2016b.eb +++ b/easybuild/easyconfigs/l/libspatialindex/libspatialindex-1.8.5-foss-2016b.eb @@ -18,29 +18,3 @@ sanity_check_paths = { } moduleclass = 'lib' - -# Build statistics -buildstats = [{ - "build_time": 143.61, - "command_line": ["--buildpath='/tmp/vsc40023/easybuild_build'", '--debug', "--github-user='boegel'", "--installpath='/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib'", "--job-backend='PbsPython'", "--packagepath='/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/packages'", "--prefix='/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib'", "--repositorypath='/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/ebfiles_repo'", "--robot='/vscmnt/gent_vulpix/_/user/data/gent/gvo000/gvo00002/vsc40023:/user/data/gent/vsc400/vsc40023/easybuild_easy_installed/lib/python2.7/site-packages/easybuild_easyconfigs-3.1.0-py2.7.egg/easybuild/easyconfigs'", "--robot-paths='/vscmnt/gent_vulpix/_/user/data/gent/gvo000/gvo00002/vsc40023:'", "--sourcepath='/user/data/gent/vsc400/vsc40023/EasyBuild/sources:/apps/gent/source:/nfsmuk/apps/gent/source/'", "--try-toolchain='foss,2016b'", "--use-ccache='/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/ccache/CO7/haswell-ib'", 'QGIS.eb'], - "core_count": 24, - "cpu_model": "Intel(R) Xeon(R) CPU E5-2680 v3 @ 2.50GHz", - "cpu_speed": 2500.0, - "cpu_vendor": "Intel", - "easybuild-easyblocks_version": "3.1.0", - "easybuild-framework_version": "3.1.0", - "gcc_version": "Using built-in specs.; COLLECT_GCC=/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/software/GCCcore/5.4.0/bin/gcc; COLLECT_LTO_WRAPPER=/user/scratchphanpy/gent/gvo000/gvo00002/vsc40023/easybuild_REGTEST/CO7/haswell-ib/software/GCCcore/5.4.0/bin/../libexec/gcc/x86_64-unknown-linux-gnu/5.4.0/lto-wrapper; Target: x86_64-unknown-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --prefix=/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/software/GCCcore/5.4.0 --with-local-prefix=/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/software/GCCcore/5.4.0 --enable-bootstrap --with-isl=/tmp/vsc40023/easybuild_build/GCCcore/5.4.0/dummy-/gcc-5.4.0/stage2_stuff; Thread model: posix; gcc version 5.4.0 (GCC) ; ", - "glibc_version": "2.17", - "hostname": "node2471.golett.os", - "install_size": 5693279, - "modules_tool": ('Lmod', '/usr/share/lmod/lmod/libexec/lmod', '6.6'), - "os_name": "centos linux", - "os_type": "Linux", - "os_version": "7.3.1611", - "platform_name": "x86_64-unknown-linux", - "python_version": "2.7.5 (default, Nov 6 2016, 00:28:07) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-11)]", - "system_gcc_path": "/tmp/eb-RUaDzP/tmp07Ujmt/gcc", - "system_python_path": "/usr/bin/python", - "timestamp": 1488891488, - "total_memory": 64303, -}] -- GitLab From 1cf8d4ec36e74b4eedd969376ccce569e18fd13f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Mar 2017 11:14:58 +0100 Subject: [PATCH 0297/1603] remove buildstats --- .../f/FreeXL/FreeXL-1.0.2-foss-2016b.eb | 26 ------------------- 1 file changed, 26 deletions(-) diff --git a/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.2-foss-2016b.eb b/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.2-foss-2016b.eb index 1e91b6e6f0..f20ffb2db6 100644 --- a/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.2-foss-2016b.eb +++ b/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.2-foss-2016b.eb @@ -21,29 +21,3 @@ sanity_check_paths = { } moduleclass = 'lib' - -# Build statistics -buildstats = [{ - "build_time": 55.18, - "command_line": ["--buildpath='/tmp/vsc40023/easybuild_build'", '--debug', "--github-user='boegel'", "--installpath='/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib'", "--job-backend='PbsPython'", "--packagepath='/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/packages'", "--prefix='/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib'", "--repositorypath='/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/ebfiles_repo'", "--robot='/vscmnt/gent_vulpix/_/user/data/gent/gvo000/gvo00002/vsc40023:/user/data/gent/vsc400/vsc40023/easybuild_easy_installed/lib/python2.7/site-packages/easybuild_easyconfigs-3.1.0-py2.7.egg/easybuild/easyconfigs'", "--robot-paths='/vscmnt/gent_vulpix/_/user/data/gent/gvo000/gvo00002/vsc40023:'", "--sourcepath='/user/data/gent/vsc400/vsc40023/EasyBuild/sources:/apps/gent/source:/nfsmuk/apps/gent/source/'", "--try-toolchain='foss,2016b'", "--use-ccache='/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/ccache/CO7/haswell-ib'", 'QGIS.eb'], - "core_count": 24, - "cpu_model": "Intel(R) Xeon(R) CPU E5-2680 v3 @ 2.50GHz", - "cpu_speed": 2500.0, - "cpu_vendor": "Intel", - "easybuild-easyblocks_version": "3.1.0", - "easybuild-framework_version": "3.1.0", - "gcc_version": "Using built-in specs.; COLLECT_GCC=/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/software/GCCcore/5.4.0/bin/gcc; COLLECT_LTO_WRAPPER=/user/scratchphanpy/gent/gvo000/gvo00002/vsc40023/easybuild_REGTEST/CO7/haswell-ib/software/GCCcore/5.4.0/bin/../libexec/gcc/x86_64-unknown-linux-gnu/5.4.0/lto-wrapper; Target: x86_64-unknown-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --prefix=/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/software/GCCcore/5.4.0 --with-local-prefix=/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/software/GCCcore/5.4.0 --enable-bootstrap --with-isl=/tmp/vsc40023/easybuild_build/GCCcore/5.4.0/dummy-/gcc-5.4.0/stage2_stuff; Thread model: posix; gcc version 5.4.0 (GCC) ; ", - "glibc_version": "2.17", - "hostname": "node2471.golett.os", - "install_size": 205319, - "modules_tool": ('Lmod', '/usr/share/lmod/lmod/libexec/lmod', '6.6'), - "os_name": "centos linux", - "os_type": "Linux", - "os_version": "7.3.1611", - "platform_name": "x86_64-unknown-linux", - "python_version": "2.7.5 (default, Nov 6 2016, 00:28:07) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-11)]", - "system_gcc_path": "/tmp/eb-RUaDzP/tmp6qSQU6/gcc", - "system_python_path": "/usr/bin/python", - "timestamp": 1488891543, - "total_memory": 64303, -}] -- GitLab From eb3e66959e2ab315db0c3819b436b186463b65a0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Mar 2017 11:22:06 +0100 Subject: [PATCH 0298/1603] remove commented out lines --- .../g/GDAL/GDAL-2.1.3-foss-2016b-Python-2.7.12.eb | 7 ------- 1 file changed, 7 deletions(-) diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-2.1.3-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/g/GDAL/GDAL-2.1.3-foss-2016b-Python-2.7.12.eb index 0f954c1b05..bc2162b8fb 100644 --- a/easybuild/easyconfigs/g/GDAL/GDAL-2.1.3-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/g/GDAL/GDAL-2.1.3-foss-2016b-Python-2.7.12.eb @@ -16,8 +16,6 @@ toolchainopts = {'usempi': True} source_urls = ['http://download.osgeo.org/gdal/%(version)s/'] sources = [SOURCELOWER_TAR_XZ] -#patches = ['GDAL-2.1.2_fix-vrtsources.patch'] - dependencies = [ ('Python', '2.7.12'), ('netCDF', '4.4.1.1'), @@ -38,11 +36,6 @@ configopts = '--with-expat=$EBROOTEXPAT --with-libz=$EBROOTLIBZ --with-hdf5=$EBR configopts += ' --with-xml2=$EBROOTLIBXML2 --with-geos=$EBROOTGEOS/bin/geos-config --with-jpeg=$EBROOTLIBJPEGMINTURBO' configopts += ' --with-png=$EBROOTLIBPNG --with-sqlite3=$EBROOTSQLITE --with-jasper=$EBROOTJASPER' configopts += ' --with-libtiff=$EBROOTLIBTIFF --with-pcre=$EBROOTPCRE --with-python=$EBROOTPYTHON/bin/python' -# there is a bug in the build system causing the build with libtool to fail for the moment -# (static library is also missing because of this) -#configopts += ' --without-libtool' - -#buildopts = 'CXXFLAGS="$CXXFLAGS -fpermissive"' modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} -- GitLab From 9795a9c4c7c3d4ba24cbd1f0ace84bb7b426f937 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Mar 2017 13:00:51 +0100 Subject: [PATCH 0299/1603] remove 'Built with' comments --- .../easyconfigs/g/GEOS/GEOS-3.6.1-foss-2016b-Python-2.7.12.eb | 1 - easybuild/easyconfigs/p/PROJ/PROJ-4.9.3-foss-2016b.eb | 1 - .../easyconfigs/s/SWIG/SWIG-3.0.11-foss-2016b-Python-2.7.12.eb | 1 - 3 files changed, 3 deletions(-) diff --git a/easybuild/easyconfigs/g/GEOS/GEOS-3.6.1-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/g/GEOS/GEOS-3.6.1-foss-2016b-Python-2.7.12.eb index 95a33702aa..02e7eb0e40 100644 --- a/easybuild/easyconfigs/g/GEOS/GEOS-3.6.1-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/g/GEOS/GEOS-3.6.1-foss-2016b-Python-2.7.12.eb @@ -1,4 +1,3 @@ -# Built with EasyBuild version 3.1.0 on 2017-03-07_14-08-23 easyblock = 'ConfigureMake' name = 'GEOS' diff --git a/easybuild/easyconfigs/p/PROJ/PROJ-4.9.3-foss-2016b.eb b/easybuild/easyconfigs/p/PROJ/PROJ-4.9.3-foss-2016b.eb index bd62ff7fdd..7b1bb021f3 100644 --- a/easybuild/easyconfigs/p/PROJ/PROJ-4.9.3-foss-2016b.eb +++ b/easybuild/easyconfigs/p/PROJ/PROJ-4.9.3-foss-2016b.eb @@ -1,4 +1,3 @@ -# Built with EasyBuild version 3.1.0 on 2017-03-07_13-55-44 ## # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # diff --git a/easybuild/easyconfigs/s/SWIG/SWIG-3.0.11-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/s/SWIG/SWIG-3.0.11-foss-2016b-Python-2.7.12.eb index ef67967e6e..645b771837 100644 --- a/easybuild/easyconfigs/s/SWIG/SWIG-3.0.11-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/s/SWIG/SWIG-3.0.11-foss-2016b-Python-2.7.12.eb @@ -1,4 +1,3 @@ -# Built with EasyBuild version 3.1.0 on 2017-03-07_14-01-11 name = 'SWIG' version = '3.0.11' versionsuffix = '-Python-%(pyver)s' -- GitLab From 85ee43bb91417d48bb753d3e85f0427c50f03069 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Mar 2017 13:01:56 +0100 Subject: [PATCH 0300/1603] remove 'Built with' comment --- easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.2-foss-2016b.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.2-foss-2016b.eb b/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.2-foss-2016b.eb index f20ffb2db6..2775a19a49 100644 --- a/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.2-foss-2016b.eb +++ b/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.2-foss-2016b.eb @@ -1,4 +1,3 @@ -# Built with EasyBuild version 3.1.0 on 2017-03-07_13-59-03 easyblock = 'ConfigureMake' name = 'FreeXL' -- GitLab From 62fc9ea965433cb32529fb9b5e058a6fe5805367 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Mar 2017 13:03:24 +0100 Subject: [PATCH 0301/1603] remove 'Built with' comment --- .../l/libspatialindex/libspatialindex-1.8.5-foss-2016b.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libspatialindex/libspatialindex-1.8.5-foss-2016b.eb b/easybuild/easyconfigs/l/libspatialindex/libspatialindex-1.8.5-foss-2016b.eb index 6393dbd967..5ff79fa5a7 100644 --- a/easybuild/easyconfigs/l/libspatialindex/libspatialindex-1.8.5-foss-2016b.eb +++ b/easybuild/easyconfigs/l/libspatialindex/libspatialindex-1.8.5-foss-2016b.eb @@ -1,4 +1,3 @@ -# Built with EasyBuild version 3.1.0 on 2017-03-07_13-58-08 easyblock = 'ConfigureMake' name = 'libspatialindex' -- GitLab From 7206a55c12c3eb2b748b83b94957030601c762b5 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Lopez Date: Thu, 9 Mar 2017 13:22:27 +0100 Subject: [PATCH 0302/1603] add ${CXXFLAGS} to the patch file --- easybuild/easyconfigs/g/GFOLD/gfold-1.1.4-makefile.patch | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/g/GFOLD/gfold-1.1.4-makefile.patch b/easybuild/easyconfigs/g/GFOLD/gfold-1.1.4-makefile.patch index 15699d96ba..08f6097072 100644 --- a/easybuild/easyconfigs/g/GFOLD/gfold-1.1.4-makefile.patch +++ b/easybuild/easyconfigs/g/GFOLD/gfold-1.1.4-makefile.patch @@ -8,11 +8,11 @@ diff -ru gfold.V1.1.4.orig/Makefile gfold.V1.1.4/Makefile debug: DataProcessor.hpp GFOLD.hpp Utility.hpp GeneInfo.hpp main.cc - g++ -Wall -g main.cc -o gfold -lgsl -lgslcblas -+ ${CXX} -Wall -g main.cc -o gfold -lgsl -lgslcblas ++ ${CXX} ${CXXFLAGS} -Wall -g main.cc -o gfold -lgsl -lgslcblas program: DataProcessor.hpp GFOLD.hpp Utility.hpp GeneInfo.hpp main.cc - g++ -O3 -Wall -g main.cc -o gfold -lgsl -lgslcblas -+ ${CXX} -O3 -Wall -g main.cc -o gfold -lgsl -lgslcblas ++ ${CXX} ${CXXFLAGS} -Wall -g main.cc -o gfold -lgsl -lgslcblas docu: doc/gfold.pod pod2man doc/gfold.pod > doc/gfold.man -- GitLab From 6efe46cb2ad1f6a29fb5a8268ff27a9fb7dd9c5e Mon Sep 17 00:00:00 2001 From: Pablo Escobar Lopez Date: Thu, 9 Mar 2017 13:22:50 +0100 Subject: [PATCH 0303/1603] update the patch comment --- easybuild/easyconfigs/g/GFOLD/gfold-1.1.4-makefile.patch | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GFOLD/gfold-1.1.4-makefile.patch b/easybuild/easyconfigs/g/GFOLD/gfold-1.1.4-makefile.patch index 08f6097072..23ba52ac63 100644 --- a/easybuild/easyconfigs/g/GFOLD/gfold-1.1.4-makefile.patch +++ b/easybuild/easyconfigs/g/GFOLD/gfold-1.1.4-makefile.patch @@ -1,4 +1,4 @@ -fix the hardcoded compiler +fix the hardcoded compiler and use ${CXXFLAGS} diff -ru gfold.V1.1.4.orig/Makefile gfold.V1.1.4/Makefile --- gfold.V1.1.4.orig/Makefile 2015-05-24 01:47:13.000000000 +0200 -- GitLab From ff1bba6485cfb033f60e7a58f5442b49ff854d0c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Mar 2017 13:49:40 +0100 Subject: [PATCH 0304/1603] fix minor style issue --- easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.2-foss-2016b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.2-foss-2016b.eb b/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.2-foss-2016b.eb index 2775a19a49..b7981e18c5 100644 --- a/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.2-foss-2016b.eb +++ b/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.2-foss-2016b.eb @@ -17,6 +17,6 @@ builddependencies = [('CMake', '3.7.1')] sanity_check_paths = { 'files': ['lib/libfreexl.a'], 'dirs': [] - } +} moduleclass = 'lib' -- GitLab From 76eec10c26deba272148df8e3229eab11166444c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Mar 2017 14:09:46 +0100 Subject: [PATCH 0305/1603] fix shebang in miRDeep2 Perl scripts --- easybuild/easyconfigs/m/miRDeep2/miRDeep2-2.0.0.8-intel-2016b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/m/miRDeep2/miRDeep2-2.0.0.8-intel-2016b.eb b/easybuild/easyconfigs/m/miRDeep2/miRDeep2-2.0.0.8-intel-2016b.eb index 7f489ba651..de73467658 100644 --- a/easybuild/easyconfigs/m/miRDeep2/miRDeep2-2.0.0.8-intel-2016b.eb +++ b/easybuild/easyconfigs/m/miRDeep2/miRDeep2-2.0.0.8-intel-2016b.eb @@ -21,6 +21,7 @@ dependencies = [ ] install_cmd = "cp -a mirdeep*/src %(installdir)s/bin && chmod a+x %(installdir)s/bin/*.pl && " +install_cmd += 'sed -i "s@#!/usr/bin/perl@#!$EBROOTPERL/bin/perl@" %(installdir)s/bin/*.pl && ' # scripts include a hard check for a file called 'install_successful' in the install directory... install_cmd += "touch %(installdir)s/install_successful" -- GitLab From 31b0580e2f82fe48ac5901484363f8d60bcf4fdc Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Mar 2017 14:34:50 +0100 Subject: [PATCH 0306/1603] adding easyconfigs: flex-2.6.3-GCCcore-5.4.0.eb, M4-1.4.18-GCCcore-5.4.0.eb, help2man-1.47.4-GCCcore-5.4.0.eb --- .../f/flex/flex-2.6.3-GCCcore-5.4.0.eb | 23 +++++++++++++++++ .../help2man/help2man-1.47.4-GCCcore-5.4.0.eb | 19 ++++++++++++++ .../m/M4/M4-1.4.18-GCCcore-5.4.0.eb | 25 +++++++++++++++++++ 3 files changed, 67 insertions(+) create mode 100644 easybuild/easyconfigs/f/flex/flex-2.6.3-GCCcore-5.4.0.eb create mode 100644 easybuild/easyconfigs/h/help2man/help2man-1.47.4-GCCcore-5.4.0.eb create mode 100644 easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.4.0.eb diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.3-GCCcore-5.4.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.3-GCCcore-5.4.0.eb new file mode 100644 index 0000000000..5044907def --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.6.3-GCCcore-5.4.0.eb @@ -0,0 +1,23 @@ +name = 'flex' +version = '2.6.3' + +homepage = 'http://flex.sourceforge.net/' +description = """Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, + sometimes called a tokenizer, is a program which recognizes lexical patterns in text.""" + +toolchain = {'name': 'GCCcore', 'version': '5.4.0'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['https://github.com/westes/flex/releases/download/v%(version)s/'] + +checksums = ['a5f65570cd9107ec8a8ec88f17b31bb1'] + +dependencies = [('M4', '1.4.18')] +builddependencies = [ + ('binutils', '2.26'), + ('Bison', '3.0.4'), + ('help2man', '1.47.4'), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/h/help2man/help2man-1.47.4-GCCcore-5.4.0.eb b/easybuild/easyconfigs/h/help2man/help2man-1.47.4-GCCcore-5.4.0.eb new file mode 100644 index 0000000000..7b53bd8797 --- /dev/null +++ b/easybuild/easyconfigs/h/help2man/help2man-1.47.4-GCCcore-5.4.0.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'help2man' +version = '1.47.4' + +homepage = 'https://www.gnu.org/software/help2man/' +description = """help2man produces simple manual pages from the '--help' and '--version' output of other commands.""" + +toolchain = {'name': 'GCCcore', 'version': '5.4.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_XZ] + +sanity_check_paths = { + 'files': ['bin/help2man'], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.4.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.4.0.eb new file mode 100644 index 0000000000..345402c605 --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.4.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'M4' +version = '1.4.18' + +homepage = 'http://www.gnu.org/software/m4/m4.html' +description = """GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible + although it has some extensions (for example, handling more than 9 positional parameters to macros). + GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc.""" + +toolchain = {'name': 'GCCcore', 'version': '5.4.0'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +# '-fgnu89-inline' is required to avoid linking errors with older glibc's, +# see https://github.com/hpcugent/easybuild-easyconfigs/issues/529 +configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" + +sanity_check_paths = { + 'files': ["bin/m4"], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From b35c28b493af2a252f41971c1d3b492a7000460c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Mar 2017 14:36:09 +0100 Subject: [PATCH 0307/1603] adding easyconfigs: GDAL-2.1.3-intel-2016b-Python-2.7.12.eb --- .../GDAL-2.1.3-intel-2016b-Python-2.7.12.eb | 47 +++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 easybuild/easyconfigs/g/GDAL/GDAL-2.1.3-intel-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-2.1.3-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/g/GDAL/GDAL-2.1.3-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..015f10d595 --- /dev/null +++ b/easybuild/easyconfigs/g/GDAL/GDAL-2.1.3-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,47 @@ +easyblock = 'ConfigureMake' + +name = 'GDAL' +version = '2.1.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.gdal.org/' +description = """GDAL is a translator library for raster geospatial data formats that is released under an X/MIT style + Open Source license by the Open Source Geospatial Foundation. As a library, it presents a single abstract data model + to the calling application for all supported formats. It also comes with a variety of useful commandline utilities for + data translation and processing.""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'usempi': True} + +source_urls = ['http://download.osgeo.org/gdal/%(version)s/'] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('Python', '2.7.12'), + ('netCDF', '4.4.1.1'), + ('expat', '2.2.0'), + ('GEOS', '3.6.1', versionsuffix), + ('SQLite', '3.13.0'), + ('libxml2', '2.9.4'), + ('libpng', '1.6.24'), + ('libjpeg-turbo', '1.5.0'), + ('JasPer', '1.900.1'), + ('LibTIFF', '4.0.6'), + ('zlib', '1.2.8'), + ('cURL', '7.49.1'), + ('PCRE', '8.39'), +] + +configopts = '--with-expat=$EBROOTEXPAT --with-libz=$EBROOTLIBZ --with-hdf5=$EBROOTHDF5 --with-netcdf=$EBROOTNETCDF' +configopts += ' --with-xml2=$EBROOTLIBXML2 --with-geos=$EBROOTGEOS/bin/geos-config --with-jpeg=$EBROOTLIBJPEGMINTURBO' +configopts += ' --with-png=$EBROOTLIBPNG --with-sqlite3=$EBROOTSQLITE --with-jasper=$EBROOTJASPER' +configopts += ' --with-libtiff=$EBROOTLIBTIFF --with-pcre=$EBROOTPCRE --with-python=$EBROOTPYTHON/bin/python' + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +sanity_check_paths = { + 'files': ['lib/libgdal.a', 'lib/libgdal.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include', 'lib/python%(pyshortver)s/site-packages'] +} + +moduleclass = 'data' -- GitLab From 59df1b140f4267a1b1abfac49143a39edf87063c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Mar 2017 14:38:46 +0100 Subject: [PATCH 0308/1603] adding easyconfigs: QCA-2.1.3-intel-2016b.eb --- .../q/QCA/QCA-2.1.3-intel-2016b.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/q/QCA/QCA-2.1.3-intel-2016b.eb diff --git a/easybuild/easyconfigs/q/QCA/QCA-2.1.3-intel-2016b.eb b/easybuild/easyconfigs/q/QCA/QCA-2.1.3-intel-2016b.eb new file mode 100644 index 0000000000..2b7816fd3c --- /dev/null +++ b/easybuild/easyconfigs/q/QCA/QCA-2.1.3-intel-2016b.eb @@ -0,0 +1,30 @@ +easyblock = 'CMakeMake' + +name = 'QCA' +version = '2.1.3' + +homepage = 'http://delta.affinix.com/qca/' +description = """Taking a hint from the similarly-named Java Cryptography Architecture, + QCA aims to provide a straightforward and cross-platform crypto API, using Qt datatypes + and conventions. QCA separates the API from the implementation, using plugins known as + Providers. The advantage of this model is to allow applications to avoid linking to or + explicitly depending on any particular cryptographic library. This allows one to easily + change or upgrade crypto implementations without even needing to recompile the + application! QCA should work everywhere Qt does, including Windows/Unix/MacOSX.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['http://download.kde.org/stable/qca/%(version)s/src/'] +sources = ['%(namelower)s-%(version)s.tar.xz'] + +configopts = "-DQT4_BUILD=true" + +builddependencies = [ + ('CMake', '3.7.2') +] + +dependencies = [ + ('Qt', '4.8.7') +] + +moduleclass = 'devel' -- GitLab From f4c13b9569fe8b33ab8a8ebb5a38f51846cad3a5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Mar 2017 14:39:12 +0100 Subject: [PATCH 0309/1603] adding easyconfigs: QJson-0.9.0-intel-2016b.eb --- .../q/QJson/QJson-0.9.0-intel-2016b.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/q/QJson/QJson-0.9.0-intel-2016b.eb diff --git a/easybuild/easyconfigs/q/QJson/QJson-0.9.0-intel-2016b.eb b/easybuild/easyconfigs/q/QJson/QJson-0.9.0-intel-2016b.eb new file mode 100644 index 0000000000..44efa4db59 --- /dev/null +++ b/easybuild/easyconfigs/q/QJson/QJson-0.9.0-intel-2016b.eb @@ -0,0 +1,28 @@ +easyblock = 'CMakeMake' + +name = 'QJson' +version = '0.9.0' + +homepage = 'http://qjson.sourceforge.net/' +description = "QJson is a Qt-based library that maps JSON data to QVariant objects and vice versa." + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['https://github.com/flavio/qjson/archive/'] +sources = ['%(version)s.tar.gz'] + +dependencies = [ + ('Qt', '4.8.7'), +] +builddependencies = [ + ('CMake', '3.7.1'), +] + +separate_build_dir = True + +sanity_check_paths = { + 'files': ['lib/libqjson.%s' % SHLIB_EXT], + 'dirs': ['include/qjson', 'lib/cmake', 'lib/pkgconfig'], +} + +moduleclass = 'tools' -- GitLab From 8c335a1b251205d9c90948cbdff9deca9386b26a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Mar 2017 14:39:36 +0100 Subject: [PATCH 0310/1603] adding easyconfigs: QScintilla2-2.10-intel-2016b-Python-2.7.12.eb --- ...intilla2-2.10-intel-2016b-Python-2.7.12.eb | 52 +++++++++++++++++++ 1 file changed, 52 insertions(+) create mode 100644 easybuild/easyconfigs/q/QScintilla2/QScintilla2-2.10-intel-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/q/QScintilla2/QScintilla2-2.10-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/q/QScintilla2/QScintilla2-2.10-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..be392c7b0b --- /dev/null +++ b/easybuild/easyconfigs/q/QScintilla2/QScintilla2-2.10-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,52 @@ +easyblock = 'ConfigureMake' + +name = 'QScintilla2' +version = '2.10' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://www.riverbankcomputing.com/software/qscintilla' +description = "QScintilla is a port to Qt of Neil Hodgson's Scintilla C++ editor control" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'pic': True, 'cstd': 'c++11'} + +source_urls = ['https://sourceforge.net/projects/pyqt/files/%(name)s/QScintilla-%(version)s/'] +sources = ['QScintilla_gpl-%(version)s.tar.gz'] + +patches = ['QScintilla2-%(version)s_fix-link-python-bindings.patch'] + +dependencies = [ + ('Python', '2.7.12'), + ('PyQt', '4.12', versionsuffix), +] + +start_dir = 'Qt4Qt5' + +skipsteps = ['configure'] + +prebuildopts = "sed -i 's@\$\$\[QT_INSTALL_LIBS\]@%(installdir)s/lib@g' qscintilla.pro && " +prebuildopts += "sed -i 's@\$\$\[QT_INSTALL_HEADERS\]@%(installdir)s/include@g' qscintilla.pro && " +prebuildopts += "sed -i 's@\$\$\[QT_INSTALL_TRANSLATIONS\]@%(installdir)s/trans@g' qscintilla.pro && " +prebuildopts += "sed -i 's@\$\$\[QT_INSTALL_DATA\]@%(installdir)s/data@g' qscintilla.pro && " +prebuildopts += "sed -i 's@\$\$\[QT_HOST_DATA\]@%(installdir)s/data@g' qscintilla.pro && " +prebuildopts += "qmake qscintilla.pro && " + +buildopts = 'CXXFLAGS="$CXXFLAGS \$(DEFINES)"' + +python_bindings_install_cmd = "cd ../Python && mkdir -p %(installdir)s/share/sip/PyQt4 && " +python_bindings_install_cmd += "python configure.py --destdir %(installdir)s/lib/python%(pyshortver)s/site-packages/PyQt4 --qsci-sipdir %(installdir)s/share/sip/PyQt4 --qsci-incdir %(installdir)s/include --qsci-libdir %(installdir)s/lib --pyqt-sipdir $EBROOTPYQT/share/sip/PyQt4 --apidir %(installdir)s/qsci/api/python --no-stubs && " +python_bindings_install_cmd += "make && make install && cd %(installdir)s/lib/python%(pyshortver)s/site-packages/PyQt4 && " +python_bindings_install_cmd += "for x in $(ls $EBROOTPYQT/lib/python2.7/site-packages/PyQt4); do ln -s $EBROOTPYQT/lib/python2.7/site-packages/PyQt4/$x; done && " +python_bindings_install_cmd += "rm __init__.py* && touch __init__.py" +postinstallcmds = [python_bindings_install_cmd] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +sanity_check_paths = { + 'files': ['lib/libqscintilla2_qt4.so'], + 'dirs': ['include/Qsci', 'lib/python%(pyshortver)s/site-packages/PyQt4', 'qsci/api/python', 'share/sip/PyQt4', 'trans'], +} + +sanity_check_commands = ["python -c 'import PyQt4.Qsci'"] + +moduleclass = 'vis' -- GitLab From 8a542052a3ba44588900ab6efbc20a18a457e8a1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Mar 2017 14:42:02 +0100 Subject: [PATCH 0311/1603] adding easyconfigs: QGIS-2.14.12-intel-2016b-Python-2.7.12.eb --- .../QGIS-2.14.12-intel-2016b-Python-2.7.12.eb | 53 +++++++++++++++++++ 1 file changed, 53 insertions(+) create mode 100644 easybuild/easyconfigs/q/QGIS/QGIS-2.14.12-intel-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/q/QGIS/QGIS-2.14.12-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/q/QGIS/QGIS-2.14.12-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..abd1b36a0c --- /dev/null +++ b/easybuild/easyconfigs/q/QGIS/QGIS-2.14.12-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,53 @@ +easyblock = 'CMakeMake' + +name = 'QGIS' +version = '2.14.12' +versionsuffix = '-Python-2.7.12' + +homepage = 'http://www.qgis.org/' +description = "QGIS is a user friendly Open Source Geographic Information System (GIS)" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'pic': True, 'cstd': 'gnu++11'} + +source_urls = ['http://qgis.org/downloads/'] +sources = [SOURCELOWER_TAR_BZ2] + +patches = ['QGIS-2.14.12.patch'] + +dependencies = [ + ('Qt', '4.8.7'), + ('PROJ', '4.9.3'), + ('GEOS', '3.6.1', versionsuffix), + ('SQLite', '3.13.0'), # stick to this version for compatibility with Python 2.7.12 + ('libspatialite', '4.3.0a'), + ('libspatialindex', '1.8.5'), + ('GDAL', '2.1.3', versionsuffix), + ('Qwt', '6.1.3'), + ('QwtPolar', '1.1.1'), + ('expat', '2.2.0'), + ('QCA', '2.1.3'), + ('PyQt', '4.12', versionsuffix), + # QScintilla2 must be listed after PyQt4 due to Python bindings 'overriding' those of PyQt4 + ('QScintilla2', '2.10', versionsuffix), + ('GSL', '2.3'), + ('QJson', '0.9.0'), +] +builddependencies = [ + ('CMake', '3.7.2'), + ('flex', '2.6.3'), + ('Bison', '3.0.4'), +] + +separate_build_dir = True + +configopts = '-DQJSON_DIR=$EBROOTQJSON/lib/cmake/qjson -DCMAKE_PREFIX_PATH=$EBROOTQT -DQSCINTILLA_LIBRARY=$EBROOTQSCINTILLA2/lib/libqscintilla2_qt4.so -DPYQT4_SIP_DIR=$EBROOTPYQT/share/sip/PyQt4 -DQSCI_SIP_DIR=$EBROOTQSCINTILLA2/share/sip/PyQt4' + +buildopts = "VERBOSE=1 V=1" + +sanity_check_paths = { + 'files': ['bin/qgis'], + 'dirs': [], +} + +moduleclass = 'geo' -- GitLab From bb02a546f8c3ed7ac96345ed57cb7ccf8cdfc9d5 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Lopez Date: Thu, 9 Mar 2017 14:52:18 +0100 Subject: [PATCH 0312/1603] style fixes --- .../disambiguate-1.0.0-goolf-1.7.20-Python-2.7.11.eb | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/d/disambiguate/disambiguate-1.0.0-goolf-1.7.20-Python-2.7.11.eb b/easybuild/easyconfigs/d/disambiguate/disambiguate-1.0.0-goolf-1.7.20-Python-2.7.11.eb index 08032c986d..816f774c49 100644 --- a/easybuild/easyconfigs/d/disambiguate/disambiguate-1.0.0-goolf-1.7.20-Python-2.7.11.eb +++ b/easybuild/easyconfigs/d/disambiguate/disambiguate-1.0.0-goolf-1.7.20-Python-2.7.11.eb @@ -26,8 +26,10 @@ dependencies = [ # this application provides a python implementation and a C++ implementation # in the postinstallcmds we compile the C++ version -postinstallcmds = ['$CXX -I$EBROOTBAMTOOLS/include -I./ -L$EBROOTBAMTOOLS/lib -o disambiguate dismain.cpp -lz -lbamtools', - 'cp disambiguate %(installdir)s/bin/'] +postinstallcmds = [ + '$CXX -I$EBROOTBAMTOOLS/include -I./ -L$EBROOTBAMTOOLS/lib -o disambiguate dismain.cpp -lz -lbamtools', + 'cp disambiguate %(installdir)s/bin/' +] # workaround to avoid the import sanity check options = {'modulename': 'os'} -- GitLab From 7101d3a09bda45ed7591d2231f16a6e72148ec07 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Mar 2017 16:42:59 +0100 Subject: [PATCH 0313/1603] update QScintilla easyconfig to use QScintilla easyblock, add easyconfig for QScintilla 2.9.4 --- ...cintilla-2.10-intel-2016b-Python-2.7.12.eb | 21 ++++++++ ...ntilla-2.10_fix-link-python-bindings.patch | 14 +++++ ...intilla-2.9.4-intel-2016b-Python-2.7.12.eb | 21 ++++++++ ...tilla-2.9.4_fix-link-python-bindings.patch | 14 +++++ ...intilla2-2.10-intel-2016b-Python-2.7.12.eb | 52 ------------------- 5 files changed, 70 insertions(+), 52 deletions(-) create mode 100644 easybuild/easyconfigs/q/QScintilla/QScintilla-2.10-intel-2016b-Python-2.7.12.eb create mode 100644 easybuild/easyconfigs/q/QScintilla/QScintilla-2.10_fix-link-python-bindings.patch create mode 100644 easybuild/easyconfigs/q/QScintilla/QScintilla-2.9.4-intel-2016b-Python-2.7.12.eb create mode 100644 easybuild/easyconfigs/q/QScintilla/QScintilla-2.9.4_fix-link-python-bindings.patch delete mode 100644 easybuild/easyconfigs/q/QScintilla2/QScintilla2-2.10-intel-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/q/QScintilla/QScintilla-2.10-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/q/QScintilla/QScintilla-2.10-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..a974a1c6ac --- /dev/null +++ b/easybuild/easyconfigs/q/QScintilla/QScintilla-2.10-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,21 @@ +name = 'QScintilla' +version = '2.10' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://www.riverbankcomputing.com/software/qscintilla' +description = "QScintilla is a port to Qt of Neil Hodgson's Scintilla C++ editor control" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'pic': True, 'cstd': 'c++11'} + +source_urls = ['https://sourceforge.net/projects/pyqt/files/%(name)s%(version_major)s/QScintilla-%(version)s/'] +sources = ['QScintilla_gpl-%(version)s.tar.gz'] + +patches = ['QScintilla-%(version)s_fix-link-python-bindings.patch'] + +dependencies = [ + ('Python', '2.7.12'), + ('PyQt', '4.12', versionsuffix), +] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/q/QScintilla/QScintilla-2.10_fix-link-python-bindings.patch b/easybuild/easyconfigs/q/QScintilla/QScintilla-2.10_fix-link-python-bindings.patch new file mode 100644 index 0000000000..cca6cde624 --- /dev/null +++ b/easybuild/easyconfigs/q/QScintilla/QScintilla-2.10_fix-link-python-bindings.patch @@ -0,0 +1,14 @@ +add missing link to QScintilla library to correctly build Python bindings + +author: Kenneth Hoste (HPC-UGent) +--- QScintilla_gpl-2.10/Python/configure.py.orig 2017-03-08 14:29:36.344465661 +0100 ++++ QScintilla_gpl-2.10/Python/configure.py 2017-03-08 14:36:00.439001287 +0100 +@@ -1510,7 +1510,7 @@ + + libs = qmake_config.get('LIBS') + if libs: +- pro.write('LIBS += %s\n' % libs) ++ pro.write('LIBS += %s -lqscintilla2_qt4\n' % libs) + + if not opts.static: + pro.write(''' diff --git a/easybuild/easyconfigs/q/QScintilla/QScintilla-2.9.4-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/q/QScintilla/QScintilla-2.9.4-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..e3f0cde600 --- /dev/null +++ b/easybuild/easyconfigs/q/QScintilla/QScintilla-2.9.4-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,21 @@ +name = 'QScintilla' +version = '2.9.4' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://www.riverbankcomputing.com/software/qscintilla' +description = "QScintilla is a port to Qt of Neil Hodgson's Scintilla C++ editor control" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'pic': True, 'cstd': 'c++11'} + +source_urls = ['https://sourceforge.net/projects/pyqt/files/%(name)s%(version_major)s/QScintilla-%(version)s/'] +sources = ['QScintilla_gpl-%(version)s.tar.gz'] + +patches = ['QScintilla-%(version)s_fix-link-python-bindings.patch'] + +dependencies = [ + ('Python', '2.7.12'), + ('PyQt', '4.12', versionsuffix), +] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/q/QScintilla/QScintilla-2.9.4_fix-link-python-bindings.patch b/easybuild/easyconfigs/q/QScintilla/QScintilla-2.9.4_fix-link-python-bindings.patch new file mode 100644 index 0000000000..3abd6f5965 --- /dev/null +++ b/easybuild/easyconfigs/q/QScintilla/QScintilla-2.9.4_fix-link-python-bindings.patch @@ -0,0 +1,14 @@ +add missing link to QScintilla library to correctly build Python bindings + +author: Kenneth Hoste (HPC-UGent) +--- QScintilla_gpl-2.9.4/Python/configure.py.orig 2017-03-08 14:29:36.344465661 +0100 ++++ QScintilla_gpl-2.9.4/Python/configure.py 2017-03-08 14:36:00.439001287 +0100 +@@ -1510,7 +1510,7 @@ + + libs = qmake_config.get('LIBS') + if libs: +- pro.write('LIBS += %s\n' % libs) ++ pro.write('LIBS += %s -lqscintilla2\n' % libs) + + if not opts.static: + pro.write(''' diff --git a/easybuild/easyconfigs/q/QScintilla2/QScintilla2-2.10-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/q/QScintilla2/QScintilla2-2.10-intel-2016b-Python-2.7.12.eb deleted file mode 100644 index be392c7b0b..0000000000 --- a/easybuild/easyconfigs/q/QScintilla2/QScintilla2-2.10-intel-2016b-Python-2.7.12.eb +++ /dev/null @@ -1,52 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'QScintilla2' -version = '2.10' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://www.riverbankcomputing.com/software/qscintilla' -description = "QScintilla is a port to Qt of Neil Hodgson's Scintilla C++ editor control" - -toolchain = {'name': 'intel', 'version': '2016b'} -toolchainopts = {'pic': True, 'cstd': 'c++11'} - -source_urls = ['https://sourceforge.net/projects/pyqt/files/%(name)s/QScintilla-%(version)s/'] -sources = ['QScintilla_gpl-%(version)s.tar.gz'] - -patches = ['QScintilla2-%(version)s_fix-link-python-bindings.patch'] - -dependencies = [ - ('Python', '2.7.12'), - ('PyQt', '4.12', versionsuffix), -] - -start_dir = 'Qt4Qt5' - -skipsteps = ['configure'] - -prebuildopts = "sed -i 's@\$\$\[QT_INSTALL_LIBS\]@%(installdir)s/lib@g' qscintilla.pro && " -prebuildopts += "sed -i 's@\$\$\[QT_INSTALL_HEADERS\]@%(installdir)s/include@g' qscintilla.pro && " -prebuildopts += "sed -i 's@\$\$\[QT_INSTALL_TRANSLATIONS\]@%(installdir)s/trans@g' qscintilla.pro && " -prebuildopts += "sed -i 's@\$\$\[QT_INSTALL_DATA\]@%(installdir)s/data@g' qscintilla.pro && " -prebuildopts += "sed -i 's@\$\$\[QT_HOST_DATA\]@%(installdir)s/data@g' qscintilla.pro && " -prebuildopts += "qmake qscintilla.pro && " - -buildopts = 'CXXFLAGS="$CXXFLAGS \$(DEFINES)"' - -python_bindings_install_cmd = "cd ../Python && mkdir -p %(installdir)s/share/sip/PyQt4 && " -python_bindings_install_cmd += "python configure.py --destdir %(installdir)s/lib/python%(pyshortver)s/site-packages/PyQt4 --qsci-sipdir %(installdir)s/share/sip/PyQt4 --qsci-incdir %(installdir)s/include --qsci-libdir %(installdir)s/lib --pyqt-sipdir $EBROOTPYQT/share/sip/PyQt4 --apidir %(installdir)s/qsci/api/python --no-stubs && " -python_bindings_install_cmd += "make && make install && cd %(installdir)s/lib/python%(pyshortver)s/site-packages/PyQt4 && " -python_bindings_install_cmd += "for x in $(ls $EBROOTPYQT/lib/python2.7/site-packages/PyQt4); do ln -s $EBROOTPYQT/lib/python2.7/site-packages/PyQt4/$x; done && " -python_bindings_install_cmd += "rm __init__.py* && touch __init__.py" -postinstallcmds = [python_bindings_install_cmd] - -modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} - -sanity_check_paths = { - 'files': ['lib/libqscintilla2_qt4.so'], - 'dirs': ['include/Qsci', 'lib/python%(pyshortver)s/site-packages/PyQt4', 'qsci/api/python', 'share/sip/PyQt4', 'trans'], -} - -sanity_check_commands = ["python -c 'import PyQt4.Qsci'"] - -moduleclass = 'vis' -- GitLab From 058dd65ade21434c77d9b72656ae5863f2eaf3c7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Mar 2017 16:53:26 +0100 Subject: [PATCH 0314/1603] QScintilla2 -> QScintilla, clean up configopts, enhance sanity check for QGIS --- .../QGIS-2.14.12-intel-2016b-Python-2.7.12.eb | 17 ++++++++++------- 1 file changed, 10 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/q/QGIS/QGIS-2.14.12-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/q/QGIS/QGIS-2.14.12-intel-2016b-Python-2.7.12.eb index abd1b36a0c..d97a872052 100644 --- a/easybuild/easyconfigs/q/QGIS/QGIS-2.14.12-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/q/QGIS/QGIS-2.14.12-intel-2016b-Python-2.7.12.eb @@ -28,8 +28,8 @@ dependencies = [ ('expat', '2.2.0'), ('QCA', '2.1.3'), ('PyQt', '4.12', versionsuffix), - # QScintilla2 must be listed after PyQt4 due to Python bindings 'overriding' those of PyQt4 - ('QScintilla2', '2.10', versionsuffix), + # QScintilla must be listed after PyQt4 due to Python bindings 'overriding' those of PyQt4 + ('QScintilla', '2.10', versionsuffix), ('GSL', '2.3'), ('QJson', '0.9.0'), ] @@ -41,13 +41,16 @@ builddependencies = [ separate_build_dir = True -configopts = '-DQJSON_DIR=$EBROOTQJSON/lib/cmake/qjson -DCMAKE_PREFIX_PATH=$EBROOTQT -DQSCINTILLA_LIBRARY=$EBROOTQSCINTILLA2/lib/libqscintilla2_qt4.so -DPYQT4_SIP_DIR=$EBROOTPYQT/share/sip/PyQt4 -DQSCI_SIP_DIR=$EBROOTQSCINTILLA2/share/sip/PyQt4' - -buildopts = "VERBOSE=1 V=1" +# specify locations that CMake can't figure out correctly +configopts = "-DCMAKE_PREFIX_PATH=$EBROOTQT -DQJSON_DIR=$EBROOTQJSON/lib/cmake/qjson " +configopts += "-DQSCINTILLA_LIBRARY=$EBROOTQSCINTILLA2/lib/libqscintilla2_qt4.so " +configopts += "-DPYQT4_SIP_DIR=$EBROOTPYQT/share/sip/PyQt4 -DQSCI_SIP_DIR=$EBROOTQSCINTILLA2/share/sip/PyQt4" sanity_check_paths = { - 'files': ['bin/qgis'], - 'dirs': [], + 'files': ['bin/qbrowser', 'bin/qgis', 'bin/qgis_bench', 'lib/libqgis_analysis.%s' % SHLIB_EXT, + 'lib/libqgis_app.%s' % SHLIB_EXT, 'lib/libqgis_core.%s' % SHLIB_EXT, 'lib/libqgis_gui.%s' % SHLIB_EXT, + 'lib/libqgis_networkanalysis.%s' % SHLIB_EXT, 'lib/libqgispython.%s' % SHLIB_EXT], + 'dirs': ['include/qgis', 'man', 'share/qgis'], } moduleclass = 'geo' -- GitLab From 358985ef2ee5d86074951462c0d8a6c3a3533eb9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Mar 2017 17:00:42 +0100 Subject: [PATCH 0315/1603] add patch for QGIS 2.14.12 --- .../QGIS/QGIS-2.14.12-intel-2016b-Python-2.7.12.eb | 2 +- .../q/QGIS/QGIS-2.14.12_fix-SIP-macro.patch | 14 ++++++++++++++ 2 files changed, 15 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/q/QGIS/QGIS-2.14.12_fix-SIP-macro.patch diff --git a/easybuild/easyconfigs/q/QGIS/QGIS-2.14.12-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/q/QGIS/QGIS-2.14.12-intel-2016b-Python-2.7.12.eb index d97a872052..9b31165cdc 100644 --- a/easybuild/easyconfigs/q/QGIS/QGIS-2.14.12-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/q/QGIS/QGIS-2.14.12-intel-2016b-Python-2.7.12.eb @@ -13,7 +13,7 @@ toolchainopts = {'pic': True, 'cstd': 'gnu++11'} source_urls = ['http://qgis.org/downloads/'] sources = [SOURCELOWER_TAR_BZ2] -patches = ['QGIS-2.14.12.patch'] +patches = ['QGIS-%(version)s_fix-SIP-macro.patch'] dependencies = [ ('Qt', '4.8.7'), diff --git a/easybuild/easyconfigs/q/QGIS/QGIS-2.14.12_fix-SIP-macro.patch b/easybuild/easyconfigs/q/QGIS/QGIS-2.14.12_fix-SIP-macro.patch new file mode 100644 index 0000000000..2eb3299a7d --- /dev/null +++ b/easybuild/easyconfigs/q/QGIS/QGIS-2.14.12_fix-SIP-macro.patch @@ -0,0 +1,14 @@ +include location of PyQt .sip files in SIPCMD macro + +author: Kenneth Hoste (HPC-UGent) +--- qgis-2.14.12/cmake/SIPMacros.cmake.orig 2017-03-09 12:57:14.037320233 +0100 ++++ qgis-2.14.12/cmake/SIPMacros.cmake 2017-03-09 13:05:55.739057294 +0100 +@@ -102,7 +102,7 @@ + ENDIF(PEDANTIC) + + +- SET(SIPCMD ${SIP_BINARY_PATH} ${_sip_tags} -w -e ${_sip_x} ${SIP_EXTRA_OPTIONS} -j ${SIP_CONCAT_PARTS} -c ${CMAKE_CURRENT_BINARY_DIR}/${_module_path} ${_sip_includes} ${_abs_module_sip}) ++ SET(SIPCMD ${SIP_BINARY_PATH} ${_sip_tags} -w -e ${_sip_x} ${SIP_EXTRA_OPTIONS} -j ${SIP_CONCAT_PARTS} -c ${CMAKE_CURRENT_BINARY_DIR}/${_module_path} ${_sip_includes} -I$ENV{EBROOTPYQT}/share/sip/PyQt4 ${_abs_module_sip}) + SET(SUPPRESS_SIP_WARNINGS FALSE CACHE BOOL "Hide SIP warnings") + MARK_AS_ADVANCED(SUPPRESS_SIP_WARNINGS) + IF(SUPPRESS_SIP_WARNINGS) -- GitLab From 616fe782803b18052ff11d6a1fc6eba545cb57e4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Mar 2017 17:37:13 +0100 Subject: [PATCH 0316/1603] fix $EBROOT for QScintilla --- .../q/QGIS/QGIS-2.14.12-intel-2016b-Python-2.7.12.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/q/QGIS/QGIS-2.14.12-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/q/QGIS/QGIS-2.14.12-intel-2016b-Python-2.7.12.eb index 9b31165cdc..43245eb873 100644 --- a/easybuild/easyconfigs/q/QGIS/QGIS-2.14.12-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/q/QGIS/QGIS-2.14.12-intel-2016b-Python-2.7.12.eb @@ -43,8 +43,8 @@ separate_build_dir = True # specify locations that CMake can't figure out correctly configopts = "-DCMAKE_PREFIX_PATH=$EBROOTQT -DQJSON_DIR=$EBROOTQJSON/lib/cmake/qjson " -configopts += "-DQSCINTILLA_LIBRARY=$EBROOTQSCINTILLA2/lib/libqscintilla2_qt4.so " -configopts += "-DPYQT4_SIP_DIR=$EBROOTPYQT/share/sip/PyQt4 -DQSCI_SIP_DIR=$EBROOTQSCINTILLA2/share/sip/PyQt4" +configopts += "-DQSCINTILLA_LIBRARY=$EBROOTQSCINTILLA/lib/libqscintilla2_qt4.so " +configopts += "-DPYQT4_SIP_DIR=$EBROOTPYQT/share/sip/PyQt4 -DQSCI_SIP_DIR=$EBROOTQSCINTILLA/share/sip/PyQt4" sanity_check_paths = { 'files': ['bin/qbrowser', 'bin/qgis', 'bin/qgis_bench', 'lib/libqgis_analysis.%s' % SHLIB_EXT, -- GitLab From c326a3be445d0ad2f149747707daf4addd88ff7e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Mar 2017 19:41:37 +0100 Subject: [PATCH 0317/1603] adding easyconfigs: libspatialite-4.3.0a-foss-2016b.eb --- .../libspatialite-4.3.0a-foss-2016b.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/l/libspatialite/libspatialite-4.3.0a-foss-2016b.eb diff --git a/easybuild/easyconfigs/l/libspatialite/libspatialite-4.3.0a-foss-2016b.eb b/easybuild/easyconfigs/l/libspatialite/libspatialite-4.3.0a-foss-2016b.eb new file mode 100644 index 0000000000..c87d185cc1 --- /dev/null +++ b/easybuild/easyconfigs/l/libspatialite/libspatialite-4.3.0a-foss-2016b.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'libspatialite' +version = '4.3.0a' + +homepage = "https://www.gaia-gis.it/fossil/libspatialite/home" +description = """SpatiaLite is an open source library intended to extend the SQLite core to support + fully fledged Spatial SQL capabilities.""" + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.gaia-gis.it/gaia-sins/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('FreeXL', '1.0.2'), + ('GEOS', '3.6.1', '-Python-2.7.12'), + ('SQLite', '3.13.0'), + ('PROJ', '4.9.3'), +] + +builddependencies = [('CMake', '3.7.1')] + +configopts = '--disable-geosadvanced' + +sanity_check_paths = { + 'files': ['include/spatialite.h', 'lib/libspatialite.a', 'lib/libspatialite.%s' % SHLIB_EXT], + 'dirs': ['include/spatialite'], +} + +moduleclass = 'lib' -- GitLab From de1032dfcb6d247eb98e23a8f63146c82dc6f57d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Mar 2017 19:56:54 +0100 Subject: [PATCH 0318/1603] adding easyconfigs: PyQt-4.12-foss-2016b-Python-2.7.12.eb, SIP-4.19-foss-2016b-Python-2.7.12.eb --- .../PyQt-4.12-foss-2016b-Python-2.7.12.eb | 37 +++++++++++++++++++ .../SIP/SIP-4.19-foss-2016b-Python-2.7.12.eb | 30 +++++++++++++++ 2 files changed, 67 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyQt/PyQt-4.12-foss-2016b-Python-2.7.12.eb create mode 100644 easybuild/easyconfigs/s/SIP/SIP-4.19-foss-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/p/PyQt/PyQt-4.12-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/PyQt/PyQt-4.12-foss-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..f8e50daad2 --- /dev/null +++ b/easybuild/easyconfigs/p/PyQt/PyQt-4.12-foss-2016b-Python-2.7.12.eb @@ -0,0 +1,37 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Bart Verleye +# Center for eResearch, Auckland +easyblock = 'ConfigureMakePythonPackage' + +name = 'PyQt' +version = '4.12' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.riverbankcomputing.co.uk/software/pyqt' +description = """PyQt is a set of Python v2 and v3 bindings for Digia's Qt application framework.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['http://sourceforge.net/projects/pyqt/files/PyQt4/PyQt-%(version)s'] +sources = ['PyQt4_gpl_x11-%(version)s.tar.gz'] + +dependencies = [ + ('Python', '2.7.12'), + ('SIP', '4.19', versionsuffix), + ('Qt', '4.8.7'), +] + +configopts = "configure-ng.py --confirm-license" +configopts += " --destdir=%(installdir)s/lib/python%(pyshortver)s/site-packages " +configopts += " --sipdir=%(installdir)s/share/sip/PyQt%(version_major)s" + +options = {'modulename': '%(name)s%(version_major)s'} + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s%(version_major)s'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/s/SIP/SIP-4.19-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/s/SIP/SIP-4.19-foss-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..be020214d2 --- /dev/null +++ b/easybuild/easyconfigs/s/SIP/SIP-4.19-foss-2016b-Python-2.7.12.eb @@ -0,0 +1,30 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Bart Verleye +# Center for eResearch, Auckland +easyblock = 'ConfigureMakePythonPackage' + +name = 'SIP' +version = '4.19' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.riverbankcomputing.com/software/sip/' +description = """SIP is a tool that makes it very easy to create Python bindings for C and C++ libraries.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://sourceforge.net/projects/pyqt/files/sip/sip-%(version)s'] + +dependencies = [('Python', '2.7.12')] + +configopts = "configure.py --bindir %(installdir)s/bin --incdir %(installdir)s/include " +configopts += "--destdir %(installdir)s/lib/python%(pyshortver)s/site-packages" + +sanity_check_paths = { + 'files': ['bin/sip', 'include/sip.h'] + + ['lib/python%%(pyshortver)s/site-packages/%s' % x + for x in ['sip.%s' % SHLIB_EXT, 'sipconfig.py', 'sipdistutils.py']], + 'dirs': [], +} + +moduleclass = 'lang' -- GitLab From fccbb78c76415fc8bafa07811b51c091e3bcf9a4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Mar 2017 19:57:53 +0100 Subject: [PATCH 0319/1603] also enable installation of SIP files in PyQt 4.12 easyconfig used intel/2016b --- .../easyconfigs/p/PyQt/PyQt-4.12-intel-2016b-Python-2.7.12.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PyQt/PyQt-4.12-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/PyQt/PyQt-4.12-intel-2016b-Python-2.7.12.eb index 9ea42178d7..8afd4b1225 100644 --- a/easybuild/easyconfigs/p/PyQt/PyQt-4.12-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/p/PyQt/PyQt-4.12-intel-2016b-Python-2.7.12.eb @@ -23,7 +23,7 @@ dependencies = [ configopts = "configure-ng.py --confirm-license" configopts += " --destdir=%(installdir)s/lib/python%(pyshortver)s/site-packages " -configopts += " --no-sip-files" +configopts += " --sipdir=%(installdir)s/share/sip/PyQt%(version_major)s" options = {'modulename': '%(name)s%(version_major)s'} -- GitLab From f1dba5919c4d1a1081412e33b37fa8d863b53904 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Mar 2017 20:00:15 +0100 Subject: [PATCH 0320/1603] include binutils as build dep in flex/help2man/M4 easyconfigs using GCCcore/5.4.0 --- easybuild/easyconfigs/f/flex/flex-2.6.3-GCCcore-5.4.0.eb | 3 ++- .../easyconfigs/h/help2man/help2man-1.47.4-GCCcore-5.4.0.eb | 5 +++++ easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.4.0.eb | 3 +++ 3 files changed, 10 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.3-GCCcore-5.4.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.3-GCCcore-5.4.0.eb index 5044907def..fea2687908 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.3-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.3-GCCcore-5.4.0.eb @@ -15,9 +15,10 @@ checksums = ['a5f65570cd9107ec8a8ec88f17b31bb1'] dependencies = [('M4', '1.4.18')] builddependencies = [ - ('binutils', '2.26'), ('Bison', '3.0.4'), ('help2man', '1.47.4'), + # use same binutils version that was used when building GCC toolchain + ('binutils', '2.26', '', True), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/h/help2man/help2man-1.47.4-GCCcore-5.4.0.eb b/easybuild/easyconfigs/h/help2man/help2man-1.47.4-GCCcore-5.4.0.eb index 7b53bd8797..0d730043fb 100644 --- a/easybuild/easyconfigs/h/help2man/help2man-1.47.4-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/h/help2man/help2man-1.47.4-GCCcore-5.4.0.eb @@ -11,6 +11,11 @@ toolchain = {'name': 'GCCcore', 'version': '5.4.0'} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_XZ] +builddependencies = [ + # use same binutils version that was used when building GCC toolchain + ('binutils', '2.26', '', True), +] + sanity_check_paths = { 'files': ['bin/help2man'], 'dirs': [], diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.4.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.4.0.eb index 345402c605..c1c1439bf3 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.4.0.eb @@ -13,6 +13,9 @@ toolchain = {'name': 'GCCcore', 'version': '5.4.0'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] +# use same binutils version that was used when building GCC toolchain +builddependencies = [('binutils', '2.26', '', True)] + # '-fgnu89-inline' is required to avoid linking errors with older glibc's, # see https://github.com/hpcugent/easybuild-easyconfigs/issues/529 configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" -- GitLab From dfb169134cb268f9ae36f937ba2e650e605ef173 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Mar 2017 20:05:28 +0100 Subject: [PATCH 0321/1603] adding easyconfigs: QwtPolar-1.1.1-foss-2016b.eb, Qwt-6.1.3-foss-2016b.eb --- .../easyconfigs/q/Qwt/Qwt-6.1.3-foss-2016b.eb | 29 +++++++++++++++++++ .../q/QwtPolar/QwtPolar-1.1.1-foss-2016b.eb | 29 +++++++++++++++++++ 2 files changed, 58 insertions(+) create mode 100644 easybuild/easyconfigs/q/Qwt/Qwt-6.1.3-foss-2016b.eb create mode 100644 easybuild/easyconfigs/q/QwtPolar/QwtPolar-1.1.1-foss-2016b.eb diff --git a/easybuild/easyconfigs/q/Qwt/Qwt-6.1.3-foss-2016b.eb b/easybuild/easyconfigs/q/Qwt/Qwt-6.1.3-foss-2016b.eb new file mode 100644 index 0000000000..f2b00bf192 --- /dev/null +++ b/easybuild/easyconfigs/q/Qwt/Qwt-6.1.3-foss-2016b.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'Qwt' +version = '6.1.3' + +homepage = 'http://qwt.sourceforge.net/' +description = """The Qwt library contains GUI Components and utility classes which are primarily useful for programs + with a technical background.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_BZ2] + +dependencies = [ + ('Qt', '4.8.7'), +] + +skipsteps = ['configure'] + +prebuildopts = "sed -i 's@QWT_INSTALL_PREFIX[ ]*=.*@QWT_INSTALL_PREFIX = %(installdir)s@g' qwtconfig.pri && " +prebuildopts += "qmake qwt.pro && " + +sanity_check_paths = { + 'files': ['lib/libqwt.%s' % SHLIB_EXT], + 'dirs': ['doc', 'features', 'include', 'plugins'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/q/QwtPolar/QwtPolar-1.1.1-foss-2016b.eb b/easybuild/easyconfigs/q/QwtPolar/QwtPolar-1.1.1-foss-2016b.eb new file mode 100644 index 0000000000..bf12b1ad5e --- /dev/null +++ b/easybuild/easyconfigs/q/QwtPolar/QwtPolar-1.1.1-foss-2016b.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'QwtPolar' +version = '1.1.1' + +homepage = 'http://qwtpolar.sourceforge.net/' +description = "The QwtPolar library contains classes for displaying values on a polar coordinate system." + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_BZ2] + +dependencies = [ + ('Qwt', '6.1.3'), +] + +skipsteps = ['configure'] + +prebuildopts = "sed -i 's@INSTALL_PREFIX[ ]*=.*@INSTALL_PREFIX = %(installdir)s@g' qwtpolarconfig.pri && " +prebuildopts += "sed -i 's/QwtPolarExamples//g' qwtpolarconfig.pri && " +prebuildopts += "qmake qwtpolar.pro && " + +sanity_check_paths = { + 'files': ['lib/libqwtpolar.%s' % SHLIB_EXT], + 'dirs': ['doc', 'features', 'include', 'plugins'], +} + +moduleclass = 'lib' -- GitLab From cf4446f582499934c66770414128fd17c3b1f804 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Mar 2017 20:17:17 +0100 Subject: [PATCH 0322/1603] adding easyconfigs: QJson-0.9.0-foss-2016b.eb --- .../q/QJson/QJson-0.9.0-foss-2016b.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/q/QJson/QJson-0.9.0-foss-2016b.eb diff --git a/easybuild/easyconfigs/q/QJson/QJson-0.9.0-foss-2016b.eb b/easybuild/easyconfigs/q/QJson/QJson-0.9.0-foss-2016b.eb new file mode 100644 index 0000000000..32b2329111 --- /dev/null +++ b/easybuild/easyconfigs/q/QJson/QJson-0.9.0-foss-2016b.eb @@ -0,0 +1,28 @@ +easyblock = 'CMakeMake' + +name = 'QJson' +version = '0.9.0' + +homepage = 'http://qjson.sourceforge.net/' +description = "QJson is a Qt-based library that maps JSON data to QVariant objects and vice versa." + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['https://github.com/flavio/qjson/archive/'] +sources = ['%(version)s.tar.gz'] + +dependencies = [ + ('Qt', '4.8.7'), +] +builddependencies = [ + ('CMake', '3.7.1'), +] + +separate_build_dir = True + +sanity_check_paths = { + 'files': ['lib/libqjson.%s' % SHLIB_EXT], + 'dirs': ['include/qjson', 'lib/cmake', 'lib/pkgconfig'], +} + +moduleclass = 'tools' -- GitLab From b280b34714182becf501f1b79cb4f7c83d335a63 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Mar 2017 20:17:47 +0100 Subject: [PATCH 0323/1603] adding easyconfigs: QCA-2.1.3-foss-2016b.eb --- .../easyconfigs/q/QCA/QCA-2.1.3-foss-2016b.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/q/QCA/QCA-2.1.3-foss-2016b.eb diff --git a/easybuild/easyconfigs/q/QCA/QCA-2.1.3-foss-2016b.eb b/easybuild/easyconfigs/q/QCA/QCA-2.1.3-foss-2016b.eb new file mode 100644 index 0000000000..4a94646890 --- /dev/null +++ b/easybuild/easyconfigs/q/QCA/QCA-2.1.3-foss-2016b.eb @@ -0,0 +1,30 @@ +easyblock = 'CMakeMake' + +name = 'QCA' +version = '2.1.3' + +homepage = 'http://delta.affinix.com/qca/' +description = """Taking a hint from the similarly-named Java Cryptography Architecture, + QCA aims to provide a straightforward and cross-platform crypto API, using Qt datatypes + and conventions. QCA separates the API from the implementation, using plugins known as + Providers. The advantage of this model is to allow applications to avoid linking to or + explicitly depending on any particular cryptographic library. This allows one to easily + change or upgrade crypto implementations without even needing to recompile the + application! QCA should work everywhere Qt does, including Windows/Unix/MacOSX.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['http://download.kde.org/stable/qca/%(version)s/src/'] +sources = ['%(namelower)s-%(version)s.tar.xz'] + +configopts = "-DQT4_BUILD=true" + +builddependencies = [ + ('CMake', '3.7.2') +] + +dependencies = [ + ('Qt', '4.8.7') +] + +moduleclass = 'devel' -- GitLab From c21818052a0b1ca09202778fa7b6cb5361cb15aa Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Mar 2017 22:13:51 +0100 Subject: [PATCH 0324/1603] adding easyconfigs: QScintilla-2.10-foss-2016b-Python-2.7.12.eb, QScintilla-2.9.4-foss-2016b-Python-2.7.12.eb --- ...Scintilla-2.10-foss-2016b-Python-2.7.12.eb | 21 +++++++++++++++++++ ...cintilla-2.9.4-foss-2016b-Python-2.7.12.eb | 21 +++++++++++++++++++ 2 files changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/q/QScintilla/QScintilla-2.10-foss-2016b-Python-2.7.12.eb create mode 100644 easybuild/easyconfigs/q/QScintilla/QScintilla-2.9.4-foss-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/q/QScintilla/QScintilla-2.10-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/q/QScintilla/QScintilla-2.10-foss-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..13dd45e489 --- /dev/null +++ b/easybuild/easyconfigs/q/QScintilla/QScintilla-2.10-foss-2016b-Python-2.7.12.eb @@ -0,0 +1,21 @@ +name = 'QScintilla' +version = '2.10' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://www.riverbankcomputing.com/software/qscintilla' +description = "QScintilla is a port to Qt of Neil Hodgson's Scintilla C++ editor control" + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'pic': True, 'cstd': 'c++11'} + +source_urls = ['https://sourceforge.net/projects/pyqt/files/%(name)s%(version_major)s/QScintilla-%(version)s/'] +sources = ['QScintilla_gpl-%(version)s.tar.gz'] + +patches = ['QScintilla-%(version)s_fix-link-python-bindings.patch'] + +dependencies = [ + ('Python', '2.7.12'), + ('PyQt', '4.12', versionsuffix), +] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/q/QScintilla/QScintilla-2.9.4-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/q/QScintilla/QScintilla-2.9.4-foss-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..f6edee2ee2 --- /dev/null +++ b/easybuild/easyconfigs/q/QScintilla/QScintilla-2.9.4-foss-2016b-Python-2.7.12.eb @@ -0,0 +1,21 @@ +name = 'QScintilla' +version = '2.9.4' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://www.riverbankcomputing.com/software/qscintilla' +description = "QScintilla is a port to Qt of Neil Hodgson's Scintilla C++ editor control" + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'pic': True, 'cstd': 'c++11'} + +source_urls = ['https://sourceforge.net/projects/pyqt/files/%(name)s%(version_major)s/QScintilla-%(version)s/'] +sources = ['QScintilla_gpl-%(version)s.tar.gz'] + +patches = ['QScintilla-%(version)s_fix-link-python-bindings.patch'] + +dependencies = [ + ('Python', '2.7.12'), + ('PyQt', '4.12', versionsuffix), +] + +moduleclass = 'vis' -- GitLab From 6b206c39bf1a05d066bf894be6ff0838dbe84ee8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Mar 2017 22:19:58 +0100 Subject: [PATCH 0325/1603] {geo}[foss/2016b] QGIS v2.18.4 --- .../QGIS-2.18.4-foss-2016b-Python-2.7.12.eb | 56 +++++++++++++++++++ .../q/QGIS/QGIS-2.18.4_fix-SIP-macro.patch | 14 +++++ 2 files changed, 70 insertions(+) create mode 100644 easybuild/easyconfigs/q/QGIS/QGIS-2.18.4-foss-2016b-Python-2.7.12.eb create mode 100644 easybuild/easyconfigs/q/QGIS/QGIS-2.18.4_fix-SIP-macro.patch diff --git a/easybuild/easyconfigs/q/QGIS/QGIS-2.18.4-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/q/QGIS/QGIS-2.18.4-foss-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..f6d58e7bf7 --- /dev/null +++ b/easybuild/easyconfigs/q/QGIS/QGIS-2.18.4-foss-2016b-Python-2.7.12.eb @@ -0,0 +1,56 @@ +easyblock = 'CMakeMake' + +name = 'QGIS' +version = '2.18.4' +versionsuffix = '-Python-2.7.12' + +homepage = 'http://www.qgis.org/' +description = "QGIS is a user friendly Open Source Geographic Information System (GIS)" + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'pic': True, 'cstd': 'gnu++11'} + +source_urls = ['http://qgis.org/downloads/'] +sources = [SOURCELOWER_TAR_BZ2] + +patches = ['QGIS-%(version)s_fix-SIP-macro.patch'] + +dependencies = [ + ('Qt', '4.8.7'), + ('PROJ', '4.9.3'), + ('GEOS', '3.6.1', versionsuffix), + ('SQLite', '3.13.0'), # stick to this version for compatibility with Python 2.7.12 + ('libspatialite', '4.3.0a'), + ('libspatialindex', '1.8.5'), + ('GDAL', '2.1.3', versionsuffix), + ('Qwt', '6.1.3'), + ('QwtPolar', '1.1.1'), + ('expat', '2.2.0'), + ('QCA', '2.1.3'), + ('PyQt', '4.12', versionsuffix), + # QScintilla must be listed after PyQt4 due to Python bindings 'overriding' those of PyQt4 + ('QScintilla', '2.10', versionsuffix), + ('GSL', '2.3'), + ('QJson', '0.9.0'), +] +builddependencies = [ + ('CMake', '3.7.2'), + ('flex', '2.6.3'), + ('Bison', '3.0.4'), +] + +separate_build_dir = True + +# specify locations that CMake can't figure out correctly +configopts = "-DCMAKE_PREFIX_PATH=$EBROOTQT -DQJSON_DIR=$EBROOTQJSON/lib/cmake/qjson " +configopts += "-DQSCINTILLA_LIBRARY=$EBROOTQSCINTILLA/lib/libqscintilla2_qt4.so " +configopts += "-DPYQT4_SIP_DIR=$EBROOTPYQT/share/sip/PyQt4 -DQSCI_SIP_DIR=$EBROOTQSCINTILLA/share/sip/PyQt4" + +sanity_check_paths = { + 'files': ['bin/qbrowser', 'bin/qgis', 'bin/qgis_bench', 'lib/libqgis_analysis.%s' % SHLIB_EXT, + 'lib/libqgis_app.%s' % SHLIB_EXT, 'lib/libqgis_core.%s' % SHLIB_EXT, 'lib/libqgis_gui.%s' % SHLIB_EXT, + 'lib/libqgis_networkanalysis.%s' % SHLIB_EXT, 'lib/libqgispython.%s' % SHLIB_EXT], + 'dirs': ['include/qgis', 'man', 'share/qgis'], +} + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/q/QGIS/QGIS-2.18.4_fix-SIP-macro.patch b/easybuild/easyconfigs/q/QGIS/QGIS-2.18.4_fix-SIP-macro.patch new file mode 100644 index 0000000000..5d04066fb1 --- /dev/null +++ b/easybuild/easyconfigs/q/QGIS/QGIS-2.18.4_fix-SIP-macro.patch @@ -0,0 +1,14 @@ +include location of PyQt .sip files in SIPCMD macro + +author: Kenneth Hoste (HPC-UGent) +--- qgis-2.18.4/cmake/SIPMacros.cmake.orig 2017-03-08 17:44:20.698576501 +0100 ++++ qgis-2.18.4/cmake/SIPMacros.cmake 2017-03-08 17:46:39.110172584 +0100 +@@ -96,7 +96,7 @@ + ADD_DEFINITIONS( /bigobj ) + ENDIF(MSVC) + +- SET(SIPCMD ${SIP_BINARY_PATH} ${_sip_tags} -w -e ${_sip_x} ${SIP_EXTRA_OPTIONS} -j ${SIP_CONCAT_PARTS} -c ${CMAKE_CURRENT_BINARY_DIR}/${_module_path} ${_sip_includes} ${_abs_module_sip}) ++ SET(SIPCMD ${SIP_BINARY_PATH} ${_sip_tags} -w -e ${_sip_x} ${SIP_EXTRA_OPTIONS} -j ${SIP_CONCAT_PARTS} -c ${CMAKE_CURRENT_BINARY_DIR}/${_module_path} ${_sip_includes} -I$ENV{EBROOTPYQT}/share/sip/PyQt4 ${_abs_module_sip}) + SET(SUPPRESS_SIP_WARNINGS FALSE CACHE BOOL "Hide SIP warnings") + MARK_AS_ADVANCED(SUPPRESS_SIP_WARNINGS) + IF(SUPPRESS_SIP_WARNINGS) -- GitLab From ad89278bbc144ca83fef7955ceb5580c69721100 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Mar 2017 22:37:17 +0100 Subject: [PATCH 0326/1603] also check with Tcl module syntax, Lua is the default in EasyBuild v3.x --- .travis.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.travis.yml b/.travis.yml index 13ca5c0612..07cebed738 100644 --- a/.travis.yml +++ b/.travis.yml @@ -4,11 +4,11 @@ env: matrix: - ENV_MOD_VERSION=3.2.10 EASYBUILD_MODULES_TOOL=EnvironmentModulesC EASYBUILD_MODULE_SYNTAX=Tcl - LMOD_VERSION=5.8 - - LMOD_VERSION=5.8 EASYBUILD_MODULE_SYNTAX=Lua + - LMOD_VERSION=5.8 EASYBUILD_MODULE_SYNTAX=Tcl - LMOD_VERSION=6.6.3 - - LMOD_VERSION=6.6.3 EASYBUILD_MODULE_SYNTAX=Lua + - LMOD_VERSION=6.6.3 EASYBUILD_MODULE_SYNTAX=Tcl - LMOD_VERSION=7.0 - - LMOD_VERSION=7.0 EASYBUILD_MODULE_SYNTAX=Lua + - LMOD_VERSION=7.0 EASYBUILD_MODULE_SYNTAX=Tcl matrix: # mark build as finished as soon as job has failed fast_finish: true -- GitLab From 3d6abb181ca977ede9e7f108aefa5306de1729c1 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Fri, 10 Mar 2017 13:09:41 +1300 Subject: [PATCH 0327/1603] Dependencies for Perl --- .../easyconfigs/d/DB/DB-6.0.30-foss-2015a.eb | 18 ++++++++++ .../s/SQLite/SQLite-3.8.9-foss-2015a.eb | 36 +++++++++++++++++++ 2 files changed, 54 insertions(+) create mode 100644 easybuild/easyconfigs/d/DB/DB-6.0.30-foss-2015a.eb create mode 100644 easybuild/easyconfigs/s/SQLite/SQLite-3.8.9-foss-2015a.eb diff --git a/easybuild/easyconfigs/d/DB/DB-6.0.30-foss-2015a.eb b/easybuild/easyconfigs/d/DB/DB-6.0.30-foss-2015a.eb new file mode 100644 index 0000000000..32a7842e44 --- /dev/null +++ b/easybuild/easyconfigs/d/DB/DB-6.0.30-foss-2015a.eb @@ -0,0 +1,18 @@ +name = 'DB' +version = '6.0.30' + +homepage = 'http://www.oracle.com/technetwork/products/berkeleydb' +description = """Berkeley DB enables the development of custom data management solutions, + without the overhead traditionally associated with such custom projects.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +# download via http://www.oracle.com/technetwork/products/berkeleydb/downloads/, requires registration +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': ["include/db.h"], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.9-foss-2015a.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.9-foss-2015a.eb new file mode 100644 index 0000000000..45f98b9cdb --- /dev/null +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.9-foss-2015a.eb @@ -0,0 +1,36 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg/Luxembourg Centre for Systems Biomedicine +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## + +name = 'SQLite' +version = '3.8.9' + +easyblock = 'ConfigureMake' + +homepage = 'http://www.hwaci.com/sw/sqlite/' +description = "SQLite: SQL Database Engine in a C Library" + +# eg. http://www.hwaci.com/sw/sqlite/2013/sqlite-autoconf-3080100.tar.gz +source_urls = ['http://www.hwaci.com/sw/sqlite/2013'] +sources = ['sqlite-autoconf-%s0%s0%s00.tar.gz' % tuple(version.split('.'))] # very weird way to calculate your filename + +toolchain = {'name': 'foss', 'version': '2015a'} + +dependencies = [ + ('libreadline', '6.2'), +] + +sanity_check_paths = { + 'files': ['bin/sqlite3'], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From 54f70e4c1d48ee5844f94817091e0cd3b343bc9c Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Fri, 10 Mar 2017 13:13:00 +1300 Subject: [PATCH 0328/1603] Perl and two dependencies for the gimkl-2017a toolchain; includes version updates of Perl extensions --- .../easyconfigs/d/DB/DB-6.2.23-gimkl-2017a.eb | 18 + .../p/Perl/Perl-5.24.1-gimkl-2017a.eb | 1194 +++++++++++++++++ .../s/SAMtools/SAMtools-0.1.19-gimkl-2017a.eb | 21 + 3 files changed, 1233 insertions(+) create mode 100644 easybuild/easyconfigs/d/DB/DB-6.2.23-gimkl-2017a.eb create mode 100644 easybuild/easyconfigs/p/Perl/Perl-5.24.1-gimkl-2017a.eb create mode 100644 easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.19-gimkl-2017a.eb diff --git a/easybuild/easyconfigs/d/DB/DB-6.2.23-gimkl-2017a.eb b/easybuild/easyconfigs/d/DB/DB-6.2.23-gimkl-2017a.eb new file mode 100644 index 0000000000..f6a2ef8db6 --- /dev/null +++ b/easybuild/easyconfigs/d/DB/DB-6.2.23-gimkl-2017a.eb @@ -0,0 +1,18 @@ +name = 'DB' +version = '6.2.23' + +homepage = 'http://www.oracle.com/technetwork/products/berkeleydb' +description = """Berkeley DB enables the development of custom data management solutions, + without the overhead traditionally associated with such custom projects.""" + +toolchain = {'name': 'gimkl', 'version': '2017a'} + +# download via http://www.oracle.com/technetwork/products/berkeleydb/downloads/, requires registration +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': ["include/db.h"], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.24.1-gimkl-2017a.eb b/easybuild/easyconfigs/p/Perl/Perl-5.24.1-gimkl-2017a.eb new file mode 100644 index 0000000000..d4719d425a --- /dev/null +++ b/easybuild/easyconfigs/p/Perl/Perl-5.24.1-gimkl-2017a.eb @@ -0,0 +1,1194 @@ +name = 'Perl' +version = '5.24.1' +use_perl_threads = False + +homepage = 'http://www.perl.org/' +description = """Larry Wall's Practical Extraction and Report Language""" + +toolchain = {'name': 'gimkl', 'version': '2017a'} +toolchainopts = {'optarch': True, 'pic': True} + +dependencies = [ + ('DB', '6.2.23'), # for DB_File module + ('SQLite', '3.16.2'), # for DBD::SQLite module + ('expat', '2.2.0'), # for XML::Parser I think + ('libxml2', '2.9.4'), # for XML::LibXML +] +# Also zlib / readline via the other dependencies + +builddependencies = [('SAMtools', '0.1.19')] # NOT A LATER VERSION. For Bio::DB::Sam to static link to. + +source_urls = ['http://www.cpan.org/src/5.0'] +sources = [SOURCELOWER_TAR_GZ] + +# We must compile in serial so that Convert::Binary::C is installed +# in a sane manner. +maxparallel = 1 + +#runtest = 'test' # Several modules have extra dependencies for testing + +# Extension versions +acme_damn_version = '0.08' +algorithm_diff_version = '1.1903' +algorithm_munkres_version = '0.08' +aliased_version = '0.34' +anyevent_version = '7.13' +appconfig_version = '1.71' +archive_extract_version = '0.80' +archive_tar_version = '2.24' +archive_zip_version = '1.59' +array_compare_version = '3.0.0' +authen_sasl_version = '2.16' +bioperl_version = '1.007001' +bio_phylo_version = '0.58' +bio_samtools_version = '1.43' +bit_vector_version = '7.4' +boolean_version = '0.46' +bundle_bioperl_version = '2.1.9' +b_lintsubs_version = '0.06' +b_lint_version = '1.20' +capture_tiny_version = '0.46' +carp_version = '1.38' +cgi_version = '4.35' +class_accessor_version = '0.34' +class_data_inheritable_version = '0.08' +class_dbi_version = '3.0.17' +class_inspector_version = '1.31' +class_isa_version = '0.36' +class_load_version = '0.23' +class_load_xs_version = '0.09' +class_singleton_version = '1.5' +class_trigger_version = '0.14' +clone_version = '0.38' +config_general_version = '2.63' +convert_binary_c_version = '0.78' +cpanplus_version = '0.9164' +cwd_guard_version = '0.05' +data_dumper_version = '2.161' +data_optlist_version = '0.110' +data_section_simple_version = '0.07' +data_stag_version = '0.14' +data_types_version = '0.09' +data_uuid_version = '1.221' +datetime_locale_version = '1.14' +datetime_timezone_version = '2.10' +datetime_tiny_version = '1.06' +datetime_version = '1.42' +date_handler_version = '1.2' +dbd_anydata_version = '0.110' +dbd_sqlite_version = '1.54' +dbix_contextualfetch_version = '1.03' +dbix_simple_version = '1.35' +dbi_version = '1.636' +db_file_version = '1.840' +devel_checkcompiler_version = '0.07' +devel_globaldestruction_version = '0.14' +devel_stacktrace_version = '2.02' +digest_hmac_version = '1.03' +digest_sha1_version = '2.13' +dist_checkconflicts_version = '0.11' +email_date_format_version = '1.005' +encode_locale_version = '1.05' +error_version = '0.17024' +eval_closure_version = '0.14' +exception_class_version = '1.42' +expect_pm_version = '1.21' +exporter_declare_version = '0.114' +exporter_tiny_version = '0.044' +extutils_config_version = '0.008' +extutils_helpers_version = '0.026' +extutils_installpaths_version = '0.011' +extutils_makemaker_version = '7.24' +fennec_lite_version = '0.004' +file_checktree_version = '4.42' +file_copy_recursive_version = '0.38' +file_find_rule_perl_version = '1.15' +file_find_rule_version = '0.34' +file_listing_version = '6.04' +file_path_version = '2.12' +file_sharedir_install_version = '0.11' +file_slurp_tiny_version = '0.004' +file_slurp_version = '9999.19' +file_temp_version = '0.2304' +file_which_version = '1.21' +font_ttf_version = '1.06' +forks_version = '0.36' +freezethaw_version = '0.5001' +getopt_long_version = '2.49.1' +git_version = '0.41' +go_db_perl_version = '0.04' +go_perl_version = '0.15' +graph_version = '0.9704' +hash_merge_version = '0.200' +html_form_version = '6.03' +html_parser_version = '3.72' +html_tableextract_version = '2.13' +html_tagset_version = '3.20' +http_cookies_version = '6.01' +http_daemon_version = '6.01' +http_date_version = '6.02' +http_message_version = '6.11' +http_negotiate_version = '6.01' +ima_dbi_version = '0.35' +import_into_version = '1.002005' +inline_c_version = '0.76' +inline_version = '0.80' +io_all_version = '0.86' +io_html_version = '1.001' +io_prompt_version = '0.997004' +io_socket_ssl_version = '2.047' +io_stringy_version = '2.111' +io_string_version = '1.08' +io_tty_version = '1.12' +ipc_run3_version = '0.048' +ipc_run_version = '0.94' +json_version = '2.90' +libxml_perl_version = '0.08' +list_allutils_version = '0.14' +list_moreutils_version = '0.416' +local_lib_version = '2.000019' +logger_simple_version = '2.0' +log_message_simple_version = '0.10' +log_message_version = '0.08' +lwp_mediatypes_version = '6.02' +lwp_version = '6.23' +mailtools_version = '2.18' +math_bezier_version = '0.01' +math_cdf_version = '0.1' +math_round_version = '0.07' +math_vecstat_version = '0.08' +meta_builder_version = '0.003' +mime_lite_version = '3.030' +mime_types_version = '2.13' +mock_quick_version = '1.111' +module_build_tiny_version = '0.039' +module_build_version = '0.4220' +module_build_xsutil_version = '0.16' +module_implementation_version = '0.09' +module_load_conditional_version = '0.68' +module_pluggable_version = '5.2' +module_runtime_version = '0.014' +moose_version = '2.2004' +moo_version = '2.003001' +mouse_version = '2.4.9' +mro_compat_version = '0.12' +net_http_version = '6.13' +net_smtp_ssl_version = '1.04' +number_compare_version = '0.03' +number_compare_version = '0.03' +object_accessor_version = '0.48' +object_insideout_version = '4.04' +package_deprecationmanager_version = '0.17' +package_stash_version = '0.37' +package_stash_xs_version = '0.28' +parallel_forkmanager_version = '1.19' +params_util_version = '1.07' +params_validate_version = '1.26' +parse_recdescent_version = '1.967013' +pathtools_version = '3.62' +perl_unsafe_signals_version = '0.03' +pod_latex_version = '0.61' +pod_plainer_version = '1.04' +pod_pom_version = '2.01' +readonly_version = '2.05' +regexp_common_version = '2016060801' +scalar_list_utils_version = '1.47' +scalar_util_numeric_version = '0.40' +set_array_version = '0.30' +set_intervaltree_version = '0.10' +set_intspan_version = '1.19' +set_scalar_version = '1.29' +shell_version = '0.73' +spreadsheet_parseexcel_version = '0.65' +sql_statement_version = '1.410' +statistics_descriptive_version = '3.0612' +storable_version = '2.51' +strictures_version = '2.000003' +sub_exporter_progressive_version = '0.001013' +sub_exporter_version = '0.987' +sub_install_version = '0.928' +sub_name_version = '0.21' +sub_uplevel_version = '0.2600' +svg_version ='2.64' +switch_version = '2.17' +sys_sigaction_version = '0.23' +template_toolkit_version = '2.26' +term_readkey_version = '2.37' +term_ui_version = '0.46' +test_deep_version = '1.126' +test_differences_version = '0.64' +test_exception_lessclever_version = '0.009' +test_exception_version = '0.43' +test_fatal_version = '0.014' +test_harness_version = '3.36' +test_harness_version = '3.36' +test_leaktrace_version = '0.15' +test_most_version = '0.35' +test_nowarnings_version = '1.04' +test_output_version = '1.03' +test_requires_version = '0.10' +test_simple_version = '1.302078' +test_version_version = '2.05' +test_warnings_version = '0.026' +test_warn_version = '0.32' +text_diff_version = '1.44' +text_glob_version = '0.11' +text_iconv_version = '1.7' +text_soundex_version = '3.05' +tie_ixhash_version = '1.23' +timedate_version = '2.30' +time_piece_mysql_version = '0.06' +time_piece_version = '1.31' +tree_dag_node_version = '1.29' +try_tiny_version = '0.28' +universal_moniker_version = '0.08' +uri_version = '1.71' +version_version = '0.9917' +want_version = '0.29' +www_robotrules_version = '6.02' +xml_dom_version = '1.46' +xml_dom_xpath_version = '0.14' +xml_libxml_version = '2.0128' +xml_namespacesupport_version = '1.11' +xml_parser_version = '2.44' +xml_sax_base_version = '1.08' +xml_sax_version = '0.99' +xml_sax_writer_version = '0.56' +xml_simple_version = '2.22' +xml_twig_version = '3.52' +xml_writer_version = '0.625' +xml_xpath_version = '1.40' +xsloader_version = '0.24' +yaml_version = '1.23' + +exts_list = [ + ('Module::Build', module_build_version, { # std module but recent BioPerl needs a recent version for some reason + 'source_tmpl': 'Module-Build-%s.tar.gz' % module_build_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/L/LE/LEONT/'], + }), + ('ExtUtils::MakeMaker', extutils_makemaker_version, { + 'source_tmpl': 'ExtUtils-MakeMaker-%s.tar.gz' % extutils_makemaker_version, + 'source_urls': ['http://www.cpan.org/modules/by-module/ExtUtils/BINGOS/'], + }), + ('local::lib', local_lib_version, { + 'source_tmpl': 'local-lib-%s.tar.gz' % local_lib_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/H/HA/HAARG/'], + }), + ('IO::String', io_string_version, { + 'source_tmpl': 'IO-String-%s.tar.gz' % io_string_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/G/GA/GAAS/'], + }), + ('Data::Stag', data_stag_version, { + 'source_tmpl': 'Data-Stag-%s.tar.gz' % data_stag_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/C/CM/CMUNGALL/'], + }), + ('DB_File', db_file_version, { + 'source_urls': ['http://www.cpan.org/modules/by-module/DB_File/PMQS/'], + }), + ('DBI', dbi_version, { + 'source_urls': ['http://www.cpan.org/modules/by-module/DBI/TIMB/'], + }), + ('Sub::Uplevel', sub_uplevel_version, { + 'source_tmpl': 'Sub-Uplevel-%s.tar.gz' % sub_uplevel_version, + 'source_urls': ['http://www.cpan.org/modules/by-module/Sub/DAGOLDEN/'], + }), + ('Tree::DAG_Node', tree_dag_node_version, { + 'source_tmpl': 'Tree-DAG_Node-%s.tgz' % tree_dag_node_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/R/RS/RSAVAGE/'], + }), + ('Try::Tiny', try_tiny_version, { + 'source_tmpl': 'Try-Tiny-%s.tar.gz' % try_tiny_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/E/ET/ETHER/'], + }), + ('Devel::StackTrace', devel_stacktrace_version, { + 'source_tmpl': 'Devel-StackTrace-%s.tar.gz' % devel_stacktrace_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/D/DR/DROLSKY/'], + }), + ('Class::Data::Inheritable', class_data_inheritable_version, { + 'source_tmpl': 'Class-Data-Inheritable-%s.tar.gz' % class_data_inheritable_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/T/TM/TMTM/'], + }), + ('Exception::Class', exception_class_version, { + 'source_tmpl': 'Exception-Class-%s.tar.gz' % exception_class_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/D/DR/DROLSKY/'], + }), + ('Test::Fatal', test_fatal_version, { + 'source_tmpl': 'Test-Fatal-%s.tar.gz' % test_fatal_version, + 'source_urls': ['http://www.cpan.org/modules/by-module/Test/RJBS/'], + }), + ('Test::NoWarnings', test_nowarnings_version, { + 'source_tmpl': 'Test-NoWarnings-%s.tar.gz' % test_nowarnings_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/A/AD/ADAMK/'], + }), + ('Test::Deep', test_deep_version, { + 'source_tmpl': 'Test-Deep-%s.tar.gz' % test_deep_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/R/RJ/RJBS/'], + }), + ('Algorithm::Diff', algorithm_diff_version, { + 'source_tmpl': 'Algorithm-Diff-%s.tar.gz' % algorithm_diff_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/T/TY/TYEMQ/'], + }), + ('Text::Diff', text_diff_version, { + 'source_tmpl': 'Text-Diff-%s.tar.gz' % text_diff_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/N/NE/NEILB/'], + }), + ('Test::Differences', test_differences_version, { + 'source_tmpl': 'Test-Differences-%s.tar.gz' % test_differences_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/D/DC/DCANTRELL/'], + }), + ('Test::Exception', test_exception_version, { + 'source_tmpl': 'Test-Exception-%s.tar.gz' % test_exception_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/E/EX/EXODIST/'], + }), + ('Test::Warn', test_warn_version, { + 'source_tmpl': 'Test-Warn-%s.tar.gz' % test_warn_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/B/BI/BIGJ/'], + }), + ('Test::Requires', test_requires_version, { + 'source_tmpl': 'Test-Requires-%s.tar.gz' % test_requires_version, + 'source_urls': ['http://www.cpan.org/modules/by-module/Test/TOKUHIROM/'], + }), + ('Test::Tester', test_simple_version, { + 'source_tmpl': 'Test-Simple-%s.tar.gz' % test_simple_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/E/EX/EXODIST/'], + }), + ('File::Slurp::Tiny', file_slurp_tiny_version, { + 'source_tmpl': 'File-Slurp-Tiny-%s.tar.gz' % file_slurp_tiny_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/L/LE/LEONT'], + }), + ('Params::Util', params_util_version, { + 'source_tmpl': 'Params-Util-%s.tar.gz' % params_util_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/A/AD/ADAMK/'], + }), + ('Sub::Install', sub_install_version, { + 'source_tmpl': 'Sub-Install-%s.tar.gz' % sub_install_version, + 'source_urls': ['http://www.cpan.org/modules/by-module/Sub/RJBS/'], + }), + ('Data::OptList', data_optlist_version, { + 'source_tmpl': 'Data-OptList-%s.tar.gz' % data_optlist_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/R/RJ/RJBS/'], + }), + ('Sub::Exporter', sub_exporter_version, { + 'source_tmpl': 'Sub-Exporter-%s.tar.gz' % sub_exporter_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/R/RJ/RJBS/'], + }), + ('Capture::Tiny', capture_tiny_version, { + 'source_tmpl': 'Capture-Tiny-%s.tar.gz' % capture_tiny_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/D/DA/DAGOLDEN/'], + }), + ('Test::Output', test_output_version, { + 'source_tmpl': 'Test-Output-%s.tar.gz' % test_output_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/B/BD/BDFOY/'], + }), + ('Module::Runtime', module_runtime_version, { + 'source_tmpl': 'Module-Runtime-%s.tar.gz' % module_runtime_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/Z/ZE/ZEFRAM/'], + }), + ('Module::Implementation', module_implementation_version, { + 'source_tmpl': 'Module-Implementation-%s.tar.gz' % module_implementation_version, + 'source_urls': ['http://www.cpan.org/modules/by-module/Module/DROLSKY/'], + }), + ('List::MoreUtils', list_moreutils_version, { + 'source_tmpl': 'List-MoreUtils-%s.tar.gz' % list_moreutils_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/R/RE/REHSACK/'], + }), + ('Package::DeprecationManager', package_deprecationmanager_version, { + 'source_tmpl': 'Package-DeprecationManager-%s.tar.gz' % package_deprecationmanager_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/D/DR/DROLSKY/'], + }), + ('Dist::CheckConflicts', dist_checkconflicts_version, { + 'source_tmpl': 'Dist-CheckConflicts-%s.tar.gz' % dist_checkconflicts_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/D/DO/DOY/'], + }), + ('Package::Stash', package_stash_version, { + 'source_tmpl': 'Package-Stash-%s.tar.gz' % package_stash_version, + 'source_urls': ['http://www.cpan.org/modules/by-module/Package/DOY/'], + }), + ('Class::Load', class_load_version, { + 'source_tmpl': 'Class-Load-%s.tar.gz' % class_load_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/E/ET/ETHER/'], + }), + ('TAP::Harness::Env', test_harness_version, { + 'source_tmpl': 'Test-Harness-%s.tar.gz' % test_harness_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/L/LE/LEONT/'], + }), + ('ExtUtils::Helpers', extutils_helpers_version, { + 'source_tmpl': 'ExtUtils-Helpers-%s.tar.gz' % extutils_helpers_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/L/LE/LEONT'], + }), + ('ExtUtils::Config', extutils_config_version, { + 'source_tmpl': 'ExtUtils-Config-%s.tar.gz' % extutils_config_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/L/LE/LEONT'], + }), + ('ExtUtils::InstallPaths', extutils_installpaths_version, { + 'source_tmpl': 'ExtUtils-InstallPaths-%s.tar.gz' % extutils_installpaths_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/L/LE/LEONT'], + }), + ('Module::Build::Tiny', module_build_tiny_version, { + 'source_tmpl': 'Module-Build-Tiny-%s.tar.gz' % module_build_tiny_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/L/LE/LEONT/'], + }), + ('MRO::Compat', mro_compat_version, { + 'source_tmpl': 'MRO-Compat-%s.tar.gz' % mro_compat_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/B/BO/BOBTFISH/'], + }), + ('Sub::Name', sub_name_version, { + 'source_tmpl': 'Sub-Name-%s.tar.gz' % sub_name_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/E/ET/ETHER/'], + }), + ('Eval::Closure', eval_closure_version, { + 'source_tmpl': 'Eval-Closure-%s.tar.gz' % eval_closure_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/D/DO/DOY/'], + }), + ('Sub::Exporter::Progressive', sub_exporter_progressive_version, { + 'source_tmpl': 'Sub-Exporter-Progressive-%s.tar.gz' % sub_exporter_progressive_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/F/FR/FREW/'], + }), + ('Devel::GlobalDestruction', devel_globaldestruction_version, { + 'source_tmpl': 'Devel-GlobalDestruction-%s.tar.gz' % devel_globaldestruction_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/H/HA/HAARG/'], + }), + ('boolean', boolean_version, { + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/I/IN/INGY/'], + }), + ('Tie::IxHash', tie_ixhash_version, { + 'source_tmpl': 'Tie-IxHash-%s.tar.gz' % tie_ixhash_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/C/CH/CHORNY/'], + }), + ('Moose', moose_version, { + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/E/ET/ETHER/'], + }), + ('Package::Stash::XS', package_stash_xs_version, { + 'source_tmpl': 'Package-Stash-XS-%s.tar.gz' % package_stash_xs_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/D/DO/DOY/'], + }), + ('Params::Validate', params_validate_version, { + 'source_tmpl': 'Params-Validate-%s.tar.gz' % params_validate_version, + 'source_urls': ['http://www.cpan.org/modules/by-module/Params/DROLSKY/'], + }), + ('Class::Load::XS', class_load_xs_version, { + 'source_tmpl': 'Class-Load-XS-%s.tar.gz' % class_load_xs_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/E/ET/ETHER/'], + }), + # For uoa00001, Zendesk #9076 + ('Math::CDF', math_cdf_version, { + 'source_tmpl': 'Math-CDF-%s.tar.gz' % math_cdf_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/C/CA/CALLAHAN/'], + }), + ('DateTime::Locale', datetime_locale_version, { + 'source_tmpl': 'DateTime-Locale-%s.tar.gz' % datetime_locale_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/D/DR/DROLSKY/'], + }), + ('Class::Singleton', class_singleton_version, { + 'source_tmpl': 'Class-Singleton-%s.tar.gz' % class_singleton_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/S/SH/SHAY/'], + }), + ('DateTime::TimeZone', datetime_timezone_version, { + 'source_tmpl': 'DateTime-TimeZone-%s.tar.gz' % datetime_timezone_version, + 'source_urls': ['http://www.cpan.org/modules/by-module/DateTime/DROLSKY/'], + }), + ('Test::Warnings', test_warnings_version, { + 'source_tmpl': 'Test-Warnings-%s.tar.gz' % test_warnings_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/E/ET/ETHER/'], + }), + ('Data::Types', data_types_version, { + 'source_tmpl': 'Data-Types-%s.tar.gz' % data_types_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/D/DW/DWHEELER/'], + }), + ('Exporter::Tiny', exporter_tiny_version, { + 'source_tmpl': 'Exporter-Tiny-%s.tar.gz' % exporter_tiny_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/T/TO/TOBYINK/'], + }), + ('List::AllUtils', list_allutils_version, { + 'source_tmpl': 'List-AllUtils-%s.tar.gz' % list_allutils_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/D/DR/DROLSKY/'], + }), + ('DateTime', datetime_version, { + 'source_urls': ['http://www.cpan.org/modules/by-module/DateTime/DROLSKY/'], + }), + ('DateTime::Tiny', datetime_tiny_version, { + 'source_tmpl': 'DateTime-Tiny-%s.tar.gz' % datetime_tiny_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/D/DA/DAGOLDEN/'], + }), + ('File::Slurp', file_slurp_version, { + 'source_tmpl': 'File-Slurp-%s.tar.gz' % file_slurp_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/U/UR/URI/'], + }), + ('HTTP::Date', http_date_version, { + 'source_tmpl': 'HTTP-Date-%s.tar.gz' % http_date_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/G/GA/GAAS/'], + }), + ('IO::HTML', io_html_version, { + 'source_tmpl': 'IO-HTML-%s.tar.gz' % io_html_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/C/CJ/CJM/'], + }), + ('LWP::MediaTypes', lwp_mediatypes_version, { + 'source_tmpl': 'LWP-MediaTypes-%s.tar.gz' % lwp_mediatypes_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/G/GA/GAAS/'], + }), + ('URI', uri_version, { + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/E/ET/ETHER/'], + }), + ('Encode::Locale', encode_locale_version, { + 'source_tmpl': 'Encode-Locale-%s.tar.gz' % encode_locale_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/G/GA/GAAS/'], + }), + ('HTTP::Request', http_message_version, { + 'source_tmpl': 'HTTP-Message-%s.tar.gz' % http_message_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/E/ET/ETHER/'], + }), + ('HTML::Tagset', html_tagset_version, { + 'source_tmpl': 'HTML-Tagset-%s.tar.gz' % html_tagset_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/P/PE/PETDANCE/'], + }), + ('HTML::Entities', html_parser_version, { + 'source_tmpl': 'HTML-Parser-%s.tar.gz' % html_parser_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/G/GA/GAAS/'], + }), + ('File::Listing', file_listing_version, { + 'source_tmpl': 'File-Listing-%s.tar.gz' % file_listing_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/G/GA/GAAS/'], + }), + ('AnyEvent', anyevent_version, { + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/M/ML/MLEHMANN/'], + }), + ('Devel::CheckCompiler', devel_checkcompiler_version, { + 'source_tmpl': 'Devel-CheckCompiler-%s.tar.gz' % devel_checkcompiler_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/S/SY/SYOHEX'], + }), + ('File::Copy::Recursive', file_copy_recursive_version, { + 'source_tmpl': 'File-Copy-Recursive-%s.tar.gz' % file_copy_recursive_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/D/DM/DMUEY/'], + }), + ('Cwd::Guard', cwd_guard_version, { + 'source_tmpl': 'Cwd-Guard-%s.tar.gz' % cwd_guard_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/K/KA/KAZEBURO'], + }), + ('Module::Build::XSUtil', module_build_xsutil_version, { + 'source_tmpl': 'Module-Build-XSUtil-%s.tar.gz' % module_build_xsutil_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/H/HI/HIDEAKIO/'], + }), + ('LWP', lwp_version, { + 'source_tmpl': 'libwww-perl-%s.tar.gz' % lwp_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/O/OA/OALDERS/'], + }), + ('Fennec::Lite', fennec_lite_version, { + 'source_tmpl': 'Fennec-Lite-%s.tar.gz' % fennec_lite_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/E/EX/EXODIST/'], + }), + ('aliased', aliased_version, { + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/E/ET/ETHER/'], + }), + ('Meta::Builder', meta_builder_version, { + 'source_tmpl': 'Meta-Builder-%s.tar.gz' % meta_builder_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/E/EX/EXODIST/'], + }), + ('Exporter::Declare', exporter_declare_version, { + 'source_tmpl': 'Exporter-Declare-%s.tar.gz' % exporter_declare_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/E/EX/EXODIST/'], + }), + ('Mock::Quick', mock_quick_version, { + 'source_tmpl': 'Mock-Quick-%s.tar.gz' % mock_quick_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/E/EX/EXODIST/'], + }), + ('Test::Exception::LessClever', test_exception_lessclever_version, { + 'source_tmpl': 'Test-Exception-LessClever-%s.tar.gz' % test_exception_lessclever_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/E/ET/ETHER/'], + }), + ('Test::LeakTrace', test_leaktrace_version, { + 'source_tmpl': 'Test-LeakTrace-%s.tar.gz' % test_leaktrace_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/G/GF/GFUJI/'], + }), + ('Mouse', mouse_version, { + 'source_tmpl': 'Mouse-v%s.tar.gz' % mouse_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/S/SY/SYOHEX/'], + }), + ('XML::NamespaceSupport', xml_namespacesupport_version, { + 'source_tmpl': 'XML-NamespaceSupport-%s.tar.gz' % xml_namespacesupport_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/P/PE/PERIGRIN/'], + }), + ('XML::SAX::Base', xml_sax_base_version, { + 'source_tmpl': 'XML-SAX-Base-%s.tar.gz' % xml_sax_base_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/G/GR/GRANTM/'], + }), + ('XML::SAX', xml_sax_version, { + 'source_tmpl': 'XML-SAX-%s.tar.gz' % xml_sax_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/G/GR/GRANTM/'], + }), + ('XML::LibXML', xml_libxml_version, { + 'source_tmpl': 'XML-LibXML-%s.tar.gz' % xml_libxml_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/S/SH/SHLOMIF/'], + }), + ('Clone', clone_version, { + 'source_tmpl': 'Clone-%s.tar.gz' % clone_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/G/GA/GARU'], + }), + ('Parallel::ForkManager', parallel_forkmanager_version, { + 'source_tmpl': 'Parallel-ForkManager-%s.tar.gz' % parallel_forkmanager_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/Y/YA/YANICK/'], + }), + + ('Config::General', config_general_version, { + 'source_tmpl': 'Config-General-%s.tar.gz' % config_general_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/T/TL/TLINDEN/'], + }), + ('Test::Simple', test_simple_version, { + 'source_tmpl': 'Test-Simple-%s.tar.gz' % test_simple_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/E/EX/EXODIST/'], + }), + + # For Genemark + ('YAML', yaml_version, { + 'source_tmpl': 'YAML-%s.tar.gz' % yaml_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/I/IN/INGY/'], + }), + ('Hash::Merge', hash_merge_version, { + 'source_tmpl': 'Hash-Merge-%s.tar.gz' % hash_merge_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/R/RE/REHSACK/'], + }), + ('Data::Dumper', data_dumper_version, { + 'source_tmpl': 'Data-Dumper-%s.tar.gz' % data_dumper_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/S/SM/SMUELLER/'], + }), + ('Object::InsideOut', object_insideout_version, { + 'source_tmpl': 'Object-InsideOut-%s.tar.gz' % object_insideout_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/J/JD/JDHEDDEN/'], + }), + ('Logger::Simple', logger_simple_version, { + 'source_tmpl': 'Logger-Simple-%s.tar.gz' % logger_simple_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/T/TS/TSTANLEY/'], + }), + ('File::Path', file_path_version, { + 'source_tmpl': 'File-Path-%s.tar.gz' % file_path_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/R/RI/RICHE/'], + }), + ('File::Spec', pathtools_version, { + 'source_tmpl': 'PathTools-%s.tar.gz' % pathtools_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/R/RJ/RJBS/'], + }), + ('File::Temp', file_temp_version, { + 'source_tmpl': 'File-Temp-%s.tar.gz' % file_temp_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/D/DA/DAGOLDEN/'], + }), + ('XSLoader', xsloader_version, { + 'source_tmpl': 'XSLoader-%s.tar.gz' % xsloader_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/S/SA/SAPER/'], + }), + ('Carp', carp_version, { + 'source_tmpl': 'Carp-%s.tar.gz' % carp_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/R/RJ/RJBS/'], + }), + ('Storable', storable_version, { + 'source_tmpl': 'Storable-%s.tar.gz' % storable_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/A/AM/AMS/'], + }), + + ('Font::TTF', font_ttf_version, { + 'source_tmpl': 'Font-TTF-%s.tar.gz' % font_ttf_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/B/BH/BHALLISSY'], + }), + ('IO::Tty', io_tty_version, { + 'source_tmpl': 'IO-Tty-%s.tar.gz' % io_tty_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/T/TO/TODDR/'], + }), + ('Math::Bezier', math_bezier_version, { + 'source_tmpl': 'Math-Bezier-%s.tar.gz' % math_bezier_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/A/AB/ABW'], + }), + ('IPC::Run', ipc_run_version, { + 'source_tmpl': 'IPC-Run-%s.tar.gz' % ipc_run_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/T/TO/TODDR/'], + }), + ('Math::Round', math_round_version, { + 'source_tmpl': 'Math-Round-%s.tar.gz' % math_round_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/G/GR/GROMMEL'], + }), + ('B::LintSubs', b_lintsubs_version, { + 'source_tmpl': 'B-LintSubs-%s.tar.gz' % b_lintsubs_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/P/PE/PEVANS'], + }), + ('Math::VecStat', math_vecstat_version, { + 'source_tmpl': 'Math-VecStat-%s.tar.gz' % math_vecstat_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/A/AS/ASPINELLI'], + }), + ('Test::Most', test_most_version, { + 'source_tmpl': 'Test-Most-%s.tar.gz' % test_most_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/O/OV/OVID/'], + }), + ('Readonly', readonly_version, { + 'source_tmpl': 'Readonly-%s.tar.gz' % readonly_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/S/SA/SANKO/'], + }), + ('Regexp::Common', regexp_common_version, { + 'source_tmpl': 'Regexp-Common-%s.tar.gz' % regexp_common_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/A/AB/ABIGAIL'], + }), + ('Want', want_version, { + 'source_tmpl': 'Want-%s.tar.gz' % want_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/R/RO/ROBIN/'], + }), + ('DBD::SQLite', dbd_sqlite_version, { + 'source_tmpl': 'DBD-SQLite-%s.tar.gz' % dbd_sqlite_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/I/IS/ISHIGAKI/'], + }), + ('Set::IntSpan', set_intspan_version, { + 'source_tmpl': 'Set-IntSpan-%s.tar.gz' % set_intspan_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/S/SW/SWMCD'], + }), + ('forks', forks_version, { + 'source_tmpl': 'forks-%s.tar.gz' % forks_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/R/RY/RYBSKEJ/'], + }), + ('File::Which', file_which_version, { + 'source_tmpl': 'File-Which-%s.tar.gz' % file_which_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/P/PL/PLICEASE/'], + }), + ('Perl::Unsafe::Signals', perl_unsafe_signals_version, { + 'source_tmpl': 'Perl-Unsafe-Signals-%s.tar.gz' % perl_unsafe_signals_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/R/RG/RGARCIA/'], + }), + ('Bit::Vector', bit_vector_version, { + 'source_tmpl': 'Bit-Vector-%s.tar.gz' % bit_vector_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/S/ST/STBEY/'], + }), + ('Parse::RecDescent', parse_recdescent_version, { + 'source_tmpl': 'Parse-RecDescent-%s.tar.gz' % parse_recdescent_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/J/JT/JTBRAUN/'], + }), + ('Inline', inline_version, { + 'source_tmpl': 'Inline-%s.tar.gz' % inline_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/I/IN/INGY/'], + }), + ('File::ShareDir::Install', file_sharedir_install_version, { + 'source_tmpl': 'File-ShareDir-Install-%s.tar.gz' % file_sharedir_install_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/E/ET/ETHER/'], + }), + ('Inline::C', inline_c_version, { + 'source_tmpl': 'Inline-C-%s.tar.gz' % inline_c_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/I/IN/INGY/'], + }), + ('IO::All', io_all_version, { + 'source_tmpl': 'IO-All-%s.tar.gz' % io_all_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/I/IN/INGY/'], + }), + ('IO::Prompt', io_prompt_version, { + 'source_tmpl': 'IO-Prompt-%s.tar.gz' % io_prompt_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/D/DC/DCONWAY/'], + }), + ('Getopt::Long', getopt_long_version, { + 'source_tmpl': 'Getopt-Long-%s.tar.gz' % getopt_long_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/J/JV/JV/'], + }), + ('AppConfig', appconfig_version, { + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/N/NE/NEILB/'], + }), + ('Archive::Extract', archive_extract_version, { + 'source_tmpl': 'Archive-Extract-%s.tar.gz' % archive_extract_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/B/BI/BINGOS/'], + }), + ('Archive::Tar', archive_tar_version, { + 'source_tmpl': 'Archive-Tar-%s.tar.gz' % archive_tar_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/B/BI/BINGOS/'], + }), + ('Archive::Zip', archive_zip_version, { + 'source_tmpl': 'Archive-Zip-%s.tar.gz' % archive_zip_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/P/PH/PHRED/'], + }), + ('Authen::SASL', authen_sasl_version, { + 'source_tmpl': 'Authen-SASL-%s.tar.gz' % authen_sasl_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/G/GB/GBARR/'], + }), + ('B::Lint', b_lint_version, { + 'source_tmpl': 'B-Lint-%s.tar.gz' % b_lint_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/R/RJ/RJBS/'], + }), + ('Class::Accessor', class_accessor_version, { + 'source_tmpl': 'Class-Accessor-%s.tar.gz' % class_accessor_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/K/KA/KASEI/'], + }), + ('Class::DBI', class_dbi_version, { + 'source_tmpl': 'Class-DBI-v%s.tar.gz' % class_dbi_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/T/TM/TMTM/'], + }), + ('Class::Inspector', class_inspector_version, { + 'source_tmpl': 'Class-Inspector-%s.tar.gz' % class_inspector_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/P/PL/PLICEASE/'], + }), + ('Class::ISA', class_isa_version, { + 'source_tmpl': 'Class-ISA-%s.tar.gz' % class_isa_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/S/SM/SMUELLER/'], + }), + ('Class::Trigger', class_trigger_version, { + 'source_tmpl': 'Class-Trigger-%s.tar.gz' % class_trigger_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/M/MI/MIYAGAWA/'], + }), + ('CPANPLUS', cpanplus_version, { + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/B/BI/BINGOS/'], + }), + ('Data::Grove', libxml_perl_version, { + 'source_tmpl': 'libxml-perl-%s.tar.gz' % libxml_perl_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/K/KM/KMACLEOD/'], + }), + ('Data::UUID', data_uuid_version, { + 'source_tmpl': 'Data-UUID-%s.tar.gz' % data_uuid_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/R/RJ/RJBS/'], + }), + ('Date::Language', timedate_version, { + 'source_tmpl': 'TimeDate-%s.tar.gz' % timedate_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/G/GB/GBARR/'], + }), + ('Date::Handler', date_handler_version, { + 'source_tmpl': 'Date-Handler-%s.tar.gz' % date_handler_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/B/BB/BBEAUSEJ/'], + }), + ('SQL::Statement', sql_statement_version, { + 'source_tmpl': 'SQL-Statement-%s.tar.gz' % sql_statement_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/R/RE/REHSACK/'], + }), + ('Module::Pluggable', module_pluggable_version, { + 'source_tmpl': 'Module-Pluggable-%s.tar.gz' % module_pluggable_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/S/SI/SIMONW/'], + }), + ('Digest::HMAC', digest_hmac_version, { + 'source_tmpl': 'Digest-HMAC-%s.tar.gz' % digest_hmac_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/G/GA/GAAS/'], + }), + ('Digest::SHA1', digest_sha1_version, { + 'source_tmpl': 'Digest-SHA1-%s.tar.gz' % digest_sha1_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/G/GA/GAAS/'], + }), + ('Email::Date::Format', email_date_format_version, { + 'source_tmpl': 'Email-Date-Format-%s.tar.gz' % email_date_format_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/R/RJ/RJBS/'], + }), + ('Error', error_version, { + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/S/SH/SHLOMIF/'], + }), + ('Expect', expect_pm_version, { + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/R/RG/RGIERSIG/'], + }), + ('File::CheckTree', file_checktree_version, { + 'source_tmpl': 'File-CheckTree-%s.tar.gz' % file_checktree_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/R/RJ/RJBS/'], + }), + ('FreezeThaw', freezethaw_version, { + 'source_tmpl': 'FreezeThaw-%s.tar.gz' % freezethaw_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/I/IL/ILYAZ/modules/'], + }), + ('Git', git_version, { + 'source_tmpl': 'Git-%s.tar.gz' % git_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/M/MS/MSOUTH/'], + }), + ('GO::Utils', go_perl_version, { + 'source_tmpl': 'go-perl-%s.tar.gz' % go_perl_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/C/CM/CMUNGALL/'], + }), + ('GO', go_db_perl_version, { + 'source_tmpl': 'go-db-perl-%s.tar.gz' % go_db_perl_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/S/SJ/SJCARBON/'], + }), + + ('HTML::Form', html_form_version, { + 'source_tmpl': 'HTML-Form-%s.tar.gz' % html_form_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/G/GA/GAAS/'], + }), + ('HTTP::Cookies', http_cookies_version, { + 'source_tmpl': 'HTTP-Cookies-%s.tar.gz' % http_cookies_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/G/GA/GAAS/'], + }), + ('HTTP::Daemon', http_daemon_version, { + 'source_tmpl': 'HTTP-Daemon-%s.tar.gz' % http_daemon_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/G/GA/GAAS/'], + }), + ('HTTP::Negotiate', http_negotiate_version, { + 'source_tmpl': 'HTTP-Negotiate-%s.tar.gz' % http_negotiate_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/G/GA/GAAS/'], + }), + ('IO::Stringy', io_stringy_version, { + 'source_tmpl': 'IO-stringy-%s.tar.gz' % io_stringy_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/D/DS/DSKOLL/'], + }), + ('IO::Socket::SSL', io_socket_ssl_version, { + 'source_tmpl': 'IO-Socket-SSL-%s.tar.gz' % io_socket_ssl_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/S/SU/SULLR/'], + }), + ('JSON', json_version, { + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/M/MA/MAKAMAKA/'], + }), + ('Log::Message', log_message_version, { + 'source_tmpl': 'Log-Message-%s.tar.gz' % log_message_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/B/BI/BINGOS/'], + }), + ('Log::Message::Simple', log_message_simple_version, { + 'source_tmpl': 'Log-Message-Simple-%s.tar.gz' % log_message_simple_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/B/BI/BINGOS/'], + }), + ('Mail::Util', mailtools_version, { + 'source_tmpl': 'MailTools-%s.tar.gz' % mailtools_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/M/MA/MARKOV/'], + }), + ('MIME::Types', mime_types_version, { + 'source_tmpl': 'MIME-Types-%s.tar.gz' % mime_types_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/M/MA/MARKOV/'], + }), + ('MIME::Lite', mime_lite_version, { + 'source_tmpl': 'MIME-Lite-%s.tar.gz' % mime_lite_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/R/RJ/RJBS/'], + }), + ('Net::HTTP', net_http_version, { + 'source_tmpl': 'Net-HTTP-%s.tar.gz' % net_http_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/O/OA/OALDERS/'], + }), + ('Net::SMTP::SSL', net_smtp_ssl_version, { + 'source_tmpl': 'Net-SMTP-SSL-%s.tar.gz' % net_smtp_ssl_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/R/RJ/RJBS/'], + }), + ('Object::Accessor', object_accessor_version, { + 'source_tmpl': 'Object-Accessor-%s.tar.gz' % object_accessor_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/B/BI/BINGOS/'], + }), + ('Pod::LaTeX', pod_latex_version, { + 'source_tmpl': 'Pod-LaTeX-%s.tar.gz' % pod_latex_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/T/TJ/TJENNESS/'], + }), + ('Pod::Plainer', pod_plainer_version, { + 'source_tmpl': 'Pod-Plainer-%s.tar.gz' % pod_plainer_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/R/RM/RMBARKER/'], + }), + ('Pod::POM', pod_pom_version, { + 'source_tmpl': 'Pod-POM-%s.tar.gz' % pod_pom_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/N/NE/NEILB/'], + }), + ('Shell', shell_version, { + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/F/FE/FERREIRA/'], + }), + ('Statistics::Descriptive', statistics_descriptive_version, { + 'source_tmpl': 'Statistics-Descriptive-%s.tar.gz' % statistics_descriptive_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/S/SH/SHLOMIF/'], + }), + ('Switch', switch_version, { + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/C/CH/CHORNY/'], + }), + ('Template', template_toolkit_version, { + 'source_tmpl': 'Template-Toolkit-%s.tar.gz' % template_toolkit_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/A/AB/ABW/'], + }), + ('Term::UI', term_ui_version, { + 'source_tmpl': 'Term-UI-%s.tar.gz' % term_ui_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/B/BI/BINGOS/'], + }), + ('Text::Iconv', text_iconv_version, { + 'source_tmpl': 'Text-Iconv-%s.tar.gz' % text_iconv_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/M/MP/MPIOTR/'], + }), + ('Text::Soundex', text_soundex_version, { + 'source_tmpl': 'Text-Soundex-%s.tar.gz' % text_soundex_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/R/RJ/RJBS/'], + }), + ('Time::Piece', time_piece_version, { + 'source_tmpl': 'Time-Piece-%s.tar.gz' % time_piece_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/E/ES/ESAYM/'], + }), + ('Time::Piece::MySQL', time_piece_mysql_version, { + 'source_tmpl': 'Time-Piece-MySQL-%s.tar.gz' % time_piece_mysql_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/K/KA/KASEI/'], + }), + ('UNIVERSAL::moniker', universal_moniker_version, { + 'source_tmpl': 'UNIVERSAL-moniker-%s.tar.gz' % universal_moniker_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/K/KA/KASEI/'], + }), + ('version', version_version, { + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/J/JP/JPEACOCK/'], + }), + ('WWW::RobotRules', www_robotrules_version, { + 'source_tmpl': 'WWW-RobotRules-%s.tar.gz' % www_robotrules_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/G/GA/GAAS/'], + }), + ('XML::SAX::Writer', xml_sax_writer_version, { + 'source_tmpl': 'XML-SAX-Writer-%s.tar.gz' % xml_sax_writer_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/P/PE/PERIGRIN/'], + }), + ('XML::Simple', xml_simple_version, { + 'source_tmpl': 'XML-Simple-%s.tar.gz' % xml_simple_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/G/GR/GRANTM/'], + }), + ('XML::XPath', xml_xpath_version, { + 'source_tmpl': 'XML-XPath-%s.tar.gz' % xml_xpath_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/M/MA/MANWAR/'], + }), + ('DBD::AnyData', dbd_anydata_version, { + 'source_tmpl': 'DBD-AnyData-%s.tar.gz' % dbd_anydata_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/R/RE/REHSACK/'], + }), + ('Ima::DBI', ima_dbi_version, { + 'source_tmpl': 'Ima-DBI-%s.tar.gz' % ima_dbi_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/P/PE/PERRIN/'], + }), + ('DBIx::ContextualFetch', dbix_contextualfetch_version, { + 'source_tmpl': 'DBIx-ContextualFetch-%s.tar.gz' % dbix_contextualfetch_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/T/TM/TMTM/'], + }), + ('DBIx::Simple', dbix_simple_version, { + 'source_tmpl': 'DBIx-Simple-%s.tar.gz' % dbix_simple_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/J/JU/JUERD/'], + }), + ('Term::ReadKey', term_readkey_version, { + 'source_tmpl': 'TermReadKey-%s.tar.gz' % term_readkey_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/J/JS/JSTOWE/'], +# 'patches': ['TermReadKey-2.32.patch'], + }), + ('Moo', moo_version, { + 'source_tmpl': 'Moo-%s.tar.gz' % moo_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/H/HA/HAARG/'], + }), + ('strictures', strictures_version, { + 'source_tmpl': 'strictures-%s.tar.gz' % strictures_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/H/HA/HAARG/'], + }), + ('File::Find::Rule::Perl', file_find_rule_perl_version, { + 'source_tmpl': 'File-Find-Rule-Perl-%s.tar.gz' % file_find_rule_perl_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/E/ET/ETHER/'], + }), + ('Test::Version', test_version_version, { + 'source_tmpl': 'Test-Version-%s.tar.gz' % test_version_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/P/PL/PLICEASE/'], + }), + ('Test::Harness', test_harness_version, { + 'source_tmpl': 'Test-Harness-%s.tar.gz' % test_harness_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/L/LE/LEONT/'], + }), + ('Import::Into', import_into_version, { + 'source_tmpl': 'Import-Into-%s.tar.gz' % import_into_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/H/HA/HAARG/'], + }), + ('File::Find::Rule', file_find_rule_version, { + 'source_tmpl': 'File-Find-Rule-%s.tar.gz' % file_find_rule_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/R/RC/RCLAMP/'], + }), + ('Data::Section::Simple', data_section_simple_version, { + 'source_tmpl': 'Data-Section-Simple-%s.tar.gz' % data_section_simple_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/M/MI/MIYAGAWA/'], + }), + ('Text::Glob', text_glob_version, { + 'source_tmpl': 'Text-Glob-%s.tar.gz' % text_glob_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/R/RC/RCLAMP/'], + }), + ('Number::Compare', number_compare_version, { + 'source_tmpl': 'Number-Compare-%s.tar.gz' % number_compare_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/R/RC/RCLAMP/'], + }), + ('IPC::Run3', ipc_run3_version, { + 'source_tmpl': 'IPC-Run3-%s.tar.gz' % ipc_run3_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/R/RJ/RJBS/'], + }), + ('Set::Array', set_array_version, { + 'source_tmpl': 'Set-Array-%s.tgz' % set_array_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/R/RS/RSAVAGE/'], + }), + ('Bundle::BioPerl', bundle_bioperl_version, { + 'source_tmpl': 'Bundle-BioPerl-%s.tar.gz' % bundle_bioperl_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/C/CJ/CJFIELDS/'], + }), + ('Algorithm::Munkres', algorithm_munkres_version, { + 'source_tmpl': 'Algorithm-Munkres-%s.tar.gz' % algorithm_munkres_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/T/TP/TPEDERSE/'], + }), +# Lots of deps: Types::Standard etc. +# ('Array::Compare', array_compare_version, { +# 'source_tmpl': 'Array-Compare-v%s.tar.gz' % array_compare_version, +# 'source_urls': ['http://search.cpan.org/CPAN/authors/id/D/DA/DAVECROSS/'], +# }), + ('Graph', graph_version, { + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/J/JH/JHI/'], + }), + ('Set::Scalar', set_scalar_version, { + 'source_tmpl': 'Set-Scalar-%s.tar.gz' % set_scalar_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/D/DA/DAVIDO/'], + }), + ('CGI', cgi_version, { + 'source_tmpl': 'CGI-%s.tar.gz' % cgi_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/L/LE/LEEJO/'], + }), + ('Bio::Phylo', bio_phylo_version, { + 'source_tmpl': 'Bio-Phylo-%s.tar.gz' % bio_phylo_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/R/RV/RVOSA/'], + }), + ('SVG', svg_version, { + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/S/SZ/SZABGAB/'], + }), + ('XML::DOM', xml_dom_version, { + 'source_tmpl': 'XML-DOM-%s.tar.gz' % xml_dom_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/T/TJ/TJMATHER/'], + }), + ('XML::DOM::XPath', xml_dom_xpath_version, { + 'source_tmpl': 'XML-DOM-XPath-%s.tar.gz' % xml_dom_xpath_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/M/MI/MIROD/'], + }), + ('XML::Parser::PerlSAX', libxml_perl_version, { + 'source_tmpl': 'libxml-perl-%s.tar.gz' % libxml_perl_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/K/KM/KMACLEOD/'], + }), + ('XML::Parser', xml_parser_version, { + 'source_tmpl': 'XML-Parser-%s.tar.gz' % xml_parser_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/T/TO/TODDR/'], + }), + ('XML::Twig', xml_twig_version, { + 'source_tmpl': 'XML-Twig-%s.tar.gz' % xml_twig_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/M/MI/MIROD/'], + }), + ('XML::Writer', xml_writer_version, { + 'source_tmpl': 'XML-Writer-%s.tar.gz' % xml_writer_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/J/JO/JOSEPHW/'], + }), + ('Spreadsheet::ParseExcel', spreadsheet_parseexcel_version, { + 'source_tmpl': 'Spreadsheet-ParseExcel-%s.tar.gz' % spreadsheet_parseexcel_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/D/DO/DOUGW/'], + }), + ('Convert::Binary::C', convert_binary_c_version, { + 'source_tmpl': 'Convert-Binary-C-%s.tar.gz' % convert_binary_c_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/M/MH/MHX/'], + }), + ('Sys::SigAction.pm', sys_sigaction_version, { + 'source_tmpl': 'Sys-SigAction-%s.tar.gz' % sys_sigaction_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/L/LB/LBAXTER/'], + }), + ('Acme::Damn', acme_damn_version, { + 'source_tmpl': 'Acme-Damn-%s.tar.gz' % acme_damn_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/I/IB/IBB/'], + }), + ('Set::IntervalTree', set_intervaltree_version, { + 'source_tmpl': 'Set-IntervalTree-%s.tar.gz' % set_intervaltree_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/B/BE/BENBOOTH/'], + }), + ('HTML::TableExtract', html_tableextract_version, { + 'source_tmpl': 'HTML-TableExtract-%s.tar.gz' % html_tableextract_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/M/MS/MSISK/'], + }), + ('Bio::Perl', bioperl_version, { + 'source_tmpl': 'BioPerl-%s.tar.gz' % bioperl_version, + 'source_urls': ['http://www.cpan.org/modules/by-module/Bio/CJFIELDS/'], + }), + ('Bio::DB::Sam', bio_samtools_version, { + 'source_tmpl': 'Bio-SamTools-%s.tar.gz' % bio_samtools_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/L/LD/LDS/'], + 'patches': ['Perl_SamTools_include.patch'], + }), + ('File::Spec::Functions', pathtools_version, { + 'source_tmpl': 'PathTools-%s.tar.gz' % pathtools_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/R/RJ/RJBS/'], + }), + ('List::Util', scalar_list_utils_version, { + 'source_tmpl': 'Scalar-List-Utils-%s.tar.gz' % scalar_list_utils_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/P/PE/PEVANS/'], + }), + ('Module::Load::Conditional', module_load_conditional_version, { + 'source_tmpl': 'Module-Load-Conditional-%s.tar.gz' % module_load_conditional_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/B/BI/BINGOS/'], + }), + ('Scalar::Util::Numeric', scalar_util_numeric_version, { + 'source_tmpl': 'Scalar-Util-Numeric-%s.tar.gz' % scalar_util_numeric_version, + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/C/CH/CHOCOLATE/'], + }), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.19-gimkl-2017a.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.19-gimkl-2017a.eb new file mode 100644 index 0000000000..877294f204 --- /dev/null +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.19-gimkl-2017a.eb @@ -0,0 +1,21 @@ +name = 'SAMtools' +version = '0.1.19' + +homepage = 'http://www.htslib.org/' +description = """SAM Tools provide various utilities for manipulating alignments in the SAM format, + including sorting, merging, indexing and generating alignments in a per-position format.""" + +toolchain = {'name': 'gimkl', 'version': '2017a'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = [('http://sourceforge.net/projects/samtools/files/%(namelower)s/%(version)s', 'download')] + +patches = ['SAMtools-%(version)s_Makefile-ncurses.patch'] + +dependencies = [ + ('ncurses', '6.0'), + ('zlib', '1.2.11'), +] + +moduleclass = 'bio' -- GitLab From 64f3c1865cccb676751b50727b46261ffe3b92e5 Mon Sep 17 00:00:00 2001 From: Robert Date: Fri, 10 Mar 2017 12:25:14 +1030 Subject: [PATCH 0329/1603] Style fixed --- .../{PileOMeth-0.1.11.eb => PileOMeth-0.1.11-foss-2016b.eb} | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) rename easybuild/easyconfigs/p/PileOMeth/{PileOMeth-0.1.11.eb => PileOMeth-0.1.11-foss-2016b.eb} (87%) diff --git a/easybuild/easyconfigs/p/PileOMeth/PileOMeth-0.1.11.eb b/easybuild/easyconfigs/p/PileOMeth/PileOMeth-0.1.11-foss-2016b.eb similarity index 87% rename from easybuild/easyconfigs/p/PileOMeth/PileOMeth-0.1.11.eb rename to easybuild/easyconfigs/p/PileOMeth/PileOMeth-0.1.11-foss-2016b.eb index af4dcdba98..edf4ca1f37 100644 --- a/easybuild/easyconfigs/p/PileOMeth/PileOMeth-0.1.11.eb +++ b/easybuild/easyconfigs/p/PileOMeth/PileOMeth-0.1.11-foss-2016b.eb @@ -19,17 +19,17 @@ description = """PileOMeth processes a coordinate-sorted and indexed BAM or CRAM PileOMeth extracts per-base methylation metrics from them. PileOMeth requires an indexed fasta file containing the reference genome as well. """ -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'foss', 'version': '2016b'} sources = ['%(version)s.zip'] source_urls = ['https://github.com/dpryan79/PileOMeth/archive/'] dependencies = [ - ('HTSlib', '1.2.1', '', ('foss', '2017a')) + ('HTSlib', '1.2.1') ] files_to_copy = [ - (["PileOMeth"], "bin"), "*.c", "*.h" + (["PileOMeth"], "bin"), ] sanity_check_paths = { -- GitLab From c0d6c2c7a08c93059ce58bcb0970daac4738744d Mon Sep 17 00:00:00 2001 From: Robert Date: Fri, 10 Mar 2017 12:27:59 +1030 Subject: [PATCH 0330/1603] HTSlib added --- .../h/HTSlib/HTSlib-1.2.1-foss-2016b.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/h/HTSlib/HTSlib-1.2.1-foss-2016b.eb diff --git a/easybuild/easyconfigs/h/HTSlib/HTSlib-1.2.1-foss-2016b.eb b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.2.1-foss-2016b.eb new file mode 100644 index 0000000000..66babc415c --- /dev/null +++ b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.2.1-foss-2016b.eb @@ -0,0 +1,39 @@ +## +# This is a contribution from Phoenix HPC Service, The University of Adelaide, Australia +# Homepage: https://www.adelaide.edu.au/phoenix/ +# +# Copyright:: adelaide.edu.au/phoenix +# Authors:: Robert Qiao , Exe Escobedo +# License:: +# +# Acknowledgement:: +# Original Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +## + +easyblock = 'ConfigureMake' + +name = 'HTSlib' +version = '1.2.1' + +homepage = "http://www.htslib.org/" +description = """ A C library for reading/writing high-throughput sequencing data. + This package includes the utilities bgzip and tabix +""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s/'] +sources = [SOURCELOWER_TAR_BZ2] + +dependencies = [ + ('zlib', '1.2.8'), +] + +sanity_check_paths = { + 'files': ["bin/bgzip", "bin/tabix", "lib/libhts.so"], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From 94d3b3ff4ea86240bfbb2b4a06361d80410076f5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 10 Mar 2017 10:27:41 +0100 Subject: [PATCH 0331/1603] also copy Rfam_for_miRDeep.fa to mirDeep2 bin directory --- easybuild/easyconfigs/m/miRDeep2/miRDeep2-2.0.0.8-intel-2016b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/m/miRDeep2/miRDeep2-2.0.0.8-intel-2016b.eb b/easybuild/easyconfigs/m/miRDeep2/miRDeep2-2.0.0.8-intel-2016b.eb index de73467658..466cd04f4d 100644 --- a/easybuild/easyconfigs/m/miRDeep2/miRDeep2-2.0.0.8-intel-2016b.eb +++ b/easybuild/easyconfigs/m/miRDeep2/miRDeep2-2.0.0.8-intel-2016b.eb @@ -22,6 +22,7 @@ dependencies = [ install_cmd = "cp -a mirdeep*/src %(installdir)s/bin && chmod a+x %(installdir)s/bin/*.pl && " install_cmd += 'sed -i "s@#!/usr/bin/perl@#!$EBROOTPERL/bin/perl@" %(installdir)s/bin/*.pl && ' +install_cmd += "cp -a mirdeep*/Rfam_for_miRDeep.fa %(installdir)s/bin/ && " # scripts include a hard check for a file called 'install_successful' in the install directory... install_cmd += "touch %(installdir)s/install_successful" -- GitLab From e5f020956911d15e337bfa2f7a0fd140843d84f4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 10 Mar 2017 10:36:31 +0100 Subject: [PATCH 0332/1603] adding easyconfigs: requests-2.13.0-foss-2016b-Python-2.7.12.eb, requests-2.13.0-intel-2016b-Python-2.7.12.eb --- ...equests-2.13.0-foss-2016b-Python-2.7.12.eb | 24 +++++++++++++++++++ ...quests-2.13.0-intel-2016b-Python-2.7.12.eb | 24 +++++++++++++++++++ 2 files changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/r/requests/requests-2.13.0-foss-2016b-Python-2.7.12.eb create mode 100644 easybuild/easyconfigs/r/requests/requests-2.13.0-intel-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/r/requests/requests-2.13.0-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/r/requests/requests-2.13.0-foss-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..2546a92787 --- /dev/null +++ b/easybuild/easyconfigs/r/requests/requests-2.13.0-foss-2016b-Python-2.7.12.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'requests' +version = '2.13.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pypi.python.org/pypi/requests' +description = """Python http for humans""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('Python', '2.7.12'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/r/requests/requests-2.13.0-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/r/requests/requests-2.13.0-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..3d08d7d724 --- /dev/null +++ b/easybuild/easyconfigs/r/requests/requests-2.13.0-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'requests' +version = '2.13.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pypi.python.org/pypi/requests' +description = """Python http for humans""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('Python', '2.7.12'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'devel' -- GitLab From bdee396c0c108c92a0ea57f8540ed45571e7aa4f Mon Sep 17 00:00:00 2001 From: Yann Sagon Date: Fri, 10 Mar 2017 10:46:42 +0100 Subject: [PATCH 0333/1603] fix PYTHONPATH #4239 --- easybuild/easyconfigs/r/ROOT/ROOT-v5.30.06-goolf-1.4.10.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-v5.30.06-goolf-1.4.10.eb b/easybuild/easyconfigs/r/ROOT/ROOT-v5.30.06-goolf-1.4.10.eb index a2bf4ab035..b3d257608f 100644 --- a/easybuild/easyconfigs/r/ROOT/ROOT-v5.30.06-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/r/ROOT/ROOT-v5.30.06-goolf-1.4.10.eb @@ -33,4 +33,8 @@ configopts += ' --with-fftw3-incdir=$FFTW_INC_DIR --with-fftw3-libdir=$FFTW_LIB_ configopts += ' --with-xml-incdir=$EBROOTLIBXML2/include/libxml2/libxml --with-xml-libdir=$EBROOTLIBXML2/lib' configopts += ' --with-python-libdir=$EBROOTPYTHON/lib' +sanity_check_commands = ["python -c 'import ROOT'"] + +modextrapaths = {'PYTHONPATH': 'lib/root/'} + moduleclass = 'data' -- GitLab From 398343a8cdb5277b46ab50061bb26bf009c7126e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 10 Mar 2017 10:47:44 +0100 Subject: [PATCH 0334/1603] fix PostgreSQL homepage + minor style fixes --- .../p/PostgreSQL/PostgreSQL-9.3.5-intel-2014b.eb | 15 +++++++-------- .../PostgreSQL-9.4.7-intel-2016a-Python-2.7.11.eb | 10 ++++++---- .../PostgreSQL-9.5.2-intel-2016a-Python-2.7.11.eb | 10 ++++++---- .../PostgreSQL-9.6.0-intel-2016b-Python-2.7.12.eb | 8 ++++---- 4 files changed, 23 insertions(+), 20 deletions(-) diff --git a/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.3.5-intel-2014b.eb b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.3.5-intel-2014b.eb index b694510474..8b0668a68f 100644 --- a/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.3.5-intel-2014b.eb +++ b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.3.5-intel-2014b.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'PostgreSQL' version = '9.3.5' -homepage = 'http://www.mysql.com/' +homepage = 'https://www.postgresql.org/' description = """PostgreSQL is a powerful, open source object-relational database system. It is fully ACID compliant, has full support for foreign keys, joins, views, triggers, and stored procedures (in multiple languages). @@ -18,18 +18,17 @@ sources = [SOURCELOWER_TAR_GZ] toolchain = {'name': 'intel', 'version': '2014b'} -osdependencies = [('openssl-devel', 'libssl-dev')] - -java = 'Java' -javaver = '1.7.0_60' - dependencies = [ - (java, javaver, '', True), + ('Java', '1.7.0_60', '', True), ('libreadline', '6.3'), ('zlib', '1.2.8'), - # ('OpenSSL', '1.0.1i'), # OS dependency should be preferred for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1i'), ] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + builddependencies = [ ('Bison', '3.0.2'), ('flex', '2.5.39'), diff --git a/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.4.7-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.4.7-intel-2016a-Python-2.7.11.eb index a7d2b6c4a0..6302a94b89 100644 --- a/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.4.7-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.4.7-intel-2016a-Python-2.7.11.eb @@ -4,7 +4,7 @@ name = 'PostgreSQL' version = '9.4.7' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://www.mysql.com/' +homepage = 'https://www.postgresql.org/' description = """PostgreSQL is a powerful, open source object-relational database system. It is fully ACID compliant, has full support for foreign keys, joins, views, triggers, and stored procedures (in multiple languages). @@ -19,15 +19,17 @@ sources = [SOURCELOWER_TAR_GZ] toolchain = {'name': 'intel', 'version': '2016a'} -osdependencies = [('openssl-devel', 'libssl-dev')] - dependencies = [ ('libreadline', '6.3'), ('zlib', '1.2.8'), ('Python', '2.7.11'), - # ('OpenSSL', '1.0.1i'), # OS dependency should be preferred for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1i'), ] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + builddependencies = [ ('Bison', '3.0.4'), ('flex', '2.6.0'), diff --git a/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.5.2-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.5.2-intel-2016a-Python-2.7.11.eb index 46e78c9224..c49c4abba6 100644 --- a/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.5.2-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.5.2-intel-2016a-Python-2.7.11.eb @@ -4,7 +4,7 @@ name = 'PostgreSQL' version = '9.5.2' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://www.mysql.com/' +homepage = 'https://www.postgresql.org/' description = """PostgreSQL is a powerful, open source object-relational database system. It is fully ACID compliant, has full support for foreign keys, joins, views, triggers, and stored procedures (in multiple languages). @@ -19,15 +19,17 @@ sources = [SOURCELOWER_TAR_GZ] toolchain = {'name': 'intel', 'version': '2016a'} -osdependencies = [('openssl-devel', 'libssl-dev')] - dependencies = [ ('libreadline', '6.3'), ('zlib', '1.2.8'), ('Python', '2.7.11'), - # ('OpenSSL', '1.0.1i'), # OS dependency should be preferred for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1i'), ] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + builddependencies = [ ('Bison', '3.0.4'), ('flex', '2.6.0'), diff --git a/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.6.0-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.6.0-intel-2016b-Python-2.7.12.eb index 8f8750717c..67556bd516 100644 --- a/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.6.0-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.6.0-intel-2016b-Python-2.7.12.eb @@ -4,7 +4,7 @@ name = 'PostgreSQL' version = '9.6.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://www.mysql.com/' +homepage = 'https://www.postgresql.org/' description = """PostgreSQL is a powerful, open source object-relational database system. It is fully ACID compliant, has full support for foreign keys, joins, views, triggers, and stored procedures (in multiple languages). @@ -19,13 +19,13 @@ sources = [SOURCELOWER_TAR_GZ] toolchain = {'name': 'intel', 'version': '2016b'} -osdependencies = [('openssl-devel', 'libssl-dev')] - dependencies = [ ('libreadline', '6.3'), ('zlib', '1.2.8'), ('Python', '2.7.12'), - # ('OpenSSL', '1.0.1i'), # OS dependency should be preferred for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1i'), ] builddependencies = [ -- GitLab From 51bbcc9046b2b2825a455be134d694e4bb7ba615 Mon Sep 17 00:00:00 2001 From: Yann Sagon Date: Fri, 10 Mar 2017 10:48:03 +0100 Subject: [PATCH 0335/1603] fix PYTHONPATH #4239 --- easybuild/easyconfigs/r/ROOT/ROOT-v5.34.01-goolf-1.4.10.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.01-goolf-1.4.10.eb b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.01-goolf-1.4.10.eb index f56b457e0d..99a4b3d8d6 100644 --- a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.01-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.01-goolf-1.4.10.eb @@ -33,4 +33,8 @@ configopts += ' --with-xml-incdir=$EBROOTLIBXML2/include/libxml2/libxml --with-x configopts += ' --with-fftw3-incdir=$FFTW_INC_DIR --with-fftw3-libdir=$FFTW_LIB_DIR' configopts += ' --with-python-libdir=$EBROOTPYTHON/lib' +sanity_check_commands = ["python -c 'import ROOT'"] + +modextrapaths = {'PYTHONPATH': 'lib/root/'} + moduleclass = 'data' -- GitLab From 526cbfca04174161d69fd149e9e407c9e313cc56 Mon Sep 17 00:00:00 2001 From: Yann Sagon Date: Fri, 10 Mar 2017 10:50:15 +0100 Subject: [PATCH 0336/1603] fix PYTHONPATH #4239 --- easybuild/easyconfigs/r/ROOT/ROOT-v5.34.01-intel-2015a.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.01-intel-2015a.eb b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.01-intel-2015a.eb index a263fbc4af..c111bdfea0 100644 --- a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.01-intel-2015a.eb +++ b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.01-intel-2015a.eb @@ -38,4 +38,8 @@ configopts += ' --with-fftw3-incdir=$EBROOTIMKL/mkl/include/fftw --with-fftw3-li configopts += ' --with-xml-incdir=$EBROOTLIBXML2/include/libxml2/libxml --with-xml-libdir=$EBROOTLIBXML2/lib' configopts += ' --with-python-libdir=$EBROOTPYTHON/lib' +sanity_check_commands = ["python -c 'import ROOT'"] + +modextrapaths = {'PYTHONPATH': 'lib/root/'} + moduleclass = 'data' -- GitLab From 7c1a1484d29b05d06349acaa11a8829e87a1caf0 Mon Sep 17 00:00:00 2001 From: Yann Sagon Date: Fri, 10 Mar 2017 10:51:16 +0100 Subject: [PATCH 0337/1603] fix PYTHONPATH #4239 --- easybuild/easyconfigs/r/ROOT/ROOT-v5.34.13-ictce-5.5.0.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.13-ictce-5.5.0.eb b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.13-ictce-5.5.0.eb index 4f55d64d72..a90994c1ab 100644 --- a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.13-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.13-ictce-5.5.0.eb @@ -38,4 +38,8 @@ configopts += ' --with-fftw3-incdir=$MKLROOT/mkl/include/fftw --with-fftw3-libdi configopts += ' --with-xml-incdir=$EBROOTLIBXML2/include/libxml2/libxml --with-xml-libdir=$EBROOTLIBXML2/lib' configopts += ' --with-python-libdir=$EBROOTPYTHON/lib' +sanity_check_commands = ["python -c 'import ROOT'"] + +modextrapaths = {'PYTHONPATH': 'lib/root/'} + moduleclass = 'data' -- GitLab From eaa6b52cb1d25ecd15bb5ac553cbc3771b02b9fc Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 10 Mar 2017 10:53:30 +0100 Subject: [PATCH 0338/1603] adding easyconfigs: psycopg2-2.7-intel-2016b-Python-2.7.12.eb, psycopg2-2.7-foss-2016b-Python-2.7.12.eb, PostgreSQL-9.6.2-intel-2016b-Python-2.7.12.eb, PostgreSQL-9.6.2-foss-2016b-Python-2.7.12.eb --- ...stgreSQL-9.6.2-foss-2016b-Python-2.7.12.eb | 46 +++++++++++++++++++ ...tgreSQL-9.6.2-intel-2016b-Python-2.7.12.eb | 46 +++++++++++++++++++ .../psycopg2-2.7-foss-2016b-Python-2.7.12.eb | 25 ++++++++++ .../psycopg2-2.7-intel-2016b-Python-2.7.12.eb | 25 ++++++++++ 4 files changed, 142 insertions(+) create mode 100644 easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.6.2-foss-2016b-Python-2.7.12.eb create mode 100644 easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.6.2-intel-2016b-Python-2.7.12.eb create mode 100644 easybuild/easyconfigs/p/psycopg2/psycopg2-2.7-foss-2016b-Python-2.7.12.eb create mode 100644 easybuild/easyconfigs/p/psycopg2/psycopg2-2.7-intel-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.6.2-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.6.2-foss-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..537ebb2758 --- /dev/null +++ b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.6.2-foss-2016b-Python-2.7.12.eb @@ -0,0 +1,46 @@ +easyblock = 'ConfigureMake' + +name = 'PostgreSQL' +version = '9.6.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://www.postgresql.org/' +description = """PostgreSQL is a powerful, open source object-relational database system. + It is fully ACID compliant, has full support for foreign keys, + joins, views, triggers, and stored procedures (in multiple languages). + It includes most SQL:2008 data types, including INTEGER, + NUMERIC, BOOLEAN, CHAR, VARCHAR, DATE, INTERVAL, and TIMESTAMP. + It also supports storage of binary large objects, including pictures, + sounds, or video. It has native programming interfaces for C/C++, Java, + .Net, Perl, Python, Ruby, Tcl, ODBC, among others, and exceptional documentation.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['http://ftp.postgresql.org/pub/source/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('libreadline', '6.3'), + ('zlib', '1.2.8'), + ('Python', '2.7.12'), + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.2h'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +builddependencies = [ + ('Bison', '3.0.4'), + ('flex', '2.6.0'), + ('Perl', '5.24.0'), +] + +configopts = '--with-python --with-openssl' + +sanity_check_paths = { + 'files': ['bin/psql', 'bin/pg_config', 'lib/libpq.a', 'lib/libpq.%s' % SHLIB_EXT], + 'dirs': ['share/postgresql'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.6.2-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.6.2-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..9d98aaa673 --- /dev/null +++ b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.6.2-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,46 @@ +easyblock = 'ConfigureMake' + +name = 'PostgreSQL' +version = '9.6.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://www.postgresql.org/' +description = """PostgreSQL is a powerful, open source object-relational database system. + It is fully ACID compliant, has full support for foreign keys, + joins, views, triggers, and stored procedures (in multiple languages). + It includes most SQL:2008 data types, including INTEGER, + NUMERIC, BOOLEAN, CHAR, VARCHAR, DATE, INTERVAL, and TIMESTAMP. + It also supports storage of binary large objects, including pictures, + sounds, or video. It has native programming interfaces for C/C++, Java, + .Net, Perl, Python, Ruby, Tcl, ODBC, among others, and exceptional documentation.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['http://ftp.postgresql.org/pub/source/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('libreadline', '6.3'), + ('zlib', '1.2.8'), + ('Python', '2.7.12'), + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.2h'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +builddependencies = [ + ('Bison', '3.0.4'), + ('flex', '2.6.0'), + ('Perl', '5.24.0'), +] + +configopts = '--with-python --with-openssl' + +sanity_check_paths = { + 'files': ['bin/psql', 'bin/pg_config', 'lib/libpq.a', 'lib/libpq.%s' % SHLIB_EXT], + 'dirs': ['share/postgresql'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/p/psycopg2/psycopg2-2.7-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/psycopg2/psycopg2-2.7-foss-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..948a2bd8f6 --- /dev/null +++ b/easybuild/easyconfigs/p/psycopg2/psycopg2-2.7-foss-2016b-Python-2.7.12.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'psycopg2' +version = '2.7' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://initd.org/psycopg/' +description = "Psycopg is the most popular PostgreSQL adapter for the Python programming language." + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.12'), + ('PostgreSQL', '9.6.2', versionsuffix), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/psycopg2/psycopg2-2.7-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/psycopg2/psycopg2-2.7-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..3ac0511ce1 --- /dev/null +++ b/easybuild/easyconfigs/p/psycopg2/psycopg2-2.7-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'psycopg2' +version = '2.7' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://initd.org/psycopg/' +description = "Psycopg is the most popular PostgreSQL adapter for the Python programming language." + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.12'), + ('PostgreSQL', '9.6.2', versionsuffix), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'lib' -- GitLab From ba956899575eb5c51c8ef37229213151fdcafad1 Mon Sep 17 00:00:00 2001 From: Yann Sagon Date: Fri, 10 Mar 2017 10:54:43 +0100 Subject: [PATCH 0339/1603] fix PYTHONPATH #4239 --- .../r/ROOT/ROOT-v5.34.34-intel-2015b-Python-2.7.10.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.34-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.34-intel-2015b-Python-2.7.10.eb index 81b811dc89..80a084ac4d 100644 --- a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.34-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.34-intel-2015b-Python-2.7.10.eb @@ -36,4 +36,8 @@ configopts += ' --with-fftw3-incdir=$EBROOTIMKL/mkl/include/fftw --with-fftw3-li configopts += ' --with-xml-incdir=$EBROOTLIBXML2/include/libxml2/libxml --with-xml-libdir=$EBROOTLIBXML2/lib' configopts += ' --with-python-libdir=$EBROOTPYTHON/lib' +sanity_check_commands = ["python -c 'import ROOT'"] + +modextrapaths = {'PYTHONPATH': 'lib/root/'} + moduleclass = 'data' -- GitLab From 412ba617c5167ddb3593007a38cb0820f7c1702a Mon Sep 17 00:00:00 2001 From: Yann Sagon Date: Fri, 10 Mar 2017 10:56:02 +0100 Subject: [PATCH 0340/1603] fix PYTHONPATH #4239 --- .../r/ROOT/ROOT-v5.34.34-intel-2016a-Python-2.7.11.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.34-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.34-intel-2016a-Python-2.7.11.eb index 9dd615415d..718fb2f36d 100644 --- a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.34-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.34-intel-2016a-Python-2.7.11.eb @@ -54,4 +54,8 @@ configopts += ' --with-x11-libdir=$EBROOTLIBX11/lib --with-xext-libdir=$EBROOTLI configopts += ' --with-xft-libdir=$EBROOTLIBXFT/lib' configopts += ' --with-xpm-incdir=$EBROOTLIBXPM/include --with-xpm-libdir=$EBROOTLIBXPM/lib' +sanity_check_commands = ["python -c 'import ROOT'"] + +modextrapaths = {'PYTHONPATH': 'lib/root/'} + moduleclass = 'data' -- GitLab From 83e7f94a3fea698444e22140da2fc3b7eb97f119 Mon Sep 17 00:00:00 2001 From: Yann Sagon Date: Fri, 10 Mar 2017 10:56:58 +0100 Subject: [PATCH 0341/1603] fix PYTHONPATH #4239 --- .../r/ROOT/ROOT-v5.34.36-intel-2016a-Python-2.7.11.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.36-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.36-intel-2016a-Python-2.7.11.eb index b51c955db4..d8466b4858 100644 --- a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.36-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.36-intel-2016a-Python-2.7.11.eb @@ -54,4 +54,8 @@ configopts += ' --with-x11-libdir=$EBROOTLIBX11/lib --with-xext-libdir=$EBROOTLI configopts += ' --with-xft-libdir=$EBROOTLIBXFT/lib' configopts += ' --with-xpm-incdir=$EBROOTLIBXPM/include --with-xpm-libdir=$EBROOTLIBXPM/lib' +sanity_check_commands = ["python -c 'import ROOT'"] + +modextrapaths = {'PYTHONPATH': 'lib/root/'} + moduleclass = 'data' -- GitLab From e80f2a6d6aa67ace904af25a62af8efe2646b08a Mon Sep 17 00:00:00 2001 From: Yann Sagon Date: Fri, 10 Mar 2017 10:57:41 +0100 Subject: [PATCH 0342/1603] fix PYTHONPATH #4239 --- .../r/ROOT/ROOT-v6.06.02-intel-2016b-Python-2.7.12.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-v6.06.02-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/r/ROOT/ROOT-v6.06.02-intel-2016b-Python-2.7.12.eb index 2ddf7531c8..6d3d2000b8 100644 --- a/easybuild/easyconfigs/r/ROOT/ROOT-v6.06.02-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/r/ROOT/ROOT-v6.06.02-intel-2016b-Python-2.7.12.eb @@ -52,4 +52,8 @@ configopts += ' --with-x11-libdir=$EBROOTX11/lib --with-xext-libdir=$EBROOTLIBX1 configopts += ' --with-xft-libdir=$EBROOTX11/lib' configopts += ' --with-xpm-incdir=$EBROOTX11/include --with-xpm-libdir=$EBROOTX11/lib' +sanity_check_commands = ["python -c 'import ROOT'"] + +modextrapaths = {'PYTHONPATH': 'lib/'} + moduleclass = 'data' -- GitLab From 17e252c4b0b1c3fcb5830d97cb42bcd636e394f8 Mon Sep 17 00:00:00 2001 From: Yann Sagon Date: Fri, 10 Mar 2017 11:09:37 +0100 Subject: [PATCH 0343/1603] fix PYTHONPATH #4239 --- easybuild/easyconfigs/r/ROOT/ROOT-v5.34.18-ictce-5.5.0.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.18-ictce-5.5.0.eb b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.18-ictce-5.5.0.eb index a8ab1f540d..f662b0deda 100644 --- a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.18-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.18-ictce-5.5.0.eb @@ -42,4 +42,8 @@ configopts += ' --with-fftw3-incdir=$EBROOTIMKL/mkl/include/fftw --with-fftw3-li configopts += ' --with-xml-incdir=$EBROOTLIBXML2/include/libxml2/libxml --with-xml-libdir=$EBROOTLIBXML2/lib' configopts += ' --with-python-libdir=$EBROOTPYTHON/lib' +sanity_check_commands = ["python -c 'import ROOT'"] + +modextrapaths = {'PYTHONPATH': 'lib/root/'} + moduleclass = 'data' -- GitLab From e0b7bd52bbfda4bec6fca382313bd6b7825276ef Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 10 Mar 2017 11:11:42 +0100 Subject: [PATCH 0344/1603] fix location for Rfam_for_miRDeep.fa --- .../easyconfigs/m/miRDeep2/miRDeep2-2.0.0.8-intel-2016b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/miRDeep2/miRDeep2-2.0.0.8-intel-2016b.eb b/easybuild/easyconfigs/m/miRDeep2/miRDeep2-2.0.0.8-intel-2016b.eb index 466cd04f4d..83e5129dff 100644 --- a/easybuild/easyconfigs/m/miRDeep2/miRDeep2-2.0.0.8-intel-2016b.eb +++ b/easybuild/easyconfigs/m/miRDeep2/miRDeep2-2.0.0.8-intel-2016b.eb @@ -22,7 +22,7 @@ dependencies = [ install_cmd = "cp -a mirdeep*/src %(installdir)s/bin && chmod a+x %(installdir)s/bin/*.pl && " install_cmd += 'sed -i "s@#!/usr/bin/perl@#!$EBROOTPERL/bin/perl@" %(installdir)s/bin/*.pl && ' -install_cmd += "cp -a mirdeep*/Rfam_for_miRDeep.fa %(installdir)s/bin/ && " +install_cmd += "cp -a mirdeep*/Rfam_for_miRDeep.fa %(installdir)s && " # scripts include a hard check for a file called 'install_successful' in the install directory... install_cmd += "touch %(installdir)s/install_successful" -- GitLab From f2326dc17da8f931f34c89935d2c5572dd788645 Mon Sep 17 00:00:00 2001 From: Yann Sagon Date: Fri, 10 Mar 2017 11:16:20 +0100 Subject: [PATCH 0345/1603] fix PYTHONPATH #4239 --- easybuild/easyconfigs/r/ROOT/ROOT-v5.34.26-intel-2015a.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.26-intel-2015a.eb b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.26-intel-2015a.eb index 5801dbe265..6073d0e56c 100644 --- a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.26-intel-2015a.eb +++ b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.26-intel-2015a.eb @@ -56,4 +56,8 @@ configopts += ' --with-x11-libdir=$EBROOTLIBX11/lib --with-xext-libdir=$EBROOTLI configopts += ' --with-xft-libdir=$EBROOTLIBXFT/lib' configopts += ' --with-xpm-incdir=$EBROOTLIBXPM/include --with-xpm-libdir=$EBROOTLIBXPM/lib' +sanity_check_commands = ["python -c 'import ROOT'"] + +modextrapaths = {'PYTHONPATH': 'lib/'} + moduleclass = 'data' -- GitLab From 7487ef4bd7ec0e279be25ab423ec2b9be38f1e38 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 10 Mar 2017 11:21:12 +0100 Subject: [PATCH 0346/1603] detect use of '$root', which is not compatible with module files in Lua syntax --- test/easyconfigs/easyconfigs.py | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 551695c259..993e9395ba 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -235,6 +235,11 @@ def template_easyconfig_test(self, spec): self.assertTrue(name, app.name) self.assertTrue(ec['version'], app.version) + # make sure that $root is not used, since it is not compatible with module files in Lua syntax + res = re.findall('.*\$root.*', ec.rawtxt, re.M) + error_msg = "Found use of '$root', not compatible with modules in Lua syntax, use '%%(installdir)s' instead: %s" + self.assertFalse(res, error_msg % res) + # make sure all patch files are available specdir = os.path.dirname(spec) specfn = os.path.basename(spec) -- GitLab From 667725596613b792b086d6356b7e6cdc7c22326a Mon Sep 17 00:00:00 2001 From: Pablo Escobar Lopez Date: Fri, 10 Mar 2017 11:57:26 +0100 Subject: [PATCH 0347/1603] added $CXXFLAGS --- .../disambiguate-1.0.0-goolf-1.7.20-Python-2.7.11.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/disambiguate/disambiguate-1.0.0-goolf-1.7.20-Python-2.7.11.eb b/easybuild/easyconfigs/d/disambiguate/disambiguate-1.0.0-goolf-1.7.20-Python-2.7.11.eb index 816f774c49..7de0a8ea92 100644 --- a/easybuild/easyconfigs/d/disambiguate/disambiguate-1.0.0-goolf-1.7.20-Python-2.7.11.eb +++ b/easybuild/easyconfigs/d/disambiguate/disambiguate-1.0.0-goolf-1.7.20-Python-2.7.11.eb @@ -27,7 +27,7 @@ dependencies = [ # this application provides a python implementation and a C++ implementation # in the postinstallcmds we compile the C++ version postinstallcmds = [ - '$CXX -I$EBROOTBAMTOOLS/include -I./ -L$EBROOTBAMTOOLS/lib -o disambiguate dismain.cpp -lz -lbamtools', + '$CXX $CXXFLAGS -I$EBROOTBAMTOOLS/include -I./ -L$EBROOTBAMTOOLS/lib -o disambiguate dismain.cpp -lz -lbamtools', 'cp disambiguate %(installdir)s/bin/' ] -- GitLab From 75998c8fd4ad81ef8b43d41152800e059a3adc88 Mon Sep 17 00:00:00 2001 From: Robert Date: Fri, 10 Mar 2017 21:55:20 +1030 Subject: [PATCH 0348/1603] style fixed --- easybuild/easyconfigs/h/HTSlib/HTSlib-1.2.1-foss-2016b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/h/HTSlib/HTSlib-1.2.1-foss-2016b.eb b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.2.1-foss-2016b.eb index 66babc415c..a58dae978a 100644 --- a/easybuild/easyconfigs/h/HTSlib/HTSlib-1.2.1-foss-2016b.eb +++ b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.2.1-foss-2016b.eb @@ -32,7 +32,7 @@ dependencies = [ ] sanity_check_paths = { - 'files': ["bin/bgzip", "bin/tabix", "lib/libhts.so"], + 'files': ["bin/bgzip", "bin/tabix", "lib/libhts.%s" % SHLIB_EXT], 'dirs': [], } -- GitLab From d1132ead52ea73d356501e39a3b9b603dffb4c0b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 10 Mar 2017 13:12:07 +0100 Subject: [PATCH 0349/1603] add requests and psycopg2 as dependencies for QGIS --- .../q/QGIS/QGIS-2.14.12-intel-2016b-Python-2.7.12.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/q/QGIS/QGIS-2.14.12-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/q/QGIS/QGIS-2.14.12-intel-2016b-Python-2.7.12.eb index 43245eb873..4878b7d629 100644 --- a/easybuild/easyconfigs/q/QGIS/QGIS-2.14.12-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/q/QGIS/QGIS-2.14.12-intel-2016b-Python-2.7.12.eb @@ -32,6 +32,8 @@ dependencies = [ ('QScintilla', '2.10', versionsuffix), ('GSL', '2.3'), ('QJson', '0.9.0'), + ('requests', '2.13.0', versionsuffix), + ('psycopg2', '2.7', versionsuffix), ] builddependencies = [ ('CMake', '3.7.2'), -- GitLab From 3d0c4aa8ab68e2d7fed93ce83b3f9652a7ad03f7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 10 Mar 2017 13:47:15 +0100 Subject: [PATCH 0350/1603] add requests and psycopg2 as dependencies for QGIS --- .../easyconfigs/q/QGIS/QGIS-2.18.4-foss-2016b-Python-2.7.12.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/q/QGIS/QGIS-2.18.4-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/q/QGIS/QGIS-2.18.4-foss-2016b-Python-2.7.12.eb index f6d58e7bf7..837899aa93 100644 --- a/easybuild/easyconfigs/q/QGIS/QGIS-2.18.4-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/q/QGIS/QGIS-2.18.4-foss-2016b-Python-2.7.12.eb @@ -32,6 +32,8 @@ dependencies = [ ('QScintilla', '2.10', versionsuffix), ('GSL', '2.3'), ('QJson', '0.9.0'), + ('requests', '2.13.0', versionsuffix), + ('psycopg2', '2.7', versionsuffix), ] builddependencies = [ ('CMake', '3.7.2'), -- GitLab From 674ce7782bb9b25ee3721dbe0017218df74cd31b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 10 Mar 2017 14:01:42 +0100 Subject: [PATCH 0351/1603] avoid use of '$root', replace with '%(installdir)s' --- .../a/ALPS/ALPS-2.3.0-foss-2016b-Python-2.7.12.eb | 10 +++------- .../a/ALPS/ALPS-2.3.0-foss-2016b-Python-3.5.2.eb | 10 +++------- .../MPJ-Express-0.44-foss-2016a-Java-1.8.0_92.eb | 11 +++-------- .../MPJ-Express-0.44-goolf-1.4.10-Java-1.7.0_75.eb | 11 +++-------- .../m/MView/MView-1.57-goolf-1.4.10-Perl-5.16.3.eb | 4 +--- .../easyconfigs/w/WEKA/WEKA-3.6.12-Java-1.7.0_80.eb | 4 +--- .../easyconfigs/w/WEKA/WEKA-3.7.0-Java-1.7.0_80.eb | 4 +--- 7 files changed, 15 insertions(+), 39 deletions(-) diff --git a/easybuild/easyconfigs/a/ALPS/ALPS-2.3.0-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/a/ALPS/ALPS-2.3.0-foss-2016b-Python-2.7.12.eb index 56456bbd62..4c41ac6ece 100644 --- a/easybuild/easyconfigs/a/ALPS/ALPS-2.3.0-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/a/ALPS/ALPS-2.3.0-foss-2016b-Python-2.7.12.eb @@ -25,16 +25,12 @@ dependencies = [ separate_build_dir = True -modextravars = { - 'ALPS_ROOT': '$root', -} -modextrapaths = { - 'PYTHONPATH': ['lib/'] -} - sanity_check_paths = { 'files': ['lib/libalps.%s' % SHLIB_EXT], 'dirs': ['include/alps', 'bin/', 'share/'], } +modextravars = {'ALPS_ROOT': '%(installdir)s'} +modextrapaths = {'PYTHONPATH': ['lib/']} + moduleclass = 'phys' diff --git a/easybuild/easyconfigs/a/ALPS/ALPS-2.3.0-foss-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/a/ALPS/ALPS-2.3.0-foss-2016b-Python-3.5.2.eb index f21285e25b..3d3e67389f 100644 --- a/easybuild/easyconfigs/a/ALPS/ALPS-2.3.0-foss-2016b-Python-3.5.2.eb +++ b/easybuild/easyconfigs/a/ALPS/ALPS-2.3.0-foss-2016b-Python-3.5.2.eb @@ -25,16 +25,12 @@ dependencies = [ separate_build_dir = True -modextravars = { - 'ALPS_ROOT': '$root', -} -modextrapaths = { - 'PYTHONPATH': ['lib/'] -} - sanity_check_paths = { 'files': ['lib/libalps.%s' % SHLIB_EXT], 'dirs': ['include/alps', 'bin/', 'share/'], } +modextravars = {'ALPS_ROOT': '%(installdir)s'} +modextrapaths = {'PYTHONPATH': ['lib']} + moduleclass = 'phys' diff --git a/easybuild/easyconfigs/m/MPJ-Express/MPJ-Express-0.44-foss-2016a-Java-1.8.0_92.eb b/easybuild/easyconfigs/m/MPJ-Express/MPJ-Express-0.44-foss-2016a-Java-1.8.0_92.eb index 21ae128381..6e3b23ba3c 100644 --- a/easybuild/easyconfigs/m/MPJ-Express/MPJ-Express-0.44-foss-2016a-Java-1.8.0_92.eb +++ b/easybuild/easyconfigs/m/MPJ-Express/MPJ-Express-0.44-foss-2016a-Java-1.8.0_92.eb @@ -31,17 +31,12 @@ postinstallcmds = [ "cd %(installdir)s/src/mpjdev/natmpjdev/lib/build && cmake .. && make && make install DESTDIR=%(installdir)s", ] -modextrapaths = { - 'CLASSPATH': 'lib', -} - -modextravars = { - 'MPJ_HOME': '$root', # MPJ_HOME points to install directory -} - sanity_check_paths = { 'files': ['lib/libnativempjdev.so', 'bin/mpjrun.sh'], 'dirs': [] } +modextravars = {'MPJ_HOME': '%(installdir)s'} +modextrapaths = {'CLASSPATH': 'lib'} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/MPJ-Express/MPJ-Express-0.44-goolf-1.4.10-Java-1.7.0_75.eb b/easybuild/easyconfigs/m/MPJ-Express/MPJ-Express-0.44-goolf-1.4.10-Java-1.7.0_75.eb index 41195e5042..8577e3deb4 100644 --- a/easybuild/easyconfigs/m/MPJ-Express/MPJ-Express-0.44-goolf-1.4.10-Java-1.7.0_75.eb +++ b/easybuild/easyconfigs/m/MPJ-Express/MPJ-Express-0.44-goolf-1.4.10-Java-1.7.0_75.eb @@ -34,17 +34,12 @@ postinstallcmds = [ "cd %(installdir)s/src/mpjdev/natmpjdev/lib/build && cmake .. && make && make install DESTDIR=%(installdir)s", ] -modextrapaths = { - 'CLASSPATH': 'lib', -} - -modextravars = { - 'MPJ_HOME': '$root', # MPJ_HOME points to install directory -} - sanity_check_paths = { 'files': ['lib/libnativempjdev.so', 'bin/mpjrun.sh'], 'dirs': [] } +modextravars = {'MPJ_HOME': '%(installdir)s'} +modextrapaths = {'CLASSPATH': 'lib'} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/MView/MView-1.57-goolf-1.4.10-Perl-5.16.3.eb b/easybuild/easyconfigs/m/MView/MView-1.57-goolf-1.4.10-Perl-5.16.3.eb index 44efa704ef..973e13d894 100644 --- a/easybuild/easyconfigs/m/MView/MView-1.57-goolf-1.4.10-Perl-5.16.3.eb +++ b/easybuild/easyconfigs/m/MView/MView-1.57-goolf-1.4.10-Perl-5.16.3.eb @@ -25,8 +25,6 @@ sanity_check_paths = { 'dirs': ["lib"], } -modextravars = { - 'PERL5LIB': '$root/lib' -} +modextrapaths = {'PERL5LIB': 'lib'} moduleclass = 'bio' diff --git a/easybuild/easyconfigs/w/WEKA/WEKA-3.6.12-Java-1.7.0_80.eb b/easybuild/easyconfigs/w/WEKA/WEKA-3.6.12-Java-1.7.0_80.eb index 77fe169073..c6a5e3fa14 100644 --- a/easybuild/easyconfigs/w/WEKA/WEKA-3.6.12-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/w/WEKA/WEKA-3.6.12-Java-1.7.0_80.eb @@ -31,9 +31,7 @@ sanity_check_paths = { 'dirs': [] } -modextravars = { - 'WEKAINSTALL': '$root', -} +modextravars = {'WEKAINSTALL': '%(installdir)s'} modloadmsg = "execute WEKA: java -jar $EBROOTWEKA/weka.jar\n" diff --git a/easybuild/easyconfigs/w/WEKA/WEKA-3.7.0-Java-1.7.0_80.eb b/easybuild/easyconfigs/w/WEKA/WEKA-3.7.0-Java-1.7.0_80.eb index 70198200d8..96ac9d6530 100644 --- a/easybuild/easyconfigs/w/WEKA/WEKA-3.7.0-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/w/WEKA/WEKA-3.7.0-Java-1.7.0_80.eb @@ -31,9 +31,7 @@ sanity_check_paths = { 'dirs': [] } -modextravars = { - 'WEKAINSTALL': '$root', -} +modextravars = {'WEKAINSTALL': '%(installdir)s'} modloadmsg = "execute WEKA: java -jar $EBROOTWEKA/weka.jar\n" -- GitLab From 7b5bab1965fb311d42f87d63078aa80dad41820f Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 10 Mar 2017 15:25:56 +0200 Subject: [PATCH 0352/1603] adding easyconfigs: Yasm-1.3.0-foss-2017a.eb, Yasm-1.3.0-intel-2017a.eb --- .../y/Yasm/Yasm-1.3.0-foss-2017a.eb | 31 +++++++++++++++++++ .../y/Yasm/Yasm-1.3.0-intel-2017a.eb | 31 +++++++++++++++++++ 2 files changed, 62 insertions(+) create mode 100644 easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-foss-2017a.eb create mode 100644 easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-intel-2017a.eb diff --git a/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-foss-2017a.eb b/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-foss-2017a.eb new file mode 100644 index 0000000000..bae739cbfa --- /dev/null +++ b/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-foss-2017a.eb @@ -0,0 +1,31 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-90.html +## + +easyblock = 'ConfigureMake' + +name = 'Yasm' +version = '1.3.0' + +homepage = 'http://www.tortall.net/projects/yasm/' +description = """Yasm: Complete rewrite of the NASM assembler with BSD license""" + +toolchain = {'name': 'foss', 'version': '2017a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.tortall.net/projects/yasm/releases/'] + +sanity_check_paths = { + 'files': ['bin/yasm'], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-intel-2017a.eb b/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-intel-2017a.eb new file mode 100644 index 0000000000..f0db7e8256 --- /dev/null +++ b/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-intel-2017a.eb @@ -0,0 +1,31 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-90.html +## + +easyblock = 'ConfigureMake' + +name = 'Yasm' +version = '1.3.0' + +homepage = 'http://www.tortall.net/projects/yasm/' +description = """Yasm: Complete rewrite of the NASM assembler with BSD license""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.tortall.net/projects/yasm/releases/'] + +sanity_check_paths = { + 'files': ['bin/yasm'], + 'dirs': [], +} + +moduleclass = 'lang' -- GitLab From 7ab680ea704aa1db04f7db38635b33a760437b9a Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 10 Mar 2017 16:56:47 +0200 Subject: [PATCH 0353/1603] The patch is the result of applying the upstream patch and running the maintainer scripts to regenerate the interface files. --- .../f/FFTW/FFTW-3.3.6-F03_interface_pl2.patch | 1527 +++++++++++++++++ .../f/FFTW/FFTW-3.3.6-gompi-2017a.eb | 4 + .../f/FFTW/FFTW-3.3.6-intel-2017a.eb | 29 + 3 files changed, 1560 insertions(+) create mode 100644 easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-F03_interface_pl2.patch create mode 100644 easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-intel-2017a.eb diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-F03_interface_pl2.patch b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-F03_interface_pl2.patch new file mode 100644 index 0000000000..70d5168fbf --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-F03_interface_pl2.patch @@ -0,0 +1,1527 @@ +# The scrips that generate the MPI F03 interface was broken in 3.3.6-pl1 +# The scripts were using fftw3.h from /usr/include, not ../api, and were +# failing silently if fftw3.h was not installed. This bug led to a +# fftw-3.3.6pl1 release with incomplete mpi/f03 header files. +# See commit 83092f8efbf872aefe7cfc6ee8fa43412f8e167a in FFTW upstream +# git. +# +# This patch is the result of applying that commit and running the +# maintainer mode scripts. +# +# Åke Sandgrem 2017-03-07 +diff -ru fftw-3.3.6-pl1.orig/mpi/f03api.sh fftw-3.3.6-pl1/mpi/f03api.sh +--- fftw-3.3.6-pl1.orig/mpi/f03api.sh 2017-01-15 13:03:24.000000002 +0100 ++++ fftw-3.3.6-pl1/mpi/f03api.sh 2017-03-08 15:46:56.000000002 +0100 +@@ -37,7 +37,7 @@ + + echo + echo " interface" +- grep -v 'mpi.h' fftw3-mpi.h | gcc -D__GNUC__=5 -D__i386__ -E - |grep "fftw${p}_mpi_init" |tr ';' '\n' | perl ../api/genf03.pl ++ grep -v 'mpi.h' fftw3-mpi.h | gcc -I../api -D__GNUC__=5 -D__i386__ -E - |grep "fftw${p}_mpi_init" |tr ';' '\n' | perl ../api/genf03.pl + echo " end interface" + + done +diff -ru fftw-3.3.6-pl1.orig/mpi/f03-wrap.c fftw-3.3.6-pl1/mpi/f03-wrap.c +--- fftw-3.3.6-pl1.orig/mpi/f03-wrap.c 2017-01-16 15:12:37.000000002 +0100 ++++ fftw-3.3.6-pl1/mpi/f03-wrap.c 2017-03-08 16:20:11.000000002 +0100 +@@ -3,3 +3,282 @@ + #include "fftw3-mpi.h" + #include "ifftw-mpi.h" + ++FFTW_EXTERN ptrdiff_t XM(local_size_many_transposed_f03)(int rnk, const ptrdiff_t * n, ptrdiff_t howmany, ptrdiff_t block0, ptrdiff_t block1, MPI_Fint f_comm, ptrdiff_t * local_n0, ptrdiff_t * local_0_start, ptrdiff_t * local_n1, ptrdiff_t * local_1_start); ++FFTW_EXTERN ptrdiff_t XM(local_size_many_f03)(int rnk, const ptrdiff_t * n, ptrdiff_t howmany, ptrdiff_t block0, MPI_Fint f_comm, ptrdiff_t * local_n0, ptrdiff_t * local_0_start); ++FFTW_EXTERN ptrdiff_t XM(local_size_transposed_f03)(int rnk, const ptrdiff_t * n, MPI_Fint f_comm, ptrdiff_t * local_n0, ptrdiff_t * local_0_start, ptrdiff_t * local_n1, ptrdiff_t * local_1_start); ++FFTW_EXTERN ptrdiff_t XM(local_size_f03)(int rnk, const ptrdiff_t * n, MPI_Fint f_comm, ptrdiff_t * local_n0, ptrdiff_t * local_0_start); ++FFTW_EXTERN ptrdiff_t XM(local_size_many_1d_f03)(ptrdiff_t n0, ptrdiff_t howmany, MPI_Fint f_comm, int sign, unsigned flags, ptrdiff_t * local_ni, ptrdiff_t * local_i_start, ptrdiff_t * local_no, ptrdiff_t * local_o_start); ++FFTW_EXTERN ptrdiff_t XM(local_size_1d_f03)(ptrdiff_t n0, MPI_Fint f_comm, int sign, unsigned flags, ptrdiff_t * local_ni, ptrdiff_t * local_i_start, ptrdiff_t * local_no, ptrdiff_t * local_o_start); ++FFTW_EXTERN ptrdiff_t XM(local_size_2d_f03)(ptrdiff_t n0, ptrdiff_t n1, MPI_Fint f_comm, ptrdiff_t * local_n0, ptrdiff_t * local_0_start); ++FFTW_EXTERN ptrdiff_t XM(local_size_2d_transposed_f03)(ptrdiff_t n0, ptrdiff_t n1, MPI_Fint f_comm, ptrdiff_t * local_n0, ptrdiff_t * local_0_start, ptrdiff_t * local_n1, ptrdiff_t * local_1_start); ++FFTW_EXTERN ptrdiff_t XM(local_size_3d_f03)(ptrdiff_t n0, ptrdiff_t n1, ptrdiff_t n2, MPI_Fint f_comm, ptrdiff_t * local_n0, ptrdiff_t * local_0_start); ++FFTW_EXTERN ptrdiff_t XM(local_size_3d_transposed_f03)(ptrdiff_t n0, ptrdiff_t n1, ptrdiff_t n2, MPI_Fint f_comm, ptrdiff_t * local_n0, ptrdiff_t * local_0_start, ptrdiff_t * local_n1, ptrdiff_t * local_1_start); ++FFTW_EXTERN X(plan) XM(plan_many_transpose_f03)(ptrdiff_t n0, ptrdiff_t n1, ptrdiff_t howmany, ptrdiff_t block0, ptrdiff_t block1, R * in, R * out, MPI_Fint f_comm, unsigned flags); ++FFTW_EXTERN X(plan) XM(plan_transpose_f03)(ptrdiff_t n0, ptrdiff_t n1, R * in, R * out, MPI_Fint f_comm, unsigned flags); ++FFTW_EXTERN X(plan) XM(plan_many_dft_f03)(int rnk, const ptrdiff_t * n, ptrdiff_t howmany, ptrdiff_t block, ptrdiff_t tblock, X(complex) * in, X(complex) * out, MPI_Fint f_comm, int sign, unsigned flags); ++FFTW_EXTERN X(plan) XM(plan_dft_f03)(int rnk, const ptrdiff_t * n, X(complex) * in, X(complex) * out, MPI_Fint f_comm, int sign, unsigned flags); ++FFTW_EXTERN X(plan) XM(plan_dft_1d_f03)(ptrdiff_t n0, X(complex) * in, X(complex) * out, MPI_Fint f_comm, int sign, unsigned flags); ++FFTW_EXTERN X(plan) XM(plan_dft_2d_f03)(ptrdiff_t n0, ptrdiff_t n1, X(complex) * in, X(complex) * out, MPI_Fint f_comm, int sign, unsigned flags); ++FFTW_EXTERN X(plan) XM(plan_dft_3d_f03)(ptrdiff_t n0, ptrdiff_t n1, ptrdiff_t n2, X(complex) * in, X(complex) * out, MPI_Fint f_comm, int sign, unsigned flags); ++FFTW_EXTERN X(plan) XM(plan_many_r2r_f03)(int rnk, const ptrdiff_t * n, ptrdiff_t howmany, ptrdiff_t iblock, ptrdiff_t oblock, R * in, R * out, MPI_Fint f_comm, const X(r2r_kind) * kind, unsigned flags); ++FFTW_EXTERN X(plan) XM(plan_r2r_f03)(int rnk, const ptrdiff_t * n, R * in, R * out, MPI_Fint f_comm, const X(r2r_kind) * kind, unsigned flags); ++FFTW_EXTERN X(plan) XM(plan_r2r_2d_f03)(ptrdiff_t n0, ptrdiff_t n1, R * in, R * out, MPI_Fint f_comm, X(r2r_kind) kind0, X(r2r_kind) kind1, unsigned flags); ++FFTW_EXTERN X(plan) XM(plan_r2r_3d_f03)(ptrdiff_t n0, ptrdiff_t n1, ptrdiff_t n2, R * in, R * out, MPI_Fint f_comm, X(r2r_kind) kind0, X(r2r_kind) kind1, X(r2r_kind) kind2, unsigned flags); ++FFTW_EXTERN X(plan) XM(plan_many_dft_r2c_f03)(int rnk, const ptrdiff_t * n, ptrdiff_t howmany, ptrdiff_t iblock, ptrdiff_t oblock, R * in, X(complex) * out, MPI_Fint f_comm, unsigned flags); ++FFTW_EXTERN X(plan) XM(plan_dft_r2c_f03)(int rnk, const ptrdiff_t * n, R * in, X(complex) * out, MPI_Fint f_comm, unsigned flags); ++FFTW_EXTERN X(plan) XM(plan_dft_r2c_2d_f03)(ptrdiff_t n0, ptrdiff_t n1, R * in, X(complex) * out, MPI_Fint f_comm, unsigned flags); ++FFTW_EXTERN X(plan) XM(plan_dft_r2c_3d_f03)(ptrdiff_t n0, ptrdiff_t n1, ptrdiff_t n2, R * in, X(complex) * out, MPI_Fint f_comm, unsigned flags); ++FFTW_EXTERN X(plan) XM(plan_many_dft_c2r_f03)(int rnk, const ptrdiff_t * n, ptrdiff_t howmany, ptrdiff_t iblock, ptrdiff_t oblock, X(complex) * in, R * out, MPI_Fint f_comm, unsigned flags); ++FFTW_EXTERN X(plan) XM(plan_dft_c2r_f03)(int rnk, const ptrdiff_t * n, X(complex) * in, R * out, MPI_Fint f_comm, unsigned flags); ++FFTW_EXTERN X(plan) XM(plan_dft_c2r_2d_f03)(ptrdiff_t n0, ptrdiff_t n1, X(complex) * in, R * out, MPI_Fint f_comm, unsigned flags); ++FFTW_EXTERN X(plan) XM(plan_dft_c2r_3d_f03)(ptrdiff_t n0, ptrdiff_t n1, ptrdiff_t n2, X(complex) * in, R * out, MPI_Fint f_comm, unsigned flags); ++FFTW_EXTERN void XM(gather_wisdom_f03)(MPI_Fint f_comm_); ++FFTW_EXTERN void XM(broadcast_wisdom_f03)(MPI_Fint f_comm_); ++ ++ptrdiff_t XM(local_size_many_transposed_f03)(int rnk, const ptrdiff_t * n, ptrdiff_t howmany, ptrdiff_t block0, ptrdiff_t block1, MPI_Fint f_comm, ptrdiff_t * local_n0, ptrdiff_t * local_0_start, ptrdiff_t * local_n1, ptrdiff_t * local_1_start) ++{ ++ MPI_Comm comm; ++ ++ comm = MPI_Comm_f2c(f_comm); ++ return XM(local_size_many_transposed)(rnk,n,howmany,block0,block1,comm,local_n0,local_0_start,local_n1,local_1_start); ++} ++ ++ptrdiff_t XM(local_size_many_f03)(int rnk, const ptrdiff_t * n, ptrdiff_t howmany, ptrdiff_t block0, MPI_Fint f_comm, ptrdiff_t * local_n0, ptrdiff_t * local_0_start) ++{ ++ MPI_Comm comm; ++ ++ comm = MPI_Comm_f2c(f_comm); ++ return XM(local_size_many)(rnk,n,howmany,block0,comm,local_n0,local_0_start); ++} ++ ++ptrdiff_t XM(local_size_transposed_f03)(int rnk, const ptrdiff_t * n, MPI_Fint f_comm, ptrdiff_t * local_n0, ptrdiff_t * local_0_start, ptrdiff_t * local_n1, ptrdiff_t * local_1_start) ++{ ++ MPI_Comm comm; ++ ++ comm = MPI_Comm_f2c(f_comm); ++ return XM(local_size_transposed)(rnk,n,comm,local_n0,local_0_start,local_n1,local_1_start); ++} ++ ++ptrdiff_t XM(local_size_f03)(int rnk, const ptrdiff_t * n, MPI_Fint f_comm, ptrdiff_t * local_n0, ptrdiff_t * local_0_start) ++{ ++ MPI_Comm comm; ++ ++ comm = MPI_Comm_f2c(f_comm); ++ return XM(local_size)(rnk,n,comm,local_n0,local_0_start); ++} ++ ++ptrdiff_t XM(local_size_many_1d_f03)(ptrdiff_t n0, ptrdiff_t howmany, MPI_Fint f_comm, int sign, unsigned flags, ptrdiff_t * local_ni, ptrdiff_t * local_i_start, ptrdiff_t * local_no, ptrdiff_t * local_o_start) ++{ ++ MPI_Comm comm; ++ ++ comm = MPI_Comm_f2c(f_comm); ++ return XM(local_size_many_1d)(n0,howmany,comm,sign,flags,local_ni,local_i_start,local_no,local_o_start); ++} ++ ++ptrdiff_t XM(local_size_1d_f03)(ptrdiff_t n0, MPI_Fint f_comm, int sign, unsigned flags, ptrdiff_t * local_ni, ptrdiff_t * local_i_start, ptrdiff_t * local_no, ptrdiff_t * local_o_start) ++{ ++ MPI_Comm comm; ++ ++ comm = MPI_Comm_f2c(f_comm); ++ return XM(local_size_1d)(n0,comm,sign,flags,local_ni,local_i_start,local_no,local_o_start); ++} ++ ++ptrdiff_t XM(local_size_2d_f03)(ptrdiff_t n0, ptrdiff_t n1, MPI_Fint f_comm, ptrdiff_t * local_n0, ptrdiff_t * local_0_start) ++{ ++ MPI_Comm comm; ++ ++ comm = MPI_Comm_f2c(f_comm); ++ return XM(local_size_2d)(n0,n1,comm,local_n0,local_0_start); ++} ++ ++ptrdiff_t XM(local_size_2d_transposed_f03)(ptrdiff_t n0, ptrdiff_t n1, MPI_Fint f_comm, ptrdiff_t * local_n0, ptrdiff_t * local_0_start, ptrdiff_t * local_n1, ptrdiff_t * local_1_start) ++{ ++ MPI_Comm comm; ++ ++ comm = MPI_Comm_f2c(f_comm); ++ return XM(local_size_2d_transposed)(n0,n1,comm,local_n0,local_0_start,local_n1,local_1_start); ++} ++ ++ptrdiff_t XM(local_size_3d_f03)(ptrdiff_t n0, ptrdiff_t n1, ptrdiff_t n2, MPI_Fint f_comm, ptrdiff_t * local_n0, ptrdiff_t * local_0_start) ++{ ++ MPI_Comm comm; ++ ++ comm = MPI_Comm_f2c(f_comm); ++ return XM(local_size_3d)(n0,n1,n2,comm,local_n0,local_0_start); ++} ++ ++ptrdiff_t XM(local_size_3d_transposed_f03)(ptrdiff_t n0, ptrdiff_t n1, ptrdiff_t n2, MPI_Fint f_comm, ptrdiff_t * local_n0, ptrdiff_t * local_0_start, ptrdiff_t * local_n1, ptrdiff_t * local_1_start) ++{ ++ MPI_Comm comm; ++ ++ comm = MPI_Comm_f2c(f_comm); ++ return XM(local_size_3d_transposed)(n0,n1,n2,comm,local_n0,local_0_start,local_n1,local_1_start); ++} ++ ++X(plan) XM(plan_many_transpose_f03)(ptrdiff_t n0, ptrdiff_t n1, ptrdiff_t howmany, ptrdiff_t block0, ptrdiff_t block1, R * in, R * out, MPI_Fint f_comm, unsigned flags) ++{ ++ MPI_Comm comm; ++ ++ comm = MPI_Comm_f2c(f_comm); ++ return XM(plan_many_transpose)(n0,n1,howmany,block0,block1,in,out,comm,flags); ++} ++ ++X(plan) XM(plan_transpose_f03)(ptrdiff_t n0, ptrdiff_t n1, R * in, R * out, MPI_Fint f_comm, unsigned flags) ++{ ++ MPI_Comm comm; ++ ++ comm = MPI_Comm_f2c(f_comm); ++ return XM(plan_transpose)(n0,n1,in,out,comm,flags); ++} ++ ++X(plan) XM(plan_many_dft_f03)(int rnk, const ptrdiff_t * n, ptrdiff_t howmany, ptrdiff_t block, ptrdiff_t tblock, X(complex) * in, X(complex) * out, MPI_Fint f_comm, int sign, unsigned flags) ++{ ++ MPI_Comm comm; ++ ++ comm = MPI_Comm_f2c(f_comm); ++ return XM(plan_many_dft)(rnk,n,howmany,block,tblock,in,out,comm,sign,flags); ++} ++ ++X(plan) XM(plan_dft_f03)(int rnk, const ptrdiff_t * n, X(complex) * in, X(complex) * out, MPI_Fint f_comm, int sign, unsigned flags) ++{ ++ MPI_Comm comm; ++ ++ comm = MPI_Comm_f2c(f_comm); ++ return XM(plan_dft)(rnk,n,in,out,comm,sign,flags); ++} ++ ++X(plan) XM(plan_dft_1d_f03)(ptrdiff_t n0, X(complex) * in, X(complex) * out, MPI_Fint f_comm, int sign, unsigned flags) ++{ ++ MPI_Comm comm; ++ ++ comm = MPI_Comm_f2c(f_comm); ++ return XM(plan_dft_1d)(n0,in,out,comm,sign,flags); ++} ++ ++X(plan) XM(plan_dft_2d_f03)(ptrdiff_t n0, ptrdiff_t n1, X(complex) * in, X(complex) * out, MPI_Fint f_comm, int sign, unsigned flags) ++{ ++ MPI_Comm comm; ++ ++ comm = MPI_Comm_f2c(f_comm); ++ return XM(plan_dft_2d)(n0,n1,in,out,comm,sign,flags); ++} ++ ++X(plan) XM(plan_dft_3d_f03)(ptrdiff_t n0, ptrdiff_t n1, ptrdiff_t n2, X(complex) * in, X(complex) * out, MPI_Fint f_comm, int sign, unsigned flags) ++{ ++ MPI_Comm comm; ++ ++ comm = MPI_Comm_f2c(f_comm); ++ return XM(plan_dft_3d)(n0,n1,n2,in,out,comm,sign,flags); ++} ++ ++X(plan) XM(plan_many_r2r_f03)(int rnk, const ptrdiff_t * n, ptrdiff_t howmany, ptrdiff_t iblock, ptrdiff_t oblock, R * in, R * out, MPI_Fint f_comm, const X(r2r_kind) * kind, unsigned flags) ++{ ++ MPI_Comm comm; ++ ++ comm = MPI_Comm_f2c(f_comm); ++ return XM(plan_many_r2r)(rnk,n,howmany,iblock,oblock,in,out,comm,kind,flags); ++} ++ ++X(plan) XM(plan_r2r_f03)(int rnk, const ptrdiff_t * n, R * in, R * out, MPI_Fint f_comm, const X(r2r_kind) * kind, unsigned flags) ++{ ++ MPI_Comm comm; ++ ++ comm = MPI_Comm_f2c(f_comm); ++ return XM(plan_r2r)(rnk,n,in,out,comm,kind,flags); ++} ++ ++X(plan) XM(plan_r2r_2d_f03)(ptrdiff_t n0, ptrdiff_t n1, R * in, R * out, MPI_Fint f_comm, X(r2r_kind) kind0, X(r2r_kind) kind1, unsigned flags) ++{ ++ MPI_Comm comm; ++ ++ comm = MPI_Comm_f2c(f_comm); ++ return XM(plan_r2r_2d)(n0,n1,in,out,comm,kind0,kind1,flags); ++} ++ ++X(plan) XM(plan_r2r_3d_f03)(ptrdiff_t n0, ptrdiff_t n1, ptrdiff_t n2, R * in, R * out, MPI_Fint f_comm, X(r2r_kind) kind0, X(r2r_kind) kind1, X(r2r_kind) kind2, unsigned flags) ++{ ++ MPI_Comm comm; ++ ++ comm = MPI_Comm_f2c(f_comm); ++ return XM(plan_r2r_3d)(n0,n1,n2,in,out,comm,kind0,kind1,kind2,flags); ++} ++ ++X(plan) XM(plan_many_dft_r2c_f03)(int rnk, const ptrdiff_t * n, ptrdiff_t howmany, ptrdiff_t iblock, ptrdiff_t oblock, R * in, X(complex) * out, MPI_Fint f_comm, unsigned flags) ++{ ++ MPI_Comm comm; ++ ++ comm = MPI_Comm_f2c(f_comm); ++ return XM(plan_many_dft_r2c)(rnk,n,howmany,iblock,oblock,in,out,comm,flags); ++} ++ ++X(plan) XM(plan_dft_r2c_f03)(int rnk, const ptrdiff_t * n, R * in, X(complex) * out, MPI_Fint f_comm, unsigned flags) ++{ ++ MPI_Comm comm; ++ ++ comm = MPI_Comm_f2c(f_comm); ++ return XM(plan_dft_r2c)(rnk,n,in,out,comm,flags); ++} ++ ++X(plan) XM(plan_dft_r2c_2d_f03)(ptrdiff_t n0, ptrdiff_t n1, R * in, X(complex) * out, MPI_Fint f_comm, unsigned flags) ++{ ++ MPI_Comm comm; ++ ++ comm = MPI_Comm_f2c(f_comm); ++ return XM(plan_dft_r2c_2d)(n0,n1,in,out,comm,flags); ++} ++ ++X(plan) XM(plan_dft_r2c_3d_f03)(ptrdiff_t n0, ptrdiff_t n1, ptrdiff_t n2, R * in, X(complex) * out, MPI_Fint f_comm, unsigned flags) ++{ ++ MPI_Comm comm; ++ ++ comm = MPI_Comm_f2c(f_comm); ++ return XM(plan_dft_r2c_3d)(n0,n1,n2,in,out,comm,flags); ++} ++ ++X(plan) XM(plan_many_dft_c2r_f03)(int rnk, const ptrdiff_t * n, ptrdiff_t howmany, ptrdiff_t iblock, ptrdiff_t oblock, X(complex) * in, R * out, MPI_Fint f_comm, unsigned flags) ++{ ++ MPI_Comm comm; ++ ++ comm = MPI_Comm_f2c(f_comm); ++ return XM(plan_many_dft_c2r)(rnk,n,howmany,iblock,oblock,in,out,comm,flags); ++} ++ ++X(plan) XM(plan_dft_c2r_f03)(int rnk, const ptrdiff_t * n, X(complex) * in, R * out, MPI_Fint f_comm, unsigned flags) ++{ ++ MPI_Comm comm; ++ ++ comm = MPI_Comm_f2c(f_comm); ++ return XM(plan_dft_c2r)(rnk,n,in,out,comm,flags); ++} ++ ++X(plan) XM(plan_dft_c2r_2d_f03)(ptrdiff_t n0, ptrdiff_t n1, X(complex) * in, R * out, MPI_Fint f_comm, unsigned flags) ++{ ++ MPI_Comm comm; ++ ++ comm = MPI_Comm_f2c(f_comm); ++ return XM(plan_dft_c2r_2d)(n0,n1,in,out,comm,flags); ++} ++ ++X(plan) XM(plan_dft_c2r_3d_f03)(ptrdiff_t n0, ptrdiff_t n1, ptrdiff_t n2, X(complex) * in, R * out, MPI_Fint f_comm, unsigned flags) ++{ ++ MPI_Comm comm; ++ ++ comm = MPI_Comm_f2c(f_comm); ++ return XM(plan_dft_c2r_3d)(n0,n1,n2,in,out,comm,flags); ++} ++ ++void XM(gather_wisdom_f03)(MPI_Fint f_comm_) ++{ ++ MPI_Comm comm_; ++ ++ comm_ = MPI_Comm_f2c(f_comm_); ++ XM(gather_wisdom)(comm_); ++} ++ ++void XM(broadcast_wisdom_f03)(MPI_Fint f_comm_) ++{ ++ MPI_Comm comm_; ++ ++ comm_ = MPI_Comm_f2c(f_comm_); ++ XM(broadcast_wisdom)(comm_); ++} +diff -ru fftw-3.3.6-pl1.orig/mpi/f03-wrap.sh fftw-3.3.6-pl1/mpi/f03-wrap.sh +--- fftw-3.3.6-pl1.orig/mpi/f03-wrap.sh 2017-01-15 13:03:24.000000002 +0100 ++++ fftw-3.3.6-pl1/mpi/f03-wrap.sh 2017-03-08 15:46:56.000000002 +0100 +@@ -15,8 +15,8 @@ + echo + + # Declare prototypes using FFTW_EXTERN, important for Windows DLLs +-grep -v 'mpi.h' fftw3-mpi.h | gcc -E - |grep "fftw_mpi_init" |tr ';' '\n' | grep "MPI_Comm" | perl genf03-wrap.pl | grep "MPI_Fint" | sed 's/^/FFTW_EXTERN /;s/$/;/' ++grep -v 'mpi.h' fftw3-mpi.h | gcc -E -I../api - |grep "fftw_mpi_init" |tr ';' '\n' | grep "MPI_Comm" | perl genf03-wrap.pl | grep "MPI_Fint" | sed 's/^/FFTW_EXTERN /;s/$/;/' + +-grep -v 'mpi.h' fftw3-mpi.h | gcc -E - |grep "fftw_mpi_init" |tr ';' '\n' | grep "MPI_Comm" | perl genf03-wrap.pl ++grep -v 'mpi.h' fftw3-mpi.h | gcc -E -I../api - |grep "fftw_mpi_init" |tr ';' '\n' | grep "MPI_Comm" | perl genf03-wrap.pl + + +diff -ru fftw-3.3.6-pl1.orig/mpi/fftw3l-mpi.f03.in fftw-3.3.6-pl1/mpi/fftw3l-mpi.f03.in +--- fftw-3.3.6-pl1.orig/mpi/fftw3l-mpi.f03.in 2017-01-16 15:12:37.000000002 +0100 ++++ fftw-3.3.6-pl1/mpi/fftw3l-mpi.f03.in 2017-03-08 16:20:11.000000002 +0100 +@@ -8,4 +8,398 @@ + end type fftwl_mpi_ddim + + interface ++ subroutine fftwl_mpi_init() bind(C, name='fftwl_mpi_init') ++ import ++ end subroutine fftwl_mpi_init ++ ++ subroutine fftwl_mpi_cleanup() bind(C, name='fftwl_mpi_cleanup') ++ import ++ end subroutine fftwl_mpi_cleanup ++ ++ integer(C_INTPTR_T) function fftwl_mpi_local_size_many_transposed(rnk,n,howmany,block0,block1,comm,local_n0,local_0_start, & ++ local_n1,local_1_start) & ++ bind(C, name='fftwl_mpi_local_size_many_transposed_f03') ++ import ++ integer(C_INT), value :: rnk ++ integer(C_INTPTR_T), dimension(*), intent(in) :: n ++ integer(C_INTPTR_T), value :: howmany ++ integer(C_INTPTR_T), value :: block0 ++ integer(C_INTPTR_T), value :: block1 ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INTPTR_T), intent(out) :: local_n0 ++ integer(C_INTPTR_T), intent(out) :: local_0_start ++ integer(C_INTPTR_T), intent(out) :: local_n1 ++ integer(C_INTPTR_T), intent(out) :: local_1_start ++ end function fftwl_mpi_local_size_many_transposed ++ ++ integer(C_INTPTR_T) function fftwl_mpi_local_size_many(rnk,n,howmany,block0,comm,local_n0,local_0_start) & ++ bind(C, name='fftwl_mpi_local_size_many_f03') ++ import ++ integer(C_INT), value :: rnk ++ integer(C_INTPTR_T), dimension(*), intent(in) :: n ++ integer(C_INTPTR_T), value :: howmany ++ integer(C_INTPTR_T), value :: block0 ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INTPTR_T), intent(out) :: local_n0 ++ integer(C_INTPTR_T), intent(out) :: local_0_start ++ end function fftwl_mpi_local_size_many ++ ++ integer(C_INTPTR_T) function fftwl_mpi_local_size_transposed(rnk,n,comm,local_n0,local_0_start,local_n1,local_1_start) & ++ bind(C, name='fftwl_mpi_local_size_transposed_f03') ++ import ++ integer(C_INT), value :: rnk ++ integer(C_INTPTR_T), dimension(*), intent(in) :: n ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INTPTR_T), intent(out) :: local_n0 ++ integer(C_INTPTR_T), intent(out) :: local_0_start ++ integer(C_INTPTR_T), intent(out) :: local_n1 ++ integer(C_INTPTR_T), intent(out) :: local_1_start ++ end function fftwl_mpi_local_size_transposed ++ ++ integer(C_INTPTR_T) function fftwl_mpi_local_size(rnk,n,comm,local_n0,local_0_start) bind(C, name='fftwl_mpi_local_size_f03') ++ import ++ integer(C_INT), value :: rnk ++ integer(C_INTPTR_T), dimension(*), intent(in) :: n ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INTPTR_T), intent(out) :: local_n0 ++ integer(C_INTPTR_T), intent(out) :: local_0_start ++ end function fftwl_mpi_local_size ++ ++ integer(C_INTPTR_T) function fftwl_mpi_local_size_many_1d(n0,howmany,comm,sign,flags,local_ni,local_i_start,local_no, & ++ local_o_start) bind(C, name='fftwl_mpi_local_size_many_1d_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: howmany ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: sign ++ integer(C_INT), value :: flags ++ integer(C_INTPTR_T), intent(out) :: local_ni ++ integer(C_INTPTR_T), intent(out) :: local_i_start ++ integer(C_INTPTR_T), intent(out) :: local_no ++ integer(C_INTPTR_T), intent(out) :: local_o_start ++ end function fftwl_mpi_local_size_many_1d ++ ++ integer(C_INTPTR_T) function fftwl_mpi_local_size_1d(n0,comm,sign,flags,local_ni,local_i_start,local_no,local_o_start) & ++ bind(C, name='fftwl_mpi_local_size_1d_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: sign ++ integer(C_INT), value :: flags ++ integer(C_INTPTR_T), intent(out) :: local_ni ++ integer(C_INTPTR_T), intent(out) :: local_i_start ++ integer(C_INTPTR_T), intent(out) :: local_no ++ integer(C_INTPTR_T), intent(out) :: local_o_start ++ end function fftwl_mpi_local_size_1d ++ ++ integer(C_INTPTR_T) function fftwl_mpi_local_size_2d(n0,n1,comm,local_n0,local_0_start) & ++ bind(C, name='fftwl_mpi_local_size_2d_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: n1 ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INTPTR_T), intent(out) :: local_n0 ++ integer(C_INTPTR_T), intent(out) :: local_0_start ++ end function fftwl_mpi_local_size_2d ++ ++ integer(C_INTPTR_T) function fftwl_mpi_local_size_2d_transposed(n0,n1,comm,local_n0,local_0_start,local_n1,local_1_start) & ++ bind(C, name='fftwl_mpi_local_size_2d_transposed_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: n1 ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INTPTR_T), intent(out) :: local_n0 ++ integer(C_INTPTR_T), intent(out) :: local_0_start ++ integer(C_INTPTR_T), intent(out) :: local_n1 ++ integer(C_INTPTR_T), intent(out) :: local_1_start ++ end function fftwl_mpi_local_size_2d_transposed ++ ++ integer(C_INTPTR_T) function fftwl_mpi_local_size_3d(n0,n1,n2,comm,local_n0,local_0_start) & ++ bind(C, name='fftwl_mpi_local_size_3d_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: n1 ++ integer(C_INTPTR_T), value :: n2 ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INTPTR_T), intent(out) :: local_n0 ++ integer(C_INTPTR_T), intent(out) :: local_0_start ++ end function fftwl_mpi_local_size_3d ++ ++ integer(C_INTPTR_T) function fftwl_mpi_local_size_3d_transposed(n0,n1,n2,comm,local_n0,local_0_start,local_n1,local_1_start) & ++ bind(C, name='fftwl_mpi_local_size_3d_transposed_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: n1 ++ integer(C_INTPTR_T), value :: n2 ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INTPTR_T), intent(out) :: local_n0 ++ integer(C_INTPTR_T), intent(out) :: local_0_start ++ integer(C_INTPTR_T), intent(out) :: local_n1 ++ integer(C_INTPTR_T), intent(out) :: local_1_start ++ end function fftwl_mpi_local_size_3d_transposed ++ ++ type(C_PTR) function fftwl_mpi_plan_many_transpose(n0,n1,howmany,block0,block1,in,out,comm,flags) & ++ bind(C, name='fftwl_mpi_plan_many_transpose_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: n1 ++ integer(C_INTPTR_T), value :: howmany ++ integer(C_INTPTR_T), value :: block0 ++ integer(C_INTPTR_T), value :: block1 ++ real(C_LONG_DOUBLE), dimension(*), intent(out) :: in ++ real(C_LONG_DOUBLE), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: flags ++ end function fftwl_mpi_plan_many_transpose ++ ++ type(C_PTR) function fftwl_mpi_plan_transpose(n0,n1,in,out,comm,flags) bind(C, name='fftwl_mpi_plan_transpose_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: n1 ++ real(C_LONG_DOUBLE), dimension(*), intent(out) :: in ++ real(C_LONG_DOUBLE), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: flags ++ end function fftwl_mpi_plan_transpose ++ ++ type(C_PTR) function fftwl_mpi_plan_many_dft(rnk,n,howmany,block,tblock,in,out,comm,sign,flags) & ++ bind(C, name='fftwl_mpi_plan_many_dft_f03') ++ import ++ integer(C_INT), value :: rnk ++ integer(C_INTPTR_T), dimension(*), intent(in) :: n ++ integer(C_INTPTR_T), value :: howmany ++ integer(C_INTPTR_T), value :: block ++ integer(C_INTPTR_T), value :: tblock ++ complex(C_LONG_DOUBLE_COMPLEX), dimension(*), intent(out) :: in ++ complex(C_LONG_DOUBLE_COMPLEX), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: sign ++ integer(C_INT), value :: flags ++ end function fftwl_mpi_plan_many_dft ++ ++ type(C_PTR) function fftwl_mpi_plan_dft(rnk,n,in,out,comm,sign,flags) bind(C, name='fftwl_mpi_plan_dft_f03') ++ import ++ integer(C_INT), value :: rnk ++ integer(C_INTPTR_T), dimension(*), intent(in) :: n ++ complex(C_LONG_DOUBLE_COMPLEX), dimension(*), intent(out) :: in ++ complex(C_LONG_DOUBLE_COMPLEX), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: sign ++ integer(C_INT), value :: flags ++ end function fftwl_mpi_plan_dft ++ ++ type(C_PTR) function fftwl_mpi_plan_dft_1d(n0,in,out,comm,sign,flags) bind(C, name='fftwl_mpi_plan_dft_1d_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ complex(C_LONG_DOUBLE_COMPLEX), dimension(*), intent(out) :: in ++ complex(C_LONG_DOUBLE_COMPLEX), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: sign ++ integer(C_INT), value :: flags ++ end function fftwl_mpi_plan_dft_1d ++ ++ type(C_PTR) function fftwl_mpi_plan_dft_2d(n0,n1,in,out,comm,sign,flags) bind(C, name='fftwl_mpi_plan_dft_2d_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: n1 ++ complex(C_LONG_DOUBLE_COMPLEX), dimension(*), intent(out) :: in ++ complex(C_LONG_DOUBLE_COMPLEX), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: sign ++ integer(C_INT), value :: flags ++ end function fftwl_mpi_plan_dft_2d ++ ++ type(C_PTR) function fftwl_mpi_plan_dft_3d(n0,n1,n2,in,out,comm,sign,flags) bind(C, name='fftwl_mpi_plan_dft_3d_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: n1 ++ integer(C_INTPTR_T), value :: n2 ++ complex(C_LONG_DOUBLE_COMPLEX), dimension(*), intent(out) :: in ++ complex(C_LONG_DOUBLE_COMPLEX), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: sign ++ integer(C_INT), value :: flags ++ end function fftwl_mpi_plan_dft_3d ++ ++ type(C_PTR) function fftwl_mpi_plan_many_r2r(rnk,n,howmany,iblock,oblock,in,out,comm,kind,flags) & ++ bind(C, name='fftwl_mpi_plan_many_r2r_f03') ++ import ++ integer(C_INT), value :: rnk ++ integer(C_INTPTR_T), dimension(*), intent(in) :: n ++ integer(C_INTPTR_T), value :: howmany ++ integer(C_INTPTR_T), value :: iblock ++ integer(C_INTPTR_T), value :: oblock ++ real(C_LONG_DOUBLE), dimension(*), intent(out) :: in ++ real(C_LONG_DOUBLE), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_FFTW_R2R_KIND), dimension(*), intent(in) :: kind ++ integer(C_INT), value :: flags ++ end function fftwl_mpi_plan_many_r2r ++ ++ type(C_PTR) function fftwl_mpi_plan_r2r(rnk,n,in,out,comm,kind,flags) bind(C, name='fftwl_mpi_plan_r2r_f03') ++ import ++ integer(C_INT), value :: rnk ++ integer(C_INTPTR_T), dimension(*), intent(in) :: n ++ real(C_LONG_DOUBLE), dimension(*), intent(out) :: in ++ real(C_LONG_DOUBLE), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_FFTW_R2R_KIND), dimension(*), intent(in) :: kind ++ integer(C_INT), value :: flags ++ end function fftwl_mpi_plan_r2r ++ ++ type(C_PTR) function fftwl_mpi_plan_r2r_2d(n0,n1,in,out,comm,kind0,kind1,flags) bind(C, name='fftwl_mpi_plan_r2r_2d_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: n1 ++ real(C_LONG_DOUBLE), dimension(*), intent(out) :: in ++ real(C_LONG_DOUBLE), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_FFTW_R2R_KIND), value :: kind0 ++ integer(C_FFTW_R2R_KIND), value :: kind1 ++ integer(C_INT), value :: flags ++ end function fftwl_mpi_plan_r2r_2d ++ ++ type(C_PTR) function fftwl_mpi_plan_r2r_3d(n0,n1,n2,in,out,comm,kind0,kind1,kind2,flags) & ++ bind(C, name='fftwl_mpi_plan_r2r_3d_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: n1 ++ integer(C_INTPTR_T), value :: n2 ++ real(C_LONG_DOUBLE), dimension(*), intent(out) :: in ++ real(C_LONG_DOUBLE), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_FFTW_R2R_KIND), value :: kind0 ++ integer(C_FFTW_R2R_KIND), value :: kind1 ++ integer(C_FFTW_R2R_KIND), value :: kind2 ++ integer(C_INT), value :: flags ++ end function fftwl_mpi_plan_r2r_3d ++ ++ type(C_PTR) function fftwl_mpi_plan_many_dft_r2c(rnk,n,howmany,iblock,oblock,in,out,comm,flags) & ++ bind(C, name='fftwl_mpi_plan_many_dft_r2c_f03') ++ import ++ integer(C_INT), value :: rnk ++ integer(C_INTPTR_T), dimension(*), intent(in) :: n ++ integer(C_INTPTR_T), value :: howmany ++ integer(C_INTPTR_T), value :: iblock ++ integer(C_INTPTR_T), value :: oblock ++ real(C_LONG_DOUBLE), dimension(*), intent(out) :: in ++ complex(C_LONG_DOUBLE_COMPLEX), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: flags ++ end function fftwl_mpi_plan_many_dft_r2c ++ ++ type(C_PTR) function fftwl_mpi_plan_dft_r2c(rnk,n,in,out,comm,flags) bind(C, name='fftwl_mpi_plan_dft_r2c_f03') ++ import ++ integer(C_INT), value :: rnk ++ integer(C_INTPTR_T), dimension(*), intent(in) :: n ++ real(C_LONG_DOUBLE), dimension(*), intent(out) :: in ++ complex(C_LONG_DOUBLE_COMPLEX), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: flags ++ end function fftwl_mpi_plan_dft_r2c ++ ++ type(C_PTR) function fftwl_mpi_plan_dft_r2c_2d(n0,n1,in,out,comm,flags) bind(C, name='fftwl_mpi_plan_dft_r2c_2d_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: n1 ++ real(C_LONG_DOUBLE), dimension(*), intent(out) :: in ++ complex(C_LONG_DOUBLE_COMPLEX), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: flags ++ end function fftwl_mpi_plan_dft_r2c_2d ++ ++ type(C_PTR) function fftwl_mpi_plan_dft_r2c_3d(n0,n1,n2,in,out,comm,flags) bind(C, name='fftwl_mpi_plan_dft_r2c_3d_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: n1 ++ integer(C_INTPTR_T), value :: n2 ++ real(C_LONG_DOUBLE), dimension(*), intent(out) :: in ++ complex(C_LONG_DOUBLE_COMPLEX), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: flags ++ end function fftwl_mpi_plan_dft_r2c_3d ++ ++ type(C_PTR) function fftwl_mpi_plan_many_dft_c2r(rnk,n,howmany,iblock,oblock,in,out,comm,flags) & ++ bind(C, name='fftwl_mpi_plan_many_dft_c2r_f03') ++ import ++ integer(C_INT), value :: rnk ++ integer(C_INTPTR_T), dimension(*), intent(in) :: n ++ integer(C_INTPTR_T), value :: howmany ++ integer(C_INTPTR_T), value :: iblock ++ integer(C_INTPTR_T), value :: oblock ++ complex(C_LONG_DOUBLE_COMPLEX), dimension(*), intent(out) :: in ++ real(C_LONG_DOUBLE), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: flags ++ end function fftwl_mpi_plan_many_dft_c2r ++ ++ type(C_PTR) function fftwl_mpi_plan_dft_c2r(rnk,n,in,out,comm,flags) bind(C, name='fftwl_mpi_plan_dft_c2r_f03') ++ import ++ integer(C_INT), value :: rnk ++ integer(C_INTPTR_T), dimension(*), intent(in) :: n ++ complex(C_LONG_DOUBLE_COMPLEX), dimension(*), intent(out) :: in ++ real(C_LONG_DOUBLE), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: flags ++ end function fftwl_mpi_plan_dft_c2r ++ ++ type(C_PTR) function fftwl_mpi_plan_dft_c2r_2d(n0,n1,in,out,comm,flags) bind(C, name='fftwl_mpi_plan_dft_c2r_2d_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: n1 ++ complex(C_LONG_DOUBLE_COMPLEX), dimension(*), intent(out) :: in ++ real(C_LONG_DOUBLE), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: flags ++ end function fftwl_mpi_plan_dft_c2r_2d ++ ++ type(C_PTR) function fftwl_mpi_plan_dft_c2r_3d(n0,n1,n2,in,out,comm,flags) bind(C, name='fftwl_mpi_plan_dft_c2r_3d_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: n1 ++ integer(C_INTPTR_T), value :: n2 ++ complex(C_LONG_DOUBLE_COMPLEX), dimension(*), intent(out) :: in ++ real(C_LONG_DOUBLE), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: flags ++ end function fftwl_mpi_plan_dft_c2r_3d ++ ++ subroutine fftwl_mpi_gather_wisdom(comm_) bind(C, name='fftwl_mpi_gather_wisdom_f03') ++ import ++ integer(C_MPI_FINT), value :: comm_ ++ end subroutine fftwl_mpi_gather_wisdom ++ ++ subroutine fftwl_mpi_broadcast_wisdom(comm_) bind(C, name='fftwl_mpi_broadcast_wisdom_f03') ++ import ++ integer(C_MPI_FINT), value :: comm_ ++ end subroutine fftwl_mpi_broadcast_wisdom ++ ++ subroutine fftwl_mpi_execute_dft(p,in,out) bind(C, name='fftwl_mpi_execute_dft') ++ import ++ type(C_PTR), value :: p ++ complex(C_LONG_DOUBLE_COMPLEX), dimension(*), intent(inout) :: in ++ complex(C_LONG_DOUBLE_COMPLEX), dimension(*), intent(out) :: out ++ end subroutine fftwl_mpi_execute_dft ++ ++ subroutine fftwl_mpi_execute_dft_r2c(p,in,out) bind(C, name='fftwl_mpi_execute_dft_r2c') ++ import ++ type(C_PTR), value :: p ++ real(C_LONG_DOUBLE), dimension(*), intent(inout) :: in ++ complex(C_LONG_DOUBLE_COMPLEX), dimension(*), intent(out) :: out ++ end subroutine fftwl_mpi_execute_dft_r2c ++ ++ subroutine fftwl_mpi_execute_dft_c2r(p,in,out) bind(C, name='fftwl_mpi_execute_dft_c2r') ++ import ++ type(C_PTR), value :: p ++ complex(C_LONG_DOUBLE_COMPLEX), dimension(*), intent(inout) :: in ++ real(C_LONG_DOUBLE), dimension(*), intent(out) :: out ++ end subroutine fftwl_mpi_execute_dft_c2r ++ ++ subroutine fftwl_mpi_execute_r2r(p,in,out) bind(C, name='fftwl_mpi_execute_r2r') ++ import ++ type(C_PTR), value :: p ++ real(C_LONG_DOUBLE), dimension(*), intent(inout) :: in ++ real(C_LONG_DOUBLE), dimension(*), intent(out) :: out ++ end subroutine fftwl_mpi_execute_r2r ++ + end interface +diff -ru fftw-3.3.6-pl1.orig/mpi/fftw3-mpi.f03.in fftw-3.3.6-pl1/mpi/fftw3-mpi.f03.in +--- fftw-3.3.6-pl1.orig/mpi/fftw3-mpi.f03.in 2017-01-16 15:12:37.000000002 +0100 ++++ fftw-3.3.6-pl1/mpi/fftw3-mpi.f03.in 2017-03-08 16:20:11.000000002 +0100 +@@ -13,6 +13,399 @@ + end type fftw_mpi_ddim + + interface ++ subroutine fftw_mpi_init() bind(C, name='fftw_mpi_init') ++ import ++ end subroutine fftw_mpi_init ++ ++ subroutine fftw_mpi_cleanup() bind(C, name='fftw_mpi_cleanup') ++ import ++ end subroutine fftw_mpi_cleanup ++ ++ integer(C_INTPTR_T) function fftw_mpi_local_size_many_transposed(rnk,n,howmany,block0,block1,comm,local_n0,local_0_start, & ++ local_n1,local_1_start) & ++ bind(C, name='fftw_mpi_local_size_many_transposed_f03') ++ import ++ integer(C_INT), value :: rnk ++ integer(C_INTPTR_T), dimension(*), intent(in) :: n ++ integer(C_INTPTR_T), value :: howmany ++ integer(C_INTPTR_T), value :: block0 ++ integer(C_INTPTR_T), value :: block1 ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INTPTR_T), intent(out) :: local_n0 ++ integer(C_INTPTR_T), intent(out) :: local_0_start ++ integer(C_INTPTR_T), intent(out) :: local_n1 ++ integer(C_INTPTR_T), intent(out) :: local_1_start ++ end function fftw_mpi_local_size_many_transposed ++ ++ integer(C_INTPTR_T) function fftw_mpi_local_size_many(rnk,n,howmany,block0,comm,local_n0,local_0_start) & ++ bind(C, name='fftw_mpi_local_size_many_f03') ++ import ++ integer(C_INT), value :: rnk ++ integer(C_INTPTR_T), dimension(*), intent(in) :: n ++ integer(C_INTPTR_T), value :: howmany ++ integer(C_INTPTR_T), value :: block0 ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INTPTR_T), intent(out) :: local_n0 ++ integer(C_INTPTR_T), intent(out) :: local_0_start ++ end function fftw_mpi_local_size_many ++ ++ integer(C_INTPTR_T) function fftw_mpi_local_size_transposed(rnk,n,comm,local_n0,local_0_start,local_n1,local_1_start) & ++ bind(C, name='fftw_mpi_local_size_transposed_f03') ++ import ++ integer(C_INT), value :: rnk ++ integer(C_INTPTR_T), dimension(*), intent(in) :: n ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INTPTR_T), intent(out) :: local_n0 ++ integer(C_INTPTR_T), intent(out) :: local_0_start ++ integer(C_INTPTR_T), intent(out) :: local_n1 ++ integer(C_INTPTR_T), intent(out) :: local_1_start ++ end function fftw_mpi_local_size_transposed ++ ++ integer(C_INTPTR_T) function fftw_mpi_local_size(rnk,n,comm,local_n0,local_0_start) bind(C, name='fftw_mpi_local_size_f03') ++ import ++ integer(C_INT), value :: rnk ++ integer(C_INTPTR_T), dimension(*), intent(in) :: n ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INTPTR_T), intent(out) :: local_n0 ++ integer(C_INTPTR_T), intent(out) :: local_0_start ++ end function fftw_mpi_local_size ++ ++ integer(C_INTPTR_T) function fftw_mpi_local_size_many_1d(n0,howmany,comm,sign,flags,local_ni,local_i_start,local_no, & ++ local_o_start) bind(C, name='fftw_mpi_local_size_many_1d_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: howmany ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: sign ++ integer(C_INT), value :: flags ++ integer(C_INTPTR_T), intent(out) :: local_ni ++ integer(C_INTPTR_T), intent(out) :: local_i_start ++ integer(C_INTPTR_T), intent(out) :: local_no ++ integer(C_INTPTR_T), intent(out) :: local_o_start ++ end function fftw_mpi_local_size_many_1d ++ ++ integer(C_INTPTR_T) function fftw_mpi_local_size_1d(n0,comm,sign,flags,local_ni,local_i_start,local_no,local_o_start) & ++ bind(C, name='fftw_mpi_local_size_1d_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: sign ++ integer(C_INT), value :: flags ++ integer(C_INTPTR_T), intent(out) :: local_ni ++ integer(C_INTPTR_T), intent(out) :: local_i_start ++ integer(C_INTPTR_T), intent(out) :: local_no ++ integer(C_INTPTR_T), intent(out) :: local_o_start ++ end function fftw_mpi_local_size_1d ++ ++ integer(C_INTPTR_T) function fftw_mpi_local_size_2d(n0,n1,comm,local_n0,local_0_start) & ++ bind(C, name='fftw_mpi_local_size_2d_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: n1 ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INTPTR_T), intent(out) :: local_n0 ++ integer(C_INTPTR_T), intent(out) :: local_0_start ++ end function fftw_mpi_local_size_2d ++ ++ integer(C_INTPTR_T) function fftw_mpi_local_size_2d_transposed(n0,n1,comm,local_n0,local_0_start,local_n1,local_1_start) & ++ bind(C, name='fftw_mpi_local_size_2d_transposed_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: n1 ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INTPTR_T), intent(out) :: local_n0 ++ integer(C_INTPTR_T), intent(out) :: local_0_start ++ integer(C_INTPTR_T), intent(out) :: local_n1 ++ integer(C_INTPTR_T), intent(out) :: local_1_start ++ end function fftw_mpi_local_size_2d_transposed ++ ++ integer(C_INTPTR_T) function fftw_mpi_local_size_3d(n0,n1,n2,comm,local_n0,local_0_start) & ++ bind(C, name='fftw_mpi_local_size_3d_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: n1 ++ integer(C_INTPTR_T), value :: n2 ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INTPTR_T), intent(out) :: local_n0 ++ integer(C_INTPTR_T), intent(out) :: local_0_start ++ end function fftw_mpi_local_size_3d ++ ++ integer(C_INTPTR_T) function fftw_mpi_local_size_3d_transposed(n0,n1,n2,comm,local_n0,local_0_start,local_n1,local_1_start) & ++ bind(C, name='fftw_mpi_local_size_3d_transposed_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: n1 ++ integer(C_INTPTR_T), value :: n2 ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INTPTR_T), intent(out) :: local_n0 ++ integer(C_INTPTR_T), intent(out) :: local_0_start ++ integer(C_INTPTR_T), intent(out) :: local_n1 ++ integer(C_INTPTR_T), intent(out) :: local_1_start ++ end function fftw_mpi_local_size_3d_transposed ++ ++ type(C_PTR) function fftw_mpi_plan_many_transpose(n0,n1,howmany,block0,block1,in,out,comm,flags) & ++ bind(C, name='fftw_mpi_plan_many_transpose_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: n1 ++ integer(C_INTPTR_T), value :: howmany ++ integer(C_INTPTR_T), value :: block0 ++ integer(C_INTPTR_T), value :: block1 ++ real(C_DOUBLE), dimension(*), intent(out) :: in ++ real(C_DOUBLE), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: flags ++ end function fftw_mpi_plan_many_transpose ++ ++ type(C_PTR) function fftw_mpi_plan_transpose(n0,n1,in,out,comm,flags) bind(C, name='fftw_mpi_plan_transpose_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: n1 ++ real(C_DOUBLE), dimension(*), intent(out) :: in ++ real(C_DOUBLE), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: flags ++ end function fftw_mpi_plan_transpose ++ ++ type(C_PTR) function fftw_mpi_plan_many_dft(rnk,n,howmany,block,tblock,in,out,comm,sign,flags) & ++ bind(C, name='fftw_mpi_plan_many_dft_f03') ++ import ++ integer(C_INT), value :: rnk ++ integer(C_INTPTR_T), dimension(*), intent(in) :: n ++ integer(C_INTPTR_T), value :: howmany ++ integer(C_INTPTR_T), value :: block ++ integer(C_INTPTR_T), value :: tblock ++ complex(C_DOUBLE_COMPLEX), dimension(*), intent(out) :: in ++ complex(C_DOUBLE_COMPLEX), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: sign ++ integer(C_INT), value :: flags ++ end function fftw_mpi_plan_many_dft ++ ++ type(C_PTR) function fftw_mpi_plan_dft(rnk,n,in,out,comm,sign,flags) bind(C, name='fftw_mpi_plan_dft_f03') ++ import ++ integer(C_INT), value :: rnk ++ integer(C_INTPTR_T), dimension(*), intent(in) :: n ++ complex(C_DOUBLE_COMPLEX), dimension(*), intent(out) :: in ++ complex(C_DOUBLE_COMPLEX), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: sign ++ integer(C_INT), value :: flags ++ end function fftw_mpi_plan_dft ++ ++ type(C_PTR) function fftw_mpi_plan_dft_1d(n0,in,out,comm,sign,flags) bind(C, name='fftw_mpi_plan_dft_1d_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ complex(C_DOUBLE_COMPLEX), dimension(*), intent(out) :: in ++ complex(C_DOUBLE_COMPLEX), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: sign ++ integer(C_INT), value :: flags ++ end function fftw_mpi_plan_dft_1d ++ ++ type(C_PTR) function fftw_mpi_plan_dft_2d(n0,n1,in,out,comm,sign,flags) bind(C, name='fftw_mpi_plan_dft_2d_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: n1 ++ complex(C_DOUBLE_COMPLEX), dimension(*), intent(out) :: in ++ complex(C_DOUBLE_COMPLEX), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: sign ++ integer(C_INT), value :: flags ++ end function fftw_mpi_plan_dft_2d ++ ++ type(C_PTR) function fftw_mpi_plan_dft_3d(n0,n1,n2,in,out,comm,sign,flags) bind(C, name='fftw_mpi_plan_dft_3d_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: n1 ++ integer(C_INTPTR_T), value :: n2 ++ complex(C_DOUBLE_COMPLEX), dimension(*), intent(out) :: in ++ complex(C_DOUBLE_COMPLEX), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: sign ++ integer(C_INT), value :: flags ++ end function fftw_mpi_plan_dft_3d ++ ++ type(C_PTR) function fftw_mpi_plan_many_r2r(rnk,n,howmany,iblock,oblock,in,out,comm,kind,flags) & ++ bind(C, name='fftw_mpi_plan_many_r2r_f03') ++ import ++ integer(C_INT), value :: rnk ++ integer(C_INTPTR_T), dimension(*), intent(in) :: n ++ integer(C_INTPTR_T), value :: howmany ++ integer(C_INTPTR_T), value :: iblock ++ integer(C_INTPTR_T), value :: oblock ++ real(C_DOUBLE), dimension(*), intent(out) :: in ++ real(C_DOUBLE), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_FFTW_R2R_KIND), dimension(*), intent(in) :: kind ++ integer(C_INT), value :: flags ++ end function fftw_mpi_plan_many_r2r ++ ++ type(C_PTR) function fftw_mpi_plan_r2r(rnk,n,in,out,comm,kind,flags) bind(C, name='fftw_mpi_plan_r2r_f03') ++ import ++ integer(C_INT), value :: rnk ++ integer(C_INTPTR_T), dimension(*), intent(in) :: n ++ real(C_DOUBLE), dimension(*), intent(out) :: in ++ real(C_DOUBLE), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_FFTW_R2R_KIND), dimension(*), intent(in) :: kind ++ integer(C_INT), value :: flags ++ end function fftw_mpi_plan_r2r ++ ++ type(C_PTR) function fftw_mpi_plan_r2r_2d(n0,n1,in,out,comm,kind0,kind1,flags) bind(C, name='fftw_mpi_plan_r2r_2d_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: n1 ++ real(C_DOUBLE), dimension(*), intent(out) :: in ++ real(C_DOUBLE), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_FFTW_R2R_KIND), value :: kind0 ++ integer(C_FFTW_R2R_KIND), value :: kind1 ++ integer(C_INT), value :: flags ++ end function fftw_mpi_plan_r2r_2d ++ ++ type(C_PTR) function fftw_mpi_plan_r2r_3d(n0,n1,n2,in,out,comm,kind0,kind1,kind2,flags) bind(C, name='fftw_mpi_plan_r2r_3d_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: n1 ++ integer(C_INTPTR_T), value :: n2 ++ real(C_DOUBLE), dimension(*), intent(out) :: in ++ real(C_DOUBLE), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_FFTW_R2R_KIND), value :: kind0 ++ integer(C_FFTW_R2R_KIND), value :: kind1 ++ integer(C_FFTW_R2R_KIND), value :: kind2 ++ integer(C_INT), value :: flags ++ end function fftw_mpi_plan_r2r_3d ++ ++ type(C_PTR) function fftw_mpi_plan_many_dft_r2c(rnk,n,howmany,iblock,oblock,in,out,comm,flags) & ++ bind(C, name='fftw_mpi_plan_many_dft_r2c_f03') ++ import ++ integer(C_INT), value :: rnk ++ integer(C_INTPTR_T), dimension(*), intent(in) :: n ++ integer(C_INTPTR_T), value :: howmany ++ integer(C_INTPTR_T), value :: iblock ++ integer(C_INTPTR_T), value :: oblock ++ real(C_DOUBLE), dimension(*), intent(out) :: in ++ complex(C_DOUBLE_COMPLEX), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: flags ++ end function fftw_mpi_plan_many_dft_r2c ++ ++ type(C_PTR) function fftw_mpi_plan_dft_r2c(rnk,n,in,out,comm,flags) bind(C, name='fftw_mpi_plan_dft_r2c_f03') ++ import ++ integer(C_INT), value :: rnk ++ integer(C_INTPTR_T), dimension(*), intent(in) :: n ++ real(C_DOUBLE), dimension(*), intent(out) :: in ++ complex(C_DOUBLE_COMPLEX), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: flags ++ end function fftw_mpi_plan_dft_r2c ++ ++ type(C_PTR) function fftw_mpi_plan_dft_r2c_2d(n0,n1,in,out,comm,flags) bind(C, name='fftw_mpi_plan_dft_r2c_2d_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: n1 ++ real(C_DOUBLE), dimension(*), intent(out) :: in ++ complex(C_DOUBLE_COMPLEX), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: flags ++ end function fftw_mpi_plan_dft_r2c_2d ++ ++ type(C_PTR) function fftw_mpi_plan_dft_r2c_3d(n0,n1,n2,in,out,comm,flags) bind(C, name='fftw_mpi_plan_dft_r2c_3d_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: n1 ++ integer(C_INTPTR_T), value :: n2 ++ real(C_DOUBLE), dimension(*), intent(out) :: in ++ complex(C_DOUBLE_COMPLEX), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: flags ++ end function fftw_mpi_plan_dft_r2c_3d ++ ++ type(C_PTR) function fftw_mpi_plan_many_dft_c2r(rnk,n,howmany,iblock,oblock,in,out,comm,flags) & ++ bind(C, name='fftw_mpi_plan_many_dft_c2r_f03') ++ import ++ integer(C_INT), value :: rnk ++ integer(C_INTPTR_T), dimension(*), intent(in) :: n ++ integer(C_INTPTR_T), value :: howmany ++ integer(C_INTPTR_T), value :: iblock ++ integer(C_INTPTR_T), value :: oblock ++ complex(C_DOUBLE_COMPLEX), dimension(*), intent(out) :: in ++ real(C_DOUBLE), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: flags ++ end function fftw_mpi_plan_many_dft_c2r ++ ++ type(C_PTR) function fftw_mpi_plan_dft_c2r(rnk,n,in,out,comm,flags) bind(C, name='fftw_mpi_plan_dft_c2r_f03') ++ import ++ integer(C_INT), value :: rnk ++ integer(C_INTPTR_T), dimension(*), intent(in) :: n ++ complex(C_DOUBLE_COMPLEX), dimension(*), intent(out) :: in ++ real(C_DOUBLE), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: flags ++ end function fftw_mpi_plan_dft_c2r ++ ++ type(C_PTR) function fftw_mpi_plan_dft_c2r_2d(n0,n1,in,out,comm,flags) bind(C, name='fftw_mpi_plan_dft_c2r_2d_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: n1 ++ complex(C_DOUBLE_COMPLEX), dimension(*), intent(out) :: in ++ real(C_DOUBLE), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: flags ++ end function fftw_mpi_plan_dft_c2r_2d ++ ++ type(C_PTR) function fftw_mpi_plan_dft_c2r_3d(n0,n1,n2,in,out,comm,flags) bind(C, name='fftw_mpi_plan_dft_c2r_3d_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: n1 ++ integer(C_INTPTR_T), value :: n2 ++ complex(C_DOUBLE_COMPLEX), dimension(*), intent(out) :: in ++ real(C_DOUBLE), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: flags ++ end function fftw_mpi_plan_dft_c2r_3d ++ ++ subroutine fftw_mpi_gather_wisdom(comm_) bind(C, name='fftw_mpi_gather_wisdom_f03') ++ import ++ integer(C_MPI_FINT), value :: comm_ ++ end subroutine fftw_mpi_gather_wisdom ++ ++ subroutine fftw_mpi_broadcast_wisdom(comm_) bind(C, name='fftw_mpi_broadcast_wisdom_f03') ++ import ++ integer(C_MPI_FINT), value :: comm_ ++ end subroutine fftw_mpi_broadcast_wisdom ++ ++ subroutine fftw_mpi_execute_dft(p,in,out) bind(C, name='fftw_mpi_execute_dft') ++ import ++ type(C_PTR), value :: p ++ complex(C_DOUBLE_COMPLEX), dimension(*), intent(inout) :: in ++ complex(C_DOUBLE_COMPLEX), dimension(*), intent(out) :: out ++ end subroutine fftw_mpi_execute_dft ++ ++ subroutine fftw_mpi_execute_dft_r2c(p,in,out) bind(C, name='fftw_mpi_execute_dft_r2c') ++ import ++ type(C_PTR), value :: p ++ real(C_DOUBLE), dimension(*), intent(inout) :: in ++ complex(C_DOUBLE_COMPLEX), dimension(*), intent(out) :: out ++ end subroutine fftw_mpi_execute_dft_r2c ++ ++ subroutine fftw_mpi_execute_dft_c2r(p,in,out) bind(C, name='fftw_mpi_execute_dft_c2r') ++ import ++ type(C_PTR), value :: p ++ complex(C_DOUBLE_COMPLEX), dimension(*), intent(inout) :: in ++ real(C_DOUBLE), dimension(*), intent(out) :: out ++ end subroutine fftw_mpi_execute_dft_c2r ++ ++ subroutine fftw_mpi_execute_r2r(p,in,out) bind(C, name='fftw_mpi_execute_r2r') ++ import ++ type(C_PTR), value :: p ++ real(C_DOUBLE), dimension(*), intent(inout) :: in ++ real(C_DOUBLE), dimension(*), intent(out) :: out ++ end subroutine fftw_mpi_execute_r2r ++ + end interface + + type, bind(C) :: fftwf_mpi_ddim +@@ -20,4 +413,398 @@ + end type fftwf_mpi_ddim + + interface ++ subroutine fftwf_mpi_init() bind(C, name='fftwf_mpi_init') ++ import ++ end subroutine fftwf_mpi_init ++ ++ subroutine fftwf_mpi_cleanup() bind(C, name='fftwf_mpi_cleanup') ++ import ++ end subroutine fftwf_mpi_cleanup ++ ++ integer(C_INTPTR_T) function fftwf_mpi_local_size_many_transposed(rnk,n,howmany,block0,block1,comm,local_n0,local_0_start, & ++ local_n1,local_1_start) & ++ bind(C, name='fftwf_mpi_local_size_many_transposed_f03') ++ import ++ integer(C_INT), value :: rnk ++ integer(C_INTPTR_T), dimension(*), intent(in) :: n ++ integer(C_INTPTR_T), value :: howmany ++ integer(C_INTPTR_T), value :: block0 ++ integer(C_INTPTR_T), value :: block1 ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INTPTR_T), intent(out) :: local_n0 ++ integer(C_INTPTR_T), intent(out) :: local_0_start ++ integer(C_INTPTR_T), intent(out) :: local_n1 ++ integer(C_INTPTR_T), intent(out) :: local_1_start ++ end function fftwf_mpi_local_size_many_transposed ++ ++ integer(C_INTPTR_T) function fftwf_mpi_local_size_many(rnk,n,howmany,block0,comm,local_n0,local_0_start) & ++ bind(C, name='fftwf_mpi_local_size_many_f03') ++ import ++ integer(C_INT), value :: rnk ++ integer(C_INTPTR_T), dimension(*), intent(in) :: n ++ integer(C_INTPTR_T), value :: howmany ++ integer(C_INTPTR_T), value :: block0 ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INTPTR_T), intent(out) :: local_n0 ++ integer(C_INTPTR_T), intent(out) :: local_0_start ++ end function fftwf_mpi_local_size_many ++ ++ integer(C_INTPTR_T) function fftwf_mpi_local_size_transposed(rnk,n,comm,local_n0,local_0_start,local_n1,local_1_start) & ++ bind(C, name='fftwf_mpi_local_size_transposed_f03') ++ import ++ integer(C_INT), value :: rnk ++ integer(C_INTPTR_T), dimension(*), intent(in) :: n ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INTPTR_T), intent(out) :: local_n0 ++ integer(C_INTPTR_T), intent(out) :: local_0_start ++ integer(C_INTPTR_T), intent(out) :: local_n1 ++ integer(C_INTPTR_T), intent(out) :: local_1_start ++ end function fftwf_mpi_local_size_transposed ++ ++ integer(C_INTPTR_T) function fftwf_mpi_local_size(rnk,n,comm,local_n0,local_0_start) bind(C, name='fftwf_mpi_local_size_f03') ++ import ++ integer(C_INT), value :: rnk ++ integer(C_INTPTR_T), dimension(*), intent(in) :: n ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INTPTR_T), intent(out) :: local_n0 ++ integer(C_INTPTR_T), intent(out) :: local_0_start ++ end function fftwf_mpi_local_size ++ ++ integer(C_INTPTR_T) function fftwf_mpi_local_size_many_1d(n0,howmany,comm,sign,flags,local_ni,local_i_start,local_no, & ++ local_o_start) bind(C, name='fftwf_mpi_local_size_many_1d_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: howmany ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: sign ++ integer(C_INT), value :: flags ++ integer(C_INTPTR_T), intent(out) :: local_ni ++ integer(C_INTPTR_T), intent(out) :: local_i_start ++ integer(C_INTPTR_T), intent(out) :: local_no ++ integer(C_INTPTR_T), intent(out) :: local_o_start ++ end function fftwf_mpi_local_size_many_1d ++ ++ integer(C_INTPTR_T) function fftwf_mpi_local_size_1d(n0,comm,sign,flags,local_ni,local_i_start,local_no,local_o_start) & ++ bind(C, name='fftwf_mpi_local_size_1d_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: sign ++ integer(C_INT), value :: flags ++ integer(C_INTPTR_T), intent(out) :: local_ni ++ integer(C_INTPTR_T), intent(out) :: local_i_start ++ integer(C_INTPTR_T), intent(out) :: local_no ++ integer(C_INTPTR_T), intent(out) :: local_o_start ++ end function fftwf_mpi_local_size_1d ++ ++ integer(C_INTPTR_T) function fftwf_mpi_local_size_2d(n0,n1,comm,local_n0,local_0_start) & ++ bind(C, name='fftwf_mpi_local_size_2d_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: n1 ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INTPTR_T), intent(out) :: local_n0 ++ integer(C_INTPTR_T), intent(out) :: local_0_start ++ end function fftwf_mpi_local_size_2d ++ ++ integer(C_INTPTR_T) function fftwf_mpi_local_size_2d_transposed(n0,n1,comm,local_n0,local_0_start,local_n1,local_1_start) & ++ bind(C, name='fftwf_mpi_local_size_2d_transposed_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: n1 ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INTPTR_T), intent(out) :: local_n0 ++ integer(C_INTPTR_T), intent(out) :: local_0_start ++ integer(C_INTPTR_T), intent(out) :: local_n1 ++ integer(C_INTPTR_T), intent(out) :: local_1_start ++ end function fftwf_mpi_local_size_2d_transposed ++ ++ integer(C_INTPTR_T) function fftwf_mpi_local_size_3d(n0,n1,n2,comm,local_n0,local_0_start) & ++ bind(C, name='fftwf_mpi_local_size_3d_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: n1 ++ integer(C_INTPTR_T), value :: n2 ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INTPTR_T), intent(out) :: local_n0 ++ integer(C_INTPTR_T), intent(out) :: local_0_start ++ end function fftwf_mpi_local_size_3d ++ ++ integer(C_INTPTR_T) function fftwf_mpi_local_size_3d_transposed(n0,n1,n2,comm,local_n0,local_0_start,local_n1,local_1_start) & ++ bind(C, name='fftwf_mpi_local_size_3d_transposed_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: n1 ++ integer(C_INTPTR_T), value :: n2 ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INTPTR_T), intent(out) :: local_n0 ++ integer(C_INTPTR_T), intent(out) :: local_0_start ++ integer(C_INTPTR_T), intent(out) :: local_n1 ++ integer(C_INTPTR_T), intent(out) :: local_1_start ++ end function fftwf_mpi_local_size_3d_transposed ++ ++ type(C_PTR) function fftwf_mpi_plan_many_transpose(n0,n1,howmany,block0,block1,in,out,comm,flags) & ++ bind(C, name='fftwf_mpi_plan_many_transpose_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: n1 ++ integer(C_INTPTR_T), value :: howmany ++ integer(C_INTPTR_T), value :: block0 ++ integer(C_INTPTR_T), value :: block1 ++ real(C_FLOAT), dimension(*), intent(out) :: in ++ real(C_FLOAT), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: flags ++ end function fftwf_mpi_plan_many_transpose ++ ++ type(C_PTR) function fftwf_mpi_plan_transpose(n0,n1,in,out,comm,flags) bind(C, name='fftwf_mpi_plan_transpose_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: n1 ++ real(C_FLOAT), dimension(*), intent(out) :: in ++ real(C_FLOAT), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: flags ++ end function fftwf_mpi_plan_transpose ++ ++ type(C_PTR) function fftwf_mpi_plan_many_dft(rnk,n,howmany,block,tblock,in,out,comm,sign,flags) & ++ bind(C, name='fftwf_mpi_plan_many_dft_f03') ++ import ++ integer(C_INT), value :: rnk ++ integer(C_INTPTR_T), dimension(*), intent(in) :: n ++ integer(C_INTPTR_T), value :: howmany ++ integer(C_INTPTR_T), value :: block ++ integer(C_INTPTR_T), value :: tblock ++ complex(C_FLOAT_COMPLEX), dimension(*), intent(out) :: in ++ complex(C_FLOAT_COMPLEX), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: sign ++ integer(C_INT), value :: flags ++ end function fftwf_mpi_plan_many_dft ++ ++ type(C_PTR) function fftwf_mpi_plan_dft(rnk,n,in,out,comm,sign,flags) bind(C, name='fftwf_mpi_plan_dft_f03') ++ import ++ integer(C_INT), value :: rnk ++ integer(C_INTPTR_T), dimension(*), intent(in) :: n ++ complex(C_FLOAT_COMPLEX), dimension(*), intent(out) :: in ++ complex(C_FLOAT_COMPLEX), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: sign ++ integer(C_INT), value :: flags ++ end function fftwf_mpi_plan_dft ++ ++ type(C_PTR) function fftwf_mpi_plan_dft_1d(n0,in,out,comm,sign,flags) bind(C, name='fftwf_mpi_plan_dft_1d_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ complex(C_FLOAT_COMPLEX), dimension(*), intent(out) :: in ++ complex(C_FLOAT_COMPLEX), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: sign ++ integer(C_INT), value :: flags ++ end function fftwf_mpi_plan_dft_1d ++ ++ type(C_PTR) function fftwf_mpi_plan_dft_2d(n0,n1,in,out,comm,sign,flags) bind(C, name='fftwf_mpi_plan_dft_2d_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: n1 ++ complex(C_FLOAT_COMPLEX), dimension(*), intent(out) :: in ++ complex(C_FLOAT_COMPLEX), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: sign ++ integer(C_INT), value :: flags ++ end function fftwf_mpi_plan_dft_2d ++ ++ type(C_PTR) function fftwf_mpi_plan_dft_3d(n0,n1,n2,in,out,comm,sign,flags) bind(C, name='fftwf_mpi_plan_dft_3d_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: n1 ++ integer(C_INTPTR_T), value :: n2 ++ complex(C_FLOAT_COMPLEX), dimension(*), intent(out) :: in ++ complex(C_FLOAT_COMPLEX), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: sign ++ integer(C_INT), value :: flags ++ end function fftwf_mpi_plan_dft_3d ++ ++ type(C_PTR) function fftwf_mpi_plan_many_r2r(rnk,n,howmany,iblock,oblock,in,out,comm,kind,flags) & ++ bind(C, name='fftwf_mpi_plan_many_r2r_f03') ++ import ++ integer(C_INT), value :: rnk ++ integer(C_INTPTR_T), dimension(*), intent(in) :: n ++ integer(C_INTPTR_T), value :: howmany ++ integer(C_INTPTR_T), value :: iblock ++ integer(C_INTPTR_T), value :: oblock ++ real(C_FLOAT), dimension(*), intent(out) :: in ++ real(C_FLOAT), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_FFTW_R2R_KIND), dimension(*), intent(in) :: kind ++ integer(C_INT), value :: flags ++ end function fftwf_mpi_plan_many_r2r ++ ++ type(C_PTR) function fftwf_mpi_plan_r2r(rnk,n,in,out,comm,kind,flags) bind(C, name='fftwf_mpi_plan_r2r_f03') ++ import ++ integer(C_INT), value :: rnk ++ integer(C_INTPTR_T), dimension(*), intent(in) :: n ++ real(C_FLOAT), dimension(*), intent(out) :: in ++ real(C_FLOAT), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_FFTW_R2R_KIND), dimension(*), intent(in) :: kind ++ integer(C_INT), value :: flags ++ end function fftwf_mpi_plan_r2r ++ ++ type(C_PTR) function fftwf_mpi_plan_r2r_2d(n0,n1,in,out,comm,kind0,kind1,flags) bind(C, name='fftwf_mpi_plan_r2r_2d_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: n1 ++ real(C_FLOAT), dimension(*), intent(out) :: in ++ real(C_FLOAT), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_FFTW_R2R_KIND), value :: kind0 ++ integer(C_FFTW_R2R_KIND), value :: kind1 ++ integer(C_INT), value :: flags ++ end function fftwf_mpi_plan_r2r_2d ++ ++ type(C_PTR) function fftwf_mpi_plan_r2r_3d(n0,n1,n2,in,out,comm,kind0,kind1,kind2,flags) & ++ bind(C, name='fftwf_mpi_plan_r2r_3d_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: n1 ++ integer(C_INTPTR_T), value :: n2 ++ real(C_FLOAT), dimension(*), intent(out) :: in ++ real(C_FLOAT), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_FFTW_R2R_KIND), value :: kind0 ++ integer(C_FFTW_R2R_KIND), value :: kind1 ++ integer(C_FFTW_R2R_KIND), value :: kind2 ++ integer(C_INT), value :: flags ++ end function fftwf_mpi_plan_r2r_3d ++ ++ type(C_PTR) function fftwf_mpi_plan_many_dft_r2c(rnk,n,howmany,iblock,oblock,in,out,comm,flags) & ++ bind(C, name='fftwf_mpi_plan_many_dft_r2c_f03') ++ import ++ integer(C_INT), value :: rnk ++ integer(C_INTPTR_T), dimension(*), intent(in) :: n ++ integer(C_INTPTR_T), value :: howmany ++ integer(C_INTPTR_T), value :: iblock ++ integer(C_INTPTR_T), value :: oblock ++ real(C_FLOAT), dimension(*), intent(out) :: in ++ complex(C_FLOAT_COMPLEX), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: flags ++ end function fftwf_mpi_plan_many_dft_r2c ++ ++ type(C_PTR) function fftwf_mpi_plan_dft_r2c(rnk,n,in,out,comm,flags) bind(C, name='fftwf_mpi_plan_dft_r2c_f03') ++ import ++ integer(C_INT), value :: rnk ++ integer(C_INTPTR_T), dimension(*), intent(in) :: n ++ real(C_FLOAT), dimension(*), intent(out) :: in ++ complex(C_FLOAT_COMPLEX), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: flags ++ end function fftwf_mpi_plan_dft_r2c ++ ++ type(C_PTR) function fftwf_mpi_plan_dft_r2c_2d(n0,n1,in,out,comm,flags) bind(C, name='fftwf_mpi_plan_dft_r2c_2d_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: n1 ++ real(C_FLOAT), dimension(*), intent(out) :: in ++ complex(C_FLOAT_COMPLEX), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: flags ++ end function fftwf_mpi_plan_dft_r2c_2d ++ ++ type(C_PTR) function fftwf_mpi_plan_dft_r2c_3d(n0,n1,n2,in,out,comm,flags) bind(C, name='fftwf_mpi_plan_dft_r2c_3d_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: n1 ++ integer(C_INTPTR_T), value :: n2 ++ real(C_FLOAT), dimension(*), intent(out) :: in ++ complex(C_FLOAT_COMPLEX), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: flags ++ end function fftwf_mpi_plan_dft_r2c_3d ++ ++ type(C_PTR) function fftwf_mpi_plan_many_dft_c2r(rnk,n,howmany,iblock,oblock,in,out,comm,flags) & ++ bind(C, name='fftwf_mpi_plan_many_dft_c2r_f03') ++ import ++ integer(C_INT), value :: rnk ++ integer(C_INTPTR_T), dimension(*), intent(in) :: n ++ integer(C_INTPTR_T), value :: howmany ++ integer(C_INTPTR_T), value :: iblock ++ integer(C_INTPTR_T), value :: oblock ++ complex(C_FLOAT_COMPLEX), dimension(*), intent(out) :: in ++ real(C_FLOAT), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: flags ++ end function fftwf_mpi_plan_many_dft_c2r ++ ++ type(C_PTR) function fftwf_mpi_plan_dft_c2r(rnk,n,in,out,comm,flags) bind(C, name='fftwf_mpi_plan_dft_c2r_f03') ++ import ++ integer(C_INT), value :: rnk ++ integer(C_INTPTR_T), dimension(*), intent(in) :: n ++ complex(C_FLOAT_COMPLEX), dimension(*), intent(out) :: in ++ real(C_FLOAT), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: flags ++ end function fftwf_mpi_plan_dft_c2r ++ ++ type(C_PTR) function fftwf_mpi_plan_dft_c2r_2d(n0,n1,in,out,comm,flags) bind(C, name='fftwf_mpi_plan_dft_c2r_2d_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: n1 ++ complex(C_FLOAT_COMPLEX), dimension(*), intent(out) :: in ++ real(C_FLOAT), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: flags ++ end function fftwf_mpi_plan_dft_c2r_2d ++ ++ type(C_PTR) function fftwf_mpi_plan_dft_c2r_3d(n0,n1,n2,in,out,comm,flags) bind(C, name='fftwf_mpi_plan_dft_c2r_3d_f03') ++ import ++ integer(C_INTPTR_T), value :: n0 ++ integer(C_INTPTR_T), value :: n1 ++ integer(C_INTPTR_T), value :: n2 ++ complex(C_FLOAT_COMPLEX), dimension(*), intent(out) :: in ++ real(C_FLOAT), dimension(*), intent(out) :: out ++ integer(C_MPI_FINT), value :: comm ++ integer(C_INT), value :: flags ++ end function fftwf_mpi_plan_dft_c2r_3d ++ ++ subroutine fftwf_mpi_gather_wisdom(comm_) bind(C, name='fftwf_mpi_gather_wisdom_f03') ++ import ++ integer(C_MPI_FINT), value :: comm_ ++ end subroutine fftwf_mpi_gather_wisdom ++ ++ subroutine fftwf_mpi_broadcast_wisdom(comm_) bind(C, name='fftwf_mpi_broadcast_wisdom_f03') ++ import ++ integer(C_MPI_FINT), value :: comm_ ++ end subroutine fftwf_mpi_broadcast_wisdom ++ ++ subroutine fftwf_mpi_execute_dft(p,in,out) bind(C, name='fftwf_mpi_execute_dft') ++ import ++ type(C_PTR), value :: p ++ complex(C_FLOAT_COMPLEX), dimension(*), intent(inout) :: in ++ complex(C_FLOAT_COMPLEX), dimension(*), intent(out) :: out ++ end subroutine fftwf_mpi_execute_dft ++ ++ subroutine fftwf_mpi_execute_dft_r2c(p,in,out) bind(C, name='fftwf_mpi_execute_dft_r2c') ++ import ++ type(C_PTR), value :: p ++ real(C_FLOAT), dimension(*), intent(inout) :: in ++ complex(C_FLOAT_COMPLEX), dimension(*), intent(out) :: out ++ end subroutine fftwf_mpi_execute_dft_r2c ++ ++ subroutine fftwf_mpi_execute_dft_c2r(p,in,out) bind(C, name='fftwf_mpi_execute_dft_c2r') ++ import ++ type(C_PTR), value :: p ++ complex(C_FLOAT_COMPLEX), dimension(*), intent(inout) :: in ++ real(C_FLOAT), dimension(*), intent(out) :: out ++ end subroutine fftwf_mpi_execute_dft_c2r ++ ++ subroutine fftwf_mpi_execute_r2r(p,in,out) bind(C, name='fftwf_mpi_execute_r2r') ++ import ++ type(C_PTR), value :: p ++ real(C_FLOAT), dimension(*), intent(inout) :: in ++ real(C_FLOAT), dimension(*), intent(out) :: out ++ end subroutine fftwf_mpi_execute_r2r ++ + end interface diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-gompi-2017a.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-gompi-2017a.eb index 039c1bb824..4325e0c729 100644 --- a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-gompi-2017a.eb +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-gompi-2017a.eb @@ -12,6 +12,10 @@ source_urls = [homepage] sources = ['fftw-%(version)s-pl1.tar.gz'] checksums = ['682a0e78d6966ca37c7446d4ab4cc2a1'] +patches = [ + 'FFTW-3.3.6-F03_interface_pl2.patch', +] + runtest = 'check' moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-intel-2017a.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-intel-2017a.eb new file mode 100644 index 0000000000..07c5fa9224 --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-intel-2017a.eb @@ -0,0 +1,29 @@ +name = 'FFTW' +version = '3.3.6' + +homepage = 'http://www.fftw.org' +description = """FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) + in one or more dimensions, of arbitrary input size, and of both real and complex data.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = ['fftw-%(version)s-pl1.tar.gz'] +checksums = ['682a0e78d6966ca37c7446d4ab4cc2a1'] + +patches = [ + 'FFTW-3.3.6-F03_interface_pl2.patch', +] + +# no quad precision, requires GCC v4.6 or higher +# see also +# http://www.fftw.org/doc/Extended-and-quadruple-precision-in-Fortran.html +with_quad_prec = False + +# compilation fails when configuring with --enable-avx-128-fma +use_fma = False + +runtest = 'check' + +moduleclass = 'numlib' -- GitLab From 4c1ce458d807fa27d47c7f301c47abd4c02fdf9d Mon Sep 17 00:00:00 2001 From: Robert Qiao Date: Sun, 12 Mar 2017 11:59:46 +1030 Subject: [PATCH 0354/1603] style --- easybuild/easyconfigs/h/HTSlib/HTSlib-1.2.1-foss-2016b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/h/HTSlib/HTSlib-1.2.1-foss-2016b.eb b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.2.1-foss-2016b.eb index 66babc415c..a58dae978a 100644 --- a/easybuild/easyconfigs/h/HTSlib/HTSlib-1.2.1-foss-2016b.eb +++ b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.2.1-foss-2016b.eb @@ -32,7 +32,7 @@ dependencies = [ ] sanity_check_paths = { - 'files': ["bin/bgzip", "bin/tabix", "lib/libhts.so"], + 'files': ["bin/bgzip", "bin/tabix", "lib/libhts.%s" % SHLIB_EXT], 'dirs': [], } -- GitLab From fa1ffbce7c441662925f5042a6a427907f0f6285 Mon Sep 17 00:00:00 2001 From: Robert Qiao Date: Sun, 12 Mar 2017 13:14:35 +1030 Subject: [PATCH 0355/1603] Testing --- .../easyconfigs/p/PileOMeth/PileOMeth-0.1.11-foss-2016b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PileOMeth/PileOMeth-0.1.11-foss-2016b.eb b/easybuild/easyconfigs/p/PileOMeth/PileOMeth-0.1.11-foss-2016b.eb index edf4ca1f37..1a66bb0381 100644 --- a/easybuild/easyconfigs/p/PileOMeth/PileOMeth-0.1.11-foss-2016b.eb +++ b/easybuild/easyconfigs/p/PileOMeth/PileOMeth-0.1.11-foss-2016b.eb @@ -6,7 +6,7 @@ # Authors:: Robert Qiao , Exe Escobedo # License:: # -# Notes:: +# Notes:: Testing ### easyblock = 'MakeCp' -- GitLab From 6f719a74f5ac27d67427c5cc6a1063745ced50ff Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Mon, 13 Mar 2017 09:08:33 +0200 Subject: [PATCH 0356/1603] Updated the patch with the URL to the upstream commit from fftw git. --- .../easyconfigs/f/FFTW/FFTW-3.3.6-F03_interface_pl2.patch | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-F03_interface_pl2.patch b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-F03_interface_pl2.patch index 70d5168fbf..f09a971da7 100644 --- a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-F03_interface_pl2.patch +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-F03_interface_pl2.patch @@ -2,13 +2,15 @@ # The scripts were using fftw3.h from /usr/include, not ../api, and were # failing silently if fftw3.h was not installed. This bug led to a # fftw-3.3.6pl1 release with incomplete mpi/f03 header files. -# See commit 83092f8efbf872aefe7cfc6ee8fa43412f8e167a in FFTW upstream -# git. +# +# See commit +# https://github.com/FFTW/fftw3/commit/83092f8efbf872aefe7cfc6ee8fa43412f8e167a +# in FFTW upstream git. # # This patch is the result of applying that commit and running the # maintainer mode scripts. # -# Åke Sandgrem 2017-03-07 +# Åke Sandgren, 2017-03-07 diff -ru fftw-3.3.6-pl1.orig/mpi/f03api.sh fftw-3.3.6-pl1/mpi/f03api.sh --- fftw-3.3.6-pl1.orig/mpi/f03api.sh 2017-01-15 13:03:24.000000002 +0100 +++ fftw-3.3.6-pl1/mpi/f03api.sh 2017-03-08 15:46:56.000000002 +0100 -- GitLab From 4a0b7275c165adf41ab75b4d3fc1082f51388bb5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Luk=C3=A1=C5=A1=20Krup=C4=8D=C3=ADk?= Date: Mon, 13 Mar 2017 09:05:20 +0100 Subject: [PATCH 0357/1603] {tools}LSMS-3_rev237 --- easybuild/easyconfigs/l/LSMS-3_rev237.eb | 31 ++++++ easybuild/easyconfigs/l/LSMS-Makefiles.patch | 106 +++++++++++++++++++ 2 files changed, 137 insertions(+) create mode 100644 easybuild/easyconfigs/l/LSMS-3_rev237.eb create mode 100644 easybuild/easyconfigs/l/LSMS-Makefiles.patch diff --git a/easybuild/easyconfigs/l/LSMS-3_rev237.eb b/easybuild/easyconfigs/l/LSMS-3_rev237.eb new file mode 100644 index 0000000000..014f9beea4 --- /dev/null +++ b/easybuild/easyconfigs/l/LSMS-3_rev237.eb @@ -0,0 +1,31 @@ +easyblock = 'MakeCp' + +name = 'LSMS' +version = '3_rev237' + +homepage = 'https://asc.llnl.gov/CORAL-benchmarks/#lsms' +description = "LSMS benchmark, part of CORAL suite" + +toolchain = {'name': 'foss', 'version': '2015g' } + +source_urls = ['https://asc.llnl.gov/CORAL-benchmarks/Science/'] +sources = ['%(name)s_%(version)s.tar.bz2'] + +checksums = ['8c864c9223b93488663815557e61cd0b'] + +patches = ['LSMS-Makefiles.patch'] + +files_to_copy = ['bin/lsms', 'bin/wl-lsms'] + +buildopts = '-j 1' + +dependencies = [ + ('HDF5', '1.8.16'), +] + +sanity_check_paths = { + 'files': ['lsms', 'wl-lsms'], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/l/LSMS-Makefiles.patch b/easybuild/easyconfigs/l/LSMS-Makefiles.patch new file mode 100644 index 0000000000..5c1f5e5908 --- /dev/null +++ b/easybuild/easyconfigs/l/LSMS-Makefiles.patch @@ -0,0 +1,106 @@ +--- LSMS_3_rev237/CBLAS/Makefile 2012-02-09 20:17:00.000000000 +0100 ++++ LSMS_3_rev237_working/CBLAS/Makefile 2017-03-09 15:44:39.524649760 +0100 +@@ -1,6 +1,29 @@ + dlvl = ./. + include $(dlvl)/Makefile.in +-include ../architecture.h ++ ++# export USE_GPTL=1 ++export USE_OPENMP=1 ++ ++export ADD_LIBS += -L$(TOP_DIR)/lua/lib -L$(TOP_DIR)/CBLAS/lib/ -lcblas_LINUX -lmpi -lmpi_cxx -lhdf5 -lgfortran -lopenblas $(FPMPI_POST_LINK_OPTS) ++ ++export INC_PATH += -I $(TOP_DIR)/CBLAS/include -I $(TOP_DIR)/lua/include ++ ++export ADDITIONAL_TARGETS = CBLAS_target ++ ++export BOOST_ROOT=$(TOP_DIR) ++ ++ ++ifdef USE_OPENMP ++ export CXX += -g -std=c++11 -I$(BOOST_ROOT) -fopenmp ++ #export CXX=CC -I$(BOOST_ROOT) -DUSE_PAPI -fopenmp ++ #export F77=ftn -fopenmp ++ export F77 += -fopenmp ++else ++ export CXX += -std=c++11 -I$(BOOST_ROOT) ++ #export CXX=CC -I$(BOOST_ROOT) -DUSE_PAPI ++ #export F77=ftn ++endif ++export LUACXX = $(CXX) + + all: alllib alltst + +--- LSMS_3_rev237/src/Test/buildKKRMatrixTest/Makefile 2012-02-15 19:41:17.000000000 +0100 ++++ LSMS_3_rev237_working/src/Test/buildKKRMatrixTest/Makefile 2017-03-09 15:47:04.088863802 +0100 +@@ -3,7 +3,29 @@ + export INC_PATH = + export LIBS := + +-include $(TOP_DIR)/architecture.h ++# export USE_GPTL=1 ++export USE_OPENMP=1 ++ ++export ADD_LIBS += -L$(TOP_DIR)/lua/lib -L$(TOP_DIR)/CBLAS/lib/ -lcblas_LINUX -lmpi -lmpi_cxx -lhdf5 -lgfortran -lopenblas $(FPMPI_POST_LINK_OPTS) ++ ++export INC_PATH += -I $(TOP_DIR)/CBLAS/include -I $(TOP_DIR)/lua/include ++ ++export ADDITIONAL_TARGETS = CBLAS_target ++ ++export BOOST_ROOT=$(TOP_DIR) ++ ++ ++ifdef USE_OPENMP ++ export CXX += -g -std=c++11 -I$(BOOST_ROOT) -fopenmp ++ #export CXX=CC -I$(BOOST_ROOT) -DUSE_PAPI -fopenmp ++ #export F77=ftn -fopenmp ++ export F77 += -fopenmp ++else ++ export CXX += -std=c++11 -I$(BOOST_ROOT) ++ #export CXX=CC -I$(BOOST_ROOT) -DUSE_PAPI ++ #export F77=ftn ++endif ++export LUACXX = $(CXX) + + export INC_PATH += -I $(TOP_DIR)/include -I $(TOP_DIR)/src + export MISC = $(TOP_DIR)/src/Misc +--- LSMS_3_rev237/Makefile 2017-03-09 15:47:50.699882415 +0100 ++++ LSMS_3_rev237_working/Makefile 2017-03-09 14:58:44.845436772 +0100 +@@ -1,10 +1,35 @@ + + export TOP_DIR = $(shell pwd) +-export INC_PATH = + # export LIBS := -L$(TOP_DIR)/lua/lib -llua $(TOP_DIR)/mjson/mjson.a + export LIBS := $(TOP_DIR)/lua/lib/liblua.a $(TOP_DIR)/mjson/mjson.a + +-include architecture.h ++export CC = gcc ++export CXX = g++ ++export F77 = gfortran ++ ++# export USE_GPTL=1 ++export USE_OPENMP=1 ++ ++export ADD_LIBS += -L$(TOP_DIR)/lua/lib -L$(TOP_DIR)/CBLAS/lib/ -lcblas_LINUX -lmpi -lmpi_cxx -lhdf5 -lgfortran -lopenblas $(FPMPI_POST_LINK_OPTS) ++ ++export INC_PATH += -I $(TOP_DIR)/CBLAS/include -I $(TOP_DIR)/lua/include ++ ++export ADDITIONAL_TARGETS = CBLAS_target ++ ++export BOOST_ROOT=$(TOP_DIR) ++ ++ ++ifdef USE_OPENMP ++ export CXX += -g -std=c++11 -I$(BOOST_ROOT) -fopenmp ++ #export CXX=CC -I$(BOOST_ROOT) -DUSE_PAPI -fopenmp ++ #export F77=ftn -fopenmp ++ export F77 += -fopenmp ++else ++ export CXX += -std=c++11 -I$(BOOST_ROOT) ++ #export CXX=CC -I$(BOOST_ROOT) -DUSE_PAPI ++ #export F77=ftn ++endif ++export LUACXX = $(CXX) + + + all: liblua $(ADDITIONAL_TARGETS) libmjson LSMS -- GitLab From bc135bc82da4d927fa86526d64fac52b273fd338 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Luk=C3=A1=C5=A1=20Krup=C4=8D=C3=ADk?= Date: Mon, 13 Mar 2017 09:15:58 +0100 Subject: [PATCH 0358/1603] change directory and added toolchain to name --- .../l/{LSMS-3_rev237.eb => LSMS/LSMS-3_rev237-foss-2015g.eb} | 0 easybuild/easyconfigs/l/{ => LSMS}/LSMS-Makefiles.patch | 0 2 files changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/l/{LSMS-3_rev237.eb => LSMS/LSMS-3_rev237-foss-2015g.eb} (100%) rename easybuild/easyconfigs/l/{ => LSMS}/LSMS-Makefiles.patch (100%) diff --git a/easybuild/easyconfigs/l/LSMS-3_rev237.eb b/easybuild/easyconfigs/l/LSMS/LSMS-3_rev237-foss-2015g.eb similarity index 100% rename from easybuild/easyconfigs/l/LSMS-3_rev237.eb rename to easybuild/easyconfigs/l/LSMS/LSMS-3_rev237-foss-2015g.eb diff --git a/easybuild/easyconfigs/l/LSMS-Makefiles.patch b/easybuild/easyconfigs/l/LSMS/LSMS-Makefiles.patch similarity index 100% rename from easybuild/easyconfigs/l/LSMS-Makefiles.patch rename to easybuild/easyconfigs/l/LSMS/LSMS-Makefiles.patch -- GitLab From 12a958880fea5a3840959fada778f82ab132238f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Luk=C3=A1=C5=A1=20Krup=C4=8D=C3=ADk?= Date: Mon, 13 Mar 2017 09:33:54 +0100 Subject: [PATCH 0359/1603] change $root to $root/bin --- .../easyconfigs/l/LSMS/LSMS-3_rev237-foss-2015g.eb | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/l/LSMS/LSMS-3_rev237-foss-2015g.eb b/easybuild/easyconfigs/l/LSMS/LSMS-3_rev237-foss-2015g.eb index 014f9beea4..c708bb19a4 100644 --- a/easybuild/easyconfigs/l/LSMS/LSMS-3_rev237-foss-2015g.eb +++ b/easybuild/easyconfigs/l/LSMS/LSMS-3_rev237-foss-2015g.eb @@ -15,17 +15,18 @@ checksums = ['8c864c9223b93488663815557e61cd0b'] patches = ['LSMS-Makefiles.patch'] -files_to_copy = ['bin/lsms', 'bin/wl-lsms'] +#files_to_copy = ['bin/lsms', 'bin/wl-lsms'] +files_to_copy = ['bin'] buildopts = '-j 1' -dependencies = [ - ('HDF5', '1.8.16'), +dependencies = [ + ('HDF5', '1.8.16'), ] sanity_check_paths = { - 'files': ['lsms', 'wl-lsms'], + 'files': ['bin/lsms', 'bin/wl-lsms'], 'dirs': [], } - + moduleclass = 'tools' -- GitLab From 8fe97272f49beba4d341c2b087eac159294f9606 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Luk=C3=A1=C5=A1=20Krup=C4=8D=C3=ADk?= Date: Mon, 13 Mar 2017 09:45:25 +0100 Subject: [PATCH 0360/1603] remove singularity --- .../Singularity-2.2.1-GCC-6.3.0-2.27.eb | 23 ------------------- 1 file changed, 23 deletions(-) delete mode 100644 easybuild/easyconfigs/s/Singularity/Singularity-2.2.1-GCC-6.3.0-2.27.eb diff --git a/easybuild/easyconfigs/s/Singularity/Singularity-2.2.1-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/s/Singularity/Singularity-2.2.1-GCC-6.3.0-2.27.eb deleted file mode 100644 index e1e43de48b..0000000000 --- a/easybuild/easyconfigs/s/Singularity/Singularity-2.2.1-GCC-6.3.0-2.27.eb +++ /dev/null @@ -1,23 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'Singularity' -version = '2.2.1' - -homepage = 'http://gmkurtzer.github.io/singularity' -description = """Singularity is a portable application stack packaging and runtime utility.""" - -toolchain = {'name': 'GCC', 'version': '6.3.0-2.27'} - -source_urls = ['https://github.com/gmkurtzer/singularity/archive/'] -sources = ['%(version)s.tar.gz'] - -builddependencies = [('Autotools', '20150215')] - -preconfigopts = './autogen.sh && ' - -sanity_check_paths = { - 'files': ['bin/run-singularity', 'bin/singularity', 'etc/singularity/singularity.conf', 'libexec/singularity/sexec-suid'], - 'dirs': ['etc', 'libexec/singularity'], -} - -moduleclass = 'tools' -- GitLab From c4732f5b681ee9ec959c2bf50470ff9c6b24704a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Luk=C3=A1=C5=A1=20Krup=C4=8D=C3=ADk?= Date: Mon, 13 Mar 2017 10:09:46 +0100 Subject: [PATCH 0361/1603] add LSMS-3_rev237-foss-2016a --- .../l/LSMS/LSMS-3_rev237-foss-2016a.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/l/LSMS/LSMS-3_rev237-foss-2016a.eb diff --git a/easybuild/easyconfigs/l/LSMS/LSMS-3_rev237-foss-2016a.eb b/easybuild/easyconfigs/l/LSMS/LSMS-3_rev237-foss-2016a.eb new file mode 100644 index 0000000000..ff6c8b7de3 --- /dev/null +++ b/easybuild/easyconfigs/l/LSMS/LSMS-3_rev237-foss-2016a.eb @@ -0,0 +1,32 @@ +easyblock = 'MakeCp' + +name = 'LSMS' +version = '3_rev237' + +homepage = 'https://asc.llnl.gov/CORAL-benchmarks/#lsms' +description = "LSMS benchmark, part of CORAL suite" + +toolchain = {'name': 'foss', 'version': '2016a' } + +source_urls = ['https://asc.llnl.gov/CORAL-benchmarks/Science/'] +sources = ['%(name)s_%(version)s.tar.bz2'] + +checksums = ['8c864c9223b93488663815557e61cd0b'] + +patches = ['LSMS-Makefiles.patch'] + +#files_to_copy = ['bin/lsms', 'bin/wl-lsms'] +files_to_copy = ['bin'] + +buildopts = '-j 1' + +dependencies = [ + ('HDF5', '1.8.16'), +] + +sanity_check_paths = { + 'files': ['bin/lsms', 'bin/wl-lsms'], + 'dirs': [], +} + +moduleclass = 'tools' -- GitLab From a05f85ff643946fe8058d7a839a979093f2b7239 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Mon, 13 Mar 2017 11:31:59 +0200 Subject: [PATCH 0362/1603] adding easyconfigs: arpack-ng-3.4.0-foss-2017a.eb, arpack-ng-3.4.0-intel-2017a.eb --- .../a/arpack-ng/arpack-ng-3.4.0-foss-2017a.eb | 25 +++++++++++++++++++ .../arpack-ng/arpack-ng-3.4.0-intel-2017a.eb | 25 +++++++++++++++++++ 2 files changed, 50 insertions(+) create mode 100644 easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.4.0-foss-2017a.eb create mode 100644 easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.4.0-intel-2017a.eb diff --git a/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.4.0-foss-2017a.eb b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.4.0-foss-2017a.eb new file mode 100644 index 0000000000..12081625ca --- /dev/null +++ b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.4.0-foss-2017a.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'arpack-ng' +version = '3.4.0' + +homepage = 'http://forge.scilab.org/index.php/p/arpack-ng/' +description = """ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems.""" + +toolchain = {'name': 'foss', 'version': '2017a'} +toolchainopts = {'opt': True, 'pic': True, 'usempi': True} + +source_urls = ['https://github.com/opencollab/arpack-ng/archive/'] +sources = ['%(version)s.tar.gz'] + +builddependencies = [('Autotools', '20150215')] + +preconfigopts = "sh bootstrap && " +configopts = '--with-pic --with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK"' + +sanity_check_paths = { + 'files': ["lib/libarpack.a", "lib/libarpack.so"], + 'dirs': [] +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.4.0-intel-2017a.eb b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.4.0-intel-2017a.eb new file mode 100644 index 0000000000..f92abdeafa --- /dev/null +++ b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.4.0-intel-2017a.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'arpack-ng' +version = '3.4.0' + +homepage = 'http://forge.scilab.org/index.php/p/arpack-ng/' +description = """ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'opt': True, 'pic': True, 'usempi': True} + +source_urls = ['https://github.com/opencollab/arpack-ng/archive/'] +sources = ['%(version)s.tar.gz'] + +builddependencies = [('Autotools', '20150215')] + +preconfigopts = "sh bootstrap && " +configopts = '--with-pic --with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK"' + +sanity_check_paths = { + 'files': ["lib/libarpack.a", "lib/libarpack.so"], + 'dirs': [] +} + +moduleclass = 'numlib' -- GitLab From 587c000e0c2e3dfc7f6e6c6f03713a725841813f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Luk=C3=A1=C5=A1=20Krup=C4=8D=C3=ADk?= Date: Mon, 13 Mar 2017 10:35:36 +0100 Subject: [PATCH 0363/1603] remove #... comment --- easybuild/easyconfigs/l/LSMS/LSMS-3_rev237-foss-2015g.eb | 1 - easybuild/easyconfigs/l/LSMS/LSMS-3_rev237-foss-2016a.eb | 1 - 2 files changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/l/LSMS/LSMS-3_rev237-foss-2015g.eb b/easybuild/easyconfigs/l/LSMS/LSMS-3_rev237-foss-2015g.eb index c708bb19a4..34bdeac5c9 100644 --- a/easybuild/easyconfigs/l/LSMS/LSMS-3_rev237-foss-2015g.eb +++ b/easybuild/easyconfigs/l/LSMS/LSMS-3_rev237-foss-2015g.eb @@ -15,7 +15,6 @@ checksums = ['8c864c9223b93488663815557e61cd0b'] patches = ['LSMS-Makefiles.patch'] -#files_to_copy = ['bin/lsms', 'bin/wl-lsms'] files_to_copy = ['bin'] buildopts = '-j 1' diff --git a/easybuild/easyconfigs/l/LSMS/LSMS-3_rev237-foss-2016a.eb b/easybuild/easyconfigs/l/LSMS/LSMS-3_rev237-foss-2016a.eb index ff6c8b7de3..fa65d19eb5 100644 --- a/easybuild/easyconfigs/l/LSMS/LSMS-3_rev237-foss-2016a.eb +++ b/easybuild/easyconfigs/l/LSMS/LSMS-3_rev237-foss-2016a.eb @@ -15,7 +15,6 @@ checksums = ['8c864c9223b93488663815557e61cd0b'] patches = ['LSMS-Makefiles.patch'] -#files_to_copy = ['bin/lsms', 'bin/wl-lsms'] files_to_copy = ['bin'] buildopts = '-j 1' -- GitLab From 91015b03a8a9dd192e46e16e20c22a47a8d55c00 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Luk=C3=A1=C5=A1=20Krup=C4=8D=C3=ADk?= Date: Mon, 13 Mar 2017 10:46:11 +0100 Subject: [PATCH 0364/1603] remove eb for LSMS-3_rev237-foss-2015g.eb --- .../l/LSMS/LSMS-3_rev237-foss-2015g.eb | 31 ------------------- 1 file changed, 31 deletions(-) delete mode 100644 easybuild/easyconfigs/l/LSMS/LSMS-3_rev237-foss-2015g.eb diff --git a/easybuild/easyconfigs/l/LSMS/LSMS-3_rev237-foss-2015g.eb b/easybuild/easyconfigs/l/LSMS/LSMS-3_rev237-foss-2015g.eb deleted file mode 100644 index 34bdeac5c9..0000000000 --- a/easybuild/easyconfigs/l/LSMS/LSMS-3_rev237-foss-2015g.eb +++ /dev/null @@ -1,31 +0,0 @@ -easyblock = 'MakeCp' - -name = 'LSMS' -version = '3_rev237' - -homepage = 'https://asc.llnl.gov/CORAL-benchmarks/#lsms' -description = "LSMS benchmark, part of CORAL suite" - -toolchain = {'name': 'foss', 'version': '2015g' } - -source_urls = ['https://asc.llnl.gov/CORAL-benchmarks/Science/'] -sources = ['%(name)s_%(version)s.tar.bz2'] - -checksums = ['8c864c9223b93488663815557e61cd0b'] - -patches = ['LSMS-Makefiles.patch'] - -files_to_copy = ['bin'] - -buildopts = '-j 1' - -dependencies = [ - ('HDF5', '1.8.16'), -] - -sanity_check_paths = { - 'files': ['bin/lsms', 'bin/wl-lsms'], - 'dirs': [], -} - -moduleclass = 'tools' -- GitLab From 8b8979ea29dd134984613cb79ebbb6e54216e1f7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 13 Mar 2017 10:50:16 +0100 Subject: [PATCH 0365/1603] adding easyconfigs: SWASH-4.01-intel-2017a-mpi.eb --- .../s/SWASH/SWASH-4.01-intel-2017a-mpi.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/s/SWASH/SWASH-4.01-intel-2017a-mpi.eb diff --git a/easybuild/easyconfigs/s/SWASH/SWASH-4.01-intel-2017a-mpi.eb b/easybuild/easyconfigs/s/SWASH/SWASH-4.01-intel-2017a-mpi.eb new file mode 100644 index 0000000000..57c47cdddd --- /dev/null +++ b/easybuild/easyconfigs/s/SWASH/SWASH-4.01-intel-2017a-mpi.eb @@ -0,0 +1,31 @@ +easyblock = 'MakeCp' + +name = 'SWASH' +version = '4.01' +versionsuffix = '-mpi' + +homepage = 'http://swash.sourceforge.net/' +description = """SWASH is a general-purpose numerical tool for simulating unsteady, non-hydrostatic, free-surface, + rotational flow and transport phenomena in coastal waters as driven by waves, tides, buoyancy and wind forces.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'usempi': True} + +source_urls = ['http://swash.sourceforge.net/download/zip/'] +sources = [SOURCELOWER_TAR_GZ] + +prebuildopts = "unset FC && make config && " +buildopts = 'mpi' + +parallel = 1 + +files_to_copy = [(['swash.exe', 'swashrun', 'SWASHRUN.README'], 'bin')] + +postinstallcmds = ["chmod a+rx %(installdir)s/bin/swash.exe %(installdir)s/bin/swashrun"] + +sanity_check_paths = { + 'files': ['bin/swash.exe', 'bin/swashrun', 'bin/SWASHRUN.README'], + 'dirs': [], +} + +moduleclass = 'cae' -- GitLab From 5129611740578748995df814108c604e645b9f98 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Mon, 13 Mar 2017 10:56:56 +0100 Subject: [PATCH 0366/1603] fixed homepage and source_urls --- .../easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-goolf-1.4.10.eb | 4 ++-- .../easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-ictce-5.3.0.eb | 4 ++-- .../easyconfigs/v/ViennaRNA/ViennaRNA-2.1.6-ictce-5.5.0.eb | 4 ++-- .../easyconfigs/v/ViennaRNA/ViennaRNA-2.2.3-intel-2016b.eb | 4 ++-- 4 files changed, 8 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-goolf-1.4.10.eb b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-goolf-1.4.10.eb index 759ecb7840..3da591ce62 100644 --- a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-goolf-1.4.10.eb @@ -15,7 +15,7 @@ easyblock = 'ConfigureMake' name = 'ViennaRNA' version = '2.0.7' -homepage = 'http://www.tbi.univie.ac.at/~ronny/RNA/vrna2.html' +homepage = 'http://www.tbi.univie.ac.at/RNA/' description = """The Vienna RNA Package consists of a C code library and several stand-alone programs for the prediction and comparison of RNA secondary structures.""" @@ -23,7 +23,7 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'optarch': True, 'pic': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://www.tbi.univie.ac.at/~ronny/RNA'] +source_urls = ['http://www.tbi.univie.ac.at/RNA/download/sourcecode/2_0_x/'] # Prevents the "make install" step from trying to copy to _global_ perl dir and thus make easybuild fail. configopts = '--without-perl' diff --git a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-ictce-5.3.0.eb b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-ictce-5.3.0.eb index f0b4020253..d13e7d8912 100644 --- a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-ictce-5.3.0.eb @@ -15,7 +15,7 @@ easyblock = 'ConfigureMake' name = 'ViennaRNA' version = '2.0.7' -homepage = 'http://www.tbi.univie.ac.at/~ronny/RNA/vrna2.html' +homepage = 'http://www.tbi.univie.ac.at/RNA/' description = """The Vienna RNA Package consists of a C code library and several stand-alone programs for the prediction and comparison of RNA secondary structures.""" @@ -24,7 +24,7 @@ toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'optarch': True, 'pic': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://www.tbi.univie.ac.at/~ronny/RNA'] +source_urls = ['http://www.tbi.univie.ac.at/RNA/download/sourcecode/2_0_x/'] patches = ['ViennaRNA_ictce-pragma.patch'] diff --git a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.1.6-ictce-5.5.0.eb b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.1.6-ictce-5.5.0.eb index 106d2f71e3..3e54d3ed83 100644 --- a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.1.6-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.1.6-ictce-5.5.0.eb @@ -15,7 +15,7 @@ easyblock = 'ConfigureMake' name = 'ViennaRNA' version = '2.1.6' -homepage = 'http://www.tbi.univie.ac.at/~ronny/RNA/vrna2.html' +homepage = 'http://www.tbi.univie.ac.at/RNA/' description = """The Vienna RNA Package consists of a C code library and several stand-alone programs for the prediction and comparison of RNA secondary structures.""" @@ -23,7 +23,7 @@ toolchain = {'name': 'ictce', 'version': '5.5.0'} toolchainopts = {'optarch': True, 'pic': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://www.tbi.univie.ac.at/~ronny/RNA/packages/source'] +source_urls = ['http://www.tbi.univie.ac.at/RNA/download/sourcecode/2_1_x/'] patches = ['ViennaRNA-2.1.6_ictce.patch'] diff --git a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.2.3-intel-2016b.eb b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.2.3-intel-2016b.eb index 714f3edc9e..1988a82b1e 100644 --- a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.2.3-intel-2016b.eb +++ b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.2.3-intel-2016b.eb @@ -15,7 +15,7 @@ easyblock = 'ConfigureMake' name = 'ViennaRNA' version = '2.2.3' -homepage = 'http://www.tbi.univie.ac.at/~ronny/RNA/vrna2.html' +homepage = 'http://www.tbi.univie.ac.at/RNA/' description = """The Vienna RNA Package consists of a C code library and several stand-alone programs for the prediction and comparison of RNA secondary structures.""" @@ -23,7 +23,7 @@ toolchain = {'name': 'intel', 'version': '2016b'} toolchainopts = {'pic': True, 'openmp': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://www.tbi.univie.ac.at/~ronny/RNA/packages/source'] +source_urls = ['http://www.tbi.univie.ac.at/RNA/download/sourcecode/2_2_x/'] patches = ['ViennaRNA-%(version)s_fix-pragma.patch'] -- GitLab From 773a85389fae914ab1520ec122b738c621bc8cd0 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Mon, 13 Mar 2017 10:57:22 +0100 Subject: [PATCH 0367/1603] added ViennaRNA-2.3.4-foss-2016b --- .../v/ViennaRNA/ViennaRNA-2.3.4-foss-2016b.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.3.4-foss-2016b.eb diff --git a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.3.4-foss-2016b.eb b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.3.4-foss-2016b.eb new file mode 100644 index 0000000000..5b2bac1762 --- /dev/null +++ b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.3.4-foss-2016b.eb @@ -0,0 +1,36 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild + +easyblock = 'ConfigureMake' + +name = 'ViennaRNA' +version = '2.3.4' + +homepage = 'http://www.tbi.univie.ac.at/RNA/' +description = """The Vienna RNA Package consists of a C code library and several +stand-alone programs for the prediction and comparison of RNA secondary structures.""" + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'pic': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://www.tbi.univie.ac.at/RNA/download/sourcecode/2_3_x/'] + +checksums = ['c77bff267606d22557a4f867df635822'] + +# Prevents the "make install" step from trying to copy to _global_ perl dir and thus make easybuild fail. +configopts = '--without-perl' +# Alternatively, you may want to use the following to copy the perl-module to a "local" directory +# Code NOT yet tested, therefor left here for future recycling +# preconfigopts = 'env PERLPREFIX="/path/where/the/perl/module/shoud/go"' + +sanity_check_paths = { + 'files': ['bin/RNA%s' % x for x in ['fold', 'eval', 'heat', 'pdist', 'distance', + 'inverse', 'plot', 'subopt', 'Lfold', 'cofold', + 'paln', 'duplex', 'alifold', 'plfold', 'up', + 'aliduplex', 'Lalifold', '2Dfold', 'parconv', + 'PKplex', 'plex', 'snoop', 'forester']] + + ['bin/Kinfold'], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From a3afeb3f7dcda784d5a8e79ebb8a7365edf912f9 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Mon, 13 Mar 2017 12:22:05 +0200 Subject: [PATCH 0368/1603] Use SHLIB_EXT instead of hardcoded ".so" --- easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.4.0-foss-2017a.eb | 2 +- .../easyconfigs/a/arpack-ng/arpack-ng-3.4.0-intel-2017a.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.4.0-foss-2017a.eb b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.4.0-foss-2017a.eb index 12081625ca..f7c3095a50 100644 --- a/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.4.0-foss-2017a.eb +++ b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.4.0-foss-2017a.eb @@ -18,7 +18,7 @@ preconfigopts = "sh bootstrap && " configopts = '--with-pic --with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK"' sanity_check_paths = { - 'files': ["lib/libarpack.a", "lib/libarpack.so"], + 'files': ["lib/libarpack.a", "lib/libarpack.%s" % SHLIB_EXT], 'dirs': [] } diff --git a/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.4.0-intel-2017a.eb b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.4.0-intel-2017a.eb index f92abdeafa..17c7254907 100644 --- a/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.4.0-intel-2017a.eb +++ b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.4.0-intel-2017a.eb @@ -18,7 +18,7 @@ preconfigopts = "sh bootstrap && " configopts = '--with-pic --with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK"' sanity_check_paths = { - 'files': ["lib/libarpack.a", "lib/libarpack.so"], + 'files': ["lib/libarpack.a", "lib/libarpack.%s" % SHLIB_EXT], 'dirs': [] } -- GitLab From 6760a85f0f6e38d783af94b074b4c2d684bf579b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 13 Mar 2017 11:22:55 +0100 Subject: [PATCH 0369/1603] pass $FFLAGS to $FLAGS_OPT for SWASH --- easybuild/easyconfigs/s/SWASH/SWASH-4.01-intel-2017a-mpi.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SWASH/SWASH-4.01-intel-2017a-mpi.eb b/easybuild/easyconfigs/s/SWASH/SWASH-4.01-intel-2017a-mpi.eb index 57c47cdddd..58632f03e4 100644 --- a/easybuild/easyconfigs/s/SWASH/SWASH-4.01-intel-2017a-mpi.eb +++ b/easybuild/easyconfigs/s/SWASH/SWASH-4.01-intel-2017a-mpi.eb @@ -15,7 +15,7 @@ source_urls = ['http://swash.sourceforge.net/download/zip/'] sources = [SOURCELOWER_TAR_GZ] prebuildopts = "unset FC && make config && " -buildopts = 'mpi' +buildopts = 'mpi FLAGS_OPT="$FFLAGS"' parallel = 1 -- GitLab From 7ed9150a0c5b3a194039f14ba74a46484abe55dd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 13 Mar 2017 11:57:00 +0100 Subject: [PATCH 0370/1603] {lib}[intel/2016b] Tensorflow v1.0.1 w/ Python 2.7.12 + 3.5.2 --- ...sorflow-1.0.1-intel-2016b-Python-2.7.12.eb | 35 +++++++++++++++++++ ...nsorflow-1.0.1-intel-2016b-Python-3.5.2.eb | 35 +++++++++++++++++++ 2 files changed, 70 insertions(+) create mode 100755 easybuild/easyconfigs/t/Tensorflow/Tensorflow-1.0.1-intel-2016b-Python-2.7.12.eb create mode 100755 easybuild/easyconfigs/t/Tensorflow/Tensorflow-1.0.1-intel-2016b-Python-3.5.2.eb diff --git a/easybuild/easyconfigs/t/Tensorflow/Tensorflow-1.0.1-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/t/Tensorflow/Tensorflow-1.0.1-intel-2016b-Python-2.7.12.eb new file mode 100755 index 0000000000..f1c3f15e89 --- /dev/null +++ b/easybuild/easyconfigs/t/Tensorflow/Tensorflow-1.0.1-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonPackage' + +name = 'Tensorflow' +version = '1.0.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://www.tensorflow.org/' +description = "An open-source software library for Machine Intelligence" + +toolchain = {'name': 'intel', 'version': '2016b'} + +pymaj = '2' +pymin = '7' +pymajmin = pymaj + pymin + +source_urls = ['https://pypi.python.org/packages/7e/7c/f398393beab1647be0a5e6974b8a34e4ea2d3cb7bd9e38bd43a657ed27d1/'] +sources = [ + 'tensorflow-%%(version)s-cp%(pymajmin)s-cp%(pymajmin)smu-manylinux1_x86_64.whl' % {'pymajmin': pymajmin}, +] +checksums = ['5c88e656fcd34cd89d4cf48d3ec7dd67'] + +dependencies = [ + ('Python', '%s.%s.12' % (pymaj, pymin)), + ('protobuf-python', '3.2.0', versionsuffix), +] + +use_pip = True +unpack_sources = False + +sanity_check_paths = { + 'files': ['bin/tensorboard'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/Tensorflow/Tensorflow-1.0.1-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/t/Tensorflow/Tensorflow-1.0.1-intel-2016b-Python-3.5.2.eb new file mode 100755 index 0000000000..2d9a2afe66 --- /dev/null +++ b/easybuild/easyconfigs/t/Tensorflow/Tensorflow-1.0.1-intel-2016b-Python-3.5.2.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonPackage' + +name = 'Tensorflow' +version = '1.0.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://www.tensorflow.org/' +description = "An open-source software library for Machine Intelligence" + +toolchain = {'name': 'intel', 'version': '2016b'} + +pymaj = '3' +pymin = '5' +pymajmin = pymaj + pymin + +source_urls = ['https://pypi.python.org/packages/1f/38/c255432f18005362dd2459e3bff2b2411eb7d02ca09fa20ee1dd1311f69f/'] +sources = [ + 'tensorflow-%%(version)s-cp%(pymajmin)s-cp%(pymajmin)smu-manylinux1_x86_64.whl' % {'pymajmin': pymajmin}, +] +checksums = ['bccff4d9b87331d4dcecafa43c970b89'] + +dependencies = [ + ('Python', '%s.%s.2' % (pymaj, pymin)), + ('protobuf-python', '3.2.0', versionsuffix), +] + +use_pip = True +unpack_sources = False + +sanity_check_paths = { + 'files': ['bin/tensorboard'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'lib' -- GitLab From fe7e8ddf7a2583411547d522ce9b297a07bc9cb1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 13 Mar 2017 11:59:35 +0100 Subject: [PATCH 0371/1603] fix sources spec for Tensorflow 1.0.1 w/ Python 3.5.2 --- .../t/Tensorflow/Tensorflow-1.0.1-intel-2016b-Python-3.5.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/Tensorflow/Tensorflow-1.0.1-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/t/Tensorflow/Tensorflow-1.0.1-intel-2016b-Python-3.5.2.eb index 2d9a2afe66..42b703619c 100755 --- a/easybuild/easyconfigs/t/Tensorflow/Tensorflow-1.0.1-intel-2016b-Python-3.5.2.eb +++ b/easybuild/easyconfigs/t/Tensorflow/Tensorflow-1.0.1-intel-2016b-Python-3.5.2.eb @@ -15,7 +15,7 @@ pymajmin = pymaj + pymin source_urls = ['https://pypi.python.org/packages/1f/38/c255432f18005362dd2459e3bff2b2411eb7d02ca09fa20ee1dd1311f69f/'] sources = [ - 'tensorflow-%%(version)s-cp%(pymajmin)s-cp%(pymajmin)smu-manylinux1_x86_64.whl' % {'pymajmin': pymajmin}, + 'tensorflow-%%(version)s-cp%(pymajmin)s-cp%(pymajmin)sm-manylinux1_x86_64.whl' % {'pymajmin': pymajmin}, ] checksums = ['bccff4d9b87331d4dcecafa43c970b89'] -- GitLab From 689d70e53f565ae1b0a6a5917182b633f72be48a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 13 Mar 2017 13:24:33 +0100 Subject: [PATCH 0372/1603] pass down $FFLAGS via FLAGS_OPT in SWASH easyconfigs --- easybuild/easyconfigs/s/SWASH/SWASH-3.14-intel-2015b-mpi.eb | 2 +- easybuild/easyconfigs/s/SWASH/SWASH-3.14-intel-2015b-mt.eb | 2 +- easybuild/easyconfigs/s/SWASH/SWASH-3.14-intel-2015b-serial.eb | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/s/SWASH/SWASH-3.14-intel-2015b-mpi.eb b/easybuild/easyconfigs/s/SWASH/SWASH-3.14-intel-2015b-mpi.eb index 767e04327d..c01885134c 100644 --- a/easybuild/easyconfigs/s/SWASH/SWASH-3.14-intel-2015b-mpi.eb +++ b/easybuild/easyconfigs/s/SWASH/SWASH-3.14-intel-2015b-mpi.eb @@ -15,7 +15,7 @@ source_urls = ['http://swash.sourceforge.net/download/zip/'] sources = [SOURCELOWER_TAR_GZ] prebuildopts = "unset FC && make config && " -buildopts = 'mpi' +buildopts = 'mpi FLAGS_OPT="$FFLAGS"' parallel = 1 diff --git a/easybuild/easyconfigs/s/SWASH/SWASH-3.14-intel-2015b-mt.eb b/easybuild/easyconfigs/s/SWASH/SWASH-3.14-intel-2015b-mt.eb index a9d434ebd1..b19bb39b27 100644 --- a/easybuild/easyconfigs/s/SWASH/SWASH-3.14-intel-2015b-mt.eb +++ b/easybuild/easyconfigs/s/SWASH/SWASH-3.14-intel-2015b-mt.eb @@ -15,7 +15,7 @@ source_urls = ['http://swash.sourceforge.net/download/zip/'] sources = [SOURCELOWER_TAR_GZ] prebuildopts = "make config && " -buildopts = 'omp' +buildopts = 'omp FLAGS_OPT="$FFLAGS"' parallel = 1 diff --git a/easybuild/easyconfigs/s/SWASH/SWASH-3.14-intel-2015b-serial.eb b/easybuild/easyconfigs/s/SWASH/SWASH-3.14-intel-2015b-serial.eb index ad04f26f31..1ff3f68105 100644 --- a/easybuild/easyconfigs/s/SWASH/SWASH-3.14-intel-2015b-serial.eb +++ b/easybuild/easyconfigs/s/SWASH/SWASH-3.14-intel-2015b-serial.eb @@ -14,7 +14,7 @@ source_urls = ['http://swash.sourceforge.net/download/zip/'] sources = [SOURCELOWER_TAR_GZ] prebuildopts = "make config && " -buildopts = 'ser' +buildopts = 'ser FLAGS_OPT="$FFLAGS"' parallel = 1 -- GitLab From d12d27667f6a522666539d2d5a0e44993c18b7d0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 13 Mar 2017 13:47:47 +0100 Subject: [PATCH 0373/1603] adding easyconfigs: ImageJ-1.51k.eb --- .../easyconfigs/i/ImageJ/ImageJ-1.51k.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/i/ImageJ/ImageJ-1.51k.eb diff --git a/easybuild/easyconfigs/i/ImageJ/ImageJ-1.51k.eb b/easybuild/easyconfigs/i/ImageJ/ImageJ-1.51k.eb new file mode 100644 index 0000000000..ec975dfc22 --- /dev/null +++ b/easybuild/easyconfigs/i/ImageJ/ImageJ-1.51k.eb @@ -0,0 +1,40 @@ +easyblock = 'PackedBinary' + +name = 'ImageJ' +version = '1.51k' + +homepage = 'https://imagej.nih.gov/ij' +description = "Image Processing and Analysis in Java" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = [ + 'https://imagej.nih.gov/ij/download/src/', + 'http://www.mecourse.com/landinig/software/', +] +sources = [ + 'ij%(version_major)s%(version_minor)s-src.zip', + 'morphology.zip', +] +checksums = [ + 'e7b634bd1d46cec7694a6990180c5cd9', # ij151k-src.zip + '21491b55bbef5cc50ebff495a4d2b420', # morphology.zip +] + +dependencies = [ + ('Java', '1.8.0_121'), +] + +builddependencies = [('ant', '1.10.1', '-Java-%(javaver)s')] + +install_cmd = "cd source && ant build && cp ij.jar %(installdir)s && " +install_cmd += "mkdir -p %(installdir)s/plugins && cp -a %(builddir)s/Morphology/* %(installdir)s/plugins/" + +sanity_check_paths = { + 'files': ['ij.jar'], + 'dirs': ['plugins'], +} + +modloadmsg = "To use ImageJ, run 'java -jar $EBROOTIMAGEJ/ij.jar -Dplugins.dir=$EBROOTIMAGE/plugins'\n" + +moduleclass = 'tools' -- GitLab From a57f5ac9fda2e860342fcd32051027934120b5a9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 13 Mar 2017 14:04:35 +0100 Subject: [PATCH 0374/1603] correctly specify location of plugins for ImageJ --- easybuild/easyconfigs/i/ImageJ/ImageJ-1.51k.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/i/ImageJ/ImageJ-1.51k.eb b/easybuild/easyconfigs/i/ImageJ/ImageJ-1.51k.eb index ec975dfc22..9875b136f1 100644 --- a/easybuild/easyconfigs/i/ImageJ/ImageJ-1.51k.eb +++ b/easybuild/easyconfigs/i/ImageJ/ImageJ-1.51k.eb @@ -35,6 +35,6 @@ sanity_check_paths = { 'dirs': ['plugins'], } -modloadmsg = "To use ImageJ, run 'java -jar $EBROOTIMAGEJ/ij.jar -Dplugins.dir=$EBROOTIMAGE/plugins'\n" +modloadmsg = "To use ImageJ, run 'java -jar $EBROOTIMAGEJ/ij.jar -Dij1.plugins.dir=$EBROOTIMAGE/plugins'\n" moduleclass = 'tools' -- GitLab From 50d330cc3ae39f3ef14a287c0e92ffa9d7782cd6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 13 Mar 2017 14:09:10 +0100 Subject: [PATCH 0375/1603] add easyconfigs for ant/JUnit build deps for ImageJ 1.51k --- .../a/ant/ant-1.10.1-Java-1.8.0_121.eb | 26 +++++++++++++++++++ .../j/JUnit/JUnit-4.12-Java-1.8.0_121.eb | 22 ++++++++++++++++ 2 files changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/a/ant/ant-1.10.1-Java-1.8.0_121.eb create mode 100644 easybuild/easyconfigs/j/JUnit/JUnit-4.12-Java-1.8.0_121.eb diff --git a/easybuild/easyconfigs/a/ant/ant-1.10.1-Java-1.8.0_121.eb b/easybuild/easyconfigs/a/ant/ant-1.10.1-Java-1.8.0_121.eb new file mode 100644 index 0000000000..42ed3e6196 --- /dev/null +++ b/easybuild/easyconfigs/a/ant/ant-1.10.1-Java-1.8.0_121.eb @@ -0,0 +1,26 @@ +name = 'ant' +version = '1.10.1' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'http://ant.apache.org/' +description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in + build files as targets and extension points dependent upon each other. The main known usage of Ant is the build of + Java applications.""" + +toolchain = {'name': 'dummy', 'version': ''} + +sources = ['apache-%(name)s-%(version)s-src.tar.gz'] +source_urls = ['http://archive.apache.org/dist/%(name)s/source/'] + +dependencies = [('Java', '1.8.0_121')] + +builddependencies = [('JUnit', '4.12', versionsuffix)] + +sanity_check_paths = { + 'files': ['bin/ant', 'lib/ant.jar', 'lib/ant.jar'], + 'dirs': [], +} + +modextravars = {'ANT_HOME': '%(installdir)s'} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/j/JUnit/JUnit-4.12-Java-1.8.0_121.eb b/easybuild/easyconfigs/j/JUnit/JUnit-4.12-Java-1.8.0_121.eb new file mode 100644 index 0000000000..43aa70ed7b --- /dev/null +++ b/easybuild/easyconfigs/j/JUnit/JUnit-4.12-Java-1.8.0_121.eb @@ -0,0 +1,22 @@ +easyblock = 'JAR' + +name = 'JUnit' +version = '4.12' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'http://sourceforge.net/projects/junit' +description = """A programmer-oriented testing framework for Java.""" + +toolchain = {'name': 'dummy', 'version': ''} + +sources = ['%(namelower)s-%(version)s.jar'] +source_urls = ['http://search.maven.org/remotecontent?filepath=junit/junit/%(version)s/'] + +dependencies = [('Java', '1.8.0_121')] + +sanity_check_paths = { + 'files': sources, + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From a22fd2b0ff22c524c032bbe7974ef910699cb6bb Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Luk=C3=A1=C5=A1=20Krup=C4=8D=C3=ADk?= Date: Mon, 13 Mar 2017 15:02:55 +0100 Subject: [PATCH 0376/1603] @boegel LSMS-3_rev237-foss-2016a.eb - buildopts = '-j 1' -> parallel = 1 && move dependencies, below patches --- .../easyconfigs/l/LSMS/LSMS-3_rev237-foss-2016a.eb | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/l/LSMS/LSMS-3_rev237-foss-2016a.eb b/easybuild/easyconfigs/l/LSMS/LSMS-3_rev237-foss-2016a.eb index fa65d19eb5..3ca77887d0 100644 --- a/easybuild/easyconfigs/l/LSMS/LSMS-3_rev237-foss-2016a.eb +++ b/easybuild/easyconfigs/l/LSMS/LSMS-3_rev237-foss-2016a.eb @@ -15,13 +15,13 @@ checksums = ['8c864c9223b93488663815557e61cd0b'] patches = ['LSMS-Makefiles.patch'] -files_to_copy = ['bin'] +dependencies = [ + ('HDF5', '1.8.16'), +] -buildopts = '-j 1' +files_to_copy = ['bin'] -dependencies = [ - ('HDF5', '1.8.16'), -] +parallel = 1 sanity_check_paths = { 'files': ['bin/lsms', 'bin/wl-lsms'], -- GitLab From 9c29e8517e77273ba61625703c06025da2dcb73b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Luk=C3=A1=C5=A1=20Krup=C4=8D=C3=ADk?= Date: Mon, 13 Mar 2017 15:06:38 +0100 Subject: [PATCH 0377/1603] {tools}LSMS-3_rev237 renamed LSMS-Makefiles.patch -> LSMS-3_rev237_fix-Makefiles.patch --- easybuild/easyconfigs/l/LSMS/LSMS-3_rev237-foss-2016a.eb | 2 +- .../{LSMS-Makefiles.patch => LSMS-3_rev237_fix-Makefiles.patch} | 0 2 files changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/l/LSMS/{LSMS-Makefiles.patch => LSMS-3_rev237_fix-Makefiles.patch} (100%) diff --git a/easybuild/easyconfigs/l/LSMS/LSMS-3_rev237-foss-2016a.eb b/easybuild/easyconfigs/l/LSMS/LSMS-3_rev237-foss-2016a.eb index 3ca77887d0..198945fde4 100644 --- a/easybuild/easyconfigs/l/LSMS/LSMS-3_rev237-foss-2016a.eb +++ b/easybuild/easyconfigs/l/LSMS/LSMS-3_rev237-foss-2016a.eb @@ -13,7 +13,7 @@ sources = ['%(name)s_%(version)s.tar.bz2'] checksums = ['8c864c9223b93488663815557e61cd0b'] -patches = ['LSMS-Makefiles.patch'] +patches = ['LSMS-3_rev237_fix-Makefiles.patch'] dependencies = [ ('HDF5', '1.8.16'), diff --git a/easybuild/easyconfigs/l/LSMS/LSMS-Makefiles.patch b/easybuild/easyconfigs/l/LSMS/LSMS-3_rev237_fix-Makefiles.patch similarity index 100% rename from easybuild/easyconfigs/l/LSMS/LSMS-Makefiles.patch rename to easybuild/easyconfigs/l/LSMS/LSMS-3_rev237_fix-Makefiles.patch -- GitLab From d3026219c7e50a7fa5e18488b33dd77711ffb30f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Luk=C3=A1=C5=A1=20Krup=C4=8D=C3=ADk?= Date: Mon, 13 Mar 2017 15:18:43 +0100 Subject: [PATCH 0378/1603] {tools}LSMS-3_rev237 add head LSMS-3_rev237_fix-Makefiles.patch --- easybuild/easyconfigs/l/LSMS/LSMS-3_rev237_fix-Makefiles.patch | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/l/LSMS/LSMS-3_rev237_fix-Makefiles.patch b/easybuild/easyconfigs/l/LSMS/LSMS-3_rev237_fix-Makefiles.patch index 5c1f5e5908..e650269d91 100644 --- a/easybuild/easyconfigs/l/LSMS/LSMS-3_rev237_fix-Makefiles.patch +++ b/easybuild/easyconfigs/l/LSMS/LSMS-3_rev237_fix-Makefiles.patch @@ -1,3 +1,5 @@ +#change PATH and exports +#Golasowski Martin, martin.golasowski@vsb.cz, 2016 IT4Innovations --- LSMS_3_rev237/CBLAS/Makefile 2012-02-09 20:17:00.000000000 +0100 +++ LSMS_3_rev237_working/CBLAS/Makefile 2017-03-09 15:44:39.524649760 +0100 @@ -1,6 +1,29 @@ -- GitLab From 31b9523262215334f596cde4ac75aae9242e2798 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Luk=C3=A1=C5=A1=20Krup=C4=8D=C3=ADk?= Date: Mon, 13 Mar 2017 15:25:21 +0100 Subject: [PATCH 0379/1603] {tools}LSMS-3_rev237 2016 -> 2017 --- easybuild/easyconfigs/l/LSMS/LSMS-3_rev237_fix-Makefiles.patch | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/LSMS/LSMS-3_rev237_fix-Makefiles.patch b/easybuild/easyconfigs/l/LSMS/LSMS-3_rev237_fix-Makefiles.patch index e650269d91..191092dc63 100644 --- a/easybuild/easyconfigs/l/LSMS/LSMS-3_rev237_fix-Makefiles.patch +++ b/easybuild/easyconfigs/l/LSMS/LSMS-3_rev237_fix-Makefiles.patch @@ -1,5 +1,5 @@ #change PATH and exports -#Golasowski Martin, martin.golasowski@vsb.cz, 2016 IT4Innovations +#Golasowski Martin, martin.golasowski@vsb.cz, 2017 IT4Innovations --- LSMS_3_rev237/CBLAS/Makefile 2012-02-09 20:17:00.000000000 +0100 +++ LSMS_3_rev237_working/CBLAS/Makefile 2017-03-09 15:44:39.524649760 +0100 @@ -1,6 +1,29 @@ -- GitLab From a1bc03948dde0ab43e356d72a91f8d543f6c4202 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Mon, 13 Mar 2017 15:32:02 +0100 Subject: [PATCH 0380/1603] changed source_urls to use templates --- .../easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-goolf-1.4.10.eb | 2 +- .../easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-ictce-5.3.0.eb | 2 +- .../easyconfigs/v/ViennaRNA/ViennaRNA-2.1.6-ictce-5.5.0.eb | 2 +- .../easyconfigs/v/ViennaRNA/ViennaRNA-2.2.3-intel-2016b.eb | 2 +- easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.3.4-foss-2016b.eb | 2 +- 5 files changed, 5 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-goolf-1.4.10.eb b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-goolf-1.4.10.eb index 3da591ce62..45a8cbb1a5 100644 --- a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-goolf-1.4.10.eb @@ -23,7 +23,7 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'optarch': True, 'pic': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://www.tbi.univie.ac.at/RNA/download/sourcecode/2_0_x/'] +source_urls = ['http://www.tbi.univie.ac.at/RNA/download/sourcecode/%(version_major)s_%(version_minor)s_x/'] # Prevents the "make install" step from trying to copy to _global_ perl dir and thus make easybuild fail. configopts = '--without-perl' diff --git a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-ictce-5.3.0.eb b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-ictce-5.3.0.eb index d13e7d8912..fafae9335e 100644 --- a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-ictce-5.3.0.eb @@ -24,7 +24,7 @@ toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'optarch': True, 'pic': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://www.tbi.univie.ac.at/RNA/download/sourcecode/2_0_x/'] +source_urls = ['http://www.tbi.univie.ac.at/RNA/download/sourcecode/%(version_major)s_%(version_minor)s_x/'] patches = ['ViennaRNA_ictce-pragma.patch'] diff --git a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.1.6-ictce-5.5.0.eb b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.1.6-ictce-5.5.0.eb index 3e54d3ed83..29c51c1030 100644 --- a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.1.6-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.1.6-ictce-5.5.0.eb @@ -23,7 +23,7 @@ toolchain = {'name': 'ictce', 'version': '5.5.0'} toolchainopts = {'optarch': True, 'pic': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://www.tbi.univie.ac.at/RNA/download/sourcecode/2_1_x/'] +source_urls = ['http://www.tbi.univie.ac.at/RNA/download/sourcecode/%(version_major)s_%(version_minor)s_x/'] patches = ['ViennaRNA-2.1.6_ictce.patch'] diff --git a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.2.3-intel-2016b.eb b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.2.3-intel-2016b.eb index 1988a82b1e..3214395e25 100644 --- a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.2.3-intel-2016b.eb +++ b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.2.3-intel-2016b.eb @@ -23,7 +23,7 @@ toolchain = {'name': 'intel', 'version': '2016b'} toolchainopts = {'pic': True, 'openmp': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://www.tbi.univie.ac.at/RNA/download/sourcecode/2_2_x/'] +source_urls = ['http://www.tbi.univie.ac.at/RNA/download/sourcecode/%(version_major)s_%(version_minor)s_x/'] patches = ['ViennaRNA-%(version)s_fix-pragma.patch'] diff --git a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.3.4-foss-2016b.eb b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.3.4-foss-2016b.eb index 5b2bac1762..ec625ff6c6 100644 --- a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.3.4-foss-2016b.eb +++ b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.3.4-foss-2016b.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'foss', 'version': '2016b'} toolchainopts = {'pic': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://www.tbi.univie.ac.at/RNA/download/sourcecode/2_3_x/'] +source_urls = ['http://www.tbi.univie.ac.at/RNA/download/sourcecode/%(version_major)s_%(version_minor)s_x/'] checksums = ['c77bff267606d22557a4f867df635822'] -- GitLab From 7a01868d8490d06d2ef9786713232c44550a0cb6 Mon Sep 17 00:00:00 2001 From: Joachim Hein Date: Mon, 13 Mar 2017 17:19:43 +0100 Subject: [PATCH 0381/1603] HDF5 1.10.0 patch1 for golfs incl. dependencies This is a simple port from foss/2016b - same gcc compiler --- .../HDF5/HDF5-1.10.0-patch1-goolfc-2016.10.eb | 22 ++++++++++++++++++ .../s/Szip/Szip-2.1-goolfc-2016.10.eb | 23 +++++++++++++++++++ 2 files changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.10.0-patch1-goolfc-2016.10.eb create mode 100644 easybuild/easyconfigs/s/Szip/Szip-2.1-goolfc-2016.10.eb diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.10.0-patch1-goolfc-2016.10.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.0-patch1-goolfc-2016.10.eb new file mode 100644 index 0000000000..a728a33f56 --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.0-patch1-goolfc-2016.10.eb @@ -0,0 +1,22 @@ +name = 'HDF5' +version = '1.10.0-patch1' + +homepage = 'http://www.hdfgroup.org/HDF5/' +description = """HDF5 is a unique technology suite that makes possible the management of + extremely large and complex data collections.""" + +toolchain = {'name': 'goolfc', 'version': '2016.10'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['9180ff0ef8dc2ef3f61bd37a7404f295'] + +buildopts = 'CXXFLAGS="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK"' + +dependencies = [ + ('zlib', '1.2.8'), + ('Szip', '2.1'), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1-goolfc-2016.10.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1-goolfc-2016.10.eb new file mode 100644 index 0000000000..c2c5a38e56 --- /dev/null +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1-goolfc-2016.10.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'Szip' +version = '2.1' + +homepage = 'http://www.hdfgroup.org/doc_resource/SZIP/' +description = "Szip compression software, providing lossless compression of scientific data" + +toolchain = {'name': 'goolfc', 'version': '2016.10'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = "--with-pic" + +sanity_check_paths = { + 'files': ["lib/libsz.a", "lib/libsz.%s" % SHLIB_EXT] + + ["include/%s" % x for x in ["ricehdf.h", "szip_adpt.h", "szlib.h"]], + 'dirs': [], +} + +moduleclass = 'tools' -- GitLab From 22f34275ebd33b371a33756d06860e01290f056e Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Tue, 14 Mar 2017 12:10:16 +1300 Subject: [PATCH 0382/1603] libreadline dependency for Perl --- .../libreadline/libreadline-6.2-foss-2015a.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/l/libreadline/libreadline-6.2-foss-2015a.eb diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-foss-2015a.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-foss-2015a.eb new file mode 100644 index 0000000000..45a556ffec --- /dev/null +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-foss-2015a.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'libreadline' +version = '6.2' + +homepage = 'http://cnswww.cns.cwru.edu/php/chet/readline/rltop.html' +description = """The GNU Readline library provides a set of functions for use by applications that + allow users to edit command lines as they are typed in. Both Emacs and vi editing modes are available. + The Readline library includes additional functions to maintain a list of previously-entered command lines, + to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands.""" + +toolchain = {'name': 'foss', 'version': '2015a'} +toolchainopts = {'pic': True} + +sources = ['readline-%(version)s.tar.gz'] +source_urls = ['http://ftp.gnu.org/gnu/readline'] + +dependencies = [('ncurses', '5.9')] + +sanity_check_paths = { + 'files' : ['lib/libreadline.a', 'lib/libhistory.a'] + + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + 'dirs' : [], +} + +moduleclass = 'lib' -- GitLab From 774f17a8c7232229bdf1d3520a30a1608c94fda3 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Luk=C3=A1=C5=A1=20Krup=C4=8D=C3=ADk?= Date: Tue, 14 Mar 2017 07:33:04 +0100 Subject: [PATCH 0383/1603] {tools}LSMS-3_rev237 change LSMS-3_rev237_fix-Makefiles.patch -> LSMS-%(version)s_fix-Makefiles.patch --- easybuild/easyconfigs/l/LSMS/LSMS-3_rev237-foss-2016a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/LSMS/LSMS-3_rev237-foss-2016a.eb b/easybuild/easyconfigs/l/LSMS/LSMS-3_rev237-foss-2016a.eb index 198945fde4..b39dd8a48b 100644 --- a/easybuild/easyconfigs/l/LSMS/LSMS-3_rev237-foss-2016a.eb +++ b/easybuild/easyconfigs/l/LSMS/LSMS-3_rev237-foss-2016a.eb @@ -13,7 +13,7 @@ sources = ['%(name)s_%(version)s.tar.bz2'] checksums = ['8c864c9223b93488663815557e61cd0b'] -patches = ['LSMS-3_rev237_fix-Makefiles.patch'] +patches = ['LSMS-%(version)s_fix-Makefiles.patch'] dependencies = [ ('HDF5', '1.8.16'), -- GitLab From addeb7730bc97daee66649abeea0fa38e18c01e9 Mon Sep 17 00:00:00 2001 From: Robert Qiao Date: Tue, 14 Mar 2017 19:17:30 +1030 Subject: [PATCH 0384/1603] Revert "Testing" This reverts commit fa1ffbce7c441662925f5042a6a427907f0f6285. --- .../easyconfigs/p/PileOMeth/PileOMeth-0.1.11-foss-2016b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PileOMeth/PileOMeth-0.1.11-foss-2016b.eb b/easybuild/easyconfigs/p/PileOMeth/PileOMeth-0.1.11-foss-2016b.eb index 1a66bb0381..edf4ca1f37 100644 --- a/easybuild/easyconfigs/p/PileOMeth/PileOMeth-0.1.11-foss-2016b.eb +++ b/easybuild/easyconfigs/p/PileOMeth/PileOMeth-0.1.11-foss-2016b.eb @@ -6,7 +6,7 @@ # Authors:: Robert Qiao , Exe Escobedo # License:: # -# Notes:: Testing +# Notes:: ### easyblock = 'MakeCp' -- GitLab From 152c3f7593cef4db3a1197f42adef4734a8c12a7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Mar 2017 15:20:50 +0100 Subject: [PATCH 0385/1603] remove unneeded CMake easyconfig --- .../c/CMake/CMake-3.6.2-GCCcore-6.3.0.eb | 36 ------------------- 1 file changed, 36 deletions(-) delete mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.6.2-GCCcore-6.3.0.eb diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.6.2-GCCcore-6.3.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.6.2-GCCcore-6.3.0.eb deleted file mode 100644 index 50e2df64aa..0000000000 --- a/easybuild/easyconfigs/c/CMake/CMake-3.6.2-GCCcore-6.3.0.eb +++ /dev/null @@ -1,36 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'CMake' -version = '3.6.2' - -homepage = 'http://www.cmake.org' -description = """CMake, the cross-platform, open-source build system. - CMake is a family of tools designed to build, test and package software.""" - -toolchain = {'name': 'GCCcore', 'version': '6.3.0'} - -source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] -sources = [SOURCELOWER_TAR_GZ] - -configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' - -builddependencies = [ - ('binutils', '2.27'), -] - - -dependencies = [ - ('ncurses', '6.0'), - # OS dependency should be preferred if the os version is more recent then this version, - # it's nice to have an up to date openssl for security reasons - #('OpenSSL', '1.1.0c'), -] - -osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] - -sanity_check_paths = { - 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], - 'dirs': [], -} - -moduleclass = 'devel' -- GitLab From 40f76e4b2f7d9e80850d6b94f5dfdec20bf15c99 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 14 Mar 2017 16:21:25 +0200 Subject: [PATCH 0386/1603] adding easyconfigs: GROMACS-2016.3-foss-2017a.eb --- .../g/GROMACS/GROMACS-2016.3-foss-2017a.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-2016.3-foss-2017a.eb diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.3-foss-2017a.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.3-foss-2017a.eb new file mode 100644 index 0000000000..c3f26a2915 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.3-foss-2017a.eb @@ -0,0 +1,36 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2016 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, +# Ghent University / The Francis Crick Institute +# Authors:: +# * Wiktor Jurkowski +# * Fotis Georgatos +# * George Tsouloupas +# * Kenneth Hoste +# * Adam Huffman +# License:: MIT/GPL +## + +name = 'GROMACS' +version = '2016.3' + +homepage = 'http://www.gromacs.org' +description = """ +GROMACS is a versatile package to perform molecular dynamics, + i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. + +This is CPU only build, containing both MPI and threadMPI builds. +""" + +toolchain = {'name': 'foss', 'version': '2017a'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = ['ftp://ftp.gromacs.org/pub/gromacs/'] +sources = [SOURCELOWER_TAR_GZ] + +builddependencies = [ + ('CMake', '3.7.2'), +] + +moduleclass = 'bio' -- GitLab From 3d561c8d11759dda93628cbd5ddea9f294e1537c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Mar 2017 16:30:25 +0100 Subject: [PATCH 0387/1603] adding easyconfigs: GROMACS-2016.3-intel-2017a.eb --- .../g/GROMACS/GROMACS-2016.3-intel-2017a.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-2016.3-intel-2017a.eb diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.3-intel-2017a.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.3-intel-2017a.eb new file mode 100644 index 0000000000..edcd456df0 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.3-intel-2017a.eb @@ -0,0 +1,36 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2016 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, +# Ghent University / The Francis Crick Institute +# Authors:: +# * Wiktor Jurkowski +# * Fotis Georgatos +# * George Tsouloupas +# * Kenneth Hoste +# * Adam Huffman +# License:: MIT/GPL +## + +name = 'GROMACS' +version = '2016.3' + +homepage = 'http://www.gromacs.org' +description = """ +GROMACS is a versatile package to perform molecular dynamics, + i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. + +This is CPU only build, containing both MPI and threadMPI builds. +""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = ['ftp://ftp.gromacs.org/pub/gromacs/'] +sources = [SOURCELOWER_TAR_GZ] + +builddependencies = [ + ('CMake', '3.7.2'), +] + +moduleclass = 'bio' -- GitLab From 13d0854b39af72736c182706b19fb7ee83ddcec8 Mon Sep 17 00:00:00 2001 From: Maxime Boissonneault Date: Tue, 14 Mar 2017 18:32:41 +0000 Subject: [PATCH 0388/1603] Updated PETSc recipe to the modified version of the download install feature. --- .../PETSc/PETSc-3.7.5-intel-2016a-download.eb | 34 ++++++++++--------- 1 file changed, 18 insertions(+), 16 deletions(-) diff --git a/easybuild/easyconfigs/p/PETSc/PETSc-3.7.5-intel-2016a-download.eb b/easybuild/easyconfigs/p/PETSc/PETSc-3.7.5-intel-2016a-download.eb index a59522d52f..111a8d2edd 100644 --- a/easybuild/easyconfigs/p/PETSc/PETSc-3.7.5-intel-2016a-download.eb +++ b/easybuild/easyconfigs/p/PETSc/PETSc-3.7.5-intel-2016a-download.eb @@ -1,5 +1,6 @@ name = 'PETSc' version = '3.7.5' +versionsuffix = '-downloaded_deps' homepage = 'http://www.mcs.anl.gov/petsc' description = """PETSc, pronounced PET-see (the S is silent), is a suite of data structures and routines for the @@ -11,31 +12,32 @@ toolchainopts = {'usempi': True, 'pic': True} source_urls = ['http://ftp.mcs.anl.gov/pub/petsc/release-snapshots'] sources = [SOURCELOWER_TAR_GZ] +builddependencies = [('CMake', '3.5.2')] shared_libs = 1 pic = 1 downloadinstall = True +# For these dependencies, we do not download them dependencies = [('HDF5','1.8.18')] - configopts = "" -# compiles PETSc shared configopts += "--with-mkl_pardiso=1 --with-mkl_pardiso-dir=$MKLROOT " configopts += "--with-hdf5=1 --with-hdf5-dir=$EBROOTHDF5" -# external packages that are downloaded -external_packages = ['mumps', 'ptscotch', 'superlu', 'superlu_dist', 'parmetis', 'metis', 'ml', 'suitesparse', 'hypre', 'prometheus'] -# compiles the external dependencies non-shared -external_packages_shared = "no" -for p in external_packages: - configopts += "--download-%s=yes --download-%s-shared=%s " % (p,p,external_packages_shared) -configopts += "--download-triangle=yes" # download-triangle-shared is not supported - -builddependencies = [('CMake', '3.5.2')] +# external packages that are downloaded with --download-=1 and --download--static=1 +download_deps_static = [ + 'hypre', + 'metis', + 'ml', + 'mumps', + 'parmetis', + 'prometheus', + 'ptscotch', + 'suitesparse', + 'superlu', + 'superlu_dist' +] +# triangle cannot be downloaded with --download-triangle-static because it fails +download_deps = ['triangle'] moduleclass = 'numlib' - -modluafooter = """ -family("petsc") -""" - -- GitLab From 1b637c106ee87738d65c9d15d33774d5e618c237 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Wed, 15 Mar 2017 09:46:39 +1300 Subject: [PATCH 0389/1603] Remove files related to new gimkl-2017a Perl build --- .../easyconfigs/d/DB/DB-6.2.23-gimkl-2017a.eb | 18 - .../p/Perl/Perl-5.24.1-gimkl-2017a.eb | 1194 ----------------- .../s/SAMtools/SAMtools-0.1.19-gimkl-2017a.eb | 21 - 3 files changed, 1233 deletions(-) delete mode 100644 easybuild/easyconfigs/d/DB/DB-6.2.23-gimkl-2017a.eb delete mode 100644 easybuild/easyconfigs/p/Perl/Perl-5.24.1-gimkl-2017a.eb delete mode 100644 easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.19-gimkl-2017a.eb diff --git a/easybuild/easyconfigs/d/DB/DB-6.2.23-gimkl-2017a.eb b/easybuild/easyconfigs/d/DB/DB-6.2.23-gimkl-2017a.eb deleted file mode 100644 index f6a2ef8db6..0000000000 --- a/easybuild/easyconfigs/d/DB/DB-6.2.23-gimkl-2017a.eb +++ /dev/null @@ -1,18 +0,0 @@ -name = 'DB' -version = '6.2.23' - -homepage = 'http://www.oracle.com/technetwork/products/berkeleydb' -description = """Berkeley DB enables the development of custom data management solutions, - without the overhead traditionally associated with such custom projects.""" - -toolchain = {'name': 'gimkl', 'version': '2017a'} - -# download via http://www.oracle.com/technetwork/products/berkeleydb/downloads/, requires registration -sources = [SOURCELOWER_TAR_GZ] - -sanity_check_paths = { - 'files': ["include/db.h"], - 'dirs': [], -} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.24.1-gimkl-2017a.eb b/easybuild/easyconfigs/p/Perl/Perl-5.24.1-gimkl-2017a.eb deleted file mode 100644 index d4719d425a..0000000000 --- a/easybuild/easyconfigs/p/Perl/Perl-5.24.1-gimkl-2017a.eb +++ /dev/null @@ -1,1194 +0,0 @@ -name = 'Perl' -version = '5.24.1' -use_perl_threads = False - -homepage = 'http://www.perl.org/' -description = """Larry Wall's Practical Extraction and Report Language""" - -toolchain = {'name': 'gimkl', 'version': '2017a'} -toolchainopts = {'optarch': True, 'pic': True} - -dependencies = [ - ('DB', '6.2.23'), # for DB_File module - ('SQLite', '3.16.2'), # for DBD::SQLite module - ('expat', '2.2.0'), # for XML::Parser I think - ('libxml2', '2.9.4'), # for XML::LibXML -] -# Also zlib / readline via the other dependencies - -builddependencies = [('SAMtools', '0.1.19')] # NOT A LATER VERSION. For Bio::DB::Sam to static link to. - -source_urls = ['http://www.cpan.org/src/5.0'] -sources = [SOURCELOWER_TAR_GZ] - -# We must compile in serial so that Convert::Binary::C is installed -# in a sane manner. -maxparallel = 1 - -#runtest = 'test' # Several modules have extra dependencies for testing - -# Extension versions -acme_damn_version = '0.08' -algorithm_diff_version = '1.1903' -algorithm_munkres_version = '0.08' -aliased_version = '0.34' -anyevent_version = '7.13' -appconfig_version = '1.71' -archive_extract_version = '0.80' -archive_tar_version = '2.24' -archive_zip_version = '1.59' -array_compare_version = '3.0.0' -authen_sasl_version = '2.16' -bioperl_version = '1.007001' -bio_phylo_version = '0.58' -bio_samtools_version = '1.43' -bit_vector_version = '7.4' -boolean_version = '0.46' -bundle_bioperl_version = '2.1.9' -b_lintsubs_version = '0.06' -b_lint_version = '1.20' -capture_tiny_version = '0.46' -carp_version = '1.38' -cgi_version = '4.35' -class_accessor_version = '0.34' -class_data_inheritable_version = '0.08' -class_dbi_version = '3.0.17' -class_inspector_version = '1.31' -class_isa_version = '0.36' -class_load_version = '0.23' -class_load_xs_version = '0.09' -class_singleton_version = '1.5' -class_trigger_version = '0.14' -clone_version = '0.38' -config_general_version = '2.63' -convert_binary_c_version = '0.78' -cpanplus_version = '0.9164' -cwd_guard_version = '0.05' -data_dumper_version = '2.161' -data_optlist_version = '0.110' -data_section_simple_version = '0.07' -data_stag_version = '0.14' -data_types_version = '0.09' -data_uuid_version = '1.221' -datetime_locale_version = '1.14' -datetime_timezone_version = '2.10' -datetime_tiny_version = '1.06' -datetime_version = '1.42' -date_handler_version = '1.2' -dbd_anydata_version = '0.110' -dbd_sqlite_version = '1.54' -dbix_contextualfetch_version = '1.03' -dbix_simple_version = '1.35' -dbi_version = '1.636' -db_file_version = '1.840' -devel_checkcompiler_version = '0.07' -devel_globaldestruction_version = '0.14' -devel_stacktrace_version = '2.02' -digest_hmac_version = '1.03' -digest_sha1_version = '2.13' -dist_checkconflicts_version = '0.11' -email_date_format_version = '1.005' -encode_locale_version = '1.05' -error_version = '0.17024' -eval_closure_version = '0.14' -exception_class_version = '1.42' -expect_pm_version = '1.21' -exporter_declare_version = '0.114' -exporter_tiny_version = '0.044' -extutils_config_version = '0.008' -extutils_helpers_version = '0.026' -extutils_installpaths_version = '0.011' -extutils_makemaker_version = '7.24' -fennec_lite_version = '0.004' -file_checktree_version = '4.42' -file_copy_recursive_version = '0.38' -file_find_rule_perl_version = '1.15' -file_find_rule_version = '0.34' -file_listing_version = '6.04' -file_path_version = '2.12' -file_sharedir_install_version = '0.11' -file_slurp_tiny_version = '0.004' -file_slurp_version = '9999.19' -file_temp_version = '0.2304' -file_which_version = '1.21' -font_ttf_version = '1.06' -forks_version = '0.36' -freezethaw_version = '0.5001' -getopt_long_version = '2.49.1' -git_version = '0.41' -go_db_perl_version = '0.04' -go_perl_version = '0.15' -graph_version = '0.9704' -hash_merge_version = '0.200' -html_form_version = '6.03' -html_parser_version = '3.72' -html_tableextract_version = '2.13' -html_tagset_version = '3.20' -http_cookies_version = '6.01' -http_daemon_version = '6.01' -http_date_version = '6.02' -http_message_version = '6.11' -http_negotiate_version = '6.01' -ima_dbi_version = '0.35' -import_into_version = '1.002005' -inline_c_version = '0.76' -inline_version = '0.80' -io_all_version = '0.86' -io_html_version = '1.001' -io_prompt_version = '0.997004' -io_socket_ssl_version = '2.047' -io_stringy_version = '2.111' -io_string_version = '1.08' -io_tty_version = '1.12' -ipc_run3_version = '0.048' -ipc_run_version = '0.94' -json_version = '2.90' -libxml_perl_version = '0.08' -list_allutils_version = '0.14' -list_moreutils_version = '0.416' -local_lib_version = '2.000019' -logger_simple_version = '2.0' -log_message_simple_version = '0.10' -log_message_version = '0.08' -lwp_mediatypes_version = '6.02' -lwp_version = '6.23' -mailtools_version = '2.18' -math_bezier_version = '0.01' -math_cdf_version = '0.1' -math_round_version = '0.07' -math_vecstat_version = '0.08' -meta_builder_version = '0.003' -mime_lite_version = '3.030' -mime_types_version = '2.13' -mock_quick_version = '1.111' -module_build_tiny_version = '0.039' -module_build_version = '0.4220' -module_build_xsutil_version = '0.16' -module_implementation_version = '0.09' -module_load_conditional_version = '0.68' -module_pluggable_version = '5.2' -module_runtime_version = '0.014' -moose_version = '2.2004' -moo_version = '2.003001' -mouse_version = '2.4.9' -mro_compat_version = '0.12' -net_http_version = '6.13' -net_smtp_ssl_version = '1.04' -number_compare_version = '0.03' -number_compare_version = '0.03' -object_accessor_version = '0.48' -object_insideout_version = '4.04' -package_deprecationmanager_version = '0.17' -package_stash_version = '0.37' -package_stash_xs_version = '0.28' -parallel_forkmanager_version = '1.19' -params_util_version = '1.07' -params_validate_version = '1.26' -parse_recdescent_version = '1.967013' -pathtools_version = '3.62' -perl_unsafe_signals_version = '0.03' -pod_latex_version = '0.61' -pod_plainer_version = '1.04' -pod_pom_version = '2.01' -readonly_version = '2.05' -regexp_common_version = '2016060801' -scalar_list_utils_version = '1.47' -scalar_util_numeric_version = '0.40' -set_array_version = '0.30' -set_intervaltree_version = '0.10' -set_intspan_version = '1.19' -set_scalar_version = '1.29' -shell_version = '0.73' -spreadsheet_parseexcel_version = '0.65' -sql_statement_version = '1.410' -statistics_descriptive_version = '3.0612' -storable_version = '2.51' -strictures_version = '2.000003' -sub_exporter_progressive_version = '0.001013' -sub_exporter_version = '0.987' -sub_install_version = '0.928' -sub_name_version = '0.21' -sub_uplevel_version = '0.2600' -svg_version ='2.64' -switch_version = '2.17' -sys_sigaction_version = '0.23' -template_toolkit_version = '2.26' -term_readkey_version = '2.37' -term_ui_version = '0.46' -test_deep_version = '1.126' -test_differences_version = '0.64' -test_exception_lessclever_version = '0.009' -test_exception_version = '0.43' -test_fatal_version = '0.014' -test_harness_version = '3.36' -test_harness_version = '3.36' -test_leaktrace_version = '0.15' -test_most_version = '0.35' -test_nowarnings_version = '1.04' -test_output_version = '1.03' -test_requires_version = '0.10' -test_simple_version = '1.302078' -test_version_version = '2.05' -test_warnings_version = '0.026' -test_warn_version = '0.32' -text_diff_version = '1.44' -text_glob_version = '0.11' -text_iconv_version = '1.7' -text_soundex_version = '3.05' -tie_ixhash_version = '1.23' -timedate_version = '2.30' -time_piece_mysql_version = '0.06' -time_piece_version = '1.31' -tree_dag_node_version = '1.29' -try_tiny_version = '0.28' -universal_moniker_version = '0.08' -uri_version = '1.71' -version_version = '0.9917' -want_version = '0.29' -www_robotrules_version = '6.02' -xml_dom_version = '1.46' -xml_dom_xpath_version = '0.14' -xml_libxml_version = '2.0128' -xml_namespacesupport_version = '1.11' -xml_parser_version = '2.44' -xml_sax_base_version = '1.08' -xml_sax_version = '0.99' -xml_sax_writer_version = '0.56' -xml_simple_version = '2.22' -xml_twig_version = '3.52' -xml_writer_version = '0.625' -xml_xpath_version = '1.40' -xsloader_version = '0.24' -yaml_version = '1.23' - -exts_list = [ - ('Module::Build', module_build_version, { # std module but recent BioPerl needs a recent version for some reason - 'source_tmpl': 'Module-Build-%s.tar.gz' % module_build_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/L/LE/LEONT/'], - }), - ('ExtUtils::MakeMaker', extutils_makemaker_version, { - 'source_tmpl': 'ExtUtils-MakeMaker-%s.tar.gz' % extutils_makemaker_version, - 'source_urls': ['http://www.cpan.org/modules/by-module/ExtUtils/BINGOS/'], - }), - ('local::lib', local_lib_version, { - 'source_tmpl': 'local-lib-%s.tar.gz' % local_lib_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/H/HA/HAARG/'], - }), - ('IO::String', io_string_version, { - 'source_tmpl': 'IO-String-%s.tar.gz' % io_string_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/G/GA/GAAS/'], - }), - ('Data::Stag', data_stag_version, { - 'source_tmpl': 'Data-Stag-%s.tar.gz' % data_stag_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/C/CM/CMUNGALL/'], - }), - ('DB_File', db_file_version, { - 'source_urls': ['http://www.cpan.org/modules/by-module/DB_File/PMQS/'], - }), - ('DBI', dbi_version, { - 'source_urls': ['http://www.cpan.org/modules/by-module/DBI/TIMB/'], - }), - ('Sub::Uplevel', sub_uplevel_version, { - 'source_tmpl': 'Sub-Uplevel-%s.tar.gz' % sub_uplevel_version, - 'source_urls': ['http://www.cpan.org/modules/by-module/Sub/DAGOLDEN/'], - }), - ('Tree::DAG_Node', tree_dag_node_version, { - 'source_tmpl': 'Tree-DAG_Node-%s.tgz' % tree_dag_node_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/R/RS/RSAVAGE/'], - }), - ('Try::Tiny', try_tiny_version, { - 'source_tmpl': 'Try-Tiny-%s.tar.gz' % try_tiny_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/E/ET/ETHER/'], - }), - ('Devel::StackTrace', devel_stacktrace_version, { - 'source_tmpl': 'Devel-StackTrace-%s.tar.gz' % devel_stacktrace_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/D/DR/DROLSKY/'], - }), - ('Class::Data::Inheritable', class_data_inheritable_version, { - 'source_tmpl': 'Class-Data-Inheritable-%s.tar.gz' % class_data_inheritable_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/T/TM/TMTM/'], - }), - ('Exception::Class', exception_class_version, { - 'source_tmpl': 'Exception-Class-%s.tar.gz' % exception_class_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/D/DR/DROLSKY/'], - }), - ('Test::Fatal', test_fatal_version, { - 'source_tmpl': 'Test-Fatal-%s.tar.gz' % test_fatal_version, - 'source_urls': ['http://www.cpan.org/modules/by-module/Test/RJBS/'], - }), - ('Test::NoWarnings', test_nowarnings_version, { - 'source_tmpl': 'Test-NoWarnings-%s.tar.gz' % test_nowarnings_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/A/AD/ADAMK/'], - }), - ('Test::Deep', test_deep_version, { - 'source_tmpl': 'Test-Deep-%s.tar.gz' % test_deep_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/R/RJ/RJBS/'], - }), - ('Algorithm::Diff', algorithm_diff_version, { - 'source_tmpl': 'Algorithm-Diff-%s.tar.gz' % algorithm_diff_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/T/TY/TYEMQ/'], - }), - ('Text::Diff', text_diff_version, { - 'source_tmpl': 'Text-Diff-%s.tar.gz' % text_diff_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/N/NE/NEILB/'], - }), - ('Test::Differences', test_differences_version, { - 'source_tmpl': 'Test-Differences-%s.tar.gz' % test_differences_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/D/DC/DCANTRELL/'], - }), - ('Test::Exception', test_exception_version, { - 'source_tmpl': 'Test-Exception-%s.tar.gz' % test_exception_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/E/EX/EXODIST/'], - }), - ('Test::Warn', test_warn_version, { - 'source_tmpl': 'Test-Warn-%s.tar.gz' % test_warn_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/B/BI/BIGJ/'], - }), - ('Test::Requires', test_requires_version, { - 'source_tmpl': 'Test-Requires-%s.tar.gz' % test_requires_version, - 'source_urls': ['http://www.cpan.org/modules/by-module/Test/TOKUHIROM/'], - }), - ('Test::Tester', test_simple_version, { - 'source_tmpl': 'Test-Simple-%s.tar.gz' % test_simple_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/E/EX/EXODIST/'], - }), - ('File::Slurp::Tiny', file_slurp_tiny_version, { - 'source_tmpl': 'File-Slurp-Tiny-%s.tar.gz' % file_slurp_tiny_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/L/LE/LEONT'], - }), - ('Params::Util', params_util_version, { - 'source_tmpl': 'Params-Util-%s.tar.gz' % params_util_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/A/AD/ADAMK/'], - }), - ('Sub::Install', sub_install_version, { - 'source_tmpl': 'Sub-Install-%s.tar.gz' % sub_install_version, - 'source_urls': ['http://www.cpan.org/modules/by-module/Sub/RJBS/'], - }), - ('Data::OptList', data_optlist_version, { - 'source_tmpl': 'Data-OptList-%s.tar.gz' % data_optlist_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/R/RJ/RJBS/'], - }), - ('Sub::Exporter', sub_exporter_version, { - 'source_tmpl': 'Sub-Exporter-%s.tar.gz' % sub_exporter_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/R/RJ/RJBS/'], - }), - ('Capture::Tiny', capture_tiny_version, { - 'source_tmpl': 'Capture-Tiny-%s.tar.gz' % capture_tiny_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/D/DA/DAGOLDEN/'], - }), - ('Test::Output', test_output_version, { - 'source_tmpl': 'Test-Output-%s.tar.gz' % test_output_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/B/BD/BDFOY/'], - }), - ('Module::Runtime', module_runtime_version, { - 'source_tmpl': 'Module-Runtime-%s.tar.gz' % module_runtime_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/Z/ZE/ZEFRAM/'], - }), - ('Module::Implementation', module_implementation_version, { - 'source_tmpl': 'Module-Implementation-%s.tar.gz' % module_implementation_version, - 'source_urls': ['http://www.cpan.org/modules/by-module/Module/DROLSKY/'], - }), - ('List::MoreUtils', list_moreutils_version, { - 'source_tmpl': 'List-MoreUtils-%s.tar.gz' % list_moreutils_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/R/RE/REHSACK/'], - }), - ('Package::DeprecationManager', package_deprecationmanager_version, { - 'source_tmpl': 'Package-DeprecationManager-%s.tar.gz' % package_deprecationmanager_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/D/DR/DROLSKY/'], - }), - ('Dist::CheckConflicts', dist_checkconflicts_version, { - 'source_tmpl': 'Dist-CheckConflicts-%s.tar.gz' % dist_checkconflicts_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/D/DO/DOY/'], - }), - ('Package::Stash', package_stash_version, { - 'source_tmpl': 'Package-Stash-%s.tar.gz' % package_stash_version, - 'source_urls': ['http://www.cpan.org/modules/by-module/Package/DOY/'], - }), - ('Class::Load', class_load_version, { - 'source_tmpl': 'Class-Load-%s.tar.gz' % class_load_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/E/ET/ETHER/'], - }), - ('TAP::Harness::Env', test_harness_version, { - 'source_tmpl': 'Test-Harness-%s.tar.gz' % test_harness_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/L/LE/LEONT/'], - }), - ('ExtUtils::Helpers', extutils_helpers_version, { - 'source_tmpl': 'ExtUtils-Helpers-%s.tar.gz' % extutils_helpers_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/L/LE/LEONT'], - }), - ('ExtUtils::Config', extutils_config_version, { - 'source_tmpl': 'ExtUtils-Config-%s.tar.gz' % extutils_config_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/L/LE/LEONT'], - }), - ('ExtUtils::InstallPaths', extutils_installpaths_version, { - 'source_tmpl': 'ExtUtils-InstallPaths-%s.tar.gz' % extutils_installpaths_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/L/LE/LEONT'], - }), - ('Module::Build::Tiny', module_build_tiny_version, { - 'source_tmpl': 'Module-Build-Tiny-%s.tar.gz' % module_build_tiny_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/L/LE/LEONT/'], - }), - ('MRO::Compat', mro_compat_version, { - 'source_tmpl': 'MRO-Compat-%s.tar.gz' % mro_compat_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/B/BO/BOBTFISH/'], - }), - ('Sub::Name', sub_name_version, { - 'source_tmpl': 'Sub-Name-%s.tar.gz' % sub_name_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/E/ET/ETHER/'], - }), - ('Eval::Closure', eval_closure_version, { - 'source_tmpl': 'Eval-Closure-%s.tar.gz' % eval_closure_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/D/DO/DOY/'], - }), - ('Sub::Exporter::Progressive', sub_exporter_progressive_version, { - 'source_tmpl': 'Sub-Exporter-Progressive-%s.tar.gz' % sub_exporter_progressive_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/F/FR/FREW/'], - }), - ('Devel::GlobalDestruction', devel_globaldestruction_version, { - 'source_tmpl': 'Devel-GlobalDestruction-%s.tar.gz' % devel_globaldestruction_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/H/HA/HAARG/'], - }), - ('boolean', boolean_version, { - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/I/IN/INGY/'], - }), - ('Tie::IxHash', tie_ixhash_version, { - 'source_tmpl': 'Tie-IxHash-%s.tar.gz' % tie_ixhash_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/C/CH/CHORNY/'], - }), - ('Moose', moose_version, { - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/E/ET/ETHER/'], - }), - ('Package::Stash::XS', package_stash_xs_version, { - 'source_tmpl': 'Package-Stash-XS-%s.tar.gz' % package_stash_xs_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/D/DO/DOY/'], - }), - ('Params::Validate', params_validate_version, { - 'source_tmpl': 'Params-Validate-%s.tar.gz' % params_validate_version, - 'source_urls': ['http://www.cpan.org/modules/by-module/Params/DROLSKY/'], - }), - ('Class::Load::XS', class_load_xs_version, { - 'source_tmpl': 'Class-Load-XS-%s.tar.gz' % class_load_xs_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/E/ET/ETHER/'], - }), - # For uoa00001, Zendesk #9076 - ('Math::CDF', math_cdf_version, { - 'source_tmpl': 'Math-CDF-%s.tar.gz' % math_cdf_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/C/CA/CALLAHAN/'], - }), - ('DateTime::Locale', datetime_locale_version, { - 'source_tmpl': 'DateTime-Locale-%s.tar.gz' % datetime_locale_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/D/DR/DROLSKY/'], - }), - ('Class::Singleton', class_singleton_version, { - 'source_tmpl': 'Class-Singleton-%s.tar.gz' % class_singleton_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/S/SH/SHAY/'], - }), - ('DateTime::TimeZone', datetime_timezone_version, { - 'source_tmpl': 'DateTime-TimeZone-%s.tar.gz' % datetime_timezone_version, - 'source_urls': ['http://www.cpan.org/modules/by-module/DateTime/DROLSKY/'], - }), - ('Test::Warnings', test_warnings_version, { - 'source_tmpl': 'Test-Warnings-%s.tar.gz' % test_warnings_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/E/ET/ETHER/'], - }), - ('Data::Types', data_types_version, { - 'source_tmpl': 'Data-Types-%s.tar.gz' % data_types_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/D/DW/DWHEELER/'], - }), - ('Exporter::Tiny', exporter_tiny_version, { - 'source_tmpl': 'Exporter-Tiny-%s.tar.gz' % exporter_tiny_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/T/TO/TOBYINK/'], - }), - ('List::AllUtils', list_allutils_version, { - 'source_tmpl': 'List-AllUtils-%s.tar.gz' % list_allutils_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/D/DR/DROLSKY/'], - }), - ('DateTime', datetime_version, { - 'source_urls': ['http://www.cpan.org/modules/by-module/DateTime/DROLSKY/'], - }), - ('DateTime::Tiny', datetime_tiny_version, { - 'source_tmpl': 'DateTime-Tiny-%s.tar.gz' % datetime_tiny_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/D/DA/DAGOLDEN/'], - }), - ('File::Slurp', file_slurp_version, { - 'source_tmpl': 'File-Slurp-%s.tar.gz' % file_slurp_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/U/UR/URI/'], - }), - ('HTTP::Date', http_date_version, { - 'source_tmpl': 'HTTP-Date-%s.tar.gz' % http_date_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/G/GA/GAAS/'], - }), - ('IO::HTML', io_html_version, { - 'source_tmpl': 'IO-HTML-%s.tar.gz' % io_html_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/C/CJ/CJM/'], - }), - ('LWP::MediaTypes', lwp_mediatypes_version, { - 'source_tmpl': 'LWP-MediaTypes-%s.tar.gz' % lwp_mediatypes_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/G/GA/GAAS/'], - }), - ('URI', uri_version, { - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/E/ET/ETHER/'], - }), - ('Encode::Locale', encode_locale_version, { - 'source_tmpl': 'Encode-Locale-%s.tar.gz' % encode_locale_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/G/GA/GAAS/'], - }), - ('HTTP::Request', http_message_version, { - 'source_tmpl': 'HTTP-Message-%s.tar.gz' % http_message_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/E/ET/ETHER/'], - }), - ('HTML::Tagset', html_tagset_version, { - 'source_tmpl': 'HTML-Tagset-%s.tar.gz' % html_tagset_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/P/PE/PETDANCE/'], - }), - ('HTML::Entities', html_parser_version, { - 'source_tmpl': 'HTML-Parser-%s.tar.gz' % html_parser_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/G/GA/GAAS/'], - }), - ('File::Listing', file_listing_version, { - 'source_tmpl': 'File-Listing-%s.tar.gz' % file_listing_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/G/GA/GAAS/'], - }), - ('AnyEvent', anyevent_version, { - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/M/ML/MLEHMANN/'], - }), - ('Devel::CheckCompiler', devel_checkcompiler_version, { - 'source_tmpl': 'Devel-CheckCompiler-%s.tar.gz' % devel_checkcompiler_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/S/SY/SYOHEX'], - }), - ('File::Copy::Recursive', file_copy_recursive_version, { - 'source_tmpl': 'File-Copy-Recursive-%s.tar.gz' % file_copy_recursive_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/D/DM/DMUEY/'], - }), - ('Cwd::Guard', cwd_guard_version, { - 'source_tmpl': 'Cwd-Guard-%s.tar.gz' % cwd_guard_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/K/KA/KAZEBURO'], - }), - ('Module::Build::XSUtil', module_build_xsutil_version, { - 'source_tmpl': 'Module-Build-XSUtil-%s.tar.gz' % module_build_xsutil_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/H/HI/HIDEAKIO/'], - }), - ('LWP', lwp_version, { - 'source_tmpl': 'libwww-perl-%s.tar.gz' % lwp_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/O/OA/OALDERS/'], - }), - ('Fennec::Lite', fennec_lite_version, { - 'source_tmpl': 'Fennec-Lite-%s.tar.gz' % fennec_lite_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/E/EX/EXODIST/'], - }), - ('aliased', aliased_version, { - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/E/ET/ETHER/'], - }), - ('Meta::Builder', meta_builder_version, { - 'source_tmpl': 'Meta-Builder-%s.tar.gz' % meta_builder_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/E/EX/EXODIST/'], - }), - ('Exporter::Declare', exporter_declare_version, { - 'source_tmpl': 'Exporter-Declare-%s.tar.gz' % exporter_declare_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/E/EX/EXODIST/'], - }), - ('Mock::Quick', mock_quick_version, { - 'source_tmpl': 'Mock-Quick-%s.tar.gz' % mock_quick_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/E/EX/EXODIST/'], - }), - ('Test::Exception::LessClever', test_exception_lessclever_version, { - 'source_tmpl': 'Test-Exception-LessClever-%s.tar.gz' % test_exception_lessclever_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/E/ET/ETHER/'], - }), - ('Test::LeakTrace', test_leaktrace_version, { - 'source_tmpl': 'Test-LeakTrace-%s.tar.gz' % test_leaktrace_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/G/GF/GFUJI/'], - }), - ('Mouse', mouse_version, { - 'source_tmpl': 'Mouse-v%s.tar.gz' % mouse_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/S/SY/SYOHEX/'], - }), - ('XML::NamespaceSupport', xml_namespacesupport_version, { - 'source_tmpl': 'XML-NamespaceSupport-%s.tar.gz' % xml_namespacesupport_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/P/PE/PERIGRIN/'], - }), - ('XML::SAX::Base', xml_sax_base_version, { - 'source_tmpl': 'XML-SAX-Base-%s.tar.gz' % xml_sax_base_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/G/GR/GRANTM/'], - }), - ('XML::SAX', xml_sax_version, { - 'source_tmpl': 'XML-SAX-%s.tar.gz' % xml_sax_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/G/GR/GRANTM/'], - }), - ('XML::LibXML', xml_libxml_version, { - 'source_tmpl': 'XML-LibXML-%s.tar.gz' % xml_libxml_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/S/SH/SHLOMIF/'], - }), - ('Clone', clone_version, { - 'source_tmpl': 'Clone-%s.tar.gz' % clone_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/G/GA/GARU'], - }), - ('Parallel::ForkManager', parallel_forkmanager_version, { - 'source_tmpl': 'Parallel-ForkManager-%s.tar.gz' % parallel_forkmanager_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/Y/YA/YANICK/'], - }), - - ('Config::General', config_general_version, { - 'source_tmpl': 'Config-General-%s.tar.gz' % config_general_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/T/TL/TLINDEN/'], - }), - ('Test::Simple', test_simple_version, { - 'source_tmpl': 'Test-Simple-%s.tar.gz' % test_simple_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/E/EX/EXODIST/'], - }), - - # For Genemark - ('YAML', yaml_version, { - 'source_tmpl': 'YAML-%s.tar.gz' % yaml_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/I/IN/INGY/'], - }), - ('Hash::Merge', hash_merge_version, { - 'source_tmpl': 'Hash-Merge-%s.tar.gz' % hash_merge_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/R/RE/REHSACK/'], - }), - ('Data::Dumper', data_dumper_version, { - 'source_tmpl': 'Data-Dumper-%s.tar.gz' % data_dumper_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/S/SM/SMUELLER/'], - }), - ('Object::InsideOut', object_insideout_version, { - 'source_tmpl': 'Object-InsideOut-%s.tar.gz' % object_insideout_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/J/JD/JDHEDDEN/'], - }), - ('Logger::Simple', logger_simple_version, { - 'source_tmpl': 'Logger-Simple-%s.tar.gz' % logger_simple_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/T/TS/TSTANLEY/'], - }), - ('File::Path', file_path_version, { - 'source_tmpl': 'File-Path-%s.tar.gz' % file_path_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/R/RI/RICHE/'], - }), - ('File::Spec', pathtools_version, { - 'source_tmpl': 'PathTools-%s.tar.gz' % pathtools_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/R/RJ/RJBS/'], - }), - ('File::Temp', file_temp_version, { - 'source_tmpl': 'File-Temp-%s.tar.gz' % file_temp_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/D/DA/DAGOLDEN/'], - }), - ('XSLoader', xsloader_version, { - 'source_tmpl': 'XSLoader-%s.tar.gz' % xsloader_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/S/SA/SAPER/'], - }), - ('Carp', carp_version, { - 'source_tmpl': 'Carp-%s.tar.gz' % carp_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/R/RJ/RJBS/'], - }), - ('Storable', storable_version, { - 'source_tmpl': 'Storable-%s.tar.gz' % storable_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/A/AM/AMS/'], - }), - - ('Font::TTF', font_ttf_version, { - 'source_tmpl': 'Font-TTF-%s.tar.gz' % font_ttf_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/B/BH/BHALLISSY'], - }), - ('IO::Tty', io_tty_version, { - 'source_tmpl': 'IO-Tty-%s.tar.gz' % io_tty_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/T/TO/TODDR/'], - }), - ('Math::Bezier', math_bezier_version, { - 'source_tmpl': 'Math-Bezier-%s.tar.gz' % math_bezier_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/A/AB/ABW'], - }), - ('IPC::Run', ipc_run_version, { - 'source_tmpl': 'IPC-Run-%s.tar.gz' % ipc_run_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/T/TO/TODDR/'], - }), - ('Math::Round', math_round_version, { - 'source_tmpl': 'Math-Round-%s.tar.gz' % math_round_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/G/GR/GROMMEL'], - }), - ('B::LintSubs', b_lintsubs_version, { - 'source_tmpl': 'B-LintSubs-%s.tar.gz' % b_lintsubs_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/P/PE/PEVANS'], - }), - ('Math::VecStat', math_vecstat_version, { - 'source_tmpl': 'Math-VecStat-%s.tar.gz' % math_vecstat_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/A/AS/ASPINELLI'], - }), - ('Test::Most', test_most_version, { - 'source_tmpl': 'Test-Most-%s.tar.gz' % test_most_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/O/OV/OVID/'], - }), - ('Readonly', readonly_version, { - 'source_tmpl': 'Readonly-%s.tar.gz' % readonly_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/S/SA/SANKO/'], - }), - ('Regexp::Common', regexp_common_version, { - 'source_tmpl': 'Regexp-Common-%s.tar.gz' % regexp_common_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/A/AB/ABIGAIL'], - }), - ('Want', want_version, { - 'source_tmpl': 'Want-%s.tar.gz' % want_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/R/RO/ROBIN/'], - }), - ('DBD::SQLite', dbd_sqlite_version, { - 'source_tmpl': 'DBD-SQLite-%s.tar.gz' % dbd_sqlite_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/I/IS/ISHIGAKI/'], - }), - ('Set::IntSpan', set_intspan_version, { - 'source_tmpl': 'Set-IntSpan-%s.tar.gz' % set_intspan_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/S/SW/SWMCD'], - }), - ('forks', forks_version, { - 'source_tmpl': 'forks-%s.tar.gz' % forks_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/R/RY/RYBSKEJ/'], - }), - ('File::Which', file_which_version, { - 'source_tmpl': 'File-Which-%s.tar.gz' % file_which_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/P/PL/PLICEASE/'], - }), - ('Perl::Unsafe::Signals', perl_unsafe_signals_version, { - 'source_tmpl': 'Perl-Unsafe-Signals-%s.tar.gz' % perl_unsafe_signals_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/R/RG/RGARCIA/'], - }), - ('Bit::Vector', bit_vector_version, { - 'source_tmpl': 'Bit-Vector-%s.tar.gz' % bit_vector_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/S/ST/STBEY/'], - }), - ('Parse::RecDescent', parse_recdescent_version, { - 'source_tmpl': 'Parse-RecDescent-%s.tar.gz' % parse_recdescent_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/J/JT/JTBRAUN/'], - }), - ('Inline', inline_version, { - 'source_tmpl': 'Inline-%s.tar.gz' % inline_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/I/IN/INGY/'], - }), - ('File::ShareDir::Install', file_sharedir_install_version, { - 'source_tmpl': 'File-ShareDir-Install-%s.tar.gz' % file_sharedir_install_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/E/ET/ETHER/'], - }), - ('Inline::C', inline_c_version, { - 'source_tmpl': 'Inline-C-%s.tar.gz' % inline_c_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/I/IN/INGY/'], - }), - ('IO::All', io_all_version, { - 'source_tmpl': 'IO-All-%s.tar.gz' % io_all_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/I/IN/INGY/'], - }), - ('IO::Prompt', io_prompt_version, { - 'source_tmpl': 'IO-Prompt-%s.tar.gz' % io_prompt_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/D/DC/DCONWAY/'], - }), - ('Getopt::Long', getopt_long_version, { - 'source_tmpl': 'Getopt-Long-%s.tar.gz' % getopt_long_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/J/JV/JV/'], - }), - ('AppConfig', appconfig_version, { - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/N/NE/NEILB/'], - }), - ('Archive::Extract', archive_extract_version, { - 'source_tmpl': 'Archive-Extract-%s.tar.gz' % archive_extract_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/B/BI/BINGOS/'], - }), - ('Archive::Tar', archive_tar_version, { - 'source_tmpl': 'Archive-Tar-%s.tar.gz' % archive_tar_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/B/BI/BINGOS/'], - }), - ('Archive::Zip', archive_zip_version, { - 'source_tmpl': 'Archive-Zip-%s.tar.gz' % archive_zip_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/P/PH/PHRED/'], - }), - ('Authen::SASL', authen_sasl_version, { - 'source_tmpl': 'Authen-SASL-%s.tar.gz' % authen_sasl_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/G/GB/GBARR/'], - }), - ('B::Lint', b_lint_version, { - 'source_tmpl': 'B-Lint-%s.tar.gz' % b_lint_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/R/RJ/RJBS/'], - }), - ('Class::Accessor', class_accessor_version, { - 'source_tmpl': 'Class-Accessor-%s.tar.gz' % class_accessor_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/K/KA/KASEI/'], - }), - ('Class::DBI', class_dbi_version, { - 'source_tmpl': 'Class-DBI-v%s.tar.gz' % class_dbi_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/T/TM/TMTM/'], - }), - ('Class::Inspector', class_inspector_version, { - 'source_tmpl': 'Class-Inspector-%s.tar.gz' % class_inspector_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/P/PL/PLICEASE/'], - }), - ('Class::ISA', class_isa_version, { - 'source_tmpl': 'Class-ISA-%s.tar.gz' % class_isa_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/S/SM/SMUELLER/'], - }), - ('Class::Trigger', class_trigger_version, { - 'source_tmpl': 'Class-Trigger-%s.tar.gz' % class_trigger_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/M/MI/MIYAGAWA/'], - }), - ('CPANPLUS', cpanplus_version, { - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/B/BI/BINGOS/'], - }), - ('Data::Grove', libxml_perl_version, { - 'source_tmpl': 'libxml-perl-%s.tar.gz' % libxml_perl_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/K/KM/KMACLEOD/'], - }), - ('Data::UUID', data_uuid_version, { - 'source_tmpl': 'Data-UUID-%s.tar.gz' % data_uuid_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/R/RJ/RJBS/'], - }), - ('Date::Language', timedate_version, { - 'source_tmpl': 'TimeDate-%s.tar.gz' % timedate_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/G/GB/GBARR/'], - }), - ('Date::Handler', date_handler_version, { - 'source_tmpl': 'Date-Handler-%s.tar.gz' % date_handler_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/B/BB/BBEAUSEJ/'], - }), - ('SQL::Statement', sql_statement_version, { - 'source_tmpl': 'SQL-Statement-%s.tar.gz' % sql_statement_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/R/RE/REHSACK/'], - }), - ('Module::Pluggable', module_pluggable_version, { - 'source_tmpl': 'Module-Pluggable-%s.tar.gz' % module_pluggable_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/S/SI/SIMONW/'], - }), - ('Digest::HMAC', digest_hmac_version, { - 'source_tmpl': 'Digest-HMAC-%s.tar.gz' % digest_hmac_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/G/GA/GAAS/'], - }), - ('Digest::SHA1', digest_sha1_version, { - 'source_tmpl': 'Digest-SHA1-%s.tar.gz' % digest_sha1_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/G/GA/GAAS/'], - }), - ('Email::Date::Format', email_date_format_version, { - 'source_tmpl': 'Email-Date-Format-%s.tar.gz' % email_date_format_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/R/RJ/RJBS/'], - }), - ('Error', error_version, { - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/S/SH/SHLOMIF/'], - }), - ('Expect', expect_pm_version, { - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/R/RG/RGIERSIG/'], - }), - ('File::CheckTree', file_checktree_version, { - 'source_tmpl': 'File-CheckTree-%s.tar.gz' % file_checktree_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/R/RJ/RJBS/'], - }), - ('FreezeThaw', freezethaw_version, { - 'source_tmpl': 'FreezeThaw-%s.tar.gz' % freezethaw_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/I/IL/ILYAZ/modules/'], - }), - ('Git', git_version, { - 'source_tmpl': 'Git-%s.tar.gz' % git_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/M/MS/MSOUTH/'], - }), - ('GO::Utils', go_perl_version, { - 'source_tmpl': 'go-perl-%s.tar.gz' % go_perl_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/C/CM/CMUNGALL/'], - }), - ('GO', go_db_perl_version, { - 'source_tmpl': 'go-db-perl-%s.tar.gz' % go_db_perl_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/S/SJ/SJCARBON/'], - }), - - ('HTML::Form', html_form_version, { - 'source_tmpl': 'HTML-Form-%s.tar.gz' % html_form_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/G/GA/GAAS/'], - }), - ('HTTP::Cookies', http_cookies_version, { - 'source_tmpl': 'HTTP-Cookies-%s.tar.gz' % http_cookies_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/G/GA/GAAS/'], - }), - ('HTTP::Daemon', http_daemon_version, { - 'source_tmpl': 'HTTP-Daemon-%s.tar.gz' % http_daemon_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/G/GA/GAAS/'], - }), - ('HTTP::Negotiate', http_negotiate_version, { - 'source_tmpl': 'HTTP-Negotiate-%s.tar.gz' % http_negotiate_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/G/GA/GAAS/'], - }), - ('IO::Stringy', io_stringy_version, { - 'source_tmpl': 'IO-stringy-%s.tar.gz' % io_stringy_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/D/DS/DSKOLL/'], - }), - ('IO::Socket::SSL', io_socket_ssl_version, { - 'source_tmpl': 'IO-Socket-SSL-%s.tar.gz' % io_socket_ssl_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/S/SU/SULLR/'], - }), - ('JSON', json_version, { - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/M/MA/MAKAMAKA/'], - }), - ('Log::Message', log_message_version, { - 'source_tmpl': 'Log-Message-%s.tar.gz' % log_message_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/B/BI/BINGOS/'], - }), - ('Log::Message::Simple', log_message_simple_version, { - 'source_tmpl': 'Log-Message-Simple-%s.tar.gz' % log_message_simple_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/B/BI/BINGOS/'], - }), - ('Mail::Util', mailtools_version, { - 'source_tmpl': 'MailTools-%s.tar.gz' % mailtools_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/M/MA/MARKOV/'], - }), - ('MIME::Types', mime_types_version, { - 'source_tmpl': 'MIME-Types-%s.tar.gz' % mime_types_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/M/MA/MARKOV/'], - }), - ('MIME::Lite', mime_lite_version, { - 'source_tmpl': 'MIME-Lite-%s.tar.gz' % mime_lite_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/R/RJ/RJBS/'], - }), - ('Net::HTTP', net_http_version, { - 'source_tmpl': 'Net-HTTP-%s.tar.gz' % net_http_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/O/OA/OALDERS/'], - }), - ('Net::SMTP::SSL', net_smtp_ssl_version, { - 'source_tmpl': 'Net-SMTP-SSL-%s.tar.gz' % net_smtp_ssl_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/R/RJ/RJBS/'], - }), - ('Object::Accessor', object_accessor_version, { - 'source_tmpl': 'Object-Accessor-%s.tar.gz' % object_accessor_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/B/BI/BINGOS/'], - }), - ('Pod::LaTeX', pod_latex_version, { - 'source_tmpl': 'Pod-LaTeX-%s.tar.gz' % pod_latex_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/T/TJ/TJENNESS/'], - }), - ('Pod::Plainer', pod_plainer_version, { - 'source_tmpl': 'Pod-Plainer-%s.tar.gz' % pod_plainer_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/R/RM/RMBARKER/'], - }), - ('Pod::POM', pod_pom_version, { - 'source_tmpl': 'Pod-POM-%s.tar.gz' % pod_pom_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/N/NE/NEILB/'], - }), - ('Shell', shell_version, { - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/F/FE/FERREIRA/'], - }), - ('Statistics::Descriptive', statistics_descriptive_version, { - 'source_tmpl': 'Statistics-Descriptive-%s.tar.gz' % statistics_descriptive_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/S/SH/SHLOMIF/'], - }), - ('Switch', switch_version, { - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/C/CH/CHORNY/'], - }), - ('Template', template_toolkit_version, { - 'source_tmpl': 'Template-Toolkit-%s.tar.gz' % template_toolkit_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/A/AB/ABW/'], - }), - ('Term::UI', term_ui_version, { - 'source_tmpl': 'Term-UI-%s.tar.gz' % term_ui_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/B/BI/BINGOS/'], - }), - ('Text::Iconv', text_iconv_version, { - 'source_tmpl': 'Text-Iconv-%s.tar.gz' % text_iconv_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/M/MP/MPIOTR/'], - }), - ('Text::Soundex', text_soundex_version, { - 'source_tmpl': 'Text-Soundex-%s.tar.gz' % text_soundex_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/R/RJ/RJBS/'], - }), - ('Time::Piece', time_piece_version, { - 'source_tmpl': 'Time-Piece-%s.tar.gz' % time_piece_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/E/ES/ESAYM/'], - }), - ('Time::Piece::MySQL', time_piece_mysql_version, { - 'source_tmpl': 'Time-Piece-MySQL-%s.tar.gz' % time_piece_mysql_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/K/KA/KASEI/'], - }), - ('UNIVERSAL::moniker', universal_moniker_version, { - 'source_tmpl': 'UNIVERSAL-moniker-%s.tar.gz' % universal_moniker_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/K/KA/KASEI/'], - }), - ('version', version_version, { - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/J/JP/JPEACOCK/'], - }), - ('WWW::RobotRules', www_robotrules_version, { - 'source_tmpl': 'WWW-RobotRules-%s.tar.gz' % www_robotrules_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/G/GA/GAAS/'], - }), - ('XML::SAX::Writer', xml_sax_writer_version, { - 'source_tmpl': 'XML-SAX-Writer-%s.tar.gz' % xml_sax_writer_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/P/PE/PERIGRIN/'], - }), - ('XML::Simple', xml_simple_version, { - 'source_tmpl': 'XML-Simple-%s.tar.gz' % xml_simple_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/G/GR/GRANTM/'], - }), - ('XML::XPath', xml_xpath_version, { - 'source_tmpl': 'XML-XPath-%s.tar.gz' % xml_xpath_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/M/MA/MANWAR/'], - }), - ('DBD::AnyData', dbd_anydata_version, { - 'source_tmpl': 'DBD-AnyData-%s.tar.gz' % dbd_anydata_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/R/RE/REHSACK/'], - }), - ('Ima::DBI', ima_dbi_version, { - 'source_tmpl': 'Ima-DBI-%s.tar.gz' % ima_dbi_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/P/PE/PERRIN/'], - }), - ('DBIx::ContextualFetch', dbix_contextualfetch_version, { - 'source_tmpl': 'DBIx-ContextualFetch-%s.tar.gz' % dbix_contextualfetch_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/T/TM/TMTM/'], - }), - ('DBIx::Simple', dbix_simple_version, { - 'source_tmpl': 'DBIx-Simple-%s.tar.gz' % dbix_simple_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/J/JU/JUERD/'], - }), - ('Term::ReadKey', term_readkey_version, { - 'source_tmpl': 'TermReadKey-%s.tar.gz' % term_readkey_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/J/JS/JSTOWE/'], -# 'patches': ['TermReadKey-2.32.patch'], - }), - ('Moo', moo_version, { - 'source_tmpl': 'Moo-%s.tar.gz' % moo_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/H/HA/HAARG/'], - }), - ('strictures', strictures_version, { - 'source_tmpl': 'strictures-%s.tar.gz' % strictures_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/H/HA/HAARG/'], - }), - ('File::Find::Rule::Perl', file_find_rule_perl_version, { - 'source_tmpl': 'File-Find-Rule-Perl-%s.tar.gz' % file_find_rule_perl_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/E/ET/ETHER/'], - }), - ('Test::Version', test_version_version, { - 'source_tmpl': 'Test-Version-%s.tar.gz' % test_version_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/P/PL/PLICEASE/'], - }), - ('Test::Harness', test_harness_version, { - 'source_tmpl': 'Test-Harness-%s.tar.gz' % test_harness_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/L/LE/LEONT/'], - }), - ('Import::Into', import_into_version, { - 'source_tmpl': 'Import-Into-%s.tar.gz' % import_into_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/H/HA/HAARG/'], - }), - ('File::Find::Rule', file_find_rule_version, { - 'source_tmpl': 'File-Find-Rule-%s.tar.gz' % file_find_rule_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/R/RC/RCLAMP/'], - }), - ('Data::Section::Simple', data_section_simple_version, { - 'source_tmpl': 'Data-Section-Simple-%s.tar.gz' % data_section_simple_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/M/MI/MIYAGAWA/'], - }), - ('Text::Glob', text_glob_version, { - 'source_tmpl': 'Text-Glob-%s.tar.gz' % text_glob_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/R/RC/RCLAMP/'], - }), - ('Number::Compare', number_compare_version, { - 'source_tmpl': 'Number-Compare-%s.tar.gz' % number_compare_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/R/RC/RCLAMP/'], - }), - ('IPC::Run3', ipc_run3_version, { - 'source_tmpl': 'IPC-Run3-%s.tar.gz' % ipc_run3_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/R/RJ/RJBS/'], - }), - ('Set::Array', set_array_version, { - 'source_tmpl': 'Set-Array-%s.tgz' % set_array_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/R/RS/RSAVAGE/'], - }), - ('Bundle::BioPerl', bundle_bioperl_version, { - 'source_tmpl': 'Bundle-BioPerl-%s.tar.gz' % bundle_bioperl_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/C/CJ/CJFIELDS/'], - }), - ('Algorithm::Munkres', algorithm_munkres_version, { - 'source_tmpl': 'Algorithm-Munkres-%s.tar.gz' % algorithm_munkres_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/T/TP/TPEDERSE/'], - }), -# Lots of deps: Types::Standard etc. -# ('Array::Compare', array_compare_version, { -# 'source_tmpl': 'Array-Compare-v%s.tar.gz' % array_compare_version, -# 'source_urls': ['http://search.cpan.org/CPAN/authors/id/D/DA/DAVECROSS/'], -# }), - ('Graph', graph_version, { - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/J/JH/JHI/'], - }), - ('Set::Scalar', set_scalar_version, { - 'source_tmpl': 'Set-Scalar-%s.tar.gz' % set_scalar_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/D/DA/DAVIDO/'], - }), - ('CGI', cgi_version, { - 'source_tmpl': 'CGI-%s.tar.gz' % cgi_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/L/LE/LEEJO/'], - }), - ('Bio::Phylo', bio_phylo_version, { - 'source_tmpl': 'Bio-Phylo-%s.tar.gz' % bio_phylo_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/R/RV/RVOSA/'], - }), - ('SVG', svg_version, { - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/S/SZ/SZABGAB/'], - }), - ('XML::DOM', xml_dom_version, { - 'source_tmpl': 'XML-DOM-%s.tar.gz' % xml_dom_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/T/TJ/TJMATHER/'], - }), - ('XML::DOM::XPath', xml_dom_xpath_version, { - 'source_tmpl': 'XML-DOM-XPath-%s.tar.gz' % xml_dom_xpath_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/M/MI/MIROD/'], - }), - ('XML::Parser::PerlSAX', libxml_perl_version, { - 'source_tmpl': 'libxml-perl-%s.tar.gz' % libxml_perl_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/K/KM/KMACLEOD/'], - }), - ('XML::Parser', xml_parser_version, { - 'source_tmpl': 'XML-Parser-%s.tar.gz' % xml_parser_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/T/TO/TODDR/'], - }), - ('XML::Twig', xml_twig_version, { - 'source_tmpl': 'XML-Twig-%s.tar.gz' % xml_twig_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/M/MI/MIROD/'], - }), - ('XML::Writer', xml_writer_version, { - 'source_tmpl': 'XML-Writer-%s.tar.gz' % xml_writer_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/J/JO/JOSEPHW/'], - }), - ('Spreadsheet::ParseExcel', spreadsheet_parseexcel_version, { - 'source_tmpl': 'Spreadsheet-ParseExcel-%s.tar.gz' % spreadsheet_parseexcel_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/D/DO/DOUGW/'], - }), - ('Convert::Binary::C', convert_binary_c_version, { - 'source_tmpl': 'Convert-Binary-C-%s.tar.gz' % convert_binary_c_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/M/MH/MHX/'], - }), - ('Sys::SigAction.pm', sys_sigaction_version, { - 'source_tmpl': 'Sys-SigAction-%s.tar.gz' % sys_sigaction_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/L/LB/LBAXTER/'], - }), - ('Acme::Damn', acme_damn_version, { - 'source_tmpl': 'Acme-Damn-%s.tar.gz' % acme_damn_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/I/IB/IBB/'], - }), - ('Set::IntervalTree', set_intervaltree_version, { - 'source_tmpl': 'Set-IntervalTree-%s.tar.gz' % set_intervaltree_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/B/BE/BENBOOTH/'], - }), - ('HTML::TableExtract', html_tableextract_version, { - 'source_tmpl': 'HTML-TableExtract-%s.tar.gz' % html_tableextract_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/M/MS/MSISK/'], - }), - ('Bio::Perl', bioperl_version, { - 'source_tmpl': 'BioPerl-%s.tar.gz' % bioperl_version, - 'source_urls': ['http://www.cpan.org/modules/by-module/Bio/CJFIELDS/'], - }), - ('Bio::DB::Sam', bio_samtools_version, { - 'source_tmpl': 'Bio-SamTools-%s.tar.gz' % bio_samtools_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/L/LD/LDS/'], - 'patches': ['Perl_SamTools_include.patch'], - }), - ('File::Spec::Functions', pathtools_version, { - 'source_tmpl': 'PathTools-%s.tar.gz' % pathtools_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/R/RJ/RJBS/'], - }), - ('List::Util', scalar_list_utils_version, { - 'source_tmpl': 'Scalar-List-Utils-%s.tar.gz' % scalar_list_utils_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/P/PE/PEVANS/'], - }), - ('Module::Load::Conditional', module_load_conditional_version, { - 'source_tmpl': 'Module-Load-Conditional-%s.tar.gz' % module_load_conditional_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/B/BI/BINGOS/'], - }), - ('Scalar::Util::Numeric', scalar_util_numeric_version, { - 'source_tmpl': 'Scalar-Util-Numeric-%s.tar.gz' % scalar_util_numeric_version, - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/C/CH/CHOCOLATE/'], - }), -] - -moduleclass = 'lang' diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.19-gimkl-2017a.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.19-gimkl-2017a.eb deleted file mode 100644 index 877294f204..0000000000 --- a/easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.19-gimkl-2017a.eb +++ /dev/null @@ -1,21 +0,0 @@ -name = 'SAMtools' -version = '0.1.19' - -homepage = 'http://www.htslib.org/' -description = """SAM Tools provide various utilities for manipulating alignments in the SAM format, - including sorting, merging, indexing and generating alignments in a per-position format.""" - -toolchain = {'name': 'gimkl', 'version': '2017a'} -toolchainopts = {'optarch': True, 'pic': True} - -sources = [SOURCELOWER_TAR_BZ2] -source_urls = [('http://sourceforge.net/projects/samtools/files/%(namelower)s/%(version)s', 'download')] - -patches = ['SAMtools-%(version)s_Makefile-ncurses.patch'] - -dependencies = [ - ('ncurses', '6.0'), - ('zlib', '1.2.11'), -] - -moduleclass = 'bio' -- GitLab From 11c424082a6f064552f34bc0e74a766cebbbd695 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 15 Mar 2017 11:25:33 +0100 Subject: [PATCH 0390/1603] Add kaiju/1.5.0 --- .../k/Kaiju/kaiju-1.5.0-intel-2016b.eb | 27 ++++++++++++++++ .../k/Kaiju/kaiju-1.5.0-makefile.patch | 31 +++++++++++++++++++ 2 files changed, 58 insertions(+) create mode 100644 easybuild/easyconfigs/k/Kaiju/kaiju-1.5.0-intel-2016b.eb create mode 100644 easybuild/easyconfigs/k/Kaiju/kaiju-1.5.0-makefile.patch diff --git a/easybuild/easyconfigs/k/Kaiju/kaiju-1.5.0-intel-2016b.eb b/easybuild/easyconfigs/k/Kaiju/kaiju-1.5.0-intel-2016b.eb new file mode 100644 index 0000000000..1a3e1acaed --- /dev/null +++ b/easybuild/easyconfigs/k/Kaiju/kaiju-1.5.0-intel-2016b.eb @@ -0,0 +1,27 @@ +easyblock = 'MakeCp' + +name = 'Kaiju' +version = '1.5.0' + +homepage = 'http://kaiju.binf.ku.dk/' +description = """Kaiju is a program for sensitive taxonomic classification of high-throughput +sequencing reads from metagenomic whole genome sequencing experiments""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'cstd': 'c++11'} + +sources = ['v%(version)s.tar.gz'] +source_urls = ['https://github.com/bioinformatics-centre/kaiju/archive/'] + +patches = ['kaiju-%(version)s-makefile.patch'] + +start_dir = 'src' + +files_to_copy = ['bin'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['kaiju', 'kaiju2krona', 'kaijup', 'kaijuReport', 'kaijux']], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/k/Kaiju/kaiju-1.5.0-makefile.patch b/easybuild/easyconfigs/k/Kaiju/kaiju-1.5.0-makefile.patch new file mode 100644 index 0000000000..3ae20a25b6 --- /dev/null +++ b/easybuild/easyconfigs/k/Kaiju/kaiju-1.5.0-makefile.patch @@ -0,0 +1,31 @@ +diff -ur kaiju-1.5.0.orig/src/bwt/Makefile kaiju-1.5.0/src/bwt/Makefile +--- kaiju-1.5.0.orig/src/bwt/Makefile 2017-02-20 16:22:04.000000000 +0100 ++++ kaiju-1.5.0/src/bwt/Makefile 2017-03-15 11:20:22.174636137 +0100 +@@ -1,7 +1,7 @@ +-CC = gcc ++CC ?= gcc + #CFLAGS = -g +-CFLAGS = -O3 -g -Wno-unused-result +-LDLIBS = -lpthread -lm ++CFLAGS ?= -O3 -g -Wno-unused-result ++LDLIBS ?= -lpthread -lm + + all: mkbwt mkfmi Makefile + +diff -ur kaiju-1.5.0.orig/src/makefile kaiju-1.5.0/src/makefile +--- kaiju-1.5.0.orig/src/makefile 2017-02-20 16:22:04.000000000 +0100 ++++ kaiju-1.5.0/src/makefile 2017-03-15 11:20:10.710515853 +0100 +@@ -1,8 +1,8 @@ +-CC = gcc +-CXX = g++ +-CFLAGS = -g -O3 -DNDEBUG -Wall -Wno-uninitialized +-CXXFLAGS = -ansi -pedantic -O3 -pthread -std=c++11 -g -DNDEBUG -Wall -Wconversion -Wno-unused-function +-LDLIBS = -lpthread ++CC ?= gcc ++CXX ?= g++ ++CFLAGS ?= -g -O3 -DNDEBUG -Wall -Wno-uninitialized ++CXXFLAGS ?= -ansi -pedantic -O3 -pthread -std=c++11 -g -DNDEBUG -Wall -Wconversion -Wno-unused-function ++LDLIBS ?= -lpthread + INCLUDES = -I./include/ProducerConsumerQueue/src -I./include/ncbi-blast+ + + BLASTOBJS = include/ncbi-blast+/algo/blast/core/pattern.o \ -- GitLab From 1042b8e7ef4cf2bd8866e1ab43a2d8b3ecd918f4 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 15 Mar 2017 11:35:58 +0100 Subject: [PATCH 0391/1603] Use capitals for easyconfig file --- .../{kaiju-1.5.0-intel-2016b.eb => Kaiju-1.5.0-intel-2016b.eb} | 0 .../{kaiju-1.5.0-makefile.patch => Kaiju-1.5.0-makefile.patch} | 0 2 files changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/k/Kaiju/{kaiju-1.5.0-intel-2016b.eb => Kaiju-1.5.0-intel-2016b.eb} (100%) rename easybuild/easyconfigs/k/Kaiju/{kaiju-1.5.0-makefile.patch => Kaiju-1.5.0-makefile.patch} (100%) diff --git a/easybuild/easyconfigs/k/Kaiju/kaiju-1.5.0-intel-2016b.eb b/easybuild/easyconfigs/k/Kaiju/Kaiju-1.5.0-intel-2016b.eb similarity index 100% rename from easybuild/easyconfigs/k/Kaiju/kaiju-1.5.0-intel-2016b.eb rename to easybuild/easyconfigs/k/Kaiju/Kaiju-1.5.0-intel-2016b.eb diff --git a/easybuild/easyconfigs/k/Kaiju/kaiju-1.5.0-makefile.patch b/easybuild/easyconfigs/k/Kaiju/Kaiju-1.5.0-makefile.patch similarity index 100% rename from easybuild/easyconfigs/k/Kaiju/kaiju-1.5.0-makefile.patch rename to easybuild/easyconfigs/k/Kaiju/Kaiju-1.5.0-makefile.patch -- GitLab From 868ea7d2d5d5be6bdef3d33e8a91b89e1c230127 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 15 Mar 2017 11:45:23 +0100 Subject: [PATCH 0392/1603] Fix name of patch --- easybuild/easyconfigs/k/Kaiju/Kaiju-1.5.0-intel-2016b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/k/Kaiju/Kaiju-1.5.0-intel-2016b.eb b/easybuild/easyconfigs/k/Kaiju/Kaiju-1.5.0-intel-2016b.eb index 1a3e1acaed..7f4e002400 100644 --- a/easybuild/easyconfigs/k/Kaiju/Kaiju-1.5.0-intel-2016b.eb +++ b/easybuild/easyconfigs/k/Kaiju/Kaiju-1.5.0-intel-2016b.eb @@ -13,7 +13,7 @@ toolchainopts = {'cstd': 'c++11'} sources = ['v%(version)s.tar.gz'] source_urls = ['https://github.com/bioinformatics-centre/kaiju/archive/'] -patches = ['kaiju-%(version)s-makefile.patch'] +patches = ['%(name)s-%(version)s-makefile.patch'] start_dir = 'src' -- GitLab From fd9d12a31ff48581a75fe834c0c6bff21e99f62b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Luk=C3=A1=C5=A1=20Krup=C4=8D=C3=ADk?= Date: Wed, 15 Mar 2017 15:14:09 +0100 Subject: [PATCH 0393/1603] {tools}Singularity-2.2.1-GCC-6.3.0 added --- .../Singularity-2.2.1-GCC-6.3.0-2.27.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/s/Singularity/Singularity-2.2.1-GCC-6.3.0-2.27.eb diff --git a/easybuild/easyconfigs/s/Singularity/Singularity-2.2.1-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/s/Singularity/Singularity-2.2.1-GCC-6.3.0-2.27.eb new file mode 100644 index 0000000000..e1e43de48b --- /dev/null +++ b/easybuild/easyconfigs/s/Singularity/Singularity-2.2.1-GCC-6.3.0-2.27.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'Singularity' +version = '2.2.1' + +homepage = 'http://gmkurtzer.github.io/singularity' +description = """Singularity is a portable application stack packaging and runtime utility.""" + +toolchain = {'name': 'GCC', 'version': '6.3.0-2.27'} + +source_urls = ['https://github.com/gmkurtzer/singularity/archive/'] +sources = ['%(version)s.tar.gz'] + +builddependencies = [('Autotools', '20150215')] + +preconfigopts = './autogen.sh && ' + +sanity_check_paths = { + 'files': ['bin/run-singularity', 'bin/singularity', 'etc/singularity/singularity.conf', 'libexec/singularity/sexec-suid'], + 'dirs': ['etc', 'libexec/singularity'], +} + +moduleclass = 'tools' -- GitLab From d388e8264a2f10668639379434435e81beb41709 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Luk=C3=A1=C5=A1=20Krup=C4=8D=C3=ADk?= Date: Wed, 15 Mar 2017 15:20:01 +0100 Subject: [PATCH 0394/1603] {tools}Singularity-2.2.1-GCC-6.3.0 added comment `next steps after instalations` --- .../s/Singularity/Singularity-2.2.1-GCC-6.3.0-2.27.eb | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/s/Singularity/Singularity-2.2.1-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/s/Singularity/Singularity-2.2.1-GCC-6.3.0-2.27.eb index e1e43de48b..8c36b33253 100644 --- a/easybuild/easyconfigs/s/Singularity/Singularity-2.2.1-GCC-6.3.0-2.27.eb +++ b/easybuild/easyconfigs/s/Singularity/Singularity-2.2.1-GCC-6.3.0-2.27.eb @@ -20,4 +20,10 @@ sanity_check_paths = { 'dirs': ['etc', 'libexec/singularity'], } +# next steps after instalations +# INSTALATION_PATH=your_instalation_path +# chown root:root $INSTALATION_PATH/Singularity/*/etc/singularity/singularity.conf +# chown root:root $INSTALATION_PATH/Singularity/*/libexec/singularity/sexec-suid +# chmod +s $INSTALATION_PATH/Singularity/*/libexec/singularity/sexec-suid + moduleclass = 'tools' -- GitLab From 765acc339dc67081c2630070b3f5c726609a375f Mon Sep 17 00:00:00 2001 From: Damian Alvarez Date: Thu, 16 Mar 2017 09:32:27 +0100 Subject: [PATCH 0395/1603] Fixed wrong sanity check in Mesa --- .../m/Mesa/Mesa-10.4.5-intel-2015a-Python-2.7.9.eb | 5 ++--- .../m/Mesa/Mesa-10.5.5-intel-2015a-Python-2.7.10.eb | 5 ++--- .../m/Mesa/Mesa-11.0.2-intel-2015b-Python-2.7.10.eb | 7 +++---- .../m/Mesa/Mesa-11.0.8-intel-2015b-Python-2.7.11.eb | 7 +++---- .../easyconfigs/m/Mesa/Mesa-11.1.2-foss-2016a.eb | 11 +++++++---- .../easyconfigs/m/Mesa/Mesa-11.1.2-gimkl-2.11.5.eb | 11 +++++++---- .../easyconfigs/m/Mesa/Mesa-11.1.2-intel-2016a.eb | 11 +++++++---- .../easyconfigs/m/Mesa/Mesa-11.2.1-foss-2016a.eb | 11 +++++++---- .../easyconfigs/m/Mesa/Mesa-11.2.1-intel-2016a.eb | 11 +++++++---- .../easyconfigs/m/Mesa/Mesa-12.0.2-foss-2016b.eb | 11 +++++++---- .../easyconfigs/m/Mesa/Mesa-12.0.2-intel-2016b.eb | 11 +++++++---- .../m/Mesa/Mesa-7.11.2-goolf-1.4.10-Python-2.7.3.eb | 11 +++++++---- .../m/Mesa/Mesa-7.11.2-ictce-5.3.0-Python-2.7.3.eb | 11 +++++++---- .../m/Mesa/Mesa-7.11.2-ictce-5.5.0-Python-2.7.6.eb | 10 ++++++---- 14 files changed, 79 insertions(+), 54 deletions(-) diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-10.4.5-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/m/Mesa/Mesa-10.4.5-intel-2015a-Python-2.7.9.eb index 41d6a64d37..d8ac10c171 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-10.4.5-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-10.4.5-intel-2015a-Python-2.7.9.eb @@ -64,9 +64,8 @@ prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm:$CPATH" ' sanity_check_paths = { 'files': ['lib/libGL.%s' % SHLIB_EXT, 'include/GL/glext.h', 'include/GL/gl_mangle.h', 'include/GL/glx.h', 'include/GL/osmesa.h', - 'include/GL/wglext.h', 'include/GL/gl.h', - 'include/GL/glxext.h', 'include/GL/glx_mangle.h', - 'include/GL/wmesa.h'], + 'include/GL/gl.h', 'include/GL/glxext.h', + 'include/GL/glx_mangle.h', ^'include/GL/wmesa.h'], 'dirs': [] } diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-10.5.5-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/m/Mesa/Mesa-10.5.5-intel-2015a-Python-2.7.10.eb index 8b03ae9140..d3f8230305 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-10.5.5-intel-2015a-Python-2.7.10.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-10.5.5-intel-2015a-Python-2.7.10.eb @@ -64,9 +64,8 @@ sanity_check_paths = { 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libOSMesa.%s' % SHLIB_EXT, 'include/GL/glext.h', 'include/GL/gl_mangle.h', 'include/GL/glx.h', 'include/GL/osmesa.h', - 'include/GL/wglext.h', 'include/GL/gl.h', - 'include/GL/glxext.h', 'include/GL/glx_mangle.h', - 'include/GL/wmesa.h'], + 'include/GL/gl.h', 'include/GL/glxext.h', + 'include/GL/glx_mangle.h', ^'include/GL/wmesa.h'], 'dirs': [] } diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-11.0.2-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/m/Mesa/Mesa-11.0.2-intel-2015b-Python-2.7.10.eb index 5224023e11..7d75f18d6f 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-11.0.2-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-11.0.2-intel-2015b-Python-2.7.10.eb @@ -64,10 +64,9 @@ sanity_check_paths = { 'lib/libGLESv1_CM.%s' % SHLIB_EXT, 'lib/libGLESv2.%s' % SHLIB_EXT, 'include/GL/glext.h', 'include/GL/gl_mangle.h', 'include/GL/glx.h', 'include/GL/osmesa.h', - 'include/GL/wglext.h', 'include/GL/gl.h', - 'include/GL/glxext.h', 'include/GL/glx_mangle.h', - 'include/GLES/gl.h', 'include/GLES2/gl2.h', - 'include/GLES3/gl3.h'], + 'include/GL/gl.h', 'include/GL/glxext.h', + 'include/GL/glx_mangle.h', 'include/GLES/gl.h', + 'include/GLES2/gl2.h', 'include/GLES3/gl3.h'], 'dirs': [] } diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-11.0.8-intel-2015b-Python-2.7.11.eb b/easybuild/easyconfigs/m/Mesa/Mesa-11.0.8-intel-2015b-Python-2.7.11.eb index ec21cce29c..346166fe00 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-11.0.8-intel-2015b-Python-2.7.11.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-11.0.8-intel-2015b-Python-2.7.11.eb @@ -64,10 +64,9 @@ sanity_check_paths = { 'lib/libGLESv1_CM.so', 'lib/libGLESv2.so', 'include/GL/glext.h', 'include/GL/gl_mangle.h', 'include/GL/glx.h', 'include/GL/osmesa.h', - 'include/GL/wglext.h', 'include/GL/gl.h', - 'include/GL/glxext.h', 'include/GL/glx_mangle.h', - 'include/GLES/gl.h', 'include/GLES2/gl2.h', - 'include/GLES3/gl3.h'], + 'include/GL/gl.h', 'include/GL/glxext.h', + 'include/GL/glx_mangle.h', 'include/GLES/gl.h', + 'include/GLES2/gl2.h', 'include/GLES3/gl3.h'], 'dirs': [] } diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-foss-2016a.eb b/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-foss-2016a.eb index 81337fce92..9b02d2b02b 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-foss-2016a.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-foss-2016a.eb @@ -56,10 +56,13 @@ preconfigopts = ' libtoolize && ' prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm:$CPATH" ' sanity_check_paths = { - 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libOSMesa.%s' % SHLIB_EXT, 'lib/libGLESv1_CM.%s' % SHLIB_EXT, - 'lib/libGLESv2.%s' % SHLIB_EXT, 'include/GL/glext.h', 'include/GL/gl_mangle.h', 'include/GL/glx.h', - 'include/GL/osmesa.h', 'include/GL/wglext.h', 'include/GL/gl.h', 'include/GL/glxext.h', - 'include/GL/glx_mangle.h', 'include/GLES/gl.h', 'include/GLES2/gl2.h', 'include/GLES3/gl3.h'], + 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libOSMesa.%s' % SHLIB_EXT, + 'lib/libGLESv1_CM.%s' % SHLIB_EXT, 'lib/libGLESv2.%s' % SHLIB_EXT, + 'include/GL/glext.h', 'include/GL/gl_mangle.h', + 'include/GL/glx.h', 'include/GL/osmesa.h', + 'include/GL/gl.h', 'include/GL/glxext.h', + 'include/GL/glx_mangle.h', 'include/GLES/gl.h', + 'include/GLES2/gl2.h', 'include/GLES3/gl3.h'], 'dirs': [] } diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-gimkl-2.11.5.eb b/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-gimkl-2.11.5.eb index 84db881b8b..45545e7c83 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-gimkl-2.11.5.eb @@ -56,10 +56,13 @@ preconfigopts = ' libtoolize && ' prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm:$CPATH" ' sanity_check_paths = { - 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libOSMesa.%s' % SHLIB_EXT, 'lib/libGLESv1_CM.%s' % SHLIB_EXT, - 'lib/libGLESv2.%s' % SHLIB_EXT, 'include/GL/glext.h', 'include/GL/gl_mangle.h', 'include/GL/glx.h', - 'include/GL/osmesa.h', 'include/GL/wglext.h', 'include/GL/gl.h', 'include/GL/glxext.h', - 'include/GL/glx_mangle.h', 'include/GLES/gl.h', 'include/GLES2/gl2.h', 'include/GLES3/gl3.h'], + 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libOSMesa.%s' % SHLIB_EXT, + 'lib/libGLESv1_CM.%s' % SHLIB_EXT, 'lib/libGLESv2.%s' % SHLIB_EXT, + 'include/GL/glext.h', 'include/GL/gl_mangle.h', + 'include/GL/glx.h', 'include/GL/osmesa.h', + 'include/GL/gl.h', 'include/GL/glxext.h', + 'include/GL/glx_mangle.h', 'include/GLES/gl.h', + 'include/GLES2/gl2.h', 'include/GLES3/gl3.h'], 'dirs': [] } diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-intel-2016a.eb b/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-intel-2016a.eb index 9a2892bda4..92703769fd 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-intel-2016a.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-11.1.2-intel-2016a.eb @@ -56,10 +56,13 @@ preconfigopts = ' libtoolize && ' prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm:$CPATH" ' sanity_check_paths = { - 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libOSMesa.%s' % SHLIB_EXT, 'lib/libGLESv1_CM.%s' % SHLIB_EXT, - 'lib/libGLESv2.%s' % SHLIB_EXT, 'include/GL/glext.h', 'include/GL/gl_mangle.h', 'include/GL/glx.h', - 'include/GL/osmesa.h', 'include/GL/wglext.h', 'include/GL/gl.h', 'include/GL/glxext.h', - 'include/GL/glx_mangle.h', 'include/GLES/gl.h', 'include/GLES2/gl2.h', 'include/GLES3/gl3.h'], + 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libOSMesa.%s' % SHLIB_EXT, + 'lib/libGLESv1_CM.%s' % SHLIB_EXT, 'lib/libGLESv2.%s' % SHLIB_EXT, + 'include/GL/glext.h', 'include/GL/gl_mangle.h', + 'include/GL/glx.h', 'include/GL/osmesa.h', + 'include/GL/gl.h', 'include/GL/glxext.h', + 'include/GL/glx_mangle.h', 'include/GLES/gl.h', + 'include/GLES2/gl2.h', 'include/GLES3/gl3.h'], 'dirs': [] } diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-11.2.1-foss-2016a.eb b/easybuild/easyconfigs/m/Mesa/Mesa-11.2.1-foss-2016a.eb index 8fe85b43fb..61b180d1ef 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-11.2.1-foss-2016a.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-11.2.1-foss-2016a.eb @@ -56,10 +56,13 @@ preconfigopts = ' libtoolize && ' prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm:$CPATH" ' sanity_check_paths = { - 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libOSMesa.%s' % SHLIB_EXT, 'lib/libGLESv1_CM.%s' % SHLIB_EXT, - 'lib/libGLESv2.%s' % SHLIB_EXT, 'include/GL/glext.h', 'include/GL/gl_mangle.h', 'include/GL/glx.h', - 'include/GL/osmesa.h', 'include/GL/wglext.h', 'include/GL/gl.h', 'include/GL/glxext.h', - 'include/GL/glx_mangle.h', 'include/GLES/gl.h', 'include/GLES2/gl2.h', 'include/GLES3/gl3.h'], + 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libOSMesa.%s' % SHLIB_EXT, + 'lib/libGLESv1_CM.%s' % SHLIB_EXT, 'lib/libGLESv2.%s' % SHLIB_EXT, + 'include/GL/glext.h', 'include/GL/gl_mangle.h', + 'include/GL/glx.h', 'include/GL/osmesa.h', + 'include/GL/gl.h', 'include/GL/glxext.h', + 'include/GL/glx_mangle.h', 'include/GLES/gl.h', + 'include/GLES2/gl2.h', 'include/GLES3/gl3.h'], 'dirs': [] } diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-11.2.1-intel-2016a.eb b/easybuild/easyconfigs/m/Mesa/Mesa-11.2.1-intel-2016a.eb index c0ae4f1fc2..6660454e4c 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-11.2.1-intel-2016a.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-11.2.1-intel-2016a.eb @@ -56,10 +56,13 @@ preconfigopts = ' libtoolize && ' prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm:$CPATH" ' sanity_check_paths = { - 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libOSMesa.%s' % SHLIB_EXT, 'lib/libGLESv1_CM.%s' % SHLIB_EXT, - 'lib/libGLESv2.%s' % SHLIB_EXT, 'include/GL/glext.h', 'include/GL/gl_mangle.h', 'include/GL/glx.h', - 'include/GL/osmesa.h', 'include/GL/wglext.h', 'include/GL/gl.h', 'include/GL/glxext.h', - 'include/GL/glx_mangle.h', 'include/GLES/gl.h', 'include/GLES2/gl2.h', 'include/GLES3/gl3.h'], + 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libOSMesa.%s' % SHLIB_EXT, + 'lib/libGLESv1_CM.%s' % SHLIB_EXT, 'lib/libGLESv2.%s' % SHLIB_EXT, + 'include/GL/glext.h', 'include/GL/gl_mangle.h', + 'include/GL/glx.h', 'include/GL/osmesa.h', + 'include/GL/gl.h', 'include/GL/glxext.h', + 'include/GL/glx_mangle.h', 'include/GLES/gl.h', + 'include/GLES2/gl2.h', 'include/GLES3/gl3.h'], 'dirs': [] } diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-12.0.2-foss-2016b.eb b/easybuild/easyconfigs/m/Mesa/Mesa-12.0.2-foss-2016b.eb index b8a0ae2d3f..8376070490 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-12.0.2-foss-2016b.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-12.0.2-foss-2016b.eb @@ -49,10 +49,13 @@ configopts += " --disable-driglx-direct --with-gallium-drivers='swrast,swr' --di configopts += " --with-osmesa-bits=32 --enable-texture-float --enable-llvm-shared-libs " sanity_check_paths = { - 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libOSMesa.%s' % SHLIB_EXT, 'lib/libGLESv1_CM.%s' % SHLIB_EXT, - 'lib/libGLESv2.%s' % SHLIB_EXT, 'include/GL/glext.h', 'include/GL/gl_mangle.h', 'include/GL/glx.h', - 'include/GL/osmesa.h', 'include/GL/wglext.h', 'include/GL/gl.h', 'include/GL/glxext.h', - 'include/GL/glx_mangle.h', 'include/GLES/gl.h', 'include/GLES2/gl2.h', 'include/GLES3/gl3.h'], + 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libOSMesa.%s' % SHLIB_EXT, + 'lib/libGLESv1_CM.%s' % SHLIB_EXT, 'lib/libGLESv2.%s' % SHLIB_EXT, + 'include/GL/glext.h', 'include/GL/gl_mangle.h', + 'include/GL/glx.h', 'include/GL/osmesa.h', + 'include/GL/gl.h', 'include/GL/glxext.h', + 'include/GL/glx_mangle.h', 'include/GLES/gl.h', + 'include/GLES2/gl2.h', 'include/GLES3/gl3.h'], 'dirs': [] } diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-12.0.2-intel-2016b.eb b/easybuild/easyconfigs/m/Mesa/Mesa-12.0.2-intel-2016b.eb index d9578ef42b..2ac60cb5d0 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-12.0.2-intel-2016b.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-12.0.2-intel-2016b.eb @@ -49,10 +49,13 @@ configopts += " --disable-driglx-direct --with-gallium-drivers='swrast,swr' --di configopts += " --with-osmesa-bits=32 --enable-texture-float --enable-llvm-shared-libs " sanity_check_paths = { - 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libOSMesa.%s' % SHLIB_EXT, 'lib/libGLESv1_CM.%s' % SHLIB_EXT, - 'lib/libGLESv2.%s' % SHLIB_EXT, 'include/GL/glext.h', 'include/GL/gl_mangle.h', 'include/GL/glx.h', - 'include/GL/osmesa.h', 'include/GL/wglext.h', 'include/GL/gl.h', 'include/GL/glxext.h', - 'include/GL/glx_mangle.h', 'include/GLES/gl.h', 'include/GLES2/gl2.h', 'include/GLES3/gl3.h'], + 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libOSMesa.%s' % SHLIB_EXT, + 'lib/libGLESv1_CM.%s' % SHLIB_EXT, 'lib/libGLESv2.%s' % SHLIB_EXT, + 'include/GL/glext.h', 'include/GL/gl_mangle.h', + 'include/GL/glx.h', 'include/GL/osmesa.h', + 'include/GL/gl.h', 'include/GL/glxext.h', + 'include/GL/glx_mangle.h', 'include/GLES/gl.h', + 'include/GLES2/gl2.h', 'include/GLES3/gl3.h'], 'dirs': [] } diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-goolf-1.4.10-Python-2.7.3.eb index ea99e518c2..a2555dbfc0 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-goolf-1.4.10-Python-2.7.3.eb @@ -47,10 +47,13 @@ preconfigopts = ' PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/s prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm:$CPATH" ' sanity_check_paths = { - 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libGLU.%s' % SHLIB_EXT, 'include/GL/glext.h', 'include/GL/gl_mangle.h', - 'include/GL/glu_mangle.h', 'include/GL/glx.h', 'include/GL/osmesa.h', 'include/GL/wglext.h', - 'include/GL/gl.h', 'include/GL/glu.h', 'include/GL/glxext.h', 'include/GL/glx_mangle.h', - 'include/GL/vms_x_fix.h', 'include/GL/wmesa.h'], + 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libGLU.%s' % SHLIB_EXT, + 'include/GL/glext.h', 'include/GL/gl_mangle.h', + 'include/GL/glu_mangle.h', 'include/GL/glx.h', + 'include/GL/osmesa.h', 'include/GL/gl.h', + 'include/GL/glu.h', 'include/GL/glxext.h', + 'include/GL/glx_mangle.h', 'include/GL/vms_x_fix.h', + 'include/GL/wmesa.h'], 'dirs': [], } diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-5.3.0-Python-2.7.3.eb index 55c990890f..1ef5829725 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-5.3.0-Python-2.7.3.eb @@ -48,10 +48,13 @@ preconfigopts = ' PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/s prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm:$CPATH" ' sanity_check_paths = { - 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libGLU.%s' % SHLIB_EXT, 'include/GL/glext.h', 'include/GL/gl_mangle.h', - 'include/GL/glu_mangle.h', 'include/GL/glx.h', 'include/GL/osmesa.h', 'include/GL/wglext.h', - 'include/GL/gl.h', 'include/GL/glu.h', 'include/GL/glxext.h', 'include/GL/glx_mangle.h', - 'include/GL/vms_x_fix.h', 'include/GL/wmesa.h'], + 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libGLU.%s' % SHLIB_EXT, + 'include/GL/glext.h', 'include/GL/gl_mangle.h', + 'include/GL/glu_mangle.h', 'include/GL/glx.h', + 'include/GL/osmesa.h', 'include/GL/gl.h', + 'include/GL/glu.h', 'include/GL/glxext.h', + 'include/GL/glx_mangle.h', 'include/GL/vms_x_fix.h', + 'include/GL/wmesa.h'], 'dirs': [], } diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-5.5.0-Python-2.7.6.eb b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-5.5.0-Python-2.7.6.eb index 4b5ad07db8..6f68f37b53 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-5.5.0-Python-2.7.6.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-5.5.0-Python-2.7.6.eb @@ -48,10 +48,12 @@ preconfigopts = ' PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/s prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm:$CPATH" ' sanity_check_paths = { - 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libGLU.%s' % SHLIB_EXT, 'include/GL/glext.h', 'include/GL/gl_mangle.h', - 'include/GL/glu_mangle.h', 'include/GL/glx.h', 'include/GL/osmesa.h', - 'include/GL/wglext.h', 'include/GL/gl.h', 'include/GL/glu.h', - 'include/GL/glxext.h', 'include/GL/glx_mangle.h', 'include/GL/vms_x_fix.h', + 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libGLU.%s' % SHLIB_EXT, + 'include/GL/glext.h', 'include/GL/gl_mangle.h', + 'include/GL/glu_mangle.h', 'include/GL/glx.h', + 'include/GL/osmesa.h', 'include/GL/gl.h', + 'include/GL/glu.h', 'include/GL/glxext.h', + 'include/GL/glx_mangle.h', 'include/GL/vms_x_fix.h', 'include/GL/wmesa.h'], 'dirs': [] } -- GitLab From 2234ef0dd76e1809483f978a790f39731dc593c7 Mon Sep 17 00:00:00 2001 From: Damian Alvarez Date: Thu, 16 Mar 2017 10:02:28 +0100 Subject: [PATCH 0396/1603] Fixed a character introduced by mistake --- .../easyconfigs/m/Mesa/Mesa-10.4.5-intel-2015a-Python-2.7.9.eb | 2 +- .../easyconfigs/m/Mesa/Mesa-10.5.5-intel-2015a-Python-2.7.10.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-10.4.5-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/m/Mesa/Mesa-10.4.5-intel-2015a-Python-2.7.9.eb index d8ac10c171..8757076334 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-10.4.5-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-10.4.5-intel-2015a-Python-2.7.9.eb @@ -65,7 +65,7 @@ sanity_check_paths = { 'files': ['lib/libGL.%s' % SHLIB_EXT, 'include/GL/glext.h', 'include/GL/gl_mangle.h', 'include/GL/glx.h', 'include/GL/osmesa.h', 'include/GL/gl.h', 'include/GL/glxext.h', - 'include/GL/glx_mangle.h', ^'include/GL/wmesa.h'], + 'include/GL/glx_mangle.h', 'include/GL/wmesa.h'], 'dirs': [] } diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-10.5.5-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/m/Mesa/Mesa-10.5.5-intel-2015a-Python-2.7.10.eb index d3f8230305..ffc67154d8 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-10.5.5-intel-2015a-Python-2.7.10.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-10.5.5-intel-2015a-Python-2.7.10.eb @@ -65,7 +65,7 @@ sanity_check_paths = { 'include/GL/glext.h', 'include/GL/gl_mangle.h', 'include/GL/glx.h', 'include/GL/osmesa.h', 'include/GL/gl.h', 'include/GL/glxext.h', - 'include/GL/glx_mangle.h', ^'include/GL/wmesa.h'], + 'include/GL/glx_mangle.h', 'include/GL/wmesa.h'], 'dirs': [] } -- GitLab From e782dc8c1ec30ea348a225a9fa1dc9ce8d7651f5 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 16 Mar 2017 11:35:45 +0100 Subject: [PATCH 0397/1603] Explain what patch does --- easybuild/easyconfigs/k/Kaiju/Kaiju-1.5.0-makefile.patch | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/k/Kaiju/Kaiju-1.5.0-makefile.patch b/easybuild/easyconfigs/k/Kaiju/Kaiju-1.5.0-makefile.patch index 3ae20a25b6..94fd3d70c6 100644 --- a/easybuild/easyconfigs/k/Kaiju/Kaiju-1.5.0-makefile.patch +++ b/easybuild/easyconfigs/k/Kaiju/Kaiju-1.5.0-makefile.patch @@ -1,3 +1,5 @@ +# Let the makefiles use EB provides values if they are set +# wpoely86@gmail.com diff -ur kaiju-1.5.0.orig/src/bwt/Makefile kaiju-1.5.0/src/bwt/Makefile --- kaiju-1.5.0.orig/src/bwt/Makefile 2017-02-20 16:22:04.000000000 +0100 +++ kaiju-1.5.0/src/bwt/Makefile 2017-03-15 11:20:22.174636137 +0100 @@ -9,9 +11,9 @@ diff -ur kaiju-1.5.0.orig/src/bwt/Makefile kaiju-1.5.0/src/bwt/Makefile -LDLIBS = -lpthread -lm +CFLAGS ?= -O3 -g -Wno-unused-result +LDLIBS ?= -lpthread -lm - + all: mkbwt mkfmi Makefile - + diff -ur kaiju-1.5.0.orig/src/makefile kaiju-1.5.0/src/makefile --- kaiju-1.5.0.orig/src/makefile 2017-02-20 16:22:04.000000000 +0100 +++ kaiju-1.5.0/src/makefile 2017-03-15 11:20:10.710515853 +0100 @@ -27,5 +29,5 @@ diff -ur kaiju-1.5.0.orig/src/makefile kaiju-1.5.0/src/makefile +CXXFLAGS ?= -ansi -pedantic -O3 -pthread -std=c++11 -g -DNDEBUG -Wall -Wconversion -Wno-unused-function +LDLIBS ?= -lpthread INCLUDES = -I./include/ProducerConsumerQueue/src -I./include/ncbi-blast+ - + BLASTOBJS = include/ncbi-blast+/algo/blast/core/pattern.o \ -- GitLab From aa621c0d62036c47acd1ef0843033cc6e8f532f6 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 16 Mar 2017 11:44:38 +0100 Subject: [PATCH 0398/1603] Fix patch again (dropped whitespace) --- easybuild/easyconfigs/k/Kaiju/Kaiju-1.5.0-makefile.patch | 8 +++----- 1 file changed, 3 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/k/Kaiju/Kaiju-1.5.0-makefile.patch b/easybuild/easyconfigs/k/Kaiju/Kaiju-1.5.0-makefile.patch index 94fd3d70c6..3ae20a25b6 100644 --- a/easybuild/easyconfigs/k/Kaiju/Kaiju-1.5.0-makefile.patch +++ b/easybuild/easyconfigs/k/Kaiju/Kaiju-1.5.0-makefile.patch @@ -1,5 +1,3 @@ -# Let the makefiles use EB provides values if they are set -# wpoely86@gmail.com diff -ur kaiju-1.5.0.orig/src/bwt/Makefile kaiju-1.5.0/src/bwt/Makefile --- kaiju-1.5.0.orig/src/bwt/Makefile 2017-02-20 16:22:04.000000000 +0100 +++ kaiju-1.5.0/src/bwt/Makefile 2017-03-15 11:20:22.174636137 +0100 @@ -11,9 +9,9 @@ diff -ur kaiju-1.5.0.orig/src/bwt/Makefile kaiju-1.5.0/src/bwt/Makefile -LDLIBS = -lpthread -lm +CFLAGS ?= -O3 -g -Wno-unused-result +LDLIBS ?= -lpthread -lm - + all: mkbwt mkfmi Makefile - + diff -ur kaiju-1.5.0.orig/src/makefile kaiju-1.5.0/src/makefile --- kaiju-1.5.0.orig/src/makefile 2017-02-20 16:22:04.000000000 +0100 +++ kaiju-1.5.0/src/makefile 2017-03-15 11:20:10.710515853 +0100 @@ -29,5 +27,5 @@ diff -ur kaiju-1.5.0.orig/src/makefile kaiju-1.5.0/src/makefile +CXXFLAGS ?= -ansi -pedantic -O3 -pthread -std=c++11 -g -DNDEBUG -Wall -Wconversion -Wno-unused-function +LDLIBS ?= -lpthread INCLUDES = -I./include/ProducerConsumerQueue/src -I./include/ncbi-blast+ - + BLASTOBJS = include/ncbi-blast+/algo/blast/core/pattern.o \ -- GitLab From 7db1bd4556ffbe3ed7aa2e128be29cb1016da9b6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 16 Mar 2017 12:26:50 +0100 Subject: [PATCH 0399/1603] adding easyconfigs: MyMediaLite-3.12-intel-2017a.eb, Mono-4.8.0.495-intel-2017a.eb --- .../m/Mono/Mono-4.8.0.495-intel-2017a.eb | 21 +++++++++++++++++++ .../MyMediaLite-3.12-intel-2017a.eb | 14 +++++++++++++ 2 files changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/m/Mono/Mono-4.8.0.495-intel-2017a.eb create mode 100644 easybuild/easyconfigs/m/MyMediaLite/MyMediaLite-3.12-intel-2017a.eb diff --git a/easybuild/easyconfigs/m/Mono/Mono-4.8.0.495-intel-2017a.eb b/easybuild/easyconfigs/m/Mono/Mono-4.8.0.495-intel-2017a.eb new file mode 100644 index 0000000000..7b8956bcd6 --- /dev/null +++ b/easybuild/easyconfigs/m/Mono/Mono-4.8.0.495-intel-2017a.eb @@ -0,0 +1,21 @@ +name = 'Mono' +version = '4.8.0.495' + +homepage = 'http://www.mono-project.com/' +description = """An open source, cross-platform, implementation of C# and the CLR that is + binary compatible with Microsoft.NET.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['http://download.mono-project.com/sources/mono/'] +sources = [SOURCELOWER_TAR_BZ2] + +builddependencies = [ + ('Autotools', '20150215'), + ('CMake', '3.7.2'), + ('gettext', '0.19.8.1'), +] + +configopts = "--with-large-heap=yes --without-x" + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/m/MyMediaLite/MyMediaLite-3.12-intel-2017a.eb b/easybuild/easyconfigs/m/MyMediaLite/MyMediaLite-3.12-intel-2017a.eb new file mode 100644 index 0000000000..63966d2c9c --- /dev/null +++ b/easybuild/easyconfigs/m/MyMediaLite/MyMediaLite-3.12-intel-2017a.eb @@ -0,0 +1,14 @@ +name = 'MyMediaLite' +version = '3.12' + +homepage = 'http://www.ismll.uni-hildesheim.de/mymedialite/' +description = """MyMediaLite is a lightweight, multi-purpose library of recommender system algorithms.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['https://github.com/zenogantner/MyMediaLite/archive/'] +sources = ['v%(version)s.tar.gz'] + +dependencies = [('Mono', '4.8.0.495')] + +moduleclass = 'lib' -- GitLab From 1c713b31d319cec1b07ac27b14befb58054f2b04 Mon Sep 17 00:00:00 2001 From: HPC core facility CalcUA Date: Thu, 16 Mar 2017 16:39:42 +0100 Subject: [PATCH 0400/1603] SAMtools 1.4 - 2 additional dependencies (additional compression algorithms), but also needs a modified easyblock as errmod.h and kprobaln.h are no loger provided nor needed. --- .../s/SAMtools/SAMtools-1.4-intel-2016b.eb | 40 +++++++++++++++++++ .../s/SAMtools/SAMtools-1.4_Makefile.patch | 21 ++++++++++ 2 files changed, 61 insertions(+) create mode 100644 easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-intel-2016b.eb create mode 100644 easybuild/easyconfigs/s/SAMtools/SAMtools-1.4_Makefile.patch diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-intel-2016b.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-intel-2016b.eb new file mode 100644 index 0000000000..28fabf7d41 --- /dev/null +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-intel-2016b.eb @@ -0,0 +1,40 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Robert Schmidt , Cedric Laczny , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# Modified by: Adam Huffman +# The Francis Crick Institute +# +# Modified for version 1.4 by: Kurt Lust, UAntwerpen +# +## +name = 'SAMtools' +version = '1.4' + +homepage = 'http://www.htslib.org/' +description = """SAM Tools provide various utilities for manipulating alignments in the SAM format, + including sorting, merging, indexing and generating alignments in a per-position format.""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s'] +sources = [SOURCELOWER_TAR_BZ2] + +# Patch Makefile to link against zlib provided by EB +patches = ['SAMtools-%(version)s_Makefile.patch'] + +# The htslib component of SAMtools 1.4 uses zlib, bzip2 and lzma compression. +# The latter is currently provided by XZ. +dependencies = [ + ('ncurses', '6.0'), + ('zlib', '1.2.8'), + ('bzip2', '1.0.6'), + ('XZ', '5.2.2'), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4_Makefile.patch b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4_Makefile.patch new file mode 100644 index 0000000000..321f1c822c --- /dev/null +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4_Makefile.patch @@ -0,0 +1,21 @@ +# Use EB modules for zlib and ncurses +# Author: Kurt Lust, UAntwerpen +# Developed from the 1.3.1 patch by Adam Huffman of The Francis Crick Institute +--- samtools-1.4-orig/Makefile 2017-03-16 15:11:35.236460000 +0100 ++++ samtools-1.4/Makefile 2017-03-16 15:14:45.964895969 +0100 +@@ -86,13 +86,13 @@ + + ALL_CPPFLAGS = -I. $(HTSLIB_CPPFLAGS) $(CPPFLAGS) + ALL_LDFLAGS = $(HTSLIB_LDFLAGS) $(LDFLAGS) +-ALL_LIBS = -lz $(LIBS) ++ALL_LIBS = -L$(EBROOTZLIB) -lz $(LIBS) + + # Usually config.mk and config.h are generated by running configure + # or config.status, but if those aren't used create defaults here. + + config.mk: +- @sed -e '/^prefix/,/^LIBS/d;s/@Hsource@//;s/@Hinstall@/#/;s#@HTSDIR@#htslib-1.4#g;s/@HTSLIB_CPPFLAGS@/-I$$(HTSDIR)/g;s/@CURSES_LIB@/-lcurses/g' config.mk.in > $@ ++ @sed -e '/^prefix/,/^LIBS/d;s/@Hsource@//;s/@Hinstall@/#/;s#@HTSDIR@#htslib-1.4#g;s/@HTSLIB_CPPFLAGS@/-I$$(HTSDIR)/g;s/@CURSES_LIB@/-L$$(EBROOTNCURSES)\/lib -lcurses/g' config.mk.in > $@ + + config.h: + echo '/* Basic config.h generated by Makefile */' > $@ -- GitLab From bb9402e3934ef52a1cfa253c9eddae1cbff90600 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Fri, 17 Mar 2017 08:41:47 +0100 Subject: [PATCH 0401/1603] {lang}[foss/2016b] R/3.3.3 w/ X11-20160819 (REVIEW) --- easybuild/easyconfigs/r/R/Cairo-1.5-9.patch | 33 ++ .../r/R/R-3.3.3-foss-2016b-X11-20160819.eb | 509 ++++++++++++++++++ 2 files changed, 542 insertions(+) create mode 100644 easybuild/easyconfigs/r/R/Cairo-1.5-9.patch create mode 100644 easybuild/easyconfigs/r/R/R-3.3.3-foss-2016b-X11-20160819.eb diff --git a/easybuild/easyconfigs/r/R/Cairo-1.5-9.patch b/easybuild/easyconfigs/r/R/Cairo-1.5-9.patch new file mode 100644 index 0000000000..e88f9455e6 --- /dev/null +++ b/easybuild/easyconfigs/r/R/Cairo-1.5-9.patch @@ -0,0 +1,33 @@ +# pkg-config --libs cairo-pdf +# and +# pkg-config --libs cairo-ps +# should return zlib library location, otherwise configure would use system zlib for cairo compilation tests +# (but not for the builds) +# in the cairo-{ps,pdf} +# Requires: cairo +# sould be +# Reuires: cairo zlib +# So It might be a cairo/pkg-config issue +# March 16th 2017 by B. Hajgato (Free Univeristy Brussels - VUB) +--- Cairo/MD5.org 2015-09-26 09:05:40.000000000 +0200 ++++ Cairo/MD5 2017-03-16 20:28:51.181957519 +0100 +@@ -4,7 +4,7 @@ + 652a130cdb89035bd21add505f09ff6c *R/Cairo.R + 45f780dde83799bfd5ec2d67659fded4 *R/imgtools.R + a9008f9a9abd726e834484d834008b47 *R/zzz.R +-c5196eb2ad5615b9198965124fbbc2f7 *configure ++0eb0d0ae1f7558f449dc797d3e37677d *configure + 938f465e81a73126bac6eabfdfce8ea0 *configure.ac + 9ab259fe324885b6524858aa98ab51ef *configure.win + 9b9c0bd04bd4f6444182d8a4b8e209b5 *man/Cairo.Rd +--- Cairo/configure.org 2015-09-25 19:49:11.000000000 +0200 ++++ Cairo/configure 2017-03-16 20:25:42.687704125 +0100 +@@ -3479,7 +3479,7 @@ + { $as_echo "$as_me:${as_lineno-$LINENO}: result: ${modlist}" >&5 + $as_echo "${modlist}" >&6; } + CAIRO_CFLAGS=`"${PKGCONF}" --cflags ${modlist}` +- CAIRO_LIBS=`"${PKGCONF}" --libs ${modlist}` ++ CAIRO_LIBS="-L$EBROOTZLIB/lib `"${PKGCONF}" --libs ${modlist}`" + else + { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 + $as_echo "no" >&6; } diff --git a/easybuild/easyconfigs/r/R/R-3.3.3-foss-2016b-X11-20160819.eb b/easybuild/easyconfigs/r/R/R-3.3.3-foss-2016b-X11-20160819.eb new file mode 100644 index 0000000000..2584758870 --- /dev/null +++ b/easybuild/easyconfigs/r/R/R-3.3.3-foss-2016b-X11-20160819.eb @@ -0,0 +1,509 @@ +name = 'R' +version = '3.3.3' +x11ver = '20160819' +versionsuffix = '-X11-%s' % x11ver + +homepage = 'http://www.r-project.org/' +description = """R is a free software environment for statistical computing and graphics.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://cran.us.r-project.org/src/base/R-%(version_major)s'] + +preconfigopts = 'BLAS_LIBS="$LIBBLAS" LAPACK_LIBS="$LIBLAPACK"' +configopts = "--with-lapack --with-blas --with-pic --enable-threads --with-x=no --enable-R-shlib" +#Actually use Tcl/Tk +configopts += ' --with-tcl-config=$EBROOTTCL/lib/tclConfig.sh --with-tk-config=$EBROOTTK/lib/tkConfig.sh ' +# Enable graphics capabilities for plotting. +configopts += " --with-cairo --with-libpng --with-jpeglib --with-libtiff" +# some recommended packages may fail in a parallel build (e.g. Matrix), and we're installing them anyway below +configopts += " --with-recommended-packages=no" + +dependencies = [ + ('X11', x11ver), + ('Mesa', '12.0.2'), + ('libGLU', '9.0.0'), + ('cairo', '1.14.6'), + ('libreadline', '6.3'), + ('ncurses', '6.0'), + ('bzip2', '1.0.6'), + ('XZ', '5.2.2'), + ('zlib', '1.2.8'), + ('SQLite', '3.13.0'), + ('PCRE', '8.39'), + ('libpng', '1.6.24'), # for plotting in R + ('libjpeg-turbo', '1.5.0'), # for plottting in R + ('LibTIFF', '4.0.6'), + ('Java', '1.8.0_92', '', True), # Java bindings are built if Java is found, might as well provide it + ('Tcl', '8.6.5'), # for tcltk + ('Tk', '8.6.5'), # for tcltk + ('cURL', '7.49.1'), # for RCurl + ('libxml2', '2.9.4'), # for XML + ('GDAL', '2.1.0'), # for rgdal + ('PROJ', '4.9.2'), # for rgdal + ('GMP', '6.1.1'), # for igraph + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.2h'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +name_tmpl = '%(name)s_%(version)s.tar.gz' +ext_options = { + 'source_urls': [ + 'http://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'http://cran.r-project.org/src/contrib/', # current version of packages + 'http://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': name_tmpl, +} + +# !! order of packages is important !! +# packages updated on March 7th 2017 +exts_list = [ + # default libraries, only here to sanity check their presence + 'base', + 'datasets', + 'graphics', + 'grDevices', + 'grid', + 'methods', + 'splines', + 'stats', + 'stats4', + 'tools', + 'utils', + # non-standard libraries, should be specified with fixed versions! + ('Rmpi', '0.6-6', 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'0.51.0', ext_options), + ('DiscriMiner', '0.1-29', ext_options), + ('ellipse', '0.3-8', ext_options), + ('leaps', '3.0', ext_options), + ('nloptr', '1.0.4', ext_options), + ('lme4', '1.1-12', ext_options), + ('pbkrtest', '0.4-6', ext_options), + ('car', '2.1-4', ext_options), + ('flashClust', '1.01-2', ext_options), + ('FactoMineR', '1.35', ext_options), + ('flexclust', '1.3-4', ext_options), + ('flexmix', '2.3-13', ext_options), + ('prabclus', '2.2-6', ext_options), + ('diptest', '0.75-7', ext_options), + ('trimcluster', '0.1-2', ext_options), + ('fpc', '2.1-10', ext_options), + ('BiasedUrn', '1.07', ext_options), + ('TeachingDemos', '2.10', ext_options), + ('kohonen', '2.0.19', ext_options), + ('base64', '2.0', ext_options), + ('doRNG', '1.6', ext_options), + ('nleqslv', '3.2', ext_options), + ('RGCCA', '2.1', ext_options), + ('pheatmap', '1.0.8', ext_options), + ('openxlsx', '4.0.0', ext_options), + ('pvclust', '2.0-0', ext_options), + ('RCircos', '1.2.0', ext_options), + ('lambda.r', '1.1.9', ext_options), + ('futile.options', '1.0.0', ext_options), + ('futile.logger', '1.4.3', ext_options), + ('VennDiagram', '1.6.17', ext_options), + ('xlsxjars', '0.6.1', ext_options), + ('xlsx', '0.5.7', ext_options), + ('forecast', '8.0', ext_options), + ('fma', '2.3', ext_options), + ('expsmooth', '2.3', ext_options), + ('fpp', '0.5', ext_options), + ('maptools', '0.9-1', ext_options), + ('tensor', '1.5', ext_options), + ('polyclip', '1.5-6', ext_options), + ('goftest', '1.0-4', ext_options), + ('spatstat', '1.49-0', ext_options), + ('rgdal', '1.2-5', ext_options), + ('gdalUtils', '2.0.1.7', ext_options), + ('pracma', '1.9.9', ext_options), + ('RCurl', '1.95-4.8', ext_options), + ('bio3d', '2.3-1', ext_options), + ('AUC', '0.3.0', ext_options), + ('interpretR', '0.2.4', ext_options), + ('cvAUC', '1.1.0', ext_options), + ('SuperLearner', '2.0-21', ext_options), + ('lpSolve', '5.6.13', ext_options), + ('mediation', '4.4.5', ext_options), + ('ModelMetrics', '1.1.0', ext_options), + ('caret', '6.0-73', ext_options), + ('adabag', '4.1', ext_options), + ('parallelMap', '1.3', ext_options), + ('ParamHelpers', '1.10', ext_options), + ('ggvis', '0.4.3', ext_options), + ('mlr', '2.10', ext_options), + ('unbalanced', '2.0', ext_options), + ('RSNNS', '0.4-9', ext_options), + ('abc.data', '1.0', ext_options), + ('abc', '2.1', ext_options), + ('lhs', '0.14', ext_options), + ('tensorA', '0.36', ext_options), + ('EasyABC', '1.5', ext_options), + ('shape', '1.4.2', ext_options), + ('whisker', '0.3-2', ext_options), + ('rstudioapi', '0.6', ext_options), + ('commonmark', '1.2', ext_options), + ('desc', '1.1.0', ext_options), + ('roxygen2', '6.0.1', ext_options), + ('git2r', '0.18.0', ext_options), + ('rversions', '1.0.3', ext_options), + ('withr', '1.0.2', ext_options), + ('devtools', '1.12.0', ext_options), + ('Rook', '1.1-1', ext_options), + ('Cairo', '1.5-9', dict(ext_options.items() + [('patches', ['Cairo-1.5-9.patch'])])), + ('RMTstat', '0.3', ext_options), + ('Lmoments', '1.2-3', ext_options), + ('distillery', '1.0-2', ext_options), + ('extRemes', '2.0-8', ext_options), + ('pixmap', '0.4-11', ext_options), + ('tkrplot', '0.0-23', ext_options), + ('misc3d', '0.8-4', ext_options), + ('multicool', '0.1-10', ext_options), + ('ks', '1.10.5', ext_options), + ('logcondens', '2.1.5', ext_options), + ('Iso', '0.0-17', ext_options), + ('penalized', '0.9-50', ext_options), + ('clusterRepro', '0.5-1.1', ext_options), + ('randomForestSRC', '2.4.2', ext_options), + ('sm', '2.2-5.4', ext_options), + ('psych', '1.6.12', ext_options), + ('pbivnorm', '0.6.0', ext_options), + ('lavaan', '0.5-23.1097', ext_options), + ('matrixcalc', '1.0-3', ext_options), + ('arm', '1.9-3', ext_options), + ('mi', '1.0', ext_options), + ('visNetwork', '1.0.3', ext_options), + ('rgexf', '0.15.3', ext_options), + ('influenceR', '0.1.0', ext_options), + ('DiagrammeR', '0.9.0', ext_options), + ('sem', '3.1-8', ext_options), + ('jpeg', '0.1-8', ext_options), + ('network', '1.13.0', ext_options), + ('statnet.common', '3.3.0', ext_options), + ('sna', '2.4', ext_options), + ('glasso', '1.8', ext_options), + ('huge', '1.2.7', ext_options), + ('d3Network', '0.5.2.1', ext_options), + ('ggm', '2.3', ext_options), + ('qgraph', '1.4.2', ext_options), + ('diveRsity', '1.9.89', ext_options), + ('doSNOW', '1.0.14', ext_options), + ('phangorn', '2.1.1', ext_options), + ('geepack', '1.2-1', ext_options), + ('lubridate', '1.6.0', ext_options), + ('biom', '0.3.12', ext_options), + ('pim', '2.0.0.2', ext_options), + ('minpack.lm', '1.2-1', ext_options), + ('rootSolve', '1.7', ext_options), + ('diagram', '1.6.3', ext_options), + ('FME', '1.3.5', ext_options), + ('bmp', '0.2', ext_options), + ('readbitmap', '0.1-4', ext_options), + ('purrr', '0.2.2', ext_options), + ('imager', '0.31', ext_options), +] + +moduleclass = 'lang' + -- GitLab From 80146673bc89daf3861e7df57114c0aa32a68f23 Mon Sep 17 00:00:00 2001 From: HPC core facility CalcUA Date: Fri, 17 Mar 2017 10:03:41 +0100 Subject: [PATCH 0402/1603] Removed unnecessary patch from SAMtools 1.4 and 1.3.1 for intel/2016b and removed the 1.4 patch file from the repository. --- .../s/SAMtools/SAMtools-1.3.1-intel-2016b.eb | 3 --- .../s/SAMtools/SAMtools-1.4-intel-2016b.eb | 3 --- .../s/SAMtools/SAMtools-1.4_Makefile.patch | 21 ------------------- 3 files changed, 27 deletions(-) delete mode 100644 easybuild/easyconfigs/s/SAMtools/SAMtools-1.4_Makefile.patch diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1-intel-2016b.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1-intel-2016b.eb index 068f81d41a..ad73efb9d9 100644 --- a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1-intel-2016b.eb +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1-intel-2016b.eb @@ -22,9 +22,6 @@ toolchainopts = {'pic': True} source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s'] sources = [SOURCELOWER_TAR_BZ2] -# Patch Makefile to link against zlib provided by EB -patches = ['SAMtools-%(version)s_Makefile.patch'] - dependencies = [ ('ncurses', '6.0'), ('zlib', '1.2.8'), diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-intel-2016b.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-intel-2016b.eb index 28fabf7d41..3167310f24 100644 --- a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-intel-2016b.eb +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-intel-2016b.eb @@ -25,9 +25,6 @@ toolchainopts = {'pic': True} source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s'] sources = [SOURCELOWER_TAR_BZ2] -# Patch Makefile to link against zlib provided by EB -patches = ['SAMtools-%(version)s_Makefile.patch'] - # The htslib component of SAMtools 1.4 uses zlib, bzip2 and lzma compression. # The latter is currently provided by XZ. dependencies = [ diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4_Makefile.patch b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4_Makefile.patch deleted file mode 100644 index 321f1c822c..0000000000 --- a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4_Makefile.patch +++ /dev/null @@ -1,21 +0,0 @@ -# Use EB modules for zlib and ncurses -# Author: Kurt Lust, UAntwerpen -# Developed from the 1.3.1 patch by Adam Huffman of The Francis Crick Institute ---- samtools-1.4-orig/Makefile 2017-03-16 15:11:35.236460000 +0100 -+++ samtools-1.4/Makefile 2017-03-16 15:14:45.964895969 +0100 -@@ -86,13 +86,13 @@ - - ALL_CPPFLAGS = -I. $(HTSLIB_CPPFLAGS) $(CPPFLAGS) - ALL_LDFLAGS = $(HTSLIB_LDFLAGS) $(LDFLAGS) --ALL_LIBS = -lz $(LIBS) -+ALL_LIBS = -L$(EBROOTZLIB) -lz $(LIBS) - - # Usually config.mk and config.h are generated by running configure - # or config.status, but if those aren't used create defaults here. - - config.mk: -- @sed -e '/^prefix/,/^LIBS/d;s/@Hsource@//;s/@Hinstall@/#/;s#@HTSDIR@#htslib-1.4#g;s/@HTSLIB_CPPFLAGS@/-I$$(HTSDIR)/g;s/@CURSES_LIB@/-lcurses/g' config.mk.in > $@ -+ @sed -e '/^prefix/,/^LIBS/d;s/@Hsource@//;s/@Hinstall@/#/;s#@HTSDIR@#htslib-1.4#g;s/@HTSLIB_CPPFLAGS@/-I$$(HTSDIR)/g;s/@CURSES_LIB@/-L$$(EBROOTNCURSES)\/lib -lcurses/g' config.mk.in > $@ - - config.h: - echo '/* Basic config.h generated by Makefile */' > $@ -- GitLab From e96b2fbf0f49b0f448e32e7029def139d9143e3a Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Fri, 17 Mar 2017 17:38:10 +0800 Subject: [PATCH 0403/1603] prepare release notes for eb312 --- RELEASE_NOTES | 30 ++++++++++++++++++++++++++++++ 1 file changed, 30 insertions(+) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index 96a76caa5a..a515a07590 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -6,6 +6,36 @@ These release notes can also be consulted at http://easybuild.readthedocs.org/en The latest version of easybuild-easyconfig provides 6,647 easyconfig files, for 1,168 different software packages, 25 different (compiler) toolchains, 13 software bundles and 1 meta-package. +v3.1.2 (March 17th 2017) +------------------------ + +bugfix release +- added example easyconfig files for 12 new software packages: + - DBG2OLC (#4281), disambiguate (#4125), fqtrim (#4280), GFOLD (#4293), Kaiju (#4349), LSMS (#4335), + L_RNA_scaffolder (#4282), PileOMeth (#4289), psycopg2 (#4319), QGIS (#4307), QJson (#4305), + QScintilla (#4306, #4313) +- added additional easyconfigs for various supported software packages, including: + - BLAT v3.5, FFTW v3.3.6, flex v2.6.3, FreeXL v1.0.2, GDAL v2.1.3, GEOS v3.6.1, GROMACS v2016.2 + v2016.3, + HDF5 1.10.0-patch1, help2man v1.47.4, ImageJ v1.51k, libspatialindex v1.8.5, libspatialite v4.3.0a, M4 v1.4.18, + Mono v4.8.0.495, MyMediaLite v3.12, PGI v17.1, PROJ v4.9.3, PyQt v4.12, QCA v2.1.3, QwtPolar v1.1.1, Qwt v6.1.3, + requests v2.13.0, SIP v4.19, SPAdes v3.10.1, STAR v2.5.2b, SWASH v4.01, SWIG v3.0.11, Tensorflow v1.0.1, + ViennaRNA 2.3.4, Yasm v1.3.0 +- various enhancements, including: + - fix style in several easyconfigs (#4267-#4271, #4274, #4275, #4277, #4279, #4286-#4288, #4318) + - pass down $FFLAGS via FLAGS_OPT in SWASH easyconfigs (#4341) +- various bug fixes, including: + - fix missing PYTHONPATH in ROOT v6.08.02 easyconfig (#4239) + - correct libjpeg turbo references in GDAL (#4276) + - fix to be sure the HDF5 provided by easybuild is used in BLASR (#4278) + - miRDeep2 scripts do a hard check for an (empty) file named 'install_successful' in the install dir... (#4291) + - fix shebang in miRDeep2 Perl scripts (#4301) + - also check with Tcl module syntax, Lua is the default in EasyBuild v3.x (#4315) + - also copy Rfam_for_miRDeep.fa to mirDeep2 directory (#4316) + - detect use of '$root', which is not compatible with module files in Lua syntax (#4330) + - correctly set $PYTHONPATH in ROOT easyconfigs (#4331) + - add requests and psycopg2 as dependencies for QGIS (#4332) + + v3.1.1 (March 7th 2017) ----------------------- -- GitLab From e3cb8e7f412614e49f061056d460adc144640bcd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 17 Mar 2017 13:28:43 +0100 Subject: [PATCH 0404/1603] adding easyconfigs: sketchmap-20170130-intel-2016b.eb --- .../sketchmap-20170130-intel-2016b.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/s/sketchmap/sketchmap-20170130-intel-2016b.eb diff --git a/easybuild/easyconfigs/s/sketchmap/sketchmap-20170130-intel-2016b.eb b/easybuild/easyconfigs/s/sketchmap/sketchmap-20170130-intel-2016b.eb new file mode 100644 index 0000000000..6caab74f6e --- /dev/null +++ b/easybuild/easyconfigs/s/sketchmap/sketchmap-20170130-intel-2016b.eb @@ -0,0 +1,25 @@ +easyblock = 'MakeCp' + +name = 'sketchmap' +version = '20170130' +commit = '7e059bd' + +homepage = 'http://sketchmap.org/' +description = """Sketch-map is a dimensionality reduction algorithm that is particularly well suited to examining + the high-dimensionality data that is routinely produced in atomistic simulations.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['https://github.com/cosmo-epfl/sketchmap/archive/'] +sources = ['%s.tar.gz' % commit] + +buildopts = 'CXX="$CXX" MAKEDEPEND="$CXX -M \$(CXXFLAGS)" LLAPACK="$LIBLAPACK_MT"' + +files_to_copy = ['bin'] + +sanity_check_paths = { + 'files': ['bin/dimdist', 'bin/dimlandmark', 'bin/dimproj', 'bin/dimred'], + 'dirs': [], +} + +moduleclass = 'tools' -- GitLab From b886e0f5e7426e7fdb73dc73aa4eba4d96d134b8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 17 Mar 2017 15:25:31 +0100 Subject: [PATCH 0405/1603] adding easyconfigs: snaphu-1.4.2-intel-2016b.eb --- .../s/snaphu/snaphu-1.4.2-intel-2016b.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/s/snaphu/snaphu-1.4.2-intel-2016b.eb diff --git a/easybuild/easyconfigs/s/snaphu/snaphu-1.4.2-intel-2016b.eb b/easybuild/easyconfigs/s/snaphu/snaphu-1.4.2-intel-2016b.eb new file mode 100644 index 0000000000..8397d4ea59 --- /dev/null +++ b/easybuild/easyconfigs/s/snaphu/snaphu-1.4.2-intel-2016b.eb @@ -0,0 +1,26 @@ +easyblock = 'MakeCp' + +name = 'snaphu' +version = '1.4.2' + +homepage = 'https://web.stanford.edu/group/radar/softwareandlinks/sw/snaphu/' +description = """SNAPHU is an implementation of the Statistical-cost, Network-flow Algorithm for Phase Unwrapping + proposed by Chen and Zebker""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['https://web.stanford.edu/group/radar/softwareandlinks/sw/snaphu/'] +sources = ['snaphu-v%(version)s.tar.gz'] + +start_dir = 'src' + +buildopts = 'CC="$CC" CFLAGS="$CFLAGS"' + +files_to_copy = ['bin', 'config', 'man'] + +sanity_check_paths = { + 'files': ['bin/snaphu'], + 'dirs': ['config', 'man'], +} + +moduleclass = 'math' -- GitLab From 5f80281a8224f78bc2f8b8544cb8fcb596f9b9ae Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 17 Mar 2017 15:25:51 +0100 Subject: [PATCH 0406/1603] adding easyconfigs: Triangle-1.6-intel-2016b.eb --- .../t/Triangle/Triangle-1.6-intel-2016b.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/t/Triangle/Triangle-1.6-intel-2016b.eb diff --git a/easybuild/easyconfigs/t/Triangle/Triangle-1.6-intel-2016b.eb b/easybuild/easyconfigs/t/Triangle/Triangle-1.6-intel-2016b.eb new file mode 100644 index 0000000000..f3df6e7173 --- /dev/null +++ b/easybuild/easyconfigs/t/Triangle/Triangle-1.6-intel-2016b.eb @@ -0,0 +1,38 @@ +easyblock = 'MakeCp' + +name = 'Triangle' +version = '1.6' + +homepage = 'http://www.cs.cmu.edu/~quake/triangle.html' +description = """Triangle generates exact Delaunay triangulations, constrained Delaunay triangulations, + conforming Delaunay triangulations, Voronoi diagrams, and high-quality triangular meshes. + The latter can be generated with no small or large angles, + and are thus suitable for finite element analysis.""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.netlib.org/voronoi/'] +sources = ['%(namelower)s.zip'] +checksums = [('md5', '10aff8d7950f5e0e2fb6dd2e340be2c9')] + +patches = ['%(name)s-%(version)s_makefile.patch'] + +dependencies = [ + ('X11', '20160819'), +] + +buildopts = 'triangle trilibrary' + +files_to_copy = [ + (['triangle', 'tricall'], 'bin'), + (['triangle.h'], 'include'), + (['libtriangle.a'], 'lib'), +] + +sanity_check_paths = { + 'files': ['bin/triangle', 'bin/tricall', 'include/triangle.h', 'lib/libtriangle.a'], + 'dirs': [] +} + +moduleclass = 'numlib' -- GitLab From 89a2a4661e0639138aef33016134925343aedb1b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 17 Mar 2017 15:32:46 +0100 Subject: [PATCH 0407/1603] remove unneeded X11 dep in Triangle easyconfig since 'showme' binary isn't being built --- easybuild/easyconfigs/t/Triangle/Triangle-1.6-intel-2016b.eb | 4 ---- 1 file changed, 4 deletions(-) diff --git a/easybuild/easyconfigs/t/Triangle/Triangle-1.6-intel-2016b.eb b/easybuild/easyconfigs/t/Triangle/Triangle-1.6-intel-2016b.eb index f3df6e7173..77785bc785 100644 --- a/easybuild/easyconfigs/t/Triangle/Triangle-1.6-intel-2016b.eb +++ b/easybuild/easyconfigs/t/Triangle/Triangle-1.6-intel-2016b.eb @@ -18,10 +18,6 @@ checksums = [('md5', '10aff8d7950f5e0e2fb6dd2e340be2c9')] patches = ['%(name)s-%(version)s_makefile.patch'] -dependencies = [ - ('X11', '20160819'), -] - buildopts = 'triangle trilibrary' files_to_copy = [ -- GitLab From a10c62c9e46d52fa47d1eae69f094c52307c559b Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Sat, 18 Mar 2017 09:33:54 +0100 Subject: [PATCH 0408/1603] adding easyconfigs: SAMtools-1.4-foss-2016b.eb --- .../s/SAMtools/SAMtools-1.4-foss-2016b.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-foss-2016b.eb diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-foss-2016b.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-foss-2016b.eb new file mode 100644 index 0000000000..340f9547b8 --- /dev/null +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-foss-2016b.eb @@ -0,0 +1,37 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Robert Schmidt , Cedric Laczny , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# Modified by: Adam Huffman +# The Francis Crick Institute +# +# Modified for version 1.4 by: Kurt Lust, UAntwerpen +# +## +name = 'SAMtools' +version = '1.4' + +homepage = 'http://www.htslib.org/' +description = """SAM Tools provide various utilities for manipulating alignments in the SAM format, + including sorting, merging, indexing and generating alignments in a per-position format.""" + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s'] +sources = [SOURCELOWER_TAR_BZ2] + +# The htslib component of SAMtools 1.4 uses zlib, bzip2 and lzma compression. +# The latter is currently provided by XZ. +dependencies = [ + ('ncurses', '6.0'), + ('zlib', '1.2.8'), + ('bzip2', '1.0.6'), + ('XZ', '5.2.2'), +] + +moduleclass = 'bio' -- GitLab From 491b626efb646f6115990fb080b7267d23737efe Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Sat, 18 Mar 2017 10:06:18 +0100 Subject: [PATCH 0409/1603] adding easyconfigs: HTSlib-1.4-foss-2016b.eb, HTSlib-1.4-intel-2016b.eb --- .../h/HTSlib/HTSlib-1.4-foss-2016b.eb | 36 +++++++++++++++++++ .../h/HTSlib/HTSlib-1.4-intel-2016b.eb | 36 +++++++++++++++++++ 2 files changed, 72 insertions(+) create mode 100644 easybuild/easyconfigs/h/HTSlib/HTSlib-1.4-foss-2016b.eb create mode 100644 easybuild/easyconfigs/h/HTSlib/HTSlib-1.4-intel-2016b.eb diff --git a/easybuild/easyconfigs/h/HTSlib/HTSlib-1.4-foss-2016b.eb b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.4-foss-2016b.eb new file mode 100644 index 0000000000..9bdb215d4c --- /dev/null +++ b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.4-foss-2016b.eb @@ -0,0 +1,36 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# 1.4 modified by: +# Adam Huffman +# The Francis Crick Institute + +easyblock = 'ConfigureMake' + +name = 'HTSlib' +version = '1.4' + +homepage = "http://www.htslib.org/" +description = """A C library for reading/writing high-throughput sequencing data. + This package includes the utilities bgzip and tabix""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s/'] +sources = [SOURCELOWER_TAR_BZ2] + +# cURL added for S3 support +dependencies = [ + ('zlib', '1.2.8'), + ('bzip2', '1.0.6'), + ('XZ', '5.2.2'), + ('cURL', '7.49.1'), +] + +sanity_check_paths = { + 'files': ["bin/bgzip", "bin/tabix", "lib/libhts.%s" % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/h/HTSlib/HTSlib-1.4-intel-2016b.eb b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.4-intel-2016b.eb new file mode 100644 index 0000000000..5c5a91710c --- /dev/null +++ b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.4-intel-2016b.eb @@ -0,0 +1,36 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# 1.4 modified by: +# Adam Huffman +# The Francis Crick Institute + +easyblock = 'ConfigureMake' + +name = 'HTSlib' +version = '1.4' + +homepage = "http://www.htslib.org/" +description = """A C library for reading/writing high-throughput sequencing data. + This package includes the utilities bgzip and tabix""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s/'] +sources = [SOURCELOWER_TAR_BZ2] + +# cURL added for S3 support +dependencies = [ + ('zlib', '1.2.8'), + ('bzip2', '1.0.6'), + ('XZ', '5.2.2'), + ('cURL', '7.49.1'), +] + +sanity_check_paths = { + 'files': ["bin/bgzip", "bin/tabix", "lib/libhts.%s" % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From 3e057c110297155dcb957faa7a10335bdc21613b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 18 Mar 2017 11:07:56 +0100 Subject: [PATCH 0410/1603] complete release notes for EasyBuild v3.1.2 & bump version --- RELEASE_NOTES | 40 ++++++++++++++++++---------------------- setup.py | 2 +- 2 files changed, 19 insertions(+), 23 deletions(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index a515a07590..1faff06d0d 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -3,43 +3,39 @@ For more detailed information, please see the git log. These release notes can also be consulted at http://easybuild.readthedocs.org/en/latest/Release_notes.html. -The latest version of easybuild-easyconfig provides 6,647 easyconfig files, for 1,168 different software packages, +The latest version of easybuild-easyconfig provides 6,718 easyconfig files, for 1,182 different software packages, 25 different (compiler) toolchains, 13 software bundles and 1 meta-package. -v3.1.2 (March 17th 2017) +v3.1.2 (March 20th 2017) ------------------------ -bugfix release -- added example easyconfig files for 12 new software packages: +bugfix/update release +- add patch to FFTW 3.3.6 easyconfigs to fix MPI F03 interface (#4334) + - note that this warrants rebuilding FFTW that is a part of foss/2017a +- added example easyconfig files for 14 new software packages: - DBG2OLC (#4281), disambiguate (#4125), fqtrim (#4280), GFOLD (#4293), Kaiju (#4349), LSMS (#4335), - L_RNA_scaffolder (#4282), PileOMeth (#4289), psycopg2 (#4319), QGIS (#4307), QJson (#4305), - QScintilla (#4306, #4313) -- added additional easyconfigs for various supported software packages, including: - - BLAT v3.5, FFTW v3.3.6, flex v2.6.3, FreeXL v1.0.2, GDAL v2.1.3, GEOS v3.6.1, GROMACS v2016.2 + v2016.3, - HDF5 1.10.0-patch1, help2man v1.47.4, ImageJ v1.51k, libspatialindex v1.8.5, libspatialite v4.3.0a, M4 v1.4.18, - Mono v4.8.0.495, MyMediaLite v3.12, PGI v17.1, PROJ v4.9.3, PyQt v4.12, QCA v2.1.3, QwtPolar v1.1.1, Qwt v6.1.3, - requests v2.13.0, SIP v4.19, SPAdes v3.10.1, STAR v2.5.2b, SWASH v4.01, SWIG v3.0.11, Tensorflow v1.0.1, - ViennaRNA 2.3.4, Yasm v1.3.0 + L_RNA_scaffolder (#4282), PileOMeth (#4289), psycopg2 (#4319), QGIS (#4307, #4332), QJson (#4305), + QScintilla (#4306, #4313), sketchmap (#4360), snaphu (#4362) +- added additional easyconfigs for various supported software packages, including GROMACS 2016.3, PGI 17.1, SAMtools 1.4 - various enhancements, including: - fix style in several easyconfigs (#4267-#4271, #4274, #4275, #4277, #4279, #4286-#4288, #4318) - - pass down $FFLAGS via FLAGS_OPT in SWASH easyconfigs (#4341) - various bug fixes, including: - - fix missing PYTHONPATH in ROOT v6.08.02 easyconfig (#4239) + - correctly set $PYTHONPATH in ROOT easyconfigs (#4239, #4331) - correct libjpeg turbo references in GDAL (#4276) - - fix to be sure the HDF5 provided by easybuild is used in BLASR (#4278) - - miRDeep2 scripts do a hard check for an (empty) file named 'install_successful' in the install dir... (#4291) - - fix shebang in miRDeep2 Perl scripts (#4301) - - also check with Tcl module syntax, Lua is the default in EasyBuild v3.x (#4315) - - also copy Rfam_for_miRDeep.fa to mirDeep2 directory (#4316) + - make sure that HDF5 provided via EasyBuild is used in BLASR easyconfigs (#4278) + - fix issues with miRDeep2 installation (#4291, #4301, #4316) + - also run tests with Tcl module syntax, Lua is the default in EasyBuild v3.x (#4315) + - fix PostgreSQL homepage + minor style fixes (#4318) - detect use of '$root', which is not compatible with module files in Lua syntax (#4330) - - correctly set $PYTHONPATH in ROOT easyconfigs (#4331) - - add requests and psycopg2 as dependencies for QGIS (#4332) + - fix homepage/source_urls for ViennaRNA (#4338) + - pass down $FFLAGS via FLAGS_OPT in SWASH easyconfigs (#4341) + - remove include/GL/wglext.h from Mesa sanity check (#4354) v3.1.1 (March 7th 2017) ----------------------- -bugfix release +bugfix/update release - added example easyconfig files for 16 new software packages: - Caffe (#3667), DIAMOND (#4107), fmt (#4131), googletest (#4132), igraph (#4172), MEGA (#4202), meRanTK (#4175), meshio (#4178), miRDeep2 (#4229, #4255), OOMPA (#4211), PBSuite (#4224, #4230), randfold (#4217), skewer (#4246), diff --git a/setup.py b/setup.py index 0683e432c9..0512590286 100644 --- a/setup.py +++ b/setup.py @@ -47,7 +47,7 @@ from distutils import log # recent setuptools versions will *TRANSFORM* something like 'X.Y.Zdev' into 'X.Y.Z.dev0', with a warning like # UserWarning: Normalizing '2.4.0dev' to '2.4.0.dev0' # This causes problems further up the dependency chain... -VERSION = '3.2.0.dev0' +VERSION = '3.1.2' API_VERSION = VERSION.split('.')[0] EB_VERSION = '.'.join(VERSION.split('.')[0:2]) -- GitLab From 4b402eaee4aa4427376aa3ab0871650e6e87758e Mon Sep 17 00:00:00 2001 From: Robert Schmidt Date: Sat, 18 Mar 2017 13:24:22 +0000 Subject: [PATCH 0411/1603] cannot have directories with trailing dot in windows --- .../s/{S.A.G.E. => SAGE}/S.A.G.E.-6.3.eb | 4 +-- easybuild/easyconfigs/s/SAGE/S.A.G.E.-6.4.eb | 25 +++++++++++++++++++ 2 files changed, 27 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/s/{S.A.G.E. => SAGE}/S.A.G.E.-6.3.eb (79%) create mode 100644 easybuild/easyconfigs/s/SAGE/S.A.G.E.-6.4.eb diff --git a/easybuild/easyconfigs/s/S.A.G.E./S.A.G.E.-6.3.eb b/easybuild/easyconfigs/s/SAGE/S.A.G.E.-6.3.eb similarity index 79% rename from easybuild/easyconfigs/s/S.A.G.E./S.A.G.E.-6.3.eb rename to easybuild/easyconfigs/s/SAGE/S.A.G.E.-6.3.eb index 28ef2c7ef6..52a2bd4d13 100644 --- a/easybuild/easyconfigs/s/S.A.G.E./S.A.G.E.-6.3.eb +++ b/easybuild/easyconfigs/s/SAGE/S.A.G.E.-6.3.eb @@ -7,14 +7,14 @@ easyblock = "Tarball" name = 'S.A.G.E.' version = '6.3' -homepage = 'https://code.google.com/archive/p/opensage/' +homepage = 'http://darwin.cwru.edu/sage/' description = """ S.A.G.E. (Statistical Analysis for Genetic Epidemiology) is free software package containing programs for use in the genetic analysis of family, pedigree and individual data.""" toolchain = {'name': 'dummy', 'version': 'dummy'} -source_urls = ['https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/opensage/'] +source_urls = ['https://github.com/elstonsage/sageCore/releases/download/v6.3'] sources = ['%(name)sv%(version)s_Linux_x86_64.tar.gz'] sanity_check_paths = { diff --git a/easybuild/easyconfigs/s/SAGE/S.A.G.E.-6.4.eb b/easybuild/easyconfigs/s/SAGE/S.A.G.E.-6.4.eb new file mode 100644 index 0000000000..7935579b22 --- /dev/null +++ b/easybuild/easyconfigs/s/SAGE/S.A.G.E.-6.4.eb @@ -0,0 +1,25 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Ravi Tripathi +# Email: ravi89@uab.edu + +easyblock = "Tarball" + +name = 'S.A.G.E.' +version = '6.4' + +homepage = 'http://darwin.cwru.edu/sage/' +description = """ S.A.G.E. (Statistical Analysis for Genetic +Epidemiology) is free software package containing programs for +use in the genetic analysis of family, pedigree and individual data.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['http://darwin.cwru.edu/sage/files/'] +sources = ['%(name)sv%(version)s_Linux_x86_64.tar.gz'] + +sanity_check_paths = { + 'files': ["bin/freq", "bin/ageon", "bin/segreg"], + 'dirs': ["data_files", "documentaion"] +} + +moduleclass = 'bio' -- GitLab From 13f84a024104777d4ef6d6aa90f158b1d37a6589 Mon Sep 17 00:00:00 2001 From: Robert Schmidt Date: Sat, 18 Mar 2017 13:31:51 +0000 Subject: [PATCH 0412/1603] rename so everything uses the non-dot names --- easybuild/easyconfigs/s/SAGE/{S.A.G.E.-6.3.eb => SAGE-6.3.eb} | 4 ++-- easybuild/easyconfigs/s/SAGE/{S.A.G.E.-6.4.eb => SAGE-6.4.eb} | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) rename easybuild/easyconfigs/s/SAGE/{S.A.G.E.-6.3.eb => SAGE-6.3.eb} (90%) rename easybuild/easyconfigs/s/SAGE/{S.A.G.E.-6.4.eb => SAGE-6.4.eb} (90%) diff --git a/easybuild/easyconfigs/s/SAGE/S.A.G.E.-6.3.eb b/easybuild/easyconfigs/s/SAGE/SAGE-6.3.eb similarity index 90% rename from easybuild/easyconfigs/s/SAGE/S.A.G.E.-6.3.eb rename to easybuild/easyconfigs/s/SAGE/SAGE-6.3.eb index 52a2bd4d13..3ff2689829 100644 --- a/easybuild/easyconfigs/s/SAGE/S.A.G.E.-6.3.eb +++ b/easybuild/easyconfigs/s/SAGE/SAGE-6.3.eb @@ -4,7 +4,7 @@ easyblock = "Tarball" -name = 'S.A.G.E.' +name = 'SAGE' version = '6.3' homepage = 'http://darwin.cwru.edu/sage/' @@ -15,7 +15,7 @@ use in the genetic analysis of family, pedigree and individual data.""" toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = ['https://github.com/elstonsage/sageCore/releases/download/v6.3'] -sources = ['%(name)sv%(version)s_Linux_x86_64.tar.gz'] +sources = ['S.A.G.E.v%(version)s_Linux_x86_64.tar.gz'] sanity_check_paths = { 'files': ["bin/freq", "bin/ageon", "bin/segreg"], diff --git a/easybuild/easyconfigs/s/SAGE/S.A.G.E.-6.4.eb b/easybuild/easyconfigs/s/SAGE/SAGE-6.4.eb similarity index 90% rename from easybuild/easyconfigs/s/SAGE/S.A.G.E.-6.4.eb rename to easybuild/easyconfigs/s/SAGE/SAGE-6.4.eb index 7935579b22..fa85d69211 100644 --- a/easybuild/easyconfigs/s/SAGE/S.A.G.E.-6.4.eb +++ b/easybuild/easyconfigs/s/SAGE/SAGE-6.4.eb @@ -4,7 +4,7 @@ easyblock = "Tarball" -name = 'S.A.G.E.' +name = 'SAGE' version = '6.4' homepage = 'http://darwin.cwru.edu/sage/' @@ -15,7 +15,7 @@ use in the genetic analysis of family, pedigree and individual data.""" toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = ['http://darwin.cwru.edu/sage/files/'] -sources = ['%(name)sv%(version)s_Linux_x86_64.tar.gz'] +sources = ['S.A.G.E.v%(version)s_Linux_x86_64.tar.gz'] sanity_check_paths = { 'files': ["bin/freq", "bin/ageon", "bin/segreg"], -- GitLab From 56f97bf6c0649519fd493ee0861496d065da3209 Mon Sep 17 00:00:00 2001 From: Robert Schmidt Date: Sat, 18 Mar 2017 13:43:24 +0000 Subject: [PATCH 0413/1603] updating with checksums --- easybuild/easyconfigs/s/SAGE/SAGE-6.3.eb | 1 + easybuild/easyconfigs/s/SAGE/SAGE-6.4.eb | 1 + 2 files changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/s/SAGE/SAGE-6.3.eb b/easybuild/easyconfigs/s/SAGE/SAGE-6.3.eb index 3ff2689829..603afb8db8 100644 --- a/easybuild/easyconfigs/s/SAGE/SAGE-6.3.eb +++ b/easybuild/easyconfigs/s/SAGE/SAGE-6.3.eb @@ -16,6 +16,7 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = ['https://github.com/elstonsage/sageCore/releases/download/v6.3'] sources = ['S.A.G.E.v%(version)s_Linux_x86_64.tar.gz'] +checksums = ['c94a0b9af656212251ce452f7b2f99ec'] sanity_check_paths = { 'files': ["bin/freq", "bin/ageon", "bin/segreg"], diff --git a/easybuild/easyconfigs/s/SAGE/SAGE-6.4.eb b/easybuild/easyconfigs/s/SAGE/SAGE-6.4.eb index fa85d69211..f518617128 100644 --- a/easybuild/easyconfigs/s/SAGE/SAGE-6.4.eb +++ b/easybuild/easyconfigs/s/SAGE/SAGE-6.4.eb @@ -16,6 +16,7 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = ['http://darwin.cwru.edu/sage/files/'] sources = ['S.A.G.E.v%(version)s_Linux_x86_64.tar.gz'] +checksums = ['da3b135389df1ab9a21288cb041ac0c3'] sanity_check_paths = { 'files': ["bin/freq", "bin/ageon", "bin/segreg"], -- GitLab From d6dc1c333d65c9336a6f0ccd622a6c05d0e0bbbe Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 18 Mar 2017 16:40:08 +0100 Subject: [PATCH 0414/1603] include #4368 in v3.1.2 release notes --- RELEASE_NOTES | 1 + 1 file changed, 1 insertion(+) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index 1faff06d0d..a56c5c3afe 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -30,6 +30,7 @@ bugfix/update release - fix homepage/source_urls for ViennaRNA (#4338) - pass down $FFLAGS via FLAGS_OPT in SWASH easyconfigs (#4341) - remove include/GL/wglext.h from Mesa sanity check (#4354) + - rename S.A.G.E. to SAGE, can't have directories with trailing dot in Windows (#4368) v3.1.1 (March 7th 2017) -- GitLab From d7ce8c79da296aef4c19d2b976caa770d7552fbc Mon Sep 17 00:00:00 2001 From: Robert Schmidt Date: Sat, 18 Mar 2017 15:43:15 +0000 Subject: [PATCH 0415/1603] update with version variable --- easybuild/easyconfigs/s/SAGE/SAGE-6.3.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SAGE/SAGE-6.3.eb b/easybuild/easyconfigs/s/SAGE/SAGE-6.3.eb index 603afb8db8..3c539b01d1 100644 --- a/easybuild/easyconfigs/s/SAGE/SAGE-6.3.eb +++ b/easybuild/easyconfigs/s/SAGE/SAGE-6.3.eb @@ -14,7 +14,7 @@ use in the genetic analysis of family, pedigree and individual data.""" toolchain = {'name': 'dummy', 'version': 'dummy'} -source_urls = ['https://github.com/elstonsage/sageCore/releases/download/v6.3'] +source_urls = ['https://github.com/elstonsage/sageCore/releases/download/v%(version)s'] sources = ['S.A.G.E.v%(version)s_Linux_x86_64.tar.gz'] checksums = ['c94a0b9af656212251ce452f7b2f99ec'] -- GitLab From ecc192ceba36db967ebf16ba3ac1131f0f1c1ec4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 19 Mar 2017 18:29:56 +0100 Subject: [PATCH 0416/1603] add missing XZ dep in easyconfig for libunwind 1.1 w/ GCC/4.9.2, sync sanity_check_paths across libunwind easyconfigs --- .../easyconfigs/l/libunwind/libunwind-1.1-GCC-4.9.2.eb | 10 ++++++++++ .../l/libunwind/libunwind-1.1-foss-2015a.eb | 2 +- .../l/libunwind/libunwind-1.1-foss-2016a.eb | 1 + .../l/libunwind/libunwind-1.1-goolf-1.4.10.eb | 1 + .../l/libunwind/libunwind-1.1-ictce-5.3.0.eb | 1 + .../l/libunwind/libunwind-1.1-intel-2016b.eb | 1 + 6 files changed, 15 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-GCC-4.9.2.eb b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-GCC-4.9.2.eb index 6bc89f03e7..43105b8275 100644 --- a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-GCC-4.9.2.eb @@ -15,6 +15,16 @@ toolchain = {'name': 'GCC', 'version': '4.9.2'} sources = [SOURCE_TAR_GZ] source_urls = [GNU_SAVANNAH_SOURCE] +checksums = [ + 'fb4ea2f6fbbe45bf032cd36e586883ce', # libunwind-1.1.tar.gz +] + +dependencies = [ + ('XZ', '5.2.2'), +] + +preconfigopts = 'export LIBS="$LIBS -llzma" && ' + sanity_check_paths = { 'files': ['include/libunwind.h', ('lib/libunwind.%s' % SHLIB_EXT, 'lib64/libunwind.%s' % SHLIB_EXT)], 'dirs': [] diff --git a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-foss-2015a.eb b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-foss-2015a.eb index 15053fb3db..fe52e32d1e 100644 --- a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-foss-2015a.eb +++ b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-foss-2015a.eb @@ -26,7 +26,7 @@ dependencies = [ preconfigopts = 'export LIBS="$LIBS -llzma" && ' sanity_check_paths = { - 'files': ["include/libunwind.h", "lib/libunwind.%s" % SHLIB_EXT], + 'files': ['include/libunwind.h', ('lib/libunwind.%s' % SHLIB_EXT, 'lib64/libunwind.%s' % SHLIB_EXT)], 'dirs': [] } diff --git a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-foss-2016a.eb b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-foss-2016a.eb index ac65492ae4..24e009d090 100644 --- a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-foss-2016a.eb @@ -27,6 +27,7 @@ preconfigopts = 'export LIBS="$LIBS -llzma" && ' sanity_check_paths = { 'files': ["include/libunwind.h", "lib/libunwind.%s" % SHLIB_EXT], + 'files': ['include/libunwind.h', ('lib/libunwind.%s' % SHLIB_EXT, 'lib64/libunwind.%s' % SHLIB_EXT)], 'dirs': [] } diff --git a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-goolf-1.4.10.eb index 6d87f10400..daf551f8aa 100644 --- a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-goolf-1.4.10.eb @@ -27,6 +27,7 @@ preconfigopts = 'export LIBS="$LIBS -llzma" && ' sanity_check_paths = { 'files': ["include/libunwind.h", "lib/libunwind.%s" % SHLIB_EXT], + 'files': ['include/libunwind.h', ('lib/libunwind.%s' % SHLIB_EXT, 'lib64/libunwind.%s' % SHLIB_EXT)], 'dirs': [] } diff --git a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-ictce-5.3.0.eb index 6e07f18865..aae5a5fed7 100644 --- a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-ictce-5.3.0.eb @@ -27,6 +27,7 @@ preconfigopts = 'export LIBS="$LIBS -llzma" && ' sanity_check_paths = { 'files': ["include/libunwind.h", "lib/libunwind.%s" % SHLIB_EXT], + 'files': ['include/libunwind.h', ('lib/libunwind.%s' % SHLIB_EXT, 'lib64/libunwind.%s' % SHLIB_EXT)], 'dirs': [] } diff --git a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-intel-2016b.eb b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-intel-2016b.eb index aea3c64e51..e201bb7758 100644 --- a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-intel-2016b.eb +++ b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-intel-2016b.eb @@ -27,6 +27,7 @@ preconfigopts = 'export LIBS="$LIBS -llzma" && ' sanity_check_paths = { 'files': ["include/libunwind.h", "lib/libunwind.%s" % SHLIB_EXT], + 'files': ['include/libunwind.h', ('lib/libunwind.%s' % SHLIB_EXT, 'lib64/libunwind.%s' % SHLIB_EXT)], 'dirs': [] } -- GitLab From ccf4d6591d7369bbba30a1af83fa1de8219b39d3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 19 Mar 2017 18:57:45 +0100 Subject: [PATCH 0417/1603] add missing XZ easyconfig --- .../easyconfigs/x/XZ/XZ-5.2.2-GCC-4.9.2.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/x/XZ/XZ-5.2.2-GCC-4.9.2.eb diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-GCC-4.9.2.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-GCC-4.9.2.eb new file mode 100644 index 0000000000..0423282a10 --- /dev/null +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-GCC-4.9.2.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'XZ' +version = '5.2.2' + +homepage = 'http://tukaani.org/xz/' +description = "xz: XZ utilities" + +toolchain = {'name': 'GCC', 'version': '4.9.2'} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://tukaani.org/xz/'] + +patches = ['XZ-%(version)s_compat-libs.patch'] + +builddependencies = [ + ('Autotools', '20150215'), + ('gettext', '0.19.8', '', True), +] + +# may become useful in non-x86 archs +# configopts = ' --disable-assembler ' + +sanity_check_paths = { + 'files': ["bin/xz", "bin/lzmainfo"], + 'dirs': [] +} + +moduleclass = 'tools' -- GitLab From 2311bc03eae3c5cf5562baff913f2b366e778a45 Mon Sep 17 00:00:00 2001 From: Yann Sagon Date: Mon, 20 Mar 2017 10:09:29 +0100 Subject: [PATCH 0418/1603] fix freetype dependency and moduleclass --- .../r/rootpy/rootpy-0.8.0-foss-2016a-Python-2.7.11.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/r/rootpy/rootpy-0.8.0-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/r/rootpy/rootpy-0.8.0-foss-2016a-Python-2.7.11.eb index d40917cf4c..e7e4443ff3 100644 --- a/easybuild/easyconfigs/r/rootpy/rootpy-0.8.0-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/r/rootpy/rootpy-0.8.0-foss-2016a-Python-2.7.11.eb @@ -21,7 +21,7 @@ sources = ['%(version)s.tar.gz'] dependencies = [ ('Python', '2.7.11'), ('ROOT','v6.08.02','-Python-%(pyver)s'), - ('matplotlib', '1.5.1', '-Python-%(pyver)s') + ('matplotlib', '1.5.1', '-freetype-2.6.3') ] sanity_check_paths = { @@ -29,4 +29,4 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages'], } -moduleclass = 'bio' +moduleclass = 'data' -- GitLab From cc70804b27f7ce9391e362ed0f27237036e51aed Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 20 Mar 2017 10:18:39 +0100 Subject: [PATCH 0419/1603] adding easyconfigs: QuTiP-4.1.0-intel-2016b-Python-2.7.12.eb --- .../QuTiP-4.1.0-intel-2016b-Python-2.7.12.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/q/QuTiP/QuTiP-4.1.0-intel-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/q/QuTiP/QuTiP-4.1.0-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/q/QuTiP/QuTiP-4.1.0-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..703fb053f6 --- /dev/null +++ b/easybuild/easyconfigs/q/QuTiP/QuTiP-4.1.0-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'QuTiP' +version = '4.1.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://qutip.org' +description = """QuTiP is open-source software for simulating the dynamics of open quantum systems.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://qutip.org/downloads/%(version)s/'] + +dependencies = [ + ('Python', '2.7.12'), + ('matplotlib', '1.5.3', versionsuffix), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'chem' -- GitLab From a797616eb175ed6650e8247579bb4f1a2f0fcbef Mon Sep 17 00:00:00 2001 From: HPC core facility CalcUA Date: Mon, 20 Mar 2017 12:37:28 +0100 Subject: [PATCH 0420/1603] Bowtie2 - With a patch to change the Makefile to use better compiler options for Intel, also based on a suggestion on the Allinea blog --- .../b/Bowtie2/Bowtie2-2.2.9-intel-2016b.eb | 45 +++++++++++++++++++ .../Bowtie2-2.2.9_optimize-intel.patch | 22 +++++++++ 2 files changed, 67 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9-intel-2016b.eb create mode 100644 easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9_optimize-intel.patch diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9-intel-2016b.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9-intel-2016b.eb new file mode 100644 index 0000000000..3817ce9c24 --- /dev/null +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9-intel-2016b.eb @@ -0,0 +1,45 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# Modified by: Robert Schmidt +# Ottawa Hospital Research Institute - Bioinformatics Team +# Modified by: Adam Huffman +# The Francis Crick Institute +# Modified by: Kurt Lust, UAntwerp: Patch for better optimization with the +# Intel compilers, based on +# https://www.allinea.com/blog/201501/tuning-bowtie2-better-performance + +easyblock = 'MakeCp' + +name = 'Bowtie2' +version = '2.2.9' + +homepage = 'http://bowtie-bio.sourceforge.net/bowtie2/index.shtml' +description = """ Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads + to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s + of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. + Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, + its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +sources = ['%(namelower)s-%(version)s-source.zip'] +source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')] + +patches = ['Bowtie2-%(version)s_optimize-intel.patch'] + +files_to_copy = [ + (["bowtie2", "bowtie2-align-l", "bowtie2-align-s", "bowtie2-build", "bowtie2-build-l", "bowtie2-build-s", + "bowtie2-inspect", "bowtie2-inspect-l", "bowtie2-inspect-s"], 'bin'), + "LICENSE", "doc", "example", "scripts", "MANUAL", "MANUAL.markdown", "NEWS"] + +sanity_check_paths = { + 'files': ["bin/bowtie2-align-l", "bin/bowtie2-build", "bin/bowtie2-inspect"], + 'dirs': [], +} + +# to add script folder to path just uncomment this line +#modextrapaths = {'PATH': 'scripts'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9_optimize-intel.patch b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9_optimize-intel.patch new file mode 100644 index 0000000000..7c5a3cf076 --- /dev/null +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9_optimize-intel.patch @@ -0,0 +1,22 @@ +# Adapt Bowtie2 makefile to use compiler flags that are suited for icpc. +# Options are derived from the options that EasyBuild choses. +# In particular, the compile is no longer restricted to SSE2 but now +# uses -xHost so that AVX/AVX2 instructions will be attempted were appropriate, +# as suggested by https://www.allinea.com/blog/201501/tuning-bowtie2-better-performance +# Author: Kurt Lust, UAntwerp. +--- bowtie2-2.2.9-orig/Makefile 2016-03-10 16:15:50.000000000 +0100 ++++ bowtie2-2.2.9/Makefile 2017-03-20 11:06:20.521070416 +0100 +@@ -165,11 +165,9 @@ + $(error bowtie2 compilation requires a 64-bit platform ) + endif + +-SSE_FLAG=-msse2 +- +-DEBUG_FLAGS = -O0 -g3 -m64 $(SSE_FLAG) ++DEBUG_FLAGS = -std=c++11 -O0 -g3 -xHost -ftz -fp-speculation=safe -fp-model source + DEBUG_DEFS = -DCOMPILER_OPTIONS="\"$(DEBUG_FLAGS) $(EXTRA_FLAGS)\"" +-RELEASE_FLAGS = -O3 -m64 $(SSE_FLAG) -funroll-loops -g3 ++RELEASE_FLAGS = -std=c++11 -O2 -xHost -ftz -fp-speculation=safe -fp-model source + RELEASE_DEFS = -DCOMPILER_OPTIONS="\"$(RELEASE_FLAGS) $(EXTRA_FLAGS)\"" + NOASSERT_FLAGS = -DNDEBUG + FILE_FLAGS = -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -- GitLab From 8a32fc2baa2a1f2e1780adbc366e0ecf34401c82 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 20 Mar 2017 13:20:17 +0100 Subject: [PATCH 0421/1603] adding easyconfigs: imbalanced-learn-0.2.1-intel-2016b-Python-3.5.2.eb --- ...ed-learn-0.2.1-intel-2016b-Python-3.5.2.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/i/imbalanced-learn/imbalanced-learn-0.2.1-intel-2016b-Python-3.5.2.eb diff --git a/easybuild/easyconfigs/i/imbalanced-learn/imbalanced-learn-0.2.1-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/i/imbalanced-learn/imbalanced-learn-0.2.1-intel-2016b-Python-3.5.2.eb new file mode 100644 index 0000000000..399d48b06b --- /dev/null +++ b/easybuild/easyconfigs/i/imbalanced-learn/imbalanced-learn-0.2.1-intel-2016b-Python-3.5.2.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'imbalanced-learn' +version = '0.2.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/scikit-learn-contrib/imbalanced-learn' +description = """imbalanced-learn is a Python package offering a number of re-sampling techniques commonly used in + datasets showing strong between-class imbalance.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '3.5.2'), + ('scikit-learn', '0.18.1', versionsuffix), +] + +options = {'modulename': 'imblearn'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' -- GitLab From 2e7c9ddb5a373c9ffdb28645e29f2708c8380efb Mon Sep 17 00:00:00 2001 From: HPC core facility CalcUA Date: Mon, 20 Mar 2017 14:02:30 +0100 Subject: [PATCH 0422/1603] Bowtie2 for Intel: Changed the easyconfig so that the patch from the previous commit is not needed; removed the patch. --- .../b/Bowtie2/Bowtie2-2.2.9-intel-2016b.eb | 6 ++++- .../Bowtie2-2.2.9_optimize-intel.patch | 22 ------------------- 2 files changed, 5 insertions(+), 23 deletions(-) delete mode 100644 easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9_optimize-intel.patch diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9-intel-2016b.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9-intel-2016b.eb index 3817ce9c24..28ad38c224 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9-intel-2016b.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9-intel-2016b.eb @@ -27,7 +27,11 @@ toolchain = {'name': 'intel', 'version': '2016b'} sources = ['%(namelower)s-%(version)s-source.zip'] source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')] -patches = ['Bowtie2-%(version)s_optimize-intel.patch'] +toolchainopts = {'cstd': 'c++11'} + +# Make sure that the Makefile uses options for intel rather than the ones for gcc coded +# in the Makefile by setting RELEASE_FLAGS. +buildopts = 'RELEASE_FLAGS="$CXXFLAGS"' files_to_copy = [ (["bowtie2", "bowtie2-align-l", "bowtie2-align-s", "bowtie2-build", "bowtie2-build-l", "bowtie2-build-s", diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9_optimize-intel.patch b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9_optimize-intel.patch deleted file mode 100644 index 7c5a3cf076..0000000000 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9_optimize-intel.patch +++ /dev/null @@ -1,22 +0,0 @@ -# Adapt Bowtie2 makefile to use compiler flags that are suited for icpc. -# Options are derived from the options that EasyBuild choses. -# In particular, the compile is no longer restricted to SSE2 but now -# uses -xHost so that AVX/AVX2 instructions will be attempted were appropriate, -# as suggested by https://www.allinea.com/blog/201501/tuning-bowtie2-better-performance -# Author: Kurt Lust, UAntwerp. ---- bowtie2-2.2.9-orig/Makefile 2016-03-10 16:15:50.000000000 +0100 -+++ bowtie2-2.2.9/Makefile 2017-03-20 11:06:20.521070416 +0100 -@@ -165,11 +165,9 @@ - $(error bowtie2 compilation requires a 64-bit platform ) - endif - --SSE_FLAG=-msse2 -- --DEBUG_FLAGS = -O0 -g3 -m64 $(SSE_FLAG) -+DEBUG_FLAGS = -std=c++11 -O0 -g3 -xHost -ftz -fp-speculation=safe -fp-model source - DEBUG_DEFS = -DCOMPILER_OPTIONS="\"$(DEBUG_FLAGS) $(EXTRA_FLAGS)\"" --RELEASE_FLAGS = -O3 -m64 $(SSE_FLAG) -funroll-loops -g3 -+RELEASE_FLAGS = -std=c++11 -O2 -xHost -ftz -fp-speculation=safe -fp-model source - RELEASE_DEFS = -DCOMPILER_OPTIONS="\"$(RELEASE_FLAGS) $(EXTRA_FLAGS)\"" - NOASSERT_FLAGS = -DNDEBUG - FILE_FLAGS = -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -- GitLab From 379f4c31ce260b1cbc92362a30c6426e81c4ef14 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 20 Mar 2017 14:19:45 +0100 Subject: [PATCH 0423/1603] adding easyconfigs: SWASH-3.14-intel-2016b-mpi.eb, SWASH-3.14-intel-2017a-mpi.eb --- .../s/SWASH/SWASH-3.14-intel-2016b-mpi.eb | 31 +++++++++++++++++++ .../s/SWASH/SWASH-3.14-intel-2017a-mpi.eb | 31 +++++++++++++++++++ 2 files changed, 62 insertions(+) create mode 100644 easybuild/easyconfigs/s/SWASH/SWASH-3.14-intel-2016b-mpi.eb create mode 100644 easybuild/easyconfigs/s/SWASH/SWASH-3.14-intel-2017a-mpi.eb diff --git a/easybuild/easyconfigs/s/SWASH/SWASH-3.14-intel-2016b-mpi.eb b/easybuild/easyconfigs/s/SWASH/SWASH-3.14-intel-2016b-mpi.eb new file mode 100644 index 0000000000..82347e4014 --- /dev/null +++ b/easybuild/easyconfigs/s/SWASH/SWASH-3.14-intel-2016b-mpi.eb @@ -0,0 +1,31 @@ +easyblock = 'MakeCp' + +name = 'SWASH' +version = '3.14' +versionsuffix = '-mpi' + +homepage = 'http://swash.sourceforge.net/' +description = """SWASH is a general-purpose numerical tool for simulating unsteady, non-hydrostatic, free-surface, + rotational flow and transport phenomena in coastal waters as driven by waves, tides, buoyancy and wind forces.""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'usempi': True} + +source_urls = ['http://swash.sourceforge.net/download/zip/'] +sources = [SOURCELOWER_TAR_GZ] + +prebuildopts = "unset FC && make config && " +buildopts = 'mpi FLAGS_OPT="$FFLAGS"' + +parallel = 1 + +files_to_copy = [(['swash.exe', 'swashrun', 'SWASHRUN.README'], 'bin')] + +postinstallcmds = ["chmod a+rx %(installdir)s/bin/swash.exe %(installdir)s/bin/swashrun"] + +sanity_check_paths = { + 'files': ['bin/swash.exe', 'bin/swashrun', 'bin/SWASHRUN.README'], + 'dirs': [], +} + +moduleclass = 'cae' diff --git a/easybuild/easyconfigs/s/SWASH/SWASH-3.14-intel-2017a-mpi.eb b/easybuild/easyconfigs/s/SWASH/SWASH-3.14-intel-2017a-mpi.eb new file mode 100644 index 0000000000..6b97716f50 --- /dev/null +++ b/easybuild/easyconfigs/s/SWASH/SWASH-3.14-intel-2017a-mpi.eb @@ -0,0 +1,31 @@ +easyblock = 'MakeCp' + +name = 'SWASH' +version = '3.14' +versionsuffix = '-mpi' + +homepage = 'http://swash.sourceforge.net/' +description = """SWASH is a general-purpose numerical tool for simulating unsteady, non-hydrostatic, free-surface, + rotational flow and transport phenomena in coastal waters as driven by waves, tides, buoyancy and wind forces.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'usempi': True} + +source_urls = ['http://swash.sourceforge.net/download/zip/'] +sources = [SOURCELOWER_TAR_GZ] + +prebuildopts = "unset FC && make config && " +buildopts = 'mpi FLAGS_OPT="$FFLAGS"' + +parallel = 1 + +files_to_copy = [(['swash.exe', 'swashrun', 'SWASHRUN.README'], 'bin')] + +postinstallcmds = ["chmod a+rx %(installdir)s/bin/swash.exe %(installdir)s/bin/swashrun"] + +sanity_check_paths = { + 'files': ['bin/swash.exe', 'bin/swashrun', 'bin/SWASHRUN.README'], + 'dirs': [], +} + +moduleclass = 'cae' -- GitLab From 69933991035c5ce2ac99a843390487cd68109eca Mon Sep 17 00:00:00 2001 From: HPC core facility CalcUA Date: Mon, 20 Mar 2017 14:38:47 +0100 Subject: [PATCH 0424/1603] Bowtie2: Modified the comments as requested in the pull request comments. --- easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9-intel-2016b.eb | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9-intel-2016b.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9-intel-2016b.eb index 28ad38c224..fa3d31dfa4 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9-intel-2016b.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9-intel-2016b.eb @@ -6,9 +6,8 @@ # Ottawa Hospital Research Institute - Bioinformatics Team # Modified by: Adam Huffman # The Francis Crick Institute -# Modified by: Kurt Lust, UAntwerp: Patch for better optimization with the -# Intel compilers, based on -# https://www.allinea.com/blog/201501/tuning-bowtie2-better-performance +# Modified by: Kurt Lust, UAntwerp: Overwrite compiler options used in the GNU-based +# Makefile with the preferred options for intel compilers. easyblock = 'MakeCp' -- GitLab From b97f2f6df4dd995e89280b15598056f4c66db77c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 20 Mar 2017 15:11:03 +0100 Subject: [PATCH 0425/1603] adding easyconfigs: EasyBuild-3.1.2.eb --- .../e/EasyBuild/EasyBuild-3.1.2.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.1.2.eb diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.1.2.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.1.2.eb new file mode 100644 index 0000000000..eaadea3b41 --- /dev/null +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.1.2.eb @@ -0,0 +1,38 @@ +easyblock = 'EB_EasyBuildMeta' + +name = 'EasyBuild' +version = '3.1.2' + +homepage = 'http://hpcugent.github.com/easybuild/' +description = """EasyBuild is a software build and installation framework + written in Python that allows you to install software in a structured, + repeatable and robust way.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = [ + # vsc-install + 'https://pypi.python.org/packages/ef/c7/640c6d791ba452321c0d1371b6626486bb495e0645bb896d33c78a09f810', + # vsc-base + 'https://pypi.python.org/packages/da/90/ee40b1a6a5bfed24139042c737500a9b45db0373a6735e76481fc860fe37', + # easybuild-framework + 'https://pypi.python.org/packages/fa/00/6a47862b38e6d921071d305deab4c494ae2eae58556c90c95e520fea28b9/', + # easybuild-easyblocks + 'https://pypi.python.org/packages/d6/55/9b6634b01fbc26edb9f5af39b06acbe7ec843da438ba5ac3063937934b3e', + # easybuild-easyconfigs + 'https://pypi.python.org/packages/5a/4c/ea8faa46c7874a3d20f28e2d222a1f4a5e97a4f8052add338a785755ec89', +] +# order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) +sources = [ + 'vsc-install-0.10.25.tar.gz', + 'vsc-base-2.5.7.tar.gz', + 'easybuild-framework-%(version)s.tar.gz', + 'easybuild-easyblocks-%(version)s.tar.gz', + 'easybuild-easyconfigs-%(version)s.tar.gz', +] + +# EasyBuild is a (set of) Python packages, so it depends on Python +# usually, we want to use the system Python, so no actual Python dependency is listed +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +moduleclass = 'tools' -- GitLab From 80350c7b4c07f77f07a1b646bbc4f45cec83d619 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 20 Mar 2017 18:06:38 +0100 Subject: [PATCH 0426/1603] bump version to v3.2.0.dev0 --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 0512590286..0683e432c9 100644 --- a/setup.py +++ b/setup.py @@ -47,7 +47,7 @@ from distutils import log # recent setuptools versions will *TRANSFORM* something like 'X.Y.Zdev' into 'X.Y.Z.dev0', with a warning like # UserWarning: Normalizing '2.4.0dev' to '2.4.0.dev0' # This causes problems further up the dependency chain... -VERSION = '3.1.2' +VERSION = '3.2.0.dev0' API_VERSION = VERSION.split('.')[0] EB_VERSION = '.'.join(VERSION.split('.')[0:2]) -- GitLab From bf8085add933e30949220dbef4b6caba7ab1c34c Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Tue, 21 Mar 2017 15:19:13 +0800 Subject: [PATCH 0427/1603] adding easyconfigs: QuantumESPRESSO-6.1-intel-2017a.eb --- .../QuantumESPRESSO-6.1-intel-2017a.eb | 59 +++++++++++++++++++ 1 file changed, 59 insertions(+) create mode 100644 easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.1-intel-2017a.eb diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.1-intel-2017a.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.1-intel-2017a.eb new file mode 100644 index 0000000000..4a105c34ef --- /dev/null +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.1-intel-2017a.eb @@ -0,0 +1,59 @@ +name = 'QuantumESPRESSO' +version = '6.1' + +homepage = 'http://www.pwscf.org/' +description = """Quantum ESPRESSO is an integrated suite of computer codes + for electronic-structure calculations and materials modeling at the nanoscale. + It is based on density-functional theory, plane waves, and pseudopotentials + (both norm-conserving and ultrasoft).""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'usempi': True} + +# major part of this list was determined from espresso/install/plugins_list +sources = [ + 'qe-%(version)s.tar.gz', + 'wannier90-2.1.0.tar.gz', + 'qe-gipaw-6.1.tar.gz', + # must be downloaded manually from + # http://qe-forge.org/gf/project/q-e/scmsvn/?action=browse&path=%2F%2Acheckout%2A%2Ftags%2FQE-5.2.1%2Fespresso%2Farchive%2Fplumed-1.3-qe.tar.gz&revision=11758 + # gets updated without changes to filename, cfr. http://qe-forge.org/pipermail/q-e-commits/2015-June/007359.html + # 'plumed-1.3-qe-r11758.tar.gz', + 'want-2.5.1-base.tar.gz', + 'West-2.0.1.tar.gz', + 'yambo-3.4.2.tgz', +] +missing_sources = [ + 'sax-2.0.3.tar.gz', # nowhere to be found +] +source_urls = [ + 'http://files.qe-forge.org/index.php?file=', # all sources, except espresso*.tar.gz + 'http://www.wannier.org/code/', # wannier90-2.1.0.tar.gz + 'http://qe-forge.org/gf/download/frsrelease/240/1075/', # qe-6.1.tar.gz + 'http://qe-forge.org/gf/download/frsrelease/153/618/', # want-2.5.1-base.tar.gz + 'http://www.west-code.org/downloads/', # West-2.0.1.tar.gz + 'http://qe-forge.org/gf/download/frsrelease/208/932/', # yambo-3.4.2.tgz +] + +patches = [ + 'QuantumESPRESSO-5.4.0_yambo-fixes.patch', +] + +# source checksums +checksums = [ + 'db398edcad76e085f8c8a3f6ecb7aaab', # qe-6.1.tar.gz + '07a81c002b41d6d0f97857e55c57d769', # wannier90-2.1.0.tar.gz + '178055353e59eb4dd8bebe27331f2927', # qe-gipaw-6.1.tar.gz + # 'f094031c6d13a0e00022daf4d7c847c7', # plumed-1.3-qe-r11758.tar.gz + 'ac365daebbe380bf4019235eacf71079', # want-2.5.1-base.tar.gz + '000abe6a5dccd1e722d1767c3dcd3996', # West-2.0.1.tar.gz + 'f0820a0f42dfc81ce3811af647bed777', # yambo-3.4.2.tgz +] + +# add plumed and uncomment the lines in sources and checksums if the package is downloaded manually +buildopts = 'all w90 epw gipaw want west yambo xspectra' # plumed + +# parallel build tends to fail +parallel = 1 + +moduleclass = 'chem' -- GitLab From 0a20d53f1dc9beebcf2f9938f2d84c9963a997a3 Mon Sep 17 00:00:00 2001 From: Yann Sagon Date: Tue, 21 Mar 2017 11:00:13 +0100 Subject: [PATCH 0428/1603] fix versionsuffix dependency matplotlib --- .../r/rootpy/rootpy-0.8.0-foss-2016a-Python-2.7.11.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/rootpy/rootpy-0.8.0-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/r/rootpy/rootpy-0.8.0-foss-2016a-Python-2.7.11.eb index e7e4443ff3..efecae95e8 100644 --- a/easybuild/easyconfigs/r/rootpy/rootpy-0.8.0-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/r/rootpy/rootpy-0.8.0-foss-2016a-Python-2.7.11.eb @@ -21,7 +21,7 @@ sources = ['%(version)s.tar.gz'] dependencies = [ ('Python', '2.7.11'), ('ROOT','v6.08.02','-Python-%(pyver)s'), - ('matplotlib', '1.5.1', '-freetype-2.6.3') + ('matplotlib', '1.5.1', versionsuffix + '-freetype-2.6.3') ] sanity_check_paths = { -- GitLab From d1b093ed3d64f2b8d2bf4a6c35a9f356da607c82 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 21 Mar 2017 13:06:07 +0100 Subject: [PATCH 0429/1603] sync Bowtie2 easyconfigs, consistently use Bowtie2 easyblock --- .../b/Bowtie2/Bowtie2-2.0.2-goolf-1.4.10.eb | 7 +++--- .../b/Bowtie2/Bowtie2-2.0.2-ictce-5.3.0.eb | 7 +++--- .../b/Bowtie2/Bowtie2-2.0.5-goolf-1.4.10.eb | 8 +------ .../b/Bowtie2/Bowtie2-2.0.6-goolf-1.4.10.eb | 8 +------ .../b/Bowtie2/Bowtie2-2.1.0-goolf-1.4.10.eb | 12 +--------- .../b/Bowtie2/Bowtie2-2.1.0-ictce-5.5.0.eb | 3 +-- .../b/Bowtie2/Bowtie2-2.2.0-goolf-1.4.10.eb | 13 +---------- .../b/Bowtie2/Bowtie2-2.2.2-goolf-1.4.10.eb | 13 +---------- .../b/Bowtie2/Bowtie2-2.2.4-goolf-1.4.10.eb | 13 +---------- .../b/Bowtie2/Bowtie2-2.2.5-goolf-1.7.20.eb | 13 +---------- .../b/Bowtie2/Bowtie2-2.2.5-intel-2015a.eb | 13 +---------- .../b/Bowtie2/Bowtie2-2.2.6-foss-2015b.eb | 13 +---------- .../b/Bowtie2/Bowtie2-2.2.6-intel-2015b.eb | 13 +---------- .../b/Bowtie2/Bowtie2-2.2.7-foss-2015b.eb | 13 +---------- .../b/Bowtie2/Bowtie2-2.2.8-foss-2015b.eb | 13 +---------- .../b/Bowtie2/Bowtie2-2.2.8-foss-2016a.eb | 13 +---------- .../b/Bowtie2/Bowtie2-2.2.9-foss-2016a.eb | 13 +---------- .../b/Bowtie2/Bowtie2-2.2.9-goolf-1.7.20.eb | 13 +---------- .../b/Bowtie2/Bowtie2-2.2.9-intel-2016b.eb | 22 ++----------------- 19 files changed, 26 insertions(+), 197 deletions(-) diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.2-goolf-1.4.10.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.2-goolf-1.4.10.eb index 13ddeb08e1..f334c5a116 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.2-goolf-1.4.10.eb @@ -12,17 +12,18 @@ name = 'Bowtie2' version = '2.0.2' -altversions = ['2.0.0-beta6', '2.0.0-beta7', '2.0.1', '2.0.2'] homepage = 'http://bowtie-bio.sourceforge.net/bowtie2/index.shtml' description = """Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} -toolchainopts = {'optarch': True, 'pic': True} +toolchainopts = {'pic': True} sources = ['%(namelower)s-%(version)s-source.zip'] source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')] -# N.B. the download option above -> required for sourceforge + +# to add scripts folder to $PATH just uncomment this line +# modextrapaths = {'PATH': 'scripts'} moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.2-ictce-5.3.0.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.2-ictce-5.3.0.eb index 7f8fbd5ca6..fa8a4e145b 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.2-ictce-5.3.0.eb @@ -12,7 +12,6 @@ name = 'Bowtie2' version = '2.0.2' -altversions = ['2.0.0-beta6', '2.0.0-beta7', '2.0.1', '2.0.2'] homepage = 'http://bowtie-bio.sourceforge.net/bowtie2/index.shtml' description = """Bowtie 2 is an ultrafast and memory-efficient tool @@ -20,10 +19,12 @@ description = """Bowtie 2 is an ultrafast and memory-efficient tool toolchain = {'name': 'ictce', 'version': '5.3.0'} -toolchainopts = {'optarch': True, 'pic': True} +toolchainopts = {'pic': True} sources = ['%(namelower)s-%(version)s-source.zip'] source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')] -# N.B. the download option above -> required for sourceforge + +# to add scripts folder to $PATH just uncomment this line +# modextrapaths = {'PATH': 'scripts'} moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.5-goolf-1.4.10.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.5-goolf-1.4.10.eb index 9469af37f5..a81247d559 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.5-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.5-goolf-1.4.10.eb @@ -3,8 +3,6 @@ # Swiss Institute of Bioinformatics # Biozentrum - University of Basel -easyblock = 'MakeCp' - name = 'Bowtie2' version = '2.0.5' @@ -16,6 +14,7 @@ description = """ Bowtie 2 is an ultrafast and memory-efficient tool for alignin its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} +toolchainopts = {'pic': True} sources = ['%(namelower)s-%(version)s-source.zip'] source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')] @@ -24,11 +23,6 @@ files_to_copy = [ (["bowtie2", "bowtie2-align", "bowtie2-build", "bowtie2-inspect"], 'bin'), "doc", "example", "scripts"] -sanity_check_paths = { - 'files': ["bin/bowtie2-align", "bin/bowtie2-build", "bin/bowtie2-inspect"], - 'dirs': [], -} - # to add scripts folder to $PATH just uncomment this line # modextrapaths = {'PATH': 'scripts'} diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.6-goolf-1.4.10.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.6-goolf-1.4.10.eb index 264b5296c0..00cfc5cb06 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.6-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.6-goolf-1.4.10.eb @@ -3,8 +3,6 @@ # Swiss Institute of Bioinformatics # Biozentrum - University of Basel -easyblock = 'MakeCp' - name = 'Bowtie2' version = '2.0.6' @@ -16,6 +14,7 @@ description = """ Bowtie 2 is an ultrafast and memory-efficient tool for alignin its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} +toolchainopts = {'pic': True} sources = ['%(namelower)s-%(version)s-source.zip'] source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')] @@ -24,11 +23,6 @@ files_to_copy = [ (["bowtie2", "bowtie2-align", "bowtie2-build", "bowtie2-inspect"], 'bin'), "doc", "example", "scripts"] -sanity_check_paths = { - 'files': ["bin/bowtie2-align", "bin/bowtie2-build", "bin/bowtie2-inspect"], - 'dirs': [], -} - # to add scripts folder to $PATH just uncomment this line # modextrapaths = {'PATH': 'scripts'} diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.1.0-goolf-1.4.10.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.1.0-goolf-1.4.10.eb index f3e4ae2e16..8f006d9054 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.1.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.1.0-goolf-1.4.10.eb @@ -3,8 +3,6 @@ # Swiss Institute of Bioinformatics # Biozentrum - University of Basel -easyblock = 'MakeCp' - name = 'Bowtie2' version = '2.1.0' @@ -16,19 +14,11 @@ description = """ Bowtie 2 is an ultrafast and memory-efficient tool for alignin its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} +toolchainopts = {'pic': True} sources = ['%(namelower)s-%(version)s-source.zip'] source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')] -files_to_copy = [ - (["bowtie2", "bowtie2-align", "bowtie2-build", "bowtie2-inspect"], 'bin'), - "doc", "example", "scripts"] - -sanity_check_paths = { - 'files': ["bin/bowtie2-align", "bin/bowtie2-build", "bin/bowtie2-inspect"], - 'dirs': [], -} - # to add scripts folder to $PATH just uncomment this line # modextrapaths = {'PATH': 'scripts'} diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.1.0-ictce-5.5.0.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.1.0-ictce-5.5.0.eb index 975220fa34..de611ce79f 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.1.0-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.1.0-ictce-5.5.0.eb @@ -12,14 +12,13 @@ name = 'Bowtie2' version = '2.1.0' -altversions = ['2.0.0-beta6', '2.0.0-beta7', '2.0.1', '2.0.2', '2.1.0'] homepage = 'http://bowtie-bio.sourceforge.net/bowtie2/index.shtml' description = """Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences.""" toolchain = {'name': 'ictce', 'version': '5.5.0'} -toolchainopts = {'optarch': True, 'pic': True} +toolchainopts = {'pic': True} # note: SOURCEFORGE_SOURCE constant doesn't work here because of bowtie-bio used in URL source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')] diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.0-goolf-1.4.10.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.0-goolf-1.4.10.eb index 3ccec7b3ec..9dc4955f2b 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.0-goolf-1.4.10.eb @@ -3,8 +3,6 @@ # Swiss Institute of Bioinformatics # Biozentrum - University of Basel -easyblock = 'MakeCp' - name = 'Bowtie2' version = '2.2.0' @@ -16,20 +14,11 @@ description = """ Bowtie 2 is an ultrafast and memory-efficient tool for alignin its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} +toolchainopts = {'pic': True} sources = ['%(namelower)s-%(version)s-source.zip'] source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')] -files_to_copy = [ - (["bowtie2", "bowtie2-align-l", "bowtie2-align-s", "bowtie2-build", "bowtie2-build-l", "bowtie2-build-s", - "bowtie2-inspect", "bowtie2-inspect-l", "bowtie2-inspect-s"], 'bin'), - "doc", "example", "scripts"] - -sanity_check_paths = { - 'files': ["bin/bowtie2-align-l", "bin/bowtie2-build", "bin/bowtie2-inspect"], - 'dirs': [], -} - # to add scripts folder to $PATH just uncomment this line # modextrapaths = {'PATH': 'scripts'} diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.2-goolf-1.4.10.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.2-goolf-1.4.10.eb index 37790b2b2b..535fcdd94e 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.2-goolf-1.4.10.eb @@ -3,8 +3,6 @@ # Swiss Institute of Bioinformatics # Biozentrum - University of Basel -easyblock = 'MakeCp' - name = 'Bowtie2' version = '2.2.2' @@ -16,20 +14,11 @@ description = """ Bowtie 2 is an ultrafast and memory-efficient tool for alignin its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} +toolchainopts = {'pic': True} sources = ['%(namelower)s-%(version)s-source.zip'] source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')] -files_to_copy = [ - (["bowtie2", "bowtie2-align-l", "bowtie2-align-s", "bowtie2-build", "bowtie2-build-l", "bowtie2-build-s", - "bowtie2-inspect", "bowtie2-inspect-l", "bowtie2-inspect-s"], 'bin'), - "doc", "example", "scripts", "MANUAL", "MANUAL.markdown", "NEWS"] - -sanity_check_paths = { - 'files': ["bin/bowtie2-align-l", "bin/bowtie2-build", "bin/bowtie2-inspect"], - 'dirs': [], -} - # to add script folder to path just uncomment this line # modextrapaths = {'PATH': 'scripts'} diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.4-goolf-1.4.10.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.4-goolf-1.4.10.eb index 48fab89b05..8e2370c316 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.4-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.4-goolf-1.4.10.eb @@ -5,8 +5,6 @@ # Modified by: Robert Schmidt # Ottawa Hospital Research Institute - Bioinformatics Team -easyblock = 'MakeCp' - name = 'Bowtie2' version = '2.2.4' @@ -18,20 +16,11 @@ description = """ Bowtie 2 is an ultrafast and memory-efficient tool for alignin its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} +toolchainopts = {'pic': True} sources = ['%(namelower)s-%(version)s-source.zip'] source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')] -files_to_copy = [ - (["bowtie2", "bowtie2-align-l", "bowtie2-align-s", "bowtie2-build", "bowtie2-build-l", "bowtie2-build-s", - "bowtie2-inspect", "bowtie2-inspect-l", "bowtie2-inspect-s"], 'bin'), - "doc", "example", "scripts", "MANUAL", "MANUAL.markdown", "NEWS"] - -sanity_check_paths = { - 'files': ["bin/bowtie2-align-l", "bin/bowtie2-build", "bin/bowtie2-inspect"], - 'dirs': [], -} - # to add script folder to path just uncomment this line # modextrapaths = {'PATH': 'scripts'} diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.5-goolf-1.7.20.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.5-goolf-1.7.20.eb index 3f2240e2f4..b011315af8 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.5-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.5-goolf-1.7.20.eb @@ -5,8 +5,6 @@ # Modified by: Robert Schmidt # Ottawa Hospital Research Institute - Bioinformatics Team -easyblock = 'MakeCp' - name = 'Bowtie2' version = '2.2.5' @@ -18,20 +16,11 @@ description = """ Bowtie 2 is an ultrafast and memory-efficient tool for alignin its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.""" toolchain = {'name': 'goolf', 'version': '1.7.20'} +toolchainopts = {'pic': True} sources = ['%(namelower)s-%(version)s-source.zip'] source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')] -files_to_copy = [ - (["bowtie2", "bowtie2-align-l", "bowtie2-align-s", "bowtie2-build", "bowtie2-build-l", "bowtie2-build-s", - "bowtie2-inspect", "bowtie2-inspect-l", "bowtie2-inspect-s"], 'bin'), - "doc", "example", "scripts", "MANUAL", "MANUAL.markdown", "NEWS"] - -sanity_check_paths = { - 'files': ["bin/bowtie2-align-l", "bin/bowtie2-build", "bin/bowtie2-inspect"], - 'dirs': [], -} - # to add script folder to path just uncomment this line # modextrapaths = {'PATH': 'scripts'} diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.5-intel-2015a.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.5-intel-2015a.eb index 0bb8d3c531..4dca70247f 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.5-intel-2015a.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.5-intel-2015a.eb @@ -5,8 +5,6 @@ # Modified by: Robert Schmidt # Ottawa Hospital Research Institute - Bioinformatics Team -easyblock = 'MakeCp' - name = 'Bowtie2' version = '2.2.5' @@ -18,20 +16,11 @@ description = """ Bowtie 2 is an ultrafast and memory-efficient tool for alignin its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.""" toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'pic': True} sources = ['%(namelower)s-%(version)s-source.zip'] source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')] -files_to_copy = [ - (["bowtie2", "bowtie2-align-l", "bowtie2-align-s", "bowtie2-build", "bowtie2-build-l", "bowtie2-build-s", - "bowtie2-inspect", "bowtie2-inspect-l", "bowtie2-inspect-s"], 'bin'), - "doc", "example", "scripts", "MANUAL", "MANUAL.markdown", "NEWS"] - -sanity_check_paths = { - 'files': ["bin/bowtie2-align-l", "bin/bowtie2-build", "bin/bowtie2-inspect"], - 'dirs': [], -} - # to add script folder to path just uncomment this line # modextrapaths = {'PATH': 'scripts'} diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.6-foss-2015b.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.6-foss-2015b.eb index ab7844bff7..6cd8cef8b8 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.6-foss-2015b.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.6-foss-2015b.eb @@ -5,8 +5,6 @@ # Modified by: Robert Schmidt # Ottawa Hospital Research Institute - Bioinformatics Team -easyblock = 'MakeCp' - name = 'Bowtie2' version = '2.2.6' @@ -18,20 +16,11 @@ description = """ Bowtie 2 is an ultrafast and memory-efficient tool for alignin its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.""" toolchain = {'name': 'foss', 'version': '2015b'} +toolchainopts = {'pic': True} sources = ['%(namelower)s-%(version)s-source.zip'] source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')] -files_to_copy = [ - (["bowtie2", "bowtie2-align-l", "bowtie2-align-s", "bowtie2-build", "bowtie2-build-l", "bowtie2-build-s", - "bowtie2-inspect", "bowtie2-inspect-l", "bowtie2-inspect-s"], 'bin'), - "doc", "example", "scripts", "MANUAL", "MANUAL.markdown", "NEWS"] - -sanity_check_paths = { - 'files': ["bin/bowtie2-align-l", "bin/bowtie2-build", "bin/bowtie2-inspect"], - 'dirs': [], -} - # to add script folder to path just uncomment this line # modextrapaths = {'PATH': 'scripts'} diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.6-intel-2015b.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.6-intel-2015b.eb index 9167bcb56a..5c6e44e1e9 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.6-intel-2015b.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.6-intel-2015b.eb @@ -5,8 +5,6 @@ # Modified by: Robert Schmidt # Ottawa Hospital Research Institute - Bioinformatics Team -easyblock = 'MakeCp' - name = 'Bowtie2' version = '2.2.6' @@ -18,20 +16,11 @@ description = """ Bowtie 2 is an ultrafast and memory-efficient tool for alignin its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.""" toolchain = {'name': 'intel', 'version': '2015b'} +toolchainopts = {'pic': True} sources = ['%(namelower)s-%(version)s-source.zip'] source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')] -files_to_copy = [ - (["bowtie2", "bowtie2-align-l", "bowtie2-align-s", "bowtie2-build", "bowtie2-build-l", "bowtie2-build-s", - "bowtie2-inspect", "bowtie2-inspect-l", "bowtie2-inspect-s"], 'bin'), - "doc", "example", "scripts", "MANUAL", "MANUAL.markdown", "NEWS"] - -sanity_check_paths = { - 'files': ["bin/bowtie2-align-l", "bin/bowtie2-build", "bin/bowtie2-inspect"], - 'dirs': [], -} - # to add script folder to path just uncomment this line # modextrapaths = {'PATH': 'scripts'} diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.7-foss-2015b.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.7-foss-2015b.eb index 063d865aaf..7cd080fdb1 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.7-foss-2015b.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.7-foss-2015b.eb @@ -7,8 +7,6 @@ # Modified by: Adam Huffman # The Francis Crick Institute -easyblock = 'MakeCp' - name = 'Bowtie2' version = '2.2.7' @@ -20,20 +18,11 @@ description = """ Bowtie 2 is an ultrafast and memory-efficient tool for alignin its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.""" toolchain = {'name': 'foss', 'version': '2015b'} +toolchainopts = {'pic': True} sources = ['%(namelower)s-%(version)s-source.zip'] source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')] -files_to_copy = [ - (["bowtie2", "bowtie2-align-l", "bowtie2-align-s", "bowtie2-build", "bowtie2-build-l", "bowtie2-build-s", - "bowtie2-inspect", "bowtie2-inspect-l", "bowtie2-inspect-s"], 'bin'), - "doc", "example", "scripts", "MANUAL", "MANUAL.markdown", "NEWS"] - -sanity_check_paths = { - 'files': ["bin/bowtie2-align-l", "bin/bowtie2-build", "bin/bowtie2-inspect"], - 'dirs': [], -} - # to add script folder to path just uncomment this line # modextrapaths = {'PATH': 'scripts'} diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.8-foss-2015b.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.8-foss-2015b.eb index 7309705748..e6c1bebf90 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.8-foss-2015b.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.8-foss-2015b.eb @@ -7,8 +7,6 @@ # Modified by: Adam Huffman # The Francis Crick Institute -easyblock = 'MakeCp' - name = 'Bowtie2' version = '2.2.8' @@ -20,20 +18,11 @@ description = """ Bowtie 2 is an ultrafast and memory-efficient tool for alignin its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.""" toolchain = {'name': 'foss', 'version': '2015b'} +toolchainopts = {'pic': True} sources = ['%(namelower)s-%(version)s-source.zip'] source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')] -files_to_copy = [ - (["bowtie2", "bowtie2-align-l", "bowtie2-align-s", "bowtie2-build", "bowtie2-build-l", "bowtie2-build-s", - "bowtie2-inspect", "bowtie2-inspect-l", "bowtie2-inspect-s"], 'bin'), - "doc", "example", "scripts", "MANUAL", "MANUAL.markdown", "NEWS"] - -sanity_check_paths = { - 'files': ["bin/bowtie2-align-l", "bin/bowtie2-build", "bin/bowtie2-inspect"], - 'dirs': [], -} - # to add script folder to path just uncomment this line # modextrapaths = {'PATH': 'scripts'} diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.8-foss-2016a.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.8-foss-2016a.eb index 4a280ff234..4982ab4d19 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.8-foss-2016a.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.8-foss-2016a.eb @@ -7,8 +7,6 @@ # Modified by: Adam Huffman # The Francis Crick Institute -easyblock = 'MakeCp' - name = 'Bowtie2' version = '2.2.8' @@ -20,20 +18,11 @@ description = """ Bowtie 2 is an ultrafast and memory-efficient tool for alignin its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.""" toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'pic': True} sources = ['%(namelower)s-%(version)s-source.zip'] source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')] -files_to_copy = [ - (["bowtie2", "bowtie2-align-l", "bowtie2-align-s", "bowtie2-build", "bowtie2-build-l", "bowtie2-build-s", - "bowtie2-inspect", "bowtie2-inspect-l", "bowtie2-inspect-s"], 'bin'), - "doc", "example", "scripts", "MANUAL", "MANUAL.markdown", "NEWS"] - -sanity_check_paths = { - 'files': ["bin/bowtie2-align-l", "bin/bowtie2-build", "bin/bowtie2-inspect"], - 'dirs': [], -} - # to add script folder to path just uncomment this line # modextrapaths = {'PATH': 'scripts'} diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9-foss-2016a.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9-foss-2016a.eb index 7f469a05ee..cf2e82b71c 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9-foss-2016a.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9-foss-2016a.eb @@ -7,8 +7,6 @@ # Modified by: Adam Huffman # The Francis Crick Institute -easyblock = 'MakeCp' - name = 'Bowtie2' version = '2.2.9' @@ -20,20 +18,11 @@ description = """ Bowtie 2 is an ultrafast and memory-efficient tool for alignin its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.""" toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'pic': True, 'cstd': 'c++11'} sources = ['%(namelower)s-%(version)s-source.zip'] source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')] -files_to_copy = [ - (["bowtie2", "bowtie2-align-l", "bowtie2-align-s", "bowtie2-build", "bowtie2-build-l", "bowtie2-build-s", - "bowtie2-inspect", "bowtie2-inspect-l", "bowtie2-inspect-s"], 'bin'), - "doc", "example", "scripts", "MANUAL", "MANUAL.markdown", "NEWS"] - -sanity_check_paths = { - 'files': ["bin/bowtie2-align-l", "bin/bowtie2-build", "bin/bowtie2-inspect"], - 'dirs': [], -} - # to add script folder to path just uncomment this line # modextrapaths = {'PATH': 'scripts'} diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9-goolf-1.7.20.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9-goolf-1.7.20.eb index c03250720b..637e625710 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9-goolf-1.7.20.eb @@ -7,8 +7,6 @@ # Modified by: Adam Huffman # The Francis Crick Institute -easyblock = 'MakeCp' - name = 'Bowtie2' version = "2.2.9" @@ -20,20 +18,11 @@ description = """ Bowtie 2 is an ultrafast and memory-efficient tool for alignin its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.""" toolchain = {'name': 'goolf', 'version': '1.7.20'} +toolchainopts = {'pic': True, 'cstd': 'c++11'} sources = ['%(namelower)s-%(version)s-source.zip'] source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')] -files_to_copy = [ - (["bowtie2", "bowtie2-align-l", "bowtie2-align-s", "bowtie2-build", "bowtie2-build-l", "bowtie2-build-s", - "bowtie2-inspect", "bowtie2-inspect-l", "bowtie2-inspect-s"], 'bin'), - "doc", "example", "scripts", "MANUAL", "MANUAL.markdown", "NEWS"] - -sanity_check_paths = { - 'files': ["bin/bowtie2-align-l", "bin/bowtie2-build", "bin/bowtie2-inspect"], - 'dirs': [], -} - # to add script folder to path just uncomment this line # modextrapaths = {'PATH': 'scripts'} diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9-intel-2016b.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9-intel-2016b.eb index fa3d31dfa4..826bc88a15 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9-intel-2016b.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9-intel-2016b.eb @@ -6,10 +6,7 @@ # Ottawa Hospital Research Institute - Bioinformatics Team # Modified by: Adam Huffman # The Francis Crick Institute -# Modified by: Kurt Lust, UAntwerp: Overwrite compiler options used in the GNU-based -# Makefile with the preferred options for intel compilers. - -easyblock = 'MakeCp' +# Modified by: Kurt Lust, UAntwerp name = 'Bowtie2' version = '2.2.9' @@ -22,26 +19,11 @@ description = """ Bowtie 2 is an ultrafast and memory-efficient tool for alignin its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.""" toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'pic': True, 'cstd': 'c++11'} sources = ['%(namelower)s-%(version)s-source.zip'] source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')] -toolchainopts = {'cstd': 'c++11'} - -# Make sure that the Makefile uses options for intel rather than the ones for gcc coded -# in the Makefile by setting RELEASE_FLAGS. -buildopts = 'RELEASE_FLAGS="$CXXFLAGS"' - -files_to_copy = [ - (["bowtie2", "bowtie2-align-l", "bowtie2-align-s", "bowtie2-build", "bowtie2-build-l", "bowtie2-build-s", - "bowtie2-inspect", "bowtie2-inspect-l", "bowtie2-inspect-s"], 'bin'), - "LICENSE", "doc", "example", "scripts", "MANUAL", "MANUAL.markdown", "NEWS"] - -sanity_check_paths = { - 'files': ["bin/bowtie2-align-l", "bin/bowtie2-build", "bin/bowtie2-inspect"], - 'dirs': [], -} - # to add script folder to path just uncomment this line #modextrapaths = {'PATH': 'scripts'} -- GitLab From e5d137194f7e4d46ed8578d0a0a25f4c2c4be089 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 21 Mar 2017 14:25:53 +0100 Subject: [PATCH 0430/1603] adding easyconfigs: JasPer-2.0.12-intel-2017a.eb --- .../j/JasPer/JasPer-2.0.12-intel-2017a.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/j/JasPer/JasPer-2.0.12-intel-2017a.eb diff --git a/easybuild/easyconfigs/j/JasPer/JasPer-2.0.12-intel-2017a.eb b/easybuild/easyconfigs/j/JasPer/JasPer-2.0.12-intel-2017a.eb new file mode 100644 index 0000000000..668f15ccad --- /dev/null +++ b/easybuild/easyconfigs/j/JasPer/JasPer-2.0.12-intel-2017a.eb @@ -0,0 +1,25 @@ +easyblock = 'CMakeMake' + +name = 'JasPer' +version = '2.0.12' + +homepage = 'http://www.ece.uvic.ca/~frodo/jasper/' +description = """The JasPer Project is an open-source initiative to provide a free + software-based reference implementation of the codec specified in the JPEG-2000 Part-1 standard.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.ece.uvic.ca/~frodo/jasper/software/'] + +builddependencies = [('CMake', '3.7.2')] + +separate_build_dir = True + +sanity_check_paths = { + 'files': ['bin/jasper', 'lib64/libjasper.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'vis' -- GitLab From 721d136ab9753a345adfd377e5f391fbd0e97833 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 21 Mar 2017 14:40:34 +0100 Subject: [PATCH 0431/1603] adding easyconfigs: HDF5-1.10.0-patch1-intel-2017a.eb, Szip-2.1-intel-2017a.eb --- .../h/HDF5/HDF5-1.10.0-patch1-intel-2017a.eb | 22 ++++++++++++++++++ .../s/Szip/Szip-2.1-intel-2017a.eb | 23 +++++++++++++++++++ 2 files changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.10.0-patch1-intel-2017a.eb create mode 100644 easybuild/easyconfigs/s/Szip/Szip-2.1-intel-2017a.eb diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.10.0-patch1-intel-2017a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.0-patch1-intel-2017a.eb new file mode 100644 index 0000000000..bc132a2144 --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.0-patch1-intel-2017a.eb @@ -0,0 +1,22 @@ +name = 'HDF5' +version = '1.10.0-patch1' + +homepage = 'http://www.hdfgroup.org/HDF5/' +description = """HDF5 is a unique technology suite that makes possible the management of + extremely large and complex data collections.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['9180ff0ef8dc2ef3f61bd37a7404f295'] + +buildopts = 'CXXFLAGS="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK"' + +dependencies = [ + ('zlib', '1.2.11'), + ('Szip', '2.1'), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1-intel-2017a.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1-intel-2017a.eb new file mode 100644 index 0000000000..7a02acddee --- /dev/null +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1-intel-2017a.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'Szip' +version = '2.1' + +homepage = 'http://www.hdfgroup.org/doc_resource/SZIP/' +description = "Szip compression software, providing lossless compression of scientific data" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = "--with-pic" + +sanity_check_paths = { + 'files': ["lib/libsz.a", "lib/libsz.%s" % SHLIB_EXT] + + ["include/%s" % x for x in ["ricehdf.h", "szip_adpt.h", "szlib.h"]], + 'dirs': [], +} + +moduleclass = 'tools' -- GitLab From b5f873be346781802822e6f839239e35ebb22dff Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 21 Mar 2017 14:49:54 +0100 Subject: [PATCH 0432/1603] adding easyconfigs: netCDF-4.4.1.1-intel-2017a.eb, netCDF-Fortran-4.4.4-intel-2017a.eb, cURL-7.53.1-GCCcore-6.3.0.eb, Doxygen-1.8.13-GCCcore-6.3.0.eb --- .../c/cURL/cURL-7.53.1-GCCcore-6.3.0.eb | 34 +++++++++++++++++++ .../d/Doxygen/Doxygen-1.8.13-GCCcore-6.3.0.eb | 23 +++++++++++++ .../netCDF-Fortran-4.4.4-intel-2017a.eb | 17 ++++++++++ .../n/netCDF/netCDF-4.4.1.1-intel-2017a.eb | 34 +++++++++++++++++++ 4 files changed, 108 insertions(+) create mode 100644 easybuild/easyconfigs/c/cURL/cURL-7.53.1-GCCcore-6.3.0.eb create mode 100644 easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.13-GCCcore-6.3.0.eb create mode 100644 easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.4-intel-2017a.eb create mode 100644 easybuild/easyconfigs/n/netCDF/netCDF-4.4.1.1-intel-2017a.eb diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.53.1-GCCcore-6.3.0.eb b/easybuild/easyconfigs/c/cURL/cURL-7.53.1-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..09811fccde --- /dev/null +++ b/easybuild/easyconfigs/c/cURL/cURL-7.53.1-GCCcore-6.3.0.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'cURL' +version = '7.53.1' + +homepage = 'http://curl.haxx.se' +description = """libcurl is a free and easy-to-use client-side URL transfer library, + supporting DICT, FILE, FTP, FTPS, Gopher, HTTP, HTTPS, IMAP, IMAPS, LDAP, LDAPS, + POP3, POP3S, RTMP, RTSP, SCP, SFTP, SMTP, SMTPS, Telnet and TFTP. libcurl supports + SSL certificates, HTTP POST, HTTP PUT, FTP uploading, HTTP form based upload, + proxies, cookies, user+password authentication (Basic, Digest, NTLM, Negotiate, + Kerberos), file transfer resume, http proxy tunneling and more.""" + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://curl.haxx.se/download/'] + +# use same binutils version that was used when building GCC toolchain +builddependencies = [('binutils', '2.27', '', True)] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# dependencies = [('OpenSSL', '1.1.0e')] +# configopts = "--with-ssl=$EBROOTOPENSSL" + +modextravars = {'CURL_INCLUDES': '%(installdir)s/include'} + +sanity_check_paths = { + 'files': ['bin/curl', 'lib/libcurl.a', 'lib/libcurl.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.13-GCCcore-6.3.0.eb b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.13-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..00e9535d4b --- /dev/null +++ b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.13-GCCcore-6.3.0.eb @@ -0,0 +1,23 @@ +name = 'Doxygen' +version = '1.8.13' + +homepage = 'http://www.doxygen.org' +description = """Doxygen is a documentation system for C++, C, Java, Objective-C, Python, + IDL (Corba and Microsoft flavors), Fortran, VHDL, PHP, C#, and to some extent D.""" + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} + +sources = ['%(namelower)s-%(version)s.src.tar.gz'] +source_urls = ['http://ftp.stack.nl/pub/users/dimitri/'] + +builddependencies = [ + # use same binutils version that was used when building GCC toolchain + ('binutils', '2.27', '', True), + ('CMake', '3.7.2'), + ('flex', '2.6.3'), + ('Bison', '3.0.4'), +] + +parallel = 1 + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.4-intel-2017a.eb b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.4-intel-2017a.eb new file mode 100644 index 0000000000..fa3d6fe963 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.4-intel-2017a.eb @@ -0,0 +1,17 @@ +name = 'netCDF-Fortran' +version = '4.4.4' + +homepage = 'http://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/Unidata/netcdf-fortran/archive/'] +sources = ['v%(version)s.tar.gz'] + +dependencies = [('netCDF', '4.4.1.1')] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.4.1.1-intel-2017a.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.4.1.1-intel-2017a.eb new file mode 100644 index 0000000000..d30a65ec63 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.4.1.1-intel-2017a.eb @@ -0,0 +1,34 @@ +name = 'netCDF' +version = '4.4.1.1' + +homepage = 'http://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True, 'usempi': True} + +sources = ['v%(version)s.tar.gz'] +source_urls = [ + 'https://github.com/Unidata/netcdf-c/archive/' +] + +dependencies = [ + ('HDF5', '1.10.0-patch1'), + ('cURL', '7.53.1'), + ('Szip', '2.1'), +] + +builddependencies = [ + ('CMake', '3.7.2'), + ('Doxygen', '1.8.13'), +] + +# make sure both static and shared libs are built +configopts = [ + "-DBUILD_SHARED_LIBS=OFF ", + "-DBUILD_SHARED_LIBS=ON ", +] + +moduleclass = 'data' -- GitLab From 5762444b72a33f59fe9ba453c4d5eca6ffb80f25 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 21 Mar 2017 16:31:10 +0100 Subject: [PATCH 0433/1603] collapse checksums to a single line to make @wpoely86 happy --- easybuild/easyconfigs/l/libunwind/libunwind-1.1-GCC-4.9.2.eb | 4 +--- easybuild/easyconfigs/l/libunwind/libunwind-1.1-foss-2015a.eb | 4 +--- easybuild/easyconfigs/l/libunwind/libunwind-1.1-foss-2016a.eb | 4 +--- .../easyconfigs/l/libunwind/libunwind-1.1-goolf-1.4.10.eb | 4 +--- .../easyconfigs/l/libunwind/libunwind-1.1-ictce-5.3.0.eb | 4 +--- .../easyconfigs/l/libunwind/libunwind-1.1-intel-2016b.eb | 4 +--- 6 files changed, 6 insertions(+), 18 deletions(-) diff --git a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-GCC-4.9.2.eb b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-GCC-4.9.2.eb index 43105b8275..396cb5364f 100644 --- a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-GCC-4.9.2.eb @@ -15,9 +15,7 @@ toolchain = {'name': 'GCC', 'version': '4.9.2'} sources = [SOURCE_TAR_GZ] source_urls = [GNU_SAVANNAH_SOURCE] -checksums = [ - 'fb4ea2f6fbbe45bf032cd36e586883ce', # libunwind-1.1.tar.gz -] +checksums = ['fb4ea2f6fbbe45bf032cd36e586883ce'] dependencies = [ ('XZ', '5.2.2'), diff --git a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-foss-2015a.eb b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-foss-2015a.eb index fe52e32d1e..19a10c8362 100644 --- a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-foss-2015a.eb +++ b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-foss-2015a.eb @@ -15,9 +15,7 @@ toolchain = {'version': '2015a', 'name': 'foss'} sources = [SOURCE_TAR_GZ] source_urls = [GNU_SAVANNAH_SOURCE] -checksums = [ - 'fb4ea2f6fbbe45bf032cd36e586883ce', # libunwind-1.1.tar.gz -] +checksums = ['fb4ea2f6fbbe45bf032cd36e586883ce'] dependencies = [ ('XZ', '5.2.2'), diff --git a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-foss-2016a.eb b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-foss-2016a.eb index 24e009d090..9cbc7f2bbf 100644 --- a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-foss-2016a.eb @@ -15,9 +15,7 @@ toolchain = {'name': 'foss', 'version': '2016a'} sources = [SOURCE_TAR_GZ] source_urls = [GNU_SAVANNAH_SOURCE] -checksums = [ - 'fb4ea2f6fbbe45bf032cd36e586883ce', # libunwind-1.1.tar.gz -] +checksums = ['fb4ea2f6fbbe45bf032cd36e586883ce'] dependencies = [ ('XZ', '5.2.2'), diff --git a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-goolf-1.4.10.eb index daf551f8aa..97bdf43906 100644 --- a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-goolf-1.4.10.eb @@ -15,9 +15,7 @@ toolchain = {'version': '1.4.10', 'name': 'goolf'} sources = [SOURCE_TAR_GZ] source_urls = [GNU_SAVANNAH_SOURCE] -checksums = [ - 'fb4ea2f6fbbe45bf032cd36e586883ce', # libunwind-1.1.tar.gz -] +checksums = ['fb4ea2f6fbbe45bf032cd36e586883ce'] dependencies = [ ('XZ', '5.2.2'), diff --git a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-ictce-5.3.0.eb index aae5a5fed7..5b2faed557 100644 --- a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-ictce-5.3.0.eb @@ -15,9 +15,7 @@ toolchain = {'name': 'ictce', 'version': '5.3.0'} sources = [SOURCE_TAR_GZ] source_urls = [GNU_SAVANNAH_SOURCE] -checksums = [ - 'fb4ea2f6fbbe45bf032cd36e586883ce', # libunwind-1.1.tar.gz -] +checksums = ['fb4ea2f6fbbe45bf032cd36e586883ce'] dependencies = [ ('XZ', '5.2.2'), diff --git a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-intel-2016b.eb b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-intel-2016b.eb index e201bb7758..ba5d709769 100644 --- a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-intel-2016b.eb +++ b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-intel-2016b.eb @@ -15,9 +15,7 @@ toolchain = {'name': 'intel', 'version': '2016b'} sources = [SOURCE_TAR_GZ] source_urls = [GNU_SAVANNAH_SOURCE] -checksums = [ - 'fb4ea2f6fbbe45bf032cd36e586883ce', # libunwind-1.1.tar.gz -] +checksums = ['fb4ea2f6fbbe45bf032cd36e586883ce'] dependencies = [ ('XZ', '5.2.2'), -- GitLab From 1e610f306de5153e933712cb219a377d1dfe9947 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 21 Mar 2017 19:49:40 +0100 Subject: [PATCH 0434/1603] use 'use_fma4' rather than deprecated 'use_fma' easyconfig parameter in FFTW easyconfigs using intel toolchain --- easybuild/easyconfigs/f/FFTW/FFTW-3.3.5-intel-2016b.eb | 4 ++-- easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-intel-2017a.eb | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.5-intel-2016b.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.5-intel-2016b.eb index aba6939866..f931b781ea 100644 --- a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.5-intel-2016b.eb +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.5-intel-2016b.eb @@ -15,8 +15,8 @@ source_urls = [homepage] # see also http://www.fftw.org/doc/Extended-and-quadruple-precision-in-Fortran.html with_quad_prec = False -# compilation fails when configuring with --enable-avx-128-fma -use_fma = False +# compilation fails when configuring with --enable-avx-128-fma, Intel compilers do not support FMA4 instructions +use_fma4 = False runtest = 'check' diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-intel-2017a.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-intel-2017a.eb index 07c5fa9224..da857e5ca5 100644 --- a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-intel-2017a.eb +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-intel-2017a.eb @@ -21,8 +21,8 @@ patches = [ # http://www.fftw.org/doc/Extended-and-quadruple-precision-in-Fortran.html with_quad_prec = False -# compilation fails when configuring with --enable-avx-128-fma -use_fma = False +# compilation fails when configuring with --enable-avx-128-fma, Intel compilers do not support FMA4 instructions +use_fma4 = False runtest = 'check' -- GitLab From baae366171417e854889d108e8f266afeaec8e98 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 21 Mar 2017 22:26:58 +0100 Subject: [PATCH 0435/1603] adding easyconfigs: WRF-3.8.0-intel-2016b-dmpar.eb, tcsh-6.20.00-GCCcore-5.4.0.eb --- .../t/tcsh/tcsh-6.20.00-GCCcore-5.4.0.eb | 41 +++++++++++++++++++ .../w/WRF/WRF-3.8.0-intel-2016b-dmpar.eb | 39 ++++++++++++++++++ 2 files changed, 80 insertions(+) create mode 100644 easybuild/easyconfigs/t/tcsh/tcsh-6.20.00-GCCcore-5.4.0.eb create mode 100644 easybuild/easyconfigs/w/WRF/WRF-3.8.0-intel-2016b-dmpar.eb diff --git a/easybuild/easyconfigs/t/tcsh/tcsh-6.20.00-GCCcore-5.4.0.eb b/easybuild/easyconfigs/t/tcsh/tcsh-6.20.00-GCCcore-5.4.0.eb new file mode 100644 index 0000000000..1413bb1d34 --- /dev/null +++ b/easybuild/easyconfigs/t/tcsh/tcsh-6.20.00-GCCcore-5.4.0.eb @@ -0,0 +1,41 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg/Computer Science and Communications Research Unit +# Authors:: Valentin Plugaru +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_05-06.html +## +easyblock = 'ConfigureMake' + +name = 'tcsh' +version = '6.20.00' + +homepage = 'http://www.tcsh.org' +description = """Tcsh is an enhanced, but completely compatible version of the Berkeley UNIX C shell (csh). + It is a command language interpreter usable both as an interactive login shell and a shell script command + processor. It includes a command-line editor, programmable word completion, spelling correction, a history + mechanism, job control and a C-like syntax.""" + +toolchain = {'name': 'GCCcore', 'version': '5.4.0'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [ + 'ftp://ftp.astron.com/pub/%(namelower)s', + 'ftp://ftp.astron.com/pub/%(namelower)s/old', +] + +# use same binutils version that was used when building GCC toolchain +builddependencies = [('binutils', '2.26', '', True)] + +dependencies = [('ncurses', '6.0')] + +sanity_check_paths = { + 'files': ["bin/tcsh"], + 'dirs': [] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/w/WRF/WRF-3.8.0-intel-2016b-dmpar.eb b/easybuild/easyconfigs/w/WRF/WRF-3.8.0-intel-2016b-dmpar.eb new file mode 100644 index 0000000000..9f07b0effa --- /dev/null +++ b/easybuild/easyconfigs/w/WRF/WRF-3.8.0-intel-2016b-dmpar.eb @@ -0,0 +1,39 @@ +name = 'WRF' +version = '3.8.0' +buildtype = "dmpar" +versionsuffix = '-%s' % buildtype + +homepage = 'http://www.wrf-model.org' +description = """The Weather Research and Forecasting (WRF) Model is a next-generation mesoscale + numerical weather prediction system designed to serve both operational forecasting and atmospheric + research needs.""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'opt': False} # don't use agressive optimization, stick to -O2 + +sources = ['%(name)sV%(version_major_minor)s.TAR.gz'] +source_urls = [ + 'http://www2.mmm.ucar.edu/wrf/src/', + 'http://www.mmm.ucar.edu/wrf/src/', +] + +# csh is used by WRF install scripts +builddependencies = [('tcsh', '6.20.00')] + +dependencies = [ + ('JasPer', '2.0.10'), + ('netCDF', '4.4.1.1'), + ('netCDF-Fortran', '4.4.4'), +] + +patches = [ + 'WRF_parallel_build_fix.patch', + 'WRF_tests_limit-runtimes.patch', + 'WRF-%(version)s_netCDF-Fortran_separate_path.patch', + 'WRF-%(version)s_known_problems.patch', +] + +# limit parallel build to 20 +maxparallel = 20 + +moduleclass = 'geo' -- GitLab From b8c0b56d34346a63dbd7933630ad5ef2e8e68299 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 21 Mar 2017 22:39:04 +0100 Subject: [PATCH 0436/1603] fix netCDF version in dependencies --- easybuild/easyconfigs/w/WRF/WRF-3.8.0-intel-2016b-dmpar.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/w/WRF/WRF-3.8.0-intel-2016b-dmpar.eb b/easybuild/easyconfigs/w/WRF/WRF-3.8.0-intel-2016b-dmpar.eb index 9f07b0effa..09959e26a3 100644 --- a/easybuild/easyconfigs/w/WRF/WRF-3.8.0-intel-2016b-dmpar.eb +++ b/easybuild/easyconfigs/w/WRF/WRF-3.8.0-intel-2016b-dmpar.eb @@ -22,7 +22,7 @@ builddependencies = [('tcsh', '6.20.00')] dependencies = [ ('JasPer', '2.0.10'), - ('netCDF', '4.4.1.1'), + ('netCDF', '4.4.1'), ('netCDF-Fortran', '4.4.4'), ] -- GitLab From 800c673582b5a3203d6a073f4a2800e82199ee9e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 22 Mar 2017 20:04:21 +0100 Subject: [PATCH 0437/1603] adding easyconfigs: ACTC-1.1-intel-2016b.eb --- .../a/ACTC/ACTC-1.1-intel-2016b.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/a/ACTC/ACTC-1.1-intel-2016b.eb diff --git a/easybuild/easyconfigs/a/ACTC/ACTC-1.1-intel-2016b.eb b/easybuild/easyconfigs/a/ACTC/ACTC-1.1-intel-2016b.eb new file mode 100644 index 0000000000..88e0e00942 --- /dev/null +++ b/easybuild/easyconfigs/a/ACTC/ACTC-1.1-intel-2016b.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'ACTC' +version = '1.1' + +homepage = 'https://sourceforge.net/projects/actc' +description = "ACTC converts independent triangles into triangle strips or fans." + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +skipsteps = ['configure'] + +buildopts = 'CC="$CC" CFLAGS="$CFLAGS"' + +installopts = "INCDEST=%(installdir)s/include/ac/ LIBDEST=%(installdir)s/lib && " +installopts += "mv %(installdir)s/lib/tc.h %(installdir)s/include/ac/ && " +installopts += "mkdir %(installdir)s/bin && cp -a {tcsample,tctest,tctest2} %(installdir)s/bin && " +installopts += "cp -a {COPYRIGHT,manual.html,prims.gif,README} %(installdir)s/" + +sanity_check_paths = { + 'files': ['bin/tctest', 'bin/tctest2', 'bin/tcsample', 'include/ac/tc.h', 'lib/libactc.a', + 'COPYRIGHT', 'manual.html', 'prims.gif', 'README'], + 'dirs': [], +} + +moduleclass = 'lib' -- GitLab From 933287b2503f1828df80efc7277958dcf53f559f Mon Sep 17 00:00:00 2001 From: Maxime Boissonneault Date: Wed, 22 Mar 2017 19:21:18 +0000 Subject: [PATCH 0438/1603] renamed recipe to match convention --- ...2016a-download.eb => PETSc-3.7.5-intel-2016a-download_deps.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/p/PETSc/{PETSc-3.7.5-intel-2016a-download.eb => PETSc-3.7.5-intel-2016a-download_deps.eb} (100%) diff --git a/easybuild/easyconfigs/p/PETSc/PETSc-3.7.5-intel-2016a-download.eb b/easybuild/easyconfigs/p/PETSc/PETSc-3.7.5-intel-2016a-download_deps.eb similarity index 100% rename from easybuild/easyconfigs/p/PETSc/PETSc-3.7.5-intel-2016a-download.eb rename to easybuild/easyconfigs/p/PETSc/PETSc-3.7.5-intel-2016a-download_deps.eb -- GitLab From cb193298f3defbc6c268e7e7f2aa6f1f42156fdf Mon Sep 17 00:00:00 2001 From: Maxime Boissonneault Date: Wed, 22 Mar 2017 19:21:59 +0000 Subject: [PATCH 0439/1603] renamed recipe to match convention --- ...ownload_deps.eb => PETSc-3.7.5-intel-2016a-downloaded_deps.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/p/PETSc/{PETSc-3.7.5-intel-2016a-download_deps.eb => PETSc-3.7.5-intel-2016a-downloaded_deps.eb} (100%) diff --git a/easybuild/easyconfigs/p/PETSc/PETSc-3.7.5-intel-2016a-download_deps.eb b/easybuild/easyconfigs/p/PETSc/PETSc-3.7.5-intel-2016a-downloaded_deps.eb similarity index 100% rename from easybuild/easyconfigs/p/PETSc/PETSc-3.7.5-intel-2016a-download_deps.eb rename to easybuild/easyconfigs/p/PETSc/PETSc-3.7.5-intel-2016a-downloaded_deps.eb -- GitLab From d78a9a2c5fb56e58eb9c44aa60ad3365b503b0d7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 23 Mar 2017 10:26:12 +0100 Subject: [PATCH 0440/1603] adding easyconfigs: OpenMPI-2.1.0-GCC-6.3.0-2.28.eb, hwloc-1.11.6-GCC-6.3.0-2.28.eb, GCC-6.3.0-2.28.eb --- easybuild/easyconfigs/g/GCC/GCC-6.3.0-2.28.eb | 25 ++++++++++++++ .../h/hwloc/hwloc-1.11.6-GCC-6.3.0-2.28.eb | 23 +++++++++++++ .../o/OpenMPI/OpenMPI-2.1.0-GCC-6.3.0-2.28.eb | 34 +++++++++++++++++++ 3 files changed, 82 insertions(+) create mode 100644 easybuild/easyconfigs/g/GCC/GCC-6.3.0-2.28.eb create mode 100644 easybuild/easyconfigs/h/hwloc/hwloc-1.11.6-GCC-6.3.0-2.28.eb create mode 100644 easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.0-GCC-6.3.0-2.28.eb diff --git a/easybuild/easyconfigs/g/GCC/GCC-6.3.0-2.28.eb b/easybuild/easyconfigs/g/GCC/GCC-6.3.0-2.28.eb new file mode 100644 index 0000000000..bac0785b8c --- /dev/null +++ b/easybuild/easyconfigs/g/GCC/GCC-6.3.0-2.28.eb @@ -0,0 +1,25 @@ +easyblock = 'Bundle' + +name = 'GCC' +version = '6.3.0' + +binutilsver = '2.28' +versionsuffix = '-%s' % binutilsver + +homepage = 'http://gcc.gnu.org/' +description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, + as well as libraries for these languages (libstdc++, libgcj,...).""" + +toolchain = {'name': 'dummy', 'version': ''} + +dependencies = [ + ('GCCcore', version), + # binutils built on top of GCCcore, which was built on top of (dummy-built) binutils + ('binutils', binutilsver, '', ('GCCcore', version)), +] + +altroot = 'GCCcore' +altversion = 'GCCcore' + +# this bundle serves as a compiler-only toolchain, so it should be marked as compiler (important for HMNS) +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.6-GCC-6.3.0-2.28.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.6-GCC-6.3.0-2.28.eb new file mode 100644 index 0000000000..93ceada29d --- /dev/null +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.6-GCC-6.3.0-2.28.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'hwloc' +version = '1.11.6' + +homepage = 'http://www.open-mpi.org/projects/hwloc/' +description = """The Portable Hardware Locality (hwloc) software package provides a portable abstraction +(across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including +NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various +system attributes such as cache and memory information as well as the locality of I/O devices such as +network interfaces, InfiniBand HCAs or GPUs. It primarily aims at helping applications with gathering +information about modern computing hardware so as to exploit it accordingly and efficiently.""" + +toolchain = {'name': 'GCC', 'version': '6.3.0-2.28'} + +source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [('numactl', '2.0.11')] + +configopts = "--enable-libnuma=$EBROOTNUMACTL" + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.0-GCC-6.3.0-2.28.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.0-GCC-6.3.0-2.28.eb new file mode 100644 index 0000000000..f0864ac518 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.0-GCC-6.3.0-2.28.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'OpenMPI' +version = '2.1.0' + +homepage = 'http://www.open-mpi.org/' +description = """The Open MPI Project is an open source MPI-2 implementation.""" + +toolchain = {'name': 'GCC', 'version': '6.3.0-2.28'} + +source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] +sources = [SOURCELOWER_TAR_GZ] + +checksums = ['c058052b53d209c7521079e3d2da613b'] + +dependencies = [('hwloc', '1.11.6')] + +configopts = '--enable-shared --enable-mpi-thread-multiple --with-verbs ' +configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path +configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support +configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading + +# needed for --with-verbs +osdependencies = [('libibverbs-dev', 'libibverbs-devel')] + +libs = ["mpi_mpifh", "mpi", "ompitrace", "open-pal", "open-rte"] +sanity_check_paths = { + 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] + + ["include/%s.h" % x for x in ["mpi-ext", "mpif-config", "mpif", "mpi", "mpi_portable_platform"]], + 'dirs': [], +} + +moduleclass = 'mpi' -- GitLab From 3f38e052bc47c21c631e125a8bf556792bce9e0d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 23 Mar 2017 11:26:13 +0100 Subject: [PATCH 0441/1603] correctly update $CPATH in ACTC easyconfig --- easybuild/easyconfigs/a/ACTC/ACTC-1.1-intel-2016b.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/a/ACTC/ACTC-1.1-intel-2016b.eb b/easybuild/easyconfigs/a/ACTC/ACTC-1.1-intel-2016b.eb index 88e0e00942..c94517dc29 100644 --- a/easybuild/easyconfigs/a/ACTC/ACTC-1.1-intel-2016b.eb +++ b/easybuild/easyconfigs/a/ACTC/ACTC-1.1-intel-2016b.eb @@ -26,4 +26,6 @@ sanity_check_paths = { 'dirs': [], } +modextrapaths = {'CPATH': 'include/ac'} + moduleclass = 'lib' -- GitLab From 5d143002ba0dde7c4e197453c88c488e9c431ea8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 23 Mar 2017 11:49:15 +0100 Subject: [PATCH 0442/1603] adding easyconfigs: HISAT2-2.0.5-intel-2017a.eb, NGS-1.3.0-intel-2017a.eb, ncbi-vdb-2.8.2-intel-2017a.eb, file-5.30-intel-2017a.eb --- .../f/file/file-5.30-intel-2017a.eb | 25 ++++++++++++ .../h/HISAT2/HISAT2-2.0.5-intel-2017a.eb | 36 ++++++++++++++++++ .../n/NGS/NGS-1.3.0-intel-2017a.eb | 35 +++++++++++++++++ .../n/ncbi-vdb/ncbi-vdb-2.8.2-intel-2017a.eb | 38 +++++++++++++++++++ 4 files changed, 134 insertions(+) create mode 100644 easybuild/easyconfigs/f/file/file-5.30-intel-2017a.eb create mode 100644 easybuild/easyconfigs/h/HISAT2/HISAT2-2.0.5-intel-2017a.eb create mode 100644 easybuild/easyconfigs/n/NGS/NGS-1.3.0-intel-2017a.eb create mode 100644 easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-2.8.2-intel-2017a.eb diff --git a/easybuild/easyconfigs/f/file/file-5.30-intel-2017a.eb b/easybuild/easyconfigs/f/file/file-5.30-intel-2017a.eb new file mode 100644 index 0000000000..cab481c6f4 --- /dev/null +++ b/easybuild/easyconfigs/f/file/file-5.30-intel-2017a.eb @@ -0,0 +1,25 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +## + +easyblock = 'ConfigureMake' + +name = 'file' +version = '5.30' + +homepage = 'http://www.darwinsys.com/file/' +description = """The file command is 'a file type guesser', that is, a command-line tool + that tells you in words what kind of data a file contains.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['ftp://ftp.astron.com/pub/file/'] +sources = [SOURCE_TAR_GZ] + +sanity_check_paths = { + 'files': ['bin/file', 'include/magic.h', 'lib/libmagic.%s' % SHLIB_EXT], + 'dirs': ['share'] +} + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/h/HISAT2/HISAT2-2.0.5-intel-2017a.eb b/easybuild/easyconfigs/h/HISAT2/HISAT2-2.0.5-intel-2017a.eb new file mode 100644 index 0000000000..a0d6f2ef27 --- /dev/null +++ b/easybuild/easyconfigs/h/HISAT2/HISAT2-2.0.5-intel-2017a.eb @@ -0,0 +1,36 @@ +easyblock = 'MakeCp' + +name = 'HISAT2' +version = '2.0.5' + +homepage = 'https://ccb.jhu.edu/software/hisat2/index.shtml' +description = """HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads + (both DNA and RNA) against the general human population (as well as against a single reference genome).""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +sources = ['%(namelower)s-%(version)s-source.zip'] +source_urls = ['ftp://ftp.ccb.jhu.edu/pub/infphilo/%(namelower)s/downloads/'] + +patches = ['HISAT2-%(version)s_intel-fixes.patch'] + +checksums = ['b6d867e1f8463012d1de3d1472573906'] + +dependencies = [ + ('NGS', '1.3.0'), + ('ncbi-vdb', '2.8.2'), +] + +buildopts = 'CC="$CC" CPP="$CXX" RELEASE_FLAGS="$CFLAGS" ' +buildopts += "USE_SRA=1 NCBI_NGS_DIR=$EBROOTNGS NCBI_VDB_DIR=$EBROOTNCBIMINVDB" + +executables = ['hisat2', 'hisat2-align-l', 'hisat2-align-s', 'hisat2-build', 'hisat2-build-l', 'hisat2-build-s', + 'hisat2-inspect', 'hisat2-inspect-s', 'hisat2-inspect-l'] +files_to_copy = [(executables, 'bin')] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in executables], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/n/NGS/NGS-1.3.0-intel-2017a.eb b/easybuild/easyconfigs/n/NGS/NGS-1.3.0-intel-2017a.eb new file mode 100644 index 0000000000..8d0219a742 --- /dev/null +++ b/easybuild/easyconfigs/n/NGS/NGS-1.3.0-intel-2017a.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'NGS' +version = '1.3.0' + +homepage = 'https://github.com/ncbi/ngs' +description = """NGS is a new, domain-specific API for accessing reads, alignments and pileups produced from + Next Generation Sequencing.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['https://github.com/ncbi/ngs/archive/'] +sources = ['%(version)s.tar.gz'] + +dependencies = [('Java', '1.8.0_121', '', True)] + +# override default of using $HOME/ncbi-outdir +configopts = "--build-prefix=%(builddir)s/ncbi-outdir" + +buildopts = 'CC="$CC -c" CPP="$CXX" CP="$CXX -c" -C ngs-sdk && ' +buildopts += 'make CC="$CC -c" CPP="$CXX" CP="$CXX -c" -C ngs-java' + +installopts = "-C ngs-sdk && make install -C ngs-java" + +parallel = 1 + +sanity_check_paths = { + 'files': ['jar/ngs-java.jar', ('lib/libngs-sdk.%s' % SHLIB_EXT, 'lib64/libngs-sdk.%s' % SHLIB_EXT), + ('lib/libngs-adapt-c++.a', 'lib64/libngs-adapt-c++.a'), ('lib/libngs-c++.a', 'lib64/libngs-c++.a')], + 'dirs': ['include/ngs', 'share'], +} + +modextrapaths = {'CLASSPATH': 'jar/ngs-java.jar'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-2.8.2-intel-2017a.eb b/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-2.8.2-intel-2017a.eb new file mode 100644 index 0000000000..5bfe59a4db --- /dev/null +++ b/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-2.8.2-intel-2017a.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'ncbi-vdb' +version = '2.8.2' + +homepage = 'https://github.com/ncbi/ncbi-vdb' +description = """The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for + using data in the INSDC Sequence Read Archives.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['https://github.com/ncbi/ncbi-vdb/archive/'] +sources = ['%(version)s.tar.gz'] + +dependencies = [ + ('libxml2', '2.9.4'), + ('file', '5.30'), # provides libmagic + ('HDF5', '1.10.0-patch1'), + ('NGS', '1.3.0'), +] + +# override default of using $HOME/ncbi-outdir +configopts = "--build-prefix=%(builddir)s/ncbi-outdir " + +configopts += "--with-ngs-sdk-prefix=$EBROOTNGS --with-ngs-java-prefix=$EBROOTNGS " +configopts += "--with-hdf5-prefix=$EBROOTHDF5 --with-xml2-prefix=$EBROOTLIBXML2" + +parallel = 1 + +sanity_check_paths = { + 'files': ['include/ncbi-vdb/NGS.hpp', ('lib/libncbi-vdb.%s' % SHLIB_EXT, 'lib64/libncbi-vdb.%s' % SHLIB_EXT), + ('lib/libncbi-wvdb.%s' % SHLIB_EXT, 'lib64/libncbi-wvdb.%s' % SHLIB_EXT), + ('lib/libncbi-ngs-c++.a', 'lib64/libncbi-ngs-c++.a'), ('lib/libncbi-vdb.a', 'lib64/libncbi-vdb.a'), + ('lib/libncbi-wvdb.a', 'lib64/libncbi-wvdb.a')], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From 399938d27b6370d98c81312cd0c3699e76360be8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 23 Mar 2017 12:20:18 +0100 Subject: [PATCH 0443/1603] add missing patch file for HISAT2 --- .../h/HISAT2/HISAT2-2.0.5_intel-fixes.patch | 15 +++++++++++++++ 1 file changed, 15 insertions(+) create mode 100644 easybuild/easyconfigs/h/HISAT2/HISAT2-2.0.5_intel-fixes.patch diff --git a/easybuild/easyconfigs/h/HISAT2/HISAT2-2.0.5_intel-fixes.patch b/easybuild/easyconfigs/h/HISAT2/HISAT2-2.0.5_intel-fixes.patch new file mode 100644 index 0000000000..571fc956b3 --- /dev/null +++ b/easybuild/easyconfigs/h/HISAT2/HISAT2-2.0.5_intel-fixes.patch @@ -0,0 +1,15 @@ +fix Intel compiler error due to wrong cast to void*, should be int* +author: Kenneth Hoste (HPC-UGent) +--- hisat2-2.0.5/processor_support.h.orig 2017-03-23 11:39:02.647104669 +0100 ++++ hisat2-2.0.5/processor_support.h 2017-03-23 11:39:23.727376802 +0100 +@@ -44,8 +44,8 @@ + + try { + #if ( defined(USING_INTEL_COMPILER) || defined(USING_MSC_COMPILER) ) +- __cpuid((void *) ®s,0); // test if __cpuid() works, if not catch the exception +- __cpuid((void *) ®s,0x1); // POPCNT bit is bit 23 in ECX ++ __cpuid((int *) ®s,0); // test if __cpuid() works, if not catch the exception ++ __cpuid((int *) ®s,0x1); // POPCNT bit is bit 23 in ECX + #elif defined(USING_GCC_COMPILER) + __get_cpuid(0x1, ®s.EAX, ®s.EBX, ®s.ECX, ®s.EDX); + #else -- GitLab From 0caaed423383193b70eb9765c15c4d55ba479f66 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 23 Mar 2017 12:21:08 +0100 Subject: [PATCH 0444/1603] {bio}[intel/2017a] SAMtools 1.4 --- .../s/SAMtools/SAMtools-1.4-intel-2017a.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-intel-2017a.eb diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-intel-2017a.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-intel-2017a.eb new file mode 100644 index 0000000000..86a737bc61 --- /dev/null +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-intel-2017a.eb @@ -0,0 +1,37 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Robert Schmidt , Cedric Laczny , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# Modified by: Adam Huffman +# The Francis Crick Institute +# +# Modified for version 1.4 by: Kurt Lust, UAntwerpen +# +## +name = 'SAMtools' +version = '1.4' + +homepage = 'http://www.htslib.org/' +description = """SAM Tools provide various utilities for manipulating alignments in the SAM format, + including sorting, merging, indexing and generating alignments in a per-position format.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s'] +sources = [SOURCELOWER_TAR_BZ2] + +# The htslib component of SAMtools 1.4 uses zlib, bzip2 and lzma compression. +# The latter is currently provided by XZ. +dependencies = [ + ('ncurses', '6.0'), + ('zlib', '1.2.11'), + ('bzip2', '1.0.6'), + ('XZ', '5.2.3'), +] + +moduleclass = 'bio' -- GitLab From f9903bade05e9e83af1538b4ebe64a3916fc55cb Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 23 Mar 2017 12:21:29 +0100 Subject: [PATCH 0445/1603] also patch XZ 5.2.3 to include symbols required by rpm command --- easybuild/easyconfigs/x/XZ/XZ-5.2.3-GCCcore-6.3.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.3-GCCcore-6.3.0.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.3-GCCcore-6.3.0.eb index 0e517cfb0f..735c3cbe5b 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.3-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.3-GCCcore-6.3.0.eb @@ -11,6 +11,8 @@ toolchain = {'name': 'GCCcore', 'version': '6.3.0'} sources = [SOURCELOWER_TAR_BZ2] source_urls = ['http://tukaani.org/xz/'] +patches = ['XZ-5.2.2_compat-libs.patch'] + builddependencies = [ ('gettext', '0.19.8.1', '', True), # use same binutils version that was used when building GCCcore toolchain -- GitLab From 732a70a17a353521a2a9128c5acb8d766c06417c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 23 Mar 2017 13:43:23 +0100 Subject: [PATCH 0446/1603] use MakeCp for ACTC --- .../easyconfigs/a/ACTC/ACTC-1.1-intel-2016b.eb | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/a/ACTC/ACTC-1.1-intel-2016b.eb b/easybuild/easyconfigs/a/ACTC/ACTC-1.1-intel-2016b.eb index c94517dc29..47b6a5d46f 100644 --- a/easybuild/easyconfigs/a/ACTC/ACTC-1.1-intel-2016b.eb +++ b/easybuild/easyconfigs/a/ACTC/ACTC-1.1-intel-2016b.eb @@ -1,4 +1,4 @@ -easyblock = 'ConfigureMake' +easyblock = 'MakeCp' name = 'ACTC' version = '1.1' @@ -11,14 +11,14 @@ toolchain = {'name': 'intel', 'version': '2016b'} source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCELOWER_TAR_GZ] -skipsteps = ['configure'] - buildopts = 'CC="$CC" CFLAGS="$CFLAGS"' -installopts = "INCDEST=%(installdir)s/include/ac/ LIBDEST=%(installdir)s/lib && " -installopts += "mv %(installdir)s/lib/tc.h %(installdir)s/include/ac/ && " -installopts += "mkdir %(installdir)s/bin && cp -a {tcsample,tctest,tctest2} %(installdir)s/bin && " -installopts += "cp -a {COPYRIGHT,manual.html,prims.gif,README} %(installdir)s/" +files_to_copy = [ + (['tcsample', 'tctest', 'tctest2'], 'bin'), + (['tc.h'], 'include/ac'), + (['libactc.a'], 'lib'), + 'COPYRIGHT', 'manual.html', 'prims.gif', 'README', +] sanity_check_paths = { 'files': ['bin/tctest', 'bin/tctest2', 'bin/tcsample', 'include/ac/tc.h', 'lib/libactc.a', -- GitLab From 27497f51ac83dddbba0c8be081f7d94ebe9a26d1 Mon Sep 17 00:00:00 2001 From: Maxime Boissonneault Date: Thu, 23 Mar 2017 13:07:11 +0000 Subject: [PATCH 0447/1603] changed toolchain so that HDF5 1.8.18 is found by the bot --- ...oaded_deps.eb => PETSc-3.7.5-intel-2016b-downloaded_deps.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/p/PETSc/{PETSc-3.7.5-intel-2016a-downloaded_deps.eb => PETSc-3.7.5-intel-2016b-downloaded_deps.eb} (96%) diff --git a/easybuild/easyconfigs/p/PETSc/PETSc-3.7.5-intel-2016a-downloaded_deps.eb b/easybuild/easyconfigs/p/PETSc/PETSc-3.7.5-intel-2016b-downloaded_deps.eb similarity index 96% rename from easybuild/easyconfigs/p/PETSc/PETSc-3.7.5-intel-2016a-downloaded_deps.eb rename to easybuild/easyconfigs/p/PETSc/PETSc-3.7.5-intel-2016b-downloaded_deps.eb index 111a8d2edd..f864b6e767 100644 --- a/easybuild/easyconfigs/p/PETSc/PETSc-3.7.5-intel-2016a-downloaded_deps.eb +++ b/easybuild/easyconfigs/p/PETSc/PETSc-3.7.5-intel-2016b-downloaded_deps.eb @@ -6,7 +6,7 @@ homepage = 'http://www.mcs.anl.gov/petsc' description = """PETSc, pronounced PET-see (the S is silent), is a suite of data structures and routines for the scalable (parallel) solution of scientific applications modeled by partial differential equations.""" -toolchain = {'name': 'intel', 'version': '2016a'} +toolchain = {'name': 'intel', 'version': '2016b'} toolchainopts = {'usempi': True, 'pic': True} source_urls = ['http://ftp.mcs.anl.gov/pub/petsc/release-snapshots'] -- GitLab From cd45943e036bb52b2bab419b4d529947949eb272 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 23 Mar 2017 14:30:07 +0100 Subject: [PATCH 0448/1603] {vis}[intel/2016b] VMD 1.9.3 --- .../v/VMD/VMD-1.9.3-intel-2016b.eb | 34 +++++ .../v/VMD/VMD-1.9.3_configure.patch | 116 ++++++++++++++++++ 2 files changed, 150 insertions(+) create mode 100644 easybuild/easyconfigs/v/VMD/VMD-1.9.3-intel-2016b.eb create mode 100644 easybuild/easyconfigs/v/VMD/VMD-1.9.3_configure.patch diff --git a/easybuild/easyconfigs/v/VMD/VMD-1.9.3-intel-2016b.eb b/easybuild/easyconfigs/v/VMD/VMD-1.9.3-intel-2016b.eb new file mode 100644 index 0000000000..2a5279436b --- /dev/null +++ b/easybuild/easyconfigs/v/VMD/VMD-1.9.3-intel-2016b.eb @@ -0,0 +1,34 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Authors:: Stephane Thiell +## +name = 'VMD' +version = '1.9.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.ks.uiuc.edu/Research/vmd' +description = """VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular + systems using 3-D graphics and built-in scripting.""" + +toolchain= {'name': 'intel' , 'version': '2016b'} + +# downloading requires registration +sources = [('%(namelower)s-%(version)s.src.tar.gz', "tar xfv %s")] + +patches = [ + 'VMD-%(version)s_configure.patch', +] + +dependencies = [ + ('Tcl', '8.6.5'), + ('Tk', '8.6.5'), + ('FLTK', '1.3.3'), + ('Python', '2.7.12'), + ('Mesa', '12.0.2'), + ('netCDF', '4.4.1.1'), + ('FFmpeg', '3.1.3'), + ('ImageMagick', '7.0.3-1'), + ('ACTC', '1.1'), +] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/v/VMD/VMD-1.9.3_configure.patch b/easybuild/easyconfigs/v/VMD/VMD-1.9.3_configure.patch new file mode 100644 index 0000000000..23f1311b5b --- /dev/null +++ b/easybuild/easyconfigs/v/VMD/VMD-1.9.3_configure.patch @@ -0,0 +1,116 @@ +fix hardcoded stuff in VMD configure script +authors: Stephane Thiell (Stanford University), Kenneth Hoste (HPC-UGent) +--- vmd-1.9.3/configure.orig 2016-12-01 08:11:33.000000000 +0100 ++++ vmd-1.9.3/configure 2017-03-23 13:36:41.501910996 +0100 +@@ -466,7 +476,7 @@ + + $arch_cc = "cc"; + $arch_ccpp = "CC"; +-$arch_nvcc = "/usr/local/cuda-8.0/bin/nvcc"; ++$arch_nvcc = "nvcc"; + $arch_nvccflags = "--ptxas-options=-v " . + "-gencode arch=compute_30,code=compute_30 " . + "-gencode arch=compute_30,code=sm_35 " . +@@ -581,17 +591,17 @@ + # location of Mesa library and include files; basically does the same + # as OpenGL. This is based on the default instructions from the Mesa + # README; the include files should by default be in /usr/local/include/GL. +-$mesa_dir = "$vmd_library_dir/Mesa"; ++$mesa_dir = $ENV{'EBROOTMESA'}; + $mesa_include = "-I$mesa_dir/include"; + $mesa_library = "-L$mesa_dir/lib_$config_arch"; + #$mesa_libs = "-lMesaGL -lMesaGLU"; +-$mesa_libs = "-lMesaGL"; ++$mesa_libs = "-lGL -lGLU"; + $mesa_defines = "-DUSELINEAXES -DVMDMESA -DVMDOPENGL"; + @mesa_cc = (); + @mesa_cu = (); +-@mesa_ccpp = @opengl_ccpp; +-@mesa_h = @opengl_h; +-@mesa_extra = @opengl_extra; ++@mesa_ccpp = (); ++@mesa_h = (); ++@mesa_extra = (); + + + # +@@ -666,10 +676,10 @@ + + ################ FLTK GUI + $fltk_defines = "-DVMDGUI -DVMDFLTK"; +-$fltk_dir = "$vmd_library_dir/fltk"; ++$fltk_dir = $ENV{'EBROOTFLTK'}; + $fltk_include = "-I$fltk_dir/include"; + $fltk_library = "-L$fltk_dir/$config_arch"; +-$fltk_libs = "-lfltk -lX11"; ++$fltk_libs = "-lfltk -lX11 -lXfixes -lXcursor -lXinerama"; + #@fltk_cc = ('forms_ui.c'); + @fltk_cu = (); + @fltk_ccpp = ( 'ColorFltkMenu.C', +@@ -729,8 +739,8 @@ + if ($config_tk) { $tcl_include .= " -I$stock_tk_include_dir"; } + $tcl_library = "-L$stock_tcl_library_dir"; + if ($config_tk) { $tcl_library .= " -L$stock_tk_library_dir"; } +-$tcl_libs = "-ltcl8.5"; +-if ($config_tk) { $tcl_libs = "-ltk8.5 -lX11 " . $tcl_libs; } ++$tcl_libs = "-ltcl8.6"; ++if ($config_tk) { $tcl_libs = "-ltk8.6 -lX11 " . $tcl_libs; } + + @tcl_cc = (); + @tcl_cu = (); +@@ -922,7 +932,7 @@ + # This option enables the use of CUDA GPU acceleration functions. + ####################### + $cuda_defines = "-DVMDCUDA -DMSMPOT_CUDA"; +-$cuda_dir = "/usr/local/cuda-8.0"; ++$cuda_dir = "$CUDA_HOME"; + $cuda_include = ""; + $cuda_library = ""; + $cuda_libs = "-Wl,-rpath -Wl,\$\$ORIGIN/ -lcudart_static"; +@@ -1042,7 +1052,7 @@ + # $liboptix_dir = "/usr/local/encap/NVIDIA-OptiX-SDK-3.6.3-linux64"; + # $liboptix_dir = "/usr/local/encap/NVIDIA-OptiX-SDK-3.8.0-linux64"; + # $liboptix_dir = "/usr/local/encap/NVIDIA-OptiX-SDK-3.9.0-linux64"; +-$liboptix_dir = "/usr/local/encap/NVIDIA-OptiX-SDK-4.0.1-linux64"; ++$liboptix_dir = "$ENV{'EBROOTOPTIX'}"; + # NCSA Blue Waters + # $liboptix_dir = "/u/sciteam/stonej/local/NVIDIA-OptiX-SDK-3.6.3-linux64"; + # $liboptix_dir = "/u/sciteam/stonej/local/NVIDIA-OptiX-SDK-3.8.0-linux64"; +@@ -1310,8 +1320,8 @@ + ####################### + $actc_defines = "-DVMDACTC"; + $actc_dir = "$vmd_library_dir/actc"; +-$actc_include = "-I$actc_dir/include"; +-$actc_library = "-L$actc_dir/lib_$config_arch"; ++$actc_include = "-I$actc_dir"; ++$actc_library = "-L$actc_dir"; + $actc_libs = "-lactc"; + @actc_cc = (); + @actc_cu = (); +@@ -1388,7 +1398,7 @@ + $python_defines = "-DVMDPYTHON"; + $python_include = "-I$stock_python_include_dir -I$stock_numpy_include_dir -I$stock_numpy_library_dir"; + $python_library = "-L$stock_python_library_dir"; +-$python_libs = "-lpython2.5 -lpthread"; ++$python_libs = "-lpython2.7 -lpthread"; + @python_h = ('PythonTextInterp.h', + 'VMDTkinterMenu.h', + 'py_commands.h', +@@ -2173,7 +2183,7 @@ + + if ($config_static) { + $arch_lopts = "-static"; +- $mesa_libs = "-lMesaGL -L/usr/X11R6/lib -lXext -lX11"; ++ $mesa_libs = "-lGL -lGLU -L/usr/X11R6/lib64 -lXext -lX11"; + } else { + $arch_lopts = ""; + # -rpath causes problems for people running Chromium.. +@@ -2303,7 +2313,7 @@ + # they likely serve no useful purpose going forward. + if (!$config_opengl_dispatch) { + $opengl_dep_libs = "-L/usr/X11R6/lib64 -lGL -lX11"; +- $mesa_libs = "-lMesaGL -L/usr/X11R6/lib64 -lXext -lX11"; ++ $mesa_libs = "-lGL -lGLU -L/usr/X11R6/lib64 -lXext -lX11"; + } + + # this is to make tcl happy -- GitLab From 84b686e27ad0f9e554a6cf078d652a77c11913b1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 23 Mar 2017 17:03:48 +0100 Subject: [PATCH 0449/1603] style fixes in PETSc easyconfig that downloads deps --- ...ETSc-3.7.5-intel-2016b-downloaded-deps.eb} | 31 ++++++------------- 1 file changed, 9 insertions(+), 22 deletions(-) rename easybuild/easyconfigs/p/PETSc/{PETSc-3.7.5-intel-2016b-downloaded_deps.eb => PETSc-3.7.5-intel-2016b-downloaded-deps.eb} (68%) diff --git a/easybuild/easyconfigs/p/PETSc/PETSc-3.7.5-intel-2016b-downloaded_deps.eb b/easybuild/easyconfigs/p/PETSc/PETSc-3.7.5-intel-2016b-downloaded-deps.eb similarity index 68% rename from easybuild/easyconfigs/p/PETSc/PETSc-3.7.5-intel-2016b-downloaded_deps.eb rename to easybuild/easyconfigs/p/PETSc/PETSc-3.7.5-intel-2016b-downloaded-deps.eb index f864b6e767..87e4b65750 100644 --- a/easybuild/easyconfigs/p/PETSc/PETSc-3.7.5-intel-2016b-downloaded_deps.eb +++ b/easybuild/easyconfigs/p/PETSc/PETSc-3.7.5-intel-2016b-downloaded-deps.eb @@ -1,6 +1,6 @@ name = 'PETSc' version = '3.7.5' -versionsuffix = '-downloaded_deps' +versionsuffix = '-downloaded-deps' homepage = 'http://www.mcs.anl.gov/petsc' description = """PETSc, pronounced PET-see (the S is silent), is a suite of data structures and routines for the @@ -12,32 +12,19 @@ toolchainopts = {'usempi': True, 'pic': True} source_urls = ['http://ftp.mcs.anl.gov/pub/petsc/release-snapshots'] sources = [SOURCELOWER_TAR_GZ] +# (build) dependencies provided through EasyBuild builddependencies = [('CMake', '3.5.2')] -shared_libs = 1 -pic = 1 - -downloadinstall = True - -# For these dependencies, we do not download them dependencies = [('HDF5','1.8.18')] -configopts = "" -configopts += "--with-mkl_pardiso=1 --with-mkl_pardiso-dir=$MKLROOT " -configopts += "--with-hdf5=1 --with-hdf5-dir=$EBROOTHDF5" # external packages that are downloaded with --download-=1 and --download--static=1 -download_deps_static = [ - 'hypre', - 'metis', - 'ml', - 'mumps', - 'parmetis', - 'prometheus', - 'ptscotch', - 'suitesparse', - 'superlu', - 'superlu_dist' -] +download_deps_static = ['hypre', 'metis', 'ml', 'mumps', 'parmetis', 'prometheus', 'ptscotch', 'suitesparse', + 'superlu', 'superlu_dist'] # triangle cannot be downloaded with --download-triangle-static because it fails download_deps = ['triangle'] +configopts = "--with-mkl_pardiso=1 --with-mkl_pardiso-dir=$MKLROOT " +configopts += "--with-hdf5=1 --with-hdf5-dir=$EBROOTHDF5" + +shared_libs = True + moduleclass = 'numlib' -- GitLab From bca436c37aa54ec9ae171066f4d480a701f664f1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 23 Mar 2017 17:41:36 +0100 Subject: [PATCH 0450/1603] add checksum for VMD 1.9.3 sources --- easybuild/easyconfigs/v/VMD/VMD-1.9.3-intel-2016b.eb | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/v/VMD/VMD-1.9.3-intel-2016b.eb b/easybuild/easyconfigs/v/VMD/VMD-1.9.3-intel-2016b.eb index 2a5279436b..3e3df4bec4 100644 --- a/easybuild/easyconfigs/v/VMD/VMD-1.9.3-intel-2016b.eb +++ b/easybuild/easyconfigs/v/VMD/VMD-1.9.3-intel-2016b.eb @@ -13,11 +13,11 @@ description = """VMD is a molecular visualization program for displaying, animat toolchain= {'name': 'intel' , 'version': '2016b'} # downloading requires registration -sources = [('%(namelower)s-%(version)s.src.tar.gz', "tar xfv %s")] +sources = ['vmd-%(version)s.src.tar.gz'] -patches = [ - 'VMD-%(version)s_configure.patch', -] +patches = ['VMD-%(version)s_configure.patch'] + +checksums = ['5706f88b9b77cc5fafda6fef3a82d6fa'] dependencies = [ ('Tcl', '8.6.5'), -- GitLab From 3d41143457e45e0b7c720954adf981364f9ab72a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 23 Mar 2017 18:44:18 +0100 Subject: [PATCH 0451/1603] fix easyconfig filename for VMD --- ....9.3-intel-2016b.eb => VMD-1.9.3-intel-2016b-Python-2.7.12.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/v/VMD/{VMD-1.9.3-intel-2016b.eb => VMD-1.9.3-intel-2016b-Python-2.7.12.eb} (100%) diff --git a/easybuild/easyconfigs/v/VMD/VMD-1.9.3-intel-2016b.eb b/easybuild/easyconfigs/v/VMD/VMD-1.9.3-intel-2016b-Python-2.7.12.eb similarity index 100% rename from easybuild/easyconfigs/v/VMD/VMD-1.9.3-intel-2016b.eb rename to easybuild/easyconfigs/v/VMD/VMD-1.9.3-intel-2016b-Python-2.7.12.eb -- GitLab From 3e03d88c9300b4a346ca39a28fbbad235b9e75f7 Mon Sep 17 00:00:00 2001 From: Daniel Navarro-Gomez Date: Fri, 24 Mar 2017 12:33:43 -0400 Subject: [PATCH 0452/1603] Added SAMtools-1.4-goolf-1.4.10.eb and ncurses-6.0-goolf-1.4.10.eb, the second one is a dependece of the first. By Daniel Navarro-Gomez, MEEI Bioinformatics Center new file: easyconfigs/n/ncurses/ncurses-6.0-goolf-1.4.10.eb new file: easyconfigs/s/SAMtools/SAMtools-1.4-goolf-1.4.10.eb --- .../n/ncurses/ncurses-6.0-goolf-1.4.10.eb | 38 ++++++++++++++++++ .../s/SAMtools/SAMtools-1.4-goolf-1.4.10.eb | 40 +++++++++++++++++++ 2 files changed, 78 insertions(+) create mode 100644 easybuild/easyconfigs/n/ncurses/ncurses-6.0-goolf-1.4.10.eb create mode 100644 easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.0-goolf-1.4.10.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-goolf-1.4.10.eb new file mode 100644 index 0000000000..6b10da13e5 --- /dev/null +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-goolf-1.4.10.eb @@ -0,0 +1,38 @@ +# Modified for goolf-1.4.10 by: Daniel Navarro-Gomez, MEEI Bioinformatics Center (MBC) + +easyblock = 'ConfigureMake' + +name = 'ncurses' +version = '6.0' + +homepage = 'http://www.gnu.org/software/ncurses/' +description = """The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, + and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and + function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} +toolchainopts = {'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] + +patches = ['ncurses-%(version)s_gcc-5.patch'] + +configopts = [ + # default build + '--with-shared --enable-overwrite', + # the UTF-8 enabled version (ncursesw) + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses%(version_major)s-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-goolf-1.4.10.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-goolf-1.4.10.eb new file mode 100644 index 0000000000..f620000661 --- /dev/null +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-goolf-1.4.10.eb @@ -0,0 +1,40 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Robert Schmidt , Cedric Laczny , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# Modified by: Adam Huffman +# The Francis Crick Institute +# +# Modified for version 1.4 by: Kurt Lust, UAntwerpen +# +# Modified for goolf-1.4.10 by: Daniel Navarro-Gomez, MEEI Bioinformatics Center (MBC) +# +## +name = 'SAMtools' +version = '1.4' + +homepage = 'http://www.htslib.org/' +description = """SAM Tools provide various utilities for manipulating alignments in the SAM format, + including sorting, merging, indexing and generating alignments in a per-position format.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s'] +sources = [SOURCELOWER_TAR_BZ2] + +# The htslib component of SAMtools 1.4 uses zlib, bzip2 and lzma compression. +# The latter is currently provided by XZ. +# +dependencies = [ + ('ncurses', '6.0'), + ('zlib', '1.2.7'), + ('bzip2', '1.0.6'), + ('XZ', '5.2.2'), +] + +moduleclass = 'bio' -- GitLab From 8f63e326929541c6c9f8911357c81019aea0bde8 Mon Sep 17 00:00:00 2001 From: Maxime Boissonneault Date: Fri, 24 Mar 2017 19:27:45 +0000 Subject: [PATCH 0453/1603] added recipe for repasthpc --- .../r/RepastHPC/RepastHPC-2.2.0-foss-2016a.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/r/RepastHPC/RepastHPC-2.2.0-foss-2016a.eb diff --git a/easybuild/easyconfigs/r/RepastHPC/RepastHPC-2.2.0-foss-2016a.eb b/easybuild/easyconfigs/r/RepastHPC/RepastHPC-2.2.0-foss-2016a.eb new file mode 100644 index 0000000000..d01d3cb5a2 --- /dev/null +++ b/easybuild/easyconfigs/r/RepastHPC/RepastHPC-2.2.0-foss-2016a.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'RepastHPC' +version = '2.2.0' + +homepage = 'https://repast.github.io/' +description = """The Repast Suite is a family of advanced, free, and open source agent-based modeling and simulation platforms that have collectively been under continuous development for over 15 years: +Repast for High Performance Computing 2.2.0, released on 30 September 2016, is a lean and expert-focused C++-based modeling system that is designed for use on large computing clusters and supercomputers.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'usempi': True} + +sources = ["repast_hpc-%s.tgz" % version] +source_urls = ['https://github.com/Repast/repast.hpc/releases/download/v%s' % version] + +dependencies = [ + ('netCDF-C++','4.2'), + ('Boost', '1.60.0'), +] + +configopts = '--with-boost=$EBROOTBOOST --with-netcdf=$EBROOTNETCDFMINCPLUSPLUS' + +sanity_check_paths = { + 'files': ['lib/librepast_hpc-%s.so' % version, 'lib/librelogo-%s.so' % version], + 'dirs': ['include','lib','bin/zombie', 'bin/rumor'], +} + +moduleclass = 'bio' -- GitLab From 933e11553203ffe64b2c29128734b3631ce6fe77 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Mon, 27 Mar 2017 12:00:12 +0800 Subject: [PATCH 0454/1603] adding easyconfigs: Wannier90-2.1.0-intel-2017a.eb --- .../Wannier90/Wannier90-2.1.0-intel-2017a.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/w/Wannier90/Wannier90-2.1.0-intel-2017a.eb diff --git a/easybuild/easyconfigs/w/Wannier90/Wannier90-2.1.0-intel-2017a.eb b/easybuild/easyconfigs/w/Wannier90/Wannier90-2.1.0-intel-2017a.eb new file mode 100644 index 0000000000..4945212393 --- /dev/null +++ b/easybuild/easyconfigs/w/Wannier90/Wannier90-2.1.0-intel-2017a.eb @@ -0,0 +1,29 @@ +easyblock = 'MakeCp' + +name = 'Wannier90' +version = '2.1.0' + +homepage = 'http://www.wannier.org' +description = """A tool for obtaining maximally-localised Wannier functions""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.wannier.org/code'] +checksums = ['07a81c002b41d6d0f97857e55c57d769'] + +prebuildopts = 'cp ./config/make.inc.ifort ./make.inc && ' + +buildopts = 'all F90=$F90 MPIF90=$MPIF90 FCOPTS="$FFLAGS" LDOPTS="$FFLAGS" ' +buildopts += 'LIBDIR="$LAPACK_LIB_DIR" LIBS="$LIBLAPACK" ' +buildopts += 'COMMS=mpi' + +files_to_copy = [(['wannier90.x', 'postw90.x'], 'bin'), (['libwannier.a'], 'lib')] + +sanity_check_paths = { + 'files': ['bin/wannier90.x', 'bin/postw90.x', 'lib/libwannier.a'], + 'dirs': [] +} + +moduleclass = 'chem' -- GitLab From 33de8679402f5de09a5ce0d7bcdb5bbddd34f302 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Mon, 27 Mar 2017 18:03:08 +0800 Subject: [PATCH 0455/1603] adding easyconfigs: DFTB+-1.3.1-intel-2017a.eb --- .../d/DFTB+/DFTB+-1.3.1-intel-2017a.eb | 47 +++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 easybuild/easyconfigs/d/DFTB+/DFTB+-1.3.1-intel-2017a.eb diff --git a/easybuild/easyconfigs/d/DFTB+/DFTB+-1.3.1-intel-2017a.eb b/easybuild/easyconfigs/d/DFTB+/DFTB+-1.3.1-intel-2017a.eb new file mode 100644 index 0000000000..35d80f5918 --- /dev/null +++ b/easybuild/easyconfigs/d/DFTB+/DFTB+-1.3.1-intel-2017a.eb @@ -0,0 +1,47 @@ +easyblock = 'MakeCp' + +name = 'DFTB+' +version = '1.3.1' + +homepage = 'https://www.dftb-plus.info' +description = """DFTB+ is a fast and efficient versatile quantum mechanical simulation package. It is based on the + Density Functional Tight Binding (DFTB) method, containing almost all of the useful extensions which have been + developed for the DFTB framework so far. Using DFTB+ you can carry out quantum mechanical simulations like with + ab-initio density functional theory based packages, but in an approximate way gaining typically around two order of + magnitude in speed.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['https://www.dftb-plus.info/download/dftb-13'] # requires registration +sources = [ + 'dftbplus-%(version)s-src.tar.xz', + 'dftbplus-%(version)s-extlib.tar.xz', + 'dftbplus-%(version)s-autotest.tar.xz', +] + +checksums = [ + 'b821ed7406a2a4b35c0a48974e18667f', # dftbplus-1.3.1-src.tar.xz + '2333f1ff826a3c4776e1e77a28f17004', # dftbplus-1.3.1-extlib.tar.xz + 'abaf8a2f94c74a13a0d8d19e9b022e40', # dftbplus-1.3.1-autotest.tar.xz +] + +dependencies = [ + ('arpack-ng', '3.4.0'), +] + +subdir = '%dftbplus-%(version)s' + +prebuildopts = "sed 's/ARCH = x86_64-linux-intel/ARCH = user/' Makefile.user.template > Makefile.user && " +prebuildopts += "cp sysmakes/make.x86_64-linux-intel sysmakes/make.user && " +prebuildopts += "sed -i 's|LNOPT = -static|#LNOPT = -static|' sysmakes/make.user && " +prebuildopts += "sed -i 's|/opt/intel/mkl/10.2.6.038/lib/em64t|$(MKLROOT)|' sysmakes/make.user && " +prebuildopts += "cd prg_dftb && " + +files_to_copy = [(['prg_dftb/_obj_user/dftb+'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/dftb+'], + 'dirs': [] +} + +moduleclass = 'phys' -- GitLab From 341613bcd83198517aa20bc7e728f356df2ad5f4 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Mon, 27 Mar 2017 18:09:07 +0800 Subject: [PATCH 0456/1603] adding easyconfigs: BerkeleyGW-1.2.0-intel-2017a.eb --- .../BerkeleyGW-1.2.0-intel-2017a.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.2.0-intel-2017a.eb diff --git a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.2.0-intel-2017a.eb b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.2.0-intel-2017a.eb new file mode 100644 index 0000000000..21a5da2750 --- /dev/null +++ b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.2.0-intel-2017a.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'BerkeleyGW' +version = "1.2.0" + +homepage = 'http://www.berkeleygw.org' +description = """The BerkeleyGW Package is a set of computer codes that calculates the quasiparticle + properties and the optical responses of a large variety of materials from bulk periodic crystals to + nanostructures such as slabs, wires and molecules.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'usempi': True} + +source_urls = ['http://www.berkeleygw.org/releases/'] # requires registration +sources = ['BGW-%(version)s.tar.gz'] +checksums = ['0bfcac62ebe486374b37d04a131453d7'] + +skipsteps = ['configure'] + +prebuildopts = 'cp config/generic.mpi.linux.mk arch.mk && ' + +buildopts = 'all-flavors COMPFLAG=-DINTEL PARAFLAG="-DMPI -DOMP" DEBUGFLAG="" F90free="$MPIF90 -free" LINK="$MPIF90" ' +buildopts += 'FOPTS="$FFLAGS -qopenmp" MOD_OPT="-module " C_PARAFLAG="$PARAFLAG" CC_COMP="$MPICXX" C_COMP="$MPICC" ' +buildopts += 'C_LINK="$MPICXX" C_OPTS="$CFLAGS -qopenmp" MKLPATH="$MKLROOT" LAPACKLIB="$LIBLAPACK" ' +buildopts += 'BLACSDIR="$BLACS_LIB_DIR" BLACS="$LIBBLACS" SCALAPACKLIB="$LIBSCALAPACK" ' +buildopts += 'FFTWINCLUDE="$FFTW_INC_DIR" FFTWLIB="$MKLROOT/lib/intel64/libfftw2xf_double_intel.a" ' + +# "all-flavors" cleans and compiles everything again +preinstallopts = 'sed -i "s/install: all-flavors/install: all/" Makefile && ' + +installopts = 'INSTDIR=%(installdir)s' + +sanity_check_paths = { + 'files': ['bin/' + prog + '.' + flavor + '.x' + for prog in ['epsilon', 'sigma', 'kernel', 'absorption', 'nonlinearoptics'] + for flavor in ['real', 'cplx']], + 'dirs': [] +} + +moduleclass = 'phys' -- GitLab From f9818b855274e1615306b3fde48bcbdbc3b27865 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Mon, 27 Mar 2017 23:45:22 +0800 Subject: [PATCH 0457/1603] simplify prebuildopts --- easybuild/easyconfigs/d/DFTB+/DFTB+-1.3.1-intel-2017a.eb | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/d/DFTB+/DFTB+-1.3.1-intel-2017a.eb b/easybuild/easyconfigs/d/DFTB+/DFTB+-1.3.1-intel-2017a.eb index 35d80f5918..15d96ddf6e 100644 --- a/easybuild/easyconfigs/d/DFTB+/DFTB+-1.3.1-intel-2017a.eb +++ b/easybuild/easyconfigs/d/DFTB+/DFTB+-1.3.1-intel-2017a.eb @@ -31,12 +31,11 @@ dependencies = [ subdir = '%dftbplus-%(version)s' -prebuildopts = "sed 's/ARCH = x86_64-linux-intel/ARCH = user/' Makefile.user.template > Makefile.user && " -prebuildopts += "cp sysmakes/make.x86_64-linux-intel sysmakes/make.user && " -prebuildopts += "sed -i 's|LNOPT = -static|#LNOPT = -static|' sysmakes/make.user && " -prebuildopts += "sed -i 's|/opt/intel/mkl/10.2.6.038/lib/em64t|$(MKLROOT)|' sysmakes/make.user && " +prebuildopts = "cp sysmakes/make.x86_64-linux-intel sysmakes/make.user && " prebuildopts += "cd prg_dftb && " +buildopts = "ARCH=user MKL_LIBDIR=$MKLROOT LNOPT= " + files_to_copy = [(['prg_dftb/_obj_user/dftb+'], 'bin')] sanity_check_paths = { -- GitLab From 92fd0795325dd52804826307a09bcc0fcd9cf979 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 27 Mar 2017 17:54:49 +0200 Subject: [PATCH 0458/1603] adding easyconfigs: ED2-20170201-intel-2017a.eb --- .../e/ED2/ED2-20170201-intel-2017a.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/e/ED2/ED2-20170201-intel-2017a.eb diff --git a/easybuild/easyconfigs/e/ED2/ED2-20170201-intel-2017a.eb b/easybuild/easyconfigs/e/ED2/ED2-20170201-intel-2017a.eb new file mode 100644 index 0000000000..e02aad07d9 --- /dev/null +++ b/easybuild/easyconfigs/e/ED2/ED2-20170201-intel-2017a.eb @@ -0,0 +1,37 @@ +easyblock = 'MakeCp' + +name = 'ED2' +version = '20170201' +commit = '0146fa4' + +homepage = 'https://github.com/EDmodel/ED2' +description = """The Ecosystem Demography Biosphere Model (ED2) is an integrated terrestrial biosphere model + incorporating hydrology, land-surface biophysics, vegetation dynamics, and soil carbon and nitrogen biogeochemistry""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/EDmodel/ED2/archive/'] +sources = ['%s.tar.gz' % commit] + +patches = ['ED2.patch'] + +dependencies = [('HDF5', '1.10.0-patch1')] + +start_dir = 'ED/build' + +# rely on install.sh to prepare everything, but run 'make' command ourselves to take control over compiler options +prebuildopts = "sed -i 's/^make OPT/#make OPT/g' install.sh && ./install.sh --kind E --platform intel --gitoff && " +prebuildopts += "cd bin-opt-E && " + +buildopts = "OPT=opt KIND_COMP=E GIT_TAG= HDF5_PATH=$EBROOTHDF5 PAR_LIBS='' " +buildopts += 'F_COMP="$FC" C_COMP="$CC" LOADER="$FC" F_OPTS="$FFLAGS" C_OPTS="$CFLAGS" F_LOWO_OPTS="$FFLAGS" && cd -' + +files_to_copy = [(['ED/build/ed_2.1-opt'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/ed_2.1-opt'], + 'dirs': [], +} + +moduleclass = 'geo' -- GitLab From 5ec6dcd34db0e99be4c4ba8a7cae4a12b533d4c4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 27 Mar 2017 18:18:56 +0200 Subject: [PATCH 0459/1603] add patches for ED2 --- .../e/ED2/ED2-20170201-intel-2017a.eb | 8 ++++--- .../easyconfigs/e/ED2/ED2_fix-type.patch | 13 ++++++++++ .../e/ED2/ED2_install-without-make.patch | 24 +++++++++++++++++++ 3 files changed, 42 insertions(+), 3 deletions(-) create mode 100644 easybuild/easyconfigs/e/ED2/ED2_fix-type.patch create mode 100644 easybuild/easyconfigs/e/ED2/ED2_install-without-make.patch diff --git a/easybuild/easyconfigs/e/ED2/ED2-20170201-intel-2017a.eb b/easybuild/easyconfigs/e/ED2/ED2-20170201-intel-2017a.eb index e02aad07d9..eed367500a 100644 --- a/easybuild/easyconfigs/e/ED2/ED2-20170201-intel-2017a.eb +++ b/easybuild/easyconfigs/e/ED2/ED2-20170201-intel-2017a.eb @@ -14,15 +14,17 @@ toolchainopts = {'usempi': True} source_urls = ['https://github.com/EDmodel/ED2/archive/'] sources = ['%s.tar.gz' % commit] -patches = ['ED2.patch'] +patches = [ + 'ED2_install-without-make.patch', + 'ED2_fix-type.patch', +] dependencies = [('HDF5', '1.10.0-patch1')] start_dir = 'ED/build' # rely on install.sh to prepare everything, but run 'make' command ourselves to take control over compiler options -prebuildopts = "sed -i 's/^make OPT/#make OPT/g' install.sh && ./install.sh --kind E --platform intel --gitoff && " -prebuildopts += "cd bin-opt-E && " +prebuildopts = "./install.sh --kind E --platform intel --gitoff && cd bin-opt-E && " buildopts = "OPT=opt KIND_COMP=E GIT_TAG= HDF5_PATH=$EBROOTHDF5 PAR_LIBS='' " buildopts += 'F_COMP="$FC" C_COMP="$CC" LOADER="$FC" F_OPTS="$FFLAGS" C_OPTS="$CFLAGS" F_LOWO_OPTS="$FFLAGS" && cd -' diff --git a/easybuild/easyconfigs/e/ED2/ED2_fix-type.patch b/easybuild/easyconfigs/e/ED2/ED2_fix-type.patch new file mode 100644 index 0000000000..4f73ca3487 --- /dev/null +++ b/easybuild/easyconfigs/e/ED2/ED2_fix-type.patch @@ -0,0 +1,13 @@ +fix type for argument to h5dget_type_f call +see https://github.com/EDmodel/ED2/issues/153 and https://github.com/crollinson/ED2/commit/48b9e8132b992460aa8afeca222fd4c12f01cfe4 +--- ED/src/utils/hdf5_utils.F90.orig 2017-02-01 22:00:01.000000000 +0100 ++++ ED/src/utils/hdf5_utils.F90 2017-03-27 11:56:38.579744327 +0200 +@@ -432,7 +432,7 @@ + character(len=2) :: ctype + + logical :: convert = .false. +- integer :: type_id ++ integer(HID_T) :: type_id + real(kind=8), allocatable, dimension(:) :: dvaraTEMP + + ! Find which data type will be read diff --git a/easybuild/easyconfigs/e/ED2/ED2_install-without-make.patch b/easybuild/easyconfigs/e/ED2/ED2_install-without-make.patch new file mode 100644 index 0000000000..601e93e788 --- /dev/null +++ b/easybuild/easyconfigs/e/ED2/ED2_install-without-make.patch @@ -0,0 +1,24 @@ +avoid install.sh calling 'make' (and hard set GIT_EXIST) +author: Kenneth Hoste (HPC-UGent) +--- ED/build/install.sh.orig 2017-03-27 12:00:10.321077952 +0200 ++++ ED/build/install.sh 2017-03-27 11:59:40.200888391 +0200 +@@ -94,8 +94,8 @@ + esac + + # Tag executables with a git version and branch name if possible. +-GIT_EXIST=`git rev-parse --is-inside-work-tree` +-if [ ${GIT_EXIST} == "true" -a ${USE_GIT} ] ++GIT_EXIST="" ++if [ "${GIT_EXIST}" == "true" -a ${USE_GIT} ] + then + GIT_TAG=`git branch -v | awk '/\*/ {print "-" $2 "-" $3}'` + GIT_TAG=`echo ${GIT_TAG} | tr -d '()/[]'` +@@ -122,7 +122,7 @@ + touch dependency.mk + + #----- Launch the compiler. ---------------------------------------------------------------# +-make OPT=${OPT} KIND_COMP=${KIND} ${CLEAN} GIT_TAG=${GIT_TAG} ++#make OPT=${OPT} KIND_COMP=${KIND} ${CLEAN} GIT_TAG=${GIT_TAG} + make_exit_code=$? + #------------------------------------------------------------------------------------------# + -- GitLab From 1af6f173acf17c4edddfd3ce10b770e71ddb0346 Mon Sep 17 00:00:00 2001 From: Maxime Boissonneault Date: Mon, 27 Mar 2017 19:22:16 +0000 Subject: [PATCH 0460/1603] cosmetic changes --- .../r/RepastHPC/RepastHPC-2.2.0-foss-2016a.eb | 16 +++++++++------- 1 file changed, 9 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/r/RepastHPC/RepastHPC-2.2.0-foss-2016a.eb b/easybuild/easyconfigs/r/RepastHPC/RepastHPC-2.2.0-foss-2016a.eb index d01d3cb5a2..d533ab1e52 100644 --- a/easybuild/easyconfigs/r/RepastHPC/RepastHPC-2.2.0-foss-2016a.eb +++ b/easybuild/easyconfigs/r/RepastHPC/RepastHPC-2.2.0-foss-2016a.eb @@ -4,25 +4,27 @@ name = 'RepastHPC' version = '2.2.0' homepage = 'https://repast.github.io/' -description = """The Repast Suite is a family of advanced, free, and open source agent-based modeling and simulation platforms that have collectively been under continuous development for over 15 years: -Repast for High Performance Computing 2.2.0, released on 30 September 2016, is a lean and expert-focused C++-based modeling system that is designed for use on large computing clusters and supercomputers.""" +description = """The Repast Suite is a family of advanced, free, and open source agent-based modeling and simulation +platforms that have collectively been under continuous development for over 15 years: +Repast for High Performance Computing 2.2.0, released on 30 September 2016, is a lean and expert-focused C++-based +modeling system that is designed for use on large computing clusters and supercomputers.""" toolchain = {'name': 'foss', 'version': '2016a'} toolchainopts = {'usempi': True} -sources = ["repast_hpc-%s.tgz" % version] -source_urls = ['https://github.com/Repast/repast.hpc/releases/download/v%s' % version] +sources = ["repast_hpc-%(version)s.tgz"] +source_urls = ['https://github.com/Repast/repast.hpc/releases/download/v%(version)s'] dependencies = [ - ('netCDF-C++','4.2'), + ('netCDF-C++', '4.2'), ('Boost', '1.60.0'), ] configopts = '--with-boost=$EBROOTBOOST --with-netcdf=$EBROOTNETCDFMINCPLUSPLUS' sanity_check_paths = { - 'files': ['lib/librepast_hpc-%s.so' % version, 'lib/librelogo-%s.so' % version], - 'dirs': ['include','lib','bin/zombie', 'bin/rumor'], + 'files': ['lib/librelogo-%(version)s.%s' % SHLIB_EXT, 'lib/librepast_hpc-%(version)s.%s' % SHLIB_EXT ], + 'dirs': ['bin/rumor', 'bin/zombie', 'include', 'lib'], } moduleclass = 'bio' -- GitLab From 2d8c701f3270602f9db0b3edb5cd4a4de7009159 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Tue, 28 Mar 2017 10:03:12 +0800 Subject: [PATCH 0461/1603] disable stdc-predef.h pre-include --- .../easyconfigs/b/BerkeleyGW/BerkeleyGW-1.2.0-intel-2017a.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.2.0-intel-2017a.eb b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.2.0-intel-2017a.eb index 21a5da2750..6db03e17ee 100644 --- a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.2.0-intel-2017a.eb +++ b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.2.0-intel-2017a.eb @@ -21,8 +21,8 @@ prebuildopts = 'cp config/generic.mpi.linux.mk arch.mk && ' buildopts = 'all-flavors COMPFLAG=-DINTEL PARAFLAG="-DMPI -DOMP" DEBUGFLAG="" F90free="$MPIF90 -free" LINK="$MPIF90" ' buildopts += 'FOPTS="$FFLAGS -qopenmp" MOD_OPT="-module " C_PARAFLAG="$PARAFLAG" CC_COMP="$MPICXX" C_COMP="$MPICC" ' -buildopts += 'C_LINK="$MPICXX" C_OPTS="$CFLAGS -qopenmp" MKLPATH="$MKLROOT" LAPACKLIB="$LIBLAPACK" ' -buildopts += 'BLACSDIR="$BLACS_LIB_DIR" BLACS="$LIBBLACS" SCALAPACKLIB="$LIBSCALAPACK" ' +buildopts += 'FCPP="cpp -C -P -ffreestanding" C_LINK="$MPICXX" C_OPTS="$CFLAGS -qopenmp" MKLPATH="$MKLROOT" ' +buildopts += 'LAPACKLIB="$LIBLAPACK" BLACSDIR="$BLACS_LIB_DIR" BLACS="$LIBBLACS" SCALAPACKLIB="$LIBSCALAPACK" ' buildopts += 'FFTWINCLUDE="$FFTW_INC_DIR" FFTWLIB="$MKLROOT/lib/intel64/libfftw2xf_double_intel.a" ' # "all-flavors" cleans and compiles everything again -- GitLab From e64ee749935ed6de93fde54097f4bcc9caeca1b9 Mon Sep 17 00:00:00 2001 From: easybuild Date: Tue, 28 Mar 2017 15:29:46 +0800 Subject: [PATCH 0462/1603] cleanup --- easybuild/easyconfigs/d/DFTB+/DFTB+-1.3.1-intel-2017a.eb | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/d/DFTB+/DFTB+-1.3.1-intel-2017a.eb b/easybuild/easyconfigs/d/DFTB+/DFTB+-1.3.1-intel-2017a.eb index 15d96ddf6e..7f8e07f325 100644 --- a/easybuild/easyconfigs/d/DFTB+/DFTB+-1.3.1-intel-2017a.eb +++ b/easybuild/easyconfigs/d/DFTB+/DFTB+-1.3.1-intel-2017a.eb @@ -29,10 +29,7 @@ dependencies = [ ('arpack-ng', '3.4.0'), ] -subdir = '%dftbplus-%(version)s' - -prebuildopts = "cp sysmakes/make.x86_64-linux-intel sysmakes/make.user && " -prebuildopts += "cd prg_dftb && " +prebuildopts = "cp sysmakes/make.x86_64-linux-intel sysmakes/make.user && cd prg_dftb && " buildopts = "ARCH=user MKL_LIBDIR=$MKLROOT LNOPT= " -- GitLab From a629ee133ac546cb1145364ab4dcafd4405b08f2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 28 Mar 2017 11:20:23 +0200 Subject: [PATCH 0463/1603] adding easyconfigs: WRF-Fire-20170221-intel-2016b-dmpar.eb --- .../WRF-Fire-20170221-intel-2016b-dmpar.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/w/WRF-Fire/WRF-Fire-20170221-intel-2016b-dmpar.eb diff --git a/easybuild/easyconfigs/w/WRF-Fire/WRF-Fire-20170221-intel-2016b-dmpar.eb b/easybuild/easyconfigs/w/WRF-Fire/WRF-Fire-20170221-intel-2016b-dmpar.eb new file mode 100644 index 0000000000..eeb28fe474 --- /dev/null +++ b/easybuild/easyconfigs/w/WRF-Fire/WRF-Fire-20170221-intel-2016b-dmpar.eb @@ -0,0 +1,23 @@ +name = 'WRF-Fire' +version = '20170221' +commit = 'f2db7a0' +buildtype = 'dmpar' +versionsuffix = '-' + buildtype + +homepage = 'http://www.openwfm.org/wiki/WRF-SFIRE' +description = """WRF-Fire combines the Weather Research and Forecasting model (WRF) with a fire code implementing a + surface fire behavior model, called SFIRE, based on semi-empirical formulas calculate the rate of spread of the fire + line (the interface between burning and unignited fuel) based on fuel properties, wind velocities from WRF, and + terrain slope. The fire spread is implemented by the level set method.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['https://github.com/openwfm/wrf-fire/archive/'] +sources = ['%s.tar.gz' % commit] + +dependencies = [ + ('netCDF-Fortran', '4.4.4'), +] + + +moduleclass = 'geo' -- GitLab From af3b49f341a5e52e48df92f6cfe65a3cf316c78f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 28 Mar 2017 11:49:11 +0200 Subject: [PATCH 0464/1603] add maxparallel = 10 --- .../w/WRF-Fire/WRF-Fire-20170221-intel-2016b-dmpar.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/w/WRF-Fire/WRF-Fire-20170221-intel-2016b-dmpar.eb b/easybuild/easyconfigs/w/WRF-Fire/WRF-Fire-20170221-intel-2016b-dmpar.eb index eeb28fe474..55b59e1608 100644 --- a/easybuild/easyconfigs/w/WRF-Fire/WRF-Fire-20170221-intel-2016b-dmpar.eb +++ b/easybuild/easyconfigs/w/WRF-Fire/WRF-Fire-20170221-intel-2016b-dmpar.eb @@ -19,5 +19,7 @@ dependencies = [ ('netCDF-Fortran', '4.4.4'), ] +# limit max. parallelism for build (WRF-Fire will cap to 2 if > 20) +maxparallel = 10 moduleclass = 'geo' -- GitLab From e9b358bfb426d73b3a04eae8b2a57dfb47e8ede6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 28 Mar 2017 12:41:24 +0200 Subject: [PATCH 0465/1603] adding easyconfigs: Doris-4.02-intel-2017a.eb --- .../d/Doris/Doris-4.02-intel-2017a.eb | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) create mode 100644 easybuild/easyconfigs/d/Doris/Doris-4.02-intel-2017a.eb diff --git a/easybuild/easyconfigs/d/Doris/Doris-4.02-intel-2017a.eb b/easybuild/easyconfigs/d/Doris/Doris-4.02-intel-2017a.eb new file mode 100644 index 0000000000..37cf20fd5b --- /dev/null +++ b/easybuild/easyconfigs/d/Doris/Doris-4.02-intel-2017a.eb @@ -0,0 +1,16 @@ +name = 'Doris' +version = '4.02' + +homepage = 'http://doris.tudelft.nl/' +description = "Delft object-oriented radar interferometric software" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['http://doris.tudelft.nl/software/'] +sources = ['doris_v%(version)s.tar.gz'] + +dependencies = [ + ('FFTW', '3.3.6'), +] + +moduleclass = 'geo' -- GitLab From b3fc425e503d838764466ab63d3321642070e1c9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 28 Mar 2017 14:31:38 +0200 Subject: [PATCH 0466/1603] adding easyconfigs: h5py-2.7.0-intel-2016b-Python-2.7.12.eb --- .../h5py-2.7.0-intel-2016b-Python-2.7.12.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/h/h5py/h5py-2.7.0-intel-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.7.0-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/h/h5py/h5py-2.7.0-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..adc15ffb81 --- /dev/null +++ b/easybuild/easyconfigs/h/h5py/h5py-2.7.0-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonPackage' + +name = 'h5py' +version = '2.7.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.h5py.org/' +description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, + version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous + amounts of data.""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'usempi': True} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +# to really use mpi enabled hdf5 we now seem to need a configure step +prebuildopts = ' python setup.py configure --mpi --hdf5=$EBROOTHDF5 && ' + +dependencies = [ + ('Python', '2.7.12'), + ('HDF5', '1.10.0-patch1'), + ('pkgconfig', '1.1.0', '-Python-%(pyver)s'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +moduleclass = 'data' -- GitLab From ad6485b3fbe49817a1543a16dbb87ad2b171c876 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 28 Mar 2017 14:32:03 +0200 Subject: [PATCH 0467/1603] adding easyconfigs: SpiceyPy-1.1.0-intel-2016b-Python-2.7.12.eb --- ...piceyPy-1.1.0-intel-2016b-Python-2.7.12.eb | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/s/SpiceyPy/SpiceyPy-1.1.0-intel-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/s/SpiceyPy/SpiceyPy-1.1.0-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/s/SpiceyPy/SpiceyPy-1.1.0-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..9ffb950100 --- /dev/null +++ b/easybuild/easyconfigs/s/SpiceyPy/SpiceyPy-1.1.0-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,22 @@ +easyblock = 'PythonPackage' + +name = 'SpiceyPy' +version = '1.1.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/AndrewAnnex/SpiceyPy' +description = "SpiceyPy is a Python wrapper for the NAIF C SPICE Toolkit (N65)" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('Python', '2.7.12')] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'geo' -- GitLab From 6f50fca325bea7be094393d39e28bdc2c94b19ce Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 28 Mar 2017 14:32:29 +0200 Subject: [PATCH 0468/1603] adding easyconfigs: FFTW-3.3.6-intel-2016b.eb --- .../f/FFTW/FFTW-3.3.6-intel-2016b.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-intel-2016b.eb diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-intel-2016b.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-intel-2016b.eb new file mode 100644 index 0000000000..14ebd120a4 --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-intel-2016b.eb @@ -0,0 +1,29 @@ +name = 'FFTW' +version = '3.3.6' + +homepage = 'http://www.fftw.org' +description = """FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) + in one or more dimensions, of arbitrary input size, and of both real and complex data.""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = ['fftw-%(version)s-pl1.tar.gz'] +checksums = ['682a0e78d6966ca37c7446d4ab4cc2a1'] + +patches = [ + 'FFTW-3.3.6-F03_interface_pl2.patch', +] + +# no quad precision, requires GCC v4.6 or higher +# see also +# http://www.fftw.org/doc/Extended-and-quadruple-precision-in-Fortran.html +with_quad_prec = False + +# compilation fails when configuring with --enable-avx-128-fma, Intel compilers do not support FMA4 instructions +use_fma4 = False + +runtest = 'check' + +moduleclass = 'numlib' -- GitLab From 4757aa658eebdd42897f500ee38fbea0e652d2c4 Mon Sep 17 00:00:00 2001 From: Maxime Boissonneault Date: Tue, 28 Mar 2017 12:52:24 +0000 Subject: [PATCH 0469/1603] escaped % --- easybuild/easyconfigs/r/RepastHPC/RepastHPC-2.2.0-foss-2016a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/RepastHPC/RepastHPC-2.2.0-foss-2016a.eb b/easybuild/easyconfigs/r/RepastHPC/RepastHPC-2.2.0-foss-2016a.eb index d533ab1e52..fc07069bff 100644 --- a/easybuild/easyconfigs/r/RepastHPC/RepastHPC-2.2.0-foss-2016a.eb +++ b/easybuild/easyconfigs/r/RepastHPC/RepastHPC-2.2.0-foss-2016a.eb @@ -23,7 +23,7 @@ dependencies = [ configopts = '--with-boost=$EBROOTBOOST --with-netcdf=$EBROOTNETCDFMINCPLUSPLUS' sanity_check_paths = { - 'files': ['lib/librelogo-%(version)s.%s' % SHLIB_EXT, 'lib/librepast_hpc-%(version)s.%s' % SHLIB_EXT ], + 'files': ['lib/librelogo-%%(version)s.%s' % SHLIB_EXT, 'lib/librepast_hpc-%%(version)s.%s' % SHLIB_EXT ], 'dirs': ['bin/rumor', 'bin/zombie', 'include', 'lib'], } -- GitLab From 61c407afe0e0c14abfcbb085a78030d4a1b6bf86 Mon Sep 17 00:00:00 2001 From: easybuild Date: Wed, 29 Mar 2017 08:58:45 +0800 Subject: [PATCH 0470/1603] remove -qopenmp and enable openmp toolchain option --- .../easyconfigs/b/BerkeleyGW/BerkeleyGW-1.2.0-intel-2017a.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.2.0-intel-2017a.eb b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.2.0-intel-2017a.eb index 6db03e17ee..94e1cd433d 100644 --- a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.2.0-intel-2017a.eb +++ b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.2.0-intel-2017a.eb @@ -9,7 +9,7 @@ description = """The BerkeleyGW Package is a set of computer codes that calculat nanostructures such as slabs, wires and molecules.""" toolchain = {'name': 'intel', 'version': '2017a'} -toolchainopts = {'usempi': True} +toolchainopts = {'usempi': True, 'openmp': True} source_urls = ['http://www.berkeleygw.org/releases/'] # requires registration sources = ['BGW-%(version)s.tar.gz'] @@ -21,7 +21,7 @@ prebuildopts = 'cp config/generic.mpi.linux.mk arch.mk && ' buildopts = 'all-flavors COMPFLAG=-DINTEL PARAFLAG="-DMPI -DOMP" DEBUGFLAG="" F90free="$MPIF90 -free" LINK="$MPIF90" ' buildopts += 'FOPTS="$FFLAGS -qopenmp" MOD_OPT="-module " C_PARAFLAG="$PARAFLAG" CC_COMP="$MPICXX" C_COMP="$MPICC" ' -buildopts += 'FCPP="cpp -C -P -ffreestanding" C_LINK="$MPICXX" C_OPTS="$CFLAGS -qopenmp" MKLPATH="$MKLROOT" ' +buildopts += 'FCPP="cpp -C -P -ffreestanding" C_LINK="$MPICXX" C_OPTS="$CFLAGS" MKLPATH="$MKLROOT" ' buildopts += 'LAPACKLIB="$LIBLAPACK" BLACSDIR="$BLACS_LIB_DIR" BLACS="$LIBBLACS" SCALAPACKLIB="$LIBSCALAPACK" ' buildopts += 'FFTWINCLUDE="$FFTW_INC_DIR" FFTWLIB="$MKLROOT/lib/intel64/libfftw2xf_double_intel.a" ' -- GitLab From e665b67632d148ef30590adec9b871b6cc74c9b1 Mon Sep 17 00:00:00 2001 From: easybuild Date: Wed, 29 Mar 2017 14:31:28 +0800 Subject: [PATCH 0471/1603] remove the other -qopenmp --- .../easyconfigs/b/BerkeleyGW/BerkeleyGW-1.2.0-intel-2017a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.2.0-intel-2017a.eb b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.2.0-intel-2017a.eb index 94e1cd433d..2eb57382c1 100644 --- a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.2.0-intel-2017a.eb +++ b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.2.0-intel-2017a.eb @@ -20,7 +20,7 @@ skipsteps = ['configure'] prebuildopts = 'cp config/generic.mpi.linux.mk arch.mk && ' buildopts = 'all-flavors COMPFLAG=-DINTEL PARAFLAG="-DMPI -DOMP" DEBUGFLAG="" F90free="$MPIF90 -free" LINK="$MPIF90" ' -buildopts += 'FOPTS="$FFLAGS -qopenmp" MOD_OPT="-module " C_PARAFLAG="$PARAFLAG" CC_COMP="$MPICXX" C_COMP="$MPICC" ' +buildopts += 'FOPTS="$FFLAGS" MOD_OPT="-module " C_PARAFLAG="$PARAFLAG" CC_COMP="$MPICXX" C_COMP="$MPICC" ' buildopts += 'FCPP="cpp -C -P -ffreestanding" C_LINK="$MPICXX" C_OPTS="$CFLAGS" MKLPATH="$MKLROOT" ' buildopts += 'LAPACKLIB="$LIBLAPACK" BLACSDIR="$BLACS_LIB_DIR" BLACS="$LIBBLACS" SCALAPACKLIB="$LIBSCALAPACK" ' buildopts += 'FFTWINCLUDE="$FFTW_INC_DIR" FFTWLIB="$MKLROOT/lib/intel64/libfftw2xf_double_intel.a" ' -- GitLab From 1fd96d8483783fe062547963cb0baee7a49ed8db Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 29 Mar 2017 18:32:53 +0200 Subject: [PATCH 0472/1603] adding easyconfigs: ROI_PAC-3.0.1-intel-2016b-Perl-5.24.0.eb --- .../ROI_PAC-3.0.1-intel-2016b-Perl-5.24.0.eb | 47 +++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 easybuild/easyconfigs/r/ROI_PAC/ROI_PAC-3.0.1-intel-2016b-Perl-5.24.0.eb diff --git a/easybuild/easyconfigs/r/ROI_PAC/ROI_PAC-3.0.1-intel-2016b-Perl-5.24.0.eb b/easybuild/easyconfigs/r/ROI_PAC/ROI_PAC-3.0.1-intel-2016b-Perl-5.24.0.eb new file mode 100644 index 0000000000..367e778dfc --- /dev/null +++ b/easybuild/easyconfigs/r/ROI_PAC/ROI_PAC-3.0.1-intel-2016b-Perl-5.24.0.eb @@ -0,0 +1,47 @@ +easyblock = 'ConfigureMake' + +name = 'ROI_PAC' +version = '3.0.1' +versionsuffix = '-Perl-%(perlver)s' + +homepage = 'http://roipac.org/' +description = """Repeat Orbit Interferometry PACkage (ROI_PAC), software for processing synthetic aperture radar data + to produce differential interferograms""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +# download requires registration, see http://www.openchannelfoundation.org/projects/ROI_PAC +sources = ['ROI_PAC_%s.tgz' % '_'.join(version.split('.'))] + +# FIXME: http://roipac.org/cgi-bin/moin.cgi/Patches + +builddependencies = [('Autotools', '20150215')] +dependencies = [ + ('FFTW', '3.3.6'), + ('GETORB', '2.3.2'), + ('Perl', '5.24.0'), +] + +start_dir = 'ROI_PAC' + +postinstallcmds = [ + # symlink to getorb requires in /bin subdirectory + "cd %(installdir)s/bin && ln -s $(which getorb)", + # also copy scripts and make sure they're excutable + "cp -a INT_SCR/* %(installdir)s/bin", + # fix shebang in Perl scripts + "sed -i 's@^#!.*/bin/perl.*@#!/usr/bin/env perl@g' %(installdir)s//bin/*.pl", +] + +sanity_check_paths = { + 'files': ['bin/getorb', 'bin/make_raw.pl', 'bin/roi'], + 'dirs': [], +} + +modextrapaths = {'PERL5LIB': 'bin'} +modextravars = { + 'INT_BIN': '%(installdir)s/bin', + 'INT_SCR': '%(installdir)s/bin', +} + +moduleclass = 'geo' -- GitLab From fc0f4ff96ff2a60bbb800af32366c28229941270 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 29 Mar 2017 18:34:36 +0200 Subject: [PATCH 0473/1603] adding easyconfigs: jemalloc-4.5.0-intel-2017a.eb --- .../j/jemalloc/jemalloc-4.5.0-intel-2017a.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/j/jemalloc/jemalloc-4.5.0-intel-2017a.eb diff --git a/easybuild/easyconfigs/j/jemalloc/jemalloc-4.5.0-intel-2017a.eb b/easybuild/easyconfigs/j/jemalloc/jemalloc-4.5.0-intel-2017a.eb new file mode 100644 index 0000000000..45f685672f --- /dev/null +++ b/easybuild/easyconfigs/j/jemalloc/jemalloc-4.5.0-intel-2017a.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'jemalloc' +version = '4.5.0' + +homepage = 'http://www.canonware.com/jemalloc' +description = """jemalloc is a general purpose malloc(3) implementation that emphasizes fragmentation avoidance and + scalable concurrency support.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['https://github.com/jemalloc/jemalloc/archive'] +sources = ['%(version)s.tar.gz'] + +builddependencies = [('Autotools', '20150215')] + +preconfigopts = "./autogen.sh && " +prebuildopts = "make dist && " + +sanity_check_paths = { + 'files': ['bin/jeprof', 'lib/libjemalloc.a', 'lib/libjemalloc_pic.a', 'lib/libjemalloc.%s' % SHLIB_EXT, + 'include/jemalloc/jemalloc.h'], + 'dirs': ['share'], +} + +modextrapaths = {'LD_PRELOAD': ['lib/libjemalloc.%s' % SHLIB_EXT]} + +moduleclass = 'lib' -- GitLab From 16bdb31b1f2f30a4a25c0a601176e39348a2a341 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 29 Mar 2017 20:04:44 +0200 Subject: [PATCH 0474/1603] add easyconfig for GETORB dependency for ROI_PAC --- .../g/GETORB/GETORB-2.3.2-intel-2016b.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/g/GETORB/GETORB-2.3.2-intel-2016b.eb diff --git a/easybuild/easyconfigs/g/GETORB/GETORB-2.3.2-intel-2016b.eb b/easybuild/easyconfigs/g/GETORB/GETORB-2.3.2-intel-2016b.eb new file mode 100644 index 0000000000..61b3b12249 --- /dev/null +++ b/easybuild/easyconfigs/g/GETORB/GETORB-2.3.2-intel-2016b.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'GETORB' +version = '2.3.2' + +homepage = 'http://www.deos.tudelft.nl/ers/precorbs/tools/getorb_pack.shtml' +description = "GETORB software package contains programs to handle the orbital data records (ODRs)" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['http://www.deos.tudelft.nl/ers/precorbs/tools/'] +sources = ['getorb_%(version)s.tar.gz'] + +skipsteps = ['configure'] + +preinstallopts = "mkdir %(installdir)s/bin && " +installopts = 'BIN_DIR=%(installdir)s/bin' + +sanity_check_paths = { + 'files': ['bin/getorb', 'bin/lodr', 'bin/mdate'], + 'dirs': [], +} + +moduleclass = 'tools' -- GitLab From 5ae48b9b752d2c302000a1a64f9ed58c9da4f585 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 30 Mar 2017 10:31:21 +0200 Subject: [PATCH 0475/1603] disable parallel building for GETORB, tends to break --- easybuild/easyconfigs/g/GETORB/GETORB-2.3.2-intel-2016b.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/g/GETORB/GETORB-2.3.2-intel-2016b.eb b/easybuild/easyconfigs/g/GETORB/GETORB-2.3.2-intel-2016b.eb index 61b3b12249..2e648643f9 100644 --- a/easybuild/easyconfigs/g/GETORB/GETORB-2.3.2-intel-2016b.eb +++ b/easybuild/easyconfigs/g/GETORB/GETORB-2.3.2-intel-2016b.eb @@ -13,6 +13,8 @@ sources = ['getorb_%(version)s.tar.gz'] skipsteps = ['configure'] +parallel = 1 + preinstallopts = "mkdir %(installdir)s/bin && " installopts = 'BIN_DIR=%(installdir)s/bin' -- GitLab From 07b52f5f937b0962931ac68e1ff50ef6567a3ddb Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 30 Mar 2017 10:57:46 +0200 Subject: [PATCH 0476/1603] apply fixes for ROI_PAC described at http://roipac.org/cgi-bin/moin.cgi/Patches --- .../ROI_PAC/ROI_PAC-3.0.1-intel-2016b-Perl-5.24.0.eb | 12 +++++++++--- 1 file changed, 9 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/r/ROI_PAC/ROI_PAC-3.0.1-intel-2016b-Perl-5.24.0.eb b/easybuild/easyconfigs/r/ROI_PAC/ROI_PAC-3.0.1-intel-2016b-Perl-5.24.0.eb index 367e778dfc..30adf12039 100644 --- a/easybuild/easyconfigs/r/ROI_PAC/ROI_PAC-3.0.1-intel-2016b-Perl-5.24.0.eb +++ b/easybuild/easyconfigs/r/ROI_PAC/ROI_PAC-3.0.1-intel-2016b-Perl-5.24.0.eb @@ -10,10 +10,14 @@ description = """Repeat Orbit Interferometry PACkage (ROI_PAC), software for pro toolchain = {'name': 'intel', 'version': '2016b'} -# download requires registration, see http://www.openchannelfoundation.org/projects/ROI_PAC +# download of ROI_PAC tarball requires registration, see http://www.openchannelfoundation.org/projects/ROI_PAC sources = ['ROI_PAC_%s.tgz' % '_'.join(version.split('.'))] -# FIXME: http://roipac.org/cgi-bin/moin.cgi/Patches +# make_raw_alos.pl via http://roipac.org/cgi-bin/moin.cgi/ALOS_PALSAR?action=AttachFile&do=get&target=make_raw_alos.pl +patches = [ + 'ROI_PAC-%(version)s_fix-IntSim.patch', + ('make_raw_alos.pl', 'ROI_PAC/INT_SCR'), +] builddependencies = [('Autotools', '20150215')] dependencies = [ @@ -24,6 +28,8 @@ dependencies = [ start_dir = 'ROI_PAC' +installopts = "&& cd fip && $CC $CFLAGS -o add_rmgAmpPhs add_rmgAmpPhs.c && cp -a add_rmgAmpPhs %(installdir)s/bin" + postinstallcmds = [ # symlink to getorb requires in /bin subdirectory "cd %(installdir)s/bin && ln -s $(which getorb)", @@ -34,7 +40,7 @@ postinstallcmds = [ ] sanity_check_paths = { - 'files': ['bin/getorb', 'bin/make_raw.pl', 'bin/roi'], + 'files': ['bin/add_rmgAmpPhs', 'bin/getorb', 'bin/make_raw.pl', 'bin/make_raw_alos.pl', 'bin/roi'], 'dirs': [], } -- GitLab From c1fc2295bb7312211e795a36fa9bb466465ef66d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 30 Mar 2017 11:49:06 +0200 Subject: [PATCH 0477/1603] also define $MY_BIN and $ROI_PAC in ROI_PAC easyconfig --- .../r/ROI_PAC/ROI_PAC-3.0.1-intel-2016b-Perl-5.24.0.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/r/ROI_PAC/ROI_PAC-3.0.1-intel-2016b-Perl-5.24.0.eb b/easybuild/easyconfigs/r/ROI_PAC/ROI_PAC-3.0.1-intel-2016b-Perl-5.24.0.eb index 30adf12039..89a80fb749 100644 --- a/easybuild/easyconfigs/r/ROI_PAC/ROI_PAC-3.0.1-intel-2016b-Perl-5.24.0.eb +++ b/easybuild/easyconfigs/r/ROI_PAC/ROI_PAC-3.0.1-intel-2016b-Perl-5.24.0.eb @@ -48,6 +48,10 @@ modextrapaths = {'PERL5LIB': 'bin'} modextravars = { 'INT_BIN': '%(installdir)s/bin', 'INT_SCR': '%(installdir)s/bin', + 'MY_BIN': '%(installdir)s/bin', + 'ROI_PAC': '%(installdir)s', } +modloadmsg = "To define: $INS_DIR, $POR_DIR, $SAR_ODR_DIR, $SAR_PRC_DIR, $VOR_DIR\n" + moduleclass = 'geo' -- GitLab From 58efec1edfc3367d40113a41898e9c66a597f816 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 30 Mar 2017 11:53:29 +0200 Subject: [PATCH 0478/1603] add easyconfig for SQLite 3.17.0 as dep for Python 2.7.13 --- .../s/SQLite/SQLite-3.17.0-GCCcore-6.3.0.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/s/SQLite/SQLite-3.17.0-GCCcore-6.3.0.eb diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.17.0-GCCcore-6.3.0.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.17.0-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..41b5a58bd2 --- /dev/null +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.17.0-GCCcore-6.3.0.eb @@ -0,0 +1,44 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## + +easyblock = 'ConfigureMake' + +name = 'SQLite' +version = '3.17.0' + +homepage = 'http://www.sqlite.org/' +description = 'SQLite: SQL Database Engine in a C Library' + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} + +source_urls = ['http://www.sqlite.org/2017/'] +version_minor_etc = version.split('.')[1:] +version_minor_etc += '0' * (3 - len(version_minor_etc)) +version_str = '%(version_major)s' + ''.join('%02d' % int(x) for x in version_minor_etc) +sources = ['sqlite-autoconf-%s.tar.gz' % version_str] + +builddependencies = [ + ('binutils', '2.27'), +] + +dependencies = [ + ('libreadline', '7.0'), + ('Tcl', '8.6.6'), +] + +sanity_check_paths = { + 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', 'lib/libsqlite3.a', + 'lib/libsqlite3.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'devel' -- GitLab From fb829371d5936654f861cad99145ed7ca41ab1f6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 30 Mar 2017 11:58:41 +0200 Subject: [PATCH 0479/1603] no need to patch libreadline 7.0 --- .../easyconfigs/l/libreadline/libreadline-7.0-GCCcore-6.3.0.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-7.0-GCCcore-6.3.0.eb b/easybuild/easyconfigs/l/libreadline/libreadline-7.0-GCCcore-6.3.0.eb index a64400af8e..66d703c987 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-7.0-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-7.0-GCCcore-6.3.0.eb @@ -15,8 +15,6 @@ toolchainopts = {'pic': True} sources = ['readline-%(version)s.tar.gz'] source_urls = ['http://ftp.gnu.org/gnu/readline'] -patches = ['libreadline-%(version)s-bugfix.patch'] - builddependencies = [('binutils', '2.27')] dependencies = [('ncurses', '6.0')] -- GitLab From ca1a4fafff488db98e9293a6d4f93b9ee6cde90f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 30 Mar 2017 13:11:17 +0200 Subject: [PATCH 0480/1603] update extensions in Python 2.7.13 easyconfig, mainly to include numpy 1.12.1 and scipy 0.19.0 --- .../p/Python/Python-2.7.13-intel-2017a.eb | 12 +++++++----- 1 file changed, 7 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.13-intel-2017a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.13-intel-2017a.eb index 31e0d3d932..8d585acc42 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.13-intel-2017a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.13-intel-2017a.eb @@ -28,7 +28,7 @@ dependencies = [ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! -# package versions updated March 6th 2017 +# package versions updated March 30th 2017 exts_list = [ # note: more recent versions of setuptools (v34.x) can not be installed from source anymore, # see https://github.com/pypa/setuptools/issues/980 @@ -42,13 +42,14 @@ exts_list = [ ('nose', '1.3.7', { 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), - ('numpy', '1.12.0', { + ('numpy', '1.12.1', { 'source_urls': ['https://pypi.python.org/packages/source/n/numpy'], 'source_tmpl': '%(name)s-%(version)s.zip', 'patches': ['numpy-1.12.0-mkl.patch'], }), - ('scipy', '0.18.1', { + ('scipy', '0.19.0', { 'source_urls': ['https://pypi.python.org/packages/source/s/scipy'], + 'source_tmpl': '%(name)s-%(version)s.zip', }), ('blist', '1.3.6', { 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], @@ -90,7 +91,7 @@ exts_list = [ ('ecdsa', '0.13', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], }), - ('cryptography', '1.7.2', { + ('cryptography', '1.8.1', { 'source_urls': ['https://pypi.python.org/packages/source/c/cryptography/'], }), ('paramiko', '2.1.2', { @@ -111,8 +112,9 @@ exts_list = [ ('mock', '2.0.0', { 'source_urls': ['https://pypi.python.org/packages/source/m/mock'], }), - ('pytz', '2016.10', { + ('pytz', '2017.2', { 'source_urls': ['https://pypi.python.org/packages/source/p/pytz'], + 'source_tmpl': '%(name)s-%(version)s.zip', }), ('pandas', '0.19.2', { 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], -- GitLab From c51102c55e1c7cb3641db800e8c2ac005121464d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 30 Mar 2017 16:39:09 +0200 Subject: [PATCH 0481/1603] adding easyconfigs: Mesa-17.0.2-intel-2017a.eb, LLVM-4.0.0-intel-2017a.eb, nettle-3.3-intel-2017a.eb, libdrm-2.4.76-intel-2017a.eb, Mako-1.0.6-intel-2017a-Python-2.7.13.eb, libxml2-2.9.4-intel-2017a-Python-2.7.13.eb --- .../l/LLVM/LLVM-4.0.0-intel-2017a.eb | 42 +++++++++++++ .../l/libdrm/libdrm-2.4.76-intel-2017a.eb | 24 +++++++ ...libxml2-2.9.4-intel-2017a-Python-2.7.13.eb | 24 +++++++ .../Mako-1.0.6-intel-2017a-Python-2.7.13.eb | 22 +++++++ .../m/Mesa/Mesa-17.0.2-intel-2017a.eb | 63 +++++++++++++++++++ .../n/nettle/nettle-3.3-intel-2017a.eb | 28 +++++++++ 6 files changed, 203 insertions(+) create mode 100644 easybuild/easyconfigs/l/LLVM/LLVM-4.0.0-intel-2017a.eb create mode 100644 easybuild/easyconfigs/l/libdrm/libdrm-2.4.76-intel-2017a.eb create mode 100644 easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-intel-2017a-Python-2.7.13.eb create mode 100644 easybuild/easyconfigs/m/Mako/Mako-1.0.6-intel-2017a-Python-2.7.13.eb create mode 100644 easybuild/easyconfigs/m/Mesa/Mesa-17.0.2-intel-2017a.eb create mode 100644 easybuild/easyconfigs/n/nettle/nettle-3.3-intel-2017a.eb diff --git a/easybuild/easyconfigs/l/LLVM/LLVM-4.0.0-intel-2017a.eb b/easybuild/easyconfigs/l/LLVM/LLVM-4.0.0-intel-2017a.eb new file mode 100644 index 0000000000..5fba0f28fc --- /dev/null +++ b/easybuild/easyconfigs/l/LLVM/LLVM-4.0.0-intel-2017a.eb @@ -0,0 +1,42 @@ +easyblock = 'CMakeMake' + +name = 'LLVM' +version = '4.0.0' + +homepage = "http://llvm.org/" +description = """The LLVM Core libraries provide a modern source- and target-independent + optimizer, along with code generation support for many popular CPUs + (as well as some less common ones!) These libraries are built around a well + specified code representation known as the LLVM intermediate representation + ("LLVM IR"). The LLVM Core libraries are well documented, and it is + particularly easy to invent your own language (or port an existing compiler) + to use LLVM as an optimizer and code generator.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'cstd': 'gnu++11'} + +source_urls = ["http://llvm.org/releases/%(version)s"] +sources = ["llvm-%(version)s.src.tar.xz"] + +builddependencies = [ + ('CMake', '3.7.2'), + ('Python', '2.7.13'), +] + +dependencies = [ + ('ncurses', '6.0'), + ('zlib', '1.2.11'), +] + +configopts = '-DBUILD_SHARED_LIBS=ON -DCMAKE_EXE_LINKER_FLAGS="$LDFLAGS -shared-intel" ' +# required to install extra tools in bin/ +configopts += "-DLLVM_INSTALL_UTILS=ON -DLLVM_TARGETS_TO_BUILD=X86 -DLLVM_ENABLE_ZLIB=ON" + +sanity_check_paths = { + 'files': ['bin/llvm-ar', 'bin/FileCheck'], + 'dirs': ['include/llvm', 'include/llvm-c'], +} + +separate_build_dir = True + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.76-intel-2017a.eb b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.76-intel-2017a.eb new file mode 100644 index 0000000000..be5c5321ff --- /dev/null +++ b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.76-intel-2017a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'libdrm' +version = '2.4.76' + +homepage = 'http://dri.freedesktop.org' +description = """Direct Rendering Manager runtime library.""" + +source_urls = ['http://dri.freedesktop.org/libdrm/'] +sources = [SOURCELOWER_TAR_GZ] + +toolchain = {'name': 'intel', 'version': '2017a'} + +dependencies = [ + ('X11', '20170129'), +] + +sanity_check_paths = { + 'files': ['include/xf86drm.h', 'include/xf86drmMode.h', 'lib/libdrm_intel.%s' % SHLIB_EXT, + 'lib/libdrm_radeon.%s' % SHLIB_EXT, 'lib/libdrm.%s' % SHLIB_EXT, 'lib/libkms.%s' % SHLIB_EXT], + 'dirs': ['include/libdrm', 'include/libkms', 'lib/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..8eeb402547 --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,24 @@ +name = 'libxml2' +version = '2.9.4' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://xmlsoft.org/' +description = """Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable + outside of the Gnome platform).""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('zlib', '1.2.11'), + ('XZ', '5.2.3'), + ('Python', '2.7.13'), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/Mako/Mako-1.0.6-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/m/Mako/Mako-1.0.6-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..9bae465168 --- /dev/null +++ b/easybuild/easyconfigs/m/Mako/Mako-1.0.6-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,22 @@ +easyblock = 'PythonPackage' + +name = 'Mako' +version = '1.0.6' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.makotemplates.org' +description = """A super-fast templating language that borrows the best ideas from the existing templating languages""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [('Python', '2.7.13')] + +sanity_check_paths = { + 'files': ['bin/mako-render'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s-%(version)s-py%(pyshortver)s.egg'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-17.0.2-intel-2017a.eb b/easybuild/easyconfigs/m/Mesa/Mesa-17.0.2-intel-2017a.eb new file mode 100644 index 0000000000..70b8bcc2b4 --- /dev/null +++ b/easybuild/easyconfigs/m/Mesa/Mesa-17.0.2-intel-2017a.eb @@ -0,0 +1,63 @@ +# the purpose of the easyconfig is to build a Mesa for software rendering, +# not hardware rendering. This means you want at least SSE4.2. We build: +# - llvmpipe: the high-performance Gallium LLVM driver +# - swr: Intel's OpenSWR +# it will try to use the llvmpipe by default. It you want swr, do: +# GALLIUM_DRIVER=swr + +easyblock = 'ConfigureMake' + +name = 'Mesa' +version = '17.0.2' + +homepage = 'http://www.mesa3d.org/' +description = """Mesa is an open-source implementation of the OpenGL specification - + a system for rendering interactive 3D graphics.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +# swr detects and builds parts specific for AVX and AVX2. If we use +# -xHost, this always gets overwritten and will fail. +toolchainopts = {'optarch': False} + +sources = [SOURCELOWER_TAR_XZ] +source_urls = [ + 'https://mesa.freedesktop.org/archive/', + 'https://mesa.freedesktop.org/archive/%(version)s', + 'ftp://ftp.freedesktop.org/pub/mesa/%(version)s', + 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x/%(version)s', +] + +builddependencies = [ + ('flex', '2.6.3'), + ('Bison', '3.0.4'), + ('Autotools', '20150215'), + ('pkg-config', '0.29.1'), + ('Mako', '1.0.6', '-Python-2.7.13'), + ('libxml2', '2.9.4', '-Python-2.7.13'), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('nettle', '3.3'), + ('libdrm', '2.4.76'), + ('LLVM', '4.0.0'), + ('X11', '20170129'), +] + +# GLU is not part anymore of Mesa package! +configopts = " --disable-osmesa --enable-gallium-osmesa --enable-gallium-llvm --enable-glx --disable-dri" +configopts += " --disable-gbm --disable-driglx-direct --with-gallium-drivers='swrast,swr' --disable-egl" +configopts += " --with-osmesa-bits=32 --enable-texture-float --enable-llvm-shared-libs " + +sanity_check_paths = { + 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libOSMesa.%s' % SHLIB_EXT, + 'lib/libGLESv1_CM.%s' % SHLIB_EXT, 'lib/libGLESv2.%s' % SHLIB_EXT, + 'include/GL/glext.h', 'include/GL/gl_mangle.h', + 'include/GL/glx.h', 'include/GL/osmesa.h', + 'include/GL/gl.h', 'include/GL/glxext.h', + 'include/GL/glx_mangle.h', 'include/GLES/gl.h', + 'include/GLES2/gl2.h', 'include/GLES3/gl3.h'], + 'dirs': [] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/n/nettle/nettle-3.3-intel-2017a.eb b/easybuild/easyconfigs/n/nettle/nettle-3.3-intel-2017a.eb new file mode 100644 index 0000000000..d8f9e8fc31 --- /dev/null +++ b/easybuild/easyconfigs/n/nettle/nettle-3.3-intel-2017a.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'nettle' +version = '3.3' + +homepage = 'http://www.lysator.liu.se/~nisse/nettle/' +description = """Nettle is a cryptographic library that is designed to fit easily + in more or less any context: In crypto toolkits for object-oriented + languages (C++, Python, Pike, ...), in applications like LSH or GNUPG, + or even in kernel space.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('GMP', '6.1.2'), +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['nettle-hash', 'nettle-lfib-stream', 'pkcs1-conv', 'sexp-conv']] + + ['lib64/libhogweed.a', 'lib64/libhogweed.%s' % SHLIB_EXT, + 'lib64/libnettle.a', 'lib64/libnettle.%s' % SHLIB_EXT], + 'dirs': ['include/nettle'], +} + +moduleclass = 'lib' -- GitLab From 65ed10a7fb122fd9bbde169b3234337aedb587c9 Mon Sep 17 00:00:00 2001 From: John Donners Date: Thu, 30 Mar 2017 18:55:11 +0200 Subject: [PATCH 0482/1603] adding easyconfigs: SCOTCH-6.0.4-intel-2016b.eb --- easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-intel-2016b.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-intel-2016b.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-intel-2016b.eb index 20bc255b1a..5df84b7224 100644 --- a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-intel-2016b.eb +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-intel-2016b.eb @@ -11,4 +11,8 @@ toolchainopts = {'pic': True} source_urls = ['http://gforge.inria.fr/frs/download.php/file/34618/'] sources = ['%(namelower)s_%(version)s.tar.gz'] +dependencies = [ + ('zlib', '1.2.8'), +] + moduleclass = 'math' -- GitLab From dd3c0ab7262f61bf0d5187f1ce8307bd4c3afda4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 31 Mar 2017 10:34:22 +0200 Subject: [PATCH 0483/1603] adding easyconfigs: PGI-17.3-GCC-6.3.0-2.28.eb --- .../p/PGI/PGI-17.3-GCC-6.3.0-2.28.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/p/PGI/PGI-17.3-GCC-6.3.0-2.28.eb diff --git a/easybuild/easyconfigs/p/PGI/PGI-17.3-GCC-6.3.0-2.28.eb b/easybuild/easyconfigs/p/PGI/PGI-17.3-GCC-6.3.0-2.28.eb new file mode 100644 index 0000000000..fd7e68ba06 --- /dev/null +++ b/easybuild/easyconfigs/p/PGI/PGI-17.3-GCC-6.3.0-2.28.eb @@ -0,0 +1,25 @@ +name = 'PGI' +version = '17.3' + +homepage = 'http://www.pgroup.com/' +description = "C, C++ and Fortran compilers from The Portland Group - PGI" + +toolchain = {'name': 'dummy', 'version': ''} + +sources = ['pgilinux-20%(version_major)s-%(version_major)s%(version_minor)s-x86_64.tar.gz'] +checksums = ['6eefc42f85e756cbaba76467ed640902'] + +gccver = '6.3.0' +binutilsver = '2.28' +versionsuffix = '-GCC-%s-%s' % (gccver, binutilsver) + +dependencies = [ + ('GCCcore', gccver), + ('binutils', binutilsver, '', ('GCCcore', gccver)), + ('numactl', '2.0.11', '', ('GCCcore', gccver)), +] + +# license file +license_file = HOME + '/licenses/pgi/license.dat' + +moduleclass = 'compiler' -- GitLab From 22f66c09d8737d5987422a44069c798e5702ac5f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 31 Mar 2017 11:52:19 +0200 Subject: [PATCH 0484/1603] adding easyconfigs: VTune-2017_update2.eb --- .../easyconfigs/v/VTune/VTune-2017_update2.eb | 15 +++++++++++++++ 1 file changed, 15 insertions(+) create mode 100644 easybuild/easyconfigs/v/VTune/VTune-2017_update2.eb diff --git a/easybuild/easyconfigs/v/VTune/VTune-2017_update2.eb b/easybuild/easyconfigs/v/VTune/VTune-2017_update2.eb new file mode 100644 index 0000000000..5db4d180ba --- /dev/null +++ b/easybuild/easyconfigs/v/VTune/VTune-2017_update2.eb @@ -0,0 +1,15 @@ +name = 'VTune' +version = '2017_update2' + +homepage = 'http://software.intel.com/en-us/intel-vtune-amplifier-xe' +description = """Intel VTune Amplifier XE is the premier performance profiler for C, C++, C#, Fortran, + Assembly and Java.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['vtune_amplifier_xe_%(version)s.tar.gz'] +checksums = ['1ef91898e107a1da015305def80091e4'] + +license_file = HOME + '/licenses/intel/license.lic' + +moduleclass = 'tools' -- GitLab From 21c7598a04c602939937779d872a9e59ca0f717c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 31 Mar 2017 15:43:48 +0200 Subject: [PATCH 0485/1603] add patch to fix build of Mesa 17.0.2 with Intel compilers --- .../easyconfigs/m/Mesa/Mesa-17.0.2-intel-2017a.eb | 3 +++ .../m/Mesa/Mesa-17.0.2_fix-strip-llvm-flags.patch | 14 ++++++++++++++ 2 files changed, 17 insertions(+) create mode 100644 easybuild/easyconfigs/m/Mesa/Mesa-17.0.2_fix-strip-llvm-flags.patch diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-17.0.2-intel-2017a.eb b/easybuild/easyconfigs/m/Mesa/Mesa-17.0.2-intel-2017a.eb index 70b8bcc2b4..f2828371e3 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-17.0.2-intel-2017a.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-17.0.2-intel-2017a.eb @@ -26,6 +26,7 @@ source_urls = [ 'ftp://ftp.freedesktop.org/pub/mesa/%(version)s', 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x/%(version)s', ] +patches = ['Mesa-%(version)s_fix-strip-llvm-flags.patch'] builddependencies = [ ('flex', '2.6.3'), @@ -49,6 +50,8 @@ configopts = " --disable-osmesa --enable-gallium-osmesa --enable-gallium-llvm -- configopts += " --disable-gbm --disable-driglx-direct --with-gallium-drivers='swrast,swr' --disable-egl" configopts += " --with-osmesa-bits=32 --enable-texture-float --enable-llvm-shared-libs " +buildopts = 'V=1' + sanity_check_paths = { 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libOSMesa.%s' % SHLIB_EXT, 'lib/libGLESv1_CM.%s' % SHLIB_EXT, 'lib/libGLESv2.%s' % SHLIB_EXT, diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-17.0.2_fix-strip-llvm-flags.patch b/easybuild/easyconfigs/m/Mesa/Mesa-17.0.2_fix-strip-llvm-flags.patch new file mode 100644 index 0000000000..d0aae3dd9c --- /dev/null +++ b/easybuild/easyconfigs/m/Mesa/Mesa-17.0.2_fix-strip-llvm-flags.patch @@ -0,0 +1,14 @@ +strip out '-fp-model source' as a whole, rather than only stripping out '-fp-model' which leads to compilation errors: +"File not found: 'source'" + +author: Ward Poelmans (VUB) +--- mesa-17.0.2/configure.orig 2017-03-31 15:08:32.677119063 +0200 ++++ mesa-17.0.2/configure 2017-03-31 15:09:03.797577051 +0200 +@@ -22317,6 +22317,7 @@ + -e 's/\s\+-O\S*//g' \ + -e 's/\s\+-g\S*//g' \ + -e 's/-fno-rtti\>/-Fno-rtti/g' \ ++ -e 's/\s\+-fp-model \S*//g' \ + -e 's/\s\+-f\S*//g' \ + -e 's/-Fno-rtti\>/-fno-rtti/g' \ + -e 's/^ //' -- GitLab From d9dad61ddaf59e678a9abf97cc7fa9ee16318a9f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 31 Mar 2017 17:28:15 +0200 Subject: [PATCH 0486/1603] adding easyconfigs: scp-0.10.2-intel-2016b-Python-2.7.12.eb --- .../scp-0.10.2-intel-2016b-Python-2.7.12.eb | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/s/scp/scp-0.10.2-intel-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/s/scp/scp-0.10.2-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/s/scp/scp-0.10.2-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..1372c5db1e --- /dev/null +++ b/easybuild/easyconfigs/s/scp/scp-0.10.2-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,22 @@ +easyblock = 'PythonPackage' + +name = 'scp' +version = '0.10.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/jbardin/scp.py' +description = """The scp.py module uses a paramiko transport to send and recieve files via the scp1 protocol.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [('Python', '2.7.12')] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'lib' -- GitLab From f0df52802c6a87777ca2ca60a7ceff6f977cb419 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 31 Mar 2017 17:28:41 +0200 Subject: [PATCH 0487/1603] adding easyconfigs: Seaborn-0.7.1-intel-2016b-Python-2.7.12.eb --- ...Seaborn-0.7.1-intel-2016b-Python-2.7.12.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/s/Seaborn/Seaborn-0.7.1-intel-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/s/Seaborn/Seaborn-0.7.1-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/s/Seaborn/Seaborn-0.7.1-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..c0dc9e45f8 --- /dev/null +++ b/easybuild/easyconfigs/s/Seaborn/Seaborn-0.7.1-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,31 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics (SIB) +# Biozentrum - University of Basel + +easyblock = 'PythonPackage' + +name = 'Seaborn' +version = '0.7.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://stanford.edu/~mwaskom/software/seaborn/' +description = """ Seaborn is a Python visualization library based on matplotlib. + It provides a high-level interface for drawing attractive statistical graphics. """ + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('Python', '2.7.12'), + ('matplotlib', '1.5.3', versionsuffix), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'bio' -- GitLab From 77ccc1df9abe43202a2a677829df4cda59bf6b04 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 31 Mar 2017 17:34:12 +0200 Subject: [PATCH 0488/1603] {data}[intel/2017a] GDAL v2.1.3 + updated deps --- .../GDAL-2.1.3-intel-2017a-Python-2.7.13.eb | 48 +++++++++++++++++++ .../GDAL-2.1.3_fix-uchar-definition.patch | 9 ++++ .../GEOS-3.6.1-intel-2017a-Python-2.7.13.eb | 28 +++++++++++ .../l/LibTIFF/LibTIFF-4.0.7-intel-2017a.eb | 33 +++++++++++++ .../libjpeg-turbo-1.5.1-intel-2017a.eb | 30 ++++++++++++ .../l/libpng/libpng-1.6.29-GCCcore-6.3.0.eb | 29 +++++++++++ .../n/NASM/NASM-2.12.02-intel-2017a.eb | 31 ++++++++++++ .../p/PCRE/PCRE-8.40-intel-2017a.eb | 18 +++++++ .../SWIG-3.0.12-intel-2017a-Python-2.7.13.eb | 20 ++++++++ 9 files changed, 246 insertions(+) create mode 100644 easybuild/easyconfigs/g/GDAL/GDAL-2.1.3-intel-2017a-Python-2.7.13.eb create mode 100644 easybuild/easyconfigs/g/GDAL/GDAL-2.1.3_fix-uchar-definition.patch create mode 100644 easybuild/easyconfigs/g/GEOS/GEOS-3.6.1-intel-2017a-Python-2.7.13.eb create mode 100644 easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.7-intel-2017a.eb create mode 100644 easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.5.1-intel-2017a.eb create mode 100644 easybuild/easyconfigs/l/libpng/libpng-1.6.29-GCCcore-6.3.0.eb create mode 100644 easybuild/easyconfigs/n/NASM/NASM-2.12.02-intel-2017a.eb create mode 100644 easybuild/easyconfigs/p/PCRE/PCRE-8.40-intel-2017a.eb create mode 100644 easybuild/easyconfigs/s/SWIG/SWIG-3.0.12-intel-2017a-Python-2.7.13.eb diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-2.1.3-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/g/GDAL/GDAL-2.1.3-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..07385fe881 --- /dev/null +++ b/easybuild/easyconfigs/g/GDAL/GDAL-2.1.3-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,48 @@ +easyblock = 'ConfigureMake' + +name = 'GDAL' +version = '2.1.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.gdal.org/' +description = """GDAL is a translator library for raster geospatial data formats that is released under an X/MIT style + Open Source license by the Open Source Geospatial Foundation. As a library, it presents a single abstract data model + to the calling application for all supported formats. It also comes with a variety of useful commandline utilities for + data translation and processing.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'usempi': True} + +source_urls = ['http://download.osgeo.org/gdal/%(version)s/'] +sources = [SOURCELOWER_TAR_XZ] +patches = ['GDAL-%(version)s_fix-uchar-definition.patch'] + +dependencies = [ + ('Python', '2.7.13'), + ('netCDF', '4.4.1.1'), + ('expat', '2.2.0'), + ('GEOS', '3.6.1', versionsuffix), + ('SQLite', '3.17.0'), + ('libxml2', '2.9.4'), + ('libpng', '1.6.29'), + ('libjpeg-turbo', '1.5.1'), + ('JasPer', '2.0.12'), + ('LibTIFF', '4.0.7'), + ('zlib', '1.2.11'), + ('cURL', '7.53.1'), + ('PCRE', '8.40'), +] + +configopts = '--with-expat=$EBROOTEXPAT --with-libz=$EBROOTLIBZ --with-hdf5=$EBROOTHDF5 --with-netcdf=$EBROOTNETCDF' +configopts += ' --with-xml2=$EBROOTLIBXML2 --with-geos=$EBROOTGEOS/bin/geos-config --with-jpeg=$EBROOTLIBJPEGMINTURBO' +configopts += ' --with-png=$EBROOTLIBPNG --with-sqlite3=$EBROOTSQLITE --with-jasper=$EBROOTJASPER' +configopts += ' --with-libtiff=$EBROOTLIBTIFF --with-pcre=$EBROOTPCRE --with-python=$EBROOTPYTHON/bin/python' + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +sanity_check_paths = { + 'files': ['lib/libgdal.a', 'lib/libgdal.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include', 'lib/python%(pyshortver)s/site-packages'] +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-2.1.3_fix-uchar-definition.patch b/easybuild/easyconfigs/g/GDAL/GDAL-2.1.3_fix-uchar-definition.patch new file mode 100644 index 0000000000..c70a977531 --- /dev/null +++ b/easybuild/easyconfigs/g/GDAL/GDAL-2.1.3_fix-uchar-definition.patch @@ -0,0 +1,9 @@ +--- gdal-2.1.3/frmts/jpeg2000/jpeg2000_vsil_io.h.orig 2017-03-31 17:06:52.996122910 +0200 ++++ gdal-2.1.3/frmts/jpeg2000/jpeg2000_vsil_io.h 2017-03-31 17:07:06.356370202 +0200 +@@ -34,4 +34,6 @@ + + jas_stream_t *JPEG2000_VSIL_fopen(const char *filename, const char *mode); + ++#define uchar unsigned char ++ + #endif diff --git a/easybuild/easyconfigs/g/GEOS/GEOS-3.6.1-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/g/GEOS/GEOS-3.6.1-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..4483d7a5d0 --- /dev/null +++ b/easybuild/easyconfigs/g/GEOS/GEOS-3.6.1-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'GEOS' +version = '3.6.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://trac.osgeo.org/geos' +description = """GEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (JTS)""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['http://download.osgeo.org/geos/'] +sources = [SOURCELOWER_TAR_BZ2] + +dependencies = [('Python', '2.7.13')] + +builddependencies = [('SWIG', '3.0.12', versionsuffix)] + +configopts = '--enable-python' + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +sanity_check_paths = { + 'files': ['bin/geos-config', 'lib/libgeos.%s' % SHLIB_EXT, 'lib/libgeos.a', 'include/geos.h'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/geos'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.7-intel-2017a.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.7-intel-2017a.eb new file mode 100644 index 0000000000..9087c14aa4 --- /dev/null +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.7-intel-2017a.eb @@ -0,0 +1,33 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos , Alan O'Cais (JSC) +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## +easyblock = 'ConfigureMake' + +name = 'LibTIFF' +version = '4.0.7' + +homepage = 'http://www.remotesensing.org/libtiff/' +description = "tiff: Library and tools for reading and writing TIFF data files" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [ + 'http://download.osgeo.org/libtiff/', + 'ftp://ftp.remotesensing.org/pub/libtiff/', +] +sources = ['tiff-%(version)s.tar.gz'] + +sanity_check_paths = { + 'files': ['bin/tiffinfo'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.5.1-intel-2017a.eb b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.5.1-intel-2017a.eb new file mode 100644 index 0000000000..921c5c073d --- /dev/null +++ b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.5.1-intel-2017a.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'libjpeg-turbo' +version = '1.5.1' + +homepage = 'http://sourceforge.net/projects/libjpeg-turbo/' +description = """libjpeg-turbo is a fork of the original IJG libjpeg which uses SIMD to accelerate baseline JPEG +compression and decompression. libjpeg is a library that implements JPEG image encoding, decoding and transcoding. +""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('NASM', '2.12.02'), +] + +configopts = "--with-jpeg8" +runtest = "test" + +sanity_check_paths = { + 'files': ['bin/cjpeg', 'bin/djpeg', 'bin/jpegtran', 'bin/rdjpgcom', 'bin/tjbench', 'bin/wrjpgcom', + 'lib/libjpeg.a', 'lib/libjpeg.%s' % SHLIB_EXT, 'lib/libturbojpeg.a', 'lib/libturbojpeg.%s' % SHLIB_EXT], + 'dirs': ['include', 'share'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.29-GCCcore-6.3.0.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.29-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..85ea50b710 --- /dev/null +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.29-GCCcore-6.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'libpng' +version = '1.6.29' + +homepage = 'http://www.libpng.org/pub/png/libpng.html' +description = "libpng is the official PNG reference library" + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('zlib', '1.2.11')] + +# use same binutils version that was used when building GCCcore toolchain +builddependencies = [('binutils', '2.27', '', True)] + +configopts = "--with-pic" + +majminver = ''.join(version.split('.')[:2]) +sanity_check_paths = { + 'files': ['include/pngconf.h', 'include/png.h', 'include/pnglibconf.h', 'lib/libpng.a', + 'lib/libpng.%s' % SHLIB_EXT, 'lib/libpng%s.a' % majminver, 'lib/libpng%s.%s' % (majminver, SHLIB_EXT)], + 'dirs': ['bin', 'include/libpng%s' % majminver, 'share/man'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/NASM/NASM-2.12.02-intel-2017a.eb b/easybuild/easyconfigs/n/NASM/NASM-2.12.02-intel-2017a.eb new file mode 100644 index 0000000000..a4d8935beb --- /dev/null +++ b/easybuild/easyconfigs/n/NASM/NASM-2.12.02-intel-2017a.eb @@ -0,0 +1,31 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-90.html +## + +easyblock = 'ConfigureMake' + +name = 'NASM' +version = '2.12.02' + +homepage = 'http://www.nasm.us/' +description = """NASM: General-purpose x86 assembler""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://www.nasm.us/pub/nasm/releasebuilds/%(version)s'] + +sanity_check_paths = { + 'files': ['bin/nasm'], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/PCRE/PCRE-8.40-intel-2017a.eb b/easybuild/easyconfigs/p/PCRE/PCRE-8.40-intel-2017a.eb new file mode 100644 index 0000000000..b2df6c9ad9 --- /dev/null +++ b/easybuild/easyconfigs/p/PCRE/PCRE-8.40-intel-2017a.eb @@ -0,0 +1,18 @@ +easyblock = 'ConfigureMake' + +name = 'PCRE' +version = '8.40' + +homepage = 'http://www.pcre.org/' +description = """The PCRE library is a set of functions that implement regular expression pattern matching using + the same syntax and semantics as Perl 5.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +configopts = "--with-pic --disable-cpp --enable-utf --enable-unicode-properties" + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/SWIG/SWIG-3.0.12-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/s/SWIG/SWIG-3.0.12-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..b90543199e --- /dev/null +++ b/easybuild/easyconfigs/s/SWIG/SWIG-3.0.12-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,20 @@ +name = 'SWIG' +version = '3.0.12' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.swig.org/' +description = """SWIG is a software development tool that connects programs written in C and C++ with + a variety of high-level programming languages.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('Python', '2.7.13'), + ('PCRE', '8.40'), +] + +moduleclass = 'devel' -- GitLab From bbf0a5bf2bdef4672f51a6750df57ef02ed6bb41 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 31 Mar 2017 17:51:28 +0200 Subject: [PATCH 0489/1603] adding easyconfigs: LIBSVM-3.22-intel-2016b.eb --- .../l/LIBSVM/LIBSVM-3.22-intel-2016b.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/l/LIBSVM/LIBSVM-3.22-intel-2016b.eb diff --git a/easybuild/easyconfigs/l/LIBSVM/LIBSVM-3.22-intel-2016b.eb b/easybuild/easyconfigs/l/LIBSVM/LIBSVM-3.22-intel-2016b.eb new file mode 100644 index 0000000000..26b2999f95 --- /dev/null +++ b/easybuild/easyconfigs/l/LIBSVM/LIBSVM-3.22-intel-2016b.eb @@ -0,0 +1,31 @@ +easyblock = 'MakeCp' + +name = 'LIBSVM' +version = '3.22' + +homepage = 'http://www.csie.ntu.edu.tw/~cjlin/libsvm/' +description = """LIBSVM is an integrated software for support vector classification, (C-SVC, nu-SVC), regression + (epsilon-SVR, nu-SVR) and distribution estimation (one-class SVM). It supports multi-class classification.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = [homepage] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('Qt', '4.8.7')] + +buildopts = ' && cd svm-toy/qt && make MOC=$EBROOTQT/bin/moc ' +buildopts += 'CFLAGS="$CFLAGS -I$EBROOTQT/include -I$EBROOTQT/include/QtGui -lQtGui -lQtCore" && cd -' + +files_to_copy = [(['svm-*'], 'bin'), 'tools'] + +sanity_check_paths = { + 'files': ['bin/svm-%s' % x for x in ['predict', 'scale', 'train']] + ['bin/svm-toy/qt/svm-toy'], + 'dirs': ['bin/svm-toy', 'tools'], +} + +modextrapaths = { + 'PATH': ['bin', 'bin/svm-toy/qt'], +} + +moduleclass = 'lib' -- GitLab From e9b30261c84e53d6c1d33de470ad822df6a81c07 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 31 Mar 2017 18:15:56 +0200 Subject: [PATCH 0490/1603] consistently add zlib as dependency in SCOTCH easyconfigs --- .../s/SCOTCH/SCOTCH-5.1.12b_esmumps-goolf-1.4.10.eb | 4 ++++ .../s/SCOTCH/SCOTCH-5.1.12b_esmumps-ictce-5.3.0.eb | 4 ++++ .../easyconfigs/s/SCOTCH/SCOTCH-6.0.0_esmumps-goolf-1.4.10.eb | 4 ++++ .../easyconfigs/s/SCOTCH/SCOTCH-6.0.0_esmumps-ictce-5.3.0.eb | 4 ++++ .../easyconfigs/s/SCOTCH/SCOTCH-6.0.0_esmumps-ictce-5.5.0.eb | 4 ++++ .../easyconfigs/s/SCOTCH/SCOTCH-6.0.0_esmumps-ictce-6.2.5.eb | 4 ++++ .../easyconfigs/s/SCOTCH/SCOTCH-6.0.0_esmumps-intel-2014b.eb | 4 ++++ easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.3-intel-2015a.eb | 4 ++++ easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-foss-2015.05.eb | 4 ++++ easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-foss-2015b.eb | 4 ++++ easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-foss-2016a.eb | 4 ++++ easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-foss-2016b.eb | 4 ++++ easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-gimkl-2.11.5.eb | 4 ++++ easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-intel-2015a.eb | 4 ++++ .../easyconfigs/s/SCOTCH/SCOTCH-6.0.4-intel-2015b-64bitint.eb | 4 ++++ easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-intel-2015b.eb | 4 ++++ easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-intel-2016a.eb | 4 ++++ 17 files changed, 68 insertions(+) diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-5.1.12b_esmumps-goolf-1.4.10.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-5.1.12b_esmumps-goolf-1.4.10.eb index f7e1fa75af..fb8bdd5fe8 100644 --- a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-5.1.12b_esmumps-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-5.1.12b_esmumps-goolf-1.4.10.eb @@ -11,4 +11,8 @@ toolchainopts = {'pic': True} source_urls = ['https://gforge.inria.fr/frs/download.php/28978/'] sources = ['%(namelower)s_%(version)s.tar.gz'] +dependencies = [ + ('zlib', '1.2.7'), +] + moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-5.1.12b_esmumps-ictce-5.3.0.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-5.1.12b_esmumps-ictce-5.3.0.eb index 63e54d60a9..a840cb128c 100644 --- a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-5.1.12b_esmumps-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-5.1.12b_esmumps-ictce-5.3.0.eb @@ -12,4 +12,8 @@ toolchainopts = {'pic': True} source_urls = ['https://gforge.inria.fr/frs/download.php/28978/'] sources = ['%(namelower)s_%(version)s.tar.gz'] +dependencies = [ + ('zlib', '1.2.7'), +] + moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.0_esmumps-goolf-1.4.10.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.0_esmumps-goolf-1.4.10.eb index adc2bceafc..36e2a02cae 100644 --- a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.0_esmumps-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.0_esmumps-goolf-1.4.10.eb @@ -11,4 +11,8 @@ toolchainopts = {'pic': True} source_urls = ['https://gforge.inria.fr/frs/download.php/31832/'] sources = ['%(namelower)s_%(version)s.tar.gz'] +dependencies = [ + ('zlib', '1.2.7'), +] + moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.0_esmumps-ictce-5.3.0.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.0_esmumps-ictce-5.3.0.eb index 8e693c1ca4..b9f3cfb699 100644 --- a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.0_esmumps-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.0_esmumps-ictce-5.3.0.eb @@ -11,4 +11,8 @@ toolchainopts = {'pic': True} source_urls = ['https://gforge.inria.fr/frs/download.php/31832/'] sources = ['%(namelower)s_%(version)s.tar.gz'] +dependencies = [ + ('zlib', '1.2.7'), +] + moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.0_esmumps-ictce-5.5.0.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.0_esmumps-ictce-5.5.0.eb index b0d4836a13..60cfca1ccb 100644 --- a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.0_esmumps-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.0_esmumps-ictce-5.5.0.eb @@ -11,4 +11,8 @@ toolchainopts = {'pic': True} source_urls = ['https://gforge.inria.fr/frs/download.php/31832/'] sources = ['%(namelower)s_%(version)s.tar.gz'] +dependencies = [ + ('zlib', '1.2.8'), +] + moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.0_esmumps-ictce-6.2.5.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.0_esmumps-ictce-6.2.5.eb index b9f29b45c5..1a0f934621 100644 --- a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.0_esmumps-ictce-6.2.5.eb +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.0_esmumps-ictce-6.2.5.eb @@ -11,4 +11,8 @@ toolchainopts = {'pic': True} source_urls = ['https://gforge.inria.fr/frs/download.php/31832/'] sources = ['%(namelower)s_%(version)s.tar.gz'] +dependencies = [ + ('zlib', '1.2.8'), +] + moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.0_esmumps-intel-2014b.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.0_esmumps-intel-2014b.eb index 89020e5a6b..4e6810fc24 100644 --- a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.0_esmumps-intel-2014b.eb +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.0_esmumps-intel-2014b.eb @@ -11,4 +11,8 @@ toolchainopts = {'pic': True} source_urls = ['https://gforge.inria.fr/frs/download.php/31832/'] sources = ['%(namelower)s_%(version)s.tar.gz'] +dependencies = [ + ('zlib', '1.2.8'), +] + moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.3-intel-2015a.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.3-intel-2015a.eb index f4c56ce013..68499c20c9 100644 --- a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.3-intel-2015a.eb +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.3-intel-2015a.eb @@ -11,4 +11,8 @@ toolchainopts = {'pic': True} source_urls = ['http://gforge.inria.fr/frs/download.php/file/34099/'] sources = ['%(namelower)s_%(version)s.tar.gz'] +dependencies = [ + ('zlib', '1.2.8'), +] + moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-foss-2015.05.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-foss-2015.05.eb index f5bdd9828b..8e49ec9738 100644 --- a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-foss-2015.05.eb +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-foss-2015.05.eb @@ -11,4 +11,8 @@ toolchainopts = {'pic': True} source_urls = ['http://gforge.inria.fr/frs/download.php/file/34618/'] sources = ['%(namelower)s_%(version)s.tar.gz'] +dependencies = [ + ('zlib', '1.2.8'), +] + moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-foss-2015b.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-foss-2015b.eb index 3f65d37408..6646f63b1d 100644 --- a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-foss-2015b.eb +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-foss-2015b.eb @@ -11,4 +11,8 @@ toolchainopts = {'pic': True} source_urls = ['http://gforge.inria.fr/frs/download.php/file/34618/'] sources = ['%(namelower)s_%(version)s.tar.gz'] +dependencies = [ + ('zlib', '1.2.8'), +] + moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-foss-2016a.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-foss-2016a.eb index 431d04e9df..6627e15ad7 100644 --- a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-foss-2016a.eb +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-foss-2016a.eb @@ -11,4 +11,8 @@ toolchainopts = {'pic': True} source_urls = ['http://gforge.inria.fr/frs/download.php/file/34618/'] sources = ['%(namelower)s_%(version)s.tar.gz'] +dependencies = [ + ('zlib', '1.2.8'), +] + moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-foss-2016b.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-foss-2016b.eb index 9fb7233435..e19c44686d 100644 --- a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-foss-2016b.eb +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-foss-2016b.eb @@ -11,4 +11,8 @@ toolchainopts = {'pic': True} source_urls = ['http://gforge.inria.fr/frs/download.php/file/34618/'] sources = ['%(namelower)s_%(version)s.tar.gz'] +dependencies = [ + ('zlib', '1.2.8'), +] + moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-gimkl-2.11.5.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-gimkl-2.11.5.eb index b61aa3728e..4bbf975f93 100644 --- a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-gimkl-2.11.5.eb @@ -11,4 +11,8 @@ toolchainopts = {'pic': True} source_urls = ['http://gforge.inria.fr/frs/download.php/file/34618/'] sources = ['%(namelower)s_%(version)s.tar.gz'] +dependencies = [ + ('zlib', '1.2.8'), +] + moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-intel-2015a.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-intel-2015a.eb index a98a4841f7..173ec5abc6 100644 --- a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-intel-2015a.eb +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-intel-2015a.eb @@ -11,4 +11,8 @@ toolchainopts = {'pic': True} source_urls = ['http://gforge.inria.fr/frs/download.php/file/34618/'] sources = ['%(namelower)s_%(version)s.tar.gz'] +dependencies = [ + ('zlib', '1.2.8'), +] + moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-intel-2015b-64bitint.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-intel-2015b-64bitint.eb index ba1a0a43d1..a9f67fc882 100644 --- a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-intel-2015b-64bitint.eb +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-intel-2015b-64bitint.eb @@ -12,4 +12,8 @@ toolchainopts = {'pic': True, 'i8': True} source_urls = ['http://gforge.inria.fr/frs/download.php/file/34618/'] sources = ['%(namelower)s_%(version)s.tar.gz'] +dependencies = [ + ('zlib', '1.2.8'), +] + moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-intel-2015b.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-intel-2015b.eb index 34df491afd..5f4f35c9c0 100644 --- a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-intel-2015b.eb +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-intel-2015b.eb @@ -11,4 +11,8 @@ toolchainopts = {'pic': True} source_urls = ['http://gforge.inria.fr/frs/download.php/file/34618/'] sources = ['%(namelower)s_%(version)s.tar.gz'] +dependencies = [ + ('zlib', '1.2.8'), +] + moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-intel-2016a.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-intel-2016a.eb index a90bb75fa5..30e51cb632 100644 --- a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-intel-2016a.eb +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-intel-2016a.eb @@ -11,4 +11,8 @@ toolchainopts = {'pic': True} source_urls = ['http://gforge.inria.fr/frs/download.php/file/34618/'] sources = ['%(namelower)s_%(version)s.tar.gz'] +dependencies = [ + ('zlib', '1.2.8'), +] + moduleclass = 'math' -- GitLab From e11ecadb7b25a413b83103555ebe21477c841adb Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 31 Mar 2017 18:40:48 +0200 Subject: [PATCH 0491/1603] adding easyconfigs: cairo-1.14.8-intel-2017a.eb, pixman-0.34.0-GCCcore-6.3.0.eb, GLib-2.52.0-intel-2017a.eb --- .../c/cairo/cairo-1.14.8-intel-2017a.eb | 43 +++++++++++++++++++ .../g/GLib/GLib-2.52.0-intel-2017a.eb | 34 +++++++++++++++ .../p/pixman/pixman-0.34.0-GCCcore-6.3.0.eb | 23 ++++++++++ 3 files changed, 100 insertions(+) create mode 100644 easybuild/easyconfigs/c/cairo/cairo-1.14.8-intel-2017a.eb create mode 100644 easybuild/easyconfigs/g/GLib/GLib-2.52.0-intel-2017a.eb create mode 100644 easybuild/easyconfigs/p/pixman/pixman-0.34.0-GCCcore-6.3.0.eb diff --git a/easybuild/easyconfigs/c/cairo/cairo-1.14.8-intel-2017a.eb b/easybuild/easyconfigs/c/cairo/cairo-1.14.8-intel-2017a.eb new file mode 100644 index 0000000000..6f9eb993e3 --- /dev/null +++ b/easybuild/easyconfigs/c/cairo/cairo-1.14.8-intel-2017a.eb @@ -0,0 +1,43 @@ +easyblock = 'ConfigureMake' + +name = 'cairo' +version = '1.14.8' + +homepage = 'http://cairographics.org' +description = """Cairo is a 2D graphics library with support for multiple output devices. + Currently supported output targets include the X Window System (via both Xlib and XCB), Quartz, Win32, image buffers, + PostScript, PDF, and SVG file output. Experimental backends include OpenGL, BeOS, OS/2, and DirectFB""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['http://cairographics.org/releases/'] +sources = [SOURCE_TAR_XZ] + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.11'), + ('libpng', '1.6.29'), + ('freetype', '2.7.1'), + ('pixman', '0.34.0'), + ('expat', '2.2.0'), + ('GLib', '2.52.0'), + ('X11', '20170129'), +] + +# disable symbol lookup, which requires -lbfd, to avoid link issues with (non-PIC) libiberty.a provided by GCC +configopts = "--enable-symbol-lookup=no --enable-gobject=yes --enable-svg=yes --enable-tee=yes --enable-xlib-xcb " + +# workaround for "hidden symbol .* in .* is referenced by DSO" and "ld: final link failed: Bad value" +buildopts = 'LD="$CC" LDFLAGS="$LDFLAGS -shared-intel"' + +sanity_check_paths = { + 'files': ['bin/cairo-trace', 'lib/cairo/libcairo-trace.so', 'lib/cairo/libcairo-trace.a', + 'lib/libcairo.a', 'lib/libcairo-gobject.a', 'lib/libcairo-script-interpreter.a', + 'lib/libcairo-gobject.so', 'lib/libcairo-script-interpreter.so', 'lib/libcairo.so'] + + ['include/cairo/cairo%s.h' % x for x in ['', '-deprecated', '-features', '-ft', '-gobject', '-pdf', '-ps', + '-script', '-script-interpreter', '-svg', '-version', '-xcb', + '-xlib', '-xlib-xrender']], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.52.0-intel-2017a.eb b/easybuild/easyconfigs/g/GLib/GLib-2.52.0-intel-2017a.eb new file mode 100644 index 0000000000..dcffcd7dec --- /dev/null +++ b/easybuild/easyconfigs/g/GLib/GLib-2.52.0-intel-2017a.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'GLib' +version = '2.52.0' + +homepage = 'http://www.gtk.org/' +description = """GLib is one of the base libraries of the GTK+ project""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('libffi', '3.2.1'), + ('gettext', '0.19.8.1'), + ('libxml2', '2.9.4'), + ('PCRE', '8.40'), +] + +builddependencies = [('Python', '2.7.13')] + +configopts = "--disable-maintainer-mode --disable-silent-rules --disable-libelf --disable-systemtap " +configopts += "--enable-static --enable-shared" + +postinstallcmds = ["sed -i -e 's|#!.*python|#!/usr/bin/env python|' %(installdir)s/bin/*"] + +sanity_check_paths = { + 'files': ['lib/libglib-%(version_major)s.0.a', 'lib/libglib-%%(version_major)s.0.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/pixman/pixman-0.34.0-GCCcore-6.3.0.eb b/easybuild/easyconfigs/p/pixman/pixman-0.34.0-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..185ce92b1d --- /dev/null +++ b/easybuild/easyconfigs/p/pixman/pixman-0.34.0-GCCcore-6.3.0.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'pixman' +version = '0.34.0' + +homepage = 'http://www.pixman.org/' +description = """Pixman is a low-level software library for pixel manipulation, providing features such as image +compositing and trapezoid rasterization. Important users of pixman are the cairo graphics library and the X server.""" + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} + +source_urls = ['http://cairographics.org/releases/'] +sources = [SOURCE_TAR_GZ] + +# use same binutils version that was used when building GCCcore toolchain +builddependencies = [('binutils', '2.27', '', True)] + +sanity_check_paths = { + 'files': ['lib/libpixman-1.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'vis' -- GitLab From 8cea6ea8a6ecbc4dd325a0acdce97bd43aba31af Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 31 Mar 2017 18:41:22 +0200 Subject: [PATCH 0492/1603] adding easyconfigs: ED2-20170201-intel-2017a-serial.eb --- .../e/ED2/ED2-20170201-intel-2017a-serial.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/e/ED2/ED2-20170201-intel-2017a-serial.eb diff --git a/easybuild/easyconfigs/e/ED2/ED2-20170201-intel-2017a-serial.eb b/easybuild/easyconfigs/e/ED2/ED2-20170201-intel-2017a-serial.eb new file mode 100644 index 0000000000..0ba1a5a27b --- /dev/null +++ b/easybuild/easyconfigs/e/ED2/ED2-20170201-intel-2017a-serial.eb @@ -0,0 +1,39 @@ +easyblock = 'MakeCp' + +name = 'ED2' +version = '20170201' +commit = '0146fa4' +versionsuffix = '-serial' + +homepage = 'https://github.com/EDmodel/ED2' +description = """The Ecosystem Demography Biosphere Model (ED2) is an integrated terrestrial biosphere model + incorporating hydrology, land-surface biophysics, vegetation dynamics, and soil carbon and nitrogen biogeochemistry""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['https://github.com/EDmodel/ED2/archive/'] +sources = ['%s.tar.gz' % commit] + +patches = [ + 'ED2_install-without-make.patch', + 'ED2_fix-type.patch', +] + +dependencies = [('HDF5', '1.10.0-patch1')] + +start_dir = 'ED/build' + +# rely on install.sh to prepare everything, but run 'make' command ourselves to take control over compiler options +prebuildopts = "./install.sh --kind E --platform intel --gitoff && cd bin-opt-E && " + +buildopts = "OPT=opt KIND_COMP=E GIT_TAG= HDF5_PATH=$EBROOTHDF5 PAR_LIBS='' PAR_DEFS='' " +buildopts += 'F_COMP="$FC" C_COMP="$CC" LOADER="$FC" F_OPTS="$FFLAGS" C_OPTS="$CFLAGS" F_LOWO_OPTS="$FFLAGS" && cd -' + +files_to_copy = [(['ED/build/ed_2.1-opt'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/ed_2.1-opt'], + 'dirs': [], +} + +moduleclass = 'geo' -- GitLab From 7040ded550b1739b2a37c1ce8193dcb5c9509991 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 31 Mar 2017 19:03:15 +0200 Subject: [PATCH 0493/1603] adding easyconfigs: R-3.3.3-intel-2017a-X11-20170129.eb, libGLU-9.0.0-intel-2017a.eb, Tk-8.6.6-intel-2017a.eb, PROJ-4.9.3-intel-2017a.eb --- .../l/libGLU/libGLU-9.0.0-intel-2017a.eb | 24 + .../p/PROJ/PROJ-4.9.3-intel-2017a.eb | 30 ++ .../r/R/R-3.3.3-intel-2017a-X11-20170129.eb | 509 ++++++++++++++++++ .../easyconfigs/t/Tk/Tk-8.6.6-intel-2017a.eb | 27 + 4 files changed, 590 insertions(+) create mode 100644 easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-intel-2017a.eb create mode 100644 easybuild/easyconfigs/p/PROJ/PROJ-4.9.3-intel-2017a.eb create mode 100644 easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170129.eb create mode 100644 easybuild/easyconfigs/t/Tk/Tk-8.6.6-intel-2017a.eb diff --git a/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-intel-2017a.eb b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-intel-2017a.eb new file mode 100644 index 0000000000..7dff238507 --- /dev/null +++ b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-intel-2017a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'libGLU' +version = '9.0.0' + +homepage = 'ftp://ftp.freedesktop.org/pub/mesa/glu/' +description = """The OpenGL Utility Library (GLU) is a computer graphics library for OpenGL. """ + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True} + +source_urls = ['ftp://ftp.freedesktop.org/pub/mesa/glu/'] +sources = ['glu-%(version)s.tar.bz2'] + +dependencies = [ + ('Mesa', '17.0.2'), +] + +sanity_check_paths = { + 'files': ['lib/libGLU.so.1'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/PROJ/PROJ-4.9.3-intel-2017a.eb b/easybuild/easyconfigs/p/PROJ/PROJ-4.9.3-intel-2017a.eb new file mode 100644 index 0000000000..07a9a99e42 --- /dev/null +++ b/easybuild/easyconfigs/p/PROJ/PROJ-4.9.3-intel-2017a.eb @@ -0,0 +1,30 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2014-2015 The Cyprus Institute +# Authors:: Thekla Loizou +# License:: MIT/GPL +# +## +easyblock = 'ConfigureMake' + +name = 'PROJ' +version = '4.9.3' + +homepage = 'http://trac.osgeo.org/proj/' +description = """Program proj is a standard Unix filter function which converts +geographic longitude and latitude coordinates into cartesian coordinates""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['http://download.osgeo.org/proj/'] +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': ['bin/cs2cs', 'bin/geod', 'bin/invgeod', 'bin/invproj', + 'bin/nad2bin', 'bin/proj'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170129.eb b/easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170129.eb new file mode 100644 index 0000000000..e0614dfdd9 --- /dev/null +++ b/easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170129.eb @@ -0,0 +1,509 @@ +name = 'R' +version = '3.3.3' +x11ver = '20170129' +versionsuffix = '-X11-%s' % x11ver + +homepage = 'http://www.r-project.org/' +description = """R is a free software environment for statistical computing and graphics.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://cran.us.r-project.org/src/base/R-%(version_major)s'] + +preconfigopts = 'BLAS_LIBS="$LIBBLAS" LAPACK_LIBS="$LIBLAPACK"' +configopts = "--with-lapack --with-blas --with-pic --enable-threads --with-x=no --enable-R-shlib" +#Actually use Tcl/Tk +configopts += ' --with-tcl-config=$EBROOTTCL/lib/tclConfig.sh --with-tk-config=$EBROOTTK/lib/tkConfig.sh ' +# Enable graphics capabilities for plotting. +configopts += " --with-cairo --with-libpng --with-jpeglib --with-libtiff" +# some recommended packages may fail in a parallel build (e.g. Matrix), and we're installing them anyway below +configopts += " --with-recommended-packages=no" + +dependencies = [ + ('X11', x11ver), + ('Mesa', '17.0.2'), + ('libGLU', '9.0.0'), + ('cairo', '1.14.8'), + ('libreadline', '7.0'), + ('ncurses', '6.0'), + ('bzip2', '1.0.6'), + ('XZ', '5.2.3'), + ('zlib', '1.2.11'), + ('SQLite', '3.17.0'), + ('PCRE', '8.40'), + ('libpng', '1.6.29'), # for plotting in R + ('libjpeg-turbo', '1.5.1'), # for plottting in R + ('LibTIFF', '4.0.7'), + ('Java', '1.8.0_121', '', True), # Java bindings are built if Java is found, might as well provide it + ('Tcl', '8.6.6'), # for tcltk + ('Tk', '8.6.6'), # for tcltk + ('cURL', '7.53.1'), # for RCurl + ('libxml2', '2.9.4'), # for XML + ('GDAL', '2.1.3', '-Python-2.7.13'), # for rgdal + ('PROJ', '4.9.3'), # for rgdal + ('GMP', '6.1.2'), # for igraph + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.2h'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +name_tmpl = '%(name)s_%(version)s.tar.gz' +ext_options = { + 'source_urls': [ + 'http://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'http://cran.r-project.org/src/contrib/', # current version of packages + 'http://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': name_tmpl, +} + +# !! order of packages is important !! +# packages updated on March 7th 2017 +exts_list = [ + # default libraries, only here to sanity check their presence + 'base', + 'datasets', + 'graphics', + 'grDevices', + 'grid', + 'methods', + 'splines', + 'stats', + 'stats4', + 'tools', + 'utils', + # non-standard libraries, should be specified with fixed versions! + ('Rmpi', '0.6-6', ext_options), + ('abind', '1.4-5', ext_options), + ('magic', '1.5-6', ext_options), + ('geometry', '0.3-6', ext_options), + ('bit', '1.1-12', ext_options), + ('filehash', '2.3', ext_options), + ('ff', '2.2-13', ext_options), + ('bnlearn', '4.1', ext_options), + ('bootstrap', '2017.2', ext_options), + ('combinat', '0.0-8', ext_options), + ('deal', '1.2-37', ext_options), + ('fdrtool', '1.2.15', ext_options), + ('formatR', '1.4', ext_options), + ('gtools', '3.5.0', ext_options), + ('gdata', '2.17.0', ext_options), + ('GSA', '1.03', ext_options), + ('highr', '0.6', ext_options), + ('infotheo', '1.2.0', ext_options), + ('lars', '1.2', ext_options), + ('lazy', '1.2-15', ext_options), + ('kernlab', '0.9-25', ext_options), + ('mime', '0.5', ext_options), + ('markdown', '0.7.7', ext_options), + ('mlbench', '2.1-1', ext_options), + ('NLP', '0.1-10', ext_options), + ('mclust', '5.2.2', ext_options), + ('RANN', '2.5', ext_options), + ('rmeta', '2.16', ext_options), + ('segmented', '0.5-1.4', ext_options), + ('som', '0.3-5.1', ext_options), + ('SuppDists', '1.1-9.4', ext_options), + ('stabledist', '0.7-1', ext_options), + ('survivalROC', '1.0.3', ext_options), + ('pspline', '1.0-17', ext_options), + ('timeDate', '3012.100', ext_options), + ('longmemo', '1.0-0', ext_options), + ('ADGofTest', '0.3', ext_options), + ('ade4', '1.7-5', ext_options), + ('AlgDesign', '1.1-7.3', ext_options), + ('base64enc', '0.1-3', ext_options), + ('BH', '1.62.0-1', ext_options), + ('brew', '1.0-6', ext_options), + ('Brobdingnag', '1.2-4', ext_options), + ('corpcor', '1.6.8', ext_options), + ('longitudinal', '1.1.12', ext_options), + ('backports', '1.0.5', ext_options), + ('checkmate', '1.8.2', ext_options), + ('Rcpp', '0.12.9', ext_options), + ('cubature', '1.3-6', ext_options), + ('DEoptimR', '1.0-8', ext_options), + ('digest', '0.6.12', ext_options), + ('fastmatch', '1.1-0', ext_options), + ('ffbase', '0.12.3', ext_options), + ('iterators', '1.0.8', ext_options), + ('maps', '3.1.1', ext_options), + ('nnls', '1.4', ext_options), + ('sendmailR', '1.2-1', ext_options), + ('spam', '1.4-0', ext_options), + ('subplex', '1.2-2', ext_options), + ('stringi', '1.1.2', ext_options), + ('magrittr', '1.5', ext_options), + ('stringr', '1.2.0', ext_options), + ('evaluate', '0.10', ext_options), + ('logspline', '2.1.9', ext_options), + ('ncbit', '2013.03.29', ext_options), + ('permute', '0.9-4', ext_options), + ('plotrix', '3.6-4', ext_options), + ('randomForest', '4.6-12', ext_options), + ('scatterplot3d', '0.3-38', ext_options), + ('SparseM', '1.76', ext_options), + ('tripack', '1.3-8', ext_options), + ('irace', '2.1', ext_options), + ('rJava', '0.9-8', ext_options), + ('lattice', '0.20-34', ext_options), + ('RColorBrewer', '1.1-2', ext_options), + ('latticeExtra', '0.6-28', ext_options), + ('Matrix', '1.2-8', ext_options), + ('png', '0.1-7', ext_options), + ('RcppArmadillo', '0.7.700.0.0', ext_options), + ('plyr', '1.8.4', ext_options), + ('pROC', '1.9.1', ext_options), + ('quadprog', '1.5-5', ext_options), + ('BB', '2014.10-1', ext_options), + ('BBmisc', '1.11', ext_options), + ('fail', '1.3', ext_options), + ('rlecuyer', '0.3-4', ext_options), + ('snow', '0.4-2', ext_options), + ('MASS', '7.3-45', ext_options), + ('tree', '1.0-37', ext_options), + ('pls', '2.6-0', ext_options), + ('class', '7.3-14', ext_options), + ('e1071', '1.6-8', ext_options), + ('nnet', '7.3-12', ext_options), + ('nlme', '3.1-131', ext_options), + ('minqa', '1.2.4', ext_options), + ('RcppEigen', '0.3.2.9.0', ext_options), + ('MatrixModels', '0.4-1', ext_options), + ('quantreg', '5.29', ext_options), + ('mgcv', '1.8-17', ext_options), + ('colorspace', '1.3-2', ext_options), + ('robustbase', '0.92-7', ext_options), + ('sp', '1.2-4', ext_options), + ('zoo', '1.7-14', ext_options), + ('lmtest', '0.9-35', ext_options), + ('vcd', '1.4-3', ext_options), + ('snowfall', '1.84-6.1', ext_options), + ('rpart', '4.1-10', ext_options), + ('survival', '2.40-1', ext_options), + ('mice', '2.30', ext_options), + ('urca', '1.3-0', ext_options), + ('fracdiff', '1.4-2', ext_options), + ('logistf', '1.22', ext_options), + ('akima', '0.6-2', ext_options), + ('bitops', '1.0-6', ext_options), + ('boot', '1.3-18', ext_options), + ('mixtools', '1.1.0', ext_options), + ('cluster', '2.0.5', ext_options), + ('gclus', '1.3.1', ext_options), + ('coda', '0.19-1', ext_options), + ('codetools', '0.2-15', ext_options), + ('foreach', '1.4.3', ext_options), + ('doMC', '1.3.4', ext_options), + ('DBI', '0.6', ext_options), + ('foreign', '0.8-67', ext_options), + ('gam', '1.14', ext_options), + ('gamlss.data', '5.0-0', ext_options), + ('gamlss.dist', '5.0-0', ext_options), + ('hwriter', '1.3.2', ext_options), + ('KernSmooth', '2.23-15', ext_options), + ('xts', '0.9-7', ext_options), + ('TTR', '0.23-1', ext_options), + ('quantmod', '0.4-7', ext_options), + ('mnormt', '1.5-5', ext_options), + ('mvtnorm', '1.0-6', ext_options), + ('pcaPP', '1.9-61', ext_options), + ('numDeriv', '2016.8-1', ext_options), + ('lava', '1.4.7', ext_options), + ('prodlim', '1.6.1', ext_options), + ('pscl', '1.4.9', ext_options), + ('memoise', '1.0.0', ext_options), + ('plogr', '0.1-1', ext_options), + ('RSQLite', '1.1-2', ext_options), + ('BatchJobs', '1.6', ext_options), + ('sandwich', '2.3-4', ext_options), + ('sfsmisc', '1.1-0', ext_options), + ('spatial', '7.3-11', ext_options), + ('VGAM', '1.0-3', ext_options), + ('waveslim', '1.7.5', ext_options), + ('xtable', '1.8-2', ext_options), + ('profileModel', '0.5-9', ext_options), + ('brglm', '0.5-9', ext_options), + ('deSolve', '1.14', ext_options), + ('tseriesChaos', '0.1-13', ext_options), + ('tseries', '0.10-38', ext_options), + ('fastICA', '1.2-0', ext_options), + ('R.methodsS3', '1.7.1', ext_options), + ('R.oo', '1.21.0', ext_options), + ('cgdsr', '1.2.5', ext_options), + ('R.utils', '2.5.0', ext_options), + ('R.matlab', '3.6.1', ext_options), + ('gbm', '2.1.1', ext_options), + ('dichromat', '2.0-0', ext_options), + ('Formula', '1.2-1', ext_options), + ('acepack', '1.4.1', ext_options), + ('reshape2', '1.4.2', ext_options), + ('gtable', '0.2.0', ext_options), + ('munsell', '0.4.3', ext_options), + ('labeling', '0.3', ext_options), + ('scales', '0.4.1', ext_options), + ('proto', '1.0.0', ext_options), + ('lazyeval', '0.2.0', ext_options), + ('assertthat', '0.1', ext_options), + ('tibble', '1.2', ext_options), + ('ggplot2', '2.2.1', ext_options), + ('gridExtra', '2.2.1', ext_options), + ('chron', '2.3-50', ext_options), + ('data.table', '1.10.4', ext_options), + ('viridis', '0.3.4', ext_options), + ('yaml', '2.1.14', ext_options), + ('jsonlite', '1.3', ext_options), + ('htmltools', '0.3.5', ext_options), + ('htmlwidgets', '0.8', ext_options), + ('knitr', '1.15.1', ext_options), + ('htmlTable', '1.9', ext_options), + ('Hmisc', '4.0-2', ext_options), + ('fastcluster', '1.1.22', ext_options), + ('registry', '0.3', ext_options), + ('pkgmaker', '0.22', ext_options), + ('rngtools', '1.2.4', ext_options), + ('doParallel', '1.0.10', ext_options), + ('gridBase', '0.4-7', ext_options), + ('NMF', '0.20.6', ext_options), + ('irlba', '2.1.2', ext_options), + ('igraph', '1.0.1', ext_options), + ('GeneNet', '1.2.13', ext_options), + ('ape', '4.1', ext_options), + ('RJSONIO', '1.3-0', ext_options), + ('caTools', '1.17.1', ext_options), + ('gplots', '3.0.1', ext_options), + ('ROCR', '1.0-7', ext_options), + ('httpuv', '1.3.3', ext_options), + ('R6', '2.2.0', ext_options), + ('rjson', '0.2.15', ext_options), + ('sourcetools', '0.1.5', ext_options), + ('shiny', '1.0.0', ext_options), + ('seqinr', '3.3-3', ext_options), + ('LearnBayes', '2.15', ext_options), + ('deldir', '0.1-12', ext_options), + ('gmodels', '2.16.2', ext_options), + ('expm', '0.999-1', ext_options), + ('spdep', '0.6-11', ext_options), + ('dplyr', '0.5.0', ext_options), + ('vegan', '2.4-2', ext_options), + ('adegenet', '2.0.1', ext_options), + ('prettyunits', '1.0.2', ext_options), + ('progress', '1.1.2', ext_options), + ('rncl', '0.8.2', ext_options), + ('XML', '3.98-1.5', ext_options), + ('crayon', '1.3.2', ext_options), + ('praise', '1.0.0', ext_options), + ('testthat', '1.0.2', ext_options), + ('rprojroot', '1.2', ext_options), + ('rmarkdown', '1.3', ext_options), + ('curl', '2.3', ext_options), + ('openssl', '0.9.6', ext_options), + ('httr', '1.2.1', ext_options), + ('reshape', '0.8.6', ext_options), + ('xml2', '1.1.1', ext_options), + ('bold', '0.4.0', ext_options), + ('triebeard', '0.3.0', ext_options), + ('urltools', '1.6.0', ext_options), + ('httpcode', '0.2.0', ext_options), + ('crul', '0.3.0', ext_options), + ('rredlist', '0.3.0', ext_options), + ('rentrez', '1.0.4', ext_options), + ('rotl', '3.0.3', ext_options), + ('solrium', '0.4.0', ext_options), + ('ritis', '0.5.4', ext_options), + ('worrms', '0.1.0', ext_options), + ('natserv', '0.1.4', ext_options), + ('taxize', '0.8.4', ext_options), + ('tidyr', '0.6.1', ext_options), + ('uuid', '0.1-2', ext_options), + ('RNeXML', '2.0.7', ext_options), + ('phylobase', '0.8.2', ext_options), + ('adephylo', '1.1-10', ext_options), + ('animation', '2.4', ext_options), + ('bigmemory.sri', '0.1.3', ext_options), + ('bigmemory', '4.5.19', ext_options), + ('calibrate', '1.7.2', ext_options), + ('clusterGeneration', '1.3.4', ext_options), + ('raster', '2.5-8', ext_options), + ('dismo', '1.1-4', ext_options), + ('extrafontdb', '1.0', ext_options), + ('Rttf2pt1', '1.3.4', ext_options), + ('extrafont', '0.17', ext_options), + ('fields', '8.10', ext_options), + ('shapefiles', '0.7', ext_options), + ('fossil', '0.3.7', ext_options), + ('geiger', '2.0.6', ext_options), + ('glmnet', '2.0-5', ext_options), + ('rgl', '0.98.1', ext_options), + ('labdsv', '1.8-0', ext_options), + ('stabs', '0.6-2', ext_options), + ('modeltools', '0.2-21', ext_options), + ('strucchange', '1.5-1', ext_options), + ('TH.data', '1.0-8', ext_options), + ('multcomp', '1.4-6', ext_options), + ('coin', '1.1-3', ext_options), + ('party', '1.2-2', ext_options), + ('mboost', '2.7-0', ext_options), + ('msm', '1.6.4', ext_options), + ('nor1mix', '1.2-2', ext_options), + ('np', '0.60-2', ext_options), + ('polynom', '1.3-9', ext_options), + ('polspline', '1.1.12', ext_options), + ('rms', '5.1-0', ext_options), + ('RWekajars', '3.9.1-1', ext_options), + ('RWeka', '0.4-31', ext_options), + ('slam', '0.1-40', ext_options), + ('tm', '0.7-1', ext_options), + ('TraMineR', '1.8-13', ext_options), + ('chemometrics', '1.4.1', ext_options), + ('FNN', '1.1', ext_options), + ('ipred', '0.9-6', ext_options), + ('statmod', '1.4.29', ext_options), + ('miscTools', '0.6-22', ext_options), + ('maxLik', '1.3-4', ext_options), + ('mlogit', '0.2-4', ext_options), + ('getopt', '1.20.0', ext_options), + ('gsalib', '2.1', ext_options), + ('optparse', '1.3.2', ext_options), + ('klaR', '0.6-12', ext_options), + ('neuRosim', '0.2-12', ext_options), + ('locfit', '1.5-9.1', ext_options), + ('GGally', '1.3.0', ext_options), + ('beanplot', '1.2', ext_options), + ('clValid', '0.6-6', ext_options), + ('matrixStats', '0.51.0', ext_options), + ('DiscriMiner', '0.1-29', ext_options), + ('ellipse', '0.3-8', ext_options), + ('leaps', '3.0', ext_options), + ('nloptr', '1.0.4', ext_options), + ('lme4', '1.1-12', ext_options), + ('pbkrtest', '0.4-6', ext_options), + ('car', '2.1-4', ext_options), + ('flashClust', '1.01-2', ext_options), + ('FactoMineR', '1.35', ext_options), + ('flexclust', '1.3-4', ext_options), + ('flexmix', '2.3-13', ext_options), + ('prabclus', '2.2-6', ext_options), + ('diptest', '0.75-7', ext_options), + ('trimcluster', '0.1-2', ext_options), + ('fpc', '2.1-10', ext_options), + ('BiasedUrn', '1.07', ext_options), + ('TeachingDemos', '2.10', ext_options), + ('kohonen', '2.0.19', ext_options), + ('base64', '2.0', ext_options), + ('doRNG', '1.6', ext_options), + ('nleqslv', '3.2', ext_options), + ('RGCCA', '2.1', ext_options), + ('pheatmap', '1.0.8', ext_options), + ('openxlsx', '4.0.0', ext_options), + ('pvclust', '2.0-0', ext_options), + ('RCircos', '1.2.0', ext_options), + ('lambda.r', '1.1.9', ext_options), + ('futile.options', '1.0.0', ext_options), + ('futile.logger', '1.4.3', ext_options), + ('VennDiagram', '1.6.17', ext_options), + ('xlsxjars', '0.6.1', ext_options), + ('xlsx', '0.5.7', ext_options), + ('forecast', '8.0', ext_options), + ('fma', '2.3', ext_options), + ('expsmooth', '2.3', ext_options), + ('fpp', '0.5', ext_options), + ('maptools', '0.9-1', ext_options), + ('tensor', '1.5', ext_options), + ('polyclip', '1.5-6', ext_options), + ('goftest', '1.0-4', ext_options), + ('spatstat', '1.49-0', ext_options), + ('rgdal', '1.2-5', ext_options), + ('gdalUtils', '2.0.1.7', ext_options), + ('pracma', '1.9.9', ext_options), + ('RCurl', '1.95-4.8', ext_options), + ('bio3d', '2.3-1', ext_options), + ('AUC', '0.3.0', ext_options), + ('interpretR', '0.2.4', ext_options), + ('cvAUC', '1.1.0', ext_options), + ('SuperLearner', '2.0-21', ext_options), + ('lpSolve', '5.6.13', ext_options), + ('mediation', '4.4.5', ext_options), + ('ModelMetrics', '1.1.0', ext_options), + ('caret', '6.0-73', ext_options), + ('adabag', '4.1', ext_options), + ('parallelMap', '1.3', ext_options), + ('ParamHelpers', '1.10', ext_options), + ('ggvis', '0.4.3', ext_options), + ('mlr', '2.10', ext_options), + ('unbalanced', '2.0', ext_options), + ('RSNNS', '0.4-9', ext_options), + ('abc.data', '1.0', ext_options), + ('abc', '2.1', ext_options), + ('lhs', '0.14', ext_options), + ('tensorA', '0.36', ext_options), + ('EasyABC', '1.5', ext_options), + ('shape', '1.4.2', ext_options), + ('whisker', '0.3-2', ext_options), + ('rstudioapi', '0.6', ext_options), + ('commonmark', '1.2', ext_options), + ('desc', '1.1.0', ext_options), + ('roxygen2', '6.0.1', ext_options), + ('git2r', '0.18.0', ext_options), + ('rversions', '1.0.3', ext_options), + ('withr', '1.0.2', ext_options), + ('devtools', '1.12.0', ext_options), + ('Rook', '1.1-1', ext_options), + ('Cairo', '1.5-9', dict(ext_options.items() + [('patches', ['Cairo-1.5-9.patch'])])), + ('RMTstat', '0.3', ext_options), + ('Lmoments', '1.2-3', ext_options), + ('distillery', '1.0-2', ext_options), + ('extRemes', '2.0-8', ext_options), + ('pixmap', '0.4-11', ext_options), + ('tkrplot', '0.0-23', ext_options), + ('misc3d', '0.8-4', ext_options), + ('multicool', '0.1-10', ext_options), + ('ks', '1.10.5', ext_options), + ('logcondens', '2.1.5', ext_options), + ('Iso', '0.0-17', ext_options), + ('penalized', '0.9-50', ext_options), + ('clusterRepro', '0.5-1.1', ext_options), + ('randomForestSRC', '2.4.2', ext_options), + ('sm', '2.2-5.4', ext_options), + ('psych', '1.6.12', ext_options), + ('pbivnorm', '0.6.0', ext_options), + ('lavaan', '0.5-23.1097', ext_options), + ('matrixcalc', '1.0-3', ext_options), + ('arm', '1.9-3', ext_options), + ('mi', '1.0', ext_options), + ('visNetwork', '1.0.3', ext_options), + ('rgexf', '0.15.3', ext_options), + ('influenceR', '0.1.0', ext_options), + ('DiagrammeR', '0.9.0', ext_options), + ('sem', '3.1-8', ext_options), + ('jpeg', '0.1-8', ext_options), + ('network', '1.13.0', ext_options), + ('statnet.common', '3.3.0', ext_options), + ('sna', '2.4', ext_options), + ('glasso', '1.8', ext_options), + ('huge', '1.2.7', ext_options), + ('d3Network', '0.5.2.1', ext_options), + ('ggm', '2.3', ext_options), + ('qgraph', '1.4.2', ext_options), + ('diveRsity', '1.9.89', ext_options), + ('doSNOW', '1.0.14', ext_options), + ('phangorn', '2.1.1', ext_options), + ('geepack', '1.2-1', ext_options), + ('lubridate', '1.6.0', ext_options), + ('biom', '0.3.12', ext_options), + ('pim', '2.0.0.2', ext_options), + ('minpack.lm', '1.2-1', ext_options), + ('rootSolve', '1.7', ext_options), + ('diagram', '1.6.3', ext_options), + ('FME', '1.3.5', ext_options), + ('bmp', '0.2', ext_options), + ('readbitmap', '0.1-4', ext_options), + ('purrr', '0.2.2', ext_options), + ('imager', '0.31', ext_options), +] + +moduleclass = 'lang' + diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.6-intel-2017a.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.6-intel-2017a.eb new file mode 100644 index 0000000000..325e35acc9 --- /dev/null +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.6-intel-2017a.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'Tk' +version = '8.6.6' + +homepage = 'http://www.tcl.tk/' +description = """Tk is an open source, cross-platform widget toolchain that provides a library of basic elements for + building a graphical user interface (GUI) in many different programming languages.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +patches = ['Tk-8.6.4_different-prefix-with-tcl.patch'] + +dependencies = [ + ('X11', '20170129'), + ('Tcl', version), + ('zlib', '1.2.11'), +] + +configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib CFLAGS="-I$EBROOTTCL/include"' + +start_dir = 'unix' + +moduleclass = 'vis' -- GitLab From 2d73e37dd1ce05ab3f76e27bbe6c7972f3ff8f4a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 31 Mar 2017 19:03:49 +0200 Subject: [PATCH 0494/1603] add util-linux as dependency to GLib --- .../g/GLib/GLib-2.52.0-intel-2017a.eb | 1 + .../util-linux-2.29.2-intel-2017a.eb | 33 +++++++++++++++++++ 2 files changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/u/util-linux/util-linux-2.29.2-intel-2017a.eb diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.52.0-intel-2017a.eb b/easybuild/easyconfigs/g/GLib/GLib-2.52.0-intel-2017a.eb index dcffcd7dec..6b20efcba1 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.52.0-intel-2017a.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.52.0-intel-2017a.eb @@ -17,6 +17,7 @@ dependencies = [ ('gettext', '0.19.8.1'), ('libxml2', '2.9.4'), ('PCRE', '8.40'), + ('util-linux', '2.29.2'), ] builddependencies = [('Python', '2.7.13')] diff --git a/easybuild/easyconfigs/u/util-linux/util-linux-2.29.2-intel-2017a.eb b/easybuild/easyconfigs/u/util-linux/util-linux-2.29.2-intel-2017a.eb new file mode 100644 index 0000000000..3495ebee0c --- /dev/null +++ b/easybuild/easyconfigs/u/util-linux/util-linux-2.29.2-intel-2017a.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'util-linux' +version = '2.29.2' + +homepage = 'http://www.kernel.org/pub/linux/utils/util-linux' +description = """Set of Linux utilities""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['%s/v%%(version_major_minor)s' % homepage] +sources = [SOURCELOWER_TAR_GZ] + +# disable account related utilities (they need OS dependant pam-devel files) +# disable wall and friends (requires group changing permissions for install user) +# install systemd service files in install dir +# install bash completion files in install dir +configopts = "--disable-chfn-chsh --disable-login --disable-su " +configopts += "--disable-wall --disable-use-tty-group " +configopts += "--disable-makeinstall-chown --disable-makeinstall-setuid " +configopts += "--with-systemdsystemunitdir='${prefix}/systemd' " +configopts += "--with-bashcompletiondir='${prefix}/share/bash-completion/completions' " +# disable building Python bindings (since we don't include Python as a dep) +configopts += "--without-python " + +dependencies = [('ncurses', '6.0')] + +sanity_check_paths = { + 'files': ['lib/lib%s.a' % x for x in ['blkid', 'mount', 'uuid']], + 'dirs': ['include', 'bin', 'share', 'sbin'], +} + +moduleclass = 'tools' -- GitLab From 98be1ce1add0f4ccea0920abe523f5a7d3182fa8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 31 Mar 2017 20:29:25 +0200 Subject: [PATCH 0495/1603] adding easyconfigs: X11-20170314-GCCcore-6.3.0.eb, fontconfig-2.12.1-GCCcore-6.3.0-freetype-2.7.2.eb, freetype-2.7.2-GCCcore-6.3.0.eb --- ...fig-2.12.1-GCCcore-6.3.0-freetype-2.7.2.eb | 27 ++++ .../freetype/freetype-2.7.2-GCCcore-6.3.0.eb | 29 ++++ .../x/X11/X11-20170314-GCCcore-6.3.0.eb | 135 ++++++++++++++++++ 3 files changed, 191 insertions(+) create mode 100644 easybuild/easyconfigs/f/fontconfig/fontconfig-2.12.1-GCCcore-6.3.0-freetype-2.7.2.eb create mode 100644 easybuild/easyconfigs/f/freetype/freetype-2.7.2-GCCcore-6.3.0.eb create mode 100644 easybuild/easyconfigs/x/X11/X11-20170314-GCCcore-6.3.0.eb diff --git a/easybuild/easyconfigs/f/fontconfig/fontconfig-2.12.1-GCCcore-6.3.0-freetype-2.7.2.eb b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.12.1-GCCcore-6.3.0-freetype-2.7.2.eb new file mode 100644 index 0000000000..cc99c8e530 --- /dev/null +++ b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.12.1-GCCcore-6.3.0-freetype-2.7.2.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'fontconfig' +version = '2.12.1' +freetype_ver = '2.7.2' +versionsuffix = '-freetype-%s' % freetype_ver + +homepage = 'http://www.freedesktop.org/software/fontconfig' +description = """Fontconfig is a library designed to provide system-wide font configuration, customization and +application access.""" + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} + +source_urls = ['http://www.freedesktop.org/software/fontconfig/release/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('expat', '2.2.0'), + ('freetype', freetype_ver), +] + +# use same binutils version that was used when building GCCcore toolchain +builddependencies = [('binutils', '2.27', '', True)] + +configopts = '--disable-docs ' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.7.2-GCCcore-6.3.0.eb b/easybuild/easyconfigs/f/freetype/freetype-2.7.2-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..6f9485b3f0 --- /dev/null +++ b/easybuild/easyconfigs/f/freetype/freetype-2.7.2-GCCcore-6.3.0.eb @@ -0,0 +1,29 @@ +name = 'freetype' +version = '2.7.2' + +homepage = 'http://freetype.org' +description = """FreeType 2 is a software font engine that is designed to be small, efficient, highly customizable, and + portable while capable of producing high-quality output (glyph images). It can be used in graphics libraries, display + servers, font conversion tools, text image generation tools, and many other products as well.""" + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} + +source_urls = [GNU_SAVANNAH_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('bzip2', '1.0.6'), + ('libpng', '1.6.29'), + ('zlib', '1.2.11'), +] + +# use same binutils version that was used when building GCCcore toolchain +builddependencies = [('binutils', '2.27', '', True)] + +sanity_check_paths = { + 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, + 'lib/pkgconfig/freetype2.pc'], + 'dirs': ['include/freetype2'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/x/X11/X11-20170314-GCCcore-6.3.0.eb b/easybuild/easyconfigs/x/X11/X11-20170314-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..28c4d48e99 --- /dev/null +++ b/easybuild/easyconfigs/x/X11/X11-20170314-GCCcore-6.3.0.eb @@ -0,0 +1,135 @@ +easyblock = 'Bundle' + +name = 'X11' +version = '20170314' + +homepage = 'https://www.x.org' +description = "The X Window System (X11) is a windowing system for bitmap displays" + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} + +source_urls = [ + XORG_LIB_SOURCE, + XORG_PROTO_SOURCE, + 'http://xcb.freedesktop.org/dist/', + 'http://xkbcommon.org/download/', + 'http://cgit.freedesktop.org/xorg/util/macros/snapshot', +] + +dependencies = [ + ('bzip2', '1.0.6'), + ('fontconfig', '2.12.1', '-freetype-2.7.2'), + ('zlib', '1.2.11'), +] +builddependencies = [ + ('Autotools', '20150215'), + ('Bison', '3.0.4'), + ('gettext', '0.19.8.1'), + ('pkg-config', '0.29.1'), + # use same binutils version that was used when building GCCcore toolchain + ('binutils', '2.27', '', True), +] + +default_easyblock = 'ConfigureMake' + +common_specs = { + 'sources': [SOURCE_TAR_GZ], + 'start_dir': '%(name)s-%(version)s', +} +components = [ + ('xorg-macros', '1.19.1', { # 2017-01-29 + 'sources': ['util-macros-%(version)s.tar.gz'], + 'start_dir': 'util-macros-%(version)s', + }), + ('libpthread-stubs', '0.4', common_specs), # 2017-03-14 + ('bigreqsproto', '1.1.2', common_specs), # 2012-03-23 + ('compositeproto', '0.4.2', common_specs), # 2010-10-30 + ('damageproto', '1.2.1', common_specs), # 2010-10-30 + ('dmxproto', '2.3.1', common_specs), # 2011-01-06 + ('dri2proto', '2.8', common_specs), # 2012-07-11 + ('dri3proto', '1.0', common_specs), # 2013-11-01 + ('fixesproto', '5.0', common_specs), # 2011-03-08 + ('fontsproto', '2.1.3', common_specs), # 2014-04-14 + ('glproto', '1.4.17', common_specs), # 2013-12-10 + ('inputproto', '2.3.2', common_specs), # 2016-04-04 + ('kbproto', '1.0.7', common_specs), # 2015-05-01 + ('presentproto', '1.1', common_specs), # 2017-01-26 + ('randrproto', '1.5.0', common_specs), # 2015-05-17 + ('recordproto', '1.14.2', common_specs), # 2012-03-23 + ('renderproto', '0.11.1', common_specs), # 2010-08-10 + ('resourceproto', '1.2.0', common_specs), # 2011-05-28 + ('scrnsaverproto', '1.2.2', common_specs), # 2012-03-23 + ('videoproto', '2.3.3', common_specs), # 2016-03-11 + ('xcmiscproto', '1.2.2', common_specs), # 2012-03-23 + ('xextproto', '7.3.0', common_specs), # 2013-12-27 + ('xf86bigfontproto', '1.2.0', common_specs), # 2009-08-27 + ('xf86dgaproto', '2.1', common_specs), # 2009-10-01 + ('xf86driproto', '2.1.1', common_specs), # 2011-01-06 + ('xf86vidmodeproto', '2.3.1', common_specs), # 2011-01-06 + ('xineramaproto', '1.2.1', common_specs), # 2011-01-06 + ('xproto', '7.0.31', common_specs), # 2016-09-23 + ('libXau', '1.0.8', common_specs), # 2013-05-24 + ('libXdmcp', '1.1.2', common_specs), # 2015-03-21 + ('xcb-proto', '1.12', common_specs), # 2016-05-18 + ('libxcb', '1.12', common_specs), # 2016-05-18 + ('xtrans', '1.3.5', common_specs), # 2014-09-22 + ('libxkbcommon', '0.7.1', { # 2017-01-18 + 'sources': ['libxkbcommon-%(version)s.tar.xz'], + 'start_dir': 'libxkbcommon-%(version)s', + }), + ('libX11', '1.6.5', common_specs), # 2017-02-26 + ('libXext', '1.3.3', common_specs), # 2014-07-24 + ('libFS', '1.0.7', common_specs), # 2015-05-01 + ('libICE', '1.0.9', common_specs), # 2014-06-07 + ('libSM', '1.2.2', common_specs), # 2013-09-08 + ('libXScrnSaver', '1.2.2', common_specs), # 2012-03-08 + ('libXt', '1.1.5', common_specs), # 2015-05-01 + ('libXmu', '1.1.2', common_specs), # 2013-09-08 + ('libXpm', '3.5.12', common_specs), # 2016-12-15 + ('libXaw', '1.0.13', common_specs), # 2015-05-01 + ('libXfixes', '5.0.3', common_specs), # 2016-10-04 + ('libXcomposite', '0.4.4', common_specs), # 2013-01-03 + ('libXrender', '0.9.10', common_specs), # 2016-10-04 + ('libXcursor', '1.1.14', common_specs), # 2013-05-30 + ('libXdamage', '1.1.4', common_specs), # 2013-01-03 + ('libfontenc', '1.1.3', common_specs), # 2015-05-01 + ('libXfont', '1.5.2', common_specs), # 2016-08-31 + ('libXfont2', '2.0.1', common_specs), # 2015-12-11 + ('libXft', '2.3.2', common_specs), # 2014-06-06 + ('libXi', '1.7.9', common_specs), # 2017-01-23 + ('libXinerama', '1.1.3', common_specs), # 2013-05-31 + ('libXrandr', '1.5.1', common_specs), # 2016-10-04 + ('libXres', '1.0.7', common_specs), # 2013-05-31 + ('libXtst', '1.2.3', common_specs), # 2016-10-04 + ('libXv', '1.0.11', common_specs), # 2016-10-04 + ('libXvMC', '1.0.10', common_specs), # 2016-10-04 + ('libXxf86dga', '1.1.4', common_specs), # 2013-05-31 + ('libXxf86vm', '1.1.4', common_specs), # 2015-02-24 + ('libdmx', '1.1.3', common_specs), # 2013-05-28 + ('libpciaccess', '0.13.4', common_specs), # 2015-05-01 + ('libxkbfile', '1.0.9', common_specs), # 2015-05-01 + ('libxshmfence', '1.2', common_specs), # 2015-01-02 + ('xcb-util', '0.4.0', common_specs), # 2014-10-15 + ('xcb-util-image', '0.4.0', common_specs), # 2014-10-15 + ('xcb-util-keysyms', '0.4.0', common_specs), # 2014-10-01 + ('xcb-util-renderutil', '0.3.9', common_specs), # 2014-06-13 + ('xcb-util-wm', '0.4.1', common_specs), # 2014-02-19 + ('xcb-util-cursor', '0.1.3', common_specs), # 2016-05-12 +] + +# Python is required for xcb-proto +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] +pyshortver = '.'.join(SYS_PYTHON_VERSION.split('.')[0:2]) + +preconfigopts = "if [ ! -f configure ]; then ./autogen.sh; fi && " + +# specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module +full_sanity_check = True + +sanity_check_paths = { + 'files': ['include/X11/Xlib.h', 'include/X11/Xutil.h'], + 'dirs': ['include/GL', 'include/X11', 'include/X11/extensions', 'lib', + 'lib/python%s/site-packages/xcbgen' % pyshortver, 'lib/pkgconfig', 'share/pkgconfig'], +} + +moduleclass = 'vis' -- GitLab From 42b1274584aa7936846cd2f34cfd71df6a72f79c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 31 Mar 2017 21:06:20 +0200 Subject: [PATCH 0496/1603] no freetype 2.7.2 yet, change versionsuffix to -libpng-1.6.29 --- ....eb => fontconfig-2.12.1-GCCcore-6.3.0-libpng-1.6.29.eb} | 5 ++--- ...3.0.eb => freetype-2.7.1-GCCcore-6.3.0-libpng-1.6.29.eb} | 6 ++++-- easybuild/easyconfigs/x/X11/X11-20170314-GCCcore-6.3.0.eb | 3 ++- 3 files changed, 8 insertions(+), 6 deletions(-) rename easybuild/easyconfigs/f/fontconfig/{fontconfig-2.12.1-GCCcore-6.3.0-freetype-2.7.2.eb => fontconfig-2.12.1-GCCcore-6.3.0-libpng-1.6.29.eb} (86%) rename easybuild/easyconfigs/f/freetype/{freetype-2.7.2-GCCcore-6.3.0.eb => freetype-2.7.1-GCCcore-6.3.0-libpng-1.6.29.eb} (89%) diff --git a/easybuild/easyconfigs/f/fontconfig/fontconfig-2.12.1-GCCcore-6.3.0-freetype-2.7.2.eb b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.12.1-GCCcore-6.3.0-libpng-1.6.29.eb similarity index 86% rename from easybuild/easyconfigs/f/fontconfig/fontconfig-2.12.1-GCCcore-6.3.0-freetype-2.7.2.eb rename to easybuild/easyconfigs/f/fontconfig/fontconfig-2.12.1-GCCcore-6.3.0-libpng-1.6.29.eb index cc99c8e530..b9da643ed4 100644 --- a/easybuild/easyconfigs/f/fontconfig/fontconfig-2.12.1-GCCcore-6.3.0-freetype-2.7.2.eb +++ b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.12.1-GCCcore-6.3.0-libpng-1.6.29.eb @@ -2,8 +2,7 @@ easyblock = 'ConfigureMake' name = 'fontconfig' version = '2.12.1' -freetype_ver = '2.7.2' -versionsuffix = '-freetype-%s' % freetype_ver +versionsuffix = '-libpng-1.6.29' homepage = 'http://www.freedesktop.org/software/fontconfig' description = """Fontconfig is a library designed to provide system-wide font configuration, customization and @@ -16,7 +15,7 @@ sources = [SOURCE_TAR_GZ] dependencies = [ ('expat', '2.2.0'), - ('freetype', freetype_ver), + ('freetype', '2.7.1', versionsuffix), ] # use same binutils version that was used when building GCCcore toolchain diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.7.2-GCCcore-6.3.0.eb b/easybuild/easyconfigs/f/freetype/freetype-2.7.1-GCCcore-6.3.0-libpng-1.6.29.eb similarity index 89% rename from easybuild/easyconfigs/f/freetype/freetype-2.7.2-GCCcore-6.3.0.eb rename to easybuild/easyconfigs/f/freetype/freetype-2.7.1-GCCcore-6.3.0-libpng-1.6.29.eb index 6f9485b3f0..1b0dc16aba 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.7.2-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.7.1-GCCcore-6.3.0-libpng-1.6.29.eb @@ -1,5 +1,7 @@ name = 'freetype' -version = '2.7.2' +version = '2.7.1' +libpng_ver = '1.6.29' +versionsuffix = '-libpng-%s' % libpng_ver homepage = 'http://freetype.org' description = """FreeType 2 is a software font engine that is designed to be small, efficient, highly customizable, and @@ -13,7 +15,7 @@ sources = [SOURCE_TAR_GZ] dependencies = [ ('bzip2', '1.0.6'), - ('libpng', '1.6.29'), + ('libpng', libpng_ver), ('zlib', '1.2.11'), ] diff --git a/easybuild/easyconfigs/x/X11/X11-20170314-GCCcore-6.3.0.eb b/easybuild/easyconfigs/x/X11/X11-20170314-GCCcore-6.3.0.eb index 28c4d48e99..dc3461eb7f 100644 --- a/easybuild/easyconfigs/x/X11/X11-20170314-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/x/X11/X11-20170314-GCCcore-6.3.0.eb @@ -18,7 +18,8 @@ source_urls = [ dependencies = [ ('bzip2', '1.0.6'), - ('fontconfig', '2.12.1', '-freetype-2.7.2'), + ('fontconfig', '2.12.1', '-libpng-1.6.29'), + ('freetype', '2.7.1', '-libpng-1.6.29'), ('zlib', '1.2.11'), ] builddependencies = [ -- GitLab From 6c8b36edb3ad6280a15cc4cfc13bfabebeb5710c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 31 Mar 2017 21:07:15 +0200 Subject: [PATCH 0497/1603] bump X11 to version 20170314 in Mesa 17.0.2 easyconfig --- easybuild/easyconfigs/l/libdrm/libdrm-2.4.76-intel-2017a.eb | 2 +- easybuild/easyconfigs/m/Mesa/Mesa-17.0.2-intel-2017a.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.76-intel-2017a.eb b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.76-intel-2017a.eb index be5c5321ff..a8a5a109c8 100644 --- a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.76-intel-2017a.eb +++ b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.76-intel-2017a.eb @@ -12,7 +12,7 @@ sources = [SOURCELOWER_TAR_GZ] toolchain = {'name': 'intel', 'version': '2017a'} dependencies = [ - ('X11', '20170129'), + ('X11', '20170314'), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-17.0.2-intel-2017a.eb b/easybuild/easyconfigs/m/Mesa/Mesa-17.0.2-intel-2017a.eb index f2828371e3..8bb12d31a3 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-17.0.2-intel-2017a.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-17.0.2-intel-2017a.eb @@ -42,7 +42,7 @@ dependencies = [ ('nettle', '3.3'), ('libdrm', '2.4.76'), ('LLVM', '4.0.0'), - ('X11', '20170129'), + ('X11', '20170314'), ] # GLU is not part anymore of Mesa package! -- GitLab From 20ef59bf583714a6cf3719bdffc7e2978ad23024 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 31 Mar 2017 21:10:07 +0200 Subject: [PATCH 0498/1603] bump X11 dep version in cairo 1.14.8 easyconfig --- easybuild/easyconfigs/c/cairo/cairo-1.14.8-intel-2017a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/cairo/cairo-1.14.8-intel-2017a.eb b/easybuild/easyconfigs/c/cairo/cairo-1.14.8-intel-2017a.eb index 6f9eb993e3..6be8104cc5 100644 --- a/easybuild/easyconfigs/c/cairo/cairo-1.14.8-intel-2017a.eb +++ b/easybuild/easyconfigs/c/cairo/cairo-1.14.8-intel-2017a.eb @@ -21,7 +21,7 @@ dependencies = [ ('pixman', '0.34.0'), ('expat', '2.2.0'), ('GLib', '2.52.0'), - ('X11', '20170129'), + ('X11', '20170314'), ] # disable symbol lookup, which requires -lbfd, to avoid link issues with (non-PIC) libiberty.a provided by GCC -- GitLab From 22f35fb732e032fa70bcedfe12fcf01bffec2f89 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 31 Mar 2017 21:11:57 +0200 Subject: [PATCH 0499/1603] bump X11 deps to 20170314 --- ...017a-X11-20170129.eb => R-3.3.3-intel-2017a-X11-20170314.eb} | 2 +- easybuild/easyconfigs/t/Tk/Tk-8.6.6-intel-2017a.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/r/R/{R-3.3.3-intel-2017a-X11-20170129.eb => R-3.3.3-intel-2017a-X11-20170314.eb} (99%) diff --git a/easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170129.eb b/easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170314.eb similarity index 99% rename from easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170129.eb rename to easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170314.eb index e0614dfdd9..6892093317 100644 --- a/easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170129.eb +++ b/easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170314.eb @@ -1,6 +1,6 @@ name = 'R' version = '3.3.3' -x11ver = '20170129' +x11ver = '20170314' versionsuffix = '-X11-%s' % x11ver homepage = 'http://www.r-project.org/' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.6-intel-2017a.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.6-intel-2017a.eb index 325e35acc9..a01bad3db9 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.6-intel-2017a.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.6-intel-2017a.eb @@ -15,7 +15,7 @@ sources = ['%(namelower)s%(version)s-src.tar.gz'] patches = ['Tk-8.6.4_different-prefix-with-tcl.patch'] dependencies = [ - ('X11', '20170129'), + ('X11', '20170314'), ('Tcl', version), ('zlib', '1.2.11'), ] -- GitLab From 113e1afec23069c309e9b805b51809af27f54de1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 31 Mar 2017 21:47:22 +0200 Subject: [PATCH 0500/1603] fix freetype dep in cairo 1.14.8 easyconfig --- easybuild/easyconfigs/c/cairo/cairo-1.14.8-intel-2017a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/cairo/cairo-1.14.8-intel-2017a.eb b/easybuild/easyconfigs/c/cairo/cairo-1.14.8-intel-2017a.eb index 6be8104cc5..872e069d81 100644 --- a/easybuild/easyconfigs/c/cairo/cairo-1.14.8-intel-2017a.eb +++ b/easybuild/easyconfigs/c/cairo/cairo-1.14.8-intel-2017a.eb @@ -17,7 +17,7 @@ dependencies = [ ('bzip2', '1.0.6'), ('zlib', '1.2.11'), ('libpng', '1.6.29'), - ('freetype', '2.7.1'), + ('freetype', '2.7.1', '-libpng-1.6.29'), ('pixman', '0.34.0'), ('expat', '2.2.0'), ('GLib', '2.52.0'), -- GitLab From ad7470594727b093fefd925cf9cf6b40ad5e802f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 31 Mar 2017 22:32:51 +0200 Subject: [PATCH 0501/1603] include patches for R v3.3.3 extensions to fix compilation with Intel compilers --- .../r/R/R-3.3.3-intel-2017a-X11-20170314.eb | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170314.eb b/easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170314.eb index 6892093317..75250e8769 100644 --- a/easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170314.eb +++ b/easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170314.eb @@ -79,7 +79,7 @@ exts_list = [ ('Rmpi', '0.6-6', ext_options), ('abind', '1.4-5', ext_options), ('magic', '1.5-6', ext_options), - ('geometry', '0.3-6', ext_options), + ('geometry', '0.3-6', dict(ext_options.items() + [('patches', ['geometry-0.3-4-icc.patch'])])), ('bit', '1.1-12', ext_options), ('filehash', '2.3', ext_options), ('ff', '2.2-13', ext_options), @@ -324,7 +324,7 @@ exts_list = [ ('adephylo', '1.1-10', ext_options), ('animation', '2.4', ext_options), ('bigmemory.sri', '0.1.3', ext_options), - ('bigmemory', '4.5.19', ext_options), + ('bigmemory', '4.5.19', dict(ext_options.items() + [('patches', ['bigmemory-4.5.19_icpc-wd308.patch'])])), ('calibrate', '1.7.2', ext_options), ('clusterGeneration', '1.3.4', ext_options), ('raster', '2.5-8', ext_options), @@ -407,7 +407,7 @@ exts_list = [ ('VennDiagram', '1.6.17', ext_options), ('xlsxjars', '0.6.1', ext_options), ('xlsx', '0.5.7', ext_options), - ('forecast', '8.0', ext_options), + ('forecast', '8.0', dict(ext_options.items() + [('patches', ['forecast-6.1_icpc-wd308.patch'])])), ('fma', '2.3', ext_options), ('expsmooth', '2.3', ext_options), ('fpp', '0.5', ext_options), @@ -460,7 +460,7 @@ exts_list = [ ('pixmap', '0.4-11', ext_options), ('tkrplot', '0.0-23', ext_options), ('misc3d', '0.8-4', ext_options), - ('multicool', '0.1-10', ext_options), + ('multicool', '0.1-10', dict(ext_options.items() + [('patches', [('multicool-0.1-9_icpc-wd308.patch', 1)])])), ('ks', '1.10.5', ext_options), ('logcondens', '2.1.5', ext_options), ('Iso', '0.0-17', ext_options), @@ -483,7 +483,7 @@ exts_list = [ ('network', '1.13.0', ext_options), ('statnet.common', '3.3.0', ext_options), ('sna', '2.4', ext_options), - ('glasso', '1.8', ext_options), + ('glasso', '1.8', dict(ext_options.items() + [('patches', [('glasso-1.8-ifort-no-fixed.patch', 1)])])), ('huge', '1.2.7', ext_options), ('d3Network', '0.5.2.1', ext_options), ('ggm', '2.3', ext_options), -- GitLab From d845dddaa77015db0f0b283f52559461647d5738 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 1 Apr 2017 12:02:44 +0200 Subject: [PATCH 0502/1603] adding easyconfigs: Spack-0.10.0.eb --- easybuild/easyconfigs/s/Spack/Spack-0.10.0.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/s/Spack/Spack-0.10.0.eb diff --git a/easybuild/easyconfigs/s/Spack/Spack-0.10.0.eb b/easybuild/easyconfigs/s/Spack/Spack-0.10.0.eb new file mode 100644 index 0000000000..3a97b911b1 --- /dev/null +++ b/easybuild/easyconfigs/s/Spack/Spack-0.10.0.eb @@ -0,0 +1,26 @@ +easyblock = 'Tarball' + +name = 'Spack' +version = '0.10.0' + +homepage = 'https://spack.io/' +description = """Spack is a package manager for supercomputers, Linux, and macOS. It makes installing scientific + software easy. With Spack, you can build a package with multiple versions, configurations, platforms, and compilers, + and all of these builds can coexist on the same machine.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['https://github.com/LLNL/spack/archive/'] +sources = ['v%(version)s.tar.gz'] + +sanity_check_paths = { + 'files': ['bin/spack'], + 'dirs': ['etc/spack/defaults', 'lib/spack', 'share/spack', 'var/spack'], +} + +sanity_check_commands = [ + "spack list", + "spack versions gcc", +] + +moduleclass = 'devel' -- GitLab From 5c10b74a26b8517f3c9462ce128ef51f9867bf82 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 1 Apr 2017 21:19:46 +0200 Subject: [PATCH 0503/1603] fix patch for multicool-0.1-10 extension in R 3.3.3 easyconfig --- .../easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170314.eb | 2 +- .../easyconfigs/r/R/multicool-0.1-10_icpc-wd308.patch | 7 +++++++ 2 files changed, 8 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/r/R/multicool-0.1-10_icpc-wd308.patch diff --git a/easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170314.eb b/easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170314.eb index 75250e8769..eb14dda6a0 100644 --- a/easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170314.eb +++ b/easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170314.eb @@ -460,7 +460,7 @@ exts_list = [ ('pixmap', '0.4-11', ext_options), ('tkrplot', '0.0-23', ext_options), ('misc3d', '0.8-4', ext_options), - ('multicool', '0.1-10', dict(ext_options.items() + [('patches', [('multicool-0.1-9_icpc-wd308.patch', 1)])])), + ('multicool', '0.1-10', dict(ext_options.items() + [('patches', [('multicool-0.1-10_icpc-wd308.patch', 1)])])), ('ks', '1.10.5', ext_options), ('logcondens', '2.1.5', ext_options), ('Iso', '0.0-17', ext_options), diff --git a/easybuild/easyconfigs/r/R/multicool-0.1-10_icpc-wd308.patch b/easybuild/easyconfigs/r/R/multicool-0.1-10_icpc-wd308.patch new file mode 100644 index 0000000000..a86f23d77d --- /dev/null +++ b/easybuild/easyconfigs/r/R/multicool-0.1-10_icpc-wd308.patch @@ -0,0 +1,7 @@ +add -wd308 compiler option to avoid compiler warning #308 being treated as an error +author: Kenneth Hoste (HPC-UGent) +--- multicool/src/Makevars.orig 2017-04-01 21:14:54.299465099 +0200 ++++ multicool/src/Makevars 2017-04-01 21:14:54.299465099 +0200 +@@ -0,0 +1,2 @@ ++# disable Intel C++ compiler (icpc) warning/error #308, to avoid 'member "std::complex::_M_value" is inaccessible' ++PKG_CXXFLAGS = -wd308 -- GitLab From 23693fca6ad76a06c641d3110ef58445491d73f3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 1 Apr 2017 21:32:43 +0200 Subject: [PATCH 0504/1603] make sure multicool patch level can be derived --- .../easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170314.eb | 2 +- .../easyconfigs/r/R/multicool-0.1-10_icpc-wd308.patch | 7 +++++++ 2 files changed, 8 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170314.eb b/easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170314.eb index eb14dda6a0..06a44541b2 100644 --- a/easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170314.eb +++ b/easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170314.eb @@ -460,7 +460,7 @@ exts_list = [ ('pixmap', '0.4-11', ext_options), ('tkrplot', '0.0-23', ext_options), ('misc3d', '0.8-4', ext_options), - ('multicool', '0.1-10', dict(ext_options.items() + [('patches', [('multicool-0.1-10_icpc-wd308.patch', 1)])])), + ('multicool', '0.1-10', dict(ext_options.items() + [('patches', ['multicool-0.1-10_icpc-wd308.patch'])])), ('ks', '1.10.5', ext_options), ('logcondens', '2.1.5', ext_options), ('Iso', '0.0-17', ext_options), diff --git a/easybuild/easyconfigs/r/R/multicool-0.1-10_icpc-wd308.patch b/easybuild/easyconfigs/r/R/multicool-0.1-10_icpc-wd308.patch index a86f23d77d..660089c7d5 100644 --- a/easybuild/easyconfigs/r/R/multicool-0.1-10_icpc-wd308.patch +++ b/easybuild/easyconfigs/r/R/multicool-0.1-10_icpc-wd308.patch @@ -1,5 +1,12 @@ add -wd308 compiler option to avoid compiler warning #308 being treated as an error author: Kenneth Hoste (HPC-UGent) +--- multicool/MD5.orig 2017-04-01 21:30:37.105382230 +0200 ++++ multicool/MD5 2017-04-01 21:30:30.095337987 +0200 +@@ -20,3 +20,4 @@ + b18b7e9e5912cf1014aa2c2fa8e86047 *src/compositions.cpp + 994ea793adf2455b973554d9b8dacd99 *src/multicool.cpp + 8e6ea24037e92ec9c30f699f4e3f9b8a *src/multinomial.h ++b1d3a4d02405fe08c7983c479bc27f13 */src/Makevars --- multicool/src/Makevars.orig 2017-04-01 21:14:54.299465099 +0200 +++ multicool/src/Makevars 2017-04-01 21:14:54.299465099 +0200 @@ -0,0 +1,2 @@ -- GitLab From 1db6d2bc186632ac3e477de75e3620300e4364e2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 2 Apr 2017 09:43:12 +0200 Subject: [PATCH 0505/1603] add patch for imager extension in R 3.3.3 easyconfig --- .../r/R/R-3.3.3-intel-2017a-X11-20170314.eb | 2 +- .../r/R/imager-0.3_fix-icpc-bool-cast.patch | 259 ++++++++++++++++++ 2 files changed, 260 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/r/R/imager-0.3_fix-icpc-bool-cast.patch diff --git a/easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170314.eb b/easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170314.eb index 06a44541b2..01ebe2e855 100644 --- a/easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170314.eb +++ b/easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170314.eb @@ -502,7 +502,7 @@ exts_list = [ ('bmp', '0.2', ext_options), ('readbitmap', '0.1-4', ext_options), ('purrr', '0.2.2', ext_options), - ('imager', '0.31', ext_options), + ('imager', '0.31', dict(ext_options.items() + [('patches', ['imager-0.3_fix-icpc-bool-cast.patch'])])), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/imager-0.3_fix-icpc-bool-cast.patch b/easybuild/easyconfigs/r/R/imager-0.3_fix-icpc-bool-cast.patch new file mode 100644 index 0000000000..8d994cb858 --- /dev/null +++ b/easybuild/easyconfigs/r/R/imager-0.3_fix-icpc-bool-cast.patch @@ -0,0 +1,259 @@ +fix Intel compilation errors, partially based on https://github.com/dtschump/CImg/commit/d66a4e7f1b13594a572c22160c20e2bd3f231f6c +author: Kenneth Hoste (HPC-UGent) +--- imager/inst/include/CImg.h.orig 2016-08-31 16:30:10.000000000 +0200 ++++ imager/inst/include/CImg.h 2017-04-01 22:43:25.292695440 +0200 +@@ -17988,7 +17988,7 @@ + unsigned int ind = (unsigned int)mp.opcode[2]; + if (ind!=~0U) ind = (unsigned int)cimg::mod((int)_mp_arg(2),mp.listin.width()); + CImg &img = ind==~0U?mp.imgout:mp.listout[ind]; +- if (img) { ++ if ((bool)img) { + if (mp.opcode[12]!=(ulongT)-1) { + const CImg M(&_mp_arg(12) + 1,dx,dy,dz,(unsigned int)mp.opcode[13],true); + img.draw_image(x,y,z,c,S,M,opacity,(float)_mp_arg(14)); +@@ -18107,10 +18107,10 @@ + if (off<0 || off>=whds) + switch (boundary_conditions) { + case 2 : // Periodic boundary +- if (img) return (double)img[cimg::mod(off,whds)]; ++ if ((bool)img) return (double)img[cimg::mod(off,whds)]; + return 0; + case 1 : // Neumann boundary +- if (img) return (double)(off<0?*img:img.back()); ++ if ((bool)img) return (double)(off<0?*img:img.back()); + return 0; + default : // Dirichet boundary + return 0; +@@ -18184,10 +18184,10 @@ + if (off<0 || off>=whds) + switch (boundary_conditions) { + case 2 : // Periodic boundary +- if (img) return (double)img[cimg::mod(off,whds)]; ++ if ((bool)img) return (double)img[cimg::mod(off,whds)]; + return 0; + case 1 : // Neumann boundary +- if (img) return (double)(off<0?*img:img.back()); ++ if ((bool)img) return (double)(off<0?*img:img.back()); + return 0; + default : // Dirichet boundary + return 0; +@@ -18257,10 +18257,10 @@ + if (off<0 || off>=whds) + switch (boundary_conditions) { + case 2 : // Periodic boundary +- if (img) return (double)img[cimg::mod(off,whds)]; ++ if ((bool)img) return (double)img[cimg::mod(off,whds)]; + return 0; + case 1 : // Neumann boundary +- if (img) return (double)(off<0?*img:img.back()); ++ if ((bool)img) return (double)(off<0?*img:img.back()); + return 0; + default : // Dirichet boundary + return 0; +@@ -18317,10 +18317,10 @@ + if (off<0 || off>=whds) + switch (boundary_conditions) { + case 2 : // Periodic boundary +- if (img) return (double)img(ind,cimg::mod(off,whds)); ++ if ((bool)img) return (double)img(ind,cimg::mod(off,whds)); + return 0; + case 1 : // Neumann boundary +- if (img) return (double)(off<0?*img:img.back()); ++ if ((bool)img) return (double)(off<0?*img:img.back()); + return 0; + default : // Dirichet boundary + return 0; +@@ -18590,7 +18590,7 @@ + } else std::memset(ptrd,0,img._spectrum*sizeof(double)); + return cimg::type::nan(); + case 1 : // Neumann boundary +- if (img) { ++ if ((bool)img) { + ptrs = off<0?img._data:&img.back(); + cimg_forC(img,c) { *(ptrd++) = *ptrs; ptrs+=whd; } + } else std::memset(ptrd,0,img._spectrum*sizeof(double)); +@@ -18662,7 +18662,7 @@ + } else std::memset(ptrd,0,img._spectrum*sizeof(double)); + return cimg::type::nan(); + case 1 : // Neumann boundary +- if (img) { ++ if ((bool)img) { + ptrs = off<0?img._data:&img.back(); + cimg_forC(img,c) { *(ptrd++) = *ptrs; ptrs+=whd; } + } else std::memset(ptrd,0,img._spectrum*sizeof(double)); +@@ -19579,7 +19579,7 @@ + } else std::memset(ptrd,0,img._spectrum*sizeof(double)); + return cimg::type::nan(); + case 1 : // Neumann boundary +- if (img) { ++ if ((bool)img) { + ptrs = off<0?img._data:&img.back(); + cimg_forC(img,c) { *(ptrd++) = *ptrs; ptrs+=whd; } + } else std::memset(ptrd,0,img._spectrum*sizeof(double)); +@@ -19648,7 +19648,7 @@ + } else std::memset(ptrd,0,img._spectrum*sizeof(double)); + return cimg::type::nan(); + case 1 : // Neumann boundary +- if (img) { ++ if ((bool)img) { + ptrs = off<0?img._data:&img.back(); + cimg_forC(img,c) { *(ptrd++) = *ptrs; ptrs+=whd; } + } else std::memset(ptrd,0,img._spectrum*sizeof(double)); +@@ -25664,14 +25664,15 @@ + x0 = ((int)xc%width()) - width(), + y0 = ((int)yc%height()) - height(), + z0 = ((int)zc%depth()) - depth(), +- c0 = ((int)cc%spectrum()) - spectrum(); ++ c0 = ((int)cc%spectrum()) - spectrum(), ++ dx = width(), dy = height(), dz = depth(), dc = spectrum(); + #ifdef cimg_use_openmp + #pragma omp parallel for collapse(3) if (res.size()>=65536) + #endif +- for (int c = c0; c<(int)sc; c+=spectrum()) +- for (int z = z0; z<(int)sz; z+=depth()) +- for (int y = y0; y<(int)sy; y+=height()) +- for (int x = x0; x<(int)sx; x+=width()) ++ for (int c = c0; c<(int)sc; c+=dc) ++ for (int z = z0; z<(int)sz; z+=dz) ++ for (int y = y0; y<(int)sy; y+=dy) ++ for (int x = x0; x<(int)sx; x+=dx) + res.draw_image(x,y,z,c,*this); + } break; + case 1 : { // Neumann boundary. +@@ -47059,7 +47060,7 @@ + const IplImage *img = 0; + for (unsigned int i = 0; iwidthStep - 3*img->width); + assign(img->width,img->height,1,3); + const unsigned char* ptrs = (unsigned char*)img->imageData; +@@ -52636,7 +52637,7 @@ + case 'x' : { // Along the X-axis. + cimglist_for(*this,l) { + const CImg& img = (*this)[l]; +- if (img) { ++ if ((bool)img) { + dx+=img._width; + dy = cimg::max(dy,img._height); + dz = cimg::max(dz,img._depth); +@@ -52646,7 +52647,7 @@ + res.assign(dx,dy,dz,dc,0); + if (res) cimglist_for(*this,l) { + const CImg& img = (*this)[l]; +- if (img) res.draw_image(pos, ++ if ((bool)img) res.draw_image(pos, + (int)(align*(dy - img._height)), + (int)(align*(dz - img._depth)), + (int)(align*(dc - img._spectrum)), +@@ -52657,7 +52658,7 @@ + case 'y' : { // Along the Y-axis. + cimglist_for(*this,l) { + const CImg& img = (*this)[l]; +- if (img) { ++ if ((bool)img) { + dx = cimg::max(dx,img._width); + dy+=img._height; + dz = cimg::max(dz,img._depth); +@@ -52667,7 +52668,7 @@ + res.assign(dx,dy,dz,dc,0); + if (res) cimglist_for(*this,l) { + const CImg& img = (*this)[l]; +- if (img) res.draw_image((int)(align*(dx - img._width)), ++ if ((bool)img) res.draw_image((int)(align*(dx - img._width)), + pos, + (int)(align*(dz - img._depth)), + (int)(align*(dc - img._spectrum)), +@@ -52678,7 +52679,7 @@ + case 'z' : { // Along the Z-axis. + cimglist_for(*this,l) { + const CImg& img = (*this)[l]; +- if (img) { ++ if ((bool)img) { + dx = cimg::max(dx,img._width); + dy = cimg::max(dy,img._height); + dz+=img._depth; +@@ -52688,7 +52689,7 @@ + res.assign(dx,dy,dz,dc,0); + if (res) cimglist_for(*this,l) { + const CImg& img = (*this)[l]; +- if (img) res.draw_image((int)(align*(dx - img._width)), ++ if ((bool)img) res.draw_image((int)(align*(dx - img._width)), + (int)(align*(dy - img._height)), + pos, + (int)(align*(dc - img._spectrum)), +@@ -52699,7 +52700,7 @@ + default : { // Along the C-axis. + cimglist_for(*this,l) { + const CImg& img = (*this)[l]; +- if (img) { ++ if ((bool)img) { + dx = cimg::max(dx,img._width); + dy = cimg::max(dy,img._height); + dz = cimg::max(dz,img._depth); +@@ -52709,7 +52710,7 @@ + res.assign(dx,dy,dz,dc,0); + if (res) cimglist_for(*this,l) { + const CImg& img = (*this)[l]; +- if (img) res.draw_image((int)(align*(dx - img._width)), ++ if ((bool)img) res.draw_image((int)(align*(dx - img._width)), + (int)(align*(dy - img._height)), + (int)(align*(dz - img._depth)), + pos, +@@ -53957,7 +53958,7 @@ + CImg img; + try { img.load_pnm(filename_tmp2); } + catch (CImgException&) { stop_flag = true; } +- if (img) { img.move_to(*this); std::remove(filename_tmp2); } ++ if ((bool)img) { img.move_to(*this); std::remove(filename_tmp2); } + } + cimg::exception_mode(omode); + if (is_empty()) +@@ -54033,7 +54034,7 @@ + CImg img; + try { img.load_png(filename_tmp2); } + catch (CImgException&) { } +- if (img) { img.move_to(*this); std::remove(filename_tmp2); } ++ if ((bool)img) { img.move_to(*this); std::remove(filename_tmp2); } + else { // Try to read animated gif. + unsigned int i = 0; + for (bool stop_flag = false; !stop_flag; ++i) { +@@ -54042,7 +54043,7 @@ + CImg img; + try { img.load_png(filename_tmp2); } + catch (CImgException&) { stop_flag = true; } +- if (img) { img.move_to(*this); std::remove(filename_tmp2); } ++ if ((bool)img) { img.move_to(*this); std::remove(filename_tmp2); } + } + } + cimg::exception_mode(omode); +--- imager/src/Makevars.in.orig 2017-04-01 22:32:32.628591934 +0200 ++++ imager/src/Makevars.in 2017-04-01 22:32:40.968645087 +0200 +@@ -1,4 +1,5 @@ + + PKG_CPPFLAGS = @HAVE_OPENMP@ @OPENMP_CFLAGS@ @CPPFLAGS@ @HAVE_FFTW@ @FFTW_CFLAGS@ -I../inst/include -DCIMG_COMPILING -Dcimg_use_rng -Dcimg_r_mode -Dcimg_use_fftw3_singlethread -Dcimg_verbosity=1 + PKG_LIBS = @OPENMP_CFLAGS@ @LIBS@ @HAVE_FFTW@ @FFTW_LIBS@ $(RCPP_LDFLAGS) +- ++# disable Intel C++ compiler (icpc) warning/error #308, to avoid 'member "std::complex::_M_value" is inaccessible' ++PKG_CXXFLAGS = -wd308 +--- imager/MD5.orig 2016-09-12 15:08:55.000000000 +0200 ++++ imager/MD5 2017-04-01 22:44:16.943021224 +0200 +@@ -31,7 +31,7 @@ + 05e04a3bc5a858c40e001cc65b853dfc *inst/extdata/Leonardo_Birds.jpg + e1328ba2c55d5a72eb77e283c9630b90 *inst/extdata/parrots.png + daa5b7e30235689ad0444df37c88b7ff *inst/extdata/tennis_sif.mpeg +-00de9e6b4c2066d28d7f8d9e251915cd *inst/include/CImg.h ++ea9acc61a3dd73452639c570af543d29 *inst/include/CImg.h + 034a9e8aab9e05094fd31ce9ea3bbae2 *inst/include/imager.h + 0c8aae8db902f96a8f8e323043eb1418 *inst/include/wrappers.h + be39be77874a0181ecd47b1a7a9af5dd *man/FFT.Rd +@@ -140,7 +140,7 @@ + a680472a2ef1eda48c1a9b90488543b5 *man/vanvliet.Rd + 08193940e20b440f614e4c7a2dbf82fb *man/warp.Rd + 429b25a38f282c30d5d178ad9efc3b1f *man/watershed.Rd +-ab8f97aa6f15c67d1029e3eb5091853d *src/Makevars.in ++802ecbe76012c51adf729063804c793a *src/Makevars.in + 5ecf9e8577f31e535dee1c371e75a35f *src/Makevars.win + 78aff3a88c55983a329723eb1174a4ca *src/RcppExports.cpp + 8193f4fecd751c7d310d23b0faacd303 *src/colourspace.cpp -- GitLab From a5f2063b833b5bf00edccfe0167ac1a396850d5d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 2 Apr 2017 16:03:04 +0200 Subject: [PATCH 0506/1603] adding easyconfigs: ClusterShell-1.7.3.eb --- .../c/ClusterShell/ClusterShell-1.7.3.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/c/ClusterShell/ClusterShell-1.7.3.eb diff --git a/easybuild/easyconfigs/c/ClusterShell/ClusterShell-1.7.3.eb b/easybuild/easyconfigs/c/ClusterShell/ClusterShell-1.7.3.eb new file mode 100644 index 0000000000..7a6d8ed9f6 --- /dev/null +++ b/easybuild/easyconfigs/c/ClusterShell/ClusterShell-1.7.3.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'ClusterShell' +version = '1.7.3' + +homepage = 'http://cea-hpc.github.io/clustershell/' +description = """ClusterShell is an event-driven open source Python library, designed to run local or distant commands + in parallel on server farms or on large Linux clusters.""" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = [PYPI_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +options = {'modulename': 'ClusterShell'} + +pyshortver = '.'.join(SYS_PYTHON_VERSION.split('.')[:2]) +sanity_check_paths = { + 'files': ['bin/clubak', 'bin/clush', 'bin/nodeset'], + 'dirs': ['lib/python%s/site-packages' % pyshortver] +} + +moduleclass = 'tools' -- GitLab From 5663f27a280b6494a5efef3dae1bf526ec75fd1f Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 3 Apr 2017 08:13:41 +0100 Subject: [PATCH 0507/1603] adding easyconfigs: ALLPATHS-LG-52488-foss-2016a.eb --- .../ALLPATHS-LG-52488-foss-2016a.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100755 easybuild/easyconfigs/a/ALLPATHS-LG/ALLPATHS-LG-52488-foss-2016a.eb diff --git a/easybuild/easyconfigs/a/ALLPATHS-LG/ALLPATHS-LG-52488-foss-2016a.eb b/easybuild/easyconfigs/a/ALLPATHS-LG/ALLPATHS-LG-52488-foss-2016a.eb new file mode 100755 index 0000000000..3ba22f9da5 --- /dev/null +++ b/easybuild/easyconfigs/a/ALLPATHS-LG/ALLPATHS-LG-52488-foss-2016a.eb @@ -0,0 +1,37 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 The Cyprus Institute +# Authors:: Andreas Panteli , Thekla Loizou , +# George Tsouloupas +# License:: MIT/GPL +# +## +# 52488 modified by: +# Adam Huffman +# The Francis Crick Institute + +easyblock = 'ConfigureMake' + +name = 'ALLPATHS-LG' +version = '52488' + +homepage = 'http://www.broadinstitute.org/software/allpaths-lg/blog/' +description = """ALLPATHS-LG, the new short read genome assembler.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +# source is moved over time, hence multiple URLs below +source_urls = [ + 'ftp://ftp.broadinstitute.org/pub/crd/ALLPATHS/Release-LG/latest_source_code', + 'ftp://ftp.broadinstitute.org/pub/crd/ALLPATHS/Release-LG/latest_source_code/2013-06', + 'ftp://ftp.broadinstitute.org/pub/crd/ALLPATHS/Release-LG/latest_source_code/2013/2013-06', +] +sources = ['allpathslg-%(version)s.tar.gz'] + +sanity_check_paths = { + 'files': [], + 'dirs': ['bin'], +} + +moduleclass = 'bio' -- GitLab From a041d36a1b35a350727fee2733daa96baeb39e8f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 3 Apr 2017 10:48:18 +0200 Subject: [PATCH 0508/1603] adding easyconfigs: Inspector-2017_update2.eb --- .../i/Inspector/Inspector-2017_update2.eb | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) create mode 100644 easybuild/easyconfigs/i/Inspector/Inspector-2017_update2.eb diff --git a/easybuild/easyconfigs/i/Inspector/Inspector-2017_update2.eb b/easybuild/easyconfigs/i/Inspector/Inspector-2017_update2.eb new file mode 100644 index 0000000000..9ea21d95ae --- /dev/null +++ b/easybuild/easyconfigs/i/Inspector/Inspector-2017_update2.eb @@ -0,0 +1,17 @@ +name = 'Inspector' +version = '2017_update2' + +homepage = 'http://software.intel.com/en-us/intel-inspector-xe' +description = """Intel Inspector XE is an easy to use memory error checker and thread checker for serial + and parallel applications""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['inspector_%(version)s.tar.gz'] +checksums = ['d85a3bbd699b0fc77967fcd5e923ad35'] + +dontcreateinstalldir = 'True' + +license_file = HOME + '/licenses/intel/license.lic' + +moduleclass = 'tools' -- GitLab From b71a103e395e5a84fad3efd2089ffe1748da8238 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Mon, 3 Apr 2017 11:05:44 +0200 Subject: [PATCH 0509/1603] adding easyconfigs: samblaster-0.1.24-goolf-1.7.20.eb --- .../samblaster-0.1.24-goolf-1.7.20.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/s/samblaster/samblaster-0.1.24-goolf-1.7.20.eb diff --git a/easybuild/easyconfigs/s/samblaster/samblaster-0.1.24-goolf-1.7.20.eb b/easybuild/easyconfigs/s/samblaster/samblaster-0.1.24-goolf-1.7.20.eb new file mode 100644 index 0000000000..55c7310c7e --- /dev/null +++ b/easybuild/easyconfigs/s/samblaster/samblaster-0.1.24-goolf-1.7.20.eb @@ -0,0 +1,30 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'MakeCp' + +name = 'samblaster' +version = '0.1.24' + +homepage = 'https://github.com/GregoryFaust/samblaster' +description = """samblaster: a tool to mark duplicates and extract discordant and split reads from sam files""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +source_urls = ['https://github.com/GregoryFaust/samblaster/archive/'] +sources = ['v.%(version)s.tar.gz'] + +files_to_copy = [(['samblaster'], 'bin/'), + 'README.md', + 'SAMBLASTER_Supplemental.pdf', + 'LICENSE.txt', +] + +sanity_check_paths = { + 'files': ['bin/samblaster'], + 'dirs': [] +} + +moduleclass = 'bio' -- GitLab From 33a00c24c74c17fb559dcdb9cb4f6b532f95362a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 3 Apr 2017 11:29:09 +0200 Subject: [PATCH 0510/1603] adding easyconfigs: ImageMagick-7.0.5-4-intel-2017a.eb, Ghostscript-9.21-intel-2017a.eb, LittleCMS-2.8-intel-2017a.eb --- .../Ghostscript-9.21-intel-2017a.eb | 35 ++++++++++++++++ .../ImageMagick-7.0.5-4-intel-2017a.eb | 42 +++++++++++++++++++ .../l/LittleCMS/LittleCMS-2.8-intel-2017a.eb | 23 ++++++++++ 3 files changed, 100 insertions(+) create mode 100644 easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.21-intel-2017a.eb create mode 100644 easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.5-4-intel-2017a.eb create mode 100644 easybuild/easyconfigs/l/LittleCMS/LittleCMS-2.8-intel-2017a.eb diff --git a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.21-intel-2017a.eb b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.21-intel-2017a.eb new file mode 100644 index 0000000000..e055f488f1 --- /dev/null +++ b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.21-intel-2017a.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'Ghostscript' +version = '9.21' + +homepage = 'http://ghostscript.com' +description = """Ghostscript is a versatile processor for PostScript data with the ability to render PostScript to + different targets. It used to be part of the cups printing stack, but is no longer used for that.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True} + +source_urls = [ + 'https://github.com/ArtifexSoftware/ghostpdl-downloads/releases/download/gs%(version_major)s%(version_minor)s/', +] +sources = ['ghostscript-%(version)s.tar.gz'] + +dependencies = [ + ('zlib', '1.2.11'), + ('libpng', '1.6.29'), + ('freetype', '2.7.1', '-libpng-1.6.29'), + ('libjpeg-turbo', '1.5.1'), + ('expat', '2.2.0'), + ('GLib', '2.52.0'), + ('cairo', '1.14.8'), + ('LibTIFF', '4.0.7'), +] + +# Do not use local copies of zlib, jpeg, freetype, and png +preconfigopts = "mv zlib zlib.no && mv jpeg jpeg.no && mv freetype freetype.no && mv libpng libpng.no && " +preconfigopts += 'export LIBS="$LIBS -lz" && ' + +configopts = "--with-system-libtiff --enable-dynamic" + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.5-4-intel-2017a.eb b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.5-4-intel-2017a.eb new file mode 100644 index 0000000000..b01509be3a --- /dev/null +++ b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.5-4-intel-2017a.eb @@ -0,0 +1,42 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Ravi Tripathi +# Email: ravi89@uab.edu + +easyblock = 'ConfigureMake' + +name = 'ImageMagick' +version = '7.0.5-4' + +homepage = 'http://www.imagemagick.org/' +description = """ImageMagick is a software suite to create, edit, compose, or convert bitmap images""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['https://www.imagemagick.org/download/releases/'] +checksums = ['473a1e7ae37548eb6fe9cf2b1fb78011'] + +dependencies = [ + ('bzip2', '1.0.6'), + ('X11', '20170314'), + ('Ghostscript', '9.21'), + ('JasPer', '2.0.12'), + ('libjpeg-turbo', '1.5.1'), + ('LibTIFF', '4.0.7'), + ('LittleCMS', '2.8'), +] + +builddependencies = [ + ('pkg-config', '0.29.1'), +] + +configopts = "--with-gslib --with-x" + +sanity_check_paths = { + 'files': [], + 'dirs': ['bin', 'etc/%(name)s-%(version_major)s', 'include/%(name)s-%(version_major)s', 'lib', 'share'], +} + +modextravars = {'MAGICK_HOME': '%(installdir)s'} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/LittleCMS/LittleCMS-2.8-intel-2017a.eb b/easybuild/easyconfigs/l/LittleCMS/LittleCMS-2.8-intel-2017a.eb new file mode 100644 index 0000000000..338a40a66d --- /dev/null +++ b/easybuild/easyconfigs/l/LittleCMS/LittleCMS-2.8-intel-2017a.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'LittleCMS' +version = '2.8' + +homepage = 'http://www.littlecms.com/' +description = """ Little CMS intends to be an OPEN SOURCE small-footprint color management engine, + with special focus on accuracy and performance. """ + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['http://sourceforge.net/projects/lcms/files/lcms/%(version)s/'] +sources = ['lcms2-%(version)s.tar.gz'] + +dependencies = [('libjpeg-turbo', '1.5.1')] + +sanity_check_paths = { + 'files': ['bin/jpgicc', 'bin/linkicc', 'bin/psicc', 'bin/transicc', 'include/lcms2.h', 'include/lcms2_plugin.h', + 'lib/liblcms2.a', 'lib/liblcms2.%s' % SHLIB_EXT, 'lib/pkgconfig/lcms2.pc'], + 'dirs': ['share/man'], +} + +moduleclass = 'vis' -- GitLab From 674a1c51476cf8e99d35adf0eff04ac75f62cd02 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 3 Apr 2017 12:04:18 +0200 Subject: [PATCH 0511/1603] add PyYAML as dependency for ClusterShell --- .../c/ClusterShell/ClusterShell-1.7.3.eb | 1 + .../easyconfigs/l/libyaml/libyaml-0.1.7.eb | 28 +++++++++++++++++++ easybuild/easyconfigs/p/PyYAML/PyYAML-3.12.eb | 25 +++++++++++++++++ 3 files changed, 54 insertions(+) create mode 100644 easybuild/easyconfigs/l/libyaml/libyaml-0.1.7.eb create mode 100644 easybuild/easyconfigs/p/PyYAML/PyYAML-3.12.eb diff --git a/easybuild/easyconfigs/c/ClusterShell/ClusterShell-1.7.3.eb b/easybuild/easyconfigs/c/ClusterShell/ClusterShell-1.7.3.eb index 7a6d8ed9f6..26131a5764 100644 --- a/easybuild/easyconfigs/c/ClusterShell/ClusterShell-1.7.3.eb +++ b/easybuild/easyconfigs/c/ClusterShell/ClusterShell-1.7.3.eb @@ -12,6 +12,7 @@ toolchain = {'name': 'dummy', 'version': ''} source_urls = [PYPI_SOURCE] sources = [SOURCELOWER_TAR_GZ] +dependencies = [('PyYAML', '3.12')] allow_system_deps = [('Python', SYS_PYTHON_VERSION)] options = {'modulename': 'ClusterShell'} diff --git a/easybuild/easyconfigs/l/libyaml/libyaml-0.1.7.eb b/easybuild/easyconfigs/l/libyaml/libyaml-0.1.7.eb new file mode 100644 index 0000000000..44f94ecc3d --- /dev/null +++ b/easybuild/easyconfigs/l/libyaml/libyaml-0.1.7.eb @@ -0,0 +1,28 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Nils Christian +# License:: MIT/GPL +# $Id$ +## + +easyblock = 'ConfigureMake' + +name = 'libyaml' +version = '0.1.7' + +homepage = 'http://pyyaml.org/wiki/LibYAML' +description = """LibYAML is a YAML 1.1 parser and emitter written in C.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['http://pyyaml.org/download/libyaml/'] +sources = ['yaml-%(version)s.tar.gz'] + +sanity_check_paths = { + 'files': ['include/yaml.h', 'lib/libyaml.a', 'lib/libyaml.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig'] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12.eb b/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12.eb new file mode 100644 index 0000000000..8a6937f145 --- /dev/null +++ b/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'PyYAML' +version = '3.12' + +homepage = "https://pypi.python.org/pypi/PyYAML/" +description = """PyYAML is a YAML parser and emitter for the Python programming language.""" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [('libyaml', '0.1.7')] +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +options = {'modulename': 'yaml'} + +pyshortver = '.'.join(SYS_PYTHON_VERSION.split('.')[:2]) +sanity_check_paths = { + 'files': [], + 'dirs': [('lib/python%s/site-packages' % pyshortver, 'lib64/python%s/site-packages' % pyshortver)] +} + +moduleclass = 'lib' -- GitLab From 7859c40ad54c1bb3b76ec5037be59eddf796668b Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 3 Apr 2017 11:18:29 +0100 Subject: [PATCH 0512/1603] Remove obsolete FTP paths --- .../easyconfigs/a/ALLPATHS-LG/ALLPATHS-LG-52488-foss-2016a.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/a/ALLPATHS-LG/ALLPATHS-LG-52488-foss-2016a.eb b/easybuild/easyconfigs/a/ALLPATHS-LG/ALLPATHS-LG-52488-foss-2016a.eb index 3ba22f9da5..a840c61253 100755 --- a/easybuild/easyconfigs/a/ALLPATHS-LG/ALLPATHS-LG-52488-foss-2016a.eb +++ b/easybuild/easyconfigs/a/ALLPATHS-LG/ALLPATHS-LG-52488-foss-2016a.eb @@ -19,13 +19,12 @@ version = '52488' homepage = 'http://www.broadinstitute.org/software/allpaths-lg/blog/' description = """ALLPATHS-LG, the new short read genome assembler.""" +# Compilation fails with GCC 5.3 (goss-2016b) toolchain = {'name': 'foss', 'version': '2016a'} # source is moved over time, hence multiple URLs below source_urls = [ 'ftp://ftp.broadinstitute.org/pub/crd/ALLPATHS/Release-LG/latest_source_code', - 'ftp://ftp.broadinstitute.org/pub/crd/ALLPATHS/Release-LG/latest_source_code/2013-06', - 'ftp://ftp.broadinstitute.org/pub/crd/ALLPATHS/Release-LG/latest_source_code/2013/2013-06', ] sources = ['allpathslg-%(version)s.tar.gz'] -- GitLab From 36b2bfee952f02ce6b499e5f5b7ba8b5d112b5b7 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 3 Apr 2017 11:21:44 +0100 Subject: [PATCH 0513/1603] Fix typo --- .../easyconfigs/a/ALLPATHS-LG/ALLPATHS-LG-52488-foss-2016a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/ALLPATHS-LG/ALLPATHS-LG-52488-foss-2016a.eb b/easybuild/easyconfigs/a/ALLPATHS-LG/ALLPATHS-LG-52488-foss-2016a.eb index a840c61253..0227efebd7 100755 --- a/easybuild/easyconfigs/a/ALLPATHS-LG/ALLPATHS-LG-52488-foss-2016a.eb +++ b/easybuild/easyconfigs/a/ALLPATHS-LG/ALLPATHS-LG-52488-foss-2016a.eb @@ -19,7 +19,7 @@ version = '52488' homepage = 'http://www.broadinstitute.org/software/allpaths-lg/blog/' description = """ALLPATHS-LG, the new short read genome assembler.""" -# Compilation fails with GCC 5.3 (goss-2016b) +# Compilation fails with GCC 5.3 (foss-2016b) toolchain = {'name': 'foss', 'version': '2016a'} # source is moved over time, hence multiple URLs below -- GitLab From 8c68ce861deb926d89f492e0eaf100c735ef9995 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 3 Apr 2017 17:41:12 +0200 Subject: [PATCH 0514/1603] adding easyconfigs: deap-0.9.2-intel-2016b-Python-2.7.12.eb --- .../deap-0.9.2-intel-2016b-Python-2.7.12.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/d/deap/deap-0.9.2-intel-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/d/deap/deap-0.9.2-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/d/deap/deap-0.9.2-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..f639521510 --- /dev/null +++ b/easybuild/easyconfigs/d/deap/deap-0.9.2-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,23 @@ +easyblock = 'PythonPackage' + +name = 'deap' +version = '0.9.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://deap.readthedocs.org/en/master/' +description = """DEAP is a novel evolutionary computation framework for rapid prototyping and testing of ideas. + It seeks to make algorithms explicit and data structures transparent.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [('Python', '2.7.12')] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' -- GitLab From e28163397a26a71ad0c592cafa5b85b4a7b56c78 Mon Sep 17 00:00:00 2001 From: "Nathan S. Watson-Haigh" Date: Tue, 4 Apr 2017 12:14:05 +0930 Subject: [PATCH 0515/1603] Support for BioKanga 4.3.4 --- .../b/BioKanga/BioKanga-4.3.4-foss-2015b.eb | 30 +++++++++++++++++++ .../b/BioKanga/BioKanga-4.3.4_configure.patch | 29 ++++++++++++++++++ 2 files changed, 59 insertions(+) create mode 100644 easybuild/easyconfigs/b/BioKanga/BioKanga-4.3.4-foss-2015b.eb create mode 100644 easybuild/easyconfigs/b/BioKanga/BioKanga-4.3.4_configure.patch diff --git a/easybuild/easyconfigs/b/BioKanga/BioKanga-4.3.4-foss-2015b.eb b/easybuild/easyconfigs/b/BioKanga/BioKanga-4.3.4-foss-2015b.eb new file mode 100644 index 0000000000..da082e4501 --- /dev/null +++ b/easybuild/easyconfigs/b/BioKanga/BioKanga-4.3.4-foss-2015b.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'BioKanga' +version = '4.3.4' + +homepage = 'https://github.com/csiro-crop-informatics/biokanga' +description = """BioKanga is an integrated toolkit of high performance bioinformatics + subprocesses targeting the challenges of next generation sequencing analytics. + Kanga is an acronym standing for 'K-mer Adaptive Next Generation Aligner'.""" + +toolchain = {'name': 'foss', 'version': '2015b'} + +source_urls = ['https://github.com/csiro-crop-informatics/biokanga/archive/'] +sources = ['v%(version)s.tar.gz'] + +patches = ['BioKanga-4.3.4_configure.patch'] + +builddependencies = [ + ('Autoconf', '2.69'), + ('Automake', '1.15') +] + +preconfigopts = "autoreconf -f -i && " + +sanity_check_paths = { + 'files': ["bin/biokanga"], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BioKanga/BioKanga-4.3.4_configure.patch b/easybuild/easyconfigs/b/BioKanga/BioKanga-4.3.4_configure.patch new file mode 100644 index 0000000000..a88701ea28 --- /dev/null +++ b/easybuild/easyconfigs/b/BioKanga/BioKanga-4.3.4_configure.patch @@ -0,0 +1,29 @@ +--- ./configure.ac 2017-04-04 11:47:18.067209892 +0930 ++++ ./configure.ac 2017-04-04 11:47:46.719519662 +0930 +@@ -23,11 +23,10 @@ + fasta2dist/Makefile locsw/Makefile quickcount/Makefile csv2feat/Makefile + genalignref2relloci/Makefile genalignloci2core/Makefile maploci2features/Makefile + processcsvfiles/Makefile genalignconf/Makefile Loci2Phylip/Makefile blast2csv/Makefile genrollups/Makefile +- gengoterms/Makefile gengoassoc/Makefile goassoc/Makefile + genWiggle/Makefile gencentroidmetrics/Makefile proccentroids/Makefile DNAseqSitePotential/Makefile SimulateMNase/Makefile + filterreads/Makefile prednucleosomes/Makefile RNAseqSitePotential/Makefile + genDESeq/Makefile fasta2struct/Makefile kangarg/Makefile genultras/Makefile +- LocateROI/Makefile genstructprofile/Makefile genstructstats/Makefile predconfnucs/Makefile gennucstats/Makefile fastafilter/Makefile ++ LocateROI/Makefile genstructprofile/Makefile predconfnucs/Makefile gennucstats/Makefile fastafilter/Makefile + BEDMerge/Makefile BEDFilter/Makefile genElementProfiles/Makefile genzygosity/Makefile genGenomeFromAGP/Makefile genmarkers/Makefile + HammingDist/Makefile genreadsde/Makefile ufilter/Makefile uhamming/Makefile genseqcandidates/Makefile GFFfilter/Makefile loci2dist/Makefile + genNormWiggle/Makefile GTFfilter/Makefile genDiffExpr/Makefile dmpbioseq/Makefile genpseudogenome/Makefile usimdiffexpr/Makefile RNAFragSim/Makefile mergeoverlaps/Makefile +--- Makefile.am 2017-04-04 11:51:40.878045716 +0930 ++++ Makefile.am 2017-04-04 11:51:57.518224861 +0930 +@@ -8,10 +8,9 @@ + genalignref2relloci genalignloci2core maploci2features \ + processcsvfiles genalignconf Loci2Phylip blast2csv genrollups \ + genWiggle proccentroids gencentroidmetrics SimulateMNase predconfnucs \ +- gengoterms gengoassoc goassoc \ + DNAseqSitePotential RNAseqSitePotential prednucleosomes gennucstats \ + uhamming LocateROI genDESeq genGenomeFromAGP kangarg genultras \ +- genstructprofile genstructstats filterreads fasta2struct ufilter genseqcandidates genmarkers GFFfilter \ ++ genstructprofile filterreads fasta2struct ufilter genseqcandidates genmarkers GFFfilter \ + genElementProfiles BEDMerge BEDFilter loci2dist genzygosity genNormWiggle GTFfilter genDiffExpr \ + dmpbioseq genpseudogenome usimdiffexpr genreadsde HammingDist RNAFragSim mergeoverlaps fastafilter \ + kangasr kangar kangahrdx kangade kangas kangapr csv2sqlite biokanga locmarkers PEscaffold SSRdiscovery pacbiokanga -- GitLab From ed49e763dc0bd0d51fe8a687cc1dc6056c9ab11d Mon Sep 17 00:00:00 2001 From: "Nathan S. Watson-Haigh" Date: Tue, 4 Apr 2017 12:34:08 +0930 Subject: [PATCH 0516/1603] Added missing easyconfig dependencies for foss-2015b toolchain --- .../a/Autoconf/Autoconf-2.69-foss-2015b.eb | 25 ++++++++++++++ .../a/Automake/Automake-1.15-foss-2015b.eb | 33 +++++++++++++++++++ 2 files changed, 58 insertions(+) create mode 100644 easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-foss-2015b.eb create mode 100644 easybuild/easyconfigs/a/Automake/Automake-1.15-foss-2015b.eb diff --git a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-foss-2015b.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-foss-2015b.eb new file mode 100644 index 0000000000..408f488eca --- /dev/null +++ b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-foss-2015b.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'Autoconf' +version = '2.69' + +homepage = 'http://www.gnu.org/software/autoconf/' +description = """Autoconf is an extensible package of M4 macros that produce shell scripts to automatically + configure software source code packages. These scripts can adapt the packages to many kinds of UNIX-like + systems without manual user intervention. Autoconf creates a configuration script for a package from a + template file that lists the operating system features that the package can use, in the form of M4 macro calls.""" + +toolchain = {'name': 'foss', 'version': '2015b'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('M4', '1.4.17')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["autoconf", "autoheader", "autom4te", "autoreconf", + "autoscan", "autoupdate", "ifnames"]], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.15-foss-2015b.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15-foss-2015b.eb new file mode 100644 index 0000000000..543e7a0ba7 --- /dev/null +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15-foss-2015b.eb @@ -0,0 +1,33 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## + +easyblock = 'ConfigureMake' + +name = 'Automake' +version = "1.15" + +homepage = 'http://www.gnu.org/software/automake/automake.html' +description = "Automake: GNU Standards-compliant Makefile generator" + +toolchain = {'name': 'foss', 'version': '2015b'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('Autoconf', '2.69')] + +sanity_check_paths = { + 'files': ['bin/automake', 'bin/aclocal'], + 'dirs': [] +} + +moduleclass = 'devel' -- GitLab From 2c0bd091e388bc06f25908f60bdaf821e2efeb9b Mon Sep 17 00:00:00 2001 From: Edoardo Di Lorenzo Date: Tue, 4 Apr 2017 09:54:03 +0200 Subject: [PATCH 0517/1603] adding easyconfigs: Cantera-2.3.0-foss-2016b-Python-2.7.12.eb --- .../Cantera-2.3.0-foss-2016b-Python-2.7.12.eb | 50 +++++++++++++++++++ 1 file changed, 50 insertions(+) create mode 100644 easybuild/easyconfigs/c/Cantera/Cantera-2.3.0-foss-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/c/Cantera/Cantera-2.3.0-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/c/Cantera/Cantera-2.3.0-foss-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..87566ca1da --- /dev/null +++ b/easybuild/easyconfigs/c/Cantera/Cantera-2.3.0-foss-2016b-Python-2.7.12.eb @@ -0,0 +1,50 @@ +easyblock = 'SCons' + +name = 'Cantera' +version = '2.3.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/Cantera/cantera' +description = """Chemical kinetics, thermodynamics, and transport tool suite""" + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'strict': True} + +source_urls = ['https://github.com/Cantera/cantera/archive/'] +sources = ['v%(version)s.tar.gz'] + +patches = [ + 'Cantera-%(version)s_fix-bug-416.patch', + 'Cantera-%(version)s_fix-test-reprod.patch', +] + +dependencies = [ + ('Python', '2.7.12'), + ('Boost', '1.63.0', versionsuffix), + ('SUNDIALS', '2.7.0'), + ('Eigen', '3.3.2'), + ('fmt', '3.0.1'), + ('googletest', '1.8.0'), +] +builddependencies = [ + ('SCons', '2.5.1', versionsuffix), + ('3to2', '1.1.1', versionsuffix), +] + +common_opts = 'env_vars=all CC="$CC" CXX="$CXX" blas_lapack_libs=openblas blas_lapack_dir=$BLAS_LAPACK_LIB_DIR' +common_opts += ' sundials_include=$EBROOTSUNDIALS/include sundials_libdir=$EBROOTSUNDIALS/lib' +buildopts = 'build ' + common_opts +runtest = 'test ' + common_opts +installopts = 'install ' + common_opts +prefix_arg = 'prefix=' + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +sanity_check_paths = { + 'files': ['bin/mixmaster'], + 'dirs': ['include/cantera', 'lib/pkgconfig', 'lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [('python', "-c 'import cantera'")] + +moduleclass = 'chem' -- GitLab From 504315aa55cf670592a7dfaa04a662012782ee73 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 4 Apr 2017 10:03:58 +0200 Subject: [PATCH 0518/1603] {bio}[intel/2016b] Stampy v1.0.31 w/ Python 2.7.12 --- ...Stampy-1.0.31-intel-2016b-Python-2.7.12.eb | 35 ++++++++++++++++ .../Stampy/Stampy-1.0.31_fix-hardcoding.patch | 40 +++++++++++++++++++ 2 files changed, 75 insertions(+) create mode 100644 easybuild/easyconfigs/s/Stampy/Stampy-1.0.31-intel-2016b-Python-2.7.12.eb create mode 100644 easybuild/easyconfigs/s/Stampy/Stampy-1.0.31_fix-hardcoding.patch diff --git a/easybuild/easyconfigs/s/Stampy/Stampy-1.0.31-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/s/Stampy/Stampy-1.0.31-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..1c6a84db5e --- /dev/null +++ b/easybuild/easyconfigs/s/Stampy/Stampy-1.0.31-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,35 @@ +easyblock = 'MakeCp' + +name = 'Stampy' +version = '1.0.31' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.well.ox.ac.uk/stampy' +description = """Stampy is a package for the mapping of short reads from illumina sequencing machines onto + a reference genome.""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'pic': True} + +# download via http://www.well.ox.ac.uk/software-download-registration and rename from Stampy-latest.tgz +sources = ['Stampy-%(version)s.tgz'] +checksums = ['512b2da5a952a65d2e6f70220c4641dc'] + +patches = ['Stampy-%(version)s_fix-hardcoding.patch'] + +dependencies = [('Python', '2.7.12')] + +files_to_copy = ['ext', 'maptools.%s' % SHLIB_EXT, 'plugins', 'README.txt', 'Stampy', 'stampy.py'] + +sanity_check_paths = { + 'files': ['maptools.%s' % SHLIB_EXT, 'stampy.py'], + 'dirs': ['ext', 'plugins', 'Stampy'], +} + +modextrapaths = { + # add top-level install path to $PATH and $PYTHONPATH + 'PATH': [''], + 'PYTHONPATH': [''], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/Stampy/Stampy-1.0.31_fix-hardcoding.patch b/easybuild/easyconfigs/s/Stampy/Stampy-1.0.31_fix-hardcoding.patch new file mode 100644 index 0000000000..ce59a23011 --- /dev/null +++ b/easybuild/easyconfigs/s/Stampy/Stampy-1.0.31_fix-hardcoding.patch @@ -0,0 +1,40 @@ +--- stampy-1.0.31/makefile.orig 2016-12-01 17:28:32.000000000 +0100 ++++ stampy-1.0.31/makefile 2017-04-04 09:59:04.057705404 +0200 +@@ -3,6 +3,10 @@ + # Compiles with gcc 5.4.0 and Apple LLVM version 6.1.0 + # + ++CC?=gcc ++CXX?=g++ ++CFLAGS?=-O2 ++CXXFLAGS?= + SHELL=/bin/bash + python?=python + platform=`uname` +@@ -31,21 +35,21 @@ + + $(bdir)/c/%.o: + mkdir -p $(bdir)/c +- gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -fPIC `$(python)-config --includes` -c c/$*.c -o $@ ++ $(CC) -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -fPIC `$(python)-config --includes` -c c/$*.c -o $@ + + $(bdir)/pyx/%.o: + mkdir -p $(bdir)/pyx + ln -s -f `pwd`/pyx/$(ucs)/$*.c pyx/$*.c +- gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -fPIC `$(python)-config --includes` -c pyx/$*.c -o $@ ++ $(CC) -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -fPIC `$(python)-config --includes` -c pyx/$*.c -o $@ + + $(bdir)/%.o: +- gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -fPIC `$(python)-config --includes` -c ext/readalign/$*.cc -o $@ ++ $(CC) -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -fPIC `$(python)-config --includes` -c ext/readalign/$*.cc -o $@ + + build-stampy: $(objs) + cp -r build/python2.7/* . + @if [ $(platform) = Linux ]; then \ +- g++ `$(python)-config --ldflags` -pthread -shared $(objs) -o maptools.so ; \ ++ $(CXX) `$(python)-config --ldflags` -pthread -shared $(objs) -o maptools.so ; \ + else \ +- g++ `$(python)-config --ldflags` -pthread -dynamiclib $(objs) -o maptools.so ; \ ++ $(CXX) `$(python)-config --ldflags` -pthread -dynamiclib $(objs) -o maptools.so ; \ + fi + -- GitLab From 104319a4179492a63772b13e76cb8d051b248f09 Mon Sep 17 00:00:00 2001 From: iotaka Date: Tue, 4 Apr 2017 10:23:37 +0200 Subject: [PATCH 0519/1603] missing dep --- .../s/SUNDIALS/SUNDIALS-2.7.0-foss-2016b.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-2.7.0-foss-2016b.eb diff --git a/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-2.7.0-foss-2016b.eb b/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-2.7.0-foss-2016b.eb new file mode 100644 index 0000000000..21d1aa5067 --- /dev/null +++ b/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-2.7.0-foss-2016b.eb @@ -0,0 +1,29 @@ +easyblock = 'CMakeMake' + +name = 'SUNDIALS' +version = '2.7.0' + +homepage = 'http://computation.llnl.gov/projects/sundials' +description = "SUNDIALS: SUite of Nonlinear and DIfferential/ALgebraic Equation Solvers" + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = ['http://computation.llnl.gov/projects/sundials/download/'] +sources = [SOURCELOWER_TAR_GZ] + +builddependencies = [('CMake', '3.6.2')] + +separate_build_dir = True + +configopts = "-DMPI_ENABLE=ON -DOPENMP_ENABLE=ON -DLAPACK_ENABLE=ON" + +solvers = ['arkode', 'cvode', 'cvodes', 'ida', 'idas', 'kinsol'] +sanity_check_paths = { + 'files': ['lib/libsundials_%s.a' % s for s in solvers + ['nvecopenmp', 'nvecparallel', 'nvecserial']] + + ['lib/libsundials_%s.%s' % (s, SHLIB_EXT) for s in solvers + ['nvecopenmp', 'nvecparallel', 'nvecserial']], + 'dirs': ['examples/%s' % s for s in solvers] + ['include/%s' % s for s in solvers] + + ['examples/nvector', 'include/nvector', 'include/sundials'], +} + +moduleclass = 'math' -- GitLab From f37de2420a9c1c3105717e39e765a76951c55205 Mon Sep 17 00:00:00 2001 From: iotaka Date: Tue, 4 Apr 2017 10:23:57 +0200 Subject: [PATCH 0520/1603] missing dep --- .../easyconfigs/e/Eigen/Eigen-3.3.2-foss-2016b.eb | 13 +++++++++++++ 1 file changed, 13 insertions(+) create mode 100644 easybuild/easyconfigs/e/Eigen/Eigen-3.3.2-foss-2016b.eb diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.3.2-foss-2016b.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.3.2-foss-2016b.eb new file mode 100644 index 0000000000..bab8954a19 --- /dev/null +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.3.2-foss-2016b.eb @@ -0,0 +1,13 @@ +name = 'Eigen' +version = '3.3.2' + +homepage = 'http://eigen.tuxfamily.org/index.php?title=Main_Page' +description = """Eigen is a C++ template library for linear algebra: + matrices, vectors, numerical solvers, and related algorithms.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['http://bitbucket.org/%(namelower)s/%(namelower)s/get'] +sources = ['%(version)s.tar.bz2'] + +moduleclass = 'math' -- GitLab From 3be2fdf53413ebf2aa43b7df16ce006bb80cfd60 Mon Sep 17 00:00:00 2001 From: iotaka Date: Tue, 4 Apr 2017 10:24:19 +0200 Subject: [PATCH 0521/1603] missing dep --- .../easyconfigs/f/fmt/fmt-3.0.1-foss-2016b.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/f/fmt/fmt-3.0.1-foss-2016b.eb diff --git a/easybuild/easyconfigs/f/fmt/fmt-3.0.1-foss-2016b.eb b/easybuild/easyconfigs/f/fmt/fmt-3.0.1-foss-2016b.eb new file mode 100644 index 0000000000..6faff2689b --- /dev/null +++ b/easybuild/easyconfigs/f/fmt/fmt-3.0.1-foss-2016b.eb @@ -0,0 +1,24 @@ +easyblock = 'CMakeMake' + +name = 'fmt' +version = '3.0.1' + +homepage = 'http://fmtlib.net/' +description = "fmt (formerly cppformat) is an open-source formatting library." + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/fmtlib/fmt/releases/download/%(version)s/'] +sources = ['fmt-%(version)s.zip'] + +builddependencies = [('CMake', '3.7.1')] + +separate_build_dir = True + +sanity_check_paths = { + 'files': ['lib/libfmt.a'], + 'dirs': ['include/fmt', 'lib/cmake'], +} + +moduleclass = 'lib' -- GitLab From bb9e516ef8adbfa25e3e8b9bc65cd1a2118a0e97 Mon Sep 17 00:00:00 2001 From: iotaka Date: Tue, 4 Apr 2017 10:24:36 +0200 Subject: [PATCH 0522/1603] missing dep --- .../googletest/googletest-1.8.0-foss-2016b.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/g/googletest/googletest-1.8.0-foss-2016b.eb diff --git a/easybuild/easyconfigs/g/googletest/googletest-1.8.0-foss-2016b.eb b/easybuild/easyconfigs/g/googletest/googletest-1.8.0-foss-2016b.eb new file mode 100644 index 0000000000..51ca2d0db0 --- /dev/null +++ b/easybuild/easyconfigs/g/googletest/googletest-1.8.0-foss-2016b.eb @@ -0,0 +1,23 @@ +easyblock = 'CMakeMake' + +name = 'googletest' +version = '1.8.0' + +homepage = 'https://github.com/google/googletest' +description = "Google's C++ test framework" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['https://github.com/google/googletest/archive/'] +sources = ['release-%(version)s.tar.gz'] + +builddependencies = [('CMake', '3.7.1')] + +separate_build_dir = True + +sanity_check_paths = { + 'files': ['lib/libgmock.a', 'lib/libgmock_main.a', 'lib/libgtest.a', 'lib/libgtest_main.a'], + 'dirs': ['include/gmock', 'include/gtest'], +} + +moduleclass = 'tools' -- GitLab From ce46e440b36dd05543bf1c0982a03360faf138a8 Mon Sep 17 00:00:00 2001 From: iotaka Date: Tue, 4 Apr 2017 10:24:59 +0200 Subject: [PATCH 0523/1603] missing dep --- .../SCons-2.5.1-foss-2016b-Python-2.7.12.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/s/SCons/SCons-2.5.1-foss-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/s/SCons/SCons-2.5.1-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/s/SCons/SCons-2.5.1-foss-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..40cbf3c559 --- /dev/null +++ b/easybuild/easyconfigs/s/SCons/SCons-2.5.1-foss-2016b-Python-2.7.12.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'SCons' +version = '2.5.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.scons.org/' +description = "SCons is a software construction tool." + +toolchain = {'name': 'foss', 'version': '2016b'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] + +dependencies = [('Python', '2.7.12')] + +sanity_check_paths = { + 'files': ['bin/scons', 'bin/scons-time', 'bin/sconsign'], + 'dirs': ['lib/%(namelower)s-%(version)s/%(name)s'], +} + +options = {'modulename': False} + +moduleclass = 'devel' -- GitLab From e653637f60899545e584b8abce4485607356e097 Mon Sep 17 00:00:00 2001 From: iotaka Date: Tue, 4 Apr 2017 10:25:20 +0200 Subject: [PATCH 0524/1603] missing dep --- .../3to2-1.1.1-foss-2016b-Python-2.7.12.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/0/3to2/3to2-1.1.1-foss-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/0/3to2/3to2-1.1.1-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/0/3to2/3to2-1.1.1-foss-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..5236c8830e --- /dev/null +++ b/easybuild/easyconfigs/0/3to2/3to2-1.1.1-foss-2016b-Python-2.7.12.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = '3to2' +version = '1.1.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pypi.python.org/pypi/3to2' +description = """lib3to2 is a set of fixers that are intended to backport code written for Python version 3.x + into Python version 2.x.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_ZIP] + +dependencies = [('Python', '2.7.12')] + +options = {'modulename': 'lib3to2'} + +sanity_check_paths = { + 'files': ['bin/3to2'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' -- GitLab From ad5231b3ecf0c03a913ffabe6c000a7f969d3399 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Tue, 4 Apr 2017 13:10:31 +0200 Subject: [PATCH 0525/1603] adding easyconfigs: Sambamba-0.6.6.eb --- .../easyconfigs/s/Sambamba/Sambamba-0.6.6.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/s/Sambamba/Sambamba-0.6.6.eb diff --git a/easybuild/easyconfigs/s/Sambamba/Sambamba-0.6.6.eb b/easybuild/easyconfigs/s/Sambamba/Sambamba-0.6.6.eb new file mode 100644 index 0000000000..cd17c8d34d --- /dev/null +++ b/easybuild/easyconfigs/s/Sambamba/Sambamba-0.6.6.eb @@ -0,0 +1,32 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'Tarball' + +name = 'Sambamba' +version = '0.6.6' + +homepage = 'http://lomereiter.github.io/sambamba/' +description = """Sambamba is a high performance modern robust and fast tool (and library), + written in the D programming language, for working with SAM and BAM files. Current functionality + is an important subset of samtools functionality, including view, index, sort, markdup, and depth""" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = ['https://github.com/lomereiter/sambamba/releases/download/v%(version)s/'] +sources = ['%(namelower)s_v%(version)s_linux.tar.bz2'] + +sanity_check_paths = { + 'files': ['sambamba_v%(version)s'], + 'dirs': [], +} + +modextrapaths = { + 'PATH': "", +} + +postinstallcmds = ['cd %(installdir)s && ln -s sambamba_v%(version)s sambamba',] + +moduleclass = 'bio' -- GitLab From 1a436e8b4ff18fd3e7d68944ff2f6a851cd46d02 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Lopez Date: Tue, 4 Apr 2017 13:16:24 +0200 Subject: [PATCH 0526/1603] style fixes --- .../s/samblaster/samblaster-0.1.24-goolf-1.7.20.eb | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/s/samblaster/samblaster-0.1.24-goolf-1.7.20.eb b/easybuild/easyconfigs/s/samblaster/samblaster-0.1.24-goolf-1.7.20.eb index 55c7310c7e..a99c1c0912 100644 --- a/easybuild/easyconfigs/s/samblaster/samblaster-0.1.24-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/s/samblaster/samblaster-0.1.24-goolf-1.7.20.eb @@ -16,10 +16,11 @@ toolchain = {'name': 'goolf', 'version': '1.7.20'} source_urls = ['https://github.com/GregoryFaust/samblaster/archive/'] sources = ['v.%(version)s.tar.gz'] -files_to_copy = [(['samblaster'], 'bin/'), - 'README.md', - 'SAMBLASTER_Supplemental.pdf', - 'LICENSE.txt', +files_to_copy = [ + (['samblaster'], 'bin/'), + 'README.md', + 'SAMBLASTER_Supplemental.pdf', + 'LICENSE.txt', ] sanity_check_paths = { -- GitLab From e96add50c8edc330c81ed35a3bf500d241a9b126 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 4 Apr 2017 13:41:54 +0200 Subject: [PATCH 0527/1603] adding easyconfigs: Perl-5.24.1-intel-2017a.eb --- .../p/Perl/Perl-5.24.1-intel-2017a.eb | 893 ++++++++++++++++++ 1 file changed, 893 insertions(+) create mode 100644 easybuild/easyconfigs/p/Perl/Perl-5.24.1-intel-2017a.eb diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.24.1-intel-2017a.eb b/easybuild/easyconfigs/p/Perl/Perl-5.24.1-intel-2017a.eb new file mode 100644 index 0000000000..a2c5b790f2 --- /dev/null +++ b/easybuild/easyconfigs/p/Perl/Perl-5.24.1-intel-2017a.eb @@ -0,0 +1,893 @@ +name = 'Perl' +version = '5.24.1' + +homepage = 'https://www.perl.org/' +description = """Larry Wall's Practical Extraction and Report Language""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.cpan.org/src/%(version_major)s.0'] +sources = [SOURCELOWER_TAR_GZ] + +exts_list = [ + ('Config::General', '2.63', { + 'source_tmpl': 'Config-General-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TL/TLINDEN'], + }), + ('File::Listing', '6.04', { + 'source_tmpl': 'File-Listing-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('ExtUtils::InstallPaths', '0.011', { + 'source_tmpl': 'ExtUtils-InstallPaths-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('ExtUtils::Helpers', '0.026', { + 'source_tmpl': 'ExtUtils-Helpers-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('Test::Harness', '3.38', { + 'source_tmpl': 'Test-Harness-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('ExtUtils::Config', '0.008', { + 'source_tmpl': 'ExtUtils-Config-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('Module::Build::Tiny', '0.039', { + 'source_tmpl': 'Module-Build-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('aliased', '0.34', { + 'source_tmpl': 'aliased-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Text::Glob', '0.11', { + 'source_tmpl': 'Text-Glob-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RC/RCLAMP'], + }), + ('Regexp::Common', '2016060801', { + 'source_tmpl': 'Regexp-Common-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AB/ABIGAIL'], + }), + ('GO::Utils', '0.15', { + 'source_tmpl': 'go-perl-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CM/CMUNGALL'], + }), + ('Module::Pluggable', '5.2', { + 'source_tmpl': 'Module-Pluggable-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SI/SIMONW'], + }), + ('Test::Fatal', '0.014', { + 'source_tmpl': 'Test-Fatal-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Test::Warnings', '0.026', { + 'source_tmpl': 'Test-Warnings-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('File::ShareDir::Install', '0.11', { + 'source_tmpl': 'File-ShareDir-Install-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('DateTime::Locale', '1.16', { + 'source_tmpl': 'DateTime-Locale-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('DateTime::TimeZone', '2.11', { + 'source_tmpl': 'DateTime-TimeZone-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('Test::Requires', '0.10', { + 'source_tmpl': 'Test-Requires-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TOKUHIROM'], + }), + ('Module::Implementation', '0.09', { + 'source_tmpl': 'Module-Implementation-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('Module::Build', '0.4222', { + 'source_tmpl': 'Module-Build-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('Module::Runtime', '0.014', { + 'source_tmpl': 'Module-Runtime-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/Z/ZE/ZEFRAM'], + }), + ('Try::Tiny', '0.28', { + 'source_tmpl': 'Try-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Params::Validate', '1.26', { + 'source_tmpl': 'Params-Validate-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('List::MoreUtils', '0.418', { + 'source_tmpl': 'List-MoreUtils-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + }), + ('Exporter::Tiny', '0.044', { + 'source_tmpl': 'Exporter-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TOBYINK'], + }), + ('Class::Singleton', '1.5', { + 'source_tmpl': 'Class-Singleton-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHAY'], + }), + ('DateTime', '1.42', { + 'source_tmpl': 'DateTime-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('File::Find::Rule::Perl', '1.15', { + 'source_tmpl': 'File-Find-Rule-Perl-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Readonly', '2.05', { + 'source_tmpl': 'Readonly-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SA/SANKO'], + }), + ('Git', '0.41', { + 'source_tmpl': 'Git-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MS/MSOUTH'], + }), + ('Tree::DAG_Node', '1.29', { + 'source_tmpl': 'Tree-DAG_Node-%(version)s.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + }), + ('Template', '2.26', { + 'source_tmpl': 'Template-Toolkit-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AB/ABW'], + }), + ('FreezeThaw', '0.5001', { + 'source_tmpl': 'FreezeThaw-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IL/ILYAZ/modules'], + }), + ('DBI', '1.636', { + 'source_tmpl': 'DBI-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TI/TIMB'], + }), + ('DBD::SQLite', '1.54', { + 'source_tmpl': 'DBD-SQLite-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IS/ISHIGAKI'], + }), + ('Math::Bezier', '0.01', { + 'source_tmpl': 'Math-Bezier-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AB/ABW'], + }), + ('Archive::Extract', '0.80', { + 'source_tmpl': 'Archive-Extract-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + }), + ('DBIx::Simple', '1.35', { + 'source_tmpl': 'DBIx-Simple-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JU/JUERD'], + }), + ('Shell', '0.73', { + 'source_tmpl': 'Shell-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/F/FE/FERREIRA'], + }), + ('File::Spec', '3.62', { + 'source_tmpl': 'PathTools-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Test::Simple', '1.302078', { + 'source_tmpl': 'Test-Simple-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + }), + ('Set::Scalar', '1.29', { + 'source_tmpl': 'Set-Scalar-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAVIDO'], + }), + ('IO::Stringy', '2.111', { + 'source_tmpl': 'IO-stringy-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DS/DSKOLL'], + }), + ('Encode::Locale', '1.05', { + 'source_tmpl': 'Encode-Locale-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('XML::SAX::Base', '1.09', { + 'source_tmpl': 'XML-SAX-Base-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GR/GRANTM'], + }), + ('XML::NamespaceSupport', '1.12', { + 'source_tmpl': 'XML-NamespaceSupport-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PERIGRIN'], + }), + ('XML::SAX', '0.99', { + 'source_tmpl': 'XML-SAX-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GR/GRANTM'], + }), + ('Test::LeakTrace', '0.15', { + 'source_tmpl': 'Test-LeakTrace-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GF/GFUJI'], + }), + ('Test::Exception', '0.43', { + 'source_tmpl': 'Test-Exception-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + }), + ('Text::Table', '1.132', { + 'source_tmpl': 'Text-Table-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'], + }), + ('MIME::Types', '2.13', { + 'source_tmpl': 'MIME-Types-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARKOV'], + }), + ('Module::Build::XSUtil', '0.16', { + 'source_tmpl': 'Module-Build-XSUtil-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HI/HIDEAKIO'], + }), + ('Tie::Function', '0.02', { + 'source_tmpl': 'Tie-Function-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAVIDNICO/handy_tied_functions'], + }), + ('Template::Plugin::Number::Format', '1.06', { + 'source_tmpl': 'Template-Plugin-Number-Format-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DARREN'], + }), + ('HTML::Parser', '3.72', { + 'source_tmpl': 'HTML-Parser-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('Date::Handler', '1.2', { + 'source_tmpl': 'Date-Handler-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BB/BBEAUSEJ'], + }), + ('Params::Util', '1.07', { + 'source_tmpl': 'Params-Util-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + }), + ('IO::HTML', '1.001', { + 'source_tmpl': 'IO-HTML-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CJ/CJM'], + }), + ('Data::Grove', '0.08', { + 'source_tmpl': 'libxml-perl-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KM/KMACLEOD'], + }), + ('Class::ISA', '0.36', { + 'source_tmpl': 'Class-ISA-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SM/SMUELLER'], + }), + ('URI', '1.71', { + 'source_tmpl': 'URI-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Ima::DBI', '0.35', { + 'source_tmpl': 'Ima-DBI-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PERRIN'], + }), + ('Tie::IxHash', '1.23', { + 'source_tmpl': 'Tie-IxHash-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CH/CHORNY'], + }), + ('GO', '0.04', { + 'source_tmpl': 'go-db-perl-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SJ/SJCARBON'], + }), + ('Class::DBI::SQLite', '0.11', { + 'source_tmpl': 'Class-DBI-SQLite-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA'], + }), + ('Pod::POM', '2.01', { + 'source_tmpl': 'Pod-POM-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB'], + }), + ('Math::Round', '0.07', { + 'source_tmpl': 'Math-Round-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GR/GROMMEL'], + }), + ('Text::Diff', '1.44', { + 'source_tmpl': 'Text-Diff-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB'], + }), + ('Log::Message::Simple', '0.10', { + 'source_tmpl': 'Log-Message-Simple-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + }), + ('IO::Socket::SSL', '2.047', { + 'source_tmpl': 'IO-Socket-SSL-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SU/SULLR'], + }), + ('Fennec::Lite', '0.004', { + 'source_tmpl': 'Fennec-Lite-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + }), + ('Sub::Uplevel', '0.2800', { + 'source_tmpl': 'Sub-Uplevel-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + }), + ('Meta::Builder', '0.003', { + 'source_tmpl': 'Meta-Builder-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + }), + ('Exporter::Declare', '0.114', { + 'source_tmpl': 'Exporter-Declare-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + }), + ('Getopt::Long', '2.49.1', { + 'source_tmpl': 'Getopt-Long-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JV/JV'], + }), + ('Log::Message', '0.08', { + 'source_tmpl': 'Log-Message-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + }), + ('Mouse', 'v2.4.9', { + 'source_tmpl': 'Mouse-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SY/SYOHEX'], + }), + ('Test::Version', '2.05', { + 'source_tmpl': 'Test-Version-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE'], + }), + ('DBIx::Admin::TableInfo', '3.03', { + 'source_tmpl': 'DBIx-Admin-TableInfo-%(version)s.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + }), + ('Net::HTTP', '6.13', { + 'source_tmpl': 'Net-HTTP-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'], + }), + ('Test::Deep', '1.126', { + 'source_tmpl': 'Test-Deep-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Test::Warn', '0.32', { + 'source_tmpl': 'Test-Warn-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BIGJ'], + }), + ('MRO::Compat', '0.13', { + 'source_tmpl': 'MRO-Compat-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + }), + ('Moo', '2.003002', { + 'source_tmpl': 'Moo-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + }), + ('Hash::Merge', '0.200', { + 'source_tmpl': 'Hash-Merge-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + }), + ('SQL::Abstract', '1.84', { + 'source_tmpl': 'SQL-Abstract-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IL/ILMARI'], + }), + ('HTML::Form', '6.03', { + 'source_tmpl': 'HTML-Form-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('File::Copy::Recursive', '0.38', { + 'source_tmpl': 'File-Copy-Recursive-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DM/DMUEY'], + }), + ('Number::Compare', '0.03', { + 'source_tmpl': 'Number-Compare-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RC/RCLAMP'], + }), + ('IPC::Run', '0.94', { + 'source_tmpl': 'IPC-Run-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR'], + }), + ('HTML::Entities::Interpolate', '1.10', { + 'source_tmpl': 'HTML-Entities-Interpolate-%(version)s.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + }), + ('Test::ClassAPI', '1.06', { + 'source_tmpl': 'Test-ClassAPI-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + }), + ('Test::Most', '0.35', { + 'source_tmpl': 'Test-Most-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OV/OVID'], + }), + ('Class::Accessor', '0.34', { + 'source_tmpl': 'Class-Accessor-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KA/KASEI'], + }), + ('Test::Differences', '0.64', { + 'source_tmpl': 'Test-Differences-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DC/DCANTRELL'], + }), + ('HTTP::Tiny', '0.070', { + 'source_tmpl': 'HTTP-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + }), + ('Package::DeprecationManager', '0.17', { + 'source_tmpl': 'Package-DeprecationManager-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('Digest::SHA1', '2.13', { + 'source_tmpl': 'Digest-SHA1-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('Date::Language', '2.30', { + 'source_tmpl': 'TimeDate-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GB/GBARR'], + }), + ('version', '0.9917', { + 'source_tmpl': 'version-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JP/JPEACOCK'], + }), + ('Sub::Uplevel', '0.2800', { + 'source_tmpl': 'Sub-Uplevel-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + }), + ('XML::Bare', '0.53', { + 'source_tmpl': 'XML-Bare-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CO/CODECHILD'], + 'patches': ['XML-Bare-0.53_icc.patch'], + }), + ('Dist::CheckConflicts', '0.11', { + 'source_tmpl': 'Dist-CheckConflicts-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DO/DOY'], + }), + ('Sub::Name', '0.21', { + 'source_tmpl': 'Sub-Name-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Time::Piece', '1.31', { + 'source_tmpl': 'Time-Piece-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ES/ESAYM'], + }), + ('Digest::HMAC', '1.03', { + 'source_tmpl': 'Digest-HMAC-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('HTTP::Negotiate', '6.01', { + 'source_tmpl': 'HTTP-Negotiate-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('MIME::Lite', '3.030', { + 'source_tmpl': 'MIME-Lite-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Crypt::Rijndael', '1.13', { + 'source_tmpl': 'Crypt-Rijndael-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('B::Lint', '1.20', { + 'source_tmpl': 'B-Lint-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Canary::Stability', '2012', { + 'source_tmpl': 'Canary-Stability-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/ML/MLEHMANN'], + }), + ('AnyEvent', '7.13', { + 'source_tmpl': 'AnyEvent-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/ML/MLEHMANN'], + }), + ('Object::Accessor', '0.48', { + 'source_tmpl': 'Object-Accessor-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + }), + ('Data::UUID', '1.221', { + 'source_tmpl': 'Data-UUID-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Test::Pod', '1.51', { + 'source_tmpl': 'Test-Pod-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('AppConfig', '1.71', { + 'source_tmpl': 'AppConfig-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB'], + }), + ('Net::SMTP::SSL', '1.04', { + 'source_tmpl': 'Net-SMTP-SSL-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('XML::Tiny', '2.06', { + 'source_tmpl': 'XML-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DC/DCANTRELL'], + }), + ('HTML::Tagset', '3.20', { + 'source_tmpl': 'HTML-Tagset-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PETDANCE'], + }), + ('HTML::Tree', '5.03', { + 'source_tmpl': 'HTML-Tree-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CJ/CJM'], + }), + ('Devel::GlobalDestruction', '0.14', { + 'source_tmpl': 'Devel-GlobalDestruction-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + }), + ('WWW::RobotRules', '6.02', { + 'source_tmpl': 'WWW-RobotRules-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('Expect', '1.33', { + 'source_tmpl': 'Expect-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JA/JACOBY'], + }), + ('Term::UI', '0.46', { + 'source_tmpl': 'Term-UI-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + }), + ('Net::SNMP', 'v6.0.1', { + 'source_tmpl': 'Net-SNMP-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DT/DTOWN'], + }), + ('XML::SAX::Writer', '0.56', { + 'source_tmpl': 'XML-SAX-Writer-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PERIGRIN'], + }), + ('Statistics::Descriptive', '3.0612', { + 'source_tmpl': 'Statistics-Descriptive-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'], + }), + ('Class::Load', '0.23', { + 'source_tmpl': 'Class-Load-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('LWP::Simple', '6.25', { + 'source_tmpl': 'libwww-perl-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'], + }), + ('Time::Piece::MySQL', '0.06', { + 'source_tmpl': 'Time-Piece-MySQL-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KA/KASEI'], + }), + ('Package::Stash::XS', '0.28', { + 'source_tmpl': 'Package-Stash-XS-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DO/DOY'], + }), + ('GD::Graph', '1.54', { + 'source_tmpl': 'GDGraph-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RU/RUZ'], + }), + ('Set::Array', '0.30', { + 'source_tmpl': 'Set-Array-%(version)s.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + }), + ('boolean', '0.46', { + 'source_tmpl': 'boolean-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IN/INGY'], + }), + ('Number::Format', '1.75', { + 'source_tmpl': 'Number-Format-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/W/WR/WRW'], + }), + ('Data::Stag', '0.14', { + 'source_tmpl': 'Data-Stag-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CM/CMUNGALL'], + }), + ('Test::NoWarnings', '1.04', { + 'source_tmpl': 'Test-NoWarnings-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + }), + ('Crypt::DES', '2.07', { + 'source_tmpl': 'Crypt-DES-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DP/DPARIS'], + }), + ('Exporter', '5.72', { + 'source_tmpl': 'Exporter-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR'], + }), + ('Class::Inspector', '1.31', { + 'source_tmpl': 'Class-Inspector-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE'], + }), + ('Parse::RecDescent', '1.967014', { + 'source_tmpl': 'Parse-RecDescent-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JT/JTBRAUN'], + }), + ('Carp', '1.38', { + 'source_tmpl': 'Carp-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('XML::XPath', '1.40', { + 'source_tmpl': 'XML-XPath-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MANWAR'], + }), + ('Capture::Tiny', '0.46', { + 'source_tmpl': 'Capture-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + }), + ('JSON', '2.90', { + 'source_tmpl': 'JSON-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MAKAMAKA'], + }), + ('Sub::Exporter', '0.987', { + 'source_tmpl': 'Sub-Exporter-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Class::Load::XS', '0.09', { + 'source_tmpl': 'Class-Load-XS-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Set::IntSpan::Fast', '1.15', { + 'source_tmpl': 'Set-IntSpan-Fast-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AN/ANDYA'], + }), + ('Sub::Exporter::Progressive', '0.001013', { + 'source_tmpl': 'Sub-Exporter-Progressive-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/F/FR/FREW'], + }), + ('Data::Dumper::Concise', '2.022', { + 'source_tmpl': 'Data-Dumper-Concise-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/F/FR/FREW'], + }), + ('File::Slurp::Tiny', '0.004', { + 'source_tmpl': 'File-Slurp-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('Algorithm::Diff', '1.1903', { + 'source_tmpl': 'Algorithm-Diff-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TY/TYEMQ'], + }), + ('AnyData', '0.12', { + 'source_tmpl': 'AnyData-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + }), + ('Text::Iconv', '1.7', { + 'source_tmpl': 'Text-Iconv-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MP/MPIOTR'], + }), + ('Class::Data::Inheritable', '0.08', { + 'source_tmpl': 'Class-Data-Inheritable-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TM/TMTM'], + }), + ('Text::Balanced', '2.03', { + 'source_tmpl': 'Text-Balanced-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHAY'], + }), + ('strictures', '2.000003', { + 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['https://cpan.metacpan.org/authors/id/I/IS/ISHIGAKI'], + }), + ('Test::Output', '1.031', { + 'source_tmpl': 'Test-Output-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BD/BDFOY'], + }), + ('Class::DBI', 'v3.0.17', { + 'source_tmpl': 'Class-DBI-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TM/TMTM'], + }), + ('List::AllUtils', '0.14', { + 'source_tmpl': 'List-AllUtils-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('UNIVERSAL::moniker', '0.08', { + 'source_tmpl': 'UNIVERSAL-moniker-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KA/KASEI'], + }), + ('Exception::Class', '1.42', { + 'source_tmpl': 'Exception-Class-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('File::CheckTree', '4.42', { + 'source_tmpl': 'File-CheckTree-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Math::VecStat', '0.08', { + 'source_tmpl': 'Math-VecStat-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AS/ASPINELLI'], + }), + ('Pod::LaTeX', '0.61', { + 'source_tmpl': 'Pod-LaTeX-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TJ/TJENNESS'], + }), + ('Eval::Closure', '0.14', { + 'source_tmpl': 'Eval-Closure-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DO/DOY'], + }), + ('HTTP::Request', '6.11', { + 'source_tmpl': 'HTTP-Message-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('XML::Twig', '3.52', { + 'source_tmpl': 'XML-Twig-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIROD'], + }), + ('IO::String', '1.08', { + 'source_tmpl': 'IO-String-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('XML::Simple', '2.22', { + 'source_tmpl': 'XML-Simple-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GR/GRANTM'], + }), + ('Sub::Install', '0.928', { + 'source_tmpl': 'Sub-Install-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('HTTP::Cookies', '6.03', { + 'source_tmpl': 'HTTP-Cookies-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'], + }), + ('Pod::Plainer', '1.04', { + 'source_tmpl': 'Pod-Plainer-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RM/RMBARKER'], + }), + ('Test::Exception::LessClever', '0.009', { + 'source_tmpl': 'Test-Exception-LessClever-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('LWP::MediaTypes', '6.02', { + 'source_tmpl': 'LWP-MediaTypes-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('Scalar::Util', 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'Authen-SASL-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GB/GBARR'], + }), + ('Clone', '0.38', { + 'source_tmpl': 'Clone-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GARU'], + }), + ('Data::Types', '0.09', { + 'source_tmpl': 'Data-Types-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DW/DWHEELER'], + }), + ('Import::Into', '1.002005', { + 'source_tmpl': 'Import-Into-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + }), + ('DateTime::Tiny', '1.06', { + 'source_tmpl': 'DateTime-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + }), + ('DBD::AnyData', '0.110', { + 'source_tmpl': 'DBD-AnyData-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + }), + ('Text::Format', '0.60', { + 'source_tmpl': 'Text-Format-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'], + }), + ('Devel::CheckCompiler', '0.07', { + 'source_tmpl': 'Devel-CheckCompiler-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SY/SYOHEX'], + }), + ('Log::Handler', '0.88', { + 'source_tmpl': 'Log-Handler-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BL/BLOONIX'], + }), + ('DBIx::ContextualFetch', '1.03', { + 'source_tmpl': 'DBIx-ContextualFetch-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TM/TMTM'], + }), + ('Devel::StackTrace', '2.02', { + 'source_tmpl': 'Devel-StackTrace-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('Term::ReadKey', '2.14', { + 'source_tmpl': 'TermReadKey-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KJ/KJALB'], + }), + ('Set::IntSpan', '1.19', { + 'source_tmpl': 'Set-IntSpan-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SW/SWMCD'], + }), + ('Moose', '2.2004', { + 'source_tmpl': 'Moose-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Algorithm::Dependency', '1.110', { + 'source_tmpl': 'Algorithm-Dependency-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + }), + ('Font::TTF', '1.06', { + 'source_tmpl': 'Font-TTF-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BH/BHALLISSY'], + }), + ('IPC::Run3', '0.048', { + 'source_tmpl': 'IPC-Run3-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('File::Find::Rule', '0.34', { + 'source_tmpl': 'File-Find-Rule-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RC/RCLAMP'], + }), + ('SQL::Statement', '1.410', { + 'source_tmpl': 'SQL-Statement-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + }), + ('File::Slurp', '9999.19', { + 'source_tmpl': 'File-Slurp-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/U/UR/URI'], + }), + ('Package::Stash', '0.37', { + 'source_tmpl': 'Package-Stash-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DO/DOY'], + }), + ('Data::OptList', '0.110', { + 'source_tmpl': 'Data-OptList-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('CPANPLUS', '0.9164', { + 'source_tmpl': 'CPANPLUS-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + }), + ('IO::Tty', '1.12', { + 'source_tmpl': 'IO-Tty-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR'], + }), + ('Text::Soundex', '3.05', { + 'source_tmpl': 'Text-Soundex-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Lingua::EN::PluralToSingular', '0.19', { + 'source_tmpl': 'Lingua-EN-PluralToSingular-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BK/BKB'], + }), + ('Want', '0.29', { + 'source_tmpl': 'Want-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RO/ROBIN'], + }), + ('Cwd::Guard', '0.05', { + 'source_tmpl': 'Cwd-Guard-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KA/KAZEBURO'], + }), + ('Bundle::BioPerl', '2.1.9', { + 'source_tmpl': 'Bundle-BioPerl-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS'], + }), + ('Mail::Util', '2.18', { + 'source_tmpl': 'MailTools-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARKOV'], + }), + ('Text::Template', '1.47', { + 'source_tmpl': 'Text-Template-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MS/MSCHOUT'], + }), + ('PDF::API2', '2.031', { + 'source_tmpl': 'PDF-API2-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SS/SSIMMS'], + }), +] + +moduleclass = 'lang' -- GitLab From f47b5a553604438de699f09d452f750f51c4df1b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 4 Apr 2017 13:45:47 +0200 Subject: [PATCH 0528/1603] add comment with info on last update of Perl extensions --- easybuild/easyconfigs/p/Perl/Perl-5.24.1-intel-2017a.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.24.1-intel-2017a.eb b/easybuild/easyconfigs/p/Perl/Perl-5.24.1-intel-2017a.eb index a2c5b790f2..7186e3ec91 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.24.1-intel-2017a.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.24.1-intel-2017a.eb @@ -10,6 +10,8 @@ toolchainopts = {'pic': True} source_urls = ['http://www.cpan.org/src/%(version_major)s.0'] sources = [SOURCELOWER_TAR_GZ] +# !! order of extensions is important !! +# extensions updated on April 4th 2017 exts_list = [ ('Config::General', '2.63', { 'source_tmpl': 'Config-General-%(version)s.tar.gz', -- GitLab From f94439f39c75c014db0eb230041cbeac2d02d0c2 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Tue, 4 Apr 2017 14:28:30 +0100 Subject: [PATCH 0529/1603] adding easyconfigs: matplotlib-2.0.0-foss-2016b-Python-2.7.12.eb --- ...tplotlib-2.0.0-foss-2016b-Python-2.7.12.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.0-foss-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.0-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.0-foss-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..2f829b0767 --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.0-foss-2016b-Python-2.7.12.eb @@ -0,0 +1,44 @@ +easyblock = 'Bundle' + +name = 'matplotlib' +version = '2.0.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://matplotlib.org' +description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of + hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python + and ipython shell, web application servers, and six graphical user interface toolkits.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' + +dependencies = [ + ('Python', '2.7.12'), + ('freetype', '2.7'), + ('libpng', '1.6.26'), +] + +exts_list = [ + ('Cycler', '0.10.0', { + 'modulename': 'cycler', + 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], + 'source_tmpl': 'cycler-%(version)s.tar.gz', + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], + }), +] + +# specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module +full_sanity_check = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +moduleclass = 'vis' -- GitLab From 3cb81f831d69775ac510480c8dc116e468e78258 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Tue, 4 Apr 2017 14:54:03 +0100 Subject: [PATCH 0530/1603] adding easyconfigs: MultiQC-0.9-foss-2016b-Python-2.7.12.eb --- .../MultiQC-0.9-foss-2016b-Python-2.7.12.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/m/MultiQC/MultiQC-0.9-foss-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/m/MultiQC/MultiQC-0.9-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/m/MultiQC/MultiQC-0.9-foss-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..a7a94c8c8c --- /dev/null +++ b/easybuild/easyconfigs/m/MultiQC/MultiQC-0.9-foss-2016b-Python-2.7.12.eb @@ -0,0 +1,32 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Adam Huffman +# The Francis Crick Institute +easyblock = 'PythonPackage' + +name = 'MultiQC' +version = '0.9' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://multiqc.info' +description = """Aggregate results from bioinformatics analyses across many samples into a single + report. + + MultiQC searches a given directory for analysis logs and compiles a HTML report. It's a general + use tool, perfect for summarising the output from numerous bioinformatics tools.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +sources = ['v%(version)s.tar.gz'] +source_urls = ['https://github.com/ewels/MultiQC/archive'] + +dependencies = [ + ('Python', '2.7.12'), + ('matplotlib', '2.0.0', versionsuffix), +] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'] +} + +moduleclass = 'bio' -- GitLab From e9dd3eee1b8bf54fae66b954aaf7705665188d6a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 4 Apr 2017 18:45:56 +0200 Subject: [PATCH 0531/1603] update imager extensions to 0.40.1 + add patch to fix compilation with Intel compilers --- .../r/R/R-3.3.3-intel-2017a-X11-20170314.eb | 3 +- .../r/R/imager-0.3_fix-icpc-bool-cast.patch | 259 --------------- .../r/R/imager-0.40.1_fix-CImg-icpc.patch | 310 ++++++++++++++++++ 3 files changed, 312 insertions(+), 260 deletions(-) delete mode 100644 easybuild/easyconfigs/r/R/imager-0.3_fix-icpc-bool-cast.patch create mode 100644 easybuild/easyconfigs/r/R/imager-0.40.1_fix-CImg-icpc.patch diff --git a/easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170314.eb b/easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170314.eb index 01ebe2e855..7c666ff2ec 100644 --- a/easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170314.eb +++ b/easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170314.eb @@ -502,7 +502,8 @@ exts_list = [ ('bmp', '0.2', ext_options), ('readbitmap', '0.1-4', ext_options), ('purrr', '0.2.2', ext_options), - ('imager', '0.31', dict(ext_options.items() + [('patches', ['imager-0.3_fix-icpc-bool-cast.patch'])])), + ('downloader', '0.4', ext_options), + ('imager', '0.40.1', dict(ext_options.items() + [('patches', ['imager-0.40.1_fix-CImg-icpc.patch'])])), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/imager-0.3_fix-icpc-bool-cast.patch b/easybuild/easyconfigs/r/R/imager-0.3_fix-icpc-bool-cast.patch deleted file mode 100644 index 8d994cb858..0000000000 --- a/easybuild/easyconfigs/r/R/imager-0.3_fix-icpc-bool-cast.patch +++ /dev/null @@ -1,259 +0,0 @@ -fix Intel compilation errors, partially based on https://github.com/dtschump/CImg/commit/d66a4e7f1b13594a572c22160c20e2bd3f231f6c -author: Kenneth Hoste (HPC-UGent) ---- imager/inst/include/CImg.h.orig 2016-08-31 16:30:10.000000000 +0200 -+++ imager/inst/include/CImg.h 2017-04-01 22:43:25.292695440 +0200 -@@ -17988,7 +17988,7 @@ - unsigned int ind = (unsigned int)mp.opcode[2]; - if (ind!=~0U) ind = (unsigned int)cimg::mod((int)_mp_arg(2),mp.listin.width()); - CImg &img = ind==~0U?mp.imgout:mp.listout[ind]; -- if (img) { -+ if ((bool)img) { - if (mp.opcode[12]!=(ulongT)-1) { - const CImg M(&_mp_arg(12) + 1,dx,dy,dz,(unsigned int)mp.opcode[13],true); - img.draw_image(x,y,z,c,S,M,opacity,(float)_mp_arg(14)); -@@ -18107,10 +18107,10 @@ - if (off<0 || off>=whds) - switch (boundary_conditions) { - case 2 : // Periodic boundary -- if (img) return (double)img[cimg::mod(off,whds)]; -+ if ((bool)img) return (double)img[cimg::mod(off,whds)]; - return 0; - case 1 : // Neumann boundary -- if (img) return (double)(off<0?*img:img.back()); -+ if ((bool)img) return (double)(off<0?*img:img.back()); - return 0; - default : // Dirichet boundary - return 0; -@@ -18184,10 +18184,10 @@ - if (off<0 || off>=whds) - switch (boundary_conditions) { - case 2 : // Periodic boundary -- if (img) return (double)img[cimg::mod(off,whds)]; -+ if ((bool)img) return (double)img[cimg::mod(off,whds)]; - return 0; - case 1 : // Neumann boundary -- if (img) return (double)(off<0?*img:img.back()); -+ if ((bool)img) return (double)(off<0?*img:img.back()); - return 0; - default : // Dirichet boundary - return 0; -@@ -18257,10 +18257,10 @@ - if (off<0 || off>=whds) - switch (boundary_conditions) { - case 2 : // Periodic boundary -- if (img) return (double)img[cimg::mod(off,whds)]; -+ if ((bool)img) return (double)img[cimg::mod(off,whds)]; - return 0; - case 1 : // Neumann boundary -- if (img) return (double)(off<0?*img:img.back()); -+ if ((bool)img) return (double)(off<0?*img:img.back()); - return 0; - default : // Dirichet boundary - return 0; -@@ -18317,10 +18317,10 @@ - if (off<0 || off>=whds) - switch (boundary_conditions) { - case 2 : // Periodic boundary -- if (img) return (double)img(ind,cimg::mod(off,whds)); -+ if ((bool)img) return (double)img(ind,cimg::mod(off,whds)); - return 0; - case 1 : // Neumann boundary -- if (img) return (double)(off<0?*img:img.back()); -+ if ((bool)img) return (double)(off<0?*img:img.back()); - return 0; - default : // Dirichet boundary - return 0; -@@ -18590,7 +18590,7 @@ - } else std::memset(ptrd,0,img._spectrum*sizeof(double)); - return cimg::type::nan(); - case 1 : // Neumann boundary -- if (img) { -+ if ((bool)img) { - ptrs = off<0?img._data:&img.back(); - cimg_forC(img,c) { *(ptrd++) = *ptrs; ptrs+=whd; } - } else std::memset(ptrd,0,img._spectrum*sizeof(double)); -@@ -18662,7 +18662,7 @@ - } else std::memset(ptrd,0,img._spectrum*sizeof(double)); - return cimg::type::nan(); - case 1 : // Neumann boundary -- if (img) { -+ if ((bool)img) { - ptrs = off<0?img._data:&img.back(); - cimg_forC(img,c) { *(ptrd++) = *ptrs; ptrs+=whd; } - } else std::memset(ptrd,0,img._spectrum*sizeof(double)); -@@ -19579,7 +19579,7 @@ - } else std::memset(ptrd,0,img._spectrum*sizeof(double)); - return cimg::type::nan(); - case 1 : // Neumann boundary -- if (img) { -+ if ((bool)img) { - ptrs = off<0?img._data:&img.back(); - cimg_forC(img,c) { *(ptrd++) = *ptrs; ptrs+=whd; } - } else std::memset(ptrd,0,img._spectrum*sizeof(double)); -@@ -19648,7 +19648,7 @@ - } else std::memset(ptrd,0,img._spectrum*sizeof(double)); - return cimg::type::nan(); - case 1 : // Neumann boundary -- if (img) { -+ if ((bool)img) { - ptrs = off<0?img._data:&img.back(); - cimg_forC(img,c) { *(ptrd++) = *ptrs; ptrs+=whd; } - } else std::memset(ptrd,0,img._spectrum*sizeof(double)); -@@ -25664,14 +25664,15 @@ - x0 = ((int)xc%width()) - width(), - y0 = ((int)yc%height()) - height(), - z0 = ((int)zc%depth()) - depth(), -- c0 = ((int)cc%spectrum()) - spectrum(); -+ c0 = ((int)cc%spectrum()) - spectrum(), -+ dx = width(), dy = height(), dz = depth(), dc = spectrum(); - #ifdef cimg_use_openmp - #pragma omp parallel for collapse(3) if (res.size()>=65536) - #endif -- for (int c = c0; c<(int)sc; c+=spectrum()) -- for (int z = z0; z<(int)sz; z+=depth()) -- for (int y = y0; y<(int)sy; y+=height()) -- for (int x = x0; x<(int)sx; x+=width()) -+ for (int c = c0; c<(int)sc; c+=dc) -+ for (int z = z0; z<(int)sz; z+=dz) -+ for (int y = y0; y<(int)sy; y+=dy) -+ for (int x = x0; x<(int)sx; x+=dx) - res.draw_image(x,y,z,c,*this); - } break; - case 1 : { // Neumann boundary. -@@ -47059,7 +47060,7 @@ - const IplImage *img = 0; - for (unsigned int i = 0; iwidthStep - 3*img->width); - assign(img->width,img->height,1,3); - const unsigned char* ptrs = (unsigned char*)img->imageData; -@@ -52636,7 +52637,7 @@ - case 'x' : { // Along the X-axis. - cimglist_for(*this,l) { - const CImg& img = (*this)[l]; -- if (img) { -+ if ((bool)img) { - dx+=img._width; - dy = cimg::max(dy,img._height); - dz = cimg::max(dz,img._depth); -@@ -52646,7 +52647,7 @@ - res.assign(dx,dy,dz,dc,0); - if (res) cimglist_for(*this,l) { - const CImg& img = (*this)[l]; -- if (img) res.draw_image(pos, -+ if ((bool)img) res.draw_image(pos, - (int)(align*(dy - img._height)), - (int)(align*(dz - img._depth)), - (int)(align*(dc - img._spectrum)), -@@ -52657,7 +52658,7 @@ - case 'y' : { // Along the Y-axis. - cimglist_for(*this,l) { - const CImg& img = (*this)[l]; -- if (img) { -+ if ((bool)img) { - dx = cimg::max(dx,img._width); - dy+=img._height; - dz = cimg::max(dz,img._depth); -@@ -52667,7 +52668,7 @@ - res.assign(dx,dy,dz,dc,0); - if (res) cimglist_for(*this,l) { - const CImg& img = (*this)[l]; -- if (img) res.draw_image((int)(align*(dx - img._width)), -+ if ((bool)img) res.draw_image((int)(align*(dx - img._width)), - pos, - (int)(align*(dz - img._depth)), - (int)(align*(dc - img._spectrum)), -@@ -52678,7 +52679,7 @@ - case 'z' : { // Along the Z-axis. - cimglist_for(*this,l) { - const CImg& img = (*this)[l]; -- if (img) { -+ if ((bool)img) { - dx = cimg::max(dx,img._width); - dy = cimg::max(dy,img._height); - dz+=img._depth; -@@ -52688,7 +52689,7 @@ - res.assign(dx,dy,dz,dc,0); - if (res) cimglist_for(*this,l) { - const CImg& img = (*this)[l]; -- if (img) res.draw_image((int)(align*(dx - img._width)), -+ if ((bool)img) res.draw_image((int)(align*(dx - img._width)), - (int)(align*(dy - img._height)), - pos, - (int)(align*(dc - img._spectrum)), -@@ -52699,7 +52700,7 @@ - default : { // Along the C-axis. - cimglist_for(*this,l) { - const CImg& img = (*this)[l]; -- if (img) { -+ if ((bool)img) { - dx = cimg::max(dx,img._width); - dy = cimg::max(dy,img._height); - dz = cimg::max(dz,img._depth); -@@ -52709,7 +52710,7 @@ - res.assign(dx,dy,dz,dc,0); - if (res) cimglist_for(*this,l) { - const CImg& img = (*this)[l]; -- if (img) res.draw_image((int)(align*(dx - img._width)), -+ if ((bool)img) res.draw_image((int)(align*(dx - img._width)), - (int)(align*(dy - img._height)), - (int)(align*(dz - img._depth)), - pos, -@@ -53957,7 +53958,7 @@ - CImg img; - try { img.load_pnm(filename_tmp2); } - catch (CImgException&) { stop_flag = true; } -- if (img) { img.move_to(*this); std::remove(filename_tmp2); } -+ if ((bool)img) { img.move_to(*this); std::remove(filename_tmp2); } - } - cimg::exception_mode(omode); - if (is_empty()) -@@ -54033,7 +54034,7 @@ - CImg img; - try { img.load_png(filename_tmp2); } - catch (CImgException&) { } -- if (img) { img.move_to(*this); std::remove(filename_tmp2); } -+ if ((bool)img) { img.move_to(*this); std::remove(filename_tmp2); } - else { // Try to read animated gif. - unsigned int i = 0; - for (bool stop_flag = false; !stop_flag; ++i) { -@@ -54042,7 +54043,7 @@ - CImg img; - try { img.load_png(filename_tmp2); } - catch (CImgException&) { stop_flag = true; } -- if (img) { img.move_to(*this); std::remove(filename_tmp2); } -+ if ((bool)img) { img.move_to(*this); std::remove(filename_tmp2); } - } - } - cimg::exception_mode(omode); ---- imager/src/Makevars.in.orig 2017-04-01 22:32:32.628591934 +0200 -+++ imager/src/Makevars.in 2017-04-01 22:32:40.968645087 +0200 -@@ -1,4 +1,5 @@ - - PKG_CPPFLAGS = @HAVE_OPENMP@ @OPENMP_CFLAGS@ @CPPFLAGS@ @HAVE_FFTW@ @FFTW_CFLAGS@ -I../inst/include -DCIMG_COMPILING -Dcimg_use_rng -Dcimg_r_mode -Dcimg_use_fftw3_singlethread -Dcimg_verbosity=1 - PKG_LIBS = @OPENMP_CFLAGS@ @LIBS@ @HAVE_FFTW@ @FFTW_LIBS@ $(RCPP_LDFLAGS) -- -+# disable Intel C++ compiler (icpc) warning/error #308, to avoid 'member "std::complex::_M_value" is inaccessible' -+PKG_CXXFLAGS = -wd308 ---- imager/MD5.orig 2016-09-12 15:08:55.000000000 +0200 -+++ imager/MD5 2017-04-01 22:44:16.943021224 +0200 -@@ -31,7 +31,7 @@ - 05e04a3bc5a858c40e001cc65b853dfc *inst/extdata/Leonardo_Birds.jpg - e1328ba2c55d5a72eb77e283c9630b90 *inst/extdata/parrots.png - daa5b7e30235689ad0444df37c88b7ff *inst/extdata/tennis_sif.mpeg --00de9e6b4c2066d28d7f8d9e251915cd *inst/include/CImg.h -+ea9acc61a3dd73452639c570af543d29 *inst/include/CImg.h - 034a9e8aab9e05094fd31ce9ea3bbae2 *inst/include/imager.h - 0c8aae8db902f96a8f8e323043eb1418 *inst/include/wrappers.h - be39be77874a0181ecd47b1a7a9af5dd *man/FFT.Rd -@@ -140,7 +140,7 @@ - a680472a2ef1eda48c1a9b90488543b5 *man/vanvliet.Rd - 08193940e20b440f614e4c7a2dbf82fb *man/warp.Rd - 429b25a38f282c30d5d178ad9efc3b1f *man/watershed.Rd --ab8f97aa6f15c67d1029e3eb5091853d *src/Makevars.in -+802ecbe76012c51adf729063804c793a *src/Makevars.in - 5ecf9e8577f31e535dee1c371e75a35f *src/Makevars.win - 78aff3a88c55983a329723eb1174a4ca *src/RcppExports.cpp - 8193f4fecd751c7d310d23b0faacd303 *src/colourspace.cpp diff --git a/easybuild/easyconfigs/r/R/imager-0.40.1_fix-CImg-icpc.patch b/easybuild/easyconfigs/r/R/imager-0.40.1_fix-CImg-icpc.patch new file mode 100644 index 0000000000..8f3e05fe69 --- /dev/null +++ b/easybuild/easyconfigs/r/R/imager-0.40.1_fix-CImg-icpc.patch @@ -0,0 +1,310 @@ +fix compilation issues with Intel compilers in CImg.h +cfr. https://github.com/dtschump/CImg/issues/123 and https://github.com/dahtah/imager/commit/b46e96efe0a9c596c9aca9d786123b10dd83adf2 +also include extra compiler option -wd308 to avoid 'member "std::complex::_M_value" is inaccessible' errors +patched composed by Kenneth Hoste (HPC-UGent) +--- imager/src/Makevars.in.orig 2017-04-01 22:32:32.628591934 +0200 ++++ imager/src/Makevars.in 2017-04-01 22:32:40.968645087 +0200 +@@ -1,4 +1,5 @@ + + PKG_CPPFLAGS = @HAVE_OPENMP@ @OPENMP_CFLAGS@ @CPPFLAGS@ @HAVE_FFTW@ @FFTW_CFLAGS@ -I../inst/include -DCIMG_COMPILING -Dcimg_use_rng -Dcimg_r_mode -Dcimg_use_fftw3_singlethread -Dcimg_verbosity=1 + PKG_LIBS = @OPENMP_CFLAGS@ @LIBS@ @HAVE_FFTW@ @FFTW_LIBS@ $(RCPP_LDFLAGS) +- ++# disable Intel C++ compiler (icpc) warning/error #308, to avoid 'member "std::complex::_M_value" is inaccessible' ++PKG_CXXFLAGS = -wd308 +diff --git a/inst/include/CImg.h b/inst/include/CImg.h +index 213d864..922edf8 100755 +--- a/inst/include/CImg.h ++++ b/inst/include/CImg.h +@@ -15161,7 +15161,7 @@ namespace cimg_library_suffixed { + const CImg& img_input=CImg::const_empty(), CImg *const img_output=0, + const CImgList *const list_input=0, CImgList *const list_output=0, + const bool _is_fill=false): +- code(_code),p_break((CImg*)0 - 2), ++ code(_code),p_break((CImg*)(-2*sizeof(CImg))), + imgin(img_input),listin(list_input?*list_input:CImgList::const_empty()), + imgout(img_output?*img_output:CImg::empty()),listout(list_output?*list_output:CImgList::empty()), + img_stats(_img_stats),list_stats(_list_stats),list_median(_list_median),user_macro(0), +@@ -15222,6 +15222,7 @@ namespace cimg_library_suffixed { + memtype.assign(mem._width,1,1,1,0); + for (unsigned int i = 0; i<_cimg_mp_slot_x; ++i) memtype[i] = 1; + memtype[17] = 0; ++ memtype[_cimg_mp_slot_x] = memtype[_cimg_mp_slot_y] = memtype[_cimg_mp_slot_z] = memtype[_cimg_mp_slot_c] = -2; + mempos = _cimg_mp_slot_c + 1; + variable_pos.assign(8); + +@@ -15270,7 +15271,7 @@ namespace cimg_library_suffixed { + } + + _cimg_math_parser(): +- code(_code),p_code_end(0),p_break((CImg*)0 - 2), ++ code(_code),p_code_end(0),p_break((CImg*)(-2*sizeof(CImg))), + imgin(CImg::const_empty()),listin(CImgList::const_empty()), + imgout(CImg::empty()),listout(CImgList::empty()), + img_stats(_img_stats),list_stats(_list_stats),list_median(_list_median),debug_indent(0), +@@ -15301,7 +15302,7 @@ namespace cimg_library_suffixed { + unsigned int *pd = res._data; + int level = 0; + for (const char *ps = expr._data; *ps && level>=0; ++ps) { +- if (!next_is_escaped && *ps=='\\') next_is_escaped = true; ++ if (!is_escaped && !next_is_escaped && *ps=='\\') next_is_escaped = true; + if (!is_escaped && *ps=='\'') { // Non-escaped character + if (!mode && ps>expr._data && *(ps - 1)=='[') next_mode = mode = 2; // Start vector-string + else if (mode==2 && *(ps + 1)==']') next_mode = !mode; // End vector-string +@@ -20498,7 +20499,7 @@ namespace cimg_library_suffixed { + CImg S(&_mp_arg(1) + 1,dx,dy,dz,dc,true); + const float opacity = (float)_mp_arg(12); + +- if (img) { ++ if (img._data) { + if (mp.opcode[13]!=~0U) { // Opacity mask specified + const ulongT sizM = mp.opcode[14]; + if (sizM<(ulongT)dx*dy*dz) +@@ -20605,7 +20606,7 @@ namespace cimg_library_suffixed { + off = (longT)_mp_arg(2), + whds = (longT)img.size(); + if (off>=0 && off=0 && off=0 && off=0 && off::nan(); + } +- if (img) switch (boundary_conditions) { ++ if (img._data) switch (boundary_conditions) { + case 3 : { // Mirror + const longT whd2 = 2*whd, moff = cimg::mod(off,whd2); + ptrs = &img[moff::nan(); + } +- if (img) switch (boundary_conditions) { ++ if (img._data) switch (boundary_conditions) { + case 3 : { // Mirror + const longT whd2 = 2*whd, moff = cimg::mod(off,whd2); + ptrs = &img[moff::nan(); + } +- if (img) switch (boundary_conditions) { ++ if (img._data) switch (boundary_conditions) { + case 3 : { // Mirror + const longT whd2 = 2*whd, moff = cimg::mod(off,whd2); + ptrs = &img[moff::nan(); + } +- if (img) switch (boundary_conditions) { ++ if (img._data) switch (boundary_conditions) { + case 3 : { // Mirror + const longT whd2 = 2*whd, moff = cimg::mod(off,whd2); + ptrs = &img[moff=65536)) +- for (int c = c0; c<(int)sc; c+=spectrum()) +- for (int z = z0; z<(int)sz; z+=depth()) +- for (int y = y0; y<(int)sy; y+=height()) +- for (int x = x0; x<(int)sx; x+=width()) ++ for (int c = c0; c<(int)sc; c+=dc) ++ for (int z = z0; z<(int)sz; z+=dz) ++ for (int y = y0; y<(int)sy; y+=dy) ++ for (int x = x0; x<(int)sx; x+=dx) + res.draw_image(x,y,z,c,*this); + } break; + case 1 : { // Neumann +@@ -34824,8 +34826,7 @@ namespace cimg_library_suffixed { + _sigma_x = sigma_x>=0?sigma_x:-sigma_x*_width/100, + _sigma_y = sigma_y>=0?sigma_y:-sigma_y*_height/100, + _sigma_z = sigma_z>=0?sigma_z:-sigma_z*_depth/100, +- __sigma_r = sigma_r>=0?sigma_r:-sigma_r*(edge_max - edge_min)/100, +- _sigma_r = std::max(0.1f,__sigma_r), ++ _sigma_r = sigma_r>=0?sigma_r:-sigma_r*(edge_max - edge_min)/100, + _sampling_x = sampling_x?sampling_x:std::max(_sigma_x,1.0f), + _sampling_y = sampling_y?sampling_y:std::max(_sigma_y,1.0f), + _sampling_z = sampling_z?sampling_z:std::max(_sigma_z,1.0f), +@@ -48076,9 +48077,13 @@ namespace cimg_library_suffixed { + else return load_other(filename); + #else + // Open file and check for PNG validity +- const char *volatile nfilename = filename; // two 'volatile' here to remove a g++ warning due to 'setjmp'. ++#if defined __GNUC__ ++ const char *volatile nfilename = filename; // Use 'volatile' to avoid (wrong) g++ warning. + std::FILE *volatile nfile = file?file:cimg::fopen(nfilename,"rb"); +- ++#else ++ const char *nfilename = filename; ++ std::FILE *nfile = file?file:cimg::fopen(nfilename,"rb"); ++#endif + unsigned char pngCheck[8] = { 0 }; + cimg::fread(pngCheck,8,(std::FILE*)nfile); + if (png_sig_cmp(pngCheck,0,8)) { +@@ -49017,11 +49022,11 @@ namespace cimg_library_suffixed { + rdr.ndim(2)?rdr.ndim(2):1, + rdr.ndim(3)?rdr.ndim(3):1, + rdr.ndim(4)?rdr.ndim(4):1); +- if(typeid(T)==typeid(unsigned char)) ++ if (typeid(T)==typeid(unsigned char)) + rdr.setup_read_byte(); +- else if(typeid(T)==typeid(int)) ++ else if (typeid(T)==typeid(int)) + rdr.setup_read_int(); +- else if(typeid(T)==typeid(double)) ++ else if (typeid(T)==typeid(double)) + rdr.setup_read_double(); + else + rdr.setup_read_float(); +@@ -49312,7 +49317,7 @@ namespace cimg_library_suffixed { + *item = *tmp1 = *tmp2 = 0; + out[0] = std::fscanf(file,"%63s",item._data); + out[0] = out[1] = out[2] = out[3] = out[5] = 1; out[4] = out[6] = out[7] = -1; +- if(cimg::strncasecmp(item,"#INRIMAGE-4#{",13)!=0) ++ if (cimg::strncasecmp(item,"#INRIMAGE-4#{",13)!=0) + throw CImgIOException("CImg<%s>::load_inr(): INRIMAGE-4 header not found.", + pixel_type()); + +@@ -49342,17 +49347,17 @@ namespace cimg_library_suffixed { + tmp2._data); + } + } +- if(out[0]<0 || out[1]<0 || out[2]<0 || out[3]<0) ++ if (out[0]<0 || out[1]<0 || out[2]<0 || out[3]<0) + throw CImgIOException("CImg<%s>::load_inr(): Invalid dimensions (%d,%d,%d,%d) defined in header.", + pixel_type(), + out[0],out[1],out[2],out[3]); +- if(out[4]<0 || out[5]<0) ++ if (out[4]<0 || out[5]<0) + throw CImgIOException("CImg<%s>::load_inr(): Incomplete pixel type defined in header.", + pixel_type()); +- if(out[6]<0) ++ if (out[6]<0) + throw CImgIOException("CImg<%s>::load_inr(): Incomplete PIXSIZE field defined in header.", + pixel_type()); +- if(out[7]<0) ++ if (out[7]<0) + throw CImgIOException("CImg<%s>::load_inr(): Big/Little Endian coding type undefined in header.", + pixel_type()); + } +@@ -52161,9 +52166,16 @@ namespace cimg_library_suffixed { + "save_png(): Unable to save data in '(*FILE)' unless libpng is enabled.", + cimg_instance); + #else +- const char *volatile nfilename = filename; // two 'volatile' here to remove a g++ warning due to 'setjmp'. ++ ++#if defined __GNUC__ ++ const char *volatile nfilename = filename; // Use 'volatile' to avoid (wrong) g++ warning. + std::FILE *volatile nfile = file?file:cimg::fopen(nfilename,"wb"); + volatile double stmin, stmax = (double)max_min(stmin); ++#else ++ const char *nfilename = filename; ++ std::FILE *nfile = file?file:cimg::fopen(nfilename,"wb"); ++ double stmin, stmax = (double)max_min(stmin); ++#endif + + if (_depth>1) + cimg::warn(_cimg_instance +@@ -52188,7 +52200,7 @@ namespace cimg_library_suffixed { + png_error_ptr user_error_fn = 0, user_warning_fn = 0; + png_structp png_ptr = png_create_write_struct(PNG_LIBPNG_VER_STRING,user_error_ptr, user_error_fn, + user_warning_fn); +- if(!png_ptr){ ++ if (!png_ptr){ + if (!file) cimg::fclose(nfile); + throw CImgIOException(_cimg_instance + "save_png(): Failed to initialize 'png_ptr' structure when saving file '%s'.", +@@ -52921,17 +52933,17 @@ namespace cimg_library_suffixed { + wtr.open(filename, imitate_file); + else { + minc::minc_info di; +- if(width()) di.push_back(minc::dim_info(width(),width()*0.5,-1,minc::dim_info::DIM_X)); +- if(height()) di.push_back(minc::dim_info(height(),height()*0.5,-1,minc::dim_info::DIM_Y)); +- if(depth()) di.push_back(minc::dim_info(depth(),depth()*0.5,-1,minc::dim_info::DIM_Z)); +- if(spectrum()) di.push_back(minc::dim_info(spectrum(),spectrum()*0.5,-1,minc::dim_info::DIM_TIME)); ++ if (width()) di.push_back(minc::dim_info(width(),width()*0.5,-1,minc::dim_info::DIM_X)); ++ if (height()) di.push_back(minc::dim_info(height(),height()*0.5,-1,minc::dim_info::DIM_Y)); ++ if (depth()) di.push_back(minc::dim_info(depth(),depth()*0.5,-1,minc::dim_info::DIM_Z)); ++ if (spectrum()) di.push_back(minc::dim_info(spectrum(),spectrum()*0.5,-1,minc::dim_info::DIM_TIME)); + wtr.open(filename,di,1,NC_FLOAT,0); + } +- if(typeid(T)==typeid(unsigned char)) ++ if (typeid(T)==typeid(unsigned char)) + wtr.setup_write_byte(); +- else if(typeid(T)==typeid(int)) ++ else if (typeid(T)==typeid(int)) + wtr.setup_write_int(); +- else if(typeid(T)==typeid(double)) ++ else if (typeid(T)==typeid(double)) + wtr.setup_write_double(); + else + wtr.setup_write_float(); +@@ -56443,7 +56455,7 @@ namespace cimg_library_suffixed { + } + if (disp.is_resized()) { disp.resize(false); visu0.assign(); } + if (ym>=0 && ym<13) { if (!text_down) { visu.assign(); text_down = true; }} +- else if (ym>=visu.height() - 13) { if(text_down) { visu.assign(); text_down = false; }} ++ else if (ym>=visu.height() - 13) { if (text_down) { visu.assign(); text_down = false; }} + if (!exit_on_anykey && key && key!=cimg::keyESC && + (key!=cimg::keyW || (!disp.is_keyCTRLLEFT() && !disp.is_keyCTRLRIGHT()))) { + key = 0; +@@ -57564,7 +57576,7 @@ namespace cimg_library_suffixed { + if (nlast_frame>=nb_images) nlast_frame = nb_images - 1; + assign(1 + (nlast_frame - nfirst_frame)/nstep_frame); + TIFFSetDirectory(tif,0); +-#if cimg_verbosity>=3 ++#if cimg_verbosity<3 + TIFFSetWarningHandler(0); + TIFFSetErrorHandler(0); + #endif +@@ -58324,7 +58336,6 @@ namespace cimg_library_suffixed { + throw CImgIOException(_cimglist_instance + "save_gzip_external(): Specified filename is (null).", + cimglist_instance); +- + CImg command(1024), filename_tmp(256), body(256); + const char + *ext = cimg::split_filename(filename,body), +--- imager/src/Makevars.in.orig 2017-04-04 18:02:36.525410690 +0200 ++++ imager/src/Makevars.in 2017-04-04 18:04:52.818449342 +0200 +@@ -1,3 +1,5 @@ + PKG_CPPFLAGS = $(SHLIB_OPENMP_CFLAGS) @CPPFLAGS@ @HAVE_FFTW@ @FFTW_CFLAGS@ @TIFF_CFLAGS@ -I../inst/include -DCIMG_COMPILING -Dcimg_use_rng -Dcimg_use_r -Dcimg_use_fftw3_singlethread -Dcimg_verbosity=1 -Dcimg_date='""' -Dcimg_time='""' + PKG_LIBS = $(SHLIB_OPENMP_CFLAGS) @LIBS@ @HAVE_FFTW@ @FFTW_LIBS@ @TIFF_LIBS@ $(RCPP_LDFLAGS) + ++# disable Intel C++ compiler (icpc) warning/error #308, to avoid 'member "std::complex::_M_value" is inaccessible' ++PKG_CXXFLAGS = -wd308 -- GitLab From 7638aeafcfa7264556a6ad330ed7572759665261 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Lopez Date: Tue, 4 Apr 2017 19:08:33 +0200 Subject: [PATCH 0532/1603] added zlib dependency --- .../easyconfigs/f/freetype/freetype-2.5.5-goolf-1.7.20.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.5.5-goolf-1.7.20.eb b/easybuild/easyconfigs/f/freetype/freetype-2.5.5-goolf-1.7.20.eb index c3aab419f3..773f70da96 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.5.5-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.5.5-goolf-1.7.20.eb @@ -11,7 +11,10 @@ toolchain = {'name': 'goolf', 'version': '1.7.20'} source_urls = [GNU_SAVANNAH_SOURCE] sources = [SOURCE_TAR_GZ] -dependencies = [('libpng', '1.6.18')] +dependencies = [ + ('libpng', '1.6.18'), + ('zlib', '1.2.8') +] sanity_check_paths = { 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], -- GitLab From e814354fd0809d35cbf6bf1b85844bb2e267dcfc Mon Sep 17 00:00:00 2001 From: Pablo Escobar Lopez Date: Tue, 4 Apr 2017 19:09:15 +0200 Subject: [PATCH 0533/1603] added zlib dependency --- .../easyconfigs/f/freetype/freetype-2.6.2-goolf-1.7.20.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.6.2-goolf-1.7.20.eb b/easybuild/easyconfigs/f/freetype/freetype-2.6.2-goolf-1.7.20.eb index 76cd412cf3..7436cc5833 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.6.2-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.6.2-goolf-1.7.20.eb @@ -11,7 +11,10 @@ toolchain = {'name': 'goolf', 'version': '1.7.20'} source_urls = [GNU_SAVANNAH_SOURCE] sources = [SOURCE_TAR_GZ] -dependencies = [('libpng', '1.6.21')] +dependencies = [ + ('libpng', '1.6.21'), + ('zlib', '1.2.8') +] sanity_check_paths = { 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], -- GitLab From d90ac78aec452f629244a06ae4ff49c8001e7684 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Lopez Date: Tue, 4 Apr 2017 19:10:43 +0200 Subject: [PATCH 0534/1603] added custom sanity check --- .../easyconfigs/l/libpng/libpng-1.6.18-goolf-1.7.20.eb | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.18-goolf-1.7.20.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.18-goolf-1.7.20.eb index a083925f91..2a604f301f 100644 --- a/easybuild/easyconfigs/l/libpng/libpng-1.6.18-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.18-goolf-1.7.20.eb @@ -16,4 +16,11 @@ dependencies = [('zlib', '1.2.8')] configopts = "--with-pic" +majminver = ''.join(version.split('.')[:2]) +sanity_check_paths = { + 'files': ['include/pngconf.h', 'include/png.h', 'include/pnglibconf.h', 'lib/libpng.a', + 'lib/libpng.%s' % SHLIB_EXT, 'lib/libpng%s.a' % majminver, 'lib/libpng%s.%s' % (majminver, SHLIB_EXT)], + 'dirs': ['bin', 'include/libpng%s' % majminver, 'share/man'], +} + moduleclass = 'lib' -- GitLab From ab8b2b9c6a5272d9912cff51be3bb22a5eff1b3e Mon Sep 17 00:00:00 2001 From: Pablo Escobar Lopez Date: Tue, 4 Apr 2017 19:11:13 +0200 Subject: [PATCH 0535/1603] added custom sanity checks --- .../easyconfigs/l/libpng/libpng-1.6.21-goolf-1.7.20.eb | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.21-goolf-1.7.20.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.21-goolf-1.7.20.eb index cb4fbebab2..15f766ff31 100644 --- a/easybuild/easyconfigs/l/libpng/libpng-1.6.21-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.21-goolf-1.7.20.eb @@ -16,4 +16,11 @@ dependencies = [('zlib', '1.2.8')] configopts = "--with-pic" +majminver = ''.join(version.split('.')[:2]) +sanity_check_paths = { + 'files': ['include/pngconf.h', 'include/png.h', 'include/pnglibconf.h', 'lib/libpng.a', + 'lib/libpng.%s' % SHLIB_EXT, 'lib/libpng%s.a' % majminver, 'lib/libpng%s.%s' % (majminver, SHLIB_EXT)], + 'dirs': ['bin', 'include/libpng%s' % majminver, 'share/man'], +} + moduleclass = 'lib' -- GitLab From 746c112e1e9293ed92e4ea7192c1f6271ad17621 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Lopez Date: Tue, 4 Apr 2017 19:12:12 +0200 Subject: [PATCH 0536/1603] remove unneeded line --- .../m/MultiQC/MultiQC-0.7-goolf-1.7.20-Python-2.7.11.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MultiQC/MultiQC-0.7-goolf-1.7.20-Python-2.7.11.eb b/easybuild/easyconfigs/m/MultiQC/MultiQC-0.7-goolf-1.7.20-Python-2.7.11.eb index 14c2e7f378..9cef816ccd 100644 --- a/easybuild/easyconfigs/m/MultiQC/MultiQC-0.7-goolf-1.7.20-Python-2.7.11.eb +++ b/easybuild/easyconfigs/m/MultiQC/MultiQC-0.7-goolf-1.7.20-Python-2.7.11.eb @@ -24,7 +24,6 @@ dependencies = [ # this is a bundle of Python packages exts_defaultclass = 'PythonPackage' -exts_filter = ("python -c 'import %(ext_name)s'", '') exts_list = [ ('six', '1.10.0', { -- GitLab From a00d479e8b57814916e4d9078bda040ef48fe56f Mon Sep 17 00:00:00 2001 From: Pablo Escobar Lopez Date: Tue, 4 Apr 2017 19:15:01 +0200 Subject: [PATCH 0537/1603] delete unneeded LD_LIBRARY_PATH --- .../m/MultiQC/MultiQC-0.7-goolf-1.7.20-Python-2.7.11.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MultiQC/MultiQC-0.7-goolf-1.7.20-Python-2.7.11.eb b/easybuild/easyconfigs/m/MultiQC/MultiQC-0.7-goolf-1.7.20-Python-2.7.11.eb index 9cef816ccd..9565d51bb3 100644 --- a/easybuild/easyconfigs/m/MultiQC/MultiQC-0.7-goolf-1.7.20-Python-2.7.11.eb +++ b/easybuild/easyconfigs/m/MultiQC/MultiQC-0.7-goolf-1.7.20-Python-2.7.11.eb @@ -66,7 +66,6 @@ exts_list = [ modextrapaths = { 'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages'], - 'LD_LIBRARY_PATH': ['lib/python%(pyshortver)s/site-packages'] } sanity_check_paths = { -- GitLab From 4b6fe00282e6767b906ebac0a88c360b0c42300d Mon Sep 17 00:00:00 2001 From: Pablo Escobar Lopez Date: Tue, 4 Apr 2017 19:15:22 +0200 Subject: [PATCH 0538/1603] update sanity check --- .../m/MultiQC/MultiQC-0.7-goolf-1.7.20-Python-2.7.11.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MultiQC/MultiQC-0.7-goolf-1.7.20-Python-2.7.11.eb b/easybuild/easyconfigs/m/MultiQC/MultiQC-0.7-goolf-1.7.20-Python-2.7.11.eb index 9565d51bb3..52da5ecd72 100644 --- a/easybuild/easyconfigs/m/MultiQC/MultiQC-0.7-goolf-1.7.20-Python-2.7.11.eb +++ b/easybuild/easyconfigs/m/MultiQC/MultiQC-0.7-goolf-1.7.20-Python-2.7.11.eb @@ -70,7 +70,7 @@ modextrapaths = { sanity_check_paths = { 'files': ['bin/multiqc'], - 'dirs': ['lib/python%(pyshortver)s/site-packages/multiqc-%(version)s-py%(pyshortver)s.egg'] + 'dirs': ['lib/python%(pyshortver)s/site-packages/'] } moduleclass = 'bio' -- GitLab From cc5d41bc0cc73c26f134801cede7f89961d06811 Mon Sep 17 00:00:00 2001 From: "Nathan S. Watson-Haigh" Date: Wed, 5 Apr 2017 09:29:23 +0930 Subject: [PATCH 0539/1603] Easyconfig for Autotools-20150215/foss-2015b --- .../Autotools/Autotools-20150215-foss-2015b.eb | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) create mode 100644 easybuild/easyconfigs/a/Autotools/Autotools-20150215-foss-2015b.eb diff --git a/easybuild/easyconfigs/a/Autotools/Autotools-20150215-foss-2015b.eb b/easybuild/easyconfigs/a/Autotools/Autotools-20150215-foss-2015b.eb new file mode 100644 index 0000000000..ab4ec5f149 --- /dev/null +++ b/easybuild/easyconfigs/a/Autotools/Autotools-20150215-foss-2015b.eb @@ -0,0 +1,17 @@ +easyblock = 'Bundle' + +name = 'Autotools' +version = '20150215' # date of the most recent change + +homepage = 'http://autotools.io' +description = """This bundle collect the standard GNU build tools: Autoconf, Automake and libtool""" + +toolchain = {'name': 'foss', 'version': '2015b'} + +dependencies = [ + ('Autoconf', '2.69'), # 20120424 + ('Automake', '1.15'), # 20150105 + ('libtool', '2.4.6'), # 20150215 +] + +moduleclass = 'devel' -- GitLab From c65c50b2a84609923b11eebb2dfe79b7c1252752 Mon Sep 17 00:00:00 2001 From: "Nathan S. Watson-Haigh" Date: Wed, 5 Apr 2017 09:30:11 +0930 Subject: [PATCH 0540/1603] Added comment/author to patch file --- .../easyconfigs/b/BioKanga/BioKanga-4.3.4_configure.patch | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/b/BioKanga/BioKanga-4.3.4_configure.patch b/easybuild/easyconfigs/b/BioKanga/BioKanga-4.3.4_configure.patch index a88701ea28..735a5b6d0c 100644 --- a/easybuild/easyconfigs/b/BioKanga/BioKanga-4.3.4_configure.patch +++ b/easybuild/easyconfigs/b/BioKanga/BioKanga-4.3.4_configure.patch @@ -1,3 +1,6 @@ +The Open Sourcing and refactoring of BioKanga on GitHub has resulted in some build issues. This +patch removes references to code which nolonger exists in refactored code of v4.3.4 +author: Nathan S. Watson-Haigh (University of Adelaide) --- ./configure.ac 2017-04-04 11:47:18.067209892 +0930 +++ ./configure.ac 2017-04-04 11:47:46.719519662 +0930 @@ -23,11 +23,10 @@ -- GitLab From 62b4678f29b9ba66d2d7334bf916a5871aa08573 Mon Sep 17 00:00:00 2001 From: "Nathan S. Watson-Haigh" Date: Wed, 5 Apr 2017 09:31:32 +0930 Subject: [PATCH 0541/1603] Implement changes suggested by Kenneth Hoste. * Changed to use Autotools-20150215/foss-2015b as build dependency. * Use %(version)s variable in patch name instead of hardcoding. --- .../easyconfigs/b/BioKanga/BioKanga-4.3.4-foss-2015b.eb | 7 ++----- 1 file changed, 2 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/b/BioKanga/BioKanga-4.3.4-foss-2015b.eb b/easybuild/easyconfigs/b/BioKanga/BioKanga-4.3.4-foss-2015b.eb index da082e4501..b413e97fee 100644 --- a/easybuild/easyconfigs/b/BioKanga/BioKanga-4.3.4-foss-2015b.eb +++ b/easybuild/easyconfigs/b/BioKanga/BioKanga-4.3.4-foss-2015b.eb @@ -13,12 +13,9 @@ toolchain = {'name': 'foss', 'version': '2015b'} source_urls = ['https://github.com/csiro-crop-informatics/biokanga/archive/'] sources = ['v%(version)s.tar.gz'] -patches = ['BioKanga-4.3.4_configure.patch'] +patches = ['BioKanga-%(version)s_configure.patch'] -builddependencies = [ - ('Autoconf', '2.69'), - ('Automake', '1.15') -] +builddependencies = [('Autotools', '20150215')] preconfigopts = "autoreconf -f -i && " -- GitLab From fa83d2fc94fcabf75adbd75cde9c2ce86d225162 Mon Sep 17 00:00:00 2001 From: "Nathan S. Watson-Haigh" Date: Wed, 5 Apr 2017 09:49:56 +0930 Subject: [PATCH 0542/1603] Adding libtool-2.4.6/foss-2015b missing dep --- .../l/libtool/libtool-2.4.6-foss-2015b.eb | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) create mode 100644 easybuild/easyconfigs/l/libtool/libtool-2.4.6-foss-2015b.eb diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.6-foss-2015b.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-foss-2015b.eb new file mode 100644 index 0000000000..83d12ef5f8 --- /dev/null +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-foss-2015b.eb @@ -0,0 +1,17 @@ +easyblock = 'ConfigureMake' + +name = 'libtool' +version = '2.4.6' + +homepage = 'http://www.gnu.org/software/libtool' +description = """GNU libtool is a generic library support script. Libtool hides the complexity of using shared libraries + behind a consistent, portable interface.""" + +toolchain = {'name': 'foss', 'version': '2015b'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +dependencies = [('M4', '1.4.17')] + +moduleclass = 'lib' -- GitLab From 71e29e140a369ff5d938a57835bda6f4f53e5d1f Mon Sep 17 00:00:00 2001 From: Pablo Escobar Lopez Date: Wed, 5 Apr 2017 09:00:59 +0200 Subject: [PATCH 0543/1603] removed unused patches line --- .../n/numpy/numpy-1.10.1-goolf-1.7.20-Python-2.7.11.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/n/numpy/numpy-1.10.1-goolf-1.7.20-Python-2.7.11.eb b/easybuild/easyconfigs/n/numpy/numpy-1.10.1-goolf-1.7.20-Python-2.7.11.eb index b4a5ec30e9..a4c16330cb 100644 --- a/easybuild/easyconfigs/n/numpy/numpy-1.10.1-goolf-1.7.20-Python-2.7.11.eb +++ b/easybuild/easyconfigs/n/numpy/numpy-1.10.1-goolf-1.7.20-Python-2.7.11.eb @@ -14,8 +14,6 @@ toolchain = {'name': 'goolf', 'version': '1.7.20'} source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCE_TAR_GZ] -#patches = ['numpy-1.8.0-mkl.patch'] - dependencies = [ ('Python', '2.7.11'), ] -- GitLab From cad67753370e1950e1ee1c63301ea5b159276d0d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 5 Apr 2017 11:23:41 +0200 Subject: [PATCH 0544/1603] bump imager extension to 0.40.1 in R 3.3.3 easyconfig to sync it up with #4427 --- easybuild/easyconfigs/r/R/R-3.3.3-foss-2016b-X11-20160819.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R/R-3.3.3-foss-2016b-X11-20160819.eb b/easybuild/easyconfigs/r/R/R-3.3.3-foss-2016b-X11-20160819.eb index 2584758870..3b6ee9a746 100644 --- a/easybuild/easyconfigs/r/R/R-3.3.3-foss-2016b-X11-20160819.eb +++ b/easybuild/easyconfigs/r/R/R-3.3.3-foss-2016b-X11-20160819.eb @@ -502,7 +502,8 @@ exts_list = [ ('bmp', '0.2', ext_options), ('readbitmap', '0.1-4', ext_options), ('purrr', '0.2.2', ext_options), - ('imager', '0.31', ext_options), + ('downloader', '0.4', ext_options), + ('imager', '0.40.1', ext_options), ] moduleclass = 'lang' -- GitLab From fc93911bf77c7d56dcb1b7fbf7c1e01b91116208 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Lopez Date: Wed, 5 Apr 2017 13:03:36 +0200 Subject: [PATCH 0545/1603] style fixes and add symlink to the sanity check --- easybuild/easyconfigs/s/Sambamba/Sambamba-0.6.6.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/s/Sambamba/Sambamba-0.6.6.eb b/easybuild/easyconfigs/s/Sambamba/Sambamba-0.6.6.eb index cd17c8d34d..c6c18b59b8 100644 --- a/easybuild/easyconfigs/s/Sambamba/Sambamba-0.6.6.eb +++ b/easybuild/easyconfigs/s/Sambamba/Sambamba-0.6.6.eb @@ -18,8 +18,10 @@ toolchain = {'name': 'dummy', 'version': ''} source_urls = ['https://github.com/lomereiter/sambamba/releases/download/v%(version)s/'] sources = ['%(namelower)s_v%(version)s_linux.tar.bz2'] +postinstallcmds = ['cd %(installdir)s && ln -s sambamba_v%(version)s sambamba',] + sanity_check_paths = { - 'files': ['sambamba_v%(version)s'], + 'files': ['sambamba_v%(version)s', 'sambamba'], 'dirs': [], } @@ -27,6 +29,4 @@ modextrapaths = { 'PATH': "", } -postinstallcmds = ['cd %(installdir)s && ln -s sambamba_v%(version)s sambamba',] - moduleclass = 'bio' -- GitLab From ff2de14ad7c936a63b9c2b9ba092ff0912669456 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Wed, 5 Apr 2017 12:03:45 +0100 Subject: [PATCH 0546/1603] Add explicit Python extension deps, based on @pescobar's work --- .../MultiQC-0.9-foss-2016b-Python-2.7.12.eb | 54 +++++++++++++++++-- 1 file changed, 50 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/m/MultiQC/MultiQC-0.9-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/m/MultiQC/MultiQC-0.9-foss-2016b-Python-2.7.12.eb index a7a94c8c8c..4ca3af6861 100644 --- a/easybuild/easyconfigs/m/MultiQC/MultiQC-0.9-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/m/MultiQC/MultiQC-0.9-foss-2016b-Python-2.7.12.eb @@ -1,7 +1,11 @@ # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # Adam Huffman # The Francis Crick Institute -easyblock = 'PythonPackage' +# Elements derived from work by Pablo Escobar +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'Bundle' name = 'MultiQC' version = '0.9' @@ -16,14 +20,56 @@ description = """Aggregate results from bioinformatics analyses across many samp toolchain = {'name': 'foss', 'version': '2016b'} -sources = ['v%(version)s.tar.gz'] -source_urls = ['https://github.com/ewels/MultiQC/archive'] - dependencies = [ ('Python', '2.7.12'), ('matplotlib', '2.0.0', versionsuffix), ] +exts_defaultclass = 'PythonPackage' + +exts_list = [ + ('six', '1.10.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), + ('pyparsing', '2.1.9', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], + }), + ('pytz', '2016.6.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pytz/'], + }), + ('cycler', '0.10.0', { + 'source_urls': ['https://pypi.python.org/packages/source/c/cycler/'], + }), + ('python-dateutil', '2.5.3', { + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], + 'modulename': 'dateutil', + }), + ('MarkupSafe', '0.23', { + 'source_urls': ['https://pypi.python.org/packages/source/m/markupsafe'], + }), + ('click', '6.6', { + 'source_urls': ['https://pypi.python.org/packages/source/c/click/'], + }), + ('PyYAML', '3.12', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyyaml'], + 'modulename': 'yaml', + }), + ('simplejson', '3.8.2', { + 'source_urls': ['https://pypi.python.org/packages/source/s/simplejson/'], + }), + ('Jinja2', '2.8', { + 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2/'], + }), + ('multiqc', version, { + 'source_urls': ['https://pypi.python.org/packages/source/m/multiqc/'], + }), +] + +modextrapaths = { + 'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages'], +} + + sanity_check_paths = { 'files': ['bin/%(namelower)s'], 'dirs': ['lib/python%(pyshortver)s/site-packages'] -- GitLab From fa8ca0b1d95b064584aaf1b3885d72ebfc7a3366 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 5 Apr 2017 14:26:20 +0200 Subject: [PATCH 0547/1603] adding easyconfigs: vsc-mympirun-4.0.0b0.eb, vsc-base-2.5.8.eb, IPy-0.83.eb, vsc-install-0.10.25.eb --- easybuild/easyconfigs/i/IPy/IPy-0.83.eb | 23 ++++++++++++ .../easyconfigs/v/vsc-base/vsc-base-2.5.8.eb | 27 ++++++++++++++ .../v/vsc-install/vsc-install-0.10.25.eb | 23 ++++++++++++ .../v/vsc-mympirun/vsc-mympirun-4.0.0b0.eb | 35 +++++++++++++++++++ 4 files changed, 108 insertions(+) create mode 100644 easybuild/easyconfigs/i/IPy/IPy-0.83.eb create mode 100644 easybuild/easyconfigs/v/vsc-base/vsc-base-2.5.8.eb create mode 100644 easybuild/easyconfigs/v/vsc-install/vsc-install-0.10.25.eb create mode 100755 easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-4.0.0b0.eb diff --git a/easybuild/easyconfigs/i/IPy/IPy-0.83.eb b/easybuild/easyconfigs/i/IPy/IPy-0.83.eb new file mode 100644 index 0000000000..661784d022 --- /dev/null +++ b/easybuild/easyconfigs/i/IPy/IPy-0.83.eb @@ -0,0 +1,23 @@ +easyblock = 'PythonPackage' + +name = 'IPy' +version = '0.83' + +homepage = 'https://pypi.python.org/pypi/IPy' +description = """Class and tools for handling of IPv4 and IPv6 addresses and networks""" + +# purposely built with system compilers & Python +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = [SOURCE_TAR_GZ] +source_urls = [PYPI_SOURCE] + +options = {'modulename': 'IPy'} + +shortpyver = '.'.join(SYS_PYTHON_VERSION.split('.')[:2]) +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/' % shortpyver], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/v/vsc-base/vsc-base-2.5.8.eb b/easybuild/easyconfigs/v/vsc-base/vsc-base-2.5.8.eb new file mode 100644 index 0000000000..c38a164cb9 --- /dev/null +++ b/easybuild/easyconfigs/v/vsc-base/vsc-base-2.5.8.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'vsc-base' +version = '2.5.8' + +homepage = 'http://hpcugent.github.com/vsc-base/' +description = """Basic Python libraries used by UGent's HPC group""" + +# purposely built with system compilers & Python +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = [SOURCE_TAR_GZ] +source_urls = [PYPI_SOURCE] + +# install as zipped egg to make sure that tools that use this as a dependency are responsive +use_easy_install = True +zipped_egg = True + +options = {'modulename': 'vsc.utils'} + +shortpyver = '.'.join(SYS_PYTHON_VERSION.split('.')[:2]) +sanity_check_paths = { + 'files': ['lib/python%(pyver)s/site-packages/vsc_base-%%(version)s-py%(pyver)s.egg' % {'pyver': shortpyver}], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/v/vsc-install/vsc-install-0.10.25.eb b/easybuild/easyconfigs/v/vsc-install/vsc-install-0.10.25.eb new file mode 100644 index 0000000000..c821c18048 --- /dev/null +++ b/easybuild/easyconfigs/v/vsc-install/vsc-install-0.10.25.eb @@ -0,0 +1,23 @@ +easyblock = 'PythonPackage' + +name = 'vsc-install' +version = '0.10.25' + +homepage = 'http://hpcugent.github.com/vsc-install/' +description = """Shared setuptools functions and classes for python libraries developed by UGent's HPC group""" + +# purposely built with system compilers & Python +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = [SOURCE_TAR_GZ] +source_urls = [PYPI_SOURCE] + +options = {'modulename': 'vsc.install'} + +pyshortver = '.'.join(SYS_PYTHON_VERSION.split('.')[:2]) +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages' % pyshortver], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-4.0.0b0.eb b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-4.0.0b0.eb new file mode 100755 index 0000000000..58a69d638c --- /dev/null +++ b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-4.0.0b0.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonPackage' + +name = 'vsc-mympirun' +version = '4.0.0b0' + +homepage = 'https://github.com/hpcugent/vsc-mympirun' +description = """VSC-tools is a set of Python libraries and scripts that are commonly used within HPC-UGent.""" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = [PYPI_SOURCE] +sources = ['vsc-mympirun-%(version)s.tar.gz'] + +dependencies = [ + ('vsc-base', '2.5.8'), + ('IPy', '0.83'), +] +builddependencies = [('vsc-install', '0.10.25')] + +#postinstallcmds = ['echo "import pkg_resources; pkg_resources.declare_namespace(__name__)" > %(installdir)s/lib/vsc/__init__.py'] +#use_easy_install = True + +# we ship something in bin/fake +modextrapaths = {'PATH': 'bin/fake'} + +#options = {'modulename': 'vsc.mympirun'} +options = {'modulename': 'vsc'} + +pyshortver = '.'.join(SYS_PYTHON_VERSION.split('.')[:2]) +sanity_check_paths = { + 'files': ['bin/mympirun', 'bin/mympisanity'], + 'dirs': ['bin/fake', 'lib/python%s/site-packages' % pyshortver], +} + +moduleclass = 'tools' -- GitLab From 03f367f888b40140a128276d63c9ff7c7f4779bd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 5 Apr 2017 14:30:31 +0200 Subject: [PATCH 0548/1603] don't patch Makevars.in twice in patch for R imager extension --- .../easyconfigs/r/R/imager-0.40.1_fix-CImg-icpc.patch | 9 --------- 1 file changed, 9 deletions(-) diff --git a/easybuild/easyconfigs/r/R/imager-0.40.1_fix-CImg-icpc.patch b/easybuild/easyconfigs/r/R/imager-0.40.1_fix-CImg-icpc.patch index 8f3e05fe69..829b112342 100644 --- a/easybuild/easyconfigs/r/R/imager-0.40.1_fix-CImg-icpc.patch +++ b/easybuild/easyconfigs/r/R/imager-0.40.1_fix-CImg-icpc.patch @@ -2,15 +2,6 @@ fix compilation issues with Intel compilers in CImg.h cfr. https://github.com/dtschump/CImg/issues/123 and https://github.com/dahtah/imager/commit/b46e96efe0a9c596c9aca9d786123b10dd83adf2 also include extra compiler option -wd308 to avoid 'member "std::complex::_M_value" is inaccessible' errors patched composed by Kenneth Hoste (HPC-UGent) ---- imager/src/Makevars.in.orig 2017-04-01 22:32:32.628591934 +0200 -+++ imager/src/Makevars.in 2017-04-01 22:32:40.968645087 +0200 -@@ -1,4 +1,5 @@ - - PKG_CPPFLAGS = @HAVE_OPENMP@ @OPENMP_CFLAGS@ @CPPFLAGS@ @HAVE_FFTW@ @FFTW_CFLAGS@ -I../inst/include -DCIMG_COMPILING -Dcimg_use_rng -Dcimg_r_mode -Dcimg_use_fftw3_singlethread -Dcimg_verbosity=1 - PKG_LIBS = @OPENMP_CFLAGS@ @LIBS@ @HAVE_FFTW@ @FFTW_LIBS@ $(RCPP_LDFLAGS) -- -+# disable Intel C++ compiler (icpc) warning/error #308, to avoid 'member "std::complex::_M_value" is inaccessible' -+PKG_CXXFLAGS = -wd308 diff --git a/inst/include/CImg.h b/inst/include/CImg.h index 213d864..922edf8 100755 --- a/inst/include/CImg.h -- GitLab From 6806348b71dbd35af608f2da2a6644e741ae03d8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 5 Apr 2017 15:00:10 +0200 Subject: [PATCH 0549/1603] remove commented out lines, addd sanity check command to check that 'mympirun --help' works --- .../easyconfigs/v/vsc-mympirun/vsc-mympirun-4.0.0b0.eb | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-4.0.0b0.eb b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-4.0.0b0.eb index 58a69d638c..b31dee5a6e 100755 --- a/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-4.0.0b0.eb +++ b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-4.0.0b0.eb @@ -17,13 +17,10 @@ dependencies = [ ] builddependencies = [('vsc-install', '0.10.25')] -#postinstallcmds = ['echo "import pkg_resources; pkg_resources.declare_namespace(__name__)" > %(installdir)s/lib/vsc/__init__.py'] -#use_easy_install = True - # we ship something in bin/fake modextrapaths = {'PATH': 'bin/fake'} -#options = {'modulename': 'vsc.mympirun'} +# can't check for 'import vsc.mympirun' because vsc-base may be installed system-wide options = {'modulename': 'vsc'} pyshortver = '.'.join(SYS_PYTHON_VERSION.split('.')[:2]) @@ -32,4 +29,6 @@ sanity_check_paths = { 'dirs': ['bin/fake', 'lib/python%s/site-packages' % pyshortver], } +sanity_check_commands = ["mympirun --help"] + moduleclass = 'tools' -- GitLab From 372ee603a6f226341a0ee51b8a6b33cdb48156e3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 5 Apr 2017 15:14:17 +0200 Subject: [PATCH 0550/1603] bump to intel/2017a and Perl 5.24.1 in ROI_PAC easyconfig --- ....2-intel-2016b.eb => GETORB-2.3.2-intel-2017a.eb} | 2 +- ...0.eb => ROI_PAC-3.0.1-intel-2017a-Perl-5.24.1.eb} | 12 ++++++++---- 2 files changed, 9 insertions(+), 5 deletions(-) rename easybuild/easyconfigs/g/GETORB/{GETORB-2.3.2-intel-2016b.eb => GETORB-2.3.2-intel-2017a.eb} (92%) rename easybuild/easyconfigs/r/ROI_PAC/{ROI_PAC-3.0.1-intel-2016b-Perl-5.24.0.eb => ROI_PAC-3.0.1-intel-2017a-Perl-5.24.1.eb} (83%) diff --git a/easybuild/easyconfigs/g/GETORB/GETORB-2.3.2-intel-2016b.eb b/easybuild/easyconfigs/g/GETORB/GETORB-2.3.2-intel-2017a.eb similarity index 92% rename from easybuild/easyconfigs/g/GETORB/GETORB-2.3.2-intel-2016b.eb rename to easybuild/easyconfigs/g/GETORB/GETORB-2.3.2-intel-2017a.eb index 2e648643f9..f01c7d1564 100644 --- a/easybuild/easyconfigs/g/GETORB/GETORB-2.3.2-intel-2016b.eb +++ b/easybuild/easyconfigs/g/GETORB/GETORB-2.3.2-intel-2017a.eb @@ -6,7 +6,7 @@ version = '2.3.2' homepage = 'http://www.deos.tudelft.nl/ers/precorbs/tools/getorb_pack.shtml' description = "GETORB software package contains programs to handle the orbital data records (ODRs)" -toolchain = {'name': 'intel', 'version': '2016b'} +toolchain = {'name': 'intel', 'version': '2017a'} source_urls = ['http://www.deos.tudelft.nl/ers/precorbs/tools/'] sources = ['getorb_%(version)s.tar.gz'] diff --git a/easybuild/easyconfigs/r/ROI_PAC/ROI_PAC-3.0.1-intel-2016b-Perl-5.24.0.eb b/easybuild/easyconfigs/r/ROI_PAC/ROI_PAC-3.0.1-intel-2017a-Perl-5.24.1.eb similarity index 83% rename from easybuild/easyconfigs/r/ROI_PAC/ROI_PAC-3.0.1-intel-2016b-Perl-5.24.0.eb rename to easybuild/easyconfigs/r/ROI_PAC/ROI_PAC-3.0.1-intel-2017a-Perl-5.24.1.eb index 89a80fb749..351c02bb8c 100644 --- a/easybuild/easyconfigs/r/ROI_PAC/ROI_PAC-3.0.1-intel-2016b-Perl-5.24.0.eb +++ b/easybuild/easyconfigs/r/ROI_PAC/ROI_PAC-3.0.1-intel-2017a-Perl-5.24.1.eb @@ -8,22 +8,26 @@ homepage = 'http://roipac.org/' description = """Repeat Orbit Interferometry PACkage (ROI_PAC), software for processing synthetic aperture radar data to produce differential interferograms""" -toolchain = {'name': 'intel', 'version': '2016b'} +toolchain = {'name': 'intel', 'version': '2017a'} # download of ROI_PAC tarball requires registration, see http://www.openchannelfoundation.org/projects/ROI_PAC sources = ['ROI_PAC_%s.tgz' % '_'.join(version.split('.'))] # make_raw_alos.pl via http://roipac.org/cgi-bin/moin.cgi/ALOS_PALSAR?action=AttachFile&do=get&target=make_raw_alos.pl patches = [ - 'ROI_PAC-%(version)s_fix-IntSim.patch', ('make_raw_alos.pl', 'ROI_PAC/INT_SCR'), + 'ROI_PAC-%(version)s_fix-IntSim.patch', +] +checksums = [ + 'db50e9cd99183291eb9cfe7c74750cc6', # ROI_PAC_3_0_1.tgz + '284faa43c12626670810c1e14d393159', # make_raw_alos.pl ] builddependencies = [('Autotools', '20150215')] dependencies = [ ('FFTW', '3.3.6'), ('GETORB', '2.3.2'), - ('Perl', '5.24.0'), + ('Perl', '5.24.1'), ] start_dir = 'ROI_PAC' @@ -52,6 +56,6 @@ modextravars = { 'ROI_PAC': '%(installdir)s', } -modloadmsg = "To define: $INS_DIR, $POR_DIR, $SAR_ODR_DIR, $SAR_PRC_DIR, $VOR_DIR\n" +modloadmsg = "These environment variables should be defined: $INS_DIR, $POR_DIR, $SAR_ODR_DIR, $SAR_PRC_DIR, $VOR_DIR\n" moduleclass = 'geo' -- GitLab From 3db3b7b5770a9f83fd0aa56f48c62b8eb4410f80 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 5 Apr 2017 15:15:16 +0200 Subject: [PATCH 0551/1603] add missing patch file for ROI_PAC --- .../r/ROI_PAC/ROI_PAC-3.0.1_fix-IntSim.patch | 15 +++++++++++++++ 1 file changed, 15 insertions(+) create mode 100644 easybuild/easyconfigs/r/ROI_PAC/ROI_PAC-3.0.1_fix-IntSim.patch diff --git a/easybuild/easyconfigs/r/ROI_PAC/ROI_PAC-3.0.1_fix-IntSim.patch b/easybuild/easyconfigs/r/ROI_PAC/ROI_PAC-3.0.1_fix-IntSim.patch new file mode 100644 index 0000000000..f9b938a005 --- /dev/null +++ b/easybuild/easyconfigs/r/ROI_PAC/ROI_PAC-3.0.1_fix-IntSim.patch @@ -0,0 +1,15 @@ +fix bug in ROI_PAC v3.0.1, cfr. http://roipac.org/cgi-bin/moin.cgi/Patches +--- ./ROI_PAC/intsim/IntSim.f.orig 2017-03-30 10:35:09.702908447 +0200 ++++ ./ROI_PAC/intsim/IntSim.f 2017-03-30 10:36:32.204116436 +0200 +@@ -1339,6 +1339,11 @@ + ntotlonpx = ntotcpx + endif + ++! update these after padding has been applied EJF 2013/5/9 ++ nslatpx = int(dem_pixel_min(1)) ++ nslonpx = int(dem_pixel_min(2)) ++ nlatpx = nint(dem_pixel_max(1)) - nslatpx + 1 ++ nlonpx = nint(dem_pixel_max(2)) - nslonpx + 1 + + write (*,*) + write (*,*) -- GitLab From 231a282bc419ebf00eb44efadcd54d9ca68bfca1 Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Tue, 4 Apr 2017 18:48:52 +0000 Subject: [PATCH 0552/1603] Fix pkgconfig patch for Qhull to only let CMake substitute @ --- easybuild/easyconfigs/q/Qhull/Qhull_pkgconfig.patch | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/q/Qhull/Qhull_pkgconfig.patch b/easybuild/easyconfigs/q/Qhull/Qhull_pkgconfig.patch index 53f43a015d..0aa79c3083 100644 --- a/easybuild/easyconfigs/q/Qhull/Qhull_pkgconfig.patch +++ b/easybuild/easyconfigs/q/Qhull/Qhull_pkgconfig.patch @@ -3,7 +3,7 @@ requires making CMake to fill in the gaps via 'configure_file(... @ONLY)' author: Kenneth Hoste (UGent) --- qhull/CMakeLists.txt.orig 2015-09-21 15:27:38.424110227 +0200 +++ qhull/CMakeLists.txt 2015-09-21 15:27:06.403494984 +0200 -@@ -430,3 +430,9 @@ +@@ -430,3 +430,10 @@ install(FILES html/rbox.man DESTINATION ${MAN_INSTALL_DIR} RENAME rbox.1) install(FILES ${doc_FILES} DESTINATION ${DOC_INSTALL_DIR}) install(DIRECTORY html/ DESTINATION ${DOC_INSTALL_DIR}) @@ -11,6 +11,7 @@ author: Kenneth Hoste (UGent) +CONFIGURE_FILE( + "${CMAKE_CURRENT_SOURCE_DIR}/qhull.pc.in" + "${CMAKE_CURRENT_BINARY_DIR}/qhull.pc" ++ @ONLY +) +INSTALL(FILES "${CMAKE_BINARY_DIR}/qhull.pc" DESTINATION lib/pkgconfig) --- qhull/qhull.pc.in 1970-01-01 01:00:00.000000000 +0100 -- GitLab From f5d42fd9a077f9483e3e48fae1daee3bd335347e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 6 Apr 2017 00:10:18 +0200 Subject: [PATCH 0553/1603] fix comment --- .../r/ROI_PAC/ROI_PAC-3.0.1-intel-2017a-Perl-5.24.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/ROI_PAC/ROI_PAC-3.0.1-intel-2017a-Perl-5.24.1.eb b/easybuild/easyconfigs/r/ROI_PAC/ROI_PAC-3.0.1-intel-2017a-Perl-5.24.1.eb index 351c02bb8c..d772d057cf 100644 --- a/easybuild/easyconfigs/r/ROI_PAC/ROI_PAC-3.0.1-intel-2017a-Perl-5.24.1.eb +++ b/easybuild/easyconfigs/r/ROI_PAC/ROI_PAC-3.0.1-intel-2017a-Perl-5.24.1.eb @@ -37,7 +37,7 @@ installopts = "&& cd fip && $CC $CFLAGS -o add_rmgAmpPhs add_rmgAmpPhs.c && cp - postinstallcmds = [ # symlink to getorb requires in /bin subdirectory "cd %(installdir)s/bin && ln -s $(which getorb)", - # also copy scripts and make sure they're excutable + # also copy scripts "cp -a INT_SCR/* %(installdir)s/bin", # fix shebang in Perl scripts "sed -i 's@^#!.*/bin/perl.*@#!/usr/bin/env perl@g' %(installdir)s//bin/*.pl", -- GitLab From d8cc0f780474286401a29f65cc0fe227c987b28a Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Thu, 6 Apr 2017 00:51:01 +0000 Subject: [PATCH 0554/1603] Octave 4.2.1: add easyconfig for intel 2016b with updated deps incl Qt5 --- .../o/Octave/Octave-4.2.1-intel-2016b.eb | 63 +++++++++++++++++++ .../o/Octave/Octave-4.2.1_intel.patch | 47 ++++++++++++++ 2 files changed, 110 insertions(+) create mode 100644 easybuild/easyconfigs/o/Octave/Octave-4.2.1-intel-2016b.eb create mode 100644 easybuild/easyconfigs/o/Octave/Octave-4.2.1_intel.patch diff --git a/easybuild/easyconfigs/o/Octave/Octave-4.2.1-intel-2016b.eb b/easybuild/easyconfigs/o/Octave/Octave-4.2.1-intel-2016b.eb new file mode 100644 index 0000000000..5ea3487cef --- /dev/null +++ b/easybuild/easyconfigs/o/Octave/Octave-4.2.1-intel-2016b.eb @@ -0,0 +1,63 @@ +easyblock = 'ConfigureMake' + +name = 'Octave' +version = '4.2.1' + +homepage = 'http://www.gnu.org/software/octave/' +description = """GNU Octave is a high-level interpreted language, primarily intended for numerical computations.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +patches = ['%(name)s-%(version)s_intel.patch'] + +builddependencies = [ + ('Bison', '3.0.4'), + ('flex', '2.6.3'), + ('Autotools', '20150215'), + ('libtool', '2.4.6'), + ('gperf', '3.0.4'), +] + +dependencies = [ + ('X11', '20170314'), + ('PCRE', '8.40'), + ('ncurses', '6.0'), + ('libreadline', '7.0'), + ('arpack-ng', '3.4.0'), + ('cURL', '7.52.1'), + ('FLTK', '1.3.3'), + ('fontconfig', '2.12.1'), + ('freetype', '2.7'), + ('GLPK', '4.60'), + ('GL2PS', '1.3.9'), + ('gnuplot', '5.0.5'), + ('Java', '1.8.0_121', '', True), + ('zlib', '1.2.8'), + ('Mesa', '12.0.2'), + ('libGLU', '9.0.0'), + ('Qhull', '2015.2'), + ('Qt5', '5.8.0'), + ('HDF5', '1.8.17', '-serial'), + ('qrupdate', '1.1.2'), + ('SuiteSparse', '4.5.3', '-METIS-5.1.0'), + ('GraphicsMagick', '1.3.25'), + ('FFTW', '3.3.6'), +] + +configopts = 'MOC=$EBROOTQT5/bin/moc ' +configopts += 'UIC=$EBROOTQT5/bin/uic ' +configopts += 'RCC=$EBROOTQT5/bin/rcc ' +configopts += 'LRELEASE=$EBROOTQT5/bin/lrelease ' +configopts += '--with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK" --disable-docs ' + +sanity_check_paths = { + 'files': ['bin/octave'], + 'dirs': [] +} + +sanity_check_commands = [('octave', '--eval "1+2"')] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/o/Octave/Octave-4.2.1_intel.patch b/easybuild/easyconfigs/o/Octave/Octave-4.2.1_intel.patch new file mode 100644 index 0000000000..872aa06961 --- /dev/null +++ b/easybuild/easyconfigs/o/Octave/Octave-4.2.1_intel.patch @@ -0,0 +1,47 @@ +Intel compiler does not understand __builtin_*_overflow +# Oct 25th 2016 by B. Hajgato (Free University Brussels - VUB) +# Apr 4th 2017 by B. Oldeman (Compute Canada) +--- octave-4.2.1/libgnu/xalloc-oversized.h.orig 2017-02-22 18:17:37.000000000 +0000 ++++ octave-4.2.1/libgnu/xalloc-oversized.h 2017-04-04 14:29:22.020046084 +0000 +@@ -43,12 +43,12 @@ + nonnegative. This is a macro, not a function, so that it + works correctly even when SIZE_MAX < N. */ + +-#if 7 <= __GNUC__ || __has_builtin (__builtin_add_overflow_p) ++#if (7 <= __GNUC__ || __has_builtin (__builtin_add_overflow_p) && !__INTEL_COMPILER) + # define xalloc_oversized(n, s) __builtin_mul_overflow_p (n, s, (size_t) 1) + #elif ((5 <= __GNUC__ \ + || (__has_builtin (__builtin_mul_overflow) \ + && __has_builtin (__builtin_constant_p))) \ +- && !__STRICT_ANSI__) ++ && !__STRICT_ANSI__ && !__INTEL_COMPILER) + # define xalloc_oversized(n, s) \ + (__builtin_constant_p (n) && __builtin_constant_p (s) \ + ? __xalloc_oversized (n, s) \ +--- octave-4.0.3/libgnu/glob.c.orig 2016-10-24 16:11:56.437441986 +0200 ++++ octave-4.0.3/libgnu/glob.c 2016-10-24 16:12:21.127612656 +0200 +@@ -257,7 +257,7 @@ + static bool + size_add_wrapv (size_t a, size_t b, size_t *r) + { +-#if 5 <= __GNUC__ || __has_builtin (__builtin_add_overflow) ++#if ((5 <= __GNUC__ || __has_builtin (__builtin_add_overflow)) && !__INTEL_COMPILER) + return __builtin_add_overflow (a, b, r); + #else + *r = a + b; +--- octave-4.2.1/libgnu/intprops.h.orig 2017-02-22 18:17:35.000000000 +0000 ++++ octave-4.2.1/libgnu/intprops.h 2017-04-04 14:35:17.208604138 +0000 +@@ -242,11 +242,11 @@ + + /* True if __builtin_add_overflow (A, B, P) works when P is non-null. */ + #define _GL_HAS_BUILTIN_OVERFLOW \ +- (5 <= __GNUC__ || __has_builtin (__builtin_add_overflow)) ++ ((5 <= __GNUC__ || __has_builtin (__builtin_add_overflow)) && !__INTEL_COMPILER) + + /* True if __builtin_add_overflow_p (A, B, C) works. */ + #define _GL_HAS_BUILTIN_OVERFLOW_P \ +- (7 <= __GNUC__ || __has_builtin (__builtin_add_overflow_p)) ++ ((7 <= __GNUC__ || __has_builtin (__builtin_add_overflow_p)) && !__INTEL_COMPILER) + + /* The _GL*_OVERFLOW macros have the same restrictions as the + *_RANGE_OVERFLOW macros, except that they do not assume that operands -- GitLab From 8fde62045a9e2e96adb7ce875c72d3b922ee411a Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Thu, 6 Apr 2017 01:06:14 +0000 Subject: [PATCH 0555/1603] Fix irresolvable dependencies. --- easybuild/easyconfigs/o/Octave/Octave-4.2.1-intel-2016b.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/o/Octave/Octave-4.2.1-intel-2016b.eb b/easybuild/easyconfigs/o/Octave/Octave-4.2.1-intel-2016b.eb index 5ea3487cef..7cb6f50189 100644 --- a/easybuild/easyconfigs/o/Octave/Octave-4.2.1-intel-2016b.eb +++ b/easybuild/easyconfigs/o/Octave/Octave-4.2.1-intel-2016b.eb @@ -22,10 +22,10 @@ builddependencies = [ ] dependencies = [ - ('X11', '20170314'), + ('X11', '20160819'), ('PCRE', '8.40'), ('ncurses', '6.0'), - ('libreadline', '7.0'), + ('libreadline', '6.3'), ('arpack-ng', '3.4.0'), ('cURL', '7.52.1'), ('FLTK', '1.3.3'), -- GitLab From 950cd4fa74caec7d7129c9c5f17923778748f88e Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Thu, 6 Apr 2017 01:24:41 +0000 Subject: [PATCH 0556/1603] Avoid conflicts in dependencies. --- easybuild/easyconfigs/o/Octave/Octave-4.2.1-intel-2016b.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/o/Octave/Octave-4.2.1-intel-2016b.eb b/easybuild/easyconfigs/o/Octave/Octave-4.2.1-intel-2016b.eb index 7cb6f50189..e845e9c89e 100644 --- a/easybuild/easyconfigs/o/Octave/Octave-4.2.1-intel-2016b.eb +++ b/easybuild/easyconfigs/o/Octave/Octave-4.2.1-intel-2016b.eb @@ -15,7 +15,7 @@ patches = ['%(name)s-%(version)s_intel.patch'] builddependencies = [ ('Bison', '3.0.4'), - ('flex', '2.6.3'), + ('flex', '2.6.2'), ('Autotools', '20150215'), ('libtool', '2.4.6'), ('gperf', '3.0.4'), @@ -23,14 +23,14 @@ builddependencies = [ dependencies = [ ('X11', '20160819'), - ('PCRE', '8.40'), + ('PCRE', '8.39'), ('ncurses', '6.0'), ('libreadline', '6.3'), ('arpack-ng', '3.4.0'), ('cURL', '7.52.1'), ('FLTK', '1.3.3'), ('fontconfig', '2.12.1'), - ('freetype', '2.7'), + ('freetype', '2.6.5'), ('GLPK', '4.60'), ('GL2PS', '1.3.9'), ('gnuplot', '5.0.5'), -- GitLab From 16d28a2efc5c9070ab7bc996dd5221a5e676e15b Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 6 Apr 2017 07:59:23 +0200 Subject: [PATCH 0557/1603] adding easyconfigs: Autotools-20150215-GCCcore-5.4.0.eb --- .../a/Autoconf/Autoconf-2.69-GCCcore-5.4.0.eb | 29 +++++++++++++++ .../a/Automake/Automake-1.15-GCCcore-5.4.0.eb | 36 +++++++++++++++++++ .../Autotools-20150215-GCCcore-5.4.0.eb | 18 ++++++++++ .../l/libtool/libtool-2.4.6-GCCcore-5.4.0.eb | 20 +++++++++++ 4 files changed, 103 insertions(+) create mode 100644 easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-5.4.0.eb create mode 100644 easybuild/easyconfigs/a/Automake/Automake-1.15-GCCcore-5.4.0.eb create mode 100644 easybuild/easyconfigs/a/Autotools/Autotools-20150215-GCCcore-5.4.0.eb create mode 100644 easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-5.4.0.eb diff --git a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-5.4.0.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-5.4.0.eb new file mode 100644 index 0000000000..765fe6f2fd --- /dev/null +++ b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-5.4.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'Autoconf' +version = '2.69' + +homepage = 'http://www.gnu.org/software/autoconf/' +description = """Autoconf is an extensible package of M4 macros that produce shell scripts + to automatically configure software source code packages. These scripts can adapt the + packages to many kinds of UNIX-like systems without manual user intervention. Autoconf + creates a configuration script for a package from a template file that lists the + operating system features that the package can use, in the form of M4 macro calls.""" + +toolchain = {'name': 'GCCcore', 'version': '5.4.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('M4', '1.4.18')] + +# use same binutils version that was used when building GCCcore toolchain +builddependencies = [('binutils', '2.26', '', True)] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["autoconf", "autoheader", "autom4te", "autoreconf", "autoscan", + "autoupdate", "ifnames"]], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.15-GCCcore-5.4.0.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15-GCCcore-5.4.0.eb new file mode 100644 index 0000000000..0d4c530534 --- /dev/null +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15-GCCcore-5.4.0.eb @@ -0,0 +1,36 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## + +easyblock = 'ConfigureMake' + +name = 'Automake' +version = "1.15" + +homepage = 'http://www.gnu.org/software/automake/automake.html' +description = "Automake: GNU Standards-compliant Makefile generator" + +toolchain = {'name': 'GCCcore', 'version': '5.4.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('Autoconf', '2.69')] + +# use same binutils version that was used when building GCCcore toolchain +builddependencies = [('binutils', '2.26', '', True)] + +sanity_check_paths = { + 'files': ['bin/automake', 'bin/aclocal'], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/a/Autotools/Autotools-20150215-GCCcore-5.4.0.eb b/easybuild/easyconfigs/a/Autotools/Autotools-20150215-GCCcore-5.4.0.eb new file mode 100644 index 0000000000..79f6723eb6 --- /dev/null +++ b/easybuild/easyconfigs/a/Autotools/Autotools-20150215-GCCcore-5.4.0.eb @@ -0,0 +1,18 @@ +easyblock = 'Bundle' + +name = 'Autotools' +version = '20150215' # date of the most recent change + +homepage = 'http://autotools.io' +description = """This bundle collect the standard GNU build tools: Autoconf, Automake and libtool""" + +toolchain = {'name': 'GCCcore', 'version': '5.4.0'} + +dependencies = [ + ('Autoconf', '2.69'), # 20120424 + ('Automake', '1.15'), # 20150105 + ('libtool', '2.4.6'), # 20150215 +] +# Pure bundle -- no need to specify 'binutils' used when building GCCcore toolchain as build dependency + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-5.4.0.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-5.4.0.eb new file mode 100644 index 0000000000..677b163091 --- /dev/null +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-5.4.0.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'libtool' +version = '2.4.6' + +homepage = 'http://www.gnu.org/software/libtool' +description = """GNU libtool is a generic library support script. Libtool hides the complexity of using shared libraries + behind a consistent, portable interface.""" + +toolchain = {'name': 'GCCcore', 'version': '5.4.0'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +dependencies = [('M4', '1.4.18')] + +# use same binutils version that was used when building GCCcore toolchain +builddependencies = [('binutils', '2.26', '', True)] + +moduleclass = 'lib' -- GitLab From 5e3ae80f025fa5ee94d3d58603d6b2f037b68c10 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 6 Apr 2017 08:52:34 +0200 Subject: [PATCH 0558/1603] adding easyconfigs: StaMPS-3.3b1-intel-2017a-Perl-5.24.1.eb, snaphu-1.4.2-intel-2017a.eb, Triangle-1.6-intel-2017a.eb --- .../StaMPS-3.3b1-intel-2017a-Perl-5.24.1.eb | 50 +++++++++++++++++++ .../s/snaphu/snaphu-1.4.2-intel-2017a.eb | 26 ++++++++++ .../t/Triangle/Triangle-1.6-intel-2017a.eb | 34 +++++++++++++ 3 files changed, 110 insertions(+) create mode 100644 easybuild/easyconfigs/s/StaMPS/StaMPS-3.3b1-intel-2017a-Perl-5.24.1.eb create mode 100644 easybuild/easyconfigs/s/snaphu/snaphu-1.4.2-intel-2017a.eb create mode 100644 easybuild/easyconfigs/t/Triangle/Triangle-1.6-intel-2017a.eb diff --git a/easybuild/easyconfigs/s/StaMPS/StaMPS-3.3b1-intel-2017a-Perl-5.24.1.eb b/easybuild/easyconfigs/s/StaMPS/StaMPS-3.3b1-intel-2017a-Perl-5.24.1.eb new file mode 100644 index 0000000000..457a515e11 --- /dev/null +++ b/easybuild/easyconfigs/s/StaMPS/StaMPS-3.3b1-intel-2017a-Perl-5.24.1.eb @@ -0,0 +1,50 @@ +easyblock = 'ConfigureMake' + +name = 'StaMPS' +version = '3.3b1' +versionsuffix = '-Perl-%(perlver)s' + +homepage = 'http://homepages.see.leeds.ac.uk/~earahoo/stamps/' +description = """A software package to extract ground displacements from time series of synthetic aperture radar + (SAR) acquisitions.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['http://homepages.see.leeds.ac.uk/~earahoo/stamps/'] +sources = ['%(name)s_v%(version)s.tar.gz'] + +dependencies = [ + ('Perl', '5.24.1'), + ('ROI_PAC', '3.0.1', versionsuffix), + ('Doris', '4.02'), + ('Triangle', '1.6'), + ('snaphu', '1.4.2'), +] + +skipsteps = ['configure'] + +start_dir = 'src' + +buildopts = 'CC="$CXX" CFLAGS="$CXXFLAGS"' + +preinstallopts = 'cp -a ../bin %(installdir)s/bin && ' +installopts = 'INSTALL_DIR=%(installdir)s/bin && cd .. && cp -a {DORIS_SCR,matlab,ROI_PAC_SCR} %(installdir)s/' + +postinstallcmds = [ + # fix shebang in Perl scripts + "sed -i 's@^#!.*/bin/perl.*@#!/usr/bin/env perl@g' %(installdir)s//*_SCR/*.pl", +] + +sanity_check_paths = { + 'files': ['bin/calamp', 'bin/cpxsum', 'bin/pscdem', 'bin/psclonlat', 'bin/pscphase', 'bin/selpsc_patch', + 'bin/selsbc_patch', 'bin/selsbc_patch_new'], + 'dirs': ['DORIS_SCR', 'matlab', 'ROI_PAC_SCR'], +} + +modextravars = { + 'DORIS_SCR': '%(installdir)s/DORIS_SCR', + 'MY_SCR': '%(installdir)s/ROI_PAC_SCR', + 'STAMPS': '%(installdir)s', +} + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/s/snaphu/snaphu-1.4.2-intel-2017a.eb b/easybuild/easyconfigs/s/snaphu/snaphu-1.4.2-intel-2017a.eb new file mode 100644 index 0000000000..467c802a40 --- /dev/null +++ b/easybuild/easyconfigs/s/snaphu/snaphu-1.4.2-intel-2017a.eb @@ -0,0 +1,26 @@ +easyblock = 'MakeCp' + +name = 'snaphu' +version = '1.4.2' + +homepage = 'https://web.stanford.edu/group/radar/softwareandlinks/sw/snaphu/' +description = """SNAPHU is an implementation of the Statistical-cost, Network-flow Algorithm for Phase Unwrapping + proposed by Chen and Zebker""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['https://web.stanford.edu/group/radar/softwareandlinks/sw/snaphu/'] +sources = ['snaphu-v%(version)s.tar.gz'] + +start_dir = 'src' + +buildopts = 'CC="$CC" CFLAGS="$CFLAGS"' + +files_to_copy = ['bin', 'config', 'man'] + +sanity_check_paths = { + 'files': ['bin/snaphu'], + 'dirs': ['config', 'man'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/t/Triangle/Triangle-1.6-intel-2017a.eb b/easybuild/easyconfigs/t/Triangle/Triangle-1.6-intel-2017a.eb new file mode 100644 index 0000000000..166329f4f1 --- /dev/null +++ b/easybuild/easyconfigs/t/Triangle/Triangle-1.6-intel-2017a.eb @@ -0,0 +1,34 @@ +easyblock = 'MakeCp' + +name = 'Triangle' +version = '1.6' + +homepage = 'http://www.cs.cmu.edu/~quake/triangle.html' +description = """Triangle generates exact Delaunay triangulations, constrained Delaunay triangulations, + conforming Delaunay triangulations, Voronoi diagrams, and high-quality triangular meshes. + The latter can be generated with no small or large angles, + and are thus suitable for finite element analysis.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.netlib.org/voronoi/'] +sources = ['%(namelower)s.zip'] +checksums = [('md5', '10aff8d7950f5e0e2fb6dd2e340be2c9')] + +patches = ['%(name)s-%(version)s_makefile.patch'] + +buildopts = 'triangle trilibrary' + +files_to_copy = [ + (['triangle', 'tricall'], 'bin'), + (['triangle.h'], 'include'), + (['libtriangle.a'], 'lib'), +] + +sanity_check_paths = { + 'files': ['bin/triangle', 'bin/tricall', 'include/triangle.h', 'lib/libtriangle.a'], + 'dirs': [] +} + +moduleclass = 'numlib' -- GitLab From 974ebcbcc6544aac2c3e1b84ca1fe3529d85bbe9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 6 Apr 2017 09:54:44 +0200 Subject: [PATCH 0559/1603] {bio}[intel/2017a] BreakDancer 1.4.5 --- .../BreakDancer-1.4.5-intel-2017a.eb | 29 +++++++++++++++++++ ...eakDancer-1.4.5_fix-icpc-compilation.patch | 14 +++++++++ 2 files changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/b/BreakDancer/BreakDancer-1.4.5-intel-2017a.eb create mode 100644 easybuild/easyconfigs/b/BreakDancer/BreakDancer-1.4.5_fix-icpc-compilation.patch diff --git a/easybuild/easyconfigs/b/BreakDancer/BreakDancer-1.4.5-intel-2017a.eb b/easybuild/easyconfigs/b/BreakDancer/BreakDancer-1.4.5-intel-2017a.eb new file mode 100644 index 0000000000..2526494ae8 --- /dev/null +++ b/easybuild/easyconfigs/b/BreakDancer/BreakDancer-1.4.5-intel-2017a.eb @@ -0,0 +1,29 @@ +easyblock = 'CMakeMake' + +name = 'BreakDancer' +version = '1.4.5' + +homepage = 'http://gmt.genome.wustl.edu/packages/breakdancer' +description = """BreakDancer is a Perl/C++ package that provides genome-wide detection of structural variants from + next generation paired-end sequencing reads""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['https://github.com/genome/breakdancer/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['BreakDancer-%(version)s_fix-icpc-compilation.patch'] + +dependencies = [('zlib', '1.2.11')] +builddependencies = [('CMake', '3.7.2')] + +separate_build_dir = True +configopts = '-DCMAKE_BUILD_TYPE=release' + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/breakdancer-max'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BreakDancer/BreakDancer-1.4.5_fix-icpc-compilation.patch b/easybuild/easyconfigs/b/BreakDancer/BreakDancer-1.4.5_fix-icpc-compilation.patch new file mode 100644 index 0000000000..e2859dd505 --- /dev/null +++ b/easybuild/easyconfigs/b/BreakDancer/BreakDancer-1.4.5_fix-icpc-compilation.patch @@ -0,0 +1,14 @@ +fix for compilation error: +error: no instance of constructor "testing::AssertionResult::AssertionResult" matches the argument list +author: Kenneth Hoste (HPC-UGent) +--- test/lib/io/TestBam.cpp.orig 2017-04-03 18:06:43.355151223 +0200 ++++ test/lib/io/TestBam.cpp 2017-04-03 18:06:09.154756888 +0200 +@@ -107,7 +107,7 @@ + size_t size = in.tellg(); + in.seekg(0, std::ios::beg); + std::vector buf(size); +- ASSERT_TRUE(in.read(buf.data(), size)); ++ ASSERT_TRUE((bool)in.read(buf.data(), size)); + buf.push_back(0); // make sure buffer is null terminated + EXPECT_STREQ(samData.c_str(), buf.data()); + -- GitLab From f092fd499ca51fff05161c17c43d49e84315d7e7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 6 Apr 2017 10:07:38 +0200 Subject: [PATCH 0560/1603] also include $LDFLAGS --- .../s/StaMPS/StaMPS-3.3b1-intel-2017a-Perl-5.24.1.eb | 2 +- easybuild/easyconfigs/s/snaphu/snaphu-1.4.2-intel-2016b.eb | 2 +- easybuild/easyconfigs/s/snaphu/snaphu-1.4.2-intel-2017a.eb | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/s/StaMPS/StaMPS-3.3b1-intel-2017a-Perl-5.24.1.eb b/easybuild/easyconfigs/s/StaMPS/StaMPS-3.3b1-intel-2017a-Perl-5.24.1.eb index 457a515e11..122fdfc60d 100644 --- a/easybuild/easyconfigs/s/StaMPS/StaMPS-3.3b1-intel-2017a-Perl-5.24.1.eb +++ b/easybuild/easyconfigs/s/StaMPS/StaMPS-3.3b1-intel-2017a-Perl-5.24.1.eb @@ -25,7 +25,7 @@ skipsteps = ['configure'] start_dir = 'src' -buildopts = 'CC="$CXX" CFLAGS="$CXXFLAGS"' +buildopts = 'CC="$CXX" CFLAGS="$CXXFLAGS $LDFLAGS"' preinstallopts = 'cp -a ../bin %(installdir)s/bin && ' installopts = 'INSTALL_DIR=%(installdir)s/bin && cd .. && cp -a {DORIS_SCR,matlab,ROI_PAC_SCR} %(installdir)s/' diff --git a/easybuild/easyconfigs/s/snaphu/snaphu-1.4.2-intel-2016b.eb b/easybuild/easyconfigs/s/snaphu/snaphu-1.4.2-intel-2016b.eb index 8397d4ea59..c65762eb7a 100644 --- a/easybuild/easyconfigs/s/snaphu/snaphu-1.4.2-intel-2016b.eb +++ b/easybuild/easyconfigs/s/snaphu/snaphu-1.4.2-intel-2016b.eb @@ -14,7 +14,7 @@ sources = ['snaphu-v%(version)s.tar.gz'] start_dir = 'src' -buildopts = 'CC="$CC" CFLAGS="$CFLAGS"' +buildopts = 'CC="$CC" CFLAGS="$CFLAGS $LDFLAGS"' files_to_copy = ['bin', 'config', 'man'] diff --git a/easybuild/easyconfigs/s/snaphu/snaphu-1.4.2-intel-2017a.eb b/easybuild/easyconfigs/s/snaphu/snaphu-1.4.2-intel-2017a.eb index 467c802a40..3261c207aa 100644 --- a/easybuild/easyconfigs/s/snaphu/snaphu-1.4.2-intel-2017a.eb +++ b/easybuild/easyconfigs/s/snaphu/snaphu-1.4.2-intel-2017a.eb @@ -14,7 +14,7 @@ sources = ['snaphu-v%(version)s.tar.gz'] start_dir = 'src' -buildopts = 'CC="$CC" CFLAGS="$CFLAGS"' +buildopts = 'CC="$CC" CFLAGS="$CFLAGS $LDFLAGS"' files_to_copy = ['bin', 'config', 'man'] -- GitLab From 94e004a50d650754e599fc04bf206b24cfeb96ab Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 6 Apr 2017 11:33:25 +0200 Subject: [PATCH 0561/1603] adding easyconfigs: freetype-2.7.1-GCCcore-5.4.0.eb --- .../b/bzip2/bzip2-1.0.6-GCCcore-5.4.0.eb | 18 ++++++++++++ .../freetype/freetype-2.7.1-GCCcore-5.4.0.eb | 29 +++++++++++++++++++ .../l/libpng/libpng-1.6.28-GCCcore-5.4.0.eb | 29 +++++++++++++++++++ .../z/zlib/zlib-1.2.11-GCCcore-5.4.0.eb | 25 ++++++++++++++++ 4 files changed, 101 insertions(+) create mode 100644 easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCCcore-5.4.0.eb create mode 100644 easybuild/easyconfigs/f/freetype/freetype-2.7.1-GCCcore-5.4.0.eb create mode 100644 easybuild/easyconfigs/l/libpng/libpng-1.6.28-GCCcore-5.4.0.eb create mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-5.4.0.eb diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCCcore-5.4.0.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCCcore-5.4.0.eb new file mode 100644 index 0000000000..139b8c3f30 --- /dev/null +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCCcore-5.4.0.eb @@ -0,0 +1,18 @@ +name = 'bzip2' +version = '1.0.6' + +homepage = 'http://www.bzip.org/' +description = """bzip2 is a freely available, patent free, high-quality data compressor. It typically + compresses files to within 10% to 15% of the best available techniques (the PPM family of statistical + compressors), whilst being around twice as fast at compression and six times faster at decompression.""" + +toolchain = {'name': 'GCCcore', 'version': '5.4.0'} +toolchainopts = {'pic': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://www.bzip.org/%(version)s'] + +# use same binutils version that was used when building GCCcore toolchain +builddependencies = [('binutils', '2.26', '', True)] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.7.1-GCCcore-5.4.0.eb b/easybuild/easyconfigs/f/freetype/freetype-2.7.1-GCCcore-5.4.0.eb new file mode 100644 index 0000000000..fee6777ad0 --- /dev/null +++ b/easybuild/easyconfigs/f/freetype/freetype-2.7.1-GCCcore-5.4.0.eb @@ -0,0 +1,29 @@ +name = 'freetype' +version = '2.7.1' + +homepage = 'http://freetype.org' +description = """FreeType 2 is a software font engine that is designed to be small, efficient, highly customizable, and + portable while capable of producing high-quality output (glyph images). It can be used in graphics libraries, display + servers, font conversion tools, text image generation tools, and many other products as well.""" + +toolchain = {'name': 'GCCcore', 'version': '5.4.0'} + +source_urls = [GNU_SAVANNAH_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('bzip2', '1.0.6'), + ('libpng', '1.6.28'), + ('zlib', '1.2.11'), +] + +# use same binutils version that was used when building GCCcore toolchain +builddependencies = [('binutils', '2.26', '', True)] + +sanity_check_paths = { + 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, + 'lib/pkgconfig/freetype2.pc'], + 'dirs': ['include/freetype2'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.28-GCCcore-5.4.0.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.28-GCCcore-5.4.0.eb new file mode 100644 index 0000000000..3d37620c50 --- /dev/null +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.28-GCCcore-5.4.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'libpng' +version = '1.6.28' + +homepage = 'http://www.libpng.org/pub/png/libpng.html' +description = "libpng is the official PNG reference library" + +toolchain = {'name': 'GCCcore', 'version': '5.4.0'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('zlib', '1.2.11')] + +# use same binutils version that was used when building GCCcore toolchain +builddependencies = [('binutils', '2.26', '', True)] + +configopts = "--with-pic" + +majminver = ''.join(version.split('.')[:2]) +sanity_check_paths = { + 'files': ['include/pngconf.h', 'include/png.h', 'include/pnglibconf.h', 'lib/libpng.a', + 'lib/libpng.%s' % SHLIB_EXT, 'lib/libpng%s.a' % majminver, 'lib/libpng%s.%s' % (majminver, SHLIB_EXT)], + 'dirs': ['bin', 'include/libpng%s' % majminver, 'share/man'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-5.4.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-5.4.0.eb new file mode 100644 index 0000000000..8409e2aa5c --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-5.4.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'zlib' +version = '1.2.11' + +homepage = 'http://www.zlib.net/' +description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is, + not covered by any patents -- lossless data-compression library for use on virtually any + computer hardware and operating system.""" + +toolchain = {'name': 'GCCcore', 'version': '5.4.0'} +toolchainopts = {'pic': True} + +source_urls = ['http://zlib.net/fossils'] +sources = [SOURCELOWER_TAR_GZ] + +# use same binutils version that was used when building GCC toolchain +builddependencies = [('binutils', '2.26', '', True)] + +sanity_check_paths = { + 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' -- GitLab From 9b6f95e5909ef012e1853fba226f146c6b9428c7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 6 Apr 2017 12:32:58 +0200 Subject: [PATCH 0562/1603] adding easyconfigs: BLAT-3.5-intel-2017a.eb --- .../b/BLAT/BLAT-3.5-intel-2017a.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/b/BLAT/BLAT-3.5-intel-2017a.eb diff --git a/easybuild/easyconfigs/b/BLAT/BLAT-3.5-intel-2017a.eb b/easybuild/easyconfigs/b/BLAT/BLAT-3.5-intel-2017a.eb new file mode 100644 index 0000000000..7e57ded042 --- /dev/null +++ b/easybuild/easyconfigs/b/BLAT/BLAT-3.5-intel-2017a.eb @@ -0,0 +1,34 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 The Cyprus Institute +# Authors:: Andreas Panteli , Thekla Loizou +# License:: MIT/GPL +# +## + +name = 'BLAT' +version = '3.5' + +homepage = 'http://genome.ucsc.edu/FAQ/FAQblat.html' +description = """BLAT on DNA is designed to quickly find sequences of 95% and greater similarity + of length 25 bases or more.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +sources = ['%%(namelower)sSrc%s.zip' % ''.join(version.split('.'))] +source_urls = ['http://users.soe.ucsc.edu/~kent/src'] + +dependencies = [('libpng', '1.6.29')] + +buildopts = 'CC="$CC" COPT= L="$LIBS"' + +files_to_copy = ["bin", "blat", "gfClient", "gfServer", "hg", "inc", "jkOwnLib", "lib", "utils", "webBlat"] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['blat', 'faToNib', 'faToTwoBit', 'gfClient', 'gfServer', 'nibFrag', + 'pslPretty', 'pslReps', 'pslSort', 'twoBitInfo', 'twoBitToFa']], + 'dirs': files_to_copy, +} + +moduleclass = 'bio' -- GitLab From 927716f4af5f0146eb885b5debdd96c471bae27e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 6 Apr 2017 12:33:26 +0200 Subject: [PATCH 0563/1603] adding easyconfigs: BioPerl-1.7.1-intel-2017a-Perl-5.24.1.eb --- .../BioPerl-1.7.1-intel-2017a-Perl-5.24.1.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.1-intel-2017a-Perl-5.24.1.eb diff --git a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.1-intel-2017a-Perl-5.24.1.eb b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.1-intel-2017a-Perl-5.24.1.eb new file mode 100644 index 0000000000..43055f9bb9 --- /dev/null +++ b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.1-intel-2017a-Perl-5.24.1.eb @@ -0,0 +1,28 @@ +# easybuild easyconfig +# +# John Dey jfdey@fredhutch.org +# +# Fred Hutchinson Cancer Research Center + +easyblock = 'PerlModule' + +name = 'BioPerl' +version = '1.7.1' +versionsuffix = '-Perl-%(perlver)s' + +homepage = 'http://www.bioperl.org/' +description = """Bioperl is the product of a community effort to produce Perl code which is useful in biology. + Examples include Sequence objects, Alignment objects and database searching objects.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['https://github.com/bioperl/bioperl-live/archive/'] +sources = ['release-%s.zip' % version.replace('.', '-')] + +dependencies = [ + ('Perl', '5.24.1'), +] + +options = {'modulename': 'Bio::Perl'} + +moduleclass = 'bio' -- GitLab From be8d72e960b3f118bb72ba5070687d21bbf28928 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 6 Apr 2017 13:25:25 +0200 Subject: [PATCH 0564/1603] adding easyconfigs: Rascaf-1.0.2-intel-2017a.eb, SAMtools-0.1.20-intel-2017a.eb --- .../r/Rascaf/Rascaf-1.0.2-intel-2017a.eb | 33 +++++++++++++++++++ .../s/SAMtools/SAMtools-0.1.20-intel-2017a.eb | 20 +++++++++++ 2 files changed, 53 insertions(+) create mode 100644 easybuild/easyconfigs/r/Rascaf/Rascaf-1.0.2-intel-2017a.eb create mode 100644 easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.20-intel-2017a.eb diff --git a/easybuild/easyconfigs/r/Rascaf/Rascaf-1.0.2-intel-2017a.eb b/easybuild/easyconfigs/r/Rascaf/Rascaf-1.0.2-intel-2017a.eb new file mode 100644 index 0000000000..8d81791c83 --- /dev/null +++ b/easybuild/easyconfigs/r/Rascaf/Rascaf-1.0.2-intel-2017a.eb @@ -0,0 +1,33 @@ +easyblock = 'MakeCp' + +name = 'Rascaf' +version = '1.0.2' + +homepage = 'https://github.com/mourisl/Rascaf' +description = """Rascaf (RnA-seq SCAFfolder) uses continuity and order information from paired-end RNA-seq reads + to improve a draft assembly, particularly in the gene regions.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['https://github.com/mourisl/Rascaf/archive/'] +sources = ['v%(version)s.tar.gz'] + +dependencies = [ + ('zlib', '1.2.11'), + ('SAMtools', '0.1.20'), +] + +# create fake libbam.a to skip building of included SAMtools +prebuildopts = "touch samtools-0.1.19/libbam.a && " +# empty LINKPATH to avoid that included SAMtools copy is used +buildopts = 'CXX="$CXX" CXXFLAGS="$CXXFLAGS" LINKPATH=""' +parallel = 1 + +files_to_copy = [(['rascaf', 'rascaf-join'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/rascaf', 'bin/rascaf-join'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.20-intel-2017a.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.20-intel-2017a.eb new file mode 100644 index 0000000000..75a920a136 --- /dev/null +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.20-intel-2017a.eb @@ -0,0 +1,20 @@ +name = 'SAMtools' +version = '0.1.20' + +homepage = 'http://www.htslib.org/' +description = """SAM Tools provide various utilities for manipulating alignments in the SAM format, + including sorting, merging, indexing and generating alignments in a per-position format.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['https://github.com/samtools/%(namelower)s/archive/%(version)s'] + +patches = ['SAMtools-%(version)s_Makefile-ncurses.patch'] + +dependencies = [ + ('ncurses', '6.0'), + ('zlib', '1.2.11'), +] + +moduleclass = 'bio' -- GitLab From 5977c9c92fa12f6fefb43d24dc7ed36a80da51bd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 6 Apr 2017 13:41:48 +0200 Subject: [PATCH 0565/1603] adding easyconfigs: Boost-1.63.0-intel-2017a-Python-2.7.13.eb --- .../Boost-1.63.0-intel-2017a-Python-2.7.13.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.63.0-intel-2017a-Python-2.7.13.eb diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.63.0-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/b/Boost/Boost-1.63.0-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..e0340fc524 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.63.0-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,25 @@ +name = 'Boost' +version = '1.63.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.boost.org/' +description = "Boost provides free peer-reviewed portable C++ source libraries." + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'usempi': True, 'pic': True} + +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] +source_urls = ['https://sourceforge.net/projects/%(namelower)s/files/%(namelower)s/%(version)s'] + +patches = ['Boost-1.61_fix-make_array-icpc.patch'] + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.11'), + ('Python', '2.7.13'), +] + +# also build boost_mpi +boost_mpi = True + +moduleclass = 'devel' -- GitLab From 11b3a84303b558a60d035b91a785884b116774f1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 6 Apr 2017 14:11:47 +0200 Subject: [PATCH 0566/1603] adding easyconfigs: SSPACE_Basic-2.1.1-intel-2017a-Perl-5.24.1.eb --- ...ACE_Basic-2.1.1-intel-2017a-Perl-5.24.1.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/s/SSPACE_Basic/SSPACE_Basic-2.1.1-intel-2017a-Perl-5.24.1.eb diff --git a/easybuild/easyconfigs/s/SSPACE_Basic/SSPACE_Basic-2.1.1-intel-2017a-Perl-5.24.1.eb b/easybuild/easyconfigs/s/SSPACE_Basic/SSPACE_Basic-2.1.1-intel-2017a-Perl-5.24.1.eb new file mode 100644 index 0000000000..9d51ecf299 --- /dev/null +++ b/easybuild/easyconfigs/s/SSPACE_Basic/SSPACE_Basic-2.1.1-intel-2017a-Perl-5.24.1.eb @@ -0,0 +1,27 @@ +easyblock = 'Tarball' + +name = 'SSPACE_Basic' +version = '2.1.1' +versionsuffix = '-Perl-%(perlver)s' + +homepage = 'https://github.com/nsoranzo/sspace_basic' +description = "SSPACE Basic, SSAKE-based Scaffolding of Pre-Assembled Contigs after Extension" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['https://github.com/nsoranzo/sspace_basic/archive/'] +sources = ['v%(version)s.tar.gz'] + +dependencies = [ + ('Perl', '5.24.1'), + ('Bowtie', '1.1.2'), +] + +sanity_check_paths = { + 'files': ['README', 'SSPACE_Basic.pl'], + 'dirs': ['bin', 'tools'], +} + +modextrapaths = {'PATH': ''} + +moduleclass = 'bio' -- GitLab From b921145d0ec6fb2ef6480dbef2b506f4faf241c1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 6 Apr 2017 14:47:04 +0200 Subject: [PATCH 0567/1603] {bio}[intel/2017a] GapFiller v2.1.1 --- .../GapFiller/GapFiller-2.1.1-intel-2017a.eb | 30 +++++++++++++++++++ .../GapFiller/GapFillter-2.1.1_fix-typo.patch | 13 ++++++++ 2 files changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/g/GapFiller/GapFiller-2.1.1-intel-2017a.eb create mode 100644 easybuild/easyconfigs/g/GapFiller/GapFillter-2.1.1_fix-typo.patch diff --git a/easybuild/easyconfigs/g/GapFiller/GapFiller-2.1.1-intel-2017a.eb b/easybuild/easyconfigs/g/GapFiller/GapFiller-2.1.1-intel-2017a.eb new file mode 100644 index 0000000000..4e408b39dd --- /dev/null +++ b/easybuild/easyconfigs/g/GapFiller/GapFiller-2.1.1-intel-2017a.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'GapFiller' +version = '2.1.1' + +homepage = 'https://sourceforge.net/projects/gapfiller' +description = """GapFiller is a seed-and-extend local assembler to fill the gap within paired reads. + It can be used for both DNA and RNA and it has been tested on Illumina data.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +patches = ['GapFillter-%(version)s_fix-typo.patch'] + +dependencies = [ + ('Boost', '1.63.0', '-Python-2.7.13'), + ('zlib', '1.2.11'), +] + +buildopts = 'bin_PROGRAMS=GapFiller ' +buildopts += 'GapFiller_CFLAGS="$CFLAGS $LDFLAGS -lz" GapFiller_CXXFLAGS="$CXXFLAGS $LDFLAGS -lz"' +installopts = 'bin_PROGRAMS=GapFiller ' + +sanity_check_paths = { + 'files': ['bin/GapFiller'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GapFiller/GapFillter-2.1.1_fix-typo.patch b/easybuild/easyconfigs/g/GapFiller/GapFillter-2.1.1_fix-typo.patch new file mode 100644 index 0000000000..4327a994ef --- /dev/null +++ b/easybuild/easyconfigs/g/GapFiller/GapFillter-2.1.1_fix-typo.patch @@ -0,0 +1,13 @@ +fix typo that breaks compilation with Intel compilers +author: Kenneth Hoste (HPC-UGent) +--- gapfiller-2.1.1/src/data_structures/Reads.cpp.orig 2017-04-06 13:30:10.978641815 +0200 ++++ gapfiller-2.1.1/src/data_structures/Reads.cpp 2017-04-06 13:38:39.941387943 +0200 +@@ -154,7 +154,7 @@ + case 1: out.append("C"); break; + case 2: out.append("G"); break; + case 3: out.append("T"); break; +- default: cout << "strange "<< cout << "\n"; ++ default: cout << "strange " << out << "\n"; + } + } + -- GitLab From 1730f76e147bfacab9a328311e2dce727c617736 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 6 Apr 2017 14:48:15 +0200 Subject: [PATCH 0568/1603] adding easyconfigs: fqtrim-0.9.5-intel-2017a.eb --- .../f/fqtrim/fqtrim-0.9.5-intel-2017a.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/f/fqtrim/fqtrim-0.9.5-intel-2017a.eb diff --git a/easybuild/easyconfigs/f/fqtrim/fqtrim-0.9.5-intel-2017a.eb b/easybuild/easyconfigs/f/fqtrim/fqtrim-0.9.5-intel-2017a.eb new file mode 100644 index 0000000000..c00d6cd413 --- /dev/null +++ b/easybuild/easyconfigs/f/fqtrim/fqtrim-0.9.5-intel-2017a.eb @@ -0,0 +1,25 @@ +easyblock = 'MakeCp' + +name = 'fqtrim' +version = '0.9.5' + +homepage = 'http://ccb.jhu.edu/software/fqtrim/' +description = """fqtrim is a versatile stand-alone utility that can be used to trim adapters, poly-A tails, + terminal unknown bases (Ns) and low quality 3' regions in reads from high-throughput next-generation sequencing + machines.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['http://ccb.jhu.edu/software/fqtrim/dl/'] +sources = [SOURCE_TAR_GZ] + +buildopts = 'release CC="$CXX" LINKER="$CXX"' + +files_to_copy = [(['fqtrim'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/fqtrim'], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From 799702c12e239d7de2a423c2730bbb120bdbc92a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 6 Apr 2017 16:16:56 +0200 Subject: [PATCH 0569/1603] adding easyconfigs: DBG2OLC-20170208-intel-2017a.eb --- .../d/DBG2OLC/DBG2OLC-20170208-intel-2017a.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/d/DBG2OLC/DBG2OLC-20170208-intel-2017a.eb diff --git a/easybuild/easyconfigs/d/DBG2OLC/DBG2OLC-20170208-intel-2017a.eb b/easybuild/easyconfigs/d/DBG2OLC/DBG2OLC-20170208-intel-2017a.eb new file mode 100644 index 0000000000..367145a273 --- /dev/null +++ b/easybuild/easyconfigs/d/DBG2OLC/DBG2OLC-20170208-intel-2017a.eb @@ -0,0 +1,25 @@ +easyblock = 'CmdCp' + +name = 'DBG2OLC' +version = '20170208' +commit = 'b452286' + +homepage = 'https://github.com/yechengxi/DBG2OLC' +description = """DBG2OLC:Efficient Assembly of Large Genomes Using Long Erroneous Reads of the Third Generation + Sequencing Technologies""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['https://github.com/yechengxi/DBG2OLC/archive/'] +sources = ['%s.tar.gz' % commit] + +cmds_map = [('.*', "$CXX $CXXFLAGS $LDFLAGS -o DBG2OLC *.cpp")] + +files_to_copy = [(['DBG2OLC'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/DBG2OLC'], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From c827dba5e6c5962a872c23d29dc191513a343168 Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Thu, 6 Apr 2017 16:03:20 +0000 Subject: [PATCH 0570/1603] Add --enable-fortran-calling-convention=gfortran to Octave eb. --- easybuild/easyconfigs/o/Octave/Octave-4.2.1-intel-2016b.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/o/Octave/Octave-4.2.1-intel-2016b.eb b/easybuild/easyconfigs/o/Octave/Octave-4.2.1-intel-2016b.eb index e845e9c89e..534dc92f99 100644 --- a/easybuild/easyconfigs/o/Octave/Octave-4.2.1-intel-2016b.eb +++ b/easybuild/easyconfigs/o/Octave/Octave-4.2.1-intel-2016b.eb @@ -52,6 +52,8 @@ configopts += 'UIC=$EBROOTQT5/bin/uic ' configopts += 'RCC=$EBROOTQT5/bin/rcc ' configopts += 'LRELEASE=$EBROOTQT5/bin/lrelease ' configopts += '--with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK" --disable-docs ' +# correct for both GCC and Intel compilers +configopts += '--enable-fortran-calling-convention=gfortran' sanity_check_paths = { 'files': ['bin/octave'], -- GitLab From 4d1e8dcd8cac962fd799d7c7abd261952559ddef Mon Sep 17 00:00:00 2001 From: iotaka Date: Fri, 7 Apr 2017 08:55:29 +0200 Subject: [PATCH 0571/1603] Update METIS-5.1.0-foss-2016b.eb Needed for OpenFOAM # We use 32bit for indices and 64bit for content patches = ['METIS-5.1.0-use-doubles.patch'] --- easybuild/easyconfigs/m/METIS/METIS-5.1.0-foss-2016b.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/m/METIS/METIS-5.1.0-foss-2016b.eb b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-foss-2016b.eb index 1510375706..56000b7259 100644 --- a/easybuild/easyconfigs/m/METIS/METIS-5.1.0-foss-2016b.eb +++ b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-foss-2016b.eb @@ -15,6 +15,9 @@ source_urls = [ 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/OLD', ] +# We use 32bit for indices and 64bit for content +patches = ['METIS-5.1.0-use-doubles.patch'] + builddependencies = [('CMake', '3.6.1')] configopts = ['', 'shared=1'] -- GitLab From 4849064e9a0ad00a90bdce3cfaa039ef0627ced7 Mon Sep 17 00:00:00 2001 From: Robert Date: Fri, 7 Apr 2017 19:05:15 +0930 Subject: [PATCH 0572/1603] picard updated --- .../p/picard/picard-2.2.4-Java-1.8.0_71.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/p/picard/picard-2.2.4-Java-1.8.0_71.eb diff --git a/easybuild/easyconfigs/p/picard/picard-2.2.4-Java-1.8.0_71.eb b/easybuild/easyconfigs/p/picard/picard-2.2.4-Java-1.8.0_71.eb new file mode 100644 index 0000000000..9208d35f20 --- /dev/null +++ b/easybuild/easyconfigs/p/picard/picard-2.2.4-Java-1.8.0_71.eb @@ -0,0 +1,36 @@ +## +# This is a contribution from Phoenix HPC Service, The University of Adelaide, Australia +# Homepage: https://www.adelaide.edu.au/phoenix/ +# +# Copyright:: adelaide.edu.au/phoenix +# Authors:: Robert Qiao , Exe Escobedo +# License:: +# +# Notes:: +## + + +name = 'picard' +version = '2.2.4' + +homepage = 'http://sourceforge.net/projects/picard' +description = """A set of tools (in Java) for working with next generation sequencing data in the BAM format.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['https://github.com/broadinstitute/picard/releases/download/%(version)s'] +sources = ['%(name)s-tools-%(version)s.zip'] + +java = 'Java' +javaver = '1.8.0_71' +versionsuffix = '-%s-%s' % (java, javaver) +dependencies = [(java, javaver)] + +sanity_check_paths = { + 'files': ['picard.jar'], + 'dirs': [], +} + +modloadmsg = "To execute picard run: java -jar $EBROOTPICARD/%(name)s.jar" + +moduleclass = 'bio' -- GitLab From 56461268690ba56036c3a01df34157f3a2ced24e Mon Sep 17 00:00:00 2001 From: Robert Date: Fri, 7 Apr 2017 22:40:34 +0930 Subject: [PATCH 0573/1603] Java version changed --- easybuild/easyconfigs/p/picard/picard-2.2.4-Java-1.8.0_71.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/picard/picard-2.2.4-Java-1.8.0_71.eb b/easybuild/easyconfigs/p/picard/picard-2.2.4-Java-1.8.0_71.eb index 9208d35f20..bc5e0d5779 100644 --- a/easybuild/easyconfigs/p/picard/picard-2.2.4-Java-1.8.0_71.eb +++ b/easybuild/easyconfigs/p/picard/picard-2.2.4-Java-1.8.0_71.eb @@ -22,7 +22,7 @@ source_urls = ['https://github.com/broadinstitute/picard/releases/download/%(ver sources = ['%(name)s-tools-%(version)s.zip'] java = 'Java' -javaver = '1.8.0_71' +javaver = '1.8.0_92' versionsuffix = '-%s-%s' % (java, javaver) dependencies = [(java, javaver)] -- GitLab From f7cda6667810791d21a725fa2ded135d4d42f6c9 Mon Sep 17 00:00:00 2001 From: Robert Date: Sat, 8 Apr 2017 12:21:00 +0930 Subject: [PATCH 0574/1603] file name fixed --- ...icard-2.2.4-Java-1.8.0_71.eb => picard-2.2.4-Java-1.8.0_92.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/p/picard/{picard-2.2.4-Java-1.8.0_71.eb => picard-2.2.4-Java-1.8.0_92.eb} (100%) diff --git a/easybuild/easyconfigs/p/picard/picard-2.2.4-Java-1.8.0_71.eb b/easybuild/easyconfigs/p/picard/picard-2.2.4-Java-1.8.0_92.eb similarity index 100% rename from easybuild/easyconfigs/p/picard/picard-2.2.4-Java-1.8.0_71.eb rename to easybuild/easyconfigs/p/picard/picard-2.2.4-Java-1.8.0_92.eb -- GitLab From b630d75714ea12e9e328f1ed517e8b6abd3b7c23 Mon Sep 17 00:00:00 2001 From: Robert Date: Sat, 8 Apr 2017 21:48:13 +0930 Subject: [PATCH 0575/1603] PyOpenGL easyconfig added --- ...OpenGL-3.1.1a1-foss-2016b-Python-2.7.11.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyOpenGL/PyOpenGL-3.1.1a1-foss-2016b-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/p/PyOpenGL/PyOpenGL-3.1.1a1-foss-2016b-Python-2.7.11.eb b/easybuild/easyconfigs/p/PyOpenGL/PyOpenGL-3.1.1a1-foss-2016b-Python-2.7.11.eb new file mode 100644 index 0000000000..e76b799546 --- /dev/null +++ b/easybuild/easyconfigs/p/PyOpenGL/PyOpenGL-3.1.1a1-foss-2016b-Python-2.7.11.eb @@ -0,0 +1,42 @@ +## +# This is a contribution from Phoenix HPC Service, The University of Adelaide, Australia +# Homepage: https://www.adelaide.edu.au/phoenix/ +# +# Copyright:: adelaide.edu.au/phoenix +# Authors:: Robert Qiao , Exe Escobedo +# License:: +# +# Notes:: +## + +easyblock = 'PythonPackage' + +name = 'PyOpenGL' +version = '3.1.1a1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://pyopengl.sourceforge.net' +description = """PyOpenGL is the most common cross platform Python binding to OpenGL and related APIs.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +builddependencies = [ + ('bzip2', '1.0.6'), +] + +dependencies = [ + ('Python', '2.7.12'), + ('Mesa', '12.0.2'), +] + +options = {'modulename': 'OpenGL'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +moduleclass = 'vis' -- GitLab From cf285a2e857c03b7eccba850d44de4194795bac3 Mon Sep 17 00:00:00 2001 From: Robert Date: Sat, 8 Apr 2017 22:02:55 +0930 Subject: [PATCH 0576/1603] Style fixed --- ...hon-2.7.11.eb => PyOpenGL-3.1.1a1-foss-2016b-Python-2.7.12.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/p/PyOpenGL/{PyOpenGL-3.1.1a1-foss-2016b-Python-2.7.11.eb => PyOpenGL-3.1.1a1-foss-2016b-Python-2.7.12.eb} (100%) diff --git a/easybuild/easyconfigs/p/PyOpenGL/PyOpenGL-3.1.1a1-foss-2016b-Python-2.7.11.eb b/easybuild/easyconfigs/p/PyOpenGL/PyOpenGL-3.1.1a1-foss-2016b-Python-2.7.12.eb similarity index 100% rename from easybuild/easyconfigs/p/PyOpenGL/PyOpenGL-3.1.1a1-foss-2016b-Python-2.7.11.eb rename to easybuild/easyconfigs/p/PyOpenGL/PyOpenGL-3.1.1a1-foss-2016b-Python-2.7.12.eb -- GitLab From 07eb225c270bec1545e9b5cf63753a1f79f5aa7e Mon Sep 17 00:00:00 2001 From: Robert Date: Sat, 8 Apr 2017 22:05:17 +0930 Subject: [PATCH 0577/1603] lynx easyconfig added --- .../l/lynx/lynx-2.8.9-foss-2016b.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/l/lynx/lynx-2.8.9-foss-2016b.eb diff --git a/easybuild/easyconfigs/l/lynx/lynx-2.8.9-foss-2016b.eb b/easybuild/easyconfigs/l/lynx/lynx-2.8.9-foss-2016b.eb new file mode 100644 index 0000000000..cb6a046e97 --- /dev/null +++ b/easybuild/easyconfigs/l/lynx/lynx-2.8.9-foss-2016b.eb @@ -0,0 +1,33 @@ +## +# This is a contribution from Phoenix HPC Service, The University of Adelaide, Australia +# Homepage: https://www.adelaide.edu.au/phoenix/ +# +# Copyright:: adelaide.edu.au/phoenix +# Authors:: Robert Qiao , Exe Escobedo +# License:: GNU GPLv2 +# +# Notes:: +## + +easyblock = 'ConfigureMake' + +name = 'lynx' +version = '2.8.9' + +description = "lynx is an alphanumeric display oriented World-Wide Web Client" +homepage = 'http://lynx.isc.org/' + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['http://invisible-mirror.net/archives/lynx/tarballs'] +sources = ['%(name)s%(version)sdev.11.tar.bz2'] + +dependencies = [ + ('ncurses', '6.0'), +] +sanity_check_paths = { + 'files': ['bin/lynx'], + 'dirs': [], +} + +moduleclass = 'tools' -- GitLab From 74b43253719a950a3b13d30a3531754be93587b0 Mon Sep 17 00:00:00 2001 From: iotaka Date: Mon, 10 Apr 2017 09:49:43 +0200 Subject: [PATCH 0578/1603] change qt version dep --- .../ParaView/ParaView-5.3.0-foss-2016b-mpi.eb | 52 +++++++++++++++++++ 1 file changed, 52 insertions(+) create mode 100644 easybuild/easyconfigs/p/ParaView/ParaView-5.3.0-foss-2016b-mpi.eb diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-5.3.0-foss-2016b-mpi.eb b/easybuild/easyconfigs/p/ParaView/ParaView-5.3.0-foss-2016b-mpi.eb new file mode 100644 index 0000000000..b50111ff96 --- /dev/null +++ b/easybuild/easyconfigs/p/ParaView/ParaView-5.3.0-foss-2016b-mpi.eb @@ -0,0 +1,52 @@ +easyblock = 'CMakeMake' + +name = 'ParaView' +version = '5.3.0' +versionsuffix = '-mpi' + +homepage = "http://www.paraview.org" +description = "ParaView is a scientific parallel visualizer." + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'pic': True, 'usempi': True} + +download_suffix = 'download.php?submit=Download&version=v%(version_major_minor)s&type=source&os=all&downloadFile=' +source_urls = ['http://www.paraview.org/paraview-downloads/%s' % download_suffix] +sources = ["ParaView-v%(version)s.tar.gz"] + +dependencies = [ + ('X11', '20160819'), + ('Mesa', '12.0.2'), + ('libGLU', '9.0.0'), + ('Qt5', '5.7.0'), + ('zlib', '1.2.8'), + ('HDF5', '1.8.17'), + ('Python', '2.7.12'), +] + +builddependencies = [('CMake', '3.6.1')] + +separate_build_dir = True + +configopts = '-DPARAVIEW_INSTALL_DEVELOPMENT_FILES=ON -DVTK_OPENGL_HAS_OSMESA=ON -DPARAVIEW_USE_MPI=ON ' +configopts += '-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include -DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s ' % SHLIB_EXT +configopts += '-DOSMESA_INCLUDE_DIR=$EBROOTMESA/include -DOSMESA_LIBRARY=$EBROOTMESA/lib/libOSMesa.%s ' % SHLIB_EXT +configopts += '-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s ' % SHLIB_EXT +configopts += '-DVTK_USE_SYSTEM_HDF5=ON -DPARAVIEW_ENABLE_PYTHON=ON -DBUILD_SHARED_LIBS=ON ' +# if you want to build server only Paraview, uncomment the following line: +# configopts += '-DVTK_USE_X=OFF ' + +# Without internet connection turn off testing (uncomment the following line) +configopts += '-DBUILD_TESTING=OFF ' +# Or consult https://gitlab.kitware.com/vtk/vtk/blob/master/Documentation/dev/git/data.md +# and download ExternalData to $EASYBUILD_SOURCEPATH and adjust -DExternalData_OBJECT_STORES accordingly +# Without internet connection, comment the following two lines (configopts and prebuildopts) +configopts += '-DExternalData_OBJECT_STORES=%(builddir)s/ExternalData ' + +configopts += ' -DPARAVIEW_QT_VERSION=5 -DQt5_DIR=$EBROOTQT5/lib/cmake/Qt5 -DQT_QMAKE_EXECUTABLE=$EBROOTQT5/bin/qmake ' +# The ParaView server can be cranky, test downloads are quite often failing, especially in the case +# of parallel downloads. Using ; insted of && gives a second chance to download the test files, if the +# first serial attempt would fail. +prebuildopts = 'make VTKData ;' + +moduleclass = 'vis' -- GitLab From 6ac55301bd87882370344c539da5b133642f3089 Mon Sep 17 00:00:00 2001 From: iotaka Date: Mon, 10 Apr 2017 09:51:22 +0200 Subject: [PATCH 0579/1603] change ParaView version dep --- easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.0-foss-2016b.eb | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.0-foss-2016b.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.0-foss-2016b.eb index 4f9d282dad..00ba2fa1df 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.0-foss-2016b.eb +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.0-foss-2016b.eb @@ -1,7 +1,7 @@ name = 'OpenFOAM' version = '4.0' -homepage = 'http://www.openfoam.org/' +homepage = 'http://www.openfoam.com/' description = """OpenFOAM is a free, open source CFD software package. OpenFOAM has an extensive range of features to solve anything from complex fluid flows involving chemical reactions, turbulence and heat transfer, @@ -22,10 +22,9 @@ dependencies = [ ('ncurses', '6.0'), # OpenFOAM requires 64 bit METIS using 32 bit indexes (array indexes) ('METIS', '5.1.0'), - #('METIS', '5.1.0', '-32bitIDX'), ('SCOTCH', '6.0.4'), ('CGAL', '4.8.1'), - ('ParaView', '5.1.2', '-mpi'), + ('ParaView', '5.3.0', '-mpi'), ] builddependencies = [ -- GitLab From 18cb49ea57b2f04daf6f925cb00e2f9101bd260f Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 10 Apr 2017 09:28:35 +0100 Subject: [PATCH 0580/1603] adding easyconfigs: gnuplot-5.0.5-foss-2016b.eb --- .../g/gnuplot/gnuplot-5.0.5-foss-2016b.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100755 easybuild/easyconfigs/g/gnuplot/gnuplot-5.0.5-foss-2016b.eb diff --git a/easybuild/easyconfigs/g/gnuplot/gnuplot-5.0.5-foss-2016b.eb b/easybuild/easyconfigs/g/gnuplot/gnuplot-5.0.5-foss-2016b.eb new file mode 100755 index 0000000000..52cec88efd --- /dev/null +++ b/easybuild/easyconfigs/g/gnuplot/gnuplot-5.0.5-foss-2016b.eb @@ -0,0 +1,42 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg/Luxembourg Centre for Systems Biomedicine +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-97.html +## +easyblock = 'ConfigureMake' + +name = 'gnuplot' +version = '5.0.5' + +homepage = 'http://gnuplot.sourceforge.net/' +description = """Portable interactive, function plotting utility""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +sources = [SOURCE_TAR_GZ] +source_urls = [('http://sourceforge.net/projects/gnuplot/files', 'download')] + +dependencies = [ + ('cairo', '1.14.6'), + ('libjpeg-turbo', '1.5.0'), + ('libpng', '1.6.26'), + ('libgd', '2.2.3'), + ('Pango', '1.40.3'), + ('libcerf', '1.5'), + ('Qt', '4.8.7'), +] + +configopts = '--with-qt=qt4 ' + +sanity_check_paths = { + 'files': ['bin/gnuplot'], + 'dirs': [] +} + +moduleclass = 'vis' -- GitLab From a7fceb3c9b669fb14e2c23952a48482fca1b50c6 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 10 Apr 2017 09:31:00 +0100 Subject: [PATCH 0581/1603] adding easyconfigs: canu-1.4-foss-2016b.eb --- .../easyconfigs/c/canu/canu-1.4-foss-2016b.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100755 easybuild/easyconfigs/c/canu/canu-1.4-foss-2016b.eb diff --git a/easybuild/easyconfigs/c/canu/canu-1.4-foss-2016b.eb b/easybuild/easyconfigs/c/canu/canu-1.4-foss-2016b.eb new file mode 100755 index 0000000000..ff486b7b50 --- /dev/null +++ b/easybuild/easyconfigs/c/canu/canu-1.4-foss-2016b.eb @@ -0,0 +1,38 @@ +easyblock = 'MakeCp' + +name = 'canu' +version = '1.4' + +homepage = 'https://github.com/marbl/canu' +description = """Canu is a fork of the Celera Assembler, designed for high-noise single-molecule + sequencing (such as the PacBio RS II or Oxford Nanopore MinION). + + Canu is a hierarchical assembly pipeline which runs in four steps: + + Detect overlaps in high-noise sequences using MHAP + Generate corrected sequence consensus + Trim corrected sequences + Assemble trimmed corrected sequences +""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +sources = ['v%(version)s.tar.gz'] +source_urls = ['https://github.com/marbl/canu/archive/'] + +start_dir = 'src' + +files_to_copy = ['Linux-amd64/*'] + +dependencies = [ + ('Java', '1.8.0_112', '', True), + ('Perl', '5.24.0'), + ('gnuplot', '5.0.5'), +] + +sanity_check_paths = { + 'files': ['bin/canu'], + 'dirs': ["bin"] +} + +moduleclass = 'bio' -- GitLab From a38d10acbf7234f434e0c19ff59dc699bc1f57d4 Mon Sep 17 00:00:00 2001 From: Fokke Dijkstra Date: Mon, 10 Apr 2017 10:54:07 +0200 Subject: [PATCH 0582/1603] Stacks 1.45 build with the foss-2016a toolchain. --- .../s/Stacks/Stacks-1.45-foss-2016a.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/s/Stacks/Stacks-1.45-foss-2016a.eb diff --git a/easybuild/easyconfigs/s/Stacks/Stacks-1.45-foss-2016a.eb b/easybuild/easyconfigs/s/Stacks/Stacks-1.45-foss-2016a.eb new file mode 100644 index 0000000000..4f24751d68 --- /dev/null +++ b/easybuild/easyconfigs/s/Stacks/Stacks-1.45-foss-2016a.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'Stacks' +version = '1.45' + +homepage = 'http://creskolab.uoregon.edu/stacks/' +description = """Stacks is a software pipeline for building loci from short-read sequences, such as those generated on + the Illumina platform. Stacks was developed to work with restriction enzyme-based data, such as RAD-seq, + for the purpose of building genetic maps and conducting population genomics and phylogeography. +""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://catchenlab.life.illinois.edu/stacks/source/'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('zlib', '1.2.8'), + ('SAMtools', '1.3.1'), + ('sparsehash', '2.0.2'), +] + +sanity_check_paths = { + 'files': [ + 'bin/%s' % binfile for binfile in [ + 'clone_filter', 'denovo_map.pl', 'exec_velvet.pl', 'genotypes', 'index_radtags.pl', 'load_radtags.pl', + 'populations', 'process_shortreads', 'ref_map.pl', 'sstacks', 'ustacks', 'cstacks', 'estacks', + 'export_sql.pl', 'hstacks', 'kmer_filter', 'load_sequences.pl', 'process_radtags', 'pstacks', + 'sort_read_pairs.pl', 'stacks_export_notify.pl', + ] + ], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From 21dee843cc0e8baa54067ef32a50cd458268bc25 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 10 Apr 2017 15:27:16 +0200 Subject: [PATCH 0583/1603] Add Qt5/5.8 for intel/2017a --- .../pkg-config-0.29.2-intel-2017a.eb | 27 +++++++++++++++ .../q/Qt5/Qt5-5.8.0-intel-2017a.eb | 33 +++++++++++++++++++ 2 files changed, 60 insertions(+) create mode 100644 easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2-intel-2017a.eb create mode 100644 easybuild/easyconfigs/q/Qt5/Qt5-5.8.0-intel-2017a.eb diff --git a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2-intel-2017a.eb b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2-intel-2017a.eb new file mode 100644 index 0000000000..90af56a5b1 --- /dev/null +++ b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2-intel-2017a.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'pkg-config' +version = '0.29.2' + +homepage = 'http://www.freedesktop.org/wiki/Software/pkg-config/' +description = """pkg-config is a helper tool used when compiling applications and libraries. It helps you insert the + correct compiler options on the command line so an application can use + gcc -o test test.c `pkg-config --libs --cflags glib-2.0` + for instance, rather than hard-coding values on where to find glib (or other libraries).""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['https://pkg-config.freedesktop.org/releases/'] + +# don't use PAX, it might break. +tar_config_opts = True + +configopts = " --with-internal-glib" + +sanity_check_paths = { + 'files': ['bin/pkg-config'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.8.0-intel-2017a.eb b/easybuild/easyconfigs/q/Qt5/Qt5-5.8.0-intel-2017a.eb new file mode 100644 index 0000000000..fc41f1c1fd --- /dev/null +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.8.0-intel-2017a.eb @@ -0,0 +1,33 @@ +easyblock = 'EB_Qt' + +name = 'Qt5' +version = '5.8.0' + +homepage = 'http://qt.io/' +description = "Qt is a comprehensive cross-platform C++ application framework." + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [ + 'http://download.qt.io/official_releases/qt/%(version_major_minor)s/%(version)s/single/', + 'http://download.qt.io/archive/qt/%(version_major_minor)s/%(version)s/single/' +] +sources = ['qt-everywhere-opensource-src-%(version)s.tar.xz'] + +patches = ['Qt5-5.7.1_fix-nan-inf.patch'] + +builddependencies = [ + ('pkg-config', '0.29.2'), +] + +# qtgamepad needs recent kernel/libevdev (fails on RHEL 6.x) +configopts = '-skip qtgamepad' + +dependencies = [ + ('GLib', '2.52.0'), + ('libpng', '1.6.29'), + ('X11', '20170314'), #, '', ('GCCcore', '6.3.0')), + ('libGLU', '9.0.0'), +] + +moduleclass = 'devel' -- GitLab From 9406dda37ebe8a116f962078b11b46179fe977e7 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 10 Apr 2017 15:28:50 +0200 Subject: [PATCH 0584/1603] Added ParaView-5.3.0-intel-2017a-mpi --- .../c/CMake/CMake-3.7.2-intel-2017a.eb | 31 +++++++++++ .../h/HDF5/HDF5-1.8.18-intel-2017a.eb | 26 ++++++++++ .../ParaView-5.3.0-intel-2017a-mpi.eb | 52 +++++++++++++++++++ 3 files changed, 109 insertions(+) create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.7.2-intel-2017a.eb create mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.8.18-intel-2017a.eb create mode 100644 easybuild/easyconfigs/p/ParaView/ParaView-5.3.0-intel-2017a-mpi.eb diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.7.2-intel-2017a.eb b/easybuild/easyconfigs/c/CMake/CMake-3.7.2-intel-2017a.eb new file mode 100644 index 0000000000..d78b6b43f1 --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.7.2-intel-2017a.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.7.2' + +homepage = 'http://www.cmake.org' +description = """CMake, the cross-platform, open-source build system. + CMake is a family of tools designed to build, test and package software.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' + +dependencies = [ + ('ncurses', '6.0'), + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.2j'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.18-intel-2017a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.18-intel-2017a.eb new file mode 100644 index 0000000000..570e4a8ff2 --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.18-intel-2017a.eb @@ -0,0 +1,26 @@ +name = 'HDF5' +version = '1.8.18' + +homepage = 'http://www.hdfgroup.org/HDF5/' +description = """HDF5 is a unique technology suite that makes possible the management of + extremely large and complex data collections.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = [ + 'https://support.hdfgroup.org/ftp/HDF5/current18/src/', + 'https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(versions)/src/' +] + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['dd2148b740713ca0295442ec683d7b1c'] + +buildopts = 'CXXFLAGS="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK"' + +dependencies = [ + ('zlib', '1.2.11'), + ('Szip', '2.1'), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-5.3.0-intel-2017a-mpi.eb b/easybuild/easyconfigs/p/ParaView/ParaView-5.3.0-intel-2017a-mpi.eb new file mode 100644 index 0000000000..a124946808 --- /dev/null +++ b/easybuild/easyconfigs/p/ParaView/ParaView-5.3.0-intel-2017a-mpi.eb @@ -0,0 +1,52 @@ +easyblock = 'CMakeMake' + +name = 'ParaView' +version = '5.3.0' +versionsuffix = '-mpi' + +homepage = "http://www.paraview.org" +description = "ParaView is a scientific parallel visualizer." + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True, 'usempi': True} + +download_suffix = 'download.php?submit=Download&version=v%(version_major_minor)s&type=source&os=all&downloadFile=' +source_urls = ['http://www.paraview.org/paraview-downloads/%s' % download_suffix] +sources = ["ParaView-v%(version)s.tar.gz"] + +dependencies = [ + ('X11', '20170314'), + ('Mesa', '17.0.2'), + ('libGLU', '9.0.0'), + ('Qt5', '5.8.0'), + ('zlib', '1.2.11'), + ('HDF5', '1.8.18'), + ('Python', '2.7.13'), +] + +builddependencies = [('CMake', '3.7.2')] + +separate_build_dir = True + +configopts = '-DPARAVIEW_INSTALL_DEVELOPMENT_FILES=ON -DVTK_OPENGL_HAS_OSMESA=ON -DPARAVIEW_USE_MPI=ON ' +configopts += '-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include -DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s ' % SHLIB_EXT +configopts += '-DOSMESA_INCLUDE_DIR=$EBROOTMESA/include -DOSMESA_LIBRARY=$EBROOTMESA/lib/libOSMesa.%s ' % SHLIB_EXT +configopts += '-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s ' % SHLIB_EXT +configopts += '-DVTK_USE_SYSTEM_HDF5=ON -DPARAVIEW_ENABLE_PYTHON=ON -DBUILD_SHARED_LIBS=ON ' +# if you want to build server only Paraview, uncomment the following line: +# configopts += '-DVTK_USE_X=OFF ' + +# Without internet connection turn off testing (uncomment the following line) +configopts += '-DBUILD_TESTING=OFF ' +# Or consult https://gitlab.kitware.com/vtk/vtk/blob/master/Documentation/dev/git/data.md +# and download ExternalData to $EASYBUILD_SOURCEPATH and adjust -DExternalData_OBJECT_STORES accordingly +# Without internet connection, comment the following two lines (configopts and prebuildopts) +configopts += '-DExternalData_OBJECT_STORES=%(builddir)s/ExternalData ' + +configopts += ' -DPARAVIEW_QT_VERSION=5 -DQt5_DIR=$EBROOTQT5/lib/cmake/Qt5 -DQT_QMAKE_EXECUTABLE=$EBROOTQT5/bin/qmake ' +# The ParaView server can be cranky, test downloads are quite often failing, especially in the case +# of parallel downloads. Using ; insted of && gives a second chance to download the test files, if the +# first serial attempt would fail. +prebuildopts = 'make VTKData ;' + +moduleclass = 'vis' -- GitLab From 1f1e58d79e385169568b49542262db25ac27c804 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 10 Apr 2017 15:37:48 +0200 Subject: [PATCH 0585/1603] Added CGAL-4.9-intel-2017a-Python-2.7.13 --- .../CGAL-4.9-intel-2017a-Python-2.7.13.eb | 36 ++++ .../e/Eigen/Eigen-3.3.3-GCCcore-6.3.0.eb | 13 ++ .../m/MPFR/MPFR-3.1.5-20161219.patch | 174 ++++++++++++++++++ .../m/MPFR/MPFR-3.1.5-intel-2017a.eb | 29 +++ 4 files changed, 252 insertions(+) create mode 100644 easybuild/easyconfigs/c/CGAL/CGAL-4.9-intel-2017a-Python-2.7.13.eb create mode 100644 easybuild/easyconfigs/e/Eigen/Eigen-3.3.3-GCCcore-6.3.0.eb create mode 100644 easybuild/easyconfigs/m/MPFR/MPFR-3.1.5-20161219.patch create mode 100644 easybuild/easyconfigs/m/MPFR/MPFR-3.1.5-intel-2017a.eb diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.9-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.9-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..9b23706bf9 --- /dev/null +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.9-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,36 @@ +name = 'CGAL' +version = '4.9' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.cgal.org/' +description = """The goal of the CGAL Open Source Project is to provide easy access to efficient + and reliable geometric algorithms in the form of a C++ library.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'strict': True} + +source_urls = ['https://github.com/CGAL/cgal/releases/download/releases%2FCGAL-%(version)s'] +sources = [SOURCE_TAR_XZ] + +dependencies = [ + ('zlib', '1.2.11'), + ('Python', '2.7.13'), + ('Boost', '1.63.0', versionsuffix), + ('MPFR', '3.1.5'), + ('GMP', '6.1.2'), + ('libGLU', '9.0.0'), + ('Qt5', '5.8.0'), +] + +builddependencies = [ + ('CMake', '3.7.2'), + ('Eigen', '3.3.3'), +] + +configopts = "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " +configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT +configopts += "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT +configopts += "-DWITH_ZLIB=ON -DWITH_MPFR=ON -DWITH_OpenGL=ON -DWITH_Eigen3=ON " +configopts += "-DWITH_GMPXX=ON -DWITH_LAPACK=ON -DWITH_BLAS=ON " + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.3.3-GCCcore-6.3.0.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.3.3-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..86af55ba48 --- /dev/null +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.3.3-GCCcore-6.3.0.eb @@ -0,0 +1,13 @@ +name = 'Eigen' +version = '3.3.3' + +homepage = 'http://eigen.tuxfamily.org/index.php?title=Main_Page' +description = """Eigen is a C++ template library for linear algebra: + matrices, vectors, numerical solvers, and related algorithms.""" + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} + +source_urls = ['http://bitbucket.org/%(namelower)s/%(namelower)s/get'] +sources = ['%(version)s.tar.bz2'] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/MPFR/MPFR-3.1.5-20161219.patch b/easybuild/easyconfigs/m/MPFR/MPFR-3.1.5-20161219.patch new file mode 100644 index 0000000000..6b2d11466e --- /dev/null +++ b/easybuild/easyconfigs/m/MPFR/MPFR-3.1.5-20161219.patch @@ -0,0 +1,174 @@ +diff -Naurd mpfr-3.1.5-a/PATCHES mpfr-3.1.5-b/PATCHES +--- mpfr-3.1.5-a/PATCHES 2016-12-15 08:35:46.476430238 +0000 ++++ mpfr-3.1.5-b/PATCHES 2016-12-15 08:35:46.544430346 +0000 +@@ -0,0 +1 @@ ++vasprintf +diff -Naurd mpfr-3.1.5-a/VERSION mpfr-3.1.5-b/VERSION +--- mpfr-3.1.5-a/VERSION 2016-09-27 07:58:14.000000000 +0000 ++++ mpfr-3.1.5-b/VERSION 2016-12-15 08:35:46.544430346 +0000 +@@ -1 +1 @@ +-3.1.5 ++3.1.5-p1 +diff -Naurd mpfr-3.1.5-a/src/mpfr.h mpfr-3.1.5-b/src/mpfr.h +--- mpfr-3.1.5-a/src/mpfr.h 2016-09-27 07:58:15.000000000 +0000 ++++ mpfr-3.1.5-b/src/mpfr.h 2016-12-15 08:35:46.540430340 +0000 +@@ -27,7 +27,7 @@ + #define MPFR_VERSION_MAJOR 3 + #define MPFR_VERSION_MINOR 1 + #define MPFR_VERSION_PATCHLEVEL 5 +-#define MPFR_VERSION_STRING "3.1.5" ++#define MPFR_VERSION_STRING "3.1.5-p1" + + /* Macros dealing with MPFR VERSION */ + #define MPFR_VERSION_NUM(a,b,c) (((a) << 16L) | ((b) << 8) | (c)) +diff -Naurd mpfr-3.1.5-a/src/vasprintf.c mpfr-3.1.5-b/src/vasprintf.c +--- mpfr-3.1.5-a/src/vasprintf.c 2016-09-27 07:58:15.000000000 +0000 ++++ mpfr-3.1.5-b/src/vasprintf.c 2016-12-15 08:35:46.520430308 +0000 +@@ -1593,7 +1593,7 @@ + } + else if (spec.spec == 'f' || spec.spec == 'F') + { +- if (spec.prec == -1) ++ if (spec.prec < 0) + spec.prec = 6; + if (regular_fg (np, p, spec, NULL) == -1) + goto error; +diff -Naurd mpfr-3.1.5-a/src/version.c mpfr-3.1.5-b/src/version.c +--- mpfr-3.1.5-a/src/version.c 2016-09-27 07:58:15.000000000 +0000 ++++ mpfr-3.1.5-b/src/version.c 2016-12-15 08:35:46.544430346 +0000 +@@ -25,5 +25,5 @@ + const char * + mpfr_get_version (void) + { +- return "3.1.5"; ++ return "3.1.5-p1"; + } +diff -Naurd mpfr-3.1.5-a/tests/tsprintf.c mpfr-3.1.5-b/tests/tsprintf.c +--- mpfr-3.1.5-a/tests/tsprintf.c 2016-09-27 07:58:14.000000000 +0000 ++++ mpfr-3.1.5-b/tests/tsprintf.c 2016-12-15 08:35:46.520430308 +0000 +@@ -1251,6 +1251,25 @@ + check_emin_aux (MPFR_EMIN_MIN); + } + ++static void ++test20161214 (void) ++{ ++ mpfr_t x; ++ char buf[32]; ++ const char s[] = "0x0.fffffffffffff8p+1024"; ++ int r; ++ ++ mpfr_init2 (x, 64); ++ mpfr_set_str (x, s, 16, MPFR_RNDN); ++ r = mpfr_snprintf (buf, 32, "%.*RDf", -2, x); ++ MPFR_ASSERTN(r == 316); ++ r = mpfr_snprintf (buf, 32, "%.*RDf", INT_MIN + 1, x); ++ MPFR_ASSERTN(r == 316); ++ r = mpfr_snprintf (buf, 32, "%.*RDf", INT_MIN, x); ++ MPFR_ASSERTN(r == 316); ++ mpfr_clear (x); ++} ++ + int + main (int argc, char **argv) + { +@@ -1271,6 +1290,7 @@ + mixed (); + check_emax (); + check_emin (); ++ test20161214 (); + + #if defined(HAVE_LOCALE_H) && defined(HAVE_SETLOCALE) + #if MPFR_LCONV_DPTS +diff -Naurd mpfr-3.1.5-a/PATCHES mpfr-3.1.5-b/PATCHES +--- mpfr-3.1.5-a/PATCHES 2016-12-19 22:11:17.022676737 +0000 ++++ mpfr-3.1.5-b/PATCHES 2016-12-19 22:11:17.094676820 +0000 +@@ -0,0 +1 @@ ++strtofr +diff -Naurd mpfr-3.1.5-a/VERSION mpfr-3.1.5-b/VERSION +--- mpfr-3.1.5-a/VERSION 2016-12-15 08:35:46.544430346 +0000 ++++ mpfr-3.1.5-b/VERSION 2016-12-19 22:11:17.094676820 +0000 +@@ -1 +1 @@ +-3.1.5-p1 ++3.1.5-p2 +diff -Naurd mpfr-3.1.5-a/src/mpfr.h mpfr-3.1.5-b/src/mpfr.h +--- mpfr-3.1.5-a/src/mpfr.h 2016-12-15 08:35:46.540430340 +0000 ++++ mpfr-3.1.5-b/src/mpfr.h 2016-12-19 22:11:17.090676815 +0000 +@@ -27,7 +27,7 @@ + #define MPFR_VERSION_MAJOR 3 + #define MPFR_VERSION_MINOR 1 + #define MPFR_VERSION_PATCHLEVEL 5 +-#define MPFR_VERSION_STRING "3.1.5-p1" ++#define MPFR_VERSION_STRING "3.1.5-p2" + + /* Macros dealing with MPFR VERSION */ + #define MPFR_VERSION_NUM(a,b,c) (((a) << 16L) | ((b) << 8) | (c)) +diff -Naurd mpfr-3.1.5-a/src/strtofr.c mpfr-3.1.5-b/src/strtofr.c +--- mpfr-3.1.5-a/src/strtofr.c 2016-09-27 07:58:15.000000000 +0000 ++++ mpfr-3.1.5-b/src/strtofr.c 2016-12-19 22:11:17.066676788 +0000 +@@ -743,11 +743,14 @@ + of the pstr_size most significant digits of pstr->mant, with + equality in case exact is non-zero. */ + +- /* test if rounding is possible, and if so exit the loop */ +- if (exact || mpfr_can_round_raw (result, ysize, +- (pstr->negative) ? -1 : 1, +- ysize_bits - err - 1, +- MPFR_RNDN, rnd, MPFR_PREC(x))) ++ /* test if rounding is possible, and if so exit the loop. ++ Note: we also need to be able to determine the correct ternary value, ++ thus we use the MPFR_PREC(x) + (rnd == MPFR_RNDN) trick. ++ For example if result = xxx...xxx111...111 and rnd = RNDN, ++ then we know the correct rounding is xxx...xx(x+1), but we cannot know ++ the correct ternary value. */ ++ if (exact || mpfr_round_p (result, ysize, ysize_bits - err - 1, ++ MPFR_PREC(x) + (rnd == MPFR_RNDN))) + break; + + next_loop: +diff -Naurd mpfr-3.1.5-a/src/version.c mpfr-3.1.5-b/src/version.c +--- mpfr-3.1.5-a/src/version.c 2016-12-15 08:35:46.544430346 +0000 ++++ mpfr-3.1.5-b/src/version.c 2016-12-19 22:11:17.094676820 +0000 +@@ -25,5 +25,5 @@ + const char * + mpfr_get_version (void) + { +- return "3.1.5-p1"; ++ return "3.1.5-p2"; + } +diff -Naurd mpfr-3.1.5-a/tests/tstrtofr.c mpfr-3.1.5-b/tests/tstrtofr.c +--- mpfr-3.1.5-a/tests/tstrtofr.c 2016-09-27 07:58:14.000000000 +0000 ++++ mpfr-3.1.5-b/tests/tstrtofr.c 2016-12-19 22:11:17.066676788 +0000 +@@ -1191,6 +1191,24 @@ + mpfr_clears (e, x1, x2, (mpfr_ptr) 0); + } + ++/* Note: the number is 5^47/2^9. */ ++static void ++bug20161217 (void) ++{ ++ mpfr_t fp, z; ++ static const char * num = "0.1387778780781445675529539585113525390625e31"; ++ int inex; ++ ++ mpfr_init2 (fp, 110); ++ mpfr_init2 (z, 110); ++ inex = mpfr_strtofr (fp, num, NULL, 10, MPFR_RNDN); ++ MPFR_ASSERTN(inex == 0); ++ mpfr_set_str_binary (z, "10001100001000010011110110011101101001010000001011011110010001010100010100100110111101000010001011001100001101E-9"); ++ MPFR_ASSERTN(mpfr_equal_p (fp, z)); ++ mpfr_clear (fp); ++ mpfr_clear (z); ++} ++ + int + main (int argc, char *argv[]) + { +@@ -1205,6 +1223,7 @@ + test20100310 (); + bug20120814 (); + bug20120829 (); ++ bug20161217 (); + + tests_end_mpfr (); + return 0; diff --git a/easybuild/easyconfigs/m/MPFR/MPFR-3.1.5-intel-2017a.eb b/easybuild/easyconfigs/m/MPFR/MPFR-3.1.5-intel-2017a.eb new file mode 100644 index 0000000000..94a6262015 --- /dev/null +++ b/easybuild/easyconfigs/m/MPFR/MPFR-3.1.5-intel-2017a.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'MPFR' +version = '3.1.5' + +homepage = 'http://www.mpfr.org' +description = """The MPFR library is a C library for multiple-precision + floating-point computations with correct rounding.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['http://www.mpfr.org/mpfr-%(version)s/'] +sources = [SOURCELOWER_TAR_BZ2] + +patches = [ + 'MPFR_ictce_remove-deprecated-mp.patch', + '%(name)s-%(version)s-20161219.patch', +] + +dependencies = [('GMP', '6.1.2')] + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libmpfr.%s' % SHLIB_EXT, 'include/mpfr.h'], + 'dirs': [] +} + +moduleclass = 'math' -- GitLab From 7c2309cf46942ad0342bc4102db6e55fd02cef94 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 10 Apr 2017 15:40:35 +0200 Subject: [PATCH 0586/1603] Added OpenFOAM-4.1-intel-2017a --- .../m/METIS/METIS-5.1.0-intel-2017a.eb | 25 ++ .../o/OpenFOAM/OpenFOAM-4.1-cleanup.patch | 339 ++++++++++++++++++ .../o/OpenFOAM/OpenFOAM-4.1-intel-2017a.eb | 36 ++ .../s/SCOTCH/SCOTCH-6.0.4-intel-2017a.eb | 18 + 4 files changed, 418 insertions(+) create mode 100644 easybuild/easyconfigs/m/METIS/METIS-5.1.0-intel-2017a.eb create mode 100644 easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.1-cleanup.patch create mode 100644 easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.1-intel-2017a.eb create mode 100644 easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-intel-2017a.eb diff --git a/easybuild/easyconfigs/m/METIS/METIS-5.1.0-intel-2017a.eb b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-intel-2017a.eb new file mode 100644 index 0000000000..352a974db9 --- /dev/null +++ b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-intel-2017a.eb @@ -0,0 +1,25 @@ +name = 'METIS' +version = '5.1.0' + +homepage = 'http://glaros.dtc.umn.edu/gkhome/metis/metis/overview' +description = """METIS is a set of serial programs for partitioning graphs, partitioning finite element meshes, +and producing fill reducing orderings for sparse matrices. The algorithms implemented in METIS are based on the +multilevel recursive-bisection, multilevel k-way, and multi-constraint partitioning schemes.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [ + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis', + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/OLD', +] + +# We use 32bit for indices and 64bit for content +patches = ['METIS-5.1.0-use-doubles.patch'] + +builddependencies = [('CMake', '3.7.2')] + +configopts = ['', 'shared=1'] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.1-cleanup.patch b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.1-cleanup.patch new file mode 100644 index 0000000000..6c5fc1671a --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.1-cleanup.patch @@ -0,0 +1,339 @@ +# This patch removes all need for the ThirdParty files of OpenFOAM: +# we use EB dependencies for everything. It adjusts the paths, variables, etc +# We also let the install dir, compiler, etc be set by EB. +# Lastly, we also fix a small compile issue in 'ptscotchDecomp.C' +# Ward Poelmans +diff -ur OpenFOAM-4.x-version-4.1.org/applications/utilities/mesh/manipulation/setSet/Allwmake OpenFOAM-4.x-version-4.1/applications/utilities/mesh/manipulation/setSet/Allwmake +--- OpenFOAM-4.x-version-4.1.org/applications/utilities/mesh/manipulation/setSet/Allwmake 2016-10-16 16:11:45.000000000 +0200 ++++ OpenFOAM-4.x-version-4.1/applications/utilities/mesh/manipulation/setSet/Allwmake 2017-04-10 14:51:01.472221220 +0200 +@@ -9,11 +9,11 @@ + # + # use readline if available + # +-if [ -f /usr/include/readline/readline.h ] ++if [ -f $EBROOTLIBREADLINE/include/readline/readline.h ] + then + echo "Found -- enabling readline support." + export COMP_FLAGS="-DHAS_READLINE" +- export LINK_FLAGS="-lreadline" ++ export LINK_FLAGS="-L$EBROOTLIBREADLINE/lib -lreadline -L$EBROOTNCURSES -lncurses" + fi + + wmake +diff -ur OpenFOAM-4.x-version-4.1.org/applications/utilities/postProcessing/graphics/PV3Readers/PV3blockMeshReader/PV3blockMeshReader/CMakeLists.txt OpenFOAM-4.x-version-4.1/applications/utilities/postProcessing/graphics/PV3Readers/PV3blockMeshReader/PV3blockMeshReader/CMakeLists.txt +--- OpenFOAM-4.x-version-4.1.org/applications/utilities/postProcessing/graphics/PV3Readers/PV3blockMeshReader/PV3blockMeshReader/CMakeLists.txt 2016-10-16 16:11:45.000000000 +0200 ++++ OpenFOAM-4.x-version-4.1/applications/utilities/postProcessing/graphics/PV3Readers/PV3blockMeshReader/PV3blockMeshReader/CMakeLists.txt 2017-04-10 14:52:45.450160371 +0200 +@@ -41,7 +41,7 @@ + # + + # Extend the auto-generated panel +-QT4_WRAP_CPP(MOC_SRCS pqPV3blockMeshReaderPanel.h) ++QT5_WRAP_CPP(MOC_SRCS pqPV3blockMeshReaderPanel.h) + + ADD_PARAVIEW_OBJECT_PANEL(IFACES IFACE_SRCS + CLASS_NAME pqPV3blockMeshReaderPanel +diff -ur OpenFOAM-4.x-version-4.1.org/applications/utilities/postProcessing/graphics/PV3Readers/PV3FoamReader/PV3FoamReader/CMakeLists.txt OpenFOAM-4.x-version-4.1/applications/utilities/postProcessing/graphics/PV3Readers/PV3FoamReader/PV3FoamReader/CMakeLists.txt +--- OpenFOAM-4.x-version-4.1.org/applications/utilities/postProcessing/graphics/PV3Readers/PV3FoamReader/PV3FoamReader/CMakeLists.txt 2016-10-16 16:11:45.000000000 +0200 ++++ OpenFOAM-4.x-version-4.1/applications/utilities/postProcessing/graphics/PV3Readers/PV3FoamReader/PV3FoamReader/CMakeLists.txt 2017-04-10 14:52:45.450160371 +0200 +@@ -42,7 +42,7 @@ + # + + # Extend the auto-generated panel +-QT4_WRAP_CPP(MOC_SRCS pqPV3FoamReaderPanel.h) ++QT5_WRAP_CPP(MOC_SRCS pqPV3FoamReaderPanel.h) + + ADD_PARAVIEW_OBJECT_PANEL(IFACES IFACE_SRCS + CLASS_NAME pqPV3FoamReaderPanel +diff -ur OpenFOAM-4.x-version-4.1.org/applications/utilities/postProcessing/graphics/PVReaders/Allwmake OpenFOAM-4.x-version-4.1/applications/utilities/postProcessing/graphics/PVReaders/Allwmake +--- OpenFOAM-4.x-version-4.1.org/applications/utilities/postProcessing/graphics/PVReaders/Allwmake 2016-10-16 16:11:45.000000000 +0200 ++++ OpenFOAM-4.x-version-4.1/applications/utilities/postProcessing/graphics/PVReaders/Allwmake 2017-04-10 14:51:01.472221220 +0200 +@@ -16,7 +16,7 @@ + } + + # ensure CMake gets the correct C++ compiler +- [ -n "$WM_CXX" ] && export CXX="$WM_CXX" ++# [ -n "$WM_CXX" ] && export CXX="$WM_CXX" + + wmake $targetType vtkPVReaders + PVblockMeshReader/Allwmake $* +diff -ur OpenFOAM-4.x-version-4.1.org/applications/utilities/postProcessing/graphics/PVReaders/PVblockMeshReader/PVblockMeshReader/CMakeLists.txt OpenFOAM-4.x-version-4.1/applications/utilities/postProcessing/graphics/PVReaders/PVblockMeshReader/PVblockMeshReader/CMakeLists.txt +--- OpenFOAM-4.x-version-4.1.org/applications/utilities/postProcessing/graphics/PVReaders/PVblockMeshReader/PVblockMeshReader/CMakeLists.txt 2016-10-16 16:11:45.000000000 +0200 ++++ OpenFOAM-4.x-version-4.1/applications/utilities/postProcessing/graphics/PVReaders/PVblockMeshReader/PVblockMeshReader/CMakeLists.txt 2017-04-10 14:52:45.450160371 +0200 +@@ -42,7 +42,7 @@ + # + + # Extend the auto-generated panel +-QT4_WRAP_CPP(MOC_SRCS pqPVblockMeshReaderPanel.h) ++QT5_WRAP_CPP(MOC_SRCS pqPVblockMeshReaderPanel.h) + + ADD_PARAVIEW_OBJECT_PANEL(IFACES IFACE_SRCS + CLASS_NAME pqPVblockMeshReaderPanel +diff -ur OpenFOAM-4.x-version-4.1.org/applications/utilities/postProcessing/graphics/PVReaders/PVFoamReader/PVFoamReader/CMakeLists.txt OpenFOAM-4.x-version-4.1/applications/utilities/postProcessing/graphics/PVReaders/PVFoamReader/PVFoamReader/CMakeLists.txt +--- OpenFOAM-4.x-version-4.1.org/applications/utilities/postProcessing/graphics/PVReaders/PVFoamReader/PVFoamReader/CMakeLists.txt 2016-10-16 16:11:45.000000000 +0200 ++++ OpenFOAM-4.x-version-4.1/applications/utilities/postProcessing/graphics/PVReaders/PVFoamReader/PVFoamReader/CMakeLists.txt 2017-04-10 14:52:45.450160371 +0200 +@@ -43,7 +43,7 @@ + # + + # Extend the auto-generated panel +-QT4_WRAP_CPP(MOC_SRCS pqPVFoamReaderPanel.h) ++QT5_WRAP_CPP(MOC_SRCS pqPVFoamReaderPanel.h) + + ADD_PARAVIEW_OBJECT_PANEL(IFACES IFACE_SRCS + CLASS_NAME pqPVFoamReaderPanel +diff -ur OpenFOAM-4.x-version-4.1.org/etc/bashrc OpenFOAM-4.x-version-4.1/etc/bashrc +--- OpenFOAM-4.x-version-4.1.org/etc/bashrc 2016-10-16 16:11:45.000000000 +0200 ++++ OpenFOAM-4.x-version-4.1/etc/bashrc 2017-04-10 14:51:54.957704631 +0200 +@@ -42,9 +42,8 @@ + # + # Please set to the appropriate path if the default is not correct. + # +-[ $BASH_SOURCE ] && \ +-export FOAM_INST_DIR=$(cd ${BASH_SOURCE%/*/*/*} && pwd -P) || \ +-export FOAM_INST_DIR=$HOME/$WM_PROJECT ++# For Easybuild: set by the module ++# + # export FOAM_INST_DIR=~$WM_PROJECT + # export FOAM_INST_DIR=/opt/$WM_PROJECT + # export FOAM_INST_DIR=/usr/local/$WM_PROJECT +diff -ur OpenFOAM-4.x-version-4.1.org/etc/config.sh/CGAL OpenFOAM-4.x-version-4.1/etc/config.sh/CGAL +--- OpenFOAM-4.x-version-4.1.org/etc/config.sh/CGAL 2016-10-16 16:11:45.000000000 +0200 ++++ OpenFOAM-4.x-version-4.1/etc/config.sh/CGAL 2017-04-10 14:51:01.473221230 +0200 +@@ -36,37 +36,7 @@ + # + #------------------------------------------------------------------------------ + +-boost_version=boost-system +-cgal_version=cgal-system +-#cgal_version=CGAL-4.8 +- +-if [ -z "$SOURCE_CGAL_VERSIONS_ONLY" ] +-then +- +- common_path=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER +- +- export BOOST_ARCH_PATH=$common_path/$boost_version +- export CGAL_ARCH_PATH=$common_path/$cgal_version +- +- if [ "$FOAM_VERBOSE" -a "$PS1" ] +- then +- echo "Using CGAL and boost" 1>&2 +- echo " $cgal_version at $CGAL_ARCH_PATH" 1>&2 +- echo " $boost_version at $BOOST_ARCH_PATH" 1>&2 +- fi +- +- if [ -d "$CGAL_ARCH_PATH" -a "$cgal_version" != "cgal-system" ] +- then +- _foamAddLib $CGAL_ARCH_PATH/lib +- fi +- +- if [ -d "$BOOST_ARCH_PATH" -a "$boost_version" != "boost-system" ] +- then +- _foamAddLib $BOOST_ARCH_PATH/lib +- fi +- +- unset boost_version cgal_version common_path +- +-fi ++export CGAL_ARCH_PATH=$EBROOTCGAL ++export BOOST_ARCH_PATH=$EBROOTBOOST + + #------------------------------------------------------------------------------ +diff -ur OpenFOAM-4.x-version-4.1.org/etc/config.sh/gperftools OpenFOAM-4.x-version-4.1/etc/config.sh/gperftools +--- OpenFOAM-4.x-version-4.1.org/etc/config.sh/gperftools 2016-10-16 16:11:45.000000000 +0200 ++++ OpenFOAM-4.x-version-4.1/etc/config.sh/gperftools 2017-04-10 14:51:01.473221230 +0200 +@@ -29,13 +29,7 @@ + # + #------------------------------------------------------------------------------ + +-version=svn +-gperftools_install=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER +- +-GPERFTOOLS_VERSION=gperftools-$version +-GPERFTOOLS_ARCH_PATH=$gperftools_install/$GPERFTOOLS_VERSION +- +-export PATH=$GPERFTOOLS_ARCH_PATH/bin:$PATH +-export LD_LIBRARY_PATH=$GPERFTOOLS_ARCH_PATH/lib:$LD_LIBRARY_PATH ++GPERFTOOLS_VERSION=gperftools-$EBVERSIONGPERFTOOLS ++GPERFTOOLS_ARCH_PATH=$EBROOTGPERFTOOLS + + #------------------------------------------------------------------------------ +diff -ur OpenFOAM-4.x-version-4.1.org/etc/config.sh/metis OpenFOAM-4.x-version-4.1/etc/config.sh/metis +--- OpenFOAM-4.x-version-4.1.org/etc/config.sh/metis 2016-10-16 16:11:45.000000000 +0200 ++++ OpenFOAM-4.x-version-4.1/etc/config.sh/metis 2017-04-10 14:51:01.473221230 +0200 +@@ -34,7 +34,7 @@ + # + #------------------------------------------------------------------------------ + +-export METIS_VERSION=metis-5.1.0 +-export METIS_ARCH_PATH=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER$WM_PRECISION_OPTION$WM_LABEL_OPTION/$METIS_VERSION ++export METIS_VERSION=metis-$EBVERSIONMETIS ++export METIS_ARCH_PATH=$EBROOTMETIS + + #------------------------------------------------------------------------------ +diff -ur OpenFOAM-4.x-version-4.1.org/etc/config.sh/mpi OpenFOAM-4.x-version-4.1/etc/config.sh/mpi +--- OpenFOAM-4.x-version-4.1.org/etc/config.sh/mpi 2016-10-16 16:11:45.000000000 +0200 ++++ OpenFOAM-4.x-version-4.1/etc/config.sh/mpi 2017-04-10 14:51:01.473221230 +0200 +@@ -249,6 +249,9 @@ + _foamAddPath $MPI_ARCH_PATH/bin64 + _foamAddLib $MPI_ARCH_PATH/lib64 + ;; ++EASYBUILDMPI) ++ export FOAM_MPI=mpi ++ ;; + *) + export FOAM_MPI=dummy + ;; +diff -ur OpenFOAM-4.x-version-4.1.org/etc/config.sh/paraview OpenFOAM-4.x-version-4.1/etc/config.sh/paraview +--- OpenFOAM-4.x-version-4.1.org/etc/config.sh/paraview 2016-10-16 16:11:45.000000000 +0200 ++++ OpenFOAM-4.x-version-4.1/etc/config.sh/paraview 2017-04-10 14:51:01.473221230 +0200 +@@ -41,21 +41,6 @@ + ) \ + && PATH="$cleaned" + +-# Determine the cmake to be used +-unset CMAKE_HOME +-for cmake in cmake-3.2.1 cmake-2.8.12.1 cmake-2.8.8 cmake-2.8.4 cmake-2.8.3 \ +- cmake-2.8.1 +-do +- cmake=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER/$cmake +- if [ -r $cmake ] +- then +- export CMAKE_HOME=$cmake +- export CMAKE_ROOT=$cmake +- export PATH=$CMAKE_HOME/bin:$PATH +- break +- fi +-done +- + + #- ParaView version, automatically determine major version + #export ParaView_VERSION=3.12.0 +@@ -64,7 +49,7 @@ + #export ParaView_VERSION=4.3.1 + #export ParaView_VERSION=4.4.0 + #export ParaView_VERSION=5.0.0 +-export ParaView_VERSION=5.0.1 ++export ParaView_VERSION=$EBVERSIONPARAVIEW + export ParaView_MAJOR=detect + + +@@ -105,21 +90,15 @@ + paraviewInstDir=$WM_THIRD_PARTY_DIR/ParaView-$ParaView_VERSION + paraviewArchName=ParaView-$ParaView_VERSION + +-export ParaView_DIR=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER/$paraviewArchName ++export ParaView_DIR=$EBROOTPARAVIEW + + # Set paths if binaries or source are present + if [ -r $ParaView_DIR -o -r $paraviewInstDir ] + then + export ParaView_INCLUDE_DIR=$ParaView_DIR/include/paraview-$ParaView_MAJOR +- if [ ! -d $ParaView_INCLUDE_DIR -a -d $ParaView_DIR/include/paraview-3.0 ] +- then +- export ParaView_INCLUDE_DIR=$ParaView_DIR/include/paraview-3.0 +- fi + + ParaView_LIB_DIR=$ParaView_DIR/lib/paraview-$ParaView_MAJOR + +- export PATH=$ParaView_DIR/bin:$PATH +- export LD_LIBRARY_PATH=$ParaView_LIB_DIR:$LD_LIBRARY_PATH + export PV_PLUGIN_PATH=$FOAM_LIBBIN/paraview-$ParaView_MAJOR + + if [ "$FOAM_VERBOSE" -a "$PS1" ] +@@ -131,17 +110,6 @@ + echo " PV_PLUGIN_PATH : $PV_PLUGIN_PATH" + fi + +- # Add in python libraries if required +- paraviewPython=$ParaView_DIR/Utilities/VTKPythonWrapping +- if [ -r $paraviewPython ] +- then +- if [ "$PYTHONPATH" ] +- then +- export PYTHONPATH=$PYTHONPATH:$paraviewPython:$ParaView_LIB_DIR +- else +- export PYTHONPATH=$paraviewPython:$ParaView_LIB_DIR +- fi +- fi + else + unset PV_PLUGIN_PATH + fi +diff -ur OpenFOAM-4.x-version-4.1.org/etc/config.sh/scotch OpenFOAM-4.x-version-4.1/etc/config.sh/scotch +--- OpenFOAM-4.x-version-4.1.org/etc/config.sh/scotch 2016-10-16 16:11:45.000000000 +0200 ++++ OpenFOAM-4.x-version-4.1/etc/config.sh/scotch 2017-04-10 14:51:01.473221230 +0200 +@@ -37,7 +37,7 @@ + # + #------------------------------------------------------------------------------ + +-export SCOTCH_VERSION=scotch_6.0.3 +-export SCOTCH_ARCH_PATH=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER$WM_PRECISION_OPTION$WM_LABEL_OPTION/$SCOTCH_VERSION ++export SCOTCH_VERSION=scotch_$EBVERSIONSCOTCH ++export SCOTCH_ARCH_PATH=$EBROOTSCOTCH + + #------------------------------------------------------------------------------ +diff -ur OpenFOAM-4.x-version-4.1.org/etc/config.sh/settings OpenFOAM-4.x-version-4.1/etc/config.sh/settings +--- OpenFOAM-4.x-version-4.1.org/etc/config.sh/settings 2016-10-16 16:11:45.000000000 +0200 ++++ OpenFOAM-4.x-version-4.1/etc/config.sh/settings 2017-04-10 14:51:01.473221230 +0200 +@@ -56,11 +56,11 @@ + 64) + WM_ARCH=linux64 + export WM_COMPILER_LIB_ARCH=64 +- export WM_CC='gcc' +- export WM_CXX='g++' +- export WM_CFLAGS='-m64 -fPIC' +- export WM_CXXFLAGS='-m64 -fPIC -std=c++0x' +- export WM_LDFLAGS='-m64' ++ export WM_CC=$CC ++ export WM_CXX=$CXX ++ export WM_CFLAGS=$CFLAGS ++ export WM_CXXFLAGS=$CXXFLAGS ++ export WM_LDFLAGS=$LDFLAGS + ;; + *) + echo "Unknown WM_ARCH_OPTION '$WM_ARCH_OPTION', should be 32 or 64"\ +diff -ur OpenFOAM-4.x-version-4.1.org/src/parallel/decompose/ptscotchDecomp/Make/options OpenFOAM-4.x-version-4.1/src/parallel/decompose/ptscotchDecomp/Make/options +--- OpenFOAM-4.x-version-4.1.org/src/parallel/decompose/ptscotchDecomp/Make/options 2016-10-16 16:11:45.000000000 +0200 ++++ OpenFOAM-4.x-version-4.1/src/parallel/decompose/ptscotchDecomp/Make/options 2017-04-10 14:51:01.473221230 +0200 +@@ -3,10 +3,8 @@ + + EXE_INC = \ + $(PFLAGS) $(PINC) \ +- -I$(SCOTCH_ROOT)/include \ + -I$(SCOTCH_ARCH_PATH)/include/$(FOAM_MPI) \ +- -I/usr/include/scotch \ + -I../decompositionMethods/lnInclude + + LIB_LIBS = \ +- -L$(SCOTCH_ROOT)/lib -L$(FOAM_EXT_LIBBIN)/$(FOAM_MPI) -lptscotch -lptscotcherrexit -lscotch ${LINK_FLAGS} -lrt ++ -L$(SCOTCH_ARCH_PATH)/lib -L$(FOAM_EXT_LIBBIN)/$(FOAM_MPI) -lptscotch -lptscotcherrexit -lscotch ${LINK_FLAGS} -lrt +diff -ur OpenFOAM-4.x-version-4.1.org/src/parallel/decompose/ptscotchDecomp/ptscotchDecomp.C OpenFOAM-4.x-version-4.1/src/parallel/decompose/ptscotchDecomp/ptscotchDecomp.C +--- OpenFOAM-4.x-version-4.1.org/src/parallel/decompose/ptscotchDecomp/ptscotchDecomp.C 2016-10-16 16:11:45.000000000 +0200 ++++ OpenFOAM-4.x-version-4.1/src/parallel/decompose/ptscotchDecomp/ptscotchDecomp.C 2017-04-10 14:51:01.474221238 +0200 +@@ -30,10 +30,11 @@ + #include "globalIndex.H" + #include "SubField.H" + ++#include ++ + extern "C" + { + #include +- #include + #include "ptscotch.h" + } + +diff -ur OpenFOAM-4.x-version-4.1.org/src/parallel/decompose/scotchDecomp/Make/options OpenFOAM-4.x-version-4.1/src/parallel/decompose/scotchDecomp/Make/options +--- OpenFOAM-4.x-version-4.1.org/src/parallel/decompose/scotchDecomp/Make/options 2016-10-16 16:11:45.000000000 +0200 ++++ OpenFOAM-4.x-version-4.1/src/parallel/decompose/scotchDecomp/Make/options 2017-04-10 14:51:01.474221238 +0200 +@@ -7,10 +7,8 @@ + + EXE_INC = \ + $(PFLAGS) $(PINC) \ +- -I$(SCOTCH_ROOT)/include \ + -I$(SCOTCH_ARCH_PATH)/include \ +- -I/usr/include/scotch \ + -I../decompositionMethods/lnInclude + + LIB_LIBS = \ +- -L$(SCOTCH_ROOT)/lib -L$(FOAM_EXT_LIBBIN) -lscotch -lscotcherrexit -lrt ++ -L$(SCOTCH_ARCH_PATH)/lib -L$(FOAM_EXT_LIBBIN) -lscotch -lscotcherrexit -lrt diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.1-intel-2017a.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.1-intel-2017a.eb new file mode 100644 index 0000000000..214d84ba90 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.1-intel-2017a.eb @@ -0,0 +1,36 @@ +name = 'OpenFOAM' +version = '4.1' + +homepage = 'http://www.openfoam.com/' +description = """OpenFOAM is a free, open source CFD software package. + OpenFOAM has an extensive range of features to solve anything from complex fluid flows + involving chemical reactions, turbulence and heat transfer, + to solid dynamics and electromagnetics.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'cstd': 'c++11'} + +source_urls = ['https://github.com/OpenFOAM/OpenFOAM-%(version_major)s.x/archive'] +sources = ['version-%(version)s.tar.gz'] + +checksums = ['318a446c4ae6366c7296b61184acd37c'] + +patches = ['OpenFOAM-%(version)s-cleanup.patch'] + +dependencies = [ + ('libreadline', '7.0'), + ('ncurses', '6.0'), + # OpenFOAM requires 64 bit METIS using 32 bit indexes (array indexes) + ('METIS', '5.1.0'), + ('SCOTCH', '6.0.4'), + ('CGAL', '4.9', '-Python-2.7.13'), + ('ParaView', '5.3.0', '-mpi'), +] + +builddependencies = [ + ('Bison', '3.0.4'), + ('CMake', '3.7.2'), + ('flex', '2.6.3'), +] + +moduleclass = 'cae' diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-intel-2017a.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-intel-2017a.eb new file mode 100644 index 0000000000..56f2a3c362 --- /dev/null +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-intel-2017a.eb @@ -0,0 +1,18 @@ +name = 'SCOTCH' +version = '6.0.4' + +homepage = 'http://gforge.inria.fr/projects/scotch/' +description = """Software package and libraries for sequential and parallel graph partitioning, +static mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True} + +source_urls = ['http://gforge.inria.fr/frs/download.php/file/34618/'] +sources = ['%(namelower)s_%(version)s.tar.gz'] + +dependencies = [ + ('zlib', '1.2.11'), +] + +moduleclass = 'math' -- GitLab From f0c6c952907f6b57aaef620f887e0e90aabd9940 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 10 Apr 2017 15:47:12 +0200 Subject: [PATCH 0587/1603] Downgrade ParaView to 5.2 as OpenFOAM 4.1 does not work with 5.3 They uses something that has been dropped in ParaView 5.3 --- easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.1-intel-2017a.eb | 2 +- ...3.0-intel-2017a-mpi.eb => ParaView-5.2.0-intel-2017a-mpi.eb} | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/p/ParaView/{ParaView-5.3.0-intel-2017a-mpi.eb => ParaView-5.2.0-intel-2017a-mpi.eb} (99%) diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.1-intel-2017a.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.1-intel-2017a.eb index 214d84ba90..2469f2947a 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.1-intel-2017a.eb +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.1-intel-2017a.eb @@ -24,7 +24,7 @@ dependencies = [ ('METIS', '5.1.0'), ('SCOTCH', '6.0.4'), ('CGAL', '4.9', '-Python-2.7.13'), - ('ParaView', '5.3.0', '-mpi'), + ('ParaView', '5.2.0', '-mpi'), ] builddependencies = [ diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-5.3.0-intel-2017a-mpi.eb b/easybuild/easyconfigs/p/ParaView/ParaView-5.2.0-intel-2017a-mpi.eb similarity index 99% rename from easybuild/easyconfigs/p/ParaView/ParaView-5.3.0-intel-2017a-mpi.eb rename to easybuild/easyconfigs/p/ParaView/ParaView-5.2.0-intel-2017a-mpi.eb index a124946808..addfba2c58 100644 --- a/easybuild/easyconfigs/p/ParaView/ParaView-5.3.0-intel-2017a-mpi.eb +++ b/easybuild/easyconfigs/p/ParaView/ParaView-5.2.0-intel-2017a-mpi.eb @@ -1,7 +1,7 @@ easyblock = 'CMakeMake' name = 'ParaView' -version = '5.3.0' +version = '5.2.0' versionsuffix = '-mpi' homepage = "http://www.paraview.org" -- GitLab From 9f863dc507b877ed77968f9d56a47408b7f5e970 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Tue, 11 Apr 2017 10:33:06 +0200 Subject: [PATCH 0588/1603] Switch OpenFOAM 4.1 to Qt 4.x OpenFOAM doesn't work with Qt5 yet... --- .../CGAL-4.9-intel-2017a-Python-2.7.13.eb | 2 +- .../o/OpenFOAM/OpenFOAM-4.1-cleanup.patch | 48 ------------------- .../ParaView-5.2.0-intel-2017a-mpi.eb | 4 +- .../easyconfigs/q/Qt/Qt-4.8.7-intel-2017a.eb | 28 +++++++++++ 4 files changed, 31 insertions(+), 51 deletions(-) create mode 100644 easybuild/easyconfigs/q/Qt/Qt-4.8.7-intel-2017a.eb diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.9-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.9-intel-2017a-Python-2.7.13.eb index 9b23706bf9..da60ff72f0 100644 --- a/easybuild/easyconfigs/c/CGAL/CGAL-4.9-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.9-intel-2017a-Python-2.7.13.eb @@ -19,7 +19,7 @@ dependencies = [ ('MPFR', '3.1.5'), ('GMP', '6.1.2'), ('libGLU', '9.0.0'), - ('Qt5', '5.8.0'), + ('Qt', '4.8.7'), ] builddependencies = [ diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.1-cleanup.patch b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.1-cleanup.patch index 6c5fc1671a..1098db34cb 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.1-cleanup.patch +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.1-cleanup.patch @@ -20,30 +20,6 @@ diff -ur OpenFOAM-4.x-version-4.1.org/applications/utilities/mesh/manipulation/s fi wmake -diff -ur OpenFOAM-4.x-version-4.1.org/applications/utilities/postProcessing/graphics/PV3Readers/PV3blockMeshReader/PV3blockMeshReader/CMakeLists.txt OpenFOAM-4.x-version-4.1/applications/utilities/postProcessing/graphics/PV3Readers/PV3blockMeshReader/PV3blockMeshReader/CMakeLists.txt ---- OpenFOAM-4.x-version-4.1.org/applications/utilities/postProcessing/graphics/PV3Readers/PV3blockMeshReader/PV3blockMeshReader/CMakeLists.txt 2016-10-16 16:11:45.000000000 +0200 -+++ OpenFOAM-4.x-version-4.1/applications/utilities/postProcessing/graphics/PV3Readers/PV3blockMeshReader/PV3blockMeshReader/CMakeLists.txt 2017-04-10 14:52:45.450160371 +0200 -@@ -41,7 +41,7 @@ - # - - # Extend the auto-generated panel --QT4_WRAP_CPP(MOC_SRCS pqPV3blockMeshReaderPanel.h) -+QT5_WRAP_CPP(MOC_SRCS pqPV3blockMeshReaderPanel.h) - - ADD_PARAVIEW_OBJECT_PANEL(IFACES IFACE_SRCS - CLASS_NAME pqPV3blockMeshReaderPanel -diff -ur OpenFOAM-4.x-version-4.1.org/applications/utilities/postProcessing/graphics/PV3Readers/PV3FoamReader/PV3FoamReader/CMakeLists.txt OpenFOAM-4.x-version-4.1/applications/utilities/postProcessing/graphics/PV3Readers/PV3FoamReader/PV3FoamReader/CMakeLists.txt ---- OpenFOAM-4.x-version-4.1.org/applications/utilities/postProcessing/graphics/PV3Readers/PV3FoamReader/PV3FoamReader/CMakeLists.txt 2016-10-16 16:11:45.000000000 +0200 -+++ OpenFOAM-4.x-version-4.1/applications/utilities/postProcessing/graphics/PV3Readers/PV3FoamReader/PV3FoamReader/CMakeLists.txt 2017-04-10 14:52:45.450160371 +0200 -@@ -42,7 +42,7 @@ - # - - # Extend the auto-generated panel --QT4_WRAP_CPP(MOC_SRCS pqPV3FoamReaderPanel.h) -+QT5_WRAP_CPP(MOC_SRCS pqPV3FoamReaderPanel.h) - - ADD_PARAVIEW_OBJECT_PANEL(IFACES IFACE_SRCS - CLASS_NAME pqPV3FoamReaderPanel diff -ur OpenFOAM-4.x-version-4.1.org/applications/utilities/postProcessing/graphics/PVReaders/Allwmake OpenFOAM-4.x-version-4.1/applications/utilities/postProcessing/graphics/PVReaders/Allwmake --- OpenFOAM-4.x-version-4.1.org/applications/utilities/postProcessing/graphics/PVReaders/Allwmake 2016-10-16 16:11:45.000000000 +0200 +++ OpenFOAM-4.x-version-4.1/applications/utilities/postProcessing/graphics/PVReaders/Allwmake 2017-04-10 14:51:01.472221220 +0200 @@ -56,30 +32,6 @@ diff -ur OpenFOAM-4.x-version-4.1.org/applications/utilities/postProcessing/grap wmake $targetType vtkPVReaders PVblockMeshReader/Allwmake $* -diff -ur OpenFOAM-4.x-version-4.1.org/applications/utilities/postProcessing/graphics/PVReaders/PVblockMeshReader/PVblockMeshReader/CMakeLists.txt OpenFOAM-4.x-version-4.1/applications/utilities/postProcessing/graphics/PVReaders/PVblockMeshReader/PVblockMeshReader/CMakeLists.txt ---- OpenFOAM-4.x-version-4.1.org/applications/utilities/postProcessing/graphics/PVReaders/PVblockMeshReader/PVblockMeshReader/CMakeLists.txt 2016-10-16 16:11:45.000000000 +0200 -+++ OpenFOAM-4.x-version-4.1/applications/utilities/postProcessing/graphics/PVReaders/PVblockMeshReader/PVblockMeshReader/CMakeLists.txt 2017-04-10 14:52:45.450160371 +0200 -@@ -42,7 +42,7 @@ - # - - # Extend the auto-generated panel --QT4_WRAP_CPP(MOC_SRCS pqPVblockMeshReaderPanel.h) -+QT5_WRAP_CPP(MOC_SRCS pqPVblockMeshReaderPanel.h) - - ADD_PARAVIEW_OBJECT_PANEL(IFACES IFACE_SRCS - CLASS_NAME pqPVblockMeshReaderPanel -diff -ur OpenFOAM-4.x-version-4.1.org/applications/utilities/postProcessing/graphics/PVReaders/PVFoamReader/PVFoamReader/CMakeLists.txt OpenFOAM-4.x-version-4.1/applications/utilities/postProcessing/graphics/PVReaders/PVFoamReader/PVFoamReader/CMakeLists.txt ---- OpenFOAM-4.x-version-4.1.org/applications/utilities/postProcessing/graphics/PVReaders/PVFoamReader/PVFoamReader/CMakeLists.txt 2016-10-16 16:11:45.000000000 +0200 -+++ OpenFOAM-4.x-version-4.1/applications/utilities/postProcessing/graphics/PVReaders/PVFoamReader/PVFoamReader/CMakeLists.txt 2017-04-10 14:52:45.450160371 +0200 -@@ -43,7 +43,7 @@ - # - - # Extend the auto-generated panel --QT4_WRAP_CPP(MOC_SRCS pqPVFoamReaderPanel.h) -+QT5_WRAP_CPP(MOC_SRCS pqPVFoamReaderPanel.h) - - ADD_PARAVIEW_OBJECT_PANEL(IFACES IFACE_SRCS - CLASS_NAME pqPVFoamReaderPanel diff -ur OpenFOAM-4.x-version-4.1.org/etc/bashrc OpenFOAM-4.x-version-4.1/etc/bashrc --- OpenFOAM-4.x-version-4.1.org/etc/bashrc 2016-10-16 16:11:45.000000000 +0200 +++ OpenFOAM-4.x-version-4.1/etc/bashrc 2017-04-10 14:51:54.957704631 +0200 diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-5.2.0-intel-2017a-mpi.eb b/easybuild/easyconfigs/p/ParaView/ParaView-5.2.0-intel-2017a-mpi.eb index addfba2c58..903174f12f 100644 --- a/easybuild/easyconfigs/p/ParaView/ParaView-5.2.0-intel-2017a-mpi.eb +++ b/easybuild/easyconfigs/p/ParaView/ParaView-5.2.0-intel-2017a-mpi.eb @@ -18,7 +18,7 @@ dependencies = [ ('X11', '20170314'), ('Mesa', '17.0.2'), ('libGLU', '9.0.0'), - ('Qt5', '5.8.0'), + ('Qt', '4.8.7'), ('zlib', '1.2.11'), ('HDF5', '1.8.18'), ('Python', '2.7.13'), @@ -43,7 +43,7 @@ configopts += '-DBUILD_TESTING=OFF ' # Without internet connection, comment the following two lines (configopts and prebuildopts) configopts += '-DExternalData_OBJECT_STORES=%(builddir)s/ExternalData ' -configopts += ' -DPARAVIEW_QT_VERSION=5 -DQt5_DIR=$EBROOTQT5/lib/cmake/Qt5 -DQT_QMAKE_EXECUTABLE=$EBROOTQT5/bin/qmake ' +configopts += ' -DPARAVIEW_QT_VERSION=4 -DQT_QMAKE_EXECUTABLE=$EBROOTQT/bin/qmake ' # The ParaView server can be cranky, test downloads are quite often failing, especially in the case # of parallel downloads. Using ; insted of && gives a second chance to download the test files, if the # first serial attempt would fail. diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.7-intel-2017a.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.7-intel-2017a.eb new file mode 100644 index 0000000000..f45873187d --- /dev/null +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.7-intel-2017a.eb @@ -0,0 +1,28 @@ +name = 'Qt' +version = '4.8.7' + +homepage = 'http://qt.io/' +description = "Qt is a comprehensive cross-platform C++ application framework." + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [ + 'http://download.qt.io/official_releases/qt/%(version_major_minor)s/%(version)s/', + 'http://download.qt.io/archive/qt/%(version_major_minor)s/%(version)s/' +] +sources = ['%(namelower)s-everywhere-opensource-src-%(version)s.tar.gz'] + +patches = ['Qt-%(version)s_phonon-export.patch'] + +builddependencies = [ + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('GLib', '2.52.0'), + ('libpng', '1.6.29'), + ('X11', '20170314'), + ('libGLU', '9.0.0'), +] + +moduleclass = 'devel' -- GitLab From cccb215e70aba11ff7b33283085b9a4763b97c58 Mon Sep 17 00:00:00 2001 From: iotaka Date: Tue, 11 Apr 2017 12:00:50 +0200 Subject: [PATCH 0589/1603] Qt4 also for CGAL --- .../o/OpenFOAM/OpenFOAM-4.0-foss-2016b.eb | 2 +- .../ParaView/ParaView-5.2.0-foss-2016b-mpi.eb | 51 +++++++++++++++++++ 2 files changed, 52 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/p/ParaView/ParaView-5.2.0-foss-2016b-mpi.eb diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.0-foss-2016b.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.0-foss-2016b.eb index 00ba2fa1df..3db67b3e22 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.0-foss-2016b.eb +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.0-foss-2016b.eb @@ -24,7 +24,7 @@ dependencies = [ ('METIS', '5.1.0'), ('SCOTCH', '6.0.4'), ('CGAL', '4.8.1'), - ('ParaView', '5.3.0', '-mpi'), + ('ParaView', '5.2.0', '-mpi'), ] builddependencies = [ diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-5.2.0-foss-2016b-mpi.eb b/easybuild/easyconfigs/p/ParaView/ParaView-5.2.0-foss-2016b-mpi.eb new file mode 100644 index 0000000000..5dd45f28db --- /dev/null +++ b/easybuild/easyconfigs/p/ParaView/ParaView-5.2.0-foss-2016b-mpi.eb @@ -0,0 +1,51 @@ +easyblock = 'CMakeMake' + +name = 'ParaView' +version = '5.2.0' +versionsuffix = '-mpi' + +homepage = "http://www.paraview.org" +description = "ParaView is a scientific parallel visualizer." + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'pic': True, 'usempi': True} + +download_suffix = 'download.php?submit=Download&version=v%(version_major_minor)s&type=source&os=all&downloadFile=' +source_urls = ['http://www.paraview.org/paraview-downloads/%s' % download_suffix] +sources = ["ParaView-v%(version)s.tar.gz"] + +dependencies = [ + ('X11', '20160819'), + ('Mesa', '12.0.2'), + ('libGLU', '9.0.0'), + ('Qt', '4.8.7'), + ('zlib', '1.2.8'), + ('HDF5', '1.8.17'), + ('Python', '2.7.12'), +] + +builddependencies = [('CMake', '3.6.1')] + +separate_build_dir = True + +configopts = '-DPARAVIEW_INSTALL_DEVELOPMENT_FILES=ON -DVTK_OPENGL_HAS_OSMESA=ON -DPARAVIEW_USE_MPI=ON ' +configopts += '-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include -DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s ' % SHLIB_EXT +configopts += '-DOSMESA_INCLUDE_DIR=$EBROOTMESA/include -DOSMESA_LIBRARY=$EBROOTMESA/lib/libOSMesa.%s ' % SHLIB_EXT +configopts += '-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s ' % SHLIB_EXT +configopts += '-DVTK_USE_SYSTEM_HDF5=ON -DPARAVIEW_ENABLE_PYTHON=ON -DBUILD_SHARED_LIBS=ON ' +# if you want to build server only Paraview, uncomment the following line: +# configopts += '-DVTK_USE_X=OFF ' + +# Without internet connection turn off testing (uncomment the following line) +configopts += '-DBUILD_TESTING=OFF ' +# Or consult https://gitlab.kitware.com/vtk/vtk/blob/master/Documentation/dev/git/data.md +# and download ExternalData to $EASYBUILD_SOURCEPATH and adjust -DExternalData_OBJECT_STORES accordingly +# Without internet connection, comment the following two lines (configopts and prebuildopts) +configopts += '-DExternalData_OBJECT_STORES=%(builddir)s/ExternalData ' + +# The ParaView server can be cranky, test downloads are quite often failing, especially in the case +# of parallel downloads. Using ; insted of && gives a second chance to download the test files, if the +# first serial attempt would fail. +prebuildopts = 'make VTKData ;' + +moduleclass = 'vis' -- GitLab From 090054ad90088e311860cfdc0b1c228030fe1834 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Tue, 11 Apr 2017 12:51:58 +0200 Subject: [PATCH 0590/1603] Force usage of C++98 for Qt4 with intel/2017a --- easybuild/easyconfigs/q/Qt/Qt-4.8.7-intel-2017a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.7-intel-2017a.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.7-intel-2017a.eb index f45873187d..f9818f430a 100644 --- a/easybuild/easyconfigs/q/Qt/Qt-4.8.7-intel-2017a.eb +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.7-intel-2017a.eb @@ -5,6 +5,7 @@ homepage = 'http://qt.io/' description = "Qt is a comprehensive cross-platform C++ application framework." toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'cstd': 'gnu++98'} source_urls = [ 'http://download.qt.io/official_releases/qt/%(version_major_minor)s/%(version)s/', -- GitLab From d1193f3f30d6139025fa19716905c166ab9520e8 Mon Sep 17 00:00:00 2001 From: iotaka Date: Tue, 11 Apr 2017 14:37:55 +0200 Subject: [PATCH 0591/1603] Qt4 also for CGAL --- .../o/OpenFOAM/OpenFOAM-4.1-cleanup.patch | 281 ++++++++++++++++++ .../o/OpenFOAM/OpenFOAM-4.1-foss-2016b.eb | 36 +++ 2 files changed, 317 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.1-cleanup.patch create mode 100644 easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.1-foss-2016b.eb diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.1-cleanup.patch b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.1-cleanup.patch new file mode 100644 index 0000000000..d7e72b20c9 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.1-cleanup.patch @@ -0,0 +1,281 @@ +# This patch removes all need for the ThirdParty files of OpenFOAM: +# we use EB dependencies for everything. It adjusts the paths, variables, etc +# We also let the install dir, compiler, etc be set by EB. +# Lastly, we also fix a small compile issue in 'ptscotchDecomp.C' +# Ward Poelmans +diff -ur OpenFOAM-4.x-version-4.1.org/applications/utilities/mesh/manipulation/setSet/Allwmake OpenFOAM-4.x-version-4.1/applications/utilities/mesh/manipulation/setSet/Allwmake +--- OpenFOAM-4.x-version-4.1.org/applications/utilities/mesh/manipulation/setSet/Allwmake 2016-10-16 16:11:45.000000000 +0200 ++++ OpenFOAM-4.x-version-4.1/applications/utilities/mesh/manipulation/setSet/Allwmake 2017-04-10 14:51:01.472221220 +0200 +@@ -9,11 +9,11 @@ + # + # use readline if available + # +-if [ -f /usr/include/readline/readline.h ] ++if [ -f $EBROOTLIBREADLINE/include/readline/readline.h ] + then + echo "Found -- enabling readline support." + export COMP_FLAGS="-DHAS_READLINE" +- export LINK_FLAGS="-lreadline" ++ export LINK_FLAGS="-L$EBROOTLIBREADLINE/lib -lreadline -L$EBROOTNCURSES -lncurses" + fi + + wmake +diff -ur OpenFOAM-4.x-version-4.1.org/etc/bashrc OpenFOAM-4.x-version-4.1/etc/bashrc +--- OpenFOAM-4.x-version-4.1.org/etc/bashrc 2016-10-16 16:11:45.000000000 +0200 ++++ OpenFOAM-4.x-version-4.1/etc/bashrc 2017-04-10 14:51:54.957704631 +0200 +@@ -42,9 +42,8 @@ + # + # Please set to the appropriate path if the default is not correct. + # +-[ $BASH_SOURCE ] && \ +-export FOAM_INST_DIR=$(cd ${BASH_SOURCE%/*/*/*} && pwd -P) || \ +-export FOAM_INST_DIR=$HOME/$WM_PROJECT ++# For Easybuild: set by the module ++# + # export FOAM_INST_DIR=~$WM_PROJECT + # export FOAM_INST_DIR=/opt/$WM_PROJECT + # export FOAM_INST_DIR=/usr/local/$WM_PROJECT +diff -ur OpenFOAM-4.x-version-4.1.org/etc/config.sh/CGAL OpenFOAM-4.x-version-4.1/etc/config.sh/CGAL +--- OpenFOAM-4.x-version-4.1.org/etc/config.sh/CGAL 2016-10-16 16:11:45.000000000 +0200 ++++ OpenFOAM-4.x-version-4.1/etc/config.sh/CGAL 2017-04-10 14:51:01.473221230 +0200 +@@ -36,37 +36,7 @@ + # + #------------------------------------------------------------------------------ + +-boost_version=boost-system +-cgal_version=cgal-system +-#cgal_version=CGAL-4.8 +- +-if [ -z "$SOURCE_CGAL_VERSIONS_ONLY" ] +-then +- +- common_path=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER +- +- export BOOST_ARCH_PATH=$common_path/$boost_version +- export CGAL_ARCH_PATH=$common_path/$cgal_version +- +- if [ "$FOAM_VERBOSE" -a "$PS1" ] +- then +- echo "Using CGAL and boost" 1>&2 +- echo " $cgal_version at $CGAL_ARCH_PATH" 1>&2 +- echo " $boost_version at $BOOST_ARCH_PATH" 1>&2 +- fi +- +- if [ -d "$CGAL_ARCH_PATH" -a "$cgal_version" != "cgal-system" ] +- then +- _foamAddLib $CGAL_ARCH_PATH/lib +- fi +- +- if [ -d "$BOOST_ARCH_PATH" -a "$boost_version" != "boost-system" ] +- then +- _foamAddLib $BOOST_ARCH_PATH/lib +- fi +- +- unset boost_version cgal_version common_path +- +-fi ++export CGAL_ARCH_PATH=$EBROOTCGAL ++export BOOST_ARCH_PATH=$EBROOTBOOST + +#------------------------------------------------------------------------------ +diff -ur OpenFOAM-4.x-version-4.1.org/etc/config.sh/gperftools OpenFOAM-4.x-version-4.1/etc/config.sh/gperftools +--- OpenFOAM-4.x-version-4.1.org/etc/config.sh/gperftools 2016-10-16 16:11:45.000000000 +0200 ++++ OpenFOAM-4.x-version-4.1/etc/config.sh/gperftools 2017-04-10 14:51:01.473221230 +0200 +@@ -29,13 +29,7 @@ + # + #------------------------------------------------------------------------------ + +-version=svn +-gperftools_install=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER +- +-GPERFTOOLS_VERSION=gperftools-$version +-GPERFTOOLS_ARCH_PATH=$gperftools_install/$GPERFTOOLS_VERSION +- +-export PATH=$GPERFTOOLS_ARCH_PATH/bin:$PATH +-export LD_LIBRARY_PATH=$GPERFTOOLS_ARCH_PATH/lib:$LD_LIBRARY_PATH ++GPERFTOOLS_VERSION=gperftools-$EBVERSIONGPERFTOOLS ++GPERFTOOLS_ARCH_PATH=$EBROOTGPERFTOOLS + + #------------------------------------------------------------------------------ +diff -ur OpenFOAM-4.x-version-4.1.org/etc/config.sh/metis OpenFOAM-4.x-version-4.1/etc/config.sh/metis +--- OpenFOAM-4.x-version-4.1.org/etc/config.sh/metis 2016-10-16 16:11:45.000000000 +0200 ++++ OpenFOAM-4.x-version-4.1/etc/config.sh/metis 2017-04-10 14:51:01.473221230 +0200 +@@ -34,7 +34,7 @@ + # + #------------------------------------------------------------------------------ + +-export METIS_VERSION=metis-5.1.0 +-export METIS_ARCH_PATH=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER$WM_PRECISION_OPTION$WM_LABEL_OPTION/$METIS_VERSION ++export METIS_VERSION=metis-$EBVERSIONMETIS ++export METIS_ARCH_PATH=$EBROOTMETIS + + #------------------------------------------------------------------------------ +diff -ur OpenFOAM-4.x-version-4.1.org/etc/config.sh/mpi OpenFOAM-4.x-version-4.1/etc/config.sh/mpi +--- OpenFOAM-4.x-version-4.1.org/etc/config.sh/mpi 2016-10-16 16:11:45.000000000 +0200 ++++ OpenFOAM-4.x-version-4.1/etc/config.sh/mpi 2017-04-10 14:51:01.473221230 +0200 +@@ -249,6 +249,9 @@ + _foamAddPath $MPI_ARCH_PATH/bin64 + _foamAddLib $MPI_ARCH_PATH/lib64 + ;; ++EASYBUILDMPI) ++ export FOAM_MPI=mpi ++ ;; + *) + export FOAM_MPI=dummy + ;; +diff -ur OpenFOAM-4.x-version-4.1.org/etc/config.sh/paraview OpenFOAM-4.x-version-4.1/etc/config.sh/paraview +--- OpenFOAM-4.x-version-4.1.org/etc/config.sh/paraview 2016-10-16 16:11:45.000000000 +0200 ++++ OpenFOAM-4.x-version-4.1/etc/config.sh/paraview 2017-04-10 14:51:01.473221230 +0200 +@@ -41,21 +41,6 @@ + ) \ + && PATH="$cleaned" + +-# Determine the cmake to be used +-unset CMAKE_HOME +-for cmake in cmake-3.2.1 cmake-2.8.12.1 cmake-2.8.8 cmake-2.8.4 cmake-2.8.3 \ +- cmake-2.8.1 +-do +- cmake=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER/$cmake +- if [ -r $cmake ] +- then +- export CMAKE_HOME=$cmake +- export CMAKE_ROOT=$cmake +- export PATH=$CMAKE_HOME/bin:$PATH +- break +- fi +-done +- + + #- ParaView version, automatically determine major version + #export ParaView_VERSION=3.12.0 +@@ -64,7 +49,7 @@ + #export ParaView_VERSION=4.3.1 + #export ParaView_VERSION=4.4.0 + #export ParaView_VERSION=5.0.0 +-export ParaView_VERSION=5.0.1 ++export ParaView_VERSION=$EBVERSIONPARAVIEW + export ParaView_MAJOR=detect + + +@@ -105,21 +90,15 @@ + paraviewInstDir=$WM_THIRD_PARTY_DIR/ParaView-$ParaView_VERSION + paraviewArchName=ParaView-$ParaView_VERSION + +-export ParaView_DIR=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER/$paraviewArchName ++export ParaView_DIR=$EBROOTPARAVIEW + + # Set paths if binaries or source are present + if [ -r $ParaView_DIR -o -r $paraviewInstDir ] + then + export ParaView_INCLUDE_DIR=$ParaView_DIR/include/paraview-$ParaView_MAJOR +- if [ ! -d $ParaView_INCLUDE_DIR -a -d $ParaView_DIR/include/paraview-3.0 ] +- then +- export ParaView_INCLUDE_DIR=$ParaView_DIR/include/paraview-3.0 +- fi + + ParaView_LIB_DIR=$ParaView_DIR/lib/paraview-$ParaView_MAJOR + +- export PATH=$ParaView_DIR/bin:$PATH +- export LD_LIBRARY_PATH=$ParaView_LIB_DIR:$LD_LIBRARY_PATH + export PV_PLUGIN_PATH=$FOAM_LIBBIN/paraview-$ParaView_MAJOR + + if [ "$FOAM_VERBOSE" -a "$PS1" ] +@@ -131,17 +110,6 @@ + echo " PV_PLUGIN_PATH : $PV_PLUGIN_PATH" + fi + +- # Add in python libraries if required +- paraviewPython=$ParaView_DIR/Utilities/VTKPythonWrapping +- if [ -r $paraviewPython ] +- then +- if [ "$PYTHONPATH" ] +- then +- export PYTHONPATH=$PYTHONPATH:$paraviewPython:$ParaView_LIB_DIR +- else +- export PYTHONPATH=$paraviewPython:$ParaView_LIB_DIR +- fi +- fi + else + unset PV_PLUGIN_PATH + fi +diff -ur OpenFOAM-4.x-version-4.1.org/etc/config.sh/scotch OpenFOAM-4.x-version-4.1/etc/config.sh/scotch +--- OpenFOAM-4.x-version-4.1.org/etc/config.sh/scotch 2016-10-16 16:11:45.000000000 +0200 ++++ OpenFOAM-4.x-version-4.1/etc/config.sh/scotch 2017-04-10 14:51:01.473221230 +0200 +@@ -37,7 +37,7 @@ + # + #------------------------------------------------------------------------------ + +-export SCOTCH_VERSION=scotch_6.0.3 +-export SCOTCH_ARCH_PATH=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER$WM_PRECISION_OPTION$WM_LABEL_OPTION/$SCOTCH_VERSION ++export SCOTCH_VERSION=scotch_$EBVERSIONSCOTCH ++export SCOTCH_ARCH_PATH=$EBROOTSCOTCH + + #------------------------------------------------------------------------------ +diff -ur OpenFOAM-4.x-version-4.1.org/etc/config.sh/settings OpenFOAM-4.x-version-4.1/etc/config.sh/settings +--- OpenFOAM-4.x-version-4.1.org/etc/config.sh/settings 2016-10-16 16:11:45.000000000 +0200 ++++ OpenFOAM-4.x-version-4.1/etc/config.sh/settings 2017-04-10 14:51:01.473221230 +0200 +@@ -56,11 +56,11 @@ + 64) + WM_ARCH=linux64 + export WM_COMPILER_LIB_ARCH=64 +- export WM_CC='gcc' +- export WM_CXX='g++' +- export WM_CFLAGS='-m64 -fPIC' +- export WM_CXXFLAGS='-m64 -fPIC -std=c++0x' +- export WM_LDFLAGS='-m64' ++ export WM_CC=$CC ++ export WM_CXX=$CXX ++ export WM_CFLAGS=$CFLAGS ++ export WM_CXXFLAGS=$CXXFLAGS ++ export WM_LDFLAGS=$LDFLAGS + ;; + *) + echo "Unknown WM_ARCH_OPTION '$WM_ARCH_OPTION', should be 32 or 64"\ +diff -ur OpenFOAM-4.x-version-4.1.org/src/parallel/decompose/ptscotchDecomp/Make/options OpenFOAM-4.x-version-4.1/src/parallel/decompose/ptscotchDecomp/Make/options +--- OpenFOAM-4.x-version-4.1.org/src/parallel/decompose/ptscotchDecomp/Make/options 2016-10-16 16:11:45.000000000 +0200 ++++ OpenFOAM-4.x-version-4.1/src/parallel/decompose/ptscotchDecomp/Make/options 2017-04-10 14:51:01.473221230 +0200 +@@ -3,10 +3,8 @@ + + EXE_INC = \ + $(PFLAGS) $(PINC) \ +- -I$(SCOTCH_ROOT)/include \ + -I$(SCOTCH_ARCH_PATH)/include/$(FOAM_MPI) \ +- -I/usr/include/scotch \ + -I../decompositionMethods/lnInclude + + LIB_LIBS = \ +- -L$(SCOTCH_ROOT)/lib -L$(FOAM_EXT_LIBBIN)/$(FOAM_MPI) -lptscotch -lptscotcherrexit -lscotch ${LINK_FLAGS} -lrt ++ -L$(SCOTCH_ARCH_PATH)/lib -L$(FOAM_EXT_LIBBIN)/$(FOAM_MPI) -lptscotch -lptscotcherrexit -lscotch ${LINK_FLAGS} -lrt +diff -ur OpenFOAM-4.x-version-4.1.org/src/parallel/decompose/ptscotchDecomp/ptscotchDecomp.C OpenFOAM-4.x-version-4.1/src/parallel/decompose/ptscotchDecomp/ptscotchDecomp.C +--- OpenFOAM-4.x-version-4.1.org/src/parallel/decompose/ptscotchDecomp/ptscotchDecomp.C 2016-10-16 16:11:45.000000000 +0200 ++++ OpenFOAM-4.x-version-4.1/src/parallel/decompose/ptscotchDecomp/ptscotchDecomp.C 2017-04-10 14:51:01.474221238 +0200 +@@ -30,10 +30,11 @@ + #include "globalIndex.H" + #include "SubField.H" + ++#include ++ + extern "C" + { + #include +- #include + #include "ptscotch.h" + } + +diff -ur OpenFOAM-4.x-version-4.1.org/src/parallel/decompose/scotchDecomp/Make/options OpenFOAM-4.x-version-4.1/src/parallel/decompose/scotchDecomp/Make/options +--- OpenFOAM-4.x-version-4.1.org/src/parallel/decompose/scotchDecomp/Make/options 2016-10-16 16:11:45.000000000 +0200 ++++ OpenFOAM-4.x-version-4.1/src/parallel/decompose/scotchDecomp/Make/options 2017-04-10 14:51:01.474221238 +0200 +@@ -7,10 +7,8 @@ + + EXE_INC = \ + $(PFLAGS) $(PINC) \ +- -I$(SCOTCH_ROOT)/include \ + -I$(SCOTCH_ARCH_PATH)/include \ +- -I/usr/include/scotch \ + -I../decompositionMethods/lnInclude + + LIB_LIBS = \ +- -L$(SCOTCH_ROOT)/lib -L$(FOAM_EXT_LIBBIN) -lscotch -lscotcherrexit -lrt ++ -L$(SCOTCH_ARCH_PATH)/lib -L$(FOAM_EXT_LIBBIN) -lscotch -lscotcherrexit -lrt + + diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.1-foss-2016b.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.1-foss-2016b.eb new file mode 100644 index 0000000000..efc992104f --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.1-foss-2016b.eb @@ -0,0 +1,36 @@ +name = 'OpenFOAM' +version = '4.1' + +homepage = 'http://www.openfoam.com/' +description = """OpenFOAM is a free, open source CFD software package. + OpenFOAM has an extensive range of features to solve anything from complex fluid flows + involving chemical reactions, turbulence and heat transfer, + to solid dynamics and electromagnetics.""" + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'cstd': 'c++11'} + +source_urls = ['https://github.com/OpenFOAM/OpenFOAM-%(version_major)s.x/archive'] +sources = ['version-%(version)s.tar.gz'] + +checksums = ['318a446c4ae6366c7296b61184acd37c'] + +patches = ['OpenFOAM-%(version)s-cleanup.patch'] + +dependencies = [ + ('libreadline', '6.3'), + ('ncurses', '6.0'), + # OpenFOAM requires 64 bit METIS using 32 bit indexes (array indexes) + ('METIS', '5.1.0'), + ('SCOTCH', '6.0.4'), + ('CGAL', '4.8.1'), + ('ParaView', '5.1.2', '-mpi'), +] + +builddependencies = [ + ('Bison', '3.0.4'), + ('CMake', '3.6.1'), + ('flex', '2.6.0'), +] + +moduleclass = 'cae' -- GitLab From 18dd07b9caed0bb7fe11b96ec455336759009e7b Mon Sep 17 00:00:00 2001 From: Daniel Navarro-Gomez Date: Tue, 11 Apr 2017 11:10:43 -0400 Subject: [PATCH 0592/1603] Added PLINK-1.9b_4.1-x86_64.eb --- .../p/PLINK/PLINK-1.9b_4.1-x86_64.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/p/PLINK/PLINK-1.9b_4.1-x86_64.eb diff --git a/easybuild/easyconfigs/p/PLINK/PLINK-1.9b_4.1-x86_64.eb b/easybuild/easyconfigs/p/PLINK/PLINK-1.9b_4.1-x86_64.eb new file mode 100644 index 0000000000..fdc904389a --- /dev/null +++ b/easybuild/easyconfigs/p/PLINK/PLINK-1.9b_4.1-x86_64.eb @@ -0,0 +1,30 @@ +easyblock = 'PackedBinary' + +name = 'PLINK' +version = '1.9b-4.1-x86_64' + +homepage = 'https://www.cog-genomics.org/plink/1.9/' +description = 'plink-1.9-x86_64: Whole-genome association analysis toolset' + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['plink_linux_x86_64.zip'] +source_urls = ['https://www.cog-genomics.org/static/bin/plink170330/'] + +checksums = ['27e05daa4de39a15a9c7034998a35cc4'] + +files_to_copy = [ + 'plink', + 'gPLINK.jar', + 'test.map', + 'test.ped', + 'COPYING.txt', + 'README.txt', +] + +sanity_check_paths = { + 'files': ['plink', 'prettify', 'toy.map', 'toy.ped'], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From 798ff8c32a5f67ca08f3607017b8b43ef4a3c9d5 Mon Sep 17 00:00:00 2001 From: Daniel Navarro-Gomez Date: Tue, 11 Apr 2017 13:09:51 -0400 Subject: [PATCH 0593/1603] Corrected version name --- easybuild/easyconfigs/p/PLINK/PLINK-1.9b_4.1-x86_64.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PLINK/PLINK-1.9b_4.1-x86_64.eb b/easybuild/easyconfigs/p/PLINK/PLINK-1.9b_4.1-x86_64.eb index fdc904389a..1454e1f498 100644 --- a/easybuild/easyconfigs/p/PLINK/PLINK-1.9b_4.1-x86_64.eb +++ b/easybuild/easyconfigs/p/PLINK/PLINK-1.9b_4.1-x86_64.eb @@ -1,7 +1,7 @@ easyblock = 'PackedBinary' name = 'PLINK' -version = '1.9b-4.1-x86_64' +version = '1.9b_4.1-x86_64' homepage = 'https://www.cog-genomics.org/plink/1.9/' description = 'plink-1.9-x86_64: Whole-genome association analysis toolset' -- GitLab From f2ad640fea6d4242d77456cb3899a1655a0bc73e Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 12 Apr 2017 09:08:20 +0200 Subject: [PATCH 0594/1603] R extension nloptr need the NLopt lib --- .../n/NLopt/NLopt-2.4.2-intel-2017a.eb | 26 +++++++++++++++++++ .../r/R/R-3.3.3-intel-2017a-X11-20170314.eb | 1 + 2 files changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/n/NLopt/NLopt-2.4.2-intel-2017a.eb diff --git a/easybuild/easyconfigs/n/NLopt/NLopt-2.4.2-intel-2017a.eb b/easybuild/easyconfigs/n/NLopt/NLopt-2.4.2-intel-2017a.eb new file mode 100644 index 0000000000..a614e1864e --- /dev/null +++ b/easybuild/easyconfigs/n/NLopt/NLopt-2.4.2-intel-2017a.eb @@ -0,0 +1,26 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = 'ConfigureMake' + +name = 'NLopt' +version = '2.4.2' + +homepage = 'http://ab-initio.mit.edu/wiki/index.php/NLopt' +description = """ NLopt is a free/open-source library for nonlinear optimization, + providing a common interface for a number of different free optimization routines + available online as well as original implementations of various other algorithms. """ + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['http://ab-initio.mit.edu/nlopt/'] +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': ["lib/libnlopt.a", "include/nlopt.h"], + 'dirs': [""], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170314.eb b/easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170314.eb index 7c666ff2ec..963e074572 100644 --- a/easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170314.eb +++ b/easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170314.eb @@ -43,6 +43,7 @@ dependencies = [ ('GDAL', '2.1.3', '-Python-2.7.13'), # for rgdal ('PROJ', '4.9.3'), # for rgdal ('GMP', '6.1.2'), # for igraph + ('NLopt', '2.4.2'), # for nloptr # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons # ('OpenSSL', '1.0.2h'), -- GitLab From e632d08a417cf5d687a4bfae93373ebc5ba6652b Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 12 Apr 2017 09:16:03 +0200 Subject: [PATCH 0595/1603] Build shared lib for NLopt --- easybuild/easyconfigs/n/NLopt/NLopt-2.4.2-intel-2017a.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/n/NLopt/NLopt-2.4.2-intel-2017a.eb b/easybuild/easyconfigs/n/NLopt/NLopt-2.4.2-intel-2017a.eb index a614e1864e..607bdc3f75 100644 --- a/easybuild/easyconfigs/n/NLopt/NLopt-2.4.2-intel-2017a.eb +++ b/easybuild/easyconfigs/n/NLopt/NLopt-2.4.2-intel-2017a.eb @@ -18,6 +18,8 @@ toolchain = {'name': 'intel', 'version': '2017a'} source_urls = ['http://ab-initio.mit.edu/nlopt/'] sources = [SOURCELOWER_TAR_GZ] +configopts = '--enable-shared' + sanity_check_paths = { 'files': ["lib/libnlopt.a", "include/nlopt.h"], 'dirs': [""], -- GitLab From bf0d8f6148716a4b0c12bb67c20d7d189527fb40 Mon Sep 17 00:00:00 2001 From: "Nathan S. Watson-Haigh" Date: Thu, 13 Apr 2017 06:32:52 +0930 Subject: [PATCH 0596/1603] New easyconfig for BioKanga 4.3.5 --- .../b/BioKanga/BioKanga-4.3.5-foss-2015b.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/b/BioKanga/BioKanga-4.3.5-foss-2015b.eb diff --git a/easybuild/easyconfigs/b/BioKanga/BioKanga-4.3.5-foss-2015b.eb b/easybuild/easyconfigs/b/BioKanga/BioKanga-4.3.5-foss-2015b.eb new file mode 100644 index 0000000000..c614af140d --- /dev/null +++ b/easybuild/easyconfigs/b/BioKanga/BioKanga-4.3.5-foss-2015b.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'BioKanga' +version = '4.3.5' + +homepage = 'https://github.com/csiro-crop-informatics/biokanga' +description = """BioKanga is an integrated toolkit of high performance bioinformatics + subprocesses targeting the challenges of next generation sequencing analytics. + Kanga is an acronym standing for 'K-mer Adaptive Next Generation Aligner'.""" + +toolchain = {'name': 'foss', 'version': '2015b'} + +source_urls = ['https://github.com/csiro-crop-informatics/biokanga/archive/'] +sources = ['v%(version)s.tar.gz'] + +builddependencies = [('Autotools', '20150215')] + +preconfigopts = "autoreconf -f -i && " + +sanity_check_paths = { + 'files': ["bin/biokanga"], + 'dirs': [] +} + +moduleclass = 'bio' -- GitLab From eef18915f6321f45c5224f19fddb5cc35db4db51 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Thu, 13 Apr 2017 10:42:59 +0800 Subject: [PATCH 0597/1603] adding easyconfigs: atomate-0.4.4-intel-2017a-Python-2.7.13.eb, custodian-1.1.0-intel-2017a-Python-2.7.13.eb, FireWorks-1.4.2-intel-2017a-Python-2.7.13.eb, Flask-0.12-intel-2017a-Python-2.7.13.eb, Flask-paginate-0.4.5-intel-2017a-Python-2.7.13.eb, gunicorn-19.7.1-intel-2017a-Python-2.7.13.eb, Jinja2-2.9.6-intel-2017a-Python-2.7.13.eb, matplotlib-2.0.0-intel-2017a-Python-2.7.13.eb, monty-0.9.6-intel-2017a-Python-2.7.13.eb, mpmath-0.19-intel-2017a-Python-2.7.13.eb, pymatgen-4.7.3-intel-2017a-Python-2.7.13.eb, pymatgen-db-0.6.5-intel-2017a-Python-2.7.13.eb, pymongo-3.4.0-intel-2017a-Python-2.7.13.eb, PyYAML-3.12-intel-2017a-Python-2.7.13.eb, requests-2.13.0-intel-2017a-Python-2.7.13.eb, smoqe-0.1.3-intel-2017a-Python-2.7.13.eb, spglib-python-1.9.9.38-intel-2017a-Python-2.7.13.eb, sympy-1.0-intel-2017a-Python-2.7.13.eb, Werkzeug-0.12.1-intel-2017a-Python-2.7.13.eb --- ...atomate-0.4.4-intel-2017a-Python-2.7.13.eb | 28 ++++++++++++ ...stodian-1.1.0-intel-2017a-Python-2.7.13.eb | 26 +++++++++++ ...reWorks-1.4.2-intel-2017a-Python-2.7.13.eb | 31 +++++++++++++ ...aginate-0.4.5-intel-2017a-Python-2.7.13.eb | 27 ++++++++++++ .../Flask-0.12-intel-2017a-Python-2.7.13.eb | 26 +++++++++++ ...nicorn-19.7.1-intel-2017a-Python-2.7.13.eb | 24 ++++++++++ .../Jinja2-2.9.6-intel-2017a-Python-2.7.13.eb | 24 ++++++++++ ...plotlib-2.0.0-intel-2017a-Python-2.7.13.eb | 44 +++++++++++++++++++ .../monty-0.9.6-intel-2017a-Python-2.7.13.eb | 26 +++++++++++ .../mpmath-0.19-intel-2017a-Python-2.7.13.eb | 34 ++++++++++++++ .../PyYAML-3.12-intel-2017a-Python-2.7.13.eb | 27 ++++++++++++ ...tgen-db-0.6.5-intel-2017a-Python-2.7.13.eb | 29 ++++++++++++ ...ymatgen-4.7.3-intel-2017a-Python-2.7.13.eb | 32 ++++++++++++++ ...pymongo-3.4.0-intel-2017a-Python-2.7.13.eb | 24 ++++++++++ ...quests-2.13.0-intel-2017a-Python-2.7.13.eb | 24 ++++++++++ .../smoqe-0.1.3-intel-2017a-Python-2.7.13.eb | 25 +++++++++++ ...thon-1.9.9.38-intel-2017a-Python-2.7.13.eb | 26 +++++++++++ .../sympy-1.0-intel-2017a-Python-2.7.13.eb | 33 ++++++++++++++ ...rkzeug-0.12.1-intel-2017a-Python-2.7.13.eb | 24 ++++++++++ 19 files changed, 534 insertions(+) create mode 100644 easybuild/easyconfigs/a/atomate/atomate-0.4.4-intel-2017a-Python-2.7.13.eb create mode 100644 easybuild/easyconfigs/c/custodian/custodian-1.1.0-intel-2017a-Python-2.7.13.eb create mode 100644 easybuild/easyconfigs/f/FireWorks/FireWorks-1.4.2-intel-2017a-Python-2.7.13.eb create mode 100644 easybuild/easyconfigs/f/Flask-paginate/Flask-paginate-0.4.5-intel-2017a-Python-2.7.13.eb create mode 100644 easybuild/easyconfigs/f/Flask/Flask-0.12-intel-2017a-Python-2.7.13.eb create mode 100644 easybuild/easyconfigs/g/gunicorn/gunicorn-19.7.1-intel-2017a-Python-2.7.13.eb create mode 100644 easybuild/easyconfigs/j/Jinja2/Jinja2-2.9.6-intel-2017a-Python-2.7.13.eb create mode 100644 easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.0-intel-2017a-Python-2.7.13.eb create mode 100644 easybuild/easyconfigs/m/monty/monty-0.9.6-intel-2017a-Python-2.7.13.eb create mode 100644 easybuild/easyconfigs/m/mpmath/mpmath-0.19-intel-2017a-Python-2.7.13.eb create mode 100644 easybuild/easyconfigs/p/PyYAML/PyYAML-3.12-intel-2017a-Python-2.7.13.eb create mode 100644 easybuild/easyconfigs/p/pymatgen-db/pymatgen-db-0.6.5-intel-2017a-Python-2.7.13.eb create mode 100644 easybuild/easyconfigs/p/pymatgen/pymatgen-4.7.3-intel-2017a-Python-2.7.13.eb create mode 100644 easybuild/easyconfigs/p/pymongo/pymongo-3.4.0-intel-2017a-Python-2.7.13.eb create mode 100644 easybuild/easyconfigs/r/requests/requests-2.13.0-intel-2017a-Python-2.7.13.eb create mode 100644 easybuild/easyconfigs/s/smoqe/smoqe-0.1.3-intel-2017a-Python-2.7.13.eb create mode 100644 easybuild/easyconfigs/s/spglib-python/spglib-python-1.9.9.38-intel-2017a-Python-2.7.13.eb create mode 100644 easybuild/easyconfigs/s/sympy/sympy-1.0-intel-2017a-Python-2.7.13.eb create mode 100644 easybuild/easyconfigs/w/Werkzeug/Werkzeug-0.12.1-intel-2017a-Python-2.7.13.eb diff --git a/easybuild/easyconfigs/a/atomate/atomate-0.4.4-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/a/atomate/atomate-0.4.4-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..6a33cf7fb2 --- /dev/null +++ b/easybuild/easyconfigs/a/atomate/atomate-0.4.4-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,28 @@ +easyblock = "PythonPackage" + +name = 'atomate' +version = '0.4.4' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pythonhosted.org/atomate/' +description = """atomate has implementations of FireWorks workflows for Materials Science.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.13'), + ('FireWorks', '1.4.2', versionsuffix), + ('custodian', '1.1.0', versionsuffix), + ('pymatgen', '4.7.3', versionsuffix), + ('pymatgen-db', '0.6.5', versionsuffix), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'] +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/c/custodian/custodian-1.1.0-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/c/custodian/custodian-1.1.0-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..45b7389451 --- /dev/null +++ b/easybuild/easyconfigs/c/custodian/custodian-1.1.0-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,26 @@ +easyblock = "PythonPackage" + +name = 'custodian' +version = '1.1.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pypi.python.org/pypi/custodian' +description = """A simple JIT job management framework in Python.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.13'), + ('PyYAML', '3.12', versionsuffix), + ('monty', '0.9.6', versionsuffix), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/f/FireWorks/FireWorks-1.4.2-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/f/FireWorks/FireWorks-1.4.2-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..526b35054c --- /dev/null +++ b/easybuild/easyconfigs/f/FireWorks/FireWorks-1.4.2-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,31 @@ +easyblock = "PythonPackage" + +name = 'FireWorks' +version = '1.4.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pypi.python.org/pypi/FireWorks' +description = """FireWorks helps run calculation workflows, with a centralized workflow server + controlling many worker nodes.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.13'), + ('Flask', '0.12', versionsuffix), + ('Flask-paginate', '0.4.5', versionsuffix), + ('PyYAML', '3.12', versionsuffix), + ('gunicorn', '19.7.1', versionsuffix), + ('monty', '0.9.6', versionsuffix), + ('pymongo', '3.4.0', versionsuffix), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/f/Flask-paginate/Flask-paginate-0.4.5-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/f/Flask-paginate/Flask-paginate-0.4.5-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..153e1028fe --- /dev/null +++ b/easybuild/easyconfigs/f/Flask-paginate/Flask-paginate-0.4.5-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,27 @@ +easyblock = "PythonPackage" + +name = 'Flask-paginate' +version = '0.4.5' +versionsuffix = '-Python-%(pyver)s' + +homepage = "https://pypi.python.org/pypi/Flask-paginate" +description = """Simple paginate support for flask.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCELOWER_ZIP] + +dependencies = [ + ('Python', '2.7.13'), + ('Flask', '0.12', versionsuffix), +] + +options = {'modulename': 'flask_paginate'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/f/Flask/Flask-0.12-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/f/Flask/Flask-0.12-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..b305d04f47 --- /dev/null +++ b/easybuild/easyconfigs/f/Flask/Flask-0.12-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,26 @@ +easyblock = "PythonPackage" + +name = 'Flask' +version = '0.12' +versionsuffix = '-Python-%(pyver)s' + +homepage = "https://pypi.python.org/pypi/Flask" +description = """A microframework based on Werkzeug, Jinja2 and good intentions.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.13'), + ('Jinja2', '2.9.6', versionsuffix), + ('Werkzeug', '0.12.1', versionsuffix), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/gunicorn/gunicorn-19.7.1-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/g/gunicorn/gunicorn-19.7.1-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..6e2be6854a --- /dev/null +++ b/easybuild/easyconfigs/g/gunicorn/gunicorn-19.7.1-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,24 @@ +easyblock = "PythonPackage" + +name = 'gunicorn' +version = '19.7.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = "https://pypi.python.org/pypi/gunicorn" +description = """WSGI HTTP Server for UNIX.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.13'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/j/Jinja2/Jinja2-2.9.6-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/j/Jinja2/Jinja2-2.9.6-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..0069b2587c --- /dev/null +++ b/easybuild/easyconfigs/j/Jinja2/Jinja2-2.9.6-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,24 @@ +easyblock = "PythonPackage" + +name = 'Jinja2' +version = '2.9.6' +versionsuffix = '-Python-%(pyver)s' + +homepage = "https://pypi.python.org/pypi/Jinja2" +description = """A small but fast and easy to use stand-alone template engine written in pure python.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.13'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.0-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.0-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..4cff5e718d --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.0-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,44 @@ +easyblock = 'Bundle' + +name = 'matplotlib' +version = '2.0.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://matplotlib.org' +description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of + hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python + and ipython shell, web application servers, and six graphical user interface toolkits.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' + +dependencies = [ + ('Python', '2.7.13'), + ('freetype', '2.7.1'), + ('libpng', '1.6.29'), +] + +exts_list = [ + ('Cycler', '0.10.0', { + 'modulename': 'cycler', + 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], + 'source_tmpl': 'cycler-%(version)s.tar.gz', + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], + }), +] + +# specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module +full_sanity_check = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/monty/monty-0.9.6-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/m/monty/monty-0.9.6-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..64c36ac39f --- /dev/null +++ b/easybuild/easyconfigs/m/monty/monty-0.9.6-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'monty' +version = '0.9.6' +versionsuffix = '-Python-%(pyver)s' + +homepage = "https://pypi.python.org/pypi/monty/" +description = """Monty implements supplementary useful functions for Python that are not part of the standard library. + Examples include useful utilities like transparent support for zipped files, useful design patterns such as singleton + and cached_class, and many more.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.13'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s-%(version)s-py%(pyshortver)s.egg'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/mpmath/mpmath-0.19-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/m/mpmath/mpmath-0.19-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..db5a0e5289 --- /dev/null +++ b/easybuild/easyconfigs/m/mpmath/mpmath-0.19-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,34 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Author: Adam Huffman +# adam.huffman@crick.ac.uk +# The Francis Crick Institute + +easyblock = 'PythonPackage' + +name = 'mpmath' +version = '0.19' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://mpmath.org/' +description = """mpmath can be used as an arbitrary-precision substitute for Python's float/complex + types and math/cmath modules, but also does much more advanced mathematics. Almost any calculation + can be performed just as well at 10-digit or 1000-digit precision, with either real or complex + numbers, and in many cases mpmath implements efficient algorithms that scale well for extremely + high precision work.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['https://github.com/fredrik-johansson/mpmath/archive/'] +sources = ['%(version)s.tar.gz'] + +dependencies = [('Python', '2.7.13')] + +runtest = 'python -c "import mpmath; mpmath.runtests();"' + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/mpmath'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..4ff041f5c0 --- /dev/null +++ b/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'PyYAML' +version = '3.12' +versionsuffix = '-Python-%(pyver)s' + +homepage = "https://pypi.python.org/pypi/PyYAML/" +description = """PyYAML is a YAML parser and emitter for the Python programming language.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.13'), + ('libyaml', '0.1.7'), +] + +options = {'modulename': 'yaml'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/pymatgen-db/pymatgen-db-0.6.5-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/p/pymatgen-db/pymatgen-db-0.6.5-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..908d8b8ff5 --- /dev/null +++ b/easybuild/easyconfigs/p/pymatgen-db/pymatgen-db-0.6.5-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,29 @@ +easyblock = "PythonPackage" + +name = 'pymatgen-db' +version = '0.6.5' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pypi.python.org/pypi/pymatgen-db' +description = """Pymatgen-db is a database add-on for the Python Materials Genomics (pymatgen) + materials analysis library.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.13'), + ('pymatgen', '4.7.3', versionsuffix), + ('smoqe', '0.1.3', versionsuffix), +] + +options = {'modulename': 'matgendb'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'] +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/p/pymatgen/pymatgen-4.7.3-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/p/pymatgen/pymatgen-4.7.3-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..f8b263a2dd --- /dev/null +++ b/easybuild/easyconfigs/p/pymatgen/pymatgen-4.7.3-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonPackage' + +name = 'pymatgen' +version = '4.7.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pypi.python.org/pypi/pymatgen' +description = """Python Materials Genomics is a robust materials analysis code that defines core object + representations for structures and molecules with support for many electronic structure codes.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.13'), + ('PyYAML', '3.12', versionsuffix), + ('matplotlib', '2.0.0', versionsuffix), + ('monty', '0.9.6', versionsuffix), + ('mpmath', '0.19', versionsuffix), + ('requests', '2.13.0', versionsuffix), + ('spglib-python', '1.9.9.38', versionsuffix), + ('sympy', '1.0', versionsuffix), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'] +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/p/pymongo/pymongo-3.4.0-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/p/pymongo/pymongo-3.4.0-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..9bb19f1090 --- /dev/null +++ b/easybuild/easyconfigs/p/pymongo/pymongo-3.4.0-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'pymongo' +version = '3.4.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pypi.python.org/pypi/pymongo' +description = """Python driver for MongoDB.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('Python', '2.7.13'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/r/requests/requests-2.13.0-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/r/requests/requests-2.13.0-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..786bbdf2c6 --- /dev/null +++ b/easybuild/easyconfigs/r/requests/requests-2.13.0-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'requests' +version = '2.13.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pypi.python.org/pypi/requests' +description = """Python http for humans.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('Python', '2.7.13'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/smoqe/smoqe-0.1.3-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/s/smoqe/smoqe-0.1.3-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..a5ff78eb95 --- /dev/null +++ b/easybuild/easyconfigs/s/smoqe/smoqe-0.1.3-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'smoqe' +version = '0.1.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pypi.python.org/pypi/smoqe' +description = """Simple MongoDB Query Engine (SMoQE).""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('Python', '2.7.13'), + ('pymongo', '3.4.0', versionsuffix), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/spglib-python/spglib-python-1.9.9.38-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/s/spglib-python/spglib-python-1.9.9.38-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..6c2b70d3f7 --- /dev/null +++ b/easybuild/easyconfigs/s/spglib-python/spglib-python-1.9.9.38-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'spglib-python' +version = '1.9.9.38' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pypi.python.org/pypi/spglib' +description = """Spglib for Python. Spglib is a library for finding and handling crystal symmetries written in C.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['https://pypi.python.org/packages/source/%(nameletter)s/spglib'] +sources = ['spglib-%(version)s.tar.gz'] + +dependencies = [ + ('Python', '2.7.13'), +] + +options = {'modulename': 'spglib'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'] +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/s/sympy/sympy-1.0-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/s/sympy/sympy-1.0-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..444574067c --- /dev/null +++ b/easybuild/easyconfigs/s/sympy/sympy-1.0-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonPackage' + +name = 'sympy' +version = '1.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://sympy.org/' +description = """SymPy is a Python library for symbolic mathematics. It aims to + become a full-featured computer algebra system (CAS) while keeping the code as + simple as possible in order to be comprehensible and easily extensible. SymPy + is written entirely in Python and does not require any external libraries.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +# patch to fix tests +patches = ['sympy-1.0_tests-unicode.patch'] + +dependencies = [ + ('Python', '2.7.13'), + ('mpmath', '0.19', '-Python-%(pyver)s'), +] + +# runtest = 'python setup.py test' + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s-%(version)s-py%(pyshortver)s.egg/%(name)s'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/w/Werkzeug/Werkzeug-0.12.1-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/w/Werkzeug/Werkzeug-0.12.1-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..9f007d3773 --- /dev/null +++ b/easybuild/easyconfigs/w/Werkzeug/Werkzeug-0.12.1-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,24 @@ +easyblock = "PythonPackage" + +name = 'Werkzeug' +version = '0.12.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = "https://pypi.python.org/pypi/WerkZeug" +description = """The Swiss Army knife of Python web development.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.13'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'devel' -- GitLab From e64a152e2eba52d015850c2cf549afd467ca0f49 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Thu, 13 Apr 2017 11:18:23 +0800 Subject: [PATCH 0598/1603] use existing libyaml with dummy toolchain --- .../p/PyYAML/PyYAML-3.12-intel-2017a-Python-2.7.13.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12-intel-2017a-Python-2.7.13.eb index 4ff041f5c0..73b6477407 100644 --- a/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12-intel-2017a-Python-2.7.13.eb @@ -14,7 +14,7 @@ sources = [SOURCE_TAR_GZ] dependencies = [ ('Python', '2.7.13'), - ('libyaml', '0.1.7'), + ('libyaml', '0.1.7', '', True), ] options = {'modulename': 'yaml'} -- GitLab From 23807849f1af83d3d0520249a6694f0317f8515f Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Thu, 13 Apr 2017 13:13:48 +0800 Subject: [PATCH 0599/1603] remove libpng from matplotlib dependencies (already a dependency of freetype) --- .../m/matplotlib/matplotlib-2.0.0-intel-2017a-Python-2.7.13.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.0-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.0-intel-2017a-Python-2.7.13.eb index 4cff5e718d..e00702b768 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.0-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.0-intel-2017a-Python-2.7.13.eb @@ -17,7 +17,6 @@ exts_defaultclass = 'PythonPackage' dependencies = [ ('Python', '2.7.13'), ('freetype', '2.7.1'), - ('libpng', '1.6.29'), ] exts_list = [ -- GitLab From 86b92838f0b3009d1ec12ffc53e2b7f6993d0974 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Thu, 13 Apr 2017 10:20:31 +0100 Subject: [PATCH 0600/1603] Fix libpng version conflict --- easybuild/easyconfigs/g/gnuplot/gnuplot-5.0.5-foss-2016b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/gnuplot/gnuplot-5.0.5-foss-2016b.eb b/easybuild/easyconfigs/g/gnuplot/gnuplot-5.0.5-foss-2016b.eb index 52cec88efd..20416b1946 100755 --- a/easybuild/easyconfigs/g/gnuplot/gnuplot-5.0.5-foss-2016b.eb +++ b/easybuild/easyconfigs/g/gnuplot/gnuplot-5.0.5-foss-2016b.eb @@ -25,7 +25,7 @@ source_urls = [('http://sourceforge.net/projects/gnuplot/files', 'download')] dependencies = [ ('cairo', '1.14.6'), ('libjpeg-turbo', '1.5.0'), - ('libpng', '1.6.26'), + ('libpng', '1.6.24'), ('libgd', '2.2.3'), ('Pango', '1.40.3'), ('libcerf', '1.5'), -- GitLab From 08e498cb5cc4bf318ed4660616330eb391c4b42c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 18 Apr 2017 11:49:10 +0200 Subject: [PATCH 0601/1603] adding easyconfigs: bx-python-0.7.4-intel-2017a-Python-2.7.13.eb, LZO-2.10-intel-2017a.eb --- ...-python-0.7.4-intel-2017a-Python-2.7.13.eb | 47 +++++++++++++++++++ .../easyconfigs/l/LZO/LZO-2.10-intel-2017a.eb | 31 ++++++++++++ 2 files changed, 78 insertions(+) create mode 100644 easybuild/easyconfigs/b/bx-python/bx-python-0.7.4-intel-2017a-Python-2.7.13.eb create mode 100644 easybuild/easyconfigs/l/LZO/LZO-2.10-intel-2017a.eb diff --git a/easybuild/easyconfigs/b/bx-python/bx-python-0.7.4-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/b/bx-python/bx-python-0.7.4-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..8f02847ea1 --- /dev/null +++ b/easybuild/easyconfigs/b/bx-python/bx-python-0.7.4-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,47 @@ +easyblock = 'Bundle' + +name = 'bx-python' +version = '0.7.4' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/bxlab/bx-python' +description = """The bx-python project is a Python library and associated set of scripts to allow for rapid + implementation of genome scale analyses.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + + +dependencies = [ + ('Python', '2.7.13'), + ('LZO', '2.10'), +] + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' + +prebuildopts = "export CPATH=$EBROOTLZO/include/lzo:$CPATH && " + +exts_list = [ + ('python-lzo', '1.11', { + 'modulename': 'lzo', + 'source_urls': ['https://pypi.python.org/packages/source/p/python-lzo/'], + 'source_tmpl': 'python-lzo-%(version)s.tar.gz', + }), + (name, version, { + 'modulename': 'bx', + 'source_urls': ['https://github.com/bxlab/bx-python/archive/'], + 'source_tmpl': 'v%(version)s.tar.gz', + }), +] + +# specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module +full_sanity_check = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['bin', 'lib/python%(pyshortver)s/site-packages'], +} + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/l/LZO/LZO-2.10-intel-2017a.eb b/easybuild/easyconfigs/l/LZO/LZO-2.10-intel-2017a.eb new file mode 100644 index 0000000000..801057a84f --- /dev/null +++ b/easybuild/easyconfigs/l/LZO/LZO-2.10-intel-2017a.eb @@ -0,0 +1,31 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +## + +easyblock = 'ConfigureMake' + +name = 'LZO' +version = '2.10' + +homepage = 'http://www.oberhumer.com/opensource/lzo/' +description = "Portable lossless data compression library" + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [homepage + 'download/'] + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True} + +runtest = 'test' + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib', 'include'] +} + +moduleclass = 'devel' -- GitLab From ffa2d8c231fe75d6527db2440b07d8f50b250975 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 18 Apr 2017 13:14:06 +0200 Subject: [PATCH 0602/1603] {math}[intel/2016b] scipy 0.19.0 + numpy 1.12.1 w/ Python 3.5.2 --- .../n/numpy/numpy-1.12.0-mkl.patch | 55 +++++++++++++++++++ .../numpy-1.12.1-intel-2016b-Python-3.5.2.eb | 23 ++++++++ .../scipy-0.19.0-intel-2016b-Python-3.5.2.eb | 19 +++++++ 3 files changed, 97 insertions(+) create mode 100644 easybuild/easyconfigs/n/numpy/numpy-1.12.0-mkl.patch create mode 100644 easybuild/easyconfigs/n/numpy/numpy-1.12.1-intel-2016b-Python-3.5.2.eb create mode 100644 easybuild/easyconfigs/s/scipy/scipy-0.19.0-intel-2016b-Python-3.5.2.eb diff --git a/easybuild/easyconfigs/n/numpy/numpy-1.12.0-mkl.patch b/easybuild/easyconfigs/n/numpy/numpy-1.12.0-mkl.patch new file mode 100644 index 0000000000..3d09924f96 --- /dev/null +++ b/easybuild/easyconfigs/n/numpy/numpy-1.12.0-mkl.patch @@ -0,0 +1,55 @@ +fix issues in numpy distutils pkg w.r.t. detecting BLAS/LAPACK libraries +by Kenneth Hoste (HPC-UGent) +diff -ru numpy-1.12.0.orig/numpy/distutils/fcompiler/__init__.py numpy-1.12.0/numpy/distutils/fcompiler/__init__.py +--- numpy-1.12.0.orig/numpy/distutils/fcompiler/__init__.py 2017-01-15 11:39:18.000000000 +0100 ++++ numpy-1.12.0/numpy/distutils/fcompiler/__init__.py 2017-03-06 17:19:07.262810683 +0100 +@@ -628,7 +628,10 @@ + return options + + def library_option(self, lib): +- return "-l" + lib ++ if lib[0]=='-': ++ return lib ++ else: ++ return "-l" + lib + def library_dir_option(self, dir): + return "-L" + dir + +diff -ru numpy-1.12.0.orig/numpy/distutils/system_info.py numpy-1.12.0/numpy/distutils/system_info.py +--- numpy-1.12.0.orig/numpy/distutils/system_info.py 2017-01-15 11:39:18.000000000 +0100 ++++ numpy-1.12.0/numpy/distutils/system_info.py 2017-03-06 17:25:38.778143748 +0100 +@@ -675,7 +675,7 @@ + if is_string(default): + return [default] + return default +- return [b for b in [a.strip() for a in libs.split(',')] if b] ++ return [b for b in [a.strip().replace(':',',') for a in libs.split(',')] if b] + + def get_libraries(self, key='libraries'): + if hasattr(self, '_lib_names'): +@@ -756,6 +756,9 @@ + # make sure we preserve the order of libs, as it can be important + found_dirs, found_libs = [], [] + for lib in libs: ++ if lib[0] == '-': ++ found_libs.append(lib) ++ continue + for lib_dir in lib_dirs: + found_lib = self._find_lib(lib_dir, lib, exts) + if found_lib: +diff -ru numpy-1.12.0.orig/numpy/distutils/unixccompiler.py numpy-1.12.0/numpy/distutils/unixccompiler.py +--- numpy-1.12.0.orig/numpy/distutils/unixccompiler.py 2016-12-21 16:46:24.000000000 +0100 ++++ numpy-1.12.0/numpy/distutils/unixccompiler.py 2017-03-06 17:19:07.262810683 +0100 +@@ -123,3 +123,12 @@ + + replace_method(UnixCCompiler, 'create_static_lib', + UnixCCompiler_create_static_lib) ++ ++def UnixCCompiler_library_option(self, lib): ++ if lib[0]=='-': ++ return lib ++ else: ++ return "-l" + lib ++ ++replace_method(UnixCCompiler, 'library_option', ++ UnixCCompiler_library_option) diff --git a/easybuild/easyconfigs/n/numpy/numpy-1.12.1-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/n/numpy/numpy-1.12.1-intel-2016b-Python-3.5.2.eb new file mode 100644 index 0000000000..b83a080a7d --- /dev/null +++ b/easybuild/easyconfigs/n/numpy/numpy-1.12.1-intel-2016b-Python-3.5.2.eb @@ -0,0 +1,23 @@ +name = 'numpy' +version = '1.12.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.numpy.org' +description = """NumPy is the fundamental package for scientific computing with Python. It contains among other things: + a powerful N-dimensional array object, sophisticated (broadcasting) functions, tools for integrating C/C++ and Fortran + code, useful linear algebra, Fourier transform, and random number capabilities. Besides its obvious scientific uses, + NumPy can also be used as an efficient multi-dimensional container of generic data. Arbitrary data-types can be + defined. This allows NumPy to seamlessly and speedily integrate with a wide variety of databases.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_ZIP] + +patches = ['numpy-1.12.0-mkl.patch'] + +dependencies = [ + ('Python', '3.5.2'), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/scipy/scipy-0.19.0-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/s/scipy/scipy-0.19.0-intel-2016b-Python-3.5.2.eb new file mode 100644 index 0000000000..523cf018d9 --- /dev/null +++ b/easybuild/easyconfigs/s/scipy/scipy-0.19.0-intel-2016b-Python-3.5.2.eb @@ -0,0 +1,19 @@ +name = 'scipy' +version = '0.19.0' +versionsuffix = '-Python-3.5.2' + +homepage = 'http://www.scipy.org' +description = """SciPy is a collection of mathematical algorithms and convenience + functions built on the Numpy extension for Python.""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'pic': True} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_ZIP] + +dependencies = [ + ('numpy', '1.12.1', versionsuffix), +] + +moduleclass = 'math' -- GitLab From e085c578bfb1eac166f793d1b1877a36059d0491 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 18 Apr 2017 13:17:35 +0200 Subject: [PATCH 0603/1603] adding easyconfigs: Stacks-1.46-intel-2017a.eb, sparsehash-2.0.3-intel-2017a.eb --- .../s/Stacks/Stacks-1.46-intel-2017a.eb | 35 +++++++++++++++++++ .../sparsehash-2.0.3-intel-2017a.eb | 23 ++++++++++++ 2 files changed, 58 insertions(+) create mode 100644 easybuild/easyconfigs/s/Stacks/Stacks-1.46-intel-2017a.eb create mode 100644 easybuild/easyconfigs/s/sparsehash/sparsehash-2.0.3-intel-2017a.eb diff --git a/easybuild/easyconfigs/s/Stacks/Stacks-1.46-intel-2017a.eb b/easybuild/easyconfigs/s/Stacks/Stacks-1.46-intel-2017a.eb new file mode 100644 index 0000000000..341b4db710 --- /dev/null +++ b/easybuild/easyconfigs/s/Stacks/Stacks-1.46-intel-2017a.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'Stacks' +version = '1.46' + +homepage = 'http://creskolab.uoregon.edu/stacks/' +description = """Stacks is a software pipeline for building loci from short-read sequences, such as those generated on + the Illumina platform. Stacks was developed to work with restriction enzyme-based data, such as RAD-seq, + for the purpose of building genetic maps and conducting population genomics and phylogeography. +""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['http://catchenlab.life.illinois.edu/stacks/source/'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('zlib', '1.2.11'), + ('SAMtools', '1.4'), + ('sparsehash', '2.0.3'), +] + +sanity_check_paths = { + 'files': [ + 'bin/%s' % binfile for binfile in [ + 'clone_filter', 'denovo_map.pl', 'exec_velvet.pl', 'genotypes', 'index_radtags.pl', 'load_radtags.pl', + 'populations', 'process_shortreads', 'ref_map.pl', 'sstacks', 'ustacks', 'cstacks', 'estacks', + 'export_sql.pl', 'hstacks', 'kmer_filter', 'load_sequences.pl', 'process_radtags', 'pstacks', + 'sort_read_pairs.pl', 'stacks_export_notify.pl', + ] + ], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/sparsehash/sparsehash-2.0.3-intel-2017a.eb b/easybuild/easyconfigs/s/sparsehash/sparsehash-2.0.3-intel-2017a.eb new file mode 100644 index 0000000000..32f208ded5 --- /dev/null +++ b/easybuild/easyconfigs/s/sparsehash/sparsehash-2.0.3-intel-2017a.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'sparsehash' +version = '2.0.3' + +homepage = 'https://github.com/sparsehash/sparsehash' +description = """An extremely memory-efficient hash_map + implementation. 2 bits/entry overhead! The SparseHash library + contains several hash-map implementations, including + implementations that optimize for space or speed.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/sparsehash/sparsehash/archive/'] +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': ['include/google/type_traits.h'], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From 28cf85302f91dcc01e4e373f8d7a8b84ee9a0aff Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 19 Apr 2017 10:08:35 +0200 Subject: [PATCH 0604/1603] adding easyconfigs: MRtrix-0.3.15-intel-2016b-Python-2.7.12.eb, Eigen-3.2.10-intel-2016b.eb --- ...MRtrix-0.3.15-intel-2016b-Python-2.7.12.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/m/MRtrix/MRtrix-0.3.15-intel-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/m/MRtrix/MRtrix-0.3.15-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/m/MRtrix/MRtrix-0.3.15-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..bfa4a70408 --- /dev/null +++ b/easybuild/easyconfigs/m/MRtrix/MRtrix-0.3.15-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,23 @@ +name = 'MRtrix' +version = '0.3.15' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.brain.org.au/software/index.html#mrtrix' +description = """MRtrix provides a set of tools to perform diffusion-weighted MR white-matter tractography in a manner + robust to crossing fibres, using constrained spherical deconvolution (CSD) and probabilistic streamlines.""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'cstd': 'c++11'} + +source_urls = ['https://github.com/MRtrix3/mrtrix3/archive/'] +sources = ['%(version)s.tar.gz'] + +dependencies = [ + ('zlib', '1.2.8'), + ('Python', '2.7.12'), + ('Mesa', '12.0.2'), + ('Qt', '4.8.7'), + ('Eigen', '3.2.10'), +] + +moduleclass = 'bio' -- GitLab From 3ce4bc6da6754819d8706ff8d011551ddc02dbfc Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 19 Apr 2017 13:03:43 +0200 Subject: [PATCH 0605/1603] Add CUDA/8.0.61 --- .../c/CUDA/CUDA-8.0.61-GCCcore-6.3.0.eb | 18 ++++++++++++++++++ easybuild/easyconfigs/c/CUDA/CUDA-8.0.61.eb | 18 ++++++++++++++++++ 2 files changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/c/CUDA/CUDA-8.0.61-GCCcore-6.3.0.eb create mode 100644 easybuild/easyconfigs/c/CUDA/CUDA-8.0.61.eb diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-8.0.61-GCCcore-6.3.0.eb b/easybuild/easyconfigs/c/CUDA/CUDA-8.0.61-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..02ed53d7d5 --- /dev/null +++ b/easybuild/easyconfigs/c/CUDA/CUDA-8.0.61-GCCcore-6.3.0.eb @@ -0,0 +1,18 @@ +name = 'CUDA' +version = '8.0.61' + +homepage = 'https://developer.nvidia.com/cuda-toolkit' +description = """CUDA (formerly Compute Unified Device Architecture) is a parallel + computing platform and programming model created by NVIDIA and implemented by the + graphics processing units (GPUs) that they produce. CUDA gives developers access + to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs.""" + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} + +source_urls = ['https://developer.nvidia.com/compute/cuda/%(version_major_minor)s/Prod2/local_installers/'] + +sources = ['cuda_%(version)s_375.26_linux-run'] + +modextravars = {'CUDA_HOME': '%(installdir)s'} + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-8.0.61.eb b/easybuild/easyconfigs/c/CUDA/CUDA-8.0.61.eb new file mode 100644 index 0000000000..b3ad585f70 --- /dev/null +++ b/easybuild/easyconfigs/c/CUDA/CUDA-8.0.61.eb @@ -0,0 +1,18 @@ +name = 'CUDA' +version = '8.0.61' + +homepage = 'https://developer.nvidia.com/cuda-toolkit' +description = """CUDA (formerly Compute Unified Device Architecture) is a parallel + computing platform and programming model created by NVIDIA and implemented by the + graphics processing units (GPUs) that they produce. CUDA gives developers access + to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['https://developer.nvidia.com/compute/cuda/%(version_major_minor)s/Prod2/local_installers/'] + +sources = ['cuda_%(version)s_375.26_linux-run'] + +modextravars = {'CUDA_HOME': '%(installdir)s'} + +moduleclass = 'system' -- GitLab From 8307b771d0e3d26a65a442d1e3c761ccb7bdb934 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 19 Apr 2017 13:14:31 +0200 Subject: [PATCH 0606/1603] Drop Cuda easyconfig with unsupported GCC --- .../c/CUDA/CUDA-8.0.61-GCCcore-6.3.0.eb | 18 ------------------ 1 file changed, 18 deletions(-) delete mode 100644 easybuild/easyconfigs/c/CUDA/CUDA-8.0.61-GCCcore-6.3.0.eb diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-8.0.61-GCCcore-6.3.0.eb b/easybuild/easyconfigs/c/CUDA/CUDA-8.0.61-GCCcore-6.3.0.eb deleted file mode 100644 index 02ed53d7d5..0000000000 --- a/easybuild/easyconfigs/c/CUDA/CUDA-8.0.61-GCCcore-6.3.0.eb +++ /dev/null @@ -1,18 +0,0 @@ -name = 'CUDA' -version = '8.0.61' - -homepage = 'https://developer.nvidia.com/cuda-toolkit' -description = """CUDA (formerly Compute Unified Device Architecture) is a parallel - computing platform and programming model created by NVIDIA and implemented by the - graphics processing units (GPUs) that they produce. CUDA gives developers access - to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs.""" - -toolchain = {'name': 'GCCcore', 'version': '6.3.0'} - -source_urls = ['https://developer.nvidia.com/compute/cuda/%(version_major_minor)s/Prod2/local_installers/'] - -sources = ['cuda_%(version)s_375.26_linux-run'] - -modextravars = {'CUDA_HOME': '%(installdir)s'} - -moduleclass = 'system' -- GitLab From ad01055ce5e98a5dce7f62d59d7bfd360355cf18 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 19 Apr 2017 13:53:42 +0200 Subject: [PATCH 0607/1603] adding easyconfigs: JasPer-1.900.1-intel-2017a.eb --- .../j/JasPer/JasPer-1.900.1-intel-2017a.eb | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-intel-2017a.eb diff --git a/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-intel-2017a.eb b/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-intel-2017a.eb new file mode 100644 index 0000000000..80e537b9bb --- /dev/null +++ b/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-intel-2017a.eb @@ -0,0 +1,21 @@ +easyblock = 'ConfigureMake' + +name = 'JasPer' +version = '1.900.1' + +homepage = 'http://www.ece.uvic.ca/~frodo/jasper/' +description = """The JasPer Project is an open-source initiative to provide a free + software-based reference implementation of the codec specified in the JPEG-2000 Part-1 standard.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_ZIP] +source_urls = ['http://www.ece.uvic.ca/~frodo/jasper/software/'] + +sanity_check_paths = { + 'files': ["bin/jasper", "lib/libjasper.a"], + 'dirs': ["include"], +} + +moduleclass = 'vis' -- GitLab From 98c8fa75eab423831af2b64676302a7ab477997f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 19 Apr 2017 13:54:13 +0200 Subject: [PATCH 0608/1603] adding easyconfigs: makedepend-1.0.5-GCCcore-6.3.0.eb, xorg-macros-1.19.1-GCCcore-6.3.0.eb, xproto-7.0.31-GCCcore-6.3.0.eb --- .../makedepend-1.0.5-GCCcore-6.3.0.eb | 26 +++++++++++++++++ .../xorg-macros-1.19.1-GCCcore-6.3.0.eb | 27 +++++++++++++++++ .../x/xproto/xproto-7.0.31-GCCcore-6.3.0.eb | 29 +++++++++++++++++++ 3 files changed, 82 insertions(+) create mode 100644 easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-GCCcore-6.3.0.eb create mode 100755 easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.1-GCCcore-6.3.0.eb create mode 100644 easybuild/easyconfigs/x/xproto/xproto-7.0.31-GCCcore-6.3.0.eb diff --git a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-GCCcore-6.3.0.eb b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..b7d5d70c2d --- /dev/null +++ b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-GCCcore-6.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'makedepend' +version = '1.0.5' + +homepage = "http://www.linuxfromscratch.org/blfs/view/svn/x/makedepend.html" +description = "The makedepend package contains a C-preprocessor like utility to determine build-time dependencies." + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_UTIL_SOURCE] + +builddependencies = [ + # use same binutils version that was used when building GCC toolchain + ('binutils', '2.27', '', True), + ('xproto', '7.0.31'), + ('xorg-macros', '1.19.1'), +] + +sanity_check_paths = { + 'files': ['bin/makedepend'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.1-GCCcore-6.3.0.eb b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.1-GCCcore-6.3.0.eb new file mode 100755 index 0000000000..6f48acb154 --- /dev/null +++ b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.1-GCCcore-6.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'xorg-macros' +version = '1.19.1' + +homepage = 'http://cgit.freedesktop.org/xorg/util/macros' +description = """X.org macros utilities.""" + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} + +source_urls = ['http://cgit.freedesktop.org/xorg/util/macros/snapshot'] # no slash ('/') at the end! +sources = ['util-macros-%(version)s.tar.gz'] + +builddependencies = [ + # use same binutils version that was used when building GCC toolchain + ('binutils', '2.27', '', True), + ('Autotools', '20150215'), +] + +preconfigopts = './autogen.sh && ' + +sanity_check_paths = { + 'files': ['share/pkgconfig/xorg-macros.pc'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/xproto/xproto-7.0.31-GCCcore-6.3.0.eb b/easybuild/easyconfigs/x/xproto/xproto-7.0.31-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..06e2a620f7 --- /dev/null +++ b/easybuild/easyconfigs/x/xproto/xproto-7.0.31-GCCcore-6.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'xproto' +version = '7.0.31' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = "X protocol and ancillary headers" + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_PROTO_SOURCE] + +builddependencies = [ + # use same binutils version that was used when building GCC toolchain + ('binutils', '2.27', '', True), + ('xorg-macros', '1.19.1'), +] + +sanity_check_paths = { + 'files': ['include/X11/%s' % x for x in ['ap_keysym.h', 'HPkeysym.h', 'keysym.h', 'Xalloca.h', 'Xatom.h', + 'XF86keysym.h', 'Xfuncs.h', 'Xmd.h', 'Xos.h', 'Xpoll.h', 'Xprotostr.h', + 'Xw32defs.h', 'Xwindows.h', 'DECkeysym.h', 'keysymdef.h', 'Sunkeysym.h', + 'Xarch.h', 'Xdefs.h', 'Xfuncproto.h', 'X.h', 'Xosdefs.h', 'Xos_r.h', + 'Xproto.h', 'Xthreads.h', 'XWDFile.h', 'Xwinsock.h']], + 'dirs': [] +} + +moduleclass = 'devel' -- GitLab From e4c9596d4b47c878879c7413a42508d5bd897b29 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 19 Apr 2017 13:58:21 +0200 Subject: [PATCH 0609/1603] adding easyconfigs: cURL-7.54.0-GCCcore-6.3.0.eb --- .../c/cURL/cURL-7.54.0-GCCcore-6.3.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/c/cURL/cURL-7.54.0-GCCcore-6.3.0.eb diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.54.0-GCCcore-6.3.0.eb b/easybuild/easyconfigs/c/cURL/cURL-7.54.0-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..8d7f087e2b --- /dev/null +++ b/easybuild/easyconfigs/c/cURL/cURL-7.54.0-GCCcore-6.3.0.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'cURL' +version = '7.54.0' + +homepage = 'http://curl.haxx.se' +description = """libcurl is a free and easy-to-use client-side URL transfer library, + supporting DICT, FILE, FTP, FTPS, Gopher, HTTP, HTTPS, IMAP, IMAPS, LDAP, LDAPS, + POP3, POP3S, RTMP, RTSP, SCP, SFTP, SMTP, SMTPS, Telnet and TFTP. libcurl supports + SSL certificates, HTTP POST, HTTP PUT, FTP uploading, HTTP form based upload, + proxies, cookies, user+password authentication (Basic, Digest, NTLM, Negotiate, + Kerberos), file transfer resume, http proxy tunneling and more.""" + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://curl.haxx.se/download/'] + +# use same binutils version that was used when building GCC toolchain +builddependencies = [('binutils', '2.27', '', True)] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# dependencies = [('OpenSSL', '1.1.0e')] +# configopts = "--with-ssl=$EBROOTOPENSSL" + +modextravars = {'CURL_INCLUDES': '%(installdir)s/include'} + +sanity_check_paths = { + 'files': ['bin/curl', 'lib/libcurl.a', 'lib/libcurl.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'tools' -- GitLab From a38dd1652faef8092f063cfcb4a8f8c95aaa21a9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 19 Apr 2017 14:27:11 +0200 Subject: [PATCH 0610/1603] adding easyconfigs: UDUNITS-2.2.24-intel-2017a.eb --- .../u/UDUNITS/UDUNITS-2.2.24-intel-2017a.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.24-intel-2017a.eb diff --git a/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.24-intel-2017a.eb b/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.24-intel-2017a.eb new file mode 100644 index 0000000000..0e89a4b4d6 --- /dev/null +++ b/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.24-intel-2017a.eb @@ -0,0 +1,38 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg, Ghent University +# Authors:: Fotis Georgatos , Kenneth Hoste (Ghent University) +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-97.html +## + +easyblock = 'ConfigureMake' + +name = 'UDUNITS' +version = '2.2.24' + +homepage = 'http://www.unidata.ucar.edu/software/udunits/' +description = """UDUNITS supports conversion of unit specifications between formatted and binary forms, + arithmetic manipulation of units, and conversion of values between compatible scales of measurement.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['ftp://ftp.unidata.ucar.edu/pub/udunits'] + +dependencies = [('expat', '2.2.0')] + +sanity_check_paths = { + 'files': ['bin/udunits2', 'include/converter.h', 'include/udunits2.h', 'include/udunits.h', + 'lib/libudunits2.a', 'lib/libudunits2.%s' % SHLIB_EXT], + 'dirs': ['share'], +} + +parallel = 1 + +moduleclass = 'phys' -- GitLab From b1b868b9fad00772a8c991df2a84b5e91e4488e9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 19 Apr 2017 14:27:39 +0200 Subject: [PATCH 0611/1603] adding easyconfigs: HDF-4.2.12-intel-2017a.eb --- .../h/HDF/HDF-4.2.12-intel-2017a.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/h/HDF/HDF-4.2.12-intel-2017a.eb diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.12-intel-2017a.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.12-intel-2017a.eb new file mode 100644 index 0000000000..36b03f1853 --- /dev/null +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.12-intel-2017a.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'HDF' +version = '4.2.12' + +homepage = 'http://www.hdfgroup.org/products/hdf4/' +description = """HDF (also known as HDF4) is a library and multi-object file format for storing and managing data + between machines.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] + +builddependencies = [ + ('flex', '2.6.3'), + ('Bison', '3.0.4'), +] +dependencies = [ + ('Szip', '2.1'), + ('libjpeg-turbo', '1.5.1'), +] + +configopts = "--with-szlib=$EBROOTSZIP --includedir=%(installdir)s/include/%(namelower)s" + +modextrapaths = {'CPATH': 'include/hdf'} + +sanity_check_paths = { + 'files': ['lib/libdf.a', 'lib/libhdf4.settings', 'lib/libmfhdf.a'], + 'dirs': ['bin', 'include/hdf'], +} + +moduleclass = 'data' -- GitLab From db59e7eca44753a4e802ccff209fe89a4804e19d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 19 Apr 2017 14:28:06 +0200 Subject: [PATCH 0612/1603] adding easyconfigs: g2lib-1.4.0-intel-2017a.eb, g2clib-1.6.0-intel-2017a.eb --- .../g/g2clib/g2clib-1.6.0-intel-2017a.eb | 17 +++++++++++++++ .../g/g2lib/g2lib-1.4.0-intel-2017a.eb | 21 +++++++++++++++++++ 2 files changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/g/g2clib/g2clib-1.6.0-intel-2017a.eb create mode 100644 easybuild/easyconfigs/g/g2lib/g2lib-1.4.0-intel-2017a.eb diff --git a/easybuild/easyconfigs/g/g2clib/g2clib-1.6.0-intel-2017a.eb b/easybuild/easyconfigs/g/g2clib/g2clib-1.6.0-intel-2017a.eb new file mode 100644 index 0000000000..91bbbfa89b --- /dev/null +++ b/easybuild/easyconfigs/g/g2clib/g2clib-1.6.0-intel-2017a.eb @@ -0,0 +1,17 @@ +name = 'g2clib' +version = '1.6.0' + +homepage = 'http://www.nco.ncep.noaa.gov/pmb/codes/GRIB2/' +description = """Library contains GRIB2 encoder/decoder ('C' version).""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [homepage] +sources = ['%(name)s-%(version)s.tar'] + +dependencies = [('JasPer', '1.900.1')] + +# parallel build tends to fail +parallel = 1 + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/g/g2lib/g2lib-1.4.0-intel-2017a.eb b/easybuild/easyconfigs/g/g2lib/g2lib-1.4.0-intel-2017a.eb new file mode 100644 index 0000000000..c7f92d0e2b --- /dev/null +++ b/easybuild/easyconfigs/g/g2lib/g2lib-1.4.0-intel-2017a.eb @@ -0,0 +1,21 @@ +name = 'g2lib' +version = '1.4.0' + +homepage = 'http://www.nco.ncep.noaa.gov/pmb/codes/GRIB2/' +description = """Library contains GRIB2 encoder/decoder and search/indexing routines.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [homepage] +sources = ['%(name)s-%(version)s.tar'] + +patches = ['fix_makefile.patch'] + +dependencies = [('JasPer', '1.900.1')] + +buildopts = 'CFLAGS="$CFLAGS -DLINUXG95 -D__64BIT__" FFLAGS="$FFLAGS -fpp -I."' + +# parallel build tends to fail +parallel = 1 + +moduleclass = 'data' -- GitLab From 766e37c4509ed9d8de231878b0b1080dc2922fd8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 19 Apr 2017 14:47:38 +0200 Subject: [PATCH 0613/1603] {geo}[intel/2017a] ESMF 6.3.0rp1 --- .../e/ESMF/ESMF-6.3.0rp1-intel-2017a.eb | 31 +++++++++++++++++++ .../ESMF-6.3.0rp1_fix-file-open-test.patch | 13 ++++++++ .../netCDF-C++4-4.3.0-intel-2017a.eb | 24 ++++++++++++++ 3 files changed, 68 insertions(+) create mode 100644 easybuild/easyconfigs/e/ESMF/ESMF-6.3.0rp1-intel-2017a.eb create mode 100644 easybuild/easyconfigs/e/ESMF/ESMF-6.3.0rp1_fix-file-open-test.patch create mode 100644 easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.3.0-intel-2017a.eb diff --git a/easybuild/easyconfigs/e/ESMF/ESMF-6.3.0rp1-intel-2017a.eb b/easybuild/easyconfigs/e/ESMF/ESMF-6.3.0rp1-intel-2017a.eb new file mode 100644 index 0000000000..fec7e0e3f7 --- /dev/null +++ b/easybuild/easyconfigs/e/ESMF/ESMF-6.3.0rp1-intel-2017a.eb @@ -0,0 +1,31 @@ +name = 'ESMF' +version = '6.3.0rp1' + +homepage = 'http://sourceforge.net/projects/esmf' +description = """The Earth System Modeling Framework (ESMF) is software for building and coupling weather, + climate, and related models.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'usempi': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s_src.tar.gz' % '_'.join(version.split('.'))] + +patches = [ + 'ESMF-6.1.1_libopts.patch', + 'ESMF-%(version)s_fix-file-open-test.patch', +] + +dependencies = [ + ('netCDF', '4.4.1.1'), + ('netCDF-Fortran', '4.4.4'), + ('netCDF-C++4', '4.3.0'), +] + +buildopts = 'ESMF_NETCDF_INCLUDE=$EBROOTNETCDFMINFORTRAN/include ' +buildopts += 'ESMF_NETCDF_LIBS="`nc-config --libs` `nf-config --flibs` `ncxx4-config --libs`"' + +# too parallel causes the build to become really slow +maxparallel = 8 + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/e/ESMF/ESMF-6.3.0rp1_fix-file-open-test.patch b/easybuild/easyconfigs/e/ESMF/ESMF-6.3.0rp1_fix-file-open-test.patch new file mode 100644 index 0000000000..62a98e0354 --- /dev/null +++ b/easybuild/easyconfigs/e/ESMF/ESMF-6.3.0rp1_fix-file-open-test.patch @@ -0,0 +1,13 @@ +fix compilation issue with recent compilers +cfr. https://sourceforge.net/p/esmf/esmf/ci/3706bf758012daebadef83d6575c477aeff9c89b/#diff-1 +--- src/Infrastructure/Mesh/src/Moab/io/ReadABAQUS.cpp.orig 2017-04-19 13:44:03.384547426 +0200 ++++ src/Infrastructure/Mesh/src/Moab/io/ReadABAQUS.cpp 2017-04-19 13:44:16.864674576 +0200 +@@ -105,7 +105,7 @@ + ReadABAQUS::~ReadABAQUS() + { + mdbImpl->release_interface(readMeshIface); +- if (NULL != abFile) ++ if (abFile.is_open()) + abFile.close(); + } + diff --git a/easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.3.0-intel-2017a.eb b/easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.3.0-intel-2017a.eb new file mode 100644 index 0000000000..959f14667b --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.3.0-intel-2017a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'netCDF-C++4' +version = '4.3.0' + +homepage = 'http://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/Unidata/netcdf-cxx4/archive/'] +sources = ['v%(version)s.tar.gz'] + +dependencies = [('netCDF', '4.4.1.1')] + +sanity_check_paths = { + 'files': ['include/netcdf', 'lib/libnetcdf_c++4.a', 'lib/libnetcdf_c++4.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'data' -- GitLab From 4133ea658c683e1f2a46a28bb5494b71aa9765e1 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Wed, 19 Apr 2017 15:32:06 +0200 Subject: [PATCH 0614/1603] v6.0 --- .../c/cuDNN/cuDNN-6.0-CUDA-8.0.61.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/c/cuDNN/cuDNN-6.0-CUDA-8.0.61.eb diff --git a/easybuild/easyconfigs/c/cuDNN/cuDNN-6.0-CUDA-8.0.61.eb b/easybuild/easyconfigs/c/cuDNN/cuDNN-6.0-CUDA-8.0.61.eb new file mode 100644 index 0000000000..942648ea47 --- /dev/null +++ b/easybuild/easyconfigs/c/cuDNN/cuDNN-6.0-CUDA-8.0.61.eb @@ -0,0 +1,35 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Author: Stephane Thiell +## +easyblock = 'Tarball' + +name = 'cuDNN' +version = '6.0' +cuda_version = '8.0.61' + +versionsuffix = '-CUDA-%s' % cuda_version + +homepage = 'https://developer.nvidia.com/cudnn' +description = """The NVIDIA CUDA Deep Neural Network library (cuDNN) is a GPU-accelerated library of primitives for + deep neural networks.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +# Nvidia developer registration required. +# Download link: https://developer.nvidia.com/rdp/cudnn-download +sources = ['%(namelower)s-8.0-linux-x64-v%(version)s.tgz'] + +dependencies = [('CUDA', cuda_version)] + +checksums = [ + '4aacb7acb93c5e4dfa9db814df496219', # cudnn-8.0-linux-x64-v6.0.tgz, Jan 20 2017 download +] + +sanity_check_paths = { + 'files': ['include/cudnn.h', 'lib64/libcudnn_static.a'], + 'dirs': ['include', 'lib64'], +} + +moduleclass = 'numlib' -- GitLab From 695590ab4dad6e11621fcf63d0bf7152afc9ad9d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 19 Apr 2017 18:36:20 +0200 Subject: [PATCH 0615/1603] adding easyconfigs: libiconv-1.15-intel-2017a.eb --- .../l/libiconv/libiconv-1.15-intel-2017a.eb | 20 +++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 easybuild/easyconfigs/l/libiconv/libiconv-1.15-intel-2017a.eb diff --git a/easybuild/easyconfigs/l/libiconv/libiconv-1.15-intel-2017a.eb b/easybuild/easyconfigs/l/libiconv/libiconv-1.15-intel-2017a.eb new file mode 100644 index 0000000000..fb6be42e9f --- /dev/null +++ b/easybuild/easyconfigs/l/libiconv/libiconv-1.15-intel-2017a.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'libiconv' +version = '1.15' + +homepage = 'https://www.gnu.org/software/libiconv' +description = "Libiconv converts from one character encoding to another through Unicode conversion" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] + +sanity_check_paths = { + 'files': ['bin/iconv', 'include/iconv.h', 'include/libcharset.h', 'include/localcharset.h', + 'lib/libcharset.a', 'lib/libcharset.%s' % SHLIB_EXT, 'lib/libiconv.%s' % SHLIB_EXT], + 'dirs': ['share'], +} + +moduleclass = 'lib' -- GitLab From 2d502840969e2356078da89e05ac197c67ae0306 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 20 Apr 2017 10:14:45 +0200 Subject: [PATCH 0616/1603] install libiconv with GCCcore rather than intel toolchain --- ...nv-1.15-intel-2017a.eb => libiconv-1.15-GCCcore-6.3.0.eb} | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) rename easybuild/easyconfigs/l/libiconv/{libiconv-1.15-intel-2017a.eb => libiconv-1.15-GCCcore-6.3.0.eb} (75%) diff --git a/easybuild/easyconfigs/l/libiconv/libiconv-1.15-intel-2017a.eb b/easybuild/easyconfigs/l/libiconv/libiconv-1.15-GCCcore-6.3.0.eb similarity index 75% rename from easybuild/easyconfigs/l/libiconv/libiconv-1.15-intel-2017a.eb rename to easybuild/easyconfigs/l/libiconv/libiconv-1.15-GCCcore-6.3.0.eb index fb6be42e9f..c2a203f1b2 100644 --- a/easybuild/easyconfigs/l/libiconv/libiconv-1.15-intel-2017a.eb +++ b/easybuild/easyconfigs/l/libiconv/libiconv-1.15-GCCcore-6.3.0.eb @@ -6,11 +6,14 @@ version = '1.15' homepage = 'https://www.gnu.org/software/libiconv' description = "Libiconv converts from one character encoding to another through Unicode conversion" -toolchain = {'name': 'intel', 'version': '2017a'} +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +# use same binutils version that was used when building GCC toolchain +builddependencies = [('binutils', '2.27', '', True)] + sanity_check_paths = { 'files': ['bin/iconv', 'include/iconv.h', 'include/libcharset.h', 'include/localcharset.h', 'lib/libcharset.a', 'lib/libcharset.%s' % SHLIB_EXT, 'lib/libiconv.%s' % SHLIB_EXT], -- GitLab From b72075148a92dc4187d739278cb11f5f33e40709 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 20 Apr 2017 10:35:46 +0200 Subject: [PATCH 0617/1603] adding easyconfigs: numba-0.32.0-intel-2017a-Python-2.7.13.eb --- .../numba-0.32.0-intel-2017a-Python-2.7.13.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/n/numba/numba-0.32.0-intel-2017a-Python-2.7.13.eb diff --git a/easybuild/easyconfigs/n/numba/numba-0.32.0-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/n/numba/numba-0.32.0-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..dc868ad142 --- /dev/null +++ b/easybuild/easyconfigs/n/numba/numba-0.32.0-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,40 @@ +easyblock = 'Bundle' + +name = 'numba' +version = '0.32.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://numba.pydata.org/' +description = """Numba is an Open Source NumPy-aware optimizing compiler for Python sponsored by Continuum Analytics, + Inc. It uses the remarkable LLVM compiler infrastructure to compile Python syntax to machine code.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' + +dependencies = [ + ('Python', '2.7.13'), + ('LLVM', '4.0.0'), +] + +exts_list = [ + ('llvmlite', '0.17.1', { + 'source_urls': ['https://pypi.python.org/packages/source/l/llvmlite/'], + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/n/numba/'], + }), +] + +# specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module +full_sanity_check = True + +sanity_check_paths = { + 'files': ['bin/numba', 'bin/pycc'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +moduleclass = 'lang' -- GitLab From bf7342099c04a56d0715d02cdf2531ee57e1d194 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 20 Apr 2017 10:58:08 +0200 Subject: [PATCH 0618/1603] adding easyconfigs: PyZMQ-16.0.2-intel-2017a-Python-2.7.13-zmq4.eb, ZeroMQ-4.2.2-intel-2017a.eb, OpenPGM-5.2.122-intel-2017a.eb, libsodium-1.0.12-intel-2017a.eb --- .../libsodium/libsodium-1.0.12-intel-2017a.eb | 20 +++++++++++ .../o/OpenPGM/OpenPGM-5.2.122-intel-2017a.eb | 30 ++++++++++++++++ ...Q-16.0.2-intel-2017a-Python-2.7.13-zmq4.eb | 30 ++++++++++++++++ .../z/ZeroMQ/ZeroMQ-4.2.2-intel-2017a.eb | 36 +++++++++++++++++++ 4 files changed, 116 insertions(+) create mode 100644 easybuild/easyconfigs/l/libsodium/libsodium-1.0.12-intel-2017a.eb create mode 100644 easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-intel-2017a.eb create mode 100644 easybuild/easyconfigs/p/PyZMQ/PyZMQ-16.0.2-intel-2017a-Python-2.7.13-zmq4.eb create mode 100644 easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.2.2-intel-2017a.eb diff --git a/easybuild/easyconfigs/l/libsodium/libsodium-1.0.12-intel-2017a.eb b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.12-intel-2017a.eb new file mode 100644 index 0000000000..faf9cf93a1 --- /dev/null +++ b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.12-intel-2017a.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'libsodium' +version = '1.0.12' + +homepage = 'http://doc.libsodium.org/' +description = """Sodium is a modern, easy-to-use software library for encryption, decryption, signatures, + password hashing and more.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['https://download.libsodium.org/libsodium/releases/'] +sources = [SOURCE_TAR_GZ] + +sanity_check_paths = { + 'files': ['include/sodium.h', 'lib/libsodium.so', 'lib/libsodium.a'], + 'dirs': ['include/sodium', 'lib/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-intel-2017a.eb b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-intel-2017a.eb new file mode 100644 index 0000000000..d604042523 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-intel-2017a.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'OpenPGM' +version = '5.2.122' + +homepage = 'http://code.google.com/p/openpgm/' +description = """OpenPGM is an open source implementation of the Pragmatic General Multicast (PGM) + specification in RFC 3208 available at www.ietf.org. PGM is a reliable and scalable multicast protocol + that enables receivers to detect loss, request retransmission of lost data, or notify an application + of unrecoverable loss. PGM is a receiver-reliable protocol, which means the receiver is responsible + for ensuring all data is received, absolving the sender of reception responsibility.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True} + +source_urls = ['https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/openpgm/'] +sources = ['libpgm-%(version)s.tar.gz'] + +checksums = ['d7673e9ff6cc33cf42fe9fb9a7bfbffa'] + +configopts = '--with-pic' + +start_dir = 'pgm' + +sanity_check_paths = { + 'files': ['lib/libpgm.%s' % SHLIB_EXT, 'lib/libpgm.a'], + 'dirs': ['include'], +} + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/p/PyZMQ/PyZMQ-16.0.2-intel-2017a-Python-2.7.13-zmq4.eb b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-16.0.2-intel-2017a-Python-2.7.13-zmq4.eb new file mode 100644 index 0000000000..3ee565a8d9 --- /dev/null +++ b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-16.0.2-intel-2017a-Python-2.7.13-zmq4.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'PyZMQ' +version = '16.0.2' +zmqversion = '4.2.2' +versionsuffix = '-Python-%%(pyver)s-zmq%s' % zmqversion.split('.')[0] + +homepage = 'http://www.zeromq.org/bindings:python' +description = """Python bindings for ZeroMQ""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +checksums = ['9a8768b00a566a400d70318f8c359cfe'] + +dependencies = [ + ('Python', '2.7.13'), + ('ZeroMQ', zmqversion), +] + +options = {'modulename': 'zmq'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/zmq'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.2.2-intel-2017a.eb b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.2.2-intel-2017a.eb new file mode 100644 index 0000000000..165ba15944 --- /dev/null +++ b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.2.2-intel-2017a.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'ZeroMQ' +version = '4.2.2' + +homepage = 'http://www.zeromq.org/' +description = """ZeroMQ looks like an embeddable networking library but acts like a concurrency framework. + It gives you sockets that carry atomic messages across various transports like in-process, + inter-process, TCP, and multicast. You can connect sockets N-to-N with patterns like fanout, + pub-sub, task distribution, and request-reply. It's fast enough to be the fabric for clustered + products. Its asynchronous I/O model gives you scalable multicore applications, built as asynchronous + message-processing tasks. It has a score of language APIs and runs on most operating systems.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['https://github.com/zeromq/libzmq/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['52499909b29604c1e47a86f1cb6a9115'] + +# --with-pgm will use shipped OpenPGM (in foreign subdir) +configopts = '--with-pic --with-system-pgm ' +configopts += 'OpenPGM_CFLAGS="-I$EBROOTOPENPGM/include/pgm-${EBVERSIONOPENPGM%.*}" ' +configopts += 'OpenPGM_LIBS="-L$EBROOTOPENPGM/lib -lpgm -lrt -lpthread -lm" ' + +dependencies = [ + ('OpenPGM', '5.2.122'), + ('util-linux', '2.29.2'), + ('libsodium', '1.0.12'), +] + +sanity_check_paths = { + 'files': ['lib/libzmq.%s' % SHLIB_EXT, 'lib/libzmq.a'], + 'dirs': ['include', 'lib'], +} + +moduleclass = 'devel' -- GitLab From 54c21ef39805e3658819582f56a821f29ea5b96c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 20 Apr 2017 10:58:44 +0200 Subject: [PATCH 0619/1603] adding easyconfigs: GSL-2.3-intel-2017a.eb --- .../easyconfigs/g/GSL/GSL-2.3-intel-2017a.eb | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) create mode 100644 easybuild/easyconfigs/g/GSL/GSL-2.3-intel-2017a.eb diff --git a/easybuild/easyconfigs/g/GSL/GSL-2.3-intel-2017a.eb b/easybuild/easyconfigs/g/GSL/GSL-2.3-intel-2017a.eb new file mode 100644 index 0000000000..23a2fed6dc --- /dev/null +++ b/easybuild/easyconfigs/g/GSL/GSL-2.3-intel-2017a.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'GSL' +version = '2.3' + +homepage = 'http://www.gnu.org/software/gsl/' +description = """The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. + The library provides a wide range of mathematical routines such as random number generators, special functions + and least-squares fitting.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'unroll': True, 'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +configopts = "--with-pic" + +moduleclass = 'numlib' -- GitLab From 5611e1be3e27234852c0429f2a98458f8e3a0e2e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 20 Apr 2017 11:42:16 +0200 Subject: [PATCH 0620/1603] add patch to avoid configparser declaring ownership of backports namespace, fixes #3825 --- ...igparser-3.5.0-foss-2016a-Python-2.7.11.eb | 16 +++------- ...gparser-3.5.0-intel-2016b-Python-2.7.12.eb | 15 ++------- ...igparser-3.5.0-intel-2016b-Python-3.5.2.eb | 7 ++--- ...gparser-3.5.0_no-backports-namespace.patch | 31 +++++++++++++++++++ 4 files changed, 41 insertions(+), 28 deletions(-) create mode 100644 easybuild/easyconfigs/c/configparser/configparser-3.5.0_no-backports-namespace.patch diff --git a/easybuild/easyconfigs/c/configparser/configparser-3.5.0-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/c/configparser/configparser-3.5.0-foss-2016a-Python-2.7.11.eb index 8172078525..f9db925788 100644 --- a/easybuild/easyconfigs/c/configparser/configparser-3.5.0-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/c/configparser/configparser-3.5.0-foss-2016a-Python-2.7.11.eb @@ -12,26 +12,18 @@ toolchain = {'name': 'foss', 'version': '2016a'} source_urls = ['https://pypi.python.org/packages/7c/69/c2ce7e91c89dc073eb1aa74c0621c3eefbffe8216b3f9af9d3885265c01c/'] sources = ['configparser-%(version)s.tar.gz'] -dependencies = [ - ('Python', '2.7.11'), -] -builddependencies = [ - ('pip', '8.1.2', versionsuffix), -] +patches = ['configparser-%(version)s_no-backports-namespace.patch'] + +dependencies = [('Python', '2.7.11')] +builddependencies = [('pip', '8.1.2', versionsuffix)] use_pip = True -unpack_sources = False sanity_check_paths = { 'files': ['lib/python%(pyshortver)s/site-packages/configparser.py'], 'dirs': ['lib/python%(pyshortver)s/site-packages/backports/configparser'], } -# XXX: hack! for some reason the sanity check imports fail, even though the -# PYTHONPATH seems to point to the right directory?!? Creating the __init__.py -# in backports makes it pass and hopefully does not break anything. -postinstallcmds = ['touch %(installdir)s/lib/python%(pyshortver)s/site-packages/backports/__init__.py'] - sanity_check_commands = [ ('python', "-c 'import configparser'"), ('python', "-c 'from backports import configparser'"), diff --git a/easybuild/easyconfigs/c/configparser/configparser-3.5.0-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/c/configparser/configparser-3.5.0-intel-2016b-Python-2.7.12.eb index 10fc576297..bed63bcc08 100644 --- a/easybuild/easyconfigs/c/configparser/configparser-3.5.0-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/c/configparser/configparser-3.5.0-intel-2016b-Python-2.7.12.eb @@ -12,26 +12,17 @@ toolchain = {'name': 'intel', 'version': '2016b'} source_urls = ['https://pypi.python.org/packages/7c/69/c2ce7e91c89dc073eb1aa74c0621c3eefbffe8216b3f9af9d3885265c01c/'] sources = ['configparser-%(version)s.tar.gz'] -dependencies = [ - ('Python', '2.7.12'), -] -builddependencies = [ - ('pip', '8.1.2', versionsuffix), -] +patches = ['configparser-%(version)s_no-backports-namespace.patch'] + +dependencies = [('Python', '2.7.12')] use_pip = True -unpack_sources = False sanity_check_paths = { 'files': ['lib/python%(pyshortver)s/site-packages/configparser.py'], 'dirs': ['lib/python%(pyshortver)s/site-packages/backports/configparser'], } -# XXX: hack! for some reason the sanity check imports fail, even though the -# PYTHONPATH seems to point to the right directory?!? Creating the __init__.py -# in backports makes it pass and hopefully does not break anything. -postinstallcmds = ['touch %(installdir)s/lib/python%(pyshortver)s/site-packages/backports/__init__.py'] - sanity_check_commands = [ ('python', "-c 'import configparser'"), ('python', "-c 'from backports import configparser'"), diff --git a/easybuild/easyconfigs/c/configparser/configparser-3.5.0-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/c/configparser/configparser-3.5.0-intel-2016b-Python-3.5.2.eb index e3bb6d9e20..113e88c75f 100644 --- a/easybuild/easyconfigs/c/configparser/configparser-3.5.0-intel-2016b-Python-3.5.2.eb +++ b/easybuild/easyconfigs/c/configparser/configparser-3.5.0-intel-2016b-Python-3.5.2.eb @@ -12,12 +12,11 @@ toolchain = {'name': 'intel', 'version': '2016b'} source_urls = ['https://pypi.python.org/packages/7c/69/c2ce7e91c89dc073eb1aa74c0621c3eefbffe8216b3f9af9d3885265c01c/'] sources = ['configparser-%(version)s.tar.gz'] -dependencies = [ - ('Python', '3.5.2'), -] +patches = ['configparser-%(version)s_no-backports-namespace.patch'] + +dependencies = [('Python', '3.5.2')] use_pip = True -unpack_sources = False sanity_check_paths = { 'files': [], diff --git a/easybuild/easyconfigs/c/configparser/configparser-3.5.0_no-backports-namespace.patch b/easybuild/easyconfigs/c/configparser/configparser-3.5.0_no-backports-namespace.patch new file mode 100644 index 0000000000..6deccec5e6 --- /dev/null +++ b/easybuild/easyconfigs/c/configparser/configparser-3.5.0_no-backports-namespace.patch @@ -0,0 +1,31 @@ +don't let configparser define 'backports' namespace, since that interferes with other packaging that provide stuff in 'backports' + +patch obtained from https://github.com/NIXOS/nixpkgs/blob/master/pkgs/development/python-modules/configparser/0001-namespace-fix.patch +see also https://bitbucket.org/ambv/configparser/issues/17/importerror-when-used-with-other-backports +diff --git a/setup.py b/setup.py +index 3b07823..63ed25d 100644 +--- a/setup.py ++++ b/setup.py +@@ -42,7 +42,6 @@ setup( + py_modules=modules, + package_dir={'': 'src'}, + packages=find_packages('src'), +- namespace_packages=['backports'], + include_package_data=True, + zip_safe=False, + install_requires=requirements, +diff --git a/src/backports/__init__.py b/src/backports/__init__.py +index f84d25c..febdb2f 100644 +--- a/src/backports/__init__.py ++++ b/src/backports/__init__.py +@@ -3,9 +3,3 @@ + + from pkgutil import extend_path + __path__ = extend_path(__path__, __name__) +- +-try: +- import pkg_resources +- pkg_resources.declare_namespace(__name__) +-except ImportError: +- pass +-- -- GitLab From cf19458b143e485f7f38567676fccbce91806cd1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 20 Apr 2017 17:12:07 +0200 Subject: [PATCH 0621/1603] re-add nbconvert extension in IPython easyconfigs --- ...igparser-3.5.0-foss-2016b-Python-2.7.12.eb | 31 +++++++++++++++++++ ...rypoints-0.2.2-foss-2016b-Python-2.7.12.eb | 28 +++++++++++++++++ .../IPython-5.1.0-foss-2016b-Python-2.7.12.eb | 12 +++---- ...IPython-5.1.0-intel-2016b-Python-2.7.12.eb | 12 +++---- ...IPython-5.2.2-intel-2016b-Python-2.7.12.eb | 16 +++++----- 5 files changed, 75 insertions(+), 24 deletions(-) create mode 100644 easybuild/easyconfigs/c/configparser/configparser-3.5.0-foss-2016b-Python-2.7.12.eb create mode 100644 easybuild/easyconfigs/e/entrypoints/entrypoints-0.2.2-foss-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/c/configparser/configparser-3.5.0-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/c/configparser/configparser-3.5.0-foss-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..5bd3d25aab --- /dev/null +++ b/easybuild/easyconfigs/c/configparser/configparser-3.5.0-foss-2016b-Python-2.7.12.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonPackage' + +name = 'configparser' +version = '3.5.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://docs.python.org/3/library/configparser.html' +description = "configparser is a Python library that brings the updated configparser from Python 3.5 to Python 2.6-3.5" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['https://pypi.python.org/packages/7c/69/c2ce7e91c89dc073eb1aa74c0621c3eefbffe8216b3f9af9d3885265c01c/'] +sources = ['configparser-%(version)s.tar.gz'] + +patches = ['configparser-%(version)s_no-backports-namespace.patch'] + +dependencies = [('Python', '2.7.12')] + +use_pip = True + +sanity_check_paths = { + 'files': ['lib/python%(pyshortver)s/site-packages/configparser.py'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/backports/configparser'], +} + +sanity_check_commands = [ + ('python', "-c 'import configparser'"), + ('python', "-c 'from backports import configparser'"), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/e/entrypoints/entrypoints-0.2.2-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/e/entrypoints/entrypoints-0.2.2-foss-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..a82113c472 --- /dev/null +++ b/easybuild/easyconfigs/e/entrypoints/entrypoints-0.2.2-foss-2016b-Python-2.7.12.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'entrypoints' +version = '0.2.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/takluyver/entrypoints' +description = """Entry points are a way for Python packages to advertise objects with some common interface.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['https://pypi.python.org/packages/f8/ad/0e77a853c745a15981ab51fa9a0cb4eca7a7a007b4c1970106ee6ba01e0c/'] +sources = ['entrypoints-0.2.2-py2.py3-none-any.whl'] + +dependencies = [ + ('Python', '2.7.12'), + ('configparser', '3.5.0', versionsuffix), +] + +use_pip = True +unpack_sources = False + +sanity_check_paths = { + 'files': ['lib/python%(pyshortver)s/site-packages/entrypoints.py'], + 'dirs': [] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/i/IPython/IPython-5.1.0-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/i/IPython/IPython-5.1.0-foss-2016b-Python-2.7.12.eb index 15948e83d4..ec7c04c10b 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-5.1.0-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-5.1.0-foss-2016b-Python-2.7.12.eb @@ -18,9 +18,7 @@ dependencies = [ ('Python', '2.7.12'), ('PyZMQ', '16.0.2', '%s-zmq4' % versionsuffix), ('testpath', '0.3', versionsuffix), - # required by 'nbconvert', but causes problems w.r.t. 'backports' module... - # see https://github.com/hpcugent/easybuild-easyconfigs/issues/3825 - # ('entrypoints', '0.2.2', versionsuffix), + ('entrypoints', '0.2.2', versionsuffix), ('path.py', '8.2.1', versionsuffix), ('prompt-toolkit', '1.0.6', versionsuffix), ] @@ -114,11 +112,9 @@ exts_list = [ ('pexpect', '4.2.0', { 'source_urls': ['https://pypi.python.org/packages/source/p/pexpect/'], }), - # disabled because entrypoints on which this depends pull in configparser, which causes problems - # see https://github.com/hpcugent/easybuild-easyconfigs/issues/3825 - # ('nbconvert', '4.2.0', { - # 'source_urls': ['https://pypi.python.org/packages/source/n/nbconvert/'], - # }), + ('nbconvert', '4.2.0', { + 'source_urls': ['https://pypi.python.org/packages/source/n/nbconvert/'], + }), ('backports.shutil_get_terminal_size', '1.0.0', { 'source_urls': ['https://pypi.python.org/packages/source/b/backports.shutil_get_terminal_size/'], }), diff --git a/easybuild/easyconfigs/i/IPython/IPython-5.1.0-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/i/IPython/IPython-5.1.0-intel-2016b-Python-2.7.12.eb index 73b84816cd..ad14e82e32 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-5.1.0-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-5.1.0-intel-2016b-Python-2.7.12.eb @@ -18,9 +18,7 @@ dependencies = [ ('Python', '2.7.12'), ('PyZMQ', '15.4.0', '%s-zmq4' % versionsuffix), ('testpath', '0.3', versionsuffix), - # required by 'nbconvert', but causes problems w.r.t. 'backports' module... - # see https://github.com/hpcugent/easybuild-easyconfigs/issues/3825 - # ('entrypoints', '0.2.2', versionsuffix), + ('entrypoints', '0.2.2', versionsuffix), ('path.py', '8.2.1', versionsuffix), ('prompt-toolkit', '1.0.6', versionsuffix), ] @@ -114,11 +112,9 @@ exts_list = [ ('pexpect', '4.2.0', { 'source_urls': ['https://pypi.python.org/packages/source/p/pexpect/'], }), - # disabled because entrypoints on which this depends pull in configparser, which causes problems - # see https://github.com/hpcugent/easybuild-easyconfigs/issues/3825 - # ('nbconvert', '4.2.0', { - # 'source_urls': ['https://pypi.python.org/packages/source/n/nbconvert/'], - # }), + ('nbconvert', '4.2.0', { + 'source_urls': ['https://pypi.python.org/packages/source/n/nbconvert/'], + }), ('backports.shutil_get_terminal_size', '1.0.0', { 'source_urls': ['https://pypi.python.org/packages/source/b/backports.shutil_get_terminal_size/'], }), diff --git a/easybuild/easyconfigs/i/IPython/IPython-5.2.2-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/i/IPython/IPython-5.2.2-intel-2016b-Python-2.7.12.eb index 89001fc17a..01c5f93a20 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-5.2.2-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-5.2.2-intel-2016b-Python-2.7.12.eb @@ -18,9 +18,7 @@ dependencies = [ ('Python', '2.7.12'), ('PyZMQ', '16.0.2', '%s-zmq4' % versionsuffix), ('testpath', '0.3', versionsuffix), - # required by 'nbconvert', but causes problems w.r.t. 'backports' module... - # see https://github.com/hpcugent/easybuild-easyconfigs/issues/3825 - # ('entrypoints', '0.2.2', versionsuffix), + ('entrypoints', '0.2.2', versionsuffix), ('path.py', '10.1', versionsuffix), ('prompt-toolkit', '1.0.13', versionsuffix), ] @@ -111,11 +109,13 @@ exts_list = [ ('pexpect', '4.2.1', { 'source_urls': ['https://pypi.python.org/packages/source/p/pexpect/'], }), - # disabled because entrypoints on which this depends pull in configparser, which causes problems - # see https://github.com/hpcugent/easybuild-easyconfigs/issues/3825 - # ('nbconvert', '5.1.1', { - # 'source_urls': ['https://pypi.python.org/packages/source/n/nbconvert/'], - # }), + ('pandocfilters', '1.4.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pandocfilters/'], + }), + ('nbconvert', '5.1.1', { + 'source_urls': ['https://pypi.python.org/packages/source/n/nbconvert/'], + 'use_pip': True, + }), ('backports.shutil_get_terminal_size', '1.0.0', { 'source_urls': ['https://pypi.python.org/packages/source/b/backports.shutil_get_terminal_size/'], }), -- GitLab From f142dcdf9ad525403d586d37b3bf68d2a2933032 Mon Sep 17 00:00:00 2001 From: Basil Neff Date: Thu, 20 Apr 2017 17:31:03 +0200 Subject: [PATCH 0622/1603] Change source_urls of pycrypto to https://pypi.python.org/packages/source/p/pycrypto/: A crypto library should be downloaded via https, python.org seems more reliable than dlitz.net, dlitz.net is currently not online. --- easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015a.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015b.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.10-gimkl-2.11.5.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.10-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.10-goolf-1.7.20.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015a.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015b.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2015.11.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2016.03.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2015a.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2016a.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.11-gimkl-2.11.5.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.11-goolf-1.7.20.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2015b.eb | 2 +- .../easyconfigs/p/Python/Python-2.7.11-intel-2016.02-GCC-4.9.eb | 2 +- .../p/Python/Python-2.7.11-intel-2016a-libX11-1.6.3.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016a.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.11-iomkl-2016.07.eb | 2 +- .../p/Python/Python-2.7.11-iomkl-2016.09-GCC-4.9.3-2.25.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.12-foss-2016b.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.12-intel-2016b.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.12-iomkl-2017a.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.13-intel-2017a.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.3-foss-2015b.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.5.14.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.2.0.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.3.0.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.3-intel-2015a.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.5-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.3.0.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.5.0.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.6-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-5.5.0.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.8-foss-2014b.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.8-goolf-1.5.14.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.8-ictce-7.1.2.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014.06.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014b.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2015a.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.06.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.11.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015.05.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015b.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.14.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.16.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.7.20.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb | 2 +- easybuild/easyconfigs/p/Python/Python-3.2.3-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-5.3.0.eb | 2 +- easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2014b.eb | 2 +- easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2015a.eb | 2 +- easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb | 2 +- easybuild/easyconfigs/p/Python/Python-3.5.0-intel-2015b.eb | 2 +- easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2015a.eb | 2 +- easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2016a.eb | 2 +- easybuild/easyconfigs/p/Python/Python-3.5.1-intel-2016a.eb | 2 +- easybuild/easyconfigs/p/Python/Python-3.5.2-foss-2016.04.eb | 2 +- easybuild/easyconfigs/p/Python/Python-3.5.2-foss-2016b.eb | 2 +- easybuild/easyconfigs/p/Python/Python-3.5.2-intel-2016b.eb | 2 +- 61 files changed, 61 insertions(+), 61 deletions(-) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015a.eb index 0cacb5b908..6b56eb27c3 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015a.eb @@ -91,7 +91,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.13', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015b.eb index c4b91910db..8b4e1559a2 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015b.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015b.eb @@ -91,7 +91,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.13', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.10-gimkl-2.11.5.eb b/easybuild/easyconfigs/p/Python/Python-2.7.10-gimkl-2.11.5.eb index 6cb74160de..acd58a0881 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.10-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.10-gimkl-2.11.5.eb @@ -90,7 +90,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.13', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.10-goolf-1.4.10.eb b/easybuild/easyconfigs/p/Python/Python-2.7.10-goolf-1.4.10.eb index 2bf2b3c0c7..e8f04d3c24 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.10-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.10-goolf-1.4.10.eb @@ -91,7 +91,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.13', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.10-goolf-1.7.20.eb b/easybuild/easyconfigs/p/Python/Python-2.7.10-goolf-1.7.20.eb index d616f3a678..f6fb8098a2 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.10-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.10-goolf-1.7.20.eb @@ -91,7 +91,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.13', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015a.eb index 3bba96e78d..e63f73a086 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015a.eb @@ -91,7 +91,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.13', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015b.eb index 5578abe094..007214e5b0 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015b.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015b.eb @@ -90,7 +90,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.13', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2015.11.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2015.11.eb index 4289f275f3..8a60745ce6 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2015.11.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2015.11.eb @@ -93,7 +93,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.13', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2016.03.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2016.03.eb index f16c276300..f9d52e68ec 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2016.03.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2016.03.eb @@ -93,7 +93,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.13', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2015a.eb index 7ca3e0d30a..b14cb9623b 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2015a.eb @@ -90,7 +90,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.13', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2016a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2016a.eb index 90aff56172..161e0d5c72 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2016a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2016a.eb @@ -90,7 +90,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.13', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-gimkl-2.11.5.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-gimkl-2.11.5.eb index 540888954b..236dc03eb2 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-gimkl-2.11.5.eb @@ -93,7 +93,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.13', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-goolf-1.7.20.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-goolf-1.7.20.eb index 500c945db9..61b2cea7f1 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-goolf-1.7.20.eb @@ -90,7 +90,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.13', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2015b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2015b.eb index 66287172c5..15781ef44b 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2015b.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2015b.eb @@ -93,7 +93,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.13', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016.02-GCC-4.9.eb index 49ed840807..92cc06cd43 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016.02-GCC-4.9.eb @@ -93,7 +93,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.13', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016a-libX11-1.6.3.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016a-libX11-1.6.3.eb index 4fa82a32c1..2bcf51b6e3 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016a-libX11-1.6.3.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016a-libX11-1.6.3.eb @@ -95,7 +95,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.13', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016a.eb index 36a33282cc..b4d230688e 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016a.eb @@ -93,7 +93,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.13', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-iomkl-2016.07.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-iomkl-2016.07.eb index ceffc4847a..f016ee6e7a 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-iomkl-2016.07.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-iomkl-2016.07.eb @@ -92,7 +92,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.13', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-iomkl-2016.09-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-iomkl-2016.09-GCC-4.9.3-2.25.eb index 42a08985d0..7040853aa6 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-iomkl-2016.09-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-iomkl-2016.09-GCC-4.9.3-2.25.eb @@ -90,7 +90,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.13', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.12-foss-2016b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.12-foss-2016b.eb index ba6ada1467..0f7cc1242b 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.12-foss-2016b.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.12-foss-2016b.eb @@ -85,7 +85,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.13', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.12-intel-2016b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.12-intel-2016b.eb index f39ab1c056..8305709383 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.12-intel-2016b.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.12-intel-2016b.eb @@ -85,7 +85,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.13', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.12-iomkl-2017a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.12-iomkl-2017a.eb index 47c4558b9f..eb4f43f9dd 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.12-iomkl-2017a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.12-iomkl-2017a.eb @@ -85,7 +85,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.13', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.13-intel-2017a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.13-intel-2017a.eb index 8d585acc42..099f1ae1b2 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.13-intel-2017a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.13-intel-2017a.eb @@ -86,7 +86,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.13', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-foss-2015b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-foss-2015b.eb index 9cf2d30627..b98190bc1b 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-foss-2015b.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-foss-2015b.eb @@ -81,7 +81,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.8', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.4.10.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.4.10.eb index 0d7187668b..6d47c29a41 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.4.10.eb @@ -81,7 +81,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.8', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.5.14.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.5.14.eb index 1f04581f6c..5d62c714b3 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.5.14.eb @@ -81,7 +81,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.8', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.2.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.2.0.eb index d6acb56cd0..466af1fc83 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.2.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.2.0.eb @@ -79,7 +79,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.8', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.3.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.3.0.eb index 0a6a82b9fe..9112593773 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.3.0.eb @@ -79,7 +79,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.8', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-intel-2015a.eb index 78b8331206..b74b1eef65 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-intel-2015a.eb @@ -79,7 +79,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.8', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.5-goolf-1.4.10.eb b/easybuild/easyconfigs/p/Python/Python-2.7.5-goolf-1.4.10.eb index 8bc486f394..fa3597eb0f 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.5-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.5-goolf-1.4.10.eb @@ -82,7 +82,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.8', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.3.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.3.0.eb index f91d5d9be1..74108af019 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.3.0.eb @@ -82,7 +82,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.8', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.5.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.5.0.eb index 1589ad3044..7f83fbbc76 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.5.0.eb @@ -82,7 +82,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.8', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.6-goolf-1.4.10.eb b/easybuild/easyconfigs/p/Python/Python-2.7.6-goolf-1.4.10.eb index cc438001ba..d802876700 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.6-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.6-goolf-1.4.10.eb @@ -81,7 +81,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.11', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-5.5.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-5.5.0.eb index 8a3b97a885..8d651bcfeb 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-5.5.0.eb @@ -84,7 +84,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.11', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.8-foss-2014b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.8-foss-2014b.eb index ff8c4dd1f7..0ac840f64e 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.8-foss-2014b.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.8-foss-2014b.eb @@ -81,7 +81,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.11', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.8-goolf-1.5.14.eb b/easybuild/easyconfigs/p/Python/Python-2.7.8-goolf-1.5.14.eb index 400936afa7..8301c629cc 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.8-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.8-goolf-1.5.14.eb @@ -87,7 +87,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.11', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.8-ictce-7.1.2.eb b/easybuild/easyconfigs/p/Python/Python-2.7.8-ictce-7.1.2.eb index 535df5f445..fcb554f578 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.8-ictce-7.1.2.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.8-ictce-7.1.2.eb @@ -91,7 +91,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.11', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014.06.eb b/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014.06.eb index 15167c0da9..d08ab61505 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014.06.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014.06.eb @@ -88,7 +88,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.11', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014b.eb index 5da8fad6cd..3479838d18 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014b.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014b.eb @@ -88,7 +88,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.11', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2015a.eb index a19c3193df..e92ff5d69d 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2015a.eb @@ -84,7 +84,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.11', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.06.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.06.eb index c42116cc9a..0f597d584c 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.06.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.06.eb @@ -87,7 +87,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.11', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.11.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.11.eb index e020765a41..2963dc2fc7 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.11.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-2015.11.eb @@ -87,7 +87,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.11', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015.05.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015.05.eb index 0e5c8bdaf5..6953cb6dbe 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015.05.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015.05.eb @@ -87,7 +87,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['https://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.11', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a.eb index 50b5d85a22..0f287711fc 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a.eb @@ -87,7 +87,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.11', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015b.eb index 954cb1d6c9..77b75dd242 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015b.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015b.eb @@ -87,7 +87,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.11', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.14.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.14.eb index 2117038315..3ba0f79c58 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.14.eb @@ -87,7 +87,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.11', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.16.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.16.eb index de0245d75a..58ac4915cc 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.16.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.16.eb @@ -87,7 +87,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['https://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.11', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.7.20.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.7.20.eb index 39c33c3855..f324c5da55 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.7.20.eb @@ -87,7 +87,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['https://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.11', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb index dfd615f248..76e8491a9b 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb @@ -88,7 +88,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.11', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-3.2.3-goolf-1.4.10.eb b/easybuild/easyconfigs/p/Python/Python-3.2.3-goolf-1.4.10.eb index 530b345146..e15e16e66c 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.2.3-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.2.3-goolf-1.4.10.eb @@ -62,7 +62,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ] diff --git a/easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-5.3.0.eb b/easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-5.3.0.eb index 1f4aa039b5..fbcadd2903 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-5.3.0.eb @@ -62,7 +62,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ] diff --git a/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2014b.eb b/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2014b.eb index 85a061b4b2..aaa2d02a7e 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2014b.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2014b.eb @@ -93,7 +93,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.11', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2015a.eb index 43f98bbf39..80c176feab 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2015a.eb @@ -93,7 +93,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.11', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb index fa4d5db712..e220cd9cc4 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb @@ -91,7 +91,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.13', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-3.5.0-intel-2015b.eb b/easybuild/easyconfigs/p/Python/Python-3.5.0-intel-2015b.eb index 7f32b2fbd5..1fe2eb4748 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.5.0-intel-2015b.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.5.0-intel-2015b.eb @@ -93,7 +93,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.13', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2015a.eb b/easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2015a.eb index 34b680443b..3794d8056b 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2015a.eb @@ -93,7 +93,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.13', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2016a.eb b/easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2016a.eb index f17ad6e258..0ea37fde6e 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2016a.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.5.1-foss-2016a.eb @@ -93,7 +93,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.13', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-3.5.1-intel-2016a.eb b/easybuild/easyconfigs/p/Python/Python-3.5.1-intel-2016a.eb index bba87219ba..6b27ddc007 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.5.1-intel-2016a.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.5.1-intel-2016a.eb @@ -97,7 +97,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.13', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-3.5.2-foss-2016.04.eb b/easybuild/easyconfigs/p/Python/Python-3.5.2-foss-2016.04.eb index 3034157afb..0f528e0158 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.5.2-foss-2016.04.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.5.2-foss-2016.04.eb @@ -92,7 +92,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.13', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-3.5.2-foss-2016b.eb b/easybuild/easyconfigs/p/Python/Python-3.5.2-foss-2016b.eb index f40c4aab55..2fc712658f 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.5.2-foss-2016b.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.5.2-foss-2016b.eb @@ -92,7 +92,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.13', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], diff --git a/easybuild/easyconfigs/p/Python/Python-3.5.2-intel-2016b.eb b/easybuild/easyconfigs/p/Python/Python-3.5.2-intel-2016b.eb index 805061ab30..198569f10b 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.5.2-intel-2016b.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.5.2-intel-2016b.eb @@ -92,7 +92,7 @@ exts_list = [ }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], }), ('ecdsa', '0.13', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], -- GitLab From 2582246e9f15e21fffde3cf51c5c8e8f192422ef Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 20 Apr 2017 20:47:44 +0200 Subject: [PATCH 0623/1603] adding easyconfigs: IPython-5.3.0-intel-2017a-Python-2.7.13.eb --- ...IPython-5.3.0-intel-2017a-Python-2.7.13.eb | 176 ++++++++++++++++++ 1 file changed, 176 insertions(+) create mode 100644 easybuild/easyconfigs/i/IPython/IPython-5.3.0-intel-2017a-Python-2.7.13.eb diff --git a/easybuild/easyconfigs/i/IPython/IPython-5.3.0-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/i/IPython/IPython-5.3.0-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..62ef063309 --- /dev/null +++ b/easybuild/easyconfigs/i/IPython/IPython-5.3.0-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,176 @@ +easyblock = 'Bundle' + +name = 'IPython' +version = '5.3.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://ipython.org/index.html' +description = """IPython provides a rich architecture for interactive computing with: + Powerful interactive shells (terminal and Qt-based). + A browser-based notebook with support for code, text, mathematical expressions, inline plots and other rich media. + Support for interactive data visualization and use of GUI toolkits. + Flexible, embeddable interpreters to load into your own projects. + Easy to use, high performance tools for parallel computing.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +dependencies = [ + ('Python', '2.7.13'), + ('PyZMQ', '16.0.2', '%s-zmq4' % versionsuffix), +] + +exts_defaultclass = 'PythonPackage' + +exts_list = [ + ('nose', '1.3.7', { + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], + }), + ('requests', '2.13.0', { + 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], + }), + ('nbformat', '4.3.0', { + 'source_urls': ['https://pypi.python.org/packages/source/n/nbformat/'], + }), + ('Pygments', '2.2.0', { + 'source_urls': ['https://pypi.python.org/packages/source/P/Pygments/'], + 'modulename': 'pygments', + }), + ('singledispatch', '3.4.0.3', { + 'source_urls': ['https://pypi.python.org/packages/source/s/singledispatch/'], + }), + ('certifi', '2017.4.17', { + 'source_urls': ['https://pypi.python.org/packages/source/c/certifi/'], + }), + ('backports_abc', '0.5', { + 'source_urls': ['https://pypi.python.org/packages/source/b/backports_abc/'], + }), + ('tornado', '4.5', { + 'source_urls': ['https://pypi.python.org/packages/source/t/tornado/'], + }), + ('MarkupSafe', '1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/M/MarkupSafe/'], + 'modulename': 'markupsafe', + }), + ('Jinja2', '2.9.6', { + 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2/'], + 'modulename': 'jinja2', + }), + ('jupyter_client', '5.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/j/jupyter_client/'], + }), + ('functools32', '3.2.3-2', { + 'source_urls': ['https://pypi.python.org/packages/source/f/functools32/'], + }), + ('jsonschema', '2.6.0', { + 'source_urls': ['https://pypi.python.org/packages/source/j/jsonschema/'], + }), + ('mistune', '0.7.4', { + 'source_urls': ['https://pypi.python.org/packages/source/m/mistune/'], + }), + ('ptyprocess', '0.5.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/ptyprocess/'], + }), + ('terminado', '0.6', { + 'source_urls': ['https://pypi.python.org/packages/source/t/terminado/'], + }), + ('simplegeneric', '0.8.1', { + 'source_urls': ['https://pypi.python.org/packages/source/s/simplegeneric/'], + 'source_tmpl': 'simplegeneric-%(version)s.zip', + }), + ('ipython_genutils', '0.2.0', { + 'source_urls': ['https://pypi.python.org/packages/source/i/ipython_genutils/'], + }), + ('scandir', '1.5', { + 'source_urls': ['https://pypi.python.org/packages/source/s/scandir/'], + }), + ('pathlib2', '2.2.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pathlib2/'], + }), + ('pickleshare', '0.7.4', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pickleshare/'], + }), + ('traitlets', '4.3.2', { + 'source_urls': ['https://pypi.python.org/packages/source/t/traitlets/'], + }), + ('notebook', '5.0.0', { + 'source_urls': ['https://pypi.python.org/packages/source/n/notebook/'], + }), + ('jupyter_core', '4.3.0', { + 'source_urls': ['https://pypi.python.org/packages/source/j/jupyter_core/'], + }), + ('pexpect', '4.2.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pexpect/'], + }), + ('pandocfilters', '1.4.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pandocfilters/'], + }), + ('configparser', '3.5.0', { + 'source_urls': ['https://pypi.python.org/packages/source/c/configparser/'], + 'patches': ['configparser-3.5.0_no-backports-namespace.patch'], + 'use_pip': True, + }), + ('entrypoints', '0.2.2', { + 'source_urls': ['https://pypi.python.org/packages/source/e/entrypoints/'], + 'source_tmpl': 'entrypoints-%(version)s-py2.py3-none-any.whl', + 'unpack_sources': False, + 'use_pip': True, + }), + ('nbconvert', '5.1.1', { + 'source_urls': ['https://pypi.python.org/packages/source/n/nbconvert/'], + 'use_pip': True, + }), + ('backports.shutil_get_terminal_size', '1.0.0', { + 'source_urls': ['https://pypi.python.org/packages/source/b/backports.shutil_get_terminal_size/'], + }), + ('decorator', '4.0.11', { + 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], + }), + ('testpath', '0.3', { + 'source_urls': ['https://pypi.python.org/packages/py2.py3/t/testpath/'], + 'source_tmpl': 'testpath-%(version)s-py2.py3-none-any.whl', + 'unpack_sources': False, + 'use_pip': True, + }), + ('wcwidth', '0.1.7', { + 'source_urls': ['https://pypi.python.org/packages/source/w/wcwidth/'], + 'source_tmpl': 'wcwidth-%(version)s-py2.py3-none-any.whl', + 'unpack_sources': False, + 'use_pip': True, + }), + ('prompt-toolkit', '1.0.14', { + 'modulename': 'prompt_toolkit', + 'source_urls': ['https://pypi.python.org/packages/source/p/prompt_toolkit/'], + 'source_tmpl': 'prompt_toolkit-%(version)s-py2-none-any.whl', + 'unpack_sources': False, + 'use_pip': True, + }), + ('ipython', version, { + 'source_urls': ['https://pypi.python.org/packages/source/i/ipython/'], + 'modulename': 'IPython', + }), + ('ipykernel', '4.6.1', { + 'source_urls': ['https://pypi.python.org/packages/source/i/ipykernel/'], + }), + ('ipywidgets', '5.2.3', { + 'source_urls': ['https://pypi.python.org/packages/source/i/ipywidgets/'], + }), + ('widgetsnbextension', '2.0.0', { + 'source_urls': ['https://pypi.python.org/packages/source/w/widgetsnbextension/'], + }), +] + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +sanity_check_paths = { + 'files': ['bin/ipython'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/IPython'], +} + +sanity_check_commands = [ + ('ipython -h', ''), + ('ipython notebook --help', ''), + ('iptest', ''), + ('iptest2', ''), +] + +moduleclass = 'tools' -- GitLab From d9723ff8ec091b57e3ffbf11566782a52a612a75 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 20 Apr 2017 21:05:59 +0200 Subject: [PATCH 0624/1603] adding easyconfigs: ipyrad-0.6.15-intel-2017a-Python-2.7.13.eb, h5py-2.7.0-intel-2017a-Python-2.7.13.eb, pkgconfig-1.2.2-intel-2017a-Python-2.7.13.eb, pkg-config-0.29.2-GCCcore-6.3.0.eb --- .../h5py-2.7.0-intel-2017a-Python-2.7.13.eb | 32 +++++++ ...ipyrad-0.6.15-intel-2017a-Python-2.7.13.eb | 88 +++++++++++++++++++ .../pkg-config-0.29.2-GCCcore-6.3.0.eb | 32 +++++++ ...gconfig-1.2.2-intel-2017a-Python-2.7.13.eb | 26 ++++++ 4 files changed, 178 insertions(+) create mode 100644 easybuild/easyconfigs/h/h5py/h5py-2.7.0-intel-2017a-Python-2.7.13.eb create mode 100644 easybuild/easyconfigs/i/ipyrad/ipyrad-0.6.15-intel-2017a-Python-2.7.13.eb create mode 100644 easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2-GCCcore-6.3.0.eb create mode 100644 easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.2.2-intel-2017a-Python-2.7.13.eb diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.7.0-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/h/h5py/h5py-2.7.0-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..300f1e3d6e --- /dev/null +++ b/easybuild/easyconfigs/h/h5py/h5py-2.7.0-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonPackage' + +name = 'h5py' +version = '2.7.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.h5py.org/' +description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, + version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous + amounts of data.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'usempi': True} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +# to really use mpi enabled hdf5 we now seem to need a configure step +prebuildopts = ' python setup.py configure --mpi --hdf5=$EBROOTHDF5 && ' + +dependencies = [ + ('Python', '2.7.13'), + ('HDF5', '1.10.0-patch1'), + ('pkgconfig', '1.2.2', '-Python-%(pyver)s'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/i/ipyrad/ipyrad-0.6.15-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/i/ipyrad/ipyrad-0.6.15-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..d74840fcf3 --- /dev/null +++ b/easybuild/easyconfigs/i/ipyrad/ipyrad-0.6.15-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,88 @@ +easyblock = 'Bundle' + +name = 'ipyrad' +version = '0.6.15' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://ipyrad.readthedocs.io' +description = """ipyrad is an interactive toolkit for assembly and analysis of restriction-site associated genomic + data sets (e.g., RAD, ddRAD, GBS) for population genetic and phylogenetic studies.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' + +dependencies = [ + ('Python', '2.7.13'), + ('h5py', '2.7.0', versionsuffix), + ('numba', '0.32.0', versionsuffix), + ('IPython', '5.3.0', versionsuffix), +] + +exts_list = [ + ('imagesize', '0.7.1', { + 'source_urls': ['https://pypi.python.org/packages/source/i/imagesize'], + }), + ('alabaster', '0.7.10', { + 'source_urls': ['https://pypi.python.org/packages/source/a/alabaster'], + }), + ('Babel', '2.4.0', { + 'source_urls': ['https://pypi.python.org/packages/source/B/Babel'], + }), + ('snowballstemmer', '1.2.1', { + 'source_urls': ['https://pypi.python.org/packages/source/s/snowballstemmer'], + }), + ('docutils', '0.13.1', { + 'source_urls': ['https://pypi.python.org/packages/source/d/docutils'], + }), + ('Sphinx', '1.5.5', { + 'source_urls': ['https://pypi.python.org/packages/source/S/Sphinx'], + }), + ('networkx', '1.11', { + 'source_urls': ['https://pypi.python.org/packages/source/n/networkx'], + }), + ('jupyter', '1.0.0', { + 'source_urls': ['https://pypi.python.org/packages/source/j/jupyter'], + }), + ('ipyparallel', '6.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/i/ipyparallel'], + }), + ('webencodings', '0.5.1', { + 'source_urls': ['https://pypi.python.org/packages/source/w/webencodings'], + }), + ('html5lib', '0.999999999', { + 'source_urls': ['https://pypi.python.org/packages/source/h/html5lib'], + }), + ('bleach', '2.0.0', { + 'source_urls': ['https://pypi.python.org/packages/source/b/bleach'], + }), + ('jupyter-console', '5.1.0', { + 'modulename': 'jupyter_console', + 'source_urls': ['https://pypi.python.org/packages/source/j/jupyter_console'], + 'source_tmpl': 'jupyter_console-%(version)s.tar.gz', + }), + ('qtconsole', '4.3.0', { + 'source_urls': ['https://pypi.python.org/packages/source/q/qtconsole'], + }), + ('futures', '3.1.1', { + 'modulename': 'concurrent.futures', + 'source_urls': ['https://pypi.python.org/packages/source/f/futures'], + }), + (name, version, { + 'source_urls': ['https://github.com/dereneaton/ipyrad/archive/'], + 'source_tmpl': '%(version)s.tar.gz', + }), +] + +# specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module +full_sanity_check = True + +sanity_check_paths = { + 'files': ['bin/ipyrad'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2-GCCcore-6.3.0.eb b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..b75a0d85ea --- /dev/null +++ b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2-GCCcore-6.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'pkg-config' +version = '0.29.2' + +homepage = 'http://www.freedesktop.org/wiki/Software/pkg-config/' +description = """pkg-config is a helper tool used when compiling applications and libraries. It helps you insert the + correct compiler options on the command line so an application can use + gcc -o test test.c `pkg-config --libs --cflags glib-2.0` + for instance, rather than hard-coding values on where to find glib (or other libraries).""" + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['https://pkg-config.freedesktop.org/releases/'] + +builddependencies = [ + # use same binutils version that was used when building GCCcore toolchain + ('binutils', '2.27', '', True), +] + +# don't use PAX, it might break. +tar_config_opts = True + +configopts = " --with-internal-glib" + +sanity_check_paths = { + 'files': ['bin/pkg-config'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.2.2-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.2.2-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..0df86ffc84 --- /dev/null +++ b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.2.2-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'pkgconfig' +version = '1.2.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://github.com/matze/pkgconfig' +description = """pkgconfig is a Python module to interface with the pkg-config command line tool""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'usempi': True} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.13'), + ('pkg-config', '0.29.2'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +moduleclass = 'data' -- GitLab From 0be93bb3b688cde0add034758905359998691a30 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 20 Apr 2017 22:04:24 +0200 Subject: [PATCH 0625/1603] add patch file for configparser as extension in IPython easyconfig --- ...gparser-3.5.0_no-backports-namespace.patch | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/i/IPython/configparser-3.5.0_no-backports-namespace.patch diff --git a/easybuild/easyconfigs/i/IPython/configparser-3.5.0_no-backports-namespace.patch b/easybuild/easyconfigs/i/IPython/configparser-3.5.0_no-backports-namespace.patch new file mode 100644 index 0000000000..6deccec5e6 --- /dev/null +++ b/easybuild/easyconfigs/i/IPython/configparser-3.5.0_no-backports-namespace.patch @@ -0,0 +1,31 @@ +don't let configparser define 'backports' namespace, since that interferes with other packaging that provide stuff in 'backports' + +patch obtained from https://github.com/NIXOS/nixpkgs/blob/master/pkgs/development/python-modules/configparser/0001-namespace-fix.patch +see also https://bitbucket.org/ambv/configparser/issues/17/importerror-when-used-with-other-backports +diff --git a/setup.py b/setup.py +index 3b07823..63ed25d 100644 +--- a/setup.py ++++ b/setup.py +@@ -42,7 +42,6 @@ setup( + py_modules=modules, + package_dir={'': 'src'}, + packages=find_packages('src'), +- namespace_packages=['backports'], + include_package_data=True, + zip_safe=False, + install_requires=requirements, +diff --git a/src/backports/__init__.py b/src/backports/__init__.py +index f84d25c..febdb2f 100644 +--- a/src/backports/__init__.py ++++ b/src/backports/__init__.py +@@ -3,9 +3,3 @@ + + from pkgutil import extend_path + __path__ = extend_path(__path__, __name__) +- +-try: +- import pkg_resources +- pkg_resources.declare_namespace(__name__) +-except ImportError: +- pass +-- -- GitLab From 0c7c4f5c3d8938754cdf2229ab8aa6743d375d6d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 20 Apr 2017 23:28:04 +0200 Subject: [PATCH 0626/1603] add toyplot extension in ipyrad easyconfig file --- ...ipyrad-0.6.15-intel-2017a-Python-2.7.13.eb | 26 +++++++++++++++++- .../Pillow-4.1.0-intel-2017a-Python-2.7.13.eb | 27 +++++++++++++++++++ 2 files changed, 52 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/p/Pillow/Pillow-4.1.0-intel-2017a-Python-2.7.13.eb diff --git a/easybuild/easyconfigs/i/ipyrad/ipyrad-0.6.15-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/i/ipyrad/ipyrad-0.6.15-intel-2017a-Python-2.7.13.eb index d74840fcf3..ecce4b3046 100644 --- a/easybuild/easyconfigs/i/ipyrad/ipyrad-0.6.15-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/i/ipyrad/ipyrad-0.6.15-intel-2017a-Python-2.7.13.eb @@ -10,14 +10,15 @@ description = """ipyrad is an interactive toolkit for assembly and analysis of r toolchain = {'name': 'intel', 'version': '2017a'} -# this is a bundle of Python packages exts_defaultclass = 'PythonPackage' +exts_filter = ("python -c 'import %(ext_name)s'", '') dependencies = [ ('Python', '2.7.13'), ('h5py', '2.7.0', versionsuffix), ('numba', '0.32.0', versionsuffix), ('IPython', '5.3.0', versionsuffix), + ('Pillow', '4.1.0', versionsuffix), ] exts_list = [ @@ -69,6 +70,29 @@ exts_list = [ 'modulename': 'concurrent.futures', 'source_urls': ['https://pypi.python.org/packages/source/f/futures'], }), + ('arrow', '0.10.0', { + 'source_urls': ['https://pypi.python.org/packages/source/a/arrow'], + }), + ('colormath', '2.1.1', { + 'source_urls': ['https://pypi.python.org/packages/source/c/colormath'], + }), + ('multipledispatch', '0.4.9', { + 'source_urls': ['https://pypi.python.org/packages/source/m/multipledispatch'], + }), + ('pypng', '0.0.18', { + 'modulename': 'png', + 'source_urls': ['https://pypi.python.org/packages/source/p/pypng'], + }), + ('olefile', '0.44', { + 'source_urls': ['https://pypi.python.org/packages/source/o/olefile'], + 'source_tmpl': 'olefile-%(version)s.zip', + }), + ('reportlab', '3.4.0', { + 'source_urls': ['https://pypi.python.org/packages/source/r/reportlab'], + }), + ('toyplot', '0.14.0', { + 'source_urls': ['https://pypi.python.org/packages/source/t/toyplot'], + }), (name, version, { 'source_urls': ['https://github.com/dereneaton/ipyrad/archive/'], 'source_tmpl': '%(version)s.tar.gz', diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-4.1.0-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/p/Pillow/Pillow-4.1.0-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..f4cf66d2ef --- /dev/null +++ b/easybuild/easyconfigs/p/Pillow/Pillow-4.1.0-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'Pillow' +version = '4.1.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://pillow.readthedocs.org/' +description = """Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. + PIL is the Python Imaging Library by Fredrik Lundh and Contributors.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.13'), + ('libjpeg-turbo', '1.5.1'), + ('libpng', '1.6.29'), + ('zlib', '1.2.11'), + ('LibTIFF', '4.0.7'), + ('freetype', '2.7.1', '-libpng-1.6.29'), +] + +options = {'modulename': 'PIL'} + +moduleclass = 'vis' -- GitLab From 4dd8a3443ae8329b20a05bce182f2386c3053d9d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Fri, 21 Apr 2017 13:14:18 +0200 Subject: [PATCH 0627/1603] Go 1.8.1 binary version --- easybuild/easyconfigs/g/Go/Go-1.8.1.eb | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/g/Go/Go-1.8.1.eb diff --git a/easybuild/easyconfigs/g/Go/Go-1.8.1.eb b/easybuild/easyconfigs/g/Go/Go-1.8.1.eb new file mode 100644 index 0000000000..07ab4f25c4 --- /dev/null +++ b/easybuild/easyconfigs/g/Go/Go-1.8.1.eb @@ -0,0 +1,21 @@ +easyblock = 'Tarball' + +name = 'Go' +version = '1.8.1' + +homepage = 'http://www.golang.org' +description = """Go is an open source programming language that makes it easy to build + simple, reliable, and efficient software.""" + +toolchain = {'name': 'dummy', 'version': ''} + +sources = ['%(namelower)s%(version)s.linux-amd64.tar.gz'] +source_urls = ['https://storage.googleapis.com/golang/'] + +sanity_check_paths = { + 'files': ['bin/go', 'bin/gofmt'], + 'dirs': ['api', 'doc', 'lib', 'pkg'], +} + +modextravars = {'GOROOT': '%(installdir)s'} +moduleclass = 'compiler' -- GitLab From 6beb05e877f425ecaafe2fa8cbb60ff583c27dd5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Fri, 21 Apr 2017 13:43:25 +0200 Subject: [PATCH 0628/1603] added AdapterRemoval --- .../AdapterRemoval-2.2.0-foss-2016b.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/a/AdapterRemoval/AdapterRemoval-2.2.0-foss-2016b.eb diff --git a/easybuild/easyconfigs/a/AdapterRemoval/AdapterRemoval-2.2.0-foss-2016b.eb b/easybuild/easyconfigs/a/AdapterRemoval/AdapterRemoval-2.2.0-foss-2016b.eb new file mode 100644 index 0000000000..738b03c0ca --- /dev/null +++ b/easybuild/easyconfigs/a/AdapterRemoval/AdapterRemoval-2.2.0-foss-2016b.eb @@ -0,0 +1,35 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild + +easyblock = 'MakeCp' + +name = 'AdapterRemoval' +version = '2.2.0' + +homepage = 'https://github.com/MikkelSchubert/%(namelower)s' +description = """AdapterRemoval searches for and removes remnant adapter sequences + from High-Throughput Sequencing (HTS) data and (optionally) trims low quality bases + from the 3' end of reads following adapter removal.""" + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/MikkelSchubert/%(namelower)s/archive/'] +sources = ['v%(version)s.tar.gz'] + +files_to_copy = [(['build/%(name)s'], 'bin'), (['build/%(name)s.1'], 'share/man/man1')] + +checksums = ['159e5c7c527dde70eac444a87bf5fbfc'] + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), +] + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': ['share'] +} + +sanity_check_commands = [('AdapterRemoval', '--version')] + +moduleclass = 'bio' -- GitLab From 321af123d5b5f5bb627e1e067dbf730af59b4816 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 23 Apr 2017 13:16:53 +0200 Subject: [PATCH 0629/1603] adding easyconfigs: ViennaRNA-2.3.5-intel-2017a.eb --- .../ViennaRNA/ViennaRNA-2.3.5-intel-2017a.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.3.5-intel-2017a.eb diff --git a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.3.5-intel-2017a.eb b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.3.5-intel-2017a.eb new file mode 100644 index 0000000000..daafb8cd29 --- /dev/null +++ b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.3.5-intel-2017a.eb @@ -0,0 +1,44 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Cedric Laczny , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + +easyblock = 'ConfigureMake' + +name = 'ViennaRNA' +version = '2.3.5' + +homepage = 'http://www.tbi.univie.ac.at/RNA/' +description = """The Vienna RNA Package consists of a C code library and several +stand-alone programs for the prediction and comparison of RNA secondary structures.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True, 'openmp': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://www.tbi.univie.ac.at/RNA/download/sourcecode/%(version_major)s_%(version_minor)s_x/'] + +# Prevents the "make install" step from trying to copy to _global_ perl dir and thus make easybuild fail. +configopts = '--without-perl' +# Alternatively, you may want to use the following to copy the perl-module to a "local" directory +# Code NOT yet tested, therefor left here for future recycling +# preconfigopts = 'env PERLPREFIX="/path/where/the/perl/module/shoud/go"' + +sanity_check_paths = { + 'files': ['bin/RNA%s' % x for x in ['fold', 'eval', 'heat', 'pdist', 'distance', + 'inverse', 'plot', 'subopt', 'Lfold', 'cofold', + 'paln', 'duplex', 'alifold', 'plfold', 'up', + 'aliduplex', 'Lalifold', '2Dfold', 'parconv', + 'PKplex', 'plex', 'snoop', 'forester']] + + ['bin/Kinfold'], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From 28d361d3ce47585509674f61b14a5027ac94a1dc Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 24 Apr 2017 11:00:31 +0200 Subject: [PATCH 0630/1603] add checksum for ViennaRNA 2.3.5 source tarball --- .../easyconfigs/v/ViennaRNA/ViennaRNA-2.3.5-intel-2017a.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.3.5-intel-2017a.eb b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.3.5-intel-2017a.eb index daafb8cd29..fc2a6f62b8 100644 --- a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.3.5-intel-2017a.eb +++ b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.3.5-intel-2017a.eb @@ -25,6 +25,8 @@ toolchainopts = {'pic': True, 'openmp': True} sources = [SOURCE_TAR_GZ] source_urls = ['http://www.tbi.univie.ac.at/RNA/download/sourcecode/%(version_major)s_%(version_minor)s_x/'] +checksums = ['4542120adae9b7abb605e2304c2a1326'] + # Prevents the "make install" step from trying to copy to _global_ perl dir and thus make easybuild fail. configopts = '--without-perl' # Alternatively, you may want to use the following to copy the perl-module to a "local" directory -- GitLab From 513967084fe5171105b83b20c0cc16466b84346b Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Tue, 25 Apr 2017 17:12:25 +0800 Subject: [PATCH 0631/1603] bundle most of the python packages as extensions --- ...stodian-1.1.0-intel-2017a-Python-2.7.13.eb | 9 ++++- ...reWorks-1.4.2-intel-2017a-Python-2.7.13.eb | 33 +++++++++++++++--- ...aginate-0.4.5-intel-2017a-Python-2.7.13.eb | 27 --------------- .../Flask-0.12-intel-2017a-Python-2.7.13.eb | 26 -------------- ...nicorn-19.7.1-intel-2017a-Python-2.7.13.eb | 24 ------------- .../Jinja2-2.9.6-intel-2017a-Python-2.7.13.eb | 24 ------------- .../monty-0.9.6-intel-2017a-Python-2.7.13.eb | 26 -------------- .../mpmath-0.19-intel-2017a-Python-2.7.13.eb | 34 ------------------- ...tgen-db-0.6.5-intel-2017a-Python-2.7.13.eb | 9 ++++- ...ymatgen-4.7.3-intel-2017a-Python-2.7.13.eb | 32 ++++++++++++++--- ...pymongo-3.4.0-intel-2017a-Python-2.7.13.eb | 24 ------------- ...quests-2.13.0-intel-2017a-Python-2.7.13.eb | 24 ------------- .../smoqe-0.1.3-intel-2017a-Python-2.7.13.eb | 25 -------------- .../sympy-1.0-intel-2017a-Python-2.7.13.eb | 33 ------------------ .../s/sympy/sympy-1.0_tests-unicode.patch | 23 ------------- ...rkzeug-0.12.1-intel-2017a-Python-2.7.13.eb | 24 ------------- 16 files changed, 72 insertions(+), 325 deletions(-) delete mode 100644 easybuild/easyconfigs/f/Flask-paginate/Flask-paginate-0.4.5-intel-2017a-Python-2.7.13.eb delete mode 100644 easybuild/easyconfigs/f/Flask/Flask-0.12-intel-2017a-Python-2.7.13.eb delete mode 100644 easybuild/easyconfigs/g/gunicorn/gunicorn-19.7.1-intel-2017a-Python-2.7.13.eb delete mode 100644 easybuild/easyconfigs/j/Jinja2/Jinja2-2.9.6-intel-2017a-Python-2.7.13.eb delete mode 100644 easybuild/easyconfigs/m/monty/monty-0.9.6-intel-2017a-Python-2.7.13.eb delete mode 100644 easybuild/easyconfigs/m/mpmath/mpmath-0.19-intel-2017a-Python-2.7.13.eb delete mode 100644 easybuild/easyconfigs/p/pymongo/pymongo-3.4.0-intel-2017a-Python-2.7.13.eb delete mode 100644 easybuild/easyconfigs/r/requests/requests-2.13.0-intel-2017a-Python-2.7.13.eb delete mode 100644 easybuild/easyconfigs/s/smoqe/smoqe-0.1.3-intel-2017a-Python-2.7.13.eb delete mode 100644 easybuild/easyconfigs/s/sympy/sympy-1.0-intel-2017a-Python-2.7.13.eb delete mode 100644 easybuild/easyconfigs/s/sympy/sympy-1.0_tests-unicode.patch delete mode 100644 easybuild/easyconfigs/w/Werkzeug/Werkzeug-0.12.1-intel-2017a-Python-2.7.13.eb diff --git a/easybuild/easyconfigs/c/custodian/custodian-1.1.0-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/c/custodian/custodian-1.1.0-intel-2017a-Python-2.7.13.eb index 45b7389451..2a8be8856b 100644 --- a/easybuild/easyconfigs/c/custodian/custodian-1.1.0-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/c/custodian/custodian-1.1.0-intel-2017a-Python-2.7.13.eb @@ -15,7 +15,14 @@ sources = [SOURCE_TAR_GZ] dependencies = [ ('Python', '2.7.13'), ('PyYAML', '3.12', versionsuffix), - ('monty', '0.9.6', versionsuffix), +] + +exts_defaultclass = 'PythonPackage' + +exts_list = [ + ('monty', '0.9.6', { + 'source_urls': ['https://pypi.python.org/packages/source/m/monty/'], + }), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/f/FireWorks/FireWorks-1.4.2-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/f/FireWorks/FireWorks-1.4.2-intel-2017a-Python-2.7.13.eb index 526b35054c..0323b8f8c9 100644 --- a/easybuild/easyconfigs/f/FireWorks/FireWorks-1.4.2-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/f/FireWorks/FireWorks-1.4.2-intel-2017a-Python-2.7.13.eb @@ -15,12 +15,35 @@ sources = [SOURCE_TAR_GZ] dependencies = [ ('Python', '2.7.13'), - ('Flask', '0.12', versionsuffix), - ('Flask-paginate', '0.4.5', versionsuffix), ('PyYAML', '3.12', versionsuffix), - ('gunicorn', '19.7.1', versionsuffix), - ('monty', '0.9.6', versionsuffix), - ('pymongo', '3.4.0', versionsuffix), +] + +exts_defaultclass = 'PythonPackage' + +exts_list = [ + ('Flask', '0.12', { + 'source_urls': ['https://pypi.python.org/packages/source/F/Flask/'], + }), + ('Flask-paginate', '0.4.5', { + 'source_urls': ['https://pypi.python.org/packages/source/F/Flask-paginate/'], + 'source_tmpl': 'flask-paginate-%(version)s.zip', + 'modulename': 'flask_paginate', + }), + ('Jinja2', '2.9.6', { + 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2/'], + }), + ('Werkzeug', '0.12.1', { + 'source_urls': ['https://pypi.python.org/packages/source/W/Werkzeug/'], + }), + ('gunicorn', '19.7.1', { + 'source_urls': ['https://pypi.python.org/packages/source/g/gunicorn/'], + }), + ('monty', '0.9.6', { + 'source_urls': ['https://pypi.python.org/packages/source/m/monty/'], + }), + ('pymongo', '3.4.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pymongo/'], + }), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/f/Flask-paginate/Flask-paginate-0.4.5-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/f/Flask-paginate/Flask-paginate-0.4.5-intel-2017a-Python-2.7.13.eb deleted file mode 100644 index 153e1028fe..0000000000 --- a/easybuild/easyconfigs/f/Flask-paginate/Flask-paginate-0.4.5-intel-2017a-Python-2.7.13.eb +++ /dev/null @@ -1,27 +0,0 @@ -easyblock = "PythonPackage" - -name = 'Flask-paginate' -version = '0.4.5' -versionsuffix = '-Python-%(pyver)s' - -homepage = "https://pypi.python.org/pypi/Flask-paginate" -description = """Simple paginate support for flask.""" - -toolchain = {'name': 'intel', 'version': '2017a'} - -source_urls = [PYPI_SOURCE] -sources = [SOURCELOWER_ZIP] - -dependencies = [ - ('Python', '2.7.13'), - ('Flask', '0.12', versionsuffix), -] - -options = {'modulename': 'flask_paginate'} - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/f/Flask/Flask-0.12-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/f/Flask/Flask-0.12-intel-2017a-Python-2.7.13.eb deleted file mode 100644 index b305d04f47..0000000000 --- a/easybuild/easyconfigs/f/Flask/Flask-0.12-intel-2017a-Python-2.7.13.eb +++ /dev/null @@ -1,26 +0,0 @@ -easyblock = "PythonPackage" - -name = 'Flask' -version = '0.12' -versionsuffix = '-Python-%(pyver)s' - -homepage = "https://pypi.python.org/pypi/Flask" -description = """A microframework based on Werkzeug, Jinja2 and good intentions.""" - -toolchain = {'name': 'intel', 'version': '2017a'} - -source_urls = [PYPI_SOURCE] -sources = [SOURCE_TAR_GZ] - -dependencies = [ - ('Python', '2.7.13'), - ('Jinja2', '2.9.6', versionsuffix), - ('Werkzeug', '0.12.1', versionsuffix), -] - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/gunicorn/gunicorn-19.7.1-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/g/gunicorn/gunicorn-19.7.1-intel-2017a-Python-2.7.13.eb deleted file mode 100644 index 6e2be6854a..0000000000 --- a/easybuild/easyconfigs/g/gunicorn/gunicorn-19.7.1-intel-2017a-Python-2.7.13.eb +++ /dev/null @@ -1,24 +0,0 @@ -easyblock = "PythonPackage" - -name = 'gunicorn' -version = '19.7.1' -versionsuffix = '-Python-%(pyver)s' - -homepage = "https://pypi.python.org/pypi/gunicorn" -description = """WSGI HTTP Server for UNIX.""" - -toolchain = {'name': 'intel', 'version': '2017a'} - -source_urls = [PYPI_SOURCE] -sources = [SOURCE_TAR_GZ] - -dependencies = [ - ('Python', '2.7.13'), -] - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/j/Jinja2/Jinja2-2.9.6-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/j/Jinja2/Jinja2-2.9.6-intel-2017a-Python-2.7.13.eb deleted file mode 100644 index 0069b2587c..0000000000 --- a/easybuild/easyconfigs/j/Jinja2/Jinja2-2.9.6-intel-2017a-Python-2.7.13.eb +++ /dev/null @@ -1,24 +0,0 @@ -easyblock = "PythonPackage" - -name = 'Jinja2' -version = '2.9.6' -versionsuffix = '-Python-%(pyver)s' - -homepage = "https://pypi.python.org/pypi/Jinja2" -description = """A small but fast and easy to use stand-alone template engine written in pure python.""" - -toolchain = {'name': 'intel', 'version': '2017a'} - -source_urls = [PYPI_SOURCE] -sources = [SOURCE_TAR_GZ] - -dependencies = [ - ('Python', '2.7.13'), -] - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/m/monty/monty-0.9.6-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/m/monty/monty-0.9.6-intel-2017a-Python-2.7.13.eb deleted file mode 100644 index 64c36ac39f..0000000000 --- a/easybuild/easyconfigs/m/monty/monty-0.9.6-intel-2017a-Python-2.7.13.eb +++ /dev/null @@ -1,26 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'monty' -version = '0.9.6' -versionsuffix = '-Python-%(pyver)s' - -homepage = "https://pypi.python.org/pypi/monty/" -description = """Monty implements supplementary useful functions for Python that are not part of the standard library. - Examples include useful utilities like transparent support for zipped files, useful design patterns such as singleton - and cached_class, and many more.""" - -toolchain = {'name': 'intel', 'version': '2017a'} - -source_urls = [PYPI_SOURCE] -sources = [SOURCE_TAR_GZ] - -dependencies = [ - ('Python', '2.7.13'), -] - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s-%(version)s-py%(pyshortver)s.egg'], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/mpmath/mpmath-0.19-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/m/mpmath/mpmath-0.19-intel-2017a-Python-2.7.13.eb deleted file mode 100644 index db5a0e5289..0000000000 --- a/easybuild/easyconfigs/m/mpmath/mpmath-0.19-intel-2017a-Python-2.7.13.eb +++ /dev/null @@ -1,34 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild -# -# Author: Adam Huffman -# adam.huffman@crick.ac.uk -# The Francis Crick Institute - -easyblock = 'PythonPackage' - -name = 'mpmath' -version = '0.19' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'http://mpmath.org/' -description = """mpmath can be used as an arbitrary-precision substitute for Python's float/complex - types and math/cmath modules, but also does much more advanced mathematics. Almost any calculation - can be performed just as well at 10-digit or 1000-digit precision, with either real or complex - numbers, and in many cases mpmath implements efficient algorithms that scale well for extremely - high precision work.""" - -toolchain = {'name': 'intel', 'version': '2017a'} - -source_urls = ['https://github.com/fredrik-johansson/mpmath/archive/'] -sources = ['%(version)s.tar.gz'] - -dependencies = [('Python', '2.7.13')] - -runtest = 'python -c "import mpmath; mpmath.runtests();"' - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages/mpmath'], -} - -moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/pymatgen-db/pymatgen-db-0.6.5-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/p/pymatgen-db/pymatgen-db-0.6.5-intel-2017a-Python-2.7.13.eb index 908d8b8ff5..b7bde5299a 100644 --- a/easybuild/easyconfigs/p/pymatgen-db/pymatgen-db-0.6.5-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/p/pymatgen-db/pymatgen-db-0.6.5-intel-2017a-Python-2.7.13.eb @@ -16,7 +16,14 @@ sources = [SOURCE_TAR_GZ] dependencies = [ ('Python', '2.7.13'), ('pymatgen', '4.7.3', versionsuffix), - ('smoqe', '0.1.3', versionsuffix), +] + +exts_defaultclass = 'PythonPackage' + +exts_list = [ + ('smoqe', '0.1.3', { + 'source_urls': ['https://pypi.python.org/packages/source/s/smoqe/'], + }), ] options = {'modulename': 'matgendb'} diff --git a/easybuild/easyconfigs/p/pymatgen/pymatgen-4.7.3-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/p/pymatgen/pymatgen-4.7.3-intel-2017a-Python-2.7.13.eb index f8b263a2dd..c011699956 100644 --- a/easybuild/easyconfigs/p/pymatgen/pymatgen-4.7.3-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/p/pymatgen/pymatgen-4.7.3-intel-2017a-Python-2.7.13.eb @@ -17,11 +17,35 @@ dependencies = [ ('Python', '2.7.13'), ('PyYAML', '3.12', versionsuffix), ('matplotlib', '2.0.0', versionsuffix), - ('monty', '0.9.6', versionsuffix), - ('mpmath', '0.19', versionsuffix), - ('requests', '2.13.0', versionsuffix), ('spglib-python', '1.9.9.38', versionsuffix), - ('sympy', '1.0', versionsuffix), +] + +exts_defaultclass = 'PythonPackage' + +exts_list = [ + ('Flask', '0.12', { + 'source_urls': ['https://pypi.python.org/packages/source/F/Flask/'], + }), + ('Flask-paginate', '0.4.5', { + 'source_urls': ['https://pypi.python.org/packages/source/F/Flask-paginate/'], + 'source_tmpl': 'flask-paginate-%(version)s.zip', + 'modulename': 'flask_paginate', + }), + ('gunicorn', '19.7.1', { + 'source_urls': ['https://pypi.python.org/packages/source/g/gunicorn/'], + }), + ('monty', '0.9.6', { + 'source_urls': ['https://pypi.python.org/packages/source/m/monty/'], + }), + ('mpmath', '0.19', { + 'source_urls': ['https://pypi.python.org/packages/source/m/mpmath/'], + }), + ('requests', '2.13.0', { + 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], + }), + ('sympy', '1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/sympy/'], + }), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/p/pymongo/pymongo-3.4.0-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/p/pymongo/pymongo-3.4.0-intel-2017a-Python-2.7.13.eb deleted file mode 100644 index 9bb19f1090..0000000000 --- a/easybuild/easyconfigs/p/pymongo/pymongo-3.4.0-intel-2017a-Python-2.7.13.eb +++ /dev/null @@ -1,24 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'pymongo' -version = '3.4.0' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://pypi.python.org/pypi/pymongo' -description = """Python driver for MongoDB.""" - -toolchain = {'name': 'intel', 'version': '2017a'} - -source_urls = [PYPI_LOWER_SOURCE] -sources = [SOURCELOWER_TAR_GZ] - -dependencies = [ - ('Python', '2.7.13'), -] - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -moduleclass = 'data' diff --git a/easybuild/easyconfigs/r/requests/requests-2.13.0-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/r/requests/requests-2.13.0-intel-2017a-Python-2.7.13.eb deleted file mode 100644 index 786bbdf2c6..0000000000 --- a/easybuild/easyconfigs/r/requests/requests-2.13.0-intel-2017a-Python-2.7.13.eb +++ /dev/null @@ -1,24 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'requests' -version = '2.13.0' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://pypi.python.org/pypi/requests' -description = """Python http for humans.""" - -toolchain = {'name': 'intel', 'version': '2017a'} - -source_urls = [PYPI_LOWER_SOURCE] -sources = [SOURCELOWER_TAR_GZ] - -dependencies = [ - ('Python', '2.7.13'), -] - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/smoqe/smoqe-0.1.3-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/s/smoqe/smoqe-0.1.3-intel-2017a-Python-2.7.13.eb deleted file mode 100644 index a5ff78eb95..0000000000 --- a/easybuild/easyconfigs/s/smoqe/smoqe-0.1.3-intel-2017a-Python-2.7.13.eb +++ /dev/null @@ -1,25 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'smoqe' -version = '0.1.3' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://pypi.python.org/pypi/smoqe' -description = """Simple MongoDB Query Engine (SMoQE).""" - -toolchain = {'name': 'intel', 'version': '2017a'} - -source_urls = [PYPI_LOWER_SOURCE] -sources = [SOURCELOWER_TAR_GZ] - -dependencies = [ - ('Python', '2.7.13'), - ('pymongo', '3.4.0', versionsuffix), -] - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/sympy/sympy-1.0-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/s/sympy/sympy-1.0-intel-2017a-Python-2.7.13.eb deleted file mode 100644 index 444574067c..0000000000 --- a/easybuild/easyconfigs/s/sympy/sympy-1.0-intel-2017a-Python-2.7.13.eb +++ /dev/null @@ -1,33 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'sympy' -version = '1.0' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'http://sympy.org/' -description = """SymPy is a Python library for symbolic mathematics. It aims to - become a full-featured computer algebra system (CAS) while keeping the code as - simple as possible in order to be comprehensible and easily extensible. SymPy - is written entirely in Python and does not require any external libraries.""" - -toolchain = {'name': 'intel', 'version': '2017a'} - -source_urls = [PYPI_SOURCE] -sources = [SOURCE_TAR_GZ] - -# patch to fix tests -patches = ['sympy-1.0_tests-unicode.patch'] - -dependencies = [ - ('Python', '2.7.13'), - ('mpmath', '0.19', '-Python-%(pyver)s'), -] - -# runtest = 'python setup.py test' - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s-%(version)s-py%(pyshortver)s.egg/%(name)s'], -} - -moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/sympy/sympy-1.0_tests-unicode.patch b/easybuild/easyconfigs/s/sympy/sympy-1.0_tests-unicode.patch deleted file mode 100644 index 87e12a3b40..0000000000 --- a/easybuild/easyconfigs/s/sympy/sympy-1.0_tests-unicode.patch +++ /dev/null @@ -1,23 +0,0 @@ -Fix for Unicode error that causes one of the tests to fail - -For reference, see -http://stackoverflow.com/questions/21129020/how-to-fix-unicodedecodeerror-ascii-codec-cant-decode-byte -and http://nedbatchelder.com/text/unipain/unipain.html - -Patch created by: - -Adam Huffman -The Francis Crick Institute - -diff -ur sympy-sympy-1.0/sympy/utilities/autowrap.py sympy-sympy-1.0.new/sympy/utilities/autowrap.py ---- sympy-sympy-1.0/sympy/utilities/autowrap.py 2016-03-08 18:35:33.000000000 +0000 -+++ sympy-sympy-1.0.new/sympy/utilities/autowrap.py 2016-05-15 10:54:52.870235379 +0100 -@@ -164,7 +164,7 @@ - except CalledProcessError as e: - raise CodeWrapError( - "Error while executing command: %s. Command output is:\n%s" % ( -- " ".join(command), e.output.decode())) -+ " ".join(command), e.output.decode('ascii', 'ignore'))) - if not self.quiet: - print(retoutput) - diff --git a/easybuild/easyconfigs/w/Werkzeug/Werkzeug-0.12.1-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/w/Werkzeug/Werkzeug-0.12.1-intel-2017a-Python-2.7.13.eb deleted file mode 100644 index 9f007d3773..0000000000 --- a/easybuild/easyconfigs/w/Werkzeug/Werkzeug-0.12.1-intel-2017a-Python-2.7.13.eb +++ /dev/null @@ -1,24 +0,0 @@ -easyblock = "PythonPackage" - -name = 'Werkzeug' -version = '0.12.1' -versionsuffix = '-Python-%(pyver)s' - -homepage = "https://pypi.python.org/pypi/WerkZeug" -description = """The Swiss Army knife of Python web development.""" - -toolchain = {'name': 'intel', 'version': '2017a'} - -source_urls = [PYPI_SOURCE] -sources = [SOURCE_TAR_GZ] - -dependencies = [ - ('Python', '2.7.13'), -] - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -moduleclass = 'devel' -- GitLab From 5cbbbd21c3081ec7f660939e08bb4e12b23b3063 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Tue, 25 Apr 2017 18:05:52 +0800 Subject: [PATCH 0632/1603] restore erroneously deleted file --- .../s/sympy/sympy-1.0_tests-unicode.patch | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/s/sympy/sympy-1.0_tests-unicode.patch diff --git a/easybuild/easyconfigs/s/sympy/sympy-1.0_tests-unicode.patch b/easybuild/easyconfigs/s/sympy/sympy-1.0_tests-unicode.patch new file mode 100644 index 0000000000..87e12a3b40 --- /dev/null +++ b/easybuild/easyconfigs/s/sympy/sympy-1.0_tests-unicode.patch @@ -0,0 +1,23 @@ +Fix for Unicode error that causes one of the tests to fail + +For reference, see +http://stackoverflow.com/questions/21129020/how-to-fix-unicodedecodeerror-ascii-codec-cant-decode-byte +and http://nedbatchelder.com/text/unipain/unipain.html + +Patch created by: + +Adam Huffman +The Francis Crick Institute + +diff -ur sympy-sympy-1.0/sympy/utilities/autowrap.py sympy-sympy-1.0.new/sympy/utilities/autowrap.py +--- sympy-sympy-1.0/sympy/utilities/autowrap.py 2016-03-08 18:35:33.000000000 +0000 ++++ sympy-sympy-1.0.new/sympy/utilities/autowrap.py 2016-05-15 10:54:52.870235379 +0100 +@@ -164,7 +164,7 @@ + except CalledProcessError as e: + raise CodeWrapError( + "Error while executing command: %s. Command output is:\n%s" % ( +- " ".join(command), e.output.decode())) ++ " ".join(command), e.output.decode('ascii', 'ignore'))) + if not self.quiet: + print(retoutput) + -- GitLab From ce6e45a9eff79478f37e7e8dec137a229cd1c9bc Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Tue, 25 Apr 2017 18:12:09 +0800 Subject: [PATCH 0633/1603] use Bundle easyblock for easyconfigs with extensions --- .../custodian-1.1.0-intel-2017a-Python-2.7.13.eb | 14 ++++++++++---- .../FireWorks-1.4.2-intel-2017a-Python-2.7.13.eb | 14 ++++++++++---- ...pymatgen-db-0.6.5-intel-2017a-Python-2.7.13.eb | 15 ++++++++++----- .../pymatgen-4.7.3-intel-2017a-Python-2.7.13.eb | 14 ++++++++++---- 4 files changed, 40 insertions(+), 17 deletions(-) diff --git a/easybuild/easyconfigs/c/custodian/custodian-1.1.0-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/c/custodian/custodian-1.1.0-intel-2017a-Python-2.7.13.eb index 2a8be8856b..e8bf835f61 100644 --- a/easybuild/easyconfigs/c/custodian/custodian-1.1.0-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/c/custodian/custodian-1.1.0-intel-2017a-Python-2.7.13.eb @@ -1,4 +1,4 @@ -easyblock = "PythonPackage" +easyblock = 'Bundle' name = 'custodian' version = '1.1.0' @@ -9,22 +9,28 @@ description = """A simple JIT job management framework in Python.""" toolchain = {'name': 'intel', 'version': '2017a'} -source_urls = [PYPI_SOURCE] -sources = [SOURCE_TAR_GZ] - dependencies = [ ('Python', '2.7.13'), ('PyYAML', '3.12', versionsuffix), ] +# this is a bundle of Python packages exts_defaultclass = 'PythonPackage' exts_list = [ + ('custodian', version, { + 'source_urls': ['https://pypi.python.org/packages/source/c/custodian/'], + }), ('monty', '0.9.6', { 'source_urls': ['https://pypi.python.org/packages/source/m/monty/'], }), ] +# specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module +full_sanity_check = True + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + sanity_check_paths = { 'files': [], 'dirs': ['lib/python%(pyshortver)s/site-packages'] diff --git a/easybuild/easyconfigs/f/FireWorks/FireWorks-1.4.2-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/f/FireWorks/FireWorks-1.4.2-intel-2017a-Python-2.7.13.eb index 0323b8f8c9..f776bdcadf 100644 --- a/easybuild/easyconfigs/f/FireWorks/FireWorks-1.4.2-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/f/FireWorks/FireWorks-1.4.2-intel-2017a-Python-2.7.13.eb @@ -1,4 +1,4 @@ -easyblock = "PythonPackage" +easyblock = 'Bundle' name = 'FireWorks' version = '1.4.2' @@ -10,17 +10,18 @@ description = """FireWorks helps run calculation workflows, with a centralized w toolchain = {'name': 'intel', 'version': '2017a'} -source_urls = [PYPI_SOURCE] -sources = [SOURCE_TAR_GZ] - dependencies = [ ('Python', '2.7.13'), ('PyYAML', '3.12', versionsuffix), ] +# this is a bundle of Python packages exts_defaultclass = 'PythonPackage' exts_list = [ + ('FireWorks', version, { + 'source_urls': ['https://pypi.python.org/packages/source/F/FireWorks/'], + }), ('Flask', '0.12', { 'source_urls': ['https://pypi.python.org/packages/source/F/Flask/'], }), @@ -46,6 +47,11 @@ exts_list = [ }), ] +# specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module +full_sanity_check = True + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + sanity_check_paths = { 'files': [], 'dirs': ['lib/python%(pyshortver)s/site-packages'] diff --git a/easybuild/easyconfigs/p/pymatgen-db/pymatgen-db-0.6.5-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/p/pymatgen-db/pymatgen-db-0.6.5-intel-2017a-Python-2.7.13.eb index b7bde5299a..007db0084d 100644 --- a/easybuild/easyconfigs/p/pymatgen-db/pymatgen-db-0.6.5-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/p/pymatgen-db/pymatgen-db-0.6.5-intel-2017a-Python-2.7.13.eb @@ -1,4 +1,4 @@ -easyblock = "PythonPackage" +easyblock = 'Bundle' name = 'pymatgen-db' version = '0.6.5' @@ -10,23 +10,28 @@ description = """Pymatgen-db is a database add-on for the Python Materials Genom toolchain = {'name': 'intel', 'version': '2017a'} -source_urls = [PYPI_SOURCE] -sources = [SOURCE_TAR_GZ] - dependencies = [ ('Python', '2.7.13'), ('pymatgen', '4.7.3', versionsuffix), ] +# this is a bundle of Python packages exts_defaultclass = 'PythonPackage' exts_list = [ + ('pymatgen-db', '0.6.5', { + 'modulename': 'matgendb', + 'source_urls': ['https://pypi.python.org/packages/source/p/pymatgen-db/'], + }), ('smoqe', '0.1.3', { 'source_urls': ['https://pypi.python.org/packages/source/s/smoqe/'], }), ] -options = {'modulename': 'matgendb'} +# specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module +full_sanity_check = True + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} sanity_check_paths = { 'files': [], diff --git a/easybuild/easyconfigs/p/pymatgen/pymatgen-4.7.3-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/p/pymatgen/pymatgen-4.7.3-intel-2017a-Python-2.7.13.eb index c011699956..718deacce4 100644 --- a/easybuild/easyconfigs/p/pymatgen/pymatgen-4.7.3-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/p/pymatgen/pymatgen-4.7.3-intel-2017a-Python-2.7.13.eb @@ -1,4 +1,4 @@ -easyblock = 'PythonPackage' +easyblock = 'Bundle' name = 'pymatgen' version = '4.7.3' @@ -10,9 +10,6 @@ description = """Python Materials Genomics is a robust materials analysis code t toolchain = {'name': 'intel', 'version': '2017a'} -source_urls = [PYPI_SOURCE] -sources = [SOURCE_TAR_GZ] - dependencies = [ ('Python', '2.7.13'), ('PyYAML', '3.12', versionsuffix), @@ -20,6 +17,7 @@ dependencies = [ ('spglib-python', '1.9.9.38', versionsuffix), ] +# this is a bundle of Python packages exts_defaultclass = 'PythonPackage' exts_list = [ @@ -40,6 +38,9 @@ exts_list = [ ('mpmath', '0.19', { 'source_urls': ['https://pypi.python.org/packages/source/m/mpmath/'], }), + ('pymatgen', version, { + 'source_urls': ['https://pypi.python.org/packages/source/p/pymatgen/'], + }), ('requests', '2.13.0', { 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], }), @@ -48,6 +49,11 @@ exts_list = [ }), ] +# specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module +full_sanity_check = True + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + sanity_check_paths = { 'files': [], 'dirs': ['lib/python%(pyshortver)s/site-packages'] -- GitLab From 07ac52418a3dd86aaa411fb487e172b7c3ae50cb Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Tue, 25 Apr 2017 15:51:57 +0200 Subject: [PATCH 0634/1603] {chem} [dummy] ORCA/4.0.0.2 --- .../o/ORCA/ORCA-4.0.0.2-OpenMPI-2.0.2.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/o/ORCA/ORCA-4.0.0.2-OpenMPI-2.0.2.eb diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-4.0.0.2-OpenMPI-2.0.2.eb b/easybuild/easyconfigs/o/ORCA/ORCA-4.0.0.2-OpenMPI-2.0.2.eb new file mode 100644 index 0000000000..c9312c4044 --- /dev/null +++ b/easybuild/easyconfigs/o/ORCA/ORCA-4.0.0.2-OpenMPI-2.0.2.eb @@ -0,0 +1,38 @@ +easyblock = "PackedBinary" + +name = "ORCA" +version = '4.0.0.2' + +openmpiversion = '2.0.2' +versionsuffix = '-OpenMPI-%s' % openmpiversion + +homepage = 'http://cec.mpg.de/forum/' +description = """ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum chemistry + with specific emphasis on spectroscopic properties of open-shell molecules. + It features a wide variety of standard quantum chemical methods ranging from semiempirical methods to DFT to single- + and multireference correlated ab initio methods. + It can also treat environmental and relativistic effects.""" + +toolchain = {'name': 'dummy', 'version': ''} + +# Download from https://cec.mpg.de/orcadownload/index.php +sources = ['%%(namelower)s_%s_linux_x86-64_openmpi%s.tbz' % (version.replace('.', '_'), openmpiversion.replace('.', ''))] + +checksums = ['a5b8ecdd3d004af4bc8190c986f34e11'] + +dependencies = [('OpenMPI', openmpiversion, '-GCC-6.3.0-2.27')] + +sanity_check_paths = { + 'files': ['orca_%s%s' % (x, y) for x in ['anoint', 'casscf', 'cis', 'cleanup', 'cpscf', + 'eprnmr', 'gtoint', 'mdci', 'mp2', 'mrci', 'pc', + 'rocis', 'scf', 'scfgrad', 'soc'] + for y in ["", "_mpi"]] + + ['orca_%s' % x for x in ['2mkl', 'asa', 'chelpg', 'ciprep', 'eca', 'ecplib', + 'euler', 'fci', 'fitpes', 'gstep', 'loc', 'mapspc', + 'md', 'mergefrag', 'ndoint', 'numfreq', 'plot', + 'pltvib', 'pop', 'rel', 'vib', 'vpot']] + + ['orca'], + 'dirs': [], +} + +moduleclass = 'chem' -- GitLab From fb97882c1ab2909d8026a599a4ca7bf1baf576fc Mon Sep 17 00:00:00 2001 From: "\"Andreas \"" Date: Tue, 25 Apr 2017 20:19:15 +0200 Subject: [PATCH 0635/1603] adding easyconfigs: Python-2.7.12-foss-2017a.eb --- .../p/Python/Python-2.7.12-foss-2017a.eb | 293 ++++++++++++++++++ 1 file changed, 293 insertions(+) create mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.12-foss-2017a.eb diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.12-foss-2017a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.12-foss-2017a.eb new file mode 100644 index 0000000000..b8e862c97f --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.12-foss-2017a.eb @@ -0,0 +1,293 @@ +# Built with EasyBuild version 3.1.1 on 2017-04-21_17-31-01 +# Built with EasyBuild version 3.1.1 on 2017-04-20_11-17-51 +# Built with EasyBuild version 3.1.1 on 2017-04-03_09-46-50 +name = 'Python' +version = '2.7.12' + +homepage = 'http://python.org/' +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" + +toolchain = {'name': 'foss', 'version': '2017a'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +# python needs bzip2 to build the bz2 package +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.11'), + ('libreadline', '6.3'), + ('ncurses', '6.0'), + ('SQLite', '3.13.0'), + ('Tk', '8.6.5'), # this requires a full X11 stack + ('GMP', '6.1.1'), + ('libffi', '3.2.1'), + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.2h'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# order is important! +# package versions updated March 30th 2017 +# setuptools 34.3.3 zip +exts_list = [ + ('setuptools', '23.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], + }), + ('pip', '9.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], + }), + ('nose', '1.3.7', { + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], + }), + ('numpy', '1.11.1', { + 'source_urls': ['https://pypi.python.org/packages/source/n/numpy'], + 'patches': ['numpy-1.8.0-mkl.patch'], + }), + ('scipy', '0.19.0', { + 'source_tmpl': '%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/s/scipy'], + }), + ('blist', '1.3.6', { + 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], + }), + ('mpi4py', '2.0.0', { + 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + }), + ('paycheck', '1.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], + }), + ('pbr', '2.0.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], + }), + ('lockfile', '0.12.2', { + 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], + }), + ('Cython', '0.25.2', { + 'source_urls': ['https://pypi.python.org/packages/source/c/cython/'], + }), + ('six', '1.10.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), + ('dateutil', '2.6.0', { + 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], + }), + ('deap', '1.0.2', { + 'source_tmpl': '%(name)s-%(version)s.post2.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], + }), + ('decorator', '4.0.11', { + 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], + }), + ('arff', '2.1.0', { + 'source_tmpl': 'liac-%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], + }), + ('pycrypto', '2.6.1', { + 'modulename': 'Crypto', + 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + }), + ('ecdsa', '0.13', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), + ('cryptography', '1.8.1', { + 'source_urls': ['https://pypi.python.org/packages/source/c/cryptography/'], + }), + ('paramiko', '2.1.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], + }), + ('pyparsing', '2.2.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], + }), + ('netifaces', '0.10.5', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], + }), + ('netaddr', '0.7.19', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], + }), + ('funcsigs', '1.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/f/funcsigs'], + }), + ('mock', '2.0.0', { + 'source_urls': ['https://pypi.python.org/packages/source/m/mock'], + }), + ('pytz', '2017.2', { + 'source_tmpl': '%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/p/pytz'], + }), + ('pandas', '0.19.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], + }), + ('enum34', '1.1.6', { + 'modulename': 'enum', + 'source_urls': ['https://pypi.python.org/packages/source/e/enum34'], + }), + ('bitstring', '3.1.5', { + 'source_tmpl': '%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/b/bitstring'], + }), + ('virtualenv', '15.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/v/virtualenv'], + }), +] + +moduleclass = 'lang' + +# Build statistics +buildstats = [{ + "build_time": 2237.89, + "command_line": ["--buildpath='/dev/shm'", "--configfiles='/cluster/easybuild/config.cfg'", "--installpath='/cluster/easybuild'", "--module-naming-scheme='CategorizedModuleNamingScheme'", "--module-syntax='Tcl'", "--modules-tool='EnvironmentModulesC'", "--packagepath='/cluster/easybuild/packages'", "--parallel='40'", "--prefix='/cluster/easybuild'", '--rebuild', "--repository='GitRepository'", "--repositorypath='/cluster/easybuild/ebfiles_repo.git'", "--robot='/cluster/easybuild/software/EasyBuild/3.1.1/lib/python2.7/site-packages/easybuild_easyconfigs-3.1.1-py2.7.egg/easybuild/easyconfigs'", "--sourcepath='/cluster/easybuild/sources'", 'Python-2.7.12-foss-2017a-updated.eb'], + "core_count": 40, + "cpu_model": "Intel(R) 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"7.3.1611", + "platform_name": "x86_64-unknown-linux", + "python_version": "2.7.5 (default, Nov 6 2016, 00:28:07) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-11)]", + "system_gcc_path": "/cluster/easybuild/software/compiler/GCCcore/6.3.0/bin/gcc", + "system_python_path": "/usr/bin/python", + "timestamp": 1492788660, + "total_memory": 128828, +}, +] -- GitLab From 89f32f26dbe584295199ddd82dcac02a1691aaf6 Mon Sep 17 00:00:00 2001 From: "\"Andreas \"" Date: Tue, 25 Apr 2017 20:21:09 +0200 Subject: [PATCH 0636/1603] adding easyconfigs: OSU-Micro-Benchmarks-5.3.2-foss-2017a.eb --- .../OSU-Micro-Benchmarks-5.3.2-foss-2017a.eb | 51 +++++++++++++++++++ 1 file changed, 51 insertions(+) create mode 100644 easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.3.2-foss-2017a.eb diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.3.2-foss-2017a.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.3.2-foss-2017a.eb new file mode 100644 index 0000000000..773f1229f6 --- /dev/null +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.3.2-foss-2017a.eb @@ -0,0 +1,51 @@ +# Built with EasyBuild version 3.1.1 on 2017-04-04_19-59-16 +easyblock = 'ConfigureMake' + +name = 'OSU-Micro-Benchmarks' +version = '5.3.2' + +homepage = 'http://mvapich.cse.ohio-state.edu/benchmarks/' +description = """OSU Micro-Benchmarks""" + +toolchain = {'name': 'foss', 'version': '2017a'} + +source_urls = ['http://mvapich.cse.ohio-state.edu/download/mvapich/'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = 'CC="$MPICC" CXX="$MPICC"' + +benchmark_dirs = ['libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt']] +modextrapaths = {'PATH': benchmark_dirs} + +sanity_check_paths = { + 'files': [], + 'dirs': benchmark_dirs, +} + +moduleclass = 'perf' + +# Build statistics +buildstats = [{ + "build_time": 15.4, + "command_line": ["--buildpath='/dev/shm'", "--configfiles='/cluster/easybuild/config.cfg'", "--installpath='/cluster/easybuild'", "--module-naming-scheme='CategorizedModuleNamingScheme'", "--module-syntax='Tcl'", "--modules-tool='EnvironmentModulesC'", "--packagepath='/cluster/easybuild/packages'", "--parallel='40'", "--prefix='/cluster/easybuild'", "--repository='GitRepository'", "--repositorypath='/cluster/easybuild/ebfiles_repo.git'", "--robot-paths=':/cluster/easybuild/ebfiles_repo'", "--sourcepath='/cluster/easybuild/sources'", 'OSU-Micro-Benchmarks-5.3.2-foss-2017a.eb'], + "core_count": 40, + "cpu_model": "Intel(R) Xeon(R) CPU E5-2630 v4 @ 2.20GHz", + "cpu_speed": 3100.0, + "cpu_vendor": "Intel", + "easybuild-easyblocks_version": "3.1.1", + "easybuild-framework_version": "3.1.1", + "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/cluster/easybuild/software/compiler/GCCcore/6.3.0/libexec/gcc/x86_64-pc-linux-gnu/6.3.0/lto-wrapper; Target: x86_64-pc-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --with-local-prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --enable-bootstrap --with-isl=/dev/shm/GCCcore/6.3.0/dummy-/gcc-6.3.0/stage2_stuff; Thread model: posix; gcc version 6.3.0 (GCC) ; ", + "glibc_version": "2.17", + "hostname": "login23", + "install_size": 1041307, + "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'), + "os_name": "centos linux", + "os_type": "Linux", + "os_version": "7.3.1611", + "platform_name": "x86_64-unknown-linux", + "python_version": "2.7.5 (default, Nov 6 2016, 00:28:07) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-11)]", + "system_gcc_path": "/cluster/easybuild/software/compiler/GCCcore/6.3.0/bin/gcc", + "system_python_path": "/usr/bin/python", + "timestamp": 1491328756, + "total_memory": 128828, +}] -- GitLab From cb391d58e57d511606572ea9d503ca1fd6ec9802 Mon Sep 17 00:00:00 2001 From: "\"Andreas \"" Date: Tue, 25 Apr 2017 20:22:20 +0200 Subject: [PATCH 0637/1603] adding easyconfigs: LLVM-4.0.0-foss-2017a.eb, LLVM-3.9.1-foss-2017a.eb --- .../l/LLVM/LLVM-3.9.1-foss-2017a.eb | 123 +++++++ .../l/LLVM/LLVM-4.0.0-foss-2017a.eb | 301 ++++++++++++++++++ 2 files changed, 424 insertions(+) create mode 100644 easybuild/easyconfigs/l/LLVM/LLVM-3.9.1-foss-2017a.eb create mode 100644 easybuild/easyconfigs/l/LLVM/LLVM-4.0.0-foss-2017a.eb diff --git a/easybuild/easyconfigs/l/LLVM/LLVM-3.9.1-foss-2017a.eb b/easybuild/easyconfigs/l/LLVM/LLVM-3.9.1-foss-2017a.eb new file mode 100644 index 0000000000..be174d687f --- /dev/null +++ b/easybuild/easyconfigs/l/LLVM/LLVM-3.9.1-foss-2017a.eb @@ -0,0 +1,123 @@ +# Built with EasyBuild version 3.1.1 on 2017-04-22_13-55-34 +# Built with EasyBuild version 3.1.1 on 2017-04-04_11-30-48 +easyblock = 'CMakeMake' + +name = 'LLVM' +version = "3.9.1" + +homepage = "http://llvm.org/" +description = """The LLVM Core libraries provide a modern source- and target-independent + optimizer, along with code generation support for many popular CPUs + (as well as some less common ones!) These libraries are built around a well + specified code representation known as the LLVM intermediate representation + ("LLVM IR"). The LLVM Core libraries are well documented, and it is + particularly easy to invent your own language (or port an existing compiler) + to use LLVM as an optimizer and code generator.""" + +toolchain = {'name': 'foss', 'version': '2017a'} +toolchainopts = {'cstd': 'gnu++11'} + +source_urls = ["http://llvm.org/releases/%(version)s"] +sources = ["llvm-%(version)s.src.tar.xz"] + +builddependencies = [ + ('CMake', '3.7.2'), + ('Python', '2.7.12'), +] + +dependencies = [ + ('ncurses', '6.0'), + ('zlib', '1.2.11'), +] + +configopts = '-DBUILD_SHARED_LIBS=ON ' +# required to install extra tools in bin/ +configopts += '-DLLVM_INSTALL_UTILS=ON -DLLVM_TARGETS_TO_BUILD=X86 -DLLVM_ENABLE_ZLIB=ON ' +configopts += '-DCMAKE_BUILD_TYPE=Release ' + +sanity_check_paths = { + 'files': ['bin/llvm-ar', 'bin/FileCheck'], + 'dirs': ['include/llvm', 'include/llvm-c'], +} + +separate_build_dir = True + +moduleclass = 'compiler' + +# Build statistics +buildstats = [{ + "build_time": 520.33, + "command_line": ["--buildpath='/dev/shm'", "--configfiles='/cluster/easybuild/config.cfg'", "--installpath='/cluster/easybuild'", "--module-naming-scheme='CategorizedModuleNamingScheme'", "--module-syntax='Tcl'", "--modules-tool='EnvironmentModulesC'", "--packagepath='/cluster/easybuild/packages'", "--parallel='40'", "--prefix='/cluster/easybuild'", "--repository='GitRepository'", "--repositorypath='/cluster/easybuild/ebfiles_repo.git'", "--robot-paths=':/cluster/easybuild/ebfiles_repo'", "--sourcepath='/cluster/easybuild/sources'", '--use-existing-modules', 'LLVM-3.9.0-foss-2017a.eb'], + "core_count": 40, + "cpu_model": "Intel(R) Xeon(R) CPU E5-2630 v4 @ 2.20GHz", + "cpu_speed": 3100.0, + "cpu_vendor": "Intel", + "easybuild-easyblocks_version": "3.1.1", + "easybuild-framework_version": "3.1.1", + "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/cluster/easybuild/software/compiler/GCCcore/6.3.0/libexec/gcc/x86_64-pc-linux-gnu/6.3.0/lto-wrapper; Target: x86_64-pc-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --with-local-prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --enable-bootstrap --with-isl=/dev/shm/GCCcore/6.3.0/dummy-/gcc-6.3.0/stage2_stuff; Thread model: posix; gcc version 6.3.0 (GCC) ; ", + "glibc_version": "2.17", + "hostname": "login23", + "install_size": 55611227, + "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'), + "os_name": "centos linux", + "os_type": "Linux", + "os_version": "7.3.1611", + "platform_name": "x86_64-unknown-linux", + "python_version": "2.7.5 (default, Nov 6 2016, 00:28:07) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-11)]", + "system_gcc_path": "/cluster/easybuild/software/compiler/GCCcore/6.3.0/bin/gcc", + "system_python_path": "/cluster/easybuild/software/lang/Python/2.7.12-foss-2017a/bin/python", + "timestamp": 1491298248, + "total_memory": 128828, +}] + +# Build statistics +buildstats = [ +{ + "build_time": 520.33, + "command_line": ["--buildpath='/dev/shm'", "--configfiles='/cluster/easybuild/config.cfg'", "--installpath='/cluster/easybuild'", "--module-naming-scheme='CategorizedModuleNamingScheme'", "--module-syntax='Tcl'", "--modules-tool='EnvironmentModulesC'", "--packagepath='/cluster/easybuild/packages'", "--parallel='40'", "--prefix='/cluster/easybuild'", "--repository='GitRepository'", "--repositorypath='/cluster/easybuild/ebfiles_repo.git'", "--robot-paths=':/cluster/easybuild/ebfiles_repo'", "--sourcepath='/cluster/easybuild/sources'", '--use-existing-modules', 'LLVM-3.9.0-foss-2017a.eb'], + "core_count": 40, + "cpu_model": "Intel(R) Xeon(R) CPU E5-2630 v4 @ 2.20GHz", + "cpu_speed": 3100.0, + "cpu_vendor": "Intel", + "easybuild-easyblocks_version": "3.1.1", + "easybuild-framework_version": "3.1.1", + "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/cluster/easybuild/software/compiler/GCCcore/6.3.0/libexec/gcc/x86_64-pc-linux-gnu/6.3.0/lto-wrapper; Target: x86_64-pc-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --with-local-prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --enable-bootstrap --with-isl=/dev/shm/GCCcore/6.3.0/dummy-/gcc-6.3.0/stage2_stuff; Thread model: posix; gcc version 6.3.0 (GCC) ; ", + "glibc_version": "2.17", + "hostname": "login23", + "install_size": 55611227, + "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'), + "os_name": "centos linux", + "os_type": "Linux", + "os_version": "7.3.1611", + "platform_name": "x86_64-unknown-linux", + "python_version": "2.7.5 (default, Nov 6 2016, 00:28:07) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-11)]", + "system_gcc_path": "/cluster/easybuild/software/compiler/GCCcore/6.3.0/bin/gcc", + "system_python_path": "/cluster/easybuild/software/lang/Python/2.7.12-foss-2017a/bin/python", + "timestamp": 1491298248, + "total_memory": 128828, +}, +{ + "build_time": 687.87, + "command_line": ["--buildpath='/dev/shm'", "--configfiles='/cluster/easybuild/config.cfg'", '--group-writable-installdir', "--installpath='/cluster/easybuild'", '--minimal-toolchains', "--module-naming-scheme='CategorizedModuleNamingScheme'", "--module-syntax='Tcl'", "--modules-tool='EnvironmentModulesC'", "--packagepath='/cluster/easybuild/packages'", "--parallel='40'", "--prefix='/cluster/easybuild'", "--repository='GitRepository'", "--repositorypath='/cluster/easybuild/ebfiles_repo.git'", "--robot='/cluster/easybuild/ebfiles_repo:/cluster/easybuild/software/EasyBuild/3.1.1/lib/python2.7/site-packages/easybuild_easyconfigs-3.1.1-py2.7.egg/easybuild/easyconfigs'", "--robot-paths='/cluster/easybuild/ebfiles_repo:'", '--set-gid-bit', "--sourcepath='/cluster/easybuild/sources'", "--try-software-version='3.9.1'", "--umask='002'", 'LLVM-3.9.0-foss-2017a.eb'], + "core_count": 40, + "cpu_model": "Intel(R) Xeon(R) CPU E5-2630 v4 @ 2.20GHz", + "cpu_speed": 3100.0, + "cpu_vendor": "Intel", + "easybuild-easyblocks_version": "3.1.1", + "easybuild-framework_version": "3.1.1", + "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/cluster/easybuild/software/compiler/GCCcore/6.3.0/libexec/gcc/x86_64-pc-linux-gnu/6.3.0/lto-wrapper; Target: x86_64-pc-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --with-local-prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --enable-bootstrap --with-isl=/dev/shm/GCCcore/6.3.0/dummy-/gcc-6.3.0/stage2_stuff; Thread model: posix; gcc version 6.3.0 (GCC) ; ", + "glibc_version": "2.17", + "hostname": "login23", + "install_size": 55620832, + "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'), + "os_name": "centos linux", + "os_type": "Linux", + "os_version": "7.3.1611", + "platform_name": "x86_64-unknown-linux", + "python_version": "2.7.5 (default, Nov 6 2016, 00:28:07) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-11)]", + "system_gcc_path": "/cluster/easybuild/software/compiler/GCCcore/6.3.0/bin/gcc", + "system_python_path": "/cluster/easybuild/software/lang/Python/2.7.12-foss-2017a/bin/python", + "timestamp": 1492862134, + "total_memory": 128828, +}, +] diff --git a/easybuild/easyconfigs/l/LLVM/LLVM-4.0.0-foss-2017a.eb b/easybuild/easyconfigs/l/LLVM/LLVM-4.0.0-foss-2017a.eb new file mode 100644 index 0000000000..9090d26425 --- /dev/null +++ b/easybuild/easyconfigs/l/LLVM/LLVM-4.0.0-foss-2017a.eb @@ -0,0 +1,301 @@ +# Built with EasyBuild version 3.1.1 on 2017-04-22_14-33-26 +# Built with EasyBuild version 3.1.1 on 2017-04-22_13-54-52 +# Built with EasyBuild version 3.1.1 on 2017-04-21_17-49-43 +# Built with EasyBuild version 3.1.1 on 2017-04-04_11-52-35 +easyblock = 'CMakeMake' + +name = 'LLVM' +version = '4.0.0' + +homepage = "http://llvm.org/" +description = """The LLVM Core libraries provide a modern source- and target-independent + optimizer, along with code generation support for many popular CPUs + (as well as some less common ones!) These libraries are built around a well + specified code representation known as the LLVM intermediate representation + ("LLVM IR"). The LLVM Core libraries are well documented, and it is + particularly easy to invent your own language (or port an existing compiler) + to use LLVM as an optimizer and code generator.""" + +toolchain = {'name': 'foss', 'version': '2017a'} +toolchainopts = {'cstd': 'gnu++11'} + +source_urls = ["http://llvm.org/releases/%(version)s"] +sources = ["llvm-%(version)s.src.tar.xz"] + +builddependencies = [ + ('CMake', '3.7.2'), + ('Python', '2.7.12'), +] + +dependencies = [ + ('ncurses', '6.0'), + ('zlib', '1.2.11'), +] + +configopts = '-DBUILD_SHARED_LIBS=ON ' +# required to install extra tools in bin/ +configopts += '-DLLVM_INSTALL_UTILS=ON -DLLVM_TARGETS_TO_BUILD=X86 -DLLVM_ENABLE_ZLIB=ON ' +configopts += '-DCMAKE_BUILD_TYPE=Release ' + +sanity_check_paths = { + 'files': ['bin/llvm-ar', 'bin/FileCheck'], + 'dirs': ['include/llvm', 'include/llvm-c'], +} + +separate_build_dir = True + +moduleclass = 'compiler' + +# Build statistics +buildstats = [{ + "build_time": 751.68, + "command_line": ["--buildpath='/dev/shm'", "--configfiles='/cluster/easybuild/config.cfg'", "--installpath='/cluster/easybuild'", "--module-naming-scheme='CategorizedModuleNamingScheme'", "--module-syntax='Tcl'", "--modules-tool='EnvironmentModulesC'", "--packagepath='/cluster/easybuild/packages'", "--parallel='40'", "--prefix='/cluster/easybuild'", "--repository='GitRepository'", "--repositorypath='/cluster/easybuild/ebfiles_repo.git'", "--robot-paths=':/cluster/easybuild/ebfiles_repo'", "--sourcepath='/cluster/easybuild/sources'", '--use-existing-modules', 'LLVM-4.0.0-foss-2017a.eb'], + "core_count": 40, + "cpu_model": "Intel(R) Xeon(R) CPU E5-2630 v4 @ 2.20GHz", + "cpu_speed": 3100.0, + "cpu_vendor": "Intel", + "easybuild-easyblocks_version": "3.1.1", + "easybuild-framework_version": "3.1.1", + "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/cluster/easybuild/software/compiler/GCCcore/6.3.0/libexec/gcc/x86_64-pc-linux-gnu/6.3.0/lto-wrapper; Target: x86_64-pc-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --with-local-prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --enable-bootstrap --with-isl=/dev/shm/GCCcore/6.3.0/dummy-/gcc-6.3.0/stage2_stuff; Thread model: posix; gcc version 6.3.0 (GCC) ; ", + "glibc_version": "2.17", + "hostname": "login23", + "install_size": 141259484, + "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'), + "os_name": "centos linux", + "os_type": "Linux", + "os_version": "7.3.1611", + "platform_name": "x86_64-unknown-linux", + "python_version": "2.7.5 (default, Nov 6 2016, 00:28:07) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-11)]", + "system_gcc_path": "/cluster/easybuild/software/compiler/GCCcore/6.3.0/bin/gcc", + "system_python_path": "/cluster/easybuild/software/lang/Python/2.7.12-foss-2017a/bin/python", + "timestamp": 1491299554, + "total_memory": 128828, +}] + +# Build statistics +buildstats = [ +{ + "build_time": 751.68, + "command_line": ["--buildpath='/dev/shm'", "--configfiles='/cluster/easybuild/config.cfg'", "--installpath='/cluster/easybuild'", "--module-naming-scheme='CategorizedModuleNamingScheme'", "--module-syntax='Tcl'", "--modules-tool='EnvironmentModulesC'", "--packagepath='/cluster/easybuild/packages'", "--parallel='40'", "--prefix='/cluster/easybuild'", "--repository='GitRepository'", "--repositorypath='/cluster/easybuild/ebfiles_repo.git'", "--robot-paths=':/cluster/easybuild/ebfiles_repo'", "--sourcepath='/cluster/easybuild/sources'", '--use-existing-modules', 'LLVM-4.0.0-foss-2017a.eb'], + "core_count": 40, + "cpu_model": "Intel(R) Xeon(R) CPU E5-2630 v4 @ 2.20GHz", + "cpu_speed": 3100.0, + "cpu_vendor": "Intel", + "easybuild-easyblocks_version": "3.1.1", + "easybuild-framework_version": "3.1.1", + "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/cluster/easybuild/software/compiler/GCCcore/6.3.0/libexec/gcc/x86_64-pc-linux-gnu/6.3.0/lto-wrapper; Target: x86_64-pc-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --with-local-prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --enable-bootstrap --with-isl=/dev/shm/GCCcore/6.3.0/dummy-/gcc-6.3.0/stage2_stuff; Thread model: posix; gcc version 6.3.0 (GCC) ; ", + "glibc_version": "2.17", + "hostname": "login23", + "install_size": 141259484, + "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'), + "os_name": "centos linux", + "os_type": "Linux", + "os_version": "7.3.1611", + "platform_name": "x86_64-unknown-linux", + "python_version": "2.7.5 (default, Nov 6 2016, 00:28:07) ; 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[GCC 4.8.5 20150623 (Red Hat 4.8.5-11)]", + "system_gcc_path": "/cluster/easybuild/software/compiler/GCCcore/6.3.0/bin/gcc", + "system_python_path": "/cluster/easybuild/software/lang/Python/2.7.12-foss-2017a/bin/python", + "timestamp": 1492862091, + "total_memory": 128828, +}, +{ + "build_time": 395.04, + "command_line": ["--buildpath='/dev/shm'", "--configfiles='/cluster/easybuild/config.cfg'", '--group-writable-installdir', "--installpath='/cluster/easybuild'", '--minimal-toolchains', "--module-naming-scheme='CategorizedModuleNamingScheme'", "--module-syntax='Tcl'", "--modules-tool='EnvironmentModulesC'", "--packagepath='/cluster/easybuild/packages'", "--parallel='40'", "--prefix='/cluster/easybuild'", '--rebuild', "--repository='GitRepository'", "--repositorypath='/cluster/easybuild/ebfiles_repo.git'", "--robot-paths='/cluster/easybuild/ebfiles_repo:'", '--set-gid-bit', "--sourcepath='/cluster/easybuild/sources'", "--umask='002'", 'LLVM-4.0.0-foss-2017a.eb'], + "core_count": 40, + "cpu_model": "Intel(R) Xeon(R) CPU E5-2630 v4 @ 2.20GHz", + "cpu_speed": 3100.0, + "cpu_vendor": "Intel", + "easybuild-easyblocks_version": "3.1.1", + "easybuild-framework_version": "3.1.1", + "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/cluster/easybuild/software/compiler/GCCcore/6.3.0/libexec/gcc/x86_64-pc-linux-gnu/6.3.0/lto-wrapper; Target: x86_64-pc-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --with-local-prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --enable-bootstrap --with-isl=/dev/shm/GCCcore/6.3.0/dummy-/gcc-6.3.0/stage2_stuff; Thread model: posix; gcc version 6.3.0 (GCC) ; ", + "glibc_version": "2.17", + "hostname": "login23", + "install_size": 141259789, + "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'), + "os_name": "centos linux", + "os_type": "Linux", + "os_version": "7.3.1611", + "platform_name": "x86_64-unknown-linux", + "python_version": "2.7.5 (default, Nov 6 2016, 00:28:07) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-11)]", + "system_gcc_path": "/cluster/easybuild/software/compiler/GCCcore/6.3.0/bin/gcc", + "system_python_path": "/cluster/easybuild/software/lang/Python/2.7.12-foss-2017a/bin/python", + "timestamp": 1492864405, + "total_memory": 128828, +}, +] -- GitLab From 2c13ce9d66850ecf1c3f0d3eef88fdf57fb26981 Mon Sep 17 00:00:00 2001 From: "\"Andreas \"" Date: Tue, 25 Apr 2017 20:27:11 +0200 Subject: [PATCH 0638/1603] adding easyconfigs: Boost-1.63.0-foss-2017a.eb, Boost-1.63.0-foss-2017a-Python-2.7.12.eb --- .../Boost-1.63.0-foss-2017a-Python-2.7.12.eb | 103 ++++++++++++++++++ .../b/Boost/Boost-1.63.0-foss-2017a.eb | 50 +++++++++ 2 files changed, 153 insertions(+) create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.63.0-foss-2017a-Python-2.7.12.eb create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.63.0-foss-2017a.eb diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.63.0-foss-2017a-Python-2.7.12.eb b/easybuild/easyconfigs/b/Boost/Boost-1.63.0-foss-2017a-Python-2.7.12.eb new file mode 100644 index 0000000000..483520bf60 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.63.0-foss-2017a-Python-2.7.12.eb @@ -0,0 +1,103 @@ +# Built with EasyBuild version 3.1.1 on 2017-04-20_15-40-11 +# Built with EasyBuild version 3.1.1 on 2017-04-03_15-24-36 +name = 'Boost' +version = '1.63.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.boost.org/' +description = "Boost provides free peer-reviewed portable C++ source libraries." + +toolchain = {'name': 'foss', 'version': '2017a'} +toolchainopts = {'usempi': True, 'pic': True} + +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] +source_urls = ['https://sourceforge.net/projects/%(namelower)s/files/%(namelower)s/%(version)s'] + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.11'), + ('Python', '2.7.12'), +] + +# also build boost_mpi +boost_mpi = True + +moduleclass = 'devel' + +# Build statistics +buildstats = [{ + "build_time": 1537.69, + "command_line": ["--buildpath='/dev/shm'", "--configfiles='/cluster/easybuild/config.cfg'", "--installpath='/cluster/easybuild'", "--module-naming-scheme='CategorizedModuleNamingScheme'", "--module-syntax='Tcl'", "--modules-tool='EnvironmentModulesC'", "--packagepath='/cluster/easybuild/packages'", "--parallel='40'", "--prefix='/cluster/easybuild'", "--repository='GitRepository'", "--repositorypath='/cluster/easybuild/ebfiles_repo.git'", "--robot='/cluster/easybuild/software/EasyBuild/3.1.1/lib/python2.7/site-packages/easybuild_easyconfigs-3.1.1-py2.7.egg/easybuild/easyconfigs:/cluster/easybuild/ebfiles_repo'", "--robot-paths=':/cluster/easybuild/ebfiles_repo'", "--sourcepath='/cluster/easybuild/sources'", '--use-existing-modules', 'PETSc-3.7.5-foss-2017a-Python-2.7.12.eb'], + "core_count": 40, + "cpu_model": "Intel(R) Xeon(R) CPU E5-2630 v4 @ 2.20GHz", + "cpu_speed": 3100.0, + "cpu_vendor": "Intel", + "easybuild-easyblocks_version": "3.1.1", + "easybuild-framework_version": "3.1.1", + "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/cluster/easybuild/software/compiler/GCCcore/6.3.0/libexec/gcc/x86_64-pc-linux-gnu/6.3.0/lto-wrapper; Target: x86_64-pc-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --with-local-prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --enable-bootstrap --with-isl=/dev/shm/GCCcore/6.3.0/dummy-/gcc-6.3.0/stage2_stuff; Thread model: posix; gcc version 6.3.0 (GCC) ; ", + "glibc_version": "2.17", + "hostname": "login23", + "install_size": 169939518, + "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'), + "os_name": "centos linux", + "os_type": "Linux", + "os_version": "7.3.1611", + "platform_name": "x86_64-unknown-linux", + "python_version": "2.7.5 (default, Nov 6 2016, 00:28:07) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-11)]", + "system_gcc_path": "/cluster/easybuild/software/compiler/GCCcore/6.3.0/bin/gcc", + "system_python_path": "/cluster/easybuild/software/lang/Python/2.7.12-foss-2017a/bin/python", + "timestamp": 1491225875, + "total_memory": 128828, +}] + +# Build statistics +buildstats = [ +{ + "build_time": 1537.69, + "command_line": ["--buildpath='/dev/shm'", "--configfiles='/cluster/easybuild/config.cfg'", "--installpath='/cluster/easybuild'", "--module-naming-scheme='CategorizedModuleNamingScheme'", "--module-syntax='Tcl'", "--modules-tool='EnvironmentModulesC'", "--packagepath='/cluster/easybuild/packages'", "--parallel='40'", "--prefix='/cluster/easybuild'", "--repository='GitRepository'", "--repositorypath='/cluster/easybuild/ebfiles_repo.git'", "--robot='/cluster/easybuild/software/EasyBuild/3.1.1/lib/python2.7/site-packages/easybuild_easyconfigs-3.1.1-py2.7.egg/easybuild/easyconfigs:/cluster/easybuild/ebfiles_repo'", "--robot-paths=':/cluster/easybuild/ebfiles_repo'", "--sourcepath='/cluster/easybuild/sources'", '--use-existing-modules', 'PETSc-3.7.5-foss-2017a-Python-2.7.12.eb'], + "core_count": 40, + "cpu_model": "Intel(R) Xeon(R) CPU E5-2630 v4 @ 2.20GHz", + "cpu_speed": 3100.0, + "cpu_vendor": "Intel", + "easybuild-easyblocks_version": "3.1.1", + "easybuild-framework_version": "3.1.1", + "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/cluster/easybuild/software/compiler/GCCcore/6.3.0/libexec/gcc/x86_64-pc-linux-gnu/6.3.0/lto-wrapper; Target: x86_64-pc-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --with-local-prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --enable-bootstrap --with-isl=/dev/shm/GCCcore/6.3.0/dummy-/gcc-6.3.0/stage2_stuff; Thread model: posix; gcc version 6.3.0 (GCC) ; ", + "glibc_version": "2.17", + "hostname": "login23", + "install_size": 169939518, + "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'), + "os_name": "centos linux", + "os_type": "Linux", + "os_version": "7.3.1611", + "platform_name": "x86_64-unknown-linux", + "python_version": "2.7.5 (default, Nov 6 2016, 00:28:07) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-11)]", + "system_gcc_path": "/cluster/easybuild/software/compiler/GCCcore/6.3.0/bin/gcc", + "system_python_path": "/cluster/easybuild/software/lang/Python/2.7.12-foss-2017a/bin/python", + "timestamp": 1491225875, + "total_memory": 128828, +}, +{ + "build_time": 1585.32, + "command_line": ["--buildpath='/dev/shm'", "--configfiles='/cluster/easybuild/config.cfg'", '--group-writable-installdir', "--installpath='/cluster/easybuild'", "--module-naming-scheme='CategorizedModuleNamingScheme'", "--module-syntax='Tcl'", "--modules-tool='EnvironmentModulesC'", "--packagepath='/cluster/easybuild/packages'", "--parallel='40'", "--prefix='/cluster/easybuild'", '--rebuild', "--repository='GitRepository'", "--repositorypath='/cluster/easybuild/ebfiles_repo.git'", "--robot='/cluster/easybuild/ebfiles_repo:/cluster/easybuild/software/EasyBuild/3.1.1/lib/python2.7/site-packages/easybuild_easyconfigs-3.1.1-py2.7.egg/easybuild/easyconfigs'", "--robot-paths='/cluster/easybuild/ebfiles_repo:'", '--set-gid-bit', "--sourcepath='/cluster/easybuild/sources'", "--umask='002'", 'Boost/Boost-1.63.0-foss-2017a-Python-2.7.12.eb'], + "core_count": 40, + "cpu_model": "Intel(R) Xeon(R) CPU E5-2630 v4 @ 2.20GHz", + "cpu_speed": 3100.0, + "cpu_vendor": "Intel", + "easybuild-easyblocks_version": "3.1.1", + "easybuild-framework_version": "3.1.1", + "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/cluster/easybuild/software/compiler/GCCcore/6.3.0/libexec/gcc/x86_64-pc-linux-gnu/6.3.0/lto-wrapper; Target: x86_64-pc-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --with-local-prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --enable-bootstrap --with-isl=/dev/shm/GCCcore/6.3.0/dummy-/gcc-6.3.0/stage2_stuff; Thread model: posix; gcc version 6.3.0 (GCC) ; ", + "glibc_version": "2.17", + "hostname": "login24", + "install_size": 169940729, + "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'), + "os_name": "centos linux", + "os_type": "Linux", + "os_version": "7.3.1611", + "platform_name": "x86_64-unknown-linux", + "python_version": "2.7.5 (default, Nov 6 2016, 00:28:07) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-11)]", + "system_gcc_path": "/cluster/easybuild/software/compiler/GCCcore/6.3.0/bin/gcc", + "system_python_path": "/cluster/easybuild/software/lang/Python/2.7.12-foss-2017a/bin/python", + "timestamp": 1492695611, + "total_memory": 128828, +}, +] diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.63.0-foss-2017a.eb b/easybuild/easyconfigs/b/Boost/Boost-1.63.0-foss-2017a.eb new file mode 100644 index 0000000000..daa0767419 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.63.0-foss-2017a.eb @@ -0,0 +1,50 @@ +# Built with EasyBuild version 3.1.1 on 2017-04-04_18-18-26 +name = 'Boost' +version = '1.63.0' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'foss', 'version': '2017a'} +toolchainopts = {'pic': True, 'usempi': True} + +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] +source_urls = [SOURCEFORGE_SOURCE] + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.11'), +] + +configopts = '--without-libraries=python' + +# also build boost_mpi +boost_mpi = True + +moduleclass = 'devel' + +# Build statistics +buildstats = [{ + "build_time": 2759.25, + "command_line": ["--buildpath='/dev/shm'", "--configfiles='/cluster/easybuild/config.cfg'", "--installpath='/cluster/easybuild'", "--module-naming-scheme='CategorizedModuleNamingScheme'", "--module-syntax='Tcl'", "--modules-tool='EnvironmentModulesC'", "--packagepath='/cluster/easybuild/packages'", "--parallel='40'", "--prefix='/cluster/easybuild'", "--repository='GitRepository'", "--repositorypath='/cluster/easybuild/ebfiles_repo.git'", "--robot='/cluster/easybuild/software/EasyBuild/3.1.1/lib/python2.7/site-packages/easybuild_easyconfigs-3.1.1-py2.7.egg/easybuild/easyconfigs:/cluster/easybuild/ebfiles_repo'", "--robot-paths=':/cluster/easybuild/ebfiles_repo'", "--sourcepath='/cluster/easybuild/sources'", 'GROMACS-5.1.4-foss-2017a-hybrid.eb'], + "core_count": 40, + "cpu_model": "Intel(R) Xeon(R) CPU E5-2630 v4 @ 2.20GHz", + "cpu_speed": 3100.0, + "cpu_vendor": "Intel", + "easybuild-easyblocks_version": "3.1.1", + "easybuild-framework_version": "3.1.1", + "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/cluster/easybuild/software/compiler/GCCcore/6.3.0/libexec/gcc/x86_64-pc-linux-gnu/6.3.0/lto-wrapper; Target: x86_64-pc-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --with-local-prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --enable-bootstrap --with-isl=/dev/shm/GCCcore/6.3.0/dummy-/gcc-6.3.0/stage2_stuff; Thread model: posix; gcc version 6.3.0 (GCC) ; ", + "glibc_version": "2.17", + "hostname": "login23", + "install_size": 167262879, + "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'), + "os_name": "centos linux", + "os_type": "Linux", + "os_version": "7.3.1611", + "platform_name": "x86_64-unknown-linux", + "python_version": "2.7.5 (default, Nov 6 2016, 00:28:07) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-11)]", + "system_gcc_path": "/cluster/easybuild/software/compiler/GCCcore/6.3.0/bin/gcc", + "system_python_path": "/usr/bin/python", + "timestamp": 1491322705, + "total_memory": 128828, +}] -- GitLab From 0584f74e36a564f4a10893de1e84c542751ebeba Mon Sep 17 00:00:00 2001 From: "\"Andreas \"" Date: Tue, 25 Apr 2017 20:27:40 +0200 Subject: [PATCH 0639/1603] adding easyconfigs: NAMD-2.12-foss-2017a-mpi.eb --- .../n/NAMD/NAMD-2.12-foss-2017a-mpi.eb | 50 +++++++++++++++++++ 1 file changed, 50 insertions(+) create mode 100644 easybuild/easyconfigs/n/NAMD/NAMD-2.12-foss-2017a-mpi.eb diff --git a/easybuild/easyconfigs/n/NAMD/NAMD-2.12-foss-2017a-mpi.eb b/easybuild/easyconfigs/n/NAMD/NAMD-2.12-foss-2017a-mpi.eb new file mode 100644 index 0000000000..13ea1d21a4 --- /dev/null +++ b/easybuild/easyconfigs/n/NAMD/NAMD-2.12-foss-2017a-mpi.eb @@ -0,0 +1,50 @@ +# Built with EasyBuild version 3.1.1 on 2017-04-04_17-10-41 +name = 'NAMD' +version = '2.12' +versionsuffix = '-mpi' + +homepage = 'http://www.ks.uiuc.edu/Research/namd/' +description = """NAMD is a parallel molecular dynamics code designed for high-performance simulation of + large biomolecular systems.""" + +toolchain = {'name': 'foss', 'version': '2017a'} +toolchainopts = {'opt': True, 'pic': True} + +sources = ['NAMD_%(version)s_Source.tar.gz'] + +dependencies = [ + ('Tcl', '8.5.12'), +] + +# /bin/csh is required by 'config' script +osdependencies = ['tcsh'] + +charm_arch = "mpi-linux-x86_64" + +moduleclass = 'chem' + +# Build statistics +buildstats = [{ + "build_time": 269.88, + "command_line": ["--buildpath='/dev/shm'", "--configfiles='/cluster/easybuild/config.cfg'", "--installpath='/cluster/easybuild'", "--module-naming-scheme='CategorizedModuleNamingScheme'", "--module-syntax='Tcl'", "--modules-tool='EnvironmentModulesC'", "--packagepath='/cluster/easybuild/packages'", "--parallel='40'", "--prefix='/cluster/easybuild'", "--repository='GitRepository'", "--repositorypath='/cluster/easybuild/ebfiles_repo.git'", "--robot-paths=':/cluster/easybuild/ebfiles_repo'", "--sourcepath='/cluster/easybuild/sources'", 'NAMD-2.12-foss-2017a-mpi.eb'], + "core_count": 40, + "cpu_model": "Intel(R) Xeon(R) CPU E5-2630 v4 @ 2.20GHz", + "cpu_speed": 3100.0, + "cpu_vendor": "Intel", + "easybuild-easyblocks_version": "3.1.1", + "easybuild-framework_version": "3.1.1", + "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/cluster/easybuild/software/compiler/GCCcore/6.3.0/libexec/gcc/x86_64-pc-linux-gnu/6.3.0/lto-wrapper; Target: x86_64-pc-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --with-local-prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --enable-bootstrap --with-isl=/dev/shm/GCCcore/6.3.0/dummy-/gcc-6.3.0/stage2_stuff; Thread model: posix; gcc version 6.3.0 (GCC) ; ", + "glibc_version": "2.17", + "hostname": "login23", + "install_size": 45931470, + "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'), + "os_name": "centos linux", + "os_type": "Linux", + "os_version": "7.3.1611", + "platform_name": "x86_64-unknown-linux", + "python_version": "2.7.5 (default, Nov 6 2016, 00:28:07) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-11)]", + "system_gcc_path": "/cluster/easybuild/software/compiler/GCCcore/6.3.0/bin/gcc", + "system_python_path": "/usr/bin/python", + "timestamp": 1491318641, + "total_memory": 128828, +}] -- GitLab From 85190c2bda5be363fb61a927f39ffe2a9911b564 Mon Sep 17 00:00:00 2001 From: "\"Andreas \"" Date: Tue, 25 Apr 2017 20:28:39 +0200 Subject: [PATCH 0640/1603] adding easyconfigs: IMB-4.1-foss-2017a.eb --- .../easyconfigs/i/IMB/IMB-4.1-foss-2017a.eb | 57 +++++++++++++++++++ 1 file changed, 57 insertions(+) create mode 100644 easybuild/easyconfigs/i/IMB/IMB-4.1-foss-2017a.eb diff --git a/easybuild/easyconfigs/i/IMB/IMB-4.1-foss-2017a.eb b/easybuild/easyconfigs/i/IMB/IMB-4.1-foss-2017a.eb new file mode 100644 index 0000000000..87a1fa9cc3 --- /dev/null +++ b/easybuild/easyconfigs/i/IMB/IMB-4.1-foss-2017a.eb @@ -0,0 +1,57 @@ +# Built with EasyBuild version 3.1.1 on 2017-04-21_09-32-59 +easyblock = 'MakeCp' + +name = 'IMB' +version = '4.1' + +homepage = 'https://software.intel.com/en-us/articles/intel-mpi-benchmarks' +description = """ +The Intel® MPI Benchmarks perform a set of MPI performance measurements for point-to-point +and global communication operations for a range of message sizes. +""" + +toolchain = {'name': 'foss', 'version': '2017a'} + +sources = ['%(name)s_%(version)s.tgz'] +source_urls = ['https://software.intel.com/sites/default/files/managed/a3/b2/'] + +start_dir = 'src' +prebuildopts = 'export MPI_HOME=$EBROOTOPENMPI && ' +buildopts = "-f make_mpich MPI_HOME=$EBROOTOPENMPI" + +parallel = 1 + +files_to_copy = [(['src/IMB-*'], 'bin'), (['doc/IMB_Users_Guide.pdf'], 'doc')] + +sanity_check_paths = { + 'files': ['bin/%s' % binfile for binfile in ['IMB-RMA', 'IMB-EXT', 'IMB-NBC', 'IMB-MPI1']], + 'dirs': ['bin', 'doc'] +} + +moduleclass = 'perf' + +# Build statistics +buildstats = [{ + "build_time": 17.94, + "command_line": ["--buildpath='/dev/shm'", "--configfiles='/cluster/easybuild/config.cfg'", '--group-writable-installdir', "--installpath='/cluster/easybuild'", '--minimal-toolchains', "--module-naming-scheme='CategorizedModuleNamingScheme'", "--module-syntax='Tcl'", "--modules-tool='EnvironmentModulesC'", "--packagepath='/cluster/easybuild/packages'", "--parallel='40'", "--prefix='/cluster/easybuild'", "--repository='GitRepository'", "--repositorypath='/cluster/easybuild/ebfiles_repo.git'", "--robot-paths='/cluster/easybuild/ebfiles_repo:'", '--set-gid-bit', "--sourcepath='/cluster/easybuild/sources'", "--umask='002'", 'IMB-4.1-foss-2017a.eb'], + "core_count": 40, + "cpu_model": "Intel(R) Xeon(R) CPU E5-2630 v4 @ 2.20GHz", + "cpu_speed": 3100.0, + "cpu_vendor": "Intel", + "easybuild-easyblocks_version": "3.1.1", + "easybuild-framework_version": "3.1.1", + "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/cluster/easybuild/software/compiler/GCCcore/6.3.0/libexec/gcc/x86_64-pc-linux-gnu/6.3.0/lto-wrapper; Target: x86_64-pc-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --with-local-prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --enable-bootstrap --with-isl=/dev/shm/GCCcore/6.3.0/dummy-/gcc-6.3.0/stage2_stuff; Thread model: posix; gcc version 6.3.0 (GCC) ; ", + "glibc_version": "2.17", + "hostname": "login23", + "install_size": 1238017, + "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'), + "os_name": "centos linux", + "os_type": "Linux", + "os_version": "7.3.1611", + "platform_name": "x86_64-unknown-linux", + "python_version": "2.7.5 (default, Nov 6 2016, 00:28:07) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-11)]", + "system_gcc_path": "/cluster/easybuild/software/compiler/GCCcore/6.3.0/bin/gcc", + "system_python_path": "/usr/bin/python", + "timestamp": 1492759974, + "total_memory": 128828, +}] -- GitLab From a6aea5c1c8a5f4247519054b20bc9bcbc40399cd Mon Sep 17 00:00:00 2001 From: "\"Andreas \"" Date: Tue, 25 Apr 2017 20:29:53 +0200 Subject: [PATCH 0641/1603] adding easyconfigs: grib_api-1.21.0-foss-2017a.eb --- .../g/grib_api/grib_api-1.21.0-foss-2017a.eb | 51 +++++++++++++++++++ 1 file changed, 51 insertions(+) create mode 100644 easybuild/easyconfigs/g/grib_api/grib_api-1.21.0-foss-2017a.eb diff --git a/easybuild/easyconfigs/g/grib_api/grib_api-1.21.0-foss-2017a.eb b/easybuild/easyconfigs/g/grib_api/grib_api-1.21.0-foss-2017a.eb new file mode 100644 index 0000000000..c8b9bec5e8 --- /dev/null +++ b/easybuild/easyconfigs/g/grib_api/grib_api-1.21.0-foss-2017a.eb @@ -0,0 +1,51 @@ +# Built with EasyBuild version 3.1.1 on 2017-04-03_13-34-52 +easyblock = 'ConfigureMake' + +name = 'grib_api' +version = '1.21.0' + +homepage = 'https://software.ecmwf.int/wiki/display/GRIB/Home' +description = """The ECMWF GRIB API is an application program interface accessible from C, FORTRAN and Python + programs developed for encoding and decoding WMO FM-92 GRIB edition 1 and edition 2 messages. A useful set of + command line tools is also provided to give quick access to GRIB messages.""" + +toolchain = {'name': 'foss', 'version': '2017a'} + +source_urls = ['https://software.ecmwf.int/wiki/download/attachments/3473437/'] +sources = ['grib_api-%(version)s-Source.tar.gz'] + +dependencies = [ + ('JasPer', '1.900.1'), +] + +configopts = '--with-jasper=$EBROOTJASPER' + +parallel = 1 + +moduleclass = 'data' + +# Build statistics +buildstats = [{ + "build_time": 778.65, + "command_line": ["--buildpath='/dev/shm'", "--configfiles='/cluster/easybuild/config.cfg'", "--installpath='/cluster/easybuild'", "--module-naming-scheme='CategorizedModuleNamingScheme'", "--module-syntax='Tcl'", "--modules-tool='EnvironmentModulesC'", "--packagepath='/cluster/easybuild/packages'", "--parallel='40'", "--prefix='/cluster/easybuild'", "--repository='GitRepository'", "--repositorypath='/cluster/easybuild/ebfiles_repo.git'", "--robot='/cluster/easybuild/software/EasyBuild/3.1.1/lib/python2.7/site-packages/easybuild_easyconfigs-3.1.1-py2.7.egg/easybuild/easyconfigs:/cluster/easybuild/ebfiles_repo'", "--robot-paths=':/cluster/easybuild/ebfiles_repo'", "--sourcepath='/cluster/easybuild/sources'", 'grib_api-1.16.0-foss-2017a.eb'], + "core_count": 40, + "cpu_model": "Intel(R) Xeon(R) CPU E5-2630 v4 @ 2.20GHz", + "cpu_speed": 3100.0, + "cpu_vendor": "Intel", + "easybuild-easyblocks_version": "3.1.1", + "easybuild-framework_version": "3.1.1", + "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/cluster/easybuild/software/compiler/GCCcore/6.3.0/libexec/gcc/x86_64-pc-linux-gnu/6.3.0/lto-wrapper; Target: x86_64-pc-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --with-local-prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --enable-bootstrap --with-isl=/dev/shm/GCCcore/6.3.0/dummy-/gcc-6.3.0/stage2_stuff; Thread model: posix; gcc version 6.3.0 (GCC) ; ", + "glibc_version": "2.17", + "hostname": "login23", + "install_size": 27887407, + "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'), + "os_name": "centos linux", + "os_type": "Linux", + "os_version": "7.3.1611", + "platform_name": "x86_64-unknown-linux", + "python_version": "2.7.5 (default, Nov 6 2016, 00:28:07) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-11)]", + "system_gcc_path": "/cluster/easybuild/software/compiler/GCCcore/6.3.0/bin/gcc", + "system_python_path": "/usr/bin/python", + "timestamp": 1491219291, + "total_memory": 128828, +}] -- GitLab From 6c7928b649a58001999f593917825f9e51c5362e Mon Sep 17 00:00:00 2001 From: "\"Andreas \"" Date: Tue, 25 Apr 2017 20:31:20 +0200 Subject: [PATCH 0642/1603] adding easyconfigs: HDF5-1.8.18-foss-2017a.eb --- .../h/HDF5/HDF5-1.8.18-foss-2017a.eb | 53 +++++++++++++++++++ 1 file changed, 53 insertions(+) create mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.8.18-foss-2017a.eb diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.18-foss-2017a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.18-foss-2017a.eb new file mode 100644 index 0000000000..10498ad96c --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.18-foss-2017a.eb @@ -0,0 +1,53 @@ +# Built with EasyBuild version 3.1.1 on 2017-04-04_14-47-11 +name = 'HDF5' +version = '1.8.18' + +homepage = 'http://www.hdfgroup.org/HDF5/' +description = """HDF5 is a unique technology suite that makes possible the management of + extremely large and complex data collections.""" + +toolchain = {'name': 'foss', 'version': '2017a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = [ + 'https://support.hdfgroup.org/ftp/HDF5/current18/src/', + 'https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(versions)/src/' +] + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['dd2148b740713ca0295442ec683d7b1c'] + +buildopts = 'CXXFLAGS="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK"' + +dependencies = [ + ('zlib', '1.2.11'), + ('Szip', '2.1'), +] + +moduleclass = 'data' + +# Build statistics +buildstats = [{ + "build_time": 144.81, + "command_line": ["--buildpath='/dev/shm'", "--configfiles='/cluster/easybuild/config.cfg'", "--installpath='/cluster/easybuild'", "--module-naming-scheme='CategorizedModuleNamingScheme'", "--module-syntax='Tcl'", "--modules-tool='EnvironmentModulesC'", "--packagepath='/cluster/easybuild/packages'", "--parallel='40'", "--prefix='/cluster/easybuild'", '--rebuild', "--repository='GitRepository'", "--repositorypath='/cluster/easybuild/ebfiles_repo.git'", "--robot='/cluster/easybuild/software/EasyBuild/3.1.1/lib/python2.7/site-packages/easybuild_easyconfigs-3.1.1-py2.7.egg/easybuild/easyconfigs:/cluster/easybuild/ebfiles_repo'", "--robot-paths=':/cluster/easybuild/ebfiles_repo'", "--sourcepath='/cluster/easybuild/sources'", 'HDF5-1.8.18-foss-2017a.eb'], + "core_count": 40, + "cpu_model": "Intel(R) Xeon(R) CPU E5-2630 v4 @ 2.20GHz", + "cpu_speed": 3100.0, + "cpu_vendor": "Intel", + "easybuild-easyblocks_version": "3.1.1", + "easybuild-framework_version": "3.1.1", + "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/cluster/easybuild/software/compiler/GCCcore/6.3.0/libexec/gcc/x86_64-pc-linux-gnu/6.3.0/lto-wrapper; Target: x86_64-pc-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --with-local-prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --enable-bootstrap --with-isl=/dev/shm/GCCcore/6.3.0/dummy-/gcc-6.3.0/stage2_stuff; Thread model: posix; gcc version 6.3.0 (GCC) ; ", + "glibc_version": "2.17", + "hostname": "login23", + "install_size": 25911504, + "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'), + "os_name": "centos linux", + "os_type": "Linux", + "os_version": "7.3.1611", + "platform_name": "x86_64-unknown-linux", + "python_version": "2.7.5 (default, Nov 6 2016, 00:28:07) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-11)]", + "system_gcc_path": "/cluster/easybuild/software/compiler/GCCcore/6.3.0/bin/gcc", + "system_python_path": "/usr/bin/python", + "timestamp": 1491310030, + "total_memory": 128828, +}] -- GitLab From b65a2b6bb4c73feb566e0c2ffb9030263b588a14 Mon Sep 17 00:00:00 2001 From: "\"Andreas \"" Date: Tue, 25 Apr 2017 21:49:46 +0200 Subject: [PATCH 0643/1603] adding easyconfigs: SIONlib-1.7.1-foss-2017a.eb, SIONlib-1.7.1-foss-2017a-tools.eb --- .../SIONlib/SIONlib-1.7.1-foss-2017a-tools.eb | 70 +++++++++++++++++++ .../s/SIONlib/SIONlib-1.7.1-foss-2017a.eb | 64 +++++++++++++++++ 2 files changed, 134 insertions(+) create mode 100644 easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.1-foss-2017a-tools.eb create mode 100644 easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.1-foss-2017a.eb diff --git a/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.1-foss-2017a-tools.eb b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.1-foss-2017a-tools.eb new file mode 100644 index 0000000000..7d3b72d93e --- /dev/null +++ b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.1-foss-2017a-tools.eb @@ -0,0 +1,70 @@ +# Built with EasyBuild version 3.1.1 on 2017-04-25_21-35-15 +## +# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2016 Juelich Supercomputing Centre, Germany +# Authors:: Markus Geimer +# License:: 3-clause BSD +## + +easyblock = 'ConfigureMake' + +name = 'SIONlib' +version = '1.7.1' +# Provide a stripped-down version with renamed symbols for tools, +# see description for further details +versionsuffix = '-tools' + +homepage = 'http://www.fz-juelich.de/ias/jsc/EN/Expertise/Support/Software/SIONlib/_node.html' +description = """SIONlib is a scalable I/O library for parallel access to task-local files. + The library not only supports writing and reading binary data to or from several thousands of + processors into a single or a small number of physical files, but also provides global open + and close functions to access SIONlib files in parallel. This package provides a stripped-down + installation of SIONlib for use with performance tools (e.g., Score-P), with renamed symbols + to avoid conflicts when an application using SIONlib itself is linked against a tool requiring + a different SIONlib version.""" + +toolchain = {'name': 'foss', 'version': '2017a'} + +sources = ['sionlib-%(version)sl.tar.gz'] +source_urls = ['http://apps.fz-juelich.de/jsc/sionlib/download.php?version=%(version)sl'] + +checksums = [ + 'bc2ed625cdf967815007e71e732f38d1', # sionlib-1.7.1l.tar.gz +] + +configopts = '--disable-cxx --disable-fortran --disable-ompi' + +sanity_check_paths = { + 'files': ['bin/sionconfig'] + + ['lib/lib%s_64.a' % x for x in ['lsioncom', 'lsiongen', 'lsionser']], + 'dirs': [] +} + +moduleclass = 'lib' + +# Build statistics +buildstats = [{ + "build_time": 8.34, + "command_line": ["--buildpath='/dev/shm'", "--configfiles='/cluster/easybuild/config.cfg'", "--git-working-dirs-path='/home/henkela/tmp/easybuild-easyconfigs'", "--github-user='henkela'", '--group-writable-installdir', "--installpath='/cluster/easybuild'", '--minimal-toolchains', "--module-naming-scheme='CategorizedModuleNamingScheme'", "--module-syntax='Tcl'", "--modules-tool='EnvironmentModulesC'", "--packagepath='/cluster/easybuild/packages'", "--parallel='40'", "--prefix='/cluster/easybuild'", "--repository='GitRepository'", "--repositorypath='/cluster/easybuild/ebfiles_repo.git'", "--robot-paths='/cluster/easybuild/ebfiles_repo:'", '--set-gid-bit', "--sourcepath='/cluster/easybuild/sources'", "--umask='002'", 'SIONlib-1.7.1-foss-2017a-tools.eb'], + "core_count": 40, + "cpu_model": "Intel(R) Xeon(R) CPU E5-2630 v4 @ 2.20GHz", + "cpu_speed": 3100.0, + "cpu_vendor": "Intel", + "easybuild-easyblocks_version": "3.1.1", + "easybuild-framework_version": "3.1.1", + "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/cluster/easybuild/software/compiler/GCCcore/6.3.0/libexec/gcc/x86_64-pc-linux-gnu/6.3.0/lto-wrapper; Target: x86_64-pc-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --with-local-prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --enable-bootstrap --with-isl=/dev/shm/GCCcore/6.3.0/dummy-/gcc-6.3.0/stage2_stuff; Thread model: posix; gcc version 6.3.0 (GCC) ; ", + "glibc_version": "2.17", + "hostname": "login23", + "install_size": 1955553, + "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'), + "os_name": "centos linux", + "os_type": "Linux", + "os_version": "7.3.1611", + "platform_name": "x86_64-unknown-linux", + "python_version": "2.7.5 (default, Nov 6 2016, 00:28:07) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-11)]", + "system_gcc_path": "/cluster/easybuild/software/compiler/GCCcore/6.3.0/bin/gcc", + "system_python_path": "/usr/bin/python", + "timestamp": 1493148914, + "total_memory": 128828, +}] diff --git a/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.1-foss-2017a.eb b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.1-foss-2017a.eb new file mode 100644 index 0000000000..667807f3cc --- /dev/null +++ b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.1-foss-2017a.eb @@ -0,0 +1,64 @@ +# Built with EasyBuild version 3.1.1 on 2017-04-25_21-34-35 +## +# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2016 Juelich Supercomputing Centre, Germany +# Authors:: Markus Geimer +# License:: 3-clause BSD +## + +easyblock = 'ConfigureMake' + +name = 'SIONlib' +version = '1.7.1' + +homepage = 'http://www.fz-juelich.de/ias/jsc/EN/Expertise/Support/Software/SIONlib/_node.html' +description = """SIONlib is a scalable I/O library for parallel access to task-local files. + The library not only supports writing and reading binary data to or from several thousands of + processors into a single or a small number of physical files, but also provides global open + and close functions to access SIONlib files in parallel. SIONlib provides different interfaces: + parallel access using MPI, OpenMP, or their combination, and sequential access for post-processing + utilities.""" + +toolchain = {'name': 'foss', 'version': '2017a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://apps.fz-juelich.de/jsc/sionlib/download.php?version=%(version)s'] + +checksums = [ + '9d613055896af2792518d6e0cda02588', # sionlib-1.7.1.tar.gz +] + +sanity_check_paths = { + 'files': ['bin/sionconfig'] + + ['lib/lib%s_64.a' % x for x in ['sioncom', 'siongen', 'sionser']], + 'dirs': [] +} + +moduleclass = 'lib' + +# Build statistics +buildstats = [{ + "build_time": 14.02, + "command_line": ["--buildpath='/dev/shm'", "--configfiles='/cluster/easybuild/config.cfg'", "--git-working-dirs-path='/home/henkela/tmp/easybuild-easyconfigs'", "--github-user='henkela'", '--group-writable-installdir', "--installpath='/cluster/easybuild'", '--minimal-toolchains', "--module-naming-scheme='CategorizedModuleNamingScheme'", "--module-syntax='Tcl'", "--modules-tool='EnvironmentModulesC'", "--packagepath='/cluster/easybuild/packages'", "--parallel='40'", "--prefix='/cluster/easybuild'", '--rebuild', "--repository='GitRepository'", "--repositorypath='/cluster/easybuild/ebfiles_repo.git'", "--robot-paths='/cluster/easybuild/ebfiles_repo:'", '--set-gid-bit', "--sourcepath='/cluster/easybuild/sources'", "--umask='002'", 'SIONlib-1.7.1-foss-2017a.eb'], + "core_count": 40, + "cpu_model": "Intel(R) Xeon(R) CPU E5-2630 v4 @ 2.20GHz", + "cpu_speed": 3100.0, + "cpu_vendor": "Intel", + "easybuild-easyblocks_version": "3.1.1", + "easybuild-framework_version": "3.1.1", + "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/cluster/easybuild/software/compiler/GCCcore/6.3.0/libexec/gcc/x86_64-pc-linux-gnu/6.3.0/lto-wrapper; Target: x86_64-pc-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --with-local-prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --enable-bootstrap --with-isl=/dev/shm/GCCcore/6.3.0/dummy-/gcc-6.3.0/stage2_stuff; Thread model: posix; gcc version 6.3.0 (GCC) ; ", + "glibc_version": "2.17", + "hostname": "login23", + "install_size": 4336229, + "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'), + "os_name": "centos linux", + "os_type": "Linux", + "os_version": "7.3.1611", + "platform_name": "x86_64-unknown-linux", + "python_version": "2.7.5 (default, Nov 6 2016, 00:28:07) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-11)]", + "system_gcc_path": "/cluster/easybuild/software/compiler/GCCcore/6.3.0/bin/gcc", + "system_python_path": "/usr/bin/python", + "timestamp": 1493148875, + "total_memory": 128828, +}] -- GitLab From 7a5457b4666d8716ecdedc2417d645c451103a60 Mon Sep 17 00:00:00 2001 From: "\"Andreas \"" Date: Tue, 25 Apr 2017 21:50:23 +0200 Subject: [PATCH 0644/1603] adding easyconfigs: OTF2-2.0-foss-2017a.eb --- .../easyconfigs/o/OTF2/OTF2-2.0-foss-2017a.eb | 67 +++++++++++++++++++ 1 file changed, 67 insertions(+) create mode 100644 easybuild/easyconfigs/o/OTF2/OTF2-2.0-foss-2017a.eb diff --git a/easybuild/easyconfigs/o/OTF2/OTF2-2.0-foss-2017a.eb b/easybuild/easyconfigs/o/OTF2/OTF2-2.0-foss-2017a.eb new file mode 100644 index 0000000000..7d56604ccc --- /dev/null +++ b/easybuild/easyconfigs/o/OTF2/OTF2-2.0-foss-2017a.eb @@ -0,0 +1,67 @@ +# Built with EasyBuild version 3.1.1 on 2017-04-25_21-37-09 +## +# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# Copyright:: Copyright 2013-2016 Juelich Supercomputing Centre, Germany +# Authors:: Bernd Mohr +# Markus Geimer +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +## + +easyblock = 'EB_Score_minus_P' + +name = 'OTF2' +version = '2.0' + +homepage = 'http://www.score-p.org' +description = """The Open Trace Format 2 is a highly scalable, memory efficient event + trace data format plus support library. It is the new standard trace format for + Scalasca, Vampir, and TAU and is open for other tools.""" + +toolchain = {'name': 'foss', 'version': '2017a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.vi-hps.org/upload/packages/otf2/'] + +checksums = [ + '5b546188b25bc1c4e285e06dddf75dfc', # otf2-2.0.tar.gz +] + +builddependencies = [('SIONlib', '1.7.1', '-tools')] + +configopts = '--enable-shared' + +sanity_check_paths = { + 'files': ["bin/otf2-config", "include/otf2/otf2.h", ("lib/libotf2.a", "lib64/libotf2.a")], + 'dirs': [], +} + +moduleclass = 'perf' + +# Build statistics +buildstats = [{ + "build_time": 69.0, + "command_line": ["--buildpath='/dev/shm'", "--configfiles='/cluster/easybuild/config.cfg'", "--git-working-dirs-path='/home/henkela/tmp/easybuild-easyconfigs'", "--github-user='henkela'", '--group-writable-installdir', "--installpath='/cluster/easybuild'", '--minimal-toolchains', "--module-naming-scheme='CategorizedModuleNamingScheme'", "--module-syntax='Tcl'", "--modules-tool='EnvironmentModulesC'", "--packagepath='/cluster/easybuild/packages'", "--parallel='40'", "--prefix='/cluster/easybuild'", "--repository='GitRepository'", "--repositorypath='/cluster/easybuild/ebfiles_repo.git'", "--robot-paths='/cluster/easybuild/ebfiles_repo:'", '--set-gid-bit', "--sourcepath='/cluster/easybuild/sources'", "--umask='002'", 'OTF2-2.0-foss-2017a.eb'], + "core_count": 40, + "cpu_model": "Intel(R) Xeon(R) CPU E5-2630 v4 @ 2.20GHz", + "cpu_speed": 3100.0, + "cpu_vendor": "Intel", + "easybuild-easyblocks_version": "3.1.1", + "easybuild-framework_version": "3.1.1", + "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/cluster/easybuild/software/compiler/GCCcore/6.3.0/libexec/gcc/x86_64-pc-linux-gnu/6.3.0/lto-wrapper; Target: x86_64-pc-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --with-local-prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --enable-bootstrap --with-isl=/dev/shm/GCCcore/6.3.0/dummy-/gcc-6.3.0/stage2_stuff; Thread model: posix; gcc version 6.3.0 (GCC) ; ", + "glibc_version": "2.17", + "hostname": "login23", + "install_size": 19885165, + "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'), + "os_name": "centos linux", + "os_type": "Linux", + "os_version": "7.3.1611", + "platform_name": "x86_64-unknown-linux", + "python_version": "2.7.5 (default, Nov 6 2016, 00:28:07) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-11)]", + "system_gcc_path": "/cluster/easybuild/software/compiler/GCCcore/6.3.0/bin/gcc", + "system_python_path": "/usr/bin/python", + "timestamp": 1493149028, + "total_memory": 128828, +}] -- GitLab From 979674e2721a618799239d5ea2a795a9481e5aa6 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 26 Apr 2017 08:47:16 +0800 Subject: [PATCH 0645/1603] reorder extensions --- .../custodian-1.1.0-intel-2017a-Python-2.7.13.eb | 6 +++--- .../FireWorks-1.4.2-intel-2017a-Python-2.7.13.eb | 6 +++--- .../pymatgen-db-0.6.5-intel-2017a-Python-2.7.13.eb | 6 +++--- .../pymatgen/pymatgen-4.7.3-intel-2017a-Python-2.7.13.eb | 9 +++------ 4 files changed, 12 insertions(+), 15 deletions(-) diff --git a/easybuild/easyconfigs/c/custodian/custodian-1.1.0-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/c/custodian/custodian-1.1.0-intel-2017a-Python-2.7.13.eb index e8bf835f61..0c065c7d55 100644 --- a/easybuild/easyconfigs/c/custodian/custodian-1.1.0-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/c/custodian/custodian-1.1.0-intel-2017a-Python-2.7.13.eb @@ -18,12 +18,12 @@ dependencies = [ exts_defaultclass = 'PythonPackage' exts_list = [ - ('custodian', version, { - 'source_urls': ['https://pypi.python.org/packages/source/c/custodian/'], - }), ('monty', '0.9.6', { 'source_urls': ['https://pypi.python.org/packages/source/m/monty/'], }), + ('custodian', version, { + 'source_urls': ['https://pypi.python.org/packages/source/c/custodian/'], + }), ] # specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module diff --git a/easybuild/easyconfigs/f/FireWorks/FireWorks-1.4.2-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/f/FireWorks/FireWorks-1.4.2-intel-2017a-Python-2.7.13.eb index f776bdcadf..ac5fcef9e1 100644 --- a/easybuild/easyconfigs/f/FireWorks/FireWorks-1.4.2-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/f/FireWorks/FireWorks-1.4.2-intel-2017a-Python-2.7.13.eb @@ -19,9 +19,6 @@ dependencies = [ exts_defaultclass = 'PythonPackage' exts_list = [ - ('FireWorks', version, { - 'source_urls': ['https://pypi.python.org/packages/source/F/FireWorks/'], - }), ('Flask', '0.12', { 'source_urls': ['https://pypi.python.org/packages/source/F/Flask/'], }), @@ -45,6 +42,9 @@ exts_list = [ ('pymongo', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/p/pymongo/'], }), + ('FireWorks', version, { + 'source_urls': ['https://pypi.python.org/packages/source/F/FireWorks/'], + }), ] # specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module diff --git a/easybuild/easyconfigs/p/pymatgen-db/pymatgen-db-0.6.5-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/p/pymatgen-db/pymatgen-db-0.6.5-intel-2017a-Python-2.7.13.eb index 007db0084d..7c6022d3f6 100644 --- a/easybuild/easyconfigs/p/pymatgen-db/pymatgen-db-0.6.5-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/p/pymatgen-db/pymatgen-db-0.6.5-intel-2017a-Python-2.7.13.eb @@ -19,13 +19,13 @@ dependencies = [ exts_defaultclass = 'PythonPackage' exts_list = [ + ('smoqe', '0.1.3', { + 'source_urls': ['https://pypi.python.org/packages/source/s/smoqe/'], + }), ('pymatgen-db', '0.6.5', { 'modulename': 'matgendb', 'source_urls': ['https://pypi.python.org/packages/source/p/pymatgen-db/'], }), - ('smoqe', '0.1.3', { - 'source_urls': ['https://pypi.python.org/packages/source/s/smoqe/'], - }), ] # specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module diff --git a/easybuild/easyconfigs/p/pymatgen/pymatgen-4.7.3-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/p/pymatgen/pymatgen-4.7.3-intel-2017a-Python-2.7.13.eb index 718deacce4..86166ed4e4 100644 --- a/easybuild/easyconfigs/p/pymatgen/pymatgen-4.7.3-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/p/pymatgen/pymatgen-4.7.3-intel-2017a-Python-2.7.13.eb @@ -38,15 +38,12 @@ exts_list = [ ('mpmath', '0.19', { 'source_urls': ['https://pypi.python.org/packages/source/m/mpmath/'], }), - ('pymatgen', version, { - 'source_urls': ['https://pypi.python.org/packages/source/p/pymatgen/'], - }), - ('requests', '2.13.0', { - 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], - }), ('sympy', '1.0', { 'source_urls': ['https://pypi.python.org/packages/source/s/sympy/'], }), + ('pymatgen', version, { + 'source_urls': ['https://pypi.python.org/packages/source/p/pymatgen/'], + }), ] # specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module -- GitLab From cfc84bc757447be2c00d78890c4fba64817486a5 Mon Sep 17 00:00:00 2001 From: Robert Date: Wed, 26 Apr 2017 10:59:42 +0930 Subject: [PATCH 0646/1603] prodigal easyconfig added --- .../prodigal-2.6.2-GCC-4.9.3-binutils-2.25.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/p/prodigal/prodigal-2.6.2-GCC-4.9.3-binutils-2.25.eb diff --git a/easybuild/easyconfigs/p/prodigal/prodigal-2.6.2-GCC-4.9.3-binutils-2.25.eb b/easybuild/easyconfigs/p/prodigal/prodigal-2.6.2-GCC-4.9.3-binutils-2.25.eb new file mode 100644 index 0000000000..300e28ae47 --- /dev/null +++ b/easybuild/easyconfigs/p/prodigal/prodigal-2.6.2-GCC-4.9.3-binutils-2.25.eb @@ -0,0 +1,40 @@ +## +# This is a contribution from Phoenix HPC Service, The University of Adelaide, Australia +# Homepage: https://www.adelaide.edu.au/phoenix/ +# +# Copyright:: adelaide.edu.au/phoenix +# Authors:: Robert Qiao , Exe Escobedo +# License:: GPL-v3.0 +# +# Notes:: +## + + +easyblock = 'MakeCp' + +name = 'prodigal' +version = '2.6.2' + +homepage = 'http://prodigal.ornl.gov/' + +description = """Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a microbial (bacterial and archaeal) gene finding program developed at Oak Ridge National Laboratory and the University of Tennessee.""" + +toolchain = {'name': 'GCC', 'version': '4.9.3-binutils-2.25'} + +source_urls = ['https://github.com/hyattpd/Prodigal/archive/'] +sources = ['v%(version)s.tar.gz'] +#https://github.com/hyattpd/Prodigal/archive/v2.6.2.tar.gz + +files_to_copy = [ + (['prodigal'], 'bin'), + (['*.h'], 'include'), + (['LICENSE'], 'license'), +] + +sanity_check_paths = { + 'files': ['bin/prodigal'], + 'dirs': ['include', 'license'], +} + +moduleclass = 'bio' + -- GitLab From 49691e295bac00c8d5dcfa04e643f66f99257cc4 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 26 Apr 2017 13:09:36 +0200 Subject: [PATCH 0647/1603] {lang} [intel/2017a] PyCUDA/2016.1.2 --- ...CUDA-2016.1.2-intel-2017a-Python-2.7.13.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyCUDA/PyCUDA-2016.1.2-intel-2017a-Python-2.7.13.eb diff --git a/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2016.1.2-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2016.1.2-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..102a71dd89 --- /dev/null +++ b/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2016.1.2-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'PyCUDA' +version = '2016.1.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://mathema.tician.de/software/pycuda' +description = """PyCUDA lets you access Nvidia’s CUDA parallel computation API from Python.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('Python', '2.7.13'), + ('CUDA', '8.0.61', '', True), + ('Boost', '1.63.0', versionsuffix), +] + +prebuildopts = "./configure.py --cuda-root=$EBROOTCUDA --boost-inc-dir=$EBROOTBOOST/include/boost/ --boost-lib-dir=$EBROOTBOOST/lib/ --no-use-shipped-boost --boost-python-libname=boost_python && " + +options = {'modulename': '%(namelower)s'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'lang' -- GitLab From ecf4252a307ec2a48fd8b7a0d54a6f2fdfb77605 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 26 Apr 2017 18:29:34 +0200 Subject: [PATCH 0648/1603] Wrap line --- .../p/PyCUDA/PyCUDA-2016.1.2-intel-2017a-Python-2.7.13.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2016.1.2-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2016.1.2-intel-2017a-Python-2.7.13.eb index 102a71dd89..fd93f89fda 100644 --- a/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2016.1.2-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2016.1.2-intel-2017a-Python-2.7.13.eb @@ -18,7 +18,8 @@ dependencies = [ ('Boost', '1.63.0', versionsuffix), ] -prebuildopts = "./configure.py --cuda-root=$EBROOTCUDA --boost-inc-dir=$EBROOTBOOST/include/boost/ --boost-lib-dir=$EBROOTBOOST/lib/ --no-use-shipped-boost --boost-python-libname=boost_python && " +prebuildopts = "./configure.py --cuda-root=$EBROOTCUDA --boost-inc-dir=$EBROOTBOOST/include/boost/ " +prebuildopts += "--boost-lib-dir=$EBROOTBOOST/lib/ --no-use-shipped-boost --boost-python-libname=boost_python && " options = {'modulename': '%(namelower)s'} -- GitLab From 0a7cde9d50f531ed67fc85d4cfb143fe560f1ee8 Mon Sep 17 00:00:00 2001 From: "\"Andreas \"" Date: Thu, 27 Apr 2017 08:05:52 +0200 Subject: [PATCH 0649/1603] upgraded 2.7.13 instead --- .../p/Python/Python-2.7.13-foss-2017a.eb | 162 ++++++++++++++++++ 1 file changed, 162 insertions(+) create mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.13-foss-2017a.eb diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.13-foss-2017a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.13-foss-2017a.eb new file mode 100644 index 0000000000..3625e3bbd6 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.13-foss-2017a.eb @@ -0,0 +1,162 @@ +# Built with EasyBuild version 3.1.1 on 2017-04-27_06-34-41 +name = 'Python' +version = '2.7.13' + +homepage = 'http://python.org/' +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" + +toolchain = {'name': 'foss', 'version': '2017a'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +# python needs bzip2 to build the bz2 package +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.11'), + ('libreadline', '7.0'), + ('ncurses', '6.0'), + ('SQLite', '3.17.0'), + ('GMP', '6.1.2'), + ('libffi', '3.2.1'), + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.2k'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# order is important! +# package versions updated March 30th 2017 +exts_list = [ + # note: more recent versions of setuptools (v34.x) can not be installed from source anymore, + # see https://github.com/pypa/setuptools/issues/980 + ('setuptools', '33.1.1', { + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], + 'source_tmpl': '%(name)s-%(version)s.zip', + }), + ('pip', '9.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], + }), + ('nose', '1.3.7', { + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], + }), + ('numpy', '1.12.1', { + 'source_urls': ['https://pypi.python.org/packages/source/n/numpy'], + 'source_tmpl': '%(name)s-%(version)s.zip', + 'patches': ['numpy-1.12.0-mkl.patch'], + }), + ('scipy', '0.19.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/scipy'], + 'source_tmpl': '%(name)s-%(version)s.zip', + }), + ('blist', '1.3.6', { + 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], + }), + ('mpi4py', '2.0.0', { + 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + }), + ('paycheck', '1.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], + }), + ('pbr', '2.0.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], + }), + ('Cython', '0.25.2', { + 'source_urls': ['https://pypi.python.org/packages/source/c/cython/'], + }), + ('six', '1.10.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), + ('dateutil', '2.6.0', { + 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], + }), + ('deap', '1.0.2', { + 'source_tmpl': '%(name)s-%(version)s.post2.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], + }), + ('decorator', '4.0.11', { + 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], + }), + ('arff', '2.1.0', { + 'source_tmpl': 'liac-%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], + }), + ('pycrypto', '2.6.1', { + 'modulename': 'Crypto', + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], + }), + ('ecdsa', '0.13', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), + ('cryptography', '1.8.1', { + 'source_urls': ['https://pypi.python.org/packages/source/c/cryptography/'], + }), + ('paramiko', '2.1.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], + }), + ('pyparsing', '2.2.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], + }), + ('netifaces', '0.10.5', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], + }), + ('netaddr', '0.7.19', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], + }), + ('funcsigs', '1.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/f/funcsigs'], + }), + ('mock', '2.0.0', { + 'source_urls': ['https://pypi.python.org/packages/source/m/mock'], + }), + ('pytz', '2017.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pytz'], + 'source_tmpl': '%(name)s-%(version)s.zip', + }), + ('pandas', '0.19.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], + }), + ('enum34', '1.1.6', { + 'modulename': 'enum', + 'source_urls': ['https://pypi.python.org/packages/source/e/enum34'], + }), + ('bitstring', '3.1.5', { + 'source_tmpl': '%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/b/bitstring'], + }), + ('virtualenv', '15.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/v/virtualenv'], + }), +] + +moduleclass = 'lang' + +# Build statistics +buildstats = [{ + "build_time": 2019.51, + "command_line": ["--buildpath='/dev/shm'", "--configfiles='/cluster/easybuild/config.cfg'", "--git-working-dirs-path='/home/henkela/tmp/easybuild-easyconfigs'", "--github-user='henkela'", '--group-writable-installdir', "--installpath='/cluster/easybuild'", '--minimal-toolchains', "--module-naming-scheme='CategorizedModuleNamingScheme'", "--module-syntax='Tcl'", "--modules-tool='EnvironmentModulesC'", "--packagepath='/cluster/easybuild/packages'", "--parallel='40'", "--prefix='/cluster/easybuild'", "--repository='GitRepository'", "--repositorypath='/cluster/easybuild/ebfiles_repo.git'", "--robot='/cluster/easybuild/software/EasyBuild/3.1.1/lib/python2.7/site-packages/easybuild_easyconfigs-3.1.1-py2.7.egg/easybuild/easyconfigs:/home/henkela/slurm/easybuild-easyconfigs/easybuild/easyconfigs'", "--robot-paths=':/home/henkela/slurm/easybuild-easyconfigs/easybuild/easyconfigs'", '--set-gid-bit', "--sourcepath='/cluster/easybuild/sources'", "--umask='002'", 'Python-2.7.13-foss-2017a.eb'], + "core_count": 40, + "cpu_model": "Intel(R) Xeon(R) CPU E5-2630 v4 @ 2.20GHz", + "cpu_speed": 3100.0, + "cpu_vendor": "Intel", + "easybuild-easyblocks_version": "3.1.1", + "easybuild-framework_version": "3.1.1", + "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/cluster/easybuild/software/compiler/GCCcore/6.3.0/libexec/gcc/x86_64-pc-linux-gnu/6.3.0/lto-wrapper; Target: x86_64-pc-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --with-local-prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --enable-bootstrap --with-isl=/dev/shm/GCCcore/6.3.0/dummy-/gcc-6.3.0/stage2_stuff; Thread model: posix; gcc version 6.3.0 (GCC) ; ", + "glibc_version": "2.17", + "hostname": "login23", + "install_size": 409464422, + "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'), + "os_name": "centos linux", + "os_type": "Linux", + "os_version": "7.3.1611", + "platform_name": "x86_64-unknown-linux", + "python_version": "2.7.5 (default, Nov 6 2016, 00:28:07) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-11)]", + "system_gcc_path": "/cluster/easybuild/software/compiler/GCCcore/6.3.0/bin/gcc", + "system_python_path": "/usr/bin/python", + "timestamp": 1493267680, + "total_memory": 128828, +}] -- GitLab From 5fc0d21237b193085a426540bd13d4fdd264287c Mon Sep 17 00:00:00 2001 From: "\"Andreas \"" Date: Thu, 27 Apr 2017 17:00:41 +0200 Subject: [PATCH 0650/1603] removed built comments --- .../SIONlib/SIONlib-1.7.1-foss-2017a-tools.eb | 27 +------------------ .../s/SIONlib/SIONlib-1.7.1-foss-2017a.eb | 27 +------------------ 2 files changed, 2 insertions(+), 52 deletions(-) diff --git a/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.1-foss-2017a-tools.eb b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.1-foss-2017a-tools.eb index 7d3b72d93e..7e537ec0fb 100644 --- a/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.1-foss-2017a-tools.eb +++ b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.1-foss-2017a-tools.eb @@ -1,9 +1,9 @@ -# Built with EasyBuild version 3.1.1 on 2017-04-25_21-35-15 ## # This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild # # Copyright:: Copyright 2016 Juelich Supercomputing Centre, Germany # Authors:: Markus Geimer +# Modified 2017 by Andreas Henkel # License:: 3-clause BSD ## @@ -43,28 +43,3 @@ sanity_check_paths = { moduleclass = 'lib' -# Build statistics -buildstats = [{ - "build_time": 8.34, - "command_line": ["--buildpath='/dev/shm'", "--configfiles='/cluster/easybuild/config.cfg'", "--git-working-dirs-path='/home/henkela/tmp/easybuild-easyconfigs'", "--github-user='henkela'", '--group-writable-installdir', "--installpath='/cluster/easybuild'", '--minimal-toolchains', "--module-naming-scheme='CategorizedModuleNamingScheme'", "--module-syntax='Tcl'", "--modules-tool='EnvironmentModulesC'", "--packagepath='/cluster/easybuild/packages'", "--parallel='40'", "--prefix='/cluster/easybuild'", "--repository='GitRepository'", "--repositorypath='/cluster/easybuild/ebfiles_repo.git'", "--robot-paths='/cluster/easybuild/ebfiles_repo:'", '--set-gid-bit', "--sourcepath='/cluster/easybuild/sources'", "--umask='002'", 'SIONlib-1.7.1-foss-2017a-tools.eb'], - "core_count": 40, - "cpu_model": "Intel(R) Xeon(R) CPU E5-2630 v4 @ 2.20GHz", - "cpu_speed": 3100.0, - "cpu_vendor": "Intel", - "easybuild-easyblocks_version": "3.1.1", - "easybuild-framework_version": "3.1.1", - "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/cluster/easybuild/software/compiler/GCCcore/6.3.0/libexec/gcc/x86_64-pc-linux-gnu/6.3.0/lto-wrapper; Target: x86_64-pc-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --with-local-prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --enable-bootstrap --with-isl=/dev/shm/GCCcore/6.3.0/dummy-/gcc-6.3.0/stage2_stuff; Thread model: posix; gcc version 6.3.0 (GCC) ; ", - "glibc_version": "2.17", - "hostname": "login23", - "install_size": 1955553, - "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'), - "os_name": "centos linux", - "os_type": "Linux", - "os_version": "7.3.1611", - "platform_name": "x86_64-unknown-linux", - "python_version": "2.7.5 (default, Nov 6 2016, 00:28:07) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-11)]", - "system_gcc_path": "/cluster/easybuild/software/compiler/GCCcore/6.3.0/bin/gcc", - "system_python_path": "/usr/bin/python", - "timestamp": 1493148914, - "total_memory": 128828, -}] diff --git a/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.1-foss-2017a.eb b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.1-foss-2017a.eb index 667807f3cc..46e980be5f 100644 --- a/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.1-foss-2017a.eb +++ b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.1-foss-2017a.eb @@ -1,9 +1,9 @@ -# Built with EasyBuild version 3.1.1 on 2017-04-25_21-34-35 ## # This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild # # Copyright:: Copyright 2016 Juelich Supercomputing Centre, Germany # Authors:: Markus Geimer +# Modified 2017 by Andreas Henkel # License:: 3-clause BSD ## @@ -37,28 +37,3 @@ sanity_check_paths = { moduleclass = 'lib' -# Build statistics -buildstats = [{ - "build_time": 14.02, - "command_line": ["--buildpath='/dev/shm'", "--configfiles='/cluster/easybuild/config.cfg'", "--git-working-dirs-path='/home/henkela/tmp/easybuild-easyconfigs'", "--github-user='henkela'", '--group-writable-installdir', "--installpath='/cluster/easybuild'", '--minimal-toolchains', "--module-naming-scheme='CategorizedModuleNamingScheme'", "--module-syntax='Tcl'", "--modules-tool='EnvironmentModulesC'", "--packagepath='/cluster/easybuild/packages'", "--parallel='40'", "--prefix='/cluster/easybuild'", '--rebuild', "--repository='GitRepository'", "--repositorypath='/cluster/easybuild/ebfiles_repo.git'", "--robot-paths='/cluster/easybuild/ebfiles_repo:'", '--set-gid-bit', "--sourcepath='/cluster/easybuild/sources'", "--umask='002'", 'SIONlib-1.7.1-foss-2017a.eb'], - "core_count": 40, - "cpu_model": "Intel(R) Xeon(R) CPU E5-2630 v4 @ 2.20GHz", - "cpu_speed": 3100.0, - "cpu_vendor": "Intel", - "easybuild-easyblocks_version": "3.1.1", - "easybuild-framework_version": "3.1.1", - "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/cluster/easybuild/software/compiler/GCCcore/6.3.0/libexec/gcc/x86_64-pc-linux-gnu/6.3.0/lto-wrapper; Target: x86_64-pc-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --with-local-prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --enable-bootstrap --with-isl=/dev/shm/GCCcore/6.3.0/dummy-/gcc-6.3.0/stage2_stuff; Thread model: posix; gcc version 6.3.0 (GCC) ; ", - "glibc_version": "2.17", - "hostname": "login23", - "install_size": 4336229, - "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'), - "os_name": "centos linux", - "os_type": "Linux", - "os_version": "7.3.1611", - "platform_name": "x86_64-unknown-linux", - "python_version": "2.7.5 (default, Nov 6 2016, 00:28:07) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-11)]", - "system_gcc_path": "/cluster/easybuild/software/compiler/GCCcore/6.3.0/bin/gcc", - "system_python_path": "/usr/bin/python", - "timestamp": 1493148875, - "total_memory": 128828, -}] -- GitLab From 898b454611d529f69430652bb58b19dae94a9096 Mon Sep 17 00:00:00 2001 From: "\"Andreas \"" Date: Thu, 27 Apr 2017 17:03:16 +0200 Subject: [PATCH 0651/1603] removed built comments --- .../easyconfigs/i/IMB/IMB-4.1-foss-2017a.eb | 27 +---------------- .../i/IMB/IMB-4.1-intel-2017.02.eb | 29 +++++++++++++++++++ 2 files changed, 30 insertions(+), 26 deletions(-) create mode 100644 easybuild/easyconfigs/i/IMB/IMB-4.1-intel-2017.02.eb diff --git a/easybuild/easyconfigs/i/IMB/IMB-4.1-foss-2017a.eb b/easybuild/easyconfigs/i/IMB/IMB-4.1-foss-2017a.eb index 87a1fa9cc3..0a33899fe9 100644 --- a/easybuild/easyconfigs/i/IMB/IMB-4.1-foss-2017a.eb +++ b/easybuild/easyconfigs/i/IMB/IMB-4.1-foss-2017a.eb @@ -1,4 +1,3 @@ -# Built with EasyBuild version 3.1.1 on 2017-04-21_09-32-59 easyblock = 'MakeCp' name = 'IMB' @@ -30,28 +29,4 @@ sanity_check_paths = { moduleclass = 'perf' -# Build statistics -buildstats = [{ - "build_time": 17.94, - "command_line": ["--buildpath='/dev/shm'", "--configfiles='/cluster/easybuild/config.cfg'", '--group-writable-installdir', "--installpath='/cluster/easybuild'", '--minimal-toolchains', "--module-naming-scheme='CategorizedModuleNamingScheme'", "--module-syntax='Tcl'", "--modules-tool='EnvironmentModulesC'", "--packagepath='/cluster/easybuild/packages'", "--parallel='40'", "--prefix='/cluster/easybuild'", "--repository='GitRepository'", "--repositorypath='/cluster/easybuild/ebfiles_repo.git'", "--robot-paths='/cluster/easybuild/ebfiles_repo:'", '--set-gid-bit', "--sourcepath='/cluster/easybuild/sources'", "--umask='002'", 'IMB-4.1-foss-2017a.eb'], - "core_count": 40, - "cpu_model": "Intel(R) Xeon(R) CPU E5-2630 v4 @ 2.20GHz", - "cpu_speed": 3100.0, - "cpu_vendor": "Intel", - "easybuild-easyblocks_version": "3.1.1", - "easybuild-framework_version": "3.1.1", - "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/cluster/easybuild/software/compiler/GCCcore/6.3.0/libexec/gcc/x86_64-pc-linux-gnu/6.3.0/lto-wrapper; Target: x86_64-pc-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --with-local-prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --enable-bootstrap --with-isl=/dev/shm/GCCcore/6.3.0/dummy-/gcc-6.3.0/stage2_stuff; Thread model: posix; gcc version 6.3.0 (GCC) ; ", - "glibc_version": "2.17", - "hostname": "login23", - "install_size": 1238017, - "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'), - "os_name": "centos linux", - "os_type": "Linux", - "os_version": "7.3.1611", - "platform_name": "x86_64-unknown-linux", - "python_version": "2.7.5 (default, Nov 6 2016, 00:28:07) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-11)]", - "system_gcc_path": "/cluster/easybuild/software/compiler/GCCcore/6.3.0/bin/gcc", - "system_python_path": "/usr/bin/python", - "timestamp": 1492759974, - "total_memory": 128828, -}] + diff --git a/easybuild/easyconfigs/i/IMB/IMB-4.1-intel-2017.02.eb b/easybuild/easyconfigs/i/IMB/IMB-4.1-intel-2017.02.eb new file mode 100644 index 0000000000..65d5fc7e4a --- /dev/null +++ b/easybuild/easyconfigs/i/IMB/IMB-4.1-intel-2017.02.eb @@ -0,0 +1,29 @@ +easyblock = 'MakeCp' + +name = 'IMB' +version = '4.1' + +homepage = 'https://software.intel.com/en-us/articles/intel-mpi-benchmarks' +description = """The Intel MPI Benchmarks perform a set of MPI performance measurements for point-to-point and + global communication operations for a range of message sizes""" + +toolchain = {'name': 'intel', 'version': '2017.02'} +toolchainopts = {'usempi': True} + +source_urls = ['https://software.intel.com/sites/default/files/managed/34/aa/'] +sources = ['%(name)s_%(version)s.tgz'] + +prebuildopts = "cd src && " +buildopts = "all" + +parallel = 1 + +files_to_copy = [(['src/IMB-*'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/IMB-EXT', 'bin/IMB-IO', 'bin/IMB-MPI1', 'bin/IMB-NBC', 'bin/IMB-RMA'], + 'dirs': [], +} + +moduleclass = 'perf' + -- GitLab From 622f881da74b15c05d51e9e56979b3dd518756d8 Mon Sep 17 00:00:00 2001 From: "\"Andreas \"" Date: Thu, 27 Apr 2017 19:49:42 +0200 Subject: [PATCH 0652/1603] removed built comments from Python-2.7.13-foss-2017a.eb easyconfig --- .../p/Python/Python-2.7.13-foss-2017a.eb | 26 ------------------- 1 file changed, 26 deletions(-) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.13-foss-2017a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.13-foss-2017a.eb index 3625e3bbd6..166b747669 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.13-foss-2017a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.13-foss-2017a.eb @@ -1,4 +1,3 @@ -# Built with EasyBuild version 3.1.1 on 2017-04-27_06-34-41 name = 'Python' version = '2.7.13' @@ -135,28 +134,3 @@ exts_list = [ moduleclass = 'lang' -# Build statistics -buildstats = [{ - "build_time": 2019.51, - "command_line": ["--buildpath='/dev/shm'", "--configfiles='/cluster/easybuild/config.cfg'", "--git-working-dirs-path='/home/henkela/tmp/easybuild-easyconfigs'", "--github-user='henkela'", '--group-writable-installdir', "--installpath='/cluster/easybuild'", '--minimal-toolchains', "--module-naming-scheme='CategorizedModuleNamingScheme'", "--module-syntax='Tcl'", "--modules-tool='EnvironmentModulesC'", "--packagepath='/cluster/easybuild/packages'", "--parallel='40'", "--prefix='/cluster/easybuild'", "--repository='GitRepository'", "--repositorypath='/cluster/easybuild/ebfiles_repo.git'", "--robot='/cluster/easybuild/software/EasyBuild/3.1.1/lib/python2.7/site-packages/easybuild_easyconfigs-3.1.1-py2.7.egg/easybuild/easyconfigs:/home/henkela/slurm/easybuild-easyconfigs/easybuild/easyconfigs'", "--robot-paths=':/home/henkela/slurm/easybuild-easyconfigs/easybuild/easyconfigs'", '--set-gid-bit', "--sourcepath='/cluster/easybuild/sources'", "--umask='002'", 'Python-2.7.13-foss-2017a.eb'], - "core_count": 40, - "cpu_model": "Intel(R) Xeon(R) CPU E5-2630 v4 @ 2.20GHz", - "cpu_speed": 3100.0, - "cpu_vendor": "Intel", - "easybuild-easyblocks_version": "3.1.1", - "easybuild-framework_version": "3.1.1", - "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/cluster/easybuild/software/compiler/GCCcore/6.3.0/libexec/gcc/x86_64-pc-linux-gnu/6.3.0/lto-wrapper; Target: x86_64-pc-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --with-local-prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --enable-bootstrap --with-isl=/dev/shm/GCCcore/6.3.0/dummy-/gcc-6.3.0/stage2_stuff; Thread model: posix; gcc version 6.3.0 (GCC) ; ", - "glibc_version": "2.17", - "hostname": "login23", - "install_size": 409464422, - "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'), - "os_name": "centos linux", - "os_type": "Linux", - "os_version": "7.3.1611", - "platform_name": "x86_64-unknown-linux", - "python_version": "2.7.5 (default, Nov 6 2016, 00:28:07) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-11)]", - "system_gcc_path": "/cluster/easybuild/software/compiler/GCCcore/6.3.0/bin/gcc", - "system_python_path": "/usr/bin/python", - "timestamp": 1493267680, - "total_memory": 128828, -}] -- GitLab From 4c5f699986938c5a6d6770067bb8a74afb8c904d Mon Sep 17 00:00:00 2001 From: "\"Andreas \"" Date: Thu, 27 Apr 2017 19:53:37 +0200 Subject: [PATCH 0653/1603] delete Python-2.7.12-foss-2017a.eb easyconfig file --- .../p/Python/Python-2.7.12-foss-2017a.eb | 293 ------------------ 1 file changed, 293 deletions(-) delete mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.12-foss-2017a.eb diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.12-foss-2017a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.12-foss-2017a.eb deleted file mode 100644 index b8e862c97f..0000000000 --- a/easybuild/easyconfigs/p/Python/Python-2.7.12-foss-2017a.eb +++ /dev/null @@ -1,293 +0,0 @@ -# Built with EasyBuild version 3.1.1 on 2017-04-21_17-31-01 -# Built with EasyBuild version 3.1.1 on 2017-04-20_11-17-51 -# Built with EasyBuild version 3.1.1 on 2017-04-03_09-46-50 -name = 'Python' -version = '2.7.12' - -homepage = 'http://python.org/' -description = """Python is a programming language that lets you work more quickly and integrate your systems - more effectively.""" - -toolchain = {'name': 'foss', 'version': '2017a'} -toolchainopts = {'pic': True} - -source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] -sources = [SOURCE_TGZ] - -# python needs bzip2 to build the bz2 package -dependencies = [ - ('bzip2', '1.0.6'), - ('zlib', '1.2.11'), - ('libreadline', '6.3'), - ('ncurses', '6.0'), - ('SQLite', '3.13.0'), - ('Tk', '8.6.5'), # this requires a full X11 stack - ('GMP', '6.1.1'), - ('libffi', '3.2.1'), - # OS dependency should be preferred if the os version is more recent then this version, - # it's nice to have an up to date openssl for security reasons - # ('OpenSSL', '1.0.2h'), -] - -osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] - -# order is important! -# package versions updated March 30th 2017 -# setuptools 34.3.3 zip -exts_list = [ - ('setuptools', '23.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], - }), - ('pip', '9.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], - }), - ('nose', '1.3.7', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], - }), - ('numpy', '1.11.1', { - 'source_urls': ['https://pypi.python.org/packages/source/n/numpy'], - 'patches': ['numpy-1.8.0-mkl.patch'], - }), - ('scipy', '0.19.0', { - 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/s/scipy'], - }), - ('blist', '1.3.6', { - 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], - }), - ('mpi4py', '2.0.0', { - 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], - }), - ('paycheck', '1.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], - }), - ('pbr', '2.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], - }), - ('lockfile', '0.12.2', { - 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], - }), - ('Cython', '0.25.2', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cython/'], - }), - ('six', '1.10.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], - }), - ('dateutil', '2.6.0', { - 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], - }), - ('deap', '1.0.2', { - 'source_tmpl': '%(name)s-%(version)s.post2.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], - }), - ('decorator', '4.0.11', { - 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], - }), - ('arff', '2.1.0', { - 'source_tmpl': 'liac-%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], - }), - ('pycrypto', '2.6.1', { - 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], - }), - ('ecdsa', '0.13', { - 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], - }), - ('cryptography', '1.8.1', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cryptography/'], - }), - ('paramiko', '2.1.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], - }), - ('pyparsing', '2.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], - }), - ('netifaces', '0.10.5', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], - }), - ('netaddr', '0.7.19', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], - }), - ('funcsigs', '1.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/f/funcsigs'], - }), - ('mock', '2.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/m/mock'], - }), - ('pytz', '2017.2', { - 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/p/pytz'], - }), - ('pandas', 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'--group-writable-installdir', "--installpath='/cluster/easybuild'", "--module-naming-scheme='CategorizedModuleNamingScheme'", "--module-syntax='Tcl'", "--modules-tool='EnvironmentModulesC'", "--packagepath='/cluster/easybuild/packages'", "--parallel='40'", "--prefix='/cluster/easybuild'", '--rebuild', "--repository='GitRepository'", "--repositorypath='/cluster/easybuild/ebfiles_repo.git'", "--robot='/cluster/easybuild/software/EasyBuild/3.1.1/lib/python2.7/site-packages/easybuild_easyconfigs-3.1.1-py2.7.egg/easybuild/easyconfigs:/cluster/easybuild/ebfiles_repo'", "--robot-paths=':/cluster/easybuild/ebfiles_repo'", '--set-gid-bit', "--sourcepath='/cluster/easybuild/sources'", "--umask='002'", 'Python/Python-2.7.12-foss-2017a.eb'], - "core_count": 40, - "cpu_model": "Intel(R) Xeon(R) CPU E5-2630 v4 @ 2.20GHz", - "cpu_speed": 3100.0, - "cpu_vendor": "Intel", - "easybuild-easyblocks_version": "3.1.1", - "easybuild-framework_version": "3.1.1", - "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/cluster/easybuild/software/compiler/GCCcore/6.3.0/libexec/gcc/x86_64-pc-linux-gnu/6.3.0/lto-wrapper; Target: x86_64-pc-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --with-local-prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --enable-bootstrap --with-isl=/dev/shm/GCCcore/6.3.0/dummy-/gcc-6.3.0/stage2_stuff; Thread model: posix; gcc version 6.3.0 (GCC) ; ", - "glibc_version": "2.17", - "hostname": "login24", - "install_size": 404321244, - "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'), - "os_name": "centos linux", - "os_type": "Linux", - "os_version": "7.3.1611", - "platform_name": "x86_64-unknown-linux", - "python_version": "2.7.5 (default, Nov 6 2016, 00:28:07) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-11)]", - "system_gcc_path": "/cluster/easybuild/software/compiler/GCCcore/6.3.0/bin/gcc", - "system_python_path": "/usr/bin/python", - "timestamp": 1492679870, - "total_memory": 128828, -}, -{ - "build_time": 1970.68, - "command_line": ["--buildpath='/dev/shm'", "--configfiles='/cluster/easybuild/config.cfg'", '--force', '--group-writable-installdir', "--installpath='/cluster/easybuild'", '--minimal-toolchains', "--module-naming-scheme='CategorizedModuleNamingScheme'", "--module-syntax='Tcl'", "--modules-tool='EnvironmentModulesC'", "--packagepath='/cluster/easybuild/packages'", "--parallel='40'", "--prefix='/cluster/easybuild'", '--rebuild', "--repository='GitRepository'", "--repositorypath='/cluster/easybuild/ebfiles_repo.git'", "--robot='/cluster/easybuild/ebfiles_repo:/cluster/easybuild/software/EasyBuild/3.1.1/lib/python2.7/site-packages/easybuild_easyconfigs-3.1.1-py2.7.egg/easybuild/easyconfigs'", "--robot-paths='/cluster/easybuild/ebfiles_repo:'", '--set-gid-bit', "--sourcepath='/cluster/easybuild/sources'", "--umask='002'", 'Python/Python-2.7.12-foss-2017a.eb'], - "core_count": 40, - "cpu_model": "Intel(R) Xeon(R) CPU E5-2630 v4 @ 2.20GHz", - "cpu_speed": 3100.0, - "cpu_vendor": "Intel", - "easybuild-easyblocks_version": "3.1.1", - "easybuild-framework_version": "3.1.1", - "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/cluster/easybuild/software/compiler/GCCcore/6.3.0/libexec/gcc/x86_64-pc-linux-gnu/6.3.0/lto-wrapper; Target: x86_64-pc-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --with-local-prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --enable-bootstrap --with-isl=/dev/shm/GCCcore/6.3.0/dummy-/gcc-6.3.0/stage2_stuff; Thread model: posix; gcc version 6.3.0 (GCC) ; ", - "glibc_version": "2.17", - "hostname": "login23", - "install_size": 404321549, - "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'), - "os_name": "centos linux", - "os_type": "Linux", - "os_version": "7.3.1611", - "platform_name": "x86_64-unknown-linux", - "python_version": "2.7.5 (default, Nov 6 2016, 00:28:07) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-11)]", - "system_gcc_path": "/cluster/easybuild/software/compiler/GCCcore/6.3.0/bin/gcc", - "system_python_path": "/usr/bin/python", - "timestamp": 1492788660, - "total_memory": 128828, -}, -] -- GitLab From 5446fcacc7f537b151b6c2e9abf42fa9b9bec5de Mon Sep 17 00:00:00 2001 From: "\"Andreas \"" Date: Thu, 27 Apr 2017 19:57:59 +0200 Subject: [PATCH 0654/1603] removed built comments --- .../OSU-Micro-Benchmarks-5.3.2-foss-2017a.eb | 26 ------------------- 1 file changed, 26 deletions(-) diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.3.2-foss-2017a.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.3.2-foss-2017a.eb index 773f1229f6..3f1b8657b8 100644 --- a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.3.2-foss-2017a.eb +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.3.2-foss-2017a.eb @@ -1,4 +1,3 @@ -# Built with EasyBuild version 3.1.1 on 2017-04-04_19-59-16 easyblock = 'ConfigureMake' name = 'OSU-Micro-Benchmarks' @@ -24,28 +23,3 @@ sanity_check_paths = { moduleclass = 'perf' -# Build statistics -buildstats = [{ - "build_time": 15.4, - "command_line": ["--buildpath='/dev/shm'", "--configfiles='/cluster/easybuild/config.cfg'", "--installpath='/cluster/easybuild'", "--module-naming-scheme='CategorizedModuleNamingScheme'", "--module-syntax='Tcl'", "--modules-tool='EnvironmentModulesC'", "--packagepath='/cluster/easybuild/packages'", "--parallel='40'", "--prefix='/cluster/easybuild'", "--repository='GitRepository'", "--repositorypath='/cluster/easybuild/ebfiles_repo.git'", "--robot-paths=':/cluster/easybuild/ebfiles_repo'", "--sourcepath='/cluster/easybuild/sources'", 'OSU-Micro-Benchmarks-5.3.2-foss-2017a.eb'], - "core_count": 40, - "cpu_model": "Intel(R) Xeon(R) CPU E5-2630 v4 @ 2.20GHz", - "cpu_speed": 3100.0, - "cpu_vendor": "Intel", - "easybuild-easyblocks_version": "3.1.1", - "easybuild-framework_version": "3.1.1", - "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/cluster/easybuild/software/compiler/GCCcore/6.3.0/libexec/gcc/x86_64-pc-linux-gnu/6.3.0/lto-wrapper; Target: x86_64-pc-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --with-local-prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --enable-bootstrap --with-isl=/dev/shm/GCCcore/6.3.0/dummy-/gcc-6.3.0/stage2_stuff; Thread model: posix; gcc version 6.3.0 (GCC) ; ", - "glibc_version": "2.17", - "hostname": "login23", - "install_size": 1041307, - "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'), - "os_name": "centos linux", - "os_type": "Linux", - "os_version": "7.3.1611", - "platform_name": "x86_64-unknown-linux", - "python_version": "2.7.5 (default, Nov 6 2016, 00:28:07) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-11)]", - "system_gcc_path": "/cluster/easybuild/software/compiler/GCCcore/6.3.0/bin/gcc", - "system_python_path": "/usr/bin/python", - "timestamp": 1491328756, - "total_memory": 128828, -}] -- GitLab From 5516323ae59d996cf2489f0c372952e2b4c510d3 Mon Sep 17 00:00:00 2001 From: "\"Andreas \"" Date: Thu, 27 Apr 2017 20:00:49 +0200 Subject: [PATCH 0655/1603] correcting title --- easybuild/easyconfigs/p/Python/Python-2.7.13-foss-2017a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.13-foss-2017a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.13-foss-2017a.eb index 166b747669..5abe3e3e7d 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.13-foss-2017a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.13-foss-2017a.eb @@ -133,4 +133,3 @@ exts_list = [ ] moduleclass = 'lang' - -- GitLab From f1171afab1d0bf1a0ef79b28c4b1ce10e9cbd490 Mon Sep 17 00:00:00 2001 From: "\"Andreas \"" Date: Thu, 27 Apr 2017 20:27:16 +0200 Subject: [PATCH 0656/1603] removed built comments, and changed to python-2.7.13 --- .../l/LLVM/LLVM-3.9.1-foss-2017a.eb | 81 +----- .../l/LLVM/LLVM-4.0.0-foss-2017a.eb | 259 +----------------- 2 files changed, 2 insertions(+), 338 deletions(-) diff --git a/easybuild/easyconfigs/l/LLVM/LLVM-3.9.1-foss-2017a.eb b/easybuild/easyconfigs/l/LLVM/LLVM-3.9.1-foss-2017a.eb index be174d687f..6bffed0098 100644 --- a/easybuild/easyconfigs/l/LLVM/LLVM-3.9.1-foss-2017a.eb +++ b/easybuild/easyconfigs/l/LLVM/LLVM-3.9.1-foss-2017a.eb @@ -1,5 +1,3 @@ -# Built with EasyBuild version 3.1.1 on 2017-04-22_13-55-34 -# Built with EasyBuild version 3.1.1 on 2017-04-04_11-30-48 easyblock = 'CMakeMake' name = 'LLVM' @@ -22,7 +20,7 @@ sources = ["llvm-%(version)s.src.tar.xz"] builddependencies = [ ('CMake', '3.7.2'), - ('Python', '2.7.12'), + ('Python', '2.7.13'), ] dependencies = [ @@ -44,80 +42,3 @@ separate_build_dir = True moduleclass = 'compiler' -# Build statistics -buildstats = [{ - "build_time": 520.33, - "command_line": ["--buildpath='/dev/shm'", "--configfiles='/cluster/easybuild/config.cfg'", "--installpath='/cluster/easybuild'", "--module-naming-scheme='CategorizedModuleNamingScheme'", "--module-syntax='Tcl'", "--modules-tool='EnvironmentModulesC'", "--packagepath='/cluster/easybuild/packages'", "--parallel='40'", "--prefix='/cluster/easybuild'", "--repository='GitRepository'", "--repositorypath='/cluster/easybuild/ebfiles_repo.git'", "--robot-paths=':/cluster/easybuild/ebfiles_repo'", "--sourcepath='/cluster/easybuild/sources'", '--use-existing-modules', 'LLVM-3.9.0-foss-2017a.eb'], - "core_count": 40, - "cpu_model": "Intel(R) Xeon(R) CPU E5-2630 v4 @ 2.20GHz", - "cpu_speed": 3100.0, - "cpu_vendor": "Intel", - "easybuild-easyblocks_version": "3.1.1", - "easybuild-framework_version": "3.1.1", - "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/cluster/easybuild/software/compiler/GCCcore/6.3.0/libexec/gcc/x86_64-pc-linux-gnu/6.3.0/lto-wrapper; Target: x86_64-pc-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --with-local-prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --enable-bootstrap --with-isl=/dev/shm/GCCcore/6.3.0/dummy-/gcc-6.3.0/stage2_stuff; Thread model: posix; gcc version 6.3.0 (GCC) ; ", - "glibc_version": "2.17", - "hostname": "login23", - "install_size": 55611227, - "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'), - "os_name": "centos linux", - "os_type": "Linux", - "os_version": "7.3.1611", - "platform_name": "x86_64-unknown-linux", - "python_version": "2.7.5 (default, Nov 6 2016, 00:28:07) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-11)]", - "system_gcc_path": "/cluster/easybuild/software/compiler/GCCcore/6.3.0/bin/gcc", - "system_python_path": "/cluster/easybuild/software/lang/Python/2.7.12-foss-2017a/bin/python", - "timestamp": 1491298248, - "total_memory": 128828, -}] - -# Build statistics -buildstats = [ -{ - "build_time": 520.33, - "command_line": ["--buildpath='/dev/shm'", "--configfiles='/cluster/easybuild/config.cfg'", "--installpath='/cluster/easybuild'", "--module-naming-scheme='CategorizedModuleNamingScheme'", "--module-syntax='Tcl'", "--modules-tool='EnvironmentModulesC'", "--packagepath='/cluster/easybuild/packages'", "--parallel='40'", "--prefix='/cluster/easybuild'", "--repository='GitRepository'", "--repositorypath='/cluster/easybuild/ebfiles_repo.git'", "--robot-paths=':/cluster/easybuild/ebfiles_repo'", "--sourcepath='/cluster/easybuild/sources'", '--use-existing-modules', 'LLVM-3.9.0-foss-2017a.eb'], - "core_count": 40, - "cpu_model": "Intel(R) Xeon(R) CPU E5-2630 v4 @ 2.20GHz", - "cpu_speed": 3100.0, - "cpu_vendor": "Intel", - "easybuild-easyblocks_version": "3.1.1", - "easybuild-framework_version": "3.1.1", - "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/cluster/easybuild/software/compiler/GCCcore/6.3.0/libexec/gcc/x86_64-pc-linux-gnu/6.3.0/lto-wrapper; Target: x86_64-pc-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --with-local-prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --enable-bootstrap --with-isl=/dev/shm/GCCcore/6.3.0/dummy-/gcc-6.3.0/stage2_stuff; Thread model: posix; gcc version 6.3.0 (GCC) ; ", - "glibc_version": "2.17", - "hostname": "login23", - "install_size": 55611227, - "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'), - "os_name": "centos linux", - "os_type": "Linux", - "os_version": "7.3.1611", - "platform_name": "x86_64-unknown-linux", - "python_version": "2.7.5 (default, Nov 6 2016, 00:28:07) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-11)]", - "system_gcc_path": "/cluster/easybuild/software/compiler/GCCcore/6.3.0/bin/gcc", - "system_python_path": "/cluster/easybuild/software/lang/Python/2.7.12-foss-2017a/bin/python", - "timestamp": 1491298248, - "total_memory": 128828, -}, -{ - "build_time": 687.87, - "command_line": ["--buildpath='/dev/shm'", "--configfiles='/cluster/easybuild/config.cfg'", '--group-writable-installdir', "--installpath='/cluster/easybuild'", '--minimal-toolchains', "--module-naming-scheme='CategorizedModuleNamingScheme'", "--module-syntax='Tcl'", "--modules-tool='EnvironmentModulesC'", "--packagepath='/cluster/easybuild/packages'", "--parallel='40'", "--prefix='/cluster/easybuild'", "--repository='GitRepository'", "--repositorypath='/cluster/easybuild/ebfiles_repo.git'", "--robot='/cluster/easybuild/ebfiles_repo:/cluster/easybuild/software/EasyBuild/3.1.1/lib/python2.7/site-packages/easybuild_easyconfigs-3.1.1-py2.7.egg/easybuild/easyconfigs'", "--robot-paths='/cluster/easybuild/ebfiles_repo:'", '--set-gid-bit', "--sourcepath='/cluster/easybuild/sources'", "--try-software-version='3.9.1'", "--umask='002'", 'LLVM-3.9.0-foss-2017a.eb'], - "core_count": 40, - "cpu_model": "Intel(R) Xeon(R) CPU E5-2630 v4 @ 2.20GHz", - "cpu_speed": 3100.0, - "cpu_vendor": "Intel", - "easybuild-easyblocks_version": "3.1.1", - "easybuild-framework_version": "3.1.1", - "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/cluster/easybuild/software/compiler/GCCcore/6.3.0/libexec/gcc/x86_64-pc-linux-gnu/6.3.0/lto-wrapper; Target: x86_64-pc-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --with-local-prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --enable-bootstrap --with-isl=/dev/shm/GCCcore/6.3.0/dummy-/gcc-6.3.0/stage2_stuff; Thread model: posix; gcc version 6.3.0 (GCC) ; ", - "glibc_version": "2.17", - "hostname": "login23", - "install_size": 55620832, - "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'), - "os_name": "centos linux", - "os_type": "Linux", - "os_version": "7.3.1611", - "platform_name": "x86_64-unknown-linux", - "python_version": "2.7.5 (default, Nov 6 2016, 00:28:07) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-11)]", - "system_gcc_path": "/cluster/easybuild/software/compiler/GCCcore/6.3.0/bin/gcc", - "system_python_path": "/cluster/easybuild/software/lang/Python/2.7.12-foss-2017a/bin/python", - "timestamp": 1492862134, - "total_memory": 128828, -}, -] diff --git a/easybuild/easyconfigs/l/LLVM/LLVM-4.0.0-foss-2017a.eb b/easybuild/easyconfigs/l/LLVM/LLVM-4.0.0-foss-2017a.eb index 9090d26425..5a2a5553d5 100644 --- a/easybuild/easyconfigs/l/LLVM/LLVM-4.0.0-foss-2017a.eb +++ b/easybuild/easyconfigs/l/LLVM/LLVM-4.0.0-foss-2017a.eb @@ -1,7 +1,3 @@ -# Built with EasyBuild version 3.1.1 on 2017-04-22_14-33-26 -# Built with EasyBuild version 3.1.1 on 2017-04-22_13-54-52 -# Built with EasyBuild version 3.1.1 on 2017-04-21_17-49-43 -# Built with EasyBuild version 3.1.1 on 2017-04-04_11-52-35 easyblock = 'CMakeMake' name = 'LLVM' @@ -24,7 +20,7 @@ sources = ["llvm-%(version)s.src.tar.xz"] builddependencies = [ ('CMake', '3.7.2'), - ('Python', '2.7.12'), + ('Python', '2.7.13'), ] dependencies = [ @@ -46,256 +42,3 @@ separate_build_dir = True moduleclass = 'compiler' -# Build statistics -buildstats = [{ - "build_time": 751.68, - "command_line": ["--buildpath='/dev/shm'", "--configfiles='/cluster/easybuild/config.cfg'", "--installpath='/cluster/easybuild'", "--module-naming-scheme='CategorizedModuleNamingScheme'", "--module-syntax='Tcl'", "--modules-tool='EnvironmentModulesC'", "--packagepath='/cluster/easybuild/packages'", "--parallel='40'", "--prefix='/cluster/easybuild'", "--repository='GitRepository'", "--repositorypath='/cluster/easybuild/ebfiles_repo.git'", "--robot-paths=':/cluster/easybuild/ebfiles_repo'", "--sourcepath='/cluster/easybuild/sources'", '--use-existing-modules', 'LLVM-4.0.0-foss-2017a.eb'], - "core_count": 40, - "cpu_model": "Intel(R) Xeon(R) CPU E5-2630 v4 @ 2.20GHz", - "cpu_speed": 3100.0, - "cpu_vendor": "Intel", - "easybuild-easyblocks_version": "3.1.1", - "easybuild-framework_version": "3.1.1", - "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/cluster/easybuild/software/compiler/GCCcore/6.3.0/libexec/gcc/x86_64-pc-linux-gnu/6.3.0/lto-wrapper; Target: x86_64-pc-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --with-local-prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --enable-bootstrap --with-isl=/dev/shm/GCCcore/6.3.0/dummy-/gcc-6.3.0/stage2_stuff; 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COLLECT_LTO_WRAPPER=/cluster/easybuild/software/compiler/GCCcore/6.3.0/libexec/gcc/x86_64-pc-linux-gnu/6.3.0/lto-wrapper; Target: x86_64-pc-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --with-local-prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --enable-bootstrap --with-isl=/dev/shm/GCCcore/6.3.0/dummy-/gcc-6.3.0/stage2_stuff; Thread model: posix; gcc version 6.3.0 (GCC) ; ", - "glibc_version": "2.17", - "hostname": "login23", - "install_size": 141259232, - "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'), - "os_name": "centos linux", - "os_type": "Linux", - "os_version": "7.3.1611", - "platform_name": "x86_64-unknown-linux", - "python_version": "2.7.5 (default, Nov 6 2016, 00:28:07) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-11)]", - "system_gcc_path": "/cluster/easybuild/software/compiler/GCCcore/6.3.0/bin/gcc", - "system_python_path": "/cluster/easybuild/software/lang/Python/2.7.12-foss-2017a/bin/python", - "timestamp": 1492862091, - "total_memory": 128828, -}, -{ - "build_time": 395.04, - "command_line": ["--buildpath='/dev/shm'", "--configfiles='/cluster/easybuild/config.cfg'", '--group-writable-installdir', "--installpath='/cluster/easybuild'", '--minimal-toolchains', "--module-naming-scheme='CategorizedModuleNamingScheme'", "--module-syntax='Tcl'", "--modules-tool='EnvironmentModulesC'", "--packagepath='/cluster/easybuild/packages'", "--parallel='40'", "--prefix='/cluster/easybuild'", '--rebuild', "--repository='GitRepository'", "--repositorypath='/cluster/easybuild/ebfiles_repo.git'", "--robot-paths='/cluster/easybuild/ebfiles_repo:'", '--set-gid-bit', "--sourcepath='/cluster/easybuild/sources'", "--umask='002'", 'LLVM-4.0.0-foss-2017a.eb'], - "core_count": 40, - "cpu_model": "Intel(R) Xeon(R) CPU E5-2630 v4 @ 2.20GHz", - "cpu_speed": 3100.0, - "cpu_vendor": "Intel", - "easybuild-easyblocks_version": "3.1.1", - "easybuild-framework_version": "3.1.1", - "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/cluster/easybuild/software/compiler/GCCcore/6.3.0/libexec/gcc/x86_64-pc-linux-gnu/6.3.0/lto-wrapper; Target: x86_64-pc-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --with-local-prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --enable-bootstrap --with-isl=/dev/shm/GCCcore/6.3.0/dummy-/gcc-6.3.0/stage2_stuff; Thread model: posix; gcc version 6.3.0 (GCC) ; ", - "glibc_version": "2.17", - "hostname": "login23", - "install_size": 141259789, - "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'), - "os_name": "centos linux", - "os_type": "Linux", - "os_version": "7.3.1611", - "platform_name": "x86_64-unknown-linux", - "python_version": "2.7.5 (default, Nov 6 2016, 00:28:07) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-11)]", - "system_gcc_path": "/cluster/easybuild/software/compiler/GCCcore/6.3.0/bin/gcc", - "system_python_path": "/cluster/easybuild/software/lang/Python/2.7.12-foss-2017a/bin/python", - "timestamp": 1492864405, - "total_memory": 128828, -}, -] -- GitLab From 485b0eb98fcde2bb53fa971f1530deed67ace3a7 Mon Sep 17 00:00:00 2001 From: "\"Andreas \"" Date: Thu, 27 Apr 2017 20:51:09 +0200 Subject: [PATCH 0657/1603] removed comments, add jasper 1.900.1-foss-2017a dependency --- .../g/grib_api/grib_api-1.21.0-foss-2017a.eb | 26 ------------------- .../j/JasPer/JasPer-1.900.1-foss-2017a.eb | 22 ++++++++++++++++ 2 files changed, 22 insertions(+), 26 deletions(-) create mode 100644 easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-foss-2017a.eb diff --git a/easybuild/easyconfigs/g/grib_api/grib_api-1.21.0-foss-2017a.eb b/easybuild/easyconfigs/g/grib_api/grib_api-1.21.0-foss-2017a.eb index c8b9bec5e8..fa7f84d3e3 100644 --- a/easybuild/easyconfigs/g/grib_api/grib_api-1.21.0-foss-2017a.eb +++ b/easybuild/easyconfigs/g/grib_api/grib_api-1.21.0-foss-2017a.eb @@ -1,4 +1,3 @@ -# Built with EasyBuild version 3.1.1 on 2017-04-03_13-34-52 easyblock = 'ConfigureMake' name = 'grib_api' @@ -24,28 +23,3 @@ parallel = 1 moduleclass = 'data' -# Build statistics -buildstats = [{ - "build_time": 778.65, - "command_line": ["--buildpath='/dev/shm'", "--configfiles='/cluster/easybuild/config.cfg'", "--installpath='/cluster/easybuild'", "--module-naming-scheme='CategorizedModuleNamingScheme'", "--module-syntax='Tcl'", "--modules-tool='EnvironmentModulesC'", "--packagepath='/cluster/easybuild/packages'", "--parallel='40'", "--prefix='/cluster/easybuild'", "--repository='GitRepository'", "--repositorypath='/cluster/easybuild/ebfiles_repo.git'", "--robot='/cluster/easybuild/software/EasyBuild/3.1.1/lib/python2.7/site-packages/easybuild_easyconfigs-3.1.1-py2.7.egg/easybuild/easyconfigs:/cluster/easybuild/ebfiles_repo'", "--robot-paths=':/cluster/easybuild/ebfiles_repo'", "--sourcepath='/cluster/easybuild/sources'", 'grib_api-1.16.0-foss-2017a.eb'], - "core_count": 40, - "cpu_model": "Intel(R) Xeon(R) CPU E5-2630 v4 @ 2.20GHz", - "cpu_speed": 3100.0, - "cpu_vendor": "Intel", - "easybuild-easyblocks_version": "3.1.1", - "easybuild-framework_version": "3.1.1", - "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/cluster/easybuild/software/compiler/GCCcore/6.3.0/libexec/gcc/x86_64-pc-linux-gnu/6.3.0/lto-wrapper; Target: x86_64-pc-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --with-local-prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --enable-bootstrap --with-isl=/dev/shm/GCCcore/6.3.0/dummy-/gcc-6.3.0/stage2_stuff; Thread model: posix; gcc version 6.3.0 (GCC) ; ", - "glibc_version": "2.17", - "hostname": "login23", - "install_size": 27887407, - "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'), - "os_name": "centos linux", - "os_type": "Linux", - "os_version": "7.3.1611", - "platform_name": "x86_64-unknown-linux", - "python_version": "2.7.5 (default, Nov 6 2016, 00:28:07) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-11)]", - "system_gcc_path": "/cluster/easybuild/software/compiler/GCCcore/6.3.0/bin/gcc", - "system_python_path": "/usr/bin/python", - "timestamp": 1491219291, - "total_memory": 128828, -}] diff --git a/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-foss-2017a.eb b/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-foss-2017a.eb new file mode 100644 index 0000000000..73e404db1c --- /dev/null +++ b/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-foss-2017a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'JasPer' +version = '1.900.1' + +homepage = 'http://www.ece.uvic.ca/~frodo/jasper/' +description = """The JasPer Project is an open-source initiative to provide a free + software-based reference implementation of the codec specified in the JPEG-2000 Part-1 standard.""" + +toolchain = {'name': 'foss', 'version': '2017a'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_ZIP] +source_urls = ['http://www.ece.uvic.ca/~frodo/jasper/software/'] + +sanity_check_paths = { + 'files': ["bin/jasper", "lib/libjasper.a"], + 'dirs': ["include"], +} + +moduleclass = 'vis' + -- GitLab From 0378f98cce404a3d418b2ff997068c303ba29f9d Mon Sep 17 00:00:00 2001 From: "\"Andreas \"" Date: Thu, 27 Apr 2017 20:55:18 +0200 Subject: [PATCH 0658/1603] removed built comments --- .../easyconfigs/o/OTF2/OTF2-2.0-foss-2017a.eb | 28 +------------------ 1 file changed, 1 insertion(+), 27 deletions(-) diff --git a/easybuild/easyconfigs/o/OTF2/OTF2-2.0-foss-2017a.eb b/easybuild/easyconfigs/o/OTF2/OTF2-2.0-foss-2017a.eb index 7d56604ccc..c2ecdc414e 100644 --- a/easybuild/easyconfigs/o/OTF2/OTF2-2.0-foss-2017a.eb +++ b/easybuild/easyconfigs/o/OTF2/OTF2-2.0-foss-2017a.eb @@ -1,10 +1,9 @@ -# Built with EasyBuild version 3.1.1 on 2017-04-25_21-37-09 ## # This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild # Copyright:: Copyright 2013-2016 Juelich Supercomputing Centre, Germany # Authors:: Bernd Mohr # Markus Geimer -# License:: 3-clause BSD +## License:: 3-clause BSD # # This work is based on experiences from the UNITE project # http://apps.fz-juelich.de/unite/ @@ -40,28 +39,3 @@ sanity_check_paths = { moduleclass = 'perf' -# Build statistics -buildstats = [{ - "build_time": 69.0, - "command_line": ["--buildpath='/dev/shm'", "--configfiles='/cluster/easybuild/config.cfg'", "--git-working-dirs-path='/home/henkela/tmp/easybuild-easyconfigs'", "--github-user='henkela'", '--group-writable-installdir', "--installpath='/cluster/easybuild'", '--minimal-toolchains', "--module-naming-scheme='CategorizedModuleNamingScheme'", "--module-syntax='Tcl'", "--modules-tool='EnvironmentModulesC'", "--packagepath='/cluster/easybuild/packages'", "--parallel='40'", "--prefix='/cluster/easybuild'", "--repository='GitRepository'", "--repositorypath='/cluster/easybuild/ebfiles_repo.git'", "--robot-paths='/cluster/easybuild/ebfiles_repo:'", '--set-gid-bit', "--sourcepath='/cluster/easybuild/sources'", "--umask='002'", 'OTF2-2.0-foss-2017a.eb'], - "core_count": 40, - "cpu_model": "Intel(R) Xeon(R) CPU E5-2630 v4 @ 2.20GHz", - "cpu_speed": 3100.0, - "cpu_vendor": "Intel", - "easybuild-easyblocks_version": "3.1.1", - "easybuild-framework_version": "3.1.1", - "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/cluster/easybuild/software/compiler/GCCcore/6.3.0/libexec/gcc/x86_64-pc-linux-gnu/6.3.0/lto-wrapper; Target: x86_64-pc-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --with-local-prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --enable-bootstrap --with-isl=/dev/shm/GCCcore/6.3.0/dummy-/gcc-6.3.0/stage2_stuff; Thread model: posix; gcc version 6.3.0 (GCC) ; ", - "glibc_version": "2.17", - "hostname": "login23", - "install_size": 19885165, - "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'), - "os_name": "centos linux", - "os_type": "Linux", - "os_version": "7.3.1611", - "platform_name": "x86_64-unknown-linux", - "python_version": "2.7.5 (default, Nov 6 2016, 00:28:07) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-11)]", - "system_gcc_path": "/cluster/easybuild/software/compiler/GCCcore/6.3.0/bin/gcc", - "system_python_path": "/usr/bin/python", - "timestamp": 1493149028, - "total_memory": 128828, -}] -- GitLab From df93abf1c89c8562763fa53595193975553e6234 Mon Sep 17 00:00:00 2001 From: "\"Andreas \"" Date: Thu, 27 Apr 2017 20:59:28 +0200 Subject: [PATCH 0659/1603] removed built comments and added Szip-2.1-foss-2017a.eb dependency --- .../h/HDF5/HDF5-1.8.18-foss-2017a.eb | 27 ------------------- .../easyconfigs/s/Szip/Szip-2.1-foss-2017a.eb | 24 +++++++++++++++++ 2 files changed, 24 insertions(+), 27 deletions(-) create mode 100644 easybuild/easyconfigs/s/Szip/Szip-2.1-foss-2017a.eb diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.18-foss-2017a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.18-foss-2017a.eb index 10498ad96c..1febe1c832 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.18-foss-2017a.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.18-foss-2017a.eb @@ -1,4 +1,3 @@ -# Built with EasyBuild version 3.1.1 on 2017-04-04_14-47-11 name = 'HDF5' version = '1.8.18' @@ -25,29 +24,3 @@ dependencies = [ ] moduleclass = 'data' - -# Build statistics -buildstats = [{ - "build_time": 144.81, - "command_line": ["--buildpath='/dev/shm'", "--configfiles='/cluster/easybuild/config.cfg'", "--installpath='/cluster/easybuild'", "--module-naming-scheme='CategorizedModuleNamingScheme'", "--module-syntax='Tcl'", "--modules-tool='EnvironmentModulesC'", "--packagepath='/cluster/easybuild/packages'", "--parallel='40'", "--prefix='/cluster/easybuild'", '--rebuild', "--repository='GitRepository'", "--repositorypath='/cluster/easybuild/ebfiles_repo.git'", "--robot='/cluster/easybuild/software/EasyBuild/3.1.1/lib/python2.7/site-packages/easybuild_easyconfigs-3.1.1-py2.7.egg/easybuild/easyconfigs:/cluster/easybuild/ebfiles_repo'", "--robot-paths=':/cluster/easybuild/ebfiles_repo'", "--sourcepath='/cluster/easybuild/sources'", 'HDF5-1.8.18-foss-2017a.eb'], - "core_count": 40, - "cpu_model": "Intel(R) Xeon(R) CPU E5-2630 v4 @ 2.20GHz", - "cpu_speed": 3100.0, - "cpu_vendor": "Intel", - "easybuild-easyblocks_version": "3.1.1", - "easybuild-framework_version": "3.1.1", - "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/cluster/easybuild/software/compiler/GCCcore/6.3.0/libexec/gcc/x86_64-pc-linux-gnu/6.3.0/lto-wrapper; Target: x86_64-pc-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --with-local-prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --enable-bootstrap --with-isl=/dev/shm/GCCcore/6.3.0/dummy-/gcc-6.3.0/stage2_stuff; Thread model: posix; gcc version 6.3.0 (GCC) ; ", - "glibc_version": "2.17", - "hostname": "login23", - "install_size": 25911504, - "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'), - "os_name": "centos linux", - "os_type": "Linux", - "os_version": "7.3.1611", - "platform_name": "x86_64-unknown-linux", - "python_version": "2.7.5 (default, Nov 6 2016, 00:28:07) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-11)]", - "system_gcc_path": "/cluster/easybuild/software/compiler/GCCcore/6.3.0/bin/gcc", - "system_python_path": "/usr/bin/python", - "timestamp": 1491310030, - "total_memory": 128828, -}] diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1-foss-2017a.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1-foss-2017a.eb new file mode 100644 index 0000000000..9365662b36 --- /dev/null +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1-foss-2017a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'Szip' +version = '2.1' + +homepage = 'http://www.hdfgroup.org/doc_resource/SZIP/' +description = "Szip compression software, providing lossless compression of scientific data" + +toolchain = {'name': 'foss', 'version': '2017a'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = "--with-pic" + +sanity_check_paths = { + 'files': ["lib/libsz.a", "lib/libsz.%s" % SHLIB_EXT] + + ["include/%s" % x for x in ["ricehdf.h", "szip_adpt.h", "szlib.h"]], + 'dirs': [], +} + +moduleclass = 'tools' + -- GitLab From 00949b56eb8ba377a3f9adbbc96729483f1d7a0a Mon Sep 17 00:00:00 2001 From: "\"Andreas \"" Date: Thu, 27 Apr 2017 21:36:16 +0200 Subject: [PATCH 0660/1603] updated Boost-1.63.0-foss-2017a-Python-2.7.12 to 2.7.13 and removed built comments --- .../Boost-1.63.0-foss-2017a-Python-2.7.13.eb | 24 +++++++++++++++++ .../b/Boost/Boost-1.63.0-foss-2017a.eb | 26 ------------------- 2 files changed, 24 insertions(+), 26 deletions(-) create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.63.0-foss-2017a-Python-2.7.13.eb diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.63.0-foss-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/b/Boost/Boost-1.63.0-foss-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..49051608e1 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.63.0-foss-2017a-Python-2.7.13.eb @@ -0,0 +1,24 @@ +name = 'Boost' +version = '1.63.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.boost.org/' +description = "Boost provides free peer-reviewed portable C++ source libraries." + +toolchain = {'name': 'foss', 'version': '2017a'} +toolchainopts = {'usempi': True, 'pic': True} + +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] +source_urls = ['https://sourceforge.net/projects/%(namelower)s/files/%(namelower)s/%(version)s'] + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.11'), + ('Python', '2.7.13'), +] + +# also build boost_mpi +boost_mpi = True + +moduleclass = 'devel' + diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.63.0-foss-2017a.eb b/easybuild/easyconfigs/b/Boost/Boost-1.63.0-foss-2017a.eb index daa0767419..ea4624e01d 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.63.0-foss-2017a.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.63.0-foss-2017a.eb @@ -1,4 +1,3 @@ -# Built with EasyBuild version 3.1.1 on 2017-04-04_18-18-26 name = 'Boost' version = '1.63.0' @@ -23,28 +22,3 @@ boost_mpi = True moduleclass = 'devel' -# Build statistics -buildstats = [{ - "build_time": 2759.25, - "command_line": ["--buildpath='/dev/shm'", "--configfiles='/cluster/easybuild/config.cfg'", "--installpath='/cluster/easybuild'", "--module-naming-scheme='CategorizedModuleNamingScheme'", "--module-syntax='Tcl'", "--modules-tool='EnvironmentModulesC'", "--packagepath='/cluster/easybuild/packages'", "--parallel='40'", "--prefix='/cluster/easybuild'", "--repository='GitRepository'", "--repositorypath='/cluster/easybuild/ebfiles_repo.git'", "--robot='/cluster/easybuild/software/EasyBuild/3.1.1/lib/python2.7/site-packages/easybuild_easyconfigs-3.1.1-py2.7.egg/easybuild/easyconfigs:/cluster/easybuild/ebfiles_repo'", "--robot-paths=':/cluster/easybuild/ebfiles_repo'", "--sourcepath='/cluster/easybuild/sources'", 'GROMACS-5.1.4-foss-2017a-hybrid.eb'], - "core_count": 40, - "cpu_model": "Intel(R) Xeon(R) CPU E5-2630 v4 @ 2.20GHz", - "cpu_speed": 3100.0, - "cpu_vendor": "Intel", - "easybuild-easyblocks_version": "3.1.1", - "easybuild-framework_version": "3.1.1", - "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/cluster/easybuild/software/compiler/GCCcore/6.3.0/libexec/gcc/x86_64-pc-linux-gnu/6.3.0/lto-wrapper; Target: x86_64-pc-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --with-local-prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --enable-bootstrap --with-isl=/dev/shm/GCCcore/6.3.0/dummy-/gcc-6.3.0/stage2_stuff; Thread model: posix; gcc version 6.3.0 (GCC) ; ", - "glibc_version": "2.17", - "hostname": "login23", - "install_size": 167262879, - "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'), - "os_name": "centos linux", - "os_type": "Linux", - "os_version": "7.3.1611", - "platform_name": "x86_64-unknown-linux", - "python_version": "2.7.5 (default, Nov 6 2016, 00:28:07) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-11)]", - "system_gcc_path": "/cluster/easybuild/software/compiler/GCCcore/6.3.0/bin/gcc", - "system_python_path": "/usr/bin/python", - "timestamp": 1491322705, - "total_memory": 128828, -}] -- GitLab From 101e7c5c515b350678f51ac93715b0e537db32d2 Mon Sep 17 00:00:00 2001 From: "\"Andreas \"" Date: Thu, 27 Apr 2017 21:38:09 +0200 Subject: [PATCH 0661/1603] deleted Boost-1.63.0-foss-2017a-Python-2.7.12.eb --- .../Boost-1.63.0-foss-2017a-Python-2.7.12.eb | 103 ------------------ 1 file changed, 103 deletions(-) delete mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.63.0-foss-2017a-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.63.0-foss-2017a-Python-2.7.12.eb b/easybuild/easyconfigs/b/Boost/Boost-1.63.0-foss-2017a-Python-2.7.12.eb deleted file mode 100644 index 483520bf60..0000000000 --- a/easybuild/easyconfigs/b/Boost/Boost-1.63.0-foss-2017a-Python-2.7.12.eb +++ /dev/null @@ -1,103 +0,0 @@ -# Built with EasyBuild version 3.1.1 on 2017-04-20_15-40-11 -# Built with EasyBuild version 3.1.1 on 2017-04-03_15-24-36 -name = 'Boost' -version = '1.63.0' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'http://www.boost.org/' -description = "Boost provides free peer-reviewed portable C++ source libraries." - -toolchain = {'name': 'foss', 'version': '2017a'} -toolchainopts = {'usempi': True, 'pic': True} - -sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] -source_urls = ['https://sourceforge.net/projects/%(namelower)s/files/%(namelower)s/%(version)s'] - -dependencies = [ - ('bzip2', '1.0.6'), - ('zlib', '1.2.11'), - ('Python', '2.7.12'), -] - -# also build boost_mpi -boost_mpi = True - -moduleclass = 'devel' - -# Build statistics -buildstats = [{ - "build_time": 1537.69, - "command_line": ["--buildpath='/dev/shm'", "--configfiles='/cluster/easybuild/config.cfg'", "--installpath='/cluster/easybuild'", "--module-naming-scheme='CategorizedModuleNamingScheme'", "--module-syntax='Tcl'", "--modules-tool='EnvironmentModulesC'", "--packagepath='/cluster/easybuild/packages'", "--parallel='40'", "--prefix='/cluster/easybuild'", "--repository='GitRepository'", "--repositorypath='/cluster/easybuild/ebfiles_repo.git'", "--robot='/cluster/easybuild/software/EasyBuild/3.1.1/lib/python2.7/site-packages/easybuild_easyconfigs-3.1.1-py2.7.egg/easybuild/easyconfigs:/cluster/easybuild/ebfiles_repo'", "--robot-paths=':/cluster/easybuild/ebfiles_repo'", "--sourcepath='/cluster/easybuild/sources'", '--use-existing-modules', 'PETSc-3.7.5-foss-2017a-Python-2.7.12.eb'], - "core_count": 40, - "cpu_model": "Intel(R) Xeon(R) CPU E5-2630 v4 @ 2.20GHz", - "cpu_speed": 3100.0, - "cpu_vendor": "Intel", - "easybuild-easyblocks_version": "3.1.1", - "easybuild-framework_version": "3.1.1", - "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/cluster/easybuild/software/compiler/GCCcore/6.3.0/libexec/gcc/x86_64-pc-linux-gnu/6.3.0/lto-wrapper; Target: x86_64-pc-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --with-local-prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --enable-bootstrap --with-isl=/dev/shm/GCCcore/6.3.0/dummy-/gcc-6.3.0/stage2_stuff; Thread model: posix; gcc version 6.3.0 (GCC) ; ", - "glibc_version": "2.17", - "hostname": "login23", - "install_size": 169939518, - "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'), - "os_name": "centos linux", - "os_type": "Linux", - "os_version": "7.3.1611", - "platform_name": "x86_64-unknown-linux", - "python_version": "2.7.5 (default, Nov 6 2016, 00:28:07) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-11)]", - "system_gcc_path": "/cluster/easybuild/software/compiler/GCCcore/6.3.0/bin/gcc", - "system_python_path": "/cluster/easybuild/software/lang/Python/2.7.12-foss-2017a/bin/python", - "timestamp": 1491225875, - "total_memory": 128828, -}] - -# Build statistics -buildstats = [ -{ - "build_time": 1537.69, - "command_line": ["--buildpath='/dev/shm'", "--configfiles='/cluster/easybuild/config.cfg'", "--installpath='/cluster/easybuild'", "--module-naming-scheme='CategorizedModuleNamingScheme'", "--module-syntax='Tcl'", "--modules-tool='EnvironmentModulesC'", "--packagepath='/cluster/easybuild/packages'", "--parallel='40'", "--prefix='/cluster/easybuild'", "--repository='GitRepository'", "--repositorypath='/cluster/easybuild/ebfiles_repo.git'", "--robot='/cluster/easybuild/software/EasyBuild/3.1.1/lib/python2.7/site-packages/easybuild_easyconfigs-3.1.1-py2.7.egg/easybuild/easyconfigs:/cluster/easybuild/ebfiles_repo'", "--robot-paths=':/cluster/easybuild/ebfiles_repo'", "--sourcepath='/cluster/easybuild/sources'", '--use-existing-modules', 'PETSc-3.7.5-foss-2017a-Python-2.7.12.eb'], - "core_count": 40, - "cpu_model": "Intel(R) Xeon(R) CPU E5-2630 v4 @ 2.20GHz", - "cpu_speed": 3100.0, - "cpu_vendor": "Intel", - "easybuild-easyblocks_version": "3.1.1", - "easybuild-framework_version": "3.1.1", - "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/cluster/easybuild/software/compiler/GCCcore/6.3.0/libexec/gcc/x86_64-pc-linux-gnu/6.3.0/lto-wrapper; Target: x86_64-pc-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --with-local-prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --enable-bootstrap --with-isl=/dev/shm/GCCcore/6.3.0/dummy-/gcc-6.3.0/stage2_stuff; Thread model: posix; gcc version 6.3.0 (GCC) ; ", - "glibc_version": "2.17", - "hostname": "login23", - "install_size": 169939518, - "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'), - "os_name": "centos linux", - "os_type": "Linux", - "os_version": "7.3.1611", - "platform_name": "x86_64-unknown-linux", - "python_version": "2.7.5 (default, Nov 6 2016, 00:28:07) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-11)]", - "system_gcc_path": "/cluster/easybuild/software/compiler/GCCcore/6.3.0/bin/gcc", - "system_python_path": "/cluster/easybuild/software/lang/Python/2.7.12-foss-2017a/bin/python", - "timestamp": 1491225875, - "total_memory": 128828, -}, -{ - "build_time": 1585.32, - "command_line": ["--buildpath='/dev/shm'", "--configfiles='/cluster/easybuild/config.cfg'", '--group-writable-installdir', "--installpath='/cluster/easybuild'", "--module-naming-scheme='CategorizedModuleNamingScheme'", "--module-syntax='Tcl'", "--modules-tool='EnvironmentModulesC'", "--packagepath='/cluster/easybuild/packages'", "--parallel='40'", "--prefix='/cluster/easybuild'", '--rebuild', "--repository='GitRepository'", "--repositorypath='/cluster/easybuild/ebfiles_repo.git'", "--robot='/cluster/easybuild/ebfiles_repo:/cluster/easybuild/software/EasyBuild/3.1.1/lib/python2.7/site-packages/easybuild_easyconfigs-3.1.1-py2.7.egg/easybuild/easyconfigs'", "--robot-paths='/cluster/easybuild/ebfiles_repo:'", '--set-gid-bit', "--sourcepath='/cluster/easybuild/sources'", "--umask='002'", 'Boost/Boost-1.63.0-foss-2017a-Python-2.7.12.eb'], - "core_count": 40, - "cpu_model": "Intel(R) Xeon(R) CPU E5-2630 v4 @ 2.20GHz", - "cpu_speed": 3100.0, - "cpu_vendor": "Intel", - "easybuild-easyblocks_version": "3.1.1", - "easybuild-framework_version": "3.1.1", - "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/cluster/easybuild/software/compiler/GCCcore/6.3.0/libexec/gcc/x86_64-pc-linux-gnu/6.3.0/lto-wrapper; Target: x86_64-pc-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --with-local-prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --enable-bootstrap --with-isl=/dev/shm/GCCcore/6.3.0/dummy-/gcc-6.3.0/stage2_stuff; Thread model: posix; gcc version 6.3.0 (GCC) ; ", - "glibc_version": "2.17", - "hostname": "login24", - "install_size": 169940729, - "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'), - "os_name": "centos linux", - "os_type": "Linux", - "os_version": "7.3.1611", - "platform_name": "x86_64-unknown-linux", - "python_version": "2.7.5 (default, Nov 6 2016, 00:28:07) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-11)]", - "system_gcc_path": "/cluster/easybuild/software/compiler/GCCcore/6.3.0/bin/gcc", - "system_python_path": "/cluster/easybuild/software/lang/Python/2.7.12-foss-2017a/bin/python", - "timestamp": 1492695611, - "total_memory": 128828, -}, -] -- GitLab From 4eaa887d711737ff20a23ad31aa3dc194c816c33 Mon Sep 17 00:00:00 2001 From: "\"Andreas \"" Date: Fri, 28 Apr 2017 06:06:57 +0200 Subject: [PATCH 0662/1603] removed built comments and updated tcl --- .../n/NAMD/NAMD-2.12-foss-2017a-mpi.eb | 28 +------------------ .../t/Tcl/Tcl-8.5.19-foss-2017a.eb | 27 ++++++++++++++++++ 2 files changed, 28 insertions(+), 27 deletions(-) create mode 100644 easybuild/easyconfigs/t/Tcl/Tcl-8.5.19-foss-2017a.eb diff --git a/easybuild/easyconfigs/n/NAMD/NAMD-2.12-foss-2017a-mpi.eb b/easybuild/easyconfigs/n/NAMD/NAMD-2.12-foss-2017a-mpi.eb index 13ea1d21a4..6dd67416d3 100644 --- a/easybuild/easyconfigs/n/NAMD/NAMD-2.12-foss-2017a-mpi.eb +++ b/easybuild/easyconfigs/n/NAMD/NAMD-2.12-foss-2017a-mpi.eb @@ -1,4 +1,3 @@ -# Built with EasyBuild version 3.1.1 on 2017-04-04_17-10-41 name = 'NAMD' version = '2.12' versionsuffix = '-mpi' @@ -13,7 +12,7 @@ toolchainopts = {'opt': True, 'pic': True} sources = ['NAMD_%(version)s_Source.tar.gz'] dependencies = [ - ('Tcl', '8.5.12'), + ('Tcl', '8.5.19'), ] # /bin/csh is required by 'config' script @@ -23,28 +22,3 @@ charm_arch = "mpi-linux-x86_64" moduleclass = 'chem' -# Build statistics -buildstats = [{ - "build_time": 269.88, - "command_line": ["--buildpath='/dev/shm'", "--configfiles='/cluster/easybuild/config.cfg'", "--installpath='/cluster/easybuild'", "--module-naming-scheme='CategorizedModuleNamingScheme'", "--module-syntax='Tcl'", "--modules-tool='EnvironmentModulesC'", "--packagepath='/cluster/easybuild/packages'", "--parallel='40'", "--prefix='/cluster/easybuild'", "--repository='GitRepository'", "--repositorypath='/cluster/easybuild/ebfiles_repo.git'", "--robot-paths=':/cluster/easybuild/ebfiles_repo'", "--sourcepath='/cluster/easybuild/sources'", 'NAMD-2.12-foss-2017a-mpi.eb'], - "core_count": 40, - "cpu_model": "Intel(R) Xeon(R) CPU E5-2630 v4 @ 2.20GHz", - "cpu_speed": 3100.0, - "cpu_vendor": "Intel", - "easybuild-easyblocks_version": "3.1.1", - "easybuild-framework_version": "3.1.1", - "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/cluster/easybuild/software/compiler/GCCcore/6.3.0/libexec/gcc/x86_64-pc-linux-gnu/6.3.0/lto-wrapper; Target: x86_64-pc-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --with-local-prefix=/cluster/easybuild/software/compiler/GCCcore/6.3.0 --enable-bootstrap --with-isl=/dev/shm/GCCcore/6.3.0/dummy-/gcc-6.3.0/stage2_stuff; Thread model: posix; gcc version 6.3.0 (GCC) ; ", - "glibc_version": "2.17", - "hostname": "login23", - "install_size": 45931470, - "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'), - "os_name": "centos linux", - "os_type": "Linux", - "os_version": "7.3.1611", - "platform_name": "x86_64-unknown-linux", - "python_version": "2.7.5 (default, Nov 6 2016, 00:28:07) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-11)]", - "system_gcc_path": "/cluster/easybuild/software/compiler/GCCcore/6.3.0/bin/gcc", - "system_python_path": "/usr/bin/python", - "timestamp": 1491318641, - "total_memory": 128828, -}] diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.5.19-foss-2017a.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.5.19-foss-2017a.eb new file mode 100644 index 0000000000..0514b4e682 --- /dev/null +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.5.19-foss-2017a.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'Tcl' +version = "8.5.19" + +homepage = 'http://www.tcl.tk/' +description = """Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, +suitable for a very wide range of uses, including web and desktop applications, networking, administration, +testing and many more.""" + +toolchain = {'name': 'foss', 'version': '2017a'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +dependencies = [ + ('zlib', '1.2.11'), +] + +configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' + +runtest = 'test' + +start_dir = 'unix' + +moduleclass = 'lang' + -- GitLab From 1763251c00437c70b3aeff0287d6406648f30897 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 2 May 2017 10:57:26 +0200 Subject: [PATCH 0663/1603] align IMB 4.1 easyconfigs for foss/2017a and intel/2017.02 --- easybuild/easyconfigs/i/IMB/IMB-4.1-foss-2017a.eb | 14 +++++--------- .../easyconfigs/i/IMB/IMB-4.1-intel-2017.02.eb | 11 +++++------ 2 files changed, 10 insertions(+), 15 deletions(-) diff --git a/easybuild/easyconfigs/i/IMB/IMB-4.1-foss-2017a.eb b/easybuild/easyconfigs/i/IMB/IMB-4.1-foss-2017a.eb index 0a33899fe9..bcbb961f34 100644 --- a/easybuild/easyconfigs/i/IMB/IMB-4.1-foss-2017a.eb +++ b/easybuild/easyconfigs/i/IMB/IMB-4.1-foss-2017a.eb @@ -4,29 +4,25 @@ name = 'IMB' version = '4.1' homepage = 'https://software.intel.com/en-us/articles/intel-mpi-benchmarks' -description = """ -The Intel® MPI Benchmarks perform a set of MPI performance measurements for point-to-point -and global communication operations for a range of message sizes. -""" +description = """The Intel MPI Benchmarks perform a set of MPI performance measurements for point-to-point and + global communication operations for a range of message sizes""" toolchain = {'name': 'foss', 'version': '2017a'} +toolchainopts = {'usempi': True} sources = ['%(name)s_%(version)s.tgz'] source_urls = ['https://software.intel.com/sites/default/files/managed/a3/b2/'] start_dir = 'src' -prebuildopts = 'export MPI_HOME=$EBROOTOPENMPI && ' -buildopts = "-f make_mpich MPI_HOME=$EBROOTOPENMPI" +buildopts = 'all CC="$MPICC"' parallel = 1 files_to_copy = [(['src/IMB-*'], 'bin'), (['doc/IMB_Users_Guide.pdf'], 'doc')] sanity_check_paths = { - 'files': ['bin/%s' % binfile for binfile in ['IMB-RMA', 'IMB-EXT', 'IMB-NBC', 'IMB-MPI1']], + 'files': ['bin/IMB-EXT', 'bin/IMB-IO', 'bin/IMB-MPI1', 'bin/IMB-NBC', 'bin/IMB-RMA'], 'dirs': ['bin', 'doc'] } moduleclass = 'perf' - - diff --git a/easybuild/easyconfigs/i/IMB/IMB-4.1-intel-2017.02.eb b/easybuild/easyconfigs/i/IMB/IMB-4.1-intel-2017.02.eb index 65d5fc7e4a..d22113b5a9 100644 --- a/easybuild/easyconfigs/i/IMB/IMB-4.1-intel-2017.02.eb +++ b/easybuild/easyconfigs/i/IMB/IMB-4.1-intel-2017.02.eb @@ -10,20 +10,19 @@ description = """The Intel MPI Benchmarks perform a set of MPI performance measu toolchain = {'name': 'intel', 'version': '2017.02'} toolchainopts = {'usempi': True} -source_urls = ['https://software.intel.com/sites/default/files/managed/34/aa/'] sources = ['%(name)s_%(version)s.tgz'] +source_urls = ['https://software.intel.com/sites/default/files/managed/a3/b2/'] -prebuildopts = "cd src && " -buildopts = "all" +start_dir = 'src' +buildopts = 'all CC="$MPICC"' parallel = 1 -files_to_copy = [(['src/IMB-*'], 'bin')] +files_to_copy = [(['src/IMB-*'], 'bin'), (['doc/IMB_Users_Guide.pdf'], 'doc')] sanity_check_paths = { 'files': ['bin/IMB-EXT', 'bin/IMB-IO', 'bin/IMB-MPI1', 'bin/IMB-NBC', 'bin/IMB-RMA'], - 'dirs': [], + 'dirs': ['bin', 'doc'] } moduleclass = 'perf' - -- GitLab From 828a4b4be010f44678b5cc7c401ecd2b84ea51d7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 2 May 2017 11:23:30 +0200 Subject: [PATCH 0664/1603] adding easyconfigs: Boost-1.64.0-intel-2017a.eb --- .../b/Boost/Boost-1.64.0-intel-2017a.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.64.0-intel-2017a.eb diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.64.0-intel-2017a.eb b/easybuild/easyconfigs/b/Boost/Boost-1.64.0-intel-2017a.eb new file mode 100644 index 0000000000..981136de99 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.64.0-intel-2017a.eb @@ -0,0 +1,23 @@ +name = 'Boost' +version = '1.64.0' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.11'), +] + +configopts = '--without-libraries=python' + +# also build boost_mpi +boost_mpi = True + +moduleclass = 'devel' -- GitLab From d211df671be83d9fbb2740449366a1874cf44490 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 2 May 2017 12:44:47 +0200 Subject: [PATCH 0665/1603] adding easyconfigs: Python-3.6.1-intel-2017a.eb --- .../p/Python/Python-3.6.1-intel-2017a.eb | 127 ++++++++++++++++++ 1 file changed, 127 insertions(+) create mode 100644 easybuild/easyconfigs/p/Python/Python-3.6.1-intel-2017a.eb diff --git a/easybuild/easyconfigs/p/Python/Python-3.6.1-intel-2017a.eb b/easybuild/easyconfigs/p/Python/Python-3.6.1-intel-2017a.eb new file mode 100644 index 0000000000..b226f52d51 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-3.6.1-intel-2017a.eb @@ -0,0 +1,127 @@ +name = 'Python' +version = '3.6.1' + +homepage = 'http://python.org/' +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +# python needs bzip2 to build the bz2 package +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.11'), + ('libreadline', '7.0'), + ('ncurses', '6.0'), + ('SQLite', '3.17.0'), + ('GMP', '6.1.2'), + ('XZ', '5.2.3'), + ('libffi', '3.2.1'), + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.2k'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# order is important! +# package versions updated May 28th 2015 +exts_list = [ + # note: more recent versions of setuptools (v34.x) can not be installed from source anymore, + # see https://github.com/pypa/setuptools/issues/980 + ('setuptools', '33.1.1', { + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], + 'source_tmpl': '%(name)s-%(version)s.zip', + }), + ('pip', '9.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], + }), + ('nose', '1.3.7', { + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], + }), + ('numpy', '1.12.1', { + 'source_urls': ['https://pypi.python.org/packages/source/n/numpy'], + 'source_tmpl': '%(name)s-%(version)s.zip', + 'patches': ['numpy-1.12.0-mkl.patch'], + }), + ('scipy', '0.19.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/scipy'], + 'source_tmpl': '%(name)s-%(version)s.zip', + }), + ('blist', '1.3.6', { + 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], + }), + ('mpi4py', '2.0.0', { + 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + }), + ('paycheck', '1.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], + 'patches': [ + 'paycheck-1.0.2_setup-open-README-utf8.patch', + ], + }), + ('pbr', '2.0.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], + }), + ('lockfile', '0.12.2', { + 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], + }), + ('Cython', '0.25.2', { + 'source_urls': ['https://pypi.python.org/packages/source/c/cython/'], + }), + ('six', '1.10.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), + ('dateutil', '2.6.0', { + 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], + }), + ('deap', '1.0.2', { + 'source_tmpl': '%(name)s-%(version)s.post2.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], + 'patches': [ + 'deap-1.0.2_setup-open-README-utf8.patch', + ], + }), + ('decorator', '4.0.11', { + 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], + }), + ('arff', '2.1.0', { + 'source_tmpl': 'liac-%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], + }), + ('pycrypto', '2.6.1', { + 'modulename': 'Crypto', + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], + }), + ('ecdsa', '0.13', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), + ('cryptography', '1.8.1', { + 'source_urls': ['https://pypi.python.org/packages/source/c/cryptography/'], + }), + ('paramiko', '2.1.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], + }), + ('pyparsing', '2.2.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], + }), + ('netifaces', '0.10.5', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], + }), + ('netaddr', '0.7.19', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], + }), + ('pandas', '0.19.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], + }), + ('virtualenv', '15.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/v/virtualenv'], + }), +] + +moduleclass = 'lang' -- GitLab From 6d38e047d7867b3529d97081d4ff1c69857e504c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 2 May 2017 14:50:50 +0200 Subject: [PATCH 0666/1603] adding easyconfigs: BamTools-2.4.1-intel-2017a.eb, CMake-3.8.0-GCCcore-6.3.0.eb --- .../b/BamTools/BamTools-2.4.1-intel-2017a.eb | 16 +++++++++ .../c/CMake/CMake-3.8.0-GCCcore-6.3.0.eb | 36 +++++++++++++++++++ 2 files changed, 52 insertions(+) create mode 100644 easybuild/easyconfigs/b/BamTools/BamTools-2.4.1-intel-2017a.eb create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.8.0-GCCcore-6.3.0.eb diff --git a/easybuild/easyconfigs/b/BamTools/BamTools-2.4.1-intel-2017a.eb b/easybuild/easyconfigs/b/BamTools/BamTools-2.4.1-intel-2017a.eb new file mode 100644 index 0000000000..fd92ae4c8f --- /dev/null +++ b/easybuild/easyconfigs/b/BamTools/BamTools-2.4.1-intel-2017a.eb @@ -0,0 +1,16 @@ +name = 'BamTools' +version = '2.4.1' + +homepage = 'https://github.com/pezmaster31/bamtools' +description = """BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +sources = ['v%(version)s.tar.gz'] +source_urls = ['https://github.com/pezmaster31/bamtools/archive'] + +builddependencies = [('CMake', '3.8.0')] + +files_to_copy = ['bin', 'lib', 'include', 'docs', 'LICENSE', 'README'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.8.0-GCCcore-6.3.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.8.0-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..522448447c --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.8.0-GCCcore-6.3.0.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.8.0' + +homepage = 'http://www.cmake.org' +description = """CMake, the cross-platform, open-source build system. + CMake is a family of tools designed to build, test and package software.""" + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' + +builddependencies = [ + ('binutils', '2.27'), +] + + +dependencies = [ + ('ncurses', '6.0'), + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.1.0c'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From 9d66b3cd3f23021c0083ce763ee46a4b14b0dbb9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 2 May 2017 17:01:10 +0200 Subject: [PATCH 0667/1603] use pl2 source tarball for FFTW 3.3.6 which already includes patch for F03 interface --- easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-gompi-2017a.eb | 8 ++------ easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-intel-2016b.eb | 8 ++------ easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-intel-2017a.eb | 8 ++------ 3 files changed, 6 insertions(+), 18 deletions(-) diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-gompi-2017a.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-gompi-2017a.eb index 4325e0c729..ad3e944f8a 100644 --- a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-gompi-2017a.eb +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-gompi-2017a.eb @@ -9,12 +9,8 @@ toolchain = {'name': 'gompi', 'version': '2017a'} toolchainopts = {'pic': True} source_urls = [homepage] -sources = ['fftw-%(version)s-pl1.tar.gz'] -checksums = ['682a0e78d6966ca37c7446d4ab4cc2a1'] - -patches = [ - 'FFTW-3.3.6-F03_interface_pl2.patch', -] +sources = ['fftw-%(version)s-pl2.tar.gz'] +checksums = ['927e481edbb32575397eb3d62535a856'] runtest = 'check' diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-intel-2016b.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-intel-2016b.eb index 14ebd120a4..2c0fe9cb97 100644 --- a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-intel-2016b.eb +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-intel-2016b.eb @@ -9,12 +9,8 @@ toolchain = {'name': 'intel', 'version': '2016b'} toolchainopts = {'pic': True} source_urls = [homepage] -sources = ['fftw-%(version)s-pl1.tar.gz'] -checksums = ['682a0e78d6966ca37c7446d4ab4cc2a1'] - -patches = [ - 'FFTW-3.3.6-F03_interface_pl2.patch', -] +sources = ['fftw-%(version)s-pl2.tar.gz'] +checksums = ['927e481edbb32575397eb3d62535a856'] # no quad precision, requires GCC v4.6 or higher # see also diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-intel-2017a.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-intel-2017a.eb index da857e5ca5..7d5646bd9c 100644 --- a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-intel-2017a.eb +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-intel-2017a.eb @@ -9,12 +9,8 @@ toolchain = {'name': 'intel', 'version': '2017a'} toolchainopts = {'pic': True} source_urls = [homepage] -sources = ['fftw-%(version)s-pl1.tar.gz'] -checksums = ['682a0e78d6966ca37c7446d4ab4cc2a1'] - -patches = [ - 'FFTW-3.3.6-F03_interface_pl2.patch', -] +sources = ['fftw-%(version)s-pl2.tar.gz'] +checksums = ['927e481edbb32575397eb3d62535a856'] # no quad precision, requires GCC v4.6 or higher # see also -- GitLab From 8a0042c90ca5002241acabd21eae93ec86b751a2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 2 May 2017 17:24:03 +0200 Subject: [PATCH 0668/1603] adding easyconfigs: SuiteSparse-4.5.5-intel-2017a-METIS-5.1.0.eb, SuiteSparse-4.5.5-intel-2017a-ParMETIS-4.0.3.eb, METIS-5.1.0-intel-2017a.eb, ParMETIS-4.0.3-intel-2017a.eb --- .../m/METIS/METIS-5.1.0-intel-2017a.eb | 25 +++++++++++++++++++ .../p/ParMETIS/ParMETIS-4.0.3-intel-2017a.eb | 22 ++++++++++++++++ ...iteSparse-4.5.5-intel-2017a-METIS-5.1.0.eb | 19 ++++++++++++++ ...Sparse-4.5.5-intel-2017a-ParMETIS-4.0.3.eb | 19 ++++++++++++++ 4 files changed, 85 insertions(+) create mode 100644 easybuild/easyconfigs/m/METIS/METIS-5.1.0-intel-2017a.eb create mode 100644 easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-intel-2017a.eb create mode 100644 easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.5-intel-2017a-METIS-5.1.0.eb create mode 100644 easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.5-intel-2017a-ParMETIS-4.0.3.eb diff --git a/easybuild/easyconfigs/m/METIS/METIS-5.1.0-intel-2017a.eb b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-intel-2017a.eb new file mode 100644 index 0000000000..91d00f1139 --- /dev/null +++ b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-intel-2017a.eb @@ -0,0 +1,25 @@ +name = 'METIS' +version = '5.1.0' + +homepage = 'http://glaros.dtc.umn.edu/gkhome/metis/metis/overview' +description = """METIS is a set of serial programs for partitioning graphs, partitioning finite element meshes, +and producing fill reducing orderings for sparse matrices. The algorithms implemented in METIS are based on the +multilevel recursive-bisection, multilevel k-way, and multi-constraint partitioning schemes.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [ + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis', + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/OLD', +] + +# We use 32bit for indices and 64bit for content +patches = ['METIS-5.1.0-use-doubles.patch'] + +builddependencies = [('CMake', '3.8.0')] + +configopts = ['', 'shared=1'] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-intel-2017a.eb b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-intel-2017a.eb new file mode 100644 index 0000000000..239bd0fcd4 --- /dev/null +++ b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-intel-2017a.eb @@ -0,0 +1,22 @@ +name = 'ParMETIS' +version = '4.0.3' + +homepage = 'http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview' +description = """ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning + unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the + functionality provided by METIS and includes routines that are especially suited for parallel AMR computations and + large scale numerical simulations. The algorithms implemented in ParMETIS are based on the parallel multilevel k-way + graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning schemes.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'usempi': True, 'pic': True} + +source_urls = [ + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis', + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis/OLD', +] +sources = [SOURCELOWER_TAR_GZ] + +builddependencies = [('CMake', '3.8.0')] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.5-intel-2017a-METIS-5.1.0.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.5-intel-2017a-METIS-5.1.0.eb new file mode 100644 index 0000000000..3f7ce4f28f --- /dev/null +++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.5-intel-2017a-METIS-5.1.0.eb @@ -0,0 +1,19 @@ +name = 'SuiteSparse' +version = '4.5.5' +metis_ver = '5.1.0' +versionsuffix = '-METIS-%s' % metis_ver + +homepage = 'http://faculty.cse.tamu.edu/davis/suitesparse.html' +description = """SuiteSparse is a collection of libraries manipulate sparse matrices.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'unroll': True, 'pic': True} + +source_urls = ['http://faculty.cse.tamu.edu/davis/SuiteSparse/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [('METIS', metis_ver)] + +parallel = 1 + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.5-intel-2017a-ParMETIS-4.0.3.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.5-intel-2017a-ParMETIS-4.0.3.eb new file mode 100644 index 0000000000..28aa92c03a --- /dev/null +++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.5-intel-2017a-ParMETIS-4.0.3.eb @@ -0,0 +1,19 @@ +name = 'SuiteSparse' +version = '4.5.5' +metis_ver = '4.0.3' +versionsuffix = '-ParMETIS-%s' % metis_ver + +homepage = 'http://faculty.cse.tamu.edu/davis/suitesparse.html' +description = """SuiteSparse is a collection of libraries manipulate sparse matrices.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'unroll': True, 'pic': True} + +source_urls = ['http://faculty.cse.tamu.edu/davis/SuiteSparse/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [('ParMETIS', metis_ver)] + +parallel = 1 + +moduleclass = 'numlib' -- GitLab From ab62066363ea6186a345ad2c4c489dc45f355fa2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 2 May 2017 17:39:36 +0200 Subject: [PATCH 0669/1603] fix sources spec for HMMER 3.1b2 + minor style fixes --- easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-foss-2016a.eb | 9 ++++----- easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-intel-2015a.eb | 9 ++++----- 2 files changed, 8 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-foss-2016a.eb b/easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-foss-2016a.eb index 0456b6d6ce..c756d8464e 100644 --- a/easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-foss-2016a.eb +++ b/easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-foss-2016a.eb @@ -28,16 +28,15 @@ description = """HMMER is used for searching sequence databases for homologs of toolchain = {'name': 'foss', 'version': '2016a'} source_urls = ['http://eddylab.org/software/hmmer%(version_major)s/%(version)s/'] -sources = ['hmmer-%(version)s-linux-intel-x86_64.tar.gz'] +sources = ['hmmer-%(version)s.tar.gz'] + +runtest = 'check' installopts = ' && cd easel && make install' sanity_check_paths = { - 'files': ["bin/%s" % x for x in ["hmmemit", "hmmsearch", "hmmscan", - "esl-alimap", "esl-cluster", "esl-mask"]], + 'files': ['bin/esl-alimap', 'bin/esl-cluster', 'bin/esl-mask', 'bin/hmmemit', 'bin/hmmsearch', 'bin/hmmscan'], 'dirs': [] } -runtest = 'check' - moduleclass = 'bio' diff --git a/easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-intel-2015a.eb b/easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-intel-2015a.eb index da1af277a5..4211dd88a0 100644 --- a/easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-intel-2015a.eb +++ b/easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-intel-2015a.eb @@ -28,16 +28,15 @@ description = """HMMER is used for searching sequence databases for homologs of toolchain = {'name': 'intel', 'version': '2015a'} source_urls = ['http://eddylab.org/software/hmmer%(version_major)s/%(version)s/'] -sources = ['hmmer-%(version)s-linux-intel-x86_64.tar.gz'] +sources = ['hmmer-%(version)s.tar.gz'] + +runtest = 'check' installopts = ' && cd easel && make install' sanity_check_paths = { - 'files': ["bin/%s" % x for x in ["hmmemit", "hmmsearch", "hmmscan", - "esl-alimap", "esl-cluster", "esl-mask"]], + 'files': ['bin/esl-alimap', 'bin/esl-cluster', 'bin/esl-mask', 'bin/hmmemit', 'bin/hmmsearch', 'bin/hmmscan'], 'dirs': [] } -runtest = 'check' - moduleclass = 'bio' -- GitLab From 83ab75f708cba109de54b5c963959c07e8f9b33f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 2 May 2017 17:44:19 +0200 Subject: [PATCH 0670/1603] extend sanity check for HMMER 3.1b2 --- easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-foss-2016a.eb | 5 +++-- easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-intel-2015a.eb | 5 +++-- 2 files changed, 6 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-foss-2016a.eb b/easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-foss-2016a.eb index c756d8464e..aed3e32ba8 100644 --- a/easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-foss-2016a.eb +++ b/easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-foss-2016a.eb @@ -35,8 +35,9 @@ runtest = 'check' installopts = ' && cd easel && make install' sanity_check_paths = { - 'files': ['bin/esl-alimap', 'bin/esl-cluster', 'bin/esl-mask', 'bin/hmmemit', 'bin/hmmsearch', 'bin/hmmscan'], - 'dirs': [] + 'files': ['bin/esl-alimap', 'bin/esl-cluster', 'bin/esl-mask', 'bin/hmmemit', 'bin/hmmsearch', 'bin/hmmscan', + 'lib/libeasel.a', 'lib/libhmmer.a'], + 'dirs': ['include', 'share'], } moduleclass = 'bio' diff --git a/easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-intel-2015a.eb b/easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-intel-2015a.eb index 4211dd88a0..66c915507d 100644 --- a/easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-intel-2015a.eb +++ b/easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-intel-2015a.eb @@ -35,8 +35,9 @@ runtest = 'check' installopts = ' && cd easel && make install' sanity_check_paths = { - 'files': ['bin/esl-alimap', 'bin/esl-cluster', 'bin/esl-mask', 'bin/hmmemit', 'bin/hmmsearch', 'bin/hmmscan'], - 'dirs': [] + 'files': ['bin/esl-alimap', 'bin/esl-cluster', 'bin/esl-mask', 'bin/hmmemit', 'bin/hmmsearch', 'bin/hmmscan', + 'lib/libeasel.a', 'lib/libhmmer.a'], + 'dirs': ['include', 'share'], } moduleclass = 'bio' -- GitLab From 0944579f6e494a7a2e3e626638aa50ea16c951e4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 2 May 2017 17:58:00 +0200 Subject: [PATCH 0671/1603] adding easyconfigs: HMMER-3.1b2-intel-2017a.eb --- .../h/HMMER/HMMER-3.1b2-intel-2017a.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-intel-2017a.eb diff --git a/easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-intel-2017a.eb b/easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-intel-2017a.eb new file mode 100644 index 0000000000..3ca7456fc5 --- /dev/null +++ b/easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-intel-2017a.eb @@ -0,0 +1,43 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Nils Christian , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + +easyblock = 'ConfigureMake' + +name = 'HMMER' +version = '3.1b2' + +homepage = 'http://hmmer.org/' +description = """HMMER is used for searching sequence databases for homologs of protein sequences, + and for making protein sequence alignments. It implements methods using probabilistic models + called profile hidden Markov models (profile HMMs). Compared to BLAST, FASTA, and other + sequence alignment and database search tools based on older scoring methodology, + HMMER aims to be significantly more accurate and more able to detect remote homologs + because of the strength of its underlying mathematical models. In the past, this strength + came at significant computational expense, but in the new HMMER3 project, HMMER is now + essentially as fast as BLAST.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['http://eddylab.org/software/hmmer%(version_major)s/%(version)s/'] +sources = ['hmmer-%(version)s.tar.gz'] + +runtest = 'check' + +installopts = ' && cd easel && make install' + +sanity_check_paths = { + 'files': ['bin/esl-alimap', 'bin/esl-cluster', 'bin/esl-mask', 'bin/hmmemit', 'bin/hmmsearch', 'bin/hmmscan', + 'lib/libeasel.a', 'lib/libhmmer.a'], + 'dirs': ['include', 'share'], +} + +moduleclass = 'bio' -- GitLab From 6c5e0ab7620bddaf2d500c27241863c56198f9a8 Mon Sep 17 00:00:00 2001 From: "\"Andreas \"" Date: Tue, 2 May 2017 20:21:29 +0200 Subject: [PATCH 0672/1603] adding easyconfigs: OpenMPI-2.0.2-GCC-6.3.0-2.27-opa.eb --- .../OpenMPI-2.0.2-GCC-6.3.0-2.27-opa.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100755 easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.2-GCC-6.3.0-2.27-opa.eb diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.2-GCC-6.3.0-2.27-opa.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.2-GCC-6.3.0-2.27-opa.eb new file mode 100755 index 0000000000..1e3286223d --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.2-GCC-6.3.0-2.27-opa.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'OpenMPI' +version = '2.0.2' +versionsuffix= '-opa' + +homepage = 'http://www.open-mpi.org/' +description = """The Open MPI Project is an open source MPI-2 implementation.""" + +toolchain = {'name': 'GCC', 'version': '6.3.0-2.27'} + +source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] +sources = [SOURCELOWER_TAR_GZ] + +checksums = ['886698becc5bea8c151c0af2074b8392'] + +dependencies = [('hwloc', '1.11.5')] + +configopts = '--enable-shared --enable-mpi-thread-multiple --with-psm2 ' +configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path +configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support +configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading + +# needed for --with-verbs +osdependencies = [('libpsm2', 'libpsm2-devel')] + +libs = ["mpi_mpifh", "mpi", "ompitrace", "open-pal", "open-rte"] +sanity_check_paths = { + 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] + + ["include/%s.h" % x for x in ["mpi-ext", "mpif-config", "mpif", "mpi", "mpi_portable_platform"]], + 'dirs': [], +} + +moduleclass = 'mpi' -- GitLab From d8b7170e5bdc9bf19490d270f9877692a2e5d9b5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 2 May 2017 21:01:29 +0200 Subject: [PATCH 0673/1603] {compiler}[dummy] GCCcore 7.1.0 --- .../easyconfigs/g/GCCcore/GCCcore-7.1.0.eb | 54 ++++++ .../mpfr-3.1.5-allpatches-20161219.patch | 176 ++++++++++++++++++ 2 files changed, 230 insertions(+) create mode 100644 easybuild/easyconfigs/g/GCCcore/GCCcore-7.1.0.eb create mode 100644 easybuild/easyconfigs/g/GCCcore/mpfr-3.1.5-allpatches-20161219.patch diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-7.1.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-7.1.0.eb new file mode 100644 index 0000000000..6f69a58a66 --- /dev/null +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-7.1.0.eb @@ -0,0 +1,54 @@ +easyblock = 'EB_GCC' + +name = 'GCCcore' +version = '7.1.0' + +homepage = 'http://gcc.gnu.org/' +description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, + as well as libraries for these languages (libstdc++, libgcj,...).""" + +toolchain = {'name': 'dummy', 'version': ''} + +mpfr_version = '3.1.5' + +source_urls = [ + 'http://ftpmirror.gnu.org/gcc/gcc-%(version)s', # GCC auto-resolving HTTP mirror + 'http://ftpmirror.gnu.org/gmp', # idem for GMP + 'http://ftpmirror.gnu.org/mpfr', # idem for MPFR + 'http://www.multiprecision.org/mpc/download', # MPC official + 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies + 'http://gcc.cybermirror.org/infrastructure/', # HTTP mirror for GCC dependencies + 'http://isl.gforge.inria.fr/', # original HTTP source for ISL +] + +sources = [ + 'gcc-%(version)s.tar.bz2', + 'gmp-6.1.2.tar.bz2', + 'mpfr-%s.tar.bz2' % mpfr_version, + 'mpc-1.0.3.tar.gz', + 'isl-0.16.1.tar.bz2', +] + +builddependencies = [ + ('M4', '1.4.18'), + ('binutils', '2.28'), +] + +patches = [ + ('mpfr-%s-allpatches-20161219.patch' % mpfr_version, '../mpfr-%s' % mpfr_version), + 'GCCcore-6.2.0-fix-find-isl.patch', +] + +checksums = [ + '6bf56a2bca9dac9dbbf8e8d1036964a8', # gcc-7.1.0.tar.bz2 + '8ddbb26dc3bd4e2302984debba1406a5', # gmp-6.1.2.tar.bz2 + 'b1d23a55588e3b2a13e3be66bc69fd8d', # mpfr-3.1.5.tar.gz + 'd6a1d5f8ddea3abd2cc3e98f58352d26', # mpc-1.0.3.tar.gz + 'ac1f25a0677912952718a51f5bc20f32', # isl-0.16.1.tar.bz2 +] + +languages = ['c', 'c++', 'fortran'] + +withisl = True + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/GCCcore/mpfr-3.1.5-allpatches-20161219.patch b/easybuild/easyconfigs/g/GCCcore/mpfr-3.1.5-allpatches-20161219.patch new file mode 100644 index 0000000000..4e70357e4a --- /dev/null +++ b/easybuild/easyconfigs/g/GCCcore/mpfr-3.1.5-allpatches-20161219.patch @@ -0,0 +1,176 @@ +# MPFR v3.1.5 patch dated 2017-12-19 +# downloaded via https://gforge.inria.fr/frs/?group_id=136 +diff -Naurd mpfr-3.1.5-a/PATCHES mpfr-3.1.5-b/PATCHES +--- mpfr-3.1.5-a/PATCHES 2016-12-15 08:35:46.476430238 +0000 ++++ mpfr-3.1.5-b/PATCHES 2016-12-15 08:35:46.544430346 +0000 +@@ -0,0 +1 @@ ++vasprintf +diff -Naurd mpfr-3.1.5-a/VERSION mpfr-3.1.5-b/VERSION +--- mpfr-3.1.5-a/VERSION 2016-09-27 07:58:14.000000000 +0000 ++++ mpfr-3.1.5-b/VERSION 2016-12-15 08:35:46.544430346 +0000 +@@ -1 +1 @@ +-3.1.5 ++3.1.5-p1 +diff -Naurd mpfr-3.1.5-a/src/mpfr.h mpfr-3.1.5-b/src/mpfr.h +--- mpfr-3.1.5-a/src/mpfr.h 2016-09-27 07:58:15.000000000 +0000 ++++ mpfr-3.1.5-b/src/mpfr.h 2016-12-15 08:35:46.540430340 +0000 +@@ -27,7 +27,7 @@ + #define MPFR_VERSION_MAJOR 3 + #define MPFR_VERSION_MINOR 1 + #define MPFR_VERSION_PATCHLEVEL 5 +-#define MPFR_VERSION_STRING "3.1.5" ++#define MPFR_VERSION_STRING "3.1.5-p1" + + /* Macros dealing with MPFR VERSION */ + #define MPFR_VERSION_NUM(a,b,c) (((a) << 16L) | ((b) << 8) | (c)) +diff -Naurd mpfr-3.1.5-a/src/vasprintf.c mpfr-3.1.5-b/src/vasprintf.c +--- mpfr-3.1.5-a/src/vasprintf.c 2016-09-27 07:58:15.000000000 +0000 ++++ mpfr-3.1.5-b/src/vasprintf.c 2016-12-15 08:35:46.520430308 +0000 +@@ -1593,7 +1593,7 @@ + } + else if (spec.spec == 'f' || spec.spec == 'F') + { +- if (spec.prec == -1) ++ if (spec.prec < 0) + spec.prec = 6; + if (regular_fg (np, p, spec, NULL) == -1) + goto error; +diff -Naurd mpfr-3.1.5-a/src/version.c mpfr-3.1.5-b/src/version.c +--- mpfr-3.1.5-a/src/version.c 2016-09-27 07:58:15.000000000 +0000 ++++ mpfr-3.1.5-b/src/version.c 2016-12-15 08:35:46.544430346 +0000 +@@ -25,5 +25,5 @@ + const char * + mpfr_get_version (void) + { +- return "3.1.5"; ++ return "3.1.5-p1"; + } +diff -Naurd mpfr-3.1.5-a/tests/tsprintf.c mpfr-3.1.5-b/tests/tsprintf.c +--- mpfr-3.1.5-a/tests/tsprintf.c 2016-09-27 07:58:14.000000000 +0000 ++++ mpfr-3.1.5-b/tests/tsprintf.c 2016-12-15 08:35:46.520430308 +0000 +@@ -1251,6 +1251,25 @@ + check_emin_aux (MPFR_EMIN_MIN); + } + ++static void ++test20161214 (void) ++{ ++ mpfr_t x; ++ char buf[32]; ++ const char s[] = "0x0.fffffffffffff8p+1024"; ++ int r; ++ ++ mpfr_init2 (x, 64); ++ mpfr_set_str (x, s, 16, MPFR_RNDN); ++ r = mpfr_snprintf (buf, 32, "%.*RDf", -2, x); ++ MPFR_ASSERTN(r == 316); ++ r = mpfr_snprintf (buf, 32, "%.*RDf", INT_MIN + 1, x); ++ MPFR_ASSERTN(r == 316); ++ r = mpfr_snprintf (buf, 32, "%.*RDf", INT_MIN, x); ++ MPFR_ASSERTN(r == 316); ++ mpfr_clear (x); ++} ++ + int + main (int argc, char **argv) + { +@@ -1271,6 +1290,7 @@ + mixed (); + check_emax (); + check_emin (); ++ test20161214 (); + + #if defined(HAVE_LOCALE_H) && defined(HAVE_SETLOCALE) + #if MPFR_LCONV_DPTS +diff -Naurd mpfr-3.1.5-a/PATCHES mpfr-3.1.5-b/PATCHES +--- mpfr-3.1.5-a/PATCHES 2016-12-19 22:11:17.022676737 +0000 ++++ mpfr-3.1.5-b/PATCHES 2016-12-19 22:11:17.094676820 +0000 +@@ -0,0 +1 @@ ++strtofr +diff -Naurd mpfr-3.1.5-a/VERSION mpfr-3.1.5-b/VERSION +--- mpfr-3.1.5-a/VERSION 2016-12-15 08:35:46.544430346 +0000 ++++ mpfr-3.1.5-b/VERSION 2016-12-19 22:11:17.094676820 +0000 +@@ -1 +1 @@ +-3.1.5-p1 ++3.1.5-p2 +diff -Naurd mpfr-3.1.5-a/src/mpfr.h mpfr-3.1.5-b/src/mpfr.h +--- mpfr-3.1.5-a/src/mpfr.h 2016-12-15 08:35:46.540430340 +0000 ++++ mpfr-3.1.5-b/src/mpfr.h 2016-12-19 22:11:17.090676815 +0000 +@@ -27,7 +27,7 @@ + #define MPFR_VERSION_MAJOR 3 + #define MPFR_VERSION_MINOR 1 + #define MPFR_VERSION_PATCHLEVEL 5 +-#define MPFR_VERSION_STRING "3.1.5-p1" ++#define MPFR_VERSION_STRING "3.1.5-p2" + + /* Macros dealing with MPFR VERSION */ + #define MPFR_VERSION_NUM(a,b,c) (((a) << 16L) | ((b) << 8) | (c)) +diff -Naurd mpfr-3.1.5-a/src/strtofr.c mpfr-3.1.5-b/src/strtofr.c +--- mpfr-3.1.5-a/src/strtofr.c 2016-09-27 07:58:15.000000000 +0000 ++++ mpfr-3.1.5-b/src/strtofr.c 2016-12-19 22:11:17.066676788 +0000 +@@ -743,11 +743,14 @@ + of the pstr_size most significant digits of pstr->mant, with + equality in case exact is non-zero. */ + +- /* test if rounding is possible, and if so exit the loop */ +- if (exact || mpfr_can_round_raw (result, ysize, +- (pstr->negative) ? -1 : 1, +- ysize_bits - err - 1, +- MPFR_RNDN, rnd, MPFR_PREC(x))) ++ /* test if rounding is possible, and if so exit the loop. ++ Note: we also need to be able to determine the correct ternary value, ++ thus we use the MPFR_PREC(x) + (rnd == MPFR_RNDN) trick. ++ For example if result = xxx...xxx111...111 and rnd = RNDN, ++ then we know the correct rounding is xxx...xx(x+1), but we cannot know ++ the correct ternary value. */ ++ if (exact || mpfr_round_p (result, ysize, ysize_bits - err - 1, ++ MPFR_PREC(x) + (rnd == MPFR_RNDN))) + break; + + next_loop: +diff -Naurd mpfr-3.1.5-a/src/version.c mpfr-3.1.5-b/src/version.c +--- mpfr-3.1.5-a/src/version.c 2016-12-15 08:35:46.544430346 +0000 ++++ mpfr-3.1.5-b/src/version.c 2016-12-19 22:11:17.094676820 +0000 +@@ -25,5 +25,5 @@ + const char * + mpfr_get_version (void) + { +- return "3.1.5-p1"; ++ return "3.1.5-p2"; + } +diff -Naurd mpfr-3.1.5-a/tests/tstrtofr.c mpfr-3.1.5-b/tests/tstrtofr.c +--- mpfr-3.1.5-a/tests/tstrtofr.c 2016-09-27 07:58:14.000000000 +0000 ++++ mpfr-3.1.5-b/tests/tstrtofr.c 2016-12-19 22:11:17.066676788 +0000 +@@ -1191,6 +1191,24 @@ + mpfr_clears (e, x1, x2, (mpfr_ptr) 0); + } + ++/* Note: the number is 5^47/2^9. */ ++static void ++bug20161217 (void) ++{ ++ mpfr_t fp, z; ++ static const char * num = "0.1387778780781445675529539585113525390625e31"; ++ int inex; ++ ++ mpfr_init2 (fp, 110); ++ mpfr_init2 (z, 110); ++ inex = mpfr_strtofr (fp, num, NULL, 10, MPFR_RNDN); ++ MPFR_ASSERTN(inex == 0); ++ mpfr_set_str_binary (z, "10001100001000010011110110011101101001010000001011011110010001010100010100100110111101000010001011001100001101E-9"); ++ MPFR_ASSERTN(mpfr_equal_p (fp, z)); ++ mpfr_clear (fp); ++ mpfr_clear (z); ++} ++ + int + main (int argc, char *argv[]) + { +@@ -1205,6 +1223,7 @@ + test20100310 (); + bug20120814 (); + bug20120829 (); ++ bug20161217 (); + + tests_end_mpfr (); + return 0; -- GitLab From 4e6ea8705ba5ea327960feb905feefd9cbdfa3c0 Mon Sep 17 00:00:00 2001 From: "\"Andreas \"" Date: Tue, 2 May 2017 21:11:14 +0200 Subject: [PATCH 0674/1603] adding easyconfigs: METIS-5.1.0-foss-2017a.eb, ParMETIS-4.0.3-foss-2017a.eb, SuiteSparse-4.5.5-foss-2017a-METIS-5.1.0.eb, SuiteSparse-4.5.5-foss-2017a-ParMETIS-4.0.3.eb --- .../m/METIS/METIS-5.1.0-foss-2017a.eb | 22 +++++++++++++++++++ .../p/ParMETIS/ParMETIS-4.0.3-foss-2017a.eb | 22 +++++++++++++++++++ ...uiteSparse-4.5.5-foss-2017a-METIS-5.1.0.eb | 19 ++++++++++++++++ ...eSparse-4.5.5-foss-2017a-ParMETIS-4.0.3.eb | 19 ++++++++++++++++ 4 files changed, 82 insertions(+) create mode 100755 easybuild/easyconfigs/m/METIS/METIS-5.1.0-foss-2017a.eb create mode 100755 easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-foss-2017a.eb create mode 100755 easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.5-foss-2017a-METIS-5.1.0.eb create mode 100755 easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.5-foss-2017a-ParMETIS-4.0.3.eb diff --git a/easybuild/easyconfigs/m/METIS/METIS-5.1.0-foss-2017a.eb b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-foss-2017a.eb new file mode 100755 index 0000000000..03a730e5cc --- /dev/null +++ b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-foss-2017a.eb @@ -0,0 +1,22 @@ +name = 'METIS' +version = '5.1.0' + +homepage = 'http://glaros.dtc.umn.edu/gkhome/metis/metis/overview' +description = """METIS is a set of serial programs for partitioning graphs, partitioning finite element meshes, + and producing fill reducing orderings for sparse matrices. The algorithms implemented in METIS are based on the + multilevel recursive-bisection, multilevel k-way, and multi-constraint partitioning schemes.""" + +toolchain = {'name': 'foss', 'version': '2017a'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [ + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis', + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/OLD', +] + +builddependencies = [('CMake', '3.8.0')] + +configopts = ['', 'shared=1'] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-foss-2017a.eb b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-foss-2017a.eb new file mode 100755 index 0000000000..875f07389d --- /dev/null +++ b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-foss-2017a.eb @@ -0,0 +1,22 @@ +name = 'ParMETIS' +version = '4.0.3' + +homepage = 'http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview' +description = """ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning + unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the + functionality provided by METIS and includes routines that are especially suited for parallel AMR computations and + large scale numerical simulations. The algorithms implemented in ParMETIS are based on the parallel multilevel k-way + graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning schemes.""" + +toolchain = {'name': 'foss', 'version': '2017a'} +toolchainopts = {'usempi': True, 'pic': True} + +source_urls = [ + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis', + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis/OLD', +] +sources = [SOURCELOWER_TAR_GZ] + +builddependencies = [('CMake', '3.8.0')] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.5-foss-2017a-METIS-5.1.0.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.5-foss-2017a-METIS-5.1.0.eb new file mode 100755 index 0000000000..a66251bb0f --- /dev/null +++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.5-foss-2017a-METIS-5.1.0.eb @@ -0,0 +1,19 @@ +name = 'SuiteSparse' +version = '4.5.5' +metis_ver = '5.1.0' +versionsuffix = '-METIS-%s' % metis_ver + +homepage = 'http://faculty.cse.tamu.edu/davis/suitesparse.html' +description = """SuiteSparse is a collection of libraries manipulate sparse matrices.""" + +toolchain = {'name': 'foss', 'version': '2017a'} +toolchainopts = {'opt': True, 'unroll': True, 'pic': True} + +source_urls = ['http://faculty.cse.tamu.edu/davis/SuiteSparse/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [('METIS', metis_ver)] + +maxparallel = 1 + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.5-foss-2017a-ParMETIS-4.0.3.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.5-foss-2017a-ParMETIS-4.0.3.eb new file mode 100755 index 0000000000..7c7dff3356 --- /dev/null +++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.5-foss-2017a-ParMETIS-4.0.3.eb @@ -0,0 +1,19 @@ +name = 'SuiteSparse' +version = '4.5.5' +parmetis_ver = '4.0.3' +versionsuffix = '-ParMETIS-%s' % parmetis_ver + +homepage = 'http://faculty.cse.tamu.edu/davis/suitesparse.html' +description = """SuiteSparse is a collection of libraries manipulate sparse matrices.""" + +toolchain = {'name': 'foss', 'version': '2017a'} +toolchainopts = {'opt': True, 'unroll': True, 'pic': True} + +source_urls = ['http://faculty.cse.tamu.edu/davis/SuiteSparse/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [('ParMETIS', parmetis_ver)] + +maxparallel = 1 + +moduleclass = 'numlib' -- GitLab From cf7d72d4c302a22a5ee6946ec7a95f47f1cb9779 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 2 May 2017 21:32:15 +0200 Subject: [PATCH 0675/1603] fix time travelling in MPFR patch, thanks @wpoely86 --- .../easyconfigs/g/GCCcore/mpfr-3.1.5-allpatches-20161219.patch | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GCCcore/mpfr-3.1.5-allpatches-20161219.patch b/easybuild/easyconfigs/g/GCCcore/mpfr-3.1.5-allpatches-20161219.patch index 4e70357e4a..67ff28d57a 100644 --- a/easybuild/easyconfigs/g/GCCcore/mpfr-3.1.5-allpatches-20161219.patch +++ b/easybuild/easyconfigs/g/GCCcore/mpfr-3.1.5-allpatches-20161219.patch @@ -1,4 +1,4 @@ -# MPFR v3.1.5 patch dated 2017-12-19 +# MPFR v3.1.5 patch dated 2016-12-19 # downloaded via https://gforge.inria.fr/frs/?group_id=136 diff -Naurd mpfr-3.1.5-a/PATCHES mpfr-3.1.5-b/PATCHES --- mpfr-3.1.5-a/PATCHES 2016-12-15 08:35:46.476430238 +0000 -- GitLab From 42e15f650164f4faee57db07337d9dfeabf46332 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 2 May 2017 21:36:24 +0200 Subject: [PATCH 0676/1603] {compiler}[dummy] GCC 7.1.0 w/ binutils 2.28 + deps --- .../b/Bison/Bison-3.0.4-GCCcore-7.1.0.eb | 27 ++++++++++++++++++ .../b/binutils/binutils-2.28-GCCcore-7.1.0.eb | 21 ++++++++++++++ .../f/flex/flex-2.6.3-GCCcore-7.1.0.eb | 24 ++++++++++++++++ easybuild/easyconfigs/g/GCC/GCC-7.1.0-2.28.eb | 25 +++++++++++++++++ .../help2man/help2man-1.47.4-GCCcore-7.1.0.eb | 24 ++++++++++++++++ .../m/M4/M4-1.4.18-GCCcore-7.1.0.eb | 28 +++++++++++++++++++ .../z/zlib/zlib-1.2.11-GCCcore-7.1.0.eb | 25 +++++++++++++++++ 7 files changed, 174 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-7.1.0.eb create mode 100644 easybuild/easyconfigs/b/binutils/binutils-2.28-GCCcore-7.1.0.eb create mode 100644 easybuild/easyconfigs/f/flex/flex-2.6.3-GCCcore-7.1.0.eb create mode 100644 easybuild/easyconfigs/g/GCC/GCC-7.1.0-2.28.eb create mode 100644 easybuild/easyconfigs/h/help2man/help2man-1.47.4-GCCcore-7.1.0.eb create mode 100644 easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.1.0.eb create mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-7.1.0.eb diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-7.1.0.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-7.1.0.eb new file mode 100644 index 0000000000..33d3ae47a6 --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-7.1.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'Bison' +version = '3.0.4' + +homepage = 'http://www.gnu.org/software/bison' +description = """Bison is a general-purpose parser generator that converts an annotated context-free grammar + into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.""" + +toolchain = {'name': 'GCCcore', 'version': '7.1.0'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +builddependencies = [ + ('M4', '1.4.18'), + # use same binutils version that was used when building GCCcore toolchain + ('binutils', '2.28', '', True), +] + + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["bison", "yacc"]] + ["lib/liby.a"], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.28-GCCcore-7.1.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.28-GCCcore-7.1.0.eb new file mode 100644 index 0000000000..10ecc14d7a --- /dev/null +++ b/easybuild/easyconfigs/b/binutils/binutils-2.28-GCCcore-7.1.0.eb @@ -0,0 +1,21 @@ +name = 'binutils' +version = '2.28' + +homepage = 'http://directory.fsf.org/project/binutils/' +description = "binutils: GNU binary utilities" + +toolchain = {'name': 'GCCcore', 'version': '7.1.0'} + +sources = [SOURCE_TAR_GZ] +source_urls = [GNU_SOURCE] + +builddependencies = [ + ('flex', '2.6.3'), + ('Bison', '3.0.4'), + # zlib required, but being linked in statically, so not a runtime dep + ('zlib', '1.2.11'), + # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils + ('binutils', version, '', True) +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.3-GCCcore-7.1.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.3-GCCcore-7.1.0.eb new file mode 100644 index 0000000000..28c855c205 --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.6.3-GCCcore-7.1.0.eb @@ -0,0 +1,24 @@ +name = 'flex' +version = '2.6.3' + +homepage = 'http://flex.sourceforge.net/' +description = """Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, + sometimes called a tokenizer, is a program which recognizes lexical patterns in text.""" + +toolchain = {'name': 'GCCcore', 'version': '7.1.0'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['https://github.com/westes/flex/releases/download/v%(version)s/'] + +checksums = ['a5f65570cd9107ec8a8ec88f17b31bb1'] + +dependencies = [('M4', '1.4.18')] +builddependencies = [ + ('Bison', '3.0.4'), + ('help2man', '1.47.4'), + # use same binutils version that was used when building GCC toolchain + ('binutils', '2.28', '', True), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/g/GCC/GCC-7.1.0-2.28.eb b/easybuild/easyconfigs/g/GCC/GCC-7.1.0-2.28.eb new file mode 100644 index 0000000000..870e7eab31 --- /dev/null +++ b/easybuild/easyconfigs/g/GCC/GCC-7.1.0-2.28.eb @@ -0,0 +1,25 @@ +easyblock = 'Bundle' + +name = 'GCC' +version = '7.1.0' + +binutilsver = '2.28' +versionsuffix = '-%s' % binutilsver + +homepage = 'http://gcc.gnu.org/' +description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, + as well as libraries for these languages (libstdc++, libgcj,...).""" + +toolchain = {'name': 'dummy', 'version': ''} + +dependencies = [ + ('GCCcore', version), + # binutils built on top of GCCcore, which was built on top of (dummy-built) binutils + ('binutils', binutilsver, '', ('GCCcore', version)), +] + +altroot = 'GCCcore' +altversion = 'GCCcore' + +# this bundle serves as a compiler-only toolchain, so it should be marked as compiler (important for HMNS) +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/h/help2man/help2man-1.47.4-GCCcore-7.1.0.eb b/easybuild/easyconfigs/h/help2man/help2man-1.47.4-GCCcore-7.1.0.eb new file mode 100644 index 0000000000..f487ba5530 --- /dev/null +++ b/easybuild/easyconfigs/h/help2man/help2man-1.47.4-GCCcore-7.1.0.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'help2man' +version = '1.47.4' + +homepage = 'https://www.gnu.org/software/help2man/' +description = """help2man produces simple manual pages from the '--help' and '--version' output of other commands.""" + +toolchain = {'name': 'GCCcore', 'version': '7.1.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_XZ] + +builddependencies = [ + # use same binutils version that was used when building GCC toolchain + ('binutils', '2.28', '', True), +] + +sanity_check_paths = { + 'files': ['bin/help2man'], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.1.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.1.0.eb new file mode 100644 index 0000000000..18394615f9 --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.1.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'M4' +version = '1.4.18' + +homepage = 'http://www.gnu.org/software/m4/m4.html' +description = """GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible + although it has some extensions (for example, handling more than 9 positional parameters to macros). + GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc.""" + +toolchain = {'name': 'GCCcore', 'version': '7.1.0'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +# use same binutils version that was used when building GCC toolchain +builddependencies = [('binutils', '2.28', '', True)] + +# '-fgnu89-inline' is required to avoid linking errors with older glibc's, +# see https://github.com/hpcugent/easybuild-easyconfigs/issues/529 +configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" + +sanity_check_paths = { + 'files': ["bin/m4"], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-7.1.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-7.1.0.eb new file mode 100644 index 0000000000..bec9454ed8 --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-7.1.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'zlib' +version = '1.2.11' + +homepage = 'http://www.zlib.net/' +description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is, + not covered by any patents -- lossless data-compression library for use on virtually any + computer hardware and operating system.""" + +toolchain = {'name': 'GCCcore', 'version': '7.1.0'} +toolchainopts = {'pic': True} + +source_urls = ['http://zlib.net/fossils'] +sources = [SOURCELOWER_TAR_GZ] + +# use same binutils version that was used when building GCC toolchain +builddependencies = [('binutils', '2.28', '', True)] + +sanity_check_paths = { + 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' -- GitLab From 29988a028e00ce8b88a74b367cd1cfcbd1b4db80 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Wed, 3 May 2017 11:22:05 +0200 Subject: [PATCH 0677/1603] PoC for TBB open source --- .../t/tbb/tbb-2017_U5-goolf-1.7.20.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/t/tbb/tbb-2017_U5-goolf-1.7.20.eb diff --git a/easybuild/easyconfigs/t/tbb/tbb-2017_U5-goolf-1.7.20.eb b/easybuild/easyconfigs/t/tbb/tbb-2017_U5-goolf-1.7.20.eb new file mode 100644 index 0000000000..94782c17c8 --- /dev/null +++ b/easybuild/easyconfigs/t/tbb/tbb-2017_U5-goolf-1.7.20.eb @@ -0,0 +1,28 @@ +name = 'tbb' +version = '2017_U5' + +homepage = 'https://01.org/tbb/' +description = """Intel(R) Threading Building Blocks (Intel(R) TBB) lets you easily write parallel C++ programs that + take full advantage of multicore performance, that are portable, composable and have future-proof scalability.""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +source_urls = ['https://github.com/01org/tbb/archive/'] +sources = ['%(version)s.tar.gz'] + +unpack_options = '--strip-components=1' + +skipsteps = ['configure', 'install'] + +buildininstalldir = True + +buildopts = "compiler=$CC" + +#runtest = 'compiler=$CC test' + +sanity_check_paths = { + 'files': [], + 'dirs': ['.'], +} + +moduleclass = 'lib' -- GitLab From 60038da4530e4cde6809d03d02b289e8ca841a83 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 3 May 2017 11:30:23 +0200 Subject: [PATCH 0678/1603] also build IMB-IO in IMB 4.1 easyconfig using foss/2016b --- easybuild/easyconfigs/i/IMB/IMB-4.1-foss-2016a.eb | 14 ++++++-------- 1 file changed, 6 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/i/IMB/IMB-4.1-foss-2016a.eb b/easybuild/easyconfigs/i/IMB/IMB-4.1-foss-2016a.eb index f6d0b1f028..449a0d2750 100644 --- a/easybuild/easyconfigs/i/IMB/IMB-4.1-foss-2016a.eb +++ b/easybuild/easyconfigs/i/IMB/IMB-4.1-foss-2016a.eb @@ -4,26 +4,24 @@ name = 'IMB' version = '4.1' homepage = 'https://software.intel.com/en-us/articles/intel-mpi-benchmarks' -description = """ -The Intel® MPI Benchmarks perform a set of MPI performance measurements for point-to-point -and global communication operations for a range of message sizes. -""" +description = """The Intel MPI Benchmarks perform a set of MPI performance measurements for point-to-point and + global communication operations for a range of message sizes""" -toolchain = {'name': 'foss', 'version': '2016a'} +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'usempi': True} sources = ['%(name)s_%(version)s.tgz'] source_urls = ['https://software.intel.com/sites/default/files/managed/a3/b2/'] start_dir = 'src' -prebuildopts = 'export MPI_HOME=$EBROOTOPENMPI && ' -buildopts = "-f make_mpich MPI_HOME=$EBROOTOPENMPI" +buildopts = 'all CC="$MPICC"' parallel = 1 files_to_copy = [(['src/IMB-*'], 'bin'), (['doc/IMB_Users_Guide.pdf'], 'doc')] sanity_check_paths = { - 'files': ['bin/%s' % binfile for binfile in ['IMB-RMA', 'IMB-EXT', 'IMB-NBC', 'IMB-MPI1']], + 'files': ['bin/IMB-EXT', 'bin/IMB-IO', 'bin/IMB-MPI1', 'bin/IMB-NBC', 'bin/IMB-RMA'], 'dirs': ['bin', 'doc'] } -- GitLab From 9d83a3a823af6048779169f9eb4272b540b03097 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 3 May 2017 11:33:59 +0200 Subject: [PATCH 0679/1603] adding easyconfigs: IMB-4.1-intel-2017a.eb --- .../easyconfigs/i/IMB/IMB-4.1-intel-2017a.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/i/IMB/IMB-4.1-intel-2017a.eb diff --git a/easybuild/easyconfigs/i/IMB/IMB-4.1-intel-2017a.eb b/easybuild/easyconfigs/i/IMB/IMB-4.1-intel-2017a.eb new file mode 100644 index 0000000000..6636a983cd --- /dev/null +++ b/easybuild/easyconfigs/i/IMB/IMB-4.1-intel-2017a.eb @@ -0,0 +1,28 @@ +easyblock = 'MakeCp' + +name = 'IMB' +version = '4.1' + +homepage = 'https://software.intel.com/en-us/articles/intel-mpi-benchmarks' +description = """The Intel MPI Benchmarks perform a set of MPI performance measurements for point-to-point and + global communication operations for a range of message sizes""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'usempi': True} + +sources = ['%(name)s_%(version)s.tgz'] +source_urls = ['https://software.intel.com/sites/default/files/managed/a3/b2/'] + +start_dir = 'src' +buildopts = 'all CC="$MPICC"' + +parallel = 1 + +files_to_copy = [(['src/IMB-*'], 'bin'), (['doc/IMB_Users_Guide.pdf'], 'doc')] + +sanity_check_paths = { + 'files': ['bin/IMB-EXT', 'bin/IMB-IO', 'bin/IMB-MPI1', 'bin/IMB-NBC', 'bin/IMB-RMA'], + 'dirs': ['bin', 'doc'] +} + +moduleclass = 'perf' -- GitLab From 1521762763e6b6414ffd0859c553dc3337f5a038 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 3 May 2017 11:59:21 +0200 Subject: [PATCH 0680/1603] fix toolchain version --- easybuild/easyconfigs/i/IMB/IMB-4.1-foss-2016a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/i/IMB/IMB-4.1-foss-2016a.eb b/easybuild/easyconfigs/i/IMB/IMB-4.1-foss-2016a.eb index 449a0d2750..2b74ec6d38 100644 --- a/easybuild/easyconfigs/i/IMB/IMB-4.1-foss-2016a.eb +++ b/easybuild/easyconfigs/i/IMB/IMB-4.1-foss-2016a.eb @@ -7,7 +7,7 @@ homepage = 'https://software.intel.com/en-us/articles/intel-mpi-benchmarks' description = """The Intel MPI Benchmarks perform a set of MPI performance measurements for point-to-point and global communication operations for a range of message sizes""" -toolchain = {'name': 'foss', 'version': '2016b'} +toolchain = {'name': 'foss', 'version': '2016a'} toolchainopts = {'usempi': True} sources = ['%(name)s_%(version)s.tgz'] -- GitLab From a8d022261518aa55ac0044ad7e0b852f1fc55509 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 3 May 2017 14:10:11 +0200 Subject: [PATCH 0681/1603] clean up tbb easyconfig to use enhanced easyblock --- .../easyconfigs/t/tbb/tbb-2017_U5-goolf-1.7.20.eb | 15 --------------- 1 file changed, 15 deletions(-) diff --git a/easybuild/easyconfigs/t/tbb/tbb-2017_U5-goolf-1.7.20.eb b/easybuild/easyconfigs/t/tbb/tbb-2017_U5-goolf-1.7.20.eb index 94782c17c8..f90202e1b4 100644 --- a/easybuild/easyconfigs/t/tbb/tbb-2017_U5-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/t/tbb/tbb-2017_U5-goolf-1.7.20.eb @@ -10,19 +10,4 @@ toolchain = {'name': 'goolf', 'version': '1.7.20'} source_urls = ['https://github.com/01org/tbb/archive/'] sources = ['%(version)s.tar.gz'] -unpack_options = '--strip-components=1' - -skipsteps = ['configure', 'install'] - -buildininstalldir = True - -buildopts = "compiler=$CC" - -#runtest = 'compiler=$CC test' - -sanity_check_paths = { - 'files': [], - 'dirs': ['.'], -} - moduleclass = 'lib' -- GitLab From b2623eb814ff0c54f95850202907564ac4768734 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 3 May 2017 14:20:28 +0200 Subject: [PATCH 0682/1603] adding easyconfigs: tbb-2017_U5-intel-2017a.eb --- .../easyconfigs/t/tbb/tbb-2017_U5-intel-2017a.eb | 13 +++++++++++++ 1 file changed, 13 insertions(+) create mode 100644 easybuild/easyconfigs/t/tbb/tbb-2017_U5-intel-2017a.eb diff --git a/easybuild/easyconfigs/t/tbb/tbb-2017_U5-intel-2017a.eb b/easybuild/easyconfigs/t/tbb/tbb-2017_U5-intel-2017a.eb new file mode 100644 index 0000000000..fc7398b13b --- /dev/null +++ b/easybuild/easyconfigs/t/tbb/tbb-2017_U5-intel-2017a.eb @@ -0,0 +1,13 @@ +name = 'tbb' +version = '2017_U5' + +homepage = 'https://01.org/tbb/' +description = """Intel(R) Threading Building Blocks (Intel(R) TBB) lets you easily write parallel C++ programs that + take full advantage of multicore performance, that are portable, composable and have future-proof scalability.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['https://github.com/01org/tbb/archive/'] +sources = ['%(version)s.tar.gz'] + +moduleclass = 'lib' -- GitLab From 775f59f8c5345bb4ddb974790de0275d68e88e29 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 3 May 2017 16:47:33 +0200 Subject: [PATCH 0683/1603] adding easyconfigs: Node-RED-0.16.2-foss-2017a.eb, nodejs-6.10.3-foss-2017a.eb --- .../n/Node-RED/Node-RED-0.16.2-foss-2017a.eb | 28 +++++++++++++++++++ .../n/nodejs/nodejs-6.10.3-foss-2017a.eb | 26 +++++++++++++++++ 2 files changed, 54 insertions(+) create mode 100644 easybuild/easyconfigs/n/Node-RED/Node-RED-0.16.2-foss-2017a.eb create mode 100644 easybuild/easyconfigs/n/nodejs/nodejs-6.10.3-foss-2017a.eb diff --git a/easybuild/easyconfigs/n/Node-RED/Node-RED-0.16.2-foss-2017a.eb b/easybuild/easyconfigs/n/Node-RED/Node-RED-0.16.2-foss-2017a.eb new file mode 100644 index 0000000000..828c4e612b --- /dev/null +++ b/easybuild/easyconfigs/n/Node-RED/Node-RED-0.16.2-foss-2017a.eb @@ -0,0 +1,28 @@ +easyblock = 'PackedBinary' + +name = 'Node-RED' +version = '0.16.2' + +homepage = 'http://nodered.org' +description = """Node-RED is a programming tool for wiring together hardware devices, APIs and online services + in new and interesting ways.""" + +toolchain = {'name': 'foss', 'version': '2017a'} + +source_urls = ['https://github.com/node-red/node-red/releases/download/%(version)s/'] +sources = ['node-red-%(version)s.zip'] + +dependencies = [ + ('nodejs', '6.10.3'), +] + +preinstallopts = 'cd %(namelower)s-%(version)s && ' +install_cmd = 'npm install --prefix %(installdir)s -g' + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': ['lib/node_modules/%(namelower)s'], +} +sanity_check_commands = ['%(namelower)s --version'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/n/nodejs/nodejs-6.10.3-foss-2017a.eb b/easybuild/easyconfigs/n/nodejs/nodejs-6.10.3-foss-2017a.eb new file mode 100644 index 0000000000..65377857a3 --- /dev/null +++ b/easybuild/easyconfigs/n/nodejs/nodejs-6.10.3-foss-2017a.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'nodejs' +version = '6.10.3' + +homepage = 'http://nodejs.org' + +description = """Node.js is a platform built on Chrome's JavaScript runtime + for easily building fast, scalable network applications. Node.js uses an + event-driven, non-blocking I/O model that makes it lightweight and efficient, + perfect for data-intensive real-time applications that run across distributed devices.""" + +toolchain = {'name': 'foss', 'version': '2017a'} +toolchainopts = {'lowopt': True} + +source_urls = ['http://nodejs.org/dist/v%(version)s/'] +sources = ['node-v%(version)s.tar.gz'] + +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +sanity_check_paths = { + 'files': ['bin/node', 'bin/npm'], + 'dirs': ['lib/node_modules', 'include/node'] +} + +moduleclass = 'lang' -- GitLab From 012625a422c61cf81f51b20892b4413d2891039f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 3 May 2017 17:20:32 +0200 Subject: [PATCH 0684/1603] more %(namelower)s --- easybuild/easyconfigs/n/Node-RED/Node-RED-0.16.2-foss-2017a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/Node-RED/Node-RED-0.16.2-foss-2017a.eb b/easybuild/easyconfigs/n/Node-RED/Node-RED-0.16.2-foss-2017a.eb index 828c4e612b..7531db7616 100644 --- a/easybuild/easyconfigs/n/Node-RED/Node-RED-0.16.2-foss-2017a.eb +++ b/easybuild/easyconfigs/n/Node-RED/Node-RED-0.16.2-foss-2017a.eb @@ -10,7 +10,7 @@ description = """Node-RED is a programming tool for wiring together hardware dev toolchain = {'name': 'foss', 'version': '2017a'} source_urls = ['https://github.com/node-red/node-red/releases/download/%(version)s/'] -sources = ['node-red-%(version)s.zip'] +sources = ['%(namelower)s-%(version)s.zip'] dependencies = [ ('nodejs', '6.10.3'), -- GitLab From f9589ba77bc83a6b6e568a99c9de6b0958733f10 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 3 May 2017 17:27:30 +0200 Subject: [PATCH 0685/1603] use --help as sanity check command, since --version starts a Node-RED server... --- easybuild/easyconfigs/n/Node-RED/Node-RED-0.16.2-foss-2017a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/Node-RED/Node-RED-0.16.2-foss-2017a.eb b/easybuild/easyconfigs/n/Node-RED/Node-RED-0.16.2-foss-2017a.eb index 7531db7616..f11db814aa 100644 --- a/easybuild/easyconfigs/n/Node-RED/Node-RED-0.16.2-foss-2017a.eb +++ b/easybuild/easyconfigs/n/Node-RED/Node-RED-0.16.2-foss-2017a.eb @@ -23,6 +23,6 @@ sanity_check_paths = { 'files': ['bin/%(namelower)s'], 'dirs': ['lib/node_modules/%(namelower)s'], } -sanity_check_commands = ['%(namelower)s --version'] +sanity_check_commands = ['%(namelower)s --help'] moduleclass = 'tools' -- GitLab From a3a0e6c3c840bbd9e2ac747879d5fb04bceb7223 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Thu, 4 May 2017 12:21:44 +0800 Subject: [PATCH 0686/1603] prepare release notes for eb320 --- RELEASE_NOTES | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index a56c5c3afe..b25f9e1c1c 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -6,6 +6,32 @@ These release notes can also be consulted at http://easybuild.readthedocs.org/en The latest version of easybuild-easyconfig provides 6,718 easyconfig files, for 1,182 different software packages, 25 different (compiler) toolchains, 13 software bundles and 1 meta-package. +v3.2.0 (May 5th 2017) +--------------------- + +feature release +- added example easyconfig files for 33 new software packages: + - ACTC (#4386), atomate (#4484), BreakDancer (#4455), bx-python (#4486), ClusterShell (#4432), custodian (#4484), + DFTB+ (#4398), Doris (#4404), ED2 (#4402), FireWorks (#4484), GETORB (#4414), GapFiller (#4462), IPy (#4450), + imbalanced-learn (#4373), ipyrad (#4507), libiconv (#4499), MultiQC (#3564), NLopt (#1750), PyCUDA (#4523), + pymatgen-db (#4484), QuTiP (#4371), ROI_PAC (#4414), Rascaf (#4459), RepastHPC (#4395), rootpy (#4242), + SSPACE_Basic (#4461), Sambamba (#4442), Spack (#4431), SpiceyPy (#4406), StaMPS (#4454), samblaster (#4435), + VMD (#4391), WRF-Fire (#4403) +- added additional easyconfigs for various supported software packages, including ... +- various enhancements, including: + - sync Bowtie2 easyconfigs, consistently use Bowtie2 easyblock (#4380) + - use pl2 source tarball for FFTW 3.3.6 which already includes patch for F03 interface (#4529) +- various bug fixes, including: + - add missing XZ dep in easyconfig for libunwind 1.1 w/ GCC/4.9.2, sync sanity_check_paths across libunwind easyconfigs (#4369) + - use 'use_fma4' rather than deprecated 'use_fma' easyconfig parameter in FFTW easyconfigs using intel toolchain (#4384) + - fix pkgconfig patch for Qhull to only let CMake substitute (#4451) + - also use patch for METIS 5.1.0 to enable use of doubles in easyconfig for foss/2016b (#4467) + - add dependency NLopt for R extension nloptr (#4481) + - fix issue with configparser and backports namespace blocking inclusion of nbconvert with IPython (#4504) + - change source_urls of pycrypto to encrypted https://pypi.python.org/... (#4505) + - fix sources spec for HMMER 3.1b2 + minor style fixes + better sanity check (#4531) + + v3.1.2 (March 20th 2017) ------------------------ -- GitLab From 23d840436deca449424710bd1abe199149a27d7c Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Thu, 4 May 2017 13:50:49 +0800 Subject: [PATCH 0687/1603] prepare release notes for eb320 --- RELEASE_NOTES | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index b25f9e1c1c..f2fbd7d51c 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -17,7 +17,8 @@ feature release pymatgen-db (#4484), QuTiP (#4371), ROI_PAC (#4414), Rascaf (#4459), RepastHPC (#4395), rootpy (#4242), SSPACE_Basic (#4461), Sambamba (#4442), Spack (#4431), SpiceyPy (#4406), StaMPS (#4454), samblaster (#4435), VMD (#4391), WRF-Fire (#4403) -- added additional easyconfigs for various supported software packages, including ... +- added additional easyconfigs for various supported software packages, including: + - 3to2 1.1.1, ACTC 1.1, ALLPATHS-LG 52488, Autoconf 2.69, Autoconf 2.69, Automake 1.15, Automake 1.15, Autotools 20150215, Autotools 20150215, arpack-ng 3.4.0, atomate 0.4.4, BLAT 3.5, BamTools 2.4.1, BioKanga 4.3.4, BioKanga 4.3.5, BioPerl 1.7.1, Bison 3.0.4, Boost 1.63.0, Boost 1.64.0, Bowtie2 2.2.9, BreakDancer 1.4.5, binutils 2.28, bx-python , bzip2 1.0.6, CMake 3.8.0, CUDA 8.0.61.eb, Cantera 2.3.0, ClusterShell 1.7.3.eb, cURL 7.53.1, cURL 7.54.0, cairo 1.14.8, configparser 3.5.0, cuDNN 6.0, custodian 1.1.0, DBG2OLC 20170208, DFTB+ 1.3.1, Doris 4.02, Doxygen 1.8.13, deap 0.9.2, ED2 20170201, ED2 20170201, ESMF 6.3.0rp1, EasyBuild 3.1.2.eb, Eigen 3.3.2, entrypoints 0.2.2, FFTW 3.3.6, FireWorks 1.4.2, file 5.30, flex 2.6.3, fmt 3.0.1, fontconfig 2.12.1, fqtrim 0.9.5, freetype 2.5.5, freetype 2.6.2, freetype 2.7.1, freetype 2.7.1, GCC 6.3.0, GCC 7.1.0, GCCcore 7.1.0.eb, GDAL 2.1.3, GEOS 3.6.1, GETORB 2.3.2, GLib 2.52.0, GMP 6.1.2, GSL 2.3, GapFiller 2.1.1, Ghostscript 9.21, Go 1.8.1.eb, g2clib 1.6.0, g2lib 1.4.0, gnuplot 5.0.5, googletest 1.8.0, HDF 4.2.12, HDF5 1.10.0, HISAT2 2.0.5, HMMER 3.1b2, h5py 2.7.0, h5py 2.7.0, help2man 1.47.4, hwloc 1.11.6, IMB 4.1, IMB 4.1, IMB 4.1, IPy 0.83.eb, IPython 5.3.0, ImageMagick 7.0.5, Inspector 2017_update2.eb, imbalanced-learn 0.2.1, ipyrad 0.6.15, JasPer 1.900.1, JasPer 2.0.12, jemalloc 4.5.0, LIBSVM 3.22, LLVM 4.0.0, LZO 2.10, LibTIFF 4.0.7, LittleCMS 2.8, libGLU 9.0.0, libdrm 2.4.76, libiconv 1.15, libjpeg-turbo 1.5.1, libpng 1.6.18, libpng 1.6.21, libpng 1.6.28, libpng 1.6.29, libreadline 7.0, libsodium 1.0.12, libtool 2.4.6, libtool 2.4.6, libxml2 2.9.4, libyaml 0.1.7.eb, M4 1.4.18, METIS 5.1.0, MRtrix 0.3.15, Mako 1.0.6, Mesa 17.0.2, MultiQC 0.7, MultiQC 0.9, makedepend 1.0.5, matplotlib 1.5.1, matplotlib 2.0.0, matplotlib 2.0.0, NASM 2.12.02, NGS 1.3.0, NLopt 2.4.2, NLopt 2.4.2, ncbi-vdb 2.8.2, ncurses 6.0, netCDF-C++4 4.3.0, netCDF-Fortran 4.4.4, netCDF 4.4.1.1, nettle 3.3, numba 0.32.0, numpy 1.10.1, numpy 1.12.1, ORCA 4.0.0.2, Octave 4.2.1, OpenMPI 2.1.0, OpenPGM 5.2.122, PCRE 8.40, PETSc 3.7.5, PGI 17.3, PLINK 1.9b_4.1, PROJ 4.9.3, ParMETIS 4.0.3, Perl 5.24.1, Pillow 4.1.0, PyCUDA 2016.1.2, PyYAML 3.12, PyYAML 3.12.eb, PyZMQ 16.0.2, Python 2.7.13, Python 3.6.1, pixman 0.34.0, pkg-config 0.29.2, pkgconfig 1.2.2, pymatgen-db 0.6.5, pymatgen 4.7.3, QuTiP 4.1.0, QuantumESPRESSO 6.1, R 3.3.3, R 3.3.3, ROI_PAC 3.0.1, Rascaf 1.0.2, RepastHPC 2.2.0, rootpy 0.8.0, SAMtools 0.1.20, SAMtools 1.4, SAMtools 1.4, SCons 2.5.1, SIONlib 1.7.1, SIONlib 1.7.1, SQLite 3.17.0, SSPACE_Basic 2.1.1, SUNDIALS 2.7.0, SWASH 3.14, SWASH 3.14, SWIG 3.0.12, Sambamba 0.6.6.eb, Seaborn 0.7.1, Spack 0.10.0.eb, SpiceyPy 1.1.0, StaMPS 3.3b1, Stacks 1.45, Stacks 1.46, Stampy 1.0.31, SuiteSparse 4.5.5, SuiteSparse 4.5.5, Szip 2.1, samblaster 0.1.24, scipy 0.19.0, scp 0.10.2, snaphu 1.4.2, sparsehash 2.0.3, spglib-python 1.9.9.38, Tcl 8.6.6, Tk 8.6.6, Triangle 1.6, tbb 2017_U5, tbb 2017_U5, tcsh 6.20.00, UDUNITS 2.2.24, util linux, VMD 1.9.3, VTune 2017_update2.eb, ViennaRNA 2.3.5, vsc-base 2.5.8, vsc-install 0.10.25, vsc-mympirun 4.0.0b0, WRF-Fire 20170221, WRF 3.8.0, Wannier90 2.1.0, X11 20170314, XZ 5.2.2, xorg-macros 1.19.1, xproto 7.0.31, ZeroMQ 4.2.2, zlib 1.2.11, zlib 1.2.11 - various enhancements, including: - sync Bowtie2 easyconfigs, consistently use Bowtie2 easyblock (#4380) - use pl2 source tarball for FFTW 3.3.6 which already includes patch for F03 interface (#4529) -- GitLab From 64164034dc03ed67cc9cf24fef855d8a71878eb3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 4 May 2017 09:35:28 +0200 Subject: [PATCH 0688/1603] add comment on Python as build dep for nodejs --- easybuild/easyconfigs/n/nodejs/nodejs-6.10.3-foss-2017a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/n/nodejs/nodejs-6.10.3-foss-2017a.eb b/easybuild/easyconfigs/n/nodejs/nodejs-6.10.3-foss-2017a.eb index 65377857a3..b02123940f 100644 --- a/easybuild/easyconfigs/n/nodejs/nodejs-6.10.3-foss-2017a.eb +++ b/easybuild/easyconfigs/n/nodejs/nodejs-6.10.3-foss-2017a.eb @@ -16,6 +16,7 @@ toolchainopts = {'lowopt': True} source_urls = ['http://nodejs.org/dist/v%(version)s/'] sources = ['node-v%(version)s.tar.gz'] +# Python is required (only) as build dependency allow_system_deps = [('Python', SYS_PYTHON_VERSION)] sanity_check_paths = { -- GitLab From c673a9aa8a3d703806f3201b950947d051eba7c5 Mon Sep 17 00:00:00 2001 From: iotaka Date: Thu, 4 May 2017 15:51:53 +0200 Subject: [PATCH 0689/1603] adding easyconfigs: git-2.12.2-foss-2016b.eb --- .../g/git/git-2.12.2-foss-2016b.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/g/git/git-2.12.2-foss-2016b.eb diff --git a/easybuild/easyconfigs/g/git/git-2.12.2-foss-2016b.eb b/easybuild/easyconfigs/g/git/git-2.12.2-foss-2016b.eb new file mode 100644 index 0000000000..4708565849 --- /dev/null +++ b/easybuild/easyconfigs/g/git/git-2.12.2-foss-2016b.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'git' +version = '2.12.2' + +homepage = 'http://git-scm.com/' +description = """Git is a free and open source distributed version control system designed +to handle everything from small to very large projects with speed and efficiency.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +sources = ['v%(version)s.tar.gz'] +source_urls = ['https://github.com/git/git/archive'] + +dependencies = [ + ('cURL', '7.49.1'), + ('expat', '2.2.0'), + ('gettext', '0.19.8'), + ('Perl', '5.24.0', '-bare'), +] + +preconfigopts = 'make configure && ' + +# Work around git build system bug. If LIBS contains -lpthread, then configure +# will not append -lpthread to LDFLAGS, but Makefile ignores LIBS. +configopts = "--with-perl=${EBROOTPERL}/bin/perl --enable-pthreads='-lpthread'" + +sanity_check_paths = { + 'files': ['bin/git'], + 'dirs': [], +} + +moduleclass = 'tools' -- GitLab From c1912bd137f0ca05f1a33357f119144fe79d8a0e Mon Sep 17 00:00:00 2001 From: Damian Alvarez Date: Thu, 4 May 2017 16:17:20 +0200 Subject: [PATCH 0690/1603] Added memkind --- .../Coreutils/Coreutils-8.27-GCCcore-5.4.0.eb | 26 ++++++++++++++ .../m/memkind/memkind-1.5.0-GCCcore-5.4.0.eb | 34 +++++++++++++++++++ easybuild/easyconfigs/t/tbb/tbb-2017.4.174.eb | 25 ++++++++++++++ 3 files changed, 85 insertions(+) create mode 100644 easybuild/easyconfigs/c/Coreutils/Coreutils-8.27-GCCcore-5.4.0.eb create mode 100644 easybuild/easyconfigs/m/memkind/memkind-1.5.0-GCCcore-5.4.0.eb create mode 100644 easybuild/easyconfigs/t/tbb/tbb-2017.4.174.eb diff --git a/easybuild/easyconfigs/c/Coreutils/Coreutils-8.27-GCCcore-5.4.0.eb b/easybuild/easyconfigs/c/Coreutils/Coreutils-8.27-GCCcore-5.4.0.eb new file mode 100644 index 0000000000..c94e4b8ac3 --- /dev/null +++ b/easybuild/easyconfigs/c/Coreutils/Coreutils-8.27-GCCcore-5.4.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = "Coreutils" +version = "8.27" + +homepage = 'http://www.gnu.org/software/coreutils/' +description = """The GNU Core Utilities are the basic file, shell and text manipulation utilities of the + GNU operating system. These are the core utilities which are expected to exist on every operating system. + + Contact: sc@fz-juelich.de +""" + +toolchain = {'name': 'GCCcore', 'version': '5.4.0'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_XZ] + +builddependencies = [('binutils', '2.26')] + +sanity_check_paths = { + 'files': ['bin/sort', 'bin/echo', 'bin/du', 'bin/date', 'bin/true'], + 'dirs': [] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/m/memkind/memkind-1.5.0-GCCcore-5.4.0.eb b/easybuild/easyconfigs/m/memkind/memkind-1.5.0-GCCcore-5.4.0.eb new file mode 100644 index 0000000000..30d25870f8 --- /dev/null +++ b/easybuild/easyconfigs/m/memkind/memkind-1.5.0-GCCcore-5.4.0.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'memkind' +version = '1.5.0' + +homepage = 'http://memkind.github.io' +description = """User Extensible Heap Manager built on top of jemalloc which enables control of memory characteristics +and a partitioning of the heap between kinds of memory. + + Contact: sc@fz-juelich.de +""" + +toolchain = {'name': 'GCCcore', 'version': '5.4.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/memkind/memkind/archive/'] +sources = ['v%(version)s.tar.gz'] + +builddependencies = [ + ('binutils', '2.26'), + ('Coreutils', '8.27'), # needed to ensure that ./build_jemalloc.sh works properly + ('Autotools', '20150215'), # needed to ensure that ./build_jemalloc.sh works properly +] + +dependencies = [ + ('tbb', '2017.4.174', '', True), # optional, to enable the tbb heap manager +] + +# This can be also an EB dependency, but seems unnecesary +osdependencies = [('numactl-devel', 'libnuma-devel ')] + +preconfigopts = './build_jemalloc.sh && ./autogen.sh && ' + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/tbb/tbb-2017.4.174.eb b/easybuild/easyconfigs/t/tbb/tbb-2017.4.174.eb new file mode 100644 index 0000000000..54c9706aa0 --- /dev/null +++ b/easybuild/easyconfigs/t/tbb/tbb-2017.4.174.eb @@ -0,0 +1,25 @@ +name = 'tbb' +version = '2017.4.174' + +homepage = 'http://software.intel.com/en-us/articles/intel-tbb/' +description = """Intel Threading Building Blocks 4.0 (Intel TBB) + is a widely used, award-winning C++ template library for creating reliable, + portable, and scalable parallel applications. + Use Intel TBB for a simple and rapid way of developing robust task-based + parallel applications that scale to available processor cores, are compatible + with multiple environments, and are easier to maintain. + Intel TBB is the most proficient way to implement future-proof parallel applications + that tap into the power and performance of multicore and manycore hardware platforms. + + Contact: sc@fz-juelich.de +""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['l_tbb_%(version)s.tgz'] + +requires_runtime_license = False + +dontcreateinstalldir = True + +moduleclass = 'lib' -- GitLab From c183a7c624985aadebe8e70291df64825a2aaf72 Mon Sep 17 00:00:00 2001 From: Damian Alvarez Date: Thu, 4 May 2017 16:19:51 +0200 Subject: [PATCH 0691/1603] Removed contact info --- .../easyconfigs/c/Coreutils/Coreutils-8.27-GCCcore-5.4.0.eb | 2 -- easybuild/easyconfigs/m/memkind/memkind-1.5.0-GCCcore-5.4.0.eb | 2 -- easybuild/easyconfigs/t/tbb/tbb-2017.4.174.eb | 2 -- 3 files changed, 6 deletions(-) diff --git a/easybuild/easyconfigs/c/Coreutils/Coreutils-8.27-GCCcore-5.4.0.eb b/easybuild/easyconfigs/c/Coreutils/Coreutils-8.27-GCCcore-5.4.0.eb index c94e4b8ac3..e47ad52ac4 100644 --- a/easybuild/easyconfigs/c/Coreutils/Coreutils-8.27-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/c/Coreutils/Coreutils-8.27-GCCcore-5.4.0.eb @@ -6,8 +6,6 @@ version = "8.27" homepage = 'http://www.gnu.org/software/coreutils/' description = """The GNU Core Utilities are the basic file, shell and text manipulation utilities of the GNU operating system. These are the core utilities which are expected to exist on every operating system. - - Contact: sc@fz-juelich.de """ toolchain = {'name': 'GCCcore', 'version': '5.4.0'} diff --git a/easybuild/easyconfigs/m/memkind/memkind-1.5.0-GCCcore-5.4.0.eb b/easybuild/easyconfigs/m/memkind/memkind-1.5.0-GCCcore-5.4.0.eb index 30d25870f8..5522bebb7b 100644 --- a/easybuild/easyconfigs/m/memkind/memkind-1.5.0-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/m/memkind/memkind-1.5.0-GCCcore-5.4.0.eb @@ -6,8 +6,6 @@ version = '1.5.0' homepage = 'http://memkind.github.io' description = """User Extensible Heap Manager built on top of jemalloc which enables control of memory characteristics and a partitioning of the heap between kinds of memory. - - Contact: sc@fz-juelich.de """ toolchain = {'name': 'GCCcore', 'version': '5.4.0'} diff --git a/easybuild/easyconfigs/t/tbb/tbb-2017.4.174.eb b/easybuild/easyconfigs/t/tbb/tbb-2017.4.174.eb index 54c9706aa0..925ecf0fc9 100644 --- a/easybuild/easyconfigs/t/tbb/tbb-2017.4.174.eb +++ b/easybuild/easyconfigs/t/tbb/tbb-2017.4.174.eb @@ -10,8 +10,6 @@ description = """Intel Threading Building Blocks 4.0 (Intel TBB) with multiple environments, and are easier to maintain. Intel TBB is the most proficient way to implement future-proof parallel applications that tap into the power and performance of multicore and manycore hardware platforms. - - Contact: sc@fz-juelich.de """ toolchain = {'name': 'dummy', 'version': 'dummy'} -- GitLab From 27e05e5536c1a9366d61d1ed9487ad36f7e11df1 Mon Sep 17 00:00:00 2001 From: jrbosch Date: Thu, 4 May 2017 16:26:44 -0400 Subject: [PATCH 0692/1603] add easyconfig x265-2.4-foss-2016b.eb --- .../easyconfigs/x/x265/x265-2.4-foss-2016b.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/x/x265/x265-2.4-foss-2016b.eb diff --git a/easybuild/easyconfigs/x/x265/x265-2.4-foss-2016b.eb b/easybuild/easyconfigs/x/x265/x265-2.4-foss-2016b.eb new file mode 100644 index 0000000000..d0b1d74b60 --- /dev/null +++ b/easybuild/easyconfigs/x/x265/x265-2.4-foss-2016b.eb @@ -0,0 +1,29 @@ +easyblock = 'CMakeMake' + +name = 'x265' +version = '2.4' + +homepage = 'http://x265.org/' +description = """x265 is a free software library and application for encoding video streams into the H.265 + AVC compression format, and is released under the terms of the GNU GPL.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = [ + 'http://ftp.videolan.org/pub/videolan/x265/', + 'http://download.videolan.org/pub/videolan/x265/', +] +sources = ['%(name)s_%(version)s.tar.gz'] + +dependencies = [('Yasm', '1.3.0')] + +builddependencies = [('CMake', '3.7.2')] + +start_dir = 'source' + +sanity_check_paths = { + 'files': ['bin/x265', 'include/x265_config.h', 'include/x265.h', 'lib/libx265.a', 'lib/libx265.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' -- GitLab From 26710fc9b17f4bbed3ad2f9de260e16ca650da40 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 4 May 2017 22:34:40 +0200 Subject: [PATCH 0693/1603] bump version to 3.2.0 + tweak release notes --- RELEASE_NOTES | 18 ++++++++++-------- setup.py | 2 +- 2 files changed, 11 insertions(+), 9 deletions(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index f2fbd7d51c..d67162b731 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -3,34 +3,36 @@ For more detailed information, please see the git log. These release notes can also be consulted at http://easybuild.readthedocs.org/en/latest/Release_notes.html. -The latest version of easybuild-easyconfig provides 6,718 easyconfig files, for 1,182 different software packages, +The latest version of easybuild-easyconfig provides 6,943 easyconfig files, for 1,216 different software packages, 25 different (compiler) toolchains, 13 software bundles and 1 meta-package. v3.2.0 (May 5th 2017) --------------------- feature release -- added example easyconfig files for 33 new software packages: +- added example easyconfig files for 34 new software packages: - ACTC (#4386), atomate (#4484), BreakDancer (#4455), bx-python (#4486), ClusterShell (#4432), custodian (#4484), DFTB+ (#4398), Doris (#4404), ED2 (#4402), FireWorks (#4484), GETORB (#4414), GapFiller (#4462), IPy (#4450), - imbalanced-learn (#4373), ipyrad (#4507), libiconv (#4499), MultiQC (#3564), NLopt (#1750), PyCUDA (#4523), - pymatgen-db (#4484), QuTiP (#4371), ROI_PAC (#4414), Rascaf (#4459), RepastHPC (#4395), rootpy (#4242), - SSPACE_Basic (#4461), Sambamba (#4442), Spack (#4431), SpiceyPy (#4406), StaMPS (#4454), samblaster (#4435), - VMD (#4391), WRF-Fire (#4403) + imbalanced-learn (#4373), ipyrad (#4507), libiconv (#4499), MultiQC (#3564), NLopt (#1750), Node-RED (#4542), + PyCUDA (#4523), pymatgen-db (#4484), QuTiP (#4371), ROI_PAC (#4414), Rascaf (#4459), RepastHPC (#4395), + rootpy (#4242), SSPACE_Basic (#4461), Sambamba (#4442), Spack (#4431), SpiceyPy (#4406), StaMPS (#4454), + samblaster (#4435), VMD (#4391), WRF-Fire (#4403) - added additional easyconfigs for various supported software packages, including: - - 3to2 1.1.1, ACTC 1.1, ALLPATHS-LG 52488, Autoconf 2.69, Autoconf 2.69, Automake 1.15, Automake 1.15, Autotools 20150215, Autotools 20150215, arpack-ng 3.4.0, atomate 0.4.4, BLAT 3.5, BamTools 2.4.1, BioKanga 4.3.4, BioKanga 4.3.5, BioPerl 1.7.1, Bison 3.0.4, Boost 1.63.0, Boost 1.64.0, Bowtie2 2.2.9, BreakDancer 1.4.5, binutils 2.28, bx-python , bzip2 1.0.6, CMake 3.8.0, CUDA 8.0.61.eb, Cantera 2.3.0, ClusterShell 1.7.3.eb, cURL 7.53.1, cURL 7.54.0, cairo 1.14.8, configparser 3.5.0, cuDNN 6.0, custodian 1.1.0, DBG2OLC 20170208, DFTB+ 1.3.1, Doris 4.02, Doxygen 1.8.13, deap 0.9.2, ED2 20170201, ED2 20170201, ESMF 6.3.0rp1, EasyBuild 3.1.2.eb, Eigen 3.3.2, entrypoints 0.2.2, FFTW 3.3.6, FireWorks 1.4.2, file 5.30, flex 2.6.3, fmt 3.0.1, fontconfig 2.12.1, fqtrim 0.9.5, freetype 2.5.5, freetype 2.6.2, freetype 2.7.1, freetype 2.7.1, GCC 6.3.0, GCC 7.1.0, GCCcore 7.1.0.eb, GDAL 2.1.3, GEOS 3.6.1, GETORB 2.3.2, GLib 2.52.0, GMP 6.1.2, GSL 2.3, GapFiller 2.1.1, Ghostscript 9.21, Go 1.8.1.eb, g2clib 1.6.0, g2lib 1.4.0, gnuplot 5.0.5, googletest 1.8.0, HDF 4.2.12, HDF5 1.10.0, HISAT2 2.0.5, HMMER 3.1b2, h5py 2.7.0, h5py 2.7.0, help2man 1.47.4, hwloc 1.11.6, IMB 4.1, IMB 4.1, IMB 4.1, IPy 0.83.eb, IPython 5.3.0, ImageMagick 7.0.5, Inspector 2017_update2.eb, imbalanced-learn 0.2.1, ipyrad 0.6.15, JasPer 1.900.1, JasPer 2.0.12, jemalloc 4.5.0, LIBSVM 3.22, LLVM 4.0.0, LZO 2.10, LibTIFF 4.0.7, LittleCMS 2.8, libGLU 9.0.0, libdrm 2.4.76, libiconv 1.15, libjpeg-turbo 1.5.1, libpng 1.6.18, libpng 1.6.21, libpng 1.6.28, libpng 1.6.29, libreadline 7.0, libsodium 1.0.12, libtool 2.4.6, libtool 2.4.6, libxml2 2.9.4, libyaml 0.1.7.eb, M4 1.4.18, METIS 5.1.0, MRtrix 0.3.15, Mako 1.0.6, Mesa 17.0.2, MultiQC 0.7, MultiQC 0.9, makedepend 1.0.5, matplotlib 1.5.1, matplotlib 2.0.0, matplotlib 2.0.0, NASM 2.12.02, NGS 1.3.0, NLopt 2.4.2, NLopt 2.4.2, ncbi-vdb 2.8.2, ncurses 6.0, netCDF-C++4 4.3.0, netCDF-Fortran 4.4.4, netCDF 4.4.1.1, nettle 3.3, numba 0.32.0, numpy 1.10.1, numpy 1.12.1, ORCA 4.0.0.2, Octave 4.2.1, OpenMPI 2.1.0, OpenPGM 5.2.122, PCRE 8.40, PETSc 3.7.5, PGI 17.3, PLINK 1.9b_4.1, PROJ 4.9.3, ParMETIS 4.0.3, Perl 5.24.1, Pillow 4.1.0, PyCUDA 2016.1.2, PyYAML 3.12, PyYAML 3.12.eb, PyZMQ 16.0.2, Python 2.7.13, Python 3.6.1, pixman 0.34.0, pkg-config 0.29.2, pkgconfig 1.2.2, pymatgen-db 0.6.5, pymatgen 4.7.3, QuTiP 4.1.0, QuantumESPRESSO 6.1, R 3.3.3, R 3.3.3, ROI_PAC 3.0.1, Rascaf 1.0.2, RepastHPC 2.2.0, rootpy 0.8.0, SAMtools 0.1.20, SAMtools 1.4, SAMtools 1.4, SCons 2.5.1, SIONlib 1.7.1, SIONlib 1.7.1, SQLite 3.17.0, SSPACE_Basic 2.1.1, SUNDIALS 2.7.0, SWASH 3.14, SWASH 3.14, SWIG 3.0.12, Sambamba 0.6.6.eb, Seaborn 0.7.1, Spack 0.10.0.eb, SpiceyPy 1.1.0, StaMPS 3.3b1, Stacks 1.45, Stacks 1.46, Stampy 1.0.31, SuiteSparse 4.5.5, SuiteSparse 4.5.5, Szip 2.1, samblaster 0.1.24, scipy 0.19.0, scp 0.10.2, snaphu 1.4.2, sparsehash 2.0.3, spglib-python 1.9.9.38, Tcl 8.6.6, Tk 8.6.6, Triangle 1.6, tbb 2017_U5, tbb 2017_U5, tcsh 6.20.00, UDUNITS 2.2.24, util linux, VMD 1.9.3, VTune 2017_update2.eb, ViennaRNA 2.3.5, vsc-base 2.5.8, vsc-install 0.10.25, vsc-mympirun 4.0.0b0, WRF-Fire 20170221, WRF 3.8.0, Wannier90 2.1.0, X11 20170314, XZ 5.2.2, xorg-macros 1.19.1, xproto 7.0.31, ZeroMQ 4.2.2, zlib 1.2.11, zlib 1.2.11 + - BamTools 2.4.1, Boost 1.64.0, GCC 7.1.0, IPython 5.3.0, LLVM 4.0.0, Mesa 17.0.2, Octave 4.2.1, OpenMPI 2.1.0, + PETSc 3.7.5, PGI 17.3, Perl 5.24.1, Python 2.7.13 + 3.6.1 (incl. numpy 1.12.1, scipy 0.19.0), R 3.3.3, SuiteSparse 4.5.5 - various enhancements, including: - sync Bowtie2 easyconfigs, consistently use Bowtie2 easyblock (#4380) - use pl2 source tarball for FFTW 3.3.6 which already includes patch for F03 interface (#4529) - various bug fixes, including: - add missing XZ dep in easyconfig for libunwind 1.1 w/ GCC/4.9.2, sync sanity_check_paths across libunwind easyconfigs (#4369) - use 'use_fma4' rather than deprecated 'use_fma' easyconfig parameter in FFTW easyconfigs using intel toolchain (#4384) - - fix pkgconfig patch for Qhull to only let CMake substitute (#4451) + - fix pkgconfig patch for Qhull (#4451) - also use patch for METIS 5.1.0 to enable use of doubles in easyconfig for foss/2016b (#4467) - add dependency NLopt for R extension nloptr (#4481) - fix issue with configparser and backports namespace blocking inclusion of nbconvert with IPython (#4504) - change source_urls of pycrypto to encrypted https://pypi.python.org/... (#4505) - fix sources spec for HMMER 3.1b2 + minor style fixes + better sanity check (#4531) + - also build IMB-IO in IMB 4.1 easyconfig using foss/2016a (#4539) v3.1.2 (March 20th 2017) diff --git a/setup.py b/setup.py index 0683e432c9..40e8813698 100644 --- a/setup.py +++ b/setup.py @@ -47,7 +47,7 @@ from distutils import log # recent setuptools versions will *TRANSFORM* something like 'X.Y.Zdev' into 'X.Y.Z.dev0', with a warning like # UserWarning: Normalizing '2.4.0dev' to '2.4.0.dev0' # This causes problems further up the dependency chain... -VERSION = '3.2.0.dev0' +VERSION = '3.2.0' API_VERSION = VERSION.split('.')[0] EB_VERSION = '.'.join(VERSION.split('.')[0:2]) -- GitLab From 79ac6ae1634c2272cc3f821d2f56ee53ee6d67ee Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Fri, 5 May 2017 16:10:45 +0200 Subject: [PATCH 0694/1603] Bump all to CMake 3.8.0 --- .../CGAL-4.9-intel-2017a-Python-2.7.13.eb | 2 +- .../c/CMake/CMake-3.7.2-intel-2017a.eb | 31 ------------------- .../m/METIS/METIS-5.1.0-intel-2017a.eb | 2 +- .../ParaView-5.2.0-intel-2017a-mpi.eb | 2 +- 4 files changed, 3 insertions(+), 34 deletions(-) delete mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.7.2-intel-2017a.eb diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.9-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.9-intel-2017a-Python-2.7.13.eb index da60ff72f0..e83b067d66 100644 --- a/easybuild/easyconfigs/c/CGAL/CGAL-4.9-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.9-intel-2017a-Python-2.7.13.eb @@ -23,7 +23,7 @@ dependencies = [ ] builddependencies = [ - ('CMake', '3.7.2'), + ('CMake', '3.8.0'), ('Eigen', '3.3.3'), ] diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.7.2-intel-2017a.eb b/easybuild/easyconfigs/c/CMake/CMake-3.7.2-intel-2017a.eb deleted file mode 100644 index d78b6b43f1..0000000000 --- a/easybuild/easyconfigs/c/CMake/CMake-3.7.2-intel-2017a.eb +++ /dev/null @@ -1,31 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'CMake' -version = '3.7.2' - -homepage = 'http://www.cmake.org' -description = """CMake, the cross-platform, open-source build system. - CMake is a family of tools designed to build, test and package software.""" - -toolchain = {'name': 'intel', 'version': '2017a'} - -source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] -sources = [SOURCELOWER_TAR_GZ] - -configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' - -dependencies = [ - ('ncurses', '6.0'), - # OS dependency should be preferred if the os version is more recent then this version, - # it's nice to have an up to date openssl for security reasons - # ('OpenSSL', '1.0.2j'), -] - -osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] - -sanity_check_paths = { - 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], - 'dirs': [], -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/m/METIS/METIS-5.1.0-intel-2017a.eb b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-intel-2017a.eb index 352a974db9..91d00f1139 100644 --- a/easybuild/easyconfigs/m/METIS/METIS-5.1.0-intel-2017a.eb +++ b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-intel-2017a.eb @@ -18,7 +18,7 @@ source_urls = [ # We use 32bit for indices and 64bit for content patches = ['METIS-5.1.0-use-doubles.patch'] -builddependencies = [('CMake', '3.7.2')] +builddependencies = [('CMake', '3.8.0')] configopts = ['', 'shared=1'] diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-5.2.0-intel-2017a-mpi.eb b/easybuild/easyconfigs/p/ParaView/ParaView-5.2.0-intel-2017a-mpi.eb index 903174f12f..8746599786 100644 --- a/easybuild/easyconfigs/p/ParaView/ParaView-5.2.0-intel-2017a-mpi.eb +++ b/easybuild/easyconfigs/p/ParaView/ParaView-5.2.0-intel-2017a-mpi.eb @@ -24,7 +24,7 @@ dependencies = [ ('Python', '2.7.13'), ] -builddependencies = [('CMake', '3.7.2')] +builddependencies = [('CMake', '3.8.0')] separate_build_dir = True -- GitLab From 946baf954570a740f5d87d4161d1d75b0bf27b3d Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Fri, 5 May 2017 16:11:55 +0200 Subject: [PATCH 0695/1603] Bump CMake in OpenFOAM too to 3.8.0 --- easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.1-intel-2017a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.1-intel-2017a.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.1-intel-2017a.eb index 2469f2947a..c3f3f806f9 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.1-intel-2017a.eb +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.1-intel-2017a.eb @@ -29,7 +29,7 @@ dependencies = [ builddependencies = [ ('Bison', '3.0.4'), - ('CMake', '3.7.2'), + ('CMake', '3.8.0'), ('flex', '2.6.3'), ] -- GitLab From fcc2fe709d80ba7fe6a6a2d350398621c54022c7 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Fri, 5 May 2017 16:19:50 +0200 Subject: [PATCH 0696/1603] Drop old comment --- easybuild/easyconfigs/q/Qt5/Qt5-5.8.0-intel-2017a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.8.0-intel-2017a.eb b/easybuild/easyconfigs/q/Qt5/Qt5-5.8.0-intel-2017a.eb index fc41f1c1fd..ab4ae0dab8 100644 --- a/easybuild/easyconfigs/q/Qt5/Qt5-5.8.0-intel-2017a.eb +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.8.0-intel-2017a.eb @@ -26,7 +26,7 @@ configopts = '-skip qtgamepad' dependencies = [ ('GLib', '2.52.0'), ('libpng', '1.6.29'), - ('X11', '20170314'), #, '', ('GCCcore', '6.3.0')), + ('X11', '20170314'), ('libGLU', '9.0.0'), ] -- GitLab From 94fab13de92516a969d7a43238c3571870007b1e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 5 May 2017 17:29:28 +0200 Subject: [PATCH 0697/1603] adding easyconfigs: EasyBuild-3.2.0.eb --- .../e/EasyBuild/EasyBuild-3.2.0.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.2.0.eb diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.2.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.2.0.eb new file mode 100644 index 0000000000..d84e16eaba --- /dev/null +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.2.0.eb @@ -0,0 +1,38 @@ +easyblock = 'EB_EasyBuildMeta' + +name = 'EasyBuild' +version = '3.2.0' + +homepage = 'http://hpcugent.github.com/easybuild/' +description = """EasyBuild is a software build and installation framework + written in Python that allows you to install software in a structured, + repeatable and robust way.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = [ + # vsc-install + 'https://pypi.python.org/packages/82/ec/19d85d2bb91b562195d00db9ac82d7529904e7eabc0597720966bf74714f/', + # vsc-base + 'https://pypi.python.org/packages/f7/66/1ff7ecc4a93ba37e063f5bfbe395e95a547b1dec73b017c2724f4475a958/', + # easybuild-framework + 'https://pypi.python.org/packages/2c/39/4435097a0b897ca1e3c7f055000ebfa2a5dc3632e606a7cf0088b0caa2ee/', + # easybuild-easyblocks + 'https://pypi.python.org/packages/ce/49/70a1d3f419ffb21dc3a3446bdf63d2a49447753fa4e69ec0a3db5a262e67/', + # easybuild-easyconfigs + 'https://pypi.python.org/packages/97/59/b8d166b270f113ae69b0983275dac5da5bfb94bb1082a10bb26e93c78ed7/', +] +# order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) +sources = [ + 'vsc-install-0.10.26.tar.gz', + 'vsc-base-2.5.8.tar.gz', + 'easybuild-framework-%(version)s.tar.gz', + 'easybuild-easyblocks-%(version)s.tar.gz', + 'easybuild-easyconfigs-%(version)s.tar.gz', +] + +# EasyBuild is a (set of) Python packages, so it depends on Python +# usually, we want to use the system Python, so no actual Python dependency is listed +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +moduleclass = 'tools' -- GitLab From b1d56530a5bae608a28c907a43792ed3c9f85ea6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 5 May 2017 17:58:30 +0200 Subject: [PATCH 0698/1603] bump to v3.3.0.dev0 --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 40e8813698..85590c2983 100644 --- a/setup.py +++ b/setup.py @@ -47,7 +47,7 @@ from distutils import log # recent setuptools versions will *TRANSFORM* something like 'X.Y.Zdev' into 'X.Y.Z.dev0', with a warning like # UserWarning: Normalizing '2.4.0dev' to '2.4.0.dev0' # This causes problems further up the dependency chain... -VERSION = '3.2.0' +VERSION = '3.3.0.dev0' API_VERSION = VERSION.split('.')[0] EB_VERSION = '.'.join(VERSION.split('.')[0:2]) -- GitLab From 2a8958f86f854c0523d195c3bf3a34edb6615ef6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 7 May 2017 22:26:00 +0200 Subject: [PATCH 0699/1603] adding easyconfigs: OpenFOAM-2.2.2-intel-2017a.eb, flex-2.5.39-GCCcore-6.3.0.eb --- .../f/flex/flex-2.5.39-GCCcore-6.3.0.eb | 22 +++++++++++ .../o/OpenFOAM/OpenFOAM-2.2.2-intel-2017a.eb | 39 +++++++++++++++++++ 2 files changed, 61 insertions(+) create mode 100644 easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-6.3.0.eb create mode 100644 easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.2.2-intel-2017a.eb diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-6.3.0.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..f579ff8a96 --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-6.3.0.eb @@ -0,0 +1,22 @@ +name = 'flex' +version = '2.5.39' + +homepage = 'http://flex.sourceforge.net/' +description = """Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, + sometimes called a tokenizer, is a program which recognizes lexical patterns in text.""" + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] + +checksums = [ + 'e133e9ead8ec0a58d81166b461244fde', # flex-2.5.39.tar.gz +] + +dependencies = [('M4', '1.4.18')] +# use same binutils version that was used when building GCCcore toolchain +builddependencies = [('binutils', '2.27', '', True)] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.2.2-intel-2017a.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.2.2-intel-2017a.eb new file mode 100644 index 0000000000..7d4fcb2a52 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.2.2-intel-2017a.eb @@ -0,0 +1,39 @@ +name = 'OpenFOAM' +version = '2.2.2' + +homepage = 'http://www.openfoam.com/' +description = """OpenFOAM is a free, open source CFD software package. + OpenFOAM has an extensive range of features to solve anything from complex fluid flows + involving chemical reactions, turbulence and heat transfer, + to solid dynamics and electromagnetics.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['http://downloads.sourceforge.net/foam/%(version)s'] +sources = [ + SOURCE_TGZ, + 'ThirdParty-%(version)s.tgz', +] + +patches = [ + 'cleanup-OpenFOAM-%(version)s.patch', + 'OpenFOAM-2.2.0_libreadline.patch', + ('cleanup-ThirdParty-%(version)s.patch', ".."), # patch should not be applied in OpenFOAM subdir +] + +dependencies = [ + ('libreadline', '6.3'), + ('METIS', '5.1.0'), + ('ncurses', '6.0'), + ('SCOTCH', '6.0.4'), + ('Boost', '1.64.0'), +] + + +builddependencies = [ + ('flex', '2.5.39'), + ('Bison', '3.0.4'), + ('CMake', '3.8.0'), +] + +moduleclass = 'cae' -- GitLab From 0fee12a842bff40dfac37d47d96db9e9137ffb2c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 7 May 2017 22:28:24 +0200 Subject: [PATCH 0700/1603] adding easyconfigs: OpenFOAM-2.3.1-intel-2017a.eb --- .../o/OpenFOAM/OpenFOAM-2.3.1-intel-2017a.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.3.1-intel-2017a.eb diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.3.1-intel-2017a.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.3.1-intel-2017a.eb new file mode 100644 index 0000000000..22826bc9df --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.3.1-intel-2017a.eb @@ -0,0 +1,44 @@ +name = 'OpenFOAM' +version = '2.3.1' + +homepage = 'http://www.openfoam.com/' +description = """OpenFOAM is a free, open source CFD software package. + OpenFOAM has an extensive range of features to solve anything from complex fluid flows + involving chemical reactions, turbulence and heat transfer, + to solid dynamics and electromagnetics.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['http://downloads.sourceforge.net/foam/%(version)s'] +sources = [ + SOURCE_TGZ, + 'ThirdParty-%(version)s.tgz', +] + +patches = [ + 'OpenFOAM-%(version)s_cleanup.patch', + 'OpenFOAM-2.3.0_libreadline.patch', + ('ThirdParty-%(version)s_cleanup.patch', ".."), # patch should not be applied in OpenFOAM subdir +] + +# fix for cyclic symlink issue, which may cause unpacking to fail +# see also http://www.openfoam.org/mantisbt/view.php?id=1191 +# fixed in recent versions: https://github.com/OpenFOAM/OpenFOAM-2.3.x/commit/f7a485069c778495cc39b308580289f6c2d47163 +unpack_options = "--exclude=*tutorials/mesh/foamyHexMesh/mixerVessel/system/backgroundMeshDecomposition" +unpack_options += " --exclude=*tutorials/mesh/foamyHexMesh/mixerVessel/system/cellShapeControlMesh" + +dependencies = [ + ('libreadline', '6.3'), + ('METIS', '5.1.0'), + ('ncurses', '6.0'), + ('SCOTCH', '6.0.4'), + ('Boost', '1.64.0'), +] + +builddependencies = [ + ('flex', '2.5.39'), + ('Bison', '3.0.4'), + ('CMake', '3.8.0'), +] + +moduleclass = 'cae' -- GitLab From d3563b795447df65ba2eaaf239c0f332589a3c50 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 7 May 2017 22:29:03 +0200 Subject: [PATCH 0701/1603] adding easyconfigs: OpenFOAM-2.4.0-intel-2017a.eb --- .../o/OpenFOAM/OpenFOAM-2.4.0-intel-2017a.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.4.0-intel-2017a.eb diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.4.0-intel-2017a.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.4.0-intel-2017a.eb new file mode 100644 index 0000000000..dd2ccbb6b7 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.4.0-intel-2017a.eb @@ -0,0 +1,38 @@ +name = 'OpenFOAM' +version = '2.4.0' + +homepage = 'http://www.openfoam.com/' +description = """OpenFOAM is a free, open source CFD software package. + OpenFOAM has an extensive range of features to solve anything from complex fluid flows + involving chemical reactions, turbulence and heat transfer, + to solid dynamics and electromagnetics.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['http://downloads.sourceforge.net/foam/%(version)s'] +sources = [ + SOURCE_TGZ, + 'ThirdParty-%(version)s.tgz', +] + +patches = [ + 'OpenFOAM-%(version)s_cleanup.patch', + 'OpenFOAM-2.3.0_libreadline.patch', + ('ThirdParty-%(version)s_cleanup.patch', ".."), # patch should not be applied in OpenFOAM subdir +] + +dependencies = [ + ('libreadline', '6.3'), + ('METIS', '5.1.0'), + ('ncurses', '6.0'), + ('SCOTCH', '6.0.4'), + ('Boost', '1.64.0'), +] + +builddependencies = [ + ('flex', '2.5.39'), + ('Bison', '3.0.4'), + ('CMake', '3.8.0'), +] + +moduleclass = 'cae' -- GitLab From 8d7635554191701bb4b415e9a5fce845e981f221 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 8 May 2017 09:52:09 +0200 Subject: [PATCH 0702/1603] adding easyconfigs: ASE-3.13.0-intel-2017a-Python-2.7.13.eb --- .../ASE-3.13.0-intel-2017a-Python-2.7.13.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/a/ASE/ASE-3.13.0-intel-2017a-Python-2.7.13.eb diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.13.0-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/a/ASE/ASE-3.13.0-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..046d2d02c9 --- /dev/null +++ b/easybuild/easyconfigs/a/ASE/ASE-3.13.0-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'ASE' +version = '3.13.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://wiki.fysik.dtu.dk/ase/' +description = """ASE is a python package providing an open source Atomic Simulation Environment + in the Python scripting language.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('Python', '2.7.13'), +] + +sanity_check_paths = { + 'files': ['bin/ase-build', 'bin/ase-db', 'bin/ase-gui', 'bin/ase-info', 'bin/ase-run'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'chem' -- GitLab From d3dd9379507508f02b36714605f0a22ae9bc187d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 8 May 2017 10:16:35 +0200 Subject: [PATCH 0703/1603] adding easyconfigs: hanythingondemand-3.2.2-cli.eb, hanythingondemand-3.2.2-intel-2016b-Python-2.7.12.eb --- .../hanythingondemand-3.2.2-cli.eb | 42 +++++++++++++++++++ ...ndemand-3.2.2-intel-2016b-Python-2.7.12.eb | 30 +++++++++++++ 2 files changed, 72 insertions(+) create mode 100644 easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.2.2-cli.eb create mode 100644 easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.2.2-intel-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.2.2-cli.eb b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.2.2-cli.eb new file mode 100644 index 0000000000..5c43bd66c7 --- /dev/null +++ b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.2.2-cli.eb @@ -0,0 +1,42 @@ +easyblock = 'PythonPackage' + +name = 'hanythingondemand' +version = '3.2.2' +versionsuffix = '-cli' + +homepage = 'https://github.com/hpcugent/hanythingondemand' +description = """HanythingOnDemand (HOD) is a system for provisioning virtual Hadoop clusters over a large physical cluster. +It uses the Torque resource manager to do node allocation.""" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +# minimal version for interactive use: just uses system Python (netaddr/netifaces/mpi4py not required) +dependencies = [ + ('pbs_python', '4.6.0'), + ('vsc-base', '2.5.8'), +] + +use_easy_install = True +zipped_egg = True + +# use 'hod' rather than 'hanythingondemand' in module name +modaltsoftname = 'hod' + +options = {'modulename': 'hod'} + +modextravars = { + # site-specific settings, hence commented out + # specify HOD module to use in jobs (*full* HOD installation, not a minimal one) + # 'HOD_BATCH_HOD_MODULE': 'hanythingondemand/%(version)s-intel-2016b-Python-2.7.12', + # 'HOD_CREATE_HOD_MODULE': 'hanythingondemand/%(version)s-intel-2016b-Python-2.7.12', + # specify location on shared 'scratch' filesystem for HOD working directories + # 'HOD_BATCH_WORKDIR': '\$VSC_SCRATCH/hod', + # 'HOD_CREATE_WORKDIR': '\$VSC_SCRATCH/hod', +} + +sanity_check_commands = [('hod', '--help'), ('hod', 'dists')] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.2.2-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.2.2-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..ef65fdbca6 --- /dev/null +++ b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.2.2-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'hanythingondemand' +version = '3.2.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/hpcugent/hanythingondemand' +description = """HanythingOnDemand (HOD) is a system for provisioning virtual Hadoop clusters over a large physical cluster. +It uses the Torque resource manager to do node allocation.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +# a Python version with netaddr/netifaces/mpi4py + pbs_python and vsc-base/vsc-mympirun is required at runtime +dependencies = [ + ('Python', '2.7.12'), # provides netaddr, netifaces, mpi4py + ('pbs_python', '4.6.0', versionsuffix), + ('vsc-mympirun', '3.4.3', versionsuffix), +] + +use_easy_install = True +zipped_egg = True + +options = {'modulename': 'hod'} + +sanity_check_commands = [('hod', '--help'), ('hod', 'dists')] + +moduleclass = 'tools' -- GitLab From ee456a43f1d3f473ea3dcd590add6e5b5193aecc Mon Sep 17 00:00:00 2001 From: iotaka Date: Mon, 8 May 2017 11:04:19 +0200 Subject: [PATCH 0704/1603] Update OpenFOAM-4.1-foss-2016b.eb --- easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.1-foss-2016b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.1-foss-2016b.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.1-foss-2016b.eb index efc992104f..eea7c1b416 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.1-foss-2016b.eb +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.1-foss-2016b.eb @@ -24,7 +24,7 @@ dependencies = [ ('METIS', '5.1.0'), ('SCOTCH', '6.0.4'), ('CGAL', '4.8.1'), - ('ParaView', '5.1.2', '-mpi'), + ('ParaView', '5.2.0', '-mpi'), ] builddependencies = [ -- GitLab From bd572560993ad8dfd0fba752371b66d459df4116 Mon Sep 17 00:00:00 2001 From: iotaka Date: Mon, 8 May 2017 11:05:32 +0200 Subject: [PATCH 0705/1603] Update ParaView-5.2.0-foss-2016b-mpi.eb --- .../easyconfigs/p/ParaView/ParaView-5.2.0-foss-2016b-mpi.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-5.2.0-foss-2016b-mpi.eb b/easybuild/easyconfigs/p/ParaView/ParaView-5.2.0-foss-2016b-mpi.eb index 5dd45f28db..d4515369c6 100644 --- a/easybuild/easyconfigs/p/ParaView/ParaView-5.2.0-foss-2016b-mpi.eb +++ b/easybuild/easyconfigs/p/ParaView/ParaView-5.2.0-foss-2016b-mpi.eb @@ -33,6 +33,7 @@ configopts += '-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include -DOPENGL_gl_LIBRARY=$EBR configopts += '-DOSMESA_INCLUDE_DIR=$EBROOTMESA/include -DOSMESA_LIBRARY=$EBROOTMESA/lib/libOSMesa.%s ' % SHLIB_EXT configopts += '-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s ' % SHLIB_EXT configopts += '-DVTK_USE_SYSTEM_HDF5=ON -DPARAVIEW_ENABLE_PYTHON=ON -DBUILD_SHARED_LIBS=ON ' +configopts += '-DPARAVIEW_QT_VERSION=4 -DQT_QMAKE_EXECUTABLE=$EBROOTQT/bin/qmake ' # if you want to build server only Paraview, uncomment the following line: # configopts += '-DVTK_USE_X=OFF ' -- GitLab From acb79d1e16b4eb7312bbda5353605e53a86bd33c Mon Sep 17 00:00:00 2001 From: Damian Alvarez Date: Mon, 8 May 2017 12:00:47 +0200 Subject: [PATCH 0706/1603] Added tbb open source and numactl as dependencies for memkind --- .../m/memkind/memkind-1.5.0-GCCcore-5.4.0.eb | 11 +++++++---- .../t/tbb/tbb-2017_U5-GCCcore-5.4.0.eb | 17 +++++++++++++++++ 2 files changed, 24 insertions(+), 4 deletions(-) create mode 100644 easybuild/easyconfigs/t/tbb/tbb-2017_U5-GCCcore-5.4.0.eb diff --git a/easybuild/easyconfigs/m/memkind/memkind-1.5.0-GCCcore-5.4.0.eb b/easybuild/easyconfigs/m/memkind/memkind-1.5.0-GCCcore-5.4.0.eb index 5522bebb7b..6a31d17221 100644 --- a/easybuild/easyconfigs/m/memkind/memkind-1.5.0-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/m/memkind/memkind-1.5.0-GCCcore-5.4.0.eb @@ -21,12 +21,15 @@ builddependencies = [ ] dependencies = [ - ('tbb', '2017.4.174', '', True), # optional, to enable the tbb heap manager + ('tbb', '2017_U5'), # optional, to enable the tbb heap manager + ('numactl', '2.0.11') ] -# This can be also an EB dependency, but seems unnecesary -osdependencies = [('numactl-devel', 'libnuma-devel ')] - preconfigopts = './build_jemalloc.sh && ./autogen.sh && ' +sanity_check_paths = { + 'files': ["include/memkind.h", "lib/libmemkind.%s" % SHLIB_EXT], + 'dirs': [], +} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/tbb/tbb-2017_U5-GCCcore-5.4.0.eb b/easybuild/easyconfigs/t/tbb/tbb-2017_U5-GCCcore-5.4.0.eb new file mode 100644 index 0000000000..0e4e8f19f1 --- /dev/null +++ b/easybuild/easyconfigs/t/tbb/tbb-2017_U5-GCCcore-5.4.0.eb @@ -0,0 +1,17 @@ +name = 'tbb' +version = '2017_U5' + +homepage = 'https://01.org/tbb/' +description = """Intel(R) Threading Building Blocks (Intel(R) TBB) lets you easily write parallel C++ programs that + take full advantage of multicore performance, that are portable, composable and have future-proof scalability.""" + +toolchain = {'name': 'GCCcore', 'version': '5.4.0'} + +source_urls = ['https://github.com/01org/tbb/archive/'] +sources = ['%(version)s.tar.gz'] + +builddependencies = [ + ('binutils', '2.26') +] + +moduleclass = 'lib' -- GitLab From 3afbfc7bec4adf121f4e597a3f3d5e2a69d2b449 Mon Sep 17 00:00:00 2001 From: "\"Andreas \"" Date: Tue, 9 May 2017 09:28:23 +0200 Subject: [PATCH 0707/1603] updated --- .../easyconfigs/m/METIS/METIS-5.1.0-foss-2017a.eb | 4 ++++ .../SuiteSparse-4.5.5-foss-2017a-METIS-5.1.0.eb | 10 ++++++---- .../SuiteSparse-4.5.5-foss-2017a-ParMETIS-4.0.3.eb | 9 +++++---- 3 files changed, 15 insertions(+), 8 deletions(-) mode change 100755 => 100644 easybuild/easyconfigs/m/METIS/METIS-5.1.0-foss-2017a.eb mode change 100755 => 100644 easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.5-foss-2017a-METIS-5.1.0.eb diff --git a/easybuild/easyconfigs/m/METIS/METIS-5.1.0-foss-2017a.eb b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-foss-2017a.eb old mode 100755 new mode 100644 index 03a730e5cc..24c6a9c29a --- a/easybuild/easyconfigs/m/METIS/METIS-5.1.0-foss-2017a.eb +++ b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-foss-2017a.eb @@ -15,8 +15,12 @@ source_urls = [ 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/OLD', ] +#We use 32bit for indices and 64bit for content +patches = ['METIS-5.1.0-use-doubles.path'] + builddependencies = [('CMake', '3.8.0')] configopts = ['', 'shared=1'] moduleclass = 'math' + diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.5-foss-2017a-METIS-5.1.0.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.5-foss-2017a-METIS-5.1.0.eb old mode 100755 new mode 100644 index a66251bb0f..ac3303de2d --- a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.5-foss-2017a-METIS-5.1.0.eb +++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.5-foss-2017a-METIS-5.1.0.eb @@ -1,19 +1,21 @@ name = 'SuiteSparse' version = '4.5.5' -metis_ver = '5.1.0' -versionsuffix = '-METIS-%s' % metis_ver homepage = 'http://faculty.cse.tamu.edu/davis/suitesparse.html' description = """SuiteSparse is a collection of libraries manipulate sparse matrices.""" toolchain = {'name': 'foss', 'version': '2017a'} -toolchainopts = {'opt': True, 'unroll': True, 'pic': True} +toolchainopts = {'unroll': True, 'pic': True} source_urls = ['http://faculty.cse.tamu.edu/davis/SuiteSparse/'] sources = [SOURCE_TAR_GZ] -dependencies = [('METIS', metis_ver)] +metis = 'METIS' +metis_ver = '5.1.0' +versionsuffix = '-%s-%s' % (metis, metis_ver) +dependencies = [(metis, metis_ver)] maxparallel = 1 moduleclass = 'numlib' + diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.5-foss-2017a-ParMETIS-4.0.3.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.5-foss-2017a-ParMETIS-4.0.3.eb index 7c7dff3356..a24c57563a 100755 --- a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.5-foss-2017a-ParMETIS-4.0.3.eb +++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.5-foss-2017a-ParMETIS-4.0.3.eb @@ -1,18 +1,19 @@ name = 'SuiteSparse' version = '4.5.5' -parmetis_ver = '4.0.3' -versionsuffix = '-ParMETIS-%s' % parmetis_ver homepage = 'http://faculty.cse.tamu.edu/davis/suitesparse.html' description = """SuiteSparse is a collection of libraries manipulate sparse matrices.""" toolchain = {'name': 'foss', 'version': '2017a'} -toolchainopts = {'opt': True, 'unroll': True, 'pic': True} +toolchainopts = {'unroll': True, 'pic': True} source_urls = ['http://faculty.cse.tamu.edu/davis/SuiteSparse/'] sources = [SOURCE_TAR_GZ] -dependencies = [('ParMETIS', parmetis_ver)] +parmetis = 'ParMETIS' +parmetis_ver = '4.0.3' +versionsuffix = '-%s-%s' % (parmetis, parmetis_ver) +dependencies = [(parmetis, parmetis_ver)] maxparallel = 1 -- GitLab From a171247892a0d7a9b2082a7f6cd472ff99d74b8c Mon Sep 17 00:00:00 2001 From: iotaka Date: Tue, 9 May 2017 09:40:54 +0200 Subject: [PATCH 0708/1603] missing files --- .../libpciaccess-0.13.1-goolf-1.4.10.eb | 4 +--- .../libpciaccess-0.13.1-ictce-4.0.6.eb | 24 +++++++++++++++++++ .../libpciaccess-0.13.1-ictce-4.1.13.eb | 24 +++++++++++++++++++ .../libpciaccess-0.13.1-ictce-5.3.0.eb | 4 +--- .../libpciaccess-0.13.1-ictce-5.5.0.eb | 4 +--- .../libpciaccess-0.13.1-intel-2015a.eb | 4 +--- .../libpciaccess-0.13.3-intel-2015a.eb | 4 +--- .../libpciaccess-0.13.4-gimkl-2.11.5.eb | 4 +--- .../libpciaccess-0.13.4-intel-2015b.eb | 4 +--- .../libpciaccess-0.13.4-intel-2016a.eb | 4 +--- 10 files changed, 56 insertions(+), 24 deletions(-) create mode 100644 easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-ictce-4.0.6.eb create mode 100644 easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-ictce-4.1.13.eb diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-goolf-1.4.10.eb index 437954d342..9371a19f2d 100644 --- a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-goolf-1.4.10.eb @@ -6,7 +6,7 @@ version = '0.13.1' homepage = 'http://cgit.freedesktop.org/xorg/lib/libpciaccess/' description = """Generic PCI access library.""" -source_urls = ['http://cgit.freedesktop.org/xorg/lib/libpciaccess/snapshot'] +source_urls = ['https://www.x.org/releases/individual/lib/'] sources = [SOURCE_TAR_GZ] toolchain = {'name': 'goolf', 'version': '1.4.10'} @@ -16,8 +16,6 @@ builddependencies = [ ('xorg-macros', '1.17'), ] -preconfigopts = "env ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " - sanity_check_paths = { 'files': ['include/pciaccess.h', 'lib/libpciaccess.a'], 'dirs': ['lib/pkgconfig'], diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-ictce-4.0.6.eb b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-ictce-4.0.6.eb new file mode 100644 index 0000000000..adbb940942 --- /dev/null +++ b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-ictce-4.0.6.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'libpciaccess' +version = '0.13.1' + +homepage = 'http://cgit.freedesktop.org/xorg/lib/libpciaccess/' +description = """Generic PCI access library.""" + +source_urls = ['https://www.x.org/releases/individual/lib/'] +sources = [SOURCE_TAR_GZ] + +toolchain = {'name': 'ictce', 'version': '4.0.6'} + +builddependencies = [ + ('Autoconf', '2.69'), + ('xorg-macros', '1.17'), +] + +sanity_check_paths = { + 'files': ['include/pciaccess.h', 'lib/libpciaccess.a'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-ictce-4.1.13.eb b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-ictce-4.1.13.eb new file mode 100644 index 0000000000..67891759ae --- /dev/null +++ b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-ictce-4.1.13.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'libpciaccess' +version = '0.13.1' + +homepage = 'http://cgit.freedesktop.org/xorg/lib/libpciaccess/' +description = """Generic PCI access library.""" + +source_urls = ['https://www.x.org/releases/individual/lib/'] +sources = [SOURCE_TAR_GZ] + +toolchain = {'name': 'ictce', 'version': '4.1.13'} + +builddependencies = [ + ('Autoconf', '2.69'), + ('xorg-macros', '1.17'), +] + +sanity_check_paths = { + 'files': ['include/pciaccess.h', 'lib/libpciaccess.a'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-ictce-5.3.0.eb index 834a292992..cbc3f1b46c 100644 --- a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-ictce-5.3.0.eb @@ -6,7 +6,7 @@ version = '0.13.1' homepage = 'http://cgit.freedesktop.org/xorg/lib/libpciaccess/' description = """Generic PCI access library.""" -source_urls = ['http://cgit.freedesktop.org/xorg/lib/libpciaccess/snapshot'] +source_urls = ['https://www.x.org/releases/individual/lib/'] sources = [SOURCE_TAR_GZ] toolchain = {'name': 'ictce', 'version': '5.3.0'} @@ -16,8 +16,6 @@ builddependencies = [ ('xorg-macros', '1.17'), ] -preconfigopts = "env ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " - sanity_check_paths = { 'files': ['include/pciaccess.h', 'lib/libpciaccess.a'], 'dirs': ['lib/pkgconfig'], diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-ictce-5.5.0.eb b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-ictce-5.5.0.eb index c3e51b6854..1abedab086 100644 --- a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-ictce-5.5.0.eb @@ -6,7 +6,7 @@ version = '0.13.1' homepage = 'http://cgit.freedesktop.org/xorg/lib/libpciaccess/' description = """Generic PCI access library.""" -source_urls = ['http://cgit.freedesktop.org/xorg/lib/libpciaccess/snapshot'] +source_urls = ['https://www.x.org/releases/individual/lib/'] sources = [SOURCE_TAR_GZ] toolchain = {'name': 'ictce', 'version': '5.5.0'} @@ -16,8 +16,6 @@ builddependencies = [ ('xorg-macros', '1.17'), ] -preconfigopts = "env ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " - sanity_check_paths = { 'files': ['include/pciaccess.h', 'lib/libpciaccess.a'], 'dirs': ['lib/pkgconfig'], diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-intel-2015a.eb b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-intel-2015a.eb index 8f259d339a..8970daab0a 100644 --- a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-intel-2015a.eb +++ b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-intel-2015a.eb @@ -6,7 +6,7 @@ version = '0.13.1' homepage = 'http://cgit.freedesktop.org/xorg/lib/libpciaccess/' description = """Generic PCI access library.""" -source_urls = ['http://cgit.freedesktop.org/xorg/lib/libpciaccess/snapshot'] +source_urls = ['https://www.x.org/releases/individual/lib/'] sources = [SOURCE_TAR_GZ] toolchain = {'name': 'intel', 'version': '2015a'} @@ -16,8 +16,6 @@ builddependencies = [ ('xorg-macros', '1.17'), ] -preconfigopts = "env ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " - sanity_check_paths = { 'files': ['include/pciaccess.h', 'lib/libpciaccess.a'], 'dirs': ['lib/pkgconfig'], diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.3-intel-2015a.eb b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.3-intel-2015a.eb index 5f22d77a36..a36467cdf5 100644 --- a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.3-intel-2015a.eb +++ b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.3-intel-2015a.eb @@ -6,7 +6,7 @@ version = '0.13.3' homepage = 'http://cgit.freedesktop.org/xorg/lib/libpciaccess/' description = """Generic PCI access library.""" -source_urls = ['http://cgit.freedesktop.org/xorg/lib/libpciaccess/snapshot'] +source_urls = ['https://www.x.org/releases/individual/lib/'] sources = [SOURCE_TAR_GZ] toolchain = {'name': 'intel', 'version': '2015a'} @@ -16,8 +16,6 @@ builddependencies = [ ('xorg-macros', '1.19.0'), ] -preconfigopts = "env ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " - sanity_check_paths = { 'files': ['include/pciaccess.h', 'lib/libpciaccess.a'], 'dirs': ['lib/pkgconfig'], diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-gimkl-2.11.5.eb b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-gimkl-2.11.5.eb index ea05edcced..449c59f9bf 100644 --- a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-gimkl-2.11.5.eb @@ -6,7 +6,7 @@ version = '0.13.4' homepage = 'http://cgit.freedesktop.org/xorg/lib/libpciaccess/' description = """Generic PCI access library.""" -source_urls = ['http://cgit.freedesktop.org/xorg/lib/libpciaccess/snapshot'] +source_urls = ['https://www.x.org/releases/individual/lib/'] sources = [SOURCE_TAR_GZ] toolchain = {'name': 'gimkl', 'version': '2.11.5'} @@ -16,8 +16,6 @@ builddependencies = [ ('xorg-macros', '1.19.0'), ] -preconfigopts = "env ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " - sanity_check_paths = { 'files': ['include/pciaccess.h', 'lib/libpciaccess.a'], 'dirs': ['lib/pkgconfig'], diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-intel-2015b.eb b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-intel-2015b.eb index 1af83efe66..fd0fe49af5 100644 --- a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-intel-2015b.eb +++ b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-intel-2015b.eb @@ -6,7 +6,7 @@ version = '0.13.4' homepage = 'http://cgit.freedesktop.org/xorg/lib/libpciaccess/' description = """Generic PCI access library.""" -source_urls = ['http://cgit.freedesktop.org/xorg/lib/libpciaccess/snapshot'] +source_urls = ['https://www.x.org/releases/individual/lib/'] sources = [SOURCE_TAR_GZ] toolchain = {'name': 'intel', 'version': '2015b'} @@ -16,8 +16,6 @@ builddependencies = [ ('xorg-macros', '1.19.0'), ] -preconfigopts = "env ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " - sanity_check_paths = { 'files': ['include/pciaccess.h', 'lib/libpciaccess.a'], 'dirs': ['lib/pkgconfig'], diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-intel-2016a.eb b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-intel-2016a.eb index c0a23d9702..69a705ef82 100644 --- a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-intel-2016a.eb @@ -6,7 +6,7 @@ version = '0.13.4' homepage = 'http://cgit.freedesktop.org/xorg/lib/libpciaccess/' description = """Generic PCI access library.""" -source_urls = ['http://cgit.freedesktop.org/xorg/lib/libpciaccess/snapshot'] +source_urls = ['https://www.x.org/releases/individual/lib/'] sources = [SOURCE_TAR_GZ] toolchain = {'name': 'intel', 'version': '2016a'} @@ -16,8 +16,6 @@ builddependencies = [ ('xorg-macros', '1.19.0'), ] -preconfigopts = "env ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " - sanity_check_paths = { 'files': ['include/pciaccess.h', 'lib/libpciaccess.a'], 'dirs': ['lib/pkgconfig'], -- GitLab From c22ad8a61d53d5c2f32a5f02e6744227475d3416 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 9 May 2017 09:46:50 +0200 Subject: [PATCH 0709/1603] don't re-add archived libpciaccess easyconfigs --- .../libpciaccess-0.13.1-ictce-4.0.6.eb | 24 ------------------- .../libpciaccess-0.13.1-ictce-4.1.13.eb | 24 ------------------- 2 files changed, 48 deletions(-) delete mode 100644 easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-ictce-4.0.6.eb delete mode 100644 easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-ictce-4.1.13.eb diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-ictce-4.0.6.eb b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-ictce-4.0.6.eb deleted file mode 100644 index adbb940942..0000000000 --- a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-ictce-4.0.6.eb +++ /dev/null @@ -1,24 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'libpciaccess' -version = '0.13.1' - -homepage = 'http://cgit.freedesktop.org/xorg/lib/libpciaccess/' -description = """Generic PCI access library.""" - -source_urls = ['https://www.x.org/releases/individual/lib/'] -sources = [SOURCE_TAR_GZ] - -toolchain = {'name': 'ictce', 'version': '4.0.6'} - -builddependencies = [ - ('Autoconf', '2.69'), - ('xorg-macros', '1.17'), -] - -sanity_check_paths = { - 'files': ['include/pciaccess.h', 'lib/libpciaccess.a'], - 'dirs': ['lib/pkgconfig'], -} - -moduleclass = 'system' diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-ictce-4.1.13.eb b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-ictce-4.1.13.eb deleted file mode 100644 index 67891759ae..0000000000 --- a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-ictce-4.1.13.eb +++ /dev/null @@ -1,24 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'libpciaccess' -version = '0.13.1' - -homepage = 'http://cgit.freedesktop.org/xorg/lib/libpciaccess/' -description = """Generic PCI access library.""" - -source_urls = ['https://www.x.org/releases/individual/lib/'] -sources = [SOURCE_TAR_GZ] - -toolchain = {'name': 'ictce', 'version': '4.1.13'} - -builddependencies = [ - ('Autoconf', '2.69'), - ('xorg-macros', '1.17'), -] - -sanity_check_paths = { - 'files': ['include/pciaccess.h', 'lib/libpciaccess.a'], - 'dirs': ['lib/pkgconfig'], -} - -moduleclass = 'system' -- GitLab From 44b396a0cef6d3a4c19f55157e03ab3932b184bc Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 9 May 2017 09:48:20 +0200 Subject: [PATCH 0710/1603] consistent update of libpciaccess source URLs --- .../l/libpciaccess/libpciaccess-0.13.1-GCC-4.7.2.eb | 4 +--- .../l/libpciaccess/libpciaccess-0.13.4-foss-2016b.eb | 4 +--- .../l/libpciaccess/libpciaccess-0.13.4-intel-2016b.eb | 4 +--- 3 files changed, 3 insertions(+), 9 deletions(-) diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-GCC-4.7.2.eb b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-GCC-4.7.2.eb index 01c9c7b5d7..9967c64c68 100644 --- a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-GCC-4.7.2.eb +++ b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-GCC-4.7.2.eb @@ -6,7 +6,7 @@ version = '0.13.1' homepage = 'http://cgit.freedesktop.org/xorg/lib/libpciaccess/' description = """Generic PCI access library.""" -source_urls = ['http://cgit.freedesktop.org/xorg/lib/libpciaccess/snapshot'] +source_urls = ['https://www.x.org/releases/individual/lib/'] sources = [SOURCE_TAR_GZ] toolchain = {'name': 'GCC', 'version': '4.7.2'} @@ -16,8 +16,6 @@ builddependencies = [ ('xorg-macros', '1.17'), ] -preconfigopts = "env ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " - sanity_check_paths = { 'files': ['include/pciaccess.h', 'lib/libpciaccess.a'], 'dirs': ['lib/pkgconfig'], diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-foss-2016b.eb b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-foss-2016b.eb index 11ed8ea67d..76bd735f5a 100755 --- a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-foss-2016b.eb +++ b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-foss-2016b.eb @@ -6,7 +6,7 @@ version = '0.13.4' homepage = 'http://cgit.freedesktop.org/xorg/lib/libpciaccess/' description = """Generic PCI access library.""" -source_urls = ['http://cgit.freedesktop.org/xorg/lib/libpciaccess/snapshot'] +source_urls = ['https://www.x.org/releases/individual/lib/'] sources = [SOURCE_TAR_GZ] toolchain = {'name': 'foss', 'version': '2016b'} @@ -16,8 +16,6 @@ builddependencies = [ ('xorg-macros', '1.19.0'), ] -preconfigopts = "env ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " - sanity_check_paths = { 'files': ['include/pciaccess.h', 'lib/libpciaccess.a'], 'dirs': ['lib/pkgconfig'], diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-intel-2016b.eb b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-intel-2016b.eb index 9124b553ab..de4d55b188 100755 --- a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-intel-2016b.eb +++ b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-intel-2016b.eb @@ -6,7 +6,7 @@ version = '0.13.4' homepage = 'http://cgit.freedesktop.org/xorg/lib/libpciaccess/' description = """Generic PCI access library.""" -source_urls = ['http://cgit.freedesktop.org/xorg/lib/libpciaccess/snapshot'] +source_urls = ['https://www.x.org/releases/individual/lib/'] sources = [SOURCE_TAR_GZ] toolchain = {'name': 'intel', 'version': '2016b'} @@ -16,8 +16,6 @@ builddependencies = [ ('xorg-macros', '1.19.0'), ] -preconfigopts = "env ACLOCAL='aclocal -I $EBROOTXORGMINMACROS/share/aclocal' ./autogen.sh && " - sanity_check_paths = { 'files': ['include/pciaccess.h', 'lib/libpciaccess.a'], 'dirs': ['lib/pkgconfig'], -- GitLab From 3a215d2301ab7fa13a66b9899a3f3e02038d4413 Mon Sep 17 00:00:00 2001 From: iotaka Date: Tue, 9 May 2017 09:49:24 +0200 Subject: [PATCH 0711/1603] Update METIS-5.1.0-foss-2016a.eb --- easybuild/easyconfigs/m/METIS/METIS-5.1.0-foss-2016a.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/m/METIS/METIS-5.1.0-foss-2016a.eb b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-foss-2016a.eb index 2b65f31212..728e632fc1 100644 --- a/easybuild/easyconfigs/m/METIS/METIS-5.1.0-foss-2016a.eb +++ b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-foss-2016a.eb @@ -15,6 +15,9 @@ source_urls = [ 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/OLD', ] +# We use 32bit for indices and 64bit for content +patches = ['METIS-5.1.0-use-doubles.patch'] + builddependencies = [('CMake', '3.4.3')] configopts = ['', 'shared=1'] -- GitLab From 5e3ebe055d256bd61a2683a4843ab65f80687aea Mon Sep 17 00:00:00 2001 From: "\"Andreas \"" Date: Tue, 9 May 2017 09:59:39 +0200 Subject: [PATCH 0712/1603] updated usempi --- easybuild/easyconfigs/n/NAMD/NAMD-2.12-foss-2017a-mpi.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/NAMD/NAMD-2.12-foss-2017a-mpi.eb b/easybuild/easyconfigs/n/NAMD/NAMD-2.12-foss-2017a-mpi.eb index 6dd67416d3..b1ee1a4af9 100644 --- a/easybuild/easyconfigs/n/NAMD/NAMD-2.12-foss-2017a-mpi.eb +++ b/easybuild/easyconfigs/n/NAMD/NAMD-2.12-foss-2017a-mpi.eb @@ -7,7 +7,7 @@ description = """NAMD is a parallel molecular dynamics code designed for high-pe large biomolecular systems.""" toolchain = {'name': 'foss', 'version': '2017a'} -toolchainopts = {'opt': True, 'pic': True} +toolchainopts = {'usempi': True, 'pic': True} sources = ['NAMD_%(version)s_Source.tar.gz'] @@ -22,3 +22,4 @@ charm_arch = "mpi-linux-x86_64" moduleclass = 'chem' + -- GitLab From ed733c7284cfedc210d707cdf4990d9ea3ff7fa7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 9 May 2017 10:34:00 +0200 Subject: [PATCH 0713/1603] adding easyconfigs: xarray-0.9.5-intel-2017a-Python-3.6.1.eb --- .../xarray-0.9.5-intel-2017a-Python-3.6.1.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/x/xarray/xarray-0.9.5-intel-2017a-Python-3.6.1.eb diff --git a/easybuild/easyconfigs/x/xarray/xarray-0.9.5-intel-2017a-Python-3.6.1.eb b/easybuild/easyconfigs/x/xarray/xarray-0.9.5-intel-2017a-Python-3.6.1.eb new file mode 100644 index 0000000000..aba02b5499 --- /dev/null +++ b/easybuild/easyconfigs/x/xarray/xarray-0.9.5-intel-2017a-Python-3.6.1.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'xarray' +version = '0.9.5' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/pydata/xarray' +description = """xarray (formerly xray) is an open source project and Python package that aims to bring + the labeled data power of pandas to the physical sciences, by providing N-dimensional variants of the + core pandas data structures.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [('Python', '3.6.1')] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'data' -- GitLab From 1721278ce3b16a5e15f737939f20588ea7dbcf64 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 9 May 2017 11:02:07 +0200 Subject: [PATCH 0714/1603] adding easyconfigs: CMake-3.8.1-GCCcore-6.3.0.eb --- .../c/CMake/CMake-3.8.1-GCCcore-6.3.0.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.8.1-GCCcore-6.3.0.eb diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.8.1-GCCcore-6.3.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.8.1-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..4eddbf2181 --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.8.1-GCCcore-6.3.0.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.8.1' + +homepage = 'http://www.cmake.org' +description = """CMake, the cross-platform, open-source build system. + CMake is a family of tools designed to build, test and package software.""" + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' + +builddependencies = [ + ('binutils', '2.27'), +] + + +dependencies = [ + ('ncurses', '6.0'), + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.1.0c'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From 6493fbb9d6c7df667f875b49dbf17d1b72f4ce8c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 9 May 2017 11:23:56 +0200 Subject: [PATCH 0715/1603] adding easyconfigs: googletest-1.8.0-intel-2017a.eb --- .../googletest-1.8.0-intel-2017a.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/g/googletest/googletest-1.8.0-intel-2017a.eb diff --git a/easybuild/easyconfigs/g/googletest/googletest-1.8.0-intel-2017a.eb b/easybuild/easyconfigs/g/googletest/googletest-1.8.0-intel-2017a.eb new file mode 100644 index 0000000000..c0c3624868 --- /dev/null +++ b/easybuild/easyconfigs/g/googletest/googletest-1.8.0-intel-2017a.eb @@ -0,0 +1,23 @@ +easyblock = 'CMakeMake' + +name = 'googletest' +version = '1.8.0' + +homepage = 'https://github.com/google/googletest' +description = "Google's C++ test framework" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['https://github.com/google/googletest/archive/'] +sources = ['release-%(version)s.tar.gz'] + +builddependencies = [('CMake', '3.8.1')] + +separate_build_dir = True + +sanity_check_paths = { + 'files': ['lib/libgmock.a', 'lib/libgmock_main.a', 'lib/libgtest.a', 'lib/libgtest_main.a'], + 'dirs': ['include/gmock', 'include/gtest'], +} + +moduleclass = 'tools' -- GitLab From cfb7d78f7f0e3039c1c367608fcf6e6527c5ff12 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 9 May 2017 11:30:33 +0200 Subject: [PATCH 0716/1603] use GCCcore/6.3.0 toolchain for googletest --- ....0-intel-2017a.eb => googletest-1.8.0-GCCcore-6.3.0.eb} | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/g/googletest/{googletest-1.8.0-intel-2017a.eb => googletest-1.8.0-GCCcore-6.3.0.eb} (79%) diff --git a/easybuild/easyconfigs/g/googletest/googletest-1.8.0-intel-2017a.eb b/easybuild/easyconfigs/g/googletest/googletest-1.8.0-GCCcore-6.3.0.eb similarity index 79% rename from easybuild/easyconfigs/g/googletest/googletest-1.8.0-intel-2017a.eb rename to easybuild/easyconfigs/g/googletest/googletest-1.8.0-GCCcore-6.3.0.eb index c0c3624868..a63352bc58 100644 --- a/easybuild/easyconfigs/g/googletest/googletest-1.8.0-intel-2017a.eb +++ b/easybuild/easyconfigs/g/googletest/googletest-1.8.0-GCCcore-6.3.0.eb @@ -6,12 +6,15 @@ version = '1.8.0' homepage = 'https://github.com/google/googletest' description = "Google's C++ test framework" -toolchain = {'name': 'intel', 'version': '2017a'} +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} source_urls = ['https://github.com/google/googletest/archive/'] sources = ['release-%(version)s.tar.gz'] -builddependencies = [('CMake', '3.8.1')] +builddependencies = [ + ('binutils', '2.27'), + ('CMake', '3.8.1'), +] separate_build_dir = True -- GitLab From 699236a4da05466e1bf6767f266408f08c5ee8b2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 9 May 2017 12:43:20 +0200 Subject: [PATCH 0717/1603] adding easyconfigs: HDF5-1.10.1-intel-2017a.eb --- .../h/HDF5/HDF5-1.10.1-intel-2017a.eb | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.10.1-intel-2017a.eb diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.10.1-intel-2017a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.1-intel-2017a.eb new file mode 100644 index 0000000000..d72f14fe00 --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.1-intel-2017a.eb @@ -0,0 +1,22 @@ +name = 'HDF5' +version = '1.10.1' + +homepage = 'http://www.hdfgroup.org/HDF5/' +description = """HDF5 is a unique technology suite that makes possible the management of + extremely large and complex data collections.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['43a2f9466702fb1db31df98ae6677f15'] + +buildopts = 'CXXFLAGS="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK"' + +dependencies = [ + ('zlib', '1.2.11'), + ('Szip', '2.1'), +] + +moduleclass = 'data' -- GitLab From a7bf4c610f903ff28228d6b7ae027f8dea70ac93 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 9 May 2017 16:18:19 +0200 Subject: [PATCH 0718/1603] adding easyconfigs: Keras-2.0.4-intel-2017a-Python-3.6.1.eb, Theano-0.9.0-intel-2017a-Python-3.6.1.eb, h5py-2.7.0-intel-2017a-Python-3.6.1.eb, PyYAML-3.12-intel-2017a-Python-3.6.1.eb, pkgconfig-1.2.2-intel-2017a-Python-3.6.1.eb, nose-parameterized-0.6.0-intel-2017a-Python-3.6.1.eb --- .../h5py-2.7.0-intel-2017a-Python-3.6.1.eb | 32 +++++++++++++++++++ .../Keras-2.0.4-intel-2017a-Python-3.6.1.eb | 28 ++++++++++++++++ ...eterized-0.6.0-intel-2017a-Python-3.6.1.eb | 24 ++++++++++++++ .../PyYAML-3.12-intel-2017a-Python-3.6.1.eb | 27 ++++++++++++++++ ...kgconfig-1.2.2-intel-2017a-Python-3.6.1.eb | 26 +++++++++++++++ .../Theano-0.9.0-intel-2017a-Python-3.6.1.eb | 23 +++++++++++++ 6 files changed, 160 insertions(+) create mode 100644 easybuild/easyconfigs/h/h5py/h5py-2.7.0-intel-2017a-Python-3.6.1.eb create mode 100644 easybuild/easyconfigs/k/Keras/Keras-2.0.4-intel-2017a-Python-3.6.1.eb create mode 100644 easybuild/easyconfigs/n/nose-parameterized/nose-parameterized-0.6.0-intel-2017a-Python-3.6.1.eb create mode 100644 easybuild/easyconfigs/p/PyYAML/PyYAML-3.12-intel-2017a-Python-3.6.1.eb create mode 100644 easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.2.2-intel-2017a-Python-3.6.1.eb create mode 100644 easybuild/easyconfigs/t/Theano/Theano-0.9.0-intel-2017a-Python-3.6.1.eb diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.7.0-intel-2017a-Python-3.6.1.eb b/easybuild/easyconfigs/h/h5py/h5py-2.7.0-intel-2017a-Python-3.6.1.eb new file mode 100644 index 0000000000..b00f2d835b --- /dev/null +++ b/easybuild/easyconfigs/h/h5py/h5py-2.7.0-intel-2017a-Python-3.6.1.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonPackage' + +name = 'h5py' +version = '2.7.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.h5py.org/' +description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, + version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous + amounts of data.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'usempi': True} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +# to really use mpi enabled hdf5 we now seem to need a configure step +prebuildopts = ' python setup.py configure --mpi --hdf5=$EBROOTHDF5 && ' + +dependencies = [ + ('Python', '3.6.1'), + ('HDF5', '1.10.1'), + ('pkgconfig', '1.2.2', '-Python-%(pyver)s'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/k/Keras/Keras-2.0.4-intel-2017a-Python-3.6.1.eb b/easybuild/easyconfigs/k/Keras/Keras-2.0.4-intel-2017a-Python-3.6.1.eb new file mode 100644 index 0000000000..45f0be1e64 --- /dev/null +++ b/easybuild/easyconfigs/k/Keras/Keras-2.0.4-intel-2017a-Python-3.6.1.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'Keras' +version = '2.0.4' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://keras.io/' +description = """Keras is a minimalist, highly modular neural networks library, written in Python and +capable of running on top of either TensorFlow or Theano.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '3.6.1'), + ('Theano', '0.9.0', versionsuffix), + ('h5py', '2.7.0', '%(versionsuffix)s'), + ('PyYAML', '3.12', versionsuffix), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/n/nose-parameterized/nose-parameterized-0.6.0-intel-2017a-Python-3.6.1.eb b/easybuild/easyconfigs/n/nose-parameterized/nose-parameterized-0.6.0-intel-2017a-Python-3.6.1.eb new file mode 100644 index 0000000000..7877603edb --- /dev/null +++ b/easybuild/easyconfigs/n/nose-parameterized/nose-parameterized-0.6.0-intel-2017a-Python-3.6.1.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'nose-parameterized' +version = '0.6.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'hmat://github.com/wolever/nose-parameterized' +description = """Parameterized testing with any Python test framework.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [('Python', '3.6.1')] + +options = {'modulename': 'nose_parameterized'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12-intel-2017a-Python-3.6.1.eb b/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12-intel-2017a-Python-3.6.1.eb new file mode 100644 index 0000000000..6ad31707a9 --- /dev/null +++ b/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12-intel-2017a-Python-3.6.1.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'PyYAML' +version = '3.12' +versionsuffix = '-Python-%(pyver)s' + +homepage = "https://pypi.python.org/pypi/PyYAML/" +description = """PyYAML is a YAML parser and emitter for the Python programming language.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '3.6.1'), + ('libyaml', '0.1.7', '', True), +] + +options = {'modulename': 'yaml'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.2.2-intel-2017a-Python-3.6.1.eb b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.2.2-intel-2017a-Python-3.6.1.eb new file mode 100644 index 0000000000..5b31de03c1 --- /dev/null +++ b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.2.2-intel-2017a-Python-3.6.1.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'pkgconfig' +version = '1.2.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://github.com/matze/pkgconfig' +description = """pkgconfig is a Python module to interface with the pkg-config command line tool""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'usempi': True} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '3.6.1'), + ('pkg-config', '0.29.2'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/t/Theano/Theano-0.9.0-intel-2017a-Python-3.6.1.eb b/easybuild/easyconfigs/t/Theano/Theano-0.9.0-intel-2017a-Python-3.6.1.eb new file mode 100644 index 0000000000..3bd29d9876 --- /dev/null +++ b/easybuild/easyconfigs/t/Theano/Theano-0.9.0-intel-2017a-Python-3.6.1.eb @@ -0,0 +1,23 @@ +easyblock = 'PythonPackage' + +name = 'Theano' +version = '0.9.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://deeplearning.net/software/theano' +description = """Theano is a Python library that allows you to define, optimize, +and evaluate mathematical expressions involving multi-dimensional arrays efficiently.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [('Python', '3.6.1')] + +sanity_check_paths = { + 'files': ['bin/theano-cache', 'bin/theano-nose'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'math' -- GitLab From 0b5e6f8788f525168634c28e81bb9ac25fe17f7d Mon Sep 17 00:00:00 2001 From: jrbosch Date: Tue, 9 May 2017 14:00:18 -0400 Subject: [PATCH 0719/1603] convert to UNIX format --- .../easyconfigs/x/x265/x265-2.4-foss-2016b.eb | 58 +++++++++---------- 1 file changed, 29 insertions(+), 29 deletions(-) diff --git a/easybuild/easyconfigs/x/x265/x265-2.4-foss-2016b.eb b/easybuild/easyconfigs/x/x265/x265-2.4-foss-2016b.eb index d0b1d74b60..1d2f5fec38 100644 --- a/easybuild/easyconfigs/x/x265/x265-2.4-foss-2016b.eb +++ b/easybuild/easyconfigs/x/x265/x265-2.4-foss-2016b.eb @@ -1,29 +1,29 @@ -easyblock = 'CMakeMake' - -name = 'x265' -version = '2.4' - -homepage = 'http://x265.org/' -description = """x265 is a free software library and application for encoding video streams into the H.265 - AVC compression format, and is released under the terms of the GNU GPL.""" - -toolchain = {'name': 'foss', 'version': '2016b'} - -source_urls = [ - 'http://ftp.videolan.org/pub/videolan/x265/', - 'http://download.videolan.org/pub/videolan/x265/', -] -sources = ['%(name)s_%(version)s.tar.gz'] - -dependencies = [('Yasm', '1.3.0')] - -builddependencies = [('CMake', '3.7.2')] - -start_dir = 'source' - -sanity_check_paths = { - 'files': ['bin/x265', 'include/x265_config.h', 'include/x265.h', 'lib/libx265.a', 'lib/libx265.%s' % SHLIB_EXT], - 'dirs': [], -} - -moduleclass = 'vis' +easyblock = 'CMakeMake' + +name = 'x265' +version = '2.4' + +homepage = 'http://x265.org/' +description = """x265 is a free software library and application for encoding video streams into the H.265 + AVC compression format, and is released under the terms of the GNU GPL.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = [ + 'http://ftp.videolan.org/pub/videolan/x265/', + 'http://download.videolan.org/pub/videolan/x265/', +] +sources = ['%(name)s_%(version)s.tar.gz'] + +dependencies = [('Yasm', '1.3.0')] + +builddependencies = [('CMake', '3.7.2')] + +start_dir = 'source' + +sanity_check_paths = { + 'files': ['bin/x265', 'include/x265_config.h', 'include/x265.h', 'lib/libx265.a', 'lib/libx265.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' -- GitLab From 8ab7c872caf82ab348498376928e3b90480fbfc2 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 9 May 2017 21:22:35 +0200 Subject: [PATCH 0720/1603] adding easyconfigs: GROMACS-2016.1-foss-2017a-PLUMED.eb --- .../GROMACS-2016.1-foss-2017a-PLUMED.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-2016.1-foss-2017a-PLUMED.eb diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.1-foss-2017a-PLUMED.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.1-foss-2017a-PLUMED.eb new file mode 100644 index 0000000000..9fc85b8f3e --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.1-foss-2017a-PLUMED.eb @@ -0,0 +1,41 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2016 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, +# Ghent University / The Francis Crick Institute +# Authors:: +# * Wiktor Jurkowski +# * Fotis Georgatos +# * George Tsouloupas +# * Kenneth Hoste +# * Adam Huffman +# License:: MIT/GPL +## + +name = 'GROMACS' +version = '2016.1' +versionsuffix = '-PLUMED' + +homepage = 'http://www.gromacs.org' +description = """ +GROMACS is a versatile package to perform molecular dynamics, + i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. + +This is CPU only build, containing both MPI and threadMPI builds. +""" + +toolchain = {'name': 'foss', 'version': '2017a'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = ['ftp://ftp.gromacs.org/pub/gromacs/'] +sources = [SOURCELOWER_TAR_GZ] + +builddependencies = [ + ('CMake', '3.7.2'), +] + +dependencies = [ + ('PLUMED', '2.3.0'), +] + +moduleclass = 'bio' -- GitLab From 5d359bd43470955903edd5a7cb2e5ae8871d6894 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 10 May 2017 07:24:00 +0800 Subject: [PATCH 0721/1603] adding easyconfigs: Siesta-4.0-intel-2017a.eb, Siesta-4.1-b2-intel-2017a.eb --- .../s/Siesta/Siesta-4.0-intel-2017a.eb | 18 ++++++++++++++++++ .../s/Siesta/Siesta-4.1-b2-intel-2017a.eb | 18 ++++++++++++++++++ 2 files changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/s/Siesta/Siesta-4.0-intel-2017a.eb create mode 100644 easybuild/easyconfigs/s/Siesta/Siesta-4.1-b2-intel-2017a.eb diff --git a/easybuild/easyconfigs/s/Siesta/Siesta-4.0-intel-2017a.eb b/easybuild/easyconfigs/s/Siesta/Siesta-4.0-intel-2017a.eb new file mode 100644 index 0000000000..b92708a1d8 --- /dev/null +++ b/easybuild/easyconfigs/s/Siesta/Siesta-4.0-intel-2017a.eb @@ -0,0 +1,18 @@ +name = 'Siesta' +version = '4.0' + +homepage = 'http://departments.icmab.es/leem/siesta' +description = """SIESTA is both a method and its computer program implementation, to perform efficient electronic + structure calculations and ab initio molecular dynamics simulations of molecules and solids.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'usempi': True} + +sources = [SOURCELOWER_TGZ] +source_urls = ['https://launchpad.net/%(namelower)s/%(version_major_minor)s/%(version)s/+download/'] + +dependencies = [('netCDF-Fortran', '4.4.4')] + +parallel = 1 + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/s/Siesta/Siesta-4.1-b2-intel-2017a.eb b/easybuild/easyconfigs/s/Siesta/Siesta-4.1-b2-intel-2017a.eb new file mode 100644 index 0000000000..5e51c29c8b --- /dev/null +++ b/easybuild/easyconfigs/s/Siesta/Siesta-4.1-b2-intel-2017a.eb @@ -0,0 +1,18 @@ +name = 'Siesta' +version = '4.1-b2' + +homepage = 'http://departments.icmab.es/leem/siesta' +description = """SIESTA is both a method and its computer program implementation, to perform efficient electronic + structure calculations and ab initio molecular dynamics simulations of molecules and solids.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['https://launchpad.net/%(namelower)s/%(version_major)s.1/%(version)s/+download/'] + +dependencies = [('netCDF-Fortran', '4.4.4')] + +parallel = 1 + +moduleclass = 'phys' -- GitLab From 6442a465e77fd8e6c5ac2c6b62b94978ef20b422 Mon Sep 17 00:00:00 2001 From: Robert Date: Wed, 10 May 2017 12:12:32 +0930 Subject: [PATCH 0722/1603] style error corrected --- easybuild/easyconfigs/l/lynx/lynx-2.8.9-foss-2016b.eb | 5 +++-- .../easyconfigs/p/picard/picard-2.2.4-Java-1.8.0_92.eb | 4 +--- .../p/prodigal/prodigal-2.6.2-GCC-4.9.3-binutils-2.25.eb | 7 +++---- 3 files changed, 7 insertions(+), 9 deletions(-) diff --git a/easybuild/easyconfigs/l/lynx/lynx-2.8.9-foss-2016b.eb b/easybuild/easyconfigs/l/lynx/lynx-2.8.9-foss-2016b.eb index cb6a046e97..132cfc359d 100644 --- a/easybuild/easyconfigs/l/lynx/lynx-2.8.9-foss-2016b.eb +++ b/easybuild/easyconfigs/l/lynx/lynx-2.8.9-foss-2016b.eb @@ -3,7 +3,7 @@ # Homepage: https://www.adelaide.edu.au/phoenix/ # # Copyright:: adelaide.edu.au/phoenix -# Authors:: Robert Qiao , Exe Escobedo +# Authors:: Robert Qiao , Exequiel Sepulveda # License:: GNU GPLv2 # # Notes:: @@ -13,9 +13,10 @@ easyblock = 'ConfigureMake' name = 'lynx' version = '2.8.9' +versionsuffix = '-develop' description = "lynx is an alphanumeric display oriented World-Wide Web Client" -homepage = 'http://lynx.isc.org/' +homepage = 'http://lynx.browser.org/' toolchain = {'name': 'foss', 'version': '2016b'} diff --git a/easybuild/easyconfigs/p/picard/picard-2.2.4-Java-1.8.0_92.eb b/easybuild/easyconfigs/p/picard/picard-2.2.4-Java-1.8.0_92.eb index bc5e0d5779..4af929c18d 100644 --- a/easybuild/easyconfigs/p/picard/picard-2.2.4-Java-1.8.0_92.eb +++ b/easybuild/easyconfigs/p/picard/picard-2.2.4-Java-1.8.0_92.eb @@ -4,12 +4,10 @@ # # Copyright:: adelaide.edu.au/phoenix # Authors:: Robert Qiao , Exe Escobedo -# License:: +# License:: MIT # -# Notes:: ## - name = 'picard' version = '2.2.4' diff --git a/easybuild/easyconfigs/p/prodigal/prodigal-2.6.2-GCC-4.9.3-binutils-2.25.eb b/easybuild/easyconfigs/p/prodigal/prodigal-2.6.2-GCC-4.9.3-binutils-2.25.eb index 300e28ae47..e5b64245b5 100644 --- a/easybuild/easyconfigs/p/prodigal/prodigal-2.6.2-GCC-4.9.3-binutils-2.25.eb +++ b/easybuild/easyconfigs/p/prodigal/prodigal-2.6.2-GCC-4.9.3-binutils-2.25.eb @@ -9,7 +9,6 @@ # Notes:: ## - easyblock = 'MakeCp' name = 'prodigal' @@ -17,13 +16,14 @@ version = '2.6.2' homepage = 'http://prodigal.ornl.gov/' -description = """Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a microbial (bacterial and archaeal) gene finding program developed at Oak Ridge National Laboratory and the University of Tennessee.""" +description = """Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) + is a microbial (bacterial and archaeal) gene finding program developed + at Oak Ridge National Laboratory and the University of Tennessee.""" toolchain = {'name': 'GCC', 'version': '4.9.3-binutils-2.25'} source_urls = ['https://github.com/hyattpd/Prodigal/archive/'] sources = ['v%(version)s.tar.gz'] -#https://github.com/hyattpd/Prodigal/archive/v2.6.2.tar.gz files_to_copy = [ (['prodigal'], 'bin'), @@ -37,4 +37,3 @@ sanity_check_paths = { } moduleclass = 'bio' - -- GitLab From 7ffaf3184d592177d1f816179e4a2e003ed986de Mon Sep 17 00:00:00 2001 From: Robert Date: Wed, 10 May 2017 12:29:33 +0930 Subject: [PATCH 0723/1603] lynx file name corrected --- ...{lynx-2.8.9-foss-2016b.eb => lynx-2.8.9-foss-2016b-develop.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/l/lynx/{lynx-2.8.9-foss-2016b.eb => lynx-2.8.9-foss-2016b-develop.eb} (100%) diff --git a/easybuild/easyconfigs/l/lynx/lynx-2.8.9-foss-2016b.eb b/easybuild/easyconfigs/l/lynx/lynx-2.8.9-foss-2016b-develop.eb similarity index 100% rename from easybuild/easyconfigs/l/lynx/lynx-2.8.9-foss-2016b.eb rename to easybuild/easyconfigs/l/lynx/lynx-2.8.9-foss-2016b-develop.eb -- GitLab From 00cdb166ff15cf4a58f71f10473790e4c3c1436f Mon Sep 17 00:00:00 2001 From: "\"Andreas \"" Date: Wed, 10 May 2017 08:48:11 +0200 Subject: [PATCH 0724/1603] updated comments --- .../easyconfigs/o/OpenMPI/OpenMPI-2.0.2-GCC-6.3.0-2.27-opa.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) mode change 100755 => 100644 easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.2-GCC-6.3.0-2.27-opa.eb diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.2-GCC-6.3.0-2.27-opa.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.2-GCC-6.3.0-2.27-opa.eb old mode 100755 new mode 100644 index 1e3286223d..3413573e74 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.2-GCC-6.3.0-2.27-opa.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.2-GCC-6.3.0-2.27-opa.eb @@ -21,7 +21,7 @@ configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading -# needed for --with-verbs +# needed for --with-psm2 osdependencies = [('libpsm2', 'libpsm2-devel')] libs = ["mpi_mpifh", "mpi", "ompitrace", "open-pal", "open-rte"] @@ -33,3 +33,5 @@ sanity_check_paths = { } moduleclass = 'mpi' + + -- GitLab From 8d3c267dbee7f7b89edf438bd54e5e1fa7966262 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 10 May 2017 14:56:57 +0800 Subject: [PATCH 0725/1603] add checksums and make source_url more generic --- easybuild/easyconfigs/s/Siesta/Siesta-4.0-intel-2017a.eb | 4 +++- easybuild/easyconfigs/s/Siesta/Siesta-4.1-b2-intel-2017a.eb | 4 +++- 2 files changed, 6 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/Siesta/Siesta-4.0-intel-2017a.eb b/easybuild/easyconfigs/s/Siesta/Siesta-4.0-intel-2017a.eb index b92708a1d8..88fc6fad8f 100644 --- a/easybuild/easyconfigs/s/Siesta/Siesta-4.0-intel-2017a.eb +++ b/easybuild/easyconfigs/s/Siesta/Siesta-4.0-intel-2017a.eb @@ -9,7 +9,9 @@ toolchain = {'name': 'intel', 'version': '2017a'} toolchainopts = {'usempi': True} sources = [SOURCELOWER_TGZ] -source_urls = ['https://launchpad.net/%(namelower)s/%(version_major_minor)s/%(version)s/+download/'] +vl = version.split('-') +source_urls = ['https://launchpad.net/siesta/%s/%%(version)s/+download' % vl[0]] +checksums = ['c4aa5f4cf2eabefaaacd3ef6350ec8fd'] dependencies = [('netCDF-Fortran', '4.4.4')] diff --git a/easybuild/easyconfigs/s/Siesta/Siesta-4.1-b2-intel-2017a.eb b/easybuild/easyconfigs/s/Siesta/Siesta-4.1-b2-intel-2017a.eb index 5e51c29c8b..5b2e971198 100644 --- a/easybuild/easyconfigs/s/Siesta/Siesta-4.1-b2-intel-2017a.eb +++ b/easybuild/easyconfigs/s/Siesta/Siesta-4.1-b2-intel-2017a.eb @@ -9,7 +9,9 @@ toolchain = {'name': 'intel', 'version': '2017a'} toolchainopts = {'usempi': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['https://launchpad.net/%(namelower)s/%(version_major)s.1/%(version)s/+download/'] +vl = version.split('-') +source_urls = ['https://launchpad.net/siesta/%s/%%(version)s/+download' % vl[0]] +checksums = ['6dd700aa79b0da39bbd3233c220d630f'] dependencies = [('netCDF-Fortran', '4.4.4')] -- GitLab From c19bdd1337dea376a7db32ce9145cf4dfe132c74 Mon Sep 17 00:00:00 2001 From: "\"Andreas \"" Date: Wed, 10 May 2017 09:43:32 +0200 Subject: [PATCH 0726/1603] updated --- easybuild/easyconfigs/m/METIS/METIS-5.1.0-foss-2017a.eb | 2 +- .../SuiteSparse-4.5.5-foss-2017a-METIS-5.1.0.eb | 7 +++---- .../SuiteSparse-4.5.5-foss-2017a-ParMETIS-4.0.3.eb | 7 +++---- 3 files changed, 7 insertions(+), 9 deletions(-) diff --git a/easybuild/easyconfigs/m/METIS/METIS-5.1.0-foss-2017a.eb b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-foss-2017a.eb index 24c6a9c29a..b1648c008c 100644 --- a/easybuild/easyconfigs/m/METIS/METIS-5.1.0-foss-2017a.eb +++ b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-foss-2017a.eb @@ -16,7 +16,7 @@ source_urls = [ ] #We use 32bit for indices and 64bit for content -patches = ['METIS-5.1.0-use-doubles.path'] +patches = ['METIS-5.1.0-use-doubles.patch'] builddependencies = [('CMake', '3.8.0')] diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.5-foss-2017a-METIS-5.1.0.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.5-foss-2017a-METIS-5.1.0.eb index ac3303de2d..4727d14749 100644 --- a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.5-foss-2017a-METIS-5.1.0.eb +++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.5-foss-2017a-METIS-5.1.0.eb @@ -1,5 +1,7 @@ name = 'SuiteSparse' version = '4.5.5' +metis_ver = '5.1.0' +versionsuffix = '-METIS-%s' % metis_ver homepage = 'http://faculty.cse.tamu.edu/davis/suitesparse.html' description = """SuiteSparse is a collection of libraries manipulate sparse matrices.""" @@ -10,10 +12,7 @@ toolchainopts = {'unroll': True, 'pic': True} source_urls = ['http://faculty.cse.tamu.edu/davis/SuiteSparse/'] sources = [SOURCE_TAR_GZ] -metis = 'METIS' -metis_ver = '5.1.0' -versionsuffix = '-%s-%s' % (metis, metis_ver) -dependencies = [(metis, metis_ver)] +dependencies = [('METIS', metis_ver)] maxparallel = 1 diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.5-foss-2017a-ParMETIS-4.0.3.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.5-foss-2017a-ParMETIS-4.0.3.eb index a24c57563a..457bb71cde 100755 --- a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.5-foss-2017a-ParMETIS-4.0.3.eb +++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.5-foss-2017a-ParMETIS-4.0.3.eb @@ -1,5 +1,7 @@ name = 'SuiteSparse' version = '4.5.5' +parmetis_ver = '4.0.3' +versionsuffix = '-ParMETIS-%s' % parmetis_ver homepage = 'http://faculty.cse.tamu.edu/davis/suitesparse.html' description = """SuiteSparse is a collection of libraries manipulate sparse matrices.""" @@ -10,10 +12,7 @@ toolchainopts = {'unroll': True, 'pic': True} source_urls = ['http://faculty.cse.tamu.edu/davis/SuiteSparse/'] sources = [SOURCE_TAR_GZ] -parmetis = 'ParMETIS' -parmetis_ver = '4.0.3' -versionsuffix = '-%s-%s' % (parmetis, parmetis_ver) -dependencies = [(parmetis, parmetis_ver)] +dependencies = [('ParMETIS', parmetis_ver)] maxparallel = 1 -- GitLab From 84a87e68b2bfe4a5516557e54910c445299b05f5 Mon Sep 17 00:00:00 2001 From: "\"Andreas \"" Date: Wed, 10 May 2017 09:56:53 +0200 Subject: [PATCH 0727/1603] added fftw as dependency --- easybuild/easyconfigs/n/NAMD/NAMD-2.12-foss-2017a-mpi.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/n/NAMD/NAMD-2.12-foss-2017a-mpi.eb b/easybuild/easyconfigs/n/NAMD/NAMD-2.12-foss-2017a-mpi.eb index b1ee1a4af9..8c793e8447 100644 --- a/easybuild/easyconfigs/n/NAMD/NAMD-2.12-foss-2017a-mpi.eb +++ b/easybuild/easyconfigs/n/NAMD/NAMD-2.12-foss-2017a-mpi.eb @@ -13,6 +13,7 @@ sources = ['NAMD_%(version)s_Source.tar.gz'] dependencies = [ ('Tcl', '8.5.19'), + ('FFTW', '3.3.6'), ] # /bin/csh is required by 'config' script -- GitLab From f19f305be53e82db0c019889343e9614fd7042d9 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 10 May 2017 15:58:50 +0800 Subject: [PATCH 0728/1603] remove no longer necessary parallel=1 --- easybuild/easyconfigs/s/Siesta/Siesta-4.0-intel-2017a.eb | 2 -- easybuild/easyconfigs/s/Siesta/Siesta-4.1-b2-intel-2017a.eb | 2 -- 2 files changed, 4 deletions(-) diff --git a/easybuild/easyconfigs/s/Siesta/Siesta-4.0-intel-2017a.eb b/easybuild/easyconfigs/s/Siesta/Siesta-4.0-intel-2017a.eb index 88fc6fad8f..c782f5eabf 100644 --- a/easybuild/easyconfigs/s/Siesta/Siesta-4.0-intel-2017a.eb +++ b/easybuild/easyconfigs/s/Siesta/Siesta-4.0-intel-2017a.eb @@ -15,6 +15,4 @@ checksums = ['c4aa5f4cf2eabefaaacd3ef6350ec8fd'] dependencies = [('netCDF-Fortran', '4.4.4')] -parallel = 1 - moduleclass = 'phys' diff --git a/easybuild/easyconfigs/s/Siesta/Siesta-4.1-b2-intel-2017a.eb b/easybuild/easyconfigs/s/Siesta/Siesta-4.1-b2-intel-2017a.eb index 5b2e971198..3186618b3a 100644 --- a/easybuild/easyconfigs/s/Siesta/Siesta-4.1-b2-intel-2017a.eb +++ b/easybuild/easyconfigs/s/Siesta/Siesta-4.1-b2-intel-2017a.eb @@ -15,6 +15,4 @@ checksums = ['6dd700aa79b0da39bbd3233c220d630f'] dependencies = [('netCDF-Fortran', '4.4.4')] -parallel = 1 - moduleclass = 'phys' -- GitLab From 38c1c0621a437cf495f525da7c2b4d087790bedc Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 10 May 2017 13:18:00 +0200 Subject: [PATCH 0729/1603] adding easyconfigs: Tensorflow-1.1.0-intel-2017a-Python-2.7.13.eb, Tensorflow-1.1.0-intel-2017a-Python-3.6.1.eb, protobuf-3.3.0-intel-2017a.eb, protobuf-python-3.3.0-intel-2017a-Python-2.7.13.eb, protobuf-python-3.3.0-intel-2017a-Python-3.6.1.eb --- ...-python-3.3.0-intel-2017a-Python-2.7.13.eb | 29 +++++++++++++++ ...f-python-3.3.0-intel-2017a-Python-3.6.1.eb | 29 +++++++++++++++ .../p/protobuf/protobuf-3.3.0-intel-2017a.eb | 23 ++++++++++++ ...sorflow-1.1.0-intel-2017a-Python-2.7.13.eb | 35 +++++++++++++++++++ ...nsorflow-1.1.0-intel-2017a-Python-3.6.1.eb | 35 +++++++++++++++++++ 5 files changed, 151 insertions(+) create mode 100644 easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.3.0-intel-2017a-Python-2.7.13.eb create mode 100644 easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.3.0-intel-2017a-Python-3.6.1.eb create mode 100644 easybuild/easyconfigs/p/protobuf/protobuf-3.3.0-intel-2017a.eb create mode 100755 easybuild/easyconfigs/t/Tensorflow/Tensorflow-1.1.0-intel-2017a-Python-2.7.13.eb create mode 100755 easybuild/easyconfigs/t/Tensorflow/Tensorflow-1.1.0-intel-2017a-Python-3.6.1.eb diff --git a/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.3.0-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.3.0-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..e538a8e99b --- /dev/null +++ b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.3.0-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'protobuf-python' +version = '3.3.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/google/protobuf/' +description = """Python Protocol Buffers runtime library.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['https://github.com/google/protobuf/archive/v%(version)s'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.13'), + ('protobuf', version) +] + +start_dir = 'python' + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +options = {'modulename': 'google.protobuf'} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.3.0-intel-2017a-Python-3.6.1.eb b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.3.0-intel-2017a-Python-3.6.1.eb new file mode 100644 index 0000000000..4c753d376f --- /dev/null +++ b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.3.0-intel-2017a-Python-3.6.1.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'protobuf-python' +version = '3.3.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/google/protobuf/' +description = """Python Protocol Buffers runtime library.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['https://github.com/google/protobuf/archive/v%(version)s'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '3.6.1'), + ('protobuf', version) +] + +start_dir = 'python' + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +options = {'modulename': 'google.protobuf'} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/protobuf/protobuf-3.3.0-intel-2017a.eb b/easybuild/easyconfigs/p/protobuf/protobuf-3.3.0-intel-2017a.eb new file mode 100644 index 0000000000..10bedd5672 --- /dev/null +++ b/easybuild/easyconfigs/p/protobuf/protobuf-3.3.0-intel-2017a.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'protobuf' +version = '3.3.0' + +homepage = 'https://github.com/google/protobuf/' +description = """Google Protocol Buffers""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['https://github.com/google/protobuf/archive/v%(version)s/'] +sources = [SOURCE_TAR_GZ] + +builddependencies = [('Autotools', '20150215')] + +preconfigopts = "./autogen.sh && " + +sanity_check_paths = { + 'files': ['bin/protoc', 'lib/libprotobuf.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/t/Tensorflow/Tensorflow-1.1.0-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/t/Tensorflow/Tensorflow-1.1.0-intel-2017a-Python-2.7.13.eb new file mode 100755 index 0000000000..a6aec94f18 --- /dev/null +++ b/easybuild/easyconfigs/t/Tensorflow/Tensorflow-1.1.0-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonPackage' + +name = 'Tensorflow' +version = '1.1.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://www.tensorflow.org/' +description = "An open-source software library for Machine Intelligence" + +toolchain = {'name': 'intel', 'version': '2017a'} + +pymaj = '2' +pymin = '7' +pymajmin = pymaj + pymin + +source_urls = ['https://pypi.python.org/packages/8a/73/74c610decd5e0a1fd7f441a32e3561d21c28ced98fd6d3d9d5c70dbf92ce/'] +sources = [ + 'tensorflow-%%(version)s-cp%(pymajmin)s-cp%(pymajmin)smu-manylinux1_x86_64.whl' % {'pymajmin': pymajmin}, +] +checksums = ['70a7a29dbef478cbac9a9c839a18227e'] + +dependencies = [ + ('Python', '%s.%s.13' % (pymaj, pymin)), + ('protobuf-python', '3.3.0', versionsuffix), +] + +use_pip = True +unpack_sources = False + +sanity_check_paths = { + 'files': ['bin/tensorboard'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/Tensorflow/Tensorflow-1.1.0-intel-2017a-Python-3.6.1.eb b/easybuild/easyconfigs/t/Tensorflow/Tensorflow-1.1.0-intel-2017a-Python-3.6.1.eb new file mode 100755 index 0000000000..f134b5be2b --- /dev/null +++ b/easybuild/easyconfigs/t/Tensorflow/Tensorflow-1.1.0-intel-2017a-Python-3.6.1.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonPackage' + +name = 'Tensorflow' +version = '1.1.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://www.tensorflow.org/' +description = "An open-source software library for Machine Intelligence" + +toolchain = {'name': 'intel', 'version': '2017a'} + +pymaj = '3' +pymin = '6' +pymajmin = pymaj + pymin + +source_urls = ['https://pypi.python.org/packages/cd/e4/b2a8bcd1fa689489050386ec70c5c547e4a75d06f2cc2b55f45463cd092c/'] +sources = [ + 'tensorflow-%%(version)s-cp%(pymajmin)s-cp%(pymajmin)sm-manylinux1_x86_64.whl' % {'pymajmin': pymajmin}, +] +checksums = ['1f761290358dfb7fe4ec73140f4d282a'] + +dependencies = [ + ('Python', '%s.%s.1' % (pymaj, pymin)), + ('protobuf-python', '3.3.0', versionsuffix), +] + +use_pip = True +unpack_sources = False + +sanity_check_paths = { + 'files': ['bin/tensorboard'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'lib' -- GitLab From 1483de14a6df6e3641b2f740f5931682055045c8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 10 May 2017 15:08:41 +0200 Subject: [PATCH 0730/1603] adding easyconfigs: NLTK-3.2.2-intel-2017a-Python-2.7.13.eb --- .../NLTK-3.2.2-intel-2017a-Python-2.7.13.eb | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/n/NLTK/NLTK-3.2.2-intel-2017a-Python-2.7.13.eb diff --git a/easybuild/easyconfigs/n/NLTK/NLTK-3.2.2-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/n/NLTK/NLTK-3.2.2-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..1388501b14 --- /dev/null +++ b/easybuild/easyconfigs/n/NLTK/NLTK-3.2.2-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,22 @@ +easyblock = 'PythonPackage' + +name = 'NLTK' +version = '3.2.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.nltk.org/' +description = "NLTK is a leading platform for building Python programs to work with human language data." + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('Python', '2.7.13')] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' -- GitLab From 6ec3072ebf8e9ae25a8f5289def75bd636a385b6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 10 May 2017 15:16:14 +0200 Subject: [PATCH 0731/1603] adding easyconfigs: pbdagcon-20170330-intel-2017a.eb, BLASR-20170330-intel-2017a.eb, blasr_libcpp-20170426-intel-2017a.eb, pbbam-20170508-intel-2017a.eb, HTSlib-20160107-intel-2017a-PacBio.eb, HDF5-1.8.18-intel-2017a-serial.eb --- .../b/BLASR/BLASR-20170330-intel-2017a.eb | 38 ++++++++++++++ .../blasr_libcpp-20170426-intel-2017a.eb | 41 ++++++++++++++++ .../h/HDF5/HDF5-1.8.18-intel-2017a-serial.eb | 27 ++++++++++ .../HTSlib-20160107-intel-2017a-PacBio.eb | 41 ++++++++++++++++ .../p/pbbam/pbbam-20170508-intel-2017a.eb | 49 +++++++++++++++++++ .../pbdagcon/pbdagcon-20170330-intel-2017a.eb | 40 +++++++++++++++ 6 files changed, 236 insertions(+) create mode 100644 easybuild/easyconfigs/b/BLASR/BLASR-20170330-intel-2017a.eb create mode 100644 easybuild/easyconfigs/b/blasr_libcpp/blasr_libcpp-20170426-intel-2017a.eb create mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.8.18-intel-2017a-serial.eb create mode 100644 easybuild/easyconfigs/h/HTSlib/HTSlib-20160107-intel-2017a-PacBio.eb create mode 100644 easybuild/easyconfigs/p/pbbam/pbbam-20170508-intel-2017a.eb create mode 100644 easybuild/easyconfigs/p/pbdagcon/pbdagcon-20170330-intel-2017a.eb diff --git a/easybuild/easyconfigs/b/BLASR/BLASR-20170330-intel-2017a.eb b/easybuild/easyconfigs/b/BLASR/BLASR-20170330-intel-2017a.eb new file mode 100644 index 0000000000..e63d8bc616 --- /dev/null +++ b/easybuild/easyconfigs/b/BLASR/BLASR-20170330-intel-2017a.eb @@ -0,0 +1,38 @@ +easyblock = 'MakeCp' + +name = 'BLASR' +commit = 'bed926d' +version = '20170330' + +homepage = 'https://github.com/PacificBiosciences/blasr' +description = """ BLASR (Basic Local Alignment with Successive Refinement) rapidly maps + reads to genomes by finding the highest scoring local alignment or set of local alignments + between the read and the genome. Optimized for PacBio's extraordinarily long reads and + taking advantage of rich quality values, BLASR maps reads rapidly with high accuracy. """ + +toolchain = {'name': 'intel', 'version': '2017a'} +#toolchainopts = {'usempi': True} +toolchainopts = {'cstd': 'c++11'} + +source_urls = ['https://github.com/PacificBiosciences/blasr/archive/'] +sources = ['%s.tar.gz' % commit] + +dependencies = [ + ('HDF5', '1.8.18', '-serial'), + ('pbbam', '20170508'), + ('blasr_libcpp', '20170426'), +] + +prebuildopts = "./configure.py --with-szlib HDF5_INCLUDE=$EBROOTHDF5/include HDF5_LIB=$EBROOTHDF5/lib && " + +binaries = ['blasr', 'utils/loadPulses', 'utils/pls2fasta', 'utils/samFilter', 'utils/samtoh5', + 'utils/samtom4', 'utils/sawriter', 'utils/sdpMatcher', 'utils/toAfg'] +files_to_copy = [(binaries, 'bin')] + +sanity_check_paths = { + 'files': ['bin/blasr', 'bin/loadPulses', 'bin/pls2fasta', 'bin/samFilter', 'bin/samtoh5', 'bin/samtom4', + 'bin/sawriter', 'bin/sdpMatcher', 'bin/toAfg'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/blasr_libcpp/blasr_libcpp-20170426-intel-2017a.eb b/easybuild/easyconfigs/b/blasr_libcpp/blasr_libcpp-20170426-intel-2017a.eb new file mode 100644 index 0000000000..e172377121 --- /dev/null +++ b/easybuild/easyconfigs/b/blasr_libcpp/blasr_libcpp-20170426-intel-2017a.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'blasr_libcpp' +version = '20170426' +commit = 'cd49f36' + +homepage = 'https://github.com/PacificBiosciences/blasr_libcpp' +description = """Blasr_libcpp is a library used by blasr and other executables such as samtoh5, loadPulses for + analyzing PacBio sequences""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['https://github.com/PacificBiosciences/blasr_libcpp/archive/'] +sources = ['%s.tar.gz' % commit] + +dependencies = [ + ('HDF5', '1.8.18', '-serial'), + ('pbbam', '20170508'), +] + +unpack_options = "--strip-components=1" + +skipsteps = ['configure', 'install'] +buildininstalldir = True + +#prebuildopts = "NOPBBAM=1 NOHDF=1 ./configure.py && " +prebuildopts = "./configure.py && " + +sanity_check_paths = { + 'files': ['alignment/libblasr.a', 'alignment/libblasr.%s' % SHLIB_EXT, 'hdf/libpbihdf.a', + 'hdf/libpbihdf.%s' % SHLIB_EXT, 'pbdata/libpbdata.a', 'pbdata/libpbdata.%s' % SHLIB_EXT], + 'dirs': [], +} + +modextrapaths = { + 'CPATH': ['alignment', 'hdf', 'pbdata'], + 'LD_LIBRARY_PATH': ['alignment', 'hdf', 'pbdata'], + 'LIBRARY_PATH': ['alignment', 'hdf', 'pbdata'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.18-intel-2017a-serial.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.18-intel-2017a-serial.eb new file mode 100644 index 0000000000..ef054b6cdf --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.18-intel-2017a-serial.eb @@ -0,0 +1,27 @@ +name = 'HDF5' +version = '1.8.18' +versionsuffix = '-serial' + +homepage = 'http://www.hdfgroup.org/HDF5/' +description = """HDF5 is a unique technology suite that makes possible the management of + extremely large and complex data collections.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True, 'usempi': False} + +source_urls = [ + 'https://support.hdfgroup.org/ftp/HDF5/current18/src/', + 'https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(versions)/src/' +] + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['dd2148b740713ca0295442ec683d7b1c'] + +buildopts = 'CXXFLAGS="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK"' + +dependencies = [ + ('zlib', '1.2.11'), + ('Szip', '2.1'), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/HTSlib/HTSlib-20160107-intel-2017a-PacBio.eb b/easybuild/easyconfigs/h/HTSlib/HTSlib-20160107-intel-2017a-PacBio.eb new file mode 100644 index 0000000000..e9e046ddd8 --- /dev/null +++ b/easybuild/easyconfigs/h/HTSlib/HTSlib-20160107-intel-2017a-PacBio.eb @@ -0,0 +1,41 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# 1.4 modified by: +# Adam Huffman +# The Francis Crick Institute + +easyblock = 'ConfigureMake' + +name = 'HTSlib' +version = '20160107' +commit = '6b6c813' +versionsuffix = '-PacBio' + +homepage = 'https://github.com/PacificBiosciences/htslib' +description = """PacBio fork of C library for reading/writing high-throughput sequencing data. + This package includes the utilities bgzip and tabix""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['https://github.com/PacificBiosciences/htslib/archive/'] +sources = ['%s.tar.gz' % commit] + +dependencies = [ + ('zlib', '1.2.11'), + ('bzip2', '1.0.6'), + ('XZ', '5.2.3'), + ('cURL', '7.54.0'), +] + +skipsteps = ['configure'] + +installopts = ' prefix=%(installdir)s' + +sanity_check_paths = { + 'files': ['bin/bgzip', 'bin/tabix', 'lib/libhts.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/pbbam/pbbam-20170508-intel-2017a.eb b/easybuild/easyconfigs/p/pbbam/pbbam-20170508-intel-2017a.eb new file mode 100644 index 0000000000..5e218a3225 --- /dev/null +++ b/easybuild/easyconfigs/p/pbbam/pbbam-20170508-intel-2017a.eb @@ -0,0 +1,49 @@ +easyblock = 'CMakeMake' + +name = 'pbbam' +version = '20170508' +commit = 'd62e310' + +homepage = 'http://pbbam.readthedocs.io/' +description = """The pbbam software package provides components to create, query, & edit PacBio BAM files + and associated indices.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +gtest_ver = '1.8.0' +source_urls = [ + 'https://github.com/PacificBiosciences/pbbam/archive/', + 'https://github.com/google/googletest/archive/', +] +sources = [ + ('%s.tar.gz' % commit, "tar xfvz %s --strip-components=1"), # pbbam + 'release-%s.tar.gz' % gtest_ver, # googletest +] + +builddependencies = [ + ('CMake', '3.8.1'), + ('Doxygen', '1.8.13'), +] +dependencies = [ + ('zlib', '1.2.11'), + ('Boost', '1.64.0'), + ('googletest', '1.8.0'), + ('HTSlib', '20160107', '-PacBio'), +] + +skipsteps = ['install'] + +buildininstalldir = True + +configopts = "-DHTSLIB_ROOTDIR=$EBROOTHTSLIB -DGTEST_SRC_DIR=%%(builddir)s/googletest-release-%s" % gtest_ver + +runtest = 'test' + +postinstallcmds = ["rm -r googletest-release-%s" % gtest_ver] + +sanity_check_paths = { + 'files': ['bin/pbindex', 'bin/pbindexdump', 'bin/pbmerge', 'lib/libpbbam.a'], + 'dirs': ['include/pbbam'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/pbdagcon/pbdagcon-20170330-intel-2017a.eb b/easybuild/easyconfigs/p/pbdagcon/pbdagcon-20170330-intel-2017a.eb new file mode 100644 index 0000000000..51dd75d3e1 --- /dev/null +++ b/easybuild/easyconfigs/p/pbdagcon/pbdagcon-20170330-intel-2017a.eb @@ -0,0 +1,40 @@ +easyblock = 'MakeCp' + +name = 'pbdagcon' +version = '20170330' +commit = 'fd8fbad' + +homepage = 'https://github.com/PacificBiosciences/pbdagcon' +description = """pbdagcon is a tool that implements DAGCon (Directed Acyclic Graph Consensus) which is a sequence + consensus algorithm based on using directed acyclic graphs to encode multiple sequence alignment.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [ + 'https://github.com/PacificBiosciences/pbdagcon/archive/', + 'https://github.com/PacificBiosciences/DALIGNER/archive/', + 'https://github.com/PacificBiosciences/DAZZ_DB/archive/', +] +sources = [ + '%s.tar.gz' % commit, # pbdagcon + '583de37.tar.gz', # DALIGNER + '7954b44.tar.gz', # DAZZ_DB +] + +dependencies = [ + ('blasr_libcpp', '20170426'), +] + +prebuildopts = "rmdir DAZZ_DB && ln -s %(builddir)s/DAZZ_DB* DAZZ_DB && cd DAZZ_DB && pwd && make && cd .. && " +prebuildopts += "export CPATH=$PWD/DAZZ_DB:$CPATH && export LIBRARY_PATH=$PWD/DAZZ_DB:$LIBRARY_PATH && " +prebuildopts += "rmdir DALIGNER && ln -s %(builddir)s/DALIGNER* DALIGNER && cd DALIGNER && pwd && make && cd .. && " +prebuildopts += "./configure.py && export DALIGNER_SRC=$PWD/DALIGNER && export DAZZ_DB_SRC=$PWD/DAZZ_DB && " + +files_to_copy = [(['src/cpp/pbdagcon'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/pbdagcon'], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From f433280a21cca4e4c0b1a2495a6fcaa1832c0af2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 10 May 2017 15:34:11 +0200 Subject: [PATCH 0732/1603] adding easyconfigs: pyenchant-1.6.8-intel-2017a-Python-2.7.13.eb, enchant-1.6.1-intel-2017a.eb, hunspell-1.6.1-intel-2017a.eb --- .../e/enchant/enchant-1.6.1-intel-2017a.eb | 25 +++++++++++++++++ .../h/hunspell/hunspell-1.6.1-intel-2017a.eb | 25 +++++++++++++++++ ...enchant-1.6.8-intel-2017a-Python-2.7.13.eb | 27 +++++++++++++++++++ 3 files changed, 77 insertions(+) create mode 100644 easybuild/easyconfigs/e/enchant/enchant-1.6.1-intel-2017a.eb create mode 100644 easybuild/easyconfigs/h/hunspell/hunspell-1.6.1-intel-2017a.eb create mode 100644 easybuild/easyconfigs/p/pyenchant/pyenchant-1.6.8-intel-2017a-Python-2.7.13.eb diff --git a/easybuild/easyconfigs/e/enchant/enchant-1.6.1-intel-2017a.eb b/easybuild/easyconfigs/e/enchant/enchant-1.6.1-intel-2017a.eb new file mode 100644 index 0000000000..13433c2f04 --- /dev/null +++ b/easybuild/easyconfigs/e/enchant/enchant-1.6.1-intel-2017a.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'enchant' +version = '1.6.1' + +homepage = 'https://abiword.github.io/enchant/' +description = """Enchant is a library (and command-line program) that wraps a number of different spelling libraries + and programs with a consistent interface.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['https://github.com/AbiWord/enchant/releases/download/enchant-%s/' % '-'.join(version.split('.'))] +sources = [SOURCE_TAR_GZ] + +builddependencies = [('Autotools', '20150215')] +dependencies = [('hunspell', '1.6.1')] + +buildopts = "LIBTOOL='libtool --tag=CC'" + +sanity_check_paths = { + 'files': ['bin/enchant', 'lib/libenchant.a', 'lib/libenchant.%s' % SHLIB_EXT], + 'dirs': ['include/enchant', 'lib/enchant'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/hunspell/hunspell-1.6.1-intel-2017a.eb b/easybuild/easyconfigs/h/hunspell/hunspell-1.6.1-intel-2017a.eb new file mode 100644 index 0000000000..808d4c832e --- /dev/null +++ b/easybuild/easyconfigs/h/hunspell/hunspell-1.6.1-intel-2017a.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'hunspell' +version = '1.6.1' + +homepage = 'http://hunspell.github.io/' +description = """Hunspell is a spell checker and morphological analyzer library and program designed for languages + with rich morphology and complex word compounding or character encoding.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['https://github.com/hunspell/hunspell/archive/'] +sources = ['v%(version)s.tar.gz'] + +builddependencies = [('Autotools', '20150215')] + +preconfigopts = "autoreconf -vfi && " + +sanity_check_paths = { + 'files': ['bin/hunspell', 'lib/libhunspell-%(version_major_minor)s.a', + 'lib/libhunspell-%%(version_major_minor)s.%s' % SHLIB_EXT, 'lib/pkgconfig/hunspell.pc'], + 'dirs': ['include/hunspell'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/pyenchant/pyenchant-1.6.8-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/p/pyenchant/pyenchant-1.6.8-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..44fd59e0fa --- /dev/null +++ b/easybuild/easyconfigs/p/pyenchant/pyenchant-1.6.8-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'pyenchant' +version = '1.6.8' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pythonhosted.org/pyenchant/' +description = "PyEnchant is a spellchecking library for Python, based on the excellent Enchant library." + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.13'), + ('enchant', '1.6.1'), +] + +options = {'modulename': 'enchant'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'lib' -- GitLab From ae2102adbb82b9d5a4ba8d501c50ec282682c784 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 10 May 2017 16:17:26 +0200 Subject: [PATCH 0733/1603] adding easyconfigs: pandas-0.20.1-intel-2017a-Python-3.6.1.eb --- .../pandas-0.20.1-intel-2017a-Python-3.6.1.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/p/pandas/pandas-0.20.1-intel-2017a-Python-3.6.1.eb diff --git a/easybuild/easyconfigs/p/pandas/pandas-0.20.1-intel-2017a-Python-3.6.1.eb b/easybuild/easyconfigs/p/pandas/pandas-0.20.1-intel-2017a-Python-3.6.1.eb new file mode 100644 index 0000000000..ea5b45bce1 --- /dev/null +++ b/easybuild/easyconfigs/p/pandas/pandas-0.20.1-intel-2017a-Python-3.6.1.eb @@ -0,0 +1,23 @@ +easyblock = 'PythonPackage' + +name = 'pandas' +version = '0.20.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = "https://pypi.python.org/pypi/pandas/" +description = """pandas is an open source, BSD-licensed library providing high-performance, easy-to-use data structures + and data analysis tools for the Python programming language.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [('Python', '3.6.1')] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'lib' -- GitLab From 6fe5e21171575a9bddd5010a52a597d2b3b8b8f7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 10 May 2017 16:38:47 +0200 Subject: [PATCH 0734/1603] adding easyconfigs: scikit-learn-0.18.1-intel-2017a-Python-3.6.1.eb, matplotlib-2.0.1-intel-2017a-Python-3.6.1.eb --- ...tplotlib-2.0.1-intel-2017a-Python-3.6.1.eb | 43 +++++++++++++++++++ ...t-learn-0.18.1-intel-2017a-Python-3.6.1.eb | 30 +++++++++++++ 2 files changed, 73 insertions(+) create mode 100644 easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.1-intel-2017a-Python-3.6.1.eb create mode 100755 easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.18.1-intel-2017a-Python-3.6.1.eb diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.1-intel-2017a-Python-3.6.1.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.1-intel-2017a-Python-3.6.1.eb new file mode 100644 index 0000000000..a1866952ba --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.1-intel-2017a-Python-3.6.1.eb @@ -0,0 +1,43 @@ +easyblock = 'Bundle' + +name = 'matplotlib' +version = '2.0.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://matplotlib.org' +description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of + hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python + and ipython shell, web application servers, and six graphical user interface toolkits.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' + +dependencies = [ + ('Python', '3.6.1'), + ('freetype', '2.7.1'), +] + +exts_list = [ + ('Cycler', '0.10.0', { + 'modulename': 'cycler', + 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], + 'source_tmpl': 'cycler-%(version)s.tar.gz', + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], + }), +] + +# specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module +full_sanity_check = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.18.1-intel-2017a-Python-3.6.1.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.18.1-intel-2017a-Python-3.6.1.eb new file mode 100755 index 0000000000..af24f8502f --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.18.1-intel-2017a-Python-3.6.1.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'scikit-learn' +version = '0.18.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://scikit-learn.org/stable/index.html' +description = """Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, +building upon numpy, scipy, and matplotlib. As a machine-learning module, +it provides versatile tools for data mining and analysis in any field of science and engineering. +It strives to be simple and efficient, accessible to everybody, and reusable in various contexts.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '3.6.1'), + ('matplotlib', '2.0.1', versionsuffix), +] + +options = {'modulename': 'sklearn'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/sklearn'], +} + +moduleclass = 'data' -- GitLab From 33f3a414b01acd8de6e44c737dec0165a534143e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 10 May 2017 18:37:10 +0200 Subject: [PATCH 0735/1603] adding easyconfigs: RAxML-8.2.10-intel-2017a-hybrid-avx2.eb --- .../RAxML-8.2.10-intel-2017a-hybrid-avx2.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/r/RAxML/RAxML-8.2.10-intel-2017a-hybrid-avx2.eb diff --git a/easybuild/easyconfigs/r/RAxML/RAxML-8.2.10-intel-2017a-hybrid-avx2.eb b/easybuild/easyconfigs/r/RAxML/RAxML-8.2.10-intel-2017a-hybrid-avx2.eb new file mode 100644 index 0000000000..55ca13f91f --- /dev/null +++ b/easybuild/easyconfigs/r/RAxML/RAxML-8.2.10-intel-2017a-hybrid-avx2.eb @@ -0,0 +1,27 @@ +easyblock = 'MakeCp' + +name = 'RAxML' +version = '8.2.10' +versionsuffix = '-hybrid-avx2' + +homepage = 'https://github.com/stamatak/standard-RAxML' +description = "RAxML search algorithm for maximum likelihood based inference of phylogenetic trees." + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'usempi': True} + +sources = ['v%(version)s.zip'] +source_urls = ['https://github.com/stamatak/standard-RAxML/archive/'] + +buildopts = '-f Makefile.AVX2.HYBRID.gcc CC="$CC"' + +files_to_copy = [(["raxmlHPC-HYBRID-AVX2"], "bin"), "usefulScripts", "README", "manual"] + +postinstallcmds = ["cd %(installdir)s/bin && ln -s raxmlHPC-HYBRID-AVX2 raxmlHPC"] + +sanity_check_paths = { + 'files': ['bin/raxmlHPC'], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From e26314e1b0611d8031c8cec4e5272efc68677fa1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 10 May 2017 19:09:28 +0200 Subject: [PATCH 0736/1603] clean up commented out lines in BLASR & blasr_libcpp easyconfigs, no need to use cstd=c++11 for BLASR --- easybuild/easyconfigs/b/BLASR/BLASR-20170330-intel-2017a.eb | 2 -- .../b/blasr_libcpp/blasr_libcpp-20170426-intel-2017a.eb | 1 - 2 files changed, 3 deletions(-) diff --git a/easybuild/easyconfigs/b/BLASR/BLASR-20170330-intel-2017a.eb b/easybuild/easyconfigs/b/BLASR/BLASR-20170330-intel-2017a.eb index e63d8bc616..d6ce3f9ad0 100644 --- a/easybuild/easyconfigs/b/BLASR/BLASR-20170330-intel-2017a.eb +++ b/easybuild/easyconfigs/b/BLASR/BLASR-20170330-intel-2017a.eb @@ -11,8 +11,6 @@ description = """ BLASR (Basic Local Alignment with Successive Refinement) rapid taking advantage of rich quality values, BLASR maps reads rapidly with high accuracy. """ toolchain = {'name': 'intel', 'version': '2017a'} -#toolchainopts = {'usempi': True} -toolchainopts = {'cstd': 'c++11'} source_urls = ['https://github.com/PacificBiosciences/blasr/archive/'] sources = ['%s.tar.gz' % commit] diff --git a/easybuild/easyconfigs/b/blasr_libcpp/blasr_libcpp-20170426-intel-2017a.eb b/easybuild/easyconfigs/b/blasr_libcpp/blasr_libcpp-20170426-intel-2017a.eb index e172377121..c6d9e3ba4f 100644 --- a/easybuild/easyconfigs/b/blasr_libcpp/blasr_libcpp-20170426-intel-2017a.eb +++ b/easybuild/easyconfigs/b/blasr_libcpp/blasr_libcpp-20170426-intel-2017a.eb @@ -23,7 +23,6 @@ unpack_options = "--strip-components=1" skipsteps = ['configure', 'install'] buildininstalldir = True -#prebuildopts = "NOPBBAM=1 NOHDF=1 ./configure.py && " prebuildopts = "./configure.py && " sanity_check_paths = { -- GitLab From 006a5ed25c64d72593d5761c0672a4ba8bd9f34c Mon Sep 17 00:00:00 2001 From: "Nathan S. Watson-Haigh" Date: Thu, 11 May 2017 15:20:45 +0930 Subject: [PATCH 0737/1603] EasyConfig for BioKanga v4.3.6 --- .../b/BioKanga/BioKanga-4.3.6-foss-2015b.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/b/BioKanga/BioKanga-4.3.6-foss-2015b.eb diff --git a/easybuild/easyconfigs/b/BioKanga/BioKanga-4.3.6-foss-2015b.eb b/easybuild/easyconfigs/b/BioKanga/BioKanga-4.3.6-foss-2015b.eb new file mode 100644 index 0000000000..e9e6ecd9f9 --- /dev/null +++ b/easybuild/easyconfigs/b/BioKanga/BioKanga-4.3.6-foss-2015b.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'BioKanga' +version = '4.3.6' + +homepage = 'https://github.com/csiro-crop-informatics/biokanga' +description = """BioKanga is an integrated toolkit of high performance bioinformatics + subprocesses targeting the challenges of next generation sequencing analytics. + Kanga is an acronym standing for 'K-mer Adaptive Next Generation Aligner'.""" + +toolchain = {'name': 'foss', 'version': '2015b'} + +source_urls = ['https://github.com/csiro-crop-informatics/biokanga/archive/'] +sources = ['v%(version)s.tar.gz'] + +builddependencies = [('Autotools', '20150215')] + +preconfigopts = "autoreconf -f -i && " + +sanity_check_paths = { + 'files': ["bin/biokanga"], + 'dirs': [] +} + +moduleclass = 'bio' -- GitLab From a0d0507e01ead49ed4189641b597f7f0be1001a0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 11 May 2017 08:43:03 +0200 Subject: [PATCH 0738/1603] use 'data' as moduleclass --- .../easyconfigs/n/NLTK/NLTK-3.2.2-intel-2017a-Python-2.7.13.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/NLTK/NLTK-3.2.2-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/n/NLTK/NLTK-3.2.2-intel-2017a-Python-2.7.13.eb index 1388501b14..6f5ffa7a5b 100644 --- a/easybuild/easyconfigs/n/NLTK/NLTK-3.2.2-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/n/NLTK/NLTK-3.2.2-intel-2017a-Python-2.7.13.eb @@ -19,4 +19,4 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages'], } -moduleclass = 'tools' +moduleclass = 'data' -- GitLab From 65fa3ba5ecc8668bfacd8eb7bd9b6141bcaac096 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 11 May 2017 08:44:33 +0200 Subject: [PATCH 0739/1603] blank line between deps & builddeps --- easybuild/easyconfigs/e/enchant/enchant-1.6.1-intel-2017a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/e/enchant/enchant-1.6.1-intel-2017a.eb b/easybuild/easyconfigs/e/enchant/enchant-1.6.1-intel-2017a.eb index 13433c2f04..abd8322098 100644 --- a/easybuild/easyconfigs/e/enchant/enchant-1.6.1-intel-2017a.eb +++ b/easybuild/easyconfigs/e/enchant/enchant-1.6.1-intel-2017a.eb @@ -13,6 +13,7 @@ source_urls = ['https://github.com/AbiWord/enchant/releases/download/enchant-%s/ sources = [SOURCE_TAR_GZ] builddependencies = [('Autotools', '20150215')] + dependencies = [('hunspell', '1.6.1')] buildopts = "LIBTOOL='libtool --tag=CC'" -- GitLab From 64536687d1aaa8c0b42588f54367f04ed6b9da5c Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 11 May 2017 14:17:24 +0200 Subject: [PATCH 0740/1603] adding easyconfigs: goolfc-2017.01.eb --- .../CUDA/CUDA-8.0.61_375.26-GCC-5.4.0-2.26.eb | 24 ++++++++ .../f/FFTW/FFTW-3.3.6-gompic-2017.01.eb | 25 +++++++++ .../easyconfigs/g/gcccuda/gcccuda-2017.01.eb | 21 +++++++ .../easyconfigs/g/gompic/gompic-2017.01.eb | 23 ++++++++ .../easyconfigs/g/goolfc/goolfc-2017.01.eb | 38 +++++++++++++ .../h/hwloc/hwloc-1.11.5-GCC-5.4.0-2.26.eb | 23 ++++++++ ...BLAS-0.2.19-GCC-5.4.0-2.26-LAPACK-3.7.0.eb | 56 +++++++++++++++++++ .../OpenMPI/OpenMPI-2.0.2-gcccuda-2017.01.eb | 34 +++++++++++ ...ic-2017.01-OpenBLAS-0.2.19-LAPACK-3.7.0.eb | 25 +++++++++ 9 files changed, 269 insertions(+) create mode 100644 easybuild/easyconfigs/c/CUDA/CUDA-8.0.61_375.26-GCC-5.4.0-2.26.eb create mode 100644 easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-gompic-2017.01.eb create mode 100644 easybuild/easyconfigs/g/gcccuda/gcccuda-2017.01.eb create mode 100644 easybuild/easyconfigs/g/gompic/gompic-2017.01.eb create mode 100644 easybuild/easyconfigs/g/goolfc/goolfc-2017.01.eb create mode 100644 easybuild/easyconfigs/h/hwloc/hwloc-1.11.5-GCC-5.4.0-2.26.eb create mode 100644 easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-GCC-5.4.0-2.26-LAPACK-3.7.0.eb create mode 100644 easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.2-gcccuda-2017.01.eb create mode 100644 easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompic-2017.01-OpenBLAS-0.2.19-LAPACK-3.7.0.eb diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-8.0.61_375.26-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/c/CUDA/CUDA-8.0.61_375.26-GCC-5.4.0-2.26.eb new file mode 100644 index 0000000000..8bfbdd15f7 --- /dev/null +++ b/easybuild/easyconfigs/c/CUDA/CUDA-8.0.61_375.26-GCC-5.4.0-2.26.eb @@ -0,0 +1,24 @@ +name = 'CUDA' +version = '8.0.61_375.26' + +homepage = 'https://developer.nvidia.com/cuda-toolkit' +description = """CUDA (formerly Compute Unified Device Architecture) is a parallel + computing platform and programming model created by NVIDIA and implemented by the + graphics processing units (GPUs) that they produce. CUDA gives developers access + to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs.""" + +toolchain = {'name': 'GCC', 'version': '5.4.0-2.26'} + +source_urls = [ + 'https://developer.nvidia.com/compute/cuda/%(version_major_minor)s/prod/local_installers/', + 'http://developer.download.nvidia.com/compute/cuda/%(version_major_minor)s/Prod/local_installers/', + 'https://developer.nvidia.com/compute/cuda/%(version_major_minor)s/Prod2/local_installers/', +] + +sources = ['%(namelower)s_%(version)s_linux-run'] + +checksums = [ + '33e1bd980e91af4e55f3ef835c103f9b', +] + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-gompic-2017.01.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-gompic-2017.01.eb new file mode 100644 index 0000000000..98911ef733 --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-gompic-2017.01.eb @@ -0,0 +1,25 @@ +name = 'FFTW' +version = '3.3.6' + +homepage = 'http://www.fftw.org' +description = """FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) + in one or more dimensions, of arbitrary input size, and of both real and complex data.""" + +toolchain = {'name': 'gompic', 'version': '2017.01'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = ['fftw-%(version)s-pl2.tar.gz'] +checksums = ['927e481edbb32575397eb3d62535a856'] + +# no quad precision, requires GCC v4.6 or higher +# see also +# http://www.fftw.org/doc/Extended-and-quadruple-precision-in-Fortran.html +with_quad_prec = False + +# compilation fails when configuring with --enable-avx-128-fma, Intel compilers do not support FMA4 instructions +use_fma4 = False + +runtest = 'check' + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/g/gcccuda/gcccuda-2017.01.eb b/easybuild/easyconfigs/g/gcccuda/gcccuda-2017.01.eb new file mode 100644 index 0000000000..1dc8205870 --- /dev/null +++ b/easybuild/easyconfigs/g/gcccuda/gcccuda-2017.01.eb @@ -0,0 +1,21 @@ +easyblock = "Toolchain" + +name = 'gcccuda' +version = '2017.01' + +homepage = '(none)' +description = """GNU Compiler Collection (GCC) based compiler toolchain, along with CUDA toolkit.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +comp_name = 'GCC' +comp_ver = '5.4.0-2.26' +comp = (comp_name, comp_ver) + +# compiler toolchain dependencies +dependencies = [ + comp, + ('CUDA', '8.0.61_375.26', '', comp), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/g/gompic/gompic-2017.01.eb b/easybuild/easyconfigs/g/gompic/gompic-2017.01.eb new file mode 100644 index 0000000000..138f18ef6c --- /dev/null +++ b/easybuild/easyconfigs/g/gompic/gompic-2017.01.eb @@ -0,0 +1,23 @@ +easyblock = "Toolchain" + +name = 'gompic' +version = '2017.01' + +homepage = '(none)' +description = """GNU Compiler Collection (GCC) based compiler toolchain along with CUDA toolkit, + including OpenMPI for MPI support with CUDA features enabled.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +comp_name = 'GCC' +comp_ver = '5.4.0-2.26' +comp = (comp_name, comp_ver) + +# compiler toolchain dependencies +dependencies = [ + comp, # part of gcccuda + ('CUDA', '8.0.61_375.26', '', comp), # part of gcccuda + ('OpenMPI', '2.0.2', '', ('gcccuda', version)), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/g/goolfc/goolfc-2017.01.eb b/easybuild/easyconfigs/g/goolfc/goolfc-2017.01.eb new file mode 100644 index 0000000000..b8e965c62e --- /dev/null +++ b/easybuild/easyconfigs/g/goolfc/goolfc-2017.01.eb @@ -0,0 +1,38 @@ +easyblock = "Toolchain" + +name = 'goolfc' +version = '2017.01' + +homepage = '(none)' +description = """GCC based compiler toolchain __with CUDA support__, and including + OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +comp_name = 'GCC' +comp_ver = '5.4.0-2.26' +comp = (comp_name, comp_ver) + +# toolchain used to build goolfc dependencies +comp_mpi_tc_name = 'gompic' +comp_mpi_tc_ver = version +comp_mpi_tc = (comp_mpi_tc_name, comp_mpi_tc_ver) + +blaslib = 'OpenBLAS' +blasver = '0.2.19' +blassuff = '-LAPACK-3.7.0' +blas = '-%s-%s%s' % (blaslib, blasver, blassuff) + +# compiler toolchain dependencies +# we need GCC and OpenMPI as explicit dependencies instead of gompi toolchain +# because of toolchain preperation functions +dependencies = [ + comp, # part of gompic + ('CUDA', '8.0.61_375.26', '', comp), # part of gompic + ('OpenMPI', '2.0.2', '', ('gcccuda', version)), # part of gompic + (blaslib, blasver, blassuff, comp), + ('FFTW', '3.3.6', '', comp_mpi_tc), + ('ScaLAPACK', '2.0.2', blas, comp_mpi_tc), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.5-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.5-GCC-5.4.0-2.26.eb new file mode 100644 index 0000000000..547c202aa9 --- /dev/null +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.5-GCC-5.4.0-2.26.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'hwloc' +version = '1.11.5' + +homepage = 'http://www.open-mpi.org/projects/hwloc/' +description = """The Portable Hardware Locality (hwloc) software package provides a portable abstraction +(across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including +NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various +system attributes such as cache and memory information as well as the locality of I/O devices such as +network interfaces, InfiniBand HCAs or GPUs. It primarily aims at helping applications with gathering +information about modern computing hardware so as to exploit it accordingly and efficiently.""" + +toolchain = {'name': 'GCC', 'version': '5.4.0-2.26'} + +source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [('numactl', '2.0.11')] + +configopts = "--enable-libnuma=$EBROOTNUMACTL" + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-GCC-5.4.0-2.26-LAPACK-3.7.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-GCC-5.4.0-2.26-LAPACK-3.7.0.eb new file mode 100644 index 0000000000..4c55b7dc6c --- /dev/null +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-GCC-5.4.0-2.26-LAPACK-3.7.0.eb @@ -0,0 +1,56 @@ +easyblock = 'ConfigureMake' + +name = 'OpenBLAS' +version = '0.2.19' + +lapackver = '3.7.0' +versionsuffix = '-LAPACK-%s' % lapackver + +homepage = 'http://xianyi.github.com/OpenBLAS/' +description = """OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version.""" + +toolchain = {'name': 'GCC', 'version': '5.4.0-2.26'} + +lapack_src = 'lapack-%s.tgz' % lapackver +large_src = 'large.tgz' +timing_src = 'timing.tgz' + +lapack_unpack_cmd = 'cd %(name)s-%(version)s; rm -rf lapack-netlib;' +lapack_unpack_cmd += 'mkdir lapack-netlib;' +lapack_unpack_cmd += 'tar -C lapack-netlib --strip-components=1 -zxf %s; cd -' + +sources = [ + 'v%(version)s.tar.gz', + (lapack_src, lapack_unpack_cmd), + large_src, + timing_src, +] +source_urls = [ + # order matters, trying to download the LAPACK tarball from GitHub causes trouble + "http://www.netlib.org/lapack/", + "http://www.netlib.org/lapack/timing/", + "https://github.com/xianyi/OpenBLAS/archive/", +] + +patches = [ + (large_src, '.'), + (timing_src, '.'), + 'OpenBLAS-%(version)s_LAPACK-3.7.0-fixes.patch', +] + +skipsteps = ['configure'] + +buildopts = 'BINARY=64 USE_THREAD=1 CC="$CC" FC="$F77" NO_AFFINITY=1' +installopts = "USE_THREAD=1 PREFIX=%(installdir)s" + +# extensive testing can be enabled by uncommenting the line below +# runtest = 'PATH=.:$PATH lapack-timing' + +sanity_check_paths = { + 'files': ['include/cblas.h', 'include/f77blas.h', 'include/lapacke_config.h', 'include/lapacke.h', + 'include/lapacke_mangling.h', 'include/lapacke_utils.h', 'include/openblas_config.h', + 'lib/libopenblas.a', 'lib/libopenblas.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.2-gcccuda-2017.01.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.2-gcccuda-2017.01.eb new file mode 100644 index 0000000000..f4abe2cc5c --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.2-gcccuda-2017.01.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'OpenMPI' +version = '2.0.2' + +homepage = 'http://www.open-mpi.org/' +description = """The Open MPI Project is an open source MPI-2 implementation.""" + +toolchain = {'name': 'gcccuda', 'version': '2017.01'} + +source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] +sources = [SOURCELOWER_TAR_GZ] + +checksums = ['886698becc5bea8c151c0af2074b8392'] + +dependencies = [('hwloc', '1.11.5')] + +configopts = '--enable-shared --enable-mpi-thread-multiple --with-verbs ' +configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path +configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support +configopts += '--with-cuda=$CUDA_HOME ' # CUDA-aware build; N.B. --disable-dlopen is incompatible + +# needed for --with-verbs +osdependencies = [('libibverbs-dev', 'libibverbs-devel')] + +libs = ["mpi_mpifh", "mpi", "ompitrace", "open-pal", "open-rte"] +sanity_check_paths = { + 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] + + ["include/%s.h" % x for x in ["mpi-ext", "mpif-config", "mpif", "mpi", "mpi_portable_platform"]], + 'dirs': [], +} + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompic-2017.01-OpenBLAS-0.2.19-LAPACK-3.7.0.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompic-2017.01-OpenBLAS-0.2.19-LAPACK-3.7.0.eb new file mode 100644 index 0000000000..8f3ffb84de --- /dev/null +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompic-2017.01-OpenBLAS-0.2.19-LAPACK-3.7.0.eb @@ -0,0 +1,25 @@ +name = 'ScaLAPACK' +version = '2.0.2' + +homepage = 'http://www.netlib.org/scalapack/' +description = """The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines + redesigned for distributed memory MIMD parallel computers.""" + +toolchain = {'name': 'gompic', 'version': '2017.01'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = [SOURCELOWER_TGZ] + +blaslib = 'OpenBLAS' +blasver = '0.2.19' +blassuff = '-LAPACK-3.7.0' + +versionsuffix = "-%s-%s%s" % (blaslib, blasver, blassuff) + +dependencies = [(blaslib, blasver, blassuff)] + +# parallel build tends to fail, so disabling it +parallel = 1 + +moduleclass = 'numlib' -- GitLab From 1ac0a3d24973bb43c15c441e2a7e7dd018d87276 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 11 May 2017 21:17:56 +0200 Subject: [PATCH 0741/1603] adding easyconfigs: R-3.4.0-intel-2017a-X11-20170314.eb --- .../r/R/R-3.4.0-intel-2017a-X11-20170314.eb | 514 ++++++++++++++++++ 1 file changed, 514 insertions(+) create mode 100644 easybuild/easyconfigs/r/R/R-3.4.0-intel-2017a-X11-20170314.eb diff --git a/easybuild/easyconfigs/r/R/R-3.4.0-intel-2017a-X11-20170314.eb b/easybuild/easyconfigs/r/R/R-3.4.0-intel-2017a-X11-20170314.eb new file mode 100644 index 0000000000..0f9329d684 --- /dev/null +++ b/easybuild/easyconfigs/r/R/R-3.4.0-intel-2017a-X11-20170314.eb @@ -0,0 +1,514 @@ +name = 'R' +version = '3.4.0' +x11ver = '20170314' +versionsuffix = '-X11-%s' % x11ver + +homepage = 'http://www.r-project.org/' +description = """R is a free software environment for statistical computing and graphics.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://cran.us.r-project.org/src/base/R-%(version_major)s'] + +preconfigopts = 'BLAS_LIBS="$LIBBLAS" LAPACK_LIBS="$LIBLAPACK"' +configopts = "--with-lapack --with-blas --with-pic --enable-threads --with-x=no --enable-R-shlib" +#Actually use Tcl/Tk +configopts += ' --with-tcl-config=$EBROOTTCL/lib/tclConfig.sh --with-tk-config=$EBROOTTK/lib/tkConfig.sh ' +# Enable graphics capabilities for plotting. +configopts += " --with-cairo --with-libpng --with-jpeglib --with-libtiff" +# some recommended packages may fail in a parallel build (e.g. Matrix), and we're installing them anyway below +configopts += " --with-recommended-packages=no" + +dependencies = [ + ('X11', x11ver), + ('Mesa', '17.0.2'), + ('libGLU', '9.0.0'), + ('cairo', '1.14.8'), + ('libreadline', '7.0'), + ('ncurses', '6.0'), + ('bzip2', '1.0.6'), + ('XZ', '5.2.3'), + ('zlib', '1.2.11'), + ('SQLite', '3.17.0'), + ('PCRE', '8.40'), + ('libpng', '1.6.29'), # for plotting in R + ('libjpeg-turbo', '1.5.1'), # for plottting in R + ('LibTIFF', '4.0.7'), + ('Java', '1.8.0_121', '', True), # Java bindings are built if Java is found, might as well provide it + ('Tcl', '8.6.6'), # for tcltk + ('Tk', '8.6.6'), # for tcltk + ('cURL', '7.53.1'), # for RCurl + ('libxml2', '2.9.4'), # for XML + ('GDAL', '2.1.3', '-Python-2.7.13'), # for rgdal + ('PROJ', '4.9.3'), # for rgdal + ('GMP', '6.1.2'), # for igraph + ('NLopt', '2.4.2'), # for nloptr + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.2h'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +name_tmpl = '%(name)s_%(version)s.tar.gz' +ext_options = { + 'source_urls': [ + 'http://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'http://cran.r-project.org/src/contrib/', # current version of packages + 'http://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': name_tmpl, +} + +# !! order of packages is important !! +# packages updated on March 7th 2017 +exts_list = [ + # default libraries, only here to sanity check their presence + 'base', + 'datasets', + 'graphics', + 'grDevices', + 'grid', + 'methods', + 'splines', + 'stats', + 'stats4', + 'tools', + 'utils', + # non-standard libraries, should be specified with fixed versions! + ('Rmpi', '0.6-6', ext_options), + ('abind', '1.4-5', ext_options), + ('magic', '1.5-6', ext_options), + ('geometry', '0.3-6', dict(ext_options.items() + [('patches', ['geometry-0.3-4-icc.patch'])])), + ('bit', '1.1-12', ext_options), + ('filehash', '2.4-1', ext_options), + ('ff', '2.2-13', ext_options), + ('bnlearn', '4.1.1', ext_options), + ('bootstrap', '2017.2', ext_options), + ('combinat', '0.0-8', ext_options), + ('deal', '1.2-37', ext_options), + ('fdrtool', '1.2.15', ext_options), + ('formatR', '1.5', ext_options), + ('gtools', '3.5.0', ext_options), + ('gdata', '2.17.0', ext_options), + ('GSA', '1.03', ext_options), + ('highr', '0.6', ext_options), + ('infotheo', '1.2.0', ext_options), + ('lars', '1.2', ext_options), + ('lazy', '1.2-15', ext_options), + ('kernlab', '0.9-25', ext_options), + ('mime', '0.5', ext_options), + ('markdown', '0.8', ext_options), + ('mlbench', '2.1-1', ext_options), + ('NLP', '0.1-10', ext_options), + ('mclust', '5.2.3', ext_options), + ('RANN', '2.5', ext_options), + ('rmeta', '2.16', ext_options), + ('segmented', '0.5-1.4', ext_options), + ('som', '0.3-5.1', ext_options), + ('SuppDists', '1.1-9.4', ext_options), + ('stabledist', '0.7-1', ext_options), + ('survivalROC', '1.0.3', ext_options), + ('pspline', '1.0-17', ext_options), + ('timeDate', '3012.100', ext_options), + ('longmemo', '1.0-0', ext_options), + ('ADGofTest', '0.3', ext_options), + ('ade4', '1.7-6', ext_options), + ('AlgDesign', '1.1-7.3', ext_options), + ('base64enc', '0.1-3', ext_options), + ('BH', '1.62.0-1', ext_options), + ('brew', '1.0-6', ext_options), + ('Brobdingnag', '1.2-4', ext_options), + ('corpcor', '1.6.9', ext_options), + ('longitudinal', '1.1.12', ext_options), + ('backports', '1.0.5', ext_options), + ('checkmate', '1.8.2', ext_options), + ('Rcpp', '0.12.10', ext_options), + ('cubature', '1.3-8', ext_options), + ('DEoptimR', '1.0-8', ext_options), + ('digest', '0.6.12', ext_options), + ('fastmatch', '1.1-0', ext_options), + ('ffbase', '0.12.3', ext_options), + ('iterators', '1.0.8', ext_options), + ('maps', '3.1.1', ext_options), + ('nnls', '1.4', ext_options), + ('sendmailR', '1.2-1', ext_options), + ('spam', '1.4-0', ext_options), + ('subplex', '1.2-2', ext_options), + ('stringi', '1.1.5', ext_options), + ('magrittr', '1.5', ext_options), + ('stringr', '1.2.0', ext_options), + ('evaluate', '0.10', ext_options), + ('logspline', '2.1.9', ext_options), + ('ncbit', 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ext_options), + ('jpeg', '0.1-8', ext_options), + ('network', '1.13.0', ext_options), + ('statnet.common', '3.3.0', ext_options), + ('sna', '2.4', ext_options), + ('glasso', '1.8', dict(ext_options.items() + [('patches', [('glasso-1.8-ifort-no-fixed.patch', 1)])])), + ('huge', '1.2.7', ext_options), + ('d3Network', '0.5.2.1', ext_options), + ('ggm', '2.3', ext_options), + ('qgraph', '1.4.3', ext_options), + ('diveRsity', '1.9.90', ext_options), + ('doSNOW', '1.0.14', ext_options), + ('phangorn', '2.2.0', ext_options), + ('geepack', '1.2-1', ext_options), + ('lubridate', '1.6.0', ext_options), + ('biom', '0.3.12', ext_options), + ('pim', '2.0.1', ext_options), + ('minpack.lm', '1.2-1', ext_options), + ('rootSolve', '1.7', ext_options), + ('diagram', '1.6.3', ext_options), + ('FME', '1.3.5', ext_options), + ('bmp', '0.2', ext_options), + ('readbitmap', '0.1-4', ext_options), + ('purrr', '0.2.2', ext_options), + ('downloader', '0.4', ext_options), + ('imager', '0.40.2', dict(ext_options.items() + [('patches', ['imager-0.40.2_icpc-wd308.patch'])])), +] + +moduleclass = 'lang' + -- GitLab From 907e2454dc8d7bb28ef3852a02d94ab0461b1d7b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 11 May 2017 21:25:15 +0200 Subject: [PATCH 0742/1603] add missing patch files for kohoner/imager extensions in R v3.4.0 --- .../r/R/imager-0.40.2_icpc-wd308.patch | 21 +++++++++++++++++ .../r/R/kohonen-3.0.2_icpc-wd308.patch | 23 +++++++++++++++++++ 2 files changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/r/R/imager-0.40.2_icpc-wd308.patch create mode 100644 easybuild/easyconfigs/r/R/kohonen-3.0.2_icpc-wd308.patch diff --git a/easybuild/easyconfigs/r/R/imager-0.40.2_icpc-wd308.patch b/easybuild/easyconfigs/r/R/imager-0.40.2_icpc-wd308.patch new file mode 100644 index 0000000000..bdcf948b63 --- /dev/null +++ b/easybuild/easyconfigs/r/R/imager-0.40.2_icpc-wd308.patch @@ -0,0 +1,21 @@ +add -wd308 compiler option to avoid compiler warning #308 being treated as an error +author: Kenneth Hoste (HPC-UGent) +--- imager/MD5.orig 2017-05-11 19:41:40.494524499 +0200 ++++ imager/MD5 2017-05-11 19:41:57.914534000 +0200 +@@ -178,7 +178,7 @@ + ad2654de31942fed6a81372ca95c69f8 *man/warp.Rd + 175e0ff835838c3a97f4e262ea2e22a9 *man/watershed.Rd + 6d2ea6da4b089e34b2c74fa9915598ad *man/where.Rd +-2d2d7a47e364f82c3a83d1def6997313 *src/Makevars.in ++4b7df5fe6555e13b54525ca11ac3bfb7 *src/Makevars.in + 0921c95e100ceb6edfe481db8258741c *src/Makevars.win + ad6fce36dbcb58ce1a05b98b5a87f263 *src/RcppExports.cpp + cac489a7495799d378cf0c10c8db3ebd *src/colourspace.cpp +--- imager/src/Makevars.in.orig 2017-05-11 19:41:06.494524465 +0200 ++++ imager/src/Makevars.in 2017-05-11 19:41:20.957122000 +0200 +@@ -1,3 +1,5 @@ + PKG_CPPFLAGS = $(SHLIB_OPENMP_CFLAGS) @CPPFLAGS@ @HAVE_FFTW@ @FFTW_CFLAGS@ @TIFF_CFLAGS@ -I../inst/include -DCIMG_COMPILING -Dcimg_use_rng -Dcimg_use_r -Dcimg_use_fftw3_singlethread -Dcimg_verbosity=1 -Dcimg_date='""' -Dcimg_time='""' + PKG_LIBS = $(SHLIB_OPENMP_CFLAGS) @LIBS@ @HAVE_FFTW@ @FFTW_LIBS@ @TIFF_LIBS@ $(RCPP_LDFLAGS) + ++# disable Intel C++ compiler (icpc) warning/error #308, to avoid 'member "std::complex::_M_value" is inaccessible' ++PKG_CXXFLAGS = -wd308 diff --git a/easybuild/easyconfigs/r/R/kohonen-3.0.2_icpc-wd308.patch b/easybuild/easyconfigs/r/R/kohonen-3.0.2_icpc-wd308.patch new file mode 100644 index 0000000000..7c77bb7a74 --- /dev/null +++ b/easybuild/easyconfigs/r/R/kohonen-3.0.2_icpc-wd308.patch @@ -0,0 +1,23 @@ +add -wd308 compiler option to avoid compiler warning #308 being treated as an error +author: Kenneth Hoste (HPC-UGent) +--- kohonen/MD5.orig 2017-05-11 18:42:50.494520969 +0200 ++++ kohonen/MD5 2017-05-11 18:43:02.299001000 +0200 +@@ -41,7 +41,7 @@ + 4074da8d1e8ba029d52de2a9ff24124b *man/unit.distances.Rd + c7f0e4739945511e6fcd67289320eab1 *man/wines.Rd + ad838f45c3a9435e7b2229b8cc6682ae *man/yeast.Rd +-74d73c2023015c6b008d9fdd11d60b14 *src/Makevars ++803f88be6a292da8d8ab21bdf420bda0 *src/Makevars + fada3f440c7f59d360c9303e803b1460 *src/RcppExports.cpp + 0b0c395e4a39ef2e6b31d2459c449912 *src/batch-supersom.cpp + 478e89466560e680760d7781c81acbcc *src/distance-functions.cpp +--- kohonen/src/Makevars.orig 2017-05-11 18:42:07.494520926 +0200 ++++ kohonen/src/Makevars 2017-05-11 18:42:34.436276000 +0200 +@@ -1,3 +1,4 @@ +-PKG_CFLAGS = $(SHLIB_OPENMP_CFLAGS) +-PKG_CXXFLAGS = $(SHLIB_OPENMP_CFLAGS) +-PKG_LIBS = $(SHLIB_OPENMP_CFLAGS) ++# disable Intel C++ compiler (icpc) warning/error #308, to avoid 'member "std::complex::_M_value" is inaccessible' ++PKG_CFLAGS = $(SHLIB_OPENMP_CFLAGS) -wd308 ++PKG_CXXFLAGS = $(SHLIB_OPENMP_CFLAGS) -wd308 ++PKG_LIBS = $(SHLIB_OPENMP_CFLAGS) -wd308 -- GitLab From f2abe0f2e6cfb51114b25520766aad0dfa32f615 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 11 May 2017 21:30:04 +0200 Subject: [PATCH 0743/1603] adding easyconfigs: R-bundle-Bioconductor-3.5-intel-2017a-R-3.4.0.eb --- ...le-Bioconductor-3.5-intel-2017a-R-3.4.0.eb | 168 ++++++++++++++++++ 1 file changed, 168 insertions(+) create mode 100644 easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.5-intel-2017a-R-3.4.0.eb diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.5-intel-2017a-R-3.4.0.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.5-intel-2017a-R-3.4.0.eb new file mode 100644 index 0000000000..99eea4dc16 --- /dev/null +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.5-intel-2017a-R-3.4.0.eb @@ -0,0 +1,168 @@ +easyblock = 'Bundle' + +name = 'R-bundle-Bioconductor' +version = '3.5' +versionsuffix = '-R-%(rver)s' + +homepage = 'http://www.r-project.org/' +description = """R is a free software environment for statistical computing and graphics.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +dependencies = [ + ('R', '3.4.0', '-X11-20170314'), + ('HDF5', '1.10.0-patch1'), # for rhdf5 +] + +name_tmpl = '%(name)s_%(version)s.tar.gz' +ext_options = { + 'source_urls': [ + 'http://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'http://cran.r-project.org/src/contrib/', # current version of packages + 'http://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': name_tmpl, +} +bioconductor_options = { + 'source_urls': [ + 'http://bioconductor.org/packages/3.5/bioc/src/contrib/', + 'http://bioconductor.org/packages/3.5/data/annotation/src/contrib/', + 'http://bioconductor.org/packages/3.5/data/experiment/src/contrib/', + ], + 'source_tmpl': name_tmpl, +} + +exts_defaultclass = 'RPackage' +exts_filter = ("R -q --no-save", "library(%(ext_name)s)") + +# CRAN packages on which these Bioconductor packages depend are available in R module on which this depends +# !! order of packages is important !! +exts_list = [ + ('BiocGenerics', '0.22.0', bioconductor_options), + ('Biobase', '2.36.2', bioconductor_options), + ('S4Vectors', '0.14.0', bioconductor_options), + ('IRanges', '2.10.0', bioconductor_options), + ('GenomeInfoDbData', '0.99.0', bioconductor_options), + ('GenomeInfoDb', '1.12.0', bioconductor_options), + ('AnnotationDbi', '1.38.0', bioconductor_options), + ('zlibbioc', '1.22.0', bioconductor_options), + ('XVector', '0.16.0', bioconductor_options), + ('Biostrings', '2.44.0', bioconductor_options), + ('GenomicRanges', '1.28.1', bioconductor_options), + ('BiocParallel', '1.10.1', bioconductor_options), + ('Rsamtools', '1.28.0', bioconductor_options), + ('lambda.r', '1.1.9', ext_options), + ('futile.options', '1.0.0', ext_options), + ('futile.logger', '1.4.3', ext_options), + ('DelayedArray', '0.2.2', bioconductor_options), + ('SummarizedExperiment', '1.6.1', bioconductor_options), + ('GenomicAlignments', '1.12.0', bioconductor_options), + ('ShortRead', '1.34.0', bioconductor_options), + ('graph', '1.54.0', bioconductor_options), + ('affyio', '1.46.0', bioconductor_options), + ('BiocInstaller', '1.26.0', bioconductor_options), + ('preprocessCore', '1.38.1', bioconductor_options), + ('affy', '1.54.0', bioconductor_options), + ('GO.db', '3.4.1', bioconductor_options), + ('limma', '3.32.2', bioconductor_options), + ('RBGL', '1.52.0', bioconductor_options), + ('org.Hs.eg.db', '3.4.1', bioconductor_options), + ('AnnotationForge', '1.18.0', bioconductor_options), + ('KEGG.db', '3.2.3', bioconductor_options), + ('annaffy', '1.48.0', bioconductor_options), + ('gcrma', '2.48.0', bioconductor_options), + ('oligoClasses', '1.38.0', bioconductor_options), + ('edgeR', '3.18.1', bioconductor_options), + ('PFAM.db', '3.4.1', bioconductor_options), + ('perm', '1.0-0.0', ext_options), + ('baySeq', '2.10.0', bioconductor_options), + ('qvalue', '2.8.0', bioconductor_options), + ('impute', '1.50.1', bioconductor_options), + ('samr', '2.0', ext_options), + ('DEGseq', '1.30.0', bioconductor_options), + ('hgu133plus2.db', '3.2.3', bioconductor_options), + ('illuminaio', '0.18.0', bioconductor_options), + ('rtracklayer', '1.36.0', bioconductor_options), + ('biomaRt', '2.32.0', bioconductor_options), + ('GenomicFeatures', '1.28.0', bioconductor_options), + ('bumphunter', '1.16.0', bioconductor_options), + ('multtest', '2.32.0', bioconductor_options), + ('siggenes', '1.50.0', bioconductor_options), + ('DynDoc', '1.54.0', bioconductor_options), + ('genoset', '1.32.0', bioconductor_options), + ('NOISeq', '2.20.0', bioconductor_options), + ('Rgraphviz', '2.20.0', bioconductor_options), + ('RNASeqPower', '1.16.0', bioconductor_options), + ('annotate', '1.54.0', bioconductor_options), + ('GSEABase', '1.38.0', bioconductor_options), + ('genefilter', '1.58.1', bioconductor_options), + ('Category', '2.38.0', bioconductor_options), + ('GOstats', '2.42.0', bioconductor_options), + ('BSgenome', '1.44.0', bioconductor_options), + ('VariantAnnotation', '1.22.0', bioconductor_options), + ('interactiveDisplayBase', '1.14.0', bioconductor_options), + ('AnnotationHub', '2.8.1', bioconductor_options), + ('AnnotationFilter', '1.0.0', bioconductor_options), + ('ProtGenerics', '1.8.0', bioconductor_options), + ('ensembldb', '2.0.1', bioconductor_options), + ('biovizBase', '1.24.0', bioconductor_options), + ('OrganismDbi', '1.18.0', bioconductor_options), + ('ggbio', '1.24.0', bioconductor_options), + ('geneplotter', '1.54.0', bioconductor_options), + ('DESeq2', '1.16.1', bioconductor_options), + ('ReportingTools', '2.16.0', bioconductor_options), + ('affycoretools', '1.48.0', bioconductor_options), + ('TxDb.Hsapiens.UCSC.hg19.knownGene', '3.2.2', bioconductor_options), + ('Homo.sapiens', '1.3.1', bioconductor_options), + ('BSgenome.Hsapiens.UCSC.hg19', '1.4.0', bioconductor_options), + ('AgiMicroRna', '2.26.0', bioconductor_options), + ('GenomeGraphs', '1.36.0', bioconductor_options), + ('geneLenDataBase', '1.12.0', bioconductor_options), + ('goseq', '1.28.0', bioconductor_options), + ('KEGGREST', '1.16.0', bioconductor_options), + ('KEGGgraph', '1.34.0', bioconductor_options), + ('KEGGprofile', '1.18.0', bioconductor_options), + ('GEOquery', '2.42.0', bioconductor_options), + ('mixOmics', '6.1.3', ext_options), + ('minfi', '1.22.1', bioconductor_options), + ('FDb.InfiniumMethylation.hg19', '2.2.0', bioconductor_options), + ('methylumi', '2.22.0', bioconductor_options), + ('lumi', '2.28.0', bioconductor_options), + ('widgetTools', '1.54.0', bioconductor_options), + ('tkWidgets', '1.54.0', bioconductor_options), + ('Mfuzz', '2.36.0', bioconductor_options), + ('venn', '1.2', ext_options), + ('maSigPro', '1.48.0', bioconductor_options), + ('SPIA', '2.28.0', bioconductor_options), + ('Gviz', '1.20.0', bioconductor_options), + ('cummeRbund', '2.18.0', bioconductor_options), + ('GenomicFiles', '1.12.0', bioconductor_options), + ('derfinderHelper', '1.10.0', bioconductor_options), + ('derfinder', '1.10.3', bioconductor_options), + ('polyester', '1.12.0', bioconductor_options), + ('Rsubread', '1.26.0', bioconductor_options), + ('pcaMethods', '1.68.0', bioconductor_options), + ('marray', '1.54.0', bioconductor_options), + ('CGHbase', '1.36.0', bioconductor_options), + ('sigaR', '1.24.0', bioconductor_options), + ('HCsnip', '1.16.0', bioconductor_options), + ('metagenomeSeq', '1.18.0', bioconductor_options), + ('gdsfmt', '1.12.0', bioconductor_options), + ('SNPRelate', '1.10.1', dict(bioconductor_options.items() + [('patches', ['SNPRelate-1.6.5_no-SSE-intr.patch'])])), + ('rhdf5', '2.20.0', bioconductor_options), + ('biomformat', '1.4.0', bioconductor_options), + ('phyloseq', '1.20.0', bioconductor_options), + ('ALDEx2', '1.8.0', bioconductor_options), + ('RcppParallel', '4.3.20', ext_options), + ('dada2', '1.4.0', bioconductor_options), + ('LEA', '1.8.1', bioconductor_options), +] + +modextrapaths = {'R_LIBS': ''} + +sanity_check_paths = { + 'files': [], + 'dirs': ['AnnotationDbi', 'BiocInstaller', 'GenomicFeatures'], +} + +moduleclass = 'bio' -- GitLab From 5ada904273c09ec09a905f36c44ee31bc583c9a0 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Fri, 12 May 2017 09:56:28 +0800 Subject: [PATCH 0744/1603] prepare release notes for eb321 --- RELEASE_NOTES | 16 +++++++++++++++- 1 file changed, 15 insertions(+), 1 deletion(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index d67162b731..7fd5ec2c84 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -3,9 +3,23 @@ For more detailed information, please see the git log. These release notes can also be consulted at http://easybuild.readthedocs.org/en/latest/Release_notes.html. -The latest version of easybuild-easyconfig provides 6,943 easyconfig files, for 1,216 different software packages, +The latest version of easybuild-easyconfig provides 7,037 easyconfig files, for 1,228 different software packages, 25 different (compiler) toolchains, 13 software bundles and 1 meta-package. +v3.2.1 (May 12th 2017) +---------------------- + +bugfix/update release +- added example easyconfig files for 12 new software packages: + - AdapterRemoval (#4509), blasr_libcpp (#4566), canu (#4473), enchant (#4567), hunspell (#4567), memkind (#4544), + NLTK (#4565), pbbam (#4566), pbdagcon (#4566), pyenchant (#4567), Siesta (#4562), xarray (#4556) +- added additional easyconfigs for various supported software packages, including: + - ASE 3.13.0, AdapterRemoval 2.2.0, BLASR 20170330, BerkeleyGW 1.2.0, BioKanga 4.3.6, Boost 1.63.0, Boost 1.63.0, blasr_libcpp 20170426, CGAL 4.8.1, CGAL 4.9, CMake 3.8.1, CUDA 8.0.61_375.26, Coreutils 8.27, canu 1.4, EasyBuild 3.2.0.eb, Eigen 3.3.3, enchant 1.6.1, FFTW 3.3.6, flex 2.5.39, GROMACS 2016.1, gcccuda 2017.01.eb, gompic 2017.01.eb, googletest 1.8.0, goolfc 2017.01.eb, grib_api 1.21.0, HDF5 1.10.1, HDF5 1.8.18, HDF5 1.8.18, HDF5 1.8.18, HTSlib 20160107, h5py 2.7.0, hanythingondemand 3.2.2, hanythingondemand 3.2.2, hunspell 1.6.1, hwloc 1.11.5, JasPer 1.900.1, Keras 2.0.4, LLVM 3.9.1, LLVM 4.0.0, METIS 5.1.0, MPFR 3.1.5, matplotlib 2.0.1, memkind 1.5.0, NAMD 2.11, NAMD 2.12, NLTK 3.2.2, nose parameterized, OSU Micro, OTF2 2.0, OpenBLAS 0.2.19, OpenFOAM 2.2.2, OpenFOAM 2.3.1, OpenFOAM 2.4.0, OpenFOAM 4.0, OpenFOAM 4.1, OpenFOAM 4.1, OpenMPI 2.0.2, OpenMPI 2.0.2, ParMETIS 4.0.3, ParaView 5.2.0, ParaView 5.2.0, ParaView 5.3.0, PyYAML 3.12, Python 2.7.13, pandas 0.20.1, pbbam 20170508, pbdagcon 20170330, pkg config, pkgconfig 1.2.2, protobuf python, protobuf python, protobuf 3.3.0, pyenchant 1.6.8, Qt 4.8.7, Qt5 5.8.0, RAxML 8.2.10, SCOTCH 6.0.4, ScaLAPACK 2.0.2, Siesta 4.0, Siesta 4.1, SuiteSparse 4.5.5, SuiteSparse 4.5.5, Szip 2.1, scikit learn, Tcl 8.5.19, Tensorflow 1.1.0, Tensorflow 1.1.0, Theano 0.9.0, tbb 2017.4.174.eb, tbb 2017_U5, x265 2.4, xarray 0.9.5 +- minor enhancements, including: + - update source URLs in libpciaccess easyconfigs (#3960) + - enable use of double precision floating point in METIS 5.1.0 foss/2016a easyconfig (#4555) + + v3.2.0 (May 5th 2017) --------------------- -- GitLab From 9059b01edbf202cc26b0313d7f85c12ba5bd3a02 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 12 May 2017 08:51:58 +0200 Subject: [PATCH 0745/1603] fix update date for extensions in R 3.4.0 easyconfig --- easybuild/easyconfigs/r/R/R-3.4.0-intel-2017a-X11-20170314.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/r/R/R-3.4.0-intel-2017a-X11-20170314.eb b/easybuild/easyconfigs/r/R/R-3.4.0-intel-2017a-X11-20170314.eb index 0f9329d684..949ed58bbb 100644 --- a/easybuild/easyconfigs/r/R/R-3.4.0-intel-2017a-X11-20170314.eb +++ b/easybuild/easyconfigs/r/R/R-3.4.0-intel-2017a-X11-20170314.eb @@ -13,7 +13,7 @@ source_urls = ['http://cran.us.r-project.org/src/base/R-%(version_major)s'] preconfigopts = 'BLAS_LIBS="$LIBBLAS" LAPACK_LIBS="$LIBLAPACK"' configopts = "--with-lapack --with-blas --with-pic --enable-threads --with-x=no --enable-R-shlib" -#Actually use Tcl/Tk +# Actually use Tcl/Tk configopts += ' --with-tcl-config=$EBROOTTCL/lib/tclConfig.sh --with-tk-config=$EBROOTTK/lib/tkConfig.sh ' # Enable graphics capabilities for plotting. configopts += " --with-cairo --with-libpng --with-jpeglib --with-libtiff" @@ -62,7 +62,7 @@ ext_options = { } # !! order of packages is important !! -# packages updated on March 7th 2017 +# packages updated on May 11th 2017 exts_list = [ # default libraries, only here to sanity check their presence 'base', -- GitLab From 143826bdf5c4a40c95e9bb07bd20bd38f1914964 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 12 May 2017 08:53:34 +0200 Subject: [PATCH 0746/1603] add update date for extensions in R-bundle-Bioconductor 3.5 easyconfig --- .../R-bundle-Bioconductor-3.5-intel-2017a-R-3.4.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.5-intel-2017a-R-3.4.0.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.5-intel-2017a-R-3.4.0.eb index 99eea4dc16..80580237a7 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.5-intel-2017a-R-3.4.0.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.5-intel-2017a-R-3.4.0.eb @@ -37,6 +37,7 @@ exts_filter = ("R -q --no-save", "library(%(ext_name)s)") # CRAN packages on which these Bioconductor packages depend are available in R module on which this depends # !! order of packages is important !! +# packages updated on May 11th 2017 exts_list = [ ('BiocGenerics', '0.22.0', bioconductor_options), ('Biobase', '2.36.2', bioconductor_options), -- GitLab From 583d4167050a61ca7a9737d49a17bfd7a38910f6 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Fri, 12 May 2017 09:53:54 +0200 Subject: [PATCH 0747/1603] {tools}[intel/2016b] imbalanced-learn 0.2.1 /w Python 2.7.12 (REVIEW) --- ...d-learn-0.2.1-intel-2016b-Python-2.7.12.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/i/imbalanced-learn/imbalanced-learn-0.2.1-intel-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/i/imbalanced-learn/imbalanced-learn-0.2.1-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/i/imbalanced-learn/imbalanced-learn-0.2.1-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..6f8572780e --- /dev/null +++ b/easybuild/easyconfigs/i/imbalanced-learn/imbalanced-learn-0.2.1-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'imbalanced-learn' +version = '0.2.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/scikit-learn-contrib/imbalanced-learn' +description = """imbalanced-learn is a Python package offering a number of re-sampling techniques commonly used in + datasets showing strong between-class imbalance.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.12'), + ('scikit-learn', '0.18.1', versionsuffix), +] + +options = {'modulename': 'imblearn'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' -- GitLab From d637dc7a1b7d40ae4c70305b74ab3c1d3c7fc18e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 12 May 2017 10:26:08 +0200 Subject: [PATCH 0748/1603] bump version to v3.2.1 and massage release notes --- RELEASE_NOTES | 6 ++++-- setup.py | 2 +- 2 files changed, 5 insertions(+), 3 deletions(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index 7fd5ec2c84..4b1afa6117 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -3,7 +3,7 @@ For more detailed information, please see the git log. These release notes can also be consulted at http://easybuild.readthedocs.org/en/latest/Release_notes.html. -The latest version of easybuild-easyconfig provides 7,037 easyconfig files, for 1,228 different software packages, +The latest version of easybuild-easyconfig provides 7,036 easyconfig files, for 1,228 different software packages, 25 different (compiler) toolchains, 13 software bundles and 1 meta-package. v3.2.1 (May 12th 2017) @@ -13,8 +13,10 @@ bugfix/update release - added example easyconfig files for 12 new software packages: - AdapterRemoval (#4509), blasr_libcpp (#4566), canu (#4473), enchant (#4567), hunspell (#4567), memkind (#4544), NLTK (#4565), pbbam (#4566), pbdagcon (#4566), pyenchant (#4567), Siesta (#4562), xarray (#4556) +- added new easyconfigs for existing toolchains: + - goolfc 2017.01 (#4577) - added additional easyconfigs for various supported software packages, including: - - ASE 3.13.0, AdapterRemoval 2.2.0, BLASR 20170330, BerkeleyGW 1.2.0, BioKanga 4.3.6, Boost 1.63.0, Boost 1.63.0, blasr_libcpp 20170426, CGAL 4.8.1, CGAL 4.9, CMake 3.8.1, CUDA 8.0.61_375.26, Coreutils 8.27, canu 1.4, EasyBuild 3.2.0.eb, Eigen 3.3.3, enchant 1.6.1, FFTW 3.3.6, flex 2.5.39, GROMACS 2016.1, gcccuda 2017.01.eb, gompic 2017.01.eb, googletest 1.8.0, goolfc 2017.01.eb, grib_api 1.21.0, HDF5 1.10.1, HDF5 1.8.18, HDF5 1.8.18, HDF5 1.8.18, HTSlib 20160107, h5py 2.7.0, hanythingondemand 3.2.2, hanythingondemand 3.2.2, hunspell 1.6.1, hwloc 1.11.5, JasPer 1.900.1, Keras 2.0.4, LLVM 3.9.1, LLVM 4.0.0, METIS 5.1.0, MPFR 3.1.5, matplotlib 2.0.1, memkind 1.5.0, NAMD 2.11, NAMD 2.12, NLTK 3.2.2, nose parameterized, OSU Micro, OTF2 2.0, OpenBLAS 0.2.19, OpenFOAM 2.2.2, OpenFOAM 2.3.1, OpenFOAM 2.4.0, OpenFOAM 4.0, OpenFOAM 4.1, OpenFOAM 4.1, OpenMPI 2.0.2, OpenMPI 2.0.2, ParMETIS 4.0.3, ParaView 5.2.0, ParaView 5.2.0, ParaView 5.3.0, PyYAML 3.12, Python 2.7.13, pandas 0.20.1, pbbam 20170508, pbdagcon 20170330, pkg config, pkgconfig 1.2.2, protobuf python, protobuf python, protobuf 3.3.0, pyenchant 1.6.8, Qt 4.8.7, Qt5 5.8.0, RAxML 8.2.10, SCOTCH 6.0.4, ScaLAPACK 2.0.2, Siesta 4.0, Siesta 4.1, SuiteSparse 4.5.5, SuiteSparse 4.5.5, Szip 2.1, scikit learn, Tcl 8.5.19, Tensorflow 1.1.0, Tensorflow 1.1.0, Theano 0.9.0, tbb 2017.4.174.eb, tbb 2017_U5, x265 2.4, xarray 0.9.5 + - HDF5 1.10.1, NAMD 2.12, OpenFOAM 4.1, pandas 0.20.1, ParaView 5.2.0, R 3.4.0, R-bundle-Bioconductor 3.5, Tensorflow 1.1.0 - minor enhancements, including: - update source URLs in libpciaccess easyconfigs (#3960) - enable use of double precision floating point in METIS 5.1.0 foss/2016a easyconfig (#4555) diff --git a/setup.py b/setup.py index 85590c2983..cdf0d69c62 100644 --- a/setup.py +++ b/setup.py @@ -47,7 +47,7 @@ from distutils import log # recent setuptools versions will *TRANSFORM* something like 'X.Y.Zdev' into 'X.Y.Z.dev0', with a warning like # UserWarning: Normalizing '2.4.0dev' to '2.4.0.dev0' # This causes problems further up the dependency chain... -VERSION = '3.3.0.dev0' +VERSION = '3.2.1' API_VERSION = VERSION.split('.')[0] EB_VERSION = '.'.join(VERSION.split('.')[0:2]) -- GitLab From e531e19778783ca7f5285c4c8d6dc8b2485b8756 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 12 May 2017 14:26:56 +0200 Subject: [PATCH 0749/1603] (re-)bump to v3.3.0.dev0 --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index cdf0d69c62..85590c2983 100644 --- a/setup.py +++ b/setup.py @@ -47,7 +47,7 @@ from distutils import log # recent setuptools versions will *TRANSFORM* something like 'X.Y.Zdev' into 'X.Y.Z.dev0', with a warning like # UserWarning: Normalizing '2.4.0dev' to '2.4.0.dev0' # This causes problems further up the dependency chain... -VERSION = '3.2.1' +VERSION = '3.3.0.dev0' API_VERSION = VERSION.split('.')[0] EB_VERSION = '.'.join(VERSION.split('.')[0:2]) -- GitLab From ee171bc1dce094e97f1862ecc390486b82b7c86f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 12 May 2017 14:32:46 +0200 Subject: [PATCH 0750/1603] adding easyconfigs: EasyBuild-3.2.1.eb --- .../e/EasyBuild/EasyBuild-3.2.1.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.2.1.eb diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.2.1.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.2.1.eb new file mode 100644 index 0000000000..dfebb15dea --- /dev/null +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.2.1.eb @@ -0,0 +1,38 @@ +easyblock = 'EB_EasyBuildMeta' + +name = 'EasyBuild' +version = '3.2.1' + +homepage = 'http://hpcugent.github.com/easybuild/' +description = """EasyBuild is a software build and installation framework + written in Python that allows you to install software in a structured, + repeatable and robust way.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = [ + # vsc-install + 'https://pypi.python.org/packages/82/ec/19d85d2bb91b562195d00db9ac82d7529904e7eabc0597720966bf74714f/', + # vsc-base + 'https://pypi.python.org/packages/f7/66/1ff7ecc4a93ba37e063f5bfbe395e95a547b1dec73b017c2724f4475a958/', + # easybuild-framework + 'https://pypi.python.org/packages/77/a2/34beda6176a1c85e99861f6a5e881c3a5c67e68e1edc50258a7d941195e8/', + # easybuild-easyblocks + 'https://pypi.python.org/packages/3d/02/a5d239cbe7dfaecf712edc4aa53192239db174505e81d4c793e20abd96b6/', + # easybuild-easyconfigs + 'https://pypi.python.org/packages/ac/ae/185b876b02b2f2310fe52bb41539d23a00e421e5b19c246779e4b2be03a8/', +] +# order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) +sources = [ + 'vsc-install-0.10.26.tar.gz', + 'vsc-base-2.5.8.tar.gz', + 'easybuild-framework-%(version)s.tar.gz', + 'easybuild-easyblocks-%(version)s.tar.gz', + 'easybuild-easyconfigs-%(version)s.tar.gz', +] + +# EasyBuild is a (set of) Python packages, so it depends on Python +# usually, we want to use the system Python, so no actual Python dependency is listed +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +moduleclass = 'tools' -- GitLab From ee454a4d4305f08f04f7db64e5062d5b3d597a25 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 12 May 2017 21:00:25 +0200 Subject: [PATCH 0751/1603] Include patch to find NVML library on Ubuntu for Nvidia driver 367 and 375 --- .../GROMACS/GROMACS-2016.3-goolfc-2017.01.eb | 40 +++++++++++++++++++ ...ACS-2016.3_amend_search_for_nvml_lib.patch | 14 +++++++ 2 files changed, 54 insertions(+) create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-2016.3-goolfc-2017.01.eb create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-2016.3_amend_search_for_nvml_lib.patch diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.3-goolfc-2017.01.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.3-goolfc-2017.01.eb new file mode 100644 index 0000000000..24d9e0afe2 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.3-goolfc-2017.01.eb @@ -0,0 +1,40 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2016 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, +# Ghent University / The Francis Crick Institute +# Authors:: +# * Wiktor Jurkowski +# * Fotis Georgatos +# * George Tsouloupas +# * Kenneth Hoste +# * Adam Huffman +# License:: MIT/GPL +## + +name = 'GROMACS' +version = '2016.3' + +homepage = 'http://www.gromacs.org' +description = """ +GROMACS is a versatile package to perform molecular dynamics, + i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. + +This is a GPU enabled build, containing both MPI and threadMPI builds. +""" + +toolchain = {'name': 'goolfc', 'version': '2017.01'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = ['ftp://ftp.gromacs.org/pub/gromacs/'] +sources = [SOURCELOWER_TAR_GZ] + +patches = [ + 'GROMACS-%(version)s_amend_search_for_nvml_lib.patch', +] + +builddependencies = [ + ('CMake', '3.7.1'), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.3_amend_search_for_nvml_lib.patch b/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.3_amend_search_for_nvml_lib.patch new file mode 100644 index 0000000000..8ae9027f34 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.3_amend_search_for_nvml_lib.patch @@ -0,0 +1,14 @@ +# The NVML library location depends on driver version on Ubuntu +# Åke Sandgren, 2016-10-14 +diff -ru gromacs-2016.orig/cmake/FindNVML.cmake gromacs-2016/cmake/FindNVML.cmake +--- gromacs-2016.orig/cmake/FindNVML.cmake 2016-07-09 02:55:38.000000000 +0200 ++++ gromacs-2016/cmake/FindNVML.cmake 2016-10-14 21:44:08.143648879 +0200 +@@ -96,7 +96,7 @@ + # reasonably set GPU_DEPLOYMENT_KIT_ROOT_DIR to the value they + # passed to the installer, or the root where they later found the + # kit to be installed. Below, we cater for both possibilities. +- set( NVML_LIB_PATHS /usr/lib64 ) ++ set( NVML_LIB_PATHS /usr/lib64 /usr/lib/nvidia-367 /usr/lib/nvidia-375) + if(GPU_DEPLOYMENT_KIT_ROOT_DIR) + list(APPEND NVML_LIB_PATHS + "${GPU_DEPLOYMENT_KIT_ROOT_DIR}/src/gdk/nvml/lib" -- GitLab From 8aeae6284f5fe6bcb0bb5832f4a1ea0ec04ce5e2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 14 May 2017 19:39:51 +0200 Subject: [PATCH 0752/1603] adding easyconfigs: NAMD-2.12-intel-2017a-mpi.eb --- .../n/NAMD/NAMD-2.12-intel-2017a-mpi.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/n/NAMD/NAMD-2.12-intel-2017a-mpi.eb diff --git a/easybuild/easyconfigs/n/NAMD/NAMD-2.12-intel-2017a-mpi.eb b/easybuild/easyconfigs/n/NAMD/NAMD-2.12-intel-2017a-mpi.eb new file mode 100644 index 0000000000..a859f5adf4 --- /dev/null +++ b/easybuild/easyconfigs/n/NAMD/NAMD-2.12-intel-2017a-mpi.eb @@ -0,0 +1,24 @@ +name = 'NAMD' +version = '2.12' +versionsuffix = '-mpi' + +homepage = 'http://www.ks.uiuc.edu/Research/namd/' +description = """NAMD is a parallel molecular dynamics code designed for high-performance simulation of + large biomolecular systems.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'usempi': True, 'pic': True} + +sources = ['NAMD_%(version)s_Source.tar.gz'] + +dependencies = [ + ('Tcl', '8.6.6'), + ('FFTW', '3.3.6'), +] + +# /bin/csh is required by 'config' script +osdependencies = ['tcsh'] + +charm_arch = "mpi-linux-x86_64" + +moduleclass = 'chem' -- GitLab From e75dd82ba959670948e38161852763656350f6c9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 15 May 2017 10:26:16 +0200 Subject: [PATCH 0753/1603] style fixes: use single quotes, fix order in toolchainopts --- easybuild/easyconfigs/n/NAMD/NAMD-2.12-intel-2017a-mpi.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/n/NAMD/NAMD-2.12-intel-2017a-mpi.eb b/easybuild/easyconfigs/n/NAMD/NAMD-2.12-intel-2017a-mpi.eb index a859f5adf4..fd5bdbb7ed 100644 --- a/easybuild/easyconfigs/n/NAMD/NAMD-2.12-intel-2017a-mpi.eb +++ b/easybuild/easyconfigs/n/NAMD/NAMD-2.12-intel-2017a-mpi.eb @@ -7,7 +7,7 @@ description = """NAMD is a parallel molecular dynamics code designed for high-pe large biomolecular systems.""" toolchain = {'name': 'intel', 'version': '2017a'} -toolchainopts = {'usempi': True, 'pic': True} +toolchainopts = {'pic': True, 'usempi': True} sources = ['NAMD_%(version)s_Source.tar.gz'] @@ -19,6 +19,6 @@ dependencies = [ # /bin/csh is required by 'config' script osdependencies = ['tcsh'] -charm_arch = "mpi-linux-x86_64" +charm_arch = 'mpi-linux-x86_64' moduleclass = 'chem' -- GitLab From 28a58de9d80083c85473f36012476856d93edcb9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 15 May 2017 11:20:31 +0200 Subject: [PATCH 0754/1603] adding easyconfigs: STAR-2.5.3a-intel-2017a.eb --- .../s/STAR/STAR-2.5.3a-intel-2017a.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/s/STAR/STAR-2.5.3a-intel-2017a.eb diff --git a/easybuild/easyconfigs/s/STAR/STAR-2.5.3a-intel-2017a.eb b/easybuild/easyconfigs/s/STAR/STAR-2.5.3a-intel-2017a.eb new file mode 100644 index 0000000000..7bb56d5efd --- /dev/null +++ b/easybuild/easyconfigs/s/STAR/STAR-2.5.3a-intel-2017a.eb @@ -0,0 +1,43 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# Modified by: +# Adam Huffman +# The Francis Crick Institute + +easyblock = 'MakeCp' + +name = 'STAR' +version = '2.5.3a' + +homepage = 'https://github.com/alexdobin/STAR' +description = "STAR aligns RNA-seq reads to a reference genome using uncompressed suffix arrays." + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'openmp': True} + +source_urls = ['https://github.com/alexdobin/STAR/archive/'] +sources = ['%(version)s.tar.gz'] + +dependencies = [ + ('zlib', '1.2.11'), +] + +start_dir = 'source' + +buildopts = ' STAR && make STARlong' + +parallel = 1 + +files_to_copy = [ + (['source/STAR', 'source/STARlong'], 'bin'), + 'CHANGES.md', 'doc', 'extras', 'LICENSE', 'README.md', 'RELEASEnotes.md', +] + +sanity_check_paths = { + 'files': ["bin/STAR", "bin/STARlong"], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From 61ed4e7c403d624f0d85b986ff9a3818eb6371a4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 15 May 2017 11:51:15 +0200 Subject: [PATCH 0755/1603] adding easyconfigs: Velvet-1.2.10-intel-2017a-mt-kmer_37.eb --- .../Velvet-1.2.10-intel-2017a-mt-kmer_37.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2017a-mt-kmer_37.eb diff --git a/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2017a-mt-kmer_37.eb b/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2017a-mt-kmer_37.eb new file mode 100644 index 0000000000..19b58c6e52 --- /dev/null +++ b/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2017a-mt-kmer_37.eb @@ -0,0 +1,31 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA, 2012-2013 The Cyprus Institute +# Authors:: Cedric Laczny , Fotis Georgatos , +# Thekla Loizou , Andreas Panteli +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + +name = 'Velvet' +version = '1.2.10' +versionsuffix = '-mt-kmer_37' + +homepage = 'http://www.ebi.ac.uk/~zerbino/velvet/' +description = """Sequence assembler for very short reads""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'openmp': True, 'pic': True} + +sources = ['%(namelower)s_%(version)s.tgz'] +source_urls = ['http://www.ebi.ac.uk/~zerbino/%(namelower)s'] + +buildopts = "OPENMP=1 MAXKMERLENGTH=%s LONGSEQUENCES=1" % versionsuffix.split('_')[1] + +postinstallcmds = ["cd contrib/MetaVelvet-1.* && make && cd ../../ && cp -a contrib %(installdir)s/"] + +moduleclass = 'bio' -- GitLab From 7934c12a2e7fc6fd81543a7c8df06a1b6788a6b8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 15 May 2017 11:52:38 +0200 Subject: [PATCH 0756/1603] adding easyconfigs: Bpipe-0.9.9.2-intel-2017a.eb, Java-1.8.0_131.eb --- .../b/Bpipe/Bpipe-0.9.9.2-intel-2017a.eb | 21 +++++++++++++++++++ .../easyconfigs/j/Java/Java-1.8.0_131.eb | 15 +++++++++++++ 2 files changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bpipe/Bpipe-0.9.9.2-intel-2017a.eb create mode 100644 easybuild/easyconfigs/j/Java/Java-1.8.0_131.eb diff --git a/easybuild/easyconfigs/b/Bpipe/Bpipe-0.9.9.2-intel-2017a.eb b/easybuild/easyconfigs/b/Bpipe/Bpipe-0.9.9.2-intel-2017a.eb new file mode 100644 index 0000000000..b0ee97e8f9 --- /dev/null +++ b/easybuild/easyconfigs/b/Bpipe/Bpipe-0.9.9.2-intel-2017a.eb @@ -0,0 +1,21 @@ +easyblock = 'Tarball' + +name = 'Bpipe' +version = '0.9.9.2' + +homepage = 'http://docs.bpipe.org/' +description = "Bpipe - a tool for running and managing bioinformatics pipelines" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['http://download.bpipe.org/versions/'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('Java', '1.8.0_131', '', True)] + +sanity_check_paths = { + 'files': ['bin/bpipe', 'lib/bpipe.jar'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/j/Java/Java-1.8.0_131.eb b/easybuild/easyconfigs/j/Java/Java-1.8.0_131.eb new file mode 100644 index 0000000000..2bb2551e95 --- /dev/null +++ b/easybuild/easyconfigs/j/Java/Java-1.8.0_131.eb @@ -0,0 +1,15 @@ +name = 'Java' +version = '1.8.0_131' + +homepage = 'http://java.com/' +description = """Java Platform, Standard Edition (Java SE) lets you develop and deploy + Java applications on desktops and servers.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +# download the tar.gz directly from http://www.oracle.com/technetwork/java/javase/downloads/index.html +(vp, vs) = version.split('_') +altver = '%su%s' % (vp.split('.')[1], vs) +sources = ['jdk-%s-linux-x64.tar.gz' % altver] + +moduleclass = 'lang' -- GitLab From 26cd2367b99136755e104c2dd2b5063f67c5c957 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 15 May 2017 16:19:34 +0200 Subject: [PATCH 0757/1603] adding easyconfigs: netCDF-4.4.1.1-intel-2017a-HDF5-1.8.18.eb, netCDF-Fortran-4.4.4-intel-2017a-HDF5-1.8.18.eb, netCDF-C++4-4.3.0-intel-2017a-HDF5-1.8.18.eb --- ...tCDF-C++4-4.3.0-intel-2017a-HDF5-1.8.18.eb | 25 +++++++++++++ ...F-Fortran-4.4.4-intel-2017a-HDF5-1.8.18.eb | 18 ++++++++++ .../netCDF-4.4.1.1-intel-2017a-HDF5-1.8.18.eb | 36 +++++++++++++++++++ 3 files changed, 79 insertions(+) create mode 100644 easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.3.0-intel-2017a-HDF5-1.8.18.eb create mode 100644 easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.4-intel-2017a-HDF5-1.8.18.eb create mode 100644 easybuild/easyconfigs/n/netCDF/netCDF-4.4.1.1-intel-2017a-HDF5-1.8.18.eb diff --git a/easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.3.0-intel-2017a-HDF5-1.8.18.eb b/easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.3.0-intel-2017a-HDF5-1.8.18.eb new file mode 100644 index 0000000000..62c2012841 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.3.0-intel-2017a-HDF5-1.8.18.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'netCDF-C++4' +version = '4.3.0' +versionsuffix = '-HDF5-1.8.18' + +homepage = 'http://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/Unidata/netcdf-cxx4/archive/'] +sources = ['v%(version)s.tar.gz'] + +dependencies = [('netCDF', '4.4.1.1', versionsuffix)] + +sanity_check_paths = { + 'files': ['include/netcdf', 'lib/libnetcdf_c++4.a', 'lib/libnetcdf_c++4.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.4-intel-2017a-HDF5-1.8.18.eb b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.4-intel-2017a-HDF5-1.8.18.eb new file mode 100644 index 0000000000..188697273d --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.4-intel-2017a-HDF5-1.8.18.eb @@ -0,0 +1,18 @@ +name = 'netCDF-Fortran' +version = '4.4.4' +versionsuffix = '-HDF5-1.8.18' + +homepage = 'http://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/Unidata/netcdf-fortran/archive/'] +sources = ['v%(version)s.tar.gz'] + +dependencies = [('netCDF', '4.4.1.1', versionsuffix)] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.4.1.1-intel-2017a-HDF5-1.8.18.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.4.1.1-intel-2017a-HDF5-1.8.18.eb new file mode 100644 index 0000000000..8bc6d56640 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.4.1.1-intel-2017a-HDF5-1.8.18.eb @@ -0,0 +1,36 @@ +name = 'netCDF' +version = '4.4.1.1' +hdf5_ver = '1.8.18' +versionsuffix = '-HDF5-%s' % hdf5_ver + +homepage = 'http://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True, 'usempi': True} + +sources = ['v%(version)s.tar.gz'] +source_urls = [ + 'https://github.com/Unidata/netcdf-c/archive/' +] + +dependencies = [ + ('HDF5', hdf5_ver), + ('cURL', '7.53.1'), + ('Szip', '2.1'), +] + +builddependencies = [ + ('CMake', '3.7.2'), + ('Doxygen', '1.8.13'), +] + +# make sure both static and shared libs are built +configopts = [ + "-DBUILD_SHARED_LIBS=OFF ", + "-DBUILD_SHARED_LIBS=ON ", +] + +moduleclass = 'data' -- GitLab From c134dc6583580744f6a678ec0671352361d19c91 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 15 May 2017 16:52:33 +0200 Subject: [PATCH 0758/1603] adding easyconfigs: Doris-4.04beta4-intel-2017a.eb, Doris-4.06beta2-intel-2017a.eb --- .../d/Doris/Doris-4.04beta4-intel-2017a.eb | 16 ++++++++++++++++ .../d/Doris/Doris-4.06beta2-intel-2017a.eb | 16 ++++++++++++++++ 2 files changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/d/Doris/Doris-4.04beta4-intel-2017a.eb create mode 100644 easybuild/easyconfigs/d/Doris/Doris-4.06beta2-intel-2017a.eb diff --git a/easybuild/easyconfigs/d/Doris/Doris-4.04beta4-intel-2017a.eb b/easybuild/easyconfigs/d/Doris/Doris-4.04beta4-intel-2017a.eb new file mode 100644 index 0000000000..ad3c1ecff3 --- /dev/null +++ b/easybuild/easyconfigs/d/Doris/Doris-4.04beta4-intel-2017a.eb @@ -0,0 +1,16 @@ +name = 'Doris' +version = '4.04beta4' + +homepage = 'http://doris.tudelft.nl/' +description = "Delft object-oriented radar interferometric software" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['http://doris.tudelft.nl/software/'] +sources = ['doris_v%(version)s.tar.gz'] + +dependencies = [ + ('FFTW', '3.3.6'), +] + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/d/Doris/Doris-4.06beta2-intel-2017a.eb b/easybuild/easyconfigs/d/Doris/Doris-4.06beta2-intel-2017a.eb new file mode 100644 index 0000000000..190f829952 --- /dev/null +++ b/easybuild/easyconfigs/d/Doris/Doris-4.06beta2-intel-2017a.eb @@ -0,0 +1,16 @@ +name = 'Doris' +version = '4.06beta2' + +homepage = 'http://doris.tudelft.nl/' +description = "Delft object-oriented radar interferometric software" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['http://doris.tudelft.nl/software/'] +sources = ['doris_v%(version)s.tar.gz'] + +dependencies = [ + ('FFTW', '3.3.6'), +] + +moduleclass = 'geo' -- GitLab From b1d528ec317c4f012caf7d34c67ec6f25a6008b5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 15 May 2017 17:11:22 +0200 Subject: [PATCH 0759/1603] adding easyconfigs: EricScript-0.5.5-intel-2017a-R-3.4.0.eb, ada-2.0-5-intel-2017a-R-3.4.0.eb, BWA-0.7.15-intel-2017a.eb, SAMtools-1.4.1-intel-2017a.eb, BEDTools-2.26.0-intel-2017a.eb, seqtk-1.2-intel-2017a.eb --- .../a/ada/ada-2.0-5-intel-2017a-R-3.4.0.eb | 22 +++++++++++ .../b/BEDTools/BEDTools-2.26.0-intel-2017a.eb | 33 +++++++++++++++++ .../b/BWA/BWA-0.7.15-intel-2017a.eb | 32 ++++++++++++++++ .../EricScript-0.5.5-intel-2017a-R-3.4.0.eb | 34 +++++++++++++++++ .../s/SAMtools/SAMtools-1.4.1-intel-2017a.eb | 37 +++++++++++++++++++ .../s/seqtk/seqtk-1.2-intel-2017a.eb | 28 ++++++++++++++ 6 files changed, 186 insertions(+) create mode 100644 easybuild/easyconfigs/a/ada/ada-2.0-5-intel-2017a-R-3.4.0.eb create mode 100644 easybuild/easyconfigs/b/BEDTools/BEDTools-2.26.0-intel-2017a.eb create mode 100644 easybuild/easyconfigs/b/BWA/BWA-0.7.15-intel-2017a.eb create mode 100644 easybuild/easyconfigs/e/EricScript/EricScript-0.5.5-intel-2017a-R-3.4.0.eb create mode 100644 easybuild/easyconfigs/s/SAMtools/SAMtools-1.4.1-intel-2017a.eb create mode 100644 easybuild/easyconfigs/s/seqtk/seqtk-1.2-intel-2017a.eb diff --git a/easybuild/easyconfigs/a/ada/ada-2.0-5-intel-2017a-R-3.4.0.eb b/easybuild/easyconfigs/a/ada/ada-2.0-5-intel-2017a-R-3.4.0.eb new file mode 100644 index 0000000000..b1735c68ac --- /dev/null +++ b/easybuild/easyconfigs/a/ada/ada-2.0-5-intel-2017a-R-3.4.0.eb @@ -0,0 +1,22 @@ +easyblock = 'RPackage' + +name = 'ada' +version = '2.0-5' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://cran.r-project.org/web/packages/ada/index.html' +description = "Performs discrete, real, and gentle boost under both exponential and logistic loss on a given data set." + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['https://cran.r-project.org/src/contrib/'] +sources = ['ada_%(version)s.tar.gz'] + +dependencies = [('R', '3.4.0', '-X11-20170314')] + +sanity_check_paths = { + 'files': [], + 'dirs': [name], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.26.0-intel-2017a.eb b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.26.0-intel-2017a.eb new file mode 100644 index 0000000000..48be152602 --- /dev/null +++ b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.26.0-intel-2017a.eb @@ -0,0 +1,33 @@ +# Author: Maxime Schmitt, University of Luxembourg +# Author: Adam Huffman, The Francis Crick Institute +# +# Based on the work of: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics (SIB) +# Biozentrum - University of Basel + +easyblock = 'MakeCp' + +name = 'BEDTools' +version = '2.26.0' + +homepage = "https://github.com/arq5x/bedtools2" +description = """The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps + and computing coverage. The utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF, + and SAM/BAM.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +# https://github.com/arq5x/bedtools2/releases/download/v2.26.0/bedtools-2.26.0.tar.gz +source_urls = ['https://github.com/arq5x/bedtools2/releases/download/v%(version)s/'] +sources = ['bedtools-%(version)s.tar.gz'] + +buildopts = 'CXX="$CXX"' + +files_to_copy = ["bin", "docs", "data", "genomes", "scripts", "test"] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['bedtools', 'pairToBed', 'mergeBed', 'bedToBam', 'fastaFromBed']], + 'dirs': files_to_copy, +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BWA/BWA-0.7.15-intel-2017a.eb b/easybuild/easyconfigs/b/BWA/BWA-0.7.15-intel-2017a.eb new file mode 100644 index 0000000000..04f7fad391 --- /dev/null +++ b/easybuild/easyconfigs/b/BWA/BWA-0.7.15-intel-2017a.eb @@ -0,0 +1,32 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Cyprus Institute / CaSToRC, Uni.Lu/LCSB, NTUA +# Authors:: George Tsouloupas , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +# +# Version >= 0.7.15 +# Author: Adam Huffman +# The Francis Crick Institute +# +# Note that upstream development is mainly at: https://github.com/lh3/bwa +## + +name = 'BWA' +version = '0.7.15' + +homepage = 'http://bio-bwa.sourceforge.net/' +description = """Burrows-Wheeler Aligner (BWA) is an efficient program that aligns + relatively short nucleotide sequences against a long reference sequence such as the human genome.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/lh3/%(name)s/archive/'] +sources = ['v%(version)s.tar.gz'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/e/EricScript/EricScript-0.5.5-intel-2017a-R-3.4.0.eb b/easybuild/easyconfigs/e/EricScript/EricScript-0.5.5-intel-2017a-R-3.4.0.eb new file mode 100644 index 0000000000..adaed6879a --- /dev/null +++ b/easybuild/easyconfigs/e/EricScript/EricScript-0.5.5-intel-2017a-R-3.4.0.eb @@ -0,0 +1,34 @@ +easyblock = 'Tarball' + +name = 'EricScript' +version = '0.5.5' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://sites.google.com/site/bioericscript/home' +description = "EricScript is a computational framework for the discovery of gene fusions in paired end RNA-seq data." + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_BZ2] + +dependencies = [ + ('R', '3.4.0', '-X11-20170314'), + ('ada', '2.0-5', versionsuffix), + ('BWA', '0.7.15'), + ('SAMtools', '1.4.1'), + ('BEDTools', '2.26.0'), + ('seqtk', '1.2'), + ('BLAT', '3.5'), +] + +postinstallcmds = ["chmod a+rx %(installdir)s/ericscript.pl"] + +sanity_check_paths = { + 'files': ['ericscript.pl', 'LICENSE', 'README'], + 'dirs': ['lib'], +} + +modextrapaths = {'PATH': ''} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4.1-intel-2017a.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4.1-intel-2017a.eb new file mode 100644 index 0000000000..cd48ea8cde --- /dev/null +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4.1-intel-2017a.eb @@ -0,0 +1,37 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Robert Schmidt , Cedric Laczny , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# Modified by: Adam Huffman +# The Francis Crick Institute +# +# Modified for version 1.4 by: Kurt Lust, UAntwerpen +# +## +name = 'SAMtools' +version = '1.4.1' + +homepage = 'http://www.htslib.org/' +description = """SAM Tools provide various utilities for manipulating alignments in the SAM format, + including sorting, merging, indexing and generating alignments in a per-position format.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s'] +sources = [SOURCELOWER_TAR_BZ2] + +# The htslib component of SAMtools 1.4 uses zlib, bzip2 and lzma compression. +# The latter is currently provided by XZ. +dependencies = [ + ('ncurses', '6.0'), + ('zlib', '1.2.11'), + ('bzip2', '1.0.6'), + ('XZ', '5.2.3'), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/seqtk/seqtk-1.2-intel-2017a.eb b/easybuild/easyconfigs/s/seqtk/seqtk-1.2-intel-2017a.eb new file mode 100644 index 0000000000..d6c74b18dc --- /dev/null +++ b/easybuild/easyconfigs/s/seqtk/seqtk-1.2-intel-2017a.eb @@ -0,0 +1,28 @@ +easyblock = 'MakeCp' + +name = 'seqtk' +version = '1.2' + +homepage = 'https://github.com/lh3/seqtk/' +description = """Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format. + It seamlessly parses both FASTA and FASTQ files which can also be optionally compressed by gzip.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +sources = ['v%(version)s.tar.gz'] +source_urls = ['https://github.com/lh3/seqtk/archive/'] + +buildopts = 'CC="$CC" CFLAGS="$CLFAGS"' + +files_to_copy = ["seqtk"] + +sanity_check_paths = { + 'files': files_to_copy, + 'dirs': [], +} + +modextrapaths = { + 'PATH': [''], +} + +moduleclass = 'bio' -- GitLab From e1a4963d905de9962b793beed5336e14098d1577 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 15 May 2017 19:35:34 +0200 Subject: [PATCH 0760/1603] {data}[intel/2017a] NCL 6.4.0 (+ deps) --- .../ESMF-6.3.0rp1-intel-2017a-HDF5-1.8.18.eb | 32 +++++++ ...0-intel-2017a-Python-2.7.13-HDF5-1.8.18.eb | 49 ++++++++++ .../n/NCL/NCL-6.4.0-intel-2017a.eb | 40 ++++++++ .../n/NCL/NCL-6.4.0_fix-types.patch | 94 +++++++++++++++++++ 4 files changed, 215 insertions(+) create mode 100644 easybuild/easyconfigs/e/ESMF/ESMF-6.3.0rp1-intel-2017a-HDF5-1.8.18.eb create mode 100644 easybuild/easyconfigs/g/GDAL/GDAL-2.2.0-intel-2017a-Python-2.7.13-HDF5-1.8.18.eb create mode 100644 easybuild/easyconfigs/n/NCL/NCL-6.4.0-intel-2017a.eb create mode 100644 easybuild/easyconfigs/n/NCL/NCL-6.4.0_fix-types.patch diff --git a/easybuild/easyconfigs/e/ESMF/ESMF-6.3.0rp1-intel-2017a-HDF5-1.8.18.eb b/easybuild/easyconfigs/e/ESMF/ESMF-6.3.0rp1-intel-2017a-HDF5-1.8.18.eb new file mode 100644 index 0000000000..7d428e69ac --- /dev/null +++ b/easybuild/easyconfigs/e/ESMF/ESMF-6.3.0rp1-intel-2017a-HDF5-1.8.18.eb @@ -0,0 +1,32 @@ +name = 'ESMF' +version = '6.3.0rp1' +versionsuffix = '-HDF5-1.8.18' + +homepage = 'http://sourceforge.net/projects/esmf' +description = """The Earth System Modeling Framework (ESMF) is software for building and coupling weather, + climate, and related models.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'usempi': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s_src.tar.gz' % '_'.join(version.split('.'))] + +patches = [ + 'ESMF-6.1.1_libopts.patch', + 'ESMF-%(version)s_fix-file-open-test.patch', +] + +dependencies = [ + ('netCDF', '4.4.1.1', versionsuffix), + ('netCDF-Fortran', '4.4.4', versionsuffix), + ('netCDF-C++4', '4.3.0', versionsuffix), +] + +buildopts = 'ESMF_NETCDF_INCLUDE=$EBROOTNETCDFMINFORTRAN/include ' +buildopts += 'ESMF_NETCDF_LIBS="`nc-config --libs` `nf-config --flibs` `ncxx4-config --libs`"' + +# too parallel causes the build to become really slow +maxparallel = 8 + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-2.2.0-intel-2017a-Python-2.7.13-HDF5-1.8.18.eb b/easybuild/easyconfigs/g/GDAL/GDAL-2.2.0-intel-2017a-Python-2.7.13-HDF5-1.8.18.eb new file mode 100644 index 0000000000..26dd6f6835 --- /dev/null +++ b/easybuild/easyconfigs/g/GDAL/GDAL-2.2.0-intel-2017a-Python-2.7.13-HDF5-1.8.18.eb @@ -0,0 +1,49 @@ +easyblock = 'ConfigureMake' + +name = 'GDAL' +version = '2.2.0' +hdf5_ver = '1.8.18' +versionsuffix = '-Python-%%(pyver)s-HDF5-%s' % hdf5_ver + +homepage = 'http://www.gdal.org/' +description = """GDAL is a translator library for raster geospatial data formats that is released under an X/MIT style + Open Source license by the Open Source Geospatial Foundation. As a library, it presents a single abstract data model + to the calling application for all supported formats. It also comes with a variety of useful commandline utilities for + data translation and processing.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'usempi': True} + +source_urls = ['http://download.osgeo.org/gdal/%(version)s/'] +sources = [SOURCELOWER_TAR_XZ] +patches = ['GDAL-%(version)s_fix-uchar-definition.patch'] + +dependencies = [ + ('Python', '2.7.13'), + ('netCDF', '4.4.1.1', '-HDF5-%s' % hdf5_ver), + ('expat', '2.2.0'), + ('GEOS', '3.6.1', '-Python-%(pyver)s'), + ('SQLite', '3.17.0'), + ('libxml2', '2.9.4'), + ('libpng', '1.6.29'), + ('libjpeg-turbo', '1.5.1'), + ('JasPer', '1.900.1'), + ('LibTIFF', '4.0.7'), + ('zlib', '1.2.11'), + ('cURL', '7.53.1'), + ('PCRE', '8.40'), +] + +configopts = '--with-expat=$EBROOTEXPAT --with-libz=$EBROOTLIBZ --with-hdf5=$EBROOTHDF5 --with-netcdf=$EBROOTNETCDF' +configopts += ' --with-xml2=$EBROOTLIBXML2 --with-geos=$EBROOTGEOS/bin/geos-config --with-jpeg=$EBROOTLIBJPEGMINTURBO' +configopts += ' --with-png=$EBROOTLIBPNG --with-sqlite3=$EBROOTSQLITE --with-jasper=$EBROOTJASPER' +configopts += ' --with-libtiff=$EBROOTLIBTIFF --with-pcre=$EBROOTPCRE --with-python=$EBROOTPYTHON/bin/python' + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +sanity_check_paths = { + 'files': ['lib/libgdal.a', 'lib/libgdal.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include', 'lib/python%(pyshortver)s/site-packages'] +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/NCL/NCL-6.4.0-intel-2017a.eb b/easybuild/easyconfigs/n/NCL/NCL-6.4.0-intel-2017a.eb new file mode 100644 index 0000000000..69a80fc8ea --- /dev/null +++ b/easybuild/easyconfigs/n/NCL/NCL-6.4.0-intel-2017a.eb @@ -0,0 +1,40 @@ +name = 'NCL' +version = '6.4.0' + +homepage = 'http://www.ncl.ucar.edu' +description = """NCL is an interpreted language designed specifically for scientific data analysis and + visualization.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +#toolchainopts = {'pic': True, 'usempi': True, 'openmp': True} +toolchainopts = {'pic': True, 'openmp': True, 'cstd': 'c99'} + +# download via https://www.earthsystemgrid.org/dataset/ncl.html +sources = ['%(namelower)s_ncarg-%(version)s.tar.gz'] + +patches = ['NCL-%(version)s_fix-types.patch'] + +hdf5_ver = '1.8.18' +dependencies = [ + ('cURL', '7.53.1'), + ('JasPer', '1.900.1'), + ('g2lib', '1.4.0'), + ('g2clib', '1.6.0'), + ('HDF', '4.2.12'), + ('HDF5', hdf5_ver), + ('netCDF', '4.4.1.1', '-HDF5-%s' % hdf5_ver), + ('netCDF-Fortran', '4.4.4', '-HDF5-%s' % hdf5_ver), + ('Szip', '2.1'), + ('freetype', '2.7.1', '-libpng-1.6.29'), + ('zlib', '1.2.11'), + ('GDAL', '2.2.0', '-Python-2.7.13-HDF5-%s' % hdf5_ver), + ('UDUNITS', '2.2.24'), + ('ESMF', '6.3.0rp1', '-HDF5-%s' % hdf5_ver), + ('bzip2', '1.0.6'), + ('cairo', '1.14.8'), + ('libiconv', '1.15'), + ('GSL', '2.3'), +] +builddependencies = [('makedepend', '1.0.5')] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/NCL/NCL-6.4.0_fix-types.patch b/easybuild/easyconfigs/n/NCL/NCL-6.4.0_fix-types.patch new file mode 100644 index 0000000000..ecdfe831e0 --- /dev/null +++ b/easybuild/easyconfigs/n/NCL/NCL-6.4.0_fix-types.patch @@ -0,0 +1,94 @@ +fix compilation problems due to incorrect type +author: Kenneth Hoste (HPC-UGent) +--- ni/src/lib/nfp/SCRIP2KMLW.c.orig 2017-04-21 11:22:11.523861897 +0200 ++++ ni/src/lib/nfp/SCRIP2KMLW.c 2017-04-21 11:22:17.773923222 +0200 +@@ -8,17 +8,17 @@ + NhlErrorTypes SCRIP2KML_W(void) { + /* Defining the Arguments */ + /* Argument # 0 */ +- string * scrip_filename; ++ NclQuark* scrip_filename; + char * c_scrip_filename; + int ncid; + + /* Argument # 1 */ +- string * kml_filename; ++ NclQuark* kml_filename; + char * c_kml_filename; + FILE * fid; + + /* Argument # 2 */ +- string * gridname; ++ NclQuark* gridname; + char * c_gridname; + + /* End of Defining the Arguments */ +@@ -48,7 +48,7 @@ + + /* Getting Arguments values */ + /* Argument # 0 */ +- scrip_filename = (string *) NclGetArgValue( ++ scrip_filename = (NclQuark*) NclGetArgValue( + 0, + 3, + NULL, +@@ -61,7 +61,7 @@ + c_scrip_filename = NrmQuarkToString(*scrip_filename); + + /* Argument # 1 */ +- kml_filename = (string *) NclGetArgValue( ++ kml_filename = (NclQuark*) NclGetArgValue( + 1, + 3, + NULL, +@@ -74,7 +74,7 @@ + c_kml_filename = NrmQuarkToString(*kml_filename); + + /* Argument # 1 */ +- gridname = (string *) NclGetArgValue( ++ gridname = (NclQuark*) NclGetArgValue( + 2, + 3, + NULL, +@@ -212,4 +212,4 @@ + free(grid_corner_lon); + fclose(fid); + return (NhlNOERROR); +-} +\ No newline at end of file ++} +--- ni/src/lib/nfp/Unstruct2KMLW.c.orig 2017-04-21 11:20:50.403067496 +0200 ++++ ni/src/lib/nfp/Unstruct2KMLW.c 2017-04-21 11:21:34.883504667 +0200 +@@ -7,12 +7,12 @@ + NhlErrorTypes Unstruct2KML_W(void) { + /* Defining the Arguments */ + /* Argument # 0 */ +- string * filename; ++ NclQuark* filename; + char * c_filename; + FILE * fid; + + /* Argument # 1 */ +- string * gridname; ++ NclQuark* gridname; + char * c_gridname; + + /* Argument # 2 */ +@@ -50,7 +50,7 @@ + + /* Getting Arguments values */ + /* Argument # 0 */ +- filename = (string *) NclGetArgValue( ++ filename = (NclQuark*) NclGetArgValue( + 0, + 6, + NULL, +@@ -63,7 +63,7 @@ + c_filename = NrmQuarkToString(*filename); + + /* Argument # 1 */ +- gridname = (string *) NclGetArgValue( ++ gridname = (NclQuark*) NclGetArgValue( + 1, + 6, + NULL, -- GitLab From a870c28a01201cd38a21584c6f614e470204f76b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 15 May 2017 20:56:01 +0200 Subject: [PATCH 0761/1603] add missing patch file for GDAL 2.2.0 with intel/2017a --- .../g/GDAL/GDAL-2.2.0_fix-uchar-definition.patch | 11 +++++++++++ 1 file changed, 11 insertions(+) create mode 100644 easybuild/easyconfigs/g/GDAL/GDAL-2.2.0_fix-uchar-definition.patch diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-2.2.0_fix-uchar-definition.patch b/easybuild/easyconfigs/g/GDAL/GDAL-2.2.0_fix-uchar-definition.patch new file mode 100644 index 0000000000..c876781483 --- /dev/null +++ b/easybuild/easyconfigs/g/GDAL/GDAL-2.2.0_fix-uchar-definition.patch @@ -0,0 +1,11 @@ +add definition for uchar type that is not known by Intel compilers +author: Kenneth Hoste (HPC-UGent) +--- gdal-2.2.0/frmts/jpeg2000/jpeg2000_vsil_io.h.orig 2017-05-15 17:23:31.334324922 +0200 ++++ gdal-2.2.0/frmts/jpeg2000/jpeg2000_vsil_io.h 2017-05-15 17:23:52.134563207 +0200 +@@ -34,4 +34,6 @@ + + jas_stream_t *JPEG2000_VSIL_fopen(const char *filename, const char *mode); + ++#define uchar unsigned char ++ + #endif -- GitLab From f350e79564938b994f09e48b09bdbe88964ab95e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 16 May 2017 09:30:27 +0200 Subject: [PATCH 0762/1603] clean up toolchainopts in NCL 6.4.0 easyconfig --- easybuild/easyconfigs/n/NCL/NCL-6.4.0-intel-2017a.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/n/NCL/NCL-6.4.0-intel-2017a.eb b/easybuild/easyconfigs/n/NCL/NCL-6.4.0-intel-2017a.eb index 69a80fc8ea..9fa92eb87b 100644 --- a/easybuild/easyconfigs/n/NCL/NCL-6.4.0-intel-2017a.eb +++ b/easybuild/easyconfigs/n/NCL/NCL-6.4.0-intel-2017a.eb @@ -6,8 +6,7 @@ description = """NCL is an interpreted language designed specifically for scient visualization.""" toolchain = {'name': 'intel', 'version': '2017a'} -#toolchainopts = {'pic': True, 'usempi': True, 'openmp': True} -toolchainopts = {'pic': True, 'openmp': True, 'cstd': 'c99'} +toolchainopts = {'cstd': 'c99', 'openmp': True, 'pic': True} # download via https://www.earthsystemgrid.org/dataset/ncl.html sources = ['%(namelower)s_ncarg-%(version)s.tar.gz'] -- GitLab From 9b014dfe78bf42f2c5f26e82868346b9dd0bff48 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 16 May 2017 09:58:11 +0200 Subject: [PATCH 0763/1603] adding easyconfigs: SCons-2.5.1-intel-2017a.eb --- .../s/SCons/SCons-2.5.1-intel-2017a.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/s/SCons/SCons-2.5.1-intel-2017a.eb diff --git a/easybuild/easyconfigs/s/SCons/SCons-2.5.1-intel-2017a.eb b/easybuild/easyconfigs/s/SCons/SCons-2.5.1-intel-2017a.eb new file mode 100644 index 0000000000..cfdd0743d4 --- /dev/null +++ b/easybuild/easyconfigs/s/SCons/SCons-2.5.1-intel-2017a.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'SCons' +version = '2.5.1' + +homepage = 'http://www.scons.org/' +description = "SCons is a software construction tool." + +toolchain = {'name': 'intel', 'version': '2017a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] + +# SCons requires Python 2, rely on system Python so we can use SCons when module for Python 3.x is loaded +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +sanity_check_paths = { + 'files': ['bin/scons', 'bin/scons-time', 'bin/sconsign'], + 'dirs': ['lib/%(namelower)s-%(version)s/%(name)s'], +} + +options = {'modulename': False} + +moduleclass = 'devel' -- GitLab From a7191dd886149d7f146737462f4dc79bc6b58d07 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 16 May 2017 10:17:28 +0200 Subject: [PATCH 0764/1603] adding easyconfigs: SpiceyPy-1.1.1-intel-2017a-Python-3.6.1.eb --- ...SpiceyPy-1.1.1-intel-2017a-Python-3.6.1.eb | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/s/SpiceyPy/SpiceyPy-1.1.1-intel-2017a-Python-3.6.1.eb diff --git a/easybuild/easyconfigs/s/SpiceyPy/SpiceyPy-1.1.1-intel-2017a-Python-3.6.1.eb b/easybuild/easyconfigs/s/SpiceyPy/SpiceyPy-1.1.1-intel-2017a-Python-3.6.1.eb new file mode 100644 index 0000000000..e2776528bd --- /dev/null +++ b/easybuild/easyconfigs/s/SpiceyPy/SpiceyPy-1.1.1-intel-2017a-Python-3.6.1.eb @@ -0,0 +1,22 @@ +easyblock = 'PythonPackage' + +name = 'SpiceyPy' +version = '1.1.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/AndrewAnnex/SpiceyPy' +description = "SpiceyPy is a Python wrapper for the NAIF C SPICE Toolkit (N65)" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('Python', '3.6.1')] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'geo' -- GitLab From 34a5f16d1c19c76a6275b1e1e76a735243bce8c8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 16 May 2017 10:19:34 +0200 Subject: [PATCH 0765/1603] adding easyconfigs: h5py-2.7.0-intel-2017a-Python-3.6.1-HDF5-1.10.0-patch1.eb --- ...l-2017a-Python-3.6.1-HDF5-1.10.0-patch1.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/h/h5py/h5py-2.7.0-intel-2017a-Python-3.6.1-HDF5-1.10.0-patch1.eb diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.7.0-intel-2017a-Python-3.6.1-HDF5-1.10.0-patch1.eb b/easybuild/easyconfigs/h/h5py/h5py-2.7.0-intel-2017a-Python-3.6.1-HDF5-1.10.0-patch1.eb new file mode 100644 index 0000000000..22fe0fbf91 --- /dev/null +++ b/easybuild/easyconfigs/h/h5py/h5py-2.7.0-intel-2017a-Python-3.6.1-HDF5-1.10.0-patch1.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonPackage' + +name = 'h5py' +version = '2.7.0' +hdf5_ver = '1.10.0-patch1' +versionsuffix = '-Python-%%(pyver)s-HDF5-%s' % hdf5_ver + +homepage = 'http://www.h5py.org/' +description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, + version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous + amounts of data.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'usempi': True} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +# to really use mpi enabled hdf5 we now seem to need a configure step +prebuildopts = ' python setup.py configure --mpi --hdf5=$EBROOTHDF5 && ' + +dependencies = [ + ('Python', '3.6.1'), + ('HDF5', hdf5_ver), + ('pkgconfig', '1.2.2', '-Python-%(pyver)s'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +moduleclass = 'data' -- GitLab From efa22960a1721b67796cfac831401c5c0f98d8ee Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 16 May 2017 10:34:27 +0200 Subject: [PATCH 0766/1603] adding easyconfigs: GDAL-2.2.0-intel-2017a-Python-3.6.1.eb, GEOS-3.6.1-intel-2017a-Python-3.6.1.eb, SWIG-3.0.12-intel-2017a-Python-3.6.1.eb --- .../GDAL-2.2.0-intel-2017a-Python-3.6.1.eb | 48 +++++++++++++++++++ .../GEOS-3.6.1-intel-2017a-Python-3.6.1.eb | 29 +++++++++++ .../SWIG-3.0.12-intel-2017a-Python-3.6.1.eb | 20 ++++++++ 3 files changed, 97 insertions(+) create mode 100644 easybuild/easyconfigs/g/GDAL/GDAL-2.2.0-intel-2017a-Python-3.6.1.eb create mode 100644 easybuild/easyconfigs/g/GEOS/GEOS-3.6.1-intel-2017a-Python-3.6.1.eb create mode 100644 easybuild/easyconfigs/s/SWIG/SWIG-3.0.12-intel-2017a-Python-3.6.1.eb diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-2.2.0-intel-2017a-Python-3.6.1.eb b/easybuild/easyconfigs/g/GDAL/GDAL-2.2.0-intel-2017a-Python-3.6.1.eb new file mode 100644 index 0000000000..0b26815dc5 --- /dev/null +++ b/easybuild/easyconfigs/g/GDAL/GDAL-2.2.0-intel-2017a-Python-3.6.1.eb @@ -0,0 +1,48 @@ +easyblock = 'ConfigureMake' + +name = 'GDAL' +version = '2.2.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.gdal.org/' +description = """GDAL is a translator library for raster geospatial data formats that is released under an X/MIT style + Open Source license by the Open Source Geospatial Foundation. As a library, it presents a single abstract data model + to the calling application for all supported formats. It also comes with a variety of useful commandline utilities for + data translation and processing.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'usempi': True} + +source_urls = ['http://download.osgeo.org/gdal/%(version)s/'] +sources = [SOURCELOWER_TAR_XZ] +patches = ['GDAL-%(version)s_fix-uchar-definition.patch'] + +dependencies = [ + ('Python', '3.6.1'), + ('netCDF', '4.4.1.1'), + ('expat', '2.2.0'), + ('GEOS', '3.6.1', versionsuffix), + ('SQLite', '3.17.0'), + ('libxml2', '2.9.4'), + ('libpng', '1.6.29'), + ('libjpeg-turbo', '1.5.1'), + ('JasPer', '2.0.12'), + ('LibTIFF', '4.0.7'), + ('zlib', '1.2.11'), + ('cURL', '7.53.1'), + ('PCRE', '8.40'), +] + +configopts = '--with-expat=$EBROOTEXPAT --with-libz=$EBROOTLIBZ --with-hdf5=$EBROOTHDF5 --with-netcdf=$EBROOTNETCDF' +configopts += ' --with-xml2=$EBROOTLIBXML2 --with-geos=$EBROOTGEOS/bin/geos-config --with-jpeg=$EBROOTLIBJPEGMINTURBO' +configopts += ' --with-png=$EBROOTLIBPNG --with-sqlite3=$EBROOTSQLITE --with-jasper=$EBROOTJASPER' +configopts += ' --with-libtiff=$EBROOTLIBTIFF --with-pcre=$EBROOTPCRE --with-python=$EBROOTPYTHON/bin/python' + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +sanity_check_paths = { + 'files': ['lib/libgdal.a', 'lib/libgdal.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include', 'lib/python%(pyshortver)s/site-packages'] +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/g/GEOS/GEOS-3.6.1-intel-2017a-Python-3.6.1.eb b/easybuild/easyconfigs/g/GEOS/GEOS-3.6.1-intel-2017a-Python-3.6.1.eb new file mode 100644 index 0000000000..786b191d55 --- /dev/null +++ b/easybuild/easyconfigs/g/GEOS/GEOS-3.6.1-intel-2017a-Python-3.6.1.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'GEOS' +version = '3.6.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://trac.osgeo.org/geos' +description = """GEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (JTS)""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['http://download.osgeo.org/geos/'] +sources = [SOURCELOWER_TAR_BZ2] +patches = ['GEOS-%(version)s_fix-Python3.patch'] + +dependencies = [('Python', '3.6.1')] + +builddependencies = [('SWIG', '3.0.12', versionsuffix)] + +configopts = '--enable-python' + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +sanity_check_paths = { + 'files': ['bin/geos-config', 'lib/libgeos.%s' % SHLIB_EXT, 'lib/libgeos.a', 'include/geos.h'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/geos'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/SWIG/SWIG-3.0.12-intel-2017a-Python-3.6.1.eb b/easybuild/easyconfigs/s/SWIG/SWIG-3.0.12-intel-2017a-Python-3.6.1.eb new file mode 100644 index 0000000000..5c78d52fbe --- /dev/null +++ b/easybuild/easyconfigs/s/SWIG/SWIG-3.0.12-intel-2017a-Python-3.6.1.eb @@ -0,0 +1,20 @@ +name = 'SWIG' +version = '3.0.12' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.swig.org/' +description = """SWIG is a software development tool that connects programs written in C and C++ with + a variety of high-level programming languages.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('Python', '3.6.1'), + ('PCRE', '8.40'), +] + +moduleclass = 'devel' -- GitLab From 35513ec7cbaaf931910118fbf7f6567ffb5f5dbb Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 16 May 2017 10:35:59 +0200 Subject: [PATCH 0767/1603] add missing patch for GEOS --- .../g/GEOS/GEOS-3.6.1_fix-Python3.patch | 65 +++++++++++++++++++ 1 file changed, 65 insertions(+) create mode 100644 easybuild/easyconfigs/g/GEOS/GEOS-3.6.1_fix-Python3.patch diff --git a/easybuild/easyconfigs/g/GEOS/GEOS-3.6.1_fix-Python3.patch b/easybuild/easyconfigs/g/GEOS/GEOS-3.6.1_fix-Python3.patch new file mode 100644 index 0000000000..51d136b71d --- /dev/null +++ b/easybuild/easyconfigs/g/GEOS/GEOS-3.6.1_fix-Python3.patch @@ -0,0 +1,65 @@ +fix configuring with Python 3 +cfr. https://trac.osgeo.org/geos/ticket/774 +--- configure.orig 2016-12-29 17:33:15.229294313 +0100 ++++ configure 2016-12-29 18:33:27.822625611 +0100 +@@ -18329,7 +18329,7 @@ + if ${am_cv_python_version+:} false; then : + $as_echo_n "(cached) " >&6 + else +- am_cv_python_version=`$PYTHON -c "import sys; print sys.version[:3]"` ++ am_cv_python_version=`$PYTHON -c "import sys; print(sys.version[:3])"` + fi + { $as_echo "$as_me:${as_lineno-$LINENO}: result: $am_cv_python_version" >&5 + $as_echo "$am_cv_python_version" >&6; } +@@ -18348,7 +18348,7 @@ + if ${am_cv_python_platform+:} false; then : + $as_echo_n "(cached) " >&6 + else +- am_cv_python_platform=`$PYTHON -c "import sys; print sys.platform"` ++ am_cv_python_platform=`$PYTHON -c "import sys; print(sys.platform)"` + fi + { $as_echo "$as_me:${as_lineno-$LINENO}: result: $am_cv_python_platform" >&5 + $as_echo "$am_cv_python_platform" >&6; } +@@ -18362,7 +18362,7 @@ + if ${am_cv_python_pythondir+:} false; then : + $as_echo_n "(cached) " >&6 + else +- am_cv_python_pythondir=`$PYTHON -c "from distutils import sysconfig; print sysconfig.get_python_lib(0,0,prefix='$PYTHON_PREFIX')" 2>/dev/null || ++ am_cv_python_pythondir=`$PYTHON -c "from distutils import sysconfig; print(sysconfig.get_python_lib(0,0,prefix='$PYTHON_PREFIX'))" 2>/dev/null || + echo "$PYTHON_PREFIX/lib/python$PYTHON_VERSION/site-packages"` + fi + { $as_echo "$as_me:${as_lineno-$LINENO}: result: $am_cv_python_pythondir" >&5 +@@ -18379,7 +18379,7 @@ + if ${am_cv_python_pyexecdir+:} false; then : + $as_echo_n "(cached) " >&6 + else +- am_cv_python_pyexecdir=`$PYTHON -c "from distutils import sysconfig; print sysconfig.get_python_lib(1,0,prefix='$PYTHON_EXEC_PREFIX')" 2>/dev/null || ++ am_cv_python_pyexecdir=`$PYTHON -c "from distutils import sysconfig; print(sysconfig.get_python_lib(1,0,prefix='$PYTHON_EXEC_PREFIX'))" 2>/dev/null || + echo "${PYTHON_EXEC_PREFIX}/lib/python${PYTHON_VERSION}/site-packages"` + fi + { $as_echo "$as_me:${as_lineno-$LINENO}: result: $am_cv_python_pyexecdir" >&5 +@@ -18448,19 +18448,21 @@ + # Check for Python library path + { $as_echo "$as_me:${as_lineno-$LINENO}: checking for Python library path" >&5 + $as_echo_n "checking for Python library path... " >&6; } +- for i in "$base_python_path/lib/python$PYTHON_VERSION/config/" "$base_python_path/lib/python$PYTHON_VERSION/" "$base_python_path/lib/python/config/" "$base_python_path/lib/python/" "$base_python_path/" "$base_python_path/libs/" ; do +- python_path=`find $i -name libpython$PYTHON_VERSION.* -print 2> /dev/null | sed "1q"` ++ for i in "$base_python_path/lib/python$PYTHON_VERSION/config/" "$base_python_path/lib/python$PYTHON_VERSION/" "$base_python_path/lib/python/config/" "$base_python_path/lib/python/" "$base_python_path/" "$base_python_path/libs/" "$base_python_path/lib/" ; do ++ python_path=`find $i -name libpython$PYTHON_VERSION*.so* -print 2> /dev/null | sed "1q"` + if test -n "$python_path" ; then + break + fi + done ++ ++ lpython_name=`python -c "import os; print(os.path.split(\"$python_path\")[1].split(\".so\")[0].split(\"lib\")[1])"` + python_path=`echo $python_path | sed "s,/libpython.*$,,"` + { $as_echo "$as_me:${as_lineno-$LINENO}: result: $python_path" >&5 + $as_echo "$python_path" >&6; } + if test -z "$python_path" ; then + as_fn_error $? "cannot find Python library path" "$LINENO" 5 + fi +- PYTHON_LDFLAGS="-L$python_path -lpython$PYTHON_VERSION" ++ PYTHON_LDFLAGS="-L$python_path -l$lpython_name" + + # + python_site=`echo $base_python_path | sed "s/config/site-packages/"` -- GitLab From 7561b619e73b3afa2cc5bc68c2f35e798f09cbc7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 16 May 2017 10:37:19 +0200 Subject: [PATCH 0768/1603] adding easyconfigs: motif-2.3.7-intel-2017a.eb, xbitmaps-1.1.1.eb, flex-2.6.4-GCCcore-6.3.0.eb --- .../f/flex/flex-2.6.4-GCCcore-6.3.0.eb | 24 ++++++++++++ .../m/motif/motif-2.3.7-intel-2017a.eb | 39 +++++++++++++++++++ .../easyconfigs/x/xbitmaps/xbitmaps-1.1.1.eb | 19 +++++++++ 3 files changed, 82 insertions(+) create mode 100644 easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-6.3.0.eb create mode 100644 easybuild/easyconfigs/m/motif/motif-2.3.7-intel-2017a.eb create mode 100644 easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1.eb diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-6.3.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..c864ccaca1 --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-6.3.0.eb @@ -0,0 +1,24 @@ +name = 'flex' +version = '2.6.4' + +homepage = 'http://flex.sourceforge.net/' +description = """Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, + sometimes called a tokenizer, is a program which recognizes lexical patterns in text.""" + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['https://github.com/westes/flex/releases/download/v%(version)s/'] + +checksums = ['2882e3179748cc9f9c23ec593d6adc8d'] + +dependencies = [('M4', '1.4.18')] +builddependencies = [ + ('Bison', '3.0.4'), + ('help2man', '1.47.4'), + # use same binutils version that was used when building GCC toolchain + ('binutils', '2.27', '', True), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/m/motif/motif-2.3.7-intel-2017a.eb b/easybuild/easyconfigs/m/motif/motif-2.3.7-intel-2017a.eb new file mode 100644 index 0000000000..e0ba802b63 --- /dev/null +++ b/easybuild/easyconfigs/m/motif/motif-2.3.7-intel-2017a.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'motif' +version = '2.3.7' + +homepage = 'http://motif.ics.com/' +description = """Motif refers to both a graphical user interface (GUI) specification and the widget toolkit for building + applications that follow that specification under the X Window System on Unix and other POSIX-compliant systems. + It was the standard toolkit for the Common Desktop Environment and thus for Unix.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +sources = ['%(name)s-%(version)s.tar.gz'] +source_urls = [SOURCEFORGE_SOURCE] + +dependencies = [ + ('X11', '20170314'), + ('libpng', '1.6.29'), + ('xbitmaps', '1.1.1', '', True), + ('freetype', '2.7.1', '-libpng-1.6.29'), + ('libjpeg-turbo', '1.5.1'), + ('bzip2', '1.0.6'), +] +builddependencies = [ + ('Autotools', '20150215'), + ('flex', '2.6.4'), + ('Bison', '3.0.4'), + ('util-linux', '2.29.2'), +] + +# makefile is not parallel safe +parallel = 1 + +sanity_check_paths = { + 'files': ['lib/libMrm.a', 'lib/libUil.a', 'lib/libXm.a', 'bin/mwm', 'bin/uil', 'bin/xmbind'], + 'dirs': ['include/Mrm', 'include/uil', 'include/X11', 'include/Xm'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1.eb b/easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1.eb new file mode 100644 index 0000000000..b56ca14110 --- /dev/null +++ b/easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'xbitmaps' +version = '1.1.1' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """provides bitmaps for x""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_DATA_SOURCE] + +sanity_check_paths = { + 'files': ['include/X11/bitmaps/gray'], + 'dirs': [] +} + +moduleclass = 'devel' -- GitLab From 0377a1294cf02a92a3163d815860a572958fba73 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 16 May 2017 11:49:06 +0200 Subject: [PATCH 0769/1603] {bio}[intel/2017a] TopHat 2.1.1 --- .../t/TopHat/TopHat-2.1.1-intel-2017a.eb | 41 +++++++++++++++++++ .../TopHat-2.1.1_fix-templating-error.patch | 13 ++++++ 2 files changed, 54 insertions(+) create mode 100644 easybuild/easyconfigs/t/TopHat/TopHat-2.1.1-intel-2017a.eb create mode 100644 easybuild/easyconfigs/t/TopHat/TopHat-2.1.1_fix-templating-error.patch diff --git a/easybuild/easyconfigs/t/TopHat/TopHat-2.1.1-intel-2017a.eb b/easybuild/easyconfigs/t/TopHat/TopHat-2.1.1-intel-2017a.eb new file mode 100644 index 0000000000..f3be80ad62 --- /dev/null +++ b/easybuild/easyconfigs/t/TopHat/TopHat-2.1.1-intel-2017a.eb @@ -0,0 +1,41 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# Modified by: Adam Huffman +# The Francis Crick Institute + +easyblock = 'ConfigureMake' + +name = 'TopHat' +version = '2.1.1' + +homepage = 'http://ccb.jhu.edu/software/tophat/' +description = """TopHat is a fast splice junction mapper for RNA-Seq reads.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True, 'cstd': 'c++11'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://ccb.jhu.edu/software/tophat/downloads/'] + +patches = [ + 'tophat-2.0.13-zlib.patch', + 'TopHat-2.1.1_fix-templating-error.patch', +] + +dependencies = [ + ('Boost', '1.64.0'), + ('zlib', '1.2.11'), +] + +configopts = '--with-boost=$EBROOTBOOST' + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/tophat'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/TopHat/TopHat-2.1.1_fix-templating-error.patch b/easybuild/easyconfigs/t/TopHat/TopHat-2.1.1_fix-templating-error.patch new file mode 100644 index 0000000000..0abcfeeb26 --- /dev/null +++ b/easybuild/easyconfigs/t/TopHat/TopHat-2.1.1_fix-templating-error.patch @@ -0,0 +1,13 @@ +fix templating compilation error, let type inference do its job +authors: Kenneth Hoste (HPC-UGent), Ward Poelmans (VUB) +--- tophat-2.1.1/src/tophat_reports.cpp.orig 2017-05-16 11:24:21.776900497 +0200 ++++ tophat-2.1.1/src/tophat_reports.cpp 2017-05-16 11:25:31.958523978 +0200 +@@ -2705,7 +2705,7 @@ + junction_stat.gtf_match = true; + junction_stat.accepted = true; + +- gtf_junctions.insert(make_pair(Junction(ref_id, left_coord, right_coord, antisense), junction_stat)); ++ gtf_junctions.insert(make_pair(Junction(ref_id, left_coord, right_coord, antisense), junction_stat)); + } + } + fprintf(stderr, "Loaded %d GFF junctions from %s.\n", (int)(gtf_junctions.size()), gtf_juncs.c_str()); -- GitLab From 0650f1b517d052a4e93fc7b4a99b8d5e421402fd Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Tue, 16 May 2017 13:45:29 +0200 Subject: [PATCH 0770/1603] adding easyconfigs: SeqAn-2.3.2-foss-2016b.eb --- .../s/SeqAn/SeqAn-2.3.2-foss-2016b.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/s/SeqAn/SeqAn-2.3.2-foss-2016b.eb diff --git a/easybuild/easyconfigs/s/SeqAn/SeqAn-2.3.2-foss-2016b.eb b/easybuild/easyconfigs/s/SeqAn/SeqAn-2.3.2-foss-2016b.eb new file mode 100644 index 0000000000..28c6b25215 --- /dev/null +++ b/easybuild/easyconfigs/s/SeqAn/SeqAn-2.3.2-foss-2016b.eb @@ -0,0 +1,37 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = "CMakeMake" + +name = 'SeqAn' +version = '2.3.2' + +homepage = 'https://www.seqan.de/' +description = """SeqAn is an open source C++ library of efficient algorithms and data structures + for the analysis of sequences with the focus on biological data""" + +# GCC > 5 required. https://github.com/seqan/seqan#prerequisites +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['https://github.com/seqan/seqan/archive/'] +sources = ['%(namelower)s-v%(version)s.tar.gz'] + +# CMake > 3 required. CMake >= 3.4 recommended +builddependencies = [('CMake', '3.4.3')] + +dependencies = [ + ('zlib', '1.2.8'), + ('bzip2', '1.0.6') +] + +separate_build_dir = True + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["gustaf_mate_joining", "mason_materializer", "mason_variator", "rabema_prepare_sam", + "seqan_tcoffee", "s4_join", "samcat", "splazers", "yara_mapper"]], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From dc8ce7b3d0b19c872e7539e880dfaee4786e8553 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Lopez Date: Tue, 16 May 2017 15:04:01 +0200 Subject: [PATCH 0771/1603] update CMake dependency to 3.7.2 --- easybuild/easyconfigs/s/SeqAn/SeqAn-2.3.2-foss-2016b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SeqAn/SeqAn-2.3.2-foss-2016b.eb b/easybuild/easyconfigs/s/SeqAn/SeqAn-2.3.2-foss-2016b.eb index 28c6b25215..b89f6044b4 100644 --- a/easybuild/easyconfigs/s/SeqAn/SeqAn-2.3.2-foss-2016b.eb +++ b/easybuild/easyconfigs/s/SeqAn/SeqAn-2.3.2-foss-2016b.eb @@ -19,7 +19,7 @@ source_urls = ['https://github.com/seqan/seqan/archive/'] sources = ['%(namelower)s-v%(version)s.tar.gz'] # CMake > 3 required. CMake >= 3.4 recommended -builddependencies = [('CMake', '3.4.3')] +builddependencies = [('CMake', '3.7.2')] dependencies = [ ('zlib', '1.2.8'), -- GitLab From ebf4e914abd70d84f09a56acc1c20c3d638a10e6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 16 May 2017 17:07:13 +0200 Subject: [PATCH 0772/1603] adding easyconfigs: NCO-4.6.6-intel-2017a.eb, ANTLR-2.7.7-intel-2017a-Python-2.7.13.eb, libdap-3.18.1-intel-2017a.eb, LibUUID-1.0.3-intel-2017a.eb --- .../ANTLR-2.7.7-intel-2017a-Python-2.7.13.eb | 32 +++++++++++++++++ .../l/LibUUID/LibUUID-1.0.3-intel-2017a.eb | 19 ++++++++++ .../l/libdap/libdap-3.18.1-intel-2017a.eb | 32 +++++++++++++++++ .../n/NCO/NCO-4.6.6-intel-2017a.eb | 35 +++++++++++++++++++ 4 files changed, 118 insertions(+) create mode 100644 easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-intel-2017a-Python-2.7.13.eb create mode 100644 easybuild/easyconfigs/l/LibUUID/LibUUID-1.0.3-intel-2017a.eb create mode 100644 easybuild/easyconfigs/l/libdap/libdap-3.18.1-intel-2017a.eb create mode 100644 easybuild/easyconfigs/n/NCO/NCO-4.6.6-intel-2017a.eb diff --git a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..e00f225a13 --- /dev/null +++ b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'ANTLR' +version = '2.7.7' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.antlr2.org/' +description = """ANTLR, ANother Tool for Language Recognition, (formerly PCCTS) + is a language tool that provides a framework for constructing recognizers, + compilers, and translators from grammatical descriptions containing + Java, C#, C++, or Python actions.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['http://www.antlr2.org/download/'] +sources = [SOURCELOWER_TAR_GZ] + +patches = ['%(name)s-%(version)s_includes.patch'] + +dependencies = [ + ('Java', '1.8.0_131', '', True), + ('Python', '2.7.13'), +] + +configopts = '--disable-examples --disable-csharp ' + +sanity_check_paths = { + 'files': ['bin/antlr', 'bin/antlr-config'], + 'dirs': ['include'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/l/LibUUID/LibUUID-1.0.3-intel-2017a.eb b/easybuild/easyconfigs/l/LibUUID/LibUUID-1.0.3-intel-2017a.eb new file mode 100644 index 0000000000..a50ce3901e --- /dev/null +++ b/easybuild/easyconfigs/l/LibUUID/LibUUID-1.0.3-intel-2017a.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'LibUUID' +version = '1.0.3' + +homepage = 'http://sourceforge.net/projects/libuuid/' +description = """Portable uuid C library""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': ['include/uuid/uuid.h', 'lib/libuuid.a', 'lib/libuuid.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libdap/libdap-3.18.1-intel-2017a.eb b/easybuild/easyconfigs/l/libdap/libdap-3.18.1-intel-2017a.eb new file mode 100644 index 0000000000..437ea556cf --- /dev/null +++ b/easybuild/easyconfigs/l/libdap/libdap-3.18.1-intel-2017a.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'libdap' +version = '3.18.1' + +homepage = 'http://opendap.org/download/libdap' +description = """A C++ SDK which contains an implementation of DAP 2.0 + and the development versions of DAP3, up to 3.4. + This includes both Client- and Server-side support classes.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['http://www.opendap.org/pub/source/'] +sources = [SOURCE_TAR_GZ] + +builddependencies = [ + ('Bison', '3.0.4'), + ('flex', '2.6.4'), +] + +dependencies = [ + ('cURL', '7.53.1'), + ('libxml2', '2.9.4'), + ('LibUUID', '1.0.3'), +] + +sanity_check_paths = { + 'files': ['bin/getdap', 'bin/getdap4', 'bin/dap-config', 'lib/libdap.a', 'lib/libdap.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/NCO/NCO-4.6.6-intel-2017a.eb b/easybuild/easyconfigs/n/NCO/NCO-4.6.6-intel-2017a.eb new file mode 100644 index 0000000000..b9edf1373e --- /dev/null +++ b/easybuild/easyconfigs/n/NCO/NCO-4.6.6-intel-2017a.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'NCO' +version = '4.6.6' + +homepage = "http://nco.sourceforge.net" +description = """manipulates and analyzes data stored in netCDF-accessible formats, including DAP, HDF4, and HDF5""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['http://nco.sourceforge.net/src'] +sources = [SOURCELOWER_TAR_GZ] + +builddependencies = [ + ('Bison', '3.0.4'), + ('flex', '2.6.4'), +] + +dependencies = [ + ('UDUNITS', '2.2.24'), + ('expat', '2.2.0'), + ('ANTLR', '2.7.7', '-Python-2.7.13'), + ('libdap', '3.18.1'), + ('GSL', '2.3'), + ('netCDF', '4.4.1.1', '-HDF5-1.8.18'), +] + +sanity_check_paths = { + 'files': ['bin/nc%s' % x for x in ('ap', 'ap2', 'atted', 'bo', 'diff', 'ea', 'ecat', 'es', + 'flint', 'ks', 'pdq', 'ra', 'rcat', 'rename', 'wa')] + + ['lib/libnco.a', 'lib/libnco.%s' % SHLIB_EXT, 'lib/libnco_c++.a', 'lib/libnco_c++.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'tools' -- GitLab From 06bbccbc6a65622a729a53d4d1b9555487911510 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 16 May 2017 17:43:36 +0200 Subject: [PATCH 0773/1603] {data}[intel/2017a] CDO 1.8.1 + YAXT 0.5.1 --- .../c/CDO/CDO-1.8.1-intel-2017a.eb | 31 +++++++++++++++++++ .../y/YAXT/YAXT-0.5.1-intel-2017a.eb | 23 ++++++++++++++ 2 files changed, 54 insertions(+) create mode 100644 easybuild/easyconfigs/c/CDO/CDO-1.8.1-intel-2017a.eb create mode 100644 easybuild/easyconfigs/y/YAXT/YAXT-0.5.1-intel-2017a.eb diff --git a/easybuild/easyconfigs/c/CDO/CDO-1.8.1-intel-2017a.eb b/easybuild/easyconfigs/c/CDO/CDO-1.8.1-intel-2017a.eb new file mode 100644 index 0000000000..f6f33ffc90 --- /dev/null +++ b/easybuild/easyconfigs/c/CDO/CDO-1.8.1-intel-2017a.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'CDO' +version = '1.8.1' + +homepage = 'https://code.zmaw.de/projects/cdo' +description = """CDO is a collection of command line Operators to manipulate and analyse Climate and NWP model Data.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True, 'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['https://code.zmaw.de/attachments/download/14271/'] +checksums = ['54498438de788f245d47499efad7966c'] + +dependencies = [ + ('HDF5', '1.8.18'), + ('netCDF', '4.4.1.1', '-HDF5-1.8.18'), + ('YAXT', '0.5.1'), +] + +configopts = "--with-hdf5=$EBROOTHDF5 --with-netcdf=$EBROOTNETCDF" +# fix for linking issues with HDF5 libraries for libcdi, should link with both -lnetcdf and -lhdf5_hl -lhdf5 +prebuildopts = "find libcdi -name Makefile | xargs sed -i 's/^\(LIBS.*\)/\\1 -lhdf5_hl -lhdf5/g' && " + +sanity_check_paths = { + 'files': ['bin/cdo'], + 'dirs': [], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/y/YAXT/YAXT-0.5.1-intel-2017a.eb b/easybuild/easyconfigs/y/YAXT/YAXT-0.5.1-intel-2017a.eb new file mode 100644 index 0000000000..4cdb872a2c --- /dev/null +++ b/easybuild/easyconfigs/y/YAXT/YAXT-0.5.1-intel-2017a.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'YAXT' +version = '0.5.1' + +homepage = 'https://www.dkrz.de/redmine/projects/yaxt' +description = "Yet Another eXchange Tool" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['https://www.dkrz.de/redmine/attachments/download/473/'] +checksums = ['2176c5b1096146e58163656b9d83c0b3'] + +configopts = 'FC="$F90" FCFLAGS="$F90FLAGS -cpp"' + +sanity_check_paths = { + 'files': ['include/yaxt.h', 'include/yaxt.mod', 'lib/libyaxt.a', 'lib/libyaxt.%s' % SHLIB_EXT], + 'dirs': ['include/xt'], +} + +moduleclass = 'tools' -- GitLab From 0c48bec1e62a5778a068bd6bb9acdd3e4952f610 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 16 May 2017 19:44:51 +0200 Subject: [PATCH 0774/1603] simplify patching of libcdi Makefiles in CDO easyconfig --- easybuild/easyconfigs/c/CDO/CDO-1.8.1-intel-2017a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CDO/CDO-1.8.1-intel-2017a.eb b/easybuild/easyconfigs/c/CDO/CDO-1.8.1-intel-2017a.eb index f6f33ffc90..1e3e7c4c76 100644 --- a/easybuild/easyconfigs/c/CDO/CDO-1.8.1-intel-2017a.eb +++ b/easybuild/easyconfigs/c/CDO/CDO-1.8.1-intel-2017a.eb @@ -21,7 +21,7 @@ dependencies = [ configopts = "--with-hdf5=$EBROOTHDF5 --with-netcdf=$EBROOTNETCDF" # fix for linking issues with HDF5 libraries for libcdi, should link with both -lnetcdf and -lhdf5_hl -lhdf5 -prebuildopts = "find libcdi -name Makefile | xargs sed -i 's/^\(LIBS.*\)/\\1 -lhdf5_hl -lhdf5/g' && " +prebuildopts = "find libcdi -name Makefile | xargs sed -i 's/-lnetcdf -lnetcdf/-lnetcdf -lhdf5_hl -lhdf5/g' && " sanity_check_paths = { 'files': ['bin/cdo'], -- GitLab From 4aebea8ec5da414b987f37af99914dddb715ca4b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 16 May 2017 21:47:14 +0200 Subject: [PATCH 0775/1603] use 'git diff --name-only' and $TRAVIS_COMMIT_RANGE in Travis config to get list of changed files --- .travis.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.travis.yml b/.travis.yml index 07cebed738..2fcb5e365f 100644 --- a/.travis.yml +++ b/.travis.yml @@ -40,5 +40,7 @@ install: - if [ ! -z $LMOD_VERSION ]; then source $(which install_eb_dep.sh) lua-5.1.4.8 $HOME; fi - if [ ! -z $LMOD_VERSION ]; then source $(which install_eb_dep.sh) Lmod-${LMOD_VERSION} $HOME; fi script: + - echo $TRAVIS_COMMIT_RANGE + - cd $TRAVIS_BUILD_DIR; git diff --name-only $(echo $TRAVIS_COMMIT_RANGE | sed 's/\.//'); cd - > /dev/null - export PYTHONPATH=$TRAVIS_BUILD_DIR - python -O -m test.easyconfigs.suite -- GitLab From bd23642e2d2c6686caaef2b752817389437509a4 Mon Sep 17 00:00:00 2001 From: jrbosch Date: Wed, 17 May 2017 09:36:48 -0400 Subject: [PATCH 0776/1603] add FFmpeg easyconfig with support to x265 and LAME --- .../f/FFmpeg/FFmpeg-3.3.1-foss-2016b.eb | 34 +++++++++++++++++++ .../l/LAME/LAME-3.99.5-foss-2016b.eb | 30 ++++++++++++++++ 2 files changed, 64 insertions(+) create mode 100644 easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.3.1-foss-2016b.eb create mode 100644 easybuild/easyconfigs/l/LAME/LAME-3.99.5-foss-2016b.eb diff --git a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.3.1-foss-2016b.eb b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.3.1-foss-2016b.eb new file mode 100644 index 0000000000..374f64671c --- /dev/null +++ b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.3.1-foss-2016b.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'FFmpeg' +version = '3.3.1' + +homepage = 'https://www.ffmpeg.org/' +description = """A complete, cross-platform solution to record, convert and stream audio and video.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://ffmpeg.org/releases/'] + +dependencies = [ + ('NASM', '2.12.02'), + ('zlib', '1.2.8'), + ('bzip2', '1.0.6'), + ('x264', '20160614'), + ('x265', '2.4'), + ('LAME', '3.99.5'), + ('X11', '20160819'), +] + +configopts = '--enable-pic --enable-shared --enable-gpl --enable-version3 --enable-nonfree --cc="$CC" --cxx="$CXX" ' +configopts += '--enable-libx264 --enable-libx265 --enable-libmp3lame' + +sanity_check_paths = { + 'files': ['bin/ff%s' % x for x in ['mpeg', 'probe', 'server']] + + ['lib/lib%s.%s' % (x, y) for x in ['avdevice', 'avfilter', 'avformat', 'avcodec', 'postproc', + 'swresample', 'swscale', 'avutil'] for y in [SHLIB_EXT, 'a']], + 'dirs': ['include'] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/LAME/LAME-3.99.5-foss-2016b.eb b/easybuild/easyconfigs/l/LAME/LAME-3.99.5-foss-2016b.eb new file mode 100644 index 0000000000..042510cf2a --- /dev/null +++ b/easybuild/easyconfigs/l/LAME/LAME-3.99.5-foss-2016b.eb @@ -0,0 +1,30 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Author: Stephane Thiell +### + +easyblock = 'ConfigureMake' + +name = 'LAME' +version = '3.99.5' + +homepage = 'http://lame.sourceforge.net/' +description = """LAME is a high quality MPEG Audio Layer III (MP3) encoder licensed under the LGPL.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['https://sourceforge.net/projects/lame/files/lame/%(version_major_minor)s/'] + +dependencies = [('ncurses', '6.0')] + +# configure is broken: add workaround to find libncurses... +configure_cmd_prefix = "FRONTEND_LDADD='-L${EBROOTNCURSES}/lib' " + +sanity_check_paths = { + 'files': ['bin/lame', 'include/lame/lame.h', 'lib/libmp3lame.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'data' -- GitLab From 0c5e71d70e1d1ec068990eff100d8e053a267dd4 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Wed, 17 May 2017 15:46:08 +0200 Subject: [PATCH 0777/1603] adding easyconfigs: MUMmer-4.0.0beta-goolf-1.7.20.eb --- .../m/MUMmer/MUMmer-4.0.0beta-goolf-1.7.20.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/m/MUMmer/MUMmer-4.0.0beta-goolf-1.7.20.eb diff --git a/easybuild/easyconfigs/m/MUMmer/MUMmer-4.0.0beta-goolf-1.7.20.eb b/easybuild/easyconfigs/m/MUMmer/MUMmer-4.0.0beta-goolf-1.7.20.eb new file mode 100644 index 0000000000..8471838376 --- /dev/null +++ b/easybuild/easyconfigs/m/MUMmer/MUMmer-4.0.0beta-goolf-1.7.20.eb @@ -0,0 +1,23 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'ConfigureMake' + +name = 'MUMmer' +version = '4.0.0beta' + +homepage = 'http://mummer.sourceforge.net/' +description = """MUMmer is a system for rapidly aligning entire genomes, + whether in complete or draft form. AMOS makes use of it.""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} +toolchainopts = {'openmp': True} + +source_urls = ['https://github.com/gmarcais/mummer/releases/download/v%(version)s/'] +sources = ['%(namelower)s-%(version)s.tar.gz'] + +patches = ['mummer-%(version)s.patch'] + +moduleclass = 'bio' -- GitLab From 8e1bf1c361216cb5bc75de261cdc612704e3bdd9 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Wed, 17 May 2017 15:52:41 +0200 Subject: [PATCH 0778/1603] added mummer patch --- .../easyconfigs/m/MUMmer/mummer-4.0.0beta.patch | 15 +++++++++++++++ 1 file changed, 15 insertions(+) create mode 100644 easybuild/easyconfigs/m/MUMmer/mummer-4.0.0beta.patch diff --git a/easybuild/easyconfigs/m/MUMmer/mummer-4.0.0beta.patch b/easybuild/easyconfigs/m/MUMmer/mummer-4.0.0beta.patch new file mode 100644 index 0000000000..b95c705ef8 --- /dev/null +++ b/easybuild/easyconfigs/m/MUMmer/mummer-4.0.0beta.patch @@ -0,0 +1,15 @@ +Fix a compilation error in version 4.0.0beta +https://github.com/gmarcais/mummer/issues/7 + +diff -ru mummer-4.0.0beta.orig/src/essaMEM/mummer.cpp mummer-4.0.0beta/src/essaMEM/mummer.cpp +--- mummer-4.0.0beta.orig/src/essaMEM/mummer.cpp 2017-04-06 19:49:04.000000000 +0200 ++++ mummer-4.0.0beta/src/essaMEM/mummer.cpp 2017-05-17 15:36:51.998784593 +0200 +@@ -218,7 +218,7 @@ + case 22: + #ifdef VERSION + std::cout << VERSION << '\n'; +-#elif ++#else + std::cout << "\n"; + #endif + exit(0); -- GitLab From a9e81f5a5670c4b90ed5cc8f10243742b554c14e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 17 May 2017 17:40:01 +0200 Subject: [PATCH 0779/1603] adding easyconfigs: gmpy2-2.0.8-intel-2017a-Python-2.7.13.eb, MPC-1.0.3-intel-2017a.eb --- .../gmpy2-2.0.8-intel-2017a-Python-2.7.13.eb | 27 ++++++++++++++++ .../m/MPC/MPC-1.0.3-intel-2017a.eb | 32 +++++++++++++++++++ 2 files changed, 59 insertions(+) create mode 100644 easybuild/easyconfigs/g/gmpy2/gmpy2-2.0.8-intel-2017a-Python-2.7.13.eb create mode 100644 easybuild/easyconfigs/m/MPC/MPC-1.0.3-intel-2017a.eb diff --git a/easybuild/easyconfigs/g/gmpy2/gmpy2-2.0.8-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/g/gmpy2/gmpy2-2.0.8-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..d82b9f3a9d --- /dev/null +++ b/easybuild/easyconfigs/g/gmpy2/gmpy2-2.0.8-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'gmpy2' +version = '2.0.8' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/aleaxit/gmpy' +description = "GMP/MPIR, MPFR, and MPC interface to Python 2.6+ and 3.x" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_ZIP] + +dependencies = [ + ('Python', '2.7.13'), + ('GMP', '6.1.2'), + ('MPFR', '3.1.5'), + ('MPC', '1.0.3'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/MPC/MPC-1.0.3-intel-2017a.eb b/easybuild/easyconfigs/m/MPC/MPC-1.0.3-intel-2017a.eb new file mode 100644 index 0000000000..5bddb3e5d5 --- /dev/null +++ b/easybuild/easyconfigs/m/MPC/MPC-1.0.3-intel-2017a.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'MPC' +version = '1.0.3' + +homepage = 'http://www.multiprecision.org/' +description = """Gnu Mpc is a C library for the arithmetic of + complex numbers with arbitrarily high precision and correct + rounding of the result. It extends the principles of the IEEE-754 + standard for fixed precision real floating point numbers to + complex numbers, providing well-defined semantics for every + operation. At the same time, speed of operation at high precision + is a major design goal.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['http://www.multiprecision.org/mpc/download/'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('GMP', '6.1.2'), + ('MPFR', '3.1.5'), +] + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libmpc.%s' % SHLIB_EXT, 'include/mpc.h'], + 'dirs': [] +} + +moduleclass = 'math' -- GitLab From 0933fa668c99dee172f6ddae2d7349654c35dee6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 18 May 2017 09:14:09 +0200 Subject: [PATCH 0780/1603] adding easyconfigs: scikit-learn-0.18.1-intel-2017a-Python-2.7.13.eb, matplotlib-2.0.2-intel-2017a-Python-2.7.13.eb --- ...plotlib-2.0.2-intel-2017a-Python-2.7.13.eb | 43 +++++++++++++++++++ ...-learn-0.18.1-intel-2017a-Python-2.7.13.eb | 30 +++++++++++++ 2 files changed, 73 insertions(+) create mode 100644 easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.2-intel-2017a-Python-2.7.13.eb create mode 100755 easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.18.1-intel-2017a-Python-2.7.13.eb diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.2-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.2-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..fa289dd53b --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.2-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,43 @@ +easyblock = 'Bundle' + +name = 'matplotlib' +version = '2.0.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://matplotlib.org' +description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of + hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python + and ipython shell, web application servers, and six graphical user interface toolkits.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' + +dependencies = [ + ('Python', '2.7.13'), + ('freetype', '2.7.1'), +] + +exts_list = [ + ('Cycler', '0.10.0', { + 'modulename': 'cycler', + 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], + 'source_tmpl': 'cycler-%(version)s.tar.gz', + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], + }), +] + +# specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module +full_sanity_check = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.18.1-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.18.1-intel-2017a-Python-2.7.13.eb new file mode 100755 index 0000000000..388e0e3afa --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.18.1-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'scikit-learn' +version = '0.18.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://scikit-learn.org/stable/index.html' +description = """Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, +building upon numpy, scipy, and matplotlib. As a machine-learning module, +it provides versatile tools for data mining and analysis in any field of science and engineering. +It strives to be simple and efficient, accessible to everybody, and reusable in various contexts.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.13'), + ('matplotlib', '2.0.2', versionsuffix), +] + +options = {'modulename': 'sklearn'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/sklearn'], +} + +moduleclass = 'data' -- GitLab From 2bfb83215f61d130c7363fcd8412e4ed09b961da Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 18 May 2017 09:19:36 +0200 Subject: [PATCH 0781/1603] adding easyconfigs: statsmodels-0.8.0-intel-2017a-Python-2.7.13.eb --- ...smodels-0.8.0-intel-2017a-Python-2.7.13.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/s/statsmodels/statsmodels-0.8.0-intel-2017a-Python-2.7.13.eb diff --git a/easybuild/easyconfigs/s/statsmodels/statsmodels-0.8.0-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/s/statsmodels/statsmodels-0.8.0-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..85483b0005 --- /dev/null +++ b/easybuild/easyconfigs/s/statsmodels/statsmodels-0.8.0-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,36 @@ +easyblock = 'Bundle' + +name = 'statsmodels' +version = '0.8.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://statsmodels.sourceforge.net/' +description = """Statsmodels is a Python module that allows users to explore data, estimate statistical models, +and perform statistical tests.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' + +dependencies = [('Python', '2.7.13')] + +exts_list = [ + ('patsy', '0.4.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/patsy'], + 'source_tmpl': 'patsy-%(version)s.zip', + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/statsmodels'], + 'source_tmpl': 'statsmodels-%(version)s.tar.gz', + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +moduleclass = 'math' -- GitLab From 7b5e6e94f527f488a3a966a7cc397c250fa2ddf2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 18 May 2017 09:20:21 +0200 Subject: [PATCH 0782/1603] fix typo in statsmodels source url (/sources/ -> /source/) --- .../s/statsmodels/statsmodels-0.6.1-intel-2016b-Python-3.5.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/statsmodels/statsmodels-0.6.1-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/s/statsmodels/statsmodels-0.6.1-intel-2016b-Python-3.5.2.eb index 435f33a3bd..484c222815 100644 --- a/easybuild/easyconfigs/s/statsmodels/statsmodels-0.6.1-intel-2016b-Python-3.5.2.eb +++ b/easybuild/easyconfigs/s/statsmodels/statsmodels-0.6.1-intel-2016b-Python-3.5.2.eb @@ -21,7 +21,7 @@ exts_list = [ 'source_tmpl': 'patsy-%(version)s.zip', }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/sources/statsmodels'], + 'source_urls': ['https://pypi.python.org/packages/source/statsmodels'], 'source_tmpl': 'statsmodels-%(version)s.zip', }), ] -- GitLab From d76b99582a77ec30e760a41563bb7c12a398c0c9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 18 May 2017 11:25:50 +0200 Subject: [PATCH 0783/1603] adding easyconfigs: gnuplot-5.0.6-intel-2017a.eb, Pango-1.40.5-intel-2017a.eb, libgd-2.2.4-intel-2017a.eb, libcerf-1.5-intel-2017a.eb, HarfBuzz-1.3.1-intel-2017a.eb, GObject-Introspection-1.52.0-intel-2017a.eb --- ...Object-Introspection-1.52.0-intel-2017a.eb | 47 +++++++++++++++++++ .../g/gnuplot/gnuplot-5.0.6-intel-2017a.eb | 42 +++++++++++++++++ .../h/HarfBuzz/HarfBuzz-1.3.1-intel-2017a.eb | 34 ++++++++++++++ .../l/libcerf/libcerf-1.5-intel-2017a.eb | 28 +++++++++++ .../l/libgd/libgd-2.2.4-intel-2017a.eb | 26 ++++++++++ .../p/Pango/Pango-1.40.5-intel-2017a.eb | 31 ++++++++++++ 6 files changed, 208 insertions(+) create mode 100644 easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.52.0-intel-2017a.eb create mode 100644 easybuild/easyconfigs/g/gnuplot/gnuplot-5.0.6-intel-2017a.eb create mode 100644 easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.3.1-intel-2017a.eb create mode 100644 easybuild/easyconfigs/l/libcerf/libcerf-1.5-intel-2017a.eb create mode 100644 easybuild/easyconfigs/l/libgd/libgd-2.2.4-intel-2017a.eb create mode 100644 easybuild/easyconfigs/p/Pango/Pango-1.40.5-intel-2017a.eb diff --git a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.52.0-intel-2017a.eb b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.52.0-intel-2017a.eb new file mode 100644 index 0000000000..804872f657 --- /dev/null +++ b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.52.0-intel-2017a.eb @@ -0,0 +1,47 @@ +easyblock = 'ConfigureMake' + +name = 'GObject-Introspection' +version = '1.52.0' + +homepage = 'https://wiki.gnome.org/GObjectIntrospection/' +description = """GObject introspection is a middleware layer between C libraries + (using GObject) and language bindings. The C library can be scanned at + compile time and generate a metadata file, in addition to the actual + native C library. Then at runtime, language bindings can read this + metadata and automatically provide bindings to call into the C library.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('Python', '2.7.13'), + ('GLib', '2.52.0'), + ('libffi', '3.2.1'), +] + +builddependencies = [ + ('Autotools', '20150215'), + ('flex', '2.6.4'), + ('Bison', '3.0.4'), + ('cairo', '1.14.8'), +] + +preconfigopts = "env GI_SCANNER_DISABLE_CACHE=true " + +# avoid using hard-coded path to 'python' in shebang of scripts +buildopts = "PYTHON=python" + +modextrapaths = { + 'GI_TYPELIB_PATH': 'share', + 'XDG_DATA_DIRS': 'share', +} + +sanity_check_paths = { + 'files': ['bin/g-ir-%s' % x for x in ['annotation-tool', 'compiler', 'generate', 'scanner']] + + ['lib/libgirepository-1.0.%s' % x for x in ['so', 'a']], + 'dirs': ['include', 'share'] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/gnuplot/gnuplot-5.0.6-intel-2017a.eb b/easybuild/easyconfigs/g/gnuplot/gnuplot-5.0.6-intel-2017a.eb new file mode 100644 index 0000000000..22b8ccefa5 --- /dev/null +++ b/easybuild/easyconfigs/g/gnuplot/gnuplot-5.0.6-intel-2017a.eb @@ -0,0 +1,42 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg/Luxembourg Centre for Systems Biomedicine +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-97.html +## +easyblock = 'ConfigureMake' + +name = 'gnuplot' +version = '5.0.6' + +homepage = 'http://gnuplot.sourceforge.net/' +description = """Portable interactive, function plotting utility""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [('http://sourceforge.net/projects/gnuplot/files', 'download')] + +dependencies = [ + ('cairo', '1.14.8'), + ('libjpeg-turbo', '1.5.1'), + ('libpng', '1.6.29'), + ('libgd', '2.2.4'), + ('Pango', '1.40.5'), + ('libcerf', '1.5'), + ('Qt', '4.8.7'), +] + +configopts = '--with-qt=qt4 ' + +sanity_check_paths = { + 'files': ['bin/gnuplot'], + 'dirs': [] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.3.1-intel-2017a.eb b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.3.1-intel-2017a.eb new file mode 100644 index 0000000000..58049805dd --- /dev/null +++ b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.3.1-intel-2017a.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'HarfBuzz' +version = '1.3.1' + +homepage = 'http://www.freedesktop.org/wiki/Software/HarfBuzz' +description = """HarfBuzz is an OpenType text shaping engine.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['http://www.freedesktop.org/software/harfbuzz/release/'] +sources = [SOURCELOWER_TAR_BZ2] + +dependencies = [ + ('GLib', '2.52.0'), + ('cairo', '1.14.8'), + ('freetype', '2.7.1', '-libpng-1.6.29'), +] + +builddependencies = [('GObject-Introspection', '1.52.0')] + +configopts = "--enable-introspection=yes --with-gobject=yes --enable-static --enable-shared --with-cairo " + +modextrapaths = { + 'GI_TYPELIB_PATH': 'share', + 'XDG_DATA_DIRS': 'share', +} + +sanity_check_paths = { + 'files': ['lib/libharfbuzz.%s' % SHLIB_EXT, 'bin/hb-view'], + 'dirs': [] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libcerf/libcerf-1.5-intel-2017a.eb b/easybuild/easyconfigs/l/libcerf/libcerf-1.5-intel-2017a.eb new file mode 100644 index 0000000000..3c7483ca6e --- /dev/null +++ b/easybuild/easyconfigs/l/libcerf/libcerf-1.5-intel-2017a.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'libcerf' +version = '1.5' + +homepage = 'http://gnuplot.sourceforge.net/' +description = """libcerf is a self-contained numeric library that provides an efficient and accurate + implementation of complex error functions, along with Dawson, Faddeeva, and Voigt functions.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +sources = [SOURCE_TGZ] +source_urls = [ + 'http://apps.jcns.fz-juelich.de/src/libcerf/', + 'http://apps.jcns.fz-juelich.de/src/libcerf/old', +] + +builddependencies = [ + ('Autotools', '20150215'), + ('libtool', '2.4.6'), +] + +sanity_check_paths = { + 'files': ['lib/libcerf.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/l/libgd/libgd-2.2.4-intel-2017a.eb b/easybuild/easyconfigs/l/libgd/libgd-2.2.4-intel-2017a.eb new file mode 100644 index 0000000000..1a8de80eb4 --- /dev/null +++ b/easybuild/easyconfigs/l/libgd/libgd-2.2.4-intel-2017a.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'libgd' +version = '2.2.4' + +homepage = 'https://libgd.github.io/' +description = "GD is an open source code library for the dynamic creation of images by programmers." + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['https://github.com/libgd/libgd/releases/download/gd-%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('fontconfig', '2.12.1', '-libpng-1.6.29'), + ('libjpeg-turbo', '1.5.1'), + ('libpng', '1.6.29'), + ('zlib', '1.2.11'), +] + +sanity_check_paths = { + 'files': ["lib/libgd.a", "lib/libgd.%s" % SHLIB_EXT], + 'dirs': ["bin", "include"], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.40.5-intel-2017a.eb b/easybuild/easyconfigs/p/Pango/Pango-1.40.5-intel-2017a.eb new file mode 100644 index 0000000000..d7561a197b --- /dev/null +++ b/easybuild/easyconfigs/p/Pango/Pango-1.40.5-intel-2017a.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'Pango' +version = '1.40.5' + +homepage = 'http://www.pango.org/' +description = """Pango is a library for laying out and rendering of text, with an emphasis on internationalization. +Pango can be used anywhere that text layout is needed, though most of the work on Pango so far has been done in the +context of the GTK+ widget toolkit. Pango forms the core of text and font handling for GTK+-2.x.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('X11', '20170314'), + ('GLib', '2.52.0'), + ('cairo', '1.14.8'), + ('HarfBuzz', '1.3.1'), +] + +builddependencies = [('GObject-Introspection', '1.52.0')] + +configopts = "--disable-silent-rules --enable-introspection=yes --enable-static --enable-shared " + +modextrapaths = { + 'XDG_DATA_DIRS': 'share', +} + +moduleclass = 'vis' -- GitLab From ca675cca030fd8a76cc631816f5b128da4555daf Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 18 May 2017 12:08:14 +0200 Subject: [PATCH 0784/1603] Bump FSL to intel/2017a --- .../f/FSL/FSL-5.0.9-intel-2017a.eb | 24 +++++++++++++ .../f/freeglut/freeglut-3.0.0-intel-2017a.eb | 35 +++++++++++++++++++ 2 files changed, 59 insertions(+) create mode 100644 easybuild/easyconfigs/f/FSL/FSL-5.0.9-intel-2017a.eb create mode 100644 easybuild/easyconfigs/f/freeglut/freeglut-3.0.0-intel-2017a.eb diff --git a/easybuild/easyconfigs/f/FSL/FSL-5.0.9-intel-2017a.eb b/easybuild/easyconfigs/f/FSL/FSL-5.0.9-intel-2017a.eb new file mode 100644 index 0000000000..34a1890fcb --- /dev/null +++ b/easybuild/easyconfigs/f/FSL/FSL-5.0.9-intel-2017a.eb @@ -0,0 +1,24 @@ +name = 'FSL' +version = '5.0.9' + +homepage = 'http://www.fmrib.ox.ac.uk/fsl/' +description = """FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ["http://www.fmrib.ox.ac.uk/fsldownloads/"] +sources = ['%(namelower)s-%(version)s-sources.tar.gz'] + +patches = [ + 'FSL-%(version)s_makefile_fixes.patch', + 'FSL-%(version)s_missing_lib.patch', + 'FSL_icc_nan-inf_fix.patch', +] + +dependencies = [ + ('freeglut', '3.0.0'), + ('expat', '2.2.0'), + ('zlib', '1.2.11'), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/freeglut/freeglut-3.0.0-intel-2017a.eb b/easybuild/easyconfigs/f/freeglut/freeglut-3.0.0-intel-2017a.eb new file mode 100644 index 0000000000..3d404c8658 --- /dev/null +++ b/easybuild/easyconfigs/f/freeglut/freeglut-3.0.0-intel-2017a.eb @@ -0,0 +1,35 @@ +easyblock = 'CMakeMake' + +name = 'freeglut' +version = '3.0.0' + +homepage = 'http://freeglut.sourceforge.net/' +description = "freeglut is a completely OpenSourced alternative to the OpenGL Utility Toolkit (GLUT) library." + +toolchain = {'name': 'intel', 'version': '2017a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(name)s'] + +builddependencies = [('CMake', '3.8.0')] + +dependencies = [ + ('X11', '20170314'), + ('libGLU', '9.0.0'), + ('Mesa', '17.0.2'), +] + +configopts = ' -DX11_X11_LIB="$EBROOTX11/lib/libX11.so" ' +configopts += ' -DX11_X11_INCLUDE_PATH="$EBROOTX11/include/X11" ' +configopts += ' -DX11_Xext_LIB="$EBROOTX11/lib/libXext.so" ' +configopts += ' -DX11_Xrandr_LIB="$EBROOTX11/lib/libXrandr.so" ' +configopts += ' -DX11_Xrandr_INCLUDE_PATH="$EBROOTX11/include/X11/extensions/" ' +configopts += ' -DX11_Xi_LIB="$EBROOTX11/lib/libXrandr.so" ' +configopts += ' -DX11_Xi_INCLUDE_PATH="$EBROOTX11/include/X11/extensions/" ' + +sanity_check_paths = { + 'files': [('lib/libglut.a', 'lib64/libglut.a'), ('lib/libglut.%s' % SHLIB_EXT, 'lib64/libglut.%s' % SHLIB_EXT)], + 'dirs': ['include/GL'], +} + +moduleclass = 'lib' -- GitLab From 8a6b28c55b1bd5cc8e88bb7cd1a11b2084cafcff Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 18 May 2017 13:14:31 +0200 Subject: [PATCH 0785/1603] adding easyconfigs: Octave-4.2.1-intel-2017a.eb, arpack-ng-3.5.0-intel-2017a.eb, FLTK-1.3.4-intel-2017a.eb, GLPK-4.61-intel-2017a.eb, GL2PS-1.4.0-intel-2017a.eb, Qhull-2015.2-intel-2017a.eb, qrupdate-1.1.2-intel-2017a.eb, GraphicsMagick-1.3.25-intel-2017a.eb, freeglut-3.0.0-intel-2017a.eb, gperf-3.0.4-intel-2017a.eb, xprop-1.2.2-intel-2017a.eb --- .../arpack-ng/arpack-ng-3.5.0-intel-2017a.eb | 25 +++++++ .../f/FLTK/FLTK-1.3.4-intel-2017a.eb | 36 ++++++++++ .../f/freeglut/freeglut-3.0.0-intel-2017a.eb | 35 ++++++++++ .../g/GL2PS/GL2PS-1.4.0-intel-2017a.eb | 32 +++++++++ .../g/GLPK/GLPK-4.61-intel-2017a.eb | 28 ++++++++ .../GraphicsMagick-1.3.25-intel-2017a.eb | 39 +++++++++++ .../g/gperf/gperf-3.0.4-intel-2017a.eb | 22 +++++++ .../o/Octave/Octave-4.2.1-intel-2017a.eb | 65 +++++++++++++++++++ .../q/Qhull/Qhull-2015.2-intel-2017a.eb | 36 ++++++++++ .../q/qrupdate/qrupdate-1.1.2-intel-2017a.eb | 28 ++++++++ .../x/xprop/xprop-1.2.2-intel-2017a.eb | 30 +++++++++ 11 files changed, 376 insertions(+) create mode 100644 easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.5.0-intel-2017a.eb create mode 100644 easybuild/easyconfigs/f/FLTK/FLTK-1.3.4-intel-2017a.eb create mode 100644 easybuild/easyconfigs/f/freeglut/freeglut-3.0.0-intel-2017a.eb create mode 100644 easybuild/easyconfigs/g/GL2PS/GL2PS-1.4.0-intel-2017a.eb create mode 100644 easybuild/easyconfigs/g/GLPK/GLPK-4.61-intel-2017a.eb create mode 100644 easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.25-intel-2017a.eb create mode 100644 easybuild/easyconfigs/g/gperf/gperf-3.0.4-intel-2017a.eb create mode 100644 easybuild/easyconfigs/o/Octave/Octave-4.2.1-intel-2017a.eb create mode 100644 easybuild/easyconfigs/q/Qhull/Qhull-2015.2-intel-2017a.eb create mode 100644 easybuild/easyconfigs/q/qrupdate/qrupdate-1.1.2-intel-2017a.eb create mode 100644 easybuild/easyconfigs/x/xprop/xprop-1.2.2-intel-2017a.eb diff --git a/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.5.0-intel-2017a.eb b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.5.0-intel-2017a.eb new file mode 100644 index 0000000000..c2f959831c --- /dev/null +++ b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.5.0-intel-2017a.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'arpack-ng' +version = '3.5.0' + +homepage = 'http://forge.scilab.org/index.php/p/arpack-ng/' +description = """ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://github.com/opencollab/arpack-ng/archive/'] +sources = ['%(version)s.tar.gz'] + +builddependencies = [('Autotools', '20150215')] + +preconfigopts = "sh bootstrap && " +configopts = '--with-pic --with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK"' + +sanity_check_paths = { + 'files': ["lib/libarpack.a", "lib/libarpack.%s" % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/f/FLTK/FLTK-1.3.4-intel-2017a.eb b/easybuild/easyconfigs/f/FLTK/FLTK-1.3.4-intel-2017a.eb new file mode 100644 index 0000000000..95391e1838 --- /dev/null +++ b/easybuild/easyconfigs/f/FLTK/FLTK-1.3.4-intel-2017a.eb @@ -0,0 +1,36 @@ +# +# author: Dina Mahmoud Ibrahim ( Cairo University ) +# +easyblock = 'ConfigureMake' + +name = 'FLTK' +version = '1.3.4' + +homepage = 'http://www.fltk.org' +description = """FLTK is a cross-platform C++ GUI toolkit for UNIX/Linux (X11), Microsoft Windows, + and MacOS X. FLTK provides modern GUI functionality without the bloat and supports 3D graphics via OpenGL + and its built-in GLUT emulation.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = ['%(namelower)s-%(version)s-source.tar.gz'] +source_urls = ['http://fltk.org/pub/%(namelower)s/%(version)s/'] + +configopts = '--enable-shared --enable-threads --enable-xft' + +dependencies = [ + ('Mesa', '17.0.2'), + ('libGLU', '9.0.0'), + ('libpng', '1.6.29'), + ('libjpeg-turbo', '1.5.1'), + ('xprop', '1.2.2'), + ('zlib', '1.2.11'), +] + +sanity_check_paths = { + 'files': ['bin/fltk-config', 'bin/fluid', 'lib/libfltk.a', 'lib/libfltk.%s' % SHLIB_EXT], + 'dirs': ['lib'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/f/freeglut/freeglut-3.0.0-intel-2017a.eb b/easybuild/easyconfigs/f/freeglut/freeglut-3.0.0-intel-2017a.eb new file mode 100644 index 0000000000..64f67b2563 --- /dev/null +++ b/easybuild/easyconfigs/f/freeglut/freeglut-3.0.0-intel-2017a.eb @@ -0,0 +1,35 @@ +easyblock = 'CMakeMake' + +name = 'freeglut' +version = '3.0.0' + +homepage = 'http://freeglut.sourceforge.net/' +description = "freeglut is a completely OpenSourced alternative to the OpenGL Utility Toolkit (GLUT) library." + +toolchain = {'name': 'intel', 'version': '2017a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(name)s'] + +builddependencies = [('CMake', '3.8.1')] + +dependencies = [ + ('X11', '20170314'), + ('libGLU', '9.0.0'), + ('Mesa', '17.0.2'), +] + +configopts = ' -DX11_X11_LIB="$EBROOTX11/lib/libX11.so" ' +configopts += ' -DX11_X11_INCLUDE_PATH="$EBROOTX11/include/X11" ' +configopts += ' -DX11_Xext_LIB="$EBROOTX11/lib/libXext.so" ' +configopts += ' -DX11_Xrandr_LIB="$EBROOTX11/lib/libXrandr.so" ' +configopts += ' -DX11_Xrandr_INCLUDE_PATH="$EBROOTX11/include/X11/extensions/" ' +configopts += ' -DX11_Xi_LIB="$EBROOTX11/lib/libXrandr.so" ' +configopts += ' -DX11_Xi_INCLUDE_PATH="$EBROOTX11/include/X11/extensions/" ' + +sanity_check_paths = { + 'files': [('lib/libglut.a', 'lib64/libglut.a'), ('lib/libglut.%s' % SHLIB_EXT, 'lib64/libglut.%s' % SHLIB_EXT)], + 'dirs': ['include/GL'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/g/GL2PS/GL2PS-1.4.0-intel-2017a.eb b/easybuild/easyconfigs/g/GL2PS/GL2PS-1.4.0-intel-2017a.eb new file mode 100644 index 0000000000..a2bcb6dc02 --- /dev/null +++ b/easybuild/easyconfigs/g/GL2PS/GL2PS-1.4.0-intel-2017a.eb @@ -0,0 +1,32 @@ +easyblock = 'CMakeMake' + +name = 'GL2PS' +version = '1.4.0' + +homepage = 'http://www.geuz.org/gl2ps/' +description = """GL2PS: an OpenGL to PostScript printing library""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['http://geuz.org/gl2ps/src/'] +sources = [SOURCELOWER_TGZ] + +builddependencies = [ + ('CMake', '3.8.1'), +] + +dependencies = [ + ('X11', '20170314'), + ('Mesa', '17.0.2'), + ('libGLU', '9.0.0'), + ('freeglut', '3.0.0'), + ('libpng', '1.6.29'), + ('zlib', '1.2.11'), +] + +sanity_check_paths = { + 'files': ['include/gl2ps.h', 'lib/libgl2ps.so'], + 'dirs': [] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GLPK/GLPK-4.61-intel-2017a.eb b/easybuild/easyconfigs/g/GLPK/GLPK-4.61-intel-2017a.eb new file mode 100644 index 0000000000..28b87558fc --- /dev/null +++ b/easybuild/easyconfigs/g/GLPK/GLPK-4.61-intel-2017a.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'GLPK' +version = '4.61' + +homepage = 'https://www.gnu.org/software/glpk/' +description = """The GLPK (GNU Linear Programming Kit) package is intended for + solving large-scale linear programming (LP), + mixed integer programming (MIP), and other related problems. + It is a set of routines written in ANSI C + and organized in the form of a callable library.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://ftp.gnu.org/gnu/%(namelower)s/'] + +dependencies = [('GMP', '6.1.2')] + +configopts = "--with-gmp" + +sanity_check_paths = { + 'files': ['bin/glpsol', 'include/glpk.h'] + + ['lib/libglpk.%s' % x for x in [SHLIB_EXT, 'a']], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.25-intel-2017a.eb b/easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.25-intel-2017a.eb new file mode 100644 index 0000000000..e1b8b64f3a --- /dev/null +++ b/easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.25-intel-2017a.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'GraphicsMagick' +version = '1.3.25' + +homepage = 'http://www.graphicsmagick.org/' +description = """GraphicsMagick is the swiss army knife of image processing.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True} + +source_urls = [ + SOURCEFORGE_SOURCE, + 'ftp://ftp.graphicsmagick.org/pub/GraphicsMagick/%(version_major_minor)s/', +] +sources = [SOURCE_TAR_GZ] + +patches = ['%(name)s-%(version)s_intel.patch'] + +builddependencies = [ + ('libtool', '2.4.6'), +] + +dependencies = [ + ('X11', '20170314'), + ('bzip2', '1.0.6'), + ('freetype', '2.7.1', '-libpng-1.6.29'), + ('libpng', '1.6.29'), + ('libjpeg-turbo', '1.5.1'), + ('LibTIFF', '4.0.7'), + ('libxml2', '2.9.4'), + ('XZ', '5.2.3'), + ('zlib', '1.2.11'), + ('Ghostscript', '9.21'), +] + +modextrapaths = {'CPATH': ['include/GraphicsMagick']} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/gperf/gperf-3.0.4-intel-2017a.eb b/easybuild/easyconfigs/g/gperf/gperf-3.0.4-intel-2017a.eb new file mode 100644 index 0000000000..6b56add6d5 --- /dev/null +++ b/easybuild/easyconfigs/g/gperf/gperf-3.0.4-intel-2017a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'gperf' +version = '3.0.4' + +homepage = 'http://www.gnu.org/software/gperf/' +description = """GNU gperf is a perfect hash function generator. For a given list of strings, it produces a hash + function and hash table, in form of C or C++ code, for looking up a value depending on the input string. The hash + function is perfect, which means that the hash table has no collisions, and the hash table lookup needs a single + string comparison only.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': ['bin/gperf'], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/o/Octave/Octave-4.2.1-intel-2017a.eb b/easybuild/easyconfigs/o/Octave/Octave-4.2.1-intel-2017a.eb new file mode 100644 index 0000000000..b28e83ac96 --- /dev/null +++ b/easybuild/easyconfigs/o/Octave/Octave-4.2.1-intel-2017a.eb @@ -0,0 +1,65 @@ +easyblock = 'ConfigureMake' + +name = 'Octave' +version = '4.2.1' + +homepage = 'http://www.gnu.org/software/octave/' +description = """GNU Octave is a high-level interpreted language, primarily intended for numerical computations.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +patches = ['%(name)s-%(version)s_intel.patch'] + +builddependencies = [ + ('Bison', '3.0.4'), + ('flex', '2.6.4'), + ('Autotools', '20150215'), + ('libtool', '2.4.6'), + ('gperf', '3.0.4'), +] + +dependencies = [ + ('X11', '20170314'), + ('PCRE', '8.40'), + ('ncurses', '6.0'), + ('libreadline', '6.3'), + ('arpack-ng', '3.5.0'), + ('cURL', '7.53.1'), + ('FLTK', '1.3.4'), + ('fontconfig', '2.12.1', '-libpng-1.6.29'), + ('freetype', '2.7.1', '-libpng-1.6.29'), + ('GLPK', '4.61'), + ('GL2PS', '1.4.0'), + ('gnuplot', '5.0.6'), + ('Java', '1.8.0_131', '', True), + ('zlib', '1.2.11'), + ('Mesa', '17.0.2'), + ('libGLU', '9.0.0'), + ('Qhull', '2015.2'), + ('Qt5', '5.8.0'), + ('HDF5', '1.8.18', '-serial'), + ('qrupdate', '1.1.2'), + ('SuiteSparse', '4.5.5', '-METIS-5.1.0'), + ('GraphicsMagick', '1.3.25'), + ('FFTW', '3.3.6'), +] + +configopts = 'MOC=$EBROOTQT5/bin/moc ' +configopts += 'UIC=$EBROOTQT5/bin/uic ' +configopts += 'RCC=$EBROOTQT5/bin/rcc ' +configopts += 'LRELEASE=$EBROOTQT5/bin/lrelease ' +configopts += '--with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK" --disable-docs ' +# correct for both GCC and Intel compilers +configopts += '--enable-fortran-calling-convention=gfortran' + +sanity_check_paths = { + 'files': ['bin/octave'], + 'dirs': [] +} + +sanity_check_commands = [('octave', '--eval "1+2"')] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/q/Qhull/Qhull-2015.2-intel-2017a.eb b/easybuild/easyconfigs/q/Qhull/Qhull-2015.2-intel-2017a.eb new file mode 100644 index 0000000000..a35971ec3e --- /dev/null +++ b/easybuild/easyconfigs/q/Qhull/Qhull-2015.2-intel-2017a.eb @@ -0,0 +1,36 @@ +easyblock = 'CMakeMake' + +name = 'Qhull' +version = '2015.2' + +homepage = 'http://www.qhull.org' +description = """ +Qhull computes the convex hull, Delaunay triangulation, Voronoi diagram, halfspace intersection about a point, +furthest-site Delaunay triangulation, and furthest-site Voronoi diagram. The source code runs in 2-d, 3-d, 4-d, +and higher dimensions. Qhull implements the Quickhull algorithm for computing the convex hull. +""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +sources = ['%(namelower)s-%(version_major)s-src-7.%(version_minor)s.0.tgz'] +source_urls = ['http://www.qhull.org/download/'] + +patches = [ + 'Qhull-%(version)s-intel-fix.patch', + 'Qhull_pkgconfig.patch', +] + +builddependencies = [('CMake', '3.8.1')] + +sanity_check_paths = { + 'files': ['bin/qhull', 'lib/libqhull.%s' % SHLIB_EXT, 'lib/pkgconfig/qhull.pc'], + 'dirs': [], +} + +modextrapaths = { + 'CPATH': ['qhull/include'], +} + +parallel = 1 + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/q/qrupdate/qrupdate-1.1.2-intel-2017a.eb b/easybuild/easyconfigs/q/qrupdate/qrupdate-1.1.2-intel-2017a.eb new file mode 100644 index 0000000000..4f82f6763a --- /dev/null +++ b/easybuild/easyconfigs/q/qrupdate/qrupdate-1.1.2-intel-2017a.eb @@ -0,0 +1,28 @@ +easyblock = 'MakeCp' + +name = 'qrupdate' +version = '1.1.2' + +homepage = 'https://sourceforge.net/projects/qrupdate/' +description = """qrupdate is a Fortran library for fast updates of QR and Cholesky decompositions.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True} + +sources = [SOURCE_TAR_GZ] +source_urls = [SOURCEFORGE_SOURCE] + +patches = ['%(name)s-%(version)s_makeconf.patch'] + +buildopts = 'lib' + +files_to_copy = [(['libqrupdate.a'], 'lib')] + +sanity_check_paths = { + 'files': ['lib/libqrupdate.a'], + 'dirs': [], +} + +parallel = 1 + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/x/xprop/xprop-1.2.2-intel-2017a.eb b/easybuild/easyconfigs/x/xprop/xprop-1.2.2-intel-2017a.eb new file mode 100644 index 0000000000..773d17a26f --- /dev/null +++ b/easybuild/easyconfigs/x/xprop/xprop-1.2.2-intel-2017a.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'xprop' +version = '1.2.2' + +homepage = "http://www.x.org/wiki/" +description = """The xprop utility is for displaying window and font properties in an X server. + One window or font is selected using the command line arguments or possibly + in the case of a window, by clicking on the desired window. A list of + properties is then given, possibly with formatting information.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://ftp.x.org/archive/individual/app/'] + +builddependencies = [ + ('pkg-config', '0.29.1'), +] + +dependencies = [ + ('X11', '20170314'), +] + +sanity_check_paths = { + 'files': ['bin/xprop'], + 'dirs': [], +} + +moduleclass = 'vis' -- GitLab From 603325793bfd941b1aaeb1a26400880125cdedf5 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Thu, 18 May 2017 19:37:19 +0200 Subject: [PATCH 0786/1603] {math}[binary] MATLAB 2017a (REVIEW) --- .../easyconfigs/m/MATLAB/MATLAB-2017a.eb | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/m/MATLAB/MATLAB-2017a.eb diff --git a/easybuild/easyconfigs/m/MATLAB/MATLAB-2017a.eb b/easybuild/easyconfigs/m/MATLAB/MATLAB-2017a.eb new file mode 100644 index 0000000000..04d37d4f1e --- /dev/null +++ b/easybuild/easyconfigs/m/MATLAB/MATLAB-2017a.eb @@ -0,0 +1,22 @@ +name = 'MATLAB' +version = '2017a' + +homepage = 'http://www.mathworks.com/products/matlab' +description = """MATLAB is a high-level language and interactive environment + that enables you to perform computationally intensive tasks faster than with + traditional programming languages such as C, C++, and Fortran.""" + +toolchain = {'name': 'dummy', 'version': ''} + +# be sure to copy both DVD content to the SAME directory, +# including the hidden files, especially .dvd1 and .dvd2 +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('Java', '1.8.0_121')] + +import os +license_server = os.getenv('EB_MATLAB_LICENSE_SERVER', 'license.example.com') +license_server_port = os.getenv('EB_MATLAB_LICENSE_SERVER_PORT', '00000') +key = os.getenv('EB_MATLAB_KEY', '00000-00000-00000-00000-00000-00000-00000-00000-00000-00000') + +moduleclass = 'math' -- GitLab From 372b412676c7564c9f93360d7e897bd05491e24d Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Fri, 19 May 2017 12:27:56 +0200 Subject: [PATCH 0787/1603] Keras/2.0.4 for Python 2.7.13 --- .../Keras-2.0.4-intel-2017a-Python-2.7.13.eb | 28 +++++++++++++++++++ .../Theano-0.9.0-intel-2017a-Python-2.7.13.eb | 23 +++++++++++++++ 2 files changed, 51 insertions(+) create mode 100644 easybuild/easyconfigs/k/Keras/Keras-2.0.4-intel-2017a-Python-2.7.13.eb create mode 100644 easybuild/easyconfigs/t/Theano/Theano-0.9.0-intel-2017a-Python-2.7.13.eb diff --git a/easybuild/easyconfigs/k/Keras/Keras-2.0.4-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/k/Keras/Keras-2.0.4-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..7f78e14b8d --- /dev/null +++ b/easybuild/easyconfigs/k/Keras/Keras-2.0.4-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'Keras' +version = '2.0.4' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://keras.io/' +description = """Keras is a minimalist, highly modular neural networks library, written in Python and +capable of running on top of either TensorFlow or Theano.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.13'), + ('Theano', '0.9.0', versionsuffix), + ('h5py', '2.7.0', '%(versionsuffix)s'), + ('PyYAML', '3.12', versionsuffix), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/t/Theano/Theano-0.9.0-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/t/Theano/Theano-0.9.0-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..6119fbb576 --- /dev/null +++ b/easybuild/easyconfigs/t/Theano/Theano-0.9.0-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,23 @@ +easyblock = 'PythonPackage' + +name = 'Theano' +version = '0.9.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://deeplearning.net/software/theano' +description = """Theano is a Python library that allows you to define, optimize, +and evaluate mathematical expressions involving multi-dimensional arrays efficiently.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [('Python', '2.7.13')] + +sanity_check_paths = { + 'files': ['bin/theano-cache', 'bin/theano-nose'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'math' -- GitLab From c026c35e54a606aa89c99bcb1f4f50c62cfe535c Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Fri, 19 May 2017 12:44:11 +0200 Subject: [PATCH 0788/1603] Switch default backend to Theano for keras --- .../k/Keras/Keras-2.0.4-intel-2017a-Python-2.7.13.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/k/Keras/Keras-2.0.4-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/k/Keras/Keras-2.0.4-intel-2017a-Python-2.7.13.eb index 7f78e14b8d..b475663604 100644 --- a/easybuild/easyconfigs/k/Keras/Keras-2.0.4-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/k/Keras/Keras-2.0.4-intel-2017a-Python-2.7.13.eb @@ -20,6 +20,9 @@ dependencies = [ ('PyYAML', '3.12', versionsuffix), ] +# it defaults to Tensorflow +modextravars = {'KERAS_BACKEND': 'theano'} + sanity_check_paths = { 'files': [], 'dirs': ['lib/python%(pyshortver)s/site-packages'], -- GitLab From 0ff5782bb6b544645a89f85b268e3811a17ec77f Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Fri, 19 May 2017 13:53:35 +0200 Subject: [PATCH 0789/1603] Sync Py3 and Py2 easyconfigs of Keras --- .../k/Keras/Keras-2.0.4-intel-2017a-Python-3.6.1.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/k/Keras/Keras-2.0.4-intel-2017a-Python-3.6.1.eb b/easybuild/easyconfigs/k/Keras/Keras-2.0.4-intel-2017a-Python-3.6.1.eb index 45f0be1e64..d338fae1c9 100644 --- a/easybuild/easyconfigs/k/Keras/Keras-2.0.4-intel-2017a-Python-3.6.1.eb +++ b/easybuild/easyconfigs/k/Keras/Keras-2.0.4-intel-2017a-Python-3.6.1.eb @@ -20,6 +20,9 @@ dependencies = [ ('PyYAML', '3.12', versionsuffix), ] +# it defaults to Tensorflow +modextravars = {'KERAS_BACKEND': 'theano'} + sanity_check_paths = { 'files': [], 'dirs': ['lib/python%(pyshortver)s/site-packages'], -- GitLab From 3a7a795c6e3c53d91051cf3aa6195aaec67cbcbf Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 19 May 2017 14:52:01 +0200 Subject: [PATCH 0790/1603] adding easyconfigs: HPL-2.2-intel-2017.05.eb, intel-2017.05.eb, icc-2017.4.196-GCC-7.1.0-2.28.eb, ifort-2017.4.196-GCC-7.1.0-2.28.eb, impi-2017.3.196-iccifort-2017.4.196-GCC-7.1.0-2.28.eb, imkl-2017.3.196-iimpi-2017.05-GCC-7.1.0-2.28.eb, iccifort-2017.4.196-GCC-7.1.0-2.28.eb, iimpi-2017.05-GCC-7.1.0-2.28.eb --- .../h/HPL/HPL-2.2-intel-2017.05.eb | 18 ++++++++++ .../i/icc/icc-2017.4.196-GCC-7.1.0-2.28.eb | 33 +++++++++++++++++ .../iccifort-2017.4.196-GCC-7.1.0-2.28.eb | 19 ++++++++++ .../ifort/ifort-2017.4.196-GCC-7.1.0-2.28.eb | 36 +++++++++++++++++++ .../i/iimpi/iimpi-2017.05-GCC-7.1.0-2.28.eb | 20 +++++++++++ ...2017.3.196-iimpi-2017.05-GCC-7.1.0-2.28.eb | 36 +++++++++++++++++++ ....196-iccifort-2017.4.196-GCC-7.1.0-2.28.eb | 33 +++++++++++++++++ .../easyconfigs/i/intel/intel-2017.05.eb | 25 +++++++++++++ 8 files changed, 220 insertions(+) create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.2-intel-2017.05.eb create mode 100644 easybuild/easyconfigs/i/icc/icc-2017.4.196-GCC-7.1.0-2.28.eb create mode 100644 easybuild/easyconfigs/i/iccifort/iccifort-2017.4.196-GCC-7.1.0-2.28.eb create mode 100644 easybuild/easyconfigs/i/ifort/ifort-2017.4.196-GCC-7.1.0-2.28.eb create mode 100644 easybuild/easyconfigs/i/iimpi/iimpi-2017.05-GCC-7.1.0-2.28.eb create mode 100644 easybuild/easyconfigs/i/imkl/imkl-2017.3.196-iimpi-2017.05-GCC-7.1.0-2.28.eb create mode 100644 easybuild/easyconfigs/i/impi/impi-2017.3.196-iccifort-2017.4.196-GCC-7.1.0-2.28.eb create mode 100644 easybuild/easyconfigs/i/intel/intel-2017.05.eb diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.2-intel-2017.05.eb b/easybuild/easyconfigs/h/HPL/HPL-2.2-intel-2017.05.eb new file mode 100644 index 0000000000..f649fc1c6c --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.2-intel-2017.05.eb @@ -0,0 +1,18 @@ +name = 'HPL' +version = '2.2' + +homepage = 'http://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'intel', 'version': '2017.05'} +toolchainopts = {'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] + +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/i/icc/icc-2017.4.196-GCC-7.1.0-2.28.eb b/easybuild/easyconfigs/i/icc/icc-2017.4.196-GCC-7.1.0-2.28.eb new file mode 100644 index 0000000000..75482e87cf --- /dev/null +++ b/easybuild/easyconfigs/i/icc/icc-2017.4.196-GCC-7.1.0-2.28.eb @@ -0,0 +1,33 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild + +name = 'icc' +version = '2017.4.196' + +homepage = 'http://software.intel.com/en-us/intel-compilers/' +description = "C and C++ compiler from Intel" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition_for_cpp.tgz'] + +checksums = ['6b9b57dada0ec68e394866ec0a8b162c9233de18a7a6dd2dcc956d335e06acbc'] + +gccver = '7.1.0' +binutilsver = '2.28' +versionsuffix = '-GCC-%s-%s' % (gccver, binutilsver) + +dependencies = [ + ('GCCcore', gccver), + ('binutils', binutilsver, '', ('GCCcore', gccver)), +] + +# list of regex for components to install +# full list of components can be obtained from pset/mediaconfig.xml in unpacked sources +# cfr. https://software.intel.com/en-us/articles/intel-composer-xe-2015-silent-installation-guide +components = ['intel-comp', 'intel-ccomp', 'intel-icc', 'intel-openmp', 'intel-ipsc?_', 'intel-gdb(?!.*mic)'] + +dontcreateinstalldir = 'True' + +license_file = HOME + '/licenses/intel/license.lic' + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2017.4.196-GCC-7.1.0-2.28.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2017.4.196-GCC-7.1.0-2.28.eb new file mode 100644 index 0000000000..20175f1539 --- /dev/null +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2017.4.196-GCC-7.1.0-2.28.eb @@ -0,0 +1,19 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +easyblock = 'Toolchain' + +name = 'iccifort' +version = '2017.4.196' +versionsuffix = '-GCC-7.1.0-2.28' + +homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' +description = """Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and + Intel MKL""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +dependencies = [ + ('icc', version, versionsuffix), + ('ifort', version, versionsuffix), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2017.4.196-GCC-7.1.0-2.28.eb b/easybuild/easyconfigs/i/ifort/ifort-2017.4.196-GCC-7.1.0-2.28.eb new file mode 100644 index 0000000000..0ad62b89f5 --- /dev/null +++ b/easybuild/easyconfigs/i/ifort/ifort-2017.4.196-GCC-7.1.0-2.28.eb @@ -0,0 +1,36 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild + +name = 'ifort' +version = '2017.4.196' + +homepage = 'http://software.intel.com/en-us/intel-compilers/' +description = "Fortran compiler from Intel" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition_for_fortran.tgz'] + +checksums = ['0b6a222e015f776600b12b17c19506249c9e7691a8d287f44cd40a66ca9ac749'] + +# remove dependency on intel-mpi-rt-mic +patches = ['ifort_2017_no_mpi_mic_dependency.patch'] + +gccver = '7.1.0' +binutilsver = '2.28' +versionsuffix = '-GCC-%s-%s' % (gccver, binutilsver) + +dependencies = [ + ('GCCcore', gccver), + ('binutils', binutilsver, '', ('GCCcore', gccver)), +] + +# list of regex for components to install +# full list of components can be obtained from pset/mediaconfig.xml in unpacked sources +# cfr. https://software.intel.com/en-us/articles/intel-composer-xe-2015-silent-installation-guide +components = ['intel-comp', 'intel-fcomp', 'intel-ifort', 'intel-openmp', 'intel-ipsf?_', 'intel-gdb(?!.*mic)'] + +dontcreateinstalldir = 'True' + +license_file = HOME + '/licenses/intel/license.lic' + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-2017.05-GCC-7.1.0-2.28.eb b/easybuild/easyconfigs/i/iimpi/iimpi-2017.05-GCC-7.1.0-2.28.eb new file mode 100644 index 0000000000..ff25b839db --- /dev/null +++ b/easybuild/easyconfigs/i/iimpi/iimpi-2017.05-GCC-7.1.0-2.28.eb @@ -0,0 +1,20 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +easyblock = "Toolchain" + +name = 'iimpi' +version = '2017.05' +versionsuffix = '-GCC-7.1.0-2.28' + +homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' +description = """Intel C/C++ and Fortran compilers, alongside Intel MPI.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +compver = '2017.4.196' +dependencies = [ + ('icc', compver, versionsuffix), + ('ifort', compver, versionsuffix), + ('impi', '2017.3.196', '', ('iccifort', '%s%s' % (compver, versionsuffix))), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/imkl/imkl-2017.3.196-iimpi-2017.05-GCC-7.1.0-2.28.eb b/easybuild/easyconfigs/i/imkl/imkl-2017.3.196-iimpi-2017.05-GCC-7.1.0-2.28.eb new file mode 100644 index 0000000000..2793cfba56 --- /dev/null +++ b/easybuild/easyconfigs/i/imkl/imkl-2017.3.196-iimpi-2017.05-GCC-7.1.0-2.28.eb @@ -0,0 +1,36 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild + +name = 'imkl' +version = '2017.3.196' + +homepage = 'http://software.intel.com/en-us/intel-mkl/' +description = """Intel Math Kernel Library is a library of highly optimized, + extensively threaded math routines for science, engineering, and financial + applications that require maximum performance. Core math functions include + BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.""" + +toolchain = {'name': 'iimpi', 'version': '2017.05-GCC-7.1.0-2.28'} + +sources = ['l_mkl_%(version)s.tgz'] +checksums = ['fd7295870fa164d6138c9818304f25f2bb263c814a6c6539c9fe4e104055f1ca'] + +dontcreateinstalldir = 'True' + +interfaces = True + +postinstallcmds = [ + # extract the examples + 'tar xvzf %(installdir)s/mkl/examples/examples_cluster_c.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_cluster_f.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_core_c.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_core_f.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_f95.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_mic_f.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_mic_c.tgz -C %(installdir)s/mkl/examples/', +] + +modextravars = { + 'MKL_EXAMPLES': '%(installdir)s/mkl/examples/', +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/impi/impi-2017.3.196-iccifort-2017.4.196-GCC-7.1.0-2.28.eb b/easybuild/easyconfigs/i/impi/impi-2017.3.196-iccifort-2017.4.196-GCC-7.1.0-2.28.eb new file mode 100644 index 0000000000..75d92e43ef --- /dev/null +++ b/easybuild/easyconfigs/i/impi/impi-2017.3.196-iccifort-2017.4.196-GCC-7.1.0-2.28.eb @@ -0,0 +1,33 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild + +name = 'impi' +version = '2017.3.196' + +homepage = 'http://software.intel.com/en-us/intel-mpi-library/' +description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric message + passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for + Linux OS implements the Message Passing Interface, version 2 (MPI-2) specification.""" + +toolchain = {'name': 'iccifort', 'version': '2017.4.196-GCC-7.1.0-2.28'} + +sources = ['l_mpi_%(version)s.tgz'] + +checksums = ['dad9efbc5bbd3fd27cce7e1e2507ad77f342d5ecc929747ae141c890e7fb87f0'] + +dontcreateinstalldir = 'True' + +components = ['intel-mpi', 'intel-psxe', 'intel-imb'] + +# set up all the mpi commands to default to intel compilers +# set_mpi_wrappers_all = 'True' + +postinstallcmds = [ + 'ln -s %(installdir)s/lib64/libmpi.so %(installdir)s/lib64/libmpich.so', + 'ln -s %(installdir)s/lib64/libmpigc4.so %(installdir)s/lib64/libmpichcxx.so', + 'ln -s %(installdir)s/lib64/libmpigf.so %(installdir)s/lib64/libfmpich.so', + 'ln -s %(installdir)s/lib64/libmpigf.so %(installdir)s/lib64/libmpichf90.so', + 'ln -s %(installdir)s/lib64/libmpi.so %(installdir)s/lib64/libmpl.so', + 'ln -s %(installdir)s/lib64/libmpi.so %(installdir)s/lib64/libopa.so' +] + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/intel/intel-2017.05.eb b/easybuild/easyconfigs/i/intel/intel-2017.05.eb new file mode 100644 index 0000000000..6e68b4ba70 --- /dev/null +++ b/easybuild/easyconfigs/i/intel/intel-2017.05.eb @@ -0,0 +1,25 @@ +easyblock = 'Toolchain' + +name = 'intel' +version = '2017.05' + +homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & + Intel MKL.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +compver = '2017.4.196' +gccver = '7.1.0' +binutilsver = '2.28' +gccsuff = '-GCC-%s-%s' % (gccver, binutilsver) +dependencies = [ + ('GCCcore', gccver), + ('binutils', binutilsver, '-GCCcore-%s' % gccver), + ('icc', compver, gccsuff), + ('ifort', compver, gccsuff), + ('impi', '2017.3.196', '', ('iccifort', '%s%s' % (compver, gccsuff))), + ('imkl', '2017.3.196', '', ('iimpi', version + gccsuff)), +] + +moduleclass = 'toolchain' -- GitLab From bb1e24a58fbdf67a53ff89fe0bef88ca2926a58c Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Fri, 19 May 2017 15:25:59 +0200 Subject: [PATCH 0791/1603] FSL/5.0.10 for intel/2017a --- .../f/FSL/FSL-5.0.10-intel-2017a.eb | 33 + .../f/FSL/FSL-5.0.10_build_extras.patch | 13 + .../f/FSL/FSL-5.0.10_makefile_fixes.patch | 605 ++++++++++++++++++ .../g/GLibmm/GLibmm-2.53.1.1-intel-2017a.eb | 24 + .../libsigc++/libsigc++-2.10.0-intel-2017a.eb | 20 + .../l/libxml++/libxml++-2.91.3-intel-2017a.eb | 24 + 6 files changed, 719 insertions(+) create mode 100644 easybuild/easyconfigs/f/FSL/FSL-5.0.10-intel-2017a.eb create mode 100644 easybuild/easyconfigs/f/FSL/FSL-5.0.10_build_extras.patch create mode 100644 easybuild/easyconfigs/f/FSL/FSL-5.0.10_makefile_fixes.patch create mode 100644 easybuild/easyconfigs/g/GLibmm/GLibmm-2.53.1.1-intel-2017a.eb create mode 100644 easybuild/easyconfigs/l/libsigc++/libsigc++-2.10.0-intel-2017a.eb create mode 100644 easybuild/easyconfigs/l/libxml++/libxml++-2.91.3-intel-2017a.eb diff --git a/easybuild/easyconfigs/f/FSL/FSL-5.0.10-intel-2017a.eb b/easybuild/easyconfigs/f/FSL/FSL-5.0.10-intel-2017a.eb new file mode 100644 index 0000000000..b6760b7e06 --- /dev/null +++ b/easybuild/easyconfigs/f/FSL/FSL-5.0.10-intel-2017a.eb @@ -0,0 +1,33 @@ +name = 'FSL' +version = '5.0.10' + +homepage = 'http://www.fmrib.ox.ac.uk/fsl/' +description = """FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ["http://www.fmrib.ox.ac.uk/fsldownloads/"] +sources = ['%(namelower)s-%(version)s-sources.tar.gz'] + +patches = [ + 'FSL-%(version)s_makefile_fixes.patch', + 'FSL-5.0.9_missing_lib.patch', + 'FSL_icc_nan-inf_fix.patch', + 'FSL-%(version)s_build_extras.patch', +] + +dependencies = [ + ('Boost', '1.63.0', '-Python-2.7.13'), + ('libgd', '2.2.4'), + ('libxml++', '2.91.3'), + ('SQLite', '3.13.0'), + ('libpng', '1.6.29'), + ('Tk', '8.6.6'), + ('GLibmm', '2.53.1.1'), + ('NLopt', '2.4.2'), + ('freeglut', '3.0.0'), + ('expat', '2.2.0'), + ('zlib', '1.2.11'), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/FSL/FSL-5.0.10_build_extras.patch b/easybuild/easyconfigs/f/FSL/FSL-5.0.10_build_extras.patch new file mode 100644 index 0000000000..ac663c9852 --- /dev/null +++ b/easybuild/easyconfigs/f/FSL/FSL-5.0.10_build_extras.patch @@ -0,0 +1,13 @@ +# only build thing we don't provide with EasyBuild +diff -ur fsl/extras/build fsl.new/extras/build +--- fsl/extras/build 2016-11-15 15:30:21.000000000 +0100 ++++ fsl.new/extras/build 2017-05-19 15:21:07.321630239 +0200 +@@ -106,6 +106,8 @@ + fi + PROJECTS="${PROJECTS} libgd libgdc libprob libcprob newmat cprob newran fftw" + PROJECTS="${PROJECTS} boost libxml2-2.9.2 libxml++-2.34.0 libsqlite libnlopt ../include/armawrap/dummy_newmat" ++# For EasyBuild: ++PROJECTS="libprob libcprob newmat cprob newran" + for projname in $PROJECTS; do + if [ -d $FSLESRCDIR/$projname ] ; then + buildIt $FSLESRCDIR $projname 1 diff --git a/easybuild/easyconfigs/f/FSL/FSL-5.0.10_makefile_fixes.patch b/easybuild/easyconfigs/f/FSL/FSL-5.0.10_makefile_fixes.patch new file mode 100644 index 0000000000..8808344d6f --- /dev/null +++ b/easybuild/easyconfigs/f/FSL/FSL-5.0.10_makefile_fixes.patch @@ -0,0 +1,605 @@ +patch out hardcoded compiler names and options +author: kenneth hoste (hpc-ugent) +diff -ur fsl.orig/config/apple-darwin10-gcc4.2/systemvars.mk fsl/config/apple-darwin10-gcc4.2/systemvars.mk +--- fsl.orig/config/apple-darwin10-gcc4.2/systemvars.mk 2009-11-03 18:02:14.000000000 +0100 ++++ fsl/config/apple-darwin10-gcc4.2/systemvars.mk 2017-05-18 13:54:40.446975876 +0200 +@@ -3,8 +3,8 @@ + + # Compiler dependent variables + +-CC = cc +-CXX = c++ ++CC := ${CC} ++CXX := ${CXX} + CSTATICFLAGS = + CXXSTATICFLAGS = + +@@ -15,7 +15,7 @@ + + DEPENDFLAGS = -MM + +-OPTFLAGS = -O3 -fexpensive-optimizations ++OPTFLAGS := ${CFLAGS} -wd803 + MACHDBGFLAGS = -g + GNU_ANSI_FLAGS = -Wall -Wno-long-long -ansi -pedantic + SGI_ANSI_FLAGS = -ansi -fullwarn +Only in fsl/config/apple-darwin10-gcc4.2: systemvars.mk.orig +diff -ur fsl.orig/config/apple-darwin11-gcc4.2/systemvars.mk fsl/config/apple-darwin11-gcc4.2/systemvars.mk +--- fsl.orig/config/apple-darwin11-gcc4.2/systemvars.mk 2012-03-21 12:30:53.000000000 +0100 ++++ fsl/config/apple-darwin11-gcc4.2/systemvars.mk 2017-05-18 13:54:40.446975876 +0200 +@@ -15,7 +15,7 @@ + + DEPENDFLAGS = -MM + +-OPTFLAGS = -O3 ++OPTFLAGS := -O3 -wd803 + MACHDBGFLAGS = -g + GNU_ANSI_FLAGS = -Wall -Wno-long-long -ansi -pedantic + ANSI_FLAGS = ${GNU_ANSI_FLAGS} +Only in fsl/config/apple-darwin11-gcc4.2: systemvars.mk.orig +diff -ur fsl.orig/config/apple-darwin12-gcc4.2/systemvars.mk fsl/config/apple-darwin12-gcc4.2/systemvars.mk +--- fsl.orig/config/apple-darwin12-gcc4.2/systemvars.mk 2013-04-09 18:00:32.000000000 +0200 ++++ fsl/config/apple-darwin12-gcc4.2/systemvars.mk 2017-05-18 13:54:40.446975876 +0200 +@@ -15,7 +15,7 @@ + + DEPENDFLAGS = -MM + +-OPTFLAGS = -O3 ++OPTFLAGS := -O3 -wd803 + MACHDBGFLAGS = -g + GNU_ANSI_FLAGS = -Wall -Wno-long-long -ansi -pedantic + ANSI_FLAGS = ${GNU_ANSI_FLAGS} +Only in fsl/config/apple-darwin12-gcc4.2: systemvars.mk.orig +diff -ur fsl.orig/config/apple-darwin7-gcc3.1/systemvars.mk fsl/config/apple-darwin7-gcc3.1/systemvars.mk +--- fsl.orig/config/apple-darwin7-gcc3.1/systemvars.mk 2007-07-13 13:00:20.000000000 +0200 ++++ fsl/config/apple-darwin7-gcc3.1/systemvars.mk 2017-05-18 13:54:40.446975876 +0200 +@@ -7,8 +7,8 @@ + + # Compiler dependent variables + +-CC = cc +-CXX = c++ ++CC := ${CC} ++CXX := ${CXX} + CSTATICFLAGS = + CXXSTATICFLAGS = + +@@ -17,7 +17,7 @@ + + DEPENDFLAGS = -MM + +-OPTFLAGS = -O3 -fexpensive-optimizations ${ARCHFLAGS} ++OPTFLAGS := ${CFLAGS} ${ARCHFLAGS} -wd803 + MACHDBGFLAGS = -g + GNU_ANSI_FLAGS = -traditional-cpp -Wall -Wno-long-long -Wno-long-double -ansi -pedantic + SGI_ANSI_FLAGS = -ansi -fullwarn +Only in fsl/config/apple-darwin7-gcc3.1: systemvars.mk.orig +diff -ur fsl.orig/config/apple-darwin7-gcc3.3/systemvars.mk fsl/config/apple-darwin7-gcc3.3/systemvars.mk +--- fsl.orig/config/apple-darwin7-gcc3.3/systemvars.mk 2007-07-13 13:00:20.000000000 +0200 ++++ fsl/config/apple-darwin7-gcc3.3/systemvars.mk 2017-05-18 13:54:40.446975876 +0200 +@@ -7,8 +7,8 @@ + + # Compiler dependent variables + +-CC = cc +-CXX = c++ ++CC := ${CC} ++CXX := ${CXX} + CSTATICFLAGS = + CXXSTATICFLAGS = + +@@ -17,7 +17,7 @@ + + DEPENDFLAGS = -MM + +-OPTFLAGS = -O3 -fexpensive-optimizations ${ARCHFLAGS} ++OPTFLAGS := ${CFLAGS} ${ARCHFLAGS} -wd803 + MACHDBGFLAGS = -g + GNU_ANSI_FLAGS = -Wall -Wno-long-long -Wno-long-double -ansi -pedantic + SGI_ANSI_FLAGS = -ansi -fullwarn +Only in fsl/config/apple-darwin7-gcc3.3: systemvars.mk.orig +diff -ur fsl.orig/config/apple-darwin8-gcc4.0/systemvars.mk fsl/config/apple-darwin8-gcc4.0/systemvars.mk +--- fsl.orig/config/apple-darwin8-gcc4.0/systemvars.mk 2007-12-19 15:40:57.000000000 +0100 ++++ fsl/config/apple-darwin8-gcc4.0/systemvars.mk 2017-05-18 13:54:40.446975876 +0200 +@@ -3,8 +3,8 @@ + + # Compiler dependent variables + +-CC = cc +-CXX = c++ ++CC := ${CC} ++CXX := ${CXX} + CSTATICFLAGS = + CXXSTATICFLAGS = + +@@ -17,7 +17,7 @@ + + DEPENDFLAGS = -MM + +-OPTFLAGS = -O3 -fexpensive-optimizations ++OPTFLAGS := ${CFLAGS} -wd803 + MACHDBGFLAGS = -g + GNU_ANSI_FLAGS = -Wall -Wno-long-long -Wno-long-double -ansi -pedantic + SGI_ANSI_FLAGS = -ansi -fullwarn +Only in fsl/config/apple-darwin8-gcc4.0: systemvars.mk.orig +diff -ur fsl.orig/config/apple-darwin9-gcc4.0/systemvars.mk fsl/config/apple-darwin9-gcc4.0/systemvars.mk +--- fsl.orig/config/apple-darwin9-gcc4.0/systemvars.mk 2007-12-19 15:33:53.000000000 +0100 ++++ fsl/config/apple-darwin9-gcc4.0/systemvars.mk 2017-05-18 13:54:40.446975876 +0200 +@@ -3,8 +3,8 @@ + + # Compiler dependent variables + +-CC = cc +-CXX = c++ ++CC := ${CC} ++CXX := ${CXX} + CSTATICFLAGS = + CXXSTATICFLAGS = + +@@ -17,7 +17,7 @@ + + DEPENDFLAGS = -MM + +-OPTFLAGS = -O3 -fexpensive-optimizations ++OPTFLAGS := ${CFLAGS} -wd803 + MACHDBGFLAGS = -g + GNU_ANSI_FLAGS = -Wall -Wno-long-long -Wno-long-double -ansi -pedantic + SGI_ANSI_FLAGS = -ansi -fullwarn +Only in fsl/config/apple-darwin9-gcc4.0: systemvars.mk.orig +diff -ur fsl.orig/config/generic/systemvars.mk fsl/config/generic/systemvars.mk +--- fsl.orig/config/generic/systemvars.mk 2007-07-13 13:00:20.000000000 +0200 ++++ fsl/config/generic/systemvars.mk 2017-05-18 13:54:40.446975876 +0200 +@@ -16,8 +16,8 @@ + + # Compiler dependent variables + +-CC = gcc +-CXX = c++ ++CC := ${CC} ++CXX := ${CXX} + CSTATICFLAGS = -static + CXXSTATICFLAGS = -static + +@@ -25,7 +25,7 @@ + + DEPENDFLAGS = -MM + +-OPTFLAGS = -O3 -fexpensive-optimizations ${ARCHFLAGS} ++OPTFLAGS := ${CFLAGS} ${ARCHFLAGS} -wd803 + MACHDBGFLAGS = + GNU_ANSI_FLAGS = -Wall -ansi -pedantic + SGI_ANSI_FLAGS = -ansi -fullwarn +Only in fsl/config/generic: systemvars.mk.orig +diff -ur fsl.orig/config/gnu_64-gcc4.4/systemvars.mk fsl/config/gnu_64-gcc4.4/systemvars.mk +--- fsl.orig/config/gnu_64-gcc4.4/systemvars.mk 2011-04-19 10:47:52.000000000 +0200 ++++ fsl/config/gnu_64-gcc4.4/systemvars.mk 2017-05-18 13:54:40.446975876 +0200 +@@ -27,7 +27,7 @@ + + DEPENDFLAGS = -MM + +-OPTFLAGS = -O3 -fexpensive-optimizations ${ARCHFLAGS} ++OPTFLAGS := ${CFLAGS} ${ARCHFLAGS} -wd803 + MACHDBGFLAGS = -g + GNU_ANSI_FLAGS = -Wall -ansi -pedantic -Wno-long-long + SGI_ANSI_FLAGS = -ansi -fullwarn +Only in fsl/config/gnu_64-gcc4.4: systemvars.mk.orig +diff -ur fsl.orig/config/i686-pc-cygwin-gcc3.2/systemvars.mk fsl/config/i686-pc-cygwin-gcc3.2/systemvars.mk +--- fsl.orig/config/i686-pc-cygwin-gcc3.2/systemvars.mk 2007-07-13 13:00:20.000000000 +0200 ++++ fsl/config/i686-pc-cygwin-gcc3.2/systemvars.mk 2017-05-18 13:54:40.446975876 +0200 +@@ -18,8 +18,8 @@ + + # Compiler dependent variables + +-CC = gcc-2 +-CXX = c++-2 ++CC := ${CC} ++CXX := ${CXX} + CSTATICFLAGS = -static + CXXSTATICFLAGS = -static + +@@ -27,7 +27,7 @@ + + DEPENDFLAGS = -MM + +-OPTFLAGS = -O3 -fexpensive-optimizations ${ARCHFLAGS} ++OPTFLAGS := ${CFLAGS} ${ARCHFLAGS} -wd803 + MACHDBGFLAGS = -g + GNU_ANSI_FLAGS = -Wall -ansi -pedantic -Wno-deprecated + SGI_ANSI_FLAGS = -ansi -fullwarn +Only in fsl/config/i686-pc-cygwin-gcc3.2: systemvars.mk.orig +diff -ur fsl.orig/config/i686-pc-cygwin-gcc3.3/systemvars.mk fsl/config/i686-pc-cygwin-gcc3.3/systemvars.mk +--- fsl.orig/config/i686-pc-cygwin-gcc3.3/systemvars.mk 2007-07-13 13:00:20.000000000 +0200 ++++ fsl/config/i686-pc-cygwin-gcc3.3/systemvars.mk 2017-05-18 13:54:40.447975880 +0200 +@@ -18,8 +18,8 @@ + + # Compiler dependent variables + +-CC = gcc +-CXX = c++ ++CC := ${CC} ++CXX := ${CXX} + CSTATICFLAGS = -static + CXXSTATICFLAGS = -static + +@@ -27,7 +27,7 @@ + + DEPENDFLAGS = -MM + +-OPTFLAGS = -O3 -fexpensive-optimizations ${ARCHFLAGS} ++OPTFLAGS := ${CFLAGS} ${ARCHFLAGS} -wd803 + MACHDBGFLAGS = -g + GNU_ANSI_FLAGS = -Wall -ansi -pedantic -Wno-deprecated + SGI_ANSI_FLAGS = -ansi -fullwarn +Only in fsl/config/i686-pc-cygwin-gcc3.3: systemvars.mk.orig +diff -ur fsl.orig/config/i686-pc-cygwin-gcc3.4/systemvars.mk fsl/config/i686-pc-cygwin-gcc3.4/systemvars.mk +--- fsl.orig/config/i686-pc-cygwin-gcc3.4/systemvars.mk 2007-07-13 13:00:20.000000000 +0200 ++++ fsl/config/i686-pc-cygwin-gcc3.4/systemvars.mk 2017-05-18 13:54:40.447975880 +0200 +@@ -18,8 +18,8 @@ + + # Compiler dependent variables + +-CC = gcc +-CXX = c++ ++CC := ${CC} ++CXX := ${CXX} + CSTATICFLAGS = -static + CXXSTATICFLAGS = -static + +@@ -27,7 +27,7 @@ + + DEPENDFLAGS = -MM + +-OPTFLAGS = -O3 -fexpensive-optimizations ${ARCHFLAGS} ++OPTFLAGS := ${CFLAGS} ${ARCHFLAGS} -wd803 + MACHDBGFLAGS = -g + GNU_ANSI_FLAGS = -Wall -ansi -pedantic -Wno-deprecated + SGI_ANSI_FLAGS = -ansi -fullwarn +Only in fsl/config/i686-pc-cygwin-gcc3.4: systemvars.mk.orig +diff -ur fsl.orig/config/linux_32-gcc2.96/systemvars.mk fsl/config/linux_32-gcc2.96/systemvars.mk +--- fsl.orig/config/linux_32-gcc2.96/systemvars.mk 2007-07-25 17:21:07.000000000 +0200 ++++ fsl/config/linux_32-gcc2.96/systemvars.mk 2017-05-18 13:54:40.447975880 +0200 +@@ -18,8 +18,8 @@ + + # Compiler dependent variables + +-CC = gcc +-CXX = c++ ++CC := ${CC} ++CXX := ${CXX} + CSTATICFLAGS = -static + CXXSTATICFLAGS = -static + +@@ -27,7 +27,7 @@ + + DEPENDFLAGS = -MM + +-OPTFLAGS = -O3 -fexpensive-optimizations ${ARCHFLAGS} ++OPTFLAGS := ${CFLAGS} ${ARCHFLAGS} -wd803 + MACHDBGFLAGS = -g + GNU_ANSI_FLAGS = -Wall -ansi -pedantic + SGI_ANSI_FLAGS = -ansi -fullwarn +Only in fsl/config/linux_32-gcc2.96: systemvars.mk.orig +diff -ur fsl.orig/config/linux_32-gcc3.2/systemvars.mk fsl/config/linux_32-gcc3.2/systemvars.mk +--- fsl.orig/config/linux_32-gcc3.2/systemvars.mk 2007-07-25 17:21:08.000000000 +0200 ++++ fsl/config/linux_32-gcc3.2/systemvars.mk 2017-05-18 13:54:40.447975880 +0200 +@@ -18,8 +18,8 @@ + + # Compiler dependent variables + +-CC = gcc +-CXX = c++ ++CC := ${CC} ++CXX := ${CXX} + CSTATICFLAGS = -static + CXXSTATICFLAGS = -static + +@@ -27,7 +27,7 @@ + + DEPENDFLAGS = -MM + +-OPTFLAGS = -O3 -fexpensive-optimizations ${ARCHFLAGS} ++OPTFLAGS := ${CFLAGS} ${ARCHFLAGS} -wd803 + MACHDBGFLAGS = -g + GNU_ANSI_FLAGS = -Wall -ansi -pedantic + SGI_ANSI_FLAGS = -ansi -fullwarn +Only in fsl/config/linux_32-gcc3.2: systemvars.mk.orig +diff -ur fsl.orig/config/linux_32-gcc3.3/systemvars.mk fsl/config/linux_32-gcc3.3/systemvars.mk +--- fsl.orig/config/linux_32-gcc3.3/systemvars.mk 2007-07-25 17:21:09.000000000 +0200 ++++ fsl/config/linux_32-gcc3.3/systemvars.mk 2017-05-18 13:54:40.447975880 +0200 +@@ -18,8 +18,8 @@ + + # Compiler dependent variables + +-CC = gcc +-CXX = c++ ++CC := ${CC} ++CXX := ${CXX} + CSTATICFLAGS = -static + CXXSTATICFLAGS = -static + +@@ -27,7 +27,7 @@ + + DEPENDFLAGS = -MM + +-OPTFLAGS = -O3 -fexpensive-optimizations ${ARCHFLAGS} ++OPTFLAGS := ${CFLAGS} ${ARCHFLAGS} -wd803 + MACHDBGFLAGS = -g + GNU_ANSI_FLAGS = -Wall -ansi -pedantic -Wno-long-long + SGI_ANSI_FLAGS = -ansi -fullwarn +Only in fsl/config/linux_32-gcc3.3: systemvars.mk.orig +diff -ur fsl.orig/config/linux_32-gcc3.4/systemvars.mk fsl/config/linux_32-gcc3.4/systemvars.mk +--- fsl.orig/config/linux_32-gcc3.4/systemvars.mk 2007-07-25 17:21:10.000000000 +0200 ++++ fsl/config/linux_32-gcc3.4/systemvars.mk 2017-05-18 13:54:40.447975880 +0200 +@@ -18,8 +18,8 @@ + + # Compiler dependent variables + +-CC = gcc +-CXX = c++ ++CC := ${CC} ++CXX := ${CXX} + CSTATICFLAGS = -static + CXXSTATICFLAGS = -static + +@@ -27,7 +27,7 @@ + + DEPENDFLAGS = -MM + +-OPTFLAGS = -O3 -fexpensive-optimizations ${ARCHFLAGS} ++OPTFLAGS := ${CFLAGS} ${ARCHFLAGS} -wd803 + MACHDBGFLAGS = -g + GNU_ANSI_FLAGS = -Wall -ansi -pedantic -Wno-long-long + SGI_ANSI_FLAGS = -ansi -fullwarn +Only in fsl/config/linux_32-gcc3.4: systemvars.mk.orig +diff -ur fsl.orig/config/linux_32-gcc4.0/systemvars.mk fsl/config/linux_32-gcc4.0/systemvars.mk +--- fsl.orig/config/linux_32-gcc4.0/systemvars.mk 2007-07-25 17:21:11.000000000 +0200 ++++ fsl/config/linux_32-gcc4.0/systemvars.mk 2017-05-18 13:54:40.447975880 +0200 +@@ -18,8 +18,8 @@ + + # Compiler dependent variables + +-CC = gcc +-CXX = c++ ++CC := ${CC} ++CXX := ${CXX} + CSTATICFLAGS = -static + CXXSTATICFLAGS = -static + +@@ -27,7 +27,7 @@ + + DEPENDFLAGS = -MM + +-OPTFLAGS = -O3 -fexpensive-optimizations ${ARCHFLAGS} ++OPTFLAGS := ${CFLAGS} ${ARCHFLAGS} -wd803 + MACHDBGFLAGS = -g + GNU_ANSI_FLAGS = -Wall -ansi -pedantic + SGI_ANSI_FLAGS = -ansi -fullwarn +Only in fsl/config/linux_32-gcc4.0: systemvars.mk.orig +diff -ur fsl.orig/config/linux_32-gcc4.1/systemvars.mk fsl/config/linux_32-gcc4.1/systemvars.mk +--- fsl.orig/config/linux_32-gcc4.1/systemvars.mk 2012-04-20 11:37:28.000000000 +0200 ++++ fsl/config/linux_32-gcc4.1/systemvars.mk 2017-05-18 13:54:40.447975880 +0200 +@@ -18,8 +18,8 @@ + + # Compiler dependent variables + +-CC = gcc +-CXX = c++ ++CC := ${CC} ++CXX := ${CXX} + CSTATICFLAGS = -static + CXXSTATICFLAGS = -static + +@@ -27,7 +27,7 @@ + + DEPENDFLAGS = -MM + +-OPTFLAGS = -O3 -fexpensive-optimizations ${ARCHFLAGS} ++OPTFLAGS := ${CFLAGS} ${ARCHFLAGS} -wd803 + MACHDBGFLAGS = -g + GNU_ANSI_FLAGS = -Wall -ansi -pedantic -Wno-long-long + SGI_ANSI_FLAGS = -ansi -fullwarn +Only in fsl/config/linux_32-gcc4.1: systemvars.mk.orig +diff -ur fsl.orig/config/linux_64-gcc3.4/systemvars.mk fsl/config/linux_64-gcc3.4/systemvars.mk +--- fsl.orig/config/linux_64-gcc3.4/systemvars.mk 2007-07-25 17:21:12.000000000 +0200 ++++ fsl/config/linux_64-gcc3.4/systemvars.mk 2017-05-18 13:54:40.447975880 +0200 +@@ -18,8 +18,8 @@ + + # Compiler dependent variables + +-CC = gcc +-CXX = c++ ++CC := ${CC} ++CXX := ${CXX} + CSTATICFLAGS = -static + CXXSTATICFLAGS = -static + +@@ -27,7 +27,7 @@ + + DEPENDFLAGS = -MM + +-OPTFLAGS = -O3 -fexpensive-optimizations ${ARCHFLAGS} ++OPTFLAGS := ${CFLAGS} ${ARCHFLAGS} -wd803 + MACHDBGFLAGS = -g + GNU_ANSI_FLAGS = -Wall -ansi -pedantic -Wno-long-long + SGI_ANSI_FLAGS = -ansi -fullwarn +Only in fsl/config/linux_64-gcc3.4: systemvars.mk.orig +diff -ur fsl.orig/config/linux_64-gcc4.0/systemvars.mk fsl/config/linux_64-gcc4.0/systemvars.mk +--- fsl.orig/config/linux_64-gcc4.0/systemvars.mk 2007-07-25 17:21:13.000000000 +0200 ++++ fsl/config/linux_64-gcc4.0/systemvars.mk 2017-05-18 13:54:40.447975880 +0200 +@@ -18,8 +18,8 @@ + + # Compiler dependent variables + +-CC = gcc +-CXX = c++ ++CC := ${CC} ++CXX := ${CXX} + CSTATICFLAGS = -static + CXXSTATICFLAGS = -static + +@@ -27,7 +27,7 @@ + + DEPENDFLAGS = -MM + +-OPTFLAGS = -O3 -fexpensive-optimizations ${ARCHFLAGS} ++OPTFLAGS := ${CFLAGS} ${ARCHFLAGS} -wd803 + MACHDBGFLAGS = -g + GNU_ANSI_FLAGS = -Wall -ansi -pedantic -Wno-long-long + SGI_ANSI_FLAGS = -ansi -fullwarn +Only in fsl/config/linux_64-gcc4.0: systemvars.mk.orig +diff -ur fsl.orig/config/linux_64-gcc4.1/systemvars.mk fsl/config/linux_64-gcc4.1/systemvars.mk +--- fsl.orig/config/linux_64-gcc4.1/systemvars.mk 2007-07-25 11:19:45.000000000 +0200 ++++ fsl/config/linux_64-gcc4.1/systemvars.mk 2017-05-18 13:54:40.447975880 +0200 +@@ -18,8 +18,8 @@ + + # Compiler dependent variables + +-CC = gcc +-CXX = c++ ++CC := ${CC} ++CXX := ${CXX} + CSTATICFLAGS = -static + CXXSTATICFLAGS = -static + +@@ -27,7 +27,7 @@ + + DEPENDFLAGS = -MM + +-OPTFLAGS = -O3 -fexpensive-optimizations ${ARCHFLAGS} ++OPTFLAGS := ${CFLAGS} ${ARCHFLAGS} -wd803 + MACHDBGFLAGS = -g + GNU_ANSI_FLAGS = -Wall -ansi -pedantic -Wno-long-long + SGI_ANSI_FLAGS = -ansi -fullwarn +Only in fsl/config/linux_64-gcc4.1: systemvars.mk.orig +diff -ur fsl.orig/config/linux_64-gcc4.2/systemvars.mk fsl/config/linux_64-gcc4.2/systemvars.mk +--- fsl.orig/config/linux_64-gcc4.2/systemvars.mk 2008-06-26 15:25:42.000000000 +0200 ++++ fsl/config/linux_64-gcc4.2/systemvars.mk 2017-05-18 13:54:40.447975880 +0200 +@@ -18,8 +18,8 @@ + + # Compiler dependent variables + +-CC = gcc +-CXX = c++ ++CC := ${CC} ++CXX := ${CXX} + CSTATICFLAGS = -static + CXXSTATICFLAGS = -static + +@@ -27,7 +27,7 @@ + + DEPENDFLAGS = -MM + +-OPTFLAGS = -O3 -fexpensive-optimizations ${ARCHFLAGS} ++OPTFLAGS := ${CFLAGS} ${ARCHFLAGS} -wd803 + MACHDBGFLAGS = -g + GNU_ANSI_FLAGS = -Wall -ansi -pedantic -Wno-long-long + SGI_ANSI_FLAGS = -ansi -fullwarn +Only in fsl/config/linux_64-gcc4.2: systemvars.mk.orig +diff -ur fsl.orig/config/linux_64-gcc4.4/systemvars.mk fsl/config/linux_64-gcc4.4/systemvars.mk +--- fsl.orig/config/linux_64-gcc4.4/systemvars.mk 2017-01-20 16:47:17.000000000 +0100 ++++ fsl/config/linux_64-gcc4.4/systemvars.mk 2017-05-18 13:57:25.995699462 +0200 +@@ -18,8 +18,8 @@ + + # Compiler dependent variables + +-CC = gcc +-CXX = c++ ++CC := ${CC} ++CXX := ${CXX} + CXX11 = scl enable devtoolset-2 -- c++ + CSTATICFLAGS = -static + CXXSTATICFLAGS = -static +@@ -30,7 +30,7 @@ + + DEPENDFLAGS = -MM + +-OPTFLAGS = -g -O3 -fexpensive-optimizations ${ARCHFLAGS} ++OPTFLAGS := ${CFLAGS} ${ARCHFLAGS} -wd803 + MACHDBGFLAGS = -g + GNU_ANSI_FLAGS = -Wall -ansi -pedantic -Wno-long-long + SGI_ANSI_FLAGS = -ansi -fullwarn +Only in fsl/config/linux_64-gcc4.4: systemvars.mk.orig +Only in fsl/config/linux_64-gcc4.4: systemvars.mk.rej +diff -ur fsl.orig/config/sparc-solaris2.8-gcc2.95/systemvars.mk fsl/config/sparc-solaris2.8-gcc2.95/systemvars.mk +--- fsl.orig/config/sparc-solaris2.8-gcc2.95/systemvars.mk 2007-07-13 13:00:21.000000000 +0200 ++++ fsl/config/sparc-solaris2.8-gcc2.95/systemvars.mk 2017-05-18 13:54:40.448975885 +0200 +@@ -5,14 +5,14 @@ + + # Compiler dependent variables + +-CC = gcc +-CXX = c++ ++CC := ${CC} ++CXX := ${CXX} + + ARCHFLAGS = -mv8 -ffast-math -fomit-frame-pointer + + DEPENDFLAGS = -MM + +-OPTFLAGS = -O6 -fexpensive-optimizations ${ARCHFLAGS} ++OPTFLAGS := ${CFLAGS} ${ARCHFLAGS} -wd803 + MACHDBGFLAGS = + GNU_ANSI_FLAGS = -Wall -ansi -pedantic + SGI_ANSI_FLAGS = -ansi -fullwarn +Only in fsl/config/sparc-solaris2.8-gcc2.95: systemvars.mk.orig +diff -ur fsl.orig/config/sparc-solaris2.9-gcc2.95/systemvars.mk fsl/config/sparc-solaris2.9-gcc2.95/systemvars.mk +--- fsl.orig/config/sparc-solaris2.9-gcc2.95/systemvars.mk 2007-07-13 13:00:21.000000000 +0200 ++++ fsl/config/sparc-solaris2.9-gcc2.95/systemvars.mk 2017-05-18 13:54:40.448975885 +0200 +@@ -5,14 +5,14 @@ + + # Compiler dependent variables + +-CC = gcc +-CXX = c++ ++CC := ${CC} ++CXX := ${CXX} + + ARCHFLAGS = -mv8 -ffast-math -fomit-frame-pointer + ARCHLDFLAGS = -static + DEPENDFLAGS = -MM + +-OPTFLAGS = -O6 -fexpensive-optimizations ${ARCHFLAGS} ++OPTFLAGS := ${CFLAGS} ${ARCHFLAGS} -wd803 + MACHDBGFLAGS = + GNU_ANSI_FLAGS = -Wall -ansi -pedantic + SGI_ANSI_FLAGS = -ansi -fullwarn +Only in fsl/config/sparc-solaris2.9-gcc2.95: systemvars.mk.orig +diff -ur fsl.orig/src/film/Makefile fsl/src/film/Makefile +--- fsl.orig/src/film/Makefile 2017-04-20 17:01:43.000000000 +0200 ++++ fsl/src/film/Makefile 2017-05-18 13:54:40.448975885 +0200 +@@ -28,7 +28,7 @@ + ${CXX} ${CXXFLAGS} ${LDFLAGS} -o $@ ${OBJS} ftoz.o ${LIBS} + + film_gls:${OBJS} film_gls.o +- ${CXX} ${CXXFLAGS} ${LDFLAGS} -o $@ ${OBJS} film_gls.o ${LIBS} -l giftiio ++ ${CXX} ${CXXFLAGS} ${LDFLAGS} -o $@ ${OBJS} film_gls.o ${LIBS} -lgiftiio + + film_gls_res:${OBJS} film_gls_res.o + ${CXX} ${CXXFLAGS} ${LDFLAGS} -o $@ ${OBJS} film_gls_res.o ${LIBS} +Only in fsl/src/film: Makefile.orig +diff -ur fsl.orig/src/libmeshutils/Makefile fsl/src/libmeshutils/Makefile +--- fsl.orig/src/libmeshutils/Makefile 2012-07-23 15:25:20.000000000 +0200 ++++ fsl/src/libmeshutils/Makefile 2017-05-18 13:54:40.448975885 +0200 +@@ -3,7 +3,7 @@ + + PROJNAME = meshUtils + +-LD_LIBRARY_PATH=${FSLDIR}/lib ++#LD_LIBRARY_PATH=${FSLDIR}/lib + + USRINCFLAGS = -I${INC_NEWMAT} -I${INC_ZLIB} -I${INC_PROB} -I${INC_BOOST} + USRLDFLAGS = -L${LIB_PROB} -L${LIB_NEWMAT} -L${LIB_ZLIB} +Only in fsl/src/libmeshutils: Makefile.orig +diff -ur fsl.orig/src/melodic/Makefile fsl/src/melodic/Makefile +--- fsl.orig/src/melodic/Makefile 2016-09-01 17:24:32.000000000 +0200 ++++ fsl/src/melodic/Makefile 2017-05-18 13:54:40.448975885 +0200 +@@ -3,7 +3,7 @@ + include ${FSLCONFDIR}/default.mk + + OPTFLAGS = -O3 -Wno-deprecated -ggdb +-OPTFLAGS_alphaev6-dec-osf5.0-gcc2.95.2 = -O3 -mieee -mfp-trap-mode=sui ++#OPTFLAGS_alphaev6-dec-osf5.0-gcc2.95.2 = -O3 -mieee -mfp-trap-mode=sui + + PROJNAME = melodic + +Only in fsl/src/melodic: Makefile.orig diff --git a/easybuild/easyconfigs/g/GLibmm/GLibmm-2.53.1.1-intel-2017a.eb b/easybuild/easyconfigs/g/GLibmm/GLibmm-2.53.1.1-intel-2017a.eb new file mode 100644 index 0000000000..b9e19ec518 --- /dev/null +++ b/easybuild/easyconfigs/g/GLibmm/GLibmm-2.53.1.1-intel-2017a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'GLibmm' +version = '2.53.1.1' + +homepage = 'http://www.gtk.org/' +description = """GLib is one of the base libraries of the GTK+ project""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['http://ftp.gnome.org/pub/gnome/sources/glibmm/%(version_major_minor)s/'] +sources = ['%(namelower)s-%(version)s.tar.xz'] + +dependencies = [ + ('GLib', '2.52.0'), + ('libsigc++', '2.10.0'), +] + +sanity_check_paths = { + 'files': ['lib/libglibmm-2.5.%s' % SHLIB_EXT], + 'dirs': [], +} +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libsigc++/libsigc++-2.10.0-intel-2017a.eb b/easybuild/easyconfigs/l/libsigc++/libsigc++-2.10.0-intel-2017a.eb new file mode 100644 index 0000000000..bb4e33f915 --- /dev/null +++ b/easybuild/easyconfigs/l/libsigc++/libsigc++-2.10.0-intel-2017a.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'libsigc++' +version = '2.10.0' + +homepage = 'http://www.gtk.org/' +description = """The libsigc++ package implements a typesafe callback system for standard C++.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['http://ftp.gnome.org/pub/gnome/sources/%(name)s/%(version_major_minor)s/'] +sources = ['%(namelower)s-%(version)s.tar.xz'] + +sanity_check_paths = { + 'files': ['lib/libsigc-2.0.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/libxml++/libxml++-2.91.3-intel-2017a.eb b/easybuild/easyconfigs/l/libxml++/libxml++-2.91.3-intel-2017a.eb new file mode 100644 index 0000000000..8e9c13f200 --- /dev/null +++ b/easybuild/easyconfigs/l/libxml++/libxml++-2.91.3-intel-2017a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'libxml++' +version = '2.91.3' + +homepage = 'http://libxmlplusplus.sourceforge.net' +description = """ libxml++ is a C++ wrapper for the libxml XML parser library. """ + +toolchain = {'name': 'intel', 'version': '2017a'} + +sources = [SOURCE_TAR_XZ] +source_urls = ['http://www.example.com'] + +dependencies = [ + ('libxml2', '2.9.4'), + ('GLibmm', '2.53.1.1'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ["."] +} + +moduleclass = 'lib' -- GitLab From f28aafad75d4bb0e567b219ba26fd4d4e4687141 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 20 May 2017 10:35:16 +0200 Subject: [PATCH 0792/1603] get list of added/modified files using 'git diff --name-only' in Travis config --- .travis.yml | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/.travis.yml b/.travis.yml index 2fcb5e365f..accc9427b8 100644 --- a/.travis.yml +++ b/.travis.yml @@ -39,8 +39,13 @@ install: - if [ ! -z $ENV_MOD_VERSION ]; then source $(which install_eb_dep.sh) modules-${ENV_MOD_VERSION} $HOME; fi - if [ ! -z $LMOD_VERSION ]; then source $(which install_eb_dep.sh) lua-5.1.4.8 $HOME; fi - if [ ! -z $LMOD_VERSION ]; then source $(which install_eb_dep.sh) Lmod-${LMOD_VERSION} $HOME; fi +before_script: + - cd $TRAVIS_BUILD_DIR + # pull in develop so we can diff against it + - git fetch -v origin ${TRAVIS_BRANCH}:${TRAVIS_BRANCH} + # get list of filenames for modified/added files, use '...' to compare with merge base of develop and branch + - git diff --name-only --diff-filter=AM ${TRAVIS_BRANCH}...HEAD script: - - echo $TRAVIS_COMMIT_RANGE - - cd $TRAVIS_BUILD_DIR; git diff --name-only $(echo $TRAVIS_COMMIT_RANGE | sed 's/\.//'); cd - > /dev/null + - cd $HOME - export PYTHONPATH=$TRAVIS_BUILD_DIR - python -O -m test.easyconfigs.suite -- GitLab From d32172cde98fb79987a55f4abca094f33f5caa64 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Sun, 21 May 2017 20:41:43 +0200 Subject: [PATCH 0793/1603] Update Tkinter easyconfigs --- ...er-2.7.13-foss-2016b-Python-2.7.13-bare.eb | 9 +------- ...kinter-2.7.13-intel-2017a-Python-2.7.13.eb | 21 +++++++++++++++++++ 2 files changed, 22 insertions(+), 8 deletions(-) mode change 100755 => 100644 easybuild/easyconfigs/t/Tkinter/Tkinter-2.7.13-foss-2016b-Python-2.7.13-bare.eb create mode 100644 easybuild/easyconfigs/t/Tkinter/Tkinter-2.7.13-intel-2017a-Python-2.7.13.eb diff --git a/easybuild/easyconfigs/t/Tkinter/Tkinter-2.7.13-foss-2016b-Python-2.7.13-bare.eb b/easybuild/easyconfigs/t/Tkinter/Tkinter-2.7.13-foss-2016b-Python-2.7.13-bare.eb old mode 100755 new mode 100644 index 4f9e88dceb..9870eab580 --- a/easybuild/easyconfigs/t/Tkinter/Tkinter-2.7.13-foss-2016b-Python-2.7.13-bare.eb +++ b/easybuild/easyconfigs/t/Tkinter/Tkinter-2.7.13-foss-2016b-Python-2.7.13-bare.eb @@ -1,11 +1,8 @@ easyblock = 'EB_TkinterPython' -# TODO: -# only build the Tkinter parts we want -# using further easyblock customisation name = 'Tkinter' version = '2.7.13' -versionsuffix = '-Python-%(version)s-bare' +versionsuffix = '-Python-%(pyver)s-bare' homepage = 'http://python.org/' description = """Tkinter module, built with the Python buildsystem""" @@ -16,8 +13,6 @@ toolchainopts = {'pic': True} source_urls = ['http://www.python.org/ftp/python/%(version)s/'] sources = ['Python-%(version)s.tgz'] -postinstallcmds = [ ' mv %(installdir)s/lib/python%(pyshortver)s/lib-tk %(installdir)s/lib/ && mv %(installdir)s/lib/python%(pyshortver)s/lib-dynload/_tkinter.so %(installdir)s/lib/ && rm -rf %(installdir)s/lib/python%(pyshortver)s/* && mv %(installdir)s/lib/lib-tk %(installdir)s/lib/python%(pyshortver)s/ && mkdir %(installdir)s/lib/python%(pyshortver)s/lib-dynload && mv %(installdir)s/lib/_tkinter.so %(installdir)s/lib/python%(pyshortver)s/lib-dynload && rm %(installdir)s/bin/python ' ] - dependencies = [ ('Python', '2.7.13', '-bare'), ('Tcl', '8.6.5'), @@ -25,6 +20,4 @@ dependencies = [ ('xproto', '7.0.28'), ] -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/lib-dynload:lib/python%(pyshortver)s/lib-tk']} - moduleclass = 'lang' diff --git a/easybuild/easyconfigs/t/Tkinter/Tkinter-2.7.13-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/t/Tkinter/Tkinter-2.7.13-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..8b9e8501c9 --- /dev/null +++ b/easybuild/easyconfigs/t/Tkinter/Tkinter-2.7.13-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,21 @@ +easyblock = 'EB_TkinterPython' + +name = 'Tkinter' +version = '2.7.13' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://python.org/' +description = """Tkinter module, built with the Python buildsystem""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.python.org/ftp/python/%(version)s/'] +sources = ['Python-%(version)s.tgz'] + +dependencies = [ + ('Python', '2.7.13'), + ('Tk', '8.6.6'), +] + +moduleclass = 'lang' -- GitLab From 7e22d56d6410cfbf87668110ff23823ee58d8f05 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 22 May 2017 09:36:41 +0200 Subject: [PATCH 0794/1603] Use new name easyblock tkinter --- .../t/Tkinter/Tkinter-2.7.13-foss-2016b-Python-2.7.13-bare.eb | 2 -- .../t/Tkinter/Tkinter-2.7.13-intel-2017a-Python-2.7.13.eb | 2 -- 2 files changed, 4 deletions(-) diff --git a/easybuild/easyconfigs/t/Tkinter/Tkinter-2.7.13-foss-2016b-Python-2.7.13-bare.eb b/easybuild/easyconfigs/t/Tkinter/Tkinter-2.7.13-foss-2016b-Python-2.7.13-bare.eb index 9870eab580..79e3c82386 100644 --- a/easybuild/easyconfigs/t/Tkinter/Tkinter-2.7.13-foss-2016b-Python-2.7.13-bare.eb +++ b/easybuild/easyconfigs/t/Tkinter/Tkinter-2.7.13-foss-2016b-Python-2.7.13-bare.eb @@ -1,5 +1,3 @@ -easyblock = 'EB_TkinterPython' - name = 'Tkinter' version = '2.7.13' versionsuffix = '-Python-%(pyver)s-bare' diff --git a/easybuild/easyconfigs/t/Tkinter/Tkinter-2.7.13-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/t/Tkinter/Tkinter-2.7.13-intel-2017a-Python-2.7.13.eb index 8b9e8501c9..a9547d3014 100644 --- a/easybuild/easyconfigs/t/Tkinter/Tkinter-2.7.13-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/t/Tkinter/Tkinter-2.7.13-intel-2017a-Python-2.7.13.eb @@ -1,5 +1,3 @@ -easyblock = 'EB_TkinterPython' - name = 'Tkinter' version = '2.7.13' versionsuffix = '-Python-%(pyver)s' -- GitLab From 0aeb00c035456e42dc385cc3ec05efa3d8507684 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Mon, 22 May 2017 12:03:03 +0200 Subject: [PATCH 0795/1603] {vis}[intel/2017a] matplotlib 2.0.2 Python 2.7.13 w/ Qt 4.8.7 --- ....0.2-intel-2017a-Python-2.7.13-Qt-4.8.7.eb | 46 +++++++++++++++++++ .../PyQt-4.12-intel-2017a-Python-2.7.13.eb | 37 +++++++++++++++ .../SIP-4.19.2-intel-2017a-Python-2.7.13.eb | 30 ++++++++++++ 3 files changed, 113 insertions(+) create mode 100644 easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.2-intel-2017a-Python-2.7.13-Qt-4.8.7.eb create mode 100644 easybuild/easyconfigs/p/PyQt/PyQt-4.12-intel-2017a-Python-2.7.13.eb create mode 100644 easybuild/easyconfigs/s/SIP/SIP-4.19.2-intel-2017a-Python-2.7.13.eb diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.2-intel-2017a-Python-2.7.13-Qt-4.8.7.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.2-intel-2017a-Python-2.7.13-Qt-4.8.7.eb new file mode 100644 index 0000000000..591cb38e66 --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.2-intel-2017a-Python-2.7.13-Qt-4.8.7.eb @@ -0,0 +1,46 @@ +easyblock = 'Bundle' + +name = 'matplotlib' +version = '2.0.2' +qtver = '4.8.7' +versionsuffix = '-Python-%%(pyver)s-Qt-%s' % qtver + +homepage = 'http://matplotlib.org' +description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of + hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python + and ipython shell, web application servers, and six graphical user interface toolkits.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' + +dependencies = [ + ('Python', '2.7.13'), + ('Qt', qtver), + ('PyQt', '4.12', '-Python-%(pyver)s'), + ('freetype', '2.7.1', '-libpng-1.6.29'), +] + +exts_list = [ + ('Cycler', '0.10.0', { + 'modulename': 'cycler', + 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], + 'source_tmpl': 'cycler-%(version)s.tar.gz', + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], + }), +] + +# specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module +full_sanity_check = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/PyQt/PyQt-4.12-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/p/PyQt/PyQt-4.12-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..d5c9f991a7 --- /dev/null +++ b/easybuild/easyconfigs/p/PyQt/PyQt-4.12-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,37 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Bart Verleye +# Center for eResearch, Auckland +easyblock = 'ConfigureMakePythonPackage' + +name = 'PyQt' +version = '4.12' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.riverbankcomputing.co.uk/software/pyqt' +description = """PyQt is a set of Python v2 and v3 bindings for Digia's Qt application framework.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['http://sourceforge.net/projects/pyqt/files/PyQt4/PyQt-%(version)s'] +sources = ['PyQt4_gpl_x11-%(version)s.tar.gz'] + +dependencies = [ + ('Python', '2.7.13'), + ('SIP', '4.19.2', versionsuffix), + ('Qt', '4.8.7'), +] + +configopts = "configure-ng.py --confirm-license" +configopts += " --destdir=%(installdir)s/lib/python%(pyshortver)s/site-packages " +configopts += " --sipdir=%(installdir)s/share/sip/PyQt%(version_major)s" + +options = {'modulename': '%(name)s%(version_major)s'} + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s%(version_major)s'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/s/SIP/SIP-4.19.2-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/s/SIP/SIP-4.19.2-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..c113a20dd9 --- /dev/null +++ b/easybuild/easyconfigs/s/SIP/SIP-4.19.2-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,30 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Bart Verleye +# Center for eResearch, Auckland +easyblock = 'ConfigureMakePythonPackage' + +name = 'SIP' +version = '4.19.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.riverbankcomputing.com/software/sip/' +description = """SIP is a tool that makes it very easy to create Python bindings for C and C++ libraries.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://sourceforge.net/projects/pyqt/files/sip/sip-%(version)s'] + +dependencies = [('Python', '2.7.13')] + +configopts = "configure.py --bindir %(installdir)s/bin --incdir %(installdir)s/include " +configopts += "--destdir %(installdir)s/lib/python%(pyshortver)s/site-packages" + +sanity_check_paths = { + 'files': ['bin/sip', 'include/sip.h'] + + ['lib/python%%(pyshortver)s/site-packages/%s' % x + for x in ['sip.%s' % SHLIB_EXT, 'sipconfig.py', 'sipdistutils.py']], + 'dirs': [], +} + +moduleclass = 'lang' -- GitLab From 8260549ee21a50231a31746f4c3d53d4d71f1a36 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Mon, 22 May 2017 16:58:33 -0500 Subject: [PATCH 0796/1603] Added Rmpi patch file --- easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170314.eb | 2 +- easybuild/easyconfigs/r/R/R-3.4.0-intel-2017a-X11-20170314.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170314.eb b/easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170314.eb index 963e074572..dd1dc43ebf 100644 --- a/easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170314.eb +++ b/easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170314.eb @@ -77,7 +77,7 @@ exts_list = [ 'tools', 'utils', # non-standard libraries, should be specified with fixed versions! - ('Rmpi', '0.6-6', ext_options), + ('Rmpi', '0.6-6', dict(ext_options.items() + [('patches', ['Rmpi-0.6-5_impi5.patch'])])), ('abind', '1.4-5', ext_options), ('magic', '1.5-6', ext_options), ('geometry', '0.3-6', dict(ext_options.items() + [('patches', ['geometry-0.3-4-icc.patch'])])), diff --git a/easybuild/easyconfigs/r/R/R-3.4.0-intel-2017a-X11-20170314.eb b/easybuild/easyconfigs/r/R/R-3.4.0-intel-2017a-X11-20170314.eb index 949ed58bbb..2cde7eea73 100644 --- a/easybuild/easyconfigs/r/R/R-3.4.0-intel-2017a-X11-20170314.eb +++ b/easybuild/easyconfigs/r/R/R-3.4.0-intel-2017a-X11-20170314.eb @@ -77,7 +77,7 @@ exts_list = [ 'tools', 'utils', # non-standard libraries, should be specified with fixed versions! - ('Rmpi', '0.6-6', ext_options), + ('Rmpi', '0.6-6', dict(ext_options.items() + [('patches', ['Rmpi-0.6-5_impi5.patch'])])), ('abind', '1.4-5', ext_options), ('magic', '1.5-6', ext_options), ('geometry', '0.3-6', dict(ext_options.items() + [('patches', ['geometry-0.3-4-icc.patch'])])), -- GitLab From e96f924206f4f47c0d775f00daab621fbedb8d22 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Tue, 23 May 2017 13:59:20 +1200 Subject: [PATCH 0797/1603] Removed commented out references to SamTools --- .../easyconfigs/p/Perl/Perl-5.22.0-foss-2015a-mt.eb | 9 --------- .../easyconfigs/p/Perl/Perl-5.22.0-foss-2015a.eb | 11 +---------- 2 files changed, 1 insertion(+), 19 deletions(-) diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.22.0-foss-2015a-mt.eb b/easybuild/easyconfigs/p/Perl/Perl-5.22.0-foss-2015a-mt.eb index 43dbd48785..1311c9dfcc 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.22.0-foss-2015a-mt.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.22.0-foss-2015a-mt.eb @@ -16,8 +16,6 @@ dependencies = [ ('libxml2', '2.9.2'), # for XML::LibXML ] -#builddependencies = [('SAMtools', '0.1.20')] # NOT A LATER VERSION. For Bio::DB::Sam to static link to. - source_urls = ['http://www.cpan.org/src/5.0'] sources = [SOURCELOWER_TAR_GZ] #runtest = 'test' @@ -883,13 +881,6 @@ exts_list = [ 'source_tmpl': 'Set-IntervalTree-0.10.tar.gz', 'source_urls': ['http://search.cpan.org/CPAN/authors/id/B/BE/BENBOOTH/'], }), - -# Trouble finding libbam.a and bam/bam.h - try Alien::Samtools next -# ('Bio::DB::Sam', '1.41', { -# 'source_tmpl': 'Bio-SamTools-1.41.tar.gz', -# 'source_urls': ['http://cpan.metacpan.org/authors/id/L/LD/LDS/'], -# 'patches': ['Perl-Bio-SamTools.patch'], -# }), ('HTML::TableExtract', '2.13', { 'source_tmpl': 'HTML-TableExtract-2.13.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/M/MS/MSISK/'], diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.22.0-foss-2015a.eb b/easybuild/easyconfigs/p/Perl/Perl-5.22.0-foss-2015a.eb index dc4e724075..0443d98f0a 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.22.0-foss-2015a.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.22.0-foss-2015a.eb @@ -13,9 +13,7 @@ dependencies = [ ('SQLite', '3.8.9'), # for DBD::SQLite module ('expat', '2.1.0'), # for XML::Parser I think ('libxml2', '2.9.2'), # for XML::LibXML - ] - -#builddependencies = [('SAMtools', '0.1.20')] # NOT A LATER VERSION. For Bio::DB::Sam to static link to. +] source_urls = ['http://www.cpan.org/src/5.0'] sources = [SOURCELOWER_TAR_GZ] @@ -882,13 +880,6 @@ exts_list = [ 'source_tmpl': 'Set-IntervalTree-0.10.tar.gz', 'source_urls': ['http://search.cpan.org/CPAN/authors/id/B/BE/BENBOOTH/'], }), - -# Trouble finding libbam.a and bam/bam.h - try Alien::Samtools next -# ('Bio::DB::Sam', '1.41', { -# 'source_tmpl': 'Bio-SamTools-1.41.tar.gz', -# 'source_urls': ['http://cpan.metacpan.org/authors/id/L/LD/LDS/'], -# 'patches': ['Perl-Bio-SamTools.patch'], -# }), ('HTML::TableExtract', '2.13', { 'source_tmpl': 'HTML-TableExtract-2.13.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/M/MS/MSISK/'], -- GitLab From abe1231ab912c5880b7c9506b59fd55e0d36d1cd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 23 May 2017 10:42:23 +0200 Subject: [PATCH 0798/1603] adding easyconfigs: BUSCO-2.0.1-intel-2017a-Python-2.7.13.eb, AUGUSTUS-3.2.3-intel-2017a-Python-2.7.13.eb, BLAST+-2.6.0-intel-2017a-Python-2.7.13.eb, EMBOSS-6.6.0-intel-2017a.eb, lpsolve-5.5.2.5-intel-2017a.eb, libharu-2.3.0-intel-2017a.eb --- ...UGUSTUS-3.2.3-intel-2017a-Python-2.7.13.eb | 42 +++++++++++++++ .../BLAST+-2.6.0-intel-2017a-Python-2.7.13.eb | 54 +++++++++++++++++++ .../BUSCO-2.0.1-intel-2017a-Python-2.7.13.eb | 31 +++++++++++ .../e/EMBOSS/EMBOSS-6.6.0-intel-2017a.eb | 48 +++++++++++++++++ .../l/libharu/libharu-2.3.0-intel-2017a.eb | 39 ++++++++++++++ .../l/lpsolve/lpsolve-5.5.2.5-intel-2017a.eb | 32 +++++++++++ 6 files changed, 246 insertions(+) create mode 100644 easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.2.3-intel-2017a-Python-2.7.13.eb create mode 100644 easybuild/easyconfigs/b/BLAST+/BLAST+-2.6.0-intel-2017a-Python-2.7.13.eb create mode 100644 easybuild/easyconfigs/b/BUSCO/BUSCO-2.0.1-intel-2017a-Python-2.7.13.eb create mode 100644 easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-intel-2017a.eb create mode 100644 easybuild/easyconfigs/l/libharu/libharu-2.3.0-intel-2017a.eb create mode 100644 easybuild/easyconfigs/l/lpsolve/lpsolve-5.5.2.5-intel-2017a.eb diff --git a/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.2.3-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.2.3-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..e754db2e6d --- /dev/null +++ b/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.2.3-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,42 @@ +easyblock = 'ConfigureMake' + +name = 'AUGUSTUS' +version = '3.2.3' +versionsuffix = '-Python-2.7.13' + +homepage = 'http://bioinf.uni-greifswald.de/augustus/' +description = "AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['http://bioinf.uni-greifswald.de/augustus/binaries/'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['AUGUSTUS-%(version)s_fix-hardcoding.patch'] + +dependencies = [ + ('zlib', '1.2.11'), + ('Boost', '1.63.0', versionsuffix), + ('SQLite', '3.17.0'), + ('GSL', '2.3'), + ('SuiteSparse', '4.5.5', '-ParMETIS-4.0.3'), + ('lpsolve', '5.5.2.5'), + ('BamTools', '2.4.1'), +] + +skipsteps = ['configure'] + +prebuildopts = "unset LDFLAGS && unset LIBS && " +buildopts = 'COMPGENEPRED=true SQLITE=true ZIPINPUT=true CXX="$CXX" LINK.cc="$CXX"' +installopts = 'INSTALLDIR=%(installdir)s' + +sanity_check_paths = { + 'files': ['bin/aln2wig', 'bin/augustus', 'bin/bam2hints', 'bin/bam2wig', 'bin/espoca', 'bin/etraining', + 'bin/fastBlockSearch', 'bin/filterBam', 'bin/getSeq', 'bin/homGeneMapping', 'bin/joingenes', + 'bin/load2sqlitedb', 'bin/prepareAlign'], + 'dirs': ['config', 'scripts'], +} + +modextrapaths = {'PATH': 'scripts'} +modextravars = {'AUGUSTUS_CONFIG_PATH': '%(installdir)s/config'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.6.0-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.6.0-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..c6ba2de331 --- /dev/null +++ b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.6.0-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,54 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos , Kenneth Hoste (UGent) +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + +easyblock = 'ConfigureMake' + +name = 'BLAST+' +version = '2.6.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://blast.ncbi.nlm.nih.gov/' +description = """Basic Local Alignment Search Tool, or BLAST, is an algorithm + for comparing primary biological sequence information, such as the amino-acid + sequences of different proteins or the nucleotides of DNA sequences.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'cstd': 'c++14'} + +sources = ['ncbi-blast-%(version)s+-src.tar.gz'] +source_urls = ['http://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/%(version)s/'] +patches = [ + 'BLAST+-2.2.30_ictce-fixes.patch', + 'BLAST+.patch', +] + +dependencies = [ + ('zlib', '1.2.11'), + ('bzip2', '1.0.6'), + ('PCRE', '8.40'), + ('Python', '2.7.13'), + ('Boost', '1.63.0', versionsuffix), + ('GMP', '6.1.2'), + ('libpng', '1.6.29'), + ('libjpeg-turbo', '1.5.1'), +] + +configopts = "--with-64 --with-z=$EBROOTZLIB --with-bz2=$EBROOTBZIP2 --with-pcre=$EBROOTPCRE " +configopts += "--with-python=$EBROOTPYTHON --with-boost=$EBROOTBOOST --with-gmp=$EBROOTGMP --with-png=$EBROOTLIBPNG " +configopts += "--with-jpeg=$EBROOTLIBJPEGMINTURBO " + +sanity_check_paths = { + 'files': ['bin/blastn', 'bin/blastp', 'bin/blastx'], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BUSCO/BUSCO-2.0.1-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/b/BUSCO/BUSCO-2.0.1-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..3c812eb0fb --- /dev/null +++ b/easybuild/easyconfigs/b/BUSCO/BUSCO-2.0.1-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,31 @@ +easyblock = 'Tarball' + +name = 'BUSCO' +version = '2.0.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://busco.ezlab.org/' +description = "BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs" + +toolchain = {'name': 'intel', 'version': '2017a'} + +# download via https://gitlab.com/ezlab/busco/repository/archive.tar.gz?ref=2.0.1 +# rename to busco-2.0.1.tar.gz +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('Python', '2.7.13'), + ('BLAST+', '2.6.0', versionsuffix), + ('HMMER', '3.1b2'), + ('AUGUSTUS', '3.2.3', versionsuffix), + ('EMBOSS', '6.6.0'), +] + +sanity_check_paths = { + 'files': ['BUSCO.py', 'BUSCO_plot.py'], + 'dirs': ['sample_data'], +} + +modextrapaths = {'PATH': '.'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-intel-2017a.eb b/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-intel-2017a.eb new file mode 100644 index 0000000000..d6fa49965a --- /dev/null +++ b/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-intel-2017a.eb @@ -0,0 +1,48 @@ +# authors: Kenneth Hoste (Ghent University), George Tsouloupas , Fotis Georgatos +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +# foss-2016b modified by: +# Adam Huffman +# The Francis Crick Institute + +easyblock = 'ConfigureMake' + +name = 'EMBOSS' +version = '6.6.0' + +homepage = 'http://emboss.sourceforge.net/' +description = """EMBOSS is 'The European Molecular Biology Open Software Suite'. + EMBOSS is a free Open Source software analysis package specially developed for + the needs of the molecular biology (e.g. EMBnet) user community.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [ + 'ftp://emboss.open-bio.org/pub/EMBOSS/', + 'ftp://emboss.open-bio.org/pub/EMBOSS/old/%(version_major_minor)s.0', +] + +sources = [SOURCE_TAR_GZ] + +patches = ['EMBOSS_disable-embossupdate.patch'] + +dependencies = [ + ('libharu', '2.3.0'), + ('Java', '1.7.0_80', '', True), +] + +configopts = " --with-hpdf=$EBROOTLIBHARU " + +# jemboss.jar does not build in a parallel build +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['seqret', 'aligncopy', 'profit', 'prophet']] + + ['lib/lib%s.a' % x for x in ['acd', 'ajax', 'ajaxdb', 'ajaxg', 'eexpat', 'ensembl', + 'epcre', 'eplplot', 'ezlib', 'nucleus']] + + ['share/EMBOSS/jemboss/lib/jemboss.jar'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/l/libharu/libharu-2.3.0-intel-2017a.eb b/easybuild/easyconfigs/l/libharu/libharu-2.3.0-intel-2017a.eb new file mode 100644 index 0000000000..b87a22de76 --- /dev/null +++ b/easybuild/easyconfigs/l/libharu/libharu-2.3.0-intel-2017a.eb @@ -0,0 +1,39 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Cyprus Institute / CaSToRC, Uni.Lu/LCSB, NTUA +# Authors:: George Tsouloupas , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## +# Modified for foss-2016b by: +# Adam Huffman +# The Francis Crick Institute + +easyblock = 'CMakeMake' + +name = 'libharu' +version = '2.3.0' + +homepage = 'http://libharu.org/' +description = """libHaru is a free, cross platform, open source library for generating PDF files.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [' https://github.com/libharu/libharu/archive/'] +sources = ['RELEASE_%s.tar.gz' % '_'.join(version.split('.'))] + +dependencies = [('libpng', '1.6.29')] + +builddependencies = [('CMake', '3.8.1')] + +parallel = 1 + +sanity_check_paths = { + 'files': ['lib/libhpdf.%s' % SHLIB_EXT], + 'dirs': ['if', 'include', 'lib'] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/lpsolve/lpsolve-5.5.2.5-intel-2017a.eb b/easybuild/easyconfigs/l/lpsolve/lpsolve-5.5.2.5-intel-2017a.eb new file mode 100644 index 0000000000..3ca32aeeb9 --- /dev/null +++ b/easybuild/easyconfigs/l/lpsolve/lpsolve-5.5.2.5-intel-2017a.eb @@ -0,0 +1,32 @@ +easyblock = 'CmdCp' + +name = 'lpsolve' +version = '5.5.2.5' + +homepage = 'https://sourceforge.net/projects/lpsolve/' +description = "Mixed Integer Linear Programming (MILP) solver" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['lp_solve_%(version)s_source.tar.gz'] + +lpsolve_ver = '%(version_major)s%(version_minor)s' +start_dir = 'lpsolve%s' % lpsolve_ver + +comp_cmd = 'sed -i "s/^c=.*/c=\'$CC\'/g" ccc && sed -i "s/^opts=.*/opts=\'$CFLAGS\'/g" ccc && ' +comp_cmd += "sh ccc" +cmds_map = [('.*', comp_cmd)] + +lpsolve_libname = 'liblpsolve%s' % lpsolve_ver +files_to_copy = [ + (['bin/ux64/%s.a' % lpsolve_libname, 'bin/ux64/%s.%s' % (lpsolve_libname, SHLIB_EXT)], 'lib'), + (['../lp*.h'], 'include'), +] + +sanity_check_paths = { + 'files': ['lib/%s.a' % lpsolve_libname, 'lib/%s.%s' % (lpsolve_libname, SHLIB_EXT)], + 'dirs': ['include'], +} + +moduleclass = 'math' -- GitLab From 009634088181bae31d3a6d27883b45fe34246b2a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 23 May 2017 10:43:47 +0200 Subject: [PATCH 0799/1603] add patch for AUGUSTUS --- .../AUGUSTUS-3.2.3_fix-hardcoding.patch | 57 +++++++++++++++++++ 1 file changed, 57 insertions(+) create mode 100644 easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.2.3_fix-hardcoding.patch diff --git a/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.2.3_fix-hardcoding.patch b/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.2.3_fix-hardcoding.patch new file mode 100644 index 0000000000..85bff50668 --- /dev/null +++ b/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.2.3_fix-hardcoding.patch @@ -0,0 +1,57 @@ +fix hardcoded compiler names in Makefile + don't try to link binaries in /usr/local/bin +author: Kenneth Hoste (HPC-UGent) +--- augustus-3.2.3/auxprogs/compileSpliceCands/Makefile.orig 2017-05-02 20:40:04.471986962 +0200 ++++ augustus-3.2.3/auxprogs/compileSpliceCands/Makefile 2017-05-02 20:40:30.812468384 +0200 +@@ -1,8 +1,8 @@ + compileSpliceCands : compileSpliceCands.o list.h list.o +- gcc $(LDFLAGS) -o compileSpliceCands compileSpliceCands.o list.o; ++ $(CC) $(LDFLAGS) -o compileSpliceCands compileSpliceCands.o list.o; + # cp compileSpliceCands ../../bin + compileSpliceCands.o : compileSpliceCands.c +- gcc -Wall -pedantic -ansi $(CPPFLAGS) -c compileSpliceCands.c ++ $(CC) -Wall -pedantic -ansi $(CPPFLAGS) -c compileSpliceCands.c + + all : compileSpliceCands + +--- augustus-3.2.3/auxprogs/homGeneMapping/src/Makefile.orig 2017-05-04 10:12:47.633497259 +0200 ++++ augustus-3.2.3/auxprogs/homGeneMapping/src/Makefile 2017-05-04 10:12:56.313614398 +0200 +@@ -7,7 +7,7 @@ + # database access for retrieval of hints + # SQLITE = true + +-CC = g++ ++CC = $(CXX) + + # Notes: - "-Wno-sign-compare" eliminates a high number of warnings (see footnote below). Please adopt + # a strict signed-only usage strategy to avoid mistakes since we are not warned about this. +--- augustus-3.2.3/auxprogs/joingenes/Makefile.orig 2017-05-04 10:46:28.700811811 +0200 ++++ augustus-3.2.3/auxprogs/joingenes/Makefile 2017-05-04 10:46:35.380911653 +0200 +@@ -1,4 +1,4 @@ +-CC=g++ ++CC=$(CXX) + CFLAGS=-Wall -std=gnu++0x + + all: joingenes +--- augustus-3.2.3/Makefile.orig 2017-05-04 09:54:03.568352171 +0200 ++++ augustus-3.2.3/Makefile 2017-05-04 09:54:11.968330382 +0200 +@@ -17,13 +17,13 @@ + install: + install -d $(INSTALLDIR) + cp -a config bin scripts $(INSTALLDIR) +- ln -sf $(INSTALLDIR)/bin/augustus /usr/local/bin/augustus +- ln -sf $(INSTALLDIR)/bin/etraining /usr/local/bin/etraining +- ln -sf $(INSTALLDIR)/bin/prepareAlign /usr/local/bin/prepareAlign +- ln -sf $(INSTALLDIR)/bin/fastBlockSearch /usr/local/bin/fastBlockSearch +- ln -sf $(INSTALLDIR)/bin/load2db /usr/local/bin/load2db +- ln -sf $(INSTALLDIR)/bin/getSeq /usr/local/bin/getSeq +- ln -sf $(INSTALLDIR)/bin/espoca /usr/local/bin/espoca ++ #ln -sf $(INSTALLDIR)/bin/augustus /usr/local/bin/augustus ++ #ln -sf $(INSTALLDIR)/bin/etraining /usr/local/bin/etraining ++ #ln -sf $(INSTALLDIR)/bin/prepareAlign /usr/local/bin/prepareAlign ++ #ln -sf $(INSTALLDIR)/bin/fastBlockSearch /usr/local/bin/fastBlockSearch ++ #ln -sf $(INSTALLDIR)/bin/load2db /usr/local/bin/load2db ++ #ln -sf $(INSTALLDIR)/bin/getSeq /usr/local/bin/getSeq ++ #ln -sf $(INSTALLDIR)/bin/espoca /usr/local/bin/espoca + + # for internal purposes: + release: -- GitLab From 4d22e9d52139428d75e141a502bae918e19608d8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 23 May 2017 10:46:59 +0200 Subject: [PATCH 0800/1603] add patch for BLAST+ 2.6.0 (based on patch provided in #4195) --- .../BLAST+-2.6.0-intel-2017a-Python-2.7.13.eb | 2 +- .../b/BLAST+/BLAST+-2.6.0_fix-make-install.patch | 14 ++++++++++++++ 2 files changed, 15 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/b/BLAST+/BLAST+-2.6.0_fix-make-install.patch diff --git a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.6.0-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.6.0-intel-2017a-Python-2.7.13.eb index c6ba2de331..37ae5901c6 100644 --- a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.6.0-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.6.0-intel-2017a-Python-2.7.13.eb @@ -28,7 +28,7 @@ sources = ['ncbi-blast-%(version)s+-src.tar.gz'] source_urls = ['http://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/%(version)s/'] patches = [ 'BLAST+-2.2.30_ictce-fixes.patch', - 'BLAST+.patch', + 'BLAST+-%(version)s_fix-make-install.patch', ] dependencies = [ diff --git a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.6.0_fix-make-install.patch b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.6.0_fix-make-install.patch new file mode 100644 index 0000000000..61dc64608e --- /dev/null +++ b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.6.0_fix-make-install.patch @@ -0,0 +1,14 @@ +fix 'make install-toolkit' by copying header files in 'common' separately +patch created by Kenneth Hoste (HPC-UGent), based on patch by Kurt Lust (UAntwerpen) +--- ncbi-blast-2.6.0+-src/c++/src/build-system/Makefile.in.top.orig 2017-05-22 13:35:40.236430282 +0200 ++++ ncbi-blast-2.6.0+-src/c++/src/build-system/Makefile.in.top 2017-05-22 13:38:37.179080048 +0200 +@@ -51,7 +51,8 @@ + done + cd $(includedir0) && find * -name CVS -prune -o -print |\ + cpio -pd $(pincludedir) +- $(INSTALL) -m 644 $(incdir)/* $(pincludedir) ++ $(INSTALL) -m 644 $(incdir)/*.h $(pincludedir) ++ $(INSTALL) -m 644 $(incdir)/common/*.h $(pincludedir)/common + ## set up appropriate build and status directories somewhere under $(libdir)? + + install-gbench: -- GitLab From 2a15c267ab3ac4492f437d0d76b8233db0a8a31b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 23 May 2017 15:05:32 +0200 Subject: [PATCH 0801/1603] adding easyconfigs: Spyder-3.1.4-intel-2017a-Python-2.7.13.eb, PyQt5-5.8.2-intel-2017a-Python-2.7.13.eb, SIP-4.19.2-intel-2017a-Python-2.7.13.eb --- .../PyQt5-5.8.2-intel-2017a-Python-2.7.13.eb | 34 +++++ .../SIP-4.19.2-intel-2017a-Python-2.7.13.eb | 30 +++++ .../Spyder-3.1.4-intel-2017a-Python-2.7.13.eb | 117 ++++++++++++++++++ 3 files changed, 181 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyQt5/PyQt5-5.8.2-intel-2017a-Python-2.7.13.eb create mode 100644 easybuild/easyconfigs/s/SIP/SIP-4.19.2-intel-2017a-Python-2.7.13.eb create mode 100644 easybuild/easyconfigs/s/Spyder/Spyder-3.1.4-intel-2017a-Python-2.7.13.eb diff --git a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.8.2-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.8.2-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..60a9bfec1e --- /dev/null +++ b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.8.2-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMakePythonPackage' + +name = 'PyQt5' +version = '5.8.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.riverbankcomputing.co.uk/software/pyqt' +description = """PyQt5 is a set of Python bindings for v5 of the Qt application framework from The Qt Company.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['http://sourceforge.net/projects/pyqt/files/PyQt5/PyQt-%(version)s'] +sources = ['%(name)s_gpl-%(version)s.tar.gz'] + +dependencies = [ + ('Python', '2.7.13'), + ('SIP', '4.19.2', versionsuffix), + ('Qt5', '5.8.0'), +] + +configopts = "configure.py --confirm-license" +configopts += " --destdir=%(installdir)s/lib/python%(pyshortver)s/site-packages " +configopts += " --no-sip-files" + +options = {'modulename': '%(name)s'} + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/s/SIP/SIP-4.19.2-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/s/SIP/SIP-4.19.2-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..c113a20dd9 --- /dev/null +++ b/easybuild/easyconfigs/s/SIP/SIP-4.19.2-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,30 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Bart Verleye +# Center for eResearch, Auckland +easyblock = 'ConfigureMakePythonPackage' + +name = 'SIP' +version = '4.19.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.riverbankcomputing.com/software/sip/' +description = """SIP is a tool that makes it very easy to create Python bindings for C and C++ libraries.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://sourceforge.net/projects/pyqt/files/sip/sip-%(version)s'] + +dependencies = [('Python', '2.7.13')] + +configopts = "configure.py --bindir %(installdir)s/bin --incdir %(installdir)s/include " +configopts += "--destdir %(installdir)s/lib/python%(pyshortver)s/site-packages" + +sanity_check_paths = { + 'files': ['bin/sip', 'include/sip.h'] + + ['lib/python%%(pyshortver)s/site-packages/%s' % x + for x in ['sip.%s' % SHLIB_EXT, 'sipconfig.py', 'sipdistutils.py']], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/s/Spyder/Spyder-3.1.4-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/s/Spyder/Spyder-3.1.4-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..148b4a94d1 --- /dev/null +++ b/easybuild/easyconfigs/s/Spyder/Spyder-3.1.4-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,117 @@ +easyblock = 'Bundle' + +name = 'Spyder' +version = '3.1.4' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/spyder-ide/spyder' +description = """Spyder is an interactive Python development environment providing MATLAB-like features in a simple + and light-weighted software.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +dependencies = [ + ('Python', '2.7.13'), + ('PyQt5', '5.8.2', versionsuffix), + ('PyZMQ', '16.0.2', versionsuffix + '-zmq4'), +] + +exts_defaultclass = 'PythonPackage' +exts_filter = ("python -c 'import %(ext_name)s'", '') + +exts_list = [ + ('qtconsole', '4.3.0', { + 'source_urls': ['https://pypi.python.org/packages/source/q/qtconsole'], + }), + ('rope', '0.10.5', { + 'source_urls': ['https://pypi.python.org/packages/source/r/rope'], + }), + ('jedi', '0.10.2', { + 'source_urls': ['https://pypi.python.org/packages/source/j/jedi'], + }), + ('pyflakes', '1.5.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyflakes'], + }), + ('Sphinx', '1.6.1', { + 'source_urls': ['https://pypi.python.org/packages/source/s/Sphinx'], + }), + ('Pygments', '2.2.0', { + 'source_urls': ['https://pypi.python.org/packages/source/P/Pygments'], + }), + ('pylint', '1.7.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pylint'], + }), + ('pep8', '1.7.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pep8'], + }), + ('psutil', '5.2.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/psutil'], + }), + ('ipython_genutils', '0.2.0', { + 'source_urls': ['https://pypi.python.org/packages/source/i/ipython_genutils/'], + }), + ('traitlets', '4.3.2', { + 'source_urls': ['https://pypi.python.org/packages/source/t/traitlets/'], + }), + ('jsonschema', '2.6.0', { + 'source_urls': ['https://pypi.python.org/packages/source/j/jsonschema/'], + }), + ('nbformat', '4.3.0', { + 'source_urls': ['https://pypi.python.org/packages/source/n/nbformat/'], + }), + ('configparser', '3.5.0', { + 'source_urls': ['https://pypi.python.org/packages/source/c/configparser/'], + 'patches': ['configparser-3.5.0_no-backports-namespace.patch'], + 'use_pip': True, + }), + ('entrypoints', '0.2.2', { + 'source_urls': ['https://pypi.python.org/packages/source/e/entrypoints/'], + 'source_tmpl': 'entrypoints-%(version)s-py2.py3-none-any.whl', + 'unpack_sources': False, + 'use_pip': True, + }), + ('pandocfilters', '1.4.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pandocfilters/'], + }), + ('testpath', '0.3', { + 'source_urls': ['https://pypi.python.org/packages/py2.py3/t/testpath/'], + 'source_tmpl': 'testpath-%(version)s-py2.py3-none-any.whl', + 'unpack_sources': False, + 'use_pip': True, + }), + ('nbconvert', '5.1.1', { + 'source_urls': ['https://pypi.python.org/packages/source/n/nbconvert'], + 'use_pip': True, + }), + ('QtAwesome', '0.4.4', { + 'source_urls': ['https://pypi.python.org/packages/source/Q/QtAwesome'], + 'prebuildopts': "rm -r qtawesome/tests/__pycache__ && ", + }), + ('pickleshare', '0.7.4', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pickleshare'], + }), + ('QtPy', '1.2.1', { + 'source_urls': ['https://pypi.python.org/packages/source/Q/QtPy'], + }), + ('chardet', '3.0.3', { + 'source_urls': ['https://pypi.python.org/packages/source/c/chardet'], + }), + ('numpydoc', '0.6.0', { + 'source_urls': ['https://pypi.python.org/packages/source/n/numpydoc'], + }), + (name.lower(), version, { + 'source_urls': ['https://pypi.python.org/packages/source/s/spyder'], + }), +] + +# specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module +full_sanity_check = True + +sanity_check_paths = { + 'files': ['bin/spyder'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +moduleclass = 'tools' -- GitLab From ae42b680550622152b1ae579352285c80394ebbe Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 23 May 2017 15:20:20 +0200 Subject: [PATCH 0802/1603] add tuneR, seewave, soundecology extensions for R 3.4.0 (+ libsndfile as dep) --- .../libsndfile-1.0.28-intel-2017a.eb | 20 +++++++++++++++++++ .../r/R/R-3.4.0-intel-2017a-X11-20170314.eb | 14 ++++++++++++- 2 files changed, 33 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/l/libsndfile/libsndfile-1.0.28-intel-2017a.eb diff --git a/easybuild/easyconfigs/l/libsndfile/libsndfile-1.0.28-intel-2017a.eb b/easybuild/easyconfigs/l/libsndfile/libsndfile-1.0.28-intel-2017a.eb new file mode 100644 index 0000000000..0912c1995f --- /dev/null +++ b/easybuild/easyconfigs/l/libsndfile/libsndfile-1.0.28-intel-2017a.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'libsndfile' +version = '1.0.28' + +homepage = 'http://www.mega-nerd.com/libsndfile' +description = """Libsndfile is a C library for reading and writing files containing sampled sound + (such as MS Windows WAV and the Apple/SGI AIFF format) through one standard library interface.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['http://www.mega-nerd.com/libsndfile/files/'] +sources = [SOURCE_TAR_GZ] + +sanity_check_paths = { + 'files': ['include/sndfile.h', 'include/sndfile.hh', 'lib/libsndfile.a', 'lib/libsndfile.%s' % SHLIB_EXT], + 'dirs': ['bin'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/r/R/R-3.4.0-intel-2017a-X11-20170314.eb b/easybuild/easyconfigs/r/R/R-3.4.0-intel-2017a-X11-20170314.eb index 949ed58bbb..94a8307cc4 100644 --- a/easybuild/easyconfigs/r/R/R-3.4.0-intel-2017a-X11-20170314.eb +++ b/easybuild/easyconfigs/r/R/R-3.4.0-intel-2017a-X11-20170314.eb @@ -44,6 +44,8 @@ dependencies = [ ('PROJ', '4.9.3'), # for rgdal ('GMP', '6.1.2'), # for igraph ('NLopt', '2.4.2'), # for nloptr + ('FFTW', '3.3.6'), # for fftw + ('libsndfile', '1.0.28'), # for seewave # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons # ('OpenSSL', '1.0.2h'), @@ -508,7 +510,17 @@ exts_list = [ ('purrr', '0.2.2', ext_options), ('downloader', '0.4', ext_options), ('imager', '0.40.2', dict(ext_options.items() + [('patches', ['imager-0.40.2_icpc-wd308.patch'])])), + ('pracma', '2.0.4', ext_options), + ('signal', '0.7-6', ext_options), + ('tuneR', '1.3.2', ext_options), + ('pastecs', '1.3-18', ext_options), + ('audio', '0.1-5', ext_options), + ('fftw', '1.0-4', ext_options), + ('seewave', '2.0.5', ext_options), + ('gsw', '1.0-3', ext_options), + ('oce', '0.9-21', ext_options), + ('ineq', '0.2-13', ext_options), + ('soundecology', '1.3.2', ext_options), ] moduleclass = 'lang' - -- GitLab From e69694e926d3426f654dcfd7f67cd72b63430d22 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 23 May 2017 15:22:50 +0200 Subject: [PATCH 0803/1603] add missing patch for configparser --- ...gparser-3.5.0_no-backports-namespace.patch | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/s/Spyder/configparser-3.5.0_no-backports-namespace.patch diff --git a/easybuild/easyconfigs/s/Spyder/configparser-3.5.0_no-backports-namespace.patch b/easybuild/easyconfigs/s/Spyder/configparser-3.5.0_no-backports-namespace.patch new file mode 100644 index 0000000000..6deccec5e6 --- /dev/null +++ b/easybuild/easyconfigs/s/Spyder/configparser-3.5.0_no-backports-namespace.patch @@ -0,0 +1,31 @@ +don't let configparser define 'backports' namespace, since that interferes with other packaging that provide stuff in 'backports' + +patch obtained from https://github.com/NIXOS/nixpkgs/blob/master/pkgs/development/python-modules/configparser/0001-namespace-fix.patch +see also https://bitbucket.org/ambv/configparser/issues/17/importerror-when-used-with-other-backports +diff --git a/setup.py b/setup.py +index 3b07823..63ed25d 100644 +--- a/setup.py ++++ b/setup.py +@@ -42,7 +42,6 @@ setup( + py_modules=modules, + package_dir={'': 'src'}, + packages=find_packages('src'), +- namespace_packages=['backports'], + include_package_data=True, + zip_safe=False, + install_requires=requirements, +diff --git a/src/backports/__init__.py b/src/backports/__init__.py +index f84d25c..febdb2f 100644 +--- a/src/backports/__init__.py ++++ b/src/backports/__init__.py +@@ -3,9 +3,3 @@ + + from pkgutil import extend_path + __path__ = extend_path(__path__, __name__) +- +-try: +- import pkg_resources +- pkg_resources.declare_namespace(__name__) +-except ImportError: +- pass +-- -- GitLab From 3de6edbdf821c34fe4397a9ec4ffa16d0bc1e3c5 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Tue, 23 May 2017 16:04:22 +0200 Subject: [PATCH 0804/1603] Drop testing easyconfigs --- .../p/Python/Python-2.7.13-foss-2016b-bare.eb | 147 ------------------ ...er-2.7.13-foss-2016b-Python-2.7.13-bare.eb | 21 --- 2 files changed, 168 deletions(-) delete mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.13-foss-2016b-bare.eb delete mode 100644 easybuild/easyconfigs/t/Tkinter/Tkinter-2.7.13-foss-2016b-Python-2.7.13-bare.eb diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.13-foss-2016b-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.13-foss-2016b-bare.eb deleted file mode 100644 index 4c330ffc74..0000000000 --- a/easybuild/easyconfigs/p/Python/Python-2.7.13-foss-2016b-bare.eb +++ /dev/null @@ -1,147 +0,0 @@ -name = 'Python' -version = '2.7.13' -versionsuffix = '-bare' - -homepage = 'http://python.org/' -description = """Python is a programming language that lets you work more quickly and integrate your systems - more effectively. - - This is a version without Tk or X11.""" - -toolchain = {'name': 'foss', 'version': '2016b'} -toolchainopts = {'pic': True} - -source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] -sources = [SOURCE_TGZ] - -# python needs bzip2 to build the bz2 package -dependencies = [ - ('bzip2', '1.0.6'), - ('zlib', '1.2.8'), - ('libreadline', '6.3'), - ('ncurses', '6.0'), - ('SQLite', '3.13.0'), - ('GMP', '6.1.2'), - ('libffi', '3.2.1'), - # OS dependency should be preferred if the os version is more recent then this version, - # it's nice to have an up to date openssl for security reasons - # ('OpenSSL', '1.0.2h'), -] - -osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] - -# order is important! -# package versions updated 9th February 2017 -# using easy_update -# the commented out extensions were added by easy_update but broke the build -exts_list = [ - ('six', '1.10.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], - }), - #('packaging', '16.8', { - # 'source_urls': ['https://pypi.python.org/packages/source/p/packaging/'], - #}), - #('pyparsing', '2.1.10', { - # 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], - #}), - #('appdirs', '1.4.0', { - # 'source_urls': ['https://pypi.python.org/packages/source/a/appdirs/'], - #}), - ('setuptools', '32.3.1', { - 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], - }), - ('pip', '9.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], - }), - ('nose', '1.3.7', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], - }), - ('numpy', '1.12.0', { - 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/n/numpy'], - }), - ('scipy', '0.18.1', { - 'source_urls': ['https://pypi.python.org/packages/source/s/scipy'], - }), - ('blist', '1.3.6', { - 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], - }), - ('mpi4py', '2.0.0', { - 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], - }), - ('paycheck', '1.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], - }), - ('pbr', '1.10.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], - }), - ('lockfile', '0.12.2', { - 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], - }), - ('Cython', '0.25.2', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cython/'], - }), - ('dateutil', '2.5.3', { - 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], - }), - ('deap', '1.0.2', { - 'source_tmpl': '%(name)s-%(version)s.post2.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], - }), - ('decorator', '4.0.11', { - 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], - }), - ('arff', '2.1.0', { - 'source_tmpl': 'liac-%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], - }), - ('pycrypto', '2.6.1', { - 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], - }), - ('ecdsa', '0.13', { - 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], - }), - ('cryptography', '1.7.2', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cryptography/'], - }), - ('pyasn1', '0.2.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyasn1/'], - }), - ('paramiko', '2.1.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], - }), - ('netifaces', '0.10.5', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], - }), - ('netaddr', '0.7.19', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], - }), - ('funcsigs', '1.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/f/funcsigs'], - }), - ('mock', '2.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/m/mock'], - }), - ('pytz', '2016.10', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pytz'], - }), - ('pandas', '0.19.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], - }), - ('enum34', '1.1.6', { - 'modulename': 'enum', - 'source_urls': ['https://pypi.python.org/packages/source/e/enum34'], - }), - ('bitstring', '3.1.5', { - 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/b/bitstring'], - }), - ('virtualenv', '15.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/v/virtualenv'], - }), -] - -moduleclass = 'lang' diff --git a/easybuild/easyconfigs/t/Tkinter/Tkinter-2.7.13-foss-2016b-Python-2.7.13-bare.eb b/easybuild/easyconfigs/t/Tkinter/Tkinter-2.7.13-foss-2016b-Python-2.7.13-bare.eb deleted file mode 100644 index 79e3c82386..0000000000 --- a/easybuild/easyconfigs/t/Tkinter/Tkinter-2.7.13-foss-2016b-Python-2.7.13-bare.eb +++ /dev/null @@ -1,21 +0,0 @@ -name = 'Tkinter' -version = '2.7.13' -versionsuffix = '-Python-%(pyver)s-bare' - -homepage = 'http://python.org/' -description = """Tkinter module, built with the Python buildsystem""" - -toolchain = {'name': 'foss', 'version': '2016b'} -toolchainopts = {'pic': True} - -source_urls = ['http://www.python.org/ftp/python/%(version)s/'] -sources = ['Python-%(version)s.tgz'] - -dependencies = [ - ('Python', '2.7.13', '-bare'), - ('Tcl', '8.6.5'), - ('Tk', '8.6.5', '-libX11-1.6.3'), - ('xproto', '7.0.28'), -] - -moduleclass = 'lang' -- GitLab From 3a1774cff1fcb0b5d67c56e5f856c9676431b142 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Tue, 23 May 2017 17:45:12 +0200 Subject: [PATCH 0805/1603] Add VTK/7.1.1 --- .../VTK-7.1.1-intel-2017a-Python-2.7.13.eb | 59 +++++++++++++++++++ 1 file changed, 59 insertions(+) create mode 100644 easybuild/easyconfigs/v/VTK/VTK-7.1.1-intel-2017a-Python-2.7.13.eb diff --git a/easybuild/easyconfigs/v/VTK/VTK-7.1.1-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/v/VTK/VTK-7.1.1-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..79963c3515 --- /dev/null +++ b/easybuild/easyconfigs/v/VTK/VTK-7.1.1-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,59 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-97.html +## + +easyblock = 'CMakeMake' + +name = 'VTK' +version = '7.1.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.vtk.org' +description = """The Visualization Toolkit (VTK) is an open-source, freely available software system for + 3D computer graphics, image processing and visualization. VTK consists of a C++ class library and several + interpreted interface layers including Tcl/Tk, Java, and Python. VTK supports a wide variety of visualization + algorithms including: scalar, vector, tensor, texture, and volumetric methods; and advanced modeling techniques + such as: implicit modeling, polygon reduction, mesh smoothing, cutting, contouring, and Delaunay triangulation.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['http://www.vtk.org/files/release/%(version_major_minor)s'] +sources = [ + SOURCE_TAR_GZ, + '%(name)sData-%(version)s.tar.gz', +] + +builddependencies = [('CMake', '3.8.0')] + +dependencies = [ + ('Python', '2.7.13'), + ('libGLU', '9.0.0'), + ('X11', '20170314'), +] + +configopts = "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT +configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT +configopts += "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include -DVTK_WRAP_PYTHON=ON " +configopts += "-DPYTHON_LIBRARY=$EBROOTPYTHON/lib/libpython%%(pyshortver)s.%s " % SHLIB_EXT +configopts += " -DPYTHON_INCLUDE_DIR=$EBROOTPYTHON/include/python%(pyshortver)s " +preinstallopts = "mkdir -p %(installdir)s/lib/python%(pyshortver)s/site-packages/ && " +preinstallopts += "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +sanity_check_paths = { + 'files': ['bin/vtk%s-%%(version_major_minor)s' % x for x in ['EncodeString', 'HashSource']], + 'dirs': ['lib/python%(pyshortver)s/site-packages/', 'include/vtk-%(version_major_minor)s'], +} + +sanity_check_commands = [('python', "-c 'import %(namelower)s'")] + +moduleclass = 'vis' -- GitLab From e49f01daadc3275835be0ddfafb68785c1a744dc Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Tue, 23 May 2017 17:49:59 +0200 Subject: [PATCH 0806/1603] Fix FSL to actually build --- .../f/FSL/FSL-5.0.10-intel-2017a.eb | 6 +- .../f/FSL/FSL-5.0.10_build_extras.patch | 2 +- .../f/FSL/FSL-5.0.10_makefile_fixes.patch | 758 +++++------------- .../g/GLibmm/GLibmm-2.53.1.1-intel-2017a.eb | 24 - .../libsigc++/libsigc++-2.10.0-intel-2017a.eb | 20 - .../l/libxml++/libxml++-2.91.3-intel-2017a.eb | 24 - 6 files changed, 213 insertions(+), 621 deletions(-) delete mode 100644 easybuild/easyconfigs/g/GLibmm/GLibmm-2.53.1.1-intel-2017a.eb delete mode 100644 easybuild/easyconfigs/l/libsigc++/libsigc++-2.10.0-intel-2017a.eb delete mode 100644 easybuild/easyconfigs/l/libxml++/libxml++-2.91.3-intel-2017a.eb diff --git a/easybuild/easyconfigs/f/FSL/FSL-5.0.10-intel-2017a.eb b/easybuild/easyconfigs/f/FSL/FSL-5.0.10-intel-2017a.eb index b6760b7e06..5ba9750bf3 100644 --- a/easybuild/easyconfigs/f/FSL/FSL-5.0.10-intel-2017a.eb +++ b/easybuild/easyconfigs/f/FSL/FSL-5.0.10-intel-2017a.eb @@ -19,15 +19,15 @@ patches = [ dependencies = [ ('Boost', '1.63.0', '-Python-2.7.13'), ('libgd', '2.2.4'), - ('libxml++', '2.91.3'), - ('SQLite', '3.13.0'), + ('libxml2', '2.9.4'), + ('SQLite', '3.17.0'), ('libpng', '1.6.29'), ('Tk', '8.6.6'), - ('GLibmm', '2.53.1.1'), ('NLopt', '2.4.2'), ('freeglut', '3.0.0'), ('expat', '2.2.0'), ('zlib', '1.2.11'), + ('VTK', '7.1.1', '-Python-2.7.13'), ] moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/FSL/FSL-5.0.10_build_extras.patch b/easybuild/easyconfigs/f/FSL/FSL-5.0.10_build_extras.patch index ac663c9852..d545a66031 100644 --- a/easybuild/easyconfigs/f/FSL/FSL-5.0.10_build_extras.patch +++ b/easybuild/easyconfigs/f/FSL/FSL-5.0.10_build_extras.patch @@ -7,7 +7,7 @@ diff -ur fsl/extras/build fsl.new/extras/build PROJECTS="${PROJECTS} libgd libgdc libprob libcprob newmat cprob newran fftw" PROJECTS="${PROJECTS} boost libxml2-2.9.2 libxml++-2.34.0 libsqlite libnlopt ../include/armawrap/dummy_newmat" +# For EasyBuild: -+PROJECTS="libprob libcprob newmat cprob newran" ++PROJECTS="libprob libcprob newmat cprob newran libxml++-2.34.0 libgdc" for projname in $PROJECTS; do if [ -d $FSLESRCDIR/$projname ] ; then buildIt $FSLESRCDIR $projname 1 diff --git a/easybuild/easyconfigs/f/FSL/FSL-5.0.10_makefile_fixes.patch b/easybuild/easyconfigs/f/FSL/FSL-5.0.10_makefile_fixes.patch index 8808344d6f..ca470e4c17 100644 --- a/easybuild/easyconfigs/f/FSL/FSL-5.0.10_makefile_fixes.patch +++ b/easybuild/easyconfigs/f/FSL/FSL-5.0.10_makefile_fixes.patch @@ -1,605 +1,265 @@ -patch out hardcoded compiler names and options -author: kenneth hoste (hpc-ugent) -diff -ur fsl.orig/config/apple-darwin10-gcc4.2/systemvars.mk fsl/config/apple-darwin10-gcc4.2/systemvars.mk ---- fsl.orig/config/apple-darwin10-gcc4.2/systemvars.mk 2009-11-03 18:02:14.000000000 +0100 -+++ fsl/config/apple-darwin10-gcc4.2/systemvars.mk 2017-05-18 13:54:40.446975876 +0200 -@@ -3,8 +3,8 @@ - - # Compiler dependent variables - --CC = cc --CXX = c++ -+CC := ${CC} -+CXX := ${CXX} - CSTATICFLAGS = - CXXSTATICFLAGS = - -@@ -15,7 +15,7 @@ - - DEPENDFLAGS = -MM - --OPTFLAGS = -O3 -fexpensive-optimizations -+OPTFLAGS := ${CFLAGS} -wd803 - MACHDBGFLAGS = -g - GNU_ANSI_FLAGS = -Wall -Wno-long-long -ansi -pedantic - SGI_ANSI_FLAGS = -ansi -fullwarn -Only in fsl/config/apple-darwin10-gcc4.2: systemvars.mk.orig -diff -ur fsl.orig/config/apple-darwin11-gcc4.2/systemvars.mk fsl/config/apple-darwin11-gcc4.2/systemvars.mk ---- fsl.orig/config/apple-darwin11-gcc4.2/systemvars.mk 2012-03-21 12:30:53.000000000 +0100 -+++ fsl/config/apple-darwin11-gcc4.2/systemvars.mk 2017-05-18 13:54:40.446975876 +0200 -@@ -15,7 +15,7 @@ - - DEPENDFLAGS = -MM - --OPTFLAGS = -O3 -+OPTFLAGS := -O3 -wd803 - MACHDBGFLAGS = -g - GNU_ANSI_FLAGS = -Wall -Wno-long-long -ansi -pedantic - ANSI_FLAGS = ${GNU_ANSI_FLAGS} -Only in fsl/config/apple-darwin11-gcc4.2: systemvars.mk.orig -diff -ur fsl.orig/config/apple-darwin12-gcc4.2/systemvars.mk fsl/config/apple-darwin12-gcc4.2/systemvars.mk ---- fsl.orig/config/apple-darwin12-gcc4.2/systemvars.mk 2013-04-09 18:00:32.000000000 +0200 -+++ fsl/config/apple-darwin12-gcc4.2/systemvars.mk 2017-05-18 13:54:40.446975876 +0200 -@@ -15,7 +15,7 @@ - - DEPENDFLAGS = -MM - --OPTFLAGS = -O3 -+OPTFLAGS := -O3 -wd803 - MACHDBGFLAGS = -g - GNU_ANSI_FLAGS = -Wall -Wno-long-long -ansi -pedantic - ANSI_FLAGS = ${GNU_ANSI_FLAGS} -Only in fsl/config/apple-darwin12-gcc4.2: systemvars.mk.orig -diff -ur fsl.orig/config/apple-darwin7-gcc3.1/systemvars.mk fsl/config/apple-darwin7-gcc3.1/systemvars.mk ---- fsl.orig/config/apple-darwin7-gcc3.1/systemvars.mk 2007-07-13 13:00:20.000000000 +0200 -+++ fsl/config/apple-darwin7-gcc3.1/systemvars.mk 2017-05-18 13:54:40.446975876 +0200 -@@ -7,8 +7,8 @@ - - # Compiler dependent variables - --CC = cc --CXX = c++ -+CC := ${CC} -+CXX := ${CXX} - CSTATICFLAGS = - CXXSTATICFLAGS = - -@@ -17,7 +17,7 @@ - - DEPENDFLAGS = -MM - --OPTFLAGS = -O3 -fexpensive-optimizations ${ARCHFLAGS} -+OPTFLAGS := ${CFLAGS} ${ARCHFLAGS} -wd803 - MACHDBGFLAGS = -g - GNU_ANSI_FLAGS = -traditional-cpp -Wall -Wno-long-long -Wno-long-double -ansi -pedantic - SGI_ANSI_FLAGS = -ansi -fullwarn -Only in fsl/config/apple-darwin7-gcc3.1: systemvars.mk.orig -diff -ur fsl.orig/config/apple-darwin7-gcc3.3/systemvars.mk fsl/config/apple-darwin7-gcc3.3/systemvars.mk ---- fsl.orig/config/apple-darwin7-gcc3.3/systemvars.mk 2007-07-13 13:00:20.000000000 +0200 -+++ fsl/config/apple-darwin7-gcc3.3/systemvars.mk 2017-05-18 13:54:40.446975876 +0200 -@@ -7,8 +7,8 @@ - - # Compiler dependent variables - --CC = cc --CXX = c++ -+CC := ${CC} -+CXX := ${CXX} - CSTATICFLAGS = - CXXSTATICFLAGS = - -@@ -17,7 +17,7 @@ - - DEPENDFLAGS = -MM - --OPTFLAGS = -O3 -fexpensive-optimizations ${ARCHFLAGS} -+OPTFLAGS := ${CFLAGS} ${ARCHFLAGS} -wd803 - MACHDBGFLAGS = -g - GNU_ANSI_FLAGS = -Wall -Wno-long-long -Wno-long-double -ansi -pedantic - SGI_ANSI_FLAGS = -ansi -fullwarn -Only in fsl/config/apple-darwin7-gcc3.3: systemvars.mk.orig -diff -ur fsl.orig/config/apple-darwin8-gcc4.0/systemvars.mk fsl/config/apple-darwin8-gcc4.0/systemvars.mk ---- fsl.orig/config/apple-darwin8-gcc4.0/systemvars.mk 2007-12-19 15:40:57.000000000 +0100 -+++ fsl/config/apple-darwin8-gcc4.0/systemvars.mk 2017-05-18 13:54:40.446975876 +0200 -@@ -3,8 +3,8 @@ - - # Compiler dependent variables - --CC = cc --CXX = c++ -+CC := ${CC} -+CXX := ${CXX} - CSTATICFLAGS = - CXXSTATICFLAGS = - -@@ -17,7 +17,7 @@ - - DEPENDFLAGS = -MM - --OPTFLAGS = -O3 -fexpensive-optimizations -+OPTFLAGS := ${CFLAGS} -wd803 - MACHDBGFLAGS = -g - GNU_ANSI_FLAGS = -Wall -Wno-long-long -Wno-long-double -ansi -pedantic - SGI_ANSI_FLAGS = -ansi -fullwarn -Only in fsl/config/apple-darwin8-gcc4.0: systemvars.mk.orig -diff -ur fsl.orig/config/apple-darwin9-gcc4.0/systemvars.mk fsl/config/apple-darwin9-gcc4.0/systemvars.mk ---- fsl.orig/config/apple-darwin9-gcc4.0/systemvars.mk 2007-12-19 15:33:53.000000000 +0100 -+++ fsl/config/apple-darwin9-gcc4.0/systemvars.mk 2017-05-18 13:54:40.446975876 +0200 -@@ -3,8 +3,8 @@ - - # Compiler dependent variables - --CC = cc --CXX = c++ -+CC := ${CC} -+CXX := ${CXX} - CSTATICFLAGS = - CXXSTATICFLAGS = - -@@ -17,7 +17,7 @@ - - DEPENDFLAGS = -MM - --OPTFLAGS = -O3 -fexpensive-optimizations -+OPTFLAGS := ${CFLAGS} -wd803 - MACHDBGFLAGS = -g - GNU_ANSI_FLAGS = -Wall -Wno-long-long -Wno-long-double -ansi -pedantic - SGI_ANSI_FLAGS = -ansi -fullwarn -Only in fsl/config/apple-darwin9-gcc4.0: systemvars.mk.orig +# This fixes the build system of FSL. It now (mostly) uses EB. +# Ward Poelmans +diff -ur fsl.orig/config/common/vars.mk fsl/config/common/vars.mk +--- fsl.orig/config/common/vars.mk 2016-05-24 17:44:11.000000000 +0200 ++++ fsl/config/common/vars.mk 2017-05-23 10:19:55.325628385 +0200 +@@ -24,14 +24,14 @@ + USRCFLAGS = + USRCXXFLAGS = + +-LDFLAGS = ${ARCHLDFLAGS} ${USRLDFLAGS} -L. -L${DEVLIBDIR} -L${LIBDIR} ++LDFLAGS = ${EBVARLDFLAGS} ${ARCHLDFLAGS} ${USRLDFLAGS} -L. -L${DEVLIBDIR} -L${LIBDIR} + +-AccumulatedIncFlags = -I${INC_BOOST} ${USRINCFLAGS} -I. -I${DEVINCDIR} -I${INCDIR} ++AccumulatedIncFlags = ${EBVARCPPFLAGS} -I${INC_BOOST} ${USRINCFLAGS} -I. -I${DEVINCDIR} -I${INCDIR} + +-CFLAGS = ${ANSI_FLAGS} ${ANSI_CFLAGS} ${DBGFLAGS} ${USEDCSTATICFLAGS} ${USRCFLAGS} ${ARCHFLAGS} ${OPTFLAGS} \ ++CFLAGS = ${EBVARCFLAGS} ${ANSI_FLAGS} ${ANSI_CFLAGS} ${DBGFLAGS} ${USEDCSTATICFLAGS} ${USRCFLAGS} ${ARCHFLAGS} ${OPTFLAGS} \ + ${AccumulatedIncFlags} + +-CXXFLAGS = ${ANSI_FLAGS} ${ANSI_CXXFLAGS} ${DBGFLAGS} ${USEDCXXSTATICFLAGS} ${USRCXXFLAGS} ${ARCHFLAGS} ${OPTFLAGS} \ ++CXXFLAGS = ${EBVARCXXFLAGS} ${ANSI_FLAGS} ${ANSI_CXXFLAGS} ${DBGFLAGS} ${USEDCXXSTATICFLAGS} ${USRCXXFLAGS} ${ARCHFLAGS} ${OPTFLAGS} \ + ${AccumulatedIncFlags} + + HFILES = *.h diff -ur fsl.orig/config/generic/systemvars.mk fsl/config/generic/systemvars.mk --- fsl.orig/config/generic/systemvars.mk 2007-07-13 13:00:20.000000000 +0200 -+++ fsl/config/generic/systemvars.mk 2017-05-18 13:54:40.446975876 +0200 ++++ fsl/config/generic/systemvars.mk 2017-05-22 14:26:37.819705455 +0200 @@ -16,8 +16,8 @@ - + # Compiler dependent variables - + -CC = gcc -CXX = c++ +CC := ${CC} +CXX := ${CXX} CSTATICFLAGS = -static CXXSTATICFLAGS = -static - + @@ -25,7 +25,7 @@ - + DEPENDFLAGS = -MM - + -OPTFLAGS = -O3 -fexpensive-optimizations ${ARCHFLAGS} +OPTFLAGS := ${CFLAGS} ${ARCHFLAGS} -wd803 MACHDBGFLAGS = GNU_ANSI_FLAGS = -Wall -ansi -pedantic SGI_ANSI_FLAGS = -ansi -fullwarn -Only in fsl/config/generic: systemvars.mk.orig -diff -ur fsl.orig/config/gnu_64-gcc4.4/systemvars.mk fsl/config/gnu_64-gcc4.4/systemvars.mk ---- fsl.orig/config/gnu_64-gcc4.4/systemvars.mk 2011-04-19 10:47:52.000000000 +0200 -+++ fsl/config/gnu_64-gcc4.4/systemvars.mk 2017-05-18 13:54:40.446975876 +0200 -@@ -27,7 +27,7 @@ - - DEPENDFLAGS = -MM - --OPTFLAGS = -O3 -fexpensive-optimizations ${ARCHFLAGS} -+OPTFLAGS := ${CFLAGS} ${ARCHFLAGS} -wd803 - MACHDBGFLAGS = -g - GNU_ANSI_FLAGS = -Wall -ansi -pedantic -Wno-long-long - SGI_ANSI_FLAGS = -ansi -fullwarn -Only in fsl/config/gnu_64-gcc4.4: systemvars.mk.orig -diff -ur fsl.orig/config/i686-pc-cygwin-gcc3.2/systemvars.mk fsl/config/i686-pc-cygwin-gcc3.2/systemvars.mk ---- fsl.orig/config/i686-pc-cygwin-gcc3.2/systemvars.mk 2007-07-13 13:00:20.000000000 +0200 -+++ fsl/config/i686-pc-cygwin-gcc3.2/systemvars.mk 2017-05-18 13:54:40.446975876 +0200 -@@ -18,8 +18,8 @@ - - # Compiler dependent variables - --CC = gcc-2 --CXX = c++-2 -+CC := ${CC} -+CXX := ${CXX} - CSTATICFLAGS = -static - CXXSTATICFLAGS = -static - -@@ -27,7 +27,7 @@ - - DEPENDFLAGS = -MM - --OPTFLAGS = -O3 -fexpensive-optimizations ${ARCHFLAGS} -+OPTFLAGS := ${CFLAGS} ${ARCHFLAGS} -wd803 - MACHDBGFLAGS = -g - GNU_ANSI_FLAGS = -Wall -ansi -pedantic -Wno-deprecated - SGI_ANSI_FLAGS = -ansi -fullwarn -Only in fsl/config/i686-pc-cygwin-gcc3.2: systemvars.mk.orig -diff -ur fsl.orig/config/i686-pc-cygwin-gcc3.3/systemvars.mk fsl/config/i686-pc-cygwin-gcc3.3/systemvars.mk ---- fsl.orig/config/i686-pc-cygwin-gcc3.3/systemvars.mk 2007-07-13 13:00:20.000000000 +0200 -+++ fsl/config/i686-pc-cygwin-gcc3.3/systemvars.mk 2017-05-18 13:54:40.447975880 +0200 -@@ -18,8 +18,8 @@ - - # Compiler dependent variables - --CC = gcc --CXX = c++ -+CC := ${CC} -+CXX := ${CXX} - CSTATICFLAGS = -static - CXXSTATICFLAGS = -static - -@@ -27,7 +27,7 @@ - - DEPENDFLAGS = -MM - --OPTFLAGS = -O3 -fexpensive-optimizations ${ARCHFLAGS} -+OPTFLAGS := ${CFLAGS} ${ARCHFLAGS} -wd803 - MACHDBGFLAGS = -g - GNU_ANSI_FLAGS = -Wall -ansi -pedantic -Wno-deprecated - SGI_ANSI_FLAGS = -ansi -fullwarn -Only in fsl/config/i686-pc-cygwin-gcc3.3: systemvars.mk.orig -diff -ur fsl.orig/config/i686-pc-cygwin-gcc3.4/systemvars.mk fsl/config/i686-pc-cygwin-gcc3.4/systemvars.mk ---- fsl.orig/config/i686-pc-cygwin-gcc3.4/systemvars.mk 2007-07-13 13:00:20.000000000 +0200 -+++ fsl/config/i686-pc-cygwin-gcc3.4/systemvars.mk 2017-05-18 13:54:40.447975880 +0200 -@@ -18,8 +18,8 @@ - - # Compiler dependent variables - --CC = gcc --CXX = c++ -+CC := ${CC} -+CXX := ${CXX} - CSTATICFLAGS = -static - CXXSTATICFLAGS = -static - -@@ -27,7 +27,7 @@ - - DEPENDFLAGS = -MM - --OPTFLAGS = -O3 -fexpensive-optimizations ${ARCHFLAGS} -+OPTFLAGS := ${CFLAGS} ${ARCHFLAGS} -wd803 - MACHDBGFLAGS = -g - GNU_ANSI_FLAGS = -Wall -ansi -pedantic -Wno-deprecated - SGI_ANSI_FLAGS = -ansi -fullwarn -Only in fsl/config/i686-pc-cygwin-gcc3.4: systemvars.mk.orig -diff -ur fsl.orig/config/linux_32-gcc2.96/systemvars.mk fsl/config/linux_32-gcc2.96/systemvars.mk ---- fsl.orig/config/linux_32-gcc2.96/systemvars.mk 2007-07-25 17:21:07.000000000 +0200 -+++ fsl/config/linux_32-gcc2.96/systemvars.mk 2017-05-18 13:54:40.447975880 +0200 -@@ -18,8 +18,8 @@ - - # Compiler dependent variables - --CC = gcc --CXX = c++ -+CC := ${CC} -+CXX := ${CXX} - CSTATICFLAGS = -static - CXXSTATICFLAGS = -static - -@@ -27,7 +27,7 @@ - - DEPENDFLAGS = -MM - --OPTFLAGS = -O3 -fexpensive-optimizations ${ARCHFLAGS} -+OPTFLAGS := ${CFLAGS} ${ARCHFLAGS} -wd803 - MACHDBGFLAGS = -g - GNU_ANSI_FLAGS = -Wall -ansi -pedantic - SGI_ANSI_FLAGS = -ansi -fullwarn -Only in fsl/config/linux_32-gcc2.96: systemvars.mk.orig -diff -ur fsl.orig/config/linux_32-gcc3.2/systemvars.mk fsl/config/linux_32-gcc3.2/systemvars.mk ---- fsl.orig/config/linux_32-gcc3.2/systemvars.mk 2007-07-25 17:21:08.000000000 +0200 -+++ fsl/config/linux_32-gcc3.2/systemvars.mk 2017-05-18 13:54:40.447975880 +0200 -@@ -18,8 +18,8 @@ - - # Compiler dependent variables - --CC = gcc --CXX = c++ -+CC := ${CC} -+CXX := ${CXX} - CSTATICFLAGS = -static - CXXSTATICFLAGS = -static - -@@ -27,7 +27,7 @@ - - DEPENDFLAGS = -MM - --OPTFLAGS = -O3 -fexpensive-optimizations ${ARCHFLAGS} -+OPTFLAGS := ${CFLAGS} ${ARCHFLAGS} -wd803 - MACHDBGFLAGS = -g - GNU_ANSI_FLAGS = -Wall -ansi -pedantic - SGI_ANSI_FLAGS = -ansi -fullwarn -Only in fsl/config/linux_32-gcc3.2: systemvars.mk.orig -diff -ur fsl.orig/config/linux_32-gcc3.3/systemvars.mk fsl/config/linux_32-gcc3.3/systemvars.mk ---- fsl.orig/config/linux_32-gcc3.3/systemvars.mk 2007-07-25 17:21:09.000000000 +0200 -+++ fsl/config/linux_32-gcc3.3/systemvars.mk 2017-05-18 13:54:40.447975880 +0200 -@@ -18,8 +18,8 @@ - - # Compiler dependent variables - --CC = gcc --CXX = c++ -+CC := ${CC} -+CXX := ${CXX} - CSTATICFLAGS = -static - CXXSTATICFLAGS = -static - -@@ -27,7 +27,7 @@ - - DEPENDFLAGS = -MM - --OPTFLAGS = -O3 -fexpensive-optimizations ${ARCHFLAGS} -+OPTFLAGS := ${CFLAGS} ${ARCHFLAGS} -wd803 - MACHDBGFLAGS = -g - GNU_ANSI_FLAGS = -Wall -ansi -pedantic -Wno-long-long - SGI_ANSI_FLAGS = -ansi -fullwarn -Only in fsl/config/linux_32-gcc3.3: systemvars.mk.orig -diff -ur fsl.orig/config/linux_32-gcc3.4/systemvars.mk fsl/config/linux_32-gcc3.4/systemvars.mk ---- fsl.orig/config/linux_32-gcc3.4/systemvars.mk 2007-07-25 17:21:10.000000000 +0200 -+++ fsl/config/linux_32-gcc3.4/systemvars.mk 2017-05-18 13:54:40.447975880 +0200 -@@ -18,8 +18,8 @@ - - # Compiler dependent variables - --CC = gcc --CXX = c++ -+CC := ${CC} -+CXX := ${CXX} - CSTATICFLAGS = -static - CXXSTATICFLAGS = -static - -@@ -27,7 +27,7 @@ - - DEPENDFLAGS = -MM - --OPTFLAGS = -O3 -fexpensive-optimizations ${ARCHFLAGS} -+OPTFLAGS := ${CFLAGS} ${ARCHFLAGS} -wd803 - MACHDBGFLAGS = -g - GNU_ANSI_FLAGS = -Wall -ansi -pedantic -Wno-long-long - SGI_ANSI_FLAGS = -ansi -fullwarn -Only in fsl/config/linux_32-gcc3.4: systemvars.mk.orig -diff -ur fsl.orig/config/linux_32-gcc4.0/systemvars.mk fsl/config/linux_32-gcc4.0/systemvars.mk ---- fsl.orig/config/linux_32-gcc4.0/systemvars.mk 2007-07-25 17:21:11.000000000 +0200 -+++ fsl/config/linux_32-gcc4.0/systemvars.mk 2017-05-18 13:54:40.447975880 +0200 -@@ -18,8 +18,8 @@ - - # Compiler dependent variables - --CC = gcc --CXX = c++ -+CC := ${CC} -+CXX := ${CXX} - CSTATICFLAGS = -static - CXXSTATICFLAGS = -static - -@@ -27,7 +27,7 @@ - - DEPENDFLAGS = -MM - --OPTFLAGS = -O3 -fexpensive-optimizations ${ARCHFLAGS} -+OPTFLAGS := ${CFLAGS} ${ARCHFLAGS} -wd803 - MACHDBGFLAGS = -g - GNU_ANSI_FLAGS = -Wall -ansi -pedantic - SGI_ANSI_FLAGS = -ansi -fullwarn -Only in fsl/config/linux_32-gcc4.0: systemvars.mk.orig -diff -ur fsl.orig/config/linux_32-gcc4.1/systemvars.mk fsl/config/linux_32-gcc4.1/systemvars.mk ---- fsl.orig/config/linux_32-gcc4.1/systemvars.mk 2012-04-20 11:37:28.000000000 +0200 -+++ fsl/config/linux_32-gcc4.1/systemvars.mk 2017-05-18 13:54:40.447975880 +0200 -@@ -18,8 +18,8 @@ - - # Compiler dependent variables - --CC = gcc --CXX = c++ -+CC := ${CC} -+CXX := ${CXX} - CSTATICFLAGS = -static - CXXSTATICFLAGS = -static - -@@ -27,7 +27,7 @@ - - DEPENDFLAGS = -MM - --OPTFLAGS = -O3 -fexpensive-optimizations ${ARCHFLAGS} -+OPTFLAGS := ${CFLAGS} ${ARCHFLAGS} -wd803 - MACHDBGFLAGS = -g - GNU_ANSI_FLAGS = -Wall -ansi -pedantic -Wno-long-long - SGI_ANSI_FLAGS = -ansi -fullwarn -Only in fsl/config/linux_32-gcc4.1: systemvars.mk.orig -diff -ur fsl.orig/config/linux_64-gcc3.4/systemvars.mk fsl/config/linux_64-gcc3.4/systemvars.mk ---- fsl.orig/config/linux_64-gcc3.4/systemvars.mk 2007-07-25 17:21:12.000000000 +0200 -+++ fsl/config/linux_64-gcc3.4/systemvars.mk 2017-05-18 13:54:40.447975880 +0200 -@@ -18,8 +18,8 @@ - - # Compiler dependent variables - --CC = gcc --CXX = c++ -+CC := ${CC} -+CXX := ${CXX} - CSTATICFLAGS = -static - CXXSTATICFLAGS = -static - -@@ -27,7 +27,7 @@ - - DEPENDFLAGS = -MM - --OPTFLAGS = -O3 -fexpensive-optimizations ${ARCHFLAGS} -+OPTFLAGS := ${CFLAGS} ${ARCHFLAGS} -wd803 - MACHDBGFLAGS = -g - GNU_ANSI_FLAGS = -Wall -ansi -pedantic -Wno-long-long - SGI_ANSI_FLAGS = -ansi -fullwarn -Only in fsl/config/linux_64-gcc3.4: systemvars.mk.orig -diff -ur fsl.orig/config/linux_64-gcc4.0/systemvars.mk fsl/config/linux_64-gcc4.0/systemvars.mk ---- fsl.orig/config/linux_64-gcc4.0/systemvars.mk 2007-07-25 17:21:13.000000000 +0200 -+++ fsl/config/linux_64-gcc4.0/systemvars.mk 2017-05-18 13:54:40.447975880 +0200 -@@ -18,8 +18,8 @@ - - # Compiler dependent variables - --CC = gcc --CXX = c++ -+CC := ${CC} -+CXX := ${CXX} - CSTATICFLAGS = -static - CXXSTATICFLAGS = -static - -@@ -27,7 +27,7 @@ - - DEPENDFLAGS = -MM - --OPTFLAGS = -O3 -fexpensive-optimizations ${ARCHFLAGS} -+OPTFLAGS := ${CFLAGS} ${ARCHFLAGS} -wd803 - MACHDBGFLAGS = -g - GNU_ANSI_FLAGS = -Wall -ansi -pedantic -Wno-long-long - SGI_ANSI_FLAGS = -ansi -fullwarn -Only in fsl/config/linux_64-gcc4.0: systemvars.mk.orig -diff -ur fsl.orig/config/linux_64-gcc4.1/systemvars.mk fsl/config/linux_64-gcc4.1/systemvars.mk ---- fsl.orig/config/linux_64-gcc4.1/systemvars.mk 2007-07-25 11:19:45.000000000 +0200 -+++ fsl/config/linux_64-gcc4.1/systemvars.mk 2017-05-18 13:54:40.447975880 +0200 -@@ -18,8 +18,8 @@ - - # Compiler dependent variables - --CC = gcc --CXX = c++ -+CC := ${CC} -+CXX := ${CXX} - CSTATICFLAGS = -static - CXXSTATICFLAGS = -static - -@@ -27,7 +27,7 @@ - - DEPENDFLAGS = -MM - --OPTFLAGS = -O3 -fexpensive-optimizations ${ARCHFLAGS} -+OPTFLAGS := ${CFLAGS} ${ARCHFLAGS} -wd803 - MACHDBGFLAGS = -g - GNU_ANSI_FLAGS = -Wall -ansi -pedantic -Wno-long-long - SGI_ANSI_FLAGS = -ansi -fullwarn -Only in fsl/config/linux_64-gcc4.1: systemvars.mk.orig -diff -ur fsl.orig/config/linux_64-gcc4.2/systemvars.mk fsl/config/linux_64-gcc4.2/systemvars.mk ---- fsl.orig/config/linux_64-gcc4.2/systemvars.mk 2008-06-26 15:25:42.000000000 +0200 -+++ fsl/config/linux_64-gcc4.2/systemvars.mk 2017-05-18 13:54:40.447975880 +0200 -@@ -18,8 +18,8 @@ - - # Compiler dependent variables - --CC = gcc --CXX = c++ -+CC := ${CC} -+CXX := ${CXX} - CSTATICFLAGS = -static - CXXSTATICFLAGS = -static - -@@ -27,7 +27,7 @@ - - DEPENDFLAGS = -MM - --OPTFLAGS = -O3 -fexpensive-optimizations ${ARCHFLAGS} -+OPTFLAGS := ${CFLAGS} ${ARCHFLAGS} -wd803 - MACHDBGFLAGS = -g - GNU_ANSI_FLAGS = -Wall -ansi -pedantic -Wno-long-long - SGI_ANSI_FLAGS = -ansi -fullwarn -Only in fsl/config/linux_64-gcc4.2: systemvars.mk.orig -diff -ur fsl.orig/config/linux_64-gcc4.4/systemvars.mk fsl/config/linux_64-gcc4.4/systemvars.mk ---- fsl.orig/config/linux_64-gcc4.4/systemvars.mk 2017-01-20 16:47:17.000000000 +0100 -+++ fsl/config/linux_64-gcc4.4/systemvars.mk 2017-05-18 13:57:25.995699462 +0200 -@@ -18,8 +18,8 @@ - +diff -ur fsl.orig/config/linux_64-gcc4.8/externallibs.mk fsl/config/linux_64-gcc4.8/externallibs.mk +--- fsl.orig/config/linux_64-gcc4.8/externallibs.mk 2017-02-18 13:20:05.000000000 +0100 ++++ fsl/config/linux_64-gcc4.8/externallibs.mk 2017-05-23 17:11:51.141583678 +0200 +@@ -15,7 +15,7 @@ + INC_GDC = ${FSLEXTINC}/libgdc + + # LIBXML2 library +-INC_XML2 = ${FSLEXTINC}/libxml2 ++INC_XML2 = ${EBROOTLIBXML2} + + # LIBXML++ library + INC_XML++ = ${FSLEXTINC}/libxml++-2.6 +@@ -49,12 +49,12 @@ + INC_ZLIB = /usr/include + + # BOOST library +-BOOSTDIR = ${FSLEXTINC}/boost +-LIB_BOOST = ${BOOSTDIR} +-INC_BOOST = ${BOOSTDIR} ++BOOSTDIR = ${EBROOTBOOST} ++LIB_BOOST = ${BOOSTDIR}/lib ++INC_BOOST = ${BOOSTDIR}/include + + # QT library +-QTDIR = /usr/lib/qt3 ++QTDIR = ${EBROOTQT} + LIB_QT = ${QTDIR}/lib + INC_QT = ${QTDIR}/include + +@@ -64,10 +64,10 @@ + INC_QWT = ${QWTDIR}/include + + # FFTW3 library +-LIB_FFTW3 = ${FSLEXTLIB} +-INC_FFTW3 = ${FSLEXTINC}/fftw3 ++LIB_FFTW3 = ${EBVARFFTW_LIB_DIR} ++INC_FFTW3 = ${EBVARFFTW_INC_DIR} + + # VTK library +-VTKDIR_INC = /home/fs0/cowboy/var/caper_linux_64-gcc4.4/VTK7/include/vtk-7.0 +-VTKDIR_LIB = /home/fs0/cowboy/var/caper_linux_64-gcc4.4/VTK7/lib +-VTKSUFFIX = -7.0 +\ No newline at end of file ++VTKDIR_INC = ${EBROOTVTK}/include/vtk-7.1 ++VTKDIR_LIB = ${EBROOTVTK}/lib ++VTKSUFFIX = -7.1 +diff -ur fsl.orig/config/linux_64-gcc4.8/systemvars.mk fsl/config/linux_64-gcc4.8/systemvars.mk +--- fsl.orig/config/linux_64-gcc4.8/systemvars.mk 2017-02-18 13:20:05.000000000 +0100 ++++ fsl/config/linux_64-gcc4.8/systemvars.mk 2017-05-22 15:09:39.988913330 +0200 +@@ -8,7 +8,7 @@ + CP = /bin/cp + MV = /bin/mv + INSTALL = install -p +-TCLSH = ${FSLDIR}/bin/fsltclsh ++TCLSH = tclsh + RANLIB = echo + + FSLML = ${FSLDIR}/bin/fslml +@@ -18,9 +18,9 @@ + # Compiler dependent variables - + -CC = gcc -CXX = c++ +-CXX11 = scl enable devtoolset-2 -- c++ +CC := ${CC} +CXX := ${CXX} - CXX11 = scl enable devtoolset-2 -- c++ ++CXX11 = ${CXX} -std=c++11 CSTATICFLAGS = -static CXXSTATICFLAGS = -static -@@ -30,7 +30,7 @@ - + +@@ -30,16 +30,16 @@ + DEPENDFLAGS = -MM - + -OPTFLAGS = -g -O3 -fexpensive-optimizations ${ARCHFLAGS} -+OPTFLAGS := ${CFLAGS} ${ARCHFLAGS} -wd803 ++OPTFLAGS := ${OPTFLAGS} ${ARCHFLAGS} -wd803 MACHDBGFLAGS = -g GNU_ANSI_FLAGS = -Wall -ansi -pedantic -Wno-long-long SGI_ANSI_FLAGS = -ansi -fullwarn -Only in fsl/config/linux_64-gcc4.4: systemvars.mk.orig -Only in fsl/config/linux_64-gcc4.4: systemvars.mk.rej -diff -ur fsl.orig/config/sparc-solaris2.8-gcc2.95/systemvars.mk fsl/config/sparc-solaris2.8-gcc2.95/systemvars.mk ---- fsl.orig/config/sparc-solaris2.8-gcc2.95/systemvars.mk 2007-07-13 13:00:21.000000000 +0200 -+++ fsl/config/sparc-solaris2.8-gcc2.95/systemvars.mk 2017-05-18 13:54:40.448975885 +0200 -@@ -5,14 +5,14 @@ - - # Compiler dependent variables - --CC = gcc --CXX = c++ -+CC := ${CC} -+CXX := ${CXX} - - ARCHFLAGS = -mv8 -ffast-math -fomit-frame-pointer - - DEPENDFLAGS = -MM - --OPTFLAGS = -O6 -fexpensive-optimizations ${ARCHFLAGS} -+OPTFLAGS := ${CFLAGS} ${ARCHFLAGS} -wd803 - MACHDBGFLAGS = - GNU_ANSI_FLAGS = -Wall -ansi -pedantic - SGI_ANSI_FLAGS = -ansi -fullwarn -Only in fsl/config/sparc-solaris2.8-gcc2.95: systemvars.mk.orig -diff -ur fsl.orig/config/sparc-solaris2.9-gcc2.95/systemvars.mk fsl/config/sparc-solaris2.9-gcc2.95/systemvars.mk ---- fsl.orig/config/sparc-solaris2.9-gcc2.95/systemvars.mk 2007-07-13 13:00:21.000000000 +0200 -+++ fsl/config/sparc-solaris2.9-gcc2.95/systemvars.mk 2017-05-18 13:54:40.448975885 +0200 -@@ -5,14 +5,14 @@ - - # Compiler dependent variables - --CC = gcc --CXX = c++ -+CC := ${CC} -+CXX := ${CXX} - - ARCHFLAGS = -mv8 -ffast-math -fomit-frame-pointer - ARCHLDFLAGS = -static - DEPENDFLAGS = -MM - --OPTFLAGS = -O6 -fexpensive-optimizations ${ARCHFLAGS} -+OPTFLAGS := ${CFLAGS} ${ARCHFLAGS} -wd803 - MACHDBGFLAGS = - GNU_ANSI_FLAGS = -Wall -ansi -pedantic - SGI_ANSI_FLAGS = -ansi -fullwarn -Only in fsl/config/sparc-solaris2.9-gcc2.95: systemvars.mk.orig + ANSI_FLAGS = ${GNU_ANSI_FLAGS} + + # CUDA development environment +-CUDA_INSTALLATION = /opt/cuda-7.5 ++CUDA_INSTALLATION = ${EBROOTCUDA} + GENCODE_FLAGS = $(shell ${FSLDIR}/config/common/supportedGencodes.sh ${CUDA_INSTALLATION}) + LIB_CUDA = ${CUDA_INSTALLATION}/lib64 + INC_CUDA = ${CUDA_INSTALLATION}/include + NVCC = ${CUDA_INSTALLATION}/bin/nvcc +-NVCC11=scl enable devtoolset-2 -- ${CUDA_INSTALLATION}/bin/nvcc ++NVCC11= ${CUDA_INSTALLATION}/bin/nvcc +diff -ur fsl.orig/etc/fslconf/fsl.csh fsl/etc/fslconf/fsl.csh +--- fsl.orig/etc/fslconf/fsl.csh 2014-05-19 16:54:10.000000000 +0200 ++++ fsl/etc/fslconf/fsl.csh 2017-05-22 14:31:34.251256565 +0200 +@@ -25,7 +25,7 @@ + # The following variables specify paths for programs and can be changed + # or replaced by different programs ( e.g. FSLDISPLAY=open for MacOSX) + +-setenv FSLTCLSH $FSLDIR/bin/fsltclsh ++setenv FSLTCLSH tclsh + setenv FSLWISH $FSLDIR/bin/fslwish + + # The following variables are used for running code in parallel across +diff -ur fsl.orig/etc/fslconf/fsl-devel.sh fsl/etc/fslconf/fsl-devel.sh +--- fsl.orig/etc/fslconf/fsl-devel.sh 2014-05-19 16:54:10.000000000 +0200 ++++ fsl/etc/fslconf/fsl-devel.sh 2017-05-22 14:31:41.437318420 +0200 +@@ -26,7 +26,7 @@ + # The following variables specify paths for programs and can be changed + # or replaced by different programs ( e.g. FSLDISPLAY=open for MacOSX) + +-FSLTCLSH=$FSLDIR/bin/fsltclsh ++FSLTCLSH=tclsh + FSLWISH=$FSLDIR/bin/fslwish + + export FSLTCLSH FSLWISH +diff -ur fsl.orig/etc/fslconf/fsl.sh fsl/etc/fslconf/fsl.sh +--- fsl.orig/etc/fslconf/fsl.sh 2014-05-19 16:54:10.000000000 +0200 ++++ fsl/etc/fslconf/fsl.sh 2017-05-22 14:31:28.729209032 +0200 +@@ -26,7 +26,7 @@ + # The following variables specify paths for programs and can be changed + # or replaced by different programs ( e.g. FSLDISPLAY=open for MacOSX) + +-FSLTCLSH=$FSLDIR/bin/fsltclsh ++FSLTCLSH=tclsh + FSLWISH=$FSLDIR/bin/fslwish + + export FSLTCLSH FSLWISH +diff -ur fsl.orig/extras/src/libxml++-2.34.0/libxml++/io/istreamparserinputbuffer.cc fsl/extras/src/libxml++-2.34.0/libxml++/io/istreamparserinputbuffer.cc +--- fsl.orig/extras/src/libxml++-2.34.0/libxml++/io/istreamparserinputbuffer.cc 2010-12-15 11:41:27.000000000 +0100 ++++ fsl/extras/src/libxml++-2.34.0/libxml++/io/istreamparserinputbuffer.cc 2017-05-22 15:01:50.430868138 +0200 +@@ -39,6 +39,6 @@ + + bool IStreamParserInputBuffer::do_close() + { +- return input_; ++ return static_cast(input_); + } + } +diff -ur fsl.orig/extras/src/libxml++-2.34.0/libxml++/io/ostreamoutputbuffer.cc fsl/extras/src/libxml++-2.34.0/libxml++/io/ostreamoutputbuffer.cc +--- fsl.orig/extras/src/libxml++-2.34.0/libxml++/io/ostreamoutputbuffer.cc 2010-12-15 11:41:27.000000000 +0100 ++++ fsl/extras/src/libxml++-2.34.0/libxml++/io/ostreamoutputbuffer.cc 2017-05-22 15:01:50.431868146 +0200 +@@ -29,13 +29,13 @@ + // here we rely on the ostream implicit conversion to boolean, to know if the stream can be used and/or if the write succeded. + if(output_) + output_.write(buffer, len); +- return output_; ++ return static_cast(output_); + } + + bool OStreamOutputBuffer::do_close() + { + if(output_) + output_.flush(); +- return output_; ++ return static_cast(output_); + } + } diff -ur fsl.orig/src/film/Makefile fsl/src/film/Makefile --- fsl.orig/src/film/Makefile 2017-04-20 17:01:43.000000000 +0200 -+++ fsl/src/film/Makefile 2017-05-18 13:54:40.448975885 +0200 ++++ fsl/src/film/Makefile 2017-05-22 14:26:37.820705464 +0200 @@ -28,7 +28,7 @@ ${CXX} ${CXXFLAGS} ${LDFLAGS} -o $@ ${OBJS} ftoz.o ${LIBS} - + film_gls:${OBJS} film_gls.o - ${CXX} ${CXXFLAGS} ${LDFLAGS} -o $@ ${OBJS} film_gls.o ${LIBS} -l giftiio + ${CXX} ${CXXFLAGS} ${LDFLAGS} -o $@ ${OBJS} film_gls.o ${LIBS} -lgiftiio - + film_gls_res:${OBJS} film_gls_res.o ${CXX} ${CXXFLAGS} ${LDFLAGS} -o $@ ${OBJS} film_gls_res.o ${LIBS} Only in fsl/src/film: Makefile.orig diff -ur fsl.orig/src/libmeshutils/Makefile fsl/src/libmeshutils/Makefile --- fsl.orig/src/libmeshutils/Makefile 2012-07-23 15:25:20.000000000 +0200 -+++ fsl/src/libmeshutils/Makefile 2017-05-18 13:54:40.448975885 +0200 ++++ fsl/src/libmeshutils/Makefile 2017-05-22 14:26:37.820705464 +0200 @@ -3,7 +3,7 @@ - + PROJNAME = meshUtils - + -LD_LIBRARY_PATH=${FSLDIR}/lib +#LD_LIBRARY_PATH=${FSLDIR}/lib - - USRINCFLAGS = -I${INC_NEWMAT} -I${INC_ZLIB} -I${INC_PROB} -I${INC_BOOST} + + USRINCFLAGS = -I${INC_NEWMAT} -I${INC_ZLIB} -I${INC_PROB} -I${INC_BOOST} USRLDFLAGS = -L${LIB_PROB} -L${LIB_NEWMAT} -L${LIB_ZLIB} Only in fsl/src/libmeshutils: Makefile.orig diff -ur fsl.orig/src/melodic/Makefile fsl/src/melodic/Makefile --- fsl.orig/src/melodic/Makefile 2016-09-01 17:24:32.000000000 +0200 -+++ fsl/src/melodic/Makefile 2017-05-18 13:54:40.448975885 +0200 ++++ fsl/src/melodic/Makefile 2017-05-22 14:26:37.820705464 +0200 @@ -3,7 +3,7 @@ include ${FSLCONFDIR}/default.mk - + OPTFLAGS = -O3 -Wno-deprecated -ggdb -OPTFLAGS_alphaev6-dec-osf5.0-gcc2.95.2 = -O3 -mieee -mfp-trap-mode=sui +#OPTFLAGS_alphaev6-dec-osf5.0-gcc2.95.2 = -O3 -mieee -mfp-trap-mode=sui - + PROJNAME = melodic - + Only in fsl/src/melodic: Makefile.orig +diff -ur fsl.orig/src/mist-clean/Makefile fsl/src/mist-clean/Makefile +--- fsl.orig/src/mist-clean/Makefile 2017-04-20 14:17:54.000000000 +0200 ++++ fsl/src/mist-clean/Makefile 2017-05-23 16:14:14.034077875 +0200 +@@ -2,15 +2,15 @@ + + NLOPT_INC = ${FSLEXTINC} + NLOPT_LIB = ${FSLEXTLIB} +-SQLITE_INC = ${FSLEXTINC}/libsqlite +-SQLITE_LIB = ${FSLEXTLIB} ++SQLITE_INC = ${EBROOTSQLITE}/include ++SQLITE_LIB = ${EBROOTSQLITE}/lib + + PROJNAME = mist + + XFILES = mist/mist + SCRIPTS = bin/mist_1_train bin/mist_2_fit bin/mist_FA_reg bin/mist_display bin/mist_mesh_utils + +-USRCXXFLAGS = -std=c++11 ++USRCXXFLAGS = -std=c++11 -DBOOST_LOG_DYN_LINK + USRINCFLAGS = -I${FSLDIR}/include/newimage -I${INC_NEWMAT} -I${INC_ZLIB} -I${INC_GDC} -I${INC_GD} -I${SQLITE_INC} -I${NLOPT_INC} -I${VTKDIR_INC} -Icommon + USRLDFLAGS = -L${LIB_NEWMAT} -L${LIB_ZLIB} -L${LIB_BOOST} -L${LIB_GDC} -L${LIB_GD} -L${NLOPT_LIB} -L${VTKDIR_LIB} + diff --git a/easybuild/easyconfigs/g/GLibmm/GLibmm-2.53.1.1-intel-2017a.eb b/easybuild/easyconfigs/g/GLibmm/GLibmm-2.53.1.1-intel-2017a.eb deleted file mode 100644 index b9e19ec518..0000000000 --- a/easybuild/easyconfigs/g/GLibmm/GLibmm-2.53.1.1-intel-2017a.eb +++ /dev/null @@ -1,24 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'GLibmm' -version = '2.53.1.1' - -homepage = 'http://www.gtk.org/' -description = """GLib is one of the base libraries of the GTK+ project""" - -toolchain = {'name': 'intel', 'version': '2017a'} -toolchainopts = {'optarch': True, 'pic': True} - -source_urls = ['http://ftp.gnome.org/pub/gnome/sources/glibmm/%(version_major_minor)s/'] -sources = ['%(namelower)s-%(version)s.tar.xz'] - -dependencies = [ - ('GLib', '2.52.0'), - ('libsigc++', '2.10.0'), -] - -sanity_check_paths = { - 'files': ['lib/libglibmm-2.5.%s' % SHLIB_EXT], - 'dirs': [], -} -moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libsigc++/libsigc++-2.10.0-intel-2017a.eb b/easybuild/easyconfigs/l/libsigc++/libsigc++-2.10.0-intel-2017a.eb deleted file mode 100644 index bb4e33f915..0000000000 --- a/easybuild/easyconfigs/l/libsigc++/libsigc++-2.10.0-intel-2017a.eb +++ /dev/null @@ -1,20 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'libsigc++' -version = '2.10.0' - -homepage = 'http://www.gtk.org/' -description = """The libsigc++ package implements a typesafe callback system for standard C++.""" - -toolchain = {'name': 'intel', 'version': '2017a'} -toolchainopts = {'optarch': True, 'pic': True} - -source_urls = ['http://ftp.gnome.org/pub/gnome/sources/%(name)s/%(version_major_minor)s/'] -sources = ['%(namelower)s-%(version)s.tar.xz'] - -sanity_check_paths = { - 'files': ['lib/libsigc-2.0.%s' % SHLIB_EXT], - 'dirs': [], -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/libxml++/libxml++-2.91.3-intel-2017a.eb b/easybuild/easyconfigs/l/libxml++/libxml++-2.91.3-intel-2017a.eb deleted file mode 100644 index 8e9c13f200..0000000000 --- a/easybuild/easyconfigs/l/libxml++/libxml++-2.91.3-intel-2017a.eb +++ /dev/null @@ -1,24 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'libxml++' -version = '2.91.3' - -homepage = 'http://libxmlplusplus.sourceforge.net' -description = """ libxml++ is a C++ wrapper for the libxml XML parser library. """ - -toolchain = {'name': 'intel', 'version': '2017a'} - -sources = [SOURCE_TAR_XZ] -source_urls = ['http://www.example.com'] - -dependencies = [ - ('libxml2', '2.9.4'), - ('GLibmm', '2.53.1.1'), -] - -sanity_check_paths = { - 'files': [], - 'dirs': ["."] -} - -moduleclass = 'lib' -- GitLab From 2c0d4a6304f7ab97cc7077bb16d508ae81f70386 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 23 May 2017 20:24:16 +0200 Subject: [PATCH 0807/1603] adding easyconfigs: matplotlib-2.0.2-intel-2017a-Python-2.7.13-libpng-1.6.29.eb --- ...intel-2017a-Python-2.7.13-libpng-1.6.29.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.2-intel-2017a-Python-2.7.13-libpng-1.6.29.eb diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.2-intel-2017a-Python-2.7.13-libpng-1.6.29.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.2-intel-2017a-Python-2.7.13-libpng-1.6.29.eb new file mode 100644 index 0000000000..5b2a328b11 --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.2-intel-2017a-Python-2.7.13-libpng-1.6.29.eb @@ -0,0 +1,44 @@ +easyblock = 'Bundle' + +name = 'matplotlib' +version = '2.0.2' +libpng_ver = '1.6.29' +versionsuffix = '-Python-%%(pyver)s-libpng-%s' % libpng_ver + +homepage = 'http://matplotlib.org' +description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of + hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python + and ipython shell, web application servers, and six graphical user interface toolkits.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' + +dependencies = [ + ('Python', '2.7.13'), + ('freetype', '2.7.1', '-libpng-%s' % libpng_ver), +] + +exts_list = [ + ('Cycler', '0.10.0', { + 'modulename': 'cycler', + 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], + 'source_tmpl': 'cycler-%(version)s.tar.gz', + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], + }), +] + +# specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module +full_sanity_check = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +moduleclass = 'vis' -- GitLab From ef5a7c15c0843b4459a249852b5da027ee368a20 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Tue, 23 May 2017 21:47:12 +0200 Subject: [PATCH 0808/1603] Drop testing easyconfig --- .../f/FSL/FSL-5.0.9-intel-2017a.eb | 24 ------------------- 1 file changed, 24 deletions(-) delete mode 100644 easybuild/easyconfigs/f/FSL/FSL-5.0.9-intel-2017a.eb diff --git a/easybuild/easyconfigs/f/FSL/FSL-5.0.9-intel-2017a.eb b/easybuild/easyconfigs/f/FSL/FSL-5.0.9-intel-2017a.eb deleted file mode 100644 index 34a1890fcb..0000000000 --- a/easybuild/easyconfigs/f/FSL/FSL-5.0.9-intel-2017a.eb +++ /dev/null @@ -1,24 +0,0 @@ -name = 'FSL' -version = '5.0.9' - -homepage = 'http://www.fmrib.ox.ac.uk/fsl/' -description = """FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data.""" - -toolchain = {'name': 'intel', 'version': '2017a'} - -source_urls = ["http://www.fmrib.ox.ac.uk/fsldownloads/"] -sources = ['%(namelower)s-%(version)s-sources.tar.gz'] - -patches = [ - 'FSL-%(version)s_makefile_fixes.patch', - 'FSL-%(version)s_missing_lib.patch', - 'FSL_icc_nan-inf_fix.patch', -] - -dependencies = [ - ('freeglut', '3.0.0'), - ('expat', '2.2.0'), - ('zlib', '1.2.11'), -] - -moduleclass = 'bio' -- GitLab From 6dc1b3764473357dfec073a64bbd1ce6d68934e5 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Tue, 23 May 2017 22:17:41 +0200 Subject: [PATCH 0809/1603] Fix patch --- .../f/FSL/FSL-5.0.10_makefile_fixes.patch | 37 ++++++++++++------- 1 file changed, 24 insertions(+), 13 deletions(-) diff --git a/easybuild/easyconfigs/f/FSL/FSL-5.0.10_makefile_fixes.patch b/easybuild/easyconfigs/f/FSL/FSL-5.0.10_makefile_fixes.patch index ca470e4c17..a9d93a90d7 100644 --- a/easybuild/easyconfigs/f/FSL/FSL-5.0.10_makefile_fixes.patch +++ b/easybuild/easyconfigs/f/FSL/FSL-5.0.10_makefile_fixes.patch @@ -2,7 +2,7 @@ # Ward Poelmans diff -ur fsl.orig/config/common/vars.mk fsl/config/common/vars.mk --- fsl.orig/config/common/vars.mk 2016-05-24 17:44:11.000000000 +0200 -+++ fsl/config/common/vars.mk 2017-05-23 10:19:55.325628385 +0200 ++++ fsl/config/common/vars.mk 2017-05-23 22:14:37.138797842 +0200 @@ -24,14 +24,14 @@ USRCFLAGS = USRCXXFLAGS = @@ -22,9 +22,10 @@ diff -ur fsl.orig/config/common/vars.mk fsl/config/common/vars.mk ${AccumulatedIncFlags} HFILES = *.h +Only in fsl/config/common: vars.mk.orig diff -ur fsl.orig/config/generic/systemvars.mk fsl/config/generic/systemvars.mk --- fsl.orig/config/generic/systemvars.mk 2007-07-13 13:00:20.000000000 +0200 -+++ fsl/config/generic/systemvars.mk 2017-05-22 14:26:37.819705455 +0200 ++++ fsl/config/generic/systemvars.mk 2017-05-23 22:14:37.139797850 +0200 @@ -16,8 +16,8 @@ # Compiler dependent variables @@ -45,9 +46,10 @@ diff -ur fsl.orig/config/generic/systemvars.mk fsl/config/generic/systemvars.mk MACHDBGFLAGS = GNU_ANSI_FLAGS = -Wall -ansi -pedantic SGI_ANSI_FLAGS = -ansi -fullwarn +Only in fsl/config/generic: systemvars.mk.orig diff -ur fsl.orig/config/linux_64-gcc4.8/externallibs.mk fsl/config/linux_64-gcc4.8/externallibs.mk --- fsl.orig/config/linux_64-gcc4.8/externallibs.mk 2017-02-18 13:20:05.000000000 +0100 -+++ fsl/config/linux_64-gcc4.8/externallibs.mk 2017-05-23 17:11:51.141583678 +0200 ++++ fsl/config/linux_64-gcc4.8/externallibs.mk 2017-05-23 22:15:51.535436754 +0200 @@ -15,7 +15,7 @@ INC_GDC = ${FSLEXTINC}/libgdc @@ -91,9 +93,11 @@ diff -ur fsl.orig/config/linux_64-gcc4.8/externallibs.mk fsl/config/linux_64-gcc +VTKDIR_INC = ${EBROOTVTK}/include/vtk-7.1 +VTKDIR_LIB = ${EBROOTVTK}/lib +VTKSUFFIX = -7.1 +Only in fsl/config/linux_64-gcc4.8: externallibs.mk.orig +Only in fsl/config/linux_64-gcc4.8: externallibs.mk.rej diff -ur fsl.orig/config/linux_64-gcc4.8/systemvars.mk fsl/config/linux_64-gcc4.8/systemvars.mk --- fsl.orig/config/linux_64-gcc4.8/systemvars.mk 2017-02-18 13:20:05.000000000 +0100 -+++ fsl/config/linux_64-gcc4.8/systemvars.mk 2017-05-22 15:09:39.988913330 +0200 ++++ fsl/config/linux_64-gcc4.8/systemvars.mk 2017-05-23 22:14:37.139797850 +0200 @@ -8,7 +8,7 @@ CP = /bin/cp MV = /bin/mv @@ -136,9 +140,10 @@ diff -ur fsl.orig/config/linux_64-gcc4.8/systemvars.mk fsl/config/linux_64-gcc4. NVCC = ${CUDA_INSTALLATION}/bin/nvcc -NVCC11=scl enable devtoolset-2 -- ${CUDA_INSTALLATION}/bin/nvcc +NVCC11= ${CUDA_INSTALLATION}/bin/nvcc +Only in fsl/config/linux_64-gcc4.8: systemvars.mk.orig diff -ur fsl.orig/etc/fslconf/fsl.csh fsl/etc/fslconf/fsl.csh --- fsl.orig/etc/fslconf/fsl.csh 2014-05-19 16:54:10.000000000 +0200 -+++ fsl/etc/fslconf/fsl.csh 2017-05-22 14:31:34.251256565 +0200 ++++ fsl/etc/fslconf/fsl.csh 2017-05-23 22:14:37.139797850 +0200 @@ -25,7 +25,7 @@ # The following variables specify paths for programs and can be changed # or replaced by different programs ( e.g. FSLDISPLAY=open for MacOSX) @@ -148,9 +153,10 @@ diff -ur fsl.orig/etc/fslconf/fsl.csh fsl/etc/fslconf/fsl.csh setenv FSLWISH $FSLDIR/bin/fslwish # The following variables are used for running code in parallel across +Only in fsl/etc/fslconf: fsl.csh.orig diff -ur fsl.orig/etc/fslconf/fsl-devel.sh fsl/etc/fslconf/fsl-devel.sh --- fsl.orig/etc/fslconf/fsl-devel.sh 2014-05-19 16:54:10.000000000 +0200 -+++ fsl/etc/fslconf/fsl-devel.sh 2017-05-22 14:31:41.437318420 +0200 ++++ fsl/etc/fslconf/fsl-devel.sh 2017-05-23 22:14:37.139797850 +0200 @@ -26,7 +26,7 @@ # The following variables specify paths for programs and can be changed # or replaced by different programs ( e.g. FSLDISPLAY=open for MacOSX) @@ -160,9 +166,10 @@ diff -ur fsl.orig/etc/fslconf/fsl-devel.sh fsl/etc/fslconf/fsl-devel.sh FSLWISH=$FSLDIR/bin/fslwish export FSLTCLSH FSLWISH +Only in fsl/etc/fslconf: fsl-devel.sh.orig diff -ur fsl.orig/etc/fslconf/fsl.sh fsl/etc/fslconf/fsl.sh --- fsl.orig/etc/fslconf/fsl.sh 2014-05-19 16:54:10.000000000 +0200 -+++ fsl/etc/fslconf/fsl.sh 2017-05-22 14:31:28.729209032 +0200 ++++ fsl/etc/fslconf/fsl.sh 2017-05-23 22:14:37.139797850 +0200 @@ -26,7 +26,7 @@ # The following variables specify paths for programs and can be changed # or replaced by different programs ( e.g. FSLDISPLAY=open for MacOSX) @@ -172,9 +179,10 @@ diff -ur fsl.orig/etc/fslconf/fsl.sh fsl/etc/fslconf/fsl.sh FSLWISH=$FSLDIR/bin/fslwish export FSLTCLSH FSLWISH +Only in fsl/etc/fslconf: fsl.sh.orig diff -ur fsl.orig/extras/src/libxml++-2.34.0/libxml++/io/istreamparserinputbuffer.cc fsl/extras/src/libxml++-2.34.0/libxml++/io/istreamparserinputbuffer.cc --- fsl.orig/extras/src/libxml++-2.34.0/libxml++/io/istreamparserinputbuffer.cc 2010-12-15 11:41:27.000000000 +0100 -+++ fsl/extras/src/libxml++-2.34.0/libxml++/io/istreamparserinputbuffer.cc 2017-05-22 15:01:50.430868138 +0200 ++++ fsl/extras/src/libxml++-2.34.0/libxml++/io/istreamparserinputbuffer.cc 2017-05-23 22:14:37.139797850 +0200 @@ -39,6 +39,6 @@ bool IStreamParserInputBuffer::do_close() @@ -183,9 +191,10 @@ diff -ur fsl.orig/extras/src/libxml++-2.34.0/libxml++/io/istreamparserinputbuffe + return static_cast(input_); } } +Only in fsl/extras/src/libxml++-2.34.0/libxml++/io: istreamparserinputbuffer.cc.orig diff -ur fsl.orig/extras/src/libxml++-2.34.0/libxml++/io/ostreamoutputbuffer.cc fsl/extras/src/libxml++-2.34.0/libxml++/io/ostreamoutputbuffer.cc --- fsl.orig/extras/src/libxml++-2.34.0/libxml++/io/ostreamoutputbuffer.cc 2010-12-15 11:41:27.000000000 +0100 -+++ fsl/extras/src/libxml++-2.34.0/libxml++/io/ostreamoutputbuffer.cc 2017-05-22 15:01:50.431868146 +0200 ++++ fsl/extras/src/libxml++-2.34.0/libxml++/io/ostreamoutputbuffer.cc 2017-05-23 22:14:37.139797850 +0200 @@ -29,13 +29,13 @@ // here we rely on the ostream implicit conversion to boolean, to know if the stream can be used and/or if the write succeded. if(output_) @@ -202,9 +211,10 @@ diff -ur fsl.orig/extras/src/libxml++-2.34.0/libxml++/io/ostreamoutputbuffer.cc + return static_cast(output_); } } +Only in fsl/extras/src/libxml++-2.34.0/libxml++/io: ostreamoutputbuffer.cc.orig diff -ur fsl.orig/src/film/Makefile fsl/src/film/Makefile --- fsl.orig/src/film/Makefile 2017-04-20 17:01:43.000000000 +0200 -+++ fsl/src/film/Makefile 2017-05-22 14:26:37.820705464 +0200 ++++ fsl/src/film/Makefile 2017-05-23 22:14:37.139797850 +0200 @@ -28,7 +28,7 @@ ${CXX} ${CXXFLAGS} ${LDFLAGS} -o $@ ${OBJS} ftoz.o ${LIBS} @@ -217,7 +227,7 @@ diff -ur fsl.orig/src/film/Makefile fsl/src/film/Makefile Only in fsl/src/film: Makefile.orig diff -ur fsl.orig/src/libmeshutils/Makefile fsl/src/libmeshutils/Makefile --- fsl.orig/src/libmeshutils/Makefile 2012-07-23 15:25:20.000000000 +0200 -+++ fsl/src/libmeshutils/Makefile 2017-05-22 14:26:37.820705464 +0200 ++++ fsl/src/libmeshutils/Makefile 2017-05-23 22:14:37.140797859 +0200 @@ -3,7 +3,7 @@ PROJNAME = meshUtils @@ -230,7 +240,7 @@ diff -ur fsl.orig/src/libmeshutils/Makefile fsl/src/libmeshutils/Makefile Only in fsl/src/libmeshutils: Makefile.orig diff -ur fsl.orig/src/melodic/Makefile fsl/src/melodic/Makefile --- fsl.orig/src/melodic/Makefile 2016-09-01 17:24:32.000000000 +0200 -+++ fsl/src/melodic/Makefile 2017-05-22 14:26:37.820705464 +0200 ++++ fsl/src/melodic/Makefile 2017-05-23 22:14:37.140797859 +0200 @@ -3,7 +3,7 @@ include ${FSLCONFDIR}/default.mk @@ -243,7 +253,7 @@ diff -ur fsl.orig/src/melodic/Makefile fsl/src/melodic/Makefile Only in fsl/src/melodic: Makefile.orig diff -ur fsl.orig/src/mist-clean/Makefile fsl/src/mist-clean/Makefile --- fsl.orig/src/mist-clean/Makefile 2017-04-20 14:17:54.000000000 +0200 -+++ fsl/src/mist-clean/Makefile 2017-05-23 16:14:14.034077875 +0200 ++++ fsl/src/mist-clean/Makefile 2017-05-23 22:14:37.140797859 +0200 @@ -2,15 +2,15 @@ NLOPT_INC = ${FSLEXTINC} @@ -263,3 +273,4 @@ diff -ur fsl.orig/src/mist-clean/Makefile fsl/src/mist-clean/Makefile USRINCFLAGS = -I${FSLDIR}/include/newimage -I${INC_NEWMAT} -I${INC_ZLIB} -I${INC_GDC} -I${INC_GD} -I${SQLITE_INC} -I${NLOPT_INC} -I${VTKDIR_INC} -Icommon USRLDFLAGS = -L${LIB_NEWMAT} -L${LIB_ZLIB} -L${LIB_BOOST} -L${LIB_GDC} -L${LIB_GD} -L${NLOPT_LIB} -L${VTKDIR_LIB} +Only in fsl/src/mist-clean: Makefile.orig -- GitLab From 687e00080e43440cf4f3a4b7c2921812f6ad85da Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 24 May 2017 08:06:32 +0200 Subject: [PATCH 0810/1603] adding easyconfigs: xarray-0.9.5-intel-2017a-Python-2.7.13.eb --- .../xarray-0.9.5-intel-2017a-Python-2.7.13.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/x/xarray/xarray-0.9.5-intel-2017a-Python-2.7.13.eb diff --git a/easybuild/easyconfigs/x/xarray/xarray-0.9.5-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/x/xarray/xarray-0.9.5-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..10d17b9e1f --- /dev/null +++ b/easybuild/easyconfigs/x/xarray/xarray-0.9.5-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'xarray' +version = '0.9.5' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/pydata/xarray' +description = """xarray (formerly xray) is an open source project and Python package that aims to bring + the labeled data power of pandas to the physical sciences, by providing N-dimensional variants of the + core pandas data structures.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [('Python', '2.7.13')] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'data' -- GitLab From 7f12474b3edb909a36dffe5c61e7a601068587aa Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 24 May 2017 08:35:56 +0200 Subject: [PATCH 0811/1603] also copy README for GapFiller --- .../easyconfigs/g/GapFiller/GapFiller-2.1.1-intel-2017a.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GapFiller/GapFiller-2.1.1-intel-2017a.eb b/easybuild/easyconfigs/g/GapFiller/GapFiller-2.1.1-intel-2017a.eb index 4e408b39dd..28fa1604ac 100644 --- a/easybuild/easyconfigs/g/GapFiller/GapFiller-2.1.1-intel-2017a.eb +++ b/easybuild/easyconfigs/g/GapFiller/GapFiller-2.1.1-intel-2017a.eb @@ -22,8 +22,10 @@ buildopts = 'bin_PROGRAMS=GapFiller ' buildopts += 'GapFiller_CFLAGS="$CFLAGS $LDFLAGS -lz" GapFiller_CXXFLAGS="$CXXFLAGS $LDFLAGS -lz"' installopts = 'bin_PROGRAMS=GapFiller ' +postinstallcmds = ["cp -a README %(installdir)s"] + sanity_check_paths = { - 'files': ['bin/GapFiller'], + 'files': ['bin/GapFiller', 'README'], 'dirs': [], } -- GitLab From 2699a28f353017f29796c94ff951a0b103b5eea4 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 24 May 2017 09:50:09 +0200 Subject: [PATCH 0812/1603] Fix patch again --- .../f/FSL/FSL-5.0.10_makefile_fixes.patch | 69 +++++++------------ 1 file changed, 23 insertions(+), 46 deletions(-) diff --git a/easybuild/easyconfigs/f/FSL/FSL-5.0.10_makefile_fixes.patch b/easybuild/easyconfigs/f/FSL/FSL-5.0.10_makefile_fixes.patch index a9d93a90d7..6a7fdafd84 100644 --- a/easybuild/easyconfigs/f/FSL/FSL-5.0.10_makefile_fixes.patch +++ b/easybuild/easyconfigs/f/FSL/FSL-5.0.10_makefile_fixes.patch @@ -2,7 +2,7 @@ # Ward Poelmans diff -ur fsl.orig/config/common/vars.mk fsl/config/common/vars.mk --- fsl.orig/config/common/vars.mk 2016-05-24 17:44:11.000000000 +0200 -+++ fsl/config/common/vars.mk 2017-05-23 22:14:37.138797842 +0200 ++++ fsl/config/common/vars.mk 2017-05-24 09:38:05.912369589 +0200 @@ -24,14 +24,14 @@ USRCFLAGS = USRCXXFLAGS = @@ -22,10 +22,9 @@ diff -ur fsl.orig/config/common/vars.mk fsl/config/common/vars.mk ${AccumulatedIncFlags} HFILES = *.h -Only in fsl/config/common: vars.mk.orig diff -ur fsl.orig/config/generic/systemvars.mk fsl/config/generic/systemvars.mk --- fsl.orig/config/generic/systemvars.mk 2007-07-13 13:00:20.000000000 +0200 -+++ fsl/config/generic/systemvars.mk 2017-05-23 22:14:37.139797850 +0200 ++++ fsl/config/generic/systemvars.mk 2017-05-24 09:38:05.912369589 +0200 @@ -16,8 +16,8 @@ # Compiler dependent variables @@ -42,14 +41,13 @@ diff -ur fsl.orig/config/generic/systemvars.mk fsl/config/generic/systemvars.mk DEPENDFLAGS = -MM -OPTFLAGS = -O3 -fexpensive-optimizations ${ARCHFLAGS} -+OPTFLAGS := ${CFLAGS} ${ARCHFLAGS} -wd803 ++OPTFLAGS := ${CFLAGS} ${ARCHFLAGS} MACHDBGFLAGS = GNU_ANSI_FLAGS = -Wall -ansi -pedantic SGI_ANSI_FLAGS = -ansi -fullwarn -Only in fsl/config/generic: systemvars.mk.orig diff -ur fsl.orig/config/linux_64-gcc4.8/externallibs.mk fsl/config/linux_64-gcc4.8/externallibs.mk --- fsl.orig/config/linux_64-gcc4.8/externallibs.mk 2017-02-18 13:20:05.000000000 +0100 -+++ fsl/config/linux_64-gcc4.8/externallibs.mk 2017-05-23 22:15:51.535436754 +0200 ++++ fsl/config/linux_64-gcc4.8/externallibs.mk 2017-05-24 09:45:04.058907856 +0200 @@ -15,7 +15,7 @@ INC_GDC = ${FSLEXTINC}/libgdc @@ -82,22 +80,22 @@ diff -ur fsl.orig/config/linux_64-gcc4.8/externallibs.mk fsl/config/linux_64-gcc # FFTW3 library -LIB_FFTW3 = ${FSLEXTLIB} -INC_FFTW3 = ${FSLEXTINC}/fftw3 -+LIB_FFTW3 = ${EBVARFFTW_LIB_DIR} -+INC_FFTW3 = ${EBVARFFTW_INC_DIR} - - # VTK library +- +-# VTK library -VTKDIR_INC = /home/fs0/cowboy/var/caper_linux_64-gcc4.4/VTK7/include/vtk-7.0 -VTKDIR_LIB = /home/fs0/cowboy/var/caper_linux_64-gcc4.4/VTK7/lib -VTKSUFFIX = -7.0 \ No newline at end of file -+VTKDIR_INC = ${EBROOTVTK}/include/vtk-7.1 ++LIB_FFTW3 = ${EBVARFFTW_LIB_DIR} ++INC_FFTW3 = ${EBVARFFTW_INC_DIR} ++ ++ # VTK library ++VTKDIR_INC = ${EBROOTVTK}/include/vtk-`echo $EBVERSIONVTK | cut -f1-2 -d.` +VTKDIR_LIB = ${EBROOTVTK}/lib -+VTKSUFFIX = -7.1 -Only in fsl/config/linux_64-gcc4.8: externallibs.mk.orig -Only in fsl/config/linux_64-gcc4.8: externallibs.mk.rej ++VTKSUFFIX = -`echo $EBVERSIONVTK | cut -f1-2 -d.` diff -ur fsl.orig/config/linux_64-gcc4.8/systemvars.mk fsl/config/linux_64-gcc4.8/systemvars.mk --- fsl.orig/config/linux_64-gcc4.8/systemvars.mk 2017-02-18 13:20:05.000000000 +0100 -+++ fsl/config/linux_64-gcc4.8/systemvars.mk 2017-05-23 22:14:37.139797850 +0200 ++++ fsl/config/linux_64-gcc4.8/systemvars.mk 2017-05-24 09:38:05.912369589 +0200 @@ -8,7 +8,7 @@ CP = /bin/cp MV = /bin/mv @@ -125,7 +123,7 @@ diff -ur fsl.orig/config/linux_64-gcc4.8/systemvars.mk fsl/config/linux_64-gcc4. DEPENDFLAGS = -MM -OPTFLAGS = -g -O3 -fexpensive-optimizations ${ARCHFLAGS} -+OPTFLAGS := ${OPTFLAGS} ${ARCHFLAGS} -wd803 ++OPTFLAGS := ${OPTFLAGS} ${ARCHFLAGS} MACHDBGFLAGS = -g GNU_ANSI_FLAGS = -Wall -ansi -pedantic -Wno-long-long SGI_ANSI_FLAGS = -ansi -fullwarn @@ -140,10 +138,9 @@ diff -ur fsl.orig/config/linux_64-gcc4.8/systemvars.mk fsl/config/linux_64-gcc4. NVCC = ${CUDA_INSTALLATION}/bin/nvcc -NVCC11=scl enable devtoolset-2 -- ${CUDA_INSTALLATION}/bin/nvcc +NVCC11= ${CUDA_INSTALLATION}/bin/nvcc -Only in fsl/config/linux_64-gcc4.8: systemvars.mk.orig diff -ur fsl.orig/etc/fslconf/fsl.csh fsl/etc/fslconf/fsl.csh --- fsl.orig/etc/fslconf/fsl.csh 2014-05-19 16:54:10.000000000 +0200 -+++ fsl/etc/fslconf/fsl.csh 2017-05-23 22:14:37.139797850 +0200 ++++ fsl/etc/fslconf/fsl.csh 2017-05-24 09:38:05.912369589 +0200 @@ -25,7 +25,7 @@ # The following variables specify paths for programs and can be changed # or replaced by different programs ( e.g. FSLDISPLAY=open for MacOSX) @@ -153,10 +150,9 @@ diff -ur fsl.orig/etc/fslconf/fsl.csh fsl/etc/fslconf/fsl.csh setenv FSLWISH $FSLDIR/bin/fslwish # The following variables are used for running code in parallel across -Only in fsl/etc/fslconf: fsl.csh.orig diff -ur fsl.orig/etc/fslconf/fsl-devel.sh fsl/etc/fslconf/fsl-devel.sh --- fsl.orig/etc/fslconf/fsl-devel.sh 2014-05-19 16:54:10.000000000 +0200 -+++ fsl/etc/fslconf/fsl-devel.sh 2017-05-23 22:14:37.139797850 +0200 ++++ fsl/etc/fslconf/fsl-devel.sh 2017-05-24 09:38:05.912369589 +0200 @@ -26,7 +26,7 @@ # The following variables specify paths for programs and can be changed # or replaced by different programs ( e.g. FSLDISPLAY=open for MacOSX) @@ -166,10 +162,9 @@ diff -ur fsl.orig/etc/fslconf/fsl-devel.sh fsl/etc/fslconf/fsl-devel.sh FSLWISH=$FSLDIR/bin/fslwish export FSLTCLSH FSLWISH -Only in fsl/etc/fslconf: fsl-devel.sh.orig diff -ur fsl.orig/etc/fslconf/fsl.sh fsl/etc/fslconf/fsl.sh --- fsl.orig/etc/fslconf/fsl.sh 2014-05-19 16:54:10.000000000 +0200 -+++ fsl/etc/fslconf/fsl.sh 2017-05-23 22:14:37.139797850 +0200 ++++ fsl/etc/fslconf/fsl.sh 2017-05-24 09:38:05.912369589 +0200 @@ -26,7 +26,7 @@ # The following variables specify paths for programs and can be changed # or replaced by different programs ( e.g. FSLDISPLAY=open for MacOSX) @@ -179,10 +174,9 @@ diff -ur fsl.orig/etc/fslconf/fsl.sh fsl/etc/fslconf/fsl.sh FSLWISH=$FSLDIR/bin/fslwish export FSLTCLSH FSLWISH -Only in fsl/etc/fslconf: fsl.sh.orig diff -ur fsl.orig/extras/src/libxml++-2.34.0/libxml++/io/istreamparserinputbuffer.cc fsl/extras/src/libxml++-2.34.0/libxml++/io/istreamparserinputbuffer.cc --- fsl.orig/extras/src/libxml++-2.34.0/libxml++/io/istreamparserinputbuffer.cc 2010-12-15 11:41:27.000000000 +0100 -+++ fsl/extras/src/libxml++-2.34.0/libxml++/io/istreamparserinputbuffer.cc 2017-05-23 22:14:37.139797850 +0200 ++++ fsl/extras/src/libxml++-2.34.0/libxml++/io/istreamparserinputbuffer.cc 2017-05-24 09:38:05.913369598 +0200 @@ -39,6 +39,6 @@ bool IStreamParserInputBuffer::do_close() @@ -191,10 +185,9 @@ diff -ur fsl.orig/extras/src/libxml++-2.34.0/libxml++/io/istreamparserinputbuffe + return static_cast(input_); } } -Only in fsl/extras/src/libxml++-2.34.0/libxml++/io: istreamparserinputbuffer.cc.orig diff -ur fsl.orig/extras/src/libxml++-2.34.0/libxml++/io/ostreamoutputbuffer.cc fsl/extras/src/libxml++-2.34.0/libxml++/io/ostreamoutputbuffer.cc --- fsl.orig/extras/src/libxml++-2.34.0/libxml++/io/ostreamoutputbuffer.cc 2010-12-15 11:41:27.000000000 +0100 -+++ fsl/extras/src/libxml++-2.34.0/libxml++/io/ostreamoutputbuffer.cc 2017-05-23 22:14:37.139797850 +0200 ++++ fsl/extras/src/libxml++-2.34.0/libxml++/io/ostreamoutputbuffer.cc 2017-05-24 09:38:05.913369598 +0200 @@ -29,13 +29,13 @@ // here we rely on the ostream implicit conversion to boolean, to know if the stream can be used and/or if the write succeded. if(output_) @@ -211,10 +204,9 @@ diff -ur fsl.orig/extras/src/libxml++-2.34.0/libxml++/io/ostreamoutputbuffer.cc + return static_cast(output_); } } -Only in fsl/extras/src/libxml++-2.34.0/libxml++/io: ostreamoutputbuffer.cc.orig diff -ur fsl.orig/src/film/Makefile fsl/src/film/Makefile --- fsl.orig/src/film/Makefile 2017-04-20 17:01:43.000000000 +0200 -+++ fsl/src/film/Makefile 2017-05-23 22:14:37.139797850 +0200 ++++ fsl/src/film/Makefile 2017-05-24 09:38:05.913369598 +0200 @@ -28,7 +28,7 @@ ${CXX} ${CXXFLAGS} ${LDFLAGS} -o $@ ${OBJS} ftoz.o ${LIBS} @@ -224,10 +216,9 @@ diff -ur fsl.orig/src/film/Makefile fsl/src/film/Makefile film_gls_res:${OBJS} film_gls_res.o ${CXX} ${CXXFLAGS} ${LDFLAGS} -o $@ ${OBJS} film_gls_res.o ${LIBS} -Only in fsl/src/film: Makefile.orig diff -ur fsl.orig/src/libmeshutils/Makefile fsl/src/libmeshutils/Makefile --- fsl.orig/src/libmeshutils/Makefile 2012-07-23 15:25:20.000000000 +0200 -+++ fsl/src/libmeshutils/Makefile 2017-05-23 22:14:37.140797859 +0200 ++++ fsl/src/libmeshutils/Makefile 2017-05-24 09:38:05.913369598 +0200 @@ -3,7 +3,7 @@ PROJNAME = meshUtils @@ -237,23 +228,9 @@ diff -ur fsl.orig/src/libmeshutils/Makefile fsl/src/libmeshutils/Makefile USRINCFLAGS = -I${INC_NEWMAT} -I${INC_ZLIB} -I${INC_PROB} -I${INC_BOOST} USRLDFLAGS = -L${LIB_PROB} -L${LIB_NEWMAT} -L${LIB_ZLIB} -Only in fsl/src/libmeshutils: Makefile.orig -diff -ur fsl.orig/src/melodic/Makefile fsl/src/melodic/Makefile ---- fsl.orig/src/melodic/Makefile 2016-09-01 17:24:32.000000000 +0200 -+++ fsl/src/melodic/Makefile 2017-05-23 22:14:37.140797859 +0200 -@@ -3,7 +3,7 @@ - include ${FSLCONFDIR}/default.mk - - OPTFLAGS = -O3 -Wno-deprecated -ggdb --OPTFLAGS_alphaev6-dec-osf5.0-gcc2.95.2 = -O3 -mieee -mfp-trap-mode=sui -+#OPTFLAGS_alphaev6-dec-osf5.0-gcc2.95.2 = -O3 -mieee -mfp-trap-mode=sui - - PROJNAME = melodic - -Only in fsl/src/melodic: Makefile.orig diff -ur fsl.orig/src/mist-clean/Makefile fsl/src/mist-clean/Makefile --- fsl.orig/src/mist-clean/Makefile 2017-04-20 14:17:54.000000000 +0200 -+++ fsl/src/mist-clean/Makefile 2017-05-23 22:14:37.140797859 +0200 ++++ fsl/src/mist-clean/Makefile 2017-05-24 09:38:05.913369598 +0200 @@ -2,15 +2,15 @@ NLOPT_INC = ${FSLEXTINC} @@ -269,8 +246,8 @@ diff -ur fsl.orig/src/mist-clean/Makefile fsl/src/mist-clean/Makefile SCRIPTS = bin/mist_1_train bin/mist_2_fit bin/mist_FA_reg bin/mist_display bin/mist_mesh_utils -USRCXXFLAGS = -std=c++11 +# EB: needed to correctly (dynamically) link with the Boost log libs +USRCXXFLAGS = -std=c++11 -DBOOST_LOG_DYN_LINK USRINCFLAGS = -I${FSLDIR}/include/newimage -I${INC_NEWMAT} -I${INC_ZLIB} -I${INC_GDC} -I${INC_GD} -I${SQLITE_INC} -I${NLOPT_INC} -I${VTKDIR_INC} -Icommon USRLDFLAGS = -L${LIB_NEWMAT} -L${LIB_ZLIB} -L${LIB_BOOST} -L${LIB_GDC} -L${LIB_GD} -L${NLOPT_LIB} -L${VTKDIR_LIB} -Only in fsl/src/mist-clean: Makefile.orig -- GitLab From 50598e882b5c1a267ef293df6f536682fafddb26 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 24 May 2017 09:51:17 +0200 Subject: [PATCH 0813/1603] Authorship patch --- easybuild/easyconfigs/f/FSL/FSL-5.0.10_build_extras.patch | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/f/FSL/FSL-5.0.10_build_extras.patch b/easybuild/easyconfigs/f/FSL/FSL-5.0.10_build_extras.patch index d545a66031..15bc9a7922 100644 --- a/easybuild/easyconfigs/f/FSL/FSL-5.0.10_build_extras.patch +++ b/easybuild/easyconfigs/f/FSL/FSL-5.0.10_build_extras.patch @@ -1,4 +1,5 @@ # only build thing we don't provide with EasyBuild +# Ward Poelmans diff -ur fsl/extras/build fsl.new/extras/build --- fsl/extras/build 2016-11-15 15:30:21.000000000 +0100 +++ fsl.new/extras/build 2017-05-19 15:21:07.321630239 +0200 -- GitLab From d5afd3ccab3e7da38cc41acd8905104c1655024e Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 24 May 2017 09:58:04 +0200 Subject: [PATCH 0814/1603] Final? fix of patch --- .../f/FSL/FSL-5.0.10_makefile_fixes.patch | 94 +++++++++---------- 1 file changed, 47 insertions(+), 47 deletions(-) diff --git a/easybuild/easyconfigs/f/FSL/FSL-5.0.10_makefile_fixes.patch b/easybuild/easyconfigs/f/FSL/FSL-5.0.10_makefile_fixes.patch index 6a7fdafd84..c9f8391467 100644 --- a/easybuild/easyconfigs/f/FSL/FSL-5.0.10_makefile_fixes.patch +++ b/easybuild/easyconfigs/f/FSL/FSL-5.0.10_makefile_fixes.patch @@ -4,42 +4,42 @@ diff -ur fsl.orig/config/common/vars.mk fsl/config/common/vars.mk --- fsl.orig/config/common/vars.mk 2016-05-24 17:44:11.000000000 +0200 +++ fsl/config/common/vars.mk 2017-05-24 09:38:05.912369589 +0200 @@ -24,14 +24,14 @@ - USRCFLAGS = + USRCFLAGS = USRCXXFLAGS = - + -LDFLAGS = ${ARCHLDFLAGS} ${USRLDFLAGS} -L. -L${DEVLIBDIR} -L${LIBDIR} +LDFLAGS = ${EBVARLDFLAGS} ${ARCHLDFLAGS} ${USRLDFLAGS} -L. -L${DEVLIBDIR} -L${LIBDIR} - + -AccumulatedIncFlags = -I${INC_BOOST} ${USRINCFLAGS} -I. -I${DEVINCDIR} -I${INCDIR} +AccumulatedIncFlags = ${EBVARCPPFLAGS} -I${INC_BOOST} ${USRINCFLAGS} -I. -I${DEVINCDIR} -I${INCDIR} - + -CFLAGS = ${ANSI_FLAGS} ${ANSI_CFLAGS} ${DBGFLAGS} ${USEDCSTATICFLAGS} ${USRCFLAGS} ${ARCHFLAGS} ${OPTFLAGS} \ +CFLAGS = ${EBVARCFLAGS} ${ANSI_FLAGS} ${ANSI_CFLAGS} ${DBGFLAGS} ${USEDCSTATICFLAGS} ${USRCFLAGS} ${ARCHFLAGS} ${OPTFLAGS} \ ${AccumulatedIncFlags} - + -CXXFLAGS = ${ANSI_FLAGS} ${ANSI_CXXFLAGS} ${DBGFLAGS} ${USEDCXXSTATICFLAGS} ${USRCXXFLAGS} ${ARCHFLAGS} ${OPTFLAGS} \ +CXXFLAGS = ${EBVARCXXFLAGS} ${ANSI_FLAGS} ${ANSI_CXXFLAGS} ${DBGFLAGS} ${USEDCXXSTATICFLAGS} ${USRCXXFLAGS} ${ARCHFLAGS} ${OPTFLAGS} \ ${AccumulatedIncFlags} - + HFILES = *.h diff -ur fsl.orig/config/generic/systemvars.mk fsl/config/generic/systemvars.mk --- fsl.orig/config/generic/systemvars.mk 2007-07-13 13:00:20.000000000 +0200 +++ fsl/config/generic/systemvars.mk 2017-05-24 09:38:05.912369589 +0200 @@ -16,8 +16,8 @@ - + # Compiler dependent variables - + -CC = gcc -CXX = c++ +CC := ${CC} +CXX := ${CXX} CSTATICFLAGS = -static CXXSTATICFLAGS = -static - + @@ -25,7 +25,7 @@ - + DEPENDFLAGS = -MM - + -OPTFLAGS = -O3 -fexpensive-optimizations ${ARCHFLAGS} +OPTFLAGS := ${CFLAGS} ${ARCHFLAGS} MACHDBGFLAGS = @@ -50,16 +50,16 @@ diff -ur fsl.orig/config/linux_64-gcc4.8/externallibs.mk fsl/config/linux_64-gcc +++ fsl/config/linux_64-gcc4.8/externallibs.mk 2017-05-24 09:45:04.058907856 +0200 @@ -15,7 +15,7 @@ INC_GDC = ${FSLEXTINC}/libgdc - + # LIBXML2 library -INC_XML2 = ${FSLEXTINC}/libxml2 +INC_XML2 = ${EBROOTLIBXML2} - + # LIBXML++ library INC_XML++ = ${FSLEXTINC}/libxml++-2.6 @@ -49,12 +49,12 @@ INC_ZLIB = /usr/include - + # BOOST library -BOOSTDIR = ${FSLEXTINC}/boost -LIB_BOOST = ${BOOSTDIR} @@ -67,28 +67,28 @@ diff -ur fsl.orig/config/linux_64-gcc4.8/externallibs.mk fsl/config/linux_64-gcc +BOOSTDIR = ${EBROOTBOOST} +LIB_BOOST = ${BOOSTDIR}/lib +INC_BOOST = ${BOOSTDIR}/include - + # QT library -QTDIR = /usr/lib/qt3 +QTDIR = ${EBROOTQT} LIB_QT = ${QTDIR}/lib INC_QT = ${QTDIR}/include - + @@ -64,10 +64,10 @@ INC_QWT = ${QWTDIR}/include - + # FFTW3 library -LIB_FFTW3 = ${FSLEXTLIB} -INC_FFTW3 = ${FSLEXTINC}/fftw3 - --# VTK library +-# VTK library -VTKDIR_INC = /home/fs0/cowboy/var/caper_linux_64-gcc4.4/VTK7/include/vtk-7.0 -VTKDIR_LIB = /home/fs0/cowboy/var/caper_linux_64-gcc4.4/VTK7/lib -VTKSUFFIX = -7.0 \ No newline at end of file +LIB_FFTW3 = ${EBVARFFTW_LIB_DIR} +INC_FFTW3 = ${EBVARFFTW_INC_DIR} -+ ++ + # VTK library +VTKDIR_INC = ${EBROOTVTK}/include/vtk-`echo $EBVERSIONVTK | cut -f1-2 -d.` +VTKDIR_LIB = ${EBROOTVTK}/lib @@ -103,12 +103,12 @@ diff -ur fsl.orig/config/linux_64-gcc4.8/systemvars.mk fsl/config/linux_64-gcc4. -TCLSH = ${FSLDIR}/bin/fsltclsh +TCLSH = tclsh RANLIB = echo - + FSLML = ${FSLDIR}/bin/fslml @@ -18,9 +18,9 @@ - + # Compiler dependent variables - + -CC = gcc -CXX = c++ -CXX11 = scl enable devtoolset-2 -- c++ @@ -117,18 +117,18 @@ diff -ur fsl.orig/config/linux_64-gcc4.8/systemvars.mk fsl/config/linux_64-gcc4. +CXX11 = ${CXX} -std=c++11 CSTATICFLAGS = -static CXXSTATICFLAGS = -static - + @@ -30,16 +30,16 @@ - + DEPENDFLAGS = -MM - + -OPTFLAGS = -g -O3 -fexpensive-optimizations ${ARCHFLAGS} +OPTFLAGS := ${OPTFLAGS} ${ARCHFLAGS} MACHDBGFLAGS = -g GNU_ANSI_FLAGS = -Wall -ansi -pedantic -Wno-long-long SGI_ANSI_FLAGS = -ansi -fullwarn ANSI_FLAGS = ${GNU_ANSI_FLAGS} - + # CUDA development environment -CUDA_INSTALLATION = /opt/cuda-7.5 +CUDA_INSTALLATION = ${EBROOTCUDA} @@ -144,11 +144,11 @@ diff -ur fsl.orig/etc/fslconf/fsl.csh fsl/etc/fslconf/fsl.csh @@ -25,7 +25,7 @@ # The following variables specify paths for programs and can be changed # or replaced by different programs ( e.g. FSLDISPLAY=open for MacOSX) - + -setenv FSLTCLSH $FSLDIR/bin/fsltclsh +setenv FSLTCLSH tclsh setenv FSLWISH $FSLDIR/bin/fslwish - + # The following variables are used for running code in parallel across diff -ur fsl.orig/etc/fslconf/fsl-devel.sh fsl/etc/fslconf/fsl-devel.sh --- fsl.orig/etc/fslconf/fsl-devel.sh 2014-05-19 16:54:10.000000000 +0200 @@ -156,29 +156,29 @@ diff -ur fsl.orig/etc/fslconf/fsl-devel.sh fsl/etc/fslconf/fsl-devel.sh @@ -26,7 +26,7 @@ # The following variables specify paths for programs and can be changed # or replaced by different programs ( e.g. FSLDISPLAY=open for MacOSX) - + -FSLTCLSH=$FSLDIR/bin/fsltclsh +FSLTCLSH=tclsh FSLWISH=$FSLDIR/bin/fslwish - - export FSLTCLSH FSLWISH + + export FSLTCLSH FSLWISH diff -ur fsl.orig/etc/fslconf/fsl.sh fsl/etc/fslconf/fsl.sh --- fsl.orig/etc/fslconf/fsl.sh 2014-05-19 16:54:10.000000000 +0200 +++ fsl/etc/fslconf/fsl.sh 2017-05-24 09:38:05.912369589 +0200 @@ -26,7 +26,7 @@ # The following variables specify paths for programs and can be changed # or replaced by different programs ( e.g. FSLDISPLAY=open for MacOSX) - + -FSLTCLSH=$FSLDIR/bin/fsltclsh +FSLTCLSH=tclsh FSLWISH=$FSLDIR/bin/fslwish - - export FSLTCLSH FSLWISH + + export FSLTCLSH FSLWISH diff -ur fsl.orig/extras/src/libxml++-2.34.0/libxml++/io/istreamparserinputbuffer.cc fsl/extras/src/libxml++-2.34.0/libxml++/io/istreamparserinputbuffer.cc --- fsl.orig/extras/src/libxml++-2.34.0/libxml++/io/istreamparserinputbuffer.cc 2010-12-15 11:41:27.000000000 +0100 +++ fsl/extras/src/libxml++-2.34.0/libxml++/io/istreamparserinputbuffer.cc 2017-05-24 09:38:05.913369598 +0200 @@ -39,6 +39,6 @@ - + bool IStreamParserInputBuffer::do_close() { - return input_; @@ -195,7 +195,7 @@ diff -ur fsl.orig/extras/src/libxml++-2.34.0/libxml++/io/ostreamoutputbuffer.cc - return output_; + return static_cast(output_); } - + bool OStreamOutputBuffer::do_close() { if(output_) @@ -209,45 +209,45 @@ diff -ur fsl.orig/src/film/Makefile fsl/src/film/Makefile +++ fsl/src/film/Makefile 2017-05-24 09:38:05.913369598 +0200 @@ -28,7 +28,7 @@ ${CXX} ${CXXFLAGS} ${LDFLAGS} -o $@ ${OBJS} ftoz.o ${LIBS} - + film_gls:${OBJS} film_gls.o - ${CXX} ${CXXFLAGS} ${LDFLAGS} -o $@ ${OBJS} film_gls.o ${LIBS} -l giftiio + ${CXX} ${CXXFLAGS} ${LDFLAGS} -o $@ ${OBJS} film_gls.o ${LIBS} -lgiftiio - + film_gls_res:${OBJS} film_gls_res.o ${CXX} ${CXXFLAGS} ${LDFLAGS} -o $@ ${OBJS} film_gls_res.o ${LIBS} diff -ur fsl.orig/src/libmeshutils/Makefile fsl/src/libmeshutils/Makefile --- fsl.orig/src/libmeshutils/Makefile 2012-07-23 15:25:20.000000000 +0200 +++ fsl/src/libmeshutils/Makefile 2017-05-24 09:38:05.913369598 +0200 @@ -3,7 +3,7 @@ - + PROJNAME = meshUtils - + -LD_LIBRARY_PATH=${FSLDIR}/lib +#LD_LIBRARY_PATH=${FSLDIR}/lib - - USRINCFLAGS = -I${INC_NEWMAT} -I${INC_ZLIB} -I${INC_PROB} -I${INC_BOOST} + + USRINCFLAGS = -I${INC_NEWMAT} -I${INC_ZLIB} -I${INC_PROB} -I${INC_BOOST} USRLDFLAGS = -L${LIB_PROB} -L${LIB_NEWMAT} -L${LIB_ZLIB} diff -ur fsl.orig/src/mist-clean/Makefile fsl/src/mist-clean/Makefile --- fsl.orig/src/mist-clean/Makefile 2017-04-20 14:17:54.000000000 +0200 +++ fsl/src/mist-clean/Makefile 2017-05-24 09:38:05.913369598 +0200 @@ -2,15 +2,15 @@ - + NLOPT_INC = ${FSLEXTINC} NLOPT_LIB = ${FSLEXTLIB} -SQLITE_INC = ${FSLEXTINC}/libsqlite -SQLITE_LIB = ${FSLEXTLIB} +SQLITE_INC = ${EBROOTSQLITE}/include +SQLITE_LIB = ${EBROOTSQLITE}/lib - + PROJNAME = mist - + XFILES = mist/mist SCRIPTS = bin/mist_1_train bin/mist_2_fit bin/mist_FA_reg bin/mist_display bin/mist_mesh_utils - + -USRCXXFLAGS = -std=c++11 # EB: needed to correctly (dynamically) link with the Boost log libs +USRCXXFLAGS = -std=c++11 -DBOOST_LOG_DYN_LINK USRINCFLAGS = -I${FSLDIR}/include/newimage -I${INC_NEWMAT} -I${INC_ZLIB} -I${INC_GDC} -I${INC_GD} -I${SQLITE_INC} -I${NLOPT_INC} -I${VTKDIR_INC} -Icommon USRLDFLAGS = -L${LIB_NEWMAT} -L${LIB_ZLIB} -L${LIB_BOOST} -L${LIB_GDC} -L${LIB_GD} -L${NLOPT_LIB} -L${VTKDIR_LIB} - + -- GitLab From a80f9ff2b305ad2c9082e07718565629a00fe7eb Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 24 May 2017 10:55:41 +0200 Subject: [PATCH 0815/1603] Fix VTK patch in makefile --- easybuild/easyconfigs/f/FSL/FSL-5.0.10_makefile_fixes.patch | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/f/FSL/FSL-5.0.10_makefile_fixes.patch b/easybuild/easyconfigs/f/FSL/FSL-5.0.10_makefile_fixes.patch index c9f8391467..cd68478001 100644 --- a/easybuild/easyconfigs/f/FSL/FSL-5.0.10_makefile_fixes.patch +++ b/easybuild/easyconfigs/f/FSL/FSL-5.0.10_makefile_fixes.patch @@ -90,9 +90,9 @@ diff -ur fsl.orig/config/linux_64-gcc4.8/externallibs.mk fsl/config/linux_64-gcc +INC_FFTW3 = ${EBVARFFTW_INC_DIR} + + # VTK library -+VTKDIR_INC = ${EBROOTVTK}/include/vtk-`echo $EBVERSIONVTK | cut -f1-2 -d.` ++VTKDIR_INC = ${EBROOTVTK}/include/vtk-`echo ${EBVERSIONVTK} | cut -f1-2 -d.` +VTKDIR_LIB = ${EBROOTVTK}/lib -+VTKSUFFIX = -`echo $EBVERSIONVTK | cut -f1-2 -d.` ++VTKSUFFIX = -`echo ${EBVERSIONVTK} | cut -f1-2 -d.` diff -ur fsl.orig/config/linux_64-gcc4.8/systemvars.mk fsl/config/linux_64-gcc4.8/systemvars.mk --- fsl.orig/config/linux_64-gcc4.8/systemvars.mk 2017-02-18 13:20:05.000000000 +0100 +++ fsl/config/linux_64-gcc4.8/systemvars.mk 2017-05-24 09:38:05.912369589 +0200 -- GitLab From 38913dfcb6952029cc0846799fcc48c8cbfc4f6e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 24 May 2017 11:24:27 +0200 Subject: [PATCH 0816/1603] {bio}[intel/2017a] VariantMetaCaller 1.0 --- .../VariantMetaCaller-1.0-intel-2017a.eb | 24 +++++++++++++++ ...VariantMetaCaller-1.0_fix-hardcoding.patch | 29 +++++++++++++++++++ 2 files changed, 53 insertions(+) create mode 100644 easybuild/easyconfigs/v/VariantMetaCaller/VariantMetaCaller-1.0-intel-2017a.eb create mode 100644 easybuild/easyconfigs/v/VariantMetaCaller/VariantMetaCaller-1.0_fix-hardcoding.patch diff --git a/easybuild/easyconfigs/v/VariantMetaCaller/VariantMetaCaller-1.0-intel-2017a.eb b/easybuild/easyconfigs/v/VariantMetaCaller/VariantMetaCaller-1.0-intel-2017a.eb new file mode 100644 index 0000000000..122e215269 --- /dev/null +++ b/easybuild/easyconfigs/v/VariantMetaCaller/VariantMetaCaller-1.0-intel-2017a.eb @@ -0,0 +1,24 @@ +easyblock = 'MakeCp' + +name = 'VariantMetaCaller' +version = '1.0' + +homepage = 'http://bioinformatics.mit.bme.hu/VariantMetaCaller/' +description = """VariantMetaCaller automatically integrates variant calling pipelines into a better performing + overall model that also predicts accurate variant probabilities.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['http://bioinformatics.mit.bme.hu/VariantMetaCaller/'] +sources = ['%(name)s_v%(version)s.tar.gz'] + +patches = ['VariantMetaCaller-%(version)s_fix-hardcoding.patch'] + +files_to_copy = [(['VariantMetaCaller'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/VariantMetaCaller'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/v/VariantMetaCaller/VariantMetaCaller-1.0_fix-hardcoding.patch b/easybuild/easyconfigs/v/VariantMetaCaller/VariantMetaCaller-1.0_fix-hardcoding.patch new file mode 100644 index 0000000000..3d14a49394 --- /dev/null +++ b/easybuild/easyconfigs/v/VariantMetaCaller/VariantMetaCaller-1.0_fix-hardcoding.patch @@ -0,0 +1,29 @@ +fix hardcoding of g++ and optimisation flags +fix minor compilation issue "no operator "<<" matches these operands" +author: Kenneth Hoste (HPC-UGent) +diff --git a/VariantMetaCaller_v1.0/makefile.orig b/VariantMetaCaller_v1.0/makefile +index 78ff65d..c49027d 100644 +--- a/VariantMetaCaller_v1.0/makefile.orig ++++ b/VariantMetaCaller_v1.0/makefile +@@ -37,7 +37,7 @@ all: VariantMetaCaller + VariantMetaCaller: $(OBJS) $(USER_OBJS) + @echo 'Building target: $@' + @echo 'Invoking: GCC C++ Linker' +- g++ -o"VariantMetaCaller" $(OBJS) $(USER_OBJS) $(LIBS) -fopenmp ++ ${CXX} ${CXXFLAGS} -o"VariantMetaCaller" $(OBJS) $(USER_OBJS) $(LIBS) -fopenmp + @echo 'Finished building target: $@' + @echo ' ' + +diff --git a/VariantMetaCaller_v1.0/subdir.mk.orig b/VariantMetaCaller_v1.0/subdir.mk +index 530defe..110d8f3 100644 +--- a/VariantMetaCaller_v1.0/subdir.mk.orig ++++ b/VariantMetaCaller_v1.0/subdir.mk +@@ -35,7 +35,7 @@ genotypePrioritizer.d + ./%.o: %.cpp + @echo 'Building file: $<' + @echo 'Invoking: GCC C++ Compiler' +- g++ -O0 -g3 -Wall -c -fmessage-length=0 -std=c++11 -fopenmp -MMD -MP -MF"$(@:%.o=%.d)" -MT"$(@:%.o=%.d)" -o"$@" "$<" ++ ${CXX} ${CXXFLAGS} -Wall -c -fmessage-length=0 -std=c++11 -fopenmp -MMD -MP -MF"$(@:%.o=%.d)" -MT"$(@:%.o=%.d)" -o"$@" "$<" + @echo 'Finished building: $<' + @echo ' ' + -- GitLab From a1967a73483c9123654218c749ce232395927b77 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 24 May 2017 11:43:18 +0200 Subject: [PATCH 0817/1603] fix remarks --- .../v/VariantMetaCaller/VariantMetaCaller-1.0-intel-2017a.eb | 1 + .../VariantMetaCaller-1.0_fix-hardcoding.patch | 4 ++-- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/v/VariantMetaCaller/VariantMetaCaller-1.0-intel-2017a.eb b/easybuild/easyconfigs/v/VariantMetaCaller/VariantMetaCaller-1.0-intel-2017a.eb index 122e215269..d77e58e531 100644 --- a/easybuild/easyconfigs/v/VariantMetaCaller/VariantMetaCaller-1.0-intel-2017a.eb +++ b/easybuild/easyconfigs/v/VariantMetaCaller/VariantMetaCaller-1.0-intel-2017a.eb @@ -8,6 +8,7 @@ description = """VariantMetaCaller automatically integrates variant calling pipe overall model that also predicts accurate variant probabilities.""" toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'cstd': 'c++11', 'openmp': True} source_urls = ['http://bioinformatics.mit.bme.hu/VariantMetaCaller/'] sources = ['%(name)s_v%(version)s.tar.gz'] diff --git a/easybuild/easyconfigs/v/VariantMetaCaller/VariantMetaCaller-1.0_fix-hardcoding.patch b/easybuild/easyconfigs/v/VariantMetaCaller/VariantMetaCaller-1.0_fix-hardcoding.patch index 3d14a49394..efa19b4c6e 100644 --- a/easybuild/easyconfigs/v/VariantMetaCaller/VariantMetaCaller-1.0_fix-hardcoding.patch +++ b/easybuild/easyconfigs/v/VariantMetaCaller/VariantMetaCaller-1.0_fix-hardcoding.patch @@ -10,7 +10,7 @@ index 78ff65d..c49027d 100644 @echo 'Building target: $@' @echo 'Invoking: GCC C++ Linker' - g++ -o"VariantMetaCaller" $(OBJS) $(USER_OBJS) $(LIBS) -fopenmp -+ ${CXX} ${CXXFLAGS} -o"VariantMetaCaller" $(OBJS) $(USER_OBJS) $(LIBS) -fopenmp ++ ${CXX} ${CXXFLAGS} ${LDFLAGS} -o"VariantMetaCaller" $(OBJS) $(USER_OBJS) $(LIBS) @echo 'Finished building target: $@' @echo ' ' @@ -23,7 +23,7 @@ index 530defe..110d8f3 100644 @echo 'Building file: $<' @echo 'Invoking: GCC C++ Compiler' - g++ -O0 -g3 -Wall -c -fmessage-length=0 -std=c++11 -fopenmp -MMD -MP -MF"$(@:%.o=%.d)" -MT"$(@:%.o=%.d)" -o"$@" "$<" -+ ${CXX} ${CXXFLAGS} -Wall -c -fmessage-length=0 -std=c++11 -fopenmp -MMD -MP -MF"$(@:%.o=%.d)" -MT"$(@:%.o=%.d)" -o"$@" "$<" ++ ${CXX} ${CXXFLAGS} -Wall -c -fmessage-length=0 -MMD -MP -MF"$(@:%.o=%.d)" -MT"$(@:%.o=%.d)" -o"$@" "$<" @echo 'Finished building: $<' @echo ' ' -- GitLab From 0bcd09ed9c394849f9c947485b5a4e914570681d Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 24 May 2017 14:52:31 +0200 Subject: [PATCH 0818/1603] Small fixes --- .../easyconfigs/f/FSL/FSL-5.0.10_makefile_fixes.patch | 9 ++++++--- .../v/VTK/VTK-7.1.1-intel-2017a-Python-2.7.13.eb | 1 + 2 files changed, 7 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/f/FSL/FSL-5.0.10_makefile_fixes.patch b/easybuild/easyconfigs/f/FSL/FSL-5.0.10_makefile_fixes.patch index cd68478001..8801e205ce 100644 --- a/easybuild/easyconfigs/f/FSL/FSL-5.0.10_makefile_fixes.patch +++ b/easybuild/easyconfigs/f/FSL/FSL-5.0.10_makefile_fixes.patch @@ -147,7 +147,8 @@ diff -ur fsl.orig/etc/fslconf/fsl.csh fsl/etc/fslconf/fsl.csh -setenv FSLTCLSH $FSLDIR/bin/fsltclsh +setenv FSLTCLSH tclsh - setenv FSLWISH $FSLDIR/bin/fslwish +-setenv FSLWISH $FSLDIR/bin/fslwish ++setenv FSLWISH wish # The following variables are used for running code in parallel across diff -ur fsl.orig/etc/fslconf/fsl-devel.sh fsl/etc/fslconf/fsl-devel.sh @@ -159,7 +160,8 @@ diff -ur fsl.orig/etc/fslconf/fsl-devel.sh fsl/etc/fslconf/fsl-devel.sh -FSLTCLSH=$FSLDIR/bin/fsltclsh +FSLTCLSH=tclsh - FSLWISH=$FSLDIR/bin/fslwish +-FSLWISH=$FSLDIR/bin/fslwish ++FSLWISH=wish export FSLTCLSH FSLWISH diff -ur fsl.orig/etc/fslconf/fsl.sh fsl/etc/fslconf/fsl.sh @@ -171,7 +173,8 @@ diff -ur fsl.orig/etc/fslconf/fsl.sh fsl/etc/fslconf/fsl.sh -FSLTCLSH=$FSLDIR/bin/fsltclsh +FSLTCLSH=tclsh - FSLWISH=$FSLDIR/bin/fslwish +-FSLWISH=$FSLDIR/bin/fslwish ++FSLWISH=wish export FSLTCLSH FSLWISH diff -ur fsl.orig/extras/src/libxml++-2.34.0/libxml++/io/istreamparserinputbuffer.cc fsl/extras/src/libxml++-2.34.0/libxml++/io/istreamparserinputbuffer.cc diff --git a/easybuild/easyconfigs/v/VTK/VTK-7.1.1-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/v/VTK/VTK-7.1.1-intel-2017a-Python-2.7.13.eb index 79963c3515..e0221778a4 100644 --- a/easybuild/easyconfigs/v/VTK/VTK-7.1.1-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/v/VTK/VTK-7.1.1-intel-2017a-Python-2.7.13.eb @@ -34,6 +34,7 @@ sources = [ builddependencies = [('CMake', '3.8.0')] dependencies = [ + ('HDF5', '1.8.18'), ('Python', '2.7.13'), ('libGLU', '9.0.0'), ('X11', '20170314'), -- GitLab From 02dd8d32e9b5b4deeb1f2641f51973d70ae687ac Mon Sep 17 00:00:00 2001 From: jrbosch Date: Fri, 26 May 2017 11:00:51 -0400 Subject: [PATCH 0819/1603] add easyconfig Biopython 1.68 for foss 2016b Python 3.5.2 --- .../Biopython-1.68-foss-2016b-Python-3.5.2.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/b/Biopython/Biopython-1.68-foss-2016b-Python-3.5.2.eb diff --git a/easybuild/easyconfigs/b/Biopython/Biopython-1.68-foss-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/b/Biopython/Biopython-1.68-foss-2016b-Python-3.5.2.eb new file mode 100644 index 0000000000..82e737e6cf --- /dev/null +++ b/easybuild/easyconfigs/b/Biopython/Biopython-1.68-foss-2016b-Python-3.5.2.eb @@ -0,0 +1,38 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 The Cyprus Institute +# Authors:: Andreas Panteli , Thekla Loizou , +# George Tsouloupas +# License:: MIT/GPL +# +## +easyblock = 'PythonPackage' + +name = 'Biopython' +version = '1.68' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.biopython.org' +description = """Biopython is a set of freely available tools for biological computation written +in Python by an international team of developers. It is a distributed collaborative effort to +develop Python libraries and applications which address the needs of current and future work in +bioinformatics. """ + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['http://biopython.org/DIST'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('Python', '3.5.2') +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/Bio', 'lib/python%(pyshortver)s/site-packages/BioSQL'] +} + +options = {'modulename': 'Bio'} + +moduleclass = 'bio' -- GitLab From f53b549a86ae0612078bbcc138603986d7a57444 Mon Sep 17 00:00:00 2001 From: Daniel Kinnamon Date: Fri, 26 May 2017 12:11:34 -0400 Subject: [PATCH 0820/1603] adding easyconfigs: Aspera-CLI-3.7.2.354.010c3b8.eb --- .../Aspera-CLI-3.7.2.354.010c3b8.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/a/Aspera-CLI/Aspera-CLI-3.7.2.354.010c3b8.eb diff --git a/easybuild/easyconfigs/a/Aspera-CLI/Aspera-CLI-3.7.2.354.010c3b8.eb b/easybuild/easyconfigs/a/Aspera-CLI/Aspera-CLI-3.7.2.354.010c3b8.eb new file mode 100644 index 0000000000..44c70d7c08 --- /dev/null +++ b/easybuild/easyconfigs/a/Aspera-CLI/Aspera-CLI-3.7.2.354.010c3b8.eb @@ -0,0 +1,40 @@ +# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# Author: Daniel D. Kinnamon +# Division of Human Genetics +# The Ohio State University Wexner Medical Center + +easyblock = 'Tarball' + +name = 'Aspera-CLI' +version = '3.7.2' +versionsuffix = '.354.010c3b8' + +homepage = 'http://asperasoft.com' +docurls = ['http://downloads.asperasoft.com/en/documentation/62'] +description = """IBM Aspera Command-Line Interface (the Aspera CLI) is +a collection of Aspera tools for performing high-speed, secure data +transfers from the command line. The Aspera CLI is for users and +organizations who want to automate their transfer workflows.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +# Aspera CLI install script includes tarball inline and installs to a +# fixed location. Need to include custom extract command to pull +# tarball out of install script and pipe to tar. %s in the extraction +# command will be replaced by the source filename. +sources = [ + ('%(namelower)s-%(version)s%(versionsuffix)s-linux-64-release.sh', + "sed '1,/^__ARCHIVE_FOLLOWS__$/d' %s |" + + 'tar -xzpo --strip-components 1 -f -') +] +source_urls = ['http://download.asperasoft.com/download/sw/cli/%(version)s'] +checksums = ['02787ca46814fb9ae2de5c706461367e'] + +sanity_check_paths = { + 'files': ['product-info.mf'], + 'dirs': ['bin', 'certs', 'docs', 'etc', 'share/man'] +} + +sanity_check_commands = ['ascp -h', 'man ascp -P cat'] + +moduleclass = 'tools' -- GitLab From aa87ae52227decd252fb4ed609cda6d89e81fee4 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Mon, 29 May 2017 11:32:26 +1200 Subject: [PATCH 0821/1603] Add CDK version suffix --- ...GI-16.1-GCC-4.9.2-2.25.eb => PGI-16.1-CDK-GCC-4.9.2-2.25.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/p/PGI/{PGI-16.1-GCC-4.9.2-2.25.eb => PGI-16.1-CDK-GCC-4.9.2-2.25.eb} (91%) diff --git a/easybuild/easyconfigs/p/PGI/PGI-16.1-GCC-4.9.2-2.25.eb b/easybuild/easyconfigs/p/PGI/PGI-16.1-CDK-GCC-4.9.2-2.25.eb similarity index 91% rename from easybuild/easyconfigs/p/PGI/PGI-16.1-GCC-4.9.2-2.25.eb rename to easybuild/easyconfigs/p/PGI/PGI-16.1-CDK-GCC-4.9.2-2.25.eb index 5972e15b28..d25dc435ae 100644 --- a/easybuild/easyconfigs/p/PGI/PGI-16.1-GCC-4.9.2-2.25.eb +++ b/easybuild/easyconfigs/p/PGI/PGI-16.1-CDK-GCC-4.9.2-2.25.eb @@ -11,7 +11,7 @@ checksums = ['442c044b9690a84b6600cd6919480bcb'] gccver = '4.9.2' binutilsver = '2.25' -versionsuffix = '-GCC-%s-%s' % (gccver, binutilsver) +versionsuffix = '-CDK-GCC-%s-%s' % (gccver, binutilsver) dependencies = [ ('GCCcore', gccver), -- GitLab From 54f63e63bedcce71d3698b0ec7548627573358a7 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Mon, 29 May 2017 12:30:46 +0200 Subject: [PATCH 0822/1603] {bio}[intel/2017a] Bio-SamTools 1.43 w/Perl-5.24.1 (REVIEW) --- ...o-SamTools-1.43-intel-2017a-Perl-5.24.1.eb | 27 ++++++++++ .../b/Bio-SamTools/Bio-SamTools-1.43.patch | 54 +++++++++++++++++++ .../s/SAMtools/SAMtools-0.1.17-intel-2017a.eb | 21 ++++++++ 3 files changed, 102 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bio-SamTools/Bio-SamTools-1.43-intel-2017a-Perl-5.24.1.eb create mode 100644 easybuild/easyconfigs/b/Bio-SamTools/Bio-SamTools-1.43.patch create mode 100644 easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.17-intel-2017a.eb diff --git a/easybuild/easyconfigs/b/Bio-SamTools/Bio-SamTools-1.43-intel-2017a-Perl-5.24.1.eb b/easybuild/easyconfigs/b/Bio-SamTools/Bio-SamTools-1.43-intel-2017a-Perl-5.24.1.eb new file mode 100644 index 0000000000..f1f376b07b --- /dev/null +++ b/easybuild/easyconfigs/b/Bio-SamTools/Bio-SamTools-1.43-intel-2017a-Perl-5.24.1.eb @@ -0,0 +1,27 @@ +easyblock = 'PerlModule' + +name = 'Bio-SamTools' +version = '1.43' +versionsuffix = '-Perl-%(perlver)s' + +homepage = 'http://search.cpan.org/~lds/Bio-SamTools/' +description = """This is a Perl interface to the SAMtools sequence alignment interface.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True} + +source_urls = ['http://search.cpan.org/CPAN/authors/id/L/LD/LDS'] +sources = [SOURCE_TAR_GZ] +#sources = [(SOURCE_TAR_GZ, 'tar -xzf %s && chmod -R +w .')] + +patches = ['%(name)s-%(version)s.patch'] + +dependencies = [ + ('Perl', '5.24.1'), + ('BioPerl', '1.7.1', versionsuffix), + ('SAMtools', '0.1.17'), +] + +options = {'modulename': 'Bio::DB::Sam'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/Bio-SamTools/Bio-SamTools-1.43.patch b/easybuild/easyconfigs/b/Bio-SamTools/Bio-SamTools-1.43.patch new file mode 100644 index 0000000000..d1342c786b --- /dev/null +++ b/easybuild/easyconfigs/b/Bio-SamTools/Bio-SamTools-1.43.patch @@ -0,0 +1,54 @@ +--- Bio-SamTools-1.43/Build.PL.orig 2016-02-12 20:31:32.000000000 +0100 ++++ Bio-SamTools-1.43/Build.PL 2017-05-26 13:22:23.318323680 +0200 +@@ -75,7 +75,7 @@ + $sam_include = $samtools + if -e "$samtools/$HeaderFile"; + $sam_include = "$samtools/include" +- if -e "$samtools/include/$HeaderFile"; ++ if -e "$samtools/include/bam/$HeaderFile"; + $sam_lib = $samtools + if -e "$samtools/$LibFile"; + $sam_lib = "$samtools/lib" +@@ -164,7 +164,7 @@ + } + + sub _samtools { +- $ENV{SAMTOOLS} || ++ $ENV{EBROOTSAMTOOLS} || + ( can_load(modules => {'Alien::SamTools' => undef, 'File::ShareDir' => undef}) && + File::ShareDir::dist_dir('Alien-SamTools')); + } +--- Bio-SamTools-1.43/c_bin/makefile.orig 2016-02-12 20:31:32.000000000 +0100 ++++ Bio-SamTools-1.43/c_bin/makefile 2017-05-26 13:44:43.770545813 +0200 +@@ -1,5 +1,5 @@ +-CC= gcc +-CFLAGS= -g -Wall -O2 -fPIC ++CC?= gcc ++CFLAGS?= -g -Wall -O2 -fPIC + DFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 + INCLUDES= + LIBPATH= +--- Bio-SamTools-1.43/c_bin/bam2bedgraph.c.orig 2016-02-12 20:31:32.000000000 +0100 ++++ Bio-SamTools-1.43/c_bin/bam2bedgraph.c 2017-05-26 13:29:28.041584111 +0200 +@@ -1,5 +1,5 @@ + #include +-#include "sam.h" ++#include "bam/sam.h" + + typedef struct { + uint32_t ltid; +--- Bio-SamTools-1.43/lib/Bio/DB/Sam.xs.orig 2016-02-12 20:31:32.000000000 +0100 ++++ Bio-SamTools-1.43/lib/Bio/DB/Sam.xs 2017-05-29 11:56:51.145855185 +0200 +@@ -25,9 +25,9 @@ + + #include + #include +-#include "bam.h" +-#include "khash.h" +-#include "faidx.h" ++#include "bam/bam.h" ++#include "bam/khash.h" ++#include "bam/faidx.h" + + /* stolen from bam_aux.c */ + #define MAX_REGION 1<<29 diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.17-intel-2017a.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.17-intel-2017a.eb new file mode 100644 index 0000000000..0424b6875f --- /dev/null +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.17-intel-2017a.eb @@ -0,0 +1,21 @@ +name = 'SAMtools' +version = '0.1.17' + +homepage = 'http://www.htslib.org/' +description = """SAM Tools provide various utilities for manipulating alignments in the SAM format, + including sorting, merging, indexing and generating alignments in a per-position format.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['https://github.com/samtools/%(namelower)s/archive/%(version)s'] + +#patches = ['SAMtools-%(version)s_Makefile-ncurses.patch'] + +dependencies = [ + ('ncurses', '6.0'), + ('zlib', '1.2.11'), +] + +moduleclass = 'bio' -- GitLab From 19a531697a174af059efe0d0e26cccc113a6f091 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 29 May 2017 14:27:06 +0200 Subject: [PATCH 0823/1603] add location to DotLib.pm to $PERL5LIB for SSPACE Basic --- .../SSPACE_Basic-2.1.1-intel-2017a-Perl-5.24.1.eb | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/SSPACE_Basic/SSPACE_Basic-2.1.1-intel-2017a-Perl-5.24.1.eb b/easybuild/easyconfigs/s/SSPACE_Basic/SSPACE_Basic-2.1.1-intel-2017a-Perl-5.24.1.eb index 9d51ecf299..d196a375f0 100644 --- a/easybuild/easyconfigs/s/SSPACE_Basic/SSPACE_Basic-2.1.1-intel-2017a-Perl-5.24.1.eb +++ b/easybuild/easyconfigs/s/SSPACE_Basic/SSPACE_Basic-2.1.1-intel-2017a-Perl-5.24.1.eb @@ -18,10 +18,13 @@ dependencies = [ ] sanity_check_paths = { - 'files': ['README', 'SSPACE_Basic.pl'], + 'files': ['dotlib/DotLib.pm', 'README', 'SSPACE_Basic.pl'], 'dirs': ['bin', 'tools'], } -modextrapaths = {'PATH': ''} +modextrapaths = { + 'PATH': '', + 'PERL5LIB': 'dotlib', +} moduleclass = 'bio' -- GitLab From c0d8aac7fe9ebda34b5d9a20aed248b8497a0560 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 29 May 2017 19:17:31 +0200 Subject: [PATCH 0824/1603] enable inclusion of version symbol by using --enable-ld-version-script configure option for LibTIFF --- easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-goolf-1.4.10.eb | 4 +++- easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-goolf-1.7.20.eb | 4 +++- easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-ictce-5.3.0.eb | 4 +++- .../easyconfigs/l/LibTIFF/LibTIFF-4.0.3-intel-2014.06.eb | 4 +++- easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-intel-2014b.eb | 4 +++- easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-intel-2015a.eb | 4 +++- easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-intel-2015b.eb | 2 ++ easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.4-foss-2015a.eb | 2 ++ easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.4-goolf-1.7.20.eb | 4 +++- easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.4-intel-2015a.eb | 2 ++ .../easyconfigs/l/LibTIFF/LibTIFF-4.0.4beta-foss-2015a.eb | 4 +++- .../easyconfigs/l/LibTIFF/LibTIFF-4.0.4beta-intel-2015a.eb | 4 +++- easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-foss-2015a.eb | 2 ++ easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-foss-2016a.eb | 2 ++ easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-foss-2016b.eb | 2 ++ easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-intel-2016a.eb | 2 ++ easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-intel-2016b.eb | 2 ++ easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.7-intel-2017a.eb | 2 ++ 18 files changed, 45 insertions(+), 9 deletions(-) diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-goolf-1.4.10.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-goolf-1.4.10.eb index 9875af8f63..b741841310 100644 --- a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-goolf-1.4.10.eb @@ -18,13 +18,15 @@ version = '4.0.3' homepage = 'http://www.remotesensing.org/libtiff/' description = "tiff: Library and tools for reading and writing TIFF data files" +toolchain = {'name': 'goolf', 'version': '1.4.10'} + source_urls = [ 'http://download.osgeo.org/libtiff/', 'ftp://ftp.remotesensing.org/pub/libtiff/', ] sources = ['tiff-%(version)s.tar.gz'] -toolchain = {'name': 'goolf', 'version': '1.4.10'} +configopts = " --enable-ld-version-script " sanity_check_paths = { 'files': ['bin/tiffinfo'], diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-goolf-1.7.20.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-goolf-1.7.20.eb index 46a3c3ee49..1496187e7b 100644 --- a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-goolf-1.7.20.eb @@ -6,13 +6,15 @@ version = '4.0.3' homepage = 'http://www.remotesensing.org/libtiff/' description = "tiff: Library and tools for reading and writing TIFF data files" +toolchain = {'name': 'goolf', 'version': '1.7.20'} + source_urls = [ 'http://download.osgeo.org/libtiff/', 'ftp://ftp.remotesensing.org/pub/libtiff/', ] sources = ['tiff-%(version)s.tar.gz'] -toolchain = {'name': 'goolf', 'version': '1.7.20'} +configopts = " --enable-ld-version-script " sanity_check_paths = { 'files': ['bin/tiffinfo'], diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-ictce-5.3.0.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-ictce-5.3.0.eb index 87e3b72f57..3b637dfd68 100644 --- a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-ictce-5.3.0.eb @@ -18,13 +18,15 @@ version = '4.0.3' homepage = 'http://www.remotesensing.org/libtiff/' description = "tiff: Library and tools for reading and writing TIFF data files" +toolchain = {'name': 'ictce', 'version': '5.3.0'} + source_urls = [ 'http://download.osgeo.org/libtiff/', 'ftp://ftp.remotesensing.org/pub/libtiff/', ] sources = ['tiff-%(version)s.tar.gz'] -toolchain = {'name': 'ictce', 'version': '5.3.0'} +configopts = " --enable-ld-version-script " sanity_check_paths = { 'files': ['bin/tiffinfo'], diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-intel-2014.06.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-intel-2014.06.eb index e29ed51d54..2d0643c0a8 100644 --- a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-intel-2014.06.eb +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-intel-2014.06.eb @@ -17,13 +17,15 @@ version = '4.0.3' homepage = 'http://www.remotesensing.org/libtiff/' description = "tiff: Library and tools for reading and writing TIFF data files" +toolchain = {'name': 'intel', 'version': '2014.06'} + source_urls = [ 'http://download.osgeo.org/libtiff/', 'ftp://ftp.remotesensing.org/pub/libtiff/', ] sources = ['tiff-%(version)s.tar.gz'] -toolchain = {'name': 'intel', 'version': '2014.06'} +configopts = " --enable-ld-version-script " sanity_check_paths = { 'files': ['bin/tiffinfo'], diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-intel-2014b.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-intel-2014b.eb index a06a26e3be..42a3e46a06 100644 --- a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-intel-2014b.eb +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-intel-2014b.eb @@ -17,13 +17,15 @@ version = '4.0.3' homepage = 'http://www.remotesensing.org/libtiff/' description = "tiff: Library and tools for reading and writing TIFF data files" +toolchain = {'name': 'intel', 'version': '2014b'} + source_urls = [ 'http://download.osgeo.org/libtiff/', 'ftp://ftp.remotesensing.org/pub/libtiff/', ] sources = ['tiff-%(version)s.tar.gz'] -toolchain = {'name': 'intel', 'version': '2014b'} +configopts = " --enable-ld-version-script " sanity_check_paths = { 'files': ['bin/tiffinfo'], diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-intel-2015a.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-intel-2015a.eb index 36759b619b..a080abfe8e 100644 --- a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-intel-2015a.eb +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-intel-2015a.eb @@ -17,6 +17,8 @@ version = '4.0.3' homepage = 'http://www.remotesensing.org/libtiff/' description = "tiff: Library and tools for reading and writing TIFF data files" +toolchain = {'name': 'intel', 'version': '2015a'} + source_urls = [ 'http://download.osgeo.org/libtiff/', 'ftp://ftp.remotesensing.org/pub/libtiff/', @@ -24,7 +26,7 @@ source_urls = [ sources = ['tiff-%(version)s.tar.gz'] checksums = ['051c1068e6a0627f461948c365290410'] -toolchain = {'name': 'intel', 'version': '2015a'} +configopts = " --enable-ld-version-script " sanity_check_paths = { 'files': ['bin/tiffinfo'], diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-intel-2015b.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-intel-2015b.eb index 245af77e27..769d5c3bf4 100644 --- a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-intel-2015b.eb +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-intel-2015b.eb @@ -17,6 +17,8 @@ version = '4.0.3' homepage = 'http://www.remotesensing.org/libtiff/' description = "tiff: Library and tools for reading and writing TIFF data files" +configopts = " --enable-ld-version-script " + source_urls = [ 'http://download.osgeo.org/libtiff/', 'ftp://ftp.remotesensing.org/pub/libtiff/', diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.4-foss-2015a.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.4-foss-2015a.eb index 70578c5f23..9fdf349e0c 100644 --- a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.4-foss-2015a.eb +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.4-foss-2015a.eb @@ -26,6 +26,8 @@ source_urls = [ ] sources = ['tiff-%(version)s.tar.gz'] +configopts = " --enable-ld-version-script " + sanity_check_paths = { 'files': ['bin/tiffinfo'], 'dirs': [], diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.4-goolf-1.7.20.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.4-goolf-1.7.20.eb index 8858538d5a..a8769ecc26 100644 --- a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.4-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.4-goolf-1.7.20.eb @@ -6,13 +6,15 @@ version = '4.0.4' homepage = 'http://www.remotesensing.org/libtiff/' description = "tiff: Library and tools for reading and writing TIFF data files" +toolchain = {'name': 'goolf', 'version': '1.7.20'} + source_urls = [ 'http://download.osgeo.org/libtiff/', 'ftp://ftp.remotesensing.org/pub/libtiff/', ] sources = ['tiff-%(version)s.tar.gz'] -toolchain = {'name': 'goolf', 'version': '1.7.20'} +configopts = " --enable-ld-version-script " sanity_check_paths = { 'files': ['bin/tiffinfo'], diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.4-intel-2015a.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.4-intel-2015a.eb index 6b0d237d17..caf97944ef 100644 --- a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.4-intel-2015a.eb +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.4-intel-2015a.eb @@ -26,6 +26,8 @@ source_urls = [ ] sources = ['tiff-%(version)s.tar.gz'] +configopts = " --enable-ld-version-script " + sanity_check_paths = { 'files': ['bin/tiffinfo'], 'dirs': [], diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.4beta-foss-2015a.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.4beta-foss-2015a.eb index accbb2bb0a..a7ec21003e 100644 --- a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.4beta-foss-2015a.eb +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.4beta-foss-2015a.eb @@ -19,13 +19,15 @@ version = '4.0.4beta' homepage = 'http://www.remotesensing.org/libtiff/' description = "tiff: Library and tools for reading and writing TIFF data files" +toolchain = {'name': 'foss', 'version': '2015a'} + source_urls = [ 'http://download.osgeo.org/libtiff/', 'ftp://ftp.remotesensing.org/pub/libtiff/', ] sources = ['tiff-%(version)s.tar.gz'] -toolchain = {'name': 'foss', 'version': '2015a'} +configopts = " --enable-ld-version-script " sanity_check_paths = { 'files': ['bin/tiffinfo'], diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.4beta-intel-2015a.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.4beta-intel-2015a.eb index a1149ab376..2ebd87d4b6 100644 --- a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.4beta-intel-2015a.eb +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.4beta-intel-2015a.eb @@ -18,13 +18,15 @@ version = '4.0.4beta' homepage = 'http://www.remotesensing.org/libtiff/' description = "tiff: Library and tools for reading and writing TIFF data files" +toolchain = {'name': 'intel', 'version': '2015a'} + source_urls = [ 'http://download.osgeo.org/libtiff/', 'ftp://ftp.remotesensing.org/pub/libtiff/', ] sources = ['tiff-%(version)s.tar.gz'] -toolchain = {'name': 'intel', 'version': '2015a'} +configopts = " --enable-ld-version-script " sanity_check_paths = { 'files': ['bin/tiffinfo'], diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-foss-2015a.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-foss-2015a.eb index 68f9ad3dc9..259a9d8bc6 100644 --- a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-foss-2015a.eb +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-foss-2015a.eb @@ -26,6 +26,8 @@ source_urls = [ ] sources = ['tiff-%(version)s.tar.gz'] +configopts = " --enable-ld-version-script " + sanity_check_paths = { 'files': ['bin/tiffinfo'], 'dirs': [], diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-foss-2016a.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-foss-2016a.eb index d7aa3b2df4..f513557a05 100644 --- a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-foss-2016a.eb +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-foss-2016a.eb @@ -25,6 +25,8 @@ source_urls = [ ] sources = ['tiff-%(version)s.tar.gz'] +configopts = " --enable-ld-version-script " + sanity_check_paths = { 'files': ['bin/tiffinfo'], 'dirs': [], diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-foss-2016b.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-foss-2016b.eb index 07fa7682ed..a7365c221f 100644 --- a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-foss-2016b.eb +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-foss-2016b.eb @@ -25,6 +25,8 @@ source_urls = [ ] sources = ['tiff-%(version)s.tar.gz'] +configopts = " --enable-ld-version-script " + sanity_check_paths = { 'files': ['bin/tiffinfo'], 'dirs': [], diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-intel-2016a.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-intel-2016a.eb index ed490e66de..b666f47dc2 100644 --- a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-intel-2016a.eb +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-intel-2016a.eb @@ -25,6 +25,8 @@ source_urls = [ ] sources = ['tiff-%(version)s.tar.gz'] +configopts = " --enable-ld-version-script " + sanity_check_paths = { 'files': ['bin/tiffinfo'], 'dirs': [], diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-intel-2016b.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-intel-2016b.eb index d8f291e4e8..9281e4ddc9 100644 --- a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-intel-2016b.eb +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-intel-2016b.eb @@ -25,6 +25,8 @@ source_urls = [ ] sources = ['tiff-%(version)s.tar.gz'] +configopts = " --enable-ld-version-script " + sanity_check_paths = { 'files': ['bin/tiffinfo'], 'dirs': [], diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.7-intel-2017a.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.7-intel-2017a.eb index 9087c14aa4..073c1b3d60 100644 --- a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.7-intel-2017a.eb +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.7-intel-2017a.eb @@ -25,6 +25,8 @@ source_urls = [ ] sources = ['tiff-%(version)s.tar.gz'] +configopts = " --enable-ld-version-script " + sanity_check_paths = { 'files': ['bin/tiffinfo'], 'dirs': [], -- GitLab From d143cc508767eff11a422fb8ed82940694e53d1d Mon Sep 17 00:00:00 2001 From: Daniel Kinnamon Date: Mon, 29 May 2017 15:44:44 -0400 Subject: [PATCH 0825/1603] Fixed multi-line command and sanity check error with man 2.6.3 --- .../easyconfigs/a/Aspera-CLI/Aspera-CLI-3.7.2.354.010c3b8.eb | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/a/Aspera-CLI/Aspera-CLI-3.7.2.354.010c3b8.eb b/easybuild/easyconfigs/a/Aspera-CLI/Aspera-CLI-3.7.2.354.010c3b8.eb index 44c70d7c08..c5b603114d 100644 --- a/easybuild/easyconfigs/a/Aspera-CLI/Aspera-CLI-3.7.2.354.010c3b8.eb +++ b/easybuild/easyconfigs/a/Aspera-CLI/Aspera-CLI-3.7.2.354.010c3b8.eb @@ -24,8 +24,7 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} # command will be replaced by the source filename. sources = [ ('%(namelower)s-%(version)s%(versionsuffix)s-linux-64-release.sh', - "sed '1,/^__ARCHIVE_FOLLOWS__$/d' %s |" + - 'tar -xzpo --strip-components 1 -f -') + "sed '1,/^__ARCHIVE_FOLLOWS__$/d' %s | tar -xzpo --strip-components 1 -f -") ] source_urls = ['http://download.asperasoft.com/download/sw/cli/%(version)s'] checksums = ['02787ca46814fb9ae2de5c706461367e'] @@ -35,6 +34,6 @@ sanity_check_paths = { 'dirs': ['bin', 'certs', 'docs', 'etc', 'share/man'] } -sanity_check_commands = ['ascp -h', 'man ascp -P cat'] +sanity_check_commands = ['ascp -h', 'man ascp'] moduleclass = 'tools' -- GitLab From 482f3b8a3b874e208b67b90758ff4c1c8943a37d Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Tue, 30 May 2017 06:42:30 +0100 Subject: [PATCH 0826/1603] adding easyconfigs: R-bundle-Bioconductor-3.5-intel-2017a-R-3.4.0.eb --- ...le-Bioconductor-3.5-intel-2017a-R-3.4.0.eb | 22 +++++++++---------- 1 file changed, 11 insertions(+), 11 deletions(-) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.5-intel-2017a-R-3.4.0.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.5-intel-2017a-R-3.4.0.eb index 80580237a7..9125415482 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.5-intel-2017a-R-3.4.0.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.5-intel-2017a-R-3.4.0.eb @@ -37,27 +37,27 @@ exts_filter = ("R -q --no-save", "library(%(ext_name)s)") # CRAN packages on which these Bioconductor packages depend are available in R module on which this depends # !! order of packages is important !! -# packages updated on May 11th 2017 +# packages updated on May 28th 2017 exts_list = [ ('BiocGenerics', '0.22.0', bioconductor_options), ('Biobase', '2.36.2', bioconductor_options), - ('S4Vectors', '0.14.0', bioconductor_options), - ('IRanges', '2.10.0', bioconductor_options), + ('S4Vectors', '0.14.2', bioconductor_options), + ('IRanges', '2.10.2', bioconductor_options), ('GenomeInfoDbData', '0.99.0', bioconductor_options), ('GenomeInfoDb', '1.12.0', bioconductor_options), ('AnnotationDbi', '1.38.0', bioconductor_options), ('zlibbioc', '1.22.0', bioconductor_options), ('XVector', '0.16.0', bioconductor_options), ('Biostrings', '2.44.0', bioconductor_options), - ('GenomicRanges', '1.28.1', bioconductor_options), + ('GenomicRanges', '1.28.3', bioconductor_options), ('BiocParallel', '1.10.1', bioconductor_options), ('Rsamtools', '1.28.0', bioconductor_options), ('lambda.r', '1.1.9', ext_options), ('futile.options', '1.0.0', ext_options), ('futile.logger', '1.4.3', ext_options), - ('DelayedArray', '0.2.2', bioconductor_options), + ('DelayedArray', '0.2.4', bioconductor_options), ('SummarizedExperiment', '1.6.1', bioconductor_options), - ('GenomicAlignments', '1.12.0', bioconductor_options), + ('GenomicAlignments', '1.12.1', bioconductor_options), ('ShortRead', '1.34.0', bioconductor_options), ('graph', '1.54.0', bioconductor_options), ('affyio', '1.46.0', bioconductor_options), @@ -83,7 +83,7 @@ exts_list = [ ('DEGseq', '1.30.0', bioconductor_options), ('hgu133plus2.db', '3.2.3', bioconductor_options), ('illuminaio', '0.18.0', bioconductor_options), - ('rtracklayer', '1.36.0', bioconductor_options), + ('rtracklayer', '1.36.3', bioconductor_options), ('biomaRt', '2.32.0', bioconductor_options), ('GenomicFeatures', '1.28.0', bioconductor_options), ('bumphunter', '1.16.0', bioconductor_options), @@ -97,15 +97,15 @@ exts_list = [ ('annotate', '1.54.0', bioconductor_options), ('GSEABase', '1.38.0', bioconductor_options), ('genefilter', '1.58.1', bioconductor_options), - ('Category', '2.38.0', bioconductor_options), + ('Category', '2.42.0', bioconductor_options), ('GOstats', '2.42.0', bioconductor_options), ('BSgenome', '1.44.0', bioconductor_options), - ('VariantAnnotation', '1.22.0', bioconductor_options), + ('VariantAnnotation', '1.22.1', bioconductor_options), ('interactiveDisplayBase', '1.14.0', bioconductor_options), ('AnnotationHub', '2.8.1', bioconductor_options), ('AnnotationFilter', '1.0.0', bioconductor_options), ('ProtGenerics', '1.8.0', bioconductor_options), - ('ensembldb', '2.0.1', bioconductor_options), + ('ensembldb', '2.0.2', bioconductor_options), ('biovizBase', '1.24.0', bioconductor_options), ('OrganismDbi', '1.18.0', bioconductor_options), ('ggbio', '1.24.0', bioconductor_options), @@ -139,7 +139,7 @@ exts_list = [ ('cummeRbund', '2.18.0', bioconductor_options), ('GenomicFiles', '1.12.0', bioconductor_options), ('derfinderHelper', '1.10.0', bioconductor_options), - ('derfinder', '1.10.3', bioconductor_options), + ('derfinder', '1.10.4', bioconductor_options), ('polyester', '1.12.0', bioconductor_options), ('Rsubread', '1.26.0', bioconductor_options), ('pcaMethods', '1.68.0', bioconductor_options), -- GitLab From 3f0ada5a6a3e896ab3d5f024164f312bd567fd82 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 30 May 2017 09:00:31 +0200 Subject: [PATCH 0827/1603] comment added to patch, commendted line deleted, sanity check added --- .../Bio-SamTools-1.43-intel-2017a-Perl-5.24.1.eb | 6 +++++- .../easyconfigs/b/Bio-SamTools/Bio-SamTools-1.43.patch | 2 ++ 2 files changed, 7 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/Bio-SamTools/Bio-SamTools-1.43-intel-2017a-Perl-5.24.1.eb b/easybuild/easyconfigs/b/Bio-SamTools/Bio-SamTools-1.43-intel-2017a-Perl-5.24.1.eb index f1f376b07b..0ba564434a 100644 --- a/easybuild/easyconfigs/b/Bio-SamTools/Bio-SamTools-1.43-intel-2017a-Perl-5.24.1.eb +++ b/easybuild/easyconfigs/b/Bio-SamTools/Bio-SamTools-1.43-intel-2017a-Perl-5.24.1.eb @@ -12,7 +12,6 @@ toolchainopts = {'pic': True} source_urls = ['http://search.cpan.org/CPAN/authors/id/L/LD/LDS'] sources = [SOURCE_TAR_GZ] -#sources = [(SOURCE_TAR_GZ, 'tar -xzf %s && chmod -R +w .')] patches = ['%(name)s-%(version)s.patch'] @@ -24,4 +23,9 @@ dependencies = [ options = {'modulename': 'Bio::DB::Sam'} +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['bam2bedgraph', 'bamToGBrowse.pl', 'chrom_sizes.pl', 'genomeCoverageBed.pl']], + 'dirs': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/%s' % x for x in ['auto', 'Bio']], +} + moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/Bio-SamTools/Bio-SamTools-1.43.patch b/easybuild/easyconfigs/b/Bio-SamTools/Bio-SamTools-1.43.patch index d1342c786b..836cc7a688 100644 --- a/easybuild/easyconfigs/b/Bio-SamTools/Bio-SamTools-1.43.patch +++ b/easybuild/easyconfigs/b/Bio-SamTools/Bio-SamTools-1.43.patch @@ -1,3 +1,5 @@ +# Take EB provided SAMtools, and use thge correct include path. Pick EB provided CC and CFLAGS as well +# May 29th 2017 by B. Hajgato (Free University Brussles - VUB) --- Bio-SamTools-1.43/Build.PL.orig 2016-02-12 20:31:32.000000000 +0100 +++ Bio-SamTools-1.43/Build.PL 2017-05-26 13:22:23.318323680 +0200 @@ -75,7 +75,7 @@ -- GitLab From 2488a83fd7a9abff45eb9fc3646c3ffdd8f5993c Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 30 May 2017 09:02:13 +0200 Subject: [PATCH 0828/1603] commendted line deleted --- easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.17-intel-2017a.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.17-intel-2017a.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.17-intel-2017a.eb index 0424b6875f..53a5edea87 100644 --- a/easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.17-intel-2017a.eb +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.17-intel-2017a.eb @@ -11,8 +11,6 @@ toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['https://github.com/samtools/%(namelower)s/archive/%(version)s'] -#patches = ['SAMtools-%(version)s_Makefile-ncurses.patch'] - dependencies = [ ('ncurses', '6.0'), ('zlib', '1.2.11'), -- GitLab From 6b7fff6124dd480089a2e2c619ea05622bea40af Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 30 May 2017 09:05:27 +0200 Subject: [PATCH 0829/1603] Typo --- easybuild/easyconfigs/b/Bio-SamTools/Bio-SamTools-1.43.patch | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/Bio-SamTools/Bio-SamTools-1.43.patch b/easybuild/easyconfigs/b/Bio-SamTools/Bio-SamTools-1.43.patch index 836cc7a688..22981ce8a4 100644 --- a/easybuild/easyconfigs/b/Bio-SamTools/Bio-SamTools-1.43.patch +++ b/easybuild/easyconfigs/b/Bio-SamTools/Bio-SamTools-1.43.patch @@ -1,4 +1,4 @@ -# Take EB provided SAMtools, and use thge correct include path. Pick EB provided CC and CFLAGS as well +# Take EB provided SAMtools, and use the correct include path. Pick EB provided CC and CFLAGS as well. # May 29th 2017 by B. Hajgato (Free University Brussles - VUB) --- Bio-SamTools-1.43/Build.PL.orig 2016-02-12 20:31:32.000000000 +0100 +++ Bio-SamTools-1.43/Build.PL 2017-05-26 13:22:23.318323680 +0200 -- GitLab From f74a8b87473783613e05ea29b2e7a3727f4d3c0f Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 30 May 2017 10:01:52 +0200 Subject: [PATCH 0830/1603] %% --- .../b/Bio-SamTools/Bio-SamTools-1.43-intel-2017a-Perl-5.24.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/Bio-SamTools/Bio-SamTools-1.43-intel-2017a-Perl-5.24.1.eb b/easybuild/easyconfigs/b/Bio-SamTools/Bio-SamTools-1.43-intel-2017a-Perl-5.24.1.eb index 0ba564434a..870337a366 100644 --- a/easybuild/easyconfigs/b/Bio-SamTools/Bio-SamTools-1.43-intel-2017a-Perl-5.24.1.eb +++ b/easybuild/easyconfigs/b/Bio-SamTools/Bio-SamTools-1.43-intel-2017a-Perl-5.24.1.eb @@ -25,7 +25,7 @@ options = {'modulename': 'Bio::DB::Sam'} sanity_check_paths = { 'files': ['bin/%s' % x for x in ['bam2bedgraph', 'bamToGBrowse.pl', 'chrom_sizes.pl', 'genomeCoverageBed.pl']], - 'dirs': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/%s' % x for x in ['auto', 'Bio']], + 'dirs': ['lib/perl5/site_perl/%%(perlver)s/x86_64-linux-thread-multi/%s' % x for x in ['auto', 'Bio']], } moduleclass = 'bio' -- GitLab From 97a13bcb686c35c4aa438e0c8025f7e15e933f37 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 30 May 2017 14:53:01 +0200 Subject: [PATCH 0831/1603] adding easyconfigs: GDAL-2.1.3-intel-2017a-Python-3.6.1.eb --- .../GDAL-2.1.3-intel-2017a-Python-3.6.1.eb | 48 +++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/g/GDAL/GDAL-2.1.3-intel-2017a-Python-3.6.1.eb diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-2.1.3-intel-2017a-Python-3.6.1.eb b/easybuild/easyconfigs/g/GDAL/GDAL-2.1.3-intel-2017a-Python-3.6.1.eb new file mode 100644 index 0000000000..cfd1d42ed3 --- /dev/null +++ b/easybuild/easyconfigs/g/GDAL/GDAL-2.1.3-intel-2017a-Python-3.6.1.eb @@ -0,0 +1,48 @@ +easyblock = 'ConfigureMake' + +name = 'GDAL' +version = '2.1.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.gdal.org/' +description = """GDAL is a translator library for raster geospatial data formats that is released under an X/MIT style + Open Source license by the Open Source Geospatial Foundation. As a library, it presents a single abstract data model + to the calling application for all supported formats. It also comes with a variety of useful commandline utilities for + data translation and processing.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'usempi': True} + +source_urls = ['http://download.osgeo.org/gdal/%(version)s/'] +sources = [SOURCELOWER_TAR_XZ] +patches = ['GDAL-%(version)s_fix-uchar-definition.patch'] + +dependencies = [ + ('Python', '3.6.1'), + ('netCDF', '4.4.1.1'), + ('expat', '2.2.0'), + ('GEOS', '3.6.1', versionsuffix), + ('SQLite', '3.17.0'), + ('libxml2', '2.9.4'), + ('libpng', '1.6.29'), + ('libjpeg-turbo', '1.5.1'), + ('JasPer', '2.0.12'), + ('LibTIFF', '4.0.7'), + ('zlib', '1.2.11'), + ('cURL', '7.53.1'), + ('PCRE', '8.40'), +] + +configopts = '--with-expat=$EBROOTEXPAT --with-libz=$EBROOTLIBZ --with-hdf5=$EBROOTHDF5 --with-netcdf=$EBROOTNETCDF' +configopts += ' --with-xml2=$EBROOTLIBXML2 --with-geos=$EBROOTGEOS/bin/geos-config --with-jpeg=$EBROOTLIBJPEGMINTURBO' +configopts += ' --with-png=$EBROOTLIBPNG --with-sqlite3=$EBROOTSQLITE --with-jasper=$EBROOTJASPER' +configopts += ' --with-libtiff=$EBROOTLIBTIFF --with-pcre=$EBROOTPCRE --with-python=$EBROOTPYTHON/bin/python' + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +sanity_check_paths = { + 'files': ['lib/libgdal.a', 'lib/libgdal.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include', 'lib/python%(pyshortver)s/site-packages'] +} + +moduleclass = 'data' -- GitLab From 6e0a1b93609cf2adde1bcabeef52593207497f33 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Wed, 31 May 2017 14:59:12 +1200 Subject: [PATCH 0832/1603] New Easyconfig for Doxygen 1.8.13 and certain dependencies with the gimkl 2017a toolchain --- .../b/Bison/Bison-3.0.4-gimkl-2017a.eb | 22 +++++++++++++++++++ .../d/Doxygen/Doxygen-1.8.13-gimkl-2017a.eb | 21 ++++++++++++++++++ .../f/flex/flex-2.6.3-gimkl-2017a.eb | 22 +++++++++++++++++++ .../h/help2man/help2man-1.47.4-gimkl-2017a.eb | 19 ++++++++++++++++ 4 files changed, 84 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bison/Bison-3.0.4-gimkl-2017a.eb create mode 100644 easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.13-gimkl-2017a.eb create mode 100644 easybuild/easyconfigs/f/flex/flex-2.6.3-gimkl-2017a.eb create mode 100644 easybuild/easyconfigs/h/help2man/help2man-1.47.4-gimkl-2017a.eb diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.4-gimkl-2017a.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-gimkl-2017a.eb new file mode 100644 index 0000000000..7ef2e128f5 --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-gimkl-2017a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'Bison' +version = '3.0.4' + +homepage = 'http://www.gnu.org/software/bison' +description = """Bison is a general-purpose parser generator that converts an annotated context-free grammar + into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.""" + +toolchain = {'name': 'gimkl', 'version': '2017a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +builddependencies = [('M4', '1.4.17', '', True)] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["bison", "yacc"]] + ["lib/liby.a"], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.13-gimkl-2017a.eb b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.13-gimkl-2017a.eb new file mode 100644 index 0000000000..5872a02692 --- /dev/null +++ b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.13-gimkl-2017a.eb @@ -0,0 +1,21 @@ +name = 'Doxygen' +version = '1.8.13' + +homepage = 'http://www.doxygen.org' +description = """Doxygen is a documentation system for C++, C, Java, Objective-C, Python, + IDL (Corba and Microsoft flavors), Fortran, VHDL, PHP, C#, and to some extent D.""" + +toolchain = {'name': 'gimkl', 'version': '2017a'} + +sources = ['%(namelower)s-%(version)s.src.tar.gz'] +source_urls = ['http://ftp.stack.nl/pub/users/dimitri/'] + +builddependencies = [ + ('CMake', '3.6.1', '', True), + ('flex', '2.6.3'), + ('Bison', '3.0.4'), +] + +parallel = 1 + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.3-gimkl-2017a.eb b/easybuild/easyconfigs/f/flex/flex-2.6.3-gimkl-2017a.eb new file mode 100644 index 0000000000..6d9bee0a21 --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.6.3-gimkl-2017a.eb @@ -0,0 +1,22 @@ +name = 'flex' +version = '2.6.3' + +homepage = 'http://flex.sourceforge.net/' +description = """Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, + sometimes called a tokenizer, is a program which recognizes lexical patterns in text.""" + +toolchain = {'name': 'gimkl', 'version': '2017a'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['https://github.com/westes/flex/releases/download/v%(version)s/'] + +checksums = ['a5f65570cd9107ec8a8ec88f17b31bb1'] + +dependencies = [('M4', '1.4.17', '', True)] +builddependencies = [ + ('Bison', '3.0.4'), + ('help2man', '1.47.4'), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/h/help2man/help2man-1.47.4-gimkl-2017a.eb b/easybuild/easyconfigs/h/help2man/help2man-1.47.4-gimkl-2017a.eb new file mode 100644 index 0000000000..f8074a8548 --- /dev/null +++ b/easybuild/easyconfigs/h/help2man/help2man-1.47.4-gimkl-2017a.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'help2man' +version = '1.47.4' + +homepage = 'https://www.gnu.org/software/help2man/' +description = """help2man produces simple manual pages from the '--help' and '--version' output of other commands.""" + +toolchain = {'name': 'gimkl', 'version': '2017a'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_XZ] + +sanity_check_paths = { + 'files': ['bin/help2man'], + 'dirs': [], +} + +moduleclass = 'tools' -- GitLab From 2751fbdc6cdc809fe36a7f31d5e266939ff490cd Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Wed, 31 May 2017 15:42:23 +1200 Subject: [PATCH 0833/1603] A 2017a version of the gimkl toolchain --- easybuild/easyconfigs/g/gimkl/gimkl-2017a.eb | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) create mode 100644 easybuild/easyconfigs/g/gimkl/gimkl-2017a.eb diff --git a/easybuild/easyconfigs/g/gimkl/gimkl-2017a.eb b/easybuild/easyconfigs/g/gimkl/gimkl-2017a.eb new file mode 100644 index 0000000000..553786dd35 --- /dev/null +++ b/easybuild/easyconfigs/g/gimkl/gimkl-2017a.eb @@ -0,0 +1,19 @@ +easyblock = "Toolchain" + +name = 'gimkl' +version = '2017a' + +homepage = '(none)' +description = """GNU Compiler Collection (GCC) based compiler toolchain with Intel MPI and MKL""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +comp = ('GCC', '5.4.0') + +dependencies = [ + comp, + ('impi', '2017.1.132', '', comp), + ('imkl', '2017.1.132', '', ('gimpi', version)), +] + +moduleclass = 'toolchain' -- GitLab From 4971ea3b19ffb8af7a0b2e0ebf97fc357cf2c053 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Wed, 31 May 2017 15:47:40 +1200 Subject: [PATCH 0834/1603] EasyConfig for CMake 3.6.1 with no particular toolchain --- easybuild/easyconfigs/c/CMake/CMake-3.6.1.eb | 28 ++++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.6.1.eb diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.6.1.eb b/easybuild/easyconfigs/c/CMake/CMake-3.6.1.eb new file mode 100644 index 0000000000..0e73857b1d --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.6.1.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.6.1' + +homepage = 'http://www.cmake.org' +description = """CMake, the cross-platform, open-source build system. + CMake is a family of tools designed to build, test and package software.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = '-- -DCMAKE_USE_OPENSSL=1' + +# Don't depend on anything, since we will use this to build other software +# which might want different versions of the same dependency, eg: ncurses +dependencies = [] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From 53b4a44a6c1a9ffab69de2ceb4540cf012836042 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Wed, 31 May 2017 06:54:12 +0100 Subject: [PATCH 0835/1603] adding easyconfigs: buildenv-default-intel-2017a.eb --- .../b/buildenv/buildenv-default-intel-2017a.eb | 13 +++++++++++++ 1 file changed, 13 insertions(+) create mode 100755 easybuild/easyconfigs/b/buildenv/buildenv-default-intel-2017a.eb diff --git a/easybuild/easyconfigs/b/buildenv/buildenv-default-intel-2017a.eb b/easybuild/easyconfigs/b/buildenv/buildenv-default-intel-2017a.eb new file mode 100755 index 0000000000..ba8c60067e --- /dev/null +++ b/easybuild/easyconfigs/b/buildenv/buildenv-default-intel-2017a.eb @@ -0,0 +1,13 @@ +easyblock = 'BuildEnv' + +name = 'buildenv' +version = 'default' + +homepage = 'None' +description = """This module sets a group of environment variables for compilers, linkers, maths libraries, etc., that + you can use to easily transition between toolchains when building your software. To query the variables being set + please use: module show """ + +toolchain = {'name': 'intel', 'version': '2017a'} + +moduleclass = 'devel' -- GitLab From 073bc69b50039a97d6873a31137f238e1a9f4bc5 Mon Sep 17 00:00:00 2001 From: Robert Date: Wed, 31 May 2017 15:40:09 +0930 Subject: [PATCH 0836/1603] CNVnator added --- easybuild/easyconfigs/TEMPLATE.eb | 31 -------------- .../c/CNVnator/CNVnator-0.3.3-foss-2016b.eb | 40 +++++++++++++++++++ 2 files changed, 40 insertions(+), 31 deletions(-) delete mode 100644 easybuild/easyconfigs/TEMPLATE.eb create mode 100644 easybuild/easyconfigs/c/CNVnator/CNVnator-0.3.3-foss-2016b.eb diff --git a/easybuild/easyconfigs/TEMPLATE.eb b/easybuild/easyconfigs/TEMPLATE.eb deleted file mode 100644 index 69759ec8da..0000000000 --- a/easybuild/easyconfigs/TEMPLATE.eb +++ /dev/null @@ -1,31 +0,0 @@ -# Note: -# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild -# It was auto-generated based on a template easyconfig, so it should be used with care. -easyblock = 'ConfigureMake' - -name = 'NAME' -version = 'VERSION' - -homepage = 'http://www.example.com' -description = """TEMPLATE DESCRIPTION""" - -# toolchain name should be 'TEMPLATE' if this is a template, so EasyBuild knows and is willing to use it as a template -toolchain = {'name': 'TEMPLATE', 'version': 'TK_VERSION'} -toolchainopts = {} # toolchain options, e.g. opt, pic, usempi, optarch, ... - -# For sources line to work correctly with --try-software-version, you MUST employ %s OR use a construct like SOURCE_TAR_GZ -sources = ['%(name)s-%(version)s.tar.gz'] -source_urls = ['http://www.example.com'] - -patches = [] - -dependencies = [] - -# The sanity test MUST be tuned before going production and submitting your contribution to upstream git repositories -sanity_check_paths = { - 'files': [], - 'dirs': ["."] -} - -# You SHOULD change the following line; Kindly consult other easyconfigs for possible options -moduleclass = 'base' diff --git a/easybuild/easyconfigs/c/CNVnator/CNVnator-0.3.3-foss-2016b.eb b/easybuild/easyconfigs/c/CNVnator/CNVnator-0.3.3-foss-2016b.eb new file mode 100644 index 0000000000..702088ee73 --- /dev/null +++ b/easybuild/easyconfigs/c/CNVnator/CNVnator-0.3.3-foss-2016b.eb @@ -0,0 +1,40 @@ +## +# This is a contribution from Phoenix HPC Service, The University of Adelaide, Australia +# Homepage: https://www.adelaide.edu.au/phoenix/ +# +# Copyright:: Copyright 2014-2017 adelaide.edu.au/phoenix +# Authors:: Robert Qiao , Exequiel Sepulveda +# License:: CCPL +# +# Notes:: +## + +easyblock = 'MakeCp' + +name = 'CNVnator' +version = '0.3.3' + +homepage = 'https://github.com/abyzovlab/CNVnator' +description = """ a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads +""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +sources = ['v%(version)s/%(name)s_v%(version)s.zip'] +source_urls = ['https://github.com/abyzovlab/CNVnator/releases/download'] + +dependencies = [ + ('Perl', '5.24.0'), +] + +skipsteps = ['build'] + +files_to_copy = [(['cnvnator2VCF.pl'], 'bin')] + + +sanity_check_paths = { + 'files': ['bin/cnvnator2VCF.pl'] , + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From e58bb5f0388828466c00673f51c987d8907acd55 Mon Sep 17 00:00:00 2001 From: Robert Qiao Date: Wed, 31 May 2017 15:54:51 +0930 Subject: [PATCH 0837/1603] correction --- easybuild/easyconfigs/TEMPLATE.eb | 31 +++++++++++++++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/TEMPLATE.eb diff --git a/easybuild/easyconfigs/TEMPLATE.eb b/easybuild/easyconfigs/TEMPLATE.eb new file mode 100644 index 0000000000..69759ec8da --- /dev/null +++ b/easybuild/easyconfigs/TEMPLATE.eb @@ -0,0 +1,31 @@ +# Note: +# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# It was auto-generated based on a template easyconfig, so it should be used with care. +easyblock = 'ConfigureMake' + +name = 'NAME' +version = 'VERSION' + +homepage = 'http://www.example.com' +description = """TEMPLATE DESCRIPTION""" + +# toolchain name should be 'TEMPLATE' if this is a template, so EasyBuild knows and is willing to use it as a template +toolchain = {'name': 'TEMPLATE', 'version': 'TK_VERSION'} +toolchainopts = {} # toolchain options, e.g. opt, pic, usempi, optarch, ... + +# For sources line to work correctly with --try-software-version, you MUST employ %s OR use a construct like SOURCE_TAR_GZ +sources = ['%(name)s-%(version)s.tar.gz'] +source_urls = ['http://www.example.com'] + +patches = [] + +dependencies = [] + +# The sanity test MUST be tuned before going production and submitting your contribution to upstream git repositories +sanity_check_paths = { + 'files': [], + 'dirs': ["."] +} + +# You SHOULD change the following line; Kindly consult other easyconfigs for possible options +moduleclass = 'base' -- GitLab From b7117a7ee415d84ffa4312f7ea047ed3b43e1a2d Mon Sep 17 00:00:00 2001 From: Robert Date: Wed, 31 May 2017 15:57:06 +0930 Subject: [PATCH 0838/1603] style fixed --- easybuild/easyconfigs/c/CNVnator/CNVnator-0.3.3-foss-2016b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CNVnator/CNVnator-0.3.3-foss-2016b.eb b/easybuild/easyconfigs/c/CNVnator/CNVnator-0.3.3-foss-2016b.eb index 702088ee73..c3f9fc44b3 100644 --- a/easybuild/easyconfigs/c/CNVnator/CNVnator-0.3.3-foss-2016b.eb +++ b/easybuild/easyconfigs/c/CNVnator/CNVnator-0.3.3-foss-2016b.eb @@ -33,7 +33,7 @@ files_to_copy = [(['cnvnator2VCF.pl'], 'bin')] sanity_check_paths = { - 'files': ['bin/cnvnator2VCF.pl'] , + 'files': ['bin/cnvnator2VCF.pl'], 'dirs': [], } -- GitLab From 0664518e768281132e9cb8338180e0f148cf6dfc Mon Sep 17 00:00:00 2001 From: Robert Date: Wed, 31 May 2017 17:17:36 +0930 Subject: [PATCH 0839/1603] easyblock corrected --- easybuild/easyconfigs/c/CNVnator/CNVnator-0.3.3-foss-2016b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CNVnator/CNVnator-0.3.3-foss-2016b.eb b/easybuild/easyconfigs/c/CNVnator/CNVnator-0.3.3-foss-2016b.eb index c3f9fc44b3..83fea79140 100644 --- a/easybuild/easyconfigs/c/CNVnator/CNVnator-0.3.3-foss-2016b.eb +++ b/easybuild/easyconfigs/c/CNVnator/CNVnator-0.3.3-foss-2016b.eb @@ -9,7 +9,7 @@ # Notes:: ## -easyblock = 'MakeCp' +easyblock = 'CmdCp' name = 'CNVnator' version = '0.3.3' -- GitLab From ecdd4e4dfe5013664a6a7b7a33ca36f26f3a8c79 Mon Sep 17 00:00:00 2001 From: Robert Date: Wed, 31 May 2017 18:35:56 +0930 Subject: [PATCH 0840/1603] {bio}[foss/2016b] GroopM and deps --- .../b/BAMM/BAMM-2.5.0-foss-2016b.eb | 37 +++++++++++++ .../b/BWA/BWA-0.7.15-foss-2016b.eb | 26 +++++++++ .../BamM-1.7.3-foss-2016b-Python-2.7.13.eb | 38 +++++++++++++ .../Cython-0.25.2-foss-2016b-Python-2.7.13.eb | 36 ++++++++++++ .../GroopM-0.3.4-foss-2016b-Python-2.7.13.eb | 46 ++++++++++++++++ ...tplotlib-1.5.2-foss-2016b-Python-2.7.13.eb | 55 +++++++++++++++++++ .../PIL/PIL-1.1.7-foss-2016b-Python-2.7.13.eb | 43 +++++++++++++++ ...PyTables-3.2.2-foss-2016b-Python-2.7.13.eb | 46 ++++++++++++++++ .../scipy-0.17.1-foss-2016b-Python-2.7.13.eb | 30 ++++++++++ 9 files changed, 357 insertions(+) create mode 100644 easybuild/easyconfigs/b/BAMM/BAMM-2.5.0-foss-2016b.eb create mode 100644 easybuild/easyconfigs/b/BWA/BWA-0.7.15-foss-2016b.eb create mode 100644 easybuild/easyconfigs/b/BamM/BamM-1.7.3-foss-2016b-Python-2.7.13.eb create mode 100644 easybuild/easyconfigs/c/Cython/Cython-0.25.2-foss-2016b-Python-2.7.13.eb create mode 100644 easybuild/easyconfigs/g/GroopM/GroopM-0.3.4-foss-2016b-Python-2.7.13.eb create mode 100644 easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.2-foss-2016b-Python-2.7.13.eb create mode 100644 easybuild/easyconfigs/p/PIL/PIL-1.1.7-foss-2016b-Python-2.7.13.eb create mode 100644 easybuild/easyconfigs/p/PyTables/PyTables-3.2.2-foss-2016b-Python-2.7.13.eb create mode 100644 easybuild/easyconfigs/s/scipy/scipy-0.17.1-foss-2016b-Python-2.7.13.eb diff --git a/easybuild/easyconfigs/b/BAMM/BAMM-2.5.0-foss-2016b.eb b/easybuild/easyconfigs/b/BAMM/BAMM-2.5.0-foss-2016b.eb new file mode 100644 index 0000000000..67e73478f5 --- /dev/null +++ b/easybuild/easyconfigs/b/BAMM/BAMM-2.5.0-foss-2016b.eb @@ -0,0 +1,37 @@ +## +# This is a contribution from Phoenix HPC Service, The University of Adelaide, Australia +# Homepage: https://www.adelaide.edu.au/phoenix/ +# +# Copyright:: Copyright 2014-2017 adelaide.edu.au/phoenix +# Authors:: Robert Qiao , Exequiel Sepulveda +# License:: GPL-v3.0 +# +# Notes:: +## + +easyblock = 'CMakeMake' + +name = 'BAMM' +version = '2.5.0' + +homepage = 'http://bamm-project.org/' +description = """ BAMM is oriented entirely towards detecting and quantifying heterogeneity in evolutionary rates. +It uses reversible jump Markov chain Monte Carlo to automatically explore a vast universe of candidate models of +lineage diversification and trait evolution. """ + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/macroevolution/bamm/archive'] +sources = ['v%(version)s.tar.gz'] + +builddependencies = [ + ('CMake', '3.7.2'), +] + +sanity_check_paths = { + 'files': ['bin/bamm'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BWA/BWA-0.7.15-foss-2016b.eb b/easybuild/easyconfigs/b/BWA/BWA-0.7.15-foss-2016b.eb new file mode 100644 index 0000000000..ceb6b4b6b3 --- /dev/null +++ b/easybuild/easyconfigs/b/BWA/BWA-0.7.15-foss-2016b.eb @@ -0,0 +1,26 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Cyprus Institute / CaSToRC, Uni.Lu/LCSB, NTUA +# Authors:: George Tsouloupas , Fotis Georgatos +# License:: MIT/GPL +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +# Modified:: Robert Qiao @ adelaide.edu.au/phoenix +## + +name = 'BWA' +version = '0.7.15' + +homepage = 'http://bio-bwa.sourceforge.net/' +description = """Burrows-Wheeler Aligner (BWA) is an efficient program that aligns + relatively short nucleotide sequences against a long reference sequence such as the human genome.""" + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'optarch': True, 'pic': True, 'usempi': True} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = [('http://sourceforge.net/projects/bio-bwa/files/', 'download')] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BamM/BamM-1.7.3-foss-2016b-Python-2.7.13.eb b/easybuild/easyconfigs/b/BamM/BamM-1.7.3-foss-2016b-Python-2.7.13.eb new file mode 100644 index 0000000000..c73686a30c --- /dev/null +++ b/easybuild/easyconfigs/b/BamM/BamM-1.7.3-foss-2016b-Python-2.7.13.eb @@ -0,0 +1,38 @@ +## +# This is a contribution from Phoenix HPC Service, The University of Adelaide, Australia +# Homepage: https://www.adelaide.edu.au/phoenix/ +# +# Copyright:: Copyright 2014-2017 adelaide.edu.au/phoenix +# Authors:: Robert Qiao , Exequiel Sepulveda +# License:: GPL-v3.0 +# +# Notes:: +## + +easyblock = 'PythonPackage' + +name = 'BamM' +version = '1.7.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://ecogenomics.github.io/BamM/' +description = """ BamM is a c library, wrapped in python, that parses BAM files """ + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/Ecogenomics/BamM/archive'] +sources = ['%(version)s.tar.gz'] + +dependencies = [ + ('Python', '2.7.13'), + ('SAMtools', '1.3.1'), + ('BWA', '0.7.15'), +] + +sanity_check_paths = { + 'files': ['bin/bamm'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/Cython/Cython-0.25.2-foss-2016b-Python-2.7.13.eb b/easybuild/easyconfigs/c/Cython/Cython-0.25.2-foss-2016b-Python-2.7.13.eb new file mode 100644 index 0000000000..07286ce8e2 --- /dev/null +++ b/easybuild/easyconfigs/c/Cython/Cython-0.25.2-foss-2016b-Python-2.7.13.eb @@ -0,0 +1,36 @@ +## +# This is a contribution from Phoenix HPC Service, The University of Adelaide, Australia +# Homepage: https://www.adelaide.edu.au/phoenix/ +# +# Copyright:: Copyright 2014-2017 adelaide.edu.au/phoenix +# Authors:: Robert Qiao , Exequiel Sepulveda +# License:: Apache +# +# Notes:: +## + +easyblock = 'PythonPackage' + +name = 'Cython' +version = '0.25.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pypi.python.org/pypi/Cython/' +description = """The Cython language makes writing C extensions for the Python language as easy as Python itself. +Cython is a source code translator based on the well-known Pyrex, +but supports more cutting edge functionality and optimizations.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [('Python', '2.7.13')] + +cythonlibdir = 'lib/python%(pyshortver)s/site-packages/Cython-%(version)s-py%(pyshortver)s-linux-x86_64.egg' +sanity_check_paths = { + 'files': ['bin/cygdb', 'bin/cython', '%s/%%(namelower)s.py' % cythonlibdir], + 'dirs': [cythonlibdir + '/%(name)s'] +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/g/GroopM/GroopM-0.3.4-foss-2016b-Python-2.7.13.eb b/easybuild/easyconfigs/g/GroopM/GroopM-0.3.4-foss-2016b-Python-2.7.13.eb new file mode 100644 index 0000000000..e52a60624a --- /dev/null +++ b/easybuild/easyconfigs/g/GroopM/GroopM-0.3.4-foss-2016b-Python-2.7.13.eb @@ -0,0 +1,46 @@ +## +# This is a contribution from Phoenix HPC Service, The University of Adelaide, Australia +# Homepage: https://www.adelaide.edu.au/phoenix/ +# +# Copyright:: adelaide.edu.au/phoenix +# Authors:: Robert Qiao , Exe Escobedo +# License:: MIT +# +# Notes:: +### + +easyblock = 'PythonPackage' + +name = 'GroopM' +version = '0.3.4' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://ecogenomics.github.io/GroopM/' +description = """ GroopM is a metagenomic binning toolset. It leverages spatio-temoral +dynamics (differential coverage) to accurately (and almost automatically) +extract population genomes from multi-sample metagenomic datasets. +""" +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.13'), + ('Cython', '0.25.2', versionsuffix), + ('numpy', '1.11.1', versionsuffix), + ('scipy', '0.17.1', versionsuffix), + ('matplotlib', '1.5.2', versionsuffix), + ('Pysam', '0.10.0', versionsuffix), + ('PyTables', '3.2.2', versionsuffix), + ('PIL', '1.1.7', versionsuffix), + ('BamM', '1.7.3', versionsuffix), + ('GTK+', '2.24.31'), +] + +sanity_check_paths = { + 'files': ["bin/groopm"], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.2-foss-2016b-Python-2.7.13.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.2-foss-2016b-Python-2.7.13.eb new file mode 100644 index 0000000000..6e664a2059 --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.2-foss-2016b-Python-2.7.13.eb @@ -0,0 +1,55 @@ +## +# This is a contribution from Phoenix HPC Service, The University of Adelaide, Australia +# Homepage: https://www.adelaide.edu.au/phoenix/ +# +# Copyright:: Copyright 2014-2017 adelaide.edu.au/phoenix +# Authors:: Robert Qiao , Exequiel Sepulveda +# License:: Python Software Foundation (PSF) +# +# Notes:: +## + +easyblock = 'Bundle' + +name = 'matplotlib' +version = '1.5.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://matplotlib.org' +description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of + hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python + and ipython shell, web application servers, and six graphical user interface toolkits.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' + +dependencies = [ + ('Python', '2.7.13'), + ('freetype', '2.6.5'), + ('libpng', '1.6.24'), +] + +exts_list = [ + ('Cycler', '0.10.0', { + 'modulename': 'cycler', + 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], + 'source_tmpl': 'cycler-%(version)s.tar.gz', + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], + }), +] + +# specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module +full_sanity_check = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/PIL/PIL-1.1.7-foss-2016b-Python-2.7.13.eb b/easybuild/easyconfigs/p/PIL/PIL-1.1.7-foss-2016b-Python-2.7.13.eb new file mode 100644 index 0000000000..18f032a1ca --- /dev/null +++ b/easybuild/easyconfigs/p/PIL/PIL-1.1.7-foss-2016b-Python-2.7.13.eb @@ -0,0 +1,43 @@ +## +# This is a contribution from Phoenix HPC Service, The University of Adelaide, Australia +# Homepage: https://www.adelaide.edu.au/phoenix/ +# +# Copyright:: Copyright 2014-2017 adelaide.edu.au/phoenix +# Authors:: Robert Qiao , Exequiel Sepulveda +# License:: Python Imaging Library License +# +# Notes:: +## + +easyblock = 'PythonPackage' + +name = 'PIL' +version = '1.1.7' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.pythonware.com/products/pil' +description = """The Python Imaging Library (PIL) adds image processing capabilities to your Python interpreter. + This library supports many file formats, and provides powerful image processing and graphics capabilities.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['http://effbot.org/downloads/'] +sources = ['Imaging-%(version)s.tar.gz'] + +patches = ['PIL-%(version)s-find-deps.patch'] + +dependencies = [ + ('zlib', '1.2.8'), + ('Python', '2.7.13'), + ('libjpeg-turbo', '1.5.0'), + ('freetype', '2.7'), +] + +options = {'modulename': 'PIL'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['bin', 'lib/python%(pyshortver)s/site-packages/%(name)s'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/PyTables/PyTables-3.2.2-foss-2016b-Python-2.7.13.eb b/easybuild/easyconfigs/p/PyTables/PyTables-3.2.2-foss-2016b-Python-2.7.13.eb new file mode 100644 index 0000000000..2e0d15537e --- /dev/null +++ b/easybuild/easyconfigs/p/PyTables/PyTables-3.2.2-foss-2016b-Python-2.7.13.eb @@ -0,0 +1,46 @@ +## +# This is a contribution from Phoenix HPC Service, The University of Adelaide, Australia +# Homepage: https://www.adelaide.edu.au/phoenix/ +# +# Copyright:: Copyright 2014-2017 adelaide.edu.au/phoenix +# Authors:: Robert Qiao , Exequiel Sepulveda +# License:: BSD +# +# Notes:: +## + +easyblock = 'PythonPackage' + +name = 'PyTables' +version = '3.3.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.pytables.org' +description = """PyTables is a package for managing hierarchical datasets and designed to efficiently and easily cope + with extremely large amounts of data. PyTables is built on top of the HDF5 library, using the Python language and the + NumPy package. It features an object-oriented interface that, combined with C extensions for the performance-critical + parts of the code (generated using Cython), makes it a fast, yet extremely easy to use tool for interactively browse, + process and search very large amounts of data. One important feature of PyTables is that it optimizes memory and disk + resources so that data takes much less space (specially if on-flight compression is used) than other solutions such as + relational or object oriented databases.""" + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/PyTables/PyTables/archive/'] +sources = ['v%(version)s.tar.gz'] + +dependencies = [ + ('Python', '2.7.13'), + ('numexpr', '2.6.1', versionsuffix), + ('HDF5', '1.8.18'), +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['pt2to3', 'ptdump', 'ptrepack']], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +options = {'modulename': 'tables'} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/scipy/scipy-0.17.1-foss-2016b-Python-2.7.13.eb b/easybuild/easyconfigs/s/scipy/scipy-0.17.1-foss-2016b-Python-2.7.13.eb new file mode 100644 index 0000000000..9faa2de7a7 --- /dev/null +++ b/easybuild/easyconfigs/s/scipy/scipy-0.17.1-foss-2016b-Python-2.7.13.eb @@ -0,0 +1,30 @@ +## +# This is a contribution from Phoenix HPC Service, The University of Adelaide, Australia +# Homepage: https://www.adelaide.edu.au/phoenix/ +# +# Copyright:: Copyright 2014-2017 adelaide.edu.au/phoenix +# Authors:: Robert Qiao , Exequiel Sepulveda +# License:: BSD-new +# +# Notes:: +## + +name = 'scipy' +version = '0.17.1' +versionsuffix = '-Python-2.7.13' + +homepage = 'http://www.scipy.org' +description = """SciPy is a collection of mathematical algorithms and convenience + functions built on the Numpy extension for Python.""" + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'usempi': True, 'pic': True} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('numpy', '1.11.1', versionsuffix), +] + +moduleclass = 'math' -- GitLab From ec8852a1a30776e009b35c378177c3ec52cb1558 Mon Sep 17 00:00:00 2001 From: Robert Qiao Date: Wed, 31 May 2017 18:48:48 +0930 Subject: [PATCH 0841/1603] file name fixed --- ...ython-2.7.13.eb => PyTables-3.3.0-foss-2016b-Python-2.7.13.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/p/PyTables/{PyTables-3.2.2-foss-2016b-Python-2.7.13.eb => PyTables-3.3.0-foss-2016b-Python-2.7.13.eb} (100%) diff --git a/easybuild/easyconfigs/p/PyTables/PyTables-3.2.2-foss-2016b-Python-2.7.13.eb b/easybuild/easyconfigs/p/PyTables/PyTables-3.3.0-foss-2016b-Python-2.7.13.eb similarity index 100% rename from easybuild/easyconfigs/p/PyTables/PyTables-3.2.2-foss-2016b-Python-2.7.13.eb rename to easybuild/easyconfigs/p/PyTables/PyTables-3.3.0-foss-2016b-Python-2.7.13.eb -- GitLab From d4ab52de4b6d9bad913ca1ef39fb9b28d445f85a Mon Sep 17 00:00:00 2001 From: Robert Date: Wed, 31 May 2017 20:48:39 +0930 Subject: [PATCH 0842/1603] numpy added --- .../numpy-1.11.1-foss-2016b-Python-2.7.13.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/n/numpy/numpy-1.11.1-foss-2016b-Python-2.7.13.eb diff --git a/easybuild/easyconfigs/n/numpy/numpy-1.11.1-foss-2016b-Python-2.7.13.eb b/easybuild/easyconfigs/n/numpy/numpy-1.11.1-foss-2016b-Python-2.7.13.eb new file mode 100644 index 0000000000..6c272594db --- /dev/null +++ b/easybuild/easyconfigs/n/numpy/numpy-1.11.1-foss-2016b-Python-2.7.13.eb @@ -0,0 +1,43 @@ +## +# This is a contribution from Phoenix HPC Service, The University of Adelaide, Australia +# Homepage: https://www.adelaide.edu.au/phoenix/ +# +# Copyright:: Copyright 2014-2017 adelaide.edu.au/phoenix +# Authors:: Robert Qiao , Exequiel Sepulveda +# License:: BSD-new +# +# Notes:: +## + +name = 'numpy' +version = '1.11.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.numpy.org' +description = """NumPy is the fundamental package for scientific computing with Python. It contains among other things: + a powerful N-dimensional array object, sophisticated (broadcasting) functions, tools for integrating C/C++ and Fortran + code, useful linear algebra, Fourier transform, and random number capabilities. Besides its obvious scientific uses, + NumPy can also be used as an efficient multi-dimensional container of generic data. Arbitrary data-types can be + defined. This allows NumPy to seamlessly and speedily integrate with a wide variety of databases.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_GZ] + +# patches = ['numpy-1.8.0-mkl.patch'] + +dependencies = [ + ('Python', '2.7.13'), +] + +# need to use pip rather than regular 'setup.py install' +# to ensure that this numpy wins over the one in the Python installation; +# using easy_install does not work... +use_pip = True + +# install as zipped egg to get a .pth file in lib/python*/site-packages; +# this enables shadowing of the numpy that is part of the Python installation +zipped_egg = True + +moduleclass = 'math' -- GitLab From d9b6a9c87e21756ed4d7aefa831f3818f87c099e Mon Sep 17 00:00:00 2001 From: Robert Date: Wed, 31 May 2017 21:34:13 +0930 Subject: [PATCH 0843/1603] SAMtools added --- .../numpy-1.11.1-foss-2016b-Python-2.7.13.eb | 2 -- .../s/SAMtools/SAMtools-1.3.1-foss-2016b.eb | 36 +++++++++++++++++++ 2 files changed, 36 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1-foss-2016b.eb diff --git a/easybuild/easyconfigs/n/numpy/numpy-1.11.1-foss-2016b-Python-2.7.13.eb b/easybuild/easyconfigs/n/numpy/numpy-1.11.1-foss-2016b-Python-2.7.13.eb index 6c272594db..90ade3ec90 100644 --- a/easybuild/easyconfigs/n/numpy/numpy-1.11.1-foss-2016b-Python-2.7.13.eb +++ b/easybuild/easyconfigs/n/numpy/numpy-1.11.1-foss-2016b-Python-2.7.13.eb @@ -25,8 +25,6 @@ toolchain = {'name': 'foss', 'version': '2016b'} source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCE_TAR_GZ] -# patches = ['numpy-1.8.0-mkl.patch'] - dependencies = [ ('Python', '2.7.13'), ] diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1-foss-2016b.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1-foss-2016b.eb new file mode 100644 index 0000000000..d688d2f69e --- /dev/null +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1-foss-2016b.eb @@ -0,0 +1,36 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Robert Schmidt , Cedric Laczny , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# Modified by: Adam Huffman +# The Francis Crick Institute +## + +name = 'SAMtools' +version = '1.3.1' + +homepage = 'http://www.htslib.org/' +description = """SAM Tools provide various utilities for manipulating alignments in the SAM format, + including sorting, merging, indexing and generating alignments in a per-position format.""" + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s'] +sources = [SOURCELOWER_TAR_BZ2] + +# Patch Makefile to link against zlib provided by EB +patches = ['SAMtools-%(version)s_Makefile.patch'] + +dependencies = [ + ('ncurses', '6.0'), + ('zlib', '1.2.8'), + ('bzip2', '1.0.6'), + ('XZ', '5.2.2'), +] + +moduleclass = 'bio' -- GitLab From 7f6ba11aeac585c11e57486efd5960a13e437e9f Mon Sep 17 00:00:00 2001 From: builduser Date: Wed, 31 May 2017 14:18:32 +0200 Subject: [PATCH 0844/1603] adding easyconfigs: NRGLjubljana-2.4.3.23-foss-2016b.eb --- .../NRGLjubljana-2.4.3.23-foss-2016b.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/n/NRGLjubljana/NRGLjubljana-2.4.3.23-foss-2016b.eb diff --git a/easybuild/easyconfigs/n/NRGLjubljana/NRGLjubljana-2.4.3.23-foss-2016b.eb b/easybuild/easyconfigs/n/NRGLjubljana/NRGLjubljana-2.4.3.23-foss-2016b.eb new file mode 100644 index 0000000000..3880dd3342 --- /dev/null +++ b/easybuild/easyconfigs/n/NRGLjubljana/NRGLjubljana-2.4.3.23-foss-2016b.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'NRGLjubljana' +version = '2.4.3.23' + +homepage = 'http://nrgljubljana.ijs.si/' +description = """ + NRG Ljubljana is an efficient implementation of the numerical renormalization group (NRG) + technique for solving quantum impurity problems that arise as simplified models of + magnetic impurities and as effective models in the dynamical mean field theory (DMFT) + approach to bulk correlated materials. +""" + +docurls = 'http://nrgljubljana.ijs.si/examples/' +software_license = 'LicenseGPLv3' + +toolchain = {'name': 'foss', 'version': '2016b'} +#toolchainopts = { 'usempi': True, 'pic': True } +toolchainopts = { 'pic': True } + +sources = [ '%(namelower)s-%(version)s.tar.gz' ] +source_urls = [ 'http://nrgljubljana.ijs.si/' ] + +configopts = "--with-tools --with-boost-serialization=boost_serialization CXXFLAGS=\"-Ddsyev=dsyev_ -Ddsyevr=dsyevr_ -Dzheev=zheev_ -Dzheevr=zheevr_\" LDFLAGS=\"-lopenblas -L${EBROOTBOOST}/lib\"" + +dependencies = [ + ('GMP', '6.1.2'), + ('GSL', '2.3'), + ('Boost', '1.61.0') +] + +sanity_check_paths = { + 'files': ["bin/nrg2_4", "bin/nrgcmpl2_4"], + 'dirs': [], +} + +moduleclass = 'phys' -- GitLab From e72c0086c925fdbb8319bd6345bd5dee601b56ba Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 31 May 2017 14:24:04 +0200 Subject: [PATCH 0845/1603] adding easyconfigs: FFTW-2.1.5-intel-2017a.eb --- .../f/FFTW/FFTW-2.1.5-intel-2017a.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/f/FFTW/FFTW-2.1.5-intel-2017a.eb diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-2.1.5-intel-2017a.eb b/easybuild/easyconfigs/f/FFTW/FFTW-2.1.5-intel-2017a.eb new file mode 100644 index 0000000000..313bc9e8bb --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW/FFTW-2.1.5-intel-2017a.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'FFTW' +version = '2.1.5' + +homepage = 'http://www.fftw.org' +description = """FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) + in one or more dimensions, of arbitrary input size, and of both real and complex data.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [homepage] + +common_configopts = "--enable-shared --enable-type-prefix --enable-threads --with-pic" + +configopts = [ + common_configopts + " --enable-float --enable-mpi", + common_configopts + " --enable-mpi", # default as last +] + +sanity_check_paths = { + 'files': ['include/%sfftw%s.h' % (x, y) for x in ['d', 'dr', 's', 'sr'] for y in ['', '_mpi', '_threads']] + + ['lib/lib%sfftw%s.a' % (x, y) for x in ['d', 'dr', 's', 'sr'] for y in ['', '_mpi', '_threads']] + + ['lib/lib%sfftw%s.%s' % (x, y, SHLIB_EXT) for x in ['d', 'dr', 's', 'sr'] + for y in ['', '_mpi', '_threads']], + 'dirs': [], +} + +moduleclass = 'numlib' -- GitLab From ca1debbc16d59bc8d2ee55b3e2367b10a8958c96 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 31 May 2017 17:23:41 +0200 Subject: [PATCH 0846/1603] add missing /gnu/ ins ftpmirror.gnu.org source_urls, or use GNU_SOURCE where possible --- easybuild/easyconfigs/e/ed/ed-1.9-ictce-5.3.0.eb | 2 +- easybuild/easyconfigs/g/GCC/GCC-4.1.2.eb | 2 +- easybuild/easyconfigs/g/GCC/GCC-4.2.4.eb | 2 +- easybuild/easyconfigs/g/GCC/GCC-4.3.6.eb | 2 +- easybuild/easyconfigs/g/GCC/GCC-4.4.7.eb | 2 +- easybuild/easyconfigs/g/GCC/GCC-4.5.2.eb | 6 +++--- easybuild/easyconfigs/g/GCC/GCC-4.5.3-CLooG-PPL.eb | 6 +++--- easybuild/easyconfigs/g/GCC/GCC-4.5.3.eb | 6 +++--- easybuild/easyconfigs/g/GCC/GCC-4.6.0.eb | 6 +++--- easybuild/easyconfigs/g/GCC/GCC-4.6.3-CLooG-PPL.eb | 6 +++--- easybuild/easyconfigs/g/GCC/GCC-4.6.3.eb | 6 +++--- easybuild/easyconfigs/g/GCC/GCC-4.6.4.eb | 6 +++--- easybuild/easyconfigs/g/GCC/GCC-4.7.0-CLooG-PPL.eb | 6 +++--- easybuild/easyconfigs/g/GCC/GCC-4.7.0.eb | 6 +++--- easybuild/easyconfigs/g/GCC/GCC-4.7.1-CLooG-PPL.eb | 6 +++--- easybuild/easyconfigs/g/GCC/GCC-4.7.1.eb | 6 +++--- easybuild/easyconfigs/g/GCC/GCC-4.7.2.eb | 6 +++--- easybuild/easyconfigs/g/GCC/GCC-4.7.3-CLooG-PPL.eb | 6 +++--- easybuild/easyconfigs/g/GCC/GCC-4.7.3.eb | 6 +++--- easybuild/easyconfigs/g/GCC/GCC-4.7.4-CLooG-PPL.eb | 6 +++--- easybuild/easyconfigs/g/GCC/GCC-4.7.4.eb | 6 +++--- easybuild/easyconfigs/g/GCC/GCC-4.8.1-CLooG.eb | 6 +++--- easybuild/easyconfigs/g/GCC/GCC-4.8.1.eb | 6 +++--- easybuild/easyconfigs/g/GCC/GCC-4.8.2-CLooG-multilib.eb | 6 +++--- easybuild/easyconfigs/g/GCC/GCC-4.8.2-CLooG.eb | 6 +++--- easybuild/easyconfigs/g/GCC/GCC-4.8.2-multilib.eb | 6 +++--- easybuild/easyconfigs/g/GCC/GCC-4.8.2.eb | 6 +++--- easybuild/easyconfigs/g/GCC/GCC-4.8.3-CLooG-multilib.eb | 6 +++--- easybuild/easyconfigs/g/GCC/GCC-4.8.3.eb | 6 +++--- easybuild/easyconfigs/g/GCC/GCC-4.8.4-CLooG-multilib.eb | 6 +++--- easybuild/easyconfigs/g/GCC/GCC-4.8.4-CLooG.eb | 6 +++--- easybuild/easyconfigs/g/GCC/GCC-4.8.4.eb | 6 +++--- easybuild/easyconfigs/g/GCC/GCC-4.8.5.eb | 6 +++--- easybuild/easyconfigs/g/GCC/GCC-4.9.0-CLooG-multilib.eb | 6 +++--- easybuild/easyconfigs/g/GCC/GCC-4.9.0-CLooG.eb | 6 +++--- easybuild/easyconfigs/g/GCC/GCC-4.9.0.eb | 6 +++--- easybuild/easyconfigs/g/GCC/GCC-4.9.1-CLooG-multilib.eb | 6 +++--- easybuild/easyconfigs/g/GCC/GCC-4.9.1-CLooG.eb | 6 +++--- easybuild/easyconfigs/g/GCC/GCC-4.9.1.eb | 6 +++--- easybuild/easyconfigs/g/GCC/GCC-4.9.2-CLooG-multilib.eb | 6 +++--- easybuild/easyconfigs/g/GCC/GCC-4.9.2-CLooG.eb | 6 +++--- easybuild/easyconfigs/g/GCC/GCC-4.9.2-binutils-2.25.eb | 6 +++--- easybuild/easyconfigs/g/GCC/GCC-4.9.2.eb | 6 +++--- easybuild/easyconfigs/g/GCC/GCC-4.9.3-binutils-2.25.eb | 6 +++--- easybuild/easyconfigs/g/GCC/GCC-4.9.3.eb | 6 +++--- easybuild/easyconfigs/g/GCC/GCC-5.1.0-binutils-2.25.eb | 6 +++--- easybuild/easyconfigs/g/GCC/GCC-5.1.0.eb | 6 +++--- easybuild/easyconfigs/g/GCC/GCC-5.2.0.eb | 6 +++--- easybuild/easyconfigs/g/GCC/GCC-5.3.0.eb | 6 +++--- easybuild/easyconfigs/g/GCCcore/GCCcore-4.9.2.eb | 6 +++--- easybuild/easyconfigs/g/GCCcore/GCCcore-4.9.3.eb | 6 +++--- easybuild/easyconfigs/g/GCCcore/GCCcore-4.9.4.eb | 6 +++--- easybuild/easyconfigs/g/GCCcore/GCCcore-5.3.0.eb | 6 +++--- easybuild/easyconfigs/g/GCCcore/GCCcore-5.4.0.eb | 6 +++--- easybuild/easyconfigs/g/GCCcore/GCCcore-6.1.0.eb | 6 +++--- easybuild/easyconfigs/g/GCCcore/GCCcore-6.2.0.eb | 6 +++--- easybuild/easyconfigs/g/GCCcore/GCCcore-6.3.0.eb | 6 +++--- easybuild/easyconfigs/g/GCCcore/GCCcore-7.1.0.eb | 6 +++--- easybuild/easyconfigs/g/GLPK/GLPK-4.48-ictce-5.3.0.eb | 2 +- easybuild/easyconfigs/g/GLPK/GLPK-4.53-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/g/GLPK/GLPK-4.53-ictce-6.2.5.eb | 2 +- easybuild/easyconfigs/g/GLPK/GLPK-4.55-foss-2015a.eb | 2 +- easybuild/easyconfigs/g/GLPK/GLPK-4.55-intel-2015a.eb | 2 +- easybuild/easyconfigs/g/GLPK/GLPK-4.58-foss-2016a.eb | 2 +- easybuild/easyconfigs/g/GLPK/GLPK-4.58-intel-2016a.eb | 2 +- easybuild/easyconfigs/g/GLPK/GLPK-4.60-intel-2016b.eb | 2 +- easybuild/easyconfigs/g/GLPK/GLPK-4.61-intel-2017a.eb | 2 +- easybuild/easyconfigs/g/GSL/GSL-1.16-goolf-1.7.20.eb | 2 +- easybuild/easyconfigs/g/gzip/gzip-1.6-ictce-5.3.0.eb | 2 +- easybuild/easyconfigs/g/gzip/gzip-1.6-ictce-5.5.0.eb | 2 +- easybuild/easyconfigs/g/gzip/gzip-1.6-ictce-6.2.5.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.16-ictce-5.5.0.eb | 2 +- easybuild/easyconfigs/m/mutil/mutil-1.822.3-intel-2016a.eb | 2 +- 73 files changed, 179 insertions(+), 179 deletions(-) diff --git a/easybuild/easyconfigs/e/ed/ed-1.9-ictce-5.3.0.eb b/easybuild/easyconfigs/e/ed/ed-1.9-ictce-5.3.0.eb index 48f5d0b7b4..dfd1efd2bf 100644 --- a/easybuild/easyconfigs/e/ed/ed-1.9-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/e/ed/ed-1.9-ictce-5.3.0.eb @@ -9,7 +9,7 @@ description = """GNU ed is a line-oriented text editor.""" toolchain = {'name': 'ictce', 'version': '5.3.0'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://ftpmirror.gnu.org/%(name)s/'] +source_urls = [GNU_SOURCE] sanity_check_paths = { 'files': ['bin/ed'], diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.1.2.eb b/easybuild/easyconfigs/g/GCC/GCC-4.1.2.eb index 15db97e462..3353304539 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.1.2.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.1.2.eb @@ -7,7 +7,7 @@ description = """The GNU Compiler Collection includes front ends for C, C++, Obj toolchain = {'name': 'dummy', 'version': ''} # empty version to ensure that dependencies are loaded -source_urls = ['http://ftpmirror.gnu.org/%(namelower)s/%(namelower)s-%(version)s'] +source_urls = ['http://ftpmirror.gnu.org/gnu/%(namelower)s/%(namelower)s-%(version)s'] sources = [SOURCELOWER_TAR_BZ2] checksums = [ diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.2.4.eb b/easybuild/easyconfigs/g/GCC/GCC-4.2.4.eb index 690c94392b..2315380a64 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.2.4.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.2.4.eb @@ -7,7 +7,7 @@ description = """The GNU Compiler Collection includes front ends for C, C++, Obj toolchain = {'name': 'dummy', 'version': ''} # empty version to ensure that dependencies are loaded -source_urls = ['http://ftpmirror.gnu.org/%(namelower)s/%(namelower)s-%(version)s'] +source_urls = ['http://ftpmirror.gnu.org/gnu/%(namelower)s/%(namelower)s-%(version)s'] sources = [SOURCELOWER_TAR_BZ2] checksums = [ diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.3.6.eb b/easybuild/easyconfigs/g/GCC/GCC-4.3.6.eb index d2df4b4c42..49e488fc5d 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.3.6.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.3.6.eb @@ -7,7 +7,7 @@ description = """The GNU Compiler Collection includes front ends for C, C++, Obj toolchain = {'name': 'dummy', 'version': ''} # empty version to ensure that dependencies are loaded -source_urls = ['http://ftpmirror.gnu.org/%(namelower)s/%(namelower)s-%(version)s'] +source_urls = ['http://ftpmirror.gnu.org/gnu/%(namelower)s/%(namelower)s-%(version)s'] sources = [SOURCELOWER_TAR_BZ2] checksums = [ diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.4.7.eb b/easybuild/easyconfigs/g/GCC/GCC-4.4.7.eb index 584afb9b7c..9a6e1777a2 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.4.7.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.4.7.eb @@ -7,7 +7,7 @@ description = """The GNU Compiler Collection includes front ends for C, C++, Obj toolchain = {'name': 'dummy', 'version': ''} # empty version to ensure that dependencies are loaded -source_urls = ['http://ftpmirror.gnu.org/%(namelower)s/%(namelower)s-%(version)s'] +source_urls = ['http://ftpmirror.gnu.org/gnu/%(namelower)s/%(namelower)s-%(version)s'] sources = [SOURCELOWER_TAR_BZ2] checksums = [ diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.5.2.eb b/easybuild/easyconfigs/g/GCC/GCC-4.5.2.eb index 719bc6f315..e4f74a2769 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.5.2.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.5.2.eb @@ -8,9 +8,9 @@ description = """The GNU Compiler Collection includes front ends for C, C++, Obj toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = [ - 'http://ftpmirror.gnu.org/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror - 'http://ftpmirror.gnu.org/gmp', # idem for GMP - 'http://ftpmirror.gnu.org/mpfr', # idem for MPFR + 'http://ftpmirror.gnu.org/gnu/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror + 'http://ftpmirror.gnu.org/gnu/gmp', # idem for GMP + 'http://ftpmirror.gnu.org/gnu/mpfr', # idem for MPFR 'http://www.multiprecision.org/mpc/download', # MPC official ] sources = [ diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.5.3-CLooG-PPL.eb b/easybuild/easyconfigs/g/GCC/GCC-4.5.3-CLooG-PPL.eb index bcb7fd7639..137d7d524e 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.5.3-CLooG-PPL.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.5.3-CLooG-PPL.eb @@ -11,9 +11,9 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} pplver = '0.11' source_urls = [ - 'http://ftpmirror.gnu.org/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror - 'http://ftpmirror.gnu.org/gmp', # idem for GMP - 'http://ftpmirror.gnu.org/mpfr', # idem for MPFR + 'http://ftpmirror.gnu.org/gnu/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror + 'http://ftpmirror.gnu.org/gnu/gmp', # idem for GMP + 'http://ftpmirror.gnu.org/gnu/mpfr', # idem for MPFR 'http://www.multiprecision.org/mpc/download', # MPC official 'http://bugseng.com/products/ppl/download/ftp/releases/%s' % pplver, # PPL official 'http://www.bastoul.net/cloog/pages/download/count.php3?url=.', # CLooG official diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.5.3.eb b/easybuild/easyconfigs/g/GCC/GCC-4.5.3.eb index 9a31d20e93..df06986016 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.5.3.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.5.3.eb @@ -8,9 +8,9 @@ description = """The GNU Compiler Collection includes front ends for C, C++, Obj toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = [ - 'http://ftpmirror.gnu.org/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror - 'http://ftpmirror.gnu.org/gmp', # idem for GMP - 'http://ftpmirror.gnu.org/mpfr', # idem for MPFR + 'http://ftpmirror.gnu.org/gnu/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror + 'http://ftpmirror.gnu.org/gnu/gmp', # idem for GMP + 'http://ftpmirror.gnu.org/gnu/mpfr', # idem for MPFR 'http://www.multiprecision.org/mpc/download', # MPC official ] sources = [ diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.6.0.eb b/easybuild/easyconfigs/g/GCC/GCC-4.6.0.eb index f310421ff2..e34a70f28b 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.6.0.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.6.0.eb @@ -8,9 +8,9 @@ description = """The GNU Compiler Collection includes front ends for C, C++, Obj toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = [ - 'http://ftpmirror.gnu.org/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror - 'http://ftpmirror.gnu.org/gmp', # idem for GMP - 'http://ftpmirror.gnu.org/mpfr', # idem for MPFR + 'http://ftpmirror.gnu.org/gnu/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror + 'http://ftpmirror.gnu.org/gnu/gmp', # idem for GMP + 'http://ftpmirror.gnu.org/gnu/mpfr', # idem for MPFR 'http://www.multiprecision.org/mpc/download', # MPC official ] sources = [ diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.6.3-CLooG-PPL.eb b/easybuild/easyconfigs/g/GCC/GCC-4.6.3-CLooG-PPL.eb index 3a9114bc86..5955aa5fd3 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.6.3-CLooG-PPL.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.6.3-CLooG-PPL.eb @@ -11,9 +11,9 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} pplver = '0.12' source_urls = [ - 'http://ftpmirror.gnu.org/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror - 'http://ftpmirror.gnu.org/gmp', # idem for GMP - 'http://ftpmirror.gnu.org/mpfr', # idem for MPFR + 'http://ftpmirror.gnu.org/gnu/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror + 'http://ftpmirror.gnu.org/gnu/gmp', # idem for GMP + 'http://ftpmirror.gnu.org/gnu/mpfr', # idem for MPFR 'http://www.multiprecision.org/mpc/download', # MPC official 'http://bugseng.com/products/ppl/download/ftp/releases/%s' % pplver, # PPL official 'http://www.bastoul.net/cloog/pages/download/count.php3?url=.', # CLooG official diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.6.3.eb b/easybuild/easyconfigs/g/GCC/GCC-4.6.3.eb index 884bd3660e..a17723ccd7 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.6.3.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.6.3.eb @@ -8,9 +8,9 @@ description = """The GNU Compiler Collection includes front ends for C, C++, Obj toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = [ - 'http://ftpmirror.gnu.org/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror - 'http://ftpmirror.gnu.org/gmp', # idem for GMP - 'http://ftpmirror.gnu.org/mpfr', # idem for MPFR + 'http://ftpmirror.gnu.org/gnu/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror + 'http://ftpmirror.gnu.org/gnu/gmp', # idem for GMP + 'http://ftpmirror.gnu.org/gnu/mpfr', # idem for MPFR 'http://www.multiprecision.org/mpc/download', # MPC official ] sources = [ diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.6.4.eb b/easybuild/easyconfigs/g/GCC/GCC-4.6.4.eb index 6d06e3dc27..92eb1f920e 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.6.4.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.6.4.eb @@ -8,9 +8,9 @@ description = """The GNU Compiler Collection includes front ends for C, C++, Obj toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = [ - 'http://ftpmirror.gnu.org/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror - 'http://ftpmirror.gnu.org/gmp', # idem for GMP - 'http://ftpmirror.gnu.org/mpfr', # idem for MPFR + 'http://ftpmirror.gnu.org/gnu/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror + 'http://ftpmirror.gnu.org/gnu/gmp', # idem for GMP + 'http://ftpmirror.gnu.org/gnu/mpfr', # idem for MPFR 'http://www.multiprecision.org/mpc/download', # MPC official ] sources = [ diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.7.0-CLooG-PPL.eb b/easybuild/easyconfigs/g/GCC/GCC-4.7.0-CLooG-PPL.eb index b46830b3c9..8c20572741 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.7.0-CLooG-PPL.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.7.0-CLooG-PPL.eb @@ -11,9 +11,9 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} pplver = '0.12' source_urls = [ - 'http://ftpmirror.gnu.org/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror - 'http://ftpmirror.gnu.org/gmp', # idem for GMP - 'http://ftpmirror.gnu.org/mpfr', # idem for MPFR + 'http://ftpmirror.gnu.org/gnu/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror + 'http://ftpmirror.gnu.org/gnu/gmp', # idem for GMP + 'http://ftpmirror.gnu.org/gnu/mpfr', # idem for MPFR 'http://www.multiprecision.org/mpc/download', # MPC official 'http://bugseng.com/products/ppl/download/ftp/releases/%s' % pplver, # PPL official 'http://www.bastoul.net/cloog/pages/download/count.php3?url=.', # CLooG official diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.7.0.eb b/easybuild/easyconfigs/g/GCC/GCC-4.7.0.eb index 25a490f355..c5bea4cc95 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.7.0.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.7.0.eb @@ -8,9 +8,9 @@ description = """The GNU Compiler Collection includes front ends for C, C++, Obj toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = [ - 'http://ftpmirror.gnu.org/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror - 'http://ftpmirror.gnu.org/gmp', # idem for GMP - 'http://ftpmirror.gnu.org/mpfr', # idem for MPFR + 'http://ftpmirror.gnu.org/gnu/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror + 'http://ftpmirror.gnu.org/gnu/gmp', # idem for GMP + 'http://ftpmirror.gnu.org/gnu/mpfr', # idem for MPFR 'http://www.multiprecision.org/mpc/download', # MPC official ] sources = [ diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.7.1-CLooG-PPL.eb b/easybuild/easyconfigs/g/GCC/GCC-4.7.1-CLooG-PPL.eb index 6c58ae7bc6..96faf6492a 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.7.1-CLooG-PPL.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.7.1-CLooG-PPL.eb @@ -11,9 +11,9 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} pplver = '0.12' source_urls = [ - 'http://ftpmirror.gnu.org/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror - 'http://ftpmirror.gnu.org/gmp', # idem for GMP - 'http://ftpmirror.gnu.org/mpfr', # idem for MPFR + 'http://ftpmirror.gnu.org/gnu/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror + 'http://ftpmirror.gnu.org/gnu/gmp', # idem for GMP + 'http://ftpmirror.gnu.org/gnu/mpfr', # idem for MPFR 'http://www.multiprecision.org/mpc/download', # MPC official 'http://bugseng.com/products/ppl/download/ftp/releases/%s' % pplver, # PPL official 'http://www.bastoul.net/cloog/pages/download/', # CLooG official diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.7.1.eb b/easybuild/easyconfigs/g/GCC/GCC-4.7.1.eb index b3ad3f8087..b98f04d03d 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.7.1.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.7.1.eb @@ -8,9 +8,9 @@ description = """The GNU Compiler Collection includes front ends for C, C++, Obj toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = [ - 'http://ftpmirror.gnu.org/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror - 'http://ftpmirror.gnu.org/gmp', # idem for GMP - 'http://ftpmirror.gnu.org/mpfr', # idem for MPFR + 'http://ftpmirror.gnu.org/gnu/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror + 'http://ftpmirror.gnu.org/gnu/gmp', # idem for GMP + 'http://ftpmirror.gnu.org/gnu/mpfr', # idem for MPFR 'http://www.multiprecision.org/mpc/download', # MPC official ] sources = [ diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.7.2.eb b/easybuild/easyconfigs/g/GCC/GCC-4.7.2.eb index decee62a58..52df95a761 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.7.2.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.7.2.eb @@ -8,9 +8,9 @@ description = """The GNU Compiler Collection includes front ends for C, C++, Obj toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = [ - 'http://ftpmirror.gnu.org/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror - 'http://ftpmirror.gnu.org/gmp', # idem for GMP - 'http://ftpmirror.gnu.org/mpfr', # idem for MPFR + 'http://ftpmirror.gnu.org/gnu/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror + 'http://ftpmirror.gnu.org/gnu/gmp', # idem for GMP + 'http://ftpmirror.gnu.org/gnu/mpfr', # idem for MPFR 'http://www.multiprecision.org/mpc/download', # MPC official ] sources = [ diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.7.3-CLooG-PPL.eb b/easybuild/easyconfigs/g/GCC/GCC-4.7.3-CLooG-PPL.eb index 8f5cae195c..f76b5cd461 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.7.3-CLooG-PPL.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.7.3-CLooG-PPL.eb @@ -11,9 +11,9 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} pplver = '0.12.1' source_urls = [ - 'http://ftpmirror.gnu.org/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror - 'http://ftpmirror.gnu.org/gmp', # idem for GMP - 'http://ftpmirror.gnu.org/mpfr', # idem for MPFR + 'http://ftpmirror.gnu.org/gnu/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror + 'http://ftpmirror.gnu.org/gnu/gmp', # idem for GMP + 'http://ftpmirror.gnu.org/gnu/mpfr', # idem for MPFR 'http://www.multiprecision.org/mpc/download', # MPC official 'http://bugseng.com/products/ppl/download/ftp/releases/%s' % pplver, # PPL official 'http://www.bastoul.net/cloog/pages/download/', # CLooG official diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.7.3.eb b/easybuild/easyconfigs/g/GCC/GCC-4.7.3.eb index 03f65ea5f0..f082b457cb 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.7.3.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.7.3.eb @@ -8,9 +8,9 @@ description = """The GNU Compiler Collection includes front ends for C, C++, Obj toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = [ - 'http://ftpmirror.gnu.org/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror - 'http://ftpmirror.gnu.org/gmp', # idem for GMP - 'http://ftpmirror.gnu.org/mpfr', # idem for MPFR + 'http://ftpmirror.gnu.org/gnu/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror + 'http://ftpmirror.gnu.org/gnu/gmp', # idem for GMP + 'http://ftpmirror.gnu.org/gnu/mpfr', # idem for MPFR 'http://www.multiprecision.org/mpc/download', # MPC official ] sources = [ diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.7.4-CLooG-PPL.eb b/easybuild/easyconfigs/g/GCC/GCC-4.7.4-CLooG-PPL.eb index da943f7026..bf7a65c4b8 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.7.4-CLooG-PPL.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.7.4-CLooG-PPL.eb @@ -11,9 +11,9 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} pplver = '0.12.1' source_urls = [ - 'http://ftpmirror.gnu.org/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror - 'http://ftpmirror.gnu.org/gmp', # idem for GMP - 'http://ftpmirror.gnu.org/mpfr', # idem for MPFR + 'http://ftpmirror.gnu.org/gnu/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror + 'http://ftpmirror.gnu.org/gnu/gmp', # idem for GMP + 'http://ftpmirror.gnu.org/gnu/mpfr', # idem for MPFR 'http://www.multiprecision.org/mpc/download', # MPC official 'http://bugseng.com/products/ppl/download/ftp/releases/%s' % pplver, # PPL official 'http://www.bastoul.net/cloog/pages/download/', # CLooG official diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.7.4.eb b/easybuild/easyconfigs/g/GCC/GCC-4.7.4.eb index 5d688569b0..d6755a5d57 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.7.4.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.7.4.eb @@ -8,9 +8,9 @@ description = """The GNU Compiler Collection includes front ends for C, C++, Obj toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = [ - 'http://ftpmirror.gnu.org/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror - 'http://ftpmirror.gnu.org/gmp', # idem for GMP - 'http://ftpmirror.gnu.org/mpfr', # idem for MPFR + 'http://ftpmirror.gnu.org/gnu/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror + 'http://ftpmirror.gnu.org/gnu/gmp', # idem for GMP + 'http://ftpmirror.gnu.org/gnu/mpfr', # idem for MPFR 'http://www.multiprecision.org/mpc/download', # MPC official ] sources = [ diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.8.1-CLooG.eb b/easybuild/easyconfigs/g/GCC/GCC-4.8.1-CLooG.eb index 618d553031..b9384bdcfe 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.8.1-CLooG.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.8.1-CLooG.eb @@ -9,9 +9,9 @@ description = """The GNU Compiler Collection includes front ends for C, C++, Obj toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = [ - 'http://ftpmirror.gnu.org/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror - 'http://ftpmirror.gnu.org/gmp', # idem for GMP - 'http://ftpmirror.gnu.org/mpfr', # idem for MPFR + 'http://ftpmirror.gnu.org/gnu/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror + 'http://ftpmirror.gnu.org/gnu/gmp', # idem for GMP + 'http://ftpmirror.gnu.org/gnu/mpfr', # idem for MPFR 'http://www.multiprecision.org/mpc/download', # MPC official 'http://www.bastoul.net/cloog/pages/download/', # CLooG official 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.8.1.eb b/easybuild/easyconfigs/g/GCC/GCC-4.8.1.eb index 85085960e8..cfc68d66f6 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.8.1.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.8.1.eb @@ -8,9 +8,9 @@ description = """The GNU Compiler Collection includes front ends for C, C++, Obj toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = [ - 'http://ftpmirror.gnu.org/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror - 'http://ftpmirror.gnu.org/gmp', # idem for GMP - 'http://ftpmirror.gnu.org/mpfr', # idem for MPFR + 'http://ftpmirror.gnu.org/gnu/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror + 'http://ftpmirror.gnu.org/gnu/gmp', # idem for GMP + 'http://ftpmirror.gnu.org/gnu/mpfr', # idem for MPFR 'http://www.multiprecision.org/mpc/download', # MPC official ] sources = [ diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.8.2-CLooG-multilib.eb b/easybuild/easyconfigs/g/GCC/GCC-4.8.2-CLooG-multilib.eb index 6d29040095..f7ae0b63f1 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.8.2-CLooG-multilib.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.8.2-CLooG-multilib.eb @@ -9,9 +9,9 @@ description = """The GNU Compiler Collection includes front ends for C, C++, Obj toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = [ - 'http://ftpmirror.gnu.org/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror - 'http://ftpmirror.gnu.org/gmp', # idem for GMP - 'http://ftpmirror.gnu.org/mpfr', # idem for MPFR + 'http://ftpmirror.gnu.org/gnu/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror + 'http://ftpmirror.gnu.org/gnu/gmp', # idem for GMP + 'http://ftpmirror.gnu.org/gnu/mpfr', # idem for MPFR 'http://www.multiprecision.org/mpc/download', # MPC official 'http://www.bastoul.net/cloog/pages/download/', # CLooG official 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.8.2-CLooG.eb b/easybuild/easyconfigs/g/GCC/GCC-4.8.2-CLooG.eb index 9a60bde46d..53a6b802c8 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.8.2-CLooG.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.8.2-CLooG.eb @@ -9,9 +9,9 @@ description = """The GNU Compiler Collection includes front ends for C, C++, Obj toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = [ - 'http://ftpmirror.gnu.org/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror - 'http://ftpmirror.gnu.org/gmp', # idem for GMP - 'http://ftpmirror.gnu.org/mpfr', # idem for MPFR + 'http://ftpmirror.gnu.org/gnu/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror + 'http://ftpmirror.gnu.org/gnu/gmp', # idem for GMP + 'http://ftpmirror.gnu.org/gnu/mpfr', # idem for MPFR 'http://www.multiprecision.org/mpc/download', # MPC official 'http://www.bastoul.net/cloog/pages/download/', # CLooG official 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.8.2-multilib.eb b/easybuild/easyconfigs/g/GCC/GCC-4.8.2-multilib.eb index 8154896aaa..62ff1a29d8 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.8.2-multilib.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.8.2-multilib.eb @@ -9,9 +9,9 @@ description = """The GNU Compiler Collection includes front ends for C, C++, Obj toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = [ - 'http://ftpmirror.gnu.org/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror - 'http://ftpmirror.gnu.org/gmp', # idem for GMP - 'http://ftpmirror.gnu.org/mpfr', # idem for MPFR + 'http://ftpmirror.gnu.org/gnu/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror + 'http://ftpmirror.gnu.org/gnu/gmp', # idem for GMP + 'http://ftpmirror.gnu.org/gnu/mpfr', # idem for MPFR 'http://www.multiprecision.org/mpc/download', # MPC official ] sources = [ diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.8.2.eb b/easybuild/easyconfigs/g/GCC/GCC-4.8.2.eb index 525d8bbaf4..ac1ea618e1 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.8.2.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.8.2.eb @@ -8,9 +8,9 @@ description = """The GNU Compiler Collection includes front ends for C, C++, Obj toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = [ - 'http://ftpmirror.gnu.org/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror - 'http://ftpmirror.gnu.org/gmp', # idem for GMP - 'http://ftpmirror.gnu.org/mpfr', # idem for MPFR + 'http://ftpmirror.gnu.org/gnu/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror + 'http://ftpmirror.gnu.org/gnu/gmp', # idem for GMP + 'http://ftpmirror.gnu.org/gnu/mpfr', # idem for MPFR 'http://www.multiprecision.org/mpc/download', # MPC official ] sources = [ diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.8.3-CLooG-multilib.eb b/easybuild/easyconfigs/g/GCC/GCC-4.8.3-CLooG-multilib.eb index 54f482d906..55705b2a56 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.8.3-CLooG-multilib.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.8.3-CLooG-multilib.eb @@ -9,9 +9,9 @@ description = """The GNU Compiler Collection includes front ends for C, C++, Obj toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = [ - 'http://ftpmirror.gnu.org/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror - 'http://ftpmirror.gnu.org/gmp', # idem for GMP - 'http://ftpmirror.gnu.org/mpfr', # idem for MPFR + 'http://ftpmirror.gnu.org/gnu/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror + 'http://ftpmirror.gnu.org/gnu/gmp', # idem for GMP + 'http://ftpmirror.gnu.org/gnu/mpfr', # idem for MPFR 'http://www.multiprecision.org/mpc/download', # MPC official 'http://www.bastoul.net/cloog/pages/download/', # CLooG official 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.8.3.eb b/easybuild/easyconfigs/g/GCC/GCC-4.8.3.eb index d300b36d8f..47fcc28da6 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.8.3.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.8.3.eb @@ -8,9 +8,9 @@ description = """The GNU Compiler Collection includes front ends for C, C++, Obj toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = [ - 'http://ftpmirror.gnu.org/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror - 'http://ftpmirror.gnu.org/gmp', # idem for GMP - 'http://ftpmirror.gnu.org/mpfr', # idem for MPFR + 'http://ftpmirror.gnu.org/gnu/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror + 'http://ftpmirror.gnu.org/gnu/gmp', # idem for GMP + 'http://ftpmirror.gnu.org/gnu/mpfr', # idem for MPFR 'http://www.multiprecision.org/mpc/download', # MPC official ] sources = [ diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.8.4-CLooG-multilib.eb b/easybuild/easyconfigs/g/GCC/GCC-4.8.4-CLooG-multilib.eb index 89f13931a3..8bc99398c5 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.8.4-CLooG-multilib.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.8.4-CLooG-multilib.eb @@ -9,9 +9,9 @@ description = """The GNU Compiler Collection includes front ends for C, C++, Obj toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = [ - 'http://ftpmirror.gnu.org/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror - 'http://ftpmirror.gnu.org/gmp', # idem for GMP - 'http://ftpmirror.gnu.org/mpfr', # idem for MPFR + 'http://ftpmirror.gnu.org/gnu/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror + 'http://ftpmirror.gnu.org/gnu/gmp', # idem for GMP + 'http://ftpmirror.gnu.org/gnu/mpfr', # idem for MPFR 'http://www.multiprecision.org/mpc/download', # MPC official 'http://www.bastoul.net/cloog/pages/download/', # CLooG official 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.8.4-CLooG.eb b/easybuild/easyconfigs/g/GCC/GCC-4.8.4-CLooG.eb index 1fee24d2ad..d04c5b5989 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.8.4-CLooG.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.8.4-CLooG.eb @@ -9,9 +9,9 @@ description = """The GNU Compiler Collection includes front ends for C, C++, Obj toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = [ - 'http://ftpmirror.gnu.org/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror - 'http://ftpmirror.gnu.org/gmp', # idem for GMP - 'http://ftpmirror.gnu.org/mpfr', # idem for MPFR + 'http://ftpmirror.gnu.org/gnu/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror + 'http://ftpmirror.gnu.org/gnu/gmp', # idem for GMP + 'http://ftpmirror.gnu.org/gnu/mpfr', # idem for MPFR 'http://www.multiprecision.org/mpc/download', # MPC official 'http://www.bastoul.net/cloog/pages/download/', # CLooG official 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.8.4.eb b/easybuild/easyconfigs/g/GCC/GCC-4.8.4.eb index 5149d85b52..18e237e811 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.8.4.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.8.4.eb @@ -8,9 +8,9 @@ description = """The GNU Compiler Collection includes front ends for C, C++, Obj toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = [ - 'http://ftpmirror.gnu.org/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror - 'http://ftpmirror.gnu.org/gmp', # idem for GMP - 'http://ftpmirror.gnu.org/mpfr', # idem for MPFR + 'http://ftpmirror.gnu.org/gnu/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror + 'http://ftpmirror.gnu.org/gnu/gmp', # idem for GMP + 'http://ftpmirror.gnu.org/gnu/mpfr', # idem for MPFR 'http://www.multiprecision.org/mpc/download', # MPC official ] sources = [ diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.8.5.eb b/easybuild/easyconfigs/g/GCC/GCC-4.8.5.eb index 358952fcd9..7a8cd2b768 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.8.5.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.8.5.eb @@ -8,9 +8,9 @@ description = """The GNU Compiler Collection includes front ends for C, C++, Obj toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = [ - 'http://ftpmirror.gnu.org/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror - 'http://ftpmirror.gnu.org/gmp', # idem for GMP - 'http://ftpmirror.gnu.org/mpfr', # idem for MPFR + 'http://ftpmirror.gnu.org/gnu/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror + 'http://ftpmirror.gnu.org/gnu/gmp', # idem for GMP + 'http://ftpmirror.gnu.org/gnu/mpfr', # idem for MPFR 'http://www.multiprecision.org/mpc/download', # MPC official ] sources = [ diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.9.0-CLooG-multilib.eb b/easybuild/easyconfigs/g/GCC/GCC-4.9.0-CLooG-multilib.eb index c0cd444cef..3d2b9ee9c0 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.9.0-CLooG-multilib.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.9.0-CLooG-multilib.eb @@ -11,9 +11,9 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} mpfr_version = '3.1.2' source_urls = [ - 'http://ftpmirror.gnu.org/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror - 'http://ftpmirror.gnu.org/gmp', # idem for GMP - 'http://ftpmirror.gnu.org/mpfr', # idem for MPFR + 'http://ftpmirror.gnu.org/gnu/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror + 'http://ftpmirror.gnu.org/gnu/gmp', # idem for GMP + 'http://ftpmirror.gnu.org/gnu/mpfr', # idem for MPFR 'http://www.multiprecision.org/mpc/download', # MPC official 'http://www.bastoul.net/cloog/pages/download/', # CLooG official 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.9.0-CLooG.eb b/easybuild/easyconfigs/g/GCC/GCC-4.9.0-CLooG.eb index 7a4b755a4c..3d655c2b61 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.9.0-CLooG.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.9.0-CLooG.eb @@ -11,9 +11,9 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} mpfr_version = '3.1.2' source_urls = [ - 'http://ftpmirror.gnu.org/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror - 'http://ftpmirror.gnu.org/gmp', # idem for GMP - 'http://ftpmirror.gnu.org/mpfr', # idem for MPFR + 'http://ftpmirror.gnu.org/gnu/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror + 'http://ftpmirror.gnu.org/gnu/gmp', # idem for GMP + 'http://ftpmirror.gnu.org/gnu/mpfr', # idem for MPFR 'http://www.multiprecision.org/mpc/download', # MPC official 'http://www.bastoul.net/cloog/pages/download/', # CLooG official 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.9.0.eb b/easybuild/easyconfigs/g/GCC/GCC-4.9.0.eb index 288754285b..68428b6c43 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.9.0.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.9.0.eb @@ -10,9 +10,9 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} mpfr_version = '3.1.2' source_urls = [ - 'http://ftpmirror.gnu.org/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror - 'http://ftpmirror.gnu.org/gmp', # idem for GMP - 'http://ftpmirror.gnu.org/mpfr', # idem for MPFR + 'http://ftpmirror.gnu.org/gnu/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror + 'http://ftpmirror.gnu.org/gnu/gmp', # idem for GMP + 'http://ftpmirror.gnu.org/gnu/mpfr', # idem for MPFR 'http://www.multiprecision.org/mpc/download', # MPC official ] sources = [ diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.9.1-CLooG-multilib.eb b/easybuild/easyconfigs/g/GCC/GCC-4.9.1-CLooG-multilib.eb index bd08517bfa..9e22d2092e 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.9.1-CLooG-multilib.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.9.1-CLooG-multilib.eb @@ -11,9 +11,9 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} mpfr_version = '3.1.2' source_urls = [ - 'http://ftpmirror.gnu.org/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror - 'http://ftpmirror.gnu.org/gmp', # idem for GMP - 'http://ftpmirror.gnu.org/mpfr', # idem for MPFR + 'http://ftpmirror.gnu.org/gnu/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror + 'http://ftpmirror.gnu.org/gnu/gmp', # idem for GMP + 'http://ftpmirror.gnu.org/gnu/mpfr', # idem for MPFR 'http://www.multiprecision.org/mpc/download', # MPC official 'http://www.bastoul.net/cloog/pages/download/', # CLooG official 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.9.1-CLooG.eb b/easybuild/easyconfigs/g/GCC/GCC-4.9.1-CLooG.eb index 5cb7dc788a..ba83e49da7 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.9.1-CLooG.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.9.1-CLooG.eb @@ -11,9 +11,9 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} mpfr_version = '3.1.2' source_urls = [ - 'http://ftpmirror.gnu.org/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror - 'http://ftpmirror.gnu.org/gmp', # idem for GMP - 'http://ftpmirror.gnu.org/mpfr', # idem for MPFR + 'http://ftpmirror.gnu.org/gnu/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror + 'http://ftpmirror.gnu.org/gnu/gmp', # idem for GMP + 'http://ftpmirror.gnu.org/gnu/mpfr', # idem for MPFR 'http://www.multiprecision.org/mpc/download', # MPC official 'http://www.bastoul.net/cloog/pages/download/', # CLooG official 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.9.1.eb b/easybuild/easyconfigs/g/GCC/GCC-4.9.1.eb index d520b55ace..39947a23d7 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.9.1.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.9.1.eb @@ -10,9 +10,9 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} mpfr_version = '3.1.2' source_urls = [ - 'http://ftpmirror.gnu.org/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror - 'http://ftpmirror.gnu.org/gmp', # idem for GMP - 'http://ftpmirror.gnu.org/mpfr', # idem for MPFR + 'http://ftpmirror.gnu.org/gnu/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror + 'http://ftpmirror.gnu.org/gnu/gmp', # idem for GMP + 'http://ftpmirror.gnu.org/gnu/mpfr', # idem for MPFR 'http://www.multiprecision.org/mpc/download', # MPC official ] sources = [ diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.9.2-CLooG-multilib.eb b/easybuild/easyconfigs/g/GCC/GCC-4.9.2-CLooG-multilib.eb index 4b52dcc343..de353eab4d 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.9.2-CLooG-multilib.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.9.2-CLooG-multilib.eb @@ -11,9 +11,9 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} mpfr_version = '3.1.2' source_urls = [ - 'http://ftpmirror.gnu.org/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror - 'http://ftpmirror.gnu.org/gmp', # idem for GMP - 'http://ftpmirror.gnu.org/mpfr', # idem for MPFR + 'http://ftpmirror.gnu.org/gnu/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror + 'http://ftpmirror.gnu.org/gnu/gmp', # idem for GMP + 'http://ftpmirror.gnu.org/gnu/mpfr', # idem for MPFR 'http://www.multiprecision.org/mpc/download', # MPC official 'http://www.bastoul.net/cloog/pages/download/', # CLooG official 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.9.2-CLooG.eb b/easybuild/easyconfigs/g/GCC/GCC-4.9.2-CLooG.eb index 1ec5100100..b598d63b4c 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.9.2-CLooG.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.9.2-CLooG.eb @@ -11,9 +11,9 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} mpfr_version = '3.1.2' source_urls = [ - 'http://ftpmirror.gnu.org/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror - 'http://ftpmirror.gnu.org/gmp', # idem for GMP - 'http://ftpmirror.gnu.org/mpfr', # idem for MPFR + 'http://ftpmirror.gnu.org/gnu/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror + 'http://ftpmirror.gnu.org/gnu/gmp', # idem for GMP + 'http://ftpmirror.gnu.org/gnu/mpfr', # idem for MPFR 'http://www.multiprecision.org/mpc/download', # MPC official 'http://www.bastoul.net/cloog/pages/download/', # CLooG official 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.9.2-binutils-2.25.eb b/easybuild/easyconfigs/g/GCC/GCC-4.9.2-binutils-2.25.eb index 44e39d233d..62739aefa4 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.9.2-binutils-2.25.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.9.2-binutils-2.25.eb @@ -13,9 +13,9 @@ toolchain = {'name': 'dummy', 'version': ''} mpfr_version = '3.1.2' source_urls = [ - 'http://ftpmirror.gnu.org/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror - 'http://ftpmirror.gnu.org/gmp', # idem for GMP - 'http://ftpmirror.gnu.org/mpfr', # idem for MPFR + 'http://ftpmirror.gnu.org/gnu/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror + 'http://ftpmirror.gnu.org/gnu/gmp', # idem for GMP + 'http://ftpmirror.gnu.org/gnu/mpfr', # idem for MPFR 'http://www.multiprecision.org/mpc/download', # MPC official ] sources = [ diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.9.2.eb b/easybuild/easyconfigs/g/GCC/GCC-4.9.2.eb index e9df0050c0..8586c48e2c 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.9.2.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.9.2.eb @@ -10,9 +10,9 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} mpfr_version = '3.1.2' source_urls = [ - 'http://ftpmirror.gnu.org/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror - 'http://ftpmirror.gnu.org/gmp', # idem for GMP - 'http://ftpmirror.gnu.org/mpfr', # idem for MPFR + 'http://ftpmirror.gnu.org/gnu/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror + 'http://ftpmirror.gnu.org/gnu/gmp', # idem for GMP + 'http://ftpmirror.gnu.org/gnu/mpfr', # idem for MPFR 'http://www.multiprecision.org/mpc/download', # MPC official ] sources = [ diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.9.3-binutils-2.25.eb b/easybuild/easyconfigs/g/GCC/GCC-4.9.3-binutils-2.25.eb index 8c62c13920..30c0749622 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.9.3-binutils-2.25.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.9.3-binutils-2.25.eb @@ -13,9 +13,9 @@ toolchain = {'name': 'dummy', 'version': ''} mpfr_version = '3.1.2' source_urls = [ - 'http://ftpmirror.gnu.org/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror - 'http://ftpmirror.gnu.org/gmp', # idem for GMP - 'http://ftpmirror.gnu.org/mpfr', # idem for MPFR + 'http://ftpmirror.gnu.org/gnu/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror + 'http://ftpmirror.gnu.org/gnu/gmp', # idem for GMP + 'http://ftpmirror.gnu.org/gnu/mpfr', # idem for MPFR 'http://www.multiprecision.org/mpc/download', # MPC official ] sources = [ diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.9.3.eb b/easybuild/easyconfigs/g/GCC/GCC-4.9.3.eb index e36af87104..ef8f2e2c88 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.9.3.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.9.3.eb @@ -10,9 +10,9 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} mpfr_version = '3.1.2' source_urls = [ - 'http://ftpmirror.gnu.org/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror - 'http://ftpmirror.gnu.org/gmp', # idem for GMP - 'http://ftpmirror.gnu.org/mpfr', # idem for MPFR + 'http://ftpmirror.gnu.org/gnu/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror + 'http://ftpmirror.gnu.org/gnu/gmp', # idem for GMP + 'http://ftpmirror.gnu.org/gnu/mpfr', # idem for MPFR 'http://www.multiprecision.org/mpc/download', # MPC official ] sources = [ diff --git a/easybuild/easyconfigs/g/GCC/GCC-5.1.0-binutils-2.25.eb b/easybuild/easyconfigs/g/GCC/GCC-5.1.0-binutils-2.25.eb index 897ca9088c..f271d37e88 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-5.1.0-binutils-2.25.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-5.1.0-binutils-2.25.eb @@ -13,9 +13,9 @@ toolchain = {'name': 'dummy', 'version': ''} mpfr_version = '3.1.2' source_urls = [ - 'http://ftpmirror.gnu.org/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror - 'http://ftpmirror.gnu.org/gmp', # idem for GMP - 'http://ftpmirror.gnu.org/mpfr', # idem for MPFR + 'http://ftpmirror.gnu.org/gnu/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror + 'http://ftpmirror.gnu.org/gnu/gmp', # idem for GMP + 'http://ftpmirror.gnu.org/gnu/mpfr', # idem for MPFR 'http://www.multiprecision.org/mpc/download', # MPC official 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies 'http://gcc.cybermirror.org/infrastructure/', # HTTP mirror for GCC dependencies diff --git a/easybuild/easyconfigs/g/GCC/GCC-5.1.0.eb b/easybuild/easyconfigs/g/GCC/GCC-5.1.0.eb index 88c83fce42..fb056c8d3b 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-5.1.0.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-5.1.0.eb @@ -10,9 +10,9 @@ toolchain = {'name': 'dummy', 'version': ''} mpfr_version = '3.1.2' source_urls = [ - 'http://ftpmirror.gnu.org/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror - 'http://ftpmirror.gnu.org/gmp', # idem for GMP - 'http://ftpmirror.gnu.org/mpfr', # idem for MPFR + 'http://ftpmirror.gnu.org/gnu/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror + 'http://ftpmirror.gnu.org/gnu/gmp', # idem for GMP + 'http://ftpmirror.gnu.org/gnu/mpfr', # idem for MPFR 'http://www.multiprecision.org/mpc/download', # MPC official 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies 'http://gcc.cybermirror.org/infrastructure/', # HTTP mirror for GCC dependencies diff --git a/easybuild/easyconfigs/g/GCC/GCC-5.2.0.eb b/easybuild/easyconfigs/g/GCC/GCC-5.2.0.eb index 4052ab789b..66232b4383 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-5.2.0.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-5.2.0.eb @@ -10,9 +10,9 @@ toolchain = {'name': 'dummy', 'version': ''} mpfr_version = '3.1.3' source_urls = [ - 'http://ftpmirror.gnu.org/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror - 'http://ftpmirror.gnu.org/gmp', # idem for GMP - 'http://ftpmirror.gnu.org/mpfr', # idem for MPFR + 'http://ftpmirror.gnu.org/gnu/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror + 'http://ftpmirror.gnu.org/gnu/gmp', # idem for GMP + 'http://ftpmirror.gnu.org/gnu/mpfr', # idem for MPFR 'http://www.multiprecision.org/mpc/download', # MPC official 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies 'http://gcc.cybermirror.org/infrastructure/', # HTTP mirror for GCC dependencies diff --git a/easybuild/easyconfigs/g/GCC/GCC-5.3.0.eb b/easybuild/easyconfigs/g/GCC/GCC-5.3.0.eb index 30c9cc61c0..bac0b46be0 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-5.3.0.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-5.3.0.eb @@ -10,9 +10,9 @@ toolchain = {'name': 'dummy', 'version': ''} mpfr_version = '3.1.3' source_urls = [ - 'http://ftpmirror.gnu.org/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror - 'http://ftpmirror.gnu.org/gmp', # idem for GMP - 'http://ftpmirror.gnu.org/mpfr', # idem for MPFR + 'http://ftpmirror.gnu.org/gnu/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror + 'http://ftpmirror.gnu.org/gnu/gmp', # idem for GMP + 'http://ftpmirror.gnu.org/gnu/mpfr', # idem for MPFR 'http://www.multiprecision.org/mpc/download', # MPC official 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies 'http://gcc.cybermirror.org/infrastructure/', # HTTP mirror for GCC dependencies diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-4.9.2.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-4.9.2.eb index 872c6745e0..1247d0d3d2 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-4.9.2.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-4.9.2.eb @@ -13,9 +13,9 @@ mpfr_version = '3.1.2' gcc_name = 'GCC' source_urls = [ - 'http://ftpmirror.gnu.org/gcc/gcc-%s' % version, # GCC auto-resolving HTTP mirror - 'http://ftpmirror.gnu.org/gmp', # idem for GMP - 'http://ftpmirror.gnu.org/mpfr', # idem for MPFR + 'http://ftpmirror.gnu.org/gnu/gcc/gcc-%s' % version, # GCC auto-resolving HTTP mirror + 'http://ftpmirror.gnu.org/gnu/gmp', # idem for GMP + 'http://ftpmirror.gnu.org/gnu/mpfr', # idem for MPFR 'http://www.multiprecision.org/mpc/download', # MPC official ] sources = [ diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-4.9.3.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-4.9.3.eb index d0d9f1d3a7..50cc39964d 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-4.9.3.eb @@ -12,9 +12,9 @@ toolchain = {'name': 'dummy', 'version': ''} mpfr_version = '3.1.2' source_urls = [ - 'http://ftpmirror.gnu.org/gcc/gcc-%s' % version, # GCC auto-resolving HTTP mirror - 'http://ftpmirror.gnu.org/gmp', # idem for GMP - 'http://ftpmirror.gnu.org/mpfr', # idem for MPFR + 'http://ftpmirror.gnu.org/gnu/gcc/gcc-%s' % version, # GCC auto-resolving HTTP mirror + 'http://ftpmirror.gnu.org/gnu/gmp', # idem for GMP + 'http://ftpmirror.gnu.org/gnu/mpfr', # idem for MPFR 'http://www.multiprecision.org/mpc/download', # MPC official ] sources = [ diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-4.9.4.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-4.9.4.eb index 9a01aa75ef..04c34b3dcc 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-4.9.4.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-4.9.4.eb @@ -12,9 +12,9 @@ toolchain = {'name': 'dummy', 'version': ''} mpfr_version = '3.1.4' source_urls = [ - 'http://ftpmirror.gnu.org/gcc/gcc-%s' % version, # GCC auto-resolving HTTP mirror - 'http://ftpmirror.gnu.org/gmp', # idem for GMP - 'http://ftpmirror.gnu.org/mpfr', # idem for MPFR + 'http://ftpmirror.gnu.org/gnu/gcc/gcc-%s' % version, # GCC auto-resolving HTTP mirror + 'http://ftpmirror.gnu.org/gnu/gmp', # idem for GMP + 'http://ftpmirror.gnu.org/gnu/mpfr', # idem for MPFR 'http://www.multiprecision.org/mpc/download', # MPC official ] sources = [ diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-5.3.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-5.3.0.eb index 508f91d3f8..cfbd5a5779 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-5.3.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-5.3.0.eb @@ -12,9 +12,9 @@ toolchain = {'name': 'dummy', 'version': ''} mpfr_version = '3.1.3' source_urls = [ - 'http://ftpmirror.gnu.org/gcc/gcc-%(version)s', # GCC auto-resolving HTTP mirror - 'http://ftpmirror.gnu.org/gmp', # idem for GMP - 'http://ftpmirror.gnu.org/mpfr', # idem for MPFR + 'http://ftpmirror.gnu.org/gnu/gcc/gcc-%(version)s', # GCC auto-resolving HTTP mirror + 'http://ftpmirror.gnu.org/gnu/gmp', # idem for GMP + 'http://ftpmirror.gnu.org/gnu/mpfr', # idem for MPFR 'http://www.multiprecision.org/mpc/download', # MPC official 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies 'http://gcc.cybermirror.org/infrastructure/', # HTTP mirror for GCC dependencies diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-5.4.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-5.4.0.eb index 1a5cf8b884..c44b03f2db 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-5.4.0.eb @@ -12,9 +12,9 @@ toolchain = {'name': 'dummy', 'version': ''} mpfr_version = '3.1.4' source_urls = [ - 'http://ftpmirror.gnu.org/gcc/gcc-%(version)s', # GCC auto-resolving HTTP mirror - 'http://ftpmirror.gnu.org/gmp', # idem for GMP - 'http://ftpmirror.gnu.org/mpfr', # idem for MPFR + 'http://ftpmirror.gnu.org/gnu/gcc/gcc-%(version)s', # GCC auto-resolving HTTP mirror + 'http://ftpmirror.gnu.org/gnu/gmp', # idem for GMP + 'http://ftpmirror.gnu.org/gnu/mpfr', # idem for MPFR 'http://www.multiprecision.org/mpc/download', # MPC official 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies 'http://gcc.cybermirror.org/infrastructure/', # HTTP mirror for GCC dependencies diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-6.1.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-6.1.0.eb index a645d60588..b3173aaf56 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-6.1.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-6.1.0.eb @@ -12,12 +12,12 @@ toolchain = {'name': 'dummy', 'version': ''} mpfr_version = '3.1.4' source_urls = [ - 'http://ftpmirror.gnu.org/gmp', # idem for GMP - 'http://ftpmirror.gnu.org/mpfr', # idem for MPFR + 'http://ftpmirror.gnu.org/gnu/gmp', # idem for GMP + 'http://ftpmirror.gnu.org/gnu/mpfr', # idem for MPFR 'http://www.multiprecision.org/mpc/download', # MPC official 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies 'http://gcc.cybermirror.org/infrastructure/', # HTTP mirror for GCC dependencies - 'http://ftpmirror.gnu.org/gcc/gcc-%(version)s', # GCC auto-resolving HTTP mirror + 'http://ftpmirror.gnu.org/gnu/gcc/gcc-%(version)s', # GCC auto-resolving HTTP mirror 'https://ftp.gnu.org/gnu/gcc/gcc-%(version)s/', # Alternative GCC 'http://isl.gforge.inria.fr/', # original HTTP source for ISL ] diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-6.2.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-6.2.0.eb index a460408c19..8bf2b22931 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-6.2.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-6.2.0.eb @@ -12,9 +12,9 @@ toolchain = {'name': 'dummy', 'version': ''} mpfr_version = '3.1.4' source_urls = [ - 'http://ftpmirror.gnu.org/gcc/gcc-%(version)s', # GCC auto-resolving HTTP mirror - 'http://ftpmirror.gnu.org/gmp', # idem for GMP - 'http://ftpmirror.gnu.org/mpfr', # idem for MPFR + 'http://ftpmirror.gnu.org/gnu/gcc/gcc-%(version)s', # GCC auto-resolving HTTP mirror + 'http://ftpmirror.gnu.org/gnu/gmp', # idem for GMP + 'http://ftpmirror.gnu.org/gnu/mpfr', # idem for MPFR 'http://www.multiprecision.org/mpc/download', # MPC official 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies 'http://gcc.cybermirror.org/infrastructure/', # HTTP mirror for GCC dependencies diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-6.3.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-6.3.0.eb index a581540c04..603d43dcde 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-6.3.0.eb @@ -12,9 +12,9 @@ toolchain = {'name': 'dummy', 'version': ''} mpfr_version = '3.1.5' source_urls = [ - 'http://ftpmirror.gnu.org/gcc/gcc-%(version)s', # GCC auto-resolving HTTP mirror - 'http://ftpmirror.gnu.org/gmp', # idem for GMP - 'http://ftpmirror.gnu.org/mpfr', # idem for MPFR + 'http://ftpmirror.gnu.org/gnu/gcc/gcc-%(version)s', # GCC auto-resolving HTTP mirror + 'http://ftpmirror.gnu.org/gnu/gmp', # idem for GMP + 'http://ftpmirror.gnu.org/gnu/mpfr', # idem for MPFR 'http://www.multiprecision.org/mpc/download', # MPC official 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies 'http://gcc.cybermirror.org/infrastructure/', # HTTP mirror for GCC dependencies diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-7.1.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-7.1.0.eb index 6f69a58a66..198af84508 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-7.1.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-7.1.0.eb @@ -12,9 +12,9 @@ toolchain = {'name': 'dummy', 'version': ''} mpfr_version = '3.1.5' source_urls = [ - 'http://ftpmirror.gnu.org/gcc/gcc-%(version)s', # GCC auto-resolving HTTP mirror - 'http://ftpmirror.gnu.org/gmp', # idem for GMP - 'http://ftpmirror.gnu.org/mpfr', # idem for MPFR + 'http://ftpmirror.gnu.org/gnu/gcc/gcc-%(version)s', # GCC auto-resolving HTTP mirror + 'http://ftpmirror.gnu.org/gnu/gmp', # idem for GMP + 'http://ftpmirror.gnu.org/gnu/mpfr', # idem for MPFR 'http://www.multiprecision.org/mpc/download', # MPC official 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies 'http://gcc.cybermirror.org/infrastructure/', # HTTP mirror for GCC dependencies diff --git a/easybuild/easyconfigs/g/GLPK/GLPK-4.48-ictce-5.3.0.eb b/easybuild/easyconfigs/g/GLPK/GLPK-4.48-ictce-5.3.0.eb index c0b7a97231..b2cdf2a95f 100644 --- a/easybuild/easyconfigs/g/GLPK/GLPK-4.48-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/g/GLPK/GLPK-4.48-ictce-5.3.0.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'opt': True, 'optarch': True, 'pic': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://ftpmirror.gnu.org/%(namelower)s'] +source_urls = [GNU_SOURCE] dependencies = [ ('GMP', '5.1.1'), diff --git a/easybuild/easyconfigs/g/GLPK/GLPK-4.53-goolf-1.4.10.eb b/easybuild/easyconfigs/g/GLPK/GLPK-4.53-goolf-1.4.10.eb index 4525095b97..7eebd2e1b5 100644 --- a/easybuild/easyconfigs/g/GLPK/GLPK-4.53-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/g/GLPK/GLPK-4.53-goolf-1.4.10.eb @@ -11,7 +11,7 @@ written in ANSI C and organized in the form of a callable library.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://ftpmirror.gnu.org/%(namelower)s'] +source_urls = [GNU_SOURCE] dependencies = [ ('GMP', '5.1.1'), diff --git a/easybuild/easyconfigs/g/GLPK/GLPK-4.53-ictce-6.2.5.eb b/easybuild/easyconfigs/g/GLPK/GLPK-4.53-ictce-6.2.5.eb index aabef669ba..23cdf9bdeb 100644 --- a/easybuild/easyconfigs/g/GLPK/GLPK-4.53-ictce-6.2.5.eb +++ b/easybuild/easyconfigs/g/GLPK/GLPK-4.53-ictce-6.2.5.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'ictce', 'version': '6.2.5'} toolchainopts = {'opt': True, 'optarch': True, 'pic': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://ftpmirror.gnu.org/%(namelower)s'] +source_urls = [GNU_SOURCE] dependencies = [ ('GMP', '5.1.1'), diff --git a/easybuild/easyconfigs/g/GLPK/GLPK-4.55-foss-2015a.eb b/easybuild/easyconfigs/g/GLPK/GLPK-4.55-foss-2015a.eb index 270390d86d..d0490da351 100644 --- a/easybuild/easyconfigs/g/GLPK/GLPK-4.55-foss-2015a.eb +++ b/easybuild/easyconfigs/g/GLPK/GLPK-4.55-foss-2015a.eb @@ -13,7 +13,7 @@ description = """The GLPK (GNU Linear Programming Kit) package is intended for toolchain = {'name': 'foss', 'version': '2015a'} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://ftp.gnu.org/gnu/%(namelower)s/'] +source_urls = [GNU_SOURCE] dependencies = [('GMP', '6.0.0a', '', ('GCC', '4.9.2'))] diff --git a/easybuild/easyconfigs/g/GLPK/GLPK-4.55-intel-2015a.eb b/easybuild/easyconfigs/g/GLPK/GLPK-4.55-intel-2015a.eb index aef6e26abf..97c634c6e3 100644 --- a/easybuild/easyconfigs/g/GLPK/GLPK-4.55-intel-2015a.eb +++ b/easybuild/easyconfigs/g/GLPK/GLPK-4.55-intel-2015a.eb @@ -13,7 +13,7 @@ description = """The GLPK (GNU Linear Programming Kit) package is intended for toolchain = {'name': 'intel', 'version': '2015a'} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://ftp.gnu.org/gnu/%(namelower)s/'] +source_urls = [GNU_SOURCE] dependencies = [('GMP', '6.0.0a', '', ('GCC', '4.9.2'))] diff --git a/easybuild/easyconfigs/g/GLPK/GLPK-4.58-foss-2016a.eb b/easybuild/easyconfigs/g/GLPK/GLPK-4.58-foss-2016a.eb index d5751eec2a..1923d225b7 100644 --- a/easybuild/easyconfigs/g/GLPK/GLPK-4.58-foss-2016a.eb +++ b/easybuild/easyconfigs/g/GLPK/GLPK-4.58-foss-2016a.eb @@ -13,7 +13,7 @@ description = """The GLPK (GNU Linear Programming Kit) package is intended for toolchain = {'name': 'foss', 'version': '2016a'} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://ftp.gnu.org/gnu/%(namelower)s/'] +source_urls = [GNU_SOURCE] dependencies = [('GMP', '6.1.0')] diff --git a/easybuild/easyconfigs/g/GLPK/GLPK-4.58-intel-2016a.eb b/easybuild/easyconfigs/g/GLPK/GLPK-4.58-intel-2016a.eb index 07ed2e7997..391a5af632 100644 --- a/easybuild/easyconfigs/g/GLPK/GLPK-4.58-intel-2016a.eb +++ b/easybuild/easyconfigs/g/GLPK/GLPK-4.58-intel-2016a.eb @@ -13,7 +13,7 @@ description = """The GLPK (GNU Linear Programming Kit) package is intended for toolchain = {'name': 'intel', 'version': '2016a'} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://ftp.gnu.org/gnu/%(namelower)s/'] +source_urls = [GNU_SOURCE] dependencies = [('GMP', '6.1.0')] diff --git a/easybuild/easyconfigs/g/GLPK/GLPK-4.60-intel-2016b.eb b/easybuild/easyconfigs/g/GLPK/GLPK-4.60-intel-2016b.eb index 66b0f5b8f2..c1d050fb81 100644 --- a/easybuild/easyconfigs/g/GLPK/GLPK-4.60-intel-2016b.eb +++ b/easybuild/easyconfigs/g/GLPK/GLPK-4.60-intel-2016b.eb @@ -13,7 +13,7 @@ description = """The GLPK (GNU Linear Programming Kit) package is intended for toolchain = {'name': 'intel', 'version': '2016b'} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://ftp.gnu.org/gnu/%(namelower)s/'] +source_urls = [GNU_SOURCE] dependencies = [('GMP', '6.1.1')] diff --git a/easybuild/easyconfigs/g/GLPK/GLPK-4.61-intel-2017a.eb b/easybuild/easyconfigs/g/GLPK/GLPK-4.61-intel-2017a.eb index 28b87558fc..634ca00ce6 100644 --- a/easybuild/easyconfigs/g/GLPK/GLPK-4.61-intel-2017a.eb +++ b/easybuild/easyconfigs/g/GLPK/GLPK-4.61-intel-2017a.eb @@ -13,7 +13,7 @@ description = """The GLPK (GNU Linear Programming Kit) package is intended for toolchain = {'name': 'intel', 'version': '2017a'} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://ftp.gnu.org/gnu/%(namelower)s/'] +source_urls = [GNU_SOURCE] dependencies = [('GMP', '6.1.2')] diff --git a/easybuild/easyconfigs/g/GSL/GSL-1.16-goolf-1.7.20.eb b/easybuild/easyconfigs/g/GSL/GSL-1.16-goolf-1.7.20.eb index 723ea8a309..848138c178 100644 --- a/easybuild/easyconfigs/g/GSL/GSL-1.16-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/g/GSL/GSL-1.16-goolf-1.7.20.eb @@ -11,7 +11,7 @@ description = """The GNU Scientific Library (GSL) is a numerical library for C a toolchain = {'name': 'goolf', 'version': '1.7.20'} toolchainopts = {'unroll': True, 'pic': True} -source_urls = ['http://ftpmirror.gnu.org/gsl/'] +source_urls = ['http://ftpmirror.gnu.org/gnu/gsl/'] sources = [SOURCELOWER_TAR_GZ] configopts = "--with-pic" diff --git a/easybuild/easyconfigs/g/gzip/gzip-1.6-ictce-5.3.0.eb b/easybuild/easyconfigs/g/gzip/gzip-1.6-ictce-5.3.0.eb index d309818ed8..443c4e034e 100644 --- a/easybuild/easyconfigs/g/gzip/gzip-1.6-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/g/gzip/gzip-1.6-ictce-5.3.0.eb @@ -21,7 +21,7 @@ description = "gzip (GNU zip) is a popular data compression program as a replace toolchain = {'name': 'ictce', 'version': '5.3.0'} # eg. http://ftp.gnu.org/gnu/gzip/gzip-1.6.tar.gz -source_urls = ['http://ftpmirror.gnu.org/gzip'] +source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] # make sure the gzip, gunzip and compress binaries are available after installation diff --git a/easybuild/easyconfigs/g/gzip/gzip-1.6-ictce-5.5.0.eb b/easybuild/easyconfigs/g/gzip/gzip-1.6-ictce-5.5.0.eb index 5f29b035e2..ce75649419 100644 --- a/easybuild/easyconfigs/g/gzip/gzip-1.6-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/g/gzip/gzip-1.6-ictce-5.5.0.eb @@ -21,7 +21,7 @@ description = "gzip (GNU zip) is a popular data compression program as a replace toolchain = {'name': 'ictce', 'version': '5.5.0'} # eg. http://ftp.gnu.org/gnu/gzip/gzip-1.6.tar.gz -source_urls = ['http://ftpmirror.gnu.org/gzip'] +source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] # make sure the gzip, gunzip and compress binaries are available after installation diff --git a/easybuild/easyconfigs/g/gzip/gzip-1.6-ictce-6.2.5.eb b/easybuild/easyconfigs/g/gzip/gzip-1.6-ictce-6.2.5.eb index 036f697797..0b795ea36c 100644 --- a/easybuild/easyconfigs/g/gzip/gzip-1.6-ictce-6.2.5.eb +++ b/easybuild/easyconfigs/g/gzip/gzip-1.6-ictce-6.2.5.eb @@ -21,7 +21,7 @@ description = "gzip (GNU zip) is a popular data compression program as a replace toolchain = {'name': 'ictce', 'version': '6.2.5'} # eg. http://ftp.gnu.org/gnu/gzip/gzip-1.6.tar.gz -source_urls = ['http://ftpmirror.gnu.org/gzip'] +source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] # make sure the gzip, gunzip and compress binaries are available after installation diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.16-ictce-5.5.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.16-ictce-5.5.0.eb index a7f7a66b5b..9b71429dfd 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.16-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.16-ictce-5.5.0.eb @@ -11,7 +11,7 @@ description = """GNU M4 is an implementation of the traditional Unix macro proce toolchain = {'name': 'ictce', 'version': '5.5.0'} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://ftpmirror.gnu.org/m4'] +source_urls = [GNU_SOURCE] patches = ['M4-%(version)s-no-gets.patch'] diff --git a/easybuild/easyconfigs/m/mutil/mutil-1.822.3-intel-2016a.eb b/easybuild/easyconfigs/m/mutil/mutil-1.822.3-intel-2016a.eb index b4d2d3ae93..851772647c 100644 --- a/easybuild/easyconfigs/m/mutil/mutil-1.822.3-intel-2016a.eb +++ b/easybuild/easyconfigs/m/mutil/mutil-1.822.3-intel-2016a.eb @@ -17,7 +17,7 @@ sources = [ ] source_urls = [ SOURCEFORGE_SOURCE, - 'http://ftpmirror.gnu.org/coreutils', + 'http://ftpmirror.gnu.org/gnu/coreutils', ] dependencies = [ -- GitLab From f5c207b85368f0c31cf348e7e38c924b94e19942 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Wed, 31 May 2017 15:34:38 -0500 Subject: [PATCH 0847/1603] adding easyconfigs: expat-2.2.0-GCCcore-5.4.0.eb --- .../e/expat/expat-2.2.0-GCCcore-5.4.0.eb | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) create mode 100644 easybuild/easyconfigs/e/expat/expat-2.2.0-GCCcore-5.4.0.eb diff --git a/easybuild/easyconfigs/e/expat/expat-2.2.0-GCCcore-5.4.0.eb b/easybuild/easyconfigs/e/expat/expat-2.2.0-GCCcore-5.4.0.eb new file mode 100644 index 0000000000..eeff8e600b --- /dev/null +++ b/easybuild/easyconfigs/e/expat/expat-2.2.0-GCCcore-5.4.0.eb @@ -0,0 +1,18 @@ +easyblock = 'ConfigureMake' + +name = 'expat' +version = '2.2.0' + +homepage = 'http://expat.sourceforge.net/' +description = """Expat is an XML parser library written in C. It is a stream-oriented parser in which an application + registers handlers for things the parser might find in the XML document (like start tags)""" + +toolchain = {'name': 'GCCcore', 'version': '5.4.0'} +toolchainopts = {'pic': True} + +builddependencies = [('binutils', '2.26', '', True)] + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = [SOURCEFORGE_SOURCE] + +moduleclass = 'tools' -- GitLab From a17d9abdf97f0390c8205b2bc63c46f8a7dcffc4 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Wed, 31 May 2017 15:57:06 -0500 Subject: [PATCH 0848/1603] adding easyconfigs: libpng-1.6.24-GCCcore-5.4.0.eb, freetype-2.6.5-GCCcore-5.4.0.eb, fontconfig-2.12.1-GCCcore-5.4.0.eb --- .../fontconfig-2.12.1-GCCcore-5.4.0.eb | 25 +++++++++++++++++ .../freetype/freetype-2.6.5-GCCcore-5.4.0.eb | 28 +++++++++++++++++++ .../l/libpng/libpng-1.6.24-GCCcore-5.4.0.eb | 28 +++++++++++++++++++ 3 files changed, 81 insertions(+) create mode 100644 easybuild/easyconfigs/f/fontconfig/fontconfig-2.12.1-GCCcore-5.4.0.eb create mode 100644 easybuild/easyconfigs/f/freetype/freetype-2.6.5-GCCcore-5.4.0.eb create mode 100644 easybuild/easyconfigs/l/libpng/libpng-1.6.24-GCCcore-5.4.0.eb diff --git a/easybuild/easyconfigs/f/fontconfig/fontconfig-2.12.1-GCCcore-5.4.0.eb b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.12.1-GCCcore-5.4.0.eb new file mode 100644 index 0000000000..39bdb77029 --- /dev/null +++ b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.12.1-GCCcore-5.4.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'fontconfig' +version = '2.12.1' + +homepage = 'http://www.freedesktop.org/software/fontconfig' +description = """Fontconfig is a library designed to provide system-wide font configuration, customization and +application access.""" + +toolchain = {'name': 'GCCcore', 'version': '5.4.0'} + +source_urls = ['http://www.freedesktop.org/software/fontconfig/release/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('expat', '2.2.0'), + ('freetype', '2.6.5'), +] + +# use same binutils version that was used when building GCCcore toolchain +builddependencies = [('binutils', '2.26', '', True)] + +configopts = '--disable-docs ' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.6.5-GCCcore-5.4.0.eb b/easybuild/easyconfigs/f/freetype/freetype-2.6.5-GCCcore-5.4.0.eb new file mode 100644 index 0000000000..e1a17a86f6 --- /dev/null +++ b/easybuild/easyconfigs/f/freetype/freetype-2.6.5-GCCcore-5.4.0.eb @@ -0,0 +1,28 @@ +name = 'freetype' +version = '2.6.5' + +homepage = 'http://freetype.org' +description = """FreeType 2 is a software font engine that is designed to be small, efficient, highly customizable, and + portable while capable of producing high-quality output (glyph images). It can be used in graphics libraries, display + servers, font conversion tools, text image generation tools, and many other products as well.""" + +toolchain = {'name': 'GCCcore', 'version': '5.4.0'} + +source_urls = [GNU_SAVANNAH_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('libpng', '1.6.24'), + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), +] + +builddependencies = [('binutils', '2.26', '', True)] + +sanity_check_paths = { + 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, + 'lib/pkgconfig/freetype2.pc'], + 'dirs': ['include/freetype2'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.24-GCCcore-5.4.0.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.24-GCCcore-5.4.0.eb new file mode 100644 index 0000000000..c2aea84a3c --- /dev/null +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.24-GCCcore-5.4.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'libpng' +version = '1.6.24' + +homepage = 'http://www.libpng.org/pub/png/libpng.html' +description = "libpng is the official PNG reference library" + +toolchain = {'name': 'GCCcore', 'version': '5.4.0'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('zlib', '1.2.8')] + +builddependencies = [('binutils', '2.26', '', True)] + +configopts = "--with-pic" + +majminver = ''.join(version.split('.')[:2]) +sanity_check_paths = { + 'files': ['include/pngconf.h', 'include/png.h', 'include/pnglibconf.h', 'lib/libpng.a', + 'lib/libpng.%s' % SHLIB_EXT, 'lib/libpng%s.a' % majminver, 'lib/libpng%s.%s' % (majminver, SHLIB_EXT)], + 'dirs': ['bin', 'include/libpng%s' % majminver, 'share/man'], +} + +moduleclass = 'lib' -- GitLab From f2a56252d1355196f6825012b83aeda3e4854eba Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Wed, 31 May 2017 16:21:09 -0500 Subject: [PATCH 0849/1603] adding easyconfigs: gettext-0.19.8-GCCcore-5.4.0.eb, libxml2-2.9.4-GCCcore-5.4.0.eb, XZ-5.2.2-GCCcore-5.4.0.eb --- .../g/gettext/gettext-0.19.8-GCCcore-5.4.0.eb | 26 +++++++++++++++++ .../l/libxml2/libxml2-2.9.4-GCCcore-5.4.0.eb | 26 +++++++++++++++++ .../x/XZ/XZ-5.2.2-GCCcore-5.4.0.eb | 28 +++++++++++++++++++ 3 files changed, 80 insertions(+) create mode 100644 easybuild/easyconfigs/g/gettext/gettext-0.19.8-GCCcore-5.4.0.eb create mode 100644 easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-GCCcore-5.4.0.eb create mode 100644 easybuild/easyconfigs/x/XZ/XZ-5.2.2-GCCcore-5.4.0.eb diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.8-GCCcore-5.4.0.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.8-GCCcore-5.4.0.eb new file mode 100644 index 0000000000..8875bae587 --- /dev/null +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.8-GCCcore-5.4.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'gettext' +version = '0.19.8' + +homepage = 'http://www.gnu.org/software/gettext/' +description = """GNU 'gettext' is an important step for the GNU Translation Project, as it is an asset on which we may +build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools +and documentation""" + +toolchain = {'name': 'GCCcore', 'version': '5.4.0'} + +sources = [SOURCE_TAR_GZ] +source_urls = [GNU_SOURCE] + +dependencies = [ + ('libxml2', '2.9.4'), + ('ncurses', '6.0'), +] + +# use same binutils version that was used when building GCCcore toolchain +builddependencies = [('binutils', '2.26', '', True)] + +configopts = '--without-emacs --with-libxml2-prefix=$EBROOTLIBXML2' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-GCCcore-5.4.0.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-GCCcore-5.4.0.eb new file mode 100644 index 0000000000..5c02f30d48 --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-GCCcore-5.4.0.eb @@ -0,0 +1,26 @@ +name = 'libxml2' +version = '2.9.4' + +homepage = 'http://xmlsoft.org/' +description = """Libxml2 is the XML C parser and +toolchain developed for the Gnome project + (but usable outside of the Gnome platform).""" + +toolchain = {'name': 'GCCcore', 'version': '5.4.0'} +toolchainopts = {'pic': True} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('zlib', '1.2.8'), + ('XZ', '5.2.2'), +] + +# use same binutils version that was used when building GCCcore toolchain +builddependencies = [('binutils', '2.26', '', True)] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-GCCcore-5.4.0.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-GCCcore-5.4.0.eb new file mode 100644 index 0000000000..c46df20c2f --- /dev/null +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-GCCcore-5.4.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'XZ' +version = '5.2.2' + +homepage = 'http://tukaani.org/xz/' +description = "xz: XZ utilities" + +toolchain = {'name': 'GCCcore', 'version': '5.4.0'} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://tukaani.org/xz/'] + +builddependencies = [ + ('gettext', '0.19.8', '', True), + # use same binutils version that was used when building GCCcore toolchain + ('binutils', '2.26', '', True), +] + +# may become useful in non-x86 archs +# configopts = ' --disable-assembler ' + +sanity_check_paths = { + 'files': ["bin/xz", "bin/lzmainfo"], + 'dirs': [] +} + +moduleclass = 'tools' -- GitLab From 379c40fb8733c04fe402d94d347c9cf78a3b51e8 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Wed, 31 May 2017 16:23:59 -0500 Subject: [PATCH 0850/1603] adding easyconfigs: pkg-config-0.29.1-GCCcore-5.4.0.eb --- .../pkg-config-0.29.1-GCCcore-5.4.0.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1-GCCcore-5.4.0.eb diff --git a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1-GCCcore-5.4.0.eb b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1-GCCcore-5.4.0.eb new file mode 100644 index 0000000000..11d61b23f7 --- /dev/null +++ b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1-GCCcore-5.4.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'pkg-config' +version = '0.29.1' + +homepage = 'http://www.freedesktop.org/wiki/Software/pkg-config/' +description = """pkg-config is a helper tool used when compiling applications and libraries. It helps you insert the + correct compiler options on the command line so an application can use + gcc -o test test.c `pkg-config --libs --cflags glib-2.0` + for instance, rather than hard-coding values on where to find glib (or other libraries).""" + +toolchain = {'name': 'GCCcore', 'version': '5.4.0'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['https://pkg-config.freedesktop.org/releases/'] + +builddependencies = [ + # use same binutils version that was used when building GCCcore toolchain + ('binutils', '2.26', '', True), +] + +# don't use PAX, it might break. +tar_config_opts = True + +configopts = " --with-internal-glib" + +sanity_check_paths = { + 'files': ['bin/pkg-config'], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From ff583b852b1a90018a60f91aea9520173851ad2c Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Wed, 31 May 2017 17:16:39 -0500 Subject: [PATCH 0851/1603] adding easyconfigs: GMP-6.1.1-GCCcore-5.4.0.eb --- .../g/GMP/GMP-6.1.1-GCCcore-5.4.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/g/GMP/GMP-6.1.1-GCCcore-5.4.0.eb diff --git a/easybuild/easyconfigs/g/GMP/GMP-6.1.1-GCCcore-5.4.0.eb b/easybuild/easyconfigs/g/GMP/GMP-6.1.1-GCCcore-5.4.0.eb new file mode 100644 index 0000000000..6b309e5f37 --- /dev/null +++ b/easybuild/easyconfigs/g/GMP/GMP-6.1.1-GCCcore-5.4.0.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'GMP' +version = '6.1.1' + +homepage = 'http://gmplib.org/' +description = """GMP is a free library for arbitrary precision arithmetic, +operating on signed integers, rational numbers, and floating point numbers. """ + +toolchain = {'name': 'GCCcore', 'version': '5.4.0'} +toolchainopts = {'pic': True, 'precise': True} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://ftp.gnu.org/gnu/gmp'] + +builddependencies = [ + ('binutils', '2.26'), + ('Autotools', '20150215'), +] + +# enable C++ interface +configopts = '--enable-cxx' + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libgmp.%s' % SHLIB_EXT, 'include/gmp.h'], + 'dirs': [], +} + +moduleclass = 'math' -- GitLab From b02e7fe62bbeefd882c8ad270226bf1f8e9125f4 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Wed, 31 May 2017 17:18:18 -0500 Subject: [PATCH 0852/1603] adding easyconfigs: libffi-3.2.1-GCCcore-5.4.0.eb --- .../l/libffi/libffi-3.2.1-GCCcore-5.4.0.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/l/libffi/libffi-3.2.1-GCCcore-5.4.0.eb diff --git a/easybuild/easyconfigs/l/libffi/libffi-3.2.1-GCCcore-5.4.0.eb b/easybuild/easyconfigs/l/libffi/libffi-3.2.1-GCCcore-5.4.0.eb new file mode 100644 index 0000000000..c9f216298d --- /dev/null +++ b/easybuild/easyconfigs/l/libffi/libffi-3.2.1-GCCcore-5.4.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'libffi' +version = '3.2.1' + +homepage = 'http://sourceware.org/libffi/' +description = """The libffi library provides a portable, high level programming interface to various calling +conventions. This allows a programmer to call any function specified by a call interface description at run-time.""" + +toolchain = {'name': 'GCCcore', 'version': '5.4.0'} + +source_urls = [ + 'ftp://sourceware.org/pub/libffi/', + 'http://www.mirrorservice.org/sites/sourceware.org/pub/libffi/', +] +sources = [SOURCELOWER_TAR_GZ] + +builddependencies = [('binutils', '2.26', '', True)] + +sanity_check_paths = { + 'files': [('lib/libffi.%s' % SHLIB_EXT, 'lib64/libffi.%s' % SHLIB_EXT), ('lib/libffi.a', 'lib64/libffi.a')], + 'dirs': [], +} + +moduleclass = 'lib' -- GitLab From bf7ef0e281e7e157677d5417eae2b0ba46dc297a Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Wed, 31 May 2017 17:18:43 -0500 Subject: [PATCH 0853/1603] adding easyconfigs: libreadline-6.3-GCCcore-5.4.0.eb --- .../libreadline-6.3-GCCcore-5.4.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCCcore-5.4.0.eb diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCCcore-5.4.0.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCCcore-5.4.0.eb new file mode 100644 index 0000000000..a356775b1b --- /dev/null +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCCcore-5.4.0.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'libreadline' +version = '6.3' + +homepage = 'http://cnswww.cns.cwru.edu/php/chet/readline/rltop.html' +description = """The GNU Readline library provides a set of functions for use by applications that + allow users to edit command lines as they are typed in. Both Emacs and vi editing modes are available. + The Readline library includes additional functions to maintain a list of previously-entered command lines, + to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands.""" + +toolchain = {'name': 'GCCcore', 'version': '5.4.0'} +toolchainopts = {'pic': True} + +sources = ['readline-%(version)s.tar.gz'] +source_urls = ['http://ftp.gnu.org/gnu/readline'] + +patches = ['libreadline-%(version)s-bugfix.patch'] + +builddependencies = [('binutils', '2.26', '', True)] + +dependencies = [('ncurses', '6.0')] + +# for the termcap symbols, use EB ncurses +preconfigopts = "env LDFLAGS='-lncurses'" + +sanity_check_paths = { + 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + 'dirs': [], +} + +moduleclass = 'lib' -- GitLab From 41fa0eb1d9f2300d745770149525ac624a23fc38 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Thu, 1 Jun 2017 16:48:59 +1200 Subject: [PATCH 0854/1603] Add ncurses-devel as OS dependency and ccmake as sanity check --- ....1-foss-2015a-GLib-2.48.2-Python-2.7.11.eb | 38 +++++++++++++++++++ easybuild/easyconfigs/c/CMake/CMake-3.6.1.eb | 4 +- 2 files changed, 40 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/c/CGAL/CGAL-4.8.1-foss-2015a-GLib-2.48.2-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.8.1-foss-2015a-GLib-2.48.2-Python-2.7.11.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.8.1-foss-2015a-GLib-2.48.2-Python-2.7.11.eb new file mode 100644 index 0000000000..f8ab683344 --- /dev/null +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.8.1-foss-2015a-GLib-2.48.2-Python-2.7.11.eb @@ -0,0 +1,38 @@ +name = 'CGAL' +version = '4.8.1' +gmpver = '6.0.0a' + +homepage = 'http://www.cgal.org/' +description = """The goal of the CGAL Open Source Project is to provide easy access to efficient + and reliable geometric algorithms in the form of a C++ library.""" + +toolchain = {'name': 'foss', 'version': '2015a'} +toolchainopts = {'strict': True} + +# note: source URL needs to be updated for a new version (checksums too)! +source_urls = ['https://github.com/%(name)s/%(namelower)s/releases/download/releases%2F%(name)s-%(version)s'] +sources = [SOURCE_TAR_XZ] +checksums = ['1cbcb3f251822766ed3d744f923c782d'] + +dependencies = [ + ('Boost', '1.60.0'), + ('GMP', gmpver), + ('MPFR', '3.1.2', '-GMP-%s' % gmpver), +] + +configopts = "-DCMAKE_VERBOSE_MAKEFILE=ON " +configopts += "-DBoost_INCLUDE_DIR=$EBROOTBOOST/include " +configopts += "-DBoost_LIBRARY_DIRS=$EBROOTBOOST/lib " +configopts += "-DBoost_SYSTEM_LIBRARY=$EBROOTBOOST/libboost_system.%s " % SHLIB_EXT +configopts += "-DBoost_THREAD_LIBRARY=$EBROOTBOOST/libboost_thread.%s " % SHLIB_EXT +configopts += "-DMPFR_INCLUDE_DIR=$EBROOTMPFR/include " +configopts += "-DMPFR_LIBRARIES=$EBROOTMPFR/lib/libmpfr.%s " % SHLIB_EXT +configopts += "-DGMP_INCLUDE_DIR=$EBROOTGMP/include " +configopts += "-DGMP_LIBRARIES=$EBROOTGMP/lib/libgmp.%s " % SHLIB_EXT +configopts += "-DGMP_LIBRARIES_DIR=$EBROOTGMP/lib " + +builddependencies = [ + ('CMake', '3.4.1'), +] + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.6.1.eb b/easybuild/easyconfigs/c/CMake/CMake-3.6.1.eb index 0e73857b1d..71580ff227 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.6.1.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.6.1.eb @@ -18,10 +18,10 @@ configopts = '-- -DCMAKE_USE_OPENSSL=1' # which might want different versions of the same dependency, eg: ncurses dependencies = [] -osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel', 'ncurses-devel')] sanity_check_paths = { - 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'files': ["bin/%s" % x for x in ['cmake', 'ccmake', 'cpack', 'ctest']], 'dirs': [], } -- GitLab From 9b68d8c3abc8e69a5230410fc69da373615b4d90 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Thu, 1 Jun 2017 16:52:35 +1200 Subject: [PATCH 0855/1603] Delete this file - wrongly committed to this branch --- .../CGAL/CGAL-4.8.1-foss-2015a-GLib-2.48.2-Python-2.7.11.eb | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.8.1-foss-2015a-GLib-2.48.2-Python-2.7.11.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.8.1-foss-2015a-GLib-2.48.2-Python-2.7.11.eb index f8ab683344..0819922f0a 100644 --- a/easybuild/easyconfigs/c/CGAL/CGAL-4.8.1-foss-2015a-GLib-2.48.2-Python-2.7.11.eb +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.8.1-foss-2015a-GLib-2.48.2-Python-2.7.11.eb @@ -1,6 +1,9 @@ name = 'CGAL' version = '4.8.1' gmpver = '6.0.0a' +pyver = '2.7.11' +glibver = '2.48.2' +versionsuffix = '-GLib-%s-Python-%s' % (glibver, pyver) homepage = 'http://www.cgal.org/' description = """The goal of the CGAL Open Source Project is to provide easy access to efficient @@ -9,15 +12,16 @@ description = """The goal of the CGAL Open Source Project is to provide easy acc toolchain = {'name': 'foss', 'version': '2015a'} toolchainopts = {'strict': True} -# note: source URL needs to be updated for a new version (checksums too)! source_urls = ['https://github.com/%(name)s/%(namelower)s/releases/download/releases%2F%(name)s-%(version)s'] sources = [SOURCE_TAR_XZ] checksums = ['1cbcb3f251822766ed3d744f923c782d'] dependencies = [ ('Boost', '1.60.0'), + ('GLib', glibver), ('GMP', gmpver), ('MPFR', '3.1.2', '-GMP-%s' % gmpver), + ('Qt', '4.8.7', versionsuffix), ] configopts = "-DCMAKE_VERBOSE_MAKEFILE=ON " -- GitLab From 18ff6997f7d60bd9f4174732982e4d432f354283 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Thu, 1 Jun 2017 16:54:02 +1200 Subject: [PATCH 0856/1603] Delete CGAL easyconfig, again --- ....1-foss-2015a-GLib-2.48.2-Python-2.7.11.eb | 42 ------------------- 1 file changed, 42 deletions(-) delete mode 100644 easybuild/easyconfigs/c/CGAL/CGAL-4.8.1-foss-2015a-GLib-2.48.2-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.8.1-foss-2015a-GLib-2.48.2-Python-2.7.11.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.8.1-foss-2015a-GLib-2.48.2-Python-2.7.11.eb deleted file mode 100644 index 0819922f0a..0000000000 --- a/easybuild/easyconfigs/c/CGAL/CGAL-4.8.1-foss-2015a-GLib-2.48.2-Python-2.7.11.eb +++ /dev/null @@ -1,42 +0,0 @@ -name = 'CGAL' -version = '4.8.1' -gmpver = '6.0.0a' -pyver = '2.7.11' -glibver = '2.48.2' -versionsuffix = '-GLib-%s-Python-%s' % (glibver, pyver) - -homepage = 'http://www.cgal.org/' -description = """The goal of the CGAL Open Source Project is to provide easy access to efficient - and reliable geometric algorithms in the form of a C++ library.""" - -toolchain = {'name': 'foss', 'version': '2015a'} -toolchainopts = {'strict': True} - -source_urls = ['https://github.com/%(name)s/%(namelower)s/releases/download/releases%2F%(name)s-%(version)s'] -sources = [SOURCE_TAR_XZ] -checksums = ['1cbcb3f251822766ed3d744f923c782d'] - -dependencies = [ - ('Boost', '1.60.0'), - ('GLib', glibver), - ('GMP', gmpver), - ('MPFR', '3.1.2', '-GMP-%s' % gmpver), - ('Qt', '4.8.7', versionsuffix), -] - -configopts = "-DCMAKE_VERBOSE_MAKEFILE=ON " -configopts += "-DBoost_INCLUDE_DIR=$EBROOTBOOST/include " -configopts += "-DBoost_LIBRARY_DIRS=$EBROOTBOOST/lib " -configopts += "-DBoost_SYSTEM_LIBRARY=$EBROOTBOOST/libboost_system.%s " % SHLIB_EXT -configopts += "-DBoost_THREAD_LIBRARY=$EBROOTBOOST/libboost_thread.%s " % SHLIB_EXT -configopts += "-DMPFR_INCLUDE_DIR=$EBROOTMPFR/include " -configopts += "-DMPFR_LIBRARIES=$EBROOTMPFR/lib/libmpfr.%s " % SHLIB_EXT -configopts += "-DGMP_INCLUDE_DIR=$EBROOTGMP/include " -configopts += "-DGMP_LIBRARIES=$EBROOTGMP/lib/libgmp.%s " % SHLIB_EXT -configopts += "-DGMP_LIBRARIES_DIR=$EBROOTGMP/lib " - -builddependencies = [ - ('CMake', '3.4.1'), -] - -moduleclass = 'numlib' -- GitLab From 2fd2715980e85eb5489fcfc009fa5dbe6fb5056f Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Thu, 1 Jun 2017 17:12:31 +1200 Subject: [PATCH 0857/1603] Dependencies for the gimkl-2017a toolchain --- easybuild/easyconfigs/g/GCC/GCC-5.4.0.eb | 25 ++++++++++++ easybuild/easyconfigs/g/gimpi/gimpi-2017a.eb | 18 +++++++++ .../i/imkl/imkl-2017.1.132-gimpi-2017a.eb | 36 +++++++++++++++++ .../i/impi/impi-2017.1.132-GCC-5.4.0.eb | 40 +++++++++++++++++++ 4 files changed, 119 insertions(+) create mode 100644 easybuild/easyconfigs/g/GCC/GCC-5.4.0.eb create mode 100644 easybuild/easyconfigs/g/gimpi/gimpi-2017a.eb create mode 100644 easybuild/easyconfigs/i/imkl/imkl-2017.1.132-gimpi-2017a.eb create mode 100644 easybuild/easyconfigs/i/impi/impi-2017.1.132-GCC-5.4.0.eb diff --git a/easybuild/easyconfigs/g/GCC/GCC-5.4.0.eb b/easybuild/easyconfigs/g/GCC/GCC-5.4.0.eb new file mode 100644 index 0000000000..0bc33f7250 --- /dev/null +++ b/easybuild/easyconfigs/g/GCC/GCC-5.4.0.eb @@ -0,0 +1,25 @@ +easyblock = 'Bundle' + +name = 'GCC' +version = '5.4.0' + +binutilsver = '2.26' +#versionsuffix = '-%s' % binutilsver + +homepage = 'http://gcc.gnu.org/' +description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, + as well as libraries for these languages (libstdc++, libgcj,...).""" + +toolchain = {'name': 'dummy', 'version': ''} + +dependencies = [ + ('GCCcore', version), + # binutils built on top of GCCcore, which was built on top of (dummy-built) binutils + ('binutils', binutilsver, '', ('GCCcore', version)), +] + +altroot = 'GCCcore' +altversion = 'GCCcore' + +# this bundle serves as a compiler-only toolchain, so it should be marked as compiler (important for HMNS) +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/gimpi/gimpi-2017a.eb b/easybuild/easyconfigs/g/gimpi/gimpi-2017a.eb new file mode 100644 index 0000000000..394c894b37 --- /dev/null +++ b/easybuild/easyconfigs/g/gimpi/gimpi-2017a.eb @@ -0,0 +1,18 @@ +easyblock = "Toolchain" + +name = 'gimpi' +version = '2017a' + +homepage = '(none)' +description = """GNU Compiler Collection (GCC) based compiler toolchain with Intel MPI.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +comp = ('GCC', '5.4.0') + +dependencies = [ + comp, + ('impi', '2017.1.132', '', comp), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-gimpi-2017a.eb b/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-gimpi-2017a.eb new file mode 100644 index 0000000000..aaa3568ab0 --- /dev/null +++ b/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-gimpi-2017a.eb @@ -0,0 +1,36 @@ +name = 'imkl' +version = '2017.1.132' + +homepage = 'http://software.intel.com/en-us/intel-mkl/' +description = """Intel Math Kernel Library is a library of highly optimized, + extensively threaded math routines for science, engineering, and financial + applications that require maximum performance. Core math functions include + BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.""" + +toolchain = {'name': 'gimpi', 'version': '2017a'} + +sources = ['l_mkl_%(version)s.tgz'] +checksums = ['7911c0f777c4cb04225bf4518088939e'] + +dontcreateinstalldir = 'True' + +license_file = HOME + '/licenses/intel/license.lic' + +interfaces = True + +postinstallcmds = [ + # extract the examples + 'tar xvzf %(installdir)s/mkl/examples/examples_cluster_c.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_cluster_f.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_core_c.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_core_f.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_f95.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_mic_f.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_mic_c.tgz -C %(installdir)s/mkl/examples/', +] + +modextravars = { + 'MKL_EXAMPLES': '%(installdir)s/mkl/examples/', +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/impi/impi-2017.1.132-GCC-5.4.0.eb b/easybuild/easyconfigs/i/impi/impi-2017.1.132-GCC-5.4.0.eb new file mode 100644 index 0000000000..e03300b9d5 --- /dev/null +++ b/easybuild/easyconfigs/i/impi/impi-2017.1.132-GCC-5.4.0.eb @@ -0,0 +1,40 @@ +name = 'impi' +version = '2017.1.132' + +homepage = 'http://software.intel.com/en-us/intel-mpi-library/' +description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric message + passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for + Linux OS implements the Message Passing Interface, version 2 (MPI-2) specification.""" + +toolchain = {'name': 'GCC', 'version': '5.4.0'} + +sources = ['l_mpi_%(version)s.tgz'] +checksums = ['d5e941ac2bcf7c5576f85f6bcfee4c18'] + +dontcreateinstalldir = 'True' + +components = ['intel-mpi', 'intel-psxe', 'intel-imb'] + +# license file +license_file = HOME + '/licenses/intel/license.lic' + +# Set I_MPI_ variables to point at the appropriate compilers +set_mpi_wrappers_all = True + +# Are these values for modextravars site-specific? +modextravars = { + 'I_MPI_WAIT_MODE': '1', + 'I_MPI_DAPL_PROVIDER': 'ofa-v2-mlx4_0-1', + 'I_MPI_PMI_LIBRARY': '/usr/lib64/libpmi.so', +} + +postinstallcmds = [ + 'ln -s %(installdir)s/lib64/libmpi.so %(installdir)s/lib64/libmpich.so', + 'ln -s %(installdir)s/lib64/libmpigc4.so %(installdir)s/lib64/libmpichcxx.so', + 'ln -s %(installdir)s/lib64/libmpigf.so %(installdir)s/lib64/libfmpich.so', + 'ln -s %(installdir)s/lib64/libmpigf.so %(installdir)s/lib64/libmpichf90.so', + 'ln -s %(installdir)s/lib64/libmpi.so %(installdir)s/lib64/libmpl.so', + 'ln -s %(installdir)s/lib64/libmpi.so %(installdir)s/lib64/libopa.so' +] + +moduleclass = 'mpi' -- GitLab From 062930f2b303492bb31f9ab351985d78479c3345 Mon Sep 17 00:00:00 2001 From: builduser Date: Thu, 1 Jun 2017 08:58:54 +0200 Subject: [PATCH 0858/1603] Fixed line lengths, quoting and removed a commented-out line --- .../n/NRGLjubljana/NRGLjubljana-2.4.3.23-foss-2016b.eb | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/n/NRGLjubljana/NRGLjubljana-2.4.3.23-foss-2016b.eb b/easybuild/easyconfigs/n/NRGLjubljana/NRGLjubljana-2.4.3.23-foss-2016b.eb index 3880dd3342..491184693e 100644 --- a/easybuild/easyconfigs/n/NRGLjubljana/NRGLjubljana-2.4.3.23-foss-2016b.eb +++ b/easybuild/easyconfigs/n/NRGLjubljana/NRGLjubljana-2.4.3.23-foss-2016b.eb @@ -15,13 +15,14 @@ docurls = 'http://nrgljubljana.ijs.si/examples/' software_license = 'LicenseGPLv3' toolchain = {'name': 'foss', 'version': '2016b'} -#toolchainopts = { 'usempi': True, 'pic': True } toolchainopts = { 'pic': True } sources = [ '%(namelower)s-%(version)s.tar.gz' ] source_urls = [ 'http://nrgljubljana.ijs.si/' ] -configopts = "--with-tools --with-boost-serialization=boost_serialization CXXFLAGS=\"-Ddsyev=dsyev_ -Ddsyevr=dsyevr_ -Dzheev=zheev_ -Dzheevr=zheevr_\" LDFLAGS=\"-lopenblas -L${EBROOTBOOST}/lib\"" +configopts = '--with-tools --with-boost-serialization=boost_serialization' +configopts += ' CXXFLAGS="-Ddsyev=dsyev_ -Ddsyevr=dsyevr_ -Dzheev=zheev_ -Dzheevr=zheevr_"' +configopts += ' LDFLAGS="-lopenblas -L${EBROOTBOOST}/lib"' dependencies = [ ('GMP', '6.1.2'), -- GitLab From 82e901b88e3a4e4f8a26414a8144a1d32c4fbd38 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 1 Jun 2017 09:25:19 +0200 Subject: [PATCH 0859/1603] add checksum and alternate source URL for ed 1.9 --- easybuild/easyconfigs/e/ed/ed-1.9-goolf-1.4.10.eb | 6 +++++- easybuild/easyconfigs/e/ed/ed-1.9-ictce-5.3.0.eb | 6 +++++- 2 files changed, 10 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/e/ed/ed-1.9-goolf-1.4.10.eb b/easybuild/easyconfigs/e/ed/ed-1.9-goolf-1.4.10.eb index b0dc02f6dd..2c5d7fe41f 100644 --- a/easybuild/easyconfigs/e/ed/ed-1.9-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/e/ed/ed-1.9-goolf-1.4.10.eb @@ -8,8 +8,12 @@ description = """GNU ed is a line-oriented text editor.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} +source_urls = [ + 'https://launchpad.net/ed/main/%(version)s/+download/', + GNU_SOURCE, +] sources = [SOURCE_TAR_GZ] -source_urls = [GNU_SOURCE] +checksums = ['d5b372cfadf073001823772272fceac2cfa87552c5cd5a8efc1c8aae61f45a88'] sanity_check_paths = { 'files': ['bin/ed'], diff --git a/easybuild/easyconfigs/e/ed/ed-1.9-ictce-5.3.0.eb b/easybuild/easyconfigs/e/ed/ed-1.9-ictce-5.3.0.eb index dfd1efd2bf..7b11af7dc6 100644 --- a/easybuild/easyconfigs/e/ed/ed-1.9-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/e/ed/ed-1.9-ictce-5.3.0.eb @@ -8,8 +8,12 @@ description = """GNU ed is a line-oriented text editor.""" toolchain = {'name': 'ictce', 'version': '5.3.0'} +source_urls = [ + 'https://launchpad.net/ed/main/%(version)s/+download/', + GNU_SOURCE, +] sources = [SOURCE_TAR_GZ] -source_urls = [GNU_SOURCE] +checksums = ['d5b372cfadf073001823772272fceac2cfa87552c5cd5a8efc1c8aae61f45a88'] sanity_check_paths = { 'files': ['bin/ed'], -- GitLab From d0ae8e4500fa9021010e0b959ca4fb47f5ed44d3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 1 Jun 2017 09:26:51 +0200 Subject: [PATCH 0860/1603] also use GNU_SOURCE for GSL (nice catch @migueldiascosta!) --- easybuild/easyconfigs/g/GSL/GSL-1.16-goolf-1.7.20.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GSL/GSL-1.16-goolf-1.7.20.eb b/easybuild/easyconfigs/g/GSL/GSL-1.16-goolf-1.7.20.eb index 848138c178..b2099121ee 100644 --- a/easybuild/easyconfigs/g/GSL/GSL-1.16-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/g/GSL/GSL-1.16-goolf-1.7.20.eb @@ -11,7 +11,7 @@ description = """The GNU Scientific Library (GSL) is a numerical library for C a toolchain = {'name': 'goolf', 'version': '1.7.20'} toolchainopts = {'unroll': True, 'pic': True} -source_urls = ['http://ftpmirror.gnu.org/gnu/gsl/'] +source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] configopts = "--with-pic" -- GitLab From 853e9b5bf078b33b989486cc9e2927813130e48e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 1 Jun 2017 09:32:44 +0200 Subject: [PATCH 0861/1603] add patch for FFTW 2.1.5 to ensure *_f77 symbols are there --- .../easyconfigs/f/FFTW/FFTW-2.1.5-intel-2017a.eb | 4 ++++ .../FFTW-2.1.5_fix-configure-Fortran-linking.patch | 13 +++++++++++++ 2 files changed, 17 insertions(+) create mode 100644 easybuild/easyconfigs/f/FFTW/FFTW-2.1.5_fix-configure-Fortran-linking.patch diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-2.1.5-intel-2017a.eb b/easybuild/easyconfigs/f/FFTW/FFTW-2.1.5-intel-2017a.eb index 313bc9e8bb..f08bc07dde 100644 --- a/easybuild/easyconfigs/f/FFTW/FFTW-2.1.5-intel-2017a.eb +++ b/easybuild/easyconfigs/f/FFTW/FFTW-2.1.5-intel-2017a.eb @@ -13,6 +13,8 @@ toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [homepage] +patches = ['FFTW-%(version)s_fix-configure-Fortran-linking.patch'] + common_configopts = "--enable-shared --enable-type-prefix --enable-threads --with-pic" configopts = [ @@ -27,5 +29,7 @@ sanity_check_paths = { for y in ['', '_mpi', '_threads']], 'dirs': [], } +# make sure *_f77 symbols are there (patch is required to avoid --disable-fortran being used automatically) +sanity_check_commands = ["nm %(installdir)s/lib/libdfftw.a | grep _f77"] moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-2.1.5_fix-configure-Fortran-linking.patch b/easybuild/easyconfigs/f/FFTW/FFTW-2.1.5_fix-configure-Fortran-linking.patch new file mode 100644 index 0000000000..3c6ff3ce4a --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW/FFTW-2.1.5_fix-configure-Fortran-linking.patch @@ -0,0 +1,13 @@ +diff --git a/fftw-2.1.5.orig/configure b/fftw-2.1.5/configure +index f5bab28..ba60d87 100755 +--- a/fftw-2.1.5.orig/configure ++++ b/fftw-2.1.5/configure +@@ -8612,7 +8612,7 @@ _ACEOF + ac_save_FFLAGS=$FFLAGS + FFLAGS="$FFLAGS $ac_cv_prog_f77_v" + (eval echo $as_me:8614: \"$ac_link\") >&5 +-ac_f77_v_output=`eval $ac_link 5>&1 2>&1 | grep -v 'Driving:'` ++ac_f77_v_output=`eval $ac_link 5>&1 2>&1 | sed 's/"//g' | grep -v 'Driving:'` + echo "$ac_f77_v_output" >&5 + FFLAGS=$ac_save_FFLAGS + -- GitLab From c00a53d1e1655e39f9f41f740fda7c8292723a29 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 1 Jun 2017 10:37:57 +0200 Subject: [PATCH 0862/1603] add description + authorship in patch for FFTW 2.1.5 --- .../f/FFTW/FFTW-2.1.5_fix-configure-Fortran-linking.patch | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-2.1.5_fix-configure-Fortran-linking.patch b/easybuild/easyconfigs/f/FFTW/FFTW-2.1.5_fix-configure-Fortran-linking.patch index 3c6ff3ce4a..6dbbf6e91a 100644 --- a/easybuild/easyconfigs/f/FFTW/FFTW-2.1.5_fix-configure-Fortran-linking.patch +++ b/easybuild/easyconfigs/f/FFTW/FFTW-2.1.5_fix-configure-Fortran-linking.patch @@ -1,3 +1,6 @@ +remove double quotes from verbose output of Fortran compiler +required to avoid that --disable-fortran gets used automatically, resulting in missing *_f77 symbols +author: Kenneth Hoste (HPC-UGent) diff --git a/fftw-2.1.5.orig/configure b/fftw-2.1.5/configure index f5bab28..ba60d87 100755 --- a/fftw-2.1.5.orig/configure -- GitLab From 6b698c93def4e0de309d169b8d92e3fe487cac31 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 1 Jun 2017 10:52:52 +0200 Subject: [PATCH 0863/1603] adding easyconfigs: HTSlib-1.4.1-intel-2017a.eb --- .../h/HTSlib/HTSlib-1.4.1-intel-2017a.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/h/HTSlib/HTSlib-1.4.1-intel-2017a.eb diff --git a/easybuild/easyconfigs/h/HTSlib/HTSlib-1.4.1-intel-2017a.eb b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.4.1-intel-2017a.eb new file mode 100644 index 0000000000..03cac8f884 --- /dev/null +++ b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.4.1-intel-2017a.eb @@ -0,0 +1,36 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# 1.4 modified by: +# Adam Huffman +# The Francis Crick Institute + +easyblock = 'ConfigureMake' + +name = 'HTSlib' +version = '1.4.1' + +homepage = "http://www.htslib.org/" +description = """A C library for reading/writing high-throughput sequencing data. + This package includes the utilities bgzip and tabix""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s/'] +sources = [SOURCELOWER_TAR_BZ2] + +# cURL added for S3 support +dependencies = [ + ('zlib', '1.2.11'), + ('bzip2', '1.0.6'), + ('XZ', '5.2.3'), + ('cURL', '7.53.1'), +] + +sanity_check_paths = { + 'files': ["bin/bgzip", "bin/tabix", "lib/libhts.%s" % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From 4324824cf9132a34f9fd33100f4f48e4332b6613 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 1 Jun 2017 11:23:11 +0200 Subject: [PATCH 0864/1603] adding easyconfigs: Bowtie2-2.3.2-intel-2017a.eb, tbb-2017_U6-intel-2017a.eb --- .../b/Bowtie2/Bowtie2-2.3.2-intel-2017a.eb | 35 +++++++++++++++++++ .../t/tbb/tbb-2017_U6-intel-2017a.eb | 13 +++++++ 2 files changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.3.2-intel-2017a.eb create mode 100644 easybuild/easyconfigs/t/tbb/tbb-2017_U6-intel-2017a.eb diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.3.2-intel-2017a.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.3.2-intel-2017a.eb new file mode 100644 index 0000000000..98d5525da2 --- /dev/null +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.3.2-intel-2017a.eb @@ -0,0 +1,35 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# Modified by: Robert Schmidt +# Ottawa Hospital Research Institute - Bioinformatics Team +# Modified by: Adam Huffman +# The Francis Crick Institute +# Modified by: Kurt Lust, UAntwerp + +name = 'Bowtie2' +version = '2.3.2' + +homepage = 'http://bowtie-bio.sourceforge.net/bowtie2/index.shtml' +description = """ Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads + to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s + of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. + Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, + its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True, 'cstd': 'c++11'} + +sources = ['%(namelower)s-%(version)s-source.zip'] +source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')] + +dependencies = [('tbb', '2017_U6')] + +# disable warning on incompatible exception specification that is treated as an error +buildopts = "EXTRA_FLAGS='-wd809'" + +# to add script folder to path just uncomment this line +#modextrapaths = {'PATH': 'scripts'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/tbb/tbb-2017_U6-intel-2017a.eb b/easybuild/easyconfigs/t/tbb/tbb-2017_U6-intel-2017a.eb new file mode 100644 index 0000000000..9fd9a0ec5a --- /dev/null +++ b/easybuild/easyconfigs/t/tbb/tbb-2017_U6-intel-2017a.eb @@ -0,0 +1,13 @@ +name = 'tbb' +version = '2017_U6' + +homepage = 'https://01.org/tbb/' +description = """Intel(R) Threading Building Blocks (Intel(R) TBB) lets you easily write parallel C++ programs that + take full advantage of multicore performance, that are portable, composable and have future-proof scalability.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['https://github.com/01org/tbb/archive/'] +sources = ['%(version)s.tar.gz'] + +moduleclass = 'lib' -- GitLab From 4a0bef476a5d450ced0b667a2e603e74a2a33083 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 1 Jun 2017 11:29:44 +0200 Subject: [PATCH 0865/1603] adding easyconfigs: pydlpoly-20150225-intel-2017a-Python-2.7.13.eb --- ...poly-20150225-intel-2017a-Python-2.7.13.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/p/pydlpoly/pydlpoly-20150225-intel-2017a-Python-2.7.13.eb diff --git a/easybuild/easyconfigs/p/pydlpoly/pydlpoly-20150225-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/p/pydlpoly/pydlpoly-20150225-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..89fcff1c23 --- /dev/null +++ b/easybuild/easyconfigs/p/pydlpoly/pydlpoly-20150225-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,39 @@ +easyblock = 'MakeCp' + +name = 'pydlpoly' +version = '20150225' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://cmc.aci.ruhr-uni-bochum.de/cmc/' +description = """Pydlpoly is a molecular dynamics simulation package which is a modified version of DL-POLY with + a Python language interface.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'usempi': True, 'pic': True} + +sources = ['%(name)s_250215.tgz'] +checksums = ['cd84a4b563dd16823e22fe6c450b07fd95036e20e0c6b7fc308afdb347241122'] + +dependencies = [ + ('Python', '2.7.13'), # also provides mpi4py, numpy + ('h5py', '2.7.0', versionsuffix), + ('FFTW', '2.1.5'), +] + +start_dir = 'source' + +parallel = 1 +buildopts = 'FC="$FC" LD="$FC -o" LDFLAGS="$FFLAGS" FFLAGS="-c $FFLAGS" LDLIBS="-ldfftw" F2PY_COMP=intelem' + +files_to_copy = ['doc', 'py', 'scripts', 'so'] + +sanity_check_paths = { + 'files': ['so/_pydlpoly.%s' % SHLIB_EXT], + 'dirs': ['py'], +} +sanity_check_commands = ["python -c 'import pydlpoly'"] + +modextrapaths = {'PYTHONPATH': ['py', 'so']} +modextravars = {'PDLPDIR': '%(installdir)s'} + +moduleclass = 'chem' -- GitLab From 6dbb79f85a5fbfb784d6fca60b4536c15a0f2b68 Mon Sep 17 00:00:00 2001 From: Robert Date: Thu, 1 Jun 2017 19:19:38 +0930 Subject: [PATCH 0866/1603] Pysam added --- .../Pysam-0.10.0-foss-2016b-Python-2.7.12.eb | 51 +++++++++++++++++++ 1 file changed, 51 insertions(+) create mode 100644 easybuild/easyconfigs/p/Pysam/Pysam-0.10.0-foss-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/p/Pysam/Pysam-0.10.0-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/Pysam/Pysam-0.10.0-foss-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..417ee652b8 --- /dev/null +++ b/easybuild/easyconfigs/p/Pysam/Pysam-0.10.0-foss-2016b-Python-2.7.12.eb @@ -0,0 +1,51 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# 0.9.1.4: +# Modified by: Robert Qiao , Exequiel Sepulveda +# @ adelaide.edu.au/phoenix + +easyblock = 'Bundle' + +name = 'Pysam' +version = '0.10.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/pysam-developers/pysam' +description = """Pysam is a python module for reading and manipulating Samfiles. + It's a lightweight wrapper of the samtools C-API. Pysam also includes an interface for tabix.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +parallel = 1 + +dependencies = [ + ('Python', '2.7.12'), + ('Cython', '0.25.2', versionsuffix), + ('ncurses', '6.0'), + ('zlib', '1.2.8'), + ('cURL', '7.49.1'), +] + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' +exts_filter = ("python -c 'import %(ext_name)s'", '') + +exts_list = [ + ('pysam', version, { + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/pysam-developers/pysam/archive/'], + }), +] + +modextrapaths = { + 'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/pysam-%(version)s-py%(pyshortver)s-linux-x86_64.egg'], +} + +moduleclass = 'bio' -- GitLab From 490659514b75ccf3f42fdcdb6acd00f59ee2b638 Mon Sep 17 00:00:00 2001 From: Robert Date: Thu, 1 Jun 2017 19:26:33 +0930 Subject: [PATCH 0867/1603] BamM Python ext updated --- ...-Python-2.7.13.eb => BamM-1.7.3-foss-2016b-Python-2.7.12.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/b/BamM/{BamM-1.7.3-foss-2016b-Python-2.7.13.eb => BamM-1.7.3-foss-2016b-Python-2.7.12.eb} (97%) diff --git a/easybuild/easyconfigs/b/BamM/BamM-1.7.3-foss-2016b-Python-2.7.13.eb b/easybuild/easyconfigs/b/BamM/BamM-1.7.3-foss-2016b-Python-2.7.12.eb similarity index 97% rename from easybuild/easyconfigs/b/BamM/BamM-1.7.3-foss-2016b-Python-2.7.13.eb rename to easybuild/easyconfigs/b/BamM/BamM-1.7.3-foss-2016b-Python-2.7.12.eb index c73686a30c..d0986b1904 100644 --- a/easybuild/easyconfigs/b/BamM/BamM-1.7.3-foss-2016b-Python-2.7.13.eb +++ b/easybuild/easyconfigs/b/BamM/BamM-1.7.3-foss-2016b-Python-2.7.12.eb @@ -25,7 +25,7 @@ source_urls = ['https://github.com/Ecogenomics/BamM/archive'] sources = ['%(version)s.tar.gz'] dependencies = [ - ('Python', '2.7.13'), + ('Python', '2.7.12'), ('SAMtools', '1.3.1'), ('BWA', '0.7.15'), ] -- GitLab From 43d135840ec9e931966918828c3a8120b93453e8 Mon Sep 17 00:00:00 2001 From: Robert Qiao Date: Thu, 1 Jun 2017 19:27:43 +0930 Subject: [PATCH 0868/1603] Python ext updated --- ...Cython-0.25.2-foss-2016b-Python-2.7.12.eb} | 2 +- .../GroopM-0.3.4-foss-2016b-Python-2.7.13.eb | 4 +- .../numpy-1.11.1-foss-2016b-Python-2.7.13.eb | 41 ------------------- ... => PIL-1.1.7-foss-2016b-Python-2.7.12.eb} | 2 +- .../scipy-0.17.1-foss-2016b-Python-2.7.13.eb | 30 -------------- 5 files changed, 3 insertions(+), 76 deletions(-) rename easybuild/easyconfigs/c/Cython/{Cython-0.25.2-foss-2016b-Python-2.7.13.eb => Cython-0.25.2-foss-2016b-Python-2.7.12.eb} (96%) delete mode 100644 easybuild/easyconfigs/n/numpy/numpy-1.11.1-foss-2016b-Python-2.7.13.eb rename easybuild/easyconfigs/p/PIL/{PIL-1.1.7-foss-2016b-Python-2.7.13.eb => PIL-1.1.7-foss-2016b-Python-2.7.12.eb} (97%) delete mode 100644 easybuild/easyconfigs/s/scipy/scipy-0.17.1-foss-2016b-Python-2.7.13.eb diff --git a/easybuild/easyconfigs/c/Cython/Cython-0.25.2-foss-2016b-Python-2.7.13.eb b/easybuild/easyconfigs/c/Cython/Cython-0.25.2-foss-2016b-Python-2.7.12.eb similarity index 96% rename from easybuild/easyconfigs/c/Cython/Cython-0.25.2-foss-2016b-Python-2.7.13.eb rename to easybuild/easyconfigs/c/Cython/Cython-0.25.2-foss-2016b-Python-2.7.12.eb index 07286ce8e2..a99c8efcb6 100644 --- a/easybuild/easyconfigs/c/Cython/Cython-0.25.2-foss-2016b-Python-2.7.13.eb +++ b/easybuild/easyconfigs/c/Cython/Cython-0.25.2-foss-2016b-Python-2.7.12.eb @@ -25,7 +25,7 @@ toolchain = {'name': 'foss', 'version': '2016b'} source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] -dependencies = [('Python', '2.7.13')] +dependencies = [('Python', '2.7.12')] cythonlibdir = 'lib/python%(pyshortver)s/site-packages/Cython-%(version)s-py%(pyshortver)s-linux-x86_64.egg' sanity_check_paths = { diff --git a/easybuild/easyconfigs/g/GroopM/GroopM-0.3.4-foss-2016b-Python-2.7.13.eb b/easybuild/easyconfigs/g/GroopM/GroopM-0.3.4-foss-2016b-Python-2.7.13.eb index e52a60624a..ffa01c6372 100644 --- a/easybuild/easyconfigs/g/GroopM/GroopM-0.3.4-foss-2016b-Python-2.7.13.eb +++ b/easybuild/easyconfigs/g/GroopM/GroopM-0.3.4-foss-2016b-Python-2.7.13.eb @@ -28,9 +28,7 @@ sources = [SOURCE_TAR_GZ] dependencies = [ ('Python', '2.7.13'), ('Cython', '0.25.2', versionsuffix), - ('numpy', '1.11.1', versionsuffix), - ('scipy', '0.17.1', versionsuffix), - ('matplotlib', '1.5.2', versionsuffix), + ('matplotlib', '1.5.3', versionsuffix), ('Pysam', '0.10.0', versionsuffix), ('PyTables', '3.2.2', versionsuffix), ('PIL', '1.1.7', versionsuffix), diff --git a/easybuild/easyconfigs/n/numpy/numpy-1.11.1-foss-2016b-Python-2.7.13.eb b/easybuild/easyconfigs/n/numpy/numpy-1.11.1-foss-2016b-Python-2.7.13.eb deleted file mode 100644 index 90ade3ec90..0000000000 --- a/easybuild/easyconfigs/n/numpy/numpy-1.11.1-foss-2016b-Python-2.7.13.eb +++ /dev/null @@ -1,41 +0,0 @@ -## -# This is a contribution from Phoenix HPC Service, The University of Adelaide, Australia -# Homepage: https://www.adelaide.edu.au/phoenix/ -# -# Copyright:: Copyright 2014-2017 adelaide.edu.au/phoenix -# Authors:: Robert Qiao , Exequiel Sepulveda -# License:: BSD-new -# -# Notes:: -## - -name = 'numpy' -version = '1.11.1' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'http://www.numpy.org' -description = """NumPy is the fundamental package for scientific computing with Python. It contains among other things: - a powerful N-dimensional array object, sophisticated (broadcasting) functions, tools for integrating C/C++ and Fortran - code, useful linear algebra, Fourier transform, and random number capabilities. Besides its obvious scientific uses, - NumPy can also be used as an efficient multi-dimensional container of generic data. Arbitrary data-types can be - defined. This allows NumPy to seamlessly and speedily integrate with a wide variety of databases.""" - -toolchain = {'name': 'foss', 'version': '2016b'} - -source_urls = [SOURCEFORGE_SOURCE] -sources = [SOURCE_TAR_GZ] - -dependencies = [ - ('Python', '2.7.13'), -] - -# need to use pip rather than regular 'setup.py install' -# to ensure that this numpy wins over the one in the Python installation; -# using easy_install does not work... -use_pip = True - -# install as zipped egg to get a .pth file in lib/python*/site-packages; -# this enables shadowing of the numpy that is part of the Python installation -zipped_egg = True - -moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/PIL/PIL-1.1.7-foss-2016b-Python-2.7.13.eb b/easybuild/easyconfigs/p/PIL/PIL-1.1.7-foss-2016b-Python-2.7.12.eb similarity index 97% rename from easybuild/easyconfigs/p/PIL/PIL-1.1.7-foss-2016b-Python-2.7.13.eb rename to easybuild/easyconfigs/p/PIL/PIL-1.1.7-foss-2016b-Python-2.7.12.eb index 18f032a1ca..92b0c0004e 100644 --- a/easybuild/easyconfigs/p/PIL/PIL-1.1.7-foss-2016b-Python-2.7.13.eb +++ b/easybuild/easyconfigs/p/PIL/PIL-1.1.7-foss-2016b-Python-2.7.12.eb @@ -28,7 +28,7 @@ patches = ['PIL-%(version)s-find-deps.patch'] dependencies = [ ('zlib', '1.2.8'), - ('Python', '2.7.13'), + ('Python', '2.7.12'), ('libjpeg-turbo', '1.5.0'), ('freetype', '2.7'), ] diff --git a/easybuild/easyconfigs/s/scipy/scipy-0.17.1-foss-2016b-Python-2.7.13.eb b/easybuild/easyconfigs/s/scipy/scipy-0.17.1-foss-2016b-Python-2.7.13.eb deleted file mode 100644 index 9faa2de7a7..0000000000 --- a/easybuild/easyconfigs/s/scipy/scipy-0.17.1-foss-2016b-Python-2.7.13.eb +++ /dev/null @@ -1,30 +0,0 @@ -## -# This is a contribution from Phoenix HPC Service, The University of Adelaide, Australia -# Homepage: https://www.adelaide.edu.au/phoenix/ -# -# Copyright:: Copyright 2014-2017 adelaide.edu.au/phoenix -# Authors:: Robert Qiao , Exequiel Sepulveda -# License:: BSD-new -# -# Notes:: -## - -name = 'scipy' -version = '0.17.1' -versionsuffix = '-Python-2.7.13' - -homepage = 'http://www.scipy.org' -description = """SciPy is a collection of mathematical algorithms and convenience - functions built on the Numpy extension for Python.""" - -toolchain = {'name': 'foss', 'version': '2016b'} -toolchainopts = {'usempi': True, 'pic': True} - -source_urls = [PYPI_SOURCE] -sources = [SOURCE_TAR_GZ] - -dependencies = [ - ('numpy', '1.11.1', versionsuffix), -] - -moduleclass = 'math' -- GitLab From 6c13759d623f43c58ac07d121e1748f96d181536 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Thu, 1 Jun 2017 09:25:56 -0500 Subject: [PATCH 0869/1603] Added patch file --- easybuild/easyconfigs/x/XZ/XZ-5.2.2-GCCcore-5.4.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-GCCcore-5.4.0.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-GCCcore-5.4.0.eb index c46df20c2f..3f9cceef3c 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-GCCcore-5.4.0.eb @@ -11,6 +11,8 @@ toolchain = {'name': 'GCCcore', 'version': '5.4.0'} sources = [SOURCELOWER_TAR_BZ2] source_urls = ['http://tukaani.org/xz/'] +patches = ['XZ-%(version)s_compat-libs.patch'] + builddependencies = [ ('gettext', '0.19.8', '', True), # use same binutils version that was used when building GCCcore toolchain -- GitLab From ac8aa533f0100516bc03024358ad05266281e8e4 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Fri, 2 Jun 2017 10:12:15 +1200 Subject: [PATCH 0870/1603] Tweaks requested by K.H. --- easybuild/easyconfigs/c/CMake/CMake-3.6.1.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.6.1.eb b/easybuild/easyconfigs/c/CMake/CMake-3.6.1.eb index 71580ff227..d8773947c8 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.6.1.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.6.1.eb @@ -18,10 +18,10 @@ configopts = '-- -DCMAKE_USE_OPENSSL=1' # which might want different versions of the same dependency, eg: ncurses dependencies = [] -osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel', 'ncurses-devel')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel'), 'ncurses-devel'] sanity_check_paths = { - 'files': ["bin/%s" % x for x in ['cmake', 'ccmake', 'cpack', 'ctest']], + 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], 'dirs': [], } -- GitLab From 300e1c109c871025c7993c7899d48c0bf07033ec Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Fri, 2 Jun 2017 10:39:57 +1200 Subject: [PATCH 0871/1603] Change GCC-5.4.0 to GCC-5.4.0-2.26 and consequential changes --- easybuild/easyconfigs/g/GCC/GCC-5.4.0.eb | 25 ------------------- easybuild/easyconfigs/g/gimkl/gimkl-2017a.eb | 4 ++- easybuild/easyconfigs/g/gimpi/gimpi-2017a.eb | 4 ++- ...0.eb => impi-2017.1.132-GCC-5.4.0-2.26.eb} | 13 +++------- 4 files changed, 10 insertions(+), 36 deletions(-) delete mode 100644 easybuild/easyconfigs/g/GCC/GCC-5.4.0.eb rename easybuild/easyconfigs/i/impi/{impi-2017.1.132-GCC-5.4.0.eb => impi-2017.1.132-GCC-5.4.0-2.26.eb} (81%) diff --git a/easybuild/easyconfigs/g/GCC/GCC-5.4.0.eb b/easybuild/easyconfigs/g/GCC/GCC-5.4.0.eb deleted file mode 100644 index 0bc33f7250..0000000000 --- a/easybuild/easyconfigs/g/GCC/GCC-5.4.0.eb +++ /dev/null @@ -1,25 +0,0 @@ -easyblock = 'Bundle' - -name = 'GCC' -version = '5.4.0' - -binutilsver = '2.26' -#versionsuffix = '-%s' % binutilsver - -homepage = 'http://gcc.gnu.org/' -description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, - as well as libraries for these languages (libstdc++, libgcj,...).""" - -toolchain = {'name': 'dummy', 'version': ''} - -dependencies = [ - ('GCCcore', version), - # binutils built on top of GCCcore, which was built on top of (dummy-built) binutils - ('binutils', binutilsver, '', ('GCCcore', version)), -] - -altroot = 'GCCcore' -altversion = 'GCCcore' - -# this bundle serves as a compiler-only toolchain, so it should be marked as compiler (important for HMNS) -moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/gimkl/gimkl-2017a.eb b/easybuild/easyconfigs/g/gimkl/gimkl-2017a.eb index 553786dd35..1ed5c3adff 100644 --- a/easybuild/easyconfigs/g/gimkl/gimkl-2017a.eb +++ b/easybuild/easyconfigs/g/gimkl/gimkl-2017a.eb @@ -8,7 +8,9 @@ description = """GNU Compiler Collection (GCC) based compiler toolchain with Int toolchain = {'name': 'dummy', 'version': 'dummy'} -comp = ('GCC', '5.4.0') +gccver = '5.4.0' +binutilsver = '2.26' +comp = ('GCC', '%s-%s' % (gccver, binutilsver)) dependencies = [ comp, diff --git a/easybuild/easyconfigs/g/gimpi/gimpi-2017a.eb b/easybuild/easyconfigs/g/gimpi/gimpi-2017a.eb index 394c894b37..faaefc8f0b 100644 --- a/easybuild/easyconfigs/g/gimpi/gimpi-2017a.eb +++ b/easybuild/easyconfigs/g/gimpi/gimpi-2017a.eb @@ -8,7 +8,9 @@ description = """GNU Compiler Collection (GCC) based compiler toolchain with Int toolchain = {'name': 'dummy', 'version': 'dummy'} -comp = ('GCC', '5.4.0') +gccver = '5.4.0' +binutilsver = '2.26' +comp = ('GCC', '%s-%s' % (gccver, binutilsver)) dependencies = [ comp, diff --git a/easybuild/easyconfigs/i/impi/impi-2017.1.132-GCC-5.4.0.eb b/easybuild/easyconfigs/i/impi/impi-2017.1.132-GCC-5.4.0-2.26.eb similarity index 81% rename from easybuild/easyconfigs/i/impi/impi-2017.1.132-GCC-5.4.0.eb rename to easybuild/easyconfigs/i/impi/impi-2017.1.132-GCC-5.4.0-2.26.eb index e03300b9d5..596670ca45 100644 --- a/easybuild/easyconfigs/i/impi/impi-2017.1.132-GCC-5.4.0.eb +++ b/easybuild/easyconfigs/i/impi/impi-2017.1.132-GCC-5.4.0-2.26.eb @@ -6,7 +6,9 @@ description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric messag passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for Linux OS implements the Message Passing Interface, version 2 (MPI-2) specification.""" -toolchain = {'name': 'GCC', 'version': '5.4.0'} +gccver = '5.4.0' +binutilsver = '2.26' +toolchain = {'name': 'GCC', 'version': '%s-%s' % (gccver, binutilsver)} sources = ['l_mpi_%(version)s.tgz'] checksums = ['d5e941ac2bcf7c5576f85f6bcfee4c18'] @@ -19,14 +21,7 @@ components = ['intel-mpi', 'intel-psxe', 'intel-imb'] license_file = HOME + '/licenses/intel/license.lic' # Set I_MPI_ variables to point at the appropriate compilers -set_mpi_wrappers_all = True - -# Are these values for modextravars site-specific? -modextravars = { - 'I_MPI_WAIT_MODE': '1', - 'I_MPI_DAPL_PROVIDER': 'ofa-v2-mlx4_0-1', - 'I_MPI_PMI_LIBRARY': '/usr/lib64/libpmi.so', -} +#set_mpi_wrappers_all = True postinstallcmds = [ 'ln -s %(installdir)s/lib64/libmpi.so %(installdir)s/lib64/libmpich.so', -- GitLab From 274d6e6cff6edc2a3635f460081e4b111c9c5d62 Mon Sep 17 00:00:00 2001 From: Robert Qiao Date: Fri, 2 Jun 2017 13:33:45 +0930 Subject: [PATCH 0872/1603] GroopM deps version updated --- .../g/GroopM/GroopM-0.3.4-foss-2016b-Python-2.7.13.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GroopM/GroopM-0.3.4-foss-2016b-Python-2.7.13.eb b/easybuild/easyconfigs/g/GroopM/GroopM-0.3.4-foss-2016b-Python-2.7.13.eb index ffa01c6372..741c740418 100644 --- a/easybuild/easyconfigs/g/GroopM/GroopM-0.3.4-foss-2016b-Python-2.7.13.eb +++ b/easybuild/easyconfigs/g/GroopM/GroopM-0.3.4-foss-2016b-Python-2.7.13.eb @@ -26,7 +26,7 @@ source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] dependencies = [ - ('Python', '2.7.13'), + ('Python', '2.7.12'), ('Cython', '0.25.2', versionsuffix), ('matplotlib', '1.5.3', versionsuffix), ('Pysam', '0.10.0', versionsuffix), -- GitLab From 56f3c72e17f2ef085d5dc268b5d6fa3d7c99802e Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Fri, 2 Jun 2017 16:11:07 +1200 Subject: [PATCH 0873/1603] Change file permissions on two libpciaccess easyconfigs --- .../easyconfigs/l/libpciaccess/libpciaccess-0.13.4-foss-2016b.eb | 0 .../easyconfigs/l/libpciaccess/libpciaccess-0.13.4-intel-2016b.eb | 0 2 files changed, 0 insertions(+), 0 deletions(-) mode change 100755 => 100644 easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-foss-2016b.eb mode change 100755 => 100644 easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-intel-2016b.eb diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-foss-2016b.eb b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-foss-2016b.eb old mode 100755 new mode 100644 diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-intel-2016b.eb b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-intel-2016b.eb old mode 100755 new mode 100644 -- GitLab From 2076bf7ef017998e744925c083cdc3532a66478a Mon Sep 17 00:00:00 2001 From: Robert Qiao Date: Fri, 2 Jun 2017 13:52:22 +0930 Subject: [PATCH 0874/1603] GroopM version updated --- ...-Python-2.7.13.eb => GroopM-0.3.4-foss-2016b-Python-2.7.12.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/g/GroopM/{GroopM-0.3.4-foss-2016b-Python-2.7.13.eb => GroopM-0.3.4-foss-2016b-Python-2.7.12.eb} (100%) diff --git a/easybuild/easyconfigs/g/GroopM/GroopM-0.3.4-foss-2016b-Python-2.7.13.eb b/easybuild/easyconfigs/g/GroopM/GroopM-0.3.4-foss-2016b-Python-2.7.12.eb similarity index 100% rename from easybuild/easyconfigs/g/GroopM/GroopM-0.3.4-foss-2016b-Python-2.7.13.eb rename to easybuild/easyconfigs/g/GroopM/GroopM-0.3.4-foss-2016b-Python-2.7.12.eb -- GitLab From f01ff0a9d8b5164a1088d4aa9172d424c2b2c312 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Fri, 2 Jun 2017 17:16:17 +1200 Subject: [PATCH 0875/1603] Changes requested by K.H. --- ....1-foss-2015a-GLib-2.48.2-Python-2.7.11.eb | 38 +++++++++++ .../e/Eigen/Eigen-3.2.9-foss-2015a.eb | 13 ++++ .../e/eudev/eudev-3.1.5-foss-2015a.eb | 32 ++++++++++ .../g/gperf/gperf-3.0.4-foss-2015a.eb | 22 +++++++ .../l/LLVM/LLVM-3.7.1-foss-2015a.eb | 33 ++++++++++ .../l/libdrm/libdrm-2.4.68-foss-2015a.eb | 28 +++++++++ .../libpciaccess-0.13.4-foss-2015a.eb | 24 +++++++ .../m/Mesa/Mesa-11.2.1-foss-2015a.eb | 63 +++++++++++++++++++ .../makedepend/makedepend-1.0.5-foss-2015a.eb | 24 +++++++ 9 files changed, 277 insertions(+) create mode 100644 easybuild/easyconfigs/c/CGAL/CGAL-4.8.1-foss-2015a-GLib-2.48.2-Python-2.7.11.eb create mode 100644 easybuild/easyconfigs/e/Eigen/Eigen-3.2.9-foss-2015a.eb create mode 100644 easybuild/easyconfigs/e/eudev/eudev-3.1.5-foss-2015a.eb create mode 100644 easybuild/easyconfigs/g/gperf/gperf-3.0.4-foss-2015a.eb create mode 100644 easybuild/easyconfigs/l/LLVM/LLVM-3.7.1-foss-2015a.eb create mode 100644 easybuild/easyconfigs/l/libdrm/libdrm-2.4.68-foss-2015a.eb create mode 100644 easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-foss-2015a.eb create mode 100644 easybuild/easyconfigs/m/Mesa/Mesa-11.2.1-foss-2015a.eb create mode 100644 easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-foss-2015a.eb diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.8.1-foss-2015a-GLib-2.48.2-Python-2.7.11.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.8.1-foss-2015a-GLib-2.48.2-Python-2.7.11.eb new file mode 100644 index 0000000000..618170db54 --- /dev/null +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.8.1-foss-2015a-GLib-2.48.2-Python-2.7.11.eb @@ -0,0 +1,38 @@ +name = 'CGAL' +version = '4.8.1' +gmpver = '6.0.0a' +pyver = '2.7.11' +glibver = '2.48.2' +versionsuffix = '-GLib-%s-Python-%s' % (glibver, pyver) + +homepage = 'http://www.cgal.org/' +description = """The goal of the CGAL Open Source Project is to provide easy access to efficient + and reliable geometric algorithms in the form of a C++ library.""" + +toolchain = {'name': 'foss', 'version': '2015a'} +toolchainopts = {'strict': True} + +source_urls = ['https://github.com/%(name)s/%(namelower)s/releases/download/releases%2F%(name)s-%(version)s'] +sources = [SOURCE_TAR_XZ] +checksums = ['1cbcb3f251822766ed3d744f923c782d'] + +dependencies = [ + ('Boost', '1.60.0'), + ('GLib', glibver), + ('GMP', gmpver), + ('libGLU', '9.0.0', '-Mesa-11.2.1'), + ('MPFR', '3.1.2', '-GMP-%s' % gmpver), + ('Qt', '4.8.7', versionsuffix), +] + +configopts = "-DCMAKE_VERBOSE_MAKEFILE=ON " +configopts += "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " +configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT +configopts += "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT + +builddependencies = [ + ('CMake', '3.4.1'), + ('Eigen', '3.2.9'), +] + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.9-foss-2015a.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.9-foss-2015a.eb new file mode 100644 index 0000000000..308bb395d6 --- /dev/null +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.9-foss-2015a.eb @@ -0,0 +1,13 @@ +name = 'Eigen' +version = '3.2.9' + +homepage = 'http://eigen.tuxfamily.org/index.php?title=Main_Page' +description = """Eigen is a C++ template library for linear algebra: + matrices, vectors, numerical solvers, and related algorithms.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +source_urls = ['http://bitbucket.org/%(namelower)s/%(namelower)s/get'] +sources = ['%(version)s.tar.bz2'] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/e/eudev/eudev-3.1.5-foss-2015a.eb b/easybuild/easyconfigs/e/eudev/eudev-3.1.5-foss-2015a.eb new file mode 100644 index 0000000000..6fa9d11cb4 --- /dev/null +++ b/easybuild/easyconfigs/e/eudev/eudev-3.1.5-foss-2015a.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'eudev' +version = '3.1.5' + +homepage = 'https://wiki.gentoo.org/wiki/Project:Eudev' +description = """eudev is a fork of systemd-udev with the goal of obtaining + better compatibility with existing software such as + OpenRC and Upstart, older kernels, various toolchains + and anything else required by users and various distributions.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://dev.gentoo.org/~blueness/%(name)s/'] +patches = ['%(name)s-3.1.2_pre-2.6.34_kernel.patch'] + +builddependencies = [ + ('gperf', '3.0.4'), +] + +osdependencies = [('kernel-headers', 'linux-libc-dev')] + +configopts = '--disable-blkid --disable-selinux --disable-gudev --disable-manpages ' +runtest = 'check' + +sanity_check_paths = { + 'files': ['bin/udevadm', 'include/libudev.h', 'include/udev.h', 'lib/libudev.so.1'], + 'dirs': [], +} + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/g/gperf/gperf-3.0.4-foss-2015a.eb b/easybuild/easyconfigs/g/gperf/gperf-3.0.4-foss-2015a.eb new file mode 100644 index 0000000000..fa479b36e5 --- /dev/null +++ b/easybuild/easyconfigs/g/gperf/gperf-3.0.4-foss-2015a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'gperf' +version = '3.0.4' + +homepage = 'http://www.gnu.org/software/gperf/' +description = """GNU gperf is a perfect hash function generator. For a given list of strings, it produces a hash + function and hash table, in form of C or C++ code, for looking up a value depending on the input string. The hash + function is perfect, which means that the hash table has no collisions, and the hash table lookup needs a single + string comparison only.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': ['bin/gperf'], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/LLVM/LLVM-3.7.1-foss-2015a.eb b/easybuild/easyconfigs/l/LLVM/LLVM-3.7.1-foss-2015a.eb new file mode 100644 index 0000000000..031705af89 --- /dev/null +++ b/easybuild/easyconfigs/l/LLVM/LLVM-3.7.1-foss-2015a.eb @@ -0,0 +1,33 @@ +name = "LLVM" +version = "3.7.1" + +homepage = 'http://llvm.org' +description = """A collection of modular and reusable compiler and toolchain technologies""" +toolchain = {'name': 'foss', 'version': '2015a'} +toolchainopts = {} + +easyblock = 'ConfigureMake' + +sources = ['%(namelower)s-%(version)s.src.tar.xz'] +source_urls = ['http://llvm.org/releases/%(version)s'] + +builddependencies = [ + ('Python', '2.7.9'), +] + +# No build allowed in source dir +preconfigopts = "[ ! -e build ] && mkdir build && cd build &&" +configure_cmd_prefix = '../' + +# For llvmpy / Numba: +configopts = '--enable-optimized --enable-pic --enable-shared' +prebuildopts = 'cd build && REQUIRES_RTTI=1' + +preinstallopts = 'cd build &&' + +sanity_check_paths = { + 'files': ["lib/libLLVMCore.a", "include/llvm-c/Core.h"], + 'dirs': ["include/llvm", ] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.68-foss-2015a.eb b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.68-foss-2015a.eb new file mode 100644 index 0000000000..d976cb1a3f --- /dev/null +++ b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.68-foss-2015a.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'libdrm' +version = '2.4.68' + +homepage = 'http://dri.freedesktop.org' +description = """Direct Rendering Manager runtime library.""" + +source_urls = ['http://dri.freedesktop.org/libdrm/'] +sources = [SOURCELOWER_TAR_GZ] + +toolchain = {'name': 'foss', 'version': '2015a'} + +builddependencies = [ + ('libpthread-stubs', '0.3'), +] + +dependencies = [ + ('libpciaccess', '0.13.4'), +] + +sanity_check_paths = { + 'files': ['include/xf86drm.h', 'include/xf86drmMode.h', 'lib/libdrm_intel.%s' % SHLIB_EXT, + 'lib/libdrm_radeon.%s' % SHLIB_EXT, 'lib/libdrm.%s' % SHLIB_EXT, 'lib/libkms.%s' % SHLIB_EXT], + 'dirs': ['include/libdrm', 'include/libkms', 'lib/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-foss-2015a.eb b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-foss-2015a.eb new file mode 100644 index 0000000000..d0b6288597 --- /dev/null +++ b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-foss-2015a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'libpciaccess' +version = '0.13.4' + +homepage = 'http://cgit.freedesktop.org/xorg/lib/libpciaccess/' +description = """Generic PCI access library.""" + +source_urls = ['https://www.x.org/releases/individual/lib/'] +sources = [SOURCE_TAR_GZ] + +toolchain = {'name': 'foss', 'version': '2015a'} + +builddependencies = [ + ('Autotools', '20150215'), + ('X11', '20160819'), +] + +sanity_check_paths = { + 'files': ['include/pciaccess.h', 'lib/libpciaccess.a'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-11.2.1-foss-2015a.eb b/easybuild/easyconfigs/m/Mesa/Mesa-11.2.1-foss-2015a.eb new file mode 100644 index 0000000000..126c65abd6 --- /dev/null +++ b/easybuild/easyconfigs/m/Mesa/Mesa-11.2.1-foss-2015a.eb @@ -0,0 +1,63 @@ +easyblock = 'ConfigureMake' + +name = 'Mesa' +version = '11.2.1' + +homepage = 'http://www.mesa3d.org/' +description = """Mesa is an open-source implementation of the OpenGL specification - + a system for rendering interactive 3D graphics.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [ + 'https://mesa.freedesktop.org/archive/%(version)s', + 'ftp://ftp.freedesktop.org/pub/mesa/%(version)s', + 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x/%(version)s', +] + +builddependencies = [ + ('flex', '2.6.0'), + ('Bison', '3.0.4'), + ('Autotools', '20150215'), + ('pkg-config', '0.29.1'), + ('libpthread-stubs', '0.3'), + ('makedepend', '1.0.5'), +] + +dependencies = [ + ('eudev', '3.1.5'), + ('libxml2', '2.9.2'), + ('libdrm', '2.4.68'), + ('LLVM', '3.7.1'), + ('X11', '20160819'), +] + +# Use the os provided libudev or the EB provided eudev +#osdependencies = ['libudev'] + +# GLU is not part anymore of Mesa package! +configopts = " --disable-osmesa --enable-gallium-osmesa --enable-gallium-llvm --enable-glx --disable-dri" +configopts += " --enable-xlib-glx --disable-driglx-direct --with-gallium-drivers='swrast' --disable-egl" +configopts += " --with-osmesa-bits=32 --enable-texture-float " + +# package-config files for os dependencies are in an os specific place +# preconfigopts = 'libtoolize && PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' +preconfigopts = ' libtoolize && ' + +prebuildopts = 'env CPATH="$EBROOTLIBDRM/include/libdrm:$CPATH" ' + +sanity_check_paths = { + 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libOSMesa.%s' % SHLIB_EXT, + 'lib/libGLESv1_CM.%s' % SHLIB_EXT, 'lib/libGLESv2.%s' % SHLIB_EXT, + 'include/GL/glext.h', 'include/GL/gl_mangle.h', + 'include/GL/glx.h', 'include/GL/osmesa.h', + 'include/GL/gl.h', 'include/GL/glxext.h', + 'include/GL/glx_mangle.h', 'include/GLES/gl.h', + 'include/GLES2/gl2.h', 'include/GLES3/gl3.h'], + 'dirs': [] +} + +maxparallel = 1 + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-foss-2015a.eb b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-foss-2015a.eb new file mode 100644 index 0000000000..29786d5315 --- /dev/null +++ b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-foss-2015a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'makedepend' +version = '1.0.5' + +homepage = "http://www.linuxfromscratch.org/blfs/view/svn/x/makedepend.html" +description = "The makedepend package contains a C-preprocessor like utility to determine build-time dependencies." + +toolchain = {'name': 'foss', 'version': '2015a'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_UTIL_SOURCE] + +builddependencies = [ + ('X11', '20160819'), +] + +sanity_check_paths = { + 'files': ['bin/makedepend'], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From daac9037af512c7c3d482c4013f25d4cdf256aab Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Fri, 2 Jun 2017 17:34:56 +1200 Subject: [PATCH 0876/1603] Additional dependencies --- .../g/GLib/GLib-2.48.2-foss-2015a.eb | 33 +++++++++++++++++++ .../libGLU-9.0.0-foss-2015a-Mesa-11.2.1.eb | 27 +++++++++++++++ ....7-foss-2015a-GLib-2.48.2-Python-2.7.11.eb | 31 +++++++++++++++++ 3 files changed, 91 insertions(+) create mode 100644 easybuild/easyconfigs/g/GLib/GLib-2.48.2-foss-2015a.eb create mode 100644 easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-foss-2015a-Mesa-11.2.1.eb create mode 100644 easybuild/easyconfigs/q/Qt/Qt-4.8.7-foss-2015a-GLib-2.48.2-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.48.2-foss-2015a.eb b/easybuild/easyconfigs/g/GLib/GLib-2.48.2-foss-2015a.eb new file mode 100644 index 0000000000..9af7e1beb3 --- /dev/null +++ b/easybuild/easyconfigs/g/GLib/GLib-2.48.2-foss-2015a.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'GLib' +version = '2.48.2' + +homepage = 'http://www.gtk.org/' +description = """GLib is one of the base libraries of the GTK+ project""" + +toolchain = {'name': 'foss', 'version': '2015a'} +toolchainopts = {'pic': True} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('libffi', '3.2.1'), + ('gettext', '0.19.8'), + ('libxml2', '2.9.3'), + ('PCRE', '8.37'), +] + +builddependencies = [('Python', '2.7.9')] + +configopts = "--disable-maintainer-mode --disable-silent-rules --disable-libelf --enable-static --enable-shared --disable-systemtap --with-pcre=system" + +postinstallcmds = ["sed -i -e 's|#!.*python|#!/usr/bin/env python|' %(installdir)s/bin/*"] + +sanity_check_paths = { + 'files': ['lib/libglib-%(version_major)s.0.a', 'lib/libglib-%%(version_major)s.0.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-foss-2015a-Mesa-11.2.1.eb b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-foss-2015a-Mesa-11.2.1.eb new file mode 100644 index 0000000000..ffcaba3d56 --- /dev/null +++ b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-foss-2015a-Mesa-11.2.1.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'libGLU' +version = '9.0.0' + +homepage = 'ftp://ftp.freedesktop.org/pub/mesa/glu/' +description = """The OpenGL Utility Library (GLU) is a computer graphics library for OpenGL. """ + +toolchain = {'name': 'foss', 'version': '2015a'} +toolchainopts = {'pic': True} + +source_urls = ['ftp://ftp.freedesktop.org/pub/mesa/glu/'] +sources = ['glu-%(version)s.tar.bz2'] + +mesa_ver = '11.2.1' +versionsuffix = '-Mesa-%s' % mesa_ver + +dependencies = [ + ('Mesa', mesa_ver), +] + +sanity_check_paths = { + 'files': ['lib/libGLU.so.1'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.7-foss-2015a-GLib-2.48.2-Python-2.7.11.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.7-foss-2015a-GLib-2.48.2-Python-2.7.11.eb new file mode 100644 index 0000000000..ba744fff34 --- /dev/null +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.7-foss-2015a-GLib-2.48.2-Python-2.7.11.eb @@ -0,0 +1,31 @@ +name = 'Qt' +version = '4.8.7' +glib = 'GLib' +glibver = '2.48.2' +glibsuffix = '-%s-%s' % (glib, glibver) +python = 'Python' +pyver = '2.7.11' +pysuffix = '-%s-%s' % (python, pyver) +versionsuffix = '%s%s' % (glibsuffix, pysuffix) + +homepage = 'http://qt.io/' +description = "Qt is a comprehensive cross-platform C++ application framework." + +toolchain = {'name': 'foss', 'version': '2015a'} + +source_urls = [ + 'http://download.qt.io/official_releases/qt/%(version_major_minor)s/%(version)s/', + 'http://download.qt.io/archive/qt/%(version_major_minor)s/%(version)s/' +] +sources = ['%(namelower)s-everywhere-opensource-src-%(version)s.tar.gz'] + +patches = ['Qt-%(version)s_phonon-export.patch'] + +dependencies = [ + ('GLib', '2.48.2'), + ('libX11', '1.6.3', pysuffix), + ('libXt', '1.1.5', pysuffix), + ('libXrender', '0.9.9', pysuffix), +] + +moduleclass = 'devel' -- GitLab From effafc99eba76f252e9e681bf5315d93abc9eee1 Mon Sep 17 00:00:00 2001 From: Robert Qiao Date: Fri, 2 Jun 2017 15:26:56 +0930 Subject: [PATCH 0877/1603] PyTable Python version updated --- ...hon-2.7.13.eb => PyTables-3.3.0-foss-2016b-Python-2.7.12.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/p/PyTables/{PyTables-3.3.0-foss-2016b-Python-2.7.13.eb => PyTables-3.3.0-foss-2016b-Python-2.7.12.eb} (98%) diff --git a/easybuild/easyconfigs/p/PyTables/PyTables-3.3.0-foss-2016b-Python-2.7.13.eb b/easybuild/easyconfigs/p/PyTables/PyTables-3.3.0-foss-2016b-Python-2.7.12.eb similarity index 98% rename from easybuild/easyconfigs/p/PyTables/PyTables-3.3.0-foss-2016b-Python-2.7.13.eb rename to easybuild/easyconfigs/p/PyTables/PyTables-3.3.0-foss-2016b-Python-2.7.12.eb index 2e0d15537e..69afe0d8b8 100644 --- a/easybuild/easyconfigs/p/PyTables/PyTables-3.3.0-foss-2016b-Python-2.7.13.eb +++ b/easybuild/easyconfigs/p/PyTables/PyTables-3.3.0-foss-2016b-Python-2.7.12.eb @@ -31,7 +31,7 @@ source_urls = ['https://github.com/PyTables/PyTables/archive/'] sources = ['v%(version)s.tar.gz'] dependencies = [ - ('Python', '2.7.13'), + ('Python', '2.7.12'), ('numexpr', '2.6.1', versionsuffix), ('HDF5', '1.8.18'), ] -- GitLab From 9a666f09a553504a48b0172738ca06d5eae5a349 Mon Sep 17 00:00:00 2001 From: Robert Qiao Date: Fri, 2 Jun 2017 15:29:21 +0930 Subject: [PATCH 0878/1603] deps version updated --- .../g/GroopM/GroopM-0.3.4-foss-2016b-Python-2.7.12.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GroopM/GroopM-0.3.4-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/g/GroopM/GroopM-0.3.4-foss-2016b-Python-2.7.12.eb index 741c740418..2b9c9abeb7 100644 --- a/easybuild/easyconfigs/g/GroopM/GroopM-0.3.4-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/g/GroopM/GroopM-0.3.4-foss-2016b-Python-2.7.12.eb @@ -30,7 +30,7 @@ dependencies = [ ('Cython', '0.25.2', versionsuffix), ('matplotlib', '1.5.3', versionsuffix), ('Pysam', '0.10.0', versionsuffix), - ('PyTables', '3.2.2', versionsuffix), + ('PyTables', '3.3.0', versionsuffix), ('PIL', '1.1.7', versionsuffix), ('BamM', '1.7.3', versionsuffix), ('GTK+', '2.24.31'), -- GitLab From ea91b8526d698ea41601fcb15af7864f4dc778c6 Mon Sep 17 00:00:00 2001 From: Robert Qiao Date: Fri, 2 Jun 2017 16:16:19 +0930 Subject: [PATCH 0879/1603] matplotlib1.5.2 removed --- ...tplotlib-1.5.2-foss-2016b-Python-2.7.13.eb | 55 ------------------- 1 file changed, 55 deletions(-) delete mode 100644 easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.2-foss-2016b-Python-2.7.13.eb diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.2-foss-2016b-Python-2.7.13.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.2-foss-2016b-Python-2.7.13.eb deleted file mode 100644 index 6e664a2059..0000000000 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.2-foss-2016b-Python-2.7.13.eb +++ /dev/null @@ -1,55 +0,0 @@ -## -# This is a contribution from Phoenix HPC Service, The University of Adelaide, Australia -# Homepage: https://www.adelaide.edu.au/phoenix/ -# -# Copyright:: Copyright 2014-2017 adelaide.edu.au/phoenix -# Authors:: Robert Qiao , Exequiel Sepulveda -# License:: Python Software Foundation (PSF) -# -# Notes:: -## - -easyblock = 'Bundle' - -name = 'matplotlib' -version = '1.5.2' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'http://matplotlib.org' -description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of - hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python - and ipython shell, web application servers, and six graphical user interface toolkits.""" - -toolchain = {'name': 'foss', 'version': '2016b'} - -# this is a bundle of Python packages -exts_defaultclass = 'PythonPackage' - -dependencies = [ - ('Python', '2.7.13'), - ('freetype', '2.6.5'), - ('libpng', '1.6.24'), -] - -exts_list = [ - ('Cycler', '0.10.0', { - 'modulename': 'cycler', - 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], - 'source_tmpl': 'cycler-%(version)s.tar.gz', - }), - (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], - }), -] - -# specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module -full_sanity_check = True - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - -moduleclass = 'vis' -- GitLab From ad0296763fa7907b3f2c20fb4b3cd9de028b1466 Mon Sep 17 00:00:00 2001 From: Robert Qiao Date: Fri, 2 Jun 2017 17:24:02 +0930 Subject: [PATCH 0880/1603] deps version updated --- .../g/GroopM/GroopM-0.3.4-foss-2016b-Python-2.7.12.eb | 2 +- .../easyconfigs/p/PIL/PIL-1.1.7-foss-2016b-Python-2.7.12.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/g/GroopM/GroopM-0.3.4-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/g/GroopM/GroopM-0.3.4-foss-2016b-Python-2.7.12.eb index 2b9c9abeb7..508fa6454b 100644 --- a/easybuild/easyconfigs/g/GroopM/GroopM-0.3.4-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/g/GroopM/GroopM-0.3.4-foss-2016b-Python-2.7.12.eb @@ -28,7 +28,7 @@ sources = [SOURCE_TAR_GZ] dependencies = [ ('Python', '2.7.12'), ('Cython', '0.25.2', versionsuffix), - ('matplotlib', '1.5.3', versionsuffix), + ('matplotlib', '1.5.2', versionsuffix), ('Pysam', '0.10.0', versionsuffix), ('PyTables', '3.3.0', versionsuffix), ('PIL', '1.1.7', versionsuffix), diff --git a/easybuild/easyconfigs/p/PIL/PIL-1.1.7-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/PIL/PIL-1.1.7-foss-2016b-Python-2.7.12.eb index 92b0c0004e..447ed8f4a5 100644 --- a/easybuild/easyconfigs/p/PIL/PIL-1.1.7-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/p/PIL/PIL-1.1.7-foss-2016b-Python-2.7.12.eb @@ -30,7 +30,7 @@ dependencies = [ ('zlib', '1.2.8'), ('Python', '2.7.12'), ('libjpeg-turbo', '1.5.0'), - ('freetype', '2.7'), + ('freetype', '2.6.5'), ] options = {'modulename': 'PIL'} -- GitLab From 722ce562fc3fa30be225d4670301b21c465477bc Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Fri, 2 Jun 2017 13:03:54 -0500 Subject: [PATCH 0881/1603] adding easyconfigs: X11-20160819-GCCcore-5.4.0.eb --- .../x/X11/X11-20160819-GCCcore-5.4.0.eb | 134 ++++++++++++++++++ 1 file changed, 134 insertions(+) create mode 100644 easybuild/easyconfigs/x/X11/X11-20160819-GCCcore-5.4.0.eb diff --git a/easybuild/easyconfigs/x/X11/X11-20160819-GCCcore-5.4.0.eb b/easybuild/easyconfigs/x/X11/X11-20160819-GCCcore-5.4.0.eb new file mode 100644 index 0000000000..69f438faec --- /dev/null +++ b/easybuild/easyconfigs/x/X11/X11-20160819-GCCcore-5.4.0.eb @@ -0,0 +1,134 @@ +easyblock = 'Bundle' + +name = 'X11' +version = '20160819' + +homepage = 'https://www.x.org' +description = "The X Window System (X11) is a windowing system for bitmap displays" + +toolchain = {'name': 'GCCcore', 'version': '5.4.0'} + +source_urls = [ + XORG_LIB_SOURCE, + XORG_PROTO_SOURCE, + 'http://xcb.freedesktop.org/dist/', + 'http://xkbcommon.org/download/', + 'http://cgit.freedesktop.org/xorg/util/macros/snapshot', +] + +builddependencies = [ + ('Autotools', '20150215'), + ('Bison', '3.0.4'), + ('gettext', '0.19.8'), + ('pkg-config', '0.29.1'), + ('binutils', '2.26', '', True), +] +dependencies = [ + ('freetype', '2.6.5'), + ('fontconfig', '2.12.1'), + ('zlib', '1.2.8'), + ('bzip2', '1.0.6'), +] + +default_easyblock = 'ConfigureMake' + +common_specs = { + 'sources': [SOURCE_TAR_GZ], + 'start_dir': '%(name)s-%(version)s', +} +components = [ + ('xorg-macros', '1.19.0', { + 'sources': ['util-macros-%(version)s.tar.gz'], + 'start_dir': 'util-macros-%(version)s', + }), + ('libpthread-stubs', '0.3', common_specs), + ('bigreqsproto', '1.1.2', common_specs), + ('compositeproto', '0.4.2', common_specs), + ('damageproto', '1.2.1', common_specs), + ('dmxproto', '2.3.1', common_specs), + ('dri2proto', '2.8', common_specs), + ('dri3proto', '1.0', common_specs), + ('fixesproto', '5.0', common_specs), + ('fontsproto', '2.1.3', common_specs), + ('glproto', '1.4.17', common_specs), + ('inputproto', '2.3.1', common_specs), + ('kbproto', '1.0.7', common_specs), + ('presentproto', '1.0', common_specs), + ('randrproto', '1.5.0', common_specs), + ('recordproto', '1.14.2', common_specs), + ('renderproto', '0.11', common_specs), + ('resourceproto', '1.2.0', common_specs), + ('scrnsaverproto', '1.2.2', common_specs), + ('videoproto', '2.3.3', common_specs), + ('xcmiscproto', '1.2.2', common_specs), + ('xextproto', '7.3.0', common_specs), + ('xf86bigfontproto', '1.2.0', common_specs), + ('xf86dgaproto', '2.1', common_specs), + ('xf86driproto', '2.1.1', common_specs), + ('xf86vidmodeproto', '2.3.1', common_specs), + ('xineramaproto', '1.2.1', common_specs), + ('xproto', '7.0.28', common_specs), + ('libXau', '1.0.8', common_specs), + ('libXdmcp', '1.1.2', common_specs), + ('xcb-proto', '1.11', common_specs), + ('libxcb', '1.11.1', common_specs), + ('xtrans', '1.3.5', common_specs), + ('libxkbcommon', '0.6.1', { + 'sources': ['libxkbcommon-%(version)s.tar.xz'], + 'start_dir': 'libxkbcommon-%(version)s', + }), + ('libX11', '1.6.3', common_specs), + ('libXext', '1.3.3', common_specs), + ('libFS', '1.0.7', common_specs), + ('libICE', '1.0.9', common_specs), + ('libSM', '1.2.2', common_specs), + ('libXScrnSaver', '1.2.2', common_specs), + ('libXt', '1.1.5', common_specs), + ('libXmu', '1.1.2', common_specs), + ('libXpm', '3.5.11', common_specs), + ('libXaw', '1.0.13', common_specs), + ('libXfixes', '5.0.2', common_specs), + ('libXcomposite', '0.4.4', common_specs), + ('libXrender', '0.9.9', common_specs), + ('libXcursor', '1.1.14', common_specs), + ('libXdamage', '1.1.4', common_specs), + ('libfontenc', '1.1.3', common_specs), + ('libXfont', '1.5.1', common_specs), + ('libXft', '2.3.2', common_specs), + ('libXi', '1.7.6', common_specs), + ('libXinerama', '1.1.3', common_specs), + ('libXrandr', '1.5.0', common_specs), + ('libXres', '1.0.7', common_specs), + ('libXtst', '1.2.2', common_specs), + ('libXv', '1.0.10', common_specs), + ('libXvMC', '1.0.9', common_specs), + ('libXxf86dga', '1.1.4', common_specs), + ('libXxf86vm', '1.1.4', common_specs), + ('libdmx', '1.1.3', common_specs), + ('libpciaccess', '0.13.4', common_specs), + ('libxkbfile', '1.0.9', common_specs), + ('libxshmfence', '1.2', common_specs), + ('xcb-util', '0.4.0', common_specs), + ('xcb-util-image', '0.4.0', common_specs), + ('xcb-util-keysyms', '0.4.0', common_specs), + ('xcb-util-renderutil', '0.3.9', common_specs), + ('xcb-util-wm', '0.4.1', common_specs), + ('xcb-util-cursor', '0.1.3', common_specs), +] + +# Python is required for xcb-proto +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] +pyshortver = '.'.join(SYS_PYTHON_VERSION.split('.')[0:2]) + +preconfigopts = "if [ ! -f configure ]; then ./autogen.sh; fi && " + +# specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module +full_sanity_check = True + +sanity_check_paths = { + 'files': ['include/X11/Xlib.h', 'include/X11/Xutil.h'], + 'dirs': ['include/GL', 'include/X11', 'include/X11/extensions', 'lib', + 'lib/python%s/site-packages/xcbgen' % pyshortver, 'lib/pkgconfig', 'share/pkgconfig'], +} + +moduleclass = 'vis' -- GitLab From 2bf7bc8bb1026af9f14f6b968e78eca8fb3f9d08 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 3 Jun 2017 12:06:50 +0200 Subject: [PATCH 0882/1603] consistently use --with-harfbuzz=no configure option in freetype easyconfigs --- .../easyconfigs/f/freetype/freetype-2.4.10-goolf-1.4.10.eb | 2 ++ easybuild/easyconfigs/f/freetype/freetype-2.4.10-ictce-5.3.0.eb | 2 ++ .../easyconfigs/f/freetype/freetype-2.4.11-goolf-1.4.10.eb | 2 ++ easybuild/easyconfigs/f/freetype/freetype-2.4.11-ictce-5.3.0.eb | 2 ++ .../easyconfigs/f/freetype/freetype-2.5.0.1-goolf-1.4.10.eb | 2 ++ .../easyconfigs/f/freetype/freetype-2.5.0.1-ictce-5.3.0.eb | 2 ++ .../easyconfigs/f/freetype/freetype-2.5.0.1-ictce-5.5.0.eb | 2 ++ easybuild/easyconfigs/f/freetype/freetype-2.5.2-ictce-5.5.0.eb | 2 ++ easybuild/easyconfigs/f/freetype/freetype-2.5.3-foss-2014b.eb | 2 ++ easybuild/easyconfigs/f/freetype/freetype-2.5.3-goolf-1.7.20.eb | 2 ++ easybuild/easyconfigs/f/freetype/freetype-2.5.3-intel-2014b.eb | 2 ++ easybuild/easyconfigs/f/freetype/freetype-2.5.5-foss-2015a.eb | 2 ++ easybuild/easyconfigs/f/freetype/freetype-2.5.5-goolf-1.7.20.eb | 2 ++ easybuild/easyconfigs/f/freetype/freetype-2.5.5-intel-2015a.eb | 2 ++ easybuild/easyconfigs/f/freetype/freetype-2.5.5-intel-2015b.eb | 2 ++ easybuild/easyconfigs/f/freetype/freetype-2.6-foss-2015a.eb | 2 ++ easybuild/easyconfigs/f/freetype/freetype-2.6-goolf-1.7.20.eb | 2 ++ easybuild/easyconfigs/f/freetype/freetype-2.6-intel-2015a.eb | 2 ++ .../f/freetype/freetype-2.6.1-intel-2015b-libpng-1.6.19.eb | 2 ++ easybuild/easyconfigs/f/freetype/freetype-2.6.1-intel-2015b.eb | 2 ++ .../easyconfigs/f/freetype/freetype-2.6.2-CrayGNU-2015.11.eb | 2 ++ easybuild/easyconfigs/f/freetype/freetype-2.6.2-foss-2015a.eb | 2 ++ easybuild/easyconfigs/f/freetype/freetype-2.6.2-foss-2015b.eb | 2 ++ easybuild/easyconfigs/f/freetype/freetype-2.6.2-foss-2016a.eb | 2 ++ easybuild/easyconfigs/f/freetype/freetype-2.6.2-gimkl-2.11.5.eb | 2 ++ easybuild/easyconfigs/f/freetype/freetype-2.6.2-goolf-1.7.20.eb | 2 ++ easybuild/easyconfigs/f/freetype/freetype-2.6.2-intel-2015b.eb | 2 ++ easybuild/easyconfigs/f/freetype/freetype-2.6.2-intel-2016a.eb | 2 ++ easybuild/easyconfigs/f/freetype/freetype-2.6.3-foss-2016a.eb | 2 ++ easybuild/easyconfigs/f/freetype/freetype-2.6.3-intel-2016a.eb | 2 ++ .../easyconfigs/f/freetype/freetype-2.6.5-GCCcore-5.4.0.eb | 2 ++ easybuild/easyconfigs/f/freetype/freetype-2.6.5-foss-2016b.eb | 2 ++ easybuild/easyconfigs/f/freetype/freetype-2.6.5-intel-2016b.eb | 2 ++ easybuild/easyconfigs/f/freetype/freetype-2.7-foss-2016b.eb | 2 ++ easybuild/easyconfigs/f/freetype/freetype-2.7-intel-2016b.eb | 2 ++ .../easyconfigs/f/freetype/freetype-2.7.1-GCCcore-5.4.0.eb | 2 ++ .../f/freetype/freetype-2.7.1-GCCcore-6.3.0-libpng-1.6.29.eb | 2 ++ .../easyconfigs/f/freetype/freetype-2.7.1-GCCcore-6.3.0.eb | 2 ++ easybuild/easyconfigs/f/freetype/freetype-2.7.1-intel-2016b.eb | 2 ++ 39 files changed, 78 insertions(+) diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.4.10-goolf-1.4.10.eb b/easybuild/easyconfigs/f/freetype/freetype-2.4.10-goolf-1.4.10.eb index 7e51dd88f4..e8bc65d782 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.4.10-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.4.10-goolf-1.4.10.eb @@ -12,6 +12,8 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} source_urls = [GNU_SAVANNAH_SOURCE] sources = [SOURCE_TAR_GZ] +configopts = '--with-harfbuzz=no' + sanity_check_paths = { 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.4.10-ictce-5.3.0.eb b/easybuild/easyconfigs/f/freetype/freetype-2.4.10-ictce-5.3.0.eb index bcf6608413..7e75acce83 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.4.10-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.4.10-ictce-5.3.0.eb @@ -11,6 +11,8 @@ toolchain = {'name': 'ictce', 'version': '5.3.0'} source_urls = [GNU_SAVANNAH_SOURCE] sources = [SOURCE_TAR_GZ] +configopts = '--with-harfbuzz=no' + sanity_check_paths = { 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.4.11-goolf-1.4.10.eb b/easybuild/easyconfigs/f/freetype/freetype-2.4.11-goolf-1.4.10.eb index 916f1302f2..dedbe863ab 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.4.11-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.4.11-goolf-1.4.10.eb @@ -12,6 +12,8 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} source_urls = [GNU_SAVANNAH_SOURCE] sources = [SOURCE_TAR_GZ] +configopts = '--with-harfbuzz=no' + sanity_check_paths = { 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.4.11-ictce-5.3.0.eb b/easybuild/easyconfigs/f/freetype/freetype-2.4.11-ictce-5.3.0.eb index 26eaffc5f6..10444c4ad7 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.4.11-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.4.11-ictce-5.3.0.eb @@ -11,6 +11,8 @@ toolchain = {'name': 'ictce', 'version': '5.3.0'} source_urls = ['http://download.savannah.gnu.org/releases/freetype/'] sources = [SOURCE_TAR_GZ] +configopts = '--with-harfbuzz=no' + sanity_check_paths = { 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.5.0.1-goolf-1.4.10.eb b/easybuild/easyconfigs/f/freetype/freetype-2.5.0.1-goolf-1.4.10.eb index cbbe1daafc..b0e7a6a30e 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.5.0.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.5.0.1-goolf-1.4.10.eb @@ -13,6 +13,8 @@ sources = [SOURCE_TAR_GZ] dependencies = [('libpng', '1.6.6')] +configopts = '--with-harfbuzz=no' + sanity_check_paths = { 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.5.0.1-ictce-5.3.0.eb b/easybuild/easyconfigs/f/freetype/freetype-2.5.0.1-ictce-5.3.0.eb index a5e70027fa..d1983d8529 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.5.0.1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.5.0.1-ictce-5.3.0.eb @@ -13,6 +13,8 @@ sources = [SOURCE_TAR_GZ] dependencies = [('libpng', '1.6.6')] +configopts = '--with-harfbuzz=no' + sanity_check_paths = { 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.5.0.1-ictce-5.5.0.eb b/easybuild/easyconfigs/f/freetype/freetype-2.5.0.1-ictce-5.5.0.eb index 8fa382b0ca..415101e28d 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.5.0.1-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.5.0.1-ictce-5.5.0.eb @@ -13,6 +13,8 @@ sources = [SOURCE_TAR_GZ] dependencies = [('libpng', '1.6.6')] +configopts = '--with-harfbuzz=no' + sanity_check_paths = { 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.5.2-ictce-5.5.0.eb b/easybuild/easyconfigs/f/freetype/freetype-2.5.2-ictce-5.5.0.eb index 0571a145ad..64e6ea7181 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.5.2-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.5.2-ictce-5.5.0.eb @@ -13,6 +13,8 @@ sources = [SOURCE_TAR_GZ] dependencies = [('libpng', '1.6.9')] +configopts = '--with-harfbuzz=no' + sanity_check_paths = { 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.5.3-foss-2014b.eb b/easybuild/easyconfigs/f/freetype/freetype-2.5.3-foss-2014b.eb index cea107f292..0d671ee5bb 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.5.3-foss-2014b.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.5.3-foss-2014b.eb @@ -13,6 +13,8 @@ sources = [SOURCE_TAR_GZ] dependencies = [('libpng', '1.6.12')] +configopts = '--with-harfbuzz=no' + sanity_check_paths = { 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.5.3-goolf-1.7.20.eb b/easybuild/easyconfigs/f/freetype/freetype-2.5.3-goolf-1.7.20.eb index 9b0aae30b7..f35d8dc0c1 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.5.3-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.5.3-goolf-1.7.20.eb @@ -13,6 +13,8 @@ sources = [SOURCE_TAR_GZ] dependencies = [('libpng', '1.6.12')] +configopts = '--with-harfbuzz=no' + sanity_check_paths = { 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.5.3-intel-2014b.eb b/easybuild/easyconfigs/f/freetype/freetype-2.5.3-intel-2014b.eb index 45d6dc8e93..fb9b9599e8 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.5.3-intel-2014b.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.5.3-intel-2014b.eb @@ -13,6 +13,8 @@ sources = [SOURCE_TAR_GZ] dependencies = [('libpng', '1.6.12')] +configopts = '--with-harfbuzz=no' + sanity_check_paths = { 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.5.5-foss-2015a.eb b/easybuild/easyconfigs/f/freetype/freetype-2.5.5-foss-2015a.eb index c9b6e770b4..13b13e9cc7 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.5.5-foss-2015a.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.5.5-foss-2015a.eb @@ -13,6 +13,8 @@ sources = [SOURCE_TAR_GZ] dependencies = [('libpng', '1.6.16')] +configopts = '--with-harfbuzz=no' + sanity_check_paths = { 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.5.5-goolf-1.7.20.eb b/easybuild/easyconfigs/f/freetype/freetype-2.5.5-goolf-1.7.20.eb index 773f70da96..f26f3a1cf8 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.5.5-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.5.5-goolf-1.7.20.eb @@ -16,6 +16,8 @@ dependencies = [ ('zlib', '1.2.8') ] +configopts = '--with-harfbuzz=no' + sanity_check_paths = { 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], 'dirs': ['include/freetype2'], diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.5.5-intel-2015a.eb b/easybuild/easyconfigs/f/freetype/freetype-2.5.5-intel-2015a.eb index 07f4f8160c..3b19e21412 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.5.5-intel-2015a.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.5.5-intel-2015a.eb @@ -13,6 +13,8 @@ sources = [SOURCE_TAR_GZ] dependencies = [('libpng', '1.6.16')] +configopts = '--with-harfbuzz=no' + sanity_check_paths = { 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.5.5-intel-2015b.eb b/easybuild/easyconfigs/f/freetype/freetype-2.5.5-intel-2015b.eb index 44080cb0f8..6d539701a6 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.5.5-intel-2015b.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.5.5-intel-2015b.eb @@ -13,6 +13,8 @@ sources = [SOURCE_TAR_GZ] dependencies = [('libpng', '1.6.16')] +configopts = '--with-harfbuzz=no' + sanity_check_paths = { 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.6-foss-2015a.eb b/easybuild/easyconfigs/f/freetype/freetype-2.6-foss-2015a.eb index 7cfa18b2f4..352ce2f725 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.6-foss-2015a.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.6-foss-2015a.eb @@ -13,6 +13,8 @@ sources = [SOURCE_TAR_GZ] dependencies = [('libpng', '1.6.17')] +configopts = '--with-harfbuzz=no' + sanity_check_paths = { 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.6-goolf-1.7.20.eb b/easybuild/easyconfigs/f/freetype/freetype-2.6-goolf-1.7.20.eb index 78c7fb98d6..5930e1dad7 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.6-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.6-goolf-1.7.20.eb @@ -13,6 +13,8 @@ sources = [SOURCE_TAR_GZ] dependencies = [('libpng', '1.6.17')] +configopts = '--with-harfbuzz=no' + sanity_check_paths = { 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.6-intel-2015a.eb b/easybuild/easyconfigs/f/freetype/freetype-2.6-intel-2015a.eb index 4cf88e23a7..febe99790f 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.6-intel-2015a.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.6-intel-2015a.eb @@ -13,6 +13,8 @@ sources = [SOURCE_TAR_GZ] dependencies = [('libpng', '1.6.17')] +configopts = '--with-harfbuzz=no' + sanity_check_paths = { 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.6.1-intel-2015b-libpng-1.6.19.eb b/easybuild/easyconfigs/f/freetype/freetype-2.6.1-intel-2015b-libpng-1.6.19.eb index 8405a0ec93..4ed20bab25 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.6.1-intel-2015b-libpng-1.6.19.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.6.1-intel-2015b-libpng-1.6.19.eb @@ -15,6 +15,8 @@ libpngver = '1.6.19' versionsuffix = '-libpng-%s' % libpngver dependencies = [('libpng', libpngver)] +configopts = '--with-harfbuzz=no' + sanity_check_paths = { 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.6.1-intel-2015b.eb b/easybuild/easyconfigs/f/freetype/freetype-2.6.1-intel-2015b.eb index 9c9d2b2e08..2b433c8140 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.6.1-intel-2015b.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.6.1-intel-2015b.eb @@ -13,6 +13,8 @@ sources = [SOURCE_TAR_GZ] dependencies = [('libpng', '1.6.18')] +configopts = '--with-harfbuzz=no' + sanity_check_paths = { 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.6.2-CrayGNU-2015.11.eb b/easybuild/easyconfigs/f/freetype/freetype-2.6.2-CrayGNU-2015.11.eb index 7f9b603bc6..b8dc673ae8 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.6.2-CrayGNU-2015.11.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.6.2-CrayGNU-2015.11.eb @@ -13,6 +13,8 @@ sources = [SOURCE_TAR_GZ] dependencies = [('libpng', '1.6.21')] +configopts = '--with-harfbuzz=no' + sanity_check_paths = { 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.6.2-foss-2015a.eb b/easybuild/easyconfigs/f/freetype/freetype-2.6.2-foss-2015a.eb index bbfd2a2508..8d1ddddc16 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.6.2-foss-2015a.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.6.2-foss-2015a.eb @@ -13,6 +13,8 @@ sources = [SOURCE_TAR_GZ] dependencies = [('libpng', '1.6.20')] +configopts = '--with-harfbuzz=no' + sanity_check_paths = { 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.6.2-foss-2015b.eb b/easybuild/easyconfigs/f/freetype/freetype-2.6.2-foss-2015b.eb index 912f826139..446146f3b1 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.6.2-foss-2015b.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.6.2-foss-2015b.eb @@ -13,6 +13,8 @@ sources = [SOURCE_TAR_GZ] dependencies = [('libpng', '1.6.21')] +configopts = '--with-harfbuzz=no' + sanity_check_paths = { 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.6.2-foss-2016a.eb b/easybuild/easyconfigs/f/freetype/freetype-2.6.2-foss-2016a.eb index 932824a17e..75cf76d290 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.6.2-foss-2016a.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.6.2-foss-2016a.eb @@ -17,6 +17,8 @@ dependencies = [ ('zlib', '1.2.8'), ] +configopts = '--with-harfbuzz=no' + sanity_check_paths = { 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.6.2-gimkl-2.11.5.eb b/easybuild/easyconfigs/f/freetype/freetype-2.6.2-gimkl-2.11.5.eb index fec100e1f0..d00692c774 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.6.2-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.6.2-gimkl-2.11.5.eb @@ -13,6 +13,8 @@ sources = [SOURCE_TAR_GZ] dependencies = [('libpng', '1.6.21')] +configopts = '--with-harfbuzz=no' + sanity_check_paths = { 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.6.2-goolf-1.7.20.eb b/easybuild/easyconfigs/f/freetype/freetype-2.6.2-goolf-1.7.20.eb index 7436cc5833..fefd237604 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.6.2-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.6.2-goolf-1.7.20.eb @@ -16,6 +16,8 @@ dependencies = [ ('zlib', '1.2.8') ] +configopts = '--with-harfbuzz=no' + sanity_check_paths = { 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], 'dirs': ['include/freetype2'], diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.6.2-intel-2015b.eb b/easybuild/easyconfigs/f/freetype/freetype-2.6.2-intel-2015b.eb index 0811253154..896545c2ea 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.6.2-intel-2015b.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.6.2-intel-2015b.eb @@ -13,6 +13,8 @@ sources = [SOURCE_TAR_GZ] dependencies = [('libpng', '1.6.21')] +configopts = '--with-harfbuzz=no' + sanity_check_paths = { 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.6.2-intel-2016a.eb b/easybuild/easyconfigs/f/freetype/freetype-2.6.2-intel-2016a.eb index 60b3db5452..7b8aa9c093 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.6.2-intel-2016a.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.6.2-intel-2016a.eb @@ -17,6 +17,8 @@ dependencies = [ ('zlib', '1.2.8'), ] +configopts = '--with-harfbuzz=no' + sanity_check_paths = { 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.6.3-foss-2016a.eb b/easybuild/easyconfigs/f/freetype/freetype-2.6.3-foss-2016a.eb index d267c83653..1b349e2706 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.6.3-foss-2016a.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.6.3-foss-2016a.eb @@ -17,6 +17,8 @@ dependencies = [ ('zlib', '1.2.8'), ] +configopts = '--with-harfbuzz=no' + sanity_check_paths = { 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.6.3-intel-2016a.eb b/easybuild/easyconfigs/f/freetype/freetype-2.6.3-intel-2016a.eb index 3d89e4bbb1..fe187d8408 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.6.3-intel-2016a.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.6.3-intel-2016a.eb @@ -17,6 +17,8 @@ dependencies = [ ('zlib', '1.2.8'), ] +configopts = '--with-harfbuzz=no' + sanity_check_paths = { 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.6.5-GCCcore-5.4.0.eb b/easybuild/easyconfigs/f/freetype/freetype-2.6.5-GCCcore-5.4.0.eb index e1a17a86f6..5aca056975 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.6.5-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.6.5-GCCcore-5.4.0.eb @@ -19,6 +19,8 @@ dependencies = [ builddependencies = [('binutils', '2.26', '', True)] +configopts = '--with-harfbuzz=no' + sanity_check_paths = { 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.6.5-foss-2016b.eb b/easybuild/easyconfigs/f/freetype/freetype-2.6.5-foss-2016b.eb index 9156052c8f..f59391c7f9 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.6.5-foss-2016b.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.6.5-foss-2016b.eb @@ -17,6 +17,8 @@ dependencies = [ ('zlib', '1.2.8'), ] +configopts = '--with-harfbuzz=no' + sanity_check_paths = { 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.6.5-intel-2016b.eb b/easybuild/easyconfigs/f/freetype/freetype-2.6.5-intel-2016b.eb index bf9e0cfc01..68aae21c57 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.6.5-intel-2016b.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.6.5-intel-2016b.eb @@ -17,6 +17,8 @@ dependencies = [ ('zlib', '1.2.8'), ] +configopts = '--with-harfbuzz=no' + sanity_check_paths = { 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.7-foss-2016b.eb b/easybuild/easyconfigs/f/freetype/freetype-2.7-foss-2016b.eb index 8b88736d00..85f52fb15e 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.7-foss-2016b.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.7-foss-2016b.eb @@ -17,6 +17,8 @@ dependencies = [ ('zlib', '1.2.8'), ] +configopts = '--with-harfbuzz=no' + sanity_check_paths = { 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.7-intel-2016b.eb b/easybuild/easyconfigs/f/freetype/freetype-2.7-intel-2016b.eb index 52d8477931..154dcf903b 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.7-intel-2016b.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.7-intel-2016b.eb @@ -17,6 +17,8 @@ dependencies = [ ('zlib', '1.2.8'), ] +configopts = '--with-harfbuzz=no' + sanity_check_paths = { 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.7.1-GCCcore-5.4.0.eb b/easybuild/easyconfigs/f/freetype/freetype-2.7.1-GCCcore-5.4.0.eb index fee6777ad0..f01c0208b5 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.7.1-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.7.1-GCCcore-5.4.0.eb @@ -20,6 +20,8 @@ dependencies = [ # use same binutils version that was used when building GCCcore toolchain builddependencies = [('binutils', '2.26', '', True)] +configopts = '--with-harfbuzz=no' + sanity_check_paths = { 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.7.1-GCCcore-6.3.0-libpng-1.6.29.eb b/easybuild/easyconfigs/f/freetype/freetype-2.7.1-GCCcore-6.3.0-libpng-1.6.29.eb index 1b0dc16aba..8016819a78 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.7.1-GCCcore-6.3.0-libpng-1.6.29.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.7.1-GCCcore-6.3.0-libpng-1.6.29.eb @@ -22,6 +22,8 @@ dependencies = [ # use same binutils version that was used when building GCCcore toolchain builddependencies = [('binutils', '2.27', '', True)] +configopts = '--with-harfbuzz=no' + sanity_check_paths = { 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.7.1-GCCcore-6.3.0.eb b/easybuild/easyconfigs/f/freetype/freetype-2.7.1-GCCcore-6.3.0.eb index 2892f7ffb0..50a10ef694 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.7.1-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.7.1-GCCcore-6.3.0.eb @@ -20,6 +20,8 @@ dependencies = [ # use same binutils version that was used when building GCCcore toolchain builddependencies = [('binutils', '2.27', '', True)] +configopts = '--with-harfbuzz=no' + sanity_check_paths = { 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.7.1-intel-2016b.eb b/easybuild/easyconfigs/f/freetype/freetype-2.7.1-intel-2016b.eb index d3a160563e..752f791cd9 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.7.1-intel-2016b.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.7.1-intel-2016b.eb @@ -17,6 +17,8 @@ dependencies = [ ('zlib', '1.2.8'), ] +configopts = '--with-harfbuzz=no' + sanity_check_paths = { 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], -- GitLab From 3445b51503bfd360e60c2362d9a0e0f9dcece80d Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Tue, 6 Jun 2017 16:08:24 +1200 Subject: [PATCH 0883/1603] Add a comment re osdependencies and remove empty dependencies list --- easybuild/easyconfigs/c/CMake/CMake-3.6.1.eb | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.6.1.eb b/easybuild/easyconfigs/c/CMake/CMake-3.6.1.eb index d8773947c8..d199586122 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.6.1.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.6.1.eb @@ -14,10 +14,8 @@ sources = [SOURCELOWER_TAR_GZ] configopts = '-- -DCMAKE_USE_OPENSSL=1' -# Don't depend on anything, since we will use this to build other software -# which might want different versions of the same dependency, eg: ncurses -dependencies = [] - +# Use OS dependencies in order to ensure that CMake can build software that +# depends on them osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel'), 'ncurses-devel'] sanity_check_paths = { -- GitLab From 262754d0412e86ff7f5688966891b214743e8805 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Tue, 6 Jun 2017 16:14:08 +1200 Subject: [PATCH 0884/1603] Replace nonce variables with ordinary strings --- easybuild/easyconfigs/g/gimkl/gimkl-2017a.eb | 4 +--- easybuild/easyconfigs/g/gimpi/gimpi-2017a.eb | 4 +--- .../easyconfigs/i/impi/impi-2017.1.132-GCC-5.4.0-2.26.eb | 4 +--- 3 files changed, 3 insertions(+), 9 deletions(-) diff --git a/easybuild/easyconfigs/g/gimkl/gimkl-2017a.eb b/easybuild/easyconfigs/g/gimkl/gimkl-2017a.eb index 1ed5c3adff..a390890a86 100644 --- a/easybuild/easyconfigs/g/gimkl/gimkl-2017a.eb +++ b/easybuild/easyconfigs/g/gimkl/gimkl-2017a.eb @@ -8,9 +8,7 @@ description = """GNU Compiler Collection (GCC) based compiler toolchain with Int toolchain = {'name': 'dummy', 'version': 'dummy'} -gccver = '5.4.0' -binutilsver = '2.26' -comp = ('GCC', '%s-%s' % (gccver, binutilsver)) +comp = ('GCC', '5.4.0-2.26') dependencies = [ comp, diff --git a/easybuild/easyconfigs/g/gimpi/gimpi-2017a.eb b/easybuild/easyconfigs/g/gimpi/gimpi-2017a.eb index faaefc8f0b..93489e6415 100644 --- a/easybuild/easyconfigs/g/gimpi/gimpi-2017a.eb +++ b/easybuild/easyconfigs/g/gimpi/gimpi-2017a.eb @@ -8,9 +8,7 @@ description = """GNU Compiler Collection (GCC) based compiler toolchain with Int toolchain = {'name': 'dummy', 'version': 'dummy'} -gccver = '5.4.0' -binutilsver = '2.26' -comp = ('GCC', '%s-%s' % (gccver, binutilsver)) +comp = ('GCC', '5.4.0-2.26') dependencies = [ comp, diff --git a/easybuild/easyconfigs/i/impi/impi-2017.1.132-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/impi/impi-2017.1.132-GCC-5.4.0-2.26.eb index 596670ca45..106806006c 100644 --- a/easybuild/easyconfigs/i/impi/impi-2017.1.132-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/impi/impi-2017.1.132-GCC-5.4.0-2.26.eb @@ -6,9 +6,7 @@ description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric messag passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for Linux OS implements the Message Passing Interface, version 2 (MPI-2) specification.""" -gccver = '5.4.0' -binutilsver = '2.26' -toolchain = {'name': 'GCC', 'version': '%s-%s' % (gccver, binutilsver)} +toolchain = {'name': 'GCC', 'version': '5.4.0-2.26'} sources = ['l_mpi_%(version)s.tgz'] checksums = ['d5e941ac2bcf7c5576f85f6bcfee4c18'] -- GitLab From 14e336473cfce9df9703c17b03a279c7221d0669 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 6 Jun 2017 09:31:15 +0200 Subject: [PATCH 0885/1603] adding easyconfigs: Perl4-CoreLibs-0.003-intel-2017a-Perl-5.24.1.eb --- ...-CoreLibs-0.003-intel-2017a-Perl-5.24.1.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/p/Perl4-CoreLibs/Perl4-CoreLibs-0.003-intel-2017a-Perl-5.24.1.eb diff --git a/easybuild/easyconfigs/p/Perl4-CoreLibs/Perl4-CoreLibs-0.003-intel-2017a-Perl-5.24.1.eb b/easybuild/easyconfigs/p/Perl4-CoreLibs/Perl4-CoreLibs-0.003-intel-2017a-Perl-5.24.1.eb new file mode 100644 index 0000000000..5590b7d7de --- /dev/null +++ b/easybuild/easyconfigs/p/Perl4-CoreLibs/Perl4-CoreLibs-0.003-intel-2017a-Perl-5.24.1.eb @@ -0,0 +1,26 @@ +easyblock = 'PerlModule' + +name = 'Perl4-CoreLibs' +version = '0.003' +versionsuffix = '-Perl-%(perlver)s' + +homepage = 'https://metacpan.org/pod/Perl4::CoreLibs' +description = "Libraries historically supplied with Perl 4" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['http://search.cpan.org/CPAN/authors/id/Z/ZE/ZEFRAM/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Perl', '5.24.1'), +] + +options = {'modulename': 'Perl4::CoreLibs'} + +sanity_check_paths = { + 'files': ['lib/perl5/site_perl/%(perlver)s/getopts.pl'], + 'dirs': [], +} + +moduleclass = 'data' -- GitLab From 2bae87de23179653f9e6b98fa456c40be3249c3b Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Tue, 6 Jun 2017 13:46:43 +0200 Subject: [PATCH 0886/1603] ImageMagick with FOSS 2016b tool chain and FFmpeg support. --- .../ImageMagick-7.0.5-10-foss-2016b.eb | 44 +++++++++++++++++++ .../j/JasPer/JasPer-2.0.12-foss-2016b.eb | 25 +++++++++++ .../l/LibTIFF/LibTIFF-4.0.7-foss-2016b.eb | 35 +++++++++++++++ .../l/LittleCMS/LittleCMS-2.8-foss-2016b.eb | 23 ++++++++++ .../libjpeg-turbo-1.5.1-foss-2016b.eb | 30 +++++++++++++ 5 files changed, 157 insertions(+) create mode 100644 easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.5-10-foss-2016b.eb create mode 100644 easybuild/easyconfigs/j/JasPer/JasPer-2.0.12-foss-2016b.eb create mode 100644 easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.7-foss-2016b.eb create mode 100644 easybuild/easyconfigs/l/LittleCMS/LittleCMS-2.8-foss-2016b.eb create mode 100644 easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.5.1-foss-2016b.eb diff --git a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.5-10-foss-2016b.eb b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.5-10-foss-2016b.eb new file mode 100644 index 0000000000..c320486a5a --- /dev/null +++ b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.5-10-foss-2016b.eb @@ -0,0 +1,44 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Ravi Tripathi +# Email: ravi89@uab.edu + +easyblock = 'ConfigureMake' + +name = 'ImageMagick' +version = '7.0.5-10' + +homepage = 'http://www.imagemagick.org/' +description = """ImageMagick is a software suite to create, edit, compose, or convert bitmap images""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['https://www.imagemagick.org/download/releases/'] +#checksums = ['473a1e7ae37548eb6fe9cf2b1fb78011'] + +dependencies = [ + ('bzip2', '1.0.6'), + #('X11', '20170314'), # Conflicts with FFmpeg + ('X11', '20160819'), + ('Ghostscript', '9.20'), + ('JasPer', '2.0.12'), + ('libjpeg-turbo', '1.5.1'), + ('LibTIFF', '4.0.7'), + ('LittleCMS', '2.8'), + ('FFmpeg', '3.3.1'), +] + +builddependencies = [ + ('pkg-config', '0.29.1'), +] + +configopts = "--with-gslib --with-x" + +sanity_check_paths = { + 'files': [], + 'dirs': ['bin', 'etc/%(name)s-%(version_major)s', 'include/%(name)s-%(version_major)s', 'lib', 'share'], +} + +modextravars = {'MAGICK_HOME': '%(installdir)s'} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/j/JasPer/JasPer-2.0.12-foss-2016b.eb b/easybuild/easyconfigs/j/JasPer/JasPer-2.0.12-foss-2016b.eb new file mode 100644 index 0000000000..c6d030f5e7 --- /dev/null +++ b/easybuild/easyconfigs/j/JasPer/JasPer-2.0.12-foss-2016b.eb @@ -0,0 +1,25 @@ +easyblock = 'CMakeMake' + +name = 'JasPer' +version = '2.0.12' + +homepage = 'http://www.ece.uvic.ca/~frodo/jasper/' +description = """The JasPer Project is an open-source initiative to provide a free + software-based reference implementation of the codec specified in the JPEG-2000 Part-1 standard.""" + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.ece.uvic.ca/~frodo/jasper/software/'] + +builddependencies = [('CMake', '3.7.2')] + +separate_build_dir = True + +sanity_check_paths = { + 'files': ['bin/jasper', 'lib64/libjasper.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.7-foss-2016b.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.7-foss-2016b.eb new file mode 100644 index 0000000000..e74567cf30 --- /dev/null +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.7-foss-2016b.eb @@ -0,0 +1,35 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos , Alan O'Cais (JSC) +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## +easyblock = 'ConfigureMake' + +name = 'LibTIFF' +version = '4.0.7' + +homepage = 'http://www.remotesensing.org/libtiff/' +description = "tiff: Library and tools for reading and writing TIFF data files" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = [ + 'http://download.osgeo.org/libtiff/', + 'ftp://ftp.remotesensing.org/pub/libtiff/', +] +sources = ['tiff-%(version)s.tar.gz'] + +configopts = " --enable-ld-version-script " + +sanity_check_paths = { + 'files': ['bin/tiffinfo'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/LittleCMS/LittleCMS-2.8-foss-2016b.eb b/easybuild/easyconfigs/l/LittleCMS/LittleCMS-2.8-foss-2016b.eb new file mode 100644 index 0000000000..c553697d74 --- /dev/null +++ b/easybuild/easyconfigs/l/LittleCMS/LittleCMS-2.8-foss-2016b.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'LittleCMS' +version = '2.8' + +homepage = 'http://www.littlecms.com/' +description = """ Little CMS intends to be an OPEN SOURCE small-footprint color management engine, + with special focus on accuracy and performance. """ + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['http://sourceforge.net/projects/lcms/files/lcms/%(version)s/'] +sources = ['lcms2-%(version)s.tar.gz'] + +dependencies = [('libjpeg-turbo', '1.5.0')] + +sanity_check_paths = { + 'files': ['bin/jpgicc', 'bin/linkicc', 'bin/psicc', 'bin/transicc', 'include/lcms2.h', 'include/lcms2_plugin.h', + 'lib/liblcms2.a', 'lib/liblcms2.%s' % SHLIB_EXT, 'lib/pkgconfig/lcms2.pc'], + 'dirs': ['share/man'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.5.1-foss-2016b.eb b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.5.1-foss-2016b.eb new file mode 100644 index 0000000000..7544c29c96 --- /dev/null +++ b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.5.1-foss-2016b.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'libjpeg-turbo' +version = '1.5.1' + +homepage = 'http://sourceforge.net/projects/libjpeg-turbo/' +description = """libjpeg-turbo is a fork of the original IJG libjpeg which uses SIMD to accelerate baseline JPEG +compression and decompression. libjpeg is a library that implements JPEG image encoding, decoding and transcoding. +""" + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('NASM', '2.12.02'), +] + +configopts = "--with-jpeg8" +runtest = "test" + +sanity_check_paths = { + 'files': ['bin/cjpeg', 'bin/djpeg', 'bin/jpegtran', 'bin/rdjpgcom', 'bin/tjbench', 'bin/wrjpgcom', + 'lib/libjpeg.a', 'lib/libjpeg.%s' % SHLIB_EXT, 'lib/libturbojpeg.a', 'lib/libturbojpeg.%s' % SHLIB_EXT], + 'dirs': ['include', 'share'], +} + +moduleclass = 'lib' -- GitLab From 1c4c921fde96de1c75fa71272bdd7eb70f20b02e Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Wed, 7 Jun 2017 12:39:09 +1200 Subject: [PATCH 0887/1603] Remove superseded CGAL easyconfig without Qt deps etc --- .../c/CGAL/CGAL-4.8.1-foss-2015a.eb | 38 ------------------- .../libpthread-stubs-0.3-foss-2015a.eb | 20 ++++++++++ .../libpthread-stubs-0.3-foss-2016b.eb | 0 .../libpthread-stubs-0.3-intel-2016b.eb | 0 4 files changed, 20 insertions(+), 38 deletions(-) delete mode 100644 easybuild/easyconfigs/c/CGAL/CGAL-4.8.1-foss-2015a.eb create mode 100644 easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-foss-2015a.eb mode change 100755 => 100644 easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-foss-2016b.eb mode change 100755 => 100644 easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-intel-2016b.eb diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.8.1-foss-2015a.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.8.1-foss-2015a.eb deleted file mode 100644 index f8ab683344..0000000000 --- a/easybuild/easyconfigs/c/CGAL/CGAL-4.8.1-foss-2015a.eb +++ /dev/null @@ -1,38 +0,0 @@ -name = 'CGAL' -version = '4.8.1' -gmpver = '6.0.0a' - -homepage = 'http://www.cgal.org/' -description = """The goal of the CGAL Open Source Project is to provide easy access to efficient - and reliable geometric algorithms in the form of a C++ library.""" - -toolchain = {'name': 'foss', 'version': '2015a'} -toolchainopts = {'strict': True} - -# note: source URL needs to be updated for a new version (checksums too)! -source_urls = ['https://github.com/%(name)s/%(namelower)s/releases/download/releases%2F%(name)s-%(version)s'] -sources = [SOURCE_TAR_XZ] -checksums = ['1cbcb3f251822766ed3d744f923c782d'] - -dependencies = [ - ('Boost', '1.60.0'), - ('GMP', gmpver), - ('MPFR', '3.1.2', '-GMP-%s' % gmpver), -] - -configopts = "-DCMAKE_VERBOSE_MAKEFILE=ON " -configopts += "-DBoost_INCLUDE_DIR=$EBROOTBOOST/include " -configopts += "-DBoost_LIBRARY_DIRS=$EBROOTBOOST/lib " -configopts += "-DBoost_SYSTEM_LIBRARY=$EBROOTBOOST/libboost_system.%s " % SHLIB_EXT -configopts += "-DBoost_THREAD_LIBRARY=$EBROOTBOOST/libboost_thread.%s " % SHLIB_EXT -configopts += "-DMPFR_INCLUDE_DIR=$EBROOTMPFR/include " -configopts += "-DMPFR_LIBRARIES=$EBROOTMPFR/lib/libmpfr.%s " % SHLIB_EXT -configopts += "-DGMP_INCLUDE_DIR=$EBROOTGMP/include " -configopts += "-DGMP_LIBRARIES=$EBROOTGMP/lib/libgmp.%s " % SHLIB_EXT -configopts += "-DGMP_LIBRARIES_DIR=$EBROOTGMP/lib " - -builddependencies = [ - ('CMake', '3.4.1'), -] - -moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-foss-2015a.eb b/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-foss-2015a.eb new file mode 100644 index 0000000000..ab9b29a42e --- /dev/null +++ b/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-foss-2015a.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'libpthread-stubs' +version = '0.3' + +homepage = 'http://xcb.freedesktop.org/' +description = """The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, +latency hiding, direct access to the protocol, improved threading support, and extensibility.""" + +source_urls = ['http://xcb.freedesktop.org/dist/'] +sources = [SOURCELOWER_TAR_GZ] + +toolchain = {'name': 'foss', 'version': '2015a'} + +sanity_check_paths = { + 'files': ['lib/pkgconfig/pthread-stubs.pc'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-foss-2016b.eb b/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-foss-2016b.eb old mode 100755 new mode 100644 diff --git a/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-intel-2016b.eb b/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-intel-2016b.eb old mode 100755 new mode 100644 -- GitLab From ff12d96bb9c435aaa85e56a05bae48cf0fe5ddb0 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Wed, 7 Jun 2017 12:49:06 +1200 Subject: [PATCH 0888/1603] Easyconfig (hitherto missing) for gettext --- .../g/gettext/gettext-0.19.8-foss-2015a.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/g/gettext/gettext-0.19.8-foss-2015a.eb diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.8-foss-2015a.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.8-foss-2015a.eb new file mode 100644 index 0000000000..482c543fe8 --- /dev/null +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.8-foss-2015a.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'gettext' +version = '0.19.8' + +homepage = 'http://www.gnu.org/software/gettext/' +description = """GNU 'gettext' is an important step for the GNU Translation Project, as it is an asset on which we may +build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools +and documentation""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [GNU_SOURCE] + +dependencies = [ + ('libxml2', '2.9.3'), + ('ncurses', '5.9'), +] + +configopts = '--without-emacs --with-libxml2-prefix=$EBROOTLIBXML2' + +moduleclass = 'vis' -- GitLab From ab941d89a7b4c73ba1c485f266e2c0aa68b8744e Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Wed, 7 Jun 2017 13:08:18 +1200 Subject: [PATCH 0889/1603] Replace specific X11 libs with the whole X11 ensemble --- .../q/Qt/Qt-4.8.7-foss-2015a-GLib-2.48.2-Python-2.7.11.eb | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.7-foss-2015a-GLib-2.48.2-Python-2.7.11.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.7-foss-2015a-GLib-2.48.2-Python-2.7.11.eb index ba744fff34..fa6c4175a4 100644 --- a/easybuild/easyconfigs/q/Qt/Qt-4.8.7-foss-2015a-GLib-2.48.2-Python-2.7.11.eb +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.7-foss-2015a-GLib-2.48.2-Python-2.7.11.eb @@ -23,9 +23,7 @@ patches = ['Qt-%(version)s_phonon-export.patch'] dependencies = [ ('GLib', '2.48.2'), - ('libX11', '1.6.3', pysuffix), - ('libXt', '1.1.5', pysuffix), - ('libXrender', '0.9.9', pysuffix), + ('X11', '20160819'), ] moduleclass = 'devel' -- GitLab From 658e51307010c918a6da56dde208c5e87d1a710f Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Wed, 7 Jun 2017 13:33:25 +1200 Subject: [PATCH 0890/1603] Use GMP built against GCC, not against foss-2015a toolchain --- .../c/CGAL/CGAL-4.8.1-foss-2015a-GLib-2.48.2-Python-2.7.11.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.8.1-foss-2015a-GLib-2.48.2-Python-2.7.11.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.8.1-foss-2015a-GLib-2.48.2-Python-2.7.11.eb index 618170db54..462e46256b 100644 --- a/easybuild/easyconfigs/c/CGAL/CGAL-4.8.1-foss-2015a-GLib-2.48.2-Python-2.7.11.eb +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.8.1-foss-2015a-GLib-2.48.2-Python-2.7.11.eb @@ -19,7 +19,7 @@ checksums = ['1cbcb3f251822766ed3d744f923c782d'] dependencies = [ ('Boost', '1.60.0'), ('GLib', glibver), - ('GMP', gmpver), + ('GMP', gmpver, '', ('GCC', '4.9.2')), ('libGLU', '9.0.0', '-Mesa-11.2.1'), ('MPFR', '3.1.2', '-GMP-%s' % gmpver), ('Qt', '4.8.7', versionsuffix), -- GitLab From 8689888be2edfef451f561a8ee18c3425ddeadbe Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Wed, 7 Jun 2017 14:03:16 +1200 Subject: [PATCH 0891/1603] Use libxml2 2.9.3 for the sake of consistency --- easybuild/easyconfigs/m/Mesa/Mesa-11.2.1-foss-2015a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-11.2.1-foss-2015a.eb b/easybuild/easyconfigs/m/Mesa/Mesa-11.2.1-foss-2015a.eb index 126c65abd6..27ac3ec93c 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-11.2.1-foss-2015a.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-11.2.1-foss-2015a.eb @@ -27,7 +27,7 @@ builddependencies = [ dependencies = [ ('eudev', '3.1.5'), - ('libxml2', '2.9.2'), + ('libxml2', '2.9.3'), ('libdrm', '2.4.68'), ('LLVM', '3.7.1'), ('X11', '20160819'), -- GitLab From bc2f2c4ca80154ec8b8782fbd9b171ec1232abeb Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Wed, 7 Jun 2017 14:18:21 +1200 Subject: [PATCH 0892/1603] Easyconfig for ncurses 6.0 with the gimkl 2017a toolchain --- .../n/ncurses/ncurses-6.0-gimkl-2017a.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/n/ncurses/ncurses-6.0-gimkl-2017a.eb diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.0-gimkl-2017a.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-gimkl-2017a.eb new file mode 100644 index 0000000000..0f183aae81 --- /dev/null +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-gimkl-2017a.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'ncurses' +version = '6.0' + +homepage = 'http://www.gnu.org/software/ncurses/' +description = """The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, + and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and + function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.""" + +toolchain = {'version': '2017a', 'name': 'gimkl'} +toolchainopts = {'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] + +patches = ['ncurses-%(version)s_gcc-5.patch'] + +configopts = [ + # default build + '--with-shared --enable-overwrite', + # the UTF-8 enabled version (ncursesw) + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses%(version_major)s-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + +moduleclass = 'devel' -- GitLab From af20584806bf6a8daecc635ec7efd99872f68489 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Wed, 7 Jun 2017 15:54:57 +1200 Subject: [PATCH 0893/1603] Easyconfig for zlib 1.2.11 with the gimkl 2017a toolchain --- .../z/zlib/zlib-1.2.11-gimkl-2017a.eb | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.11-gimkl-2017a.eb diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.11-gimkl-2017a.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-gimkl-2017a.eb new file mode 100644 index 0000000000..1362fe53c9 --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-gimkl-2017a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'zlib' +version = '1.2.11' + +homepage = 'http://www.zlib.net/' +description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is, + not covered by any patents -- lossless data-compression library for use on virtually any + computer hardware and operating system.""" + +toolchain = {'version': '2017a', 'name': 'gimkl'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] + +sanity_check_paths = { + 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' -- GitLab From b0a05fb4b685ef205ac36d04c2779d26e0050ffc Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Wed, 7 Jun 2017 16:03:24 +1200 Subject: [PATCH 0894/1603] EasyConfigs for libxml2 2.9.4 and XZ 5.2.3 with the gimkl 2017a toolchain --- .../l/libxml2/libxml2-2.9.4-gimkl-2017a.eb | 23 ++++++++++++++ .../easyconfigs/x/XZ/XZ-5.2.3-gimkl-2017a.eb | 30 +++++++++++++++++++ 2 files changed, 53 insertions(+) create mode 100644 easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-gimkl-2017a.eb create mode 100644 easybuild/easyconfigs/x/XZ/XZ-5.2.3-gimkl-2017a.eb diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-gimkl-2017a.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-gimkl-2017a.eb new file mode 100644 index 0000000000..eaca2fc38e --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-gimkl-2017a.eb @@ -0,0 +1,23 @@ +name = 'libxml2' +version = '2.9.4' + +homepage = 'http://xmlsoft.org/' +description = """Libxml2 is the XML C parser and +toolchain developed for the Gnome project + (but usable outside of the Gnome platform).""" + +toolchain = {'name': 'gimkl', 'version': '2017a'} +toolchainopts = {'pic': True} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('zlib', '1.2.11'), + ('XZ', '5.2.3'), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.3-gimkl-2017a.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.3-gimkl-2017a.eb new file mode 100644 index 0000000000..4b1d474ab3 --- /dev/null +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.3-gimkl-2017a.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'XZ' +version = '5.2.3' + +homepage = 'http://tukaani.org/xz/' +description = "xz: XZ utilities" + +toolchain = {'version': '2017a', 'name': 'gimkl'} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://tukaani.org/xz/'] + +# non-toolchain gettext because otherwise there is a circular dependency: +# XZ (presumably its executables) depends on gettext, which depends on +# xmllib2, which depends (optionally) on XZ +builddependencies = [ + ('Autotools', '20150215', '', True), + ('gettext', '0.19.8', '', True), +] + +# may become useful in non-x86 archs +#configopts = ' --disable-assembler ' + +sanity_check_paths = { + 'files': ["bin/xz", "bin/lzmainfo"], + 'dirs': [] +} + +moduleclass = 'tools' -- GitLab From eb65c292b8dbd6ba7e36cf8d5b394db95bcfcc8a Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Wed, 7 Jun 2017 16:21:10 +1200 Subject: [PATCH 0895/1603] Easyconfig for libreadline 6.3 with the gimkl 2017a toolchain --- .../libreadline-6.3-gimkl-2017a.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/l/libreadline/libreadline-6.3-gimkl-2017a.eb diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-gimkl-2017a.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-gimkl-2017a.eb new file mode 100644 index 0000000000..3c72c2c527 --- /dev/null +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-gimkl-2017a.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'libreadline' +version = '6.3' + +homepage = 'http://cnswww.cns.cwru.edu/php/chet/readline/rltop.html' +description = """The GNU Readline library provides a set of functions for use by applications that + allow users to edit command lines as they are typed in. Both Emacs and vi editing modes are available. + The Readline library includes additional functions to maintain a list of previously-entered command lines, + to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands.""" + +toolchain = {'name': 'gimkl', 'version': '2017a'} +toolchainopts = {'pic': True} + +sources = ['readline-%(version)s.tar.gz'] +source_urls = ['http://ftp.gnu.org/gnu/readline'] + +patches = ['libreadline-%(version)s-bugfix.patch'] + +dependencies = [('ncurses', '6.0')] + +# for the termcap symbols, use EB ncurses +preconfigopts = "env LDFLAGS='-lncurses'" + +sanity_check_paths = { + 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + 'dirs': [], +} + +moduleclass = 'lib' -- GitLab From e7ce769ab6bf187a0cfc09bf03ca3ba3b41d0201 Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Wed, 7 Jun 2017 11:08:50 +0200 Subject: [PATCH 0896/1603] Fix dependency conflicts. --- .../i/ImageMagick/ImageMagick-7.0.5-10-foss-2016b.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.5-10-foss-2016b.eb b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.5-10-foss-2016b.eb index c320486a5a..c287c7aa6f 100644 --- a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.5-10-foss-2016b.eb +++ b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.5-10-foss-2016b.eb @@ -22,8 +22,8 @@ dependencies = [ ('X11', '20160819'), ('Ghostscript', '9.20'), ('JasPer', '2.0.12'), - ('libjpeg-turbo', '1.5.1'), - ('LibTIFF', '4.0.7'), + ('libjpeg-turbo', '1.5.0'), + ('LibTIFF', '4.0.6'), ('LittleCMS', '2.8'), ('FFmpeg', '3.3.1'), ] -- GitLab From 6fa82b503c46b2a8459f9c6c97bed2a3a9ffaae8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 7 Jun 2017 11:51:42 +0200 Subject: [PATCH 0897/1603] add vcfR extension in R 3.4.0 easyconfig --- easybuild/easyconfigs/r/R/R-3.4.0-intel-2017a-X11-20170314.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-3.4.0-intel-2017a-X11-20170314.eb b/easybuild/easyconfigs/r/R/R-3.4.0-intel-2017a-X11-20170314.eb index 94a8307cc4..b17ecb1531 100644 --- a/easybuild/easyconfigs/r/R/R-3.4.0-intel-2017a-X11-20170314.eb +++ b/easybuild/easyconfigs/r/R/R-3.4.0-intel-2017a-X11-20170314.eb @@ -521,6 +521,9 @@ exts_list = [ ('oce', '0.9-21', ext_options), ('ineq', '0.2-13', ext_options), ('soundecology', '1.3.2', ext_options), + ('memuse', '3.0-1', ext_options), + ('pinfsc50', '1.1.0', ext_options), + ('vcfR', '1.5.0', ext_options), ] moduleclass = 'lang' -- GitLab From 6ea80c47ebcdffea6da6b8808252977077bb38a1 Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Wed, 7 Jun 2017 12:26:14 +0200 Subject: [PATCH 0898/1603] Add checksum --- .../i/ImageMagick/ImageMagick-7.0.5-10-foss-2016b.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.5-10-foss-2016b.eb b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.5-10-foss-2016b.eb index c287c7aa6f..495de72aba 100644 --- a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.5-10-foss-2016b.eb +++ b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.5-10-foss-2016b.eb @@ -14,11 +14,10 @@ toolchain = {'name': 'foss', 'version': '2016b'} sources = [SOURCE_TAR_GZ] source_urls = ['https://www.imagemagick.org/download/releases/'] -#checksums = ['473a1e7ae37548eb6fe9cf2b1fb78011'] +checksums = ['43912034c69171882536b359a7b84f9f'] dependencies = [ ('bzip2', '1.0.6'), - #('X11', '20170314'), # Conflicts with FFmpeg ('X11', '20160819'), ('Ghostscript', '9.20'), ('JasPer', '2.0.12'), -- GitLab From fee6089eeb307248d856fc8720c3c39bd225e9e4 Mon Sep 17 00:00:00 2001 From: Robert Date: Thu, 8 Jun 2017 11:45:38 +0930 Subject: [PATCH 0899/1603] {bio}[foss/2016b] --- .../l/LUMPY/LUMPY-0.2.13-foss-2016b.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/l/LUMPY/LUMPY-0.2.13-foss-2016b.eb diff --git a/easybuild/easyconfigs/l/LUMPY/LUMPY-0.2.13-foss-2016b.eb b/easybuild/easyconfigs/l/LUMPY/LUMPY-0.2.13-foss-2016b.eb new file mode 100644 index 0000000000..a301016ab0 --- /dev/null +++ b/easybuild/easyconfigs/l/LUMPY/LUMPY-0.2.13-foss-2016b.eb @@ -0,0 +1,34 @@ +## +# This is a contribution from Phoenix HPC Service, The University of Adelaide, Australia +# Homepage: https://www.adelaide.edu.au/phoenix/ +# +# Copyright:: Copyright 2014-2017 adelaide.edu.au/phoenix +# Authors:: Robert Qiao , Exequiel Sepulveda +# License:: MIT +# +# Notes:: +## + +easyblock = 'MakeCp' + +name = 'LUMPY' +version = '0.2.13' + +homepage = 'https://github.com/arq5x/lumpy-sv' +description = """A probabilistic framework for structural variant discovery. +""" + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/arq5x/lumpy-sv/archive/'] +sources = ['%(version)s.tar.gz'] + +files_to_copy = [(['bin/*'], 'bin'), 'data', 'LICENSE'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['lumpy', 'lumpyexpress']], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From 8a9b2447b271975f6d62bdc24b3659b348720b69 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Thu, 8 Jun 2017 08:48:00 +0200 Subject: [PATCH 0900/1603] Add BEDOPS 2.4.26 easyconfig --- .../easyconfigs/b/BEDOPS/BEDOPS-2.4.26.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/b/BEDOPS/BEDOPS-2.4.26.eb diff --git a/easybuild/easyconfigs/b/BEDOPS/BEDOPS-2.4.26.eb b/easybuild/easyconfigs/b/BEDOPS/BEDOPS-2.4.26.eb new file mode 100644 index 0000000000..79cc3e49ca --- /dev/null +++ b/easybuild/easyconfigs/b/BEDOPS/BEDOPS-2.4.26.eb @@ -0,0 +1,26 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild + +easyblock = 'Tarball' + +name = 'BEDOPS' +version = '2.4.26' + +homepage = 'http://bedops.readthedocs.io/en/latest/index.html' +description = """BEDOPS is an open-source command-line toolkit that performs highly efficient + and scalable Boolean and other set operations, statistical calculations, archiving, conversion + and other management of genomic data of arbitrary scale. Tasks can be easily split by chromosome + for distributing whole-genome analyses across a computational cluster.""" + +sources = ['%(namelower)s_linux_x86_64-v%(version)s.tar.bz2'] +source_urls = ['https://github.com/%(namelower)s/%(namelower)s/releases/download/v%(version)s/'] + +checksums = ['eb39bf1dadd138dff2faa45171f8f78e'] + +sanity_check_paths = { + 'files': ['bam2bed', '%(namelower)s', 'convert2bed', 'unstarch'], + 'dirs': ['.'], +} + +modextrapaths = {'PATH': ''} + +moduleclass = 'bio' -- GitLab From 7e3ce985151b5e28940d4dd87ea01bf3c9e9565f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Thu, 8 Jun 2017 09:19:47 +0200 Subject: [PATCH 0901/1603] Add missing toolchain --- easybuild/easyconfigs/b/BEDOPS/BEDOPS-2.4.26.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/b/BEDOPS/BEDOPS-2.4.26.eb b/easybuild/easyconfigs/b/BEDOPS/BEDOPS-2.4.26.eb index 79cc3e49ca..b96f53227b 100644 --- a/easybuild/easyconfigs/b/BEDOPS/BEDOPS-2.4.26.eb +++ b/easybuild/easyconfigs/b/BEDOPS/BEDOPS-2.4.26.eb @@ -11,6 +11,8 @@ description = """BEDOPS is an open-source command-line toolkit that performs hig and other management of genomic data of arbitrary scale. Tasks can be easily split by chromosome for distributing whole-genome analyses across a computational cluster.""" +toolchain = {'version': 'dummy', 'name': 'dummy'} + sources = ['%(namelower)s_linux_x86_64-v%(version)s.tar.bz2'] source_urls = ['https://github.com/%(namelower)s/%(namelower)s/releases/download/v%(version)s/'] -- GitLab From b4d309369914562cac73f4abba5fd5980c6cf415 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Thu, 8 Jun 2017 09:44:22 +0200 Subject: [PATCH 0902/1603] Add FASTA 36.3.5e foss-2016b --- .../f/FASTA/FASTA-36.3.5e-foss-2016b.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/f/FASTA/FASTA-36.3.5e-foss-2016b.eb diff --git a/easybuild/easyconfigs/f/FASTA/FASTA-36.3.5e-foss-2016b.eb b/easybuild/easyconfigs/f/FASTA/FASTA-36.3.5e-foss-2016b.eb new file mode 100644 index 0000000000..93fe9bd8a4 --- /dev/null +++ b/easybuild/easyconfigs/f/FASTA/FASTA-36.3.5e-foss-2016b.eb @@ -0,0 +1,32 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild + +easyblock = 'MakeCp' + +name = "FASTA" +version = "36.3.5e" + +homepage = 'http://fasta.bioch.virginia.edu' +description = """The FASTA programs find regions of local or global (new) similarity between +protein or DNA sequences, either by searching Protein or DNA databases, or by identifying +local duplications within a sequence.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['http://faculty.virginia.edu/wrpearson/fasta/fasta36'] +sources = [SOURCELOWER_TAR_GZ] + +checksums = ['1c76727b3c61ca36bd19ce4da70c02fe'] + +buildopts = '-C ./src -f ../make/Makefile.linux_sse2 all' + +files_to_copy = ["bin", "conf", "data", "doc", "FASTA_LIST", "misc", "README", "seq", "sql", "test"] + +sanity_check_paths = { + 'files': ["FASTA_LIST", "README"] + ['bin/%s' % x for x in ['lav2svg', 'lav2ps', 'map_db']] + + ['bin/%s%%(version_major)s' % x for x in ['fasta', 'fastm', 'fastx', 'ggsearch', 'lalign', 'tfastf', + 'tfasts', 'tfasty', 'fastf', 'fasts', 'fasty', 'glsearch', + 'ssearch', 'tfastm', 'tfastx']], + 'dirs': ["conf", "data", "doc", "misc", "seq", "sql", "test"] +} + +moduleclass = 'bio' -- GitLab From 15b969586a2b84b0a2fab41e17a5f41c362b1217 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Thu, 8 Jun 2017 10:17:37 +0200 Subject: [PATCH 0903/1603] Add segemehl 0.2.0 foss-2016b --- .../s/segemehl/segemehl-0.2.0-foss-2016b.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/s/segemehl/segemehl-0.2.0-foss-2016b.eb diff --git a/easybuild/easyconfigs/s/segemehl/segemehl-0.2.0-foss-2016b.eb b/easybuild/easyconfigs/s/segemehl/segemehl-0.2.0-foss-2016b.eb new file mode 100644 index 0000000000..7f59d53c66 --- /dev/null +++ b/easybuild/easyconfigs/s/segemehl/segemehl-0.2.0-foss-2016b.eb @@ -0,0 +1,38 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild + +easyblock = 'MakeCp' + +name = "segemehl" +version = "0.2.0" + +homepage = 'http://www.bioinf.uni-leipzig.de/Software/segemehl/' +description = """ segemehl is a software to map short sequencer reads to reference genomes. + Unlike other methods, segemehl is able to detect not only mismatches but also insertions + and deletions. Furthermore, segemehl is not limited to a specific read length and is able + to mapprimer- or polyadenylation contaminated reads correctly. segemehl implements a matching + strategy based on enhanced suffix arrays (ESA). Segemehl now supports the SAM format, reads + gziped queries to save both disk and memory space and allows bisulfite sequencing mapping + and split read mapping. """ + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['http://www.bioinf.uni-leipzig.de/Software/segemehl/'] +sources = ['%s_%s.tar.gz' % (name, version.replace('.','_'))] + +checksums = ['fef4db00ed2742a2bf4131eed674bb08'] + +parallel = 1 + +dependencies = [ + ('ncurses', '5.9'), + ('zlib', '1.2.8'), +] + +files_to_copy = [(["lack.x", "segemehl.x", "testrealign.x"], "bin")] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["lack.x" , "segemehl.x", "testrealign.x"]], + 'dirs': ["."] +} + +moduleclass = 'bio' -- GitLab From c697d989a4751a2cec405ede613df73e3842429f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Thu, 8 Jun 2017 10:25:31 +0200 Subject: [PATCH 0904/1603] Add StringTie 1.3.3b foss-2016b --- .../StringTie/StringTie-1.3.3b-foss-2016b.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/s/StringTie/StringTie-1.3.3b-foss-2016b.eb diff --git a/easybuild/easyconfigs/s/StringTie/StringTie-1.3.3b-foss-2016b.eb b/easybuild/easyconfigs/s/StringTie/StringTie-1.3.3b-foss-2016b.eb new file mode 100644 index 0000000000..d1eb27f7fe --- /dev/null +++ b/easybuild/easyconfigs/s/StringTie/StringTie-1.3.3b-foss-2016b.eb @@ -0,0 +1,25 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild + +easyblock = 'MakeCp' + +name = 'StringTie' +version = "1.3.3b" + +homepage = 'http://ccb.jhu.edu/software/stringtie/' +description = """StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['http://ccb.jhu.edu/software/stringtie/dl/'] +sources = [SOURCELOWER_TAR_GZ] + +checksums = ['8f9ed07ff532a0641cd04b23e27eb547'] + +files_to_copy = [(['stringtie'], 'bin'), 'README', 'LICENSE'] + +sanity_check_paths = { + 'files': ['bin/stringtie'], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From aee428fc62cb76252e4a9bb5a8e3b1580bcf904d Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Thu, 8 Jun 2017 10:49:53 +0200 Subject: [PATCH 0905/1603] adding easyconfigs: DIAMOND-0.9.6-goolf-1.7.20.eb --- .../d/DIAMOND/DIAMOND-0.9.6-goolf-1.7.20.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/d/DIAMOND/DIAMOND-0.9.6-goolf-1.7.20.eb diff --git a/easybuild/easyconfigs/d/DIAMOND/DIAMOND-0.9.6-goolf-1.7.20.eb b/easybuild/easyconfigs/d/DIAMOND/DIAMOND-0.9.6-goolf-1.7.20.eb new file mode 100644 index 0000000000..bc285581b6 --- /dev/null +++ b/easybuild/easyconfigs/d/DIAMOND/DIAMOND-0.9.6-goolf-1.7.20.eb @@ -0,0 +1,32 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = "CMakeMake" + +name = 'DIAMOND' +version = '0.9.6' + +homepage = 'https://github.com/bbuchfink/diamond' +description = """Accelerated BLAST compatible local sequence aligner""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +source_urls = ['https://github.com/bbuchfink/diamond/archive/'] +sources = ['v%(version)s.tar.gz'] + +separate_build_dir = True + +builddependencies = [('CMake', '3.4.3')] + +dependencies = [ + ('zlib', '1.2.8'), +] + +sanity_check_paths = { + 'files': ['bin/diamond'], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From dec1652bd49f3019b46eeb442a0ef37b99b74c9e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Thu, 8 Jun 2017 11:29:47 +0200 Subject: [PATCH 0906/1603] Add requested changes Use ncurses 6.0 instead of 5.9 and empty sanity check directory list instead of current directory. --- easybuild/easyconfigs/s/segemehl/segemehl-0.2.0-foss-2016b.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/segemehl/segemehl-0.2.0-foss-2016b.eb b/easybuild/easyconfigs/s/segemehl/segemehl-0.2.0-foss-2016b.eb index 7f59d53c66..c7d6d5fcae 100644 --- a/easybuild/easyconfigs/s/segemehl/segemehl-0.2.0-foss-2016b.eb +++ b/easybuild/easyconfigs/s/segemehl/segemehl-0.2.0-foss-2016b.eb @@ -24,7 +24,7 @@ checksums = ['fef4db00ed2742a2bf4131eed674bb08'] parallel = 1 dependencies = [ - ('ncurses', '5.9'), + ('ncurses', '6.0'), ('zlib', '1.2.8'), ] @@ -32,7 +32,7 @@ files_to_copy = [(["lack.x", "segemehl.x", "testrealign.x"], "bin")] sanity_check_paths = { 'files': ["bin/%s" % x for x in ["lack.x" , "segemehl.x", "testrealign.x"]], - 'dirs': ["."] + 'dirs': [] } moduleclass = 'bio' -- GitLab From 3a9d057a7240d86e5de526442e819f4e7997aa32 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 8 Jun 2017 11:59:46 +0200 Subject: [PATCH 0907/1603] fix source URL for SQLite 3.8.9 --- easybuild/easyconfigs/s/SQLite/SQLite-3.8.9-foss-2015a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.9-foss-2015a.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.9-foss-2015a.eb index 45f98b9cdb..8c66a0ef4c 100644 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.9-foss-2015a.eb +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.9-foss-2015a.eb @@ -19,7 +19,7 @@ homepage = 'http://www.hwaci.com/sw/sqlite/' description = "SQLite: SQL Database Engine in a C Library" # eg. http://www.hwaci.com/sw/sqlite/2013/sqlite-autoconf-3080100.tar.gz -source_urls = ['http://www.hwaci.com/sw/sqlite/2013'] +source_urls = ['http://www.sqlite.org/2015/'] sources = ['sqlite-autoconf-%s0%s0%s00.tar.gz' % tuple(version.split('.'))] # very weird way to calculate your filename toolchain = {'name': 'foss', 'version': '2015a'} -- GitLab From 080305d7b42b72cc2651ab8e3b3292078671e400 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 8 Jun 2017 12:04:31 +0200 Subject: [PATCH 0908/1603] use cpan.metacpan.org source URLs for Perl extensions, avoid hardcoding versions in source names --- .../p/Perl/Perl-5.22.0-foss-2015a-mt.eb | 517 +++++++++--------- .../p/Perl/Perl-5.22.0-foss-2015a.eb | 516 ++++++++--------- 2 files changed, 519 insertions(+), 514 deletions(-) diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.22.0-foss-2015a-mt.eb b/easybuild/easyconfigs/p/Perl/Perl-5.22.0-foss-2015a-mt.eb index 1311c9dfcc..7b23b1c105 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.22.0-foss-2015a-mt.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.22.0-foss-2015a-mt.eb @@ -22,873 +22,876 @@ sources = [SOURCELOWER_TAR_GZ] exts_list = [ ('Module::Build', '0.4210', { # std module but recent BioPerl needs a recent version for some reason - 'source_tmpl': 'Module-Build-0.4210.tar.gz', - 'source_urls': ['http://www.cpan.org/modules/by-module/Module/LEONT/'], + 'source_tmpl': 'Module-Build-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], }), ('ExtUtils::MakeMaker', '7.04', { - 'source_tmpl': 'ExtUtils-MakeMaker-7.04.tar.gz', - 'source_urls': ['http://www.cpan.org/modules/by-module/ExtUtils/BINGOS/'], + 'source_tmpl': 'ExtUtils-MakeMaker-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], }), ('local::lib', '2.000011', { - 'source_tmpl': 'local-lib-2.000011.tar.gz', - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/E/ET/ETHER/'], - }), + 'source_tmpl': 'local-lib-%(version)s.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/E/ET/ETHER/'], + ):, ('IO::String', '1.08', { - 'source_tmpl': 'IO-String-1.08.tar.gz', + 'source_tmpl': 'IO-String-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS/'], }), ('Data::Stag', '0.14', { - 'source_tmpl': 'Data-Stag-0.14.tar.gz', + 'source_tmpl': 'Data-Stag-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/C/CM/CMUNGALL/'], }), ('DB_File', '1.835', { - 'source_urls': ['http://www.cpan.org/modules/by-module/DB_File/PMQS/'], + 'source_tmpl': 'DB_File-%(version)s.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/P/PM/PMQS/'], }), ('DBI', '1.633', { - 'source_urls': ['http://www.cpan.org/modules/by-module/DBI/TIMB/'], + 'source_tmpl': 'DBI-%(version)s.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/T/TI/TIMB/'], }), ('Sub::Uplevel', '0.25', { - 'source_tmpl': 'Sub-Uplevel-0.25.tar.gz', - 'source_urls': ['http://www.cpan.org/modules/by-module/Sub/DAGOLDEN/'], + 'source_tmpl': 'Sub-Uplevel-%(version)s.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN/'], }), ('Tree::DAG_Node', '1.26', { - 'source_tmpl': 'Tree-DAG_Node-1.26.tgz', - 'source_urls': ['http://www.cpan.org/modules/by-module/Tree/RSAVAGE/'], + 'source_tmpl': 'Tree-DAG_Node-%(version)s.tgz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RS/RSAVAGE/'], }), ('Try::Tiny', '0.22', { - 'source_tmpl': 'Try-Tiny-0.22.tar.gz', - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/D/DO/DOY/'], + 'source_tmpl': 'Try-Tiny-%(version)s.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DO/DOY/'], }), ('Devel::StackTrace', '2.00', { - 'source_tmpl': 'Devel-StackTrace-2.00.tar.gz', + 'source_tmpl': 'Devel-StackTrace-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DR/DROLSKY/'], }), ('Class::Data::Inheritable', '0.08', { - 'source_tmpl': 'Class-Data-Inheritable-0.08.tar.gz', + 'source_tmpl': 'Class-Data-Inheritable-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/T/TM/TMTM/'], }), ('Exception::Class', '1.39', { - 'source_tmpl': 'Exception-Class-1.39.tar.gz', + 'source_tmpl': 'Exception-Class-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DR/DROLSKY/'], }), ('Test::Fatal', '0.014', { - 'source_tmpl': 'Test-Fatal-0.014.tar.gz', - 'source_urls': ['http://www.cpan.org/modules/by-module/Test/RJBS/'], + 'source_tmpl': 'Test-Fatal-%(version)s.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS/'], }), ('Test::NoWarnings', '1.04', { - 'source_tmpl': 'Test-NoWarnings-1.04.tar.gz', + 'source_tmpl': 'Test-NoWarnings-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AD/ADAMK/'], }), ('Test::Deep', '0.117', { - 'source_tmpl': 'Test-Deep-0.117.tar.gz', + 'source_tmpl': 'Test-Deep-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS/'], }), ('Algorithm::Diff', '1.15', { - 'source_tmpl': 'Algorithm-Diff-1.15.tar.gz', + 'source_tmpl': 'Algorithm-Diff-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/N/NE/NEDKONZ/'], }), ('Text::Diff', '1.41', { - 'source_tmpl': 'Text-Diff-1.41.tar.gz', + 'source_tmpl': 'Text-Diff-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/O/OV/OVID/'], }), ('Test::Differences', '0.61', { - 'source_tmpl': 'Test-Differences-0.61.tar.gz', + 'source_tmpl': 'Test-Differences-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/O/OV/OVID/'], }), ('Test::Exception', '0.32', { - 'source_tmpl': 'Test-Exception-0.32.tar.gz', + 'source_tmpl': 'Test-Exception-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AD/ADIE/'], }), ('Test::Warn', '0.30', { - 'source_tmpl': 'Test-Warn-0.30.tar.gz', + 'source_tmpl': 'Test-Warn-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/C/CH/CHORNY/'], }), ('Test::Requires', '0.08', { - 'source_tmpl': 'Test-Requires-0.08.tar.gz', - 'source_urls': ['http://www.cpan.org/modules/by-module/Test/TOKUHIROM/'], + 'source_tmpl': 'Test-Requires-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TOKUHIROM'], }), ('Test::Tester', '0.109', { - 'source_tmpl': 'Test-Tester-0.109.tar.gz', - 'source_urls': ['http://www.cpan.org/modules/by-module/Test/FDALY/'], + 'source_tmpl': 'Test-Tester-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/F/FD/FDALY'], }), ('File::Slurp::Tiny', '0.003', { - 'source_tmpl': 'File-Slurp-Tiny-0.003.tar.gz', + 'source_tmpl': 'File-Slurp-Tiny-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/L/LE/LEONT'], }), ('Params::Util', '1.07', { - 'source_tmpl': 'Params-Util-1.07.tar.gz', + 'source_tmpl': 'Params-Util-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AD/ADAMK/'], }), ('Sub::Install', '0.928', { - 'source_tmpl': 'Sub-Install-0.928.tar.gz', - 'source_urls': ['http://www.cpan.org/modules/by-module/Sub/RJBS/'], + 'source_tmpl': 'Sub-Install-%(version)s.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS/'], }), ('Data::OptList', '0.109', { - 'source_tmpl': 'Data-OptList-0.109.tar.gz', + 'source_tmpl': 'Data-OptList-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS/'], }), ('Sub::Exporter', '0.987', { - 'source_tmpl': 'Sub-Exporter-0.987.tar.gz', + 'source_tmpl': 'Sub-Exporter-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS/'], }), ('Capture::Tiny', '0.30', { - 'source_tmpl': 'Capture-Tiny-0.30.tar.gz', + 'source_tmpl': 'Capture-Tiny-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN/'], }), ('Test::Output', '1.03', { - 'source_tmpl': 'Test-Output-1.03.tar.gz', + 'source_tmpl': 'Test-Output-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/B/BD/BDFOY/'], }), ('Module::Runtime', '0.014', { - 'source_tmpl': 'Module-Runtime-0.014.tar.gz', + 'source_tmpl': 'Module-Runtime-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/Z/ZE/ZEFRAM/'], }), ('Module::Implementation', '0.09', { - 'source_tmpl': 'Module-Implementation-0.09.tar.gz', - 'source_urls': ['http://www.cpan.org/modules/by-module/Module/DROLSKY/'], + 'source_tmpl': 'Module-Implementation-%(version)s.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DR/DROLSKY/'], }), ('List::MoreUtils', '0.413', { - 'source_tmpl': 'List-MoreUtils-0.413.tar.gz', + 'source_tmpl': 'List-MoreUtils-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RE/REHSACK/'], }), ('Package::DeprecationManager', '0.14', { - 'source_tmpl': 'Package-DeprecationManager-0.14.tar.gz', + 'source_tmpl': 'Package-DeprecationManager-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DR/DROLSKY/'], }), ('Dist::CheckConflicts', '0.11', { - 'source_tmpl': 'Dist-CheckConflicts-0.11.tar.gz', + 'source_tmpl': 'Dist-CheckConflicts-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DO/DOY/'], }), ('Package::Stash', '0.37', { - 'source_tmpl': 'Package-Stash-0.37.tar.gz', - 'source_urls': ['http://www.cpan.org/modules/by-module/Package/DOY/'], + 'source_tmpl': 'Package-Stash-%(version)s.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DO/DOY/'], }), ('Class::Load', '0.23', { - 'source_tmpl': 'Class-Load-0.23.tar.gz', + 'source_tmpl': 'Class-Load-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/E/ET/ETHER/'], }), ('TAP::Harness::Env', '3.35', { - 'source_tmpl': 'Test-Harness-3.35.tar.gz', + 'source_tmpl': 'Test-Harness-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/L/LE/LEONT/'], }), ('ExtUtils::Helpers', '0.022', { - 'source_tmpl': 'ExtUtils-Helpers-0.022.tar.gz', + 'source_tmpl': 'ExtUtils-Helpers-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/L/LE/LEONT'], }), ('ExtUtils::Config', '0.008', { - 'source_tmpl': 'ExtUtils-Config-0.008.tar.gz', + 'source_tmpl': 'ExtUtils-Config-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/L/LE/LEONT'], }), ('ExtUtils::InstallPaths', '0.011', { - 'source_tmpl': 'ExtUtils-InstallPaths-0.011.tar.gz', + 'source_tmpl': 'ExtUtils-InstallPaths-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/L/LE/LEONT'], }), ('Module::Build::Tiny', '0.039', { - 'source_tmpl': 'Module-Build-Tiny-0.039.tar.gz', + 'source_tmpl': 'Module-Build-Tiny-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/L/LE/LEONT/'], }), ('MRO::Compat', '0.12', { - 'source_tmpl': 'MRO-Compat-0.12.tar.gz', + 'source_tmpl': 'MRO-Compat-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/B/BO/BOBTFISH/'], }), ('Sub::Name', '0.05', { - 'source_tmpl': 'Sub-Name-0.05.tar.gz', + 'source_tmpl': 'Sub-Name-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/F/FL/FLORA/'], }), ('Eval::Closure', '0.13', { - 'source_tmpl': 'Eval-Closure-0.13.tar.gz', + 'source_tmpl': 'Eval-Closure-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DO/DOY/'], }), ('Sub::Exporter::Progressive', '0.001011', { - 'source_tmpl': 'Sub-Exporter-Progressive-0.001011.tar.gz', + 'source_tmpl': 'Sub-Exporter-Progressive-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/F/FR/FREW/'], }), ('Devel::GlobalDestruction', '0.13', { - 'source_tmpl': 'Devel-GlobalDestruction-0.13.tar.gz', - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/H/HA/HAARG/'], + 'source_tmpl': 'Devel-GlobalDestruction-%(version)s.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/H/HA/HAARG/'], }), ('boolean', '0.45', { - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/I/IN/INGY/'], + 'source_tmpl': 'boolean-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IN/INGY'], }), ('Tie::IxHash', '1.23', { - 'source_tmpl': 'Tie-IxHash-1.23.tar.gz', + 'source_tmpl': 'Tie-IxHash-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/C/CH/CHORNY/'], }), ('Moose', '2.1405', { - 'source_urls': ['http://www.cpan.org/modules/by-module/MooseX/ETHER/'], + 'source_tmpl': 'Moose-%(version)s.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/E/ET/ETHER/'], }), ('Package::Stash::XS', '0.28', { - 'source_tmpl': 'Package-Stash-XS-0.28.tar.gz', + 'source_tmpl': 'Package-Stash-XS-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DO/DOY/'], }), ('Params::Validate', '1.20', { - 'source_tmpl': 'Params-Validate-1.20.tar.gz', - 'source_urls': ['http://www.cpan.org/modules/by-module/Params/DROLSKY/'], + 'source_tmpl': 'Params-Validate-%(version)s.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DR/DROLSKY/'], }), ('Class::Load::XS', '0.09', { - 'source_tmpl': 'Class-Load-XS-0.09.tar.gz', + 'source_tmpl': 'Class-Load-XS-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/E/ET/ETHER/'], }), - # For uoa00001, Zendesk #9076 ('Math::CDF', '0.1', { - 'source_tmpl': 'Math-CDF-0.1.tar.gz', - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/C/CA/CALLAHAN/'], + 'source_tmpl': 'Math-CDF-%(version)s.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/C/CA/CALLAHAN/'], }), - ('DateTime::Locale', '0.46', { - 'source_tmpl': 'DateTime-Locale-0.46.tar.gz', + 'source_tmpl': 'DateTime-Locale-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DR/DROLSKY/'], }), ('Class::Singleton', '1.4', { - 'source_tmpl': 'Class-Singleton-1.4.tar.gz', + 'source_tmpl': 'Class-Singleton-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AB/ABW/'], }), ('DateTime::TimeZone', '1.92', { - 'source_tmpl': 'DateTime-TimeZone-1.92.tar.gz', - 'source_urls': ['http://www.cpan.org/modules/by-module/DateTime/DROLSKY/'], + 'source_tmpl': 'DateTime-TimeZone-%(version)s.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DR/DROLSKY/'], }), ('Test::Warnings', '0.021', { - 'source_tmpl': 'Test-Warnings-0.021.tar.gz', + 'source_tmpl': 'Test-Warnings-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/E/ET/ETHER/'], }), ('Data::Types', '0.09', { - 'source_tmpl': 'Data-Types-0.09.tar.gz', + 'source_tmpl': 'Data-Types-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DW/DWHEELER/'], }), ('Exporter::Tiny', '0.042', { - 'source_tmpl': 'Exporter-Tiny-0.042.tar.gz', + 'source_tmpl': 'Exporter-Tiny-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/T/TO/TOBYINK/'], }), - ('List::AllUtils', '0.09', { - 'source_tmpl': 'List-AllUtils-0.09.tar.gz', + 'source_tmpl': 'List-AllUtils-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DR/DROLSKY/'], }), ('DateTime', '1.20', { - 'source_urls': ['http://www.cpan.org/modules/by-module/DateTime/DROLSKY/'], + 'source_tmpl': 'DateTime-%(version)s.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DR/DROLSKY/'], }), ('DateTime::Tiny', '1.04', { - 'source_tmpl': 'DateTime-Tiny-1.04.tar.gz', + 'source_tmpl': 'DateTime-Tiny-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AD/ADAMK/'], }), ('File::Slurp', '9999.19', { - 'source_tmpl': 'File-Slurp-9999.19.tar.gz', + 'source_tmpl': 'File-Slurp-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/U/UR/URI/'], }), ('HTTP::Date', '6.02', { - 'source_tmpl': 'HTTP-Date-6.02.tar.gz', + 'source_tmpl': 'HTTP-Date-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS/'], }), ('IO::HTML', '1.001', { - 'source_tmpl': 'IO-HTML-1.001.tar.gz', - 'source_urls': ['http://www.cpan.org/modules/by-module/IO/CJM/'], + 'source_tmpl': 'IO-HTML-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CJ/CJM'], }), ('LWP::MediaTypes', '6.02', { - 'source_tmpl': 'LWP-MediaTypes-6.02.tar.gz', + 'source_tmpl': 'LWP-MediaTypes-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS/'], }), ('URI', '1.69', { - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/E/ET/ETHER/'], + 'source_tmpl': 'URI-%(version)s.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/E/ET/ETHER/'], }), ('Encode::Locale', '1.05', { - 'source_tmpl': 'Encode-Locale-1.05.tar.gz', + 'source_tmpl': 'Encode-Locale-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS/'], }), ('HTTP::Request', '6.06', { - 'source_tmpl': 'HTTP-Message-6.06.tar.gz', + 'source_tmpl': 'HTTP-Message-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS/'], }), ('HTML::Tagset', '3.20', { - 'source_tmpl': 'HTML-Tagset-3.20.tar.gz', + 'source_tmpl': 'HTML-Tagset-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/P/PE/PETDANCE/'], }), ('HTML::Entities', '3.71', { - 'source_tmpl': 'HTML-Parser-3.71.tar.gz', + 'source_tmpl': 'HTML-Parser-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS/'], }), ('File::Listing', '6.04', { - 'source_tmpl': 'File-Listing-6.04.tar.gz', - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/G/GA/GAAS/'], + 'source_tmpl': 'File-Listing-%(version)s.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS/'], }), ('AnyEvent', '7.09', { + 'source_tmpl': 'AnyEvent-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/M/ML/MLEHMANN/'], }), ('Devel::CheckCompiler', '0.06', { - 'source_tmpl': 'Devel-CheckCompiler-0.06.tar.gz', + 'source_tmpl': 'Devel-CheckCompiler-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/S/SY/SYOHEX'], }), ('File::Copy::Recursive', '0.38', { - 'source_tmpl': 'File-Copy-Recursive-0.38.tar.gz', + 'source_tmpl': 'File-Copy-Recursive-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DM/DMUEY/'], }), ('Cwd::Guard', '0.04', { - 'source_tmpl': 'Cwd-Guard-0.04.tar.gz', + 'source_tmpl': 'Cwd-Guard-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/K/KA/KAZEBURO'], }), ('Module::Build::XSUtil', '0.16', { - 'source_tmpl': 'Module-Build-XSUtil-0.16.tar.gz', + 'source_tmpl': 'Module-Build-XSUtil-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/H/HI/HIDEAKIO/'], }), ('LWP', '6.13', { - 'source_tmpl': 'libwww-perl-6.13.tar.gz', - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/E/ET/ETHER/'], + 'source_tmpl': 'libwww-perl-%(version)s.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/E/ET/ETHER/'], }), ('Fennec::Lite', '0.004', { - 'source_tmpl': 'Fennec-Lite-0.004.tar.gz', + 'source_tmpl': 'Fennec-Lite-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/E/EX/EXODIST/'], }), ('aliased', '0.31', { + 'source_tmpl': 'aliased-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/O/OV/OVID/'], }), ('Meta::Builder', '0.003', { - 'source_tmpl': 'Meta-Builder-0.003.tar.gz', + 'source_tmpl': 'Meta-Builder-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/E/EX/EXODIST/'], }), ('Exporter::Declare', '0.114', { - 'source_tmpl': 'Exporter-Declare-0.114.tar.gz', + 'source_tmpl': 'Exporter-Declare-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/E/EX/EXODIST/'], }), ('Mock::Quick', '1.108', { - 'source_tmpl': 'Mock-Quick-1.108.tar.gz', + 'source_tmpl': 'Mock-Quick-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/E/EX/EXODIST/'], }), ('Test::Exception::LessClever', '0.006', { - 'source_tmpl': 'Test-Exception-LessClever-0.006.tar.gz', + 'source_tmpl': 'Test-Exception-LessClever-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/E/EX/EXODIST/'], }), ('Test::LeakTrace', '0.15', { - 'source_tmpl': 'Test-LeakTrace-0.15.tar.gz', + 'source_tmpl': 'Test-LeakTrace-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GF/GFUJI/'], }), ('Mouse', '2.4.2', { + 'source_tmpl': 'Mouse-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GF/GFUJI/'], }), ('XML::NamespaceSupport', '1.11', { - 'source_tmpl': 'XML-NamespaceSupport-1.11.tar.gz', + 'source_tmpl': 'XML-NamespaceSupport-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/P/PE/PERIGRIN/'], }), ('XML::SAX::Base', '1.08', { - 'source_tmpl': 'XML-SAX-Base-1.08.tar.gz', + 'source_tmpl': 'XML-SAX-Base-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GR/GRANTM/'], }), ('XML::SAX', '0.99', { - 'source_tmpl': 'XML-SAX-0.99.tar.gz', + 'source_tmpl': 'XML-SAX-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GR/GRANTM/'], }), ('XML::LibXML', '2.0121', { - 'source_tmpl': 'XML-LibXML-2.0121.tar.gz', - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/S/SH/SHLOMIF/'], + 'source_tmpl': 'XML-LibXML-%(version)s.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/S/SH/SHLOMIF/'], }), ('Clone', '0.38', { - 'source_tmpl': 'Clone-0.38.tar.gz', + 'source_tmpl': 'Clone-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GARU'], }), ('Config::General', '2.58', { - 'source_tmpl': 'Config-General-2.58.tar.gz', + 'source_tmpl': 'Config-General-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/T/TL/TLINDEN'], }), ('Test::Simple', '0.98', { - 'source_tmpl': 'Test-Simple-0.98_05.tar.gz', + 'source_tmpl': 'Test-Simple-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/M/MS/MSCHWERN'], }), ('Font::TTF', '1.05', { - 'source_tmpl': 'Font-TTF-1.05.tar.gz', + 'source_tmpl': 'Font-TTF-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/M/MH/MHOSKEN'], }), ('IO::Tty', '1.12', { - 'source_tmpl': 'IO-Tty-1.12.tar.gz', + 'source_tmpl': 'IO-Tty-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/T/TO/TODDR'], }), ('Math::Bezier', '0.01', { - 'source_tmpl': 'Math-Bezier-0.01.tar.gz', + 'source_tmpl': 'Math-Bezier-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AB/ABW'], }), ('IPC::Run', '0.94', { - 'source_tmpl': 'IPC-Run-0.94.tar.gz', + 'source_tmpl': 'IPC-Run-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/T/TO/TODDR'], }), ('Math::Round', '0.07', { - 'source_tmpl': 'Math-Round-0.07.tar.gz', + 'source_tmpl': 'Math-Round-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GR/GROMMEL'], }), ('B::LintSubs', '0.06', { - 'source_tmpl': 'B-LintSubs-0.06.tar.gz', + 'source_tmpl': 'B-LintSubs-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/P/PE/PEVANS'], }), ('Math::VecStat', '0.08', { - 'source_tmpl': 'Math-VecStat-0.08.tar.gz', + 'source_tmpl': 'Math-VecStat-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AS/ASPINELLI'], }), ('Test::Most', '0.34', { - 'source_tmpl': 'Test-Most-0.34.tar.gz', + 'source_tmpl': 'Test-Most-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/O/OV/OVID/'], }), ('Readonly', '1.04', { - 'source_tmpl': 'Readonly-1.04.tar.gz', + 'source_tmpl': 'Readonly-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/S/SA/SANKO/'], }), ('Regexp::Common', '2013031301', { - 'source_tmpl': 'Regexp-Common-2013031301.tar.gz', + 'source_tmpl': 'Regexp-Common-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AB/ABIGAIL'], }), ('Want', '0.26', { - 'source_tmpl': 'Want-0.26.tar.gz', - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/R/RO/ROBIN/'], + 'source_tmpl': 'Want-%(version)s.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RO/ROBIN/'], }), ('DBD::SQLite', '1.48', { - 'source_tmpl': 'DBD-SQLite-1.48.tar.gz', - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/I/IS/ISHIGAKI/'], + 'source_tmpl': 'DBD-SQLite-%(version)s.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/I/IS/ISHIGAKI/'], }), ('Set::IntSpan', '1.19', { - 'source_tmpl': 'Set-IntSpan-1.19.tar.gz', + 'source_tmpl': 'Set-IntSpan-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/S/SW/SWMCD'], }), ('forks', '0.36', { - 'source_tmpl': 'forks-0.36.tar.gz', - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/R/RY/RYBSKEJ/'], + 'source_tmpl': 'forks-%(version)s.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RY/RYBSKEJ/'], }), ('File::Which', '1.09', { - 'source_tmpl': 'File-Which-1.09.tar.gz', - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/A/AD/ADAMK/'], + 'source_tmpl': 'File-Which-%(version)s.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AD/ADAMK/'], }), - ('Perl::Unsafe::Signals', '', { - 'source_tmpl': 'Perl-Unsafe-Signals-0.02.tar.gz', - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/R/RG/RGARCIA/'], + ('Perl::Unsafe::Signals', '0.02', { + 'source_tmpl': 'Perl-Unsafe-Signals-%(version)s.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RG/RGARCIA/'], }), ('Bit::Vector', '7.4', { - 'source_tmpl': 'Bit-Vector-7.4.tar.gz', - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/S/ST/STBEY/'], + 'source_tmpl': 'Bit-Vector-%(version)s.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/S/ST/STBEY/'], }), ('Parse::RecDescent', '1.967009', { - 'source_tmpl': 'Parse-RecDescent-1.967009.tar.gz', - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/J/JT/JTBRAUN/'], + 'source_tmpl': 'Parse-RecDescent-%(version)s.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/J/JT/JTBRAUN/'], }), ('Inline', '0.80', { - 'source_tmpl': 'Inline-0.80.tar.gz', - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/I/IN/INGY/'], + 'source_tmpl': 'Inline-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IN/INGY'], }), ('File::ShareDir::Install', '0.10', { - 'source_tmpl': 'File-ShareDir-Install-0.10.tar.gz', - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/G/GW/GWYN/'], + 'source_tmpl': 'File-ShareDir-Install-%(version)s.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GW/GWYN/'], }), ('Inline::C', '0.76', { - 'source_tmpl': 'Inline-C-0.76.tar.gz', - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/I/IN/INGY/'], + 'source_tmpl': 'Inline-C-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IN/INGY'], }), ('IO::All', '0.85', { - 'source_tmpl': 'IO-All-0.85.tar.gz', - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/F/FR/FREW/'], + 'source_tmpl': 'IO-All-%(version)s.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/F/FR/FREW/'], }), ('IO::Prompt', '0.997002', { - 'source_tmpl': 'IO-Prompt-0.997002.tar.gz', - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/D/DC/DCONWAY/'], + 'source_tmpl': 'IO-Prompt-%(version)s.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DC/DCONWAY/'], }), ('Getopt::Long', '2.47', { - 'source_tmpl': 'Getopt-Long-2.47.tar.gz', + 'source_tmpl': 'Getopt-Long-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/J/JV/JV/'], }), ('AppConfig', '1.66', { + 'source_tmpl': 'AppConfig-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AB/ABW/'], }), ('Archive::Extract', '0.76', { - 'source_tmpl': 'Archive-Extract-0.76.tar.gz', + 'source_tmpl': 'Archive-Extract-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/B/BI/BINGOS/'], }), ('Archive::Tar', '2.08', { - 'source_tmpl': 'Archive-Tar-2.08.tar.gz', + 'source_tmpl': 'Archive-Tar-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/B/BI/BINGOS/'], }), ('Archive::Zip', '1.57', { - 'source_tmpl': 'Archive-Zip-1.57.tar.gz', - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/P/PH/PHRED/'], + 'source_tmpl': 'Archive-Zip-%(version)s.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/P/PH/PHRED/'], }), ('Authen::SASL', '2.16', { - 'source_tmpl': 'Authen-SASL-2.16.tar.gz', + 'source_tmpl': 'Authen-SASL-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GB/GBARR/'], }), ('B::Lint', '1.20', { - 'source_tmpl': 'B-Lint-1.20.tar.gz', + 'source_tmpl': 'B-Lint-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS/'], }), # BioPerl bundle was here ('Class::Accessor', '0.34', { - 'source_tmpl': 'Class-Accessor-0.34.tar.gz', + 'source_tmpl': 'Class-Accessor-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/K/KA/KASEI/'], }), ('Class::DBI', '3.0.17', { - 'source_tmpl': 'Class-DBI-v3.0.17.tar.gz', + 'source_tmpl': 'Class-DBI-v%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/T/TM/TMTM/'], }), ('Class::Inspector', '1.28', { - 'source_tmpl': 'Class-Inspector-1.28.tar.gz', + 'source_tmpl': 'Class-Inspector-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AD/ADAMK/'], }), ('Class::ISA', '0.36', { - 'source_tmpl': 'Class-ISA-0.36.tar.gz', + 'source_tmpl': 'Class-ISA-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/S/SM/SMUELLER/'], }), ('Class::Trigger', '0.14', { - 'source_tmpl': 'Class-Trigger-0.14.tar.gz', + 'source_tmpl': 'Class-Trigger-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA/'], }), ('CPANPLUS', '0.9154', { + 'source_tmpl': 'CPANPLUS-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/B/BI/BINGOS/'], }), ('Data::Grove', '0.08', { - 'source_tmpl': 'libxml-perl-0.08.tar.gz', + 'source_tmpl': 'libxml-perl-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/K/KM/KMACLEOD/'], }), ('Data::UUID', '1.220', { - 'source_tmpl': 'Data-UUID-1.220.tar.gz', + 'source_tmpl': 'Data-UUID-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS/'], }), ('Date::Language', '2.30', { - 'source_tmpl': 'TimeDate-2.30.tar.gz', + 'source_tmpl': 'TimeDate-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GB/GBARR/'], }), ('Date::Handler', '1.2', { - 'source_tmpl': 'Date-Handler-1.2.tar.gz', + 'source_tmpl': 'Date-Handler-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/B/BB/BBEAUSEJ/'], }), ('SQL::Statement', '1.407', { - 'source_tmpl': 'SQL-Statement-1.407.tar.gz', + 'source_tmpl': 'SQL-Statement-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RE/REHSACK/'], }), ('Module::Pluggable', '5.1', { - 'source_tmpl': 'Module-Pluggable-5.1.tar.gz', + 'source_tmpl': 'Module-Pluggable-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/S/SI/SIMONW/'], }), ('Digest::HMAC', '1.03', { - 'source_tmpl': 'Digest-HMAC-1.03.tar.gz', + 'source_tmpl': 'Digest-HMAC-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS/'], }), ('Digest::SHA1', '2.13', { - 'source_tmpl': 'Digest-SHA1-2.13.tar.gz', + 'source_tmpl': 'Digest-SHA1-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS/'], }), ('Email::Date::Format', '1.005', { - 'source_tmpl': 'Email-Date-Format-1.005.tar.gz', + 'source_tmpl': 'Email-Date-Format-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS/'], }), ('Error', '0.17024', { + 'source_tmpl': 'Error-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/S/SH/SHLOMIF/'], }), ('Expect', '1.21', { + 'source_tmpl': 'Expect-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RG/RGIERSIG/'], }), ('File::CheckTree', '4.42', { - 'source_tmpl': 'File-CheckTree-4.42.tar.gz', + 'source_tmpl': 'File-CheckTree-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS/'], }), ('FreezeThaw', '0.5001', { 'source_urls': ['http://cpan.metacpan.org/authors/id/I/IL/ILYAZ/modules/'], }), ('Git', '0.41', { - 'source_tmpl': 'Git-0.41.tar.gz', + 'source_tmpl': 'Git-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/M/MS/MSOUTH/'], }), ('GO::Utils', '0.15', { - 'source_tmpl': 'go-perl-0.15.tar.gz', + 'source_tmpl': 'go-perl-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/C/CM/CMUNGALL/'], }), ('GO', '0.04', { - 'source_tmpl': 'go-db-perl-0.04.tar.gz', + 'source_tmpl': 'go-db-perl-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/S/SJ/SJCARBON/'], }), ('HTML::Form', '6.03', { - 'source_tmpl': 'HTML-Form-6.03.tar.gz', + 'source_tmpl': 'HTML-Form-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS/'], }), ('HTTP::Cookies', '6.01', { - 'source_tmpl': 'HTTP-Cookies-6.01.tar.gz', + 'source_tmpl': 'HTTP-Cookies-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS/'], }), ('HTTP::Daemon', '6.01', { - 'source_tmpl': 'HTTP-Daemon-6.01.tar.gz', + 'source_tmpl': 'HTTP-Daemon-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS/'], }), ('HTTP::Negotiate', '6.01', { - 'source_tmpl': 'HTTP-Negotiate-6.01.tar.gz', + 'source_tmpl': 'HTTP-Negotiate-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS/'], }), ('IO::Stringy', '2.111', { - 'source_tmpl': 'IO-stringy-2.111.tar.gz', + 'source_tmpl': 'IO-stringy-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DS/DSKOLL/'], }), ('IO::Socket::SSL', '2.016', { - 'source_tmpl': 'IO-Socket-SSL-2.016.tar.gz', + 'source_tmpl': 'IO-Socket-SSL-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/S/SU/SULLR/'], }), ('JSON', '2.90', { + 'source_tmpl': 'JSON-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/M/MA/MAKAMAKA/'], }), ('Log::Message', '0.08', { - 'source_tmpl': 'Log-Message-0.08.tar.gz', + 'source_tmpl': 'Log-Message-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/B/BI/BINGOS/'], }), ('Log::Message::Simple', '0.10', { - 'source_tmpl': 'Log-Message-Simple-0.10.tar.gz', + 'source_tmpl': 'Log-Message-Simple-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/B/BI/BINGOS/'], }), ('Mail::Util', '2.14', { - 'source_tmpl': 'MailTools-2.14.tar.gz', + 'source_tmpl': 'MailTools-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/M/MA/MARKOV/'], }), ('MIME::Types', '2.11', { - 'source_tmpl': 'MIME-Types-2.11.tar.gz', + 'source_tmpl': 'MIME-Types-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/M/MA/MARKOV/'], }), ('MIME::Lite', '3.030', { - 'source_tmpl': 'MIME-Lite-3.030.tar.gz', + 'source_tmpl': 'MIME-Lite-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS/'], }), ('Net::HTTP', '6.06', { - 'source_tmpl': 'Net-HTTP-6.06.tar.gz', + 'source_tmpl': 'Net-HTTP-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS/'], }), ('Net::SMTP::SSL', '1.01', { - 'source_tmpl': 'Net-SMTP-SSL-1.01.tar.gz', + 'source_tmpl': 'Net-SMTP-SSL-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/C/CW/CWEST/'], }), ('Object::Accessor', '0.48', { - 'source_tmpl': 'Object-Accessor-0.48.tar.gz', + 'source_tmpl': 'Object-Accessor-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/B/BI/BINGOS/'], }), ('Pod::LaTeX', '0.61', { - 'source_tmpl': 'Pod-LaTeX-0.61.tar.gz', + 'source_tmpl': 'Pod-LaTeX-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/T/TJ/TJENNESS/'], }), ('Pod::Plainer', '1.04', { - 'source_tmpl': 'Pod-Plainer-1.04.tar.gz', + 'source_tmpl': 'Pod-Plainer-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RM/RMBARKER/'], }), ('Pod::POM', '0.29', { - 'source_tmpl': 'Pod-POM-0.29.tar.gz', + 'source_tmpl': 'Pod-POM-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AN/ANDREWF/'], }), ('Shell', '0.72', { 'source_urls': ['http://cpan.metacpan.org/authors/id/F/FE/FERREIRA/'], }), ('Statistics::Descriptive', '3.0609', { - 'source_tmpl': 'Statistics-Descriptive-3.0609.tar.gz', + 'source_tmpl': 'Statistics-Descriptive-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/S/SH/SHLOMIF/'], }), ('Switch', '2.17', { + 'source_tmpl': 'Switch-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/C/CH/CHORNY/'], }), ('Template', '2.26', { - 'source_tmpl': 'Template-Toolkit-2.26.tar.gz', + 'source_tmpl': 'Template-Toolkit-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AB/ABW/'], }), ('Term::UI', '0.46', { - 'source_tmpl': 'Term-UI-0.46.tar.gz', + 'source_tmpl': 'Term-UI-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/B/BI/BINGOS/'], }), ('Text::Iconv', '1.7', { - 'source_tmpl': 'Text-Iconv-1.7.tar.gz', + 'source_tmpl': 'Text-Iconv-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/M/MP/MPIOTR/'], }), ('Text::Soundex', '3.04', { - 'source_tmpl': 'Text-Soundex-3.04.tar.gz', + 'source_tmpl': 'Text-Soundex-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS/'], }), ('Time::Piece', '1.30', { - 'source_tmpl': 'Time-Piece-1.30.tar.gz', + 'source_tmpl': 'Time-Piece-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS/'], }), ('Time::Piece::MySQL', '0.06', { - 'source_tmpl': 'Time-Piece-MySQL-0.06.tar.gz', + 'source_tmpl': 'Time-Piece-MySQL-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/K/KA/KASEI/'], }), ('UNIVERSAL::moniker', '0.08', { - 'source_tmpl': 'UNIVERSAL-moniker-0.08.tar.gz', + 'source_tmpl': 'UNIVERSAL-moniker-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/K/KA/KASEI/'], }), ('version', '0.9912', { 'source_urls': ['http://cpan.metacpan.org/authors/id/J/JP/JPEACOCK/'], }), ('WWW::RobotRules', '6.02', { - 'source_tmpl': 'WWW-RobotRules-6.02.tar.gz', + 'source_tmpl': 'WWW-RobotRules-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS/'], }), ('XML::SAX::Writer', '0.56', { - 'source_tmpl': 'XML-SAX-Writer-0.56.tar.gz', + 'source_tmpl': 'XML-SAX-Writer-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/P/PE/PERIGRIN/'], }), ('XML::Simple', '2.20', { - 'source_tmpl': 'XML-Simple-2.20.tar.gz', + 'source_tmpl': 'XML-Simple-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GR/GRANTM/'], }), ('XML::XPath', '1.13', { - 'source_tmpl': 'XML-XPath-1.13.tar.gz', + 'source_tmpl': 'XML-XPath-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/M/MS/MSERGEANT/'], }), ('DBD::AnyData', '0.110', { - 'source_tmpl': 'DBD-AnyData-0.110.tar.gz', + 'source_tmpl': 'DBD-AnyData-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RE/REHSACK/'], }), ('Ima::DBI', '0.35', { - 'source_tmpl': 'Ima-DBI-0.35.tar.gz', + 'source_tmpl': 'Ima-DBI-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/P/PE/PERRIN/'], }), ('DBIx::ContextualFetch', '1.03', { - 'source_tmpl': 'DBIx-ContextualFetch-1.03.tar.gz', + 'source_tmpl': 'DBIx-ContextualFetch-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/T/TM/TMTM/'], }), ('DBIx::Simple', '1.35', { - 'source_tmpl': 'DBIx-Simple-1.35.tar.gz', + 'source_tmpl': 'DBIx-Simple-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/J/JU/JUERD/'], }), ('Term::ReadKey', '2.32', { - 'source_tmpl': 'TermReadKey-2.32.tar.gz', + 'source_tmpl': 'TermReadKey-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/J/JS/JSTOWE/'], 'patches': ['TermReadKey-2.32.patch'], }), ('Moo', '2.000001', { - 'source_tmpl': 'Moo-2.000001.tar.gz', + 'source_tmpl': 'Moo-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/H/HA/HAARG/'], }), ('strictures', '2.000001', { - 'source_tmpl': 'strictures-2.000001.tar.gz', + 'source_tmpl': 'strictures-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/H/HA/HAARG/'], }), ('File::Find::Rule::Perl', '1.13', { - 'source_tmpl': 'File-Find-Rule-Perl-1.13.tar.gz', + 'source_tmpl': 'File-Find-Rule-Perl-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AD/ADAMK/'], }), ('Test::Version', '1.002004', { - 'source_tmpl': 'Test-Version-1.002004.tar.gz', + 'source_tmpl': 'Test-Version-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/X/XE/XENO/'], }), ('Test::Harness', '3.35', { - 'source_tmpl': 'Test-Harness-3.35.tar.gz', + 'source_tmpl': 'Test-Harness-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/L/LE/LEONT/'], }), ('Import::Into', '1.002004', { - 'source_tmpl': 'Import-Into-1.002004.tar.gz', + 'source_tmpl': 'Import-Into-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/E/ET/ETHER/'], }), ('File::Find::Rule', '0.33', { - 'source_tmpl': 'File-Find-Rule-0.33.tar.gz', + 'source_tmpl': 'File-Find-Rule-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RC/RCLAMP/'], }), ('Data::Section::Simple', '0.07', { - 'source_tmpl': 'Data-Section-Simple-0.07.tar.gz', + 'source_tmpl': 'Data-Section-Simple-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA/'], }), ('Text::Glob', '0.09', { - 'source_tmpl': 'Text-Glob-0.09.tar.gz', + 'source_tmpl': 'Text-Glob-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RC/RCLAMP/'], }), ('Number::Compare', '0.03', { - 'source_tmpl': 'Number-Compare-0.03.tar.gz', + 'source_tmpl': 'Number-Compare-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RC/RCLAMP/'], }), ('IPC::Run3', '0.048', { - 'source_tmpl': 'IPC-Run3-0.048.tar.gz', + 'source_tmpl': 'IPC-Run3-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS/'], }), ('Set::Array', '0.30', { - 'source_tmpl': 'Set-Array-0.30.tgz', + 'source_tmpl': 'Set-Array-%(version)s.tgz', 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RS/RSAVAGE/'], }), ('Bundle::BioPerl', '2.1.9', { - 'source_tmpl': 'Bundle-BioPerl-2.1.9.tar.gz', + 'source_tmpl': 'Bundle-BioPerl-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS/'], }), - ('Algorithm::Munkres', '0.08', { - 'source_tmpl': 'Algorithm-Munkres-0.08.tar.gz', + 'source_tmpl': 'Algorithm-Munkres-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/T/TP/TPEDERSE/'], }), -# Lots of deps: Carp, Types::Standard etc. -# ('Array::Compare', '2.11', { -# 'source_tmpl': 'Array-Compare-2.11.tar.gz', -# 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DA/DAVECROSS/'], -# }), ('Graph', '0.96', { + 'source_tmpl': 'Graph-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/J/JH/JHI/'], }), ('Set::Scalar', '1.29', { - 'source_tmpl': 'Set-Scalar-1.29.tar.gz', + 'source_tmpl': 'Set-Scalar-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DA/DAVIDO/'], }), - ('CGI', '4.21', { - 'source_tmpl': 'CGI-4.21.tar.gz', + 'source_tmpl': 'CGI-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/L/LE/LEEJO/'], }), ('Bio::Phylo', '0.58', { - 'source_tmpl': 'Bio-Phylo-0.58.tar.gz', + 'source_tmpl': 'Bio-Phylo-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RV/RVOSA/'], }), -# ('GD', '2.56', { -# 'source_urls': 'http://cpan.metacpan.org/authors/id/L/LD/LDS/'], -# }), ('SVG', '2.64', { + 'source_tmpl': 'SVG-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/S/SZ/SZABGAB/'], }), ('XML::DOM', '1.44', { - 'source_tmpl': 'XML-DOM-1.44.tar.gz', + 'source_tmpl': 'XML-DOM-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/T/TJ/TJMATHER/'], }), ('XML::DOM::XPath', '0.14', { - 'source_tmpl': 'XML-DOM-XPath-0.14.tar.gz', + 'source_tmpl': 'XML-DOM-XPath-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/M/MI/MIROD/'], }), ('XML::Parser::PerlSAX', '0.08', { - 'source_tmpl': 'libxml-perl-0.08.tar.gz', + 'source_tmpl': 'libxml-perl-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/K/KM/KMACLEOD/'], }), ('XML::Parser', '2.44', { - 'source_tmpl': 'XML-Parser-2.44.tar.gz', + 'source_tmpl': 'XML-Parser-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/T/TO/TODDR/'], }), ('XML::Twig', '3.49', { - 'source_tmpl': 'XML-Twig-3.49.tar.gz', + 'source_tmpl': 'XML-Twig-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/M/MI/MIROD/'], }), ('XML::Writer', '0.625', { - 'source_tmpl': 'XML-Writer-0.625.tar.gz', + 'source_tmpl': 'XML-Writer-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/J/JO/JOSEPHW/'], }), ('XML::DOM', '1.44', { - 'source_tmpl': 'XML-DOM-1.44.tar.gz', + 'source_tmpl': 'XML-DOM-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/T/TJ/TJMATHER/'], }), ('Spreadsheet::ParseExcel', '0.65', { - 'source_tmpl': 'Spreadsheet-ParseExcel-0.65.tar.gz', + 'source_tmpl': 'Spreadsheet-ParseExcel-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DO/DOUGW/'], }), ('XML::DOM::XPath', '0.14', { - 'source_tmpl': 'XML-DOM-XPath-0.14.tar.gz', + 'source_tmpl': 'XML-DOM-XPath-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/M/MI/MIROD/'], }), ('Convert::Binary::C', '0.77', { - 'source_tmpl': 'Convert-Binary-C-0.77.tar.gz', + 'source_tmpl': 'Convert-Binary-C-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/M/MH/MHX/'], }), ('Sys::SigAction.pm', '0.21', { - 'source_tmpl': 'Sys-SigAction-0.21.tar.gz', - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/L/LB/LBAXTER/'], + 'source_tmpl': 'Sys-SigAction-%(version)s.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/L/LB/LBAXTER/'], }), ('Acme::Damn', '0.06', { - 'source_tmpl': 'Acme-Damn-0.06.tar.gz', - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/I/IB/IBB/'], + 'source_tmpl': 'Acme-Damn-%(version)s.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/I/IB/IBB/'], }), ('Set::IntervalTree', '0.10', { - 'source_tmpl': 'Set-IntervalTree-0.10.tar.gz', - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/B/BE/BENBOOTH/'], + 'source_tmpl': 'Set-IntervalTree-%(version)s.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/B/BE/BENBOOTH/'], }), ('HTML::TableExtract', '2.13', { - 'source_tmpl': 'HTML-TableExtract-2.13.tar.gz', + 'source_tmpl': 'HTML-TableExtract-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/M/MS/MSISK/'], }), - ('Bio::Perl', '1.6.924', { - 'source_tmpl': 'BioPerl-1.6.924.tar.gz', - 'source_urls': ['http://www.cpan.org/modules/by-module/Bio/CJFIELDS/'], + 'source_tmpl': 'BioPerl-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS'], }), ] diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.22.0-foss-2015a.eb b/easybuild/easyconfigs/p/Perl/Perl-5.22.0-foss-2015a.eb index 0443d98f0a..b4c631de0e 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.22.0-foss-2015a.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.22.0-foss-2015a.eb @@ -17,877 +17,879 @@ dependencies = [ source_urls = ['http://www.cpan.org/src/5.0'] sources = [SOURCELOWER_TAR_GZ] -#runtest = 'test' exts_list = [ ('Module::Build', '0.4210', { # std module but recent BioPerl needs a recent version for some reason - 'source_tmpl': 'Module-Build-0.4210.tar.gz', - 'source_urls': ['http://www.cpan.org/modules/by-module/Module/LEONT/'], + 'source_tmpl': 'Module-Build-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], }), ('ExtUtils::MakeMaker', '7.04', { - 'source_tmpl': 'ExtUtils-MakeMaker-7.04.tar.gz', - 'source_urls': ['http://www.cpan.org/modules/by-module/ExtUtils/BINGOS/'], + 'source_tmpl': 'ExtUtils-MakeMaker-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], }), ('local::lib', '2.000011', { - 'source_tmpl': 'local-lib-2.000011.tar.gz', - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/E/ET/ETHER/'], + 'source_tmpl': 'local-lib-%(version)s.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/E/ET/ETHER/'], }), ('IO::String', '1.08', { - 'source_tmpl': 'IO-String-1.08.tar.gz', + 'source_tmpl': 'IO-String-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS/'], }), ('Data::Stag', '0.14', { - 'source_tmpl': 'Data-Stag-0.14.tar.gz', + 'source_tmpl': 'Data-Stag-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/C/CM/CMUNGALL/'], }), ('DB_File', '1.835', { - 'source_urls': ['http://www.cpan.org/modules/by-module/DB_File/PMQS/'], + 'source_tmpl': 'DB_File-%(version)s.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/P/PM/PMQS/'], }), ('DBI', '1.633', { - 'source_urls': ['http://www.cpan.org/modules/by-module/DBI/TIMB/'], + 'source_tmpl': 'DBI-%(version)s.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/T/TI/TIMB/'], }), ('Sub::Uplevel', '0.25', { - 'source_tmpl': 'Sub-Uplevel-0.25.tar.gz', - 'source_urls': ['http://www.cpan.org/modules/by-module/Sub/DAGOLDEN/'], + 'source_tmpl': 'Sub-Uplevel-%(version)s.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN/'], }), ('Tree::DAG_Node', '1.26', { - 'source_tmpl': 'Tree-DAG_Node-1.26.tgz', - 'source_urls': ['http://www.cpan.org/modules/by-module/Tree/RSAVAGE/'], + 'source_tmpl': 'Tree-DAG_Node-%(version)s.tgz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RS/RSAVAGE/'], }), ('Try::Tiny', '0.22', { - 'source_tmpl': 'Try-Tiny-0.22.tar.gz', - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/D/DO/DOY/'], + 'source_tmpl': 'Try-Tiny-%(version)s.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DO/DOY/'], }), ('Devel::StackTrace', '2.00', { - 'source_tmpl': 'Devel-StackTrace-2.00.tar.gz', + 'source_tmpl': 'Devel-StackTrace-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DR/DROLSKY/'], }), ('Class::Data::Inheritable', '0.08', { - 'source_tmpl': 'Class-Data-Inheritable-0.08.tar.gz', + 'source_tmpl': 'Class-Data-Inheritable-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/T/TM/TMTM/'], }), ('Exception::Class', '1.39', { - 'source_tmpl': 'Exception-Class-1.39.tar.gz', + 'source_tmpl': 'Exception-Class-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DR/DROLSKY/'], }), ('Test::Fatal', '0.014', { - 'source_tmpl': 'Test-Fatal-0.014.tar.gz', - 'source_urls': ['http://www.cpan.org/modules/by-module/Test/RJBS/'], + 'source_tmpl': 'Test-Fatal-%(version)s.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS/'], }), ('Test::NoWarnings', '1.04', { - 'source_tmpl': 'Test-NoWarnings-1.04.tar.gz', + 'source_tmpl': 'Test-NoWarnings-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AD/ADAMK/'], }), ('Test::Deep', '0.117', { - 'source_tmpl': 'Test-Deep-0.117.tar.gz', + 'source_tmpl': 'Test-Deep-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS/'], }), ('Algorithm::Diff', '1.15', { - 'source_tmpl': 'Algorithm-Diff-1.15.tar.gz', + 'source_tmpl': 'Algorithm-Diff-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/N/NE/NEDKONZ/'], }), ('Text::Diff', '1.41', { - 'source_tmpl': 'Text-Diff-1.41.tar.gz', + 'source_tmpl': 'Text-Diff-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/O/OV/OVID/'], }), ('Test::Differences', '0.61', { - 'source_tmpl': 'Test-Differences-0.61.tar.gz', + 'source_tmpl': 'Test-Differences-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/O/OV/OVID/'], }), ('Test::Exception', '0.32', { - 'source_tmpl': 'Test-Exception-0.32.tar.gz', + 'source_tmpl': 'Test-Exception-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AD/ADIE/'], }), ('Test::Warn', '0.30', { - 'source_tmpl': 'Test-Warn-0.30.tar.gz', + 'source_tmpl': 'Test-Warn-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/C/CH/CHORNY/'], }), ('Test::Requires', '0.08', { - 'source_tmpl': 'Test-Requires-0.08.tar.gz', - 'source_urls': ['http://www.cpan.org/modules/by-module/Test/TOKUHIROM/'], + 'source_tmpl': 'Test-Requires-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TOKUHIROM'], }), ('Test::Tester', '0.109', { - 'source_tmpl': 'Test-Tester-0.109.tar.gz', - 'source_urls': ['http://www.cpan.org/modules/by-module/Test/FDALY/'], + 'source_tmpl': 'Test-Tester-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/F/FD/FDALY'], }), ('File::Slurp::Tiny', '0.003', { - 'source_tmpl': 'File-Slurp-Tiny-0.003.tar.gz', + 'source_tmpl': 'File-Slurp-Tiny-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/L/LE/LEONT'], }), ('Params::Util', '1.07', { - 'source_tmpl': 'Params-Util-1.07.tar.gz', + 'source_tmpl': 'Params-Util-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AD/ADAMK/'], }), ('Sub::Install', '0.928', { - 'source_tmpl': 'Sub-Install-0.928.tar.gz', - 'source_urls': ['http://www.cpan.org/modules/by-module/Sub/RJBS/'], + 'source_tmpl': 'Sub-Install-%(version)s.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS/'], }), ('Data::OptList', '0.109', { - 'source_tmpl': 'Data-OptList-0.109.tar.gz', + 'source_tmpl': 'Data-OptList-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS/'], }), ('Sub::Exporter', '0.987', { - 'source_tmpl': 'Sub-Exporter-0.987.tar.gz', + 'source_tmpl': 'Sub-Exporter-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS/'], }), ('Capture::Tiny', '0.30', { - 'source_tmpl': 'Capture-Tiny-0.30.tar.gz', + 'source_tmpl': 'Capture-Tiny-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN/'], }), ('Test::Output', '1.03', { - 'source_tmpl': 'Test-Output-1.03.tar.gz', + 'source_tmpl': 'Test-Output-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/B/BD/BDFOY/'], }), ('Module::Runtime', '0.014', { - 'source_tmpl': 'Module-Runtime-0.014.tar.gz', + 'source_tmpl': 'Module-Runtime-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/Z/ZE/ZEFRAM/'], }), ('Module::Implementation', '0.09', { - 'source_tmpl': 'Module-Implementation-0.09.tar.gz', - 'source_urls': ['http://www.cpan.org/modules/by-module/Module/DROLSKY/'], + 'source_tmpl': 'Module-Implementation-%(version)s.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DR/DROLSKY/'], }), ('List::MoreUtils', '0.413', { - 'source_tmpl': 'List-MoreUtils-0.413.tar.gz', + 'source_tmpl': 'List-MoreUtils-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RE/REHSACK/'], }), ('Package::DeprecationManager', '0.14', { - 'source_tmpl': 'Package-DeprecationManager-0.14.tar.gz', + 'source_tmpl': 'Package-DeprecationManager-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DR/DROLSKY/'], }), ('Dist::CheckConflicts', '0.11', { - 'source_tmpl': 'Dist-CheckConflicts-0.11.tar.gz', + 'source_tmpl': 'Dist-CheckConflicts-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DO/DOY/'], }), ('Package::Stash', '0.37', { - 'source_tmpl': 'Package-Stash-0.37.tar.gz', - 'source_urls': ['http://www.cpan.org/modules/by-module/Package/DOY/'], + 'source_tmpl': 'Package-Stash-%(version)s.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DO/DOY/'], }), ('Class::Load', '0.23', { - 'source_tmpl': 'Class-Load-0.23.tar.gz', + 'source_tmpl': 'Class-Load-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/E/ET/ETHER/'], }), ('TAP::Harness::Env', '3.35', { - 'source_tmpl': 'Test-Harness-3.35.tar.gz', + 'source_tmpl': 'Test-Harness-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/L/LE/LEONT/'], }), ('ExtUtils::Helpers', '0.022', { - 'source_tmpl': 'ExtUtils-Helpers-0.022.tar.gz', + 'source_tmpl': 'ExtUtils-Helpers-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/L/LE/LEONT'], }), ('ExtUtils::Config', '0.008', { - 'source_tmpl': 'ExtUtils-Config-0.008.tar.gz', + 'source_tmpl': 'ExtUtils-Config-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/L/LE/LEONT'], }), ('ExtUtils::InstallPaths', '0.011', { - 'source_tmpl': 'ExtUtils-InstallPaths-0.011.tar.gz', + 'source_tmpl': 'ExtUtils-InstallPaths-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/L/LE/LEONT'], }), ('Module::Build::Tiny', '0.039', { - 'source_tmpl': 'Module-Build-Tiny-0.039.tar.gz', + 'source_tmpl': 'Module-Build-Tiny-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/L/LE/LEONT/'], }), ('MRO::Compat', '0.12', { - 'source_tmpl': 'MRO-Compat-0.12.tar.gz', + 'source_tmpl': 'MRO-Compat-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/B/BO/BOBTFISH/'], }), ('Sub::Name', '0.05', { - 'source_tmpl': 'Sub-Name-0.05.tar.gz', + 'source_tmpl': 'Sub-Name-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/F/FL/FLORA/'], }), ('Eval::Closure', '0.13', { - 'source_tmpl': 'Eval-Closure-0.13.tar.gz', + 'source_tmpl': 'Eval-Closure-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DO/DOY/'], }), ('Sub::Exporter::Progressive', '0.001011', { - 'source_tmpl': 'Sub-Exporter-Progressive-0.001011.tar.gz', + 'source_tmpl': 'Sub-Exporter-Progressive-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/F/FR/FREW/'], }), ('Devel::GlobalDestruction', '0.13', { - 'source_tmpl': 'Devel-GlobalDestruction-0.13.tar.gz', - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/H/HA/HAARG/'], + 'source_tmpl': 'Devel-GlobalDestruction-%(version)s.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/H/HA/HAARG/'], }), ('boolean', '0.45', { - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/I/IN/INGY/'], + 'source_tmpl': 'boolean-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IN/INGY'], }), ('Tie::IxHash', '1.23', { - 'source_tmpl': 'Tie-IxHash-1.23.tar.gz', + 'source_tmpl': 'Tie-IxHash-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/C/CH/CHORNY/'], }), ('Moose', '2.1405', { - 'source_urls': ['http://www.cpan.org/modules/by-module/MooseX/ETHER/'], + 'source_tmpl': 'Moose-%(version)s.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/E/ET/ETHER/'], }), ('Package::Stash::XS', '0.28', { - 'source_tmpl': 'Package-Stash-XS-0.28.tar.gz', + 'source_tmpl': 'Package-Stash-XS-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DO/DOY/'], }), ('Params::Validate', '1.20', { - 'source_tmpl': 'Params-Validate-1.20.tar.gz', - 'source_urls': ['http://www.cpan.org/modules/by-module/Params/DROLSKY/'], + 'source_tmpl': 'Params-Validate-%(version)s.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DR/DROLSKY/'], }), ('Class::Load::XS', '0.09', { - 'source_tmpl': 'Class-Load-XS-0.09.tar.gz', + 'source_tmpl': 'Class-Load-XS-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/E/ET/ETHER/'], }), - # For uoa00001, Zendesk #9076 ('Math::CDF', '0.1', { - 'source_tmpl': 'Math-CDF-0.1.tar.gz', - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/C/CA/CALLAHAN/'], + 'source_tmpl': 'Math-CDF-%(version)s.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/C/CA/CALLAHAN/'], }), - ('DateTime::Locale', '0.46', { - 'source_tmpl': 'DateTime-Locale-0.46.tar.gz', + 'source_tmpl': 'DateTime-Locale-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DR/DROLSKY/'], }), ('Class::Singleton', '1.4', { - 'source_tmpl': 'Class-Singleton-1.4.tar.gz', + 'source_tmpl': 'Class-Singleton-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AB/ABW/'], }), ('DateTime::TimeZone', '1.92', { - 'source_tmpl': 'DateTime-TimeZone-1.92.tar.gz', - 'source_urls': ['http://www.cpan.org/modules/by-module/DateTime/DROLSKY/'], + 'source_tmpl': 'DateTime-TimeZone-%(version)s.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DR/DROLSKY/'], }), ('Test::Warnings', '0.021', { - 'source_tmpl': 'Test-Warnings-0.021.tar.gz', + 'source_tmpl': 'Test-Warnings-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/E/ET/ETHER/'], }), ('Data::Types', '0.09', { - 'source_tmpl': 'Data-Types-0.09.tar.gz', + 'source_tmpl': 'Data-Types-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DW/DWHEELER/'], }), ('Exporter::Tiny', '0.042', { - 'source_tmpl': 'Exporter-Tiny-0.042.tar.gz', + 'source_tmpl': 'Exporter-Tiny-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/T/TO/TOBYINK/'], }), - ('List::AllUtils', '0.09', { - 'source_tmpl': 'List-AllUtils-0.09.tar.gz', + 'source_tmpl': 'List-AllUtils-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DR/DROLSKY/'], }), ('DateTime', '1.20', { - 'source_urls': ['http://www.cpan.org/modules/by-module/DateTime/DROLSKY/'], + 'source_tmpl': 'DateTime-%(version)s.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DR/DROLSKY/'], }), ('DateTime::Tiny', '1.04', { - 'source_tmpl': 'DateTime-Tiny-1.04.tar.gz', + 'source_tmpl': 'DateTime-Tiny-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AD/ADAMK/'], }), ('File::Slurp', '9999.19', { - 'source_tmpl': 'File-Slurp-9999.19.tar.gz', + 'source_tmpl': 'File-Slurp-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/U/UR/URI/'], }), ('HTTP::Date', '6.02', { - 'source_tmpl': 'HTTP-Date-6.02.tar.gz', + 'source_tmpl': 'HTTP-Date-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS/'], }), ('IO::HTML', '1.001', { - 'source_tmpl': 'IO-HTML-1.001.tar.gz', - 'source_urls': ['http://www.cpan.org/modules/by-module/IO/CJM/'], + 'source_tmpl': 'IO-HTML-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CJ/CJM'], }), ('LWP::MediaTypes', '6.02', { - 'source_tmpl': 'LWP-MediaTypes-6.02.tar.gz', + 'source_tmpl': 'LWP-MediaTypes-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS/'], }), ('URI', '1.69', { - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/E/ET/ETHER/'], + 'source_tmpl': 'URI-%(version)s.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/E/ET/ETHER/'], }), ('Encode::Locale', '1.05', { - 'source_tmpl': 'Encode-Locale-1.05.tar.gz', + 'source_tmpl': 'Encode-Locale-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS/'], }), ('HTTP::Request', '6.06', { - 'source_tmpl': 'HTTP-Message-6.06.tar.gz', + 'source_tmpl': 'HTTP-Message-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS/'], }), ('HTML::Tagset', '3.20', { - 'source_tmpl': 'HTML-Tagset-3.20.tar.gz', + 'source_tmpl': 'HTML-Tagset-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/P/PE/PETDANCE/'], }), ('HTML::Entities', '3.71', { - 'source_tmpl': 'HTML-Parser-3.71.tar.gz', + 'source_tmpl': 'HTML-Parser-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS/'], }), ('File::Listing', '6.04', { - 'source_tmpl': 'File-Listing-6.04.tar.gz', - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/G/GA/GAAS/'], + 'source_tmpl': 'File-Listing-%(version)s.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS/'], }), ('AnyEvent', '7.09', { + 'source_tmpl': 'AnyEvent-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/M/ML/MLEHMANN/'], }), ('Devel::CheckCompiler', '0.06', { - 'source_tmpl': 'Devel-CheckCompiler-0.06.tar.gz', + 'source_tmpl': 'Devel-CheckCompiler-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/S/SY/SYOHEX'], }), ('File::Copy::Recursive', '0.38', { - 'source_tmpl': 'File-Copy-Recursive-0.38.tar.gz', + 'source_tmpl': 'File-Copy-Recursive-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DM/DMUEY/'], }), ('Cwd::Guard', '0.04', { - 'source_tmpl': 'Cwd-Guard-0.04.tar.gz', + 'source_tmpl': 'Cwd-Guard-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/K/KA/KAZEBURO'], }), ('Module::Build::XSUtil', '0.16', { - 'source_tmpl': 'Module-Build-XSUtil-0.16.tar.gz', + 'source_tmpl': 'Module-Build-XSUtil-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/H/HI/HIDEAKIO/'], }), ('LWP', '6.13', { - 'source_tmpl': 'libwww-perl-6.13.tar.gz', - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/E/ET/ETHER/'], + 'source_tmpl': 'libwww-perl-%(version)s.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/E/ET/ETHER/'], }), ('Fennec::Lite', '0.004', { - 'source_tmpl': 'Fennec-Lite-0.004.tar.gz', + 'source_tmpl': 'Fennec-Lite-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/E/EX/EXODIST/'], }), ('aliased', '0.31', { + 'source_tmpl': 'aliased-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/O/OV/OVID/'], }), ('Meta::Builder', '0.003', { - 'source_tmpl': 'Meta-Builder-0.003.tar.gz', + 'source_tmpl': 'Meta-Builder-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/E/EX/EXODIST/'], }), ('Exporter::Declare', '0.114', { - 'source_tmpl': 'Exporter-Declare-0.114.tar.gz', + 'source_tmpl': 'Exporter-Declare-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/E/EX/EXODIST/'], }), ('Mock::Quick', '1.108', { - 'source_tmpl': 'Mock-Quick-1.108.tar.gz', + 'source_tmpl': 'Mock-Quick-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/E/EX/EXODIST/'], }), ('Test::Exception::LessClever', '0.006', { - 'source_tmpl': 'Test-Exception-LessClever-0.006.tar.gz', + 'source_tmpl': 'Test-Exception-LessClever-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/E/EX/EXODIST/'], }), ('Test::LeakTrace', '0.15', { - 'source_tmpl': 'Test-LeakTrace-0.15.tar.gz', + 'source_tmpl': 'Test-LeakTrace-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GF/GFUJI/'], }), ('Mouse', '2.4.2', { + 'source_tmpl': 'Mouse-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GF/GFUJI/'], }), ('XML::NamespaceSupport', '1.11', { - 'source_tmpl': 'XML-NamespaceSupport-1.11.tar.gz', + 'source_tmpl': 'XML-NamespaceSupport-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/P/PE/PERIGRIN/'], }), ('XML::SAX::Base', '1.08', { - 'source_tmpl': 'XML-SAX-Base-1.08.tar.gz', + 'source_tmpl': 'XML-SAX-Base-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GR/GRANTM/'], }), ('XML::SAX', '0.99', { - 'source_tmpl': 'XML-SAX-0.99.tar.gz', + 'source_tmpl': 'XML-SAX-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GR/GRANTM/'], }), ('XML::LibXML', '2.0121', { - 'source_tmpl': 'XML-LibXML-2.0121.tar.gz', - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/S/SH/SHLOMIF/'], + 'source_tmpl': 'XML-LibXML-%(version)s.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/S/SH/SHLOMIF/'], }), ('Clone', '0.38', { - 'source_tmpl': 'Clone-0.38.tar.gz', + 'source_tmpl': 'Clone-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GARU'], }), ('Config::General', '2.58', { - 'source_tmpl': 'Config-General-2.58.tar.gz', + 'source_tmpl': 'Config-General-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/T/TL/TLINDEN'], }), ('Test::Simple', '0.98', { - 'source_tmpl': 'Test-Simple-0.98_05.tar.gz', + 'source_tmpl': 'Test-Simple-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/M/MS/MSCHWERN'], }), ('Font::TTF', '1.05', { - 'source_tmpl': 'Font-TTF-1.05.tar.gz', + 'source_tmpl': 'Font-TTF-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/M/MH/MHOSKEN'], }), ('IO::Tty', '1.12', { - 'source_tmpl': 'IO-Tty-1.12.tar.gz', + 'source_tmpl': 'IO-Tty-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/T/TO/TODDR'], }), ('Math::Bezier', '0.01', { - 'source_tmpl': 'Math-Bezier-0.01.tar.gz', + 'source_tmpl': 'Math-Bezier-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AB/ABW'], }), ('IPC::Run', '0.94', { - 'source_tmpl': 'IPC-Run-0.94.tar.gz', + 'source_tmpl': 'IPC-Run-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/T/TO/TODDR'], }), ('Math::Round', '0.07', { - 'source_tmpl': 'Math-Round-0.07.tar.gz', + 'source_tmpl': 'Math-Round-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GR/GROMMEL'], }), ('B::LintSubs', '0.06', { - 'source_tmpl': 'B-LintSubs-0.06.tar.gz', + 'source_tmpl': 'B-LintSubs-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/P/PE/PEVANS'], }), ('Math::VecStat', '0.08', { - 'source_tmpl': 'Math-VecStat-0.08.tar.gz', + 'source_tmpl': 'Math-VecStat-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AS/ASPINELLI'], }), ('Test::Most', '0.34', { - 'source_tmpl': 'Test-Most-0.34.tar.gz', + 'source_tmpl': 'Test-Most-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/O/OV/OVID/'], }), ('Readonly', '1.04', { - 'source_tmpl': 'Readonly-1.04.tar.gz', + 'source_tmpl': 'Readonly-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/S/SA/SANKO/'], }), ('Regexp::Common', '2013031301', { - 'source_tmpl': 'Regexp-Common-2013031301.tar.gz', + 'source_tmpl': 'Regexp-Common-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AB/ABIGAIL'], }), ('Want', '0.26', { - 'source_tmpl': 'Want-0.26.tar.gz', - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/R/RO/ROBIN/'], + 'source_tmpl': 'Want-%(version)s.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RO/ROBIN/'], }), ('DBD::SQLite', '1.48', { - 'source_tmpl': 'DBD-SQLite-1.48.tar.gz', - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/I/IS/ISHIGAKI/'], + 'source_tmpl': 'DBD-SQLite-%(version)s.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/I/IS/ISHIGAKI/'], }), ('Set::IntSpan', '1.19', { - 'source_tmpl': 'Set-IntSpan-1.19.tar.gz', + 'source_tmpl': 'Set-IntSpan-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/S/SW/SWMCD'], }), ('forks', '0.36', { - 'source_tmpl': 'forks-0.36.tar.gz', - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/R/RY/RYBSKEJ/'], + 'source_tmpl': 'forks-%(version)s.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RY/RYBSKEJ/'], }), ('File::Which', '1.09', { - 'source_tmpl': 'File-Which-1.09.tar.gz', - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/A/AD/ADAMK/'], + 'source_tmpl': 'File-Which-%(version)s.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AD/ADAMK/'], }), - ('Perl::Unsafe::Signals', '', { - 'source_tmpl': 'Perl-Unsafe-Signals-0.02.tar.gz', - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/R/RG/RGARCIA/'], + ('Perl::Unsafe::Signals', '0.02', { + 'source_tmpl': 'Perl-Unsafe-Signals-%(version)s.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RG/RGARCIA/'], }), ('Bit::Vector', '7.4', { - 'source_tmpl': 'Bit-Vector-7.4.tar.gz', - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/S/ST/STBEY/'], + 'source_tmpl': 'Bit-Vector-%(version)s.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/S/ST/STBEY/'], }), ('Parse::RecDescent', '1.967009', { - 'source_tmpl': 'Parse-RecDescent-1.967009.tar.gz', - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/J/JT/JTBRAUN/'], + 'source_tmpl': 'Parse-RecDescent-%(version)s.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/J/JT/JTBRAUN/'], }), ('Inline', '0.80', { - 'source_tmpl': 'Inline-0.80.tar.gz', - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/I/IN/INGY/'], + 'source_tmpl': 'Inline-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IN/INGY'], }), ('File::ShareDir::Install', '0.10', { - 'source_tmpl': 'File-ShareDir-Install-0.10.tar.gz', - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/G/GW/GWYN/'], + 'source_tmpl': 'File-ShareDir-Install-%(version)s.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GW/GWYN/'], }), ('Inline::C', '0.76', { - 'source_tmpl': 'Inline-C-0.76.tar.gz', - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/I/IN/INGY/'], + 'source_tmpl': 'Inline-C-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IN/INGY'], }), ('IO::All', '0.85', { - 'source_tmpl': 'IO-All-0.85.tar.gz', - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/F/FR/FREW/'], + 'source_tmpl': 'IO-All-%(version)s.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/F/FR/FREW/'], }), ('IO::Prompt', '0.997002', { - 'source_tmpl': 'IO-Prompt-0.997002.tar.gz', - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/D/DC/DCONWAY/'], + 'source_tmpl': 'IO-Prompt-%(version)s.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DC/DCONWAY/'], }), ('Getopt::Long', '2.47', { - 'source_tmpl': 'Getopt-Long-2.47.tar.gz', + 'source_tmpl': 'Getopt-Long-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/J/JV/JV/'], }), ('AppConfig', '1.66', { + 'source_tmpl': 'AppConfig-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AB/ABW/'], }), ('Archive::Extract', '0.76', { - 'source_tmpl': 'Archive-Extract-0.76.tar.gz', + 'source_tmpl': 'Archive-Extract-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/B/BI/BINGOS/'], }), ('Archive::Tar', '2.08', { - 'source_tmpl': 'Archive-Tar-2.08.tar.gz', + 'source_tmpl': 'Archive-Tar-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/B/BI/BINGOS/'], }), ('Archive::Zip', '1.57', { - 'source_tmpl': 'Archive-Zip-1.57.tar.gz', - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/P/PH/PHRED/'], + 'source_tmpl': 'Archive-Zip-%(version)s.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/P/PH/PHRED/'], }), ('Authen::SASL', '2.16', { - 'source_tmpl': 'Authen-SASL-2.16.tar.gz', + 'source_tmpl': 'Authen-SASL-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GB/GBARR/'], }), ('B::Lint', '1.20', { - 'source_tmpl': 'B-Lint-1.20.tar.gz', + 'source_tmpl': 'B-Lint-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS/'], }), # BioPerl bundle was here ('Class::Accessor', '0.34', { - 'source_tmpl': 'Class-Accessor-0.34.tar.gz', + 'source_tmpl': 'Class-Accessor-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/K/KA/KASEI/'], }), ('Class::DBI', '3.0.17', { - 'source_tmpl': 'Class-DBI-v3.0.17.tar.gz', + 'source_tmpl': 'Class-DBI-v%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/T/TM/TMTM/'], }), ('Class::Inspector', '1.28', { - 'source_tmpl': 'Class-Inspector-1.28.tar.gz', + 'source_tmpl': 'Class-Inspector-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AD/ADAMK/'], }), ('Class::ISA', '0.36', { - 'source_tmpl': 'Class-ISA-0.36.tar.gz', + 'source_tmpl': 'Class-ISA-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/S/SM/SMUELLER/'], }), ('Class::Trigger', '0.14', { - 'source_tmpl': 'Class-Trigger-0.14.tar.gz', + 'source_tmpl': 'Class-Trigger-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA/'], }), ('CPANPLUS', '0.9154', { + 'source_tmpl': 'CPANPLUS-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/B/BI/BINGOS/'], }), ('Data::Grove', '0.08', { - 'source_tmpl': 'libxml-perl-0.08.tar.gz', + 'source_tmpl': 'libxml-perl-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/K/KM/KMACLEOD/'], }), ('Data::UUID', '1.220', { - 'source_tmpl': 'Data-UUID-1.220.tar.gz', + 'source_tmpl': 'Data-UUID-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS/'], }), ('Date::Language', '2.30', { - 'source_tmpl': 'TimeDate-2.30.tar.gz', + 'source_tmpl': 'TimeDate-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GB/GBARR/'], }), ('Date::Handler', '1.2', { - 'source_tmpl': 'Date-Handler-1.2.tar.gz', + 'source_tmpl': 'Date-Handler-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/B/BB/BBEAUSEJ/'], }), ('SQL::Statement', '1.407', { - 'source_tmpl': 'SQL-Statement-1.407.tar.gz', + 'source_tmpl': 'SQL-Statement-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RE/REHSACK/'], }), ('Module::Pluggable', '5.1', { - 'source_tmpl': 'Module-Pluggable-5.1.tar.gz', + 'source_tmpl': 'Module-Pluggable-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/S/SI/SIMONW/'], }), ('Digest::HMAC', '1.03', { - 'source_tmpl': 'Digest-HMAC-1.03.tar.gz', + 'source_tmpl': 'Digest-HMAC-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS/'], }), ('Digest::SHA1', '2.13', { - 'source_tmpl': 'Digest-SHA1-2.13.tar.gz', + 'source_tmpl': 'Digest-SHA1-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS/'], }), ('Email::Date::Format', '1.005', { - 'source_tmpl': 'Email-Date-Format-1.005.tar.gz', + 'source_tmpl': 'Email-Date-Format-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS/'], }), ('Error', '0.17024', { + 'source_tmpl': 'Error-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/S/SH/SHLOMIF/'], }), ('Expect', '1.21', { + 'source_tmpl': 'Expect-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RG/RGIERSIG/'], }), ('File::CheckTree', '4.42', { - 'source_tmpl': 'File-CheckTree-4.42.tar.gz', + 'source_tmpl': 'File-CheckTree-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS/'], }), ('FreezeThaw', '0.5001', { 'source_urls': ['http://cpan.metacpan.org/authors/id/I/IL/ILYAZ/modules/'], }), ('Git', '0.41', { - 'source_tmpl': 'Git-0.41.tar.gz', + 'source_tmpl': 'Git-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/M/MS/MSOUTH/'], }), ('GO::Utils', '0.15', { - 'source_tmpl': 'go-perl-0.15.tar.gz', + 'source_tmpl': 'go-perl-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/C/CM/CMUNGALL/'], }), ('GO', '0.04', { - 'source_tmpl': 'go-db-perl-0.04.tar.gz', + 'source_tmpl': 'go-db-perl-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/S/SJ/SJCARBON/'], }), ('HTML::Form', '6.03', { - 'source_tmpl': 'HTML-Form-6.03.tar.gz', + 'source_tmpl': 'HTML-Form-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS/'], }), ('HTTP::Cookies', '6.01', { - 'source_tmpl': 'HTTP-Cookies-6.01.tar.gz', + 'source_tmpl': 'HTTP-Cookies-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS/'], }), ('HTTP::Daemon', '6.01', { - 'source_tmpl': 'HTTP-Daemon-6.01.tar.gz', + 'source_tmpl': 'HTTP-Daemon-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS/'], }), ('HTTP::Negotiate', '6.01', { - 'source_tmpl': 'HTTP-Negotiate-6.01.tar.gz', + 'source_tmpl': 'HTTP-Negotiate-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS/'], }), ('IO::Stringy', '2.111', { - 'source_tmpl': 'IO-stringy-2.111.tar.gz', + 'source_tmpl': 'IO-stringy-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DS/DSKOLL/'], }), ('IO::Socket::SSL', '2.016', { - 'source_tmpl': 'IO-Socket-SSL-2.016.tar.gz', + 'source_tmpl': 'IO-Socket-SSL-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/S/SU/SULLR/'], }), ('JSON', '2.90', { + 'source_tmpl': 'JSON-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/M/MA/MAKAMAKA/'], }), ('Log::Message', '0.08', { - 'source_tmpl': 'Log-Message-0.08.tar.gz', + 'source_tmpl': 'Log-Message-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/B/BI/BINGOS/'], }), ('Log::Message::Simple', '0.10', { - 'source_tmpl': 'Log-Message-Simple-0.10.tar.gz', + 'source_tmpl': 'Log-Message-Simple-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/B/BI/BINGOS/'], }), ('Mail::Util', '2.14', { - 'source_tmpl': 'MailTools-2.14.tar.gz', + 'source_tmpl': 'MailTools-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/M/MA/MARKOV/'], }), ('MIME::Types', '2.11', { - 'source_tmpl': 'MIME-Types-2.11.tar.gz', + 'source_tmpl': 'MIME-Types-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/M/MA/MARKOV/'], }), ('MIME::Lite', '3.030', { - 'source_tmpl': 'MIME-Lite-3.030.tar.gz', + 'source_tmpl': 'MIME-Lite-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS/'], }), ('Net::HTTP', '6.06', { - 'source_tmpl': 'Net-HTTP-6.06.tar.gz', + 'source_tmpl': 'Net-HTTP-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS/'], }), ('Net::SMTP::SSL', '1.01', { - 'source_tmpl': 'Net-SMTP-SSL-1.01.tar.gz', + 'source_tmpl': 'Net-SMTP-SSL-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/C/CW/CWEST/'], }), ('Object::Accessor', '0.48', { - 'source_tmpl': 'Object-Accessor-0.48.tar.gz', + 'source_tmpl': 'Object-Accessor-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/B/BI/BINGOS/'], }), ('Pod::LaTeX', '0.61', { - 'source_tmpl': 'Pod-LaTeX-0.61.tar.gz', + 'source_tmpl': 'Pod-LaTeX-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/T/TJ/TJENNESS/'], }), ('Pod::Plainer', '1.04', { - 'source_tmpl': 'Pod-Plainer-1.04.tar.gz', + 'source_tmpl': 'Pod-Plainer-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RM/RMBARKER/'], }), ('Pod::POM', '0.29', { - 'source_tmpl': 'Pod-POM-0.29.tar.gz', + 'source_tmpl': 'Pod-POM-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AN/ANDREWF/'], }), ('Shell', '0.72', { 'source_urls': ['http://cpan.metacpan.org/authors/id/F/FE/FERREIRA/'], }), ('Statistics::Descriptive', '3.0609', { - 'source_tmpl': 'Statistics-Descriptive-3.0609.tar.gz', + 'source_tmpl': 'Statistics-Descriptive-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/S/SH/SHLOMIF/'], }), ('Switch', '2.17', { + 'source_tmpl': 'Switch-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/C/CH/CHORNY/'], }), ('Template', '2.26', { - 'source_tmpl': 'Template-Toolkit-2.26.tar.gz', + 'source_tmpl': 'Template-Toolkit-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AB/ABW/'], }), ('Term::UI', '0.46', { - 'source_tmpl': 'Term-UI-0.46.tar.gz', + 'source_tmpl': 'Term-UI-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/B/BI/BINGOS/'], }), ('Text::Iconv', '1.7', { - 'source_tmpl': 'Text-Iconv-1.7.tar.gz', + 'source_tmpl': 'Text-Iconv-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/M/MP/MPIOTR/'], }), ('Text::Soundex', '3.04', { - 'source_tmpl': 'Text-Soundex-3.04.tar.gz', + 'source_tmpl': 'Text-Soundex-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS/'], }), ('Time::Piece', '1.30', { - 'source_tmpl': 'Time-Piece-1.30.tar.gz', + 'source_tmpl': 'Time-Piece-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS/'], }), ('Time::Piece::MySQL', '0.06', { - 'source_tmpl': 'Time-Piece-MySQL-0.06.tar.gz', + 'source_tmpl': 'Time-Piece-MySQL-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/K/KA/KASEI/'], }), ('UNIVERSAL::moniker', '0.08', { - 'source_tmpl': 'UNIVERSAL-moniker-0.08.tar.gz', + 'source_tmpl': 'UNIVERSAL-moniker-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/K/KA/KASEI/'], }), ('version', '0.9912', { 'source_urls': ['http://cpan.metacpan.org/authors/id/J/JP/JPEACOCK/'], }), ('WWW::RobotRules', '6.02', { - 'source_tmpl': 'WWW-RobotRules-6.02.tar.gz', + 'source_tmpl': 'WWW-RobotRules-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS/'], }), ('XML::SAX::Writer', '0.56', { - 'source_tmpl': 'XML-SAX-Writer-0.56.tar.gz', + 'source_tmpl': 'XML-SAX-Writer-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/P/PE/PERIGRIN/'], }), ('XML::Simple', '2.20', { - 'source_tmpl': 'XML-Simple-2.20.tar.gz', + 'source_tmpl': 'XML-Simple-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GR/GRANTM/'], }), ('XML::XPath', '1.13', { - 'source_tmpl': 'XML-XPath-1.13.tar.gz', + 'source_tmpl': 'XML-XPath-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/M/MS/MSERGEANT/'], }), ('DBD::AnyData', '0.110', { - 'source_tmpl': 'DBD-AnyData-0.110.tar.gz', + 'source_tmpl': 'DBD-AnyData-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RE/REHSACK/'], }), ('Ima::DBI', '0.35', { - 'source_tmpl': 'Ima-DBI-0.35.tar.gz', + 'source_tmpl': 'Ima-DBI-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/P/PE/PERRIN/'], }), ('DBIx::ContextualFetch', '1.03', { - 'source_tmpl': 'DBIx-ContextualFetch-1.03.tar.gz', + 'source_tmpl': 'DBIx-ContextualFetch-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/T/TM/TMTM/'], }), ('DBIx::Simple', '1.35', { - 'source_tmpl': 'DBIx-Simple-1.35.tar.gz', + 'source_tmpl': 'DBIx-Simple-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/J/JU/JUERD/'], }), ('Term::ReadKey', '2.32', { - 'source_tmpl': 'TermReadKey-2.32.tar.gz', + 'source_tmpl': 'TermReadKey-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/J/JS/JSTOWE/'], 'patches': ['TermReadKey-2.32.patch'], }), ('Moo', '2.000001', { - 'source_tmpl': 'Moo-2.000001.tar.gz', + 'source_tmpl': 'Moo-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/H/HA/HAARG/'], }), ('strictures', '2.000001', { - 'source_tmpl': 'strictures-2.000001.tar.gz', + 'source_tmpl': 'strictures-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/H/HA/HAARG/'], }), ('File::Find::Rule::Perl', '1.13', { - 'source_tmpl': 'File-Find-Rule-Perl-1.13.tar.gz', + 'source_tmpl': 'File-Find-Rule-Perl-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AD/ADAMK/'], }), ('Test::Version', '1.002004', { - 'source_tmpl': 'Test-Version-1.002004.tar.gz', + 'source_tmpl': 'Test-Version-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/X/XE/XENO/'], }), ('Test::Harness', '3.35', { - 'source_tmpl': 'Test-Harness-3.35.tar.gz', + 'source_tmpl': 'Test-Harness-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/L/LE/LEONT/'], }), ('Import::Into', '1.002004', { - 'source_tmpl': 'Import-Into-1.002004.tar.gz', + 'source_tmpl': 'Import-Into-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/E/ET/ETHER/'], }), ('File::Find::Rule', '0.33', { - 'source_tmpl': 'File-Find-Rule-0.33.tar.gz', + 'source_tmpl': 'File-Find-Rule-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RC/RCLAMP/'], }), ('Data::Section::Simple', '0.07', { - 'source_tmpl': 'Data-Section-Simple-0.07.tar.gz', + 'source_tmpl': 'Data-Section-Simple-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA/'], }), ('Text::Glob', '0.09', { - 'source_tmpl': 'Text-Glob-0.09.tar.gz', + 'source_tmpl': 'Text-Glob-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RC/RCLAMP/'], }), ('Number::Compare', '0.03', { - 'source_tmpl': 'Number-Compare-0.03.tar.gz', + 'source_tmpl': 'Number-Compare-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RC/RCLAMP/'], }), ('IPC::Run3', '0.048', { - 'source_tmpl': 'IPC-Run3-0.048.tar.gz', + 'source_tmpl': 'IPC-Run3-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS/'], }), ('Set::Array', '0.30', { - 'source_tmpl': 'Set-Array-0.30.tgz', + 'source_tmpl': 'Set-Array-%(version)s.tgz', 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RS/RSAVAGE/'], }), ('Bundle::BioPerl', '2.1.9', { - 'source_tmpl': 'Bundle-BioPerl-2.1.9.tar.gz', + 'source_tmpl': 'Bundle-BioPerl-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS/'], }), - ('Algorithm::Munkres', '0.08', { - 'source_tmpl': 'Algorithm-Munkres-0.08.tar.gz', + 'source_tmpl': 'Algorithm-Munkres-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/T/TP/TPEDERSE/'], }), -# Lots of deps: Carp, Types::Standard etc. -# ('Array::Compare', '2.11', { -# 'source_tmpl': 'Array-Compare-2.11.tar.gz', -# 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DA/DAVECROSS/'], -# }), ('Graph', '0.96', { + 'source_tmpl': 'Graph-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/J/JH/JHI/'], }), ('Set::Scalar', '1.29', { - 'source_tmpl': 'Set-Scalar-1.29.tar.gz', + 'source_tmpl': 'Set-Scalar-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DA/DAVIDO/'], }), - ('CGI', '4.21', { - 'source_tmpl': 'CGI-4.21.tar.gz', + 'source_tmpl': 'CGI-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/L/LE/LEEJO/'], }), ('Bio::Phylo', '0.58', { - 'source_tmpl': 'Bio-Phylo-0.58.tar.gz', + 'source_tmpl': 'Bio-Phylo-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RV/RVOSA/'], }), -# ('GD', '2.56', { -# 'source_urls': 'http://cpan.metacpan.org/authors/id/L/LD/LDS/'], -# }), ('SVG', '2.64', { + 'source_tmpl': 'SVG-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/S/SZ/SZABGAB/'], }), ('XML::DOM', '1.44', { - 'source_tmpl': 'XML-DOM-1.44.tar.gz', + 'source_tmpl': 'XML-DOM-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/T/TJ/TJMATHER/'], }), ('XML::DOM::XPath', '0.14', { - 'source_tmpl': 'XML-DOM-XPath-0.14.tar.gz', + 'source_tmpl': 'XML-DOM-XPath-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/M/MI/MIROD/'], }), ('XML::Parser::PerlSAX', '0.08', { - 'source_tmpl': 'libxml-perl-0.08.tar.gz', + 'source_tmpl': 'libxml-perl-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/K/KM/KMACLEOD/'], }), ('XML::Parser', '2.44', { - 'source_tmpl': 'XML-Parser-2.44.tar.gz', + 'source_tmpl': 'XML-Parser-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/T/TO/TODDR/'], }), ('XML::Twig', '3.49', { - 'source_tmpl': 'XML-Twig-3.49.tar.gz', + 'source_tmpl': 'XML-Twig-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/M/MI/MIROD/'], }), ('XML::Writer', '0.625', { - 'source_tmpl': 'XML-Writer-0.625.tar.gz', + 'source_tmpl': 'XML-Writer-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/J/JO/JOSEPHW/'], }), ('XML::DOM', '1.44', { - 'source_tmpl': 'XML-DOM-1.44.tar.gz', + 'source_tmpl': 'XML-DOM-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/T/TJ/TJMATHER/'], }), ('Spreadsheet::ParseExcel', '0.65', { - 'source_tmpl': 'Spreadsheet-ParseExcel-0.65.tar.gz', + 'source_tmpl': 'Spreadsheet-ParseExcel-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DO/DOUGW/'], }), ('XML::DOM::XPath', '0.14', { - 'source_tmpl': 'XML-DOM-XPath-0.14.tar.gz', + 'source_tmpl': 'XML-DOM-XPath-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/M/MI/MIROD/'], }), ('Convert::Binary::C', '0.77', { - 'source_tmpl': 'Convert-Binary-C-0.77.tar.gz', + 'source_tmpl': 'Convert-Binary-C-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/M/MH/MHX/'], }), ('Sys::SigAction.pm', '0.21', { - 'source_tmpl': 'Sys-SigAction-0.21.tar.gz', - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/L/LB/LBAXTER/'], + 'source_tmpl': 'Sys-SigAction-%(version)s.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/L/LB/LBAXTER/'], }), ('Acme::Damn', '0.06', { - 'source_tmpl': 'Acme-Damn-0.06.tar.gz', - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/I/IB/IBB/'], + 'source_tmpl': 'Acme-Damn-%(version)s.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/I/IB/IBB/'], }), ('Set::IntervalTree', '0.10', { - 'source_tmpl': 'Set-IntervalTree-0.10.tar.gz', - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/B/BE/BENBOOTH/'], + 'source_tmpl': 'Set-IntervalTree-%(version)s.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/B/BE/BENBOOTH/'], }), ('HTML::TableExtract', '2.13', { - 'source_tmpl': 'HTML-TableExtract-2.13.tar.gz', + 'source_tmpl': 'HTML-TableExtract-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/M/MS/MSISK/'], }), - ('Bio::Perl', '1.6.924', { - 'source_tmpl': 'BioPerl-1.6.924.tar.gz', - 'source_urls': ['http://www.cpan.org/modules/by-module/Bio/CJFIELDS/'], + 'source_tmpl': 'BioPerl-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS'], }), ] -- GitLab From 7e605984029bc4870921c38260620edde61d5df4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 8 Jun 2017 13:18:47 +0200 Subject: [PATCH 0909/1603] add SHA256 checksums for libpciaccess --- .../l/libpciaccess/libpciaccess-0.13.1-GCC-4.7.2.eb | 5 +++-- .../l/libpciaccess/libpciaccess-0.13.1-goolf-1.4.10.eb | 5 +++-- .../l/libpciaccess/libpciaccess-0.13.1-ictce-5.3.0.eb | 5 +++-- .../l/libpciaccess/libpciaccess-0.13.1-ictce-5.5.0.eb | 5 +++-- .../l/libpciaccess/libpciaccess-0.13.1-intel-2015a.eb | 5 +++-- .../l/libpciaccess/libpciaccess-0.13.3-intel-2015a.eb | 5 +++-- .../l/libpciaccess/libpciaccess-0.13.4-foss-2016a.eb | 5 +++-- .../l/libpciaccess/libpciaccess-0.13.4-foss-2016b.eb | 5 +++-- .../l/libpciaccess/libpciaccess-0.13.4-gimkl-2.11.5.eb | 5 +++-- .../l/libpciaccess/libpciaccess-0.13.4-intel-2015b.eb | 5 +++-- .../l/libpciaccess/libpciaccess-0.13.4-intel-2016a.eb | 5 +++-- .../l/libpciaccess/libpciaccess-0.13.4-intel-2016b.eb | 5 +++-- 12 files changed, 36 insertions(+), 24 deletions(-) diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-GCC-4.7.2.eb b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-GCC-4.7.2.eb index 9967c64c68..17116e1d46 100644 --- a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-GCC-4.7.2.eb +++ b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-GCC-4.7.2.eb @@ -6,10 +6,11 @@ version = '0.13.1' homepage = 'http://cgit.freedesktop.org/xorg/lib/libpciaccess/' description = """Generic PCI access library.""" +toolchain = {'name': 'GCC', 'version': '4.7.2'} + source_urls = ['https://www.x.org/releases/individual/lib/'] sources = [SOURCE_TAR_GZ] - -toolchain = {'name': 'GCC', 'version': '4.7.2'} +checksums = ['8641a3ce37c97a6b28439d4630adb9583d8bd3e3a08c2040aa81f9932a7a76f6'] builddependencies = [ ('Autoconf', '2.69'), diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-goolf-1.4.10.eb index 9371a19f2d..05a5d755f2 100644 --- a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-goolf-1.4.10.eb @@ -6,10 +6,11 @@ version = '0.13.1' homepage = 'http://cgit.freedesktop.org/xorg/lib/libpciaccess/' description = """Generic PCI access library.""" +toolchain = {'name': 'goolf', 'version': '1.4.10'} + source_urls = ['https://www.x.org/releases/individual/lib/'] sources = [SOURCE_TAR_GZ] - -toolchain = {'name': 'goolf', 'version': '1.4.10'} +checksums = ['8641a3ce37c97a6b28439d4630adb9583d8bd3e3a08c2040aa81f9932a7a76f6'] builddependencies = [ ('Autoconf', '2.69'), diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-ictce-5.3.0.eb index cbc3f1b46c..7b5d65355f 100644 --- a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-ictce-5.3.0.eb @@ -6,10 +6,11 @@ version = '0.13.1' homepage = 'http://cgit.freedesktop.org/xorg/lib/libpciaccess/' description = """Generic PCI access library.""" +toolchain = {'name': 'ictce', 'version': '5.3.0'} + source_urls = ['https://www.x.org/releases/individual/lib/'] sources = [SOURCE_TAR_GZ] - -toolchain = {'name': 'ictce', 'version': '5.3.0'} +checksums = ['8641a3ce37c97a6b28439d4630adb9583d8bd3e3a08c2040aa81f9932a7a76f6'] builddependencies = [ ('Autoconf', '2.69'), diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-ictce-5.5.0.eb b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-ictce-5.5.0.eb index 1abedab086..a19198650c 100644 --- a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-ictce-5.5.0.eb @@ -6,10 +6,11 @@ version = '0.13.1' homepage = 'http://cgit.freedesktop.org/xorg/lib/libpciaccess/' description = """Generic PCI access library.""" +toolchain = {'name': 'ictce', 'version': '5.5.0'} + source_urls = ['https://www.x.org/releases/individual/lib/'] sources = [SOURCE_TAR_GZ] - -toolchain = {'name': 'ictce', 'version': '5.5.0'} +checksums = ['8641a3ce37c97a6b28439d4630adb9583d8bd3e3a08c2040aa81f9932a7a76f6'] builddependencies = [ ('Autoconf', '2.69'), diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-intel-2015a.eb b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-intel-2015a.eb index 8970daab0a..9afa895bc3 100644 --- a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-intel-2015a.eb +++ b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-intel-2015a.eb @@ -6,10 +6,11 @@ version = '0.13.1' homepage = 'http://cgit.freedesktop.org/xorg/lib/libpciaccess/' description = """Generic PCI access library.""" +toolchain = {'name': 'intel', 'version': '2015a'} + source_urls = ['https://www.x.org/releases/individual/lib/'] sources = [SOURCE_TAR_GZ] - -toolchain = {'name': 'intel', 'version': '2015a'} +checksums = ['8641a3ce37c97a6b28439d4630adb9583d8bd3e3a08c2040aa81f9932a7a76f6'] builddependencies = [ ('Autotools', '20150119', '', ('GCC', '4.9.2')), diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.3-intel-2015a.eb b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.3-intel-2015a.eb index a36467cdf5..1617203250 100644 --- a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.3-intel-2015a.eb +++ b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.3-intel-2015a.eb @@ -6,10 +6,11 @@ version = '0.13.3' homepage = 'http://cgit.freedesktop.org/xorg/lib/libpciaccess/' description = """Generic PCI access library.""" +toolchain = {'name': 'intel', 'version': '2015a'} + source_urls = ['https://www.x.org/releases/individual/lib/'] sources = [SOURCE_TAR_GZ] - -toolchain = {'name': 'intel', 'version': '2015a'} +checksums = ['9e0244e815dc55cbedb135baa4dc1e4b0325875276e081edfe38ff2bf61dfe02'] builddependencies = [ ('Autoconf', '2.69'), diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-foss-2016a.eb b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-foss-2016a.eb index 0baaea5ccf..d017a972c2 100644 --- a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-foss-2016a.eb @@ -6,10 +6,11 @@ version = '0.13.4' homepage = 'http://cgit.freedesktop.org/xorg/lib/libpciaccess/' description = """Generic PCI access library.""" +toolchain = {'name': 'foss', 'version': '2016a'} + source_urls = ['https://www.x.org/releases/individual/lib/'] sources = [SOURCE_TAR_GZ] - -toolchain = {'name': 'foss', 'version': '2016a'} +checksums = ['74d92bda448e6fdb64fee4e0091255f48d625d07146a121653022ed3a0ca1f2f'] builddependencies = [ ('Autotools', '20150215'), diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-foss-2016b.eb b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-foss-2016b.eb index 76bd735f5a..c55a493a71 100755 --- a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-foss-2016b.eb +++ b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-foss-2016b.eb @@ -6,10 +6,11 @@ version = '0.13.4' homepage = 'http://cgit.freedesktop.org/xorg/lib/libpciaccess/' description = """Generic PCI access library.""" +toolchain = {'name': 'foss', 'version': '2016b'} + source_urls = ['https://www.x.org/releases/individual/lib/'] sources = [SOURCE_TAR_GZ] - -toolchain = {'name': 'foss', 'version': '2016b'} +checksums = ['74d92bda448e6fdb64fee4e0091255f48d625d07146a121653022ed3a0ca1f2f'] builddependencies = [ ('Autotools', '20150215'), diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-gimkl-2.11.5.eb b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-gimkl-2.11.5.eb index 449c59f9bf..08c466e4d7 100644 --- a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-gimkl-2.11.5.eb @@ -6,10 +6,11 @@ version = '0.13.4' homepage = 'http://cgit.freedesktop.org/xorg/lib/libpciaccess/' description = """Generic PCI access library.""" +toolchain = {'name': 'gimkl', 'version': '2.11.5'} + source_urls = ['https://www.x.org/releases/individual/lib/'] sources = [SOURCE_TAR_GZ] - -toolchain = {'name': 'gimkl', 'version': '2.11.5'} +checksums = ['74d92bda448e6fdb64fee4e0091255f48d625d07146a121653022ed3a0ca1f2f'] builddependencies = [ ('Autotools', '20150215'), diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-intel-2015b.eb b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-intel-2015b.eb index fd0fe49af5..64406b5039 100644 --- a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-intel-2015b.eb +++ b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-intel-2015b.eb @@ -6,10 +6,11 @@ version = '0.13.4' homepage = 'http://cgit.freedesktop.org/xorg/lib/libpciaccess/' description = """Generic PCI access library.""" +toolchain = {'name': 'intel', 'version': '2015b'} + source_urls = ['https://www.x.org/releases/individual/lib/'] sources = [SOURCE_TAR_GZ] - -toolchain = {'name': 'intel', 'version': '2015b'} +checksums = ['74d92bda448e6fdb64fee4e0091255f48d625d07146a121653022ed3a0ca1f2f'] builddependencies = [ ('Autotools', '20150215', '', ('GNU', '4.9.3-2.25')), diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-intel-2016a.eb b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-intel-2016a.eb index 69a705ef82..1ce0816af9 100644 --- a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-intel-2016a.eb @@ -6,10 +6,11 @@ version = '0.13.4' homepage = 'http://cgit.freedesktop.org/xorg/lib/libpciaccess/' description = """Generic PCI access library.""" +toolchain = {'name': 'intel', 'version': '2016a'} + source_urls = ['https://www.x.org/releases/individual/lib/'] sources = [SOURCE_TAR_GZ] - -toolchain = {'name': 'intel', 'version': '2016a'} +checksums = ['74d92bda448e6fdb64fee4e0091255f48d625d07146a121653022ed3a0ca1f2f'] builddependencies = [ ('Autotools', '20150215'), diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-intel-2016b.eb b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-intel-2016b.eb index de4d55b188..b1b38aee06 100755 --- a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-intel-2016b.eb +++ b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.4-intel-2016b.eb @@ -6,10 +6,11 @@ version = '0.13.4' homepage = 'http://cgit.freedesktop.org/xorg/lib/libpciaccess/' description = """Generic PCI access library.""" +toolchain = {'name': 'intel', 'version': '2016b'} + source_urls = ['https://www.x.org/releases/individual/lib/'] sources = [SOURCE_TAR_GZ] - -toolchain = {'name': 'intel', 'version': '2016b'} +checksums = ['74d92bda448e6fdb64fee4e0091255f48d625d07146a121653022ed3a0ca1f2f'] builddependencies = [ ('Autotools', '20150215'), -- GitLab From a59eee0aa1d29d1c01eda712ffc3eb5ead940ca9 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Thu, 8 Jun 2017 13:54:47 +0200 Subject: [PATCH 0910/1603] {geo}[intel/2017a] GMT 5.4.1 (REVIEW) --- .../g/GMT/GMT-5.4.1-intel-2017a.eb | 61 +++++++++++++++++++ 1 file changed, 61 insertions(+) create mode 100644 easybuild/easyconfigs/g/GMT/GMT-5.4.1-intel-2017a.eb diff --git a/easybuild/easyconfigs/g/GMT/GMT-5.4.1-intel-2017a.eb b/easybuild/easyconfigs/g/GMT/GMT-5.4.1-intel-2017a.eb new file mode 100644 index 0000000000..1ae0c637c6 --- /dev/null +++ b/easybuild/easyconfigs/g/GMT/GMT-5.4.1-intel-2017a.eb @@ -0,0 +1,61 @@ +easyblock = "CMakeMake" + +name = "GMT" +version = "5.4.1" + +homepage = 'http://gmt.soest.hawaii.edu/' +description = """GMT is an open source collection of about 80 command-line tools for manipulating + geographic and Cartesian data sets (including filtering, trend fitting, gridding, projecting, + etc.) and producing PostScript illustrations ranging from simple x-y plots via contour maps + to artificially illuminated surfaces and 3D perspective views; the GMT supplements add another + 40 more specialized and discipline-specific tools. """ + +toolchain = {'name': 'intel', 'version': '2017a'} + +gshhg_ver = '2.3.6' +dcw_ver = '1.1.2' +sources = [ + 'gmt-%(version)s-src.tar.xz', + # coastlines, rivers, and political boundaries + 'gshhg-gmt-%s.tar.gz' % gshhg_ver, + # country polygons + 'dcw-gmt-%s.tar.gz' % dcw_ver, +] + +# 'http://gmt.soest.hawaii.edu/files/download?name=' needs flash enabled browser +source_urls = [ + 'ftp://ftp.soest.hawaii.edu/gmt', + 'ftp://ftp.soest.hawaii.edu/gmt/legacy', + 'ftp://ftp.soest.hawaii.edu/gshhg', + 'ftp://ftp.soest.hawaii.edu/gshhg/legacy', + 'ftp://ftp.soest.hawaii.edu/dcw', + 'ftp://ftp.soest.hawaii.edu/dcw/legacy', +] + +patches = ['GMT-5.1.2_netCDF.patch'] + +builddependencies = [('CMake', '3.8.1')] + +dependencies = [ + ('PCRE', '8.40'), + ('GDAL', '2.1.3', '-Python-2.7.13'), + ('FFTW', '3.3.6'), + ('netCDF', '4.4.1.1'), + ('Ghostscript', '9.21'), + ('cURL', '7.53.1'), + ('zlib', '1.2.11'), +] + +configopts = '-DCOPY_GSHHG=TRUE -DGSHHG_ROOT=%%(builddir)s/gshhg-gmt-%s ' % gshhg_ver +configopts += '-DCOPY_DCW=TRUE -DDCW_ROOT=%%(builddir)s/dcw-gmt-%s ' % dcw_ver + +separate_build_dir = True + +sanity_check_paths = { + 'files': ['bin/gmt', 'bin/isogmt'], + 'dirs': [] +} + +modextrapaths = {'GMTHOME': ''} + +moduleclass = 'geo' -- GitLab From 429abc826d81ba546c3a53dafc0fb6a40c686251 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 8 Jun 2017 14:07:25 +0200 Subject: [PATCH 0911/1603] adding easyconfigs: FUNWAVE-TVD-3.1-20170525-intel-2017a.eb --- .../FUNWAVE-TVD-3.1-20170525-intel-2017a.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/f/FUNWAVE-TVD/FUNWAVE-TVD-3.1-20170525-intel-2017a.eb diff --git a/easybuild/easyconfigs/f/FUNWAVE-TVD/FUNWAVE-TVD-3.1-20170525-intel-2017a.eb b/easybuild/easyconfigs/f/FUNWAVE-TVD/FUNWAVE-TVD-3.1-20170525-intel-2017a.eb new file mode 100644 index 0000000000..e8a2edef7d --- /dev/null +++ b/easybuild/easyconfigs/f/FUNWAVE-TVD/FUNWAVE-TVD-3.1-20170525-intel-2017a.eb @@ -0,0 +1,28 @@ +easyblock = 'MakeCp' + +name = 'FUNWAVE-TVD' +version = '3.1-20170525' +commit = '814107a' + +homepage = 'https://fengyanshi.github.io' +description = """FUNWAVE–TVD is the TVD version of the fully nonlinear Boussinesq wave model (FUNWAVE) + initially developed by Kirby et al.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/fengyanshi/FUNWAVE-TVD/archive/'] +sources = ['%s.tar.gz' % commit] + +start_dir = 'src' +parallel = 1 +buildopts = 'FC="$FC" FFLAGS="$FFLAGS -fpp" CPPFLAGS="-DINTEL -DMIXING -DMANNING -DVIS_KENNEDY"' + +files_to_copy = [(['mytvd'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/mytvd'], + 'dirs': [], +} + +moduleclass = 'math' -- GitLab From af0ad01045d5d19e6f347fab5226348316407c60 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Thu, 8 Jun 2017 08:38:47 -0500 Subject: [PATCH 0912/1603] adding easyconfigs: Tcl-8.6.5-iccifort-2016.3.210-GCC-5.4.0-2.26.eb, Tk-8.6.5-iccifort-2016.3.210-GCC-5.4.0-2.26.eb --- ....6.5-iccifort-2016.3.210-GCC-5.4.0-2.26.eb | 26 +++++++++++++++++++ ....6.5-iccifort-2016.3.210-GCC-5.4.0-2.26.eb | 26 +++++++++++++++++++ 2 files changed, 52 insertions(+) create mode 100644 easybuild/easyconfigs/t/Tcl/Tcl-8.6.5-iccifort-2016.3.210-GCC-5.4.0-2.26.eb create mode 100644 easybuild/easyconfigs/t/Tk/Tk-8.6.5-iccifort-2016.3.210-GCC-5.4.0-2.26.eb diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.5-iccifort-2016.3.210-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.5-iccifort-2016.3.210-GCC-5.4.0-2.26.eb new file mode 100644 index 0000000000..d9890f7017 --- /dev/null +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.5-iccifort-2016.3.210-GCC-5.4.0-2.26.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'Tcl' +version = '8.6.5' + +homepage = 'http://www.tcl.tk/' +description = """Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, +suitable for a very wide range of uses, including web and desktop applications, networking, administration, +testing and many more.""" + +toolchain = {'name': 'iccifort', 'version': '2016.3.210-GCC-5.4.0-2.26'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +dependencies = [ + ('zlib', '1.2.8'), +] + +configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' + +runtest = 'test' + +start_dir = 'unix' + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.5-iccifort-2016.3.210-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.5-iccifort-2016.3.210-GCC-5.4.0-2.26.eb new file mode 100644 index 0000000000..5f81a41eff --- /dev/null +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.5-iccifort-2016.3.210-GCC-5.4.0-2.26.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'Tk' +version = '8.6.5' + +homepage = 'http://www.tcl.tk/' +description = """Tk is an open source, cross-platform widget toolchain that provides a library of basic elements for + building a graphical user interface (GUI) in many different programming languages.""" + +toolchain = {'name': 'iccifort', 'version': '2016.3.210-GCC-5.4.0-2.26'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +patches = ['Tk-8.6.4_different-prefix-with-tcl.patch'] + +dependencies = [ + ('Tcl', version), + ('zlib', '1.2.8'), +] + +configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib CFLAGS="-I$EBROOTTCL/include"' + +start_dir = 'unix' + +moduleclass = 'vis' -- GitLab From 8f64ad53373e7f11714d8395ce6fe360d576ea70 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Thu, 8 Jun 2017 08:52:47 -0500 Subject: [PATCH 0913/1603] adding easyconfigs: SQLite-3.13.0-iccifort-2016.3.210-GCC-5.4.0-2.26.eb --- ...13.0-iccifort-2016.3.210-GCC-5.4.0-2.26.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/s/SQLite/SQLite-3.13.0-iccifort-2016.3.210-GCC-5.4.0-2.26.eb diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.13.0-iccifort-2016.3.210-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.13.0-iccifort-2016.3.210-GCC-5.4.0-2.26.eb new file mode 100644 index 0000000000..de897a790e --- /dev/null +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.13.0-iccifort-2016.3.210-GCC-5.4.0-2.26.eb @@ -0,0 +1,40 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## + +easyblock = 'ConfigureMake' + +name = 'SQLite' +version = '3.13.0' + +homepage = 'http://www.sqlite.org/' +description = 'SQLite: SQL Database Engine in a C Library' + +toolchain = {'name': 'iccifort', 'version': '2016.3.210-GCC-5.4.0-2.26'} + +source_urls = ['http://www.sqlite.org/2016/'] +version_minor_etc = version.split('.')[1:] +version_minor_etc += '0' * (3 - len(version_minor_etc)) +version_str = '%(version_major)s' + ''.join('%02d' % int(x) for x in version_minor_etc) +sources = ['sqlite-autoconf-%s.tar.gz' % version_str] + +dependencies = [ + ('libreadline', '6.3'), + ('Tcl', '8.6.5'), +] + +sanity_check_paths = { + 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', 'lib/libsqlite3.a', + 'lib/libsqlite3.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'devel' -- GitLab From 73dd65a55f1a26a53c084baf3ea7097d8a383f11 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Thu, 8 Jun 2017 10:26:20 -0500 Subject: [PATCH 0914/1603] adding easyconfigs: NASM-2.11.08-GCCcore-5.4.0.eb, libjpeg-turbo-1.5.0-GCCcore-5.4.0.eb --- .../libjpeg-turbo-1.5.0-GCCcore-5.4.0.eb | 32 +++++++++++++++++++ .../n/NASM/NASM-2.11.08-GCCcore-5.4.0.eb | 21 ++++++++++++ 2 files changed, 53 insertions(+) create mode 100644 easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.5.0-GCCcore-5.4.0.eb create mode 100644 easybuild/easyconfigs/n/NASM/NASM-2.11.08-GCCcore-5.4.0.eb diff --git a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.5.0-GCCcore-5.4.0.eb b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.5.0-GCCcore-5.4.0.eb new file mode 100644 index 0000000000..42aa366fd1 --- /dev/null +++ b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.5.0-GCCcore-5.4.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'libjpeg-turbo' +version = '1.5.0' + +homepage = 'http://sourceforge.net/projects/libjpeg-turbo/' +description = """libjpeg-turbo is a fork of the original IJG libjpeg which uses SIMD to accelerate baseline JPEG +compression and decompression. libjpeg is a library that implements JPEG image encoding, decoding and transcoding. +""" + +toolchain = {'name': 'GCCcore', 'version': '5.4.0'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('NASM', '2.11.08'), +] + +builddependencies = [('binutils', '2.26', '', True)] + +configopts = "--with-jpeg8" +runtest = "test" + +sanity_check_paths = { + 'files': ['bin/cjpeg', 'bin/djpeg', 'bin/jpegtran', 'bin/rdjpgcom', 'bin/tjbench', 'bin/wrjpgcom', + 'lib/libjpeg.a', 'lib/libjpeg.%s' % SHLIB_EXT, 'lib/libturbojpeg.a', 'lib/libturbojpeg.%s' % SHLIB_EXT], + 'dirs': ['include', 'share'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/NASM/NASM-2.11.08-GCCcore-5.4.0.eb b/easybuild/easyconfigs/n/NASM/NASM-2.11.08-GCCcore-5.4.0.eb new file mode 100644 index 0000000000..30ce2d87b8 --- /dev/null +++ b/easybuild/easyconfigs/n/NASM/NASM-2.11.08-GCCcore-5.4.0.eb @@ -0,0 +1,21 @@ +easyblock = 'ConfigureMake' + +name = 'NASM' +version = '2.11.08' + +homepage = 'http://www.nasm.us/' +description = """NASM: General-purpose x86 assembler""" + +toolchain = {'name': 'GCCcore', 'version': '5.4.0'} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://www.nasm.us/pub/nasm/releasebuilds/%(version)s'] + +builddependencies = [('binutils', '2.26', '', True)] + +sanity_check_paths = { + 'files': ['bin/nasm'], + 'dirs': [], +} + +moduleclass = 'lang' -- GitLab From 64fa7fb704f44c1848a36a46944d8777b7a10595 Mon Sep 17 00:00:00 2001 From: John Donners Date: Thu, 8 Jun 2017 21:14:01 +0200 Subject: [PATCH 0915/1603] adding easyconfigs: impi-2017.0.098-iccifort-2017.0.098-GCC-5.4.0-2.26.eb, impi-2017.1.132-GCC-5.4.0-2.26.eb, impi-2017.1.132-iccifort-2017.1.132-GCC-5.4.0-2.26.eb, impi-2017.1.132-iccifort-2017.1.132-GCC-6.3.0-2.27.eb, impi-2017.2.174-iccifort-2017.2.174-GCC-6.3.0-2.27.eb, impi-4.1.0.027.eb, impi-4.1.0.030-iccifort-2013.2.146.eb, impi-4.1.0.030-iccifort-2013.3.163.eb, impi-4.1.0.030-iccifort-2013.4.183.eb, impi-4.1.0.030.eb, impi-4.1.1.036-iccifort-2013.5.192-GCC-4.8.3.eb, impi-4.1.1.036-iccifort-2013.5.192.eb, impi-4.1.1.036.eb, impi-4.1.2.040.eb, impi-4.1.3.045-iccifort-2013_sp1.1.106.eb, impi-4.1.3.045.eb, impi-4.1.3.049-GCC-4.8.3.eb, impi-4.1.3.049-iccifort-2013.5.192-GCC-4.8.3.eb, impi-4.1.3.049-iccifort-2013_sp1.2.144.eb, impi-4.1.3.049.eb, impi-5.0.1.035-iccifort-2015.0.090-GCC-4.9.2.eb, impi-5.0.1.035-iccifort-2015.0.090.eb, impi-5.0.2.044-iccifort-2015.1.133-GCC-4.9.2.eb, impi-5.0.3.048-GCC-4.9.3.eb, impi-5.0.3.048-iccifort-2015.2.164-GCC-4.9.2.eb, impi-5.0.3.048-iccifort-2015.3.187-GNU-4.9.3-2.25.eb, impi-5.0.3.048-iccifort-2015.3.187.eb, impi-5.1.0.079-iccifort-2015.3.187.eb, impi-5.1.1.109-iccifort-2016.0.109-GCC-4.9.3-2.25.eb, impi-5.1.2.150-iccifort-2015.5.223-GCC-4.9.3-2.25.eb, impi-5.1.2.150-iccifort-2016.1.150-GCC-4.9.3-2.25.eb, impi-5.1.3.181-iccifort-2016.2.181-GCC-4.9.3-2.25.eb, impi-5.1.3.181-iccifort-2016.2.181-GCC-5.3.0-2.26.eb, impi-5.1.3.181-iccifort-2016.3.210-GCC-4.9.3-2.25.eb, impi-5.1.3.181-iccifort-2016.3.210-GCC-5.3.0-2.26.eb, impi-5.1.3.181-iccifort-2016.3.210-GCC-5.4.0-2.26.eb, impi-5.1.3.181-iccifortcuda-2016.10.eb --- .../impi/impi-2017.0.098-iccifort-2017.0.098-GCC-5.4.0-2.26.eb | 2 +- easybuild/easyconfigs/i/impi/impi-2017.1.132-GCC-5.4.0-2.26.eb | 2 +- .../impi/impi-2017.1.132-iccifort-2017.1.132-GCC-5.4.0-2.26.eb | 2 +- .../impi/impi-2017.1.132-iccifort-2017.1.132-GCC-6.3.0-2.27.eb | 2 +- .../impi/impi-2017.2.174-iccifort-2017.2.174-GCC-6.3.0-2.27.eb | 2 +- easybuild/easyconfigs/i/impi/impi-4.1.0.027.eb | 2 +- .../easyconfigs/i/impi/impi-4.1.0.030-iccifort-2013.2.146.eb | 2 +- .../easyconfigs/i/impi/impi-4.1.0.030-iccifort-2013.3.163.eb | 2 +- .../easyconfigs/i/impi/impi-4.1.0.030-iccifort-2013.4.183.eb | 2 +- easybuild/easyconfigs/i/impi/impi-4.1.0.030.eb | 2 +- .../i/impi/impi-4.1.1.036-iccifort-2013.5.192-GCC-4.8.3.eb | 2 +- .../easyconfigs/i/impi/impi-4.1.1.036-iccifort-2013.5.192.eb | 2 +- easybuild/easyconfigs/i/impi/impi-4.1.1.036.eb | 2 +- easybuild/easyconfigs/i/impi/impi-4.1.2.040.eb | 2 +- .../i/impi/impi-4.1.3.045-iccifort-2013_sp1.1.106.eb | 2 +- easybuild/easyconfigs/i/impi/impi-4.1.3.045.eb | 2 +- easybuild/easyconfigs/i/impi/impi-4.1.3.049-GCC-4.8.3.eb | 2 +- .../i/impi/impi-4.1.3.049-iccifort-2013.5.192-GCC-4.8.3.eb | 2 +- .../i/impi/impi-4.1.3.049-iccifort-2013_sp1.2.144.eb | 2 +- easybuild/easyconfigs/i/impi/impi-4.1.3.049.eb | 2 +- .../i/impi/impi-5.0.1.035-iccifort-2015.0.090-GCC-4.9.2.eb | 2 +- .../easyconfigs/i/impi/impi-5.0.1.035-iccifort-2015.0.090.eb | 2 +- .../i/impi/impi-5.0.2.044-iccifort-2015.1.133-GCC-4.9.2.eb | 2 +- easybuild/easyconfigs/i/impi/impi-5.0.3.048-GCC-4.9.3.eb | 2 +- .../i/impi/impi-5.0.3.048-iccifort-2015.2.164-GCC-4.9.2.eb | 2 +- .../i/impi/impi-5.0.3.048-iccifort-2015.3.187-GNU-4.9.3-2.25.eb | 2 +- .../easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.3.187.eb | 2 +- .../i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-4.9.3-2.25.eb | 2 +- .../i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-5.3.0-2.26.eb | 2 +- .../i/impi/impi-5.1.3.181-iccifort-2016.3.210-GCC-4.9.3-2.25.eb | 2 +- .../i/impi/impi-5.1.3.181-iccifort-2016.3.210-GCC-5.3.0-2.26.eb | 2 +- .../i/impi/impi-5.1.3.181-iccifort-2016.3.210-GCC-5.4.0-2.26.eb | 2 +- .../easyconfigs/i/impi/impi-5.1.3.181-iccifortcuda-2016.10.eb | 2 +- 33 files changed, 33 insertions(+), 33 deletions(-) diff --git a/easybuild/easyconfigs/i/impi/impi-2017.0.098-iccifort-2017.0.098-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/impi/impi-2017.0.098-iccifort-2017.0.098-GCC-5.4.0-2.26.eb index 867202a357..3457aacbc5 100644 --- a/easybuild/easyconfigs/i/impi/impi-2017.0.098-iccifort-2017.0.098-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/impi/impi-2017.0.098-iccifort-2017.0.098-GCC-5.4.0-2.26.eb @@ -6,7 +6,7 @@ version = '2017.0.098' homepage = 'http://software.intel.com/en-us/intel-mpi-library/' description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric message passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for - Linux OS implements the Message Passing Interface, version 2 (MPI-2) specification.""" + Linux OS implements the Message Passing Interface, version 3.1 (MPI-3) specification.""" toolchain = {'name': 'iccifort', 'version': '2017.0.098-GCC-5.4.0-2.26'} diff --git a/easybuild/easyconfigs/i/impi/impi-2017.1.132-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/impi/impi-2017.1.132-GCC-5.4.0-2.26.eb index 106806006c..57fd16dd93 100644 --- a/easybuild/easyconfigs/i/impi/impi-2017.1.132-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/impi/impi-2017.1.132-GCC-5.4.0-2.26.eb @@ -4,7 +4,7 @@ version = '2017.1.132' homepage = 'http://software.intel.com/en-us/intel-mpi-library/' description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric message passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for - Linux OS implements the Message Passing Interface, version 2 (MPI-2) specification.""" + Linux OS implements the Message Passing Interface, version 3.1 (MPI-3) specification.""" toolchain = {'name': 'GCC', 'version': '5.4.0-2.26'} diff --git a/easybuild/easyconfigs/i/impi/impi-2017.1.132-iccifort-2017.1.132-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/impi/impi-2017.1.132-iccifort-2017.1.132-GCC-5.4.0-2.26.eb index bebecd8cf6..aa746359e2 100644 --- a/easybuild/easyconfigs/i/impi/impi-2017.1.132-iccifort-2017.1.132-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/impi/impi-2017.1.132-iccifort-2017.1.132-GCC-5.4.0-2.26.eb @@ -6,7 +6,7 @@ version = '2017.1.132' homepage = 'http://software.intel.com/en-us/intel-mpi-library/' description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric message passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for - Linux OS implements the Message Passing Interface, version 2 (MPI-2) specification.""" + Linux OS implements the Message Passing Interface, version 3.1 (MPI-3) specification.""" toolchain = {'name': 'iccifort', 'version': '2017.1.132-GCC-5.4.0-2.26'} diff --git a/easybuild/easyconfigs/i/impi/impi-2017.1.132-iccifort-2017.1.132-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/i/impi/impi-2017.1.132-iccifort-2017.1.132-GCC-6.3.0-2.27.eb index 3193d2cc9a..48a890bbcf 100644 --- a/easybuild/easyconfigs/i/impi/impi-2017.1.132-iccifort-2017.1.132-GCC-6.3.0-2.27.eb +++ b/easybuild/easyconfigs/i/impi/impi-2017.1.132-iccifort-2017.1.132-GCC-6.3.0-2.27.eb @@ -6,7 +6,7 @@ version = '2017.1.132' homepage = 'http://software.intel.com/en-us/intel-mpi-library/' description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric message passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for - Linux OS implements the Message Passing Interface, version 2 (MPI-2) specification.""" + Linux OS implements the Message Passing Interface, version 3.1 (MPI-3) specification.""" toolchain = {'name': 'iccifort', 'version': '2017.1.132-GCC-6.3.0-2.27'} diff --git a/easybuild/easyconfigs/i/impi/impi-2017.2.174-iccifort-2017.2.174-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/i/impi/impi-2017.2.174-iccifort-2017.2.174-GCC-6.3.0-2.27.eb index 9375fca351..2d925e4ac1 100644 --- a/easybuild/easyconfigs/i/impi/impi-2017.2.174-iccifort-2017.2.174-GCC-6.3.0-2.27.eb +++ b/easybuild/easyconfigs/i/impi/impi-2017.2.174-iccifort-2017.2.174-GCC-6.3.0-2.27.eb @@ -6,7 +6,7 @@ version = '2017.2.174' homepage = 'http://software.intel.com/en-us/intel-mpi-library/' description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric message passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for - Linux OS implements the Message Passing Interface, version 2 (MPI-2) specification.""" + Linux OS implements the Message Passing Interface, version 3.1 (MPI-3) specification.""" toolchain = {'name': 'iccifort', 'version': '2017.2.174-GCC-6.3.0-2.27'} diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.0.027.eb b/easybuild/easyconfigs/i/impi/impi-4.1.0.027.eb index 209842e727..6929387be6 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.0.027.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.0.027.eb @@ -4,7 +4,7 @@ version = '4.1.0.027' homepage = 'http://software.intel.com/en-us/intel-mpi-library/' description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric message passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for - Linux OS implements the Message Passing Interface, version 2 (MPI-2) specification.""" + Linux OS implements the Message Passing Interface, version 2.2 (MPI-2) specification.""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.0.030-iccifort-2013.2.146.eb b/easybuild/easyconfigs/i/impi/impi-4.1.0.030-iccifort-2013.2.146.eb index c4e43d9fa9..ab6d7960f3 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.0.030-iccifort-2013.2.146.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.0.030-iccifort-2013.2.146.eb @@ -4,7 +4,7 @@ version = '4.1.0.030' homepage = 'http://software.intel.com/en-us/intel-mpi-library/' description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric message passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for - Linux OS implements the Message Passing Interface, version 2 (MPI-2) specification.""" + Linux OS implements the Message Passing Interface, version 2.2 (MPI-2) specification.""" toolchain = {'name': 'iccifort', 'version': '2013.2.146'} diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.0.030-iccifort-2013.3.163.eb b/easybuild/easyconfigs/i/impi/impi-4.1.0.030-iccifort-2013.3.163.eb index 9b5a71ce36..e04df8a494 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.0.030-iccifort-2013.3.163.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.0.030-iccifort-2013.3.163.eb @@ -4,7 +4,7 @@ version = '4.1.0.030' homepage = 'http://software.intel.com/en-us/intel-mpi-library/' description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric message passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for - Linux OS implements the Message Passing Interface, version 2 (MPI-2) specification.""" + Linux OS implements the Message Passing Interface, version 2.2 (MPI-2) specification.""" toolchain = {'name': 'iccifort', 'version': '2013.3.163'} diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.0.030-iccifort-2013.4.183.eb b/easybuild/easyconfigs/i/impi/impi-4.1.0.030-iccifort-2013.4.183.eb index 36a86386a0..0cb097158e 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.0.030-iccifort-2013.4.183.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.0.030-iccifort-2013.4.183.eb @@ -4,7 +4,7 @@ version = '4.1.0.030' homepage = 'http://software.intel.com/en-us/intel-mpi-library/' description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric message passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for - Linux OS implements the Message Passing Interface, version 2 (MPI-2) specification.""" + Linux OS implements the Message Passing Interface, version 2.2 (MPI-2) specification.""" toolchain = {'name': 'iccifort', 'version': '2013.4.183'} diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.0.030.eb b/easybuild/easyconfigs/i/impi/impi-4.1.0.030.eb index 3f28cb9676..159af122db 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.0.030.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.0.030.eb @@ -4,7 +4,7 @@ version = '4.1.0.030' homepage = 'http://software.intel.com/en-us/intel-mpi-library/' description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric message passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for - Linux OS implements the Message Passing Interface, version 2 (MPI-2) specification.""" + Linux OS implements the Message Passing Interface, version 2.2 (MPI-2) specification.""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.1.036-iccifort-2013.5.192-GCC-4.8.3.eb b/easybuild/easyconfigs/i/impi/impi-4.1.1.036-iccifort-2013.5.192-GCC-4.8.3.eb index ee1796488d..be19fa0081 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.1.036-iccifort-2013.5.192-GCC-4.8.3.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.1.036-iccifort-2013.5.192-GCC-4.8.3.eb @@ -4,7 +4,7 @@ version = '4.1.1.036' homepage = 'http://software.intel.com/en-us/intel-mpi-library/' description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric message passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for - Linux OS implements the Message Passing Interface, version 2 (MPI-2) specification.""" + Linux OS implements the Message Passing Interface, version 2.2 (MPI-2) specification.""" toolchain = {'name': 'iccifort', 'version': '2013.5.192-GCC-4.8.3'} diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.1.036-iccifort-2013.5.192.eb b/easybuild/easyconfigs/i/impi/impi-4.1.1.036-iccifort-2013.5.192.eb index 97573c0075..118bb8c103 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.1.036-iccifort-2013.5.192.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.1.036-iccifort-2013.5.192.eb @@ -4,7 +4,7 @@ version = '4.1.1.036' homepage = 'http://software.intel.com/en-us/intel-mpi-library/' description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric message passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for - Linux OS implements the Message Passing Interface, version 2 (MPI-2) specification.""" + Linux OS implements the Message Passing Interface, version 2.2 (MPI-2) specification.""" toolchain = {'name': 'iccifort', 'version': '2013.5.192'} diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.1.036.eb b/easybuild/easyconfigs/i/impi/impi-4.1.1.036.eb index 5524846083..6f14962150 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.1.036.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.1.036.eb @@ -4,7 +4,7 @@ version = '4.1.1.036' homepage = 'http://software.intel.com/en-us/intel-mpi-library/' description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric message passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for - Linux OS implements the Message Passing Interface, version 2 (MPI-2) specification.""" + Linux OS implements the Message Passing Interface, version 2.2 (MPI-2) specification.""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.2.040.eb b/easybuild/easyconfigs/i/impi/impi-4.1.2.040.eb index 5301684735..dd8f68cc71 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.2.040.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.2.040.eb @@ -4,7 +4,7 @@ version = '4.1.2.040' homepage = 'http://software.intel.com/en-us/intel-mpi-library/' description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric message passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for - Linux OS implements the Message Passing Interface, version 2 (MPI-2) specification.""" + Linux OS implements the Message Passing Interface, version 2.2 (MPI-2) specification.""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.3.045-iccifort-2013_sp1.1.106.eb b/easybuild/easyconfigs/i/impi/impi-4.1.3.045-iccifort-2013_sp1.1.106.eb index 3eef4c39b6..8841eb5e48 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.3.045-iccifort-2013_sp1.1.106.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.3.045-iccifort-2013_sp1.1.106.eb @@ -4,7 +4,7 @@ version = '4.1.3.045' homepage = 'http://software.intel.com/en-us/intel-mpi-library/' description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric message passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for - Linux OS implements the Message Passing Interface, version 2 (MPI-2) specification.""" + Linux OS implements the Message Passing Interface, version 2.2 (MPI-2) specification.""" toolchain = {'name': 'iccifort', 'version': '2013_sp1.1.106'} diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.3.045.eb b/easybuild/easyconfigs/i/impi/impi-4.1.3.045.eb index de266ab029..53f0e55211 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.3.045.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.3.045.eb @@ -4,7 +4,7 @@ version = '4.1.3.045' homepage = 'http://software.intel.com/en-us/intel-mpi-library/' description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric message passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for - Linux OS implements the Message Passing Interface, version 2 (MPI-2) specification.""" + Linux OS implements the Message Passing Interface, version 2.2 (MPI-2) specification.""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.3.049-GCC-4.8.3.eb b/easybuild/easyconfigs/i/impi/impi-4.1.3.049-GCC-4.8.3.eb index 81b707143d..f9f2e44736 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.3.049-GCC-4.8.3.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.3.049-GCC-4.8.3.eb @@ -4,7 +4,7 @@ version = '4.1.3.049' homepage = 'http://software.intel.com/en-us/intel-mpi-library/' description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric message passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for - Linux OS implements the Message Passing Interface, version 2 (MPI-2) specification.""" + Linux OS implements the Message Passing Interface, version 2.2 (MPI-2) specification.""" toolchain = {'name': 'GCC', 'version': '4.8.3'} diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.3.049-iccifort-2013.5.192-GCC-4.8.3.eb b/easybuild/easyconfigs/i/impi/impi-4.1.3.049-iccifort-2013.5.192-GCC-4.8.3.eb index 91e7ec80d3..db7602586f 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.3.049-iccifort-2013.5.192-GCC-4.8.3.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.3.049-iccifort-2013.5.192-GCC-4.8.3.eb @@ -4,7 +4,7 @@ version = '4.1.3.049' homepage = 'http://software.intel.com/en-us/intel-mpi-library/' description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric message passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for - Linux OS implements the Message Passing Interface, version 2 (MPI-2) specification.""" + Linux OS implements the Message Passing Interface, version 2.2 (MPI-2) specification.""" toolchain = {'name': 'iccifort', 'version': '2013.5.192-GCC-4.8.3'} diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.3.049-iccifort-2013_sp1.2.144.eb b/easybuild/easyconfigs/i/impi/impi-4.1.3.049-iccifort-2013_sp1.2.144.eb index 3b51024f12..3970ddc476 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.3.049-iccifort-2013_sp1.2.144.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.3.049-iccifort-2013_sp1.2.144.eb @@ -4,7 +4,7 @@ version = '4.1.3.049' homepage = 'http://software.intel.com/en-us/intel-mpi-library/' description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric message passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for - Linux OS implements the Message Passing Interface, version 2 (MPI-2) specification.""" + Linux OS implements the Message Passing Interface, version 2.2 (MPI-2) specification.""" toolchain = {'name': 'iccifort', 'version': '2013_sp1.2.144'} diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.3.049.eb b/easybuild/easyconfigs/i/impi/impi-4.1.3.049.eb index 7b345a78e7..8b558e1f1c 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.3.049.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.3.049.eb @@ -4,7 +4,7 @@ version = '4.1.3.049' homepage = 'http://software.intel.com/en-us/intel-mpi-library/' description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric message passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for - Linux OS implements the Message Passing Interface, version 2 (MPI-2) specification.""" + Linux OS implements the Message Passing Interface, version 2.2 (MPI-2) specification.""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/impi/impi-5.0.1.035-iccifort-2015.0.090-GCC-4.9.2.eb b/easybuild/easyconfigs/i/impi/impi-5.0.1.035-iccifort-2015.0.090-GCC-4.9.2.eb index 154d705ccf..68543c277e 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.0.1.035-iccifort-2015.0.090-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.0.1.035-iccifort-2015.0.090-GCC-4.9.2.eb @@ -4,7 +4,7 @@ version = '5.0.1.035' homepage = 'http://software.intel.com/en-us/intel-mpi-library/' description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric message passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for - Linux OS implements the Message Passing Interface, version 2 (MPI-2) specification.""" + Linux OS implements the Message Passing Interface, version 3.0 (MPI-3) specification.""" toolchain = {'name': 'iccifort', 'version': '2015.0.090-GCC-4.9.2'} diff --git a/easybuild/easyconfigs/i/impi/impi-5.0.1.035-iccifort-2015.0.090.eb b/easybuild/easyconfigs/i/impi/impi-5.0.1.035-iccifort-2015.0.090.eb index 952a3f2313..f8d4105279 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.0.1.035-iccifort-2015.0.090.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.0.1.035-iccifort-2015.0.090.eb @@ -4,7 +4,7 @@ version = '5.0.1.035' homepage = 'http://software.intel.com/en-us/intel-mpi-library/' description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric message passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for - Linux OS implements the Message Passing Interface, version 2 (MPI-2) specification.""" + Linux OS implements the Message Passing Interface, version 3.0 (MPI-3) specification.""" toolchain = {'name': 'iccifort', 'version': '2015.0.090'} diff --git a/easybuild/easyconfigs/i/impi/impi-5.0.2.044-iccifort-2015.1.133-GCC-4.9.2.eb b/easybuild/easyconfigs/i/impi/impi-5.0.2.044-iccifort-2015.1.133-GCC-4.9.2.eb index 62a9caf2ee..42da75af9c 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.0.2.044-iccifort-2015.1.133-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.0.2.044-iccifort-2015.1.133-GCC-4.9.2.eb @@ -4,7 +4,7 @@ version = '5.0.2.044' homepage = 'http://software.intel.com/en-us/intel-mpi-library/' description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric message passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for - Linux OS implements the Message Passing Interface, version 2 (MPI-2) specification.""" + Linux OS implements the Message Passing Interface, version 3.0 (MPI-3) specification.""" toolchain = {'name': 'iccifort', 'version': '2015.1.133-GCC-4.9.2'} diff --git a/easybuild/easyconfigs/i/impi/impi-5.0.3.048-GCC-4.9.3.eb b/easybuild/easyconfigs/i/impi/impi-5.0.3.048-GCC-4.9.3.eb index 46722880e7..c9221491ef 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.0.3.048-GCC-4.9.3.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.0.3.048-GCC-4.9.3.eb @@ -4,7 +4,7 @@ version = '5.0.3.048' homepage = 'http://software.intel.com/en-us/intel-mpi-library/' description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric message passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for - Linux OS implements the Message Passing Interface, version 2 (MPI-2) specification.""" + Linux OS implements the Message Passing Interface, version 3.0 (MPI-3) specification.""" toolchain = {'name': 'GCC', 'version': '4.9.3'} diff --git a/easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.2.164-GCC-4.9.2.eb b/easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.2.164-GCC-4.9.2.eb index 452ab3ddd5..8a9edd8c88 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.2.164-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.2.164-GCC-4.9.2.eb @@ -4,7 +4,7 @@ version = '5.0.3.048' homepage = 'http://software.intel.com/en-us/intel-mpi-library/' description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric message passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for - Linux OS implements the Message Passing Interface, version 2 (MPI-2) specification.""" + Linux OS implements the Message Passing Interface, version 3.0 (MPI-3) specification.""" toolchain = {'name': 'iccifort', 'version': '2015.2.164-GCC-4.9.2'} diff --git a/easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.3.187-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.3.187-GNU-4.9.3-2.25.eb index 7de5ce16aa..b10c36dc27 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.3.187-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.3.187-GNU-4.9.3-2.25.eb @@ -4,7 +4,7 @@ version = '5.0.3.048' homepage = 'http://software.intel.com/en-us/intel-mpi-library/' description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric message passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for - Linux OS implements the Message Passing Interface, version 2 (MPI-2) specification.""" + Linux OS implements the Message Passing Interface, version 3.0 (MPI-3) specification.""" toolchain = {'name': 'iccifort', 'version': '2015.3.187-GNU-4.9.3-2.25'} diff --git a/easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.3.187.eb b/easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.3.187.eb index 51baff5e35..ea4314e4dc 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.3.187.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.3.187.eb @@ -4,7 +4,7 @@ version = '5.0.3.048' homepage = 'http://software.intel.com/en-us/intel-mpi-library/' description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric message passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for - Linux OS implements the Message Passing Interface, version 2 (MPI-2) specification.""" + Linux OS implements the Message Passing Interface, version 3.0 (MPI-3) specification.""" toolchain = {'name': 'iccifort', 'version': '2015.3.187'} diff --git a/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-4.9.3-2.25.eb index 845f7631f8..ff29599396 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-4.9.3-2.25.eb @@ -6,7 +6,7 @@ version = '5.1.3.181' homepage = 'http://software.intel.com/en-us/intel-mpi-library/' description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric message passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for - Linux OS implements the Message Passing Interface, version 2 (MPI-2) specification.""" + Linux OS implements the Message Passing Interface, version 3.1 (MPI-3) specification.""" toolchain = {'name': 'iccifort', 'version': '2016.2.181-GCC-4.9.3-2.25'} diff --git a/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-5.3.0-2.26.eb index eaf9a3b7a7..b683120608 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-5.3.0-2.26.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-5.3.0-2.26.eb @@ -6,7 +6,7 @@ version = '5.1.3.181' homepage = 'http://software.intel.com/en-us/intel-mpi-library/' description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric message passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for - Linux OS implements the Message Passing Interface, version 2 (MPI-2) specification.""" + Linux OS implements the Message Passing Interface, version 3.1 (MPI-3) specification.""" toolchain = {'name': 'iccifort', 'version': '2016.2.181-GCC-5.3.0-2.26'} diff --git a/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.3.210-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.3.210-GCC-4.9.3-2.25.eb index 56d81448bf..82952d9703 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.3.210-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.3.210-GCC-4.9.3-2.25.eb @@ -6,7 +6,7 @@ version = '5.1.3.181' homepage = 'http://software.intel.com/en-us/intel-mpi-library/' description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric message passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for - Linux OS implements the Message Passing Interface, version 2 (MPI-2) specification.""" + Linux OS implements the Message Passing Interface, version 3.1 (MPI-3) specification.""" toolchain = {'name': 'iccifort', 'version': '2016.3.210-GCC-4.9.3-2.25'} diff --git a/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.3.210-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.3.210-GCC-5.3.0-2.26.eb index cc0d58235f..c9693689db 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.3.210-GCC-5.3.0-2.26.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.3.210-GCC-5.3.0-2.26.eb @@ -6,7 +6,7 @@ version = '5.1.3.181' homepage = 'http://software.intel.com/en-us/intel-mpi-library/' description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric message passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for - Linux OS implements the Message Passing Interface, version 2 (MPI-2) specification.""" + Linux OS implements the Message Passing Interface, version 3.1 (MPI-3) specification.""" toolchain = {'name': 'iccifort', 'version': '2016.3.210-GCC-5.3.0-2.26'} diff --git a/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.3.210-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.3.210-GCC-5.4.0-2.26.eb index 565380f44c..28540e5444 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.3.210-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.3.210-GCC-5.4.0-2.26.eb @@ -6,7 +6,7 @@ version = '5.1.3.181' homepage = 'http://software.intel.com/en-us/intel-mpi-library/' description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric message passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for - Linux OS implements the Message Passing Interface, version 2 (MPI-2) specification.""" + Linux OS implements the Message Passing Interface, version 3.1 (MPI-3) specification.""" toolchain = {'name': 'iccifort', 'version': '2016.3.210-GCC-5.4.0-2.26'} diff --git a/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifortcuda-2016.10.eb b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifortcuda-2016.10.eb index 292b8c704e..9873b9f096 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifortcuda-2016.10.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifortcuda-2016.10.eb @@ -6,7 +6,7 @@ version = '5.1.3.181' homepage = 'http://software.intel.com/en-us/intel-mpi-library/' description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric message passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for - Linux OS implements the Message Passing Interface, version 2 (MPI-2) specification.""" + Linux OS implements the Message Passing Interface, version 3.1 (MPI-3) specification.""" toolchain = {'name': 'iccifortcuda', 'version': '2016.10'} -- GitLab From dfd0a7ee896a9a0a1f96931842ca436897f66b5e Mon Sep 17 00:00:00 2001 From: Robert Date: Fri, 9 Jun 2017 13:30:31 +0930 Subject: [PATCH 0916/1603] {bio}{dummy} SEED added --- easybuild/easyconfigs/s/SEED/SEED-2015.eb | 36 +++++++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/s/SEED/SEED-2015.eb diff --git a/easybuild/easyconfigs/s/SEED/SEED-2015.eb b/easybuild/easyconfigs/s/SEED/SEED-2015.eb new file mode 100644 index 0000000000..b186b85f21 --- /dev/null +++ b/easybuild/easyconfigs/s/SEED/SEED-2015.eb @@ -0,0 +1,36 @@ +## +# This is a contribution from Phoenix HPC Service, The University of Adelaide, Australia +# Homepage: https://www.adelaide.edu.au/phoenix/ +# +# Copyright:: Copyright 2014-2017 adelaide.edu.au/phoenix +# Authors:: Robert Qiao , Exequiel Sepulveda +# License:: Artistic-v2.0 +# +# Notes:: +## + +easyblock = 'CmdCp' + +name = 'SEED' +version = '2015' + +homepage = 'http://www.theseed.org/wiki/Main_Page' +description = """ SEED is a software for clustering large sets of Next Generation Sequences (NGS) +with hundreds of millions of reads in a time and memory efficient manner. +Its algorithm joins highly similar sequences into clusters that can differ +by up to three mismatches and three overhanging residues. +""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['master.zip'] +source_urls = ['https://github.com/baoe/SEED/archive'] + +files_to_copy = (['SEED/SEED'], 'bin'), + +sanity_check_paths = { + 'files': ["bin/SEED"], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From 5b0f4797cfda1e3bc685e45a60701eb8131d47cf Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Fri, 9 Jun 2017 16:23:45 +1200 Subject: [PATCH 0917/1603] Ensure PREFIX is set at build, not only at install, so that NE_GLOBAL_DIR is correctly set --- easybuild/easyconfigs/n/ne/ne-3.0.1-foss-2015a.eb | 1 + easybuild/easyconfigs/n/ne/ne-3.0.1-gimkl-2017a.eb | 1 + 2 files changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/n/ne/ne-3.0.1-foss-2015a.eb b/easybuild/easyconfigs/n/ne/ne-3.0.1-foss-2015a.eb index 4898061930..ebfa1fab31 100644 --- a/easybuild/easyconfigs/n/ne/ne-3.0.1-foss-2015a.eb +++ b/easybuild/easyconfigs/n/ne/ne-3.0.1-foss-2015a.eb @@ -15,6 +15,7 @@ source_urls = ['http://ne.di.unimi.it/'] sources = [SOURCELOWER_TAR_GZ] skipsteps = ['configure'] +buildopts = "PREFIX=%(installdir)s" installopts = "PREFIX=%(installdir)s" sanity_check_paths = { diff --git a/easybuild/easyconfigs/n/ne/ne-3.0.1-gimkl-2017a.eb b/easybuild/easyconfigs/n/ne/ne-3.0.1-gimkl-2017a.eb index f6ca385967..b43f3a5a81 100644 --- a/easybuild/easyconfigs/n/ne/ne-3.0.1-gimkl-2017a.eb +++ b/easybuild/easyconfigs/n/ne/ne-3.0.1-gimkl-2017a.eb @@ -19,6 +19,7 @@ dependencies = [ ] skipsteps = ['configure'] +buildopts = "PREFIX=%(installdir)s" installopts = "PREFIX=%(installdir)s" sanity_check_paths = { -- GitLab From 04a431ff6ff6184621160ce03e90c730b54ff06c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 9 Jun 2017 15:01:28 +0200 Subject: [PATCH 0918/1603] adding easyconfigs: sleuth-0.29.0-intel-2017a-R-3.4.0.eb --- .../sleuth-0.29.0-intel-2017a-R-3.4.0.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/s/sleuth/sleuth-0.29.0-intel-2017a-R-3.4.0.eb diff --git a/easybuild/easyconfigs/s/sleuth/sleuth-0.29.0-intel-2017a-R-3.4.0.eb b/easybuild/easyconfigs/s/sleuth/sleuth-0.29.0-intel-2017a-R-3.4.0.eb new file mode 100644 index 0000000000..aba646221e --- /dev/null +++ b/easybuild/easyconfigs/s/sleuth/sleuth-0.29.0-intel-2017a-R-3.4.0.eb @@ -0,0 +1,25 @@ +easyblock = 'RPackage' + +name = 'sleuth' +version = '0.29.0' +versionsuffix = '-R-%(rver)s' + +homepage = 'http://pachterlab.github.io/sleuth' +description = """Investigate RNA-Seq transcript abundance from kallisto and perform differential expression analysis.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['https://github.com/pachterlab/sleuth/archive/'] +sources = ['v%(version)s.tar.gz'] + +dependencies = [ + ('R', '3.4.0', '-X11-20170314'), + ('R-bundle-Bioconductor', '3.5', versionsuffix), +] + +sanity_check_paths = { + 'files': [], + 'dirs': [name], +} + +moduleclass = 'bio' -- GitLab From c932408af5283c17fd34ddae5eb097910d9eb2a8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 9 Jun 2017 18:23:29 +0200 Subject: [PATCH 0919/1603] use --with-x=yes in R easyconfigs that include X11 as a dependency --- easybuild/easyconfigs/r/R/R-3.3.3-foss-2016b-X11-20160819.eb | 2 +- easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170314.eb | 2 +- easybuild/easyconfigs/r/R/R-3.4.0-intel-2017a-X11-20170314.eb | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/r/R/R-3.3.3-foss-2016b-X11-20160819.eb b/easybuild/easyconfigs/r/R/R-3.3.3-foss-2016b-X11-20160819.eb index 3b6ee9a746..17436647a4 100644 --- a/easybuild/easyconfigs/r/R/R-3.3.3-foss-2016b-X11-20160819.eb +++ b/easybuild/easyconfigs/r/R/R-3.3.3-foss-2016b-X11-20160819.eb @@ -12,7 +12,7 @@ sources = [SOURCE_TAR_GZ] source_urls = ['http://cran.us.r-project.org/src/base/R-%(version_major)s'] preconfigopts = 'BLAS_LIBS="$LIBBLAS" LAPACK_LIBS="$LIBLAPACK"' -configopts = "--with-lapack --with-blas --with-pic --enable-threads --with-x=no --enable-R-shlib" +configopts = "--with-lapack --with-blas --with-pic --enable-threads --with-x=yes --enable-R-shlib" #Actually use Tcl/Tk configopts += ' --with-tcl-config=$EBROOTTCL/lib/tclConfig.sh --with-tk-config=$EBROOTTK/lib/tkConfig.sh ' # Enable graphics capabilities for plotting. diff --git a/easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170314.eb b/easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170314.eb index 963e074572..dd6b13d0c2 100644 --- a/easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170314.eb +++ b/easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170314.eb @@ -12,7 +12,7 @@ sources = [SOURCE_TAR_GZ] source_urls = ['http://cran.us.r-project.org/src/base/R-%(version_major)s'] preconfigopts = 'BLAS_LIBS="$LIBBLAS" LAPACK_LIBS="$LIBLAPACK"' -configopts = "--with-lapack --with-blas --with-pic --enable-threads --with-x=no --enable-R-shlib" +configopts = "--with-lapack --with-blas --with-pic --enable-threads --with-x=yes --enable-R-shlib" #Actually use Tcl/Tk configopts += ' --with-tcl-config=$EBROOTTCL/lib/tclConfig.sh --with-tk-config=$EBROOTTK/lib/tkConfig.sh ' # Enable graphics capabilities for plotting. diff --git a/easybuild/easyconfigs/r/R/R-3.4.0-intel-2017a-X11-20170314.eb b/easybuild/easyconfigs/r/R/R-3.4.0-intel-2017a-X11-20170314.eb index b17ecb1531..db02d8833d 100644 --- a/easybuild/easyconfigs/r/R/R-3.4.0-intel-2017a-X11-20170314.eb +++ b/easybuild/easyconfigs/r/R/R-3.4.0-intel-2017a-X11-20170314.eb @@ -12,7 +12,7 @@ sources = [SOURCE_TAR_GZ] source_urls = ['http://cran.us.r-project.org/src/base/R-%(version_major)s'] preconfigopts = 'BLAS_LIBS="$LIBBLAS" LAPACK_LIBS="$LIBLAPACK"' -configopts = "--with-lapack --with-blas --with-pic --enable-threads --with-x=no --enable-R-shlib" +configopts = "--with-lapack --with-blas --with-pic --enable-threads --with-x=yes --enable-R-shlib" # Actually use Tcl/Tk configopts += ' --with-tcl-config=$EBROOTTCL/lib/tclConfig.sh --with-tk-config=$EBROOTTK/lib/tkConfig.sh ' # Enable graphics capabilities for plotting. -- GitLab From 8a545e4e062c77c5f35e68362f7537fa919a94fb Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Fri, 9 Jun 2017 17:07:11 -0500 Subject: [PATCH 0920/1603] adding easyconfigs: Tcl-8.6.5-iccifort-2016.3.210-GCC-5.4.0-2.26.eb, SQLite-3.13.0-iccifort-2016.3.210-GCC-5.4.0-2.26.eb, Tk-8.6.5-iccifort-2016.3.210-GCC-5.4.0-2.26.eb, Python-2.7.12-iccifort-2016.3.210-GCC-5.4.0-2.26-bare.eb --- ...iccifort-2016.3.210-GCC-5.4.0-2.26-bare.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.12-iccifort-2016.3.210-GCC-5.4.0-2.26-bare.eb diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.12-iccifort-2016.3.210-GCC-5.4.0-2.26-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.12-iccifort-2016.3.210-GCC-5.4.0-2.26-bare.eb new file mode 100644 index 0000000000..d9fd114759 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.12-iccifort-2016.3.210-GCC-5.4.0-2.26-bare.eb @@ -0,0 +1,35 @@ +name = 'Python' +version = '2.7.12' +versionsuffix = '-bare' + +homepage = 'http://python.org/' +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" + +toolchain = {'name': 'iccifort', 'version': '2016.3.210-GCC-5.4.0-2.26'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +# python needs bzip2 to build the bz2 package +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libreadline', '6.3'), + ('ncurses', '6.0'), + ('SQLite', '3.13.0'), + ('Tk', '8.6.5'), # this requires a full X11 stack + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.2h'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +modluafooter = 'family("python")' + +# bare installation: no extensions included +exts_list = [] + +moduleclass = 'lang' -- GitLab From 045e29d93edb740575e27d03287bee21f55f1e60 Mon Sep 17 00:00:00 2001 From: Robert Date: Sat, 10 Jun 2017 11:40:06 +0930 Subject: [PATCH 0921/1603] OrfM easyconfig added --- .../o/OrfM/OrfM-0.6.1-foss-2016b.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/o/OrfM/OrfM-0.6.1-foss-2016b.eb diff --git a/easybuild/easyconfigs/o/OrfM/OrfM-0.6.1-foss-2016b.eb b/easybuild/easyconfigs/o/OrfM/OrfM-0.6.1-foss-2016b.eb new file mode 100644 index 0000000000..ae95bf0649 --- /dev/null +++ b/easybuild/easyconfigs/o/OrfM/OrfM-0.6.1-foss-2016b.eb @@ -0,0 +1,37 @@ +## +# This is a contribution from Phoenix HPC Service, The University of Adelaide, Australia +# Homepage: https://www.adelaide.edu.au/phoenix/ +# +# Copyright:: Copyright 2014-2017 adelaide.edu.au/phoenix +# Authors:: Robert Qiao , Exequiel Sepulveda +# License:: LGPL-v3.0 +# +# Notes:: +## + +easyblock = 'ConfigureMake' + +name = 'OrfM' +version = '0.6.1' +namelower = 'orfm' + +homepage = 'https://github.com/wwood/OrfM' +description = """A simple and not slow open reading frame (ORF) caller. +No bells or whistles like frameshift detection, +just a straightforward goal of returning a FASTA file +of open reading frames over a certain length from a FASTA/Q file +of nucleotide sequences. +""" + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'usempi': True} + +sources = ['v%(version)s/%(namelower)s-%(version)s.tar.gz'] +source_urls = ['https://github.com/wwood/OrfM/releases/download'] + +sanity_check_paths = { + 'files': ['bin/orfm'], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From 20d3efacb6ab40bc6729d727ec861e81a01dd068 Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Fri, 9 Jun 2017 22:50:18 -0500 Subject: [PATCH 0922/1603] adding easyconfigs: tbb-2017.6.196.eb --- easybuild/easyconfigs/t/tbb/tbb-2017.6.196.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/t/tbb/tbb-2017.6.196.eb diff --git a/easybuild/easyconfigs/t/tbb/tbb-2017.6.196.eb b/easybuild/easyconfigs/t/tbb/tbb-2017.6.196.eb new file mode 100644 index 0000000000..458116d68c --- /dev/null +++ b/easybuild/easyconfigs/t/tbb/tbb-2017.6.196.eb @@ -0,0 +1,25 @@ +name = 'tbb' +version = '2017.6.196' + +homepage = 'http://software.intel.com/en-us/articles/intel-tbb/' + +description = """ + Intel Threading Building Blocks 4.0 (Intel TBB) is a widely used, + award-winning C++ template library for creating reliable, portable, and + scalable parallel applications. Use Intel TBB for a simple and rapid way + of developing robust task-based parallel applications that scale to available + processor cores, are compatible with multiple environments, and are easier to + maintain. Intel TBB is the most proficient way to implement future-proof + parallel applications that tap into the power and performance of multicore + and manycore hardware platforms. +""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['l_tbb_%(version)s.tgz'] + +requires_runtime_license = False + +dontcreateinstalldir = True + +moduleclass = 'lib' -- GitLab From 734e3e1f0706ce8edb5d0e440e96628277091d44 Mon Sep 17 00:00:00 2001 From: John Donners Date: Sat, 10 Jun 2017 10:33:06 +0200 Subject: [PATCH 0923/1603] Fixed descriptions of impi-5.1.\* --- .../easyconfigs/i/impi/impi-5.1.0.079-iccifort-2015.3.187.eb | 2 +- .../i/impi/impi-5.1.1.109-iccifort-2016.0.109-GCC-4.9.3-2.25.eb | 2 +- .../i/impi/impi-5.1.2.150-iccifort-2015.5.223-GCC-4.9.3-2.25.eb | 2 +- .../i/impi/impi-5.1.2.150-iccifort-2016.1.150-GCC-4.9.3-2.25.eb | 2 +- .../i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-4.9.3-2.25.eb | 2 +- .../i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-5.3.0-2.26.eb | 2 +- .../i/impi/impi-5.1.3.181-iccifort-2016.3.210-GCC-4.9.3-2.25.eb | 2 +- .../i/impi/impi-5.1.3.181-iccifort-2016.3.210-GCC-5.3.0-2.26.eb | 2 +- .../i/impi/impi-5.1.3.181-iccifort-2016.3.210-GCC-5.4.0-2.26.eb | 2 +- .../easyconfigs/i/impi/impi-5.1.3.181-iccifortcuda-2016.10.eb | 2 +- 10 files changed, 10 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/i/impi/impi-5.1.0.079-iccifort-2015.3.187.eb b/easybuild/easyconfigs/i/impi/impi-5.1.0.079-iccifort-2015.3.187.eb index 51936e972d..66832f4bce 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.1.0.079-iccifort-2015.3.187.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.1.0.079-iccifort-2015.3.187.eb @@ -4,7 +4,7 @@ version = '5.1.0.079' homepage = 'http://software.intel.com/en-us/intel-mpi-library/' description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric message passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for - Linux OS implements the Message Passing Interface, version 2 (MPI-2) specification.""" + Linux OS implements the Message Passing Interface, version 3.0 (MPI-3) specification.""" toolchain = {'name': 'iccifort', 'version': '2015.3.187'} diff --git a/easybuild/easyconfigs/i/impi/impi-5.1.1.109-iccifort-2016.0.109-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/impi/impi-5.1.1.109-iccifort-2016.0.109-GCC-4.9.3-2.25.eb index 8d146fd342..2a54c28eb8 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.1.1.109-iccifort-2016.0.109-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.1.1.109-iccifort-2016.0.109-GCC-4.9.3-2.25.eb @@ -6,7 +6,7 @@ version = '5.1.1.109' homepage = 'http://software.intel.com/en-us/intel-mpi-library/' description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric message passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for - Linux OS implements the Message Passing Interface, version 2 (MPI-2) specification.""" + Linux OS implements the Message Passing Interface, version 3.0 (MPI-3) specification.""" toolchain = {'name': 'iccifort', 'version': '2016.0.109-GCC-4.9.3-2.25'} diff --git a/easybuild/easyconfigs/i/impi/impi-5.1.2.150-iccifort-2015.5.223-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/impi/impi-5.1.2.150-iccifort-2015.5.223-GCC-4.9.3-2.25.eb index af79fd7190..562b27bc40 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.1.2.150-iccifort-2015.5.223-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.1.2.150-iccifort-2015.5.223-GCC-4.9.3-2.25.eb @@ -4,7 +4,7 @@ version = '5.1.2.150' homepage = 'http://software.intel.com/en-us/intel-mpi-library/' description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric message passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for - Linux OS implements the Message Passing Interface, version 2 (MPI-2) specification.""" + Linux OS implements the Message Passing Interface, version 3.0 (MPI-3) specification.""" toolchain = {'name': 'iccifort', 'version': '2015.5.223-GCC-4.9.3-2.25'} diff --git a/easybuild/easyconfigs/i/impi/impi-5.1.2.150-iccifort-2016.1.150-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/impi/impi-5.1.2.150-iccifort-2016.1.150-GCC-4.9.3-2.25.eb index 6042d117f6..71b0e15d81 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.1.2.150-iccifort-2016.1.150-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.1.2.150-iccifort-2016.1.150-GCC-4.9.3-2.25.eb @@ -6,7 +6,7 @@ version = '5.1.2.150' homepage = 'http://software.intel.com/en-us/intel-mpi-library/' description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric message passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for - Linux OS implements the Message Passing Interface, version 2 (MPI-2) specification.""" + Linux OS implements the Message Passing Interface, version 3.0 (MPI-3) specification.""" toolchain = {'name': 'iccifort', 'version': '2016.1.150-GCC-4.9.3-2.25'} diff --git a/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-4.9.3-2.25.eb index ff29599396..8f1eb713c5 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-4.9.3-2.25.eb @@ -6,7 +6,7 @@ version = '5.1.3.181' homepage = 'http://software.intel.com/en-us/intel-mpi-library/' description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric message passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for - Linux OS implements the Message Passing Interface, version 3.1 (MPI-3) specification.""" + Linux OS implements the Message Passing Interface, version 3.0 (MPI-3) specification.""" toolchain = {'name': 'iccifort', 'version': '2016.2.181-GCC-4.9.3-2.25'} diff --git a/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-5.3.0-2.26.eb index b683120608..72d570c9ae 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-5.3.0-2.26.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-5.3.0-2.26.eb @@ -6,7 +6,7 @@ version = '5.1.3.181' homepage = 'http://software.intel.com/en-us/intel-mpi-library/' description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric message passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for - Linux OS implements the Message Passing Interface, version 3.1 (MPI-3) specification.""" + Linux OS implements the Message Passing Interface, version 3.0 (MPI-3) specification.""" toolchain = {'name': 'iccifort', 'version': '2016.2.181-GCC-5.3.0-2.26'} diff --git a/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.3.210-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.3.210-GCC-4.9.3-2.25.eb index 82952d9703..212b21a522 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.3.210-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.3.210-GCC-4.9.3-2.25.eb @@ -6,7 +6,7 @@ version = '5.1.3.181' homepage = 'http://software.intel.com/en-us/intel-mpi-library/' description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric message passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for - Linux OS implements the Message Passing Interface, version 3.1 (MPI-3) specification.""" + Linux OS implements the Message Passing Interface, version 3.0 (MPI-3) specification.""" toolchain = {'name': 'iccifort', 'version': '2016.3.210-GCC-4.9.3-2.25'} diff --git a/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.3.210-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.3.210-GCC-5.3.0-2.26.eb index c9693689db..783cda572d 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.3.210-GCC-5.3.0-2.26.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.3.210-GCC-5.3.0-2.26.eb @@ -6,7 +6,7 @@ version = '5.1.3.181' homepage = 'http://software.intel.com/en-us/intel-mpi-library/' description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric message passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for - Linux OS implements the Message Passing Interface, version 3.1 (MPI-3) specification.""" + Linux OS implements the Message Passing Interface, version 3.0 (MPI-3) specification.""" toolchain = {'name': 'iccifort', 'version': '2016.3.210-GCC-5.3.0-2.26'} diff --git a/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.3.210-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.3.210-GCC-5.4.0-2.26.eb index 28540e5444..420224789e 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.3.210-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.3.210-GCC-5.4.0-2.26.eb @@ -6,7 +6,7 @@ version = '5.1.3.181' homepage = 'http://software.intel.com/en-us/intel-mpi-library/' description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric message passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for - Linux OS implements the Message Passing Interface, version 3.1 (MPI-3) specification.""" + Linux OS implements the Message Passing Interface, version 3.0 (MPI-3) specification.""" toolchain = {'name': 'iccifort', 'version': '2016.3.210-GCC-5.4.0-2.26'} diff --git a/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifortcuda-2016.10.eb b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifortcuda-2016.10.eb index 9873b9f096..b61daed0c1 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifortcuda-2016.10.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifortcuda-2016.10.eb @@ -6,7 +6,7 @@ version = '5.1.3.181' homepage = 'http://software.intel.com/en-us/intel-mpi-library/' description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric message passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for - Linux OS implements the Message Passing Interface, version 3.1 (MPI-3) specification.""" + Linux OS implements the Message Passing Interface, version 3.0 (MPI-3) specification.""" toolchain = {'name': 'iccifortcuda', 'version': '2016.10'} -- GitLab From 6e0c6e7f6755f0507de970fe643c1dacc279b39c Mon Sep 17 00:00:00 2001 From: Yann Sagon Date: Mon, 12 Jun 2017 16:56:56 +0200 Subject: [PATCH 0924/1603] MaSuRCA for foss 2016a --- .../m/MaSuRCA/MaSuRCA-3.2.2-foss-206a.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/m/MaSuRCA/MaSuRCA-3.2.2-foss-206a.eb diff --git a/easybuild/easyconfigs/m/MaSuRCA/MaSuRCA-3.2.2-foss-206a.eb b/easybuild/easyconfigs/m/MaSuRCA/MaSuRCA-3.2.2-foss-206a.eb new file mode 100644 index 0000000000..57cbf4b326 --- /dev/null +++ b/easybuild/easyconfigs/m/MaSuRCA/MaSuRCA-3.2.2-foss-206a.eb @@ -0,0 +1,44 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2017 University of Geneva +# Authors:: Yann Sagon +# License:: MIT/GPL +# $Id$ +# +## + +easyblock = 'ConfigureMake' + +name = 'MaSuRCA' +version = '3.2.2' + +homepage = 'http://www.genome.umd.edu/masurca.html' + +description = '''MaSuRCA is whole genome assembly software. It combines the efficiency of the de Bruijn graph + and Overlap-Layout-Consensus (OLC) approaches. MaSuRCA can assemble data sets containing + only short reads from Illumina sequencing or a mixture of short reads and long reads + (Sanger, 454, Pacbio and Nanopore).''' + +toolchain = {'name': 'foss', 'version': '2016a'} + +buildopts="install-special" +start_dir="global-1" + +#need a temporary url to download it. Do it manually. +source_urls = ['http://www.genome.umd.edu/masurca_form.html'] +sources = ['%(name)s-%(version)s.tar.gz'] + +dependencies = [ + ('libreadline', '6.3'), + ('Tcl', '8.6.3'), + ('Boost', '1.61.0'), + ('zlib', '1.2.8'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ["bin"], +} + +moduleclass = 'bio' -- GitLab From eb98f583f62a69a35e73ecc52ec4fbbc40cb4cc2 Mon Sep 17 00:00:00 2001 From: Yann Sagon Date: Mon, 12 Jun 2017 17:07:19 +0200 Subject: [PATCH 0925/1603] typo filename --- .../{MaSuRCA-3.2.2-foss-206a.eb => MaSuRCA-3.2.2-foss-2016a.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/m/MaSuRCA/{MaSuRCA-3.2.2-foss-206a.eb => MaSuRCA-3.2.2-foss-2016a.eb} (100%) diff --git a/easybuild/easyconfigs/m/MaSuRCA/MaSuRCA-3.2.2-foss-206a.eb b/easybuild/easyconfigs/m/MaSuRCA/MaSuRCA-3.2.2-foss-2016a.eb similarity index 100% rename from easybuild/easyconfigs/m/MaSuRCA/MaSuRCA-3.2.2-foss-206a.eb rename to easybuild/easyconfigs/m/MaSuRCA/MaSuRCA-3.2.2-foss-2016a.eb -- GitLab From 843775d27184e4e0d5292a83e886a36ba2c65adc Mon Sep 17 00:00:00 2001 From: Yann Sagon Date: Mon, 12 Jun 2017 17:21:42 +0200 Subject: [PATCH 0926/1603] fix tcl dep --- easybuild/easyconfigs/m/MaSuRCA/MaSuRCA-3.2.2-foss-2016a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MaSuRCA/MaSuRCA-3.2.2-foss-2016a.eb b/easybuild/easyconfigs/m/MaSuRCA/MaSuRCA-3.2.2-foss-2016a.eb index 57cbf4b326..56f1d8c0ac 100644 --- a/easybuild/easyconfigs/m/MaSuRCA/MaSuRCA-3.2.2-foss-2016a.eb +++ b/easybuild/easyconfigs/m/MaSuRCA/MaSuRCA-3.2.2-foss-2016a.eb @@ -31,7 +31,7 @@ sources = ['%(name)s-%(version)s.tar.gz'] dependencies = [ ('libreadline', '6.3'), - ('Tcl', '8.6.3'), + ('Tcl', '8.6.5'), ('Boost', '1.61.0'), ('zlib', '1.2.8'), ] -- GitLab From 8a90950abebac4b1d13636fd13ff8aad29faba52 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 12 Jun 2017 17:54:32 +0200 Subject: [PATCH 0927/1603] remove '4.0' in tbb description --- easybuild/easyconfigs/t/tbb/tbb-2017.2.132.eb | 2 +- easybuild/easyconfigs/t/tbb/tbb-2017.4.174.eb | 2 +- easybuild/easyconfigs/t/tbb/tbb-2017.6.196.eb | 2 +- easybuild/easyconfigs/t/tbb/tbb-4.0.0.233.eb | 2 +- easybuild/easyconfigs/t/tbb/tbb-4.0.5.339.eb | 2 +- easybuild/easyconfigs/t/tbb/tbb-4.3.6.211.eb | 2 +- easybuild/easyconfigs/t/tbb/tbb-4.4.2.152.eb | 2 +- 7 files changed, 7 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/t/tbb/tbb-2017.2.132.eb b/easybuild/easyconfigs/t/tbb/tbb-2017.2.132.eb index c81d846fca..c472a12964 100644 --- a/easybuild/easyconfigs/t/tbb/tbb-2017.2.132.eb +++ b/easybuild/easyconfigs/t/tbb/tbb-2017.2.132.eb @@ -2,7 +2,7 @@ name = 'tbb' version = '2017.2.132' homepage = 'http://software.intel.com/en-us/articles/intel-tbb/' -description = """Intel Threading Building Blocks 4.0 (Intel TBB) +description = """Intel Threading Building Blocks (Intel TBB) is a widely used, award-winning C++ template library for creating reliable, portable, and scalable parallel applications. Use Intel TBB for a simple and rapid way of developing robust task-based diff --git a/easybuild/easyconfigs/t/tbb/tbb-2017.4.174.eb b/easybuild/easyconfigs/t/tbb/tbb-2017.4.174.eb index 925ecf0fc9..3644e3125e 100644 --- a/easybuild/easyconfigs/t/tbb/tbb-2017.4.174.eb +++ b/easybuild/easyconfigs/t/tbb/tbb-2017.4.174.eb @@ -2,7 +2,7 @@ name = 'tbb' version = '2017.4.174' homepage = 'http://software.intel.com/en-us/articles/intel-tbb/' -description = """Intel Threading Building Blocks 4.0 (Intel TBB) +description = """Intel Threading Building Blocks (Intel TBB) is a widely used, award-winning C++ template library for creating reliable, portable, and scalable parallel applications. Use Intel TBB for a simple and rapid way of developing robust task-based diff --git a/easybuild/easyconfigs/t/tbb/tbb-2017.6.196.eb b/easybuild/easyconfigs/t/tbb/tbb-2017.6.196.eb index 458116d68c..8156aab23b 100644 --- a/easybuild/easyconfigs/t/tbb/tbb-2017.6.196.eb +++ b/easybuild/easyconfigs/t/tbb/tbb-2017.6.196.eb @@ -4,7 +4,7 @@ version = '2017.6.196' homepage = 'http://software.intel.com/en-us/articles/intel-tbb/' description = """ - Intel Threading Building Blocks 4.0 (Intel TBB) is a widely used, + Intel Threading Building Blocks (Intel TBB) is a widely used, award-winning C++ template library for creating reliable, portable, and scalable parallel applications. Use Intel TBB for a simple and rapid way of developing robust task-based parallel applications that scale to available diff --git a/easybuild/easyconfigs/t/tbb/tbb-4.0.0.233.eb b/easybuild/easyconfigs/t/tbb/tbb-4.0.0.233.eb index 276beb485d..fe58ba8f6d 100644 --- a/easybuild/easyconfigs/t/tbb/tbb-4.0.0.233.eb +++ b/easybuild/easyconfigs/t/tbb/tbb-4.0.0.233.eb @@ -2,7 +2,7 @@ name = 'tbb' version = '4.0.0.233' homepage = 'http://software.intel.com/en-us/articles/intel-tbb/' -description = """Intel Threading Building Blocks 4.0 (Intel TBB) +description = """Intel Threading Building Blocks (Intel TBB) is a widely used, award-winning C++ template library for creating reliable, portable, and scalable parallel applications. Use Intel TBB for a simple and rapid way of developing robust task-based diff --git a/easybuild/easyconfigs/t/tbb/tbb-4.0.5.339.eb b/easybuild/easyconfigs/t/tbb/tbb-4.0.5.339.eb index 88a0f19397..db524b2407 100644 --- a/easybuild/easyconfigs/t/tbb/tbb-4.0.5.339.eb +++ b/easybuild/easyconfigs/t/tbb/tbb-4.0.5.339.eb @@ -2,7 +2,7 @@ name = 'tbb' version = '4.0.5.339' homepage = 'http://software.intel.com/en-us/articles/intel-tbb/' -description = """Intel Threading Building Blocks 4.0 (Intel TBB) +description = """Intel Threading Building Blocks (Intel TBB) is a widely used, award-winning C++ template library for creating reliable, portable, and scalable parallel applications. Use Intel TBB for a simple and rapid way of developing robust task-based diff --git a/easybuild/easyconfigs/t/tbb/tbb-4.3.6.211.eb b/easybuild/easyconfigs/t/tbb/tbb-4.3.6.211.eb index bf885c9389..8f93bdda02 100644 --- a/easybuild/easyconfigs/t/tbb/tbb-4.3.6.211.eb +++ b/easybuild/easyconfigs/t/tbb/tbb-4.3.6.211.eb @@ -2,7 +2,7 @@ name = 'tbb' version = '4.3.6.211' homepage = 'http://software.intel.com/en-us/articles/intel-tbb/' -description = """Intel Threading Building Blocks 4.0 (Intel TBB) +description = """Intel Threading Building Blocks (Intel TBB) is a widely used, award-winning C++ template library for creating reliable, portable, and scalable parallel applications. Use Intel TBB for a simple and rapid way of developing robust task-based diff --git a/easybuild/easyconfigs/t/tbb/tbb-4.4.2.152.eb b/easybuild/easyconfigs/t/tbb/tbb-4.4.2.152.eb index c5d8deaf1f..11fd6f658a 100644 --- a/easybuild/easyconfigs/t/tbb/tbb-4.4.2.152.eb +++ b/easybuild/easyconfigs/t/tbb/tbb-4.4.2.152.eb @@ -2,7 +2,7 @@ name = 'tbb' version = '4.4.2.152' homepage = 'http://software.intel.com/en-us/articles/intel-tbb/' -description = """Intel Threading Building Blocks 4.0 (Intel TBB) +description = """Intel Threading Building Blocks (Intel TBB) is a widely used, award-winning C++ template library for creating reliable, portable, and scalable parallel applications. Use Intel TBB for a simple and rapid way of developing robust task-based -- GitLab From 988ceabc4b734b57bb6920fdc0fd22dd03fe0824 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 12 Jun 2017 17:55:21 +0200 Subject: [PATCH 0928/1603] adding easyconfigs: basemap-1.0.7-intel-2017a-Python-2.7.13.eb, PIL-1.1.7-intel-2017a-Python-2.7.13.eb --- ...basemap-1.0.7-intel-2017a-Python-2.7.13.eb | 32 +++++++++++++++++++ .../PIL-1.1.7-intel-2017a-Python-2.7.13.eb | 32 +++++++++++++++++++ 2 files changed, 64 insertions(+) create mode 100644 easybuild/easyconfigs/b/basemap/basemap-1.0.7-intel-2017a-Python-2.7.13.eb create mode 100644 easybuild/easyconfigs/p/PIL/PIL-1.1.7-intel-2017a-Python-2.7.13.eb diff --git a/easybuild/easyconfigs/b/basemap/basemap-1.0.7-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/b/basemap/basemap-1.0.7-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..69a5b6b4c4 --- /dev/null +++ b/easybuild/easyconfigs/b/basemap/basemap-1.0.7-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonPackage' + +name = 'basemap' +version = '1.0.7' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://matplotlib.org/basemap/' +description = """The matplotlib basemap toolkit is a library for plotting 2D data on maps in Python""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['https://downloads.sourceforge.net/project/matplotlib/matplotlib-toolkits/basemap-%(version)s'] + +prebuildopts = 'GEOS_DIR=$EBROOTGEOS' +preinstallopts = prebuildopts + +dependencies = [ + ('Python', '2.7.13'), + ('matplotlib', '2.0.2', versionsuffix + '-libpng-1.6.29'), + ('GEOS', '3.6.1', versionsuffix), + ('PIL', '1.1.7', versionsuffix), +] + +sanity_check_paths = { + 'files': ['lib/python%%(pyshortver)s/site-packages/_geoslib.%s' % SHLIB_EXT], + 'dirs': ['lib/python%(pyshortver)s/site-packages/mpl_toolkits/basemap'] +} + +options = {'modulename': 'mpl_toolkits.basemap'} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/PIL/PIL-1.1.7-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/p/PIL/PIL-1.1.7-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..050e2ce1af --- /dev/null +++ b/easybuild/easyconfigs/p/PIL/PIL-1.1.7-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonPackage' + +name = 'PIL' +version = '1.1.7' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.pythonware.com/products/pil' +description = """The Python Imaging Library (PIL) adds image processing capabilities to your Python interpreter. + This library supports many file formats, and provides powerful image processing and graphics capabilities.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['http://effbot.org/downloads/'] +sources = ['Imaging-%(version)s.tar.gz'] + +patches = ['PIL-%(version)s-find-deps.patch'] + +dependencies = [ + ('zlib', '1.2.11'), + ('Python', '2.7.13'), + ('libjpeg-turbo', '1.5.1'), + ('freetype', '2.7.1', '-libpng-1.6.29'), +] + +options = {'modulename': 'PIL'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['bin', 'lib/python%(pyshortver)s/site-packages/%(name)s'], +} + +moduleclass = 'vis' -- GitLab From 68112e92789b25e551e13ce5ec69384c4fbec105 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Mon, 12 Jun 2017 11:24:32 -0500 Subject: [PATCH 0929/1603] adding easyconfigs: nettle-3.2-GCCcore-5.4.0.eb --- .../n/nettle/nettle-3.2-GCCcore-5.4.0.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/n/nettle/nettle-3.2-GCCcore-5.4.0.eb diff --git a/easybuild/easyconfigs/n/nettle/nettle-3.2-GCCcore-5.4.0.eb b/easybuild/easyconfigs/n/nettle/nettle-3.2-GCCcore-5.4.0.eb new file mode 100644 index 0000000000..295f442406 --- /dev/null +++ b/easybuild/easyconfigs/n/nettle/nettle-3.2-GCCcore-5.4.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'nettle' +version = '3.2' + +homepage = 'http://www.lysator.liu.se/~nisse/nettle/' +description = """Nettle is a cryptographic library that is designed to fit easily + in more or less any context: In crypto toolkits for object-oriented + languages (C++, Python, Pike, ...), in applications like LSH or GNUPG, + or even in kernel space.""" + +toolchain = {'name': 'GCCcore', 'version': '5.4.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] + +builddependencies = [('binutils', '2.26', '', True)] + +dependencies = [ + ('GMP', '6.1.1'), +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['nettle-hash', 'nettle-lfib-stream', 'pkcs1-conv', 'sexp-conv']] + + [('lib/libhogweed.a', 'lib64/libhogweed.a'), ('lib/libhogweed.%s' % SHLIB_EXT, 'lib64/libhogweed.%s' % SHLIB_EXT), + ('lib/libnettle.a', 'lib64/libnettle.a'), ('lib/libnettle.%s' % SHLIB_EXT, 'lib64/libnettle.%s' % SHLIB_EXT)], + 'dirs': ['include/nettle'], +} + +moduleclass = 'lib' -- GitLab From 350b9c5778715a22f782d9453d046bbc9a80ff47 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Wed, 14 Jun 2017 13:51:24 +1200 Subject: [PATCH 0930/1603] Do a serial build so that Convert::Binary::C compiles --- easybuild/easyconfigs/p/Perl/Perl-5.22.0-foss-2015a-mt.eb | 7 +++++-- easybuild/easyconfigs/p/Perl/Perl-5.22.0-foss-2015a.eb | 2 ++ 2 files changed, 7 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.22.0-foss-2015a-mt.eb b/easybuild/easyconfigs/p/Perl/Perl-5.22.0-foss-2015a-mt.eb index 7b23b1c105..3fb8ef382e 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.22.0-foss-2015a-mt.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.22.0-foss-2015a-mt.eb @@ -14,10 +14,13 @@ dependencies = [ ('SQLite', '3.8.9'), # for DBD::SQLite module ('expat', '2.1.0'), # for XML::Parser I think ('libxml2', '2.9.2'), # for XML::LibXML - ] +] source_urls = ['http://www.cpan.org/src/5.0'] sources = [SOURCELOWER_TAR_GZ] + +maxparallel = 1 + #runtest = 'test' exts_list = [ @@ -32,7 +35,7 @@ exts_list = [ ('local::lib', '2.000011', { 'source_tmpl': 'local-lib-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/E/ET/ETHER/'], - ):, + }), ('IO::String', '1.08', { 'source_tmpl': 'IO-String-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS/'], diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.22.0-foss-2015a.eb b/easybuild/easyconfigs/p/Perl/Perl-5.22.0-foss-2015a.eb index b4c631de0e..519a5ec0ca 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.22.0-foss-2015a.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.22.0-foss-2015a.eb @@ -18,6 +18,8 @@ dependencies = [ source_urls = ['http://www.cpan.org/src/5.0'] sources = [SOURCELOWER_TAR_GZ] +maxparallel = 1 + exts_list = [ ('Module::Build', '0.4210', { # std module but recent BioPerl needs a recent version for some reason 'source_tmpl': 'Module-Build-%(version)s.tar.gz', -- GitLab From 6832dc15184789421d72664619744c5a8c410b2f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Wed, 14 Jun 2017 11:17:37 +0200 Subject: [PATCH 0931/1603] Add GD 2.66 with updated dependencies --- .../g/GD/GD-2.66-foss-2016b-Perl-5.24.0.eb | 31 +++++++++++++++++++ .../l/libgd/libgd-2.2.4-foss-2016b.eb | 30 ++++++++++++++++++ .../l/libpng/libpng-1.6.29-foss-2016b.eb | 30 ++++++++++++++++++ 3 files changed, 91 insertions(+) create mode 100644 easybuild/easyconfigs/g/GD/GD-2.66-foss-2016b-Perl-5.24.0.eb create mode 100644 easybuild/easyconfigs/l/libgd/libgd-2.2.4-foss-2016b.eb create mode 100644 easybuild/easyconfigs/l/libpng/libpng-1.6.29-foss-2016b.eb diff --git a/easybuild/easyconfigs/g/GD/GD-2.66-foss-2016b-Perl-5.24.0.eb b/easybuild/easyconfigs/g/GD/GD-2.66-foss-2016b-Perl-5.24.0.eb new file mode 100644 index 0000000000..d3f08d5c1c --- /dev/null +++ b/easybuild/easyconfigs/g/GD/GD-2.66-foss-2016b-Perl-5.24.0.eb @@ -0,0 +1,31 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild + +easyblock = 'PerlModule' + +name = 'GD' +version = '2.66' +versionsuffix = '-Perl-%(perlver)s' + +homepage = 'https://github.com/lstein/Perl-GD' +description = """GD.pm - Interface to Gd Graphics Library""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['https://github.com/lstein/Perl-GD/archive/'] +sources = ['release_%(version_major)s_%(version_minor)s.tar.gz'] + +checksums = ['47a1388f3364e70dd2eaab072d127835'] + +dependencies = [ + ('Perl', '5.24.0'), + ('libgd', '2.2.4'), + ('libpng', '1.6.27'), + ('libjpeg-turbo', '1.5.0'), +] + +sanity_check_paths = { + 'files': ['bin/bdf2gdfont.pl', 'lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/%(name)s.pm'], + 'dirs': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/%(name)s'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/l/libgd/libgd-2.2.4-foss-2016b.eb b/easybuild/easyconfigs/l/libgd/libgd-2.2.4-foss-2016b.eb new file mode 100644 index 0000000000..e46a716330 --- /dev/null +++ b/easybuild/easyconfigs/l/libgd/libgd-2.2.4-foss-2016b.eb @@ -0,0 +1,30 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild + +easyblock = 'ConfigureMake' + +name = 'libgd' +version = '2.2.4' + +homepage = 'http://libgd.bitbucket.org/' +description = """GD is an open source code library for the dynamic creation of images by programmers.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['https://github.com/libgd/libgd/releases/download/gd-%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] + +checksums = ['0a3c307b5075edbe1883543dd1153c02'] + +dependencies = [ + ('fontconfig', '2.12.1'), + ('libjpeg-turbo', '1.5.0'), + ('libpng', '1.6.27'), + ('zlib', '1.2.8'), +] + +sanity_check_paths = { + 'files': ['lib/libgd.a', 'lib/libgd.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.29-foss-2016b.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.29-foss-2016b.eb new file mode 100644 index 0000000000..33cd96fc7f --- /dev/null +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.29-foss-2016b.eb @@ -0,0 +1,30 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild + +easyblock = 'ConfigureMake' + +name = 'libpng' +version = '1.6.29' + +homepage = 'http://www.libpng.org/pub/png/libpng.html' +description = """libpng is the official PNG reference library""" + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +checksums = ['68553080685f812d1dd7a6b8215c37d8'] + +dependencies = [('zlib', '1.2.8')] + +configopts = '--with-pic' + +majminver = ''.join(version.split('.')[:2]) +sanity_check_paths = { + 'files': ['include/pngconf.h', 'include/png.h', 'include/pnglibconf.h', 'lib/libpng.a', + 'lib/libpng.%s' % SHLIB_EXT, 'lib/libpng%s.a' % majminver, 'lib/libpng%s.%s' % (majminver, SHLIB_EXT)], + 'dirs': ['bin', 'include/libpng%s' % majminver, 'share/man'], +} + +moduleclass = 'lib' -- GitLab From 1c51fbdd60ad6a40931aac70d8b5b1c15f1859a0 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Wed, 14 Jun 2017 11:43:08 +0200 Subject: [PATCH 0932/1603] Fix version of libpng used --- easybuild/easyconfigs/g/GD/GD-2.66-foss-2016b-Perl-5.24.0.eb | 2 +- easybuild/easyconfigs/l/libgd/libgd-2.2.4-foss-2016b.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/g/GD/GD-2.66-foss-2016b-Perl-5.24.0.eb b/easybuild/easyconfigs/g/GD/GD-2.66-foss-2016b-Perl-5.24.0.eb index d3f08d5c1c..523435b933 100644 --- a/easybuild/easyconfigs/g/GD/GD-2.66-foss-2016b-Perl-5.24.0.eb +++ b/easybuild/easyconfigs/g/GD/GD-2.66-foss-2016b-Perl-5.24.0.eb @@ -19,7 +19,7 @@ checksums = ['47a1388f3364e70dd2eaab072d127835'] dependencies = [ ('Perl', '5.24.0'), ('libgd', '2.2.4'), - ('libpng', '1.6.27'), + ('libpng', '1.6.29'), ('libjpeg-turbo', '1.5.0'), ] diff --git a/easybuild/easyconfigs/l/libgd/libgd-2.2.4-foss-2016b.eb b/easybuild/easyconfigs/l/libgd/libgd-2.2.4-foss-2016b.eb index e46a716330..5e8f0d2bfb 100644 --- a/easybuild/easyconfigs/l/libgd/libgd-2.2.4-foss-2016b.eb +++ b/easybuild/easyconfigs/l/libgd/libgd-2.2.4-foss-2016b.eb @@ -18,7 +18,7 @@ checksums = ['0a3c307b5075edbe1883543dd1153c02'] dependencies = [ ('fontconfig', '2.12.1'), ('libjpeg-turbo', '1.5.0'), - ('libpng', '1.6.27'), + ('libpng', '1.6.29'), ('zlib', '1.2.8'), ] -- GitLab From 017ed7ef5666cd18dbd8f2a707318374d5a52428 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Wed, 14 Jun 2017 12:42:45 +0200 Subject: [PATCH 0933/1603] Revert to libpng version 1.6.24 --- .../g/GD/GD-2.66-foss-2016b-Perl-5.24.0.eb | 2 +- .../l/libgd/libgd-2.2.4-foss-2016b.eb | 2 +- .../l/libpng/libpng-1.6.29-foss-2016b.eb | 30 ------------------- 3 files changed, 2 insertions(+), 32 deletions(-) delete mode 100644 easybuild/easyconfigs/l/libpng/libpng-1.6.29-foss-2016b.eb diff --git a/easybuild/easyconfigs/g/GD/GD-2.66-foss-2016b-Perl-5.24.0.eb b/easybuild/easyconfigs/g/GD/GD-2.66-foss-2016b-Perl-5.24.0.eb index 523435b933..88f756e1ce 100644 --- a/easybuild/easyconfigs/g/GD/GD-2.66-foss-2016b-Perl-5.24.0.eb +++ b/easybuild/easyconfigs/g/GD/GD-2.66-foss-2016b-Perl-5.24.0.eb @@ -19,7 +19,7 @@ checksums = ['47a1388f3364e70dd2eaab072d127835'] dependencies = [ ('Perl', '5.24.0'), ('libgd', '2.2.4'), - ('libpng', '1.6.29'), + ('libpng', '1.6.24'), ('libjpeg-turbo', '1.5.0'), ] diff --git a/easybuild/easyconfigs/l/libgd/libgd-2.2.4-foss-2016b.eb b/easybuild/easyconfigs/l/libgd/libgd-2.2.4-foss-2016b.eb index 5e8f0d2bfb..36c51236e2 100644 --- a/easybuild/easyconfigs/l/libgd/libgd-2.2.4-foss-2016b.eb +++ b/easybuild/easyconfigs/l/libgd/libgd-2.2.4-foss-2016b.eb @@ -18,7 +18,7 @@ checksums = ['0a3c307b5075edbe1883543dd1153c02'] dependencies = [ ('fontconfig', '2.12.1'), ('libjpeg-turbo', '1.5.0'), - ('libpng', '1.6.29'), + ('libpng', '1.6.24'), ('zlib', '1.2.8'), ] diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.29-foss-2016b.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.29-foss-2016b.eb deleted file mode 100644 index 33cd96fc7f..0000000000 --- a/easybuild/easyconfigs/l/libpng/libpng-1.6.29-foss-2016b.eb +++ /dev/null @@ -1,30 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild - -easyblock = 'ConfigureMake' - -name = 'libpng' -version = '1.6.29' - -homepage = 'http://www.libpng.org/pub/png/libpng.html' -description = """libpng is the official PNG reference library""" - -toolchain = {'name': 'foss', 'version': '2016b'} -toolchainopts = {'pic': True} - -source_urls = [SOURCEFORGE_SOURCE] -sources = [SOURCELOWER_TAR_GZ] - -checksums = ['68553080685f812d1dd7a6b8215c37d8'] - -dependencies = [('zlib', '1.2.8')] - -configopts = '--with-pic' - -majminver = ''.join(version.split('.')[:2]) -sanity_check_paths = { - 'files': ['include/pngconf.h', 'include/png.h', 'include/pnglibconf.h', 'lib/libpng.a', - 'lib/libpng.%s' % SHLIB_EXT, 'lib/libpng%s.a' % majminver, 'lib/libpng%s.%s' % (majminver, SHLIB_EXT)], - 'dirs': ['bin', 'include/libpng%s' % majminver, 'share/man'], -} - -moduleclass = 'lib' -- GitLab From 4b8bb3ddb4152e00e335701e11675fe9d06d903b Mon Sep 17 00:00:00 2001 From: Yann Sagon Date: Wed, 14 Jun 2017 14:20:39 +0200 Subject: [PATCH 0934/1603] changes according to requests --- .../m/MaSuRCA/MaSuRCA-3.2.2-foss-2016a.eb | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/easybuild/easyconfigs/m/MaSuRCA/MaSuRCA-3.2.2-foss-2016a.eb b/easybuild/easyconfigs/m/MaSuRCA/MaSuRCA-3.2.2-foss-2016a.eb index 56f1d8c0ac..98a1ad1c1c 100644 --- a/easybuild/easyconfigs/m/MaSuRCA/MaSuRCA-3.2.2-foss-2016a.eb +++ b/easybuild/easyconfigs/m/MaSuRCA/MaSuRCA-3.2.2-foss-2016a.eb @@ -20,13 +20,8 @@ description = '''MaSuRCA is whole genome assembly software. It combines the effi only short reads from Illumina sequencing or a mixture of short reads and long reads (Sanger, 454, Pacbio and Nanopore).''' -toolchain = {'name': 'foss', 'version': '2016a'} - -buildopts="install-special" -start_dir="global-1" - -#need a temporary url to download it. Do it manually. -source_urls = ['http://www.genome.umd.edu/masurca_form.html'] +# need a temporary url to download it. Do it manually here: +# http://www.genome.umd.edu/masurca_form.html sources = ['%(name)s-%(version)s.tar.gz'] dependencies = [ @@ -36,9 +31,14 @@ dependencies = [ ('zlib', '1.2.8'), ] +toolchain = {'name': 'foss', 'version': '2016a'} + +buildopts="install-special" +start_dir="global-1" + sanity_check_paths = { - 'files': [], - 'dirs': ["bin"], + 'files': ['bin/masurca'], + 'dirs': ['include', 'lib'], } moduleclass = 'bio' -- GitLab From f9a8f455e5ed87849c0c64fccf237fd2b94ef138 Mon Sep 17 00:00:00 2001 From: Yann Sagon Date: Thu, 15 Jun 2017 14:00:40 +0200 Subject: [PATCH 0935/1603] fix style --- easybuild/easyconfigs/m/MaSuRCA/MaSuRCA-3.2.2-foss-2016a.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/MaSuRCA/MaSuRCA-3.2.2-foss-2016a.eb b/easybuild/easyconfigs/m/MaSuRCA/MaSuRCA-3.2.2-foss-2016a.eb index 98a1ad1c1c..6a0e136d4e 100644 --- a/easybuild/easyconfigs/m/MaSuRCA/MaSuRCA-3.2.2-foss-2016a.eb +++ b/easybuild/easyconfigs/m/MaSuRCA/MaSuRCA-3.2.2-foss-2016a.eb @@ -20,6 +20,8 @@ description = '''MaSuRCA is whole genome assembly software. It combines the effi only short reads from Illumina sequencing or a mixture of short reads and long reads (Sanger, 454, Pacbio and Nanopore).''' +toolchain = {'name': 'foss', 'version': '2016a'} + # need a temporary url to download it. Do it manually here: # http://www.genome.umd.edu/masurca_form.html sources = ['%(name)s-%(version)s.tar.gz'] @@ -31,8 +33,6 @@ dependencies = [ ('zlib', '1.2.8'), ] -toolchain = {'name': 'foss', 'version': '2016a'} - buildopts="install-special" start_dir="global-1" -- GitLab From b7409f13627bfe1b8029994ca75da65e9cb8b420 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Thu, 15 Jun 2017 15:04:16 +0200 Subject: [PATCH 0936/1603] Change URL to github.io --- easybuild/easyconfigs/l/libgd/libgd-2.2.4-foss-2016b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libgd/libgd-2.2.4-foss-2016b.eb b/easybuild/easyconfigs/l/libgd/libgd-2.2.4-foss-2016b.eb index 36c51236e2..5856a57c8d 100644 --- a/easybuild/easyconfigs/l/libgd/libgd-2.2.4-foss-2016b.eb +++ b/easybuild/easyconfigs/l/libgd/libgd-2.2.4-foss-2016b.eb @@ -5,7 +5,7 @@ easyblock = 'ConfigureMake' name = 'libgd' version = '2.2.4' -homepage = 'http://libgd.bitbucket.org/' +homepage = 'https://libgd.github.io' description = """GD is an open source code library for the dynamic creation of images by programmers.""" toolchain = {'name': 'foss', 'version': '2016b'} -- GitLab From 54b9e5721079cf268683e14783e5b3514611ff0d Mon Sep 17 00:00:00 2001 From: Robert Date: Thu, 15 Jun 2017 22:49:32 +0930 Subject: [PATCH 0937/1603] error fixed --- .../o/OrfM/OrfM-0.6.1-foss-2016b.eb | 1 - easybuild/easyconfigs/s/SEED/SEED-2015.eb | 36 ------------------- 2 files changed, 37 deletions(-) delete mode 100644 easybuild/easyconfigs/s/SEED/SEED-2015.eb diff --git a/easybuild/easyconfigs/o/OrfM/OrfM-0.6.1-foss-2016b.eb b/easybuild/easyconfigs/o/OrfM/OrfM-0.6.1-foss-2016b.eb index ae95bf0649..5a1afb1351 100644 --- a/easybuild/easyconfigs/o/OrfM/OrfM-0.6.1-foss-2016b.eb +++ b/easybuild/easyconfigs/o/OrfM/OrfM-0.6.1-foss-2016b.eb @@ -13,7 +13,6 @@ easyblock = 'ConfigureMake' name = 'OrfM' version = '0.6.1' -namelower = 'orfm' homepage = 'https://github.com/wwood/OrfM' description = """A simple and not slow open reading frame (ORF) caller. diff --git a/easybuild/easyconfigs/s/SEED/SEED-2015.eb b/easybuild/easyconfigs/s/SEED/SEED-2015.eb deleted file mode 100644 index b186b85f21..0000000000 --- a/easybuild/easyconfigs/s/SEED/SEED-2015.eb +++ /dev/null @@ -1,36 +0,0 @@ -## -# This is a contribution from Phoenix HPC Service, The University of Adelaide, Australia -# Homepage: https://www.adelaide.edu.au/phoenix/ -# -# Copyright:: Copyright 2014-2017 adelaide.edu.au/phoenix -# Authors:: Robert Qiao , Exequiel Sepulveda -# License:: Artistic-v2.0 -# -# Notes:: -## - -easyblock = 'CmdCp' - -name = 'SEED' -version = '2015' - -homepage = 'http://www.theseed.org/wiki/Main_Page' -description = """ SEED is a software for clustering large sets of Next Generation Sequences (NGS) -with hundreds of millions of reads in a time and memory efficient manner. -Its algorithm joins highly similar sequences into clusters that can differ -by up to three mismatches and three overhanging residues. -""" - -toolchain = {'name': 'dummy', 'version': 'dummy'} - -sources = ['master.zip'] -source_urls = ['https://github.com/baoe/SEED/archive'] - -files_to_copy = (['SEED/SEED'], 'bin'), - -sanity_check_paths = { - 'files': ["bin/SEED"], - 'dirs': [], -} - -moduleclass = 'bio' -- GitLab From 0a472f8ad884c8ffd5be2a6f13767c8a7c040644 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Fri, 16 Jun 2017 12:10:42 +1200 Subject: [PATCH 0938/1603] New EasyConfig for expat 2.2.0 with the gimkl-2017a toolchain --- .../e/expat/expat-2.2.0-gimkl-2017a.eb | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) create mode 100644 easybuild/easyconfigs/e/expat/expat-2.2.0-gimkl-2017a.eb diff --git a/easybuild/easyconfigs/e/expat/expat-2.2.0-gimkl-2017a.eb b/easybuild/easyconfigs/e/expat/expat-2.2.0-gimkl-2017a.eb new file mode 100644 index 0000000000..555f4a3da3 --- /dev/null +++ b/easybuild/easyconfigs/e/expat/expat-2.2.0-gimkl-2017a.eb @@ -0,0 +1,16 @@ +easyblock = 'ConfigureMake' + +name = 'expat' +version = '2.2.0' + +homepage = 'http://expat.sourceforge.net/' +description = """Expat is an XML parser library written in C. It is a stream-oriented parser in which an application + registers handlers for things the parser might find in the XML document (like start tags)""" + +toolchain = {'name': 'gimkl', 'version': '2017a'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = [SOURCEFORGE_SOURCE] + +moduleclass = 'tools' -- GitLab From 6737a5e9ec0be4f3edd006a2031494e1014f6aa6 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Fri, 16 Jun 2017 12:14:22 +1200 Subject: [PATCH 0939/1603] Adjusted source URL per request from K.H. --- easybuild/easyconfigs/z/zlib/zlib-1.2.11-gimkl-2017a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.11-gimkl-2017a.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-gimkl-2017a.eb index 1362fe53c9..1346eea81c 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.11-gimkl-2017a.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-gimkl-2017a.eb @@ -12,7 +12,7 @@ toolchain = {'version': '2017a', 'name': 'gimkl'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] +source_urls = ['http://zlib.net/fossils'] sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], -- GitLab From e10ae8dc4da3d2f0cb1709678aad65933d5e464b Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Fri, 16 Jun 2017 12:17:38 +1200 Subject: [PATCH 0940/1603] Adjusted indenting on two lines per request from K.H. --- .../easyconfigs/l/libreadline/libreadline-6.3-gimkl-2017a.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-gimkl-2017a.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-gimkl-2017a.eb index 3c72c2c527..375e6cccf2 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-gimkl-2017a.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-gimkl-2017a.eb @@ -24,8 +24,8 @@ preconfigopts = "env LDFLAGS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + - ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', - 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], 'dirs': [], } -- GitLab From 7deaa57c95bb3806bb2d2399ecd53db3b2e76300 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Fri, 16 Jun 2017 12:25:44 +1200 Subject: [PATCH 0941/1603] Patch for XZ requested by K.H. to avoid breaking rpm --- easybuild/easyconfigs/x/XZ/XZ-5.2.3-gimkl-2017a.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.3-gimkl-2017a.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.3-gimkl-2017a.eb index 4b1d474ab3..8d7242f13f 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.3-gimkl-2017a.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.3-gimkl-2017a.eb @@ -11,6 +11,8 @@ toolchain = {'version': '2017a', 'name': 'gimkl'} sources = [SOURCELOWER_TAR_BZ2] source_urls = ['http://tukaani.org/xz/'] +patches = ['XZ-5.2.2_compat-libs.patch'] + # non-toolchain gettext because otherwise there is a circular dependency: # XZ (presumably its executables) depends on gettext, which depends on # xmllib2, which depends (optionally) on XZ -- GitLab From 744ace0a17291f13f3d30cd85cb943d2eb128f22 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Fri, 16 Jun 2017 13:15:25 +1200 Subject: [PATCH 0942/1603] New EasyConfig for cURL 7.52.1 with the gimkl-2017a toolchain --- .../c/cURL/cURL-7.52.1-gimkl-2017a.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/c/cURL/cURL-7.52.1-gimkl-2017a.eb diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.52.1-gimkl-2017a.eb b/easybuild/easyconfigs/c/cURL/cURL-7.52.1-gimkl-2017a.eb new file mode 100644 index 0000000000..85452813a1 --- /dev/null +++ b/easybuild/easyconfigs/c/cURL/cURL-7.52.1-gimkl-2017a.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'cURL' +version = '7.52.1' + +homepage = 'http://curl.haxx.se' +description = """libcurl is a free and easy-to-use client-side URL transfer library, + supporting DICT, FILE, FTP, FTPS, Gopher, HTTP, HTTPS, IMAP, IMAPS, LDAP, LDAPS, + POP3, POP3S, RTMP, RTSP, SCP, SFTP, SMTP, SMTPS, Telnet and TFTP. libcurl supports + SSL certificates, HTTP POST, HTTP PUT, FTP uploading, HTTP form based upload, + proxies, cookies, user+password authentication (Basic, Digest, NTLM, Negotiate, + Kerberos), file transfer resume, http proxy tunneling and more.""" + +toolchain = {'name': 'gimkl', 'version': '2017a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://curl.haxx.se/download/'] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +modextravars = {'CURL_INCLUDES': '%(installdir)s/include'} + +sanity_check_paths = { + 'files': ['bin/curl', 'lib/libcurl.a', 'lib/libcurl.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'tools' -- GitLab From b88b6a34589d8b5f53f42be33e798f758ccf95af Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Fri, 16 Jun 2017 13:34:02 +1200 Subject: [PATCH 0943/1603] New EasyConfig for FFmpeg 3.2.4 with the gimkl 2017a toolchain (plus dependencies) --- .../f/FFmpeg/FFmpeg-3.2.4-gimkl-2017a.eb | 30 ++++++++++++++++++ easybuild/easyconfigs/n/NASM/NASM-2.12.02.eb | 31 +++++++++++++++++++ .../x/x264/x264-20170406-gimkl-2017a.eb | 27 ++++++++++++++++ .../y/Yasm/Yasm-1.3.0-gimkl-2017a.eb | 31 +++++++++++++++++++ 4 files changed, 119 insertions(+) create mode 100644 easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.2.4-gimkl-2017a.eb create mode 100644 easybuild/easyconfigs/n/NASM/NASM-2.12.02.eb create mode 100644 easybuild/easyconfigs/x/x264/x264-20170406-gimkl-2017a.eb create mode 100644 easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-gimkl-2017a.eb diff --git a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.2.4-gimkl-2017a.eb b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.2.4-gimkl-2017a.eb new file mode 100644 index 0000000000..2070339683 --- /dev/null +++ b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.2.4-gimkl-2017a.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'FFmpeg' +version = '3.2.4' + +homepage = 'https://www.ffmpeg.org/' +description = """A complete, cross-platform solution to record, convert and stream audio and video.""" + +toolchain = {'name': 'gimkl', 'version': '2017a'} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://ffmpeg.org/releases/'] + +dependencies = [ + ('NASM', '2.12.02', '', True), + ('x264', '20170406'), + ('X11', '20170129'), # pulls in bzip2 and zlib +] + +configopts = '--enable-pic --enable-shared --enable-gpl --enable-version3 --enable-nonfree --cc="$CC" --cxx="$CXX" ' +configopts += '--enable-libx264' + +sanity_check_paths = { + 'files': ['bin/ff%s' % x for x in ['mpeg', 'probe', 'server']] + + ['lib/lib%s.%s' % (x, y) for x in ['avdevice', 'avfilter', 'avformat', 'avcodec', 'postproc', + 'swresample', 'swscale', 'avutil'] for y in [SHLIB_EXT, 'a']], + 'dirs': ['include'] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/n/NASM/NASM-2.12.02.eb b/easybuild/easyconfigs/n/NASM/NASM-2.12.02.eb new file mode 100644 index 0000000000..b96d1d70fb --- /dev/null +++ b/easybuild/easyconfigs/n/NASM/NASM-2.12.02.eb @@ -0,0 +1,31 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-90.html +## + +easyblock = 'ConfigureMake' + +name = 'NASM' +version = '2.12.02' + +homepage = 'http://www.nasm.us/' +description = """NASM: General-purpose x86 assembler""" + +toolchain = {'version': 'dummy', 'name': 'dummy'} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://www.nasm.us/pub/nasm/releasebuilds/%(version)s'] + +sanity_check_paths = { + 'files': ['bin/nasm'], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/x/x264/x264-20170406-gimkl-2017a.eb b/easybuild/easyconfigs/x/x264/x264-20170406-gimkl-2017a.eb new file mode 100644 index 0000000000..38fbb83df0 --- /dev/null +++ b/easybuild/easyconfigs/x/x264/x264-20170406-gimkl-2017a.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'x264' +version = '20170406' + +homepage = 'http://www.videolan.org/developers/x264.html' +description = """x264 is a free software library and application for encoding video streams into the H.264/MPEG-4 + AVC compression format, and is released under the terms of the GNU GPL.""" + +toolchain = {'name': 'gimkl', 'version': '2017a'} + +source_urls = [ + 'https://download.videolan.org/pub/videolan/x264/snapshots/', + 'ftp://ftp.videolan.org/pub/videolan/x264/snapshots/', +] +sources = ['x264-snapshot-%(version)s-2245-stable.tar.bz2'] + +dependencies = [('Yasm', '1.3.0')] + +configopts = " --enable-shared --enable-static " + +sanity_check_paths = { + 'files': ['bin/x264', 'include/x264_config.h', 'include/x264.h', 'lib/libx264.a', 'lib/libx264.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-gimkl-2017a.eb b/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-gimkl-2017a.eb new file mode 100644 index 0000000000..78f408a971 --- /dev/null +++ b/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-gimkl-2017a.eb @@ -0,0 +1,31 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-90.html +## + +easyblock = 'ConfigureMake' + +name = 'Yasm' +version = '1.3.0' + +homepage = 'http://www.tortall.net/projects/yasm/' +description = """Yasm: Complete rewrite of the NASM assembler with BSD license""" + +toolchain = {'name': 'gimkl', 'version': '2017a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.tortall.net/projects/yasm/releases/'] + +sanity_check_paths = { + 'files': ['bin/yasm'], + 'dirs': [], +} + +moduleclass = 'lang' -- GitLab From 606d6664ec88002a1f049f29cdcefc328d874a2b Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Fri, 16 Jun 2017 13:40:12 +1200 Subject: [PATCH 0944/1603] New EasyConfig for bzip2 1.0.6 with the gimkl-2017a toolchain --- .../b/bzip2/bzip2-1.0.6-gimkl-2017a.eb | 15 +++++++++++++++ 1 file changed, 15 insertions(+) create mode 100644 easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-gimkl-2017a.eb diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-gimkl-2017a.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-gimkl-2017a.eb new file mode 100644 index 0000000000..e5eb2cbd9d --- /dev/null +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-gimkl-2017a.eb @@ -0,0 +1,15 @@ +name = 'bzip2' +version = '1.0.6' + +homepage = 'http://www.bzip.org/' +description = """bzip2 is a freely available, patent free, high-quality data compressor. It typically + compresses files to within 10% to 15% of the best available techniques (the PPM family of statistical + compressors), whilst being around twice as fast at compression and six times faster at decompression.""" + +toolchain = {'version': '2017a', 'name': 'gimkl'} +toolchainopts = {'pic': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://www.bzip.org/%(version)s'] + +moduleclass = 'tools' -- GitLab From 62393710ae97e94c9a25b8f22c1c92ce70cf0a7d Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Fri, 16 Jun 2017 14:45:05 +1200 Subject: [PATCH 0945/1603] New EasyConfig for libpng 1.6.28 with the gimkl-2017a toolchain --- .../l/libpng/libpng-1.6.28-gimkl-2017a.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/l/libpng/libpng-1.6.28-gimkl-2017a.eb diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.28-gimkl-2017a.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.28-gimkl-2017a.eb new file mode 100644 index 0000000000..64f18118dd --- /dev/null +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.28-gimkl-2017a.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'libpng' +version = "1.6.28" + +homepage = 'http://www.libpng.org/pub/png/libpng.html' +description = "libpng is the official PNG reference library" + +toolchain = {'version': '2017a', 'name': 'gimkl'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('zlib', '1.2.11')] + +configopts = "--with-pic" + +majminver = ''.join(version.split('.')[:2]) +sanity_check_paths = { + 'files': ['include/pngconf.h', 'include/png.h', 'include/pnglibconf.h', 'lib/libpng.a', + 'lib/libpng.%s' % SHLIB_EXT, 'lib/libpng%s.a' % majminver, 'lib/libpng%s.%s' % (majminver, SHLIB_EXT)], + 'dirs': ['bin', 'include/libpng%s' % majminver, 'share/man'], +} + +moduleclass = 'lib' -- GitLab From fa50667be0d65d67726421f60d3a371aa66dbe16 Mon Sep 17 00:00:00 2001 From: Robert Qiao Date: Fri, 16 Jun 2017 16:08:33 +0930 Subject: [PATCH 0946/1603] format updated --- easybuild/easyconfigs/o/OrfM/OrfM-0.6.1-foss-2016b.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/o/OrfM/OrfM-0.6.1-foss-2016b.eb b/easybuild/easyconfigs/o/OrfM/OrfM-0.6.1-foss-2016b.eb index 5a1afb1351..904722c279 100644 --- a/easybuild/easyconfigs/o/OrfM/OrfM-0.6.1-foss-2016b.eb +++ b/easybuild/easyconfigs/o/OrfM/OrfM-0.6.1-foss-2016b.eb @@ -25,8 +25,8 @@ of nucleotide sequences. toolchain = {'name': 'foss', 'version': '2016b'} toolchainopts = {'usempi': True} -sources = ['v%(version)s/%(namelower)s-%(version)s.tar.gz'] -source_urls = ['https://github.com/wwood/OrfM/releases/download'] +sources = ['%(namelower)s-%(version)s.tar.gz'] +source_urls = ['https://github.com/wwood/OrfM/releases/download/v%(version)s'] sanity_check_paths = { 'files': ['bin/orfm'], -- GitLab From 6373bff93ae4157fcbf5d6bdc305902438ebc814 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Fri, 16 Jun 2017 09:54:14 -0500 Subject: [PATCH 0947/1603] Removed site customizations and redundant options --- .../Python-2.7.12-iccifort-2016.3.210-GCC-5.4.0-2.26-bare.eb | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.12-iccifort-2016.3.210-GCC-5.4.0-2.26-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.12-iccifort-2016.3.210-GCC-5.4.0-2.26-bare.eb index d9fd114759..78379d4923 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.12-iccifort-2016.3.210-GCC-5.4.0-2.26-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.12-iccifort-2016.3.210-GCC-5.4.0-2.26-bare.eb @@ -7,7 +7,7 @@ description = """Python is a programming language that lets you work more quickl more effectively.""" toolchain = {'name': 'iccifort', 'version': '2016.3.210-GCC-5.4.0-2.26'} -toolchainopts = {'pic': True, 'opt': True, 'optarch': True} +toolchainopts = {'pic': True} source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] sources = [SOURCE_TGZ] @@ -27,8 +27,6 @@ dependencies = [ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] -modluafooter = 'family("python")' - # bare installation: no extensions included exts_list = [] -- GitLab From a0ecc32a106c84fd1513530fbed7dd7cf55e8f54 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Fri, 16 Jun 2017 10:49:58 -0500 Subject: [PATCH 0948/1603] Added lib sanity check paths for debian compatibility --- easybuild/easyconfigs/n/nettle/nettle-2.6-goolf-1.4.10.eb | 4 ++-- easybuild/easyconfigs/n/nettle/nettle-3.1.1-GNU-4.9.3-2.25.eb | 4 ++-- easybuild/easyconfigs/n/nettle/nettle-3.1.1-foss-2016a.eb | 4 ++-- easybuild/easyconfigs/n/nettle/nettle-3.1.1-intel-2016a.eb | 4 ++-- easybuild/easyconfigs/n/nettle/nettle-3.2-foss-2016b.eb | 4 ++-- easybuild/easyconfigs/n/nettle/nettle-3.2-intel-2016b.eb | 4 ++-- easybuild/easyconfigs/n/nettle/nettle-3.3-intel-2017a.eb | 4 ++-- 7 files changed, 14 insertions(+), 14 deletions(-) diff --git a/easybuild/easyconfigs/n/nettle/nettle-2.6-goolf-1.4.10.eb b/easybuild/easyconfigs/n/nettle/nettle-2.6-goolf-1.4.10.eb index b72cd92143..eb26f01e29 100644 --- a/easybuild/easyconfigs/n/nettle/nettle-2.6-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/n/nettle/nettle-2.6-goolf-1.4.10.eb @@ -15,8 +15,8 @@ dependencies = [('GMP', '5.0.5')] sanity_check_paths = { 'files': ['bin/%s' % x for x in ['nettle-hash', 'nettle-lfib-stream', 'pkcs1-conv', 'sexp-conv']] + - ['lib64/libhogweed.a', 'lib64/libhogweed.%s' % SHLIB_EXT, - 'lib64/libnettle.a', 'lib64/libnettle.%s' % SHLIB_EXT], + [('lib/libhogweed.a', 'lib64/libhogweed.a'), ('lib/libhogweed.%s' % SHLIB_EXT, 'lib64/libhogweed.%s' % SHLIB_EXT), + ('lib/libnettle.a', 'lib64/libnettle.a'), ('lib/libnettle.%s' % SHLIB_EXT, 'lib64/libnettle.%s' % SHLIB_EXT)], 'dirs': ['include/nettle'], } diff --git a/easybuild/easyconfigs/n/nettle/nettle-3.1.1-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/n/nettle/nettle-3.1.1-GNU-4.9.3-2.25.eb index e764834b2d..27c65b25e8 100644 --- a/easybuild/easyconfigs/n/nettle/nettle-3.1.1-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/n/nettle/nettle-3.1.1-GNU-4.9.3-2.25.eb @@ -20,8 +20,8 @@ dependencies = [ sanity_check_paths = { 'files': ['bin/%s' % x for x in ['nettle-hash', 'nettle-lfib-stream', 'pkcs1-conv', 'sexp-conv']] + - ['lib64/libhogweed.a', 'lib64/libhogweed.%s' % SHLIB_EXT, - 'lib64/libnettle.a', 'lib64/libnettle.%s' % SHLIB_EXT], + [('lib/libhogweed.a', 'lib64/libhogweed.a'), ('lib/libhogweed.%s' % SHLIB_EXT, 'lib64/libhogweed.%s' % SHLIB_EXT), + ('lib/libnettle.a', 'lib64/libnettle.a'), ('lib/libnettle.%s' % SHLIB_EXT, 'lib64/libnettle.%s' % SHLIB_EXT)], 'dirs': ['include/nettle'], } diff --git a/easybuild/easyconfigs/n/nettle/nettle-3.1.1-foss-2016a.eb b/easybuild/easyconfigs/n/nettle/nettle-3.1.1-foss-2016a.eb index fc3be53324..f658dc22c5 100644 --- a/easybuild/easyconfigs/n/nettle/nettle-3.1.1-foss-2016a.eb +++ b/easybuild/easyconfigs/n/nettle/nettle-3.1.1-foss-2016a.eb @@ -20,8 +20,8 @@ dependencies = [ sanity_check_paths = { 'files': ['bin/%s' % x for x in ['nettle-hash', 'nettle-lfib-stream', 'pkcs1-conv', 'sexp-conv']] + - ['lib64/libhogweed.a', 'lib64/libhogweed.%s' % SHLIB_EXT, - 'lib64/libnettle.a', 'lib64/libnettle.%s' % SHLIB_EXT], + [('lib/libhogweed.a', 'lib64/libhogweed.a'), ('lib/libhogweed.%s' % SHLIB_EXT, 'lib64/libhogweed.%s' % SHLIB_EXT), + ('lib/libnettle.a', 'lib64/libnettle.a'), ('lib/libnettle.%s' % SHLIB_EXT, 'lib64/libnettle.%s' % SHLIB_EXT)], 'dirs': ['include/nettle'], } diff --git a/easybuild/easyconfigs/n/nettle/nettle-3.1.1-intel-2016a.eb b/easybuild/easyconfigs/n/nettle/nettle-3.1.1-intel-2016a.eb index c725853009..b0fd192537 100644 --- a/easybuild/easyconfigs/n/nettle/nettle-3.1.1-intel-2016a.eb +++ b/easybuild/easyconfigs/n/nettle/nettle-3.1.1-intel-2016a.eb @@ -20,8 +20,8 @@ dependencies = [ sanity_check_paths = { 'files': ['bin/%s' % x for x in ['nettle-hash', 'nettle-lfib-stream', 'pkcs1-conv', 'sexp-conv']] + - ['lib64/libhogweed.a', 'lib64/libhogweed.%s' % SHLIB_EXT, - 'lib64/libnettle.a', 'lib64/libnettle.%s' % SHLIB_EXT], + [('lib/libhogweed.a', 'lib64/libhogweed.a'), ('lib/libhogweed.%s' % SHLIB_EXT, 'lib64/libhogweed.%s' % SHLIB_EXT), + ('lib/libnettle.a', 'lib64/libnettle.a'), ('lib/libnettle.%s' % SHLIB_EXT, 'lib64/libnettle.%s' % SHLIB_EXT)], 'dirs': ['include/nettle'], } diff --git a/easybuild/easyconfigs/n/nettle/nettle-3.2-foss-2016b.eb b/easybuild/easyconfigs/n/nettle/nettle-3.2-foss-2016b.eb index d8b0e1009d..2f73f07946 100644 --- a/easybuild/easyconfigs/n/nettle/nettle-3.2-foss-2016b.eb +++ b/easybuild/easyconfigs/n/nettle/nettle-3.2-foss-2016b.eb @@ -20,8 +20,8 @@ dependencies = [ sanity_check_paths = { 'files': ['bin/%s' % x for x in ['nettle-hash', 'nettle-lfib-stream', 'pkcs1-conv', 'sexp-conv']] + - ['lib64/libhogweed.a', 'lib64/libhogweed.%s' % SHLIB_EXT, - 'lib64/libnettle.a', 'lib64/libnettle.%s' % SHLIB_EXT], + [('lib/libhogweed.a', 'lib64/libhogweed.a'), ('lib/libhogweed.%s' % SHLIB_EXT, 'lib64/libhogweed.%s' % SHLIB_EXT), + ('lib/libnettle.a', 'lib64/libnettle.a'), ('lib/libnettle.%s' % SHLIB_EXT, 'lib64/libnettle.%s' % SHLIB_EXT)], 'dirs': ['include/nettle'], } diff --git a/easybuild/easyconfigs/n/nettle/nettle-3.2-intel-2016b.eb b/easybuild/easyconfigs/n/nettle/nettle-3.2-intel-2016b.eb index 728d252367..d49da80e3c 100644 --- a/easybuild/easyconfigs/n/nettle/nettle-3.2-intel-2016b.eb +++ b/easybuild/easyconfigs/n/nettle/nettle-3.2-intel-2016b.eb @@ -20,8 +20,8 @@ dependencies = [ sanity_check_paths = { 'files': ['bin/%s' % x for x in ['nettle-hash', 'nettle-lfib-stream', 'pkcs1-conv', 'sexp-conv']] + - ['lib64/libhogweed.a', 'lib64/libhogweed.%s' % SHLIB_EXT, - 'lib64/libnettle.a', 'lib64/libnettle.%s' % SHLIB_EXT], + [('lib/libhogweed.a', 'lib64/libhogweed.a'), ('lib/libhogweed.%s' % SHLIB_EXT, 'lib64/libhogweed.%s' % SHLIB_EXT), + ('lib/libnettle.a', 'lib64/libnettle.a'), ('lib/libnettle.%s' % SHLIB_EXT, 'lib64/libnettle.%s' % SHLIB_EXT)], 'dirs': ['include/nettle'], } diff --git a/easybuild/easyconfigs/n/nettle/nettle-3.3-intel-2017a.eb b/easybuild/easyconfigs/n/nettle/nettle-3.3-intel-2017a.eb index d8f9e8fc31..9683896ee0 100644 --- a/easybuild/easyconfigs/n/nettle/nettle-3.3-intel-2017a.eb +++ b/easybuild/easyconfigs/n/nettle/nettle-3.3-intel-2017a.eb @@ -20,8 +20,8 @@ dependencies = [ sanity_check_paths = { 'files': ['bin/%s' % x for x in ['nettle-hash', 'nettle-lfib-stream', 'pkcs1-conv', 'sexp-conv']] + - ['lib64/libhogweed.a', 'lib64/libhogweed.%s' % SHLIB_EXT, - 'lib64/libnettle.a', 'lib64/libnettle.%s' % SHLIB_EXT], + [('lib/libhogweed.a', 'lib64/libhogweed.a'), ('lib/libhogweed.%s' % SHLIB_EXT, 'lib64/libhogweed.%s' % SHLIB_EXT), + ('lib/libnettle.a', 'lib64/libnettle.a'), ('lib/libnettle.%s' % SHLIB_EXT, 'lib64/libnettle.%s' % SHLIB_EXT)], 'dirs': ['include/nettle'], } -- GitLab From 5449a5d6d4f1459eb7a04f3a542ab2a5a15cf1e7 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Fri, 16 Jun 2017 12:06:33 -0500 Subject: [PATCH 0949/1603] adding easyconfigs: Python-3.5.2-iccifort-2016.3.210-GCC-5.4.0-2.26-bare.eb --- ...iccifort-2016.3.210-GCC-5.4.0-2.26-bare.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/p/Python/Python-3.5.2-iccifort-2016.3.210-GCC-5.4.0-2.26-bare.eb diff --git a/easybuild/easyconfigs/p/Python/Python-3.5.2-iccifort-2016.3.210-GCC-5.4.0-2.26-bare.eb b/easybuild/easyconfigs/p/Python/Python-3.5.2-iccifort-2016.3.210-GCC-5.4.0-2.26-bare.eb new file mode 100644 index 0000000000..7c126a4294 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-3.5.2-iccifort-2016.3.210-GCC-5.4.0-2.26-bare.eb @@ -0,0 +1,32 @@ +name = 'Python' +version = '3.5.2' +versionsuffix = '-bare' + +homepage = 'http://python.org/' +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" + +toolchain = {'name': 'iccifort', 'version': '2016.3.210-GCC-5.4.0-2.26'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libreadline', '6.3'), + ('ncurses', '6.0'), + ('SQLite', '3.13.0'), + ('Tk', '8.6.5'), # this requires a full X11 stack + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.2h'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# bare installation: no extensions included +exts_list = [] + +moduleclass = 'lang' -- GitLab From 711bb3ab39f29187ae2b536f57cec10b77cc4676 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Fri, 16 Jun 2017 12:13:04 -0500 Subject: [PATCH 0950/1603] adding easyconfigs: Python-3.5.2-GCC-5.4.0-2.26-bare.eb --- .../Python-3.5.2-GCC-5.4.0-2.26-bare.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/p/Python/Python-3.5.2-GCC-5.4.0-2.26-bare.eb diff --git a/easybuild/easyconfigs/p/Python/Python-3.5.2-GCC-5.4.0-2.26-bare.eb b/easybuild/easyconfigs/p/Python/Python-3.5.2-GCC-5.4.0-2.26-bare.eb new file mode 100644 index 0000000000..1e9fd31ecc --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-3.5.2-GCC-5.4.0-2.26-bare.eb @@ -0,0 +1,31 @@ +name = 'Python' +version = '3.5.2' +versionsuffix = '-bare' + +homepage = 'http://python.org/' +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" + +toolchain = {'name': 'GCC', 'version': '5.4.0-2.26'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libreadline', '6.3'), + ('ncurses', '6.0'), + ('SQLite', '3.13.0'), + ('Tk', '8.6.5'), # this requires a full X11 stack + ('GMP', '6.1.1'), + ('libffi', '3.2.1'), + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.2h'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +moduleclass = 'lang' -- GitLab From 222682e50bd5e1b59792aa7eaaafe53220049d4a Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Fri, 16 Jun 2017 13:18:51 -0500 Subject: [PATCH 0951/1603] adding easyconfigs: libtasn1-4.12-GCCcore-5.4.0.eb, libidn-1.32-GCCcore-5.4.0.eb, libunistring-0.9.6-GCCcore-5.4.0.eb --- .../l/libidn/libidn-1.32-GCCcore-5.4.0.eb | 21 +++++++++++++++ .../l/libtasn1/libtasn1-4.12-GCCcore-5.4.0.eb | 24 +++++++++++++++++ .../libunistring-0.9.6-GCCcore-5.4.0.eb | 26 +++++++++++++++++++ 3 files changed, 71 insertions(+) create mode 100644 easybuild/easyconfigs/l/libidn/libidn-1.32-GCCcore-5.4.0.eb create mode 100644 easybuild/easyconfigs/l/libtasn1/libtasn1-4.12-GCCcore-5.4.0.eb create mode 100644 easybuild/easyconfigs/l/libunistring/libunistring-0.9.6-GCCcore-5.4.0.eb diff --git a/easybuild/easyconfigs/l/libidn/libidn-1.32-GCCcore-5.4.0.eb b/easybuild/easyconfigs/l/libidn/libidn-1.32-GCCcore-5.4.0.eb new file mode 100644 index 0000000000..8fe50e9968 --- /dev/null +++ b/easybuild/easyconfigs/l/libidn/libidn-1.32-GCCcore-5.4.0.eb @@ -0,0 +1,21 @@ +easyblock = 'ConfigureMake' + +name = 'libidn' +version = '1.32' + +homepage = 'http://www.gnu.org/software/libidn' +description = """GNU Libidn is a fully documented implementation of the Stringprep, Punycode and IDNA specifications. +Libidn's purpose is to encode and decode internationalized domain names.""" + +toolchain = {'name': 'GCCcore', 'version': '5.4.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +builddependencies = [('binutils', '2.26', '', True)] + +sanity_check_paths = { + 'files': ['bin/idn', 'lib/libidn.%s' % SHLIB_EXT], + 'dirs': ['include'], +} +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libtasn1/libtasn1-4.12-GCCcore-5.4.0.eb b/easybuild/easyconfigs/l/libtasn1/libtasn1-4.12-GCCcore-5.4.0.eb new file mode 100644 index 0000000000..e8763aba9c --- /dev/null +++ b/easybuild/easyconfigs/l/libtasn1/libtasn1-4.12-GCCcore-5.4.0.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'libtasn1' +version = '4.12' + +homepage = 'https://www.gnu.org/software/libtasn1/' +description = """Libtasn1 is the ASN.1 library used by GnuTLS, GNU Shishi and some other packages. + It was written by Fabio Fiorina, and has been shipped as part of GnuTLS + for some time but is now a proper GNU package.""" + +toolchain = {'name': 'GCCcore', 'version': '5.4.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] + +builddependencies = [('binutils', '2.26', '', True)] + +sanity_check_paths = { + 'files': ['bin/asn1%s' % x for x in ['Coding', 'Decoding', 'Parser']] + + ['lib/libtasn1.%s' % x for x in ['a', SHLIB_EXT]], + 'dirs': ['include'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libunistring/libunistring-0.9.6-GCCcore-5.4.0.eb b/easybuild/easyconfigs/l/libunistring/libunistring-0.9.6-GCCcore-5.4.0.eb new file mode 100644 index 0000000000..c1f1541e7a --- /dev/null +++ b/easybuild/easyconfigs/l/libunistring/libunistring-0.9.6-GCCcore-5.4.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'libunistring' +version = '0.9.6' + +homepage = 'http://www.gnu.org/software/libunistring/' +description = """This library provides functions for manipulating Unicode strings and for manipulating C strings + according to the Unicode standard.""" + +toolchain = {'name': 'GCCcore', 'version': '5.4.0'} + +sources = [SOURCELOWER_TAR_XZ] +source_urls = [GNU_SOURCE] + +builddependencies = [('binutils', '2.26', '', True)] + +parallel = 1 + +sanity_check_paths = { + 'files': ['lib/libunistring.a', 'lib/libunistring.%s' % SHLIB_EXT] + + ['include/uni%s.h' % x for x in ['case', 'conv', 'ctype', 'lbrk', 'name', 'norm', + 'stdio', 'str', 'types', 'wbrk', 'width']], + 'dirs': ['include/unistring'], +} + +moduleclass = 'lib' -- GitLab From 3165263b822850b2c389d0cb46545de0dac85c86 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 19 Jun 2017 13:42:18 +0200 Subject: [PATCH 0952/1603] adding easyconfigs: VTune-2017_update3.eb --- .../easyconfigs/v/VTune/VTune-2017_update3.eb | 15 +++++++++++++++ 1 file changed, 15 insertions(+) create mode 100644 easybuild/easyconfigs/v/VTune/VTune-2017_update3.eb diff --git a/easybuild/easyconfigs/v/VTune/VTune-2017_update3.eb b/easybuild/easyconfigs/v/VTune/VTune-2017_update3.eb new file mode 100644 index 0000000000..e35eec8996 --- /dev/null +++ b/easybuild/easyconfigs/v/VTune/VTune-2017_update3.eb @@ -0,0 +1,15 @@ +name = 'VTune' +version = '2017_update3' + +homepage = 'http://software.intel.com/en-us/intel-vtune-amplifier-xe' +description = """Intel VTune Amplifier XE is the premier performance profiler for C, C++, C#, Fortran, + Assembly and Java.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['vtune_amplifier_xe_%(version)s.tar.gz'] +checksums = ['1e32ce4a591439d42b23ad2960350f3354fe5f805f96c98f21ce315b66789025'] + +license_file = HOME + '/licenses/intel/license.lic' + +moduleclass = 'tools' -- GitLab From 7a9cbedfdc2c6641973bf6fc70c006cfb6a6ed02 Mon Sep 17 00:00:00 2001 From: iotaka Date: Mon, 19 Jun 2017 15:56:03 +0200 Subject: [PATCH 0953/1603] adding easyconfigs: modred-2.0.2-foss-2016b-Python-3.5.2.eb --- .../modred-2.0.2-foss-2016b-Python-3.5.2.eb | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/m/modred/modred-2.0.2-foss-2016b-Python-3.5.2.eb diff --git a/easybuild/easyconfigs/m/modred/modred-2.0.2-foss-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/m/modred/modred-2.0.2-foss-2016b-Python-3.5.2.eb new file mode 100644 index 0000000000..d45b071d80 --- /dev/null +++ b/easybuild/easyconfigs/m/modred/modred-2.0.2-foss-2016b-Python-3.5.2.eb @@ -0,0 +1,22 @@ +easyblock = 'PythonPackage' + +name = 'modred' +version = '2.0.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = "https://pypi.python.org/pypi/modred/" +description = """Compute modal decompositions and reduced-order models, easily, efficiently, and in parallel.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [('Python', '3.5.2')] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'lib' -- GitLab From 9d21dd733f27f29d3cf88d5230d775ba8649619c Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Mon, 19 Jun 2017 11:51:22 -0500 Subject: [PATCH 0954/1603] adding easyconfigs: Guile-1.8.8-GCCcore-5.4.0.eb --- .../g/Guile/Guile-1.8.8-GCCcore-5.4.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/g/Guile/Guile-1.8.8-GCCcore-5.4.0.eb diff --git a/easybuild/easyconfigs/g/Guile/Guile-1.8.8-GCCcore-5.4.0.eb b/easybuild/easyconfigs/g/Guile/Guile-1.8.8-GCCcore-5.4.0.eb new file mode 100644 index 0000000000..4f4fa3e2f0 --- /dev/null +++ b/easybuild/easyconfigs/g/Guile/Guile-1.8.8-GCCcore-5.4.0.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'Guile' +version = '1.8.8' + +homepage = 'http://www.gnu.org/software/guile' +description = """Guile is the GNU Ubiquitous Intelligent Language for Extensions, + the official extension language for the GNU operating system.""" + +toolchain = {'name': 'GCCcore', 'version': '5.4.0'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +dependencies = [ + ('libtool', '2.4.6'), + ('GMP', '6.1.1'), + ('libunistring', '0.9.6'), + ('pkg-config', '0.29.1'), + ('libffi', '3.2.1'), + ('libreadline', '6.3'), +] + +builddependencies = [('binutils', '2.26', '', True)] + +configopts = " --enable-error-on-warning=no" + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["guile", 'guile-config', 'guile-snarf', 'guile-tools']] + + ["lib/libguile.a", "include/libguile.h"], + 'dirs': [] +} + +moduleclass = 'devel' -- GitLab From ac00de53f113e340ebb7abd62e73baa22b594bb5 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Mon, 19 Jun 2017 11:51:45 -0500 Subject: [PATCH 0955/1603] adding easyconfigs: p11-kit-0.23.2-GCCcore-5.4.0.eb --- .../p/p11-kit/p11-kit-0.23.2-GCCcore-5.4.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/p/p11-kit/p11-kit-0.23.2-GCCcore-5.4.0.eb diff --git a/easybuild/easyconfigs/p/p11-kit/p11-kit-0.23.2-GCCcore-5.4.0.eb b/easybuild/easyconfigs/p/p11-kit/p11-kit-0.23.2-GCCcore-5.4.0.eb new file mode 100644 index 0000000000..0e997ce499 --- /dev/null +++ b/easybuild/easyconfigs/p/p11-kit/p11-kit-0.23.2-GCCcore-5.4.0.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'p11-kit' +version = '0.23.2' + +homepage = 'http://p11-glue.freedesktop.org/p11-kit.html' +description = """Provides a way to load and enumerate PKCS#11 modules. + Provides a standard configuration setup for installing + PKCS#11 modules in such a way that they're discoverable. + Also solves problems with coordinating the use of PKCS#11 + by different components or libraries living in the same process.""" + +toolchain = {'name': 'GCCcore', 'version': '5.4.0'} + +source_urls = ['http://p11-glue.freedesktop.org/releases/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('libtasn1', '4.12'), + ('libffi', '3.2.1'), +] + +builddependencies = [('binutils', '2.26', '', True)] + +sanity_check_paths = { + 'files': ['bin/p11-kit', 'bin/trust'] + + ['lib/libp11-kit.%s' % SHLIB_EXT], + 'dirs': ['include/p11-kit-1/p11-kit'], +} + +moduleclass = 'lib' -- GitLab From aa6b3d0674cf37ad46f7fc7183bda66f22efc7c3 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Mon, 19 Jun 2017 14:26:27 -0500 Subject: [PATCH 0956/1603] adding easyconfigs: cURL-7.49.1-GCCcore-5.4.0.eb, Doxygen-1.8.11-GCCcore-5.4.0.eb, Szip-2.1-GCCcore-5.4.0.eb --- .../c/cURL/cURL-7.49.1-GCCcore-5.4.0.eb | 33 +++++++++++++++++++ .../d/Doxygen/Doxygen-1.8.11-GCCcore-5.4.0.eb | 21 ++++++++++++ .../s/Szip/Szip-2.1-GCCcore-5.4.0.eb | 25 ++++++++++++++ 3 files changed, 79 insertions(+) create mode 100644 easybuild/easyconfigs/c/cURL/cURL-7.49.1-GCCcore-5.4.0.eb create mode 100644 easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-GCCcore-5.4.0.eb create mode 100644 easybuild/easyconfigs/s/Szip/Szip-2.1-GCCcore-5.4.0.eb diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.49.1-GCCcore-5.4.0.eb b/easybuild/easyconfigs/c/cURL/cURL-7.49.1-GCCcore-5.4.0.eb new file mode 100644 index 0000000000..9bb277e7b1 --- /dev/null +++ b/easybuild/easyconfigs/c/cURL/cURL-7.49.1-GCCcore-5.4.0.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'cURL' +version = '7.49.1' + +homepage = 'http://curl.haxx.se' +description = """libcurl is a free and easy-to-use client-side URL transfer library, + supporting DICT, FILE, FTP, FTPS, Gopher, HTTP, HTTPS, IMAP, IMAPS, LDAP, LDAPS, + POP3, POP3S, RTMP, RTSP, SCP, SFTP, SMTP, SMTPS, Telnet and TFTP. libcurl supports + SSL certificates, HTTP POST, HTTP PUT, FTP uploading, HTTP form based upload, + proxies, cookies, user+password authentication (Basic, Digest, NTLM, Negotiate, + Kerberos), file transfer resume, http proxy tunneling and more.""" + +toolchain = {'name': 'GCCcore', 'version': '5.4.0'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://curl.haxx.se/download/'] + +builddependencies = [('binutils', '2.26', '', True)] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# dependencies = [('OpenSSL', '1.0.1t')] +# configopts = "--with-ssl=$EBROOTOPENSSL" + +modextravars = {'CURL_INCLUDES': '%(installdir)s/include'} + +sanity_check_paths = { + 'files': ['bin/curl', 'lib/libcurl.a', 'lib/libcurl.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-GCCcore-5.4.0.eb b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-GCCcore-5.4.0.eb new file mode 100644 index 0000000000..f55dbe8583 --- /dev/null +++ b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-GCCcore-5.4.0.eb @@ -0,0 +1,21 @@ +name = 'Doxygen' +version = '1.8.11' + +homepage = 'http://www.doxygen.org' +description = """Doxygen is a documentation system for C++, C, Java, Objective-C, Python, + IDL (Corba and Microsoft flavors), Fortran, VHDL, PHP, C#, and to some extent D.""" + +toolchain = {'name': 'GCCcore', 'version': '5.4.0'} + +sources = ['%(namelower)s-%(version)s.src.tar.gz'] +source_urls = ['http://ftp.stack.nl/pub/users/dimitri/'] + +builddependencies = [ + ('CMake', '3.7.1'), + ('flex', '2.6.0'), + ('Bison', '3.0.4'), +] + +parallel = 1 + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1-GCCcore-5.4.0.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1-GCCcore-5.4.0.eb new file mode 100644 index 0000000000..51caf7745b --- /dev/null +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1-GCCcore-5.4.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'Szip' +version = '2.1' + +homepage = 'http://www.hdfgroup.org/doc_resource/SZIP/' +description = "Szip compression software, providing lossless compression of scientific data" + +toolchain = {'name': 'GCCcore', 'version': '5.4.0'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = "--with-pic" + +builddependencies = [('binutils', '2.26', '', True)] + +sanity_check_paths = { + 'files': ["lib/libsz.a", "lib/libsz.%s" % SHLIB_EXT] + + ["include/%s" % x for x in ["ricehdf.h", "szip_adpt.h", "szlib.h"]], + 'dirs': [], +} + +moduleclass = 'tools' -- GitLab From 450a7f3930fa0e6167a48ab803191a5275f489ec Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Mon, 19 Jun 2017 14:31:16 -0500 Subject: [PATCH 0957/1603] adding easyconfigs: libxc-3.0.0-GCC-5.4.0-2.26.eb --- .../l/libxc/libxc-3.0.0-GCC-5.4.0-2.26.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/l/libxc/libxc-3.0.0-GCC-5.4.0-2.26.eb diff --git a/easybuild/easyconfigs/l/libxc/libxc-3.0.0-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/l/libxc/libxc-3.0.0-GCC-5.4.0-2.26.eb new file mode 100644 index 0000000000..c3570aaed3 --- /dev/null +++ b/easybuild/easyconfigs/l/libxc/libxc-3.0.0-GCC-5.4.0-2.26.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'libxc' +version = '3.0.0' + +homepage = 'http://www.tddft.org/programs/octopus/wiki/index.php/Libxc' +description = """Libxc is a library of exchange-correlation functionals for density-functional theory. + The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" + +toolchain = {'name': 'GCC', 'version': '5.4.0-2.26'} +# Results for some functionals (e.g. mgga_c_tpss) deviate with too aggressive optimization settings. +toolchainopts = {'lowopt': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] + +configopts = 'FC="$F77" FCFLAGS="$FFLAGS" --enable-shared --enable-fortran' + +# From the libxc mailing list +# To summarize: expect less tests to fail in libxc 2.0.2, but don't expect +# a fully working testsuite soon (unless someone wants to volunteer to do +# it, of course ) In the meantime, unless the majority of the tests +# fail, your build should be fine. +# runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libxc%s.%s' % (x, y) for x in ['', 'f90'] for y in ['a', SHLIB_EXT]], + 'dirs': ['include'], +} + +parallel = 1 + +moduleclass = 'chem' -- GitLab From 76a807808549fec43273cd896e8cc05d529f7989 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Mon, 19 Jun 2017 14:32:00 -0500 Subject: [PATCH 0958/1603] adding easyconfigs: libxc-3.0.0-iccifort-2016.3.210-GCC-5.4.0-2.26.eb --- ....0.0-iccifort-2016.3.210-GCC-5.4.0-2.26.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/l/libxc/libxc-3.0.0-iccifort-2016.3.210-GCC-5.4.0-2.26.eb diff --git a/easybuild/easyconfigs/l/libxc/libxc-3.0.0-iccifort-2016.3.210-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/l/libxc/libxc-3.0.0-iccifort-2016.3.210-GCC-5.4.0-2.26.eb new file mode 100644 index 0000000000..5dad1c142c --- /dev/null +++ b/easybuild/easyconfigs/l/libxc/libxc-3.0.0-iccifort-2016.3.210-GCC-5.4.0-2.26.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'libxc' +version = '3.0.0' + +homepage = 'http://www.tddft.org/programs/octopus/wiki/index.php/Libxc' +description = """Libxc is a library of exchange-correlation functionals for density-functional theory. + The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" + +toolchain = {'name': 'iccifort', 'version': '2016.3.210-GCC-5.4.0-2.26'} +# Results for some functionals (e.g. mgga_c_tpss) deviate with too aggressive optimization settings. +toolchainopts = {'lowopt': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] + +configopts = 'FC="$F77" FCFLAGS="$FFLAGS" --enable-shared --enable-fortran' + +# From the libxc mailing list +# To summarize: expect less tests to fail in libxc 2.0.2, but don't expect +# a fully working testsuite soon (unless someone wants to volunteer to do +# it, of course ) In the meantime, unless the majority of the tests +# fail, your build should be fine. +# runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libxc%s.%s' % (x, y) for x in ['', 'f90'] for y in ['a', SHLIB_EXT]], + 'dirs': ['include'], +} + +parallel = 1 + +moduleclass = 'chem' -- GitLab From 9fb4fa4582db42b986b3d2449c9a963e9ed528c8 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Mon, 19 Jun 2017 14:51:44 -0500 Subject: [PATCH 0959/1603] adding easyconfigs: ABINIT-8.2.2-foss-2016b.eb --- .../a/ABINIT/ABINIT-8.2.2-foss-2016b.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/a/ABINIT/ABINIT-8.2.2-foss-2016b.eb diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-8.2.2-foss-2016b.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-8.2.2-foss-2016b.eb new file mode 100644 index 0000000000..0042cb41f3 --- /dev/null +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-8.2.2-foss-2016b.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'ABINIT' +version = '8.2.2' + +homepage = 'http://www.abinit.org/' +description = """ABINIT is a package whose main program allows one to find the total energy, charge density and + electronic structure of systems made of electrons and nuclei (molecules and periodic solids) within Density Functional + Theory (DFT), using pseudopotentials and a planewave or wavelet basis.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['http://ftp.abinit.org/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['5f25250e06fdc0815c224ffd29858860'] + +configopts = "--with-mpi-prefix=$EBROOTOPENMPI/intel64 --with-trio-flavor='etsf_io+netcdf' --with-dft=flavor='libxc' " +configopts += '--with-netcdf-incs="-I$EBROOTNETCDF/include -I$EBROOTNETCDFMINFORTRAN/include" ' +configopts += '--with-netcdf-libs="-L$EBROOTNETCDF/lib -lnetcdf -L$EBROOTNETCDFMINFORTRAN/lib -lnetcdff" ' +configopts += '--with-libxc-incs="-I$EBROOTLIBXC/include" --with-libxc-libs="-L$EBROOTLIBXC/lib -lxc" ' +configopts += 'FCFLAGS="-ffree-line-length-none" ' + +dependencies = [ + ('libxc', '3.0.0'), + ('netCDF', '4.4.1'), + ('netCDF-Fortran', '4.4.4'), +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['abinit', 'aim', 'cut3d', 'conducti', 'mrgddb', 'mrgscr', 'optic']], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'chem' -- GitLab From 0c4ecdaf2045e4021ebe29aa803135813ec8d4d6 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Mon, 19 Jun 2017 14:58:44 -0500 Subject: [PATCH 0960/1603] adding easyconfigs: ABINIT-8.2.2-intel-2016b.eb --- .../a/ABINIT/ABINIT-8.2.2-intel-2016b.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/a/ABINIT/ABINIT-8.2.2-intel-2016b.eb diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-8.2.2-intel-2016b.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-8.2.2-intel-2016b.eb new file mode 100644 index 0000000000..5ea50a6af7 --- /dev/null +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-8.2.2-intel-2016b.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'ABINIT' +version = '8.2.2' + +homepage = 'http://www.abinit.org/' +description = """ABINIT is a package whose main program allows one to find the total energy, charge density and + electronic structure of systems made of electrons and nuclei (molecules and periodic solids) within Density Functional + Theory (DFT), using pseudopotentials and a planewave or wavelet basis.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['http://ftp.abinit.org/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['5f25250e06fdc0815c224ffd29858860'] + +configopts = "--with-mpi-prefix=$EBROOTIMPI/intel64 --with-trio-flavor='etsf_io+netcdf' --with-dft=flavor='libxc' " +configopts += '--with-netcdf-incs="-I$EBROOTNETCDF/include -I$EBROOTNETCDFMINFORTRAN/include" ' +configopts += '--with-netcdf-libs="-L$EBROOTNETCDF/lib -lnetcdf -L$EBROOTNETCDFMINFORTRAN/lib -lnetcdff" ' +configopts += '--with-libxc-incs="-I$EBROOTLIBXC/include" --with-libxc-libs="-L$EBROOTLIBXC/lib -lxc" ' + +dependencies = [ + ('libxc', '3.0.0'), + ('netCDF', '4.4.1'), + ('netCDF-Fortran', '4.4.4'), +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['abinit', 'aim', 'cut3d', 'conducti', 'mrgddb', 'mrgscr', 'optic']], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'chem' -- GitLab From 87eb3c20e106aa923e247c7a9fa30b5cbf3b55b4 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Tue, 20 Jun 2017 10:49:55 +1200 Subject: [PATCH 0961/1603] The NASM (Netwide Assembler) with no toolchain --- easybuild/easyconfigs/n/NASM/NASM-2.12.02.eb | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) create mode 100644 easybuild/easyconfigs/n/NASM/NASM-2.12.02.eb diff --git a/easybuild/easyconfigs/n/NASM/NASM-2.12.02.eb b/easybuild/easyconfigs/n/NASM/NASM-2.12.02.eb new file mode 100644 index 0000000000..3c18189624 --- /dev/null +++ b/easybuild/easyconfigs/n/NASM/NASM-2.12.02.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'NASM' +version = '2.12.02' + +homepage = 'http://www.nasm.us/' +description = """NASM: General-purpose x86 assembler""" + +toolchain = {'version': 'dummy', 'name': 'dummy'} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://www.nasm.us/pub/nasm/releasebuilds/%(version)s'] + +sanity_check_paths = { + 'files': ['bin/nasm'], + 'dirs': [], +} + +moduleclass = 'lang' -- GitLab From 73dc6584e2f75e85b49dee751275211ed71b8b4c Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Tue, 20 Jun 2017 10:59:23 +1200 Subject: [PATCH 0962/1603] New EasyConfigs for Szip and HDF5 with the gimkl-2017a toolchain --- .../h/HDF5/HDF5-1.8.18-gimkl-2017a.eb | 31 +++++++++++++++++++ .../s/Szip/Szip-2.1-gimkl-2017a.eb | 23 ++++++++++++++ 2 files changed, 54 insertions(+) create mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.8.18-gimkl-2017a.eb create mode 100644 easybuild/easyconfigs/s/Szip/Szip-2.1-gimkl-2017a.eb diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.18-gimkl-2017a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.18-gimkl-2017a.eb new file mode 100644 index 0000000000..57cd66e064 --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.18-gimkl-2017a.eb @@ -0,0 +1,31 @@ +name = 'HDF5' +version = '1.8.18' + +homepage = 'http://www.hdfgroup.org/HDF5/' +description = """HDF5 is a unique technology suite that makes possible the management of + extremely large and complex data collections.""" + +toolchain = {'name': 'gimkl', 'version': '2017a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = [ + 'https://support.hdfgroup.org/ftp/HDF5/current18/src/', + 'https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(versions)/src/' +] + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['dd2148b740713ca0295442ec683d7b1c'] + +buildopts = 'CXXFLAGS="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK"' + +dependencies = [ + ('zlib', '1.2.11'), + ('Szip', '2.1'), +] + +# Needed for h5py in Python (at least sometimes) +modextravars = { + 'HDF5_DIR': '%(installdir)s', +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1-gimkl-2017a.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1-gimkl-2017a.eb new file mode 100644 index 0000000000..4d2a5188f4 --- /dev/null +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1-gimkl-2017a.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'Szip' +version = '2.1' + +homepage = 'http://www.hdfgroup.org/doc_resource/SZIP/' +description = "Szip compression software, providing lossless compression of scientific data" + +toolchain = {'version': '2017a', 'name': 'gimkl'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = "--with-pic" + +sanity_check_paths = { + 'files': ["lib/libsz.a", "lib/libsz.%s" % SHLIB_EXT] + + ["include/%s" % x for x in ["ricehdf.h", "szip_adpt.h", "szlib.h"]], + 'dirs': [], +} + +moduleclass = 'tools' -- GitLab From 9920d9c15dc10952d8c64fd8f739b88a8dd26ebe Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Tue, 20 Jun 2017 11:13:57 +1200 Subject: [PATCH 0963/1603] Remove executable permissions on HDF5-1.8.10-ictce-5.3.0-gpfs-zlib-1.2.5.eb --- .../easyconfigs/h/HDF5/HDF5-1.8.10-ictce-5.3.0-gpfs-zlib-1.2.5.eb | 0 1 file changed, 0 insertions(+), 0 deletions(-) mode change 100755 => 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-ictce-5.3.0-gpfs-zlib-1.2.5.eb diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-ictce-5.3.0-gpfs-zlib-1.2.5.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-ictce-5.3.0-gpfs-zlib-1.2.5.eb old mode 100755 new mode 100644 -- GitLab From 4b035601e78e5cfa5095d447b19557e31d8e1d9a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 20 Jun 2017 10:07:47 +0200 Subject: [PATCH 0964/1603] adding easyconfigs: FUNWAVE-TVD-3.1-20170525-intel-2017a-no-storm.eb --- ...E-TVD-3.1-20170525-intel-2017a-no-storm.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/f/FUNWAVE-TVD/FUNWAVE-TVD-3.1-20170525-intel-2017a-no-storm.eb diff --git a/easybuild/easyconfigs/f/FUNWAVE-TVD/FUNWAVE-TVD-3.1-20170525-intel-2017a-no-storm.eb b/easybuild/easyconfigs/f/FUNWAVE-TVD/FUNWAVE-TVD-3.1-20170525-intel-2017a-no-storm.eb new file mode 100644 index 0000000000..4fd23347c3 --- /dev/null +++ b/easybuild/easyconfigs/f/FUNWAVE-TVD/FUNWAVE-TVD-3.1-20170525-intel-2017a-no-storm.eb @@ -0,0 +1,31 @@ +easyblock = 'MakeCp' + +name = 'FUNWAVE-TVD' +version = '3.1-20170525' +commit = '814107a' +versionsuffix = '-no-storm' + +homepage = 'https://fengyanshi.github.io' +description = """FUNWAVE–TVD is the TVD version of the fully nonlinear Boussinesq wave model (FUNWAVE) + initially developed by Kirby et al.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/fengyanshi/FUNWAVE-TVD/archive/'] +sources = ['%s.tar.gz' % commit] + +start_dir = 'src' +parallel = 1 +buildopts = 'FC="$FC" FFLAGS="$FFLAGS -fpp" CPPFLAGS="-DINTEL -DMIXING -DMANNING -DVIS_KENNEDY" ' +# don't use -DSTORM +buildopts += "FLAG_16='' " + +files_to_copy = [(['mytvd'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/mytvd'], + 'dirs': [], +} + +moduleclass = 'math' -- GitLab From 5bc9a78ea5bff968906d375839a81e30f342528e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 20 Jun 2017 10:31:28 +0200 Subject: [PATCH 0965/1603] adding easyconfigs: sharutils-4.15-GCCcore-6.3.0.eb --- .../sharutils/sharutils-4.15-GCCcore-6.3.0.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/s/sharutils/sharutils-4.15-GCCcore-6.3.0.eb diff --git a/easybuild/easyconfigs/s/sharutils/sharutils-4.15-GCCcore-6.3.0.eb b/easybuild/easyconfigs/s/sharutils/sharutils-4.15-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..06f3fc97f7 --- /dev/null +++ b/easybuild/easyconfigs/s/sharutils/sharutils-4.15-GCCcore-6.3.0.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'sharutils' +version = '4.15' + +homepage = 'https://www.gnu.org/software/sharutils/' +description = """GNU shar makes so-called shell archives out of many files, preparing them for transmission by + electronic mail services, while unshar helps unpacking shell archives after reception.""" + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] + +# use same binutils version that was used when building GCC toolchain +builddependencies = [('binutils', '2.27', '', True)] + +sanity_check_paths = { + 'files': ['bin/shar', 'bin/uudecode', 'bin/uuencode', 'bin/unshar'], + 'dirs': [], +} + +moduleclass = 'tools' -- GitLab From d1310b028c90f173f3ba5cd759519d2af289c84f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 20 Jun 2017 13:14:28 +0200 Subject: [PATCH 0966/1603] add glmmML & ordinal (+ ucminf) as R extensions --- easybuild/easyconfigs/r/R/R-3.4.0-intel-2017a-X11-20170314.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-3.4.0-intel-2017a-X11-20170314.eb b/easybuild/easyconfigs/r/R/R-3.4.0-intel-2017a-X11-20170314.eb index db02d8833d..5616a94b6a 100644 --- a/easybuild/easyconfigs/r/R/R-3.4.0-intel-2017a-X11-20170314.eb +++ b/easybuild/easyconfigs/r/R/R-3.4.0-intel-2017a-X11-20170314.eb @@ -524,6 +524,9 @@ exts_list = [ ('memuse', '3.0-1', ext_options), ('pinfsc50', '1.1.0', ext_options), ('vcfR', '1.5.0', ext_options), + ('glmmML', '1.0.2', ext_options), + ('ucminf', '1.1-4', ext_options), + ('ordinal', '2015.6-28', ext_options), ] moduleclass = 'lang' -- GitLab From 6bde8f4b0dbaa02cbd112f6d99f706a3a63905d8 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Tue, 20 Jun 2017 16:47:44 +0100 Subject: [PATCH 0967/1603] adding easyconfigs: Trim_Galore-0.4.4-foss-2016b.eb --- .../Trim_Galore-0.4.4-foss-2016b.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100755 easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.4.4-foss-2016b.eb diff --git a/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.4.4-foss-2016b.eb b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.4.4-foss-2016b.eb new file mode 100755 index 0000000000..ed3b679410 --- /dev/null +++ b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.4.4-foss-2016b.eb @@ -0,0 +1,33 @@ +# 0.4.2 modified by: +# Adam Huffman +# The Francis Crick Institute +# TODO: deal with the hardcoding of /usr/bin/perl + +easyblock = "PackedBinary" + +name = 'Trim_Galore' +version = '0.4.4' + +homepage = 'http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/' +description = """A wrapper tool around Cutadapt and FastQC to consistently apply + quality and adapter trimming to FastQ files, with some extra functionality for + MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +sources = ['%(namelower)s_v%(version)s.zip'] +source_urls = ['http://www.bioinformatics.babraham.ac.uk/projects/%(namelower)s'] + +install_cmd = "cp -a * %(installdir)s && chmod +x %(installdir)s/%(namelower)s" + +dependencies = [ + ('FastQC', '0.11.5', '-Java-1.7.0_80', True), + ('cutadapt', '1.9.1', '-Python-2.7.12'), +] + +sanity_check_paths = { + 'files': ["trim_galore"], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From 910a55f08aa99a644510a10708ea8ab8e317ddc1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 20 Jun 2017 20:34:47 +0200 Subject: [PATCH 0968/1603] fix source URLs for HDF5 --- .../easyconfigs/h/HDF5/HDF5-1.10.0-patch1-foss-2016b.eb | 2 +- .../h/HDF5/HDF5-1.10.0-patch1-goolfc-2016.10.eb | 2 +- .../easyconfigs/h/HDF5/HDF5-1.10.0-patch1-intel-2016b.eb | 2 +- .../easyconfigs/h/HDF5/HDF5-1.10.0-patch1-intel-2017.01.eb | 2 +- .../easyconfigs/h/HDF5/HDF5-1.10.0-patch1-intel-2017a.eb | 2 +- easybuild/easyconfigs/h/HDF5/HDF5-1.10.1-intel-2017a.eb | 2 +- .../easyconfigs/h/HDF5/HDF5-1.8.10-GCC-4.8.1-serial.eb | 4 ++-- easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-goolf-1.4.10.eb | 4 ++-- .../h/HDF5/HDF5-1.8.10-ictce-5.3.0-gpfs-zlib-1.2.5.eb | 4 ++-- .../easyconfigs/h/HDF5/HDF5-1.8.10-ictce-5.3.0-gpfs.eb | 4 ++-- .../easyconfigs/h/HDF5/HDF5-1.8.10-ictce-5.3.0-serial.eb | 4 ++-- easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-ictce-5.3.0.eb | 4 ++-- .../easyconfigs/h/HDF5/HDF5-1.8.10-ictce-5.4.0-gpfs.eb | 4 ++-- .../easyconfigs/h/HDF5/HDF5-1.8.10-ictce-5.5.0-gpfs.eb | 4 ++-- .../easyconfigs/h/HDF5/HDF5-1.8.10-ictce-6.1.5-gpfs.eb | 4 ++-- .../easyconfigs/h/HDF5/HDF5-1.8.10-intel-2014b-gpfs.eb | 4 ++-- .../easyconfigs/h/HDF5/HDF5-1.8.10-patch1-goolf-1.4.10.eb | 4 ++-- .../easyconfigs/h/HDF5/HDF5-1.8.10-patch1-goolf-1.5.14.eb | 4 ++-- .../easyconfigs/h/HDF5/HDF5-1.8.10-patch1-ictce-5.3.0.eb | 4 ++-- .../easyconfigs/h/HDF5/HDF5-1.8.11-GCC-4.8.1-serial.eb | 4 ++-- easybuild/easyconfigs/h/HDF5/HDF5-1.8.11-goolf-1.4.10.eb | 4 ++-- .../easyconfigs/h/HDF5/HDF5-1.8.11-ictce-5.3.0-serial.eb | 4 ++-- .../h/HDF5/HDF5-1.8.12-goolf-1.4.10-zlib-1.2.7.eb | 4 ++-- easybuild/easyconfigs/h/HDF5/HDF5-1.8.12-ictce-5.4.0.eb | 4 ++-- .../h/HDF5/HDF5-1.8.12-ictce-5.5.0-zlib-1.2.8.eb | 4 ++-- easybuild/easyconfigs/h/HDF5/HDF5-1.8.12-ictce-5.5.0.eb | 4 ++-- easybuild/easyconfigs/h/HDF5/HDF5-1.8.12-intel-2016b.eb | 4 ++-- easybuild/easyconfigs/h/HDF5/HDF5-1.8.13-foss-2014b.eb | 4 ++-- easybuild/easyconfigs/h/HDF5/HDF5-1.8.13-foss-2015a.eb | 4 ++-- easybuild/easyconfigs/h/HDF5/HDF5-1.8.13-intel-2014b.eb | 4 ++-- easybuild/easyconfigs/h/HDF5/HDF5-1.8.13-intel-2015a.eb | 4 ++-- easybuild/easyconfigs/h/HDF5/HDF5-1.8.13-intel-2015b.eb | 4 ++-- easybuild/easyconfigs/h/HDF5/HDF5-1.8.14-foss-2015a.eb | 4 ++-- .../easyconfigs/h/HDF5/HDF5-1.8.14-ictce-7.1.2-serial.eb | 4 ++-- easybuild/easyconfigs/h/HDF5/HDF5-1.8.14-ictce-7.1.2.eb | 4 ++-- .../easyconfigs/h/HDF5/HDF5-1.8.14-intel-2015a-serial.eb | 4 ++-- easybuild/easyconfigs/h/HDF5/HDF5-1.8.14-intel-2015a.eb | 4 ++-- easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-foss-2015a.eb | 4 ++-- easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-intel-2015a.eb | 4 ++-- easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-intel-2015b.eb | 4 ++-- .../easyconfigs/h/HDF5/HDF5-1.8.15-patch1-foss-2015a.eb | 4 ++-- .../easyconfigs/h/HDF5/HDF5-1.8.15-patch1-foss-2015b.eb | 4 ++-- .../easyconfigs/h/HDF5/HDF5-1.8.15-patch1-intel-2015a.eb | 4 ++-- .../easyconfigs/h/HDF5/HDF5-1.8.15-patch1-intel-2015b.eb | 4 ++-- easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-foss-2015a.eb | 4 ++-- .../easyconfigs/h/HDF5/HDF5-1.8.16-foss-2016a-serial.eb | 4 ++-- easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-foss-2016a.eb | 4 ++-- .../easyconfigs/h/HDF5/HDF5-1.8.16-gimkl-2.11.5-serial.eb | 4 ++-- .../easyconfigs/h/HDF5/HDF5-1.8.16-intel-2015b-serial.eb | 4 ++-- easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-intel-2015b.eb | 4 ++-- .../h/HDF5/HDF5-1.8.16-intel-2016.02-GCC-4.9.eb | 4 ++-- .../easyconfigs/h/HDF5/HDF5-1.8.16-intel-2016a-serial.eb | 4 ++-- easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-intel-2016a.eb | 4 ++-- easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-iomkl-2016.07.eb | 4 ++-- .../h/HDF5/HDF5-1.8.16-iomkl-2016.09-GCC-4.9.3-2.25.eb | 4 ++-- .../easyconfigs/h/HDF5/HDF5-1.8.17-foss-2016a-serial.eb | 4 ++-- easybuild/easyconfigs/h/HDF5/HDF5-1.8.17-foss-2016a.eb | 4 ++-- easybuild/easyconfigs/h/HDF5/HDF5-1.8.17-foss-2016b.eb | 4 ++-- easybuild/easyconfigs/h/HDF5/HDF5-1.8.17-intel-2016a.eb | 4 ++-- .../easyconfigs/h/HDF5/HDF5-1.8.17-intel-2016b-serial.eb | 4 ++-- easybuild/easyconfigs/h/HDF5/HDF5-1.8.17-intel-2016b.eb | 4 ++-- easybuild/easyconfigs/h/HDF5/HDF5-1.8.18-foss-2016b.eb | 7 ++----- easybuild/easyconfigs/h/HDF5/HDF5-1.8.18-foss-2017a.eb | 7 ++----- easybuild/easyconfigs/h/HDF5/HDF5-1.8.18-intel-2016b.eb | 7 ++----- easybuild/easyconfigs/h/HDF5/HDF5-1.8.18-intel-2017.01.eb | 7 ++----- .../easyconfigs/h/HDF5/HDF5-1.8.18-intel-2017a-serial.eb | 7 ++----- easybuild/easyconfigs/h/HDF5/HDF5-1.8.18-intel-2017a.eb | 7 ++----- easybuild/easyconfigs/h/HDF5/HDF5-1.8.7-goolf-1.4.10.eb | 4 ++-- easybuild/easyconfigs/h/HDF5/HDF5-1.8.7-ictce-5.3.0.eb | 4 ++-- easybuild/easyconfigs/h/HDF5/HDF5-1.8.9-goolf-1.4.10.eb | 4 ++-- easybuild/easyconfigs/h/HDF5/HDF5-1.8.9-goolf-1.5.16.eb | 4 ++-- easybuild/easyconfigs/h/HDF5/HDF5-1.8.9-ictce-5.2.0.eb | 4 ++-- easybuild/easyconfigs/h/HDF5/HDF5-1.8.9-ictce-5.3.0.eb | 4 ++-- easybuild/easyconfigs/h/HDF5/HDF5-1.8.9-ictce-5.4.0.eb | 4 ++-- easybuild/easyconfigs/h/HDF5/HDF5-1.8.9-intel-2014b.eb | 4 ++-- 75 files changed, 144 insertions(+), 162 deletions(-) diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.10.0-patch1-foss-2016b.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.0-patch1-foss-2016b.eb index 55975c97d5..11a5ffcadd 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.10.0-patch1-foss-2016b.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.0-patch1-foss-2016b.eb @@ -1,7 +1,7 @@ name = 'HDF5' version = '1.10.0-patch1' -homepage = 'http://www.hdfgroup.org/HDF5/' +homepage = 'https://support.hdfgroup.org/HDF5/' description = """HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections.""" diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.10.0-patch1-goolfc-2016.10.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.0-patch1-goolfc-2016.10.eb index a728a33f56..761c68b5eb 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.10.0-patch1-goolfc-2016.10.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.0-patch1-goolfc-2016.10.eb @@ -1,7 +1,7 @@ name = 'HDF5' version = '1.10.0-patch1' -homepage = 'http://www.hdfgroup.org/HDF5/' +homepage = 'https://support.hdfgroup.org/HDF5/' description = """HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections.""" diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.10.0-patch1-intel-2016b.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.0-patch1-intel-2016b.eb index 8eddf5504b..7253681751 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.10.0-patch1-intel-2016b.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.0-patch1-intel-2016b.eb @@ -1,7 +1,7 @@ name = 'HDF5' version = '1.10.0-patch1' -homepage = 'http://www.hdfgroup.org/HDF5/' +homepage = 'https://support.hdfgroup.org/HDF5/' description = """HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections.""" diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.10.0-patch1-intel-2017.01.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.0-patch1-intel-2017.01.eb index 5cf3a3e7f5..cb5285d7c5 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.10.0-patch1-intel-2017.01.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.0-patch1-intel-2017.01.eb @@ -1,7 +1,7 @@ name = 'HDF5' version = '1.10.0-patch1' -homepage = 'http://www.hdfgroup.org/HDF5/' +homepage = 'https://support.hdfgroup.org/HDF5/' description = """HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections.""" diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.10.0-patch1-intel-2017a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.0-patch1-intel-2017a.eb index bc132a2144..9d04fbcf11 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.10.0-patch1-intel-2017a.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.0-patch1-intel-2017a.eb @@ -1,7 +1,7 @@ name = 'HDF5' version = '1.10.0-patch1' -homepage = 'http://www.hdfgroup.org/HDF5/' +homepage = 'https://support.hdfgroup.org/HDF5/' description = """HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections.""" diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.10.1-intel-2017a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.1-intel-2017a.eb index d72f14fe00..2cb7193188 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.10.1-intel-2017a.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.1-intel-2017a.eb @@ -1,7 +1,7 @@ name = 'HDF5' version = '1.10.1' -homepage = 'http://www.hdfgroup.org/HDF5/' +homepage = 'https://support.hdfgroup.org/HDF5/' description = """HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections.""" diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-GCC-4.8.1-serial.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-GCC-4.8.1-serial.eb index 9d10ec816c..1e95612a1b 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-GCC-4.8.1-serial.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-GCC-4.8.1-serial.eb @@ -2,14 +2,14 @@ name = 'HDF5' version = '1.8.10' versionsuffix = '-serial' -homepage = 'http://www.hdfgroup.org/HDF5/' +homepage = 'https://support.hdfgroup.org/HDF5/' description = """HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections.""" toolchain = {'name': 'GCC', 'version': '4.8.1'} toolchainopts = {'optarch': True, 'pic': True} -source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src'] +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] dependencies = [ diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-goolf-1.4.10.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-goolf-1.4.10.eb index 288a2e47ff..1f3a15a705 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-goolf-1.4.10.eb @@ -1,14 +1,14 @@ name = 'HDF5' version = '1.8.10' -homepage = 'http://www.hdfgroup.org/HDF5/' +homepage = 'https://support.hdfgroup.org/HDF5/' description = """HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'optarch': True, 'usempi': True, 'pic': True} -source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src'] +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] dependencies = [ diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-ictce-5.3.0-gpfs-zlib-1.2.5.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-ictce-5.3.0-gpfs-zlib-1.2.5.eb index 1b26514524..9f3153cef8 100755 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-ictce-5.3.0-gpfs-zlib-1.2.5.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-ictce-5.3.0-gpfs-zlib-1.2.5.eb @@ -2,14 +2,14 @@ name = 'HDF5' version = '1.8.10' versionsuffix = "-gpfs" -homepage = 'http://www.hdfgroup.org/HDF5/' +homepage = 'https://support.hdfgroup.org/HDF5/' description = """HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections.""" toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'optarch': True, 'usempi': True, 'pic': True} -source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src'] +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] patches = [ diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-ictce-5.3.0-gpfs.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-ictce-5.3.0-gpfs.eb index 20e204943c..314870506e 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-ictce-5.3.0-gpfs.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-ictce-5.3.0-gpfs.eb @@ -2,14 +2,14 @@ name = 'HDF5' version = '1.8.10' versionsuffix = "-gpfs" -homepage = 'http://www.hdfgroup.org/HDF5/' +homepage = 'https://support.hdfgroup.org/HDF5/' description = """HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections.""" toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'optarch': True, 'usempi': True, 'pic': True} -source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src'] +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] patches = [ diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-ictce-5.3.0-serial.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-ictce-5.3.0-serial.eb index 4923cec819..54393d6cef 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-ictce-5.3.0-serial.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-ictce-5.3.0-serial.eb @@ -2,14 +2,14 @@ name = 'HDF5' version = '1.8.10' versionsuffix = '-serial' -homepage = 'http://www.hdfgroup.org/HDF5/' +homepage = 'https://support.hdfgroup.org/HDF5/' description = """HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections.""" toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'optarch': True, 'pic': True} -source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src'] +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] dependencies = [ diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-ictce-5.3.0.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-ictce-5.3.0.eb index 53c166e963..75fb24dc93 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-ictce-5.3.0.eb @@ -1,14 +1,14 @@ name = 'HDF5' version = '1.8.10' -homepage = 'http://www.hdfgroup.org/HDF5/' +homepage = 'https://support.hdfgroup.org/HDF5/' description = """HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections.""" toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'optarch': True, 'usempi': True, 'pic': True} -source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src'] +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] patches = [ diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-ictce-5.4.0-gpfs.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-ictce-5.4.0-gpfs.eb index 126e473584..2aaf800fdb 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-ictce-5.4.0-gpfs.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-ictce-5.4.0-gpfs.eb @@ -2,14 +2,14 @@ name = 'HDF5' version = '1.8.10' versionsuffix = "-gpfs" -homepage = 'http://www.hdfgroup.org/HDF5/' +homepage = 'https://support.hdfgroup.org/HDF5/' description = """HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections.""" toolchain = {'name': 'ictce', 'version': '5.4.0'} toolchainopts = {'optarch': True, 'usempi': True, 'pic': True} -source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src'] +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] patches = [ diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-ictce-5.5.0-gpfs.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-ictce-5.5.0-gpfs.eb index eec3211c35..664ac4915d 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-ictce-5.5.0-gpfs.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-ictce-5.5.0-gpfs.eb @@ -2,14 +2,14 @@ name = 'HDF5' version = '1.8.10' versionsuffix = "-gpfs" -homepage = 'http://www.hdfgroup.org/HDF5/' +homepage = 'https://support.hdfgroup.org/HDF5/' description = """HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections.""" toolchain = {'name': 'ictce', 'version': '5.5.0'} toolchainopts = {'optarch': True, 'usempi': True, 'pic': True} -source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src'] +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] patches = [ diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-ictce-6.1.5-gpfs.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-ictce-6.1.5-gpfs.eb index caf75ce765..4f6fffd29a 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-ictce-6.1.5-gpfs.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-ictce-6.1.5-gpfs.eb @@ -2,14 +2,14 @@ name = 'HDF5' version = '1.8.10' versionsuffix = "-gpfs" -homepage = 'http://www.hdfgroup.org/HDF5/' +homepage = 'https://support.hdfgroup.org/HDF5/' description = """HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections.""" toolchain = {'name': 'ictce', 'version': '6.1.5'} toolchainopts = {'optarch': True, 'usempi': True, 'pic': True} -source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src'] +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] patches = [ diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-intel-2014b-gpfs.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-intel-2014b-gpfs.eb index fa45e3d80d..55ac49288a 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-intel-2014b-gpfs.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-intel-2014b-gpfs.eb @@ -2,14 +2,14 @@ name = 'HDF5' version = '1.8.10' versionsuffix = "-gpfs" -homepage = 'http://www.hdfgroup.org/HDF5/' +homepage = 'https://support.hdfgroup.org/HDF5/' description = """HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections.""" toolchain = {'name': 'intel', 'version': '2014b'} toolchainopts = {'optarch': True, 'usempi': True, 'pic': True} -source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src'] +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] patches = [ diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-patch1-goolf-1.4.10.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-patch1-goolf-1.4.10.eb index 0f94ca89b3..ed6d0e1c4e 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-patch1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-patch1-goolf-1.4.10.eb @@ -1,14 +1,14 @@ name = 'HDF5' version = '1.8.10-patch1' -homepage = 'http://www.hdfgroup.org/HDF5/' +homepage = 'https://support.hdfgroup.org/HDF5/' description = """HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'optarch': True, 'usempi': True, 'pic': True} -source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src'] +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] patches = [ diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-patch1-goolf-1.5.14.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-patch1-goolf-1.5.14.eb index c83b2a6347..da6a6ac07e 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-patch1-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-patch1-goolf-1.5.14.eb @@ -1,14 +1,14 @@ name = 'HDF5' version = '1.8.10-patch1' -homepage = 'http://www.hdfgroup.org/HDF5/' +homepage = 'https://support.hdfgroup.org/HDF5/' description = """HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections.""" toolchain = {'name': 'goolf', 'version': '1.5.14'} toolchainopts = {'optarch': True, 'usempi': True, 'pic': True} -source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src'] +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] patches = [ diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-patch1-ictce-5.3.0.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-patch1-ictce-5.3.0.eb index 96aaf04223..df1a74ad9a 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-patch1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-patch1-ictce-5.3.0.eb @@ -1,14 +1,14 @@ name = 'HDF5' version = '1.8.10-patch1' -homepage = 'http://www.hdfgroup.org/HDF5/' +homepage = 'https://support.hdfgroup.org/HDF5/' description = """HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections.""" toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'optarch': True, 'usempi': True, 'pic': True} -source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src'] +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] patches = [ diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.11-GCC-4.8.1-serial.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.11-GCC-4.8.1-serial.eb index d4743307f6..69b3336df0 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.11-GCC-4.8.1-serial.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.11-GCC-4.8.1-serial.eb @@ -2,14 +2,14 @@ name = 'HDF5' version = '1.8.11' versionsuffix = '-serial' -homepage = 'http://www.hdfgroup.org/HDF5/' +homepage = 'https://support.hdfgroup.org/HDF5/' description = """HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections.""" toolchain = {'name': 'GCC', 'version': '4.8.1'} toolchainopts = {'optarch': True, 'pic': True} -source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src'] +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] dependencies = [ diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.11-goolf-1.4.10.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.11-goolf-1.4.10.eb index 4406c160f4..baa65b4571 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.11-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.11-goolf-1.4.10.eb @@ -1,14 +1,14 @@ name = 'HDF5' version = '1.8.11' -homepage = 'http://www.hdfgroup.org/HDF5/' +homepage = 'https://support.hdfgroup.org/HDF5/' description = """HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'optarch': True, 'pic': True} -source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src'] +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] dependencies = [ diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.11-ictce-5.3.0-serial.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.11-ictce-5.3.0-serial.eb index d1cfae6705..7095cb38b8 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.11-ictce-5.3.0-serial.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.11-ictce-5.3.0-serial.eb @@ -2,14 +2,14 @@ name = 'HDF5' version = '1.8.11' versionsuffix = '-serial' -homepage = 'http://www.hdfgroup.org/HDF5/' +homepage = 'https://support.hdfgroup.org/HDF5/' description = """HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections.""" toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'optarch': True, 'pic': True} -source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src'] +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] dependencies = [ diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.12-goolf-1.4.10-zlib-1.2.7.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.12-goolf-1.4.10-zlib-1.2.7.eb index a0a7586662..d0013da7bf 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.12-goolf-1.4.10-zlib-1.2.7.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.12-goolf-1.4.10-zlib-1.2.7.eb @@ -2,14 +2,14 @@ name = 'HDF5' version = '1.8.12' versionsuffix = '-zlib-1.2.7' -homepage = 'http://www.hdfgroup.org/HDF5/' +homepage = 'https://support.hdfgroup.org/HDF5/' description = """HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'optarch': True, 'pic': True, 'usempi': True} -source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src'] +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] patches = ['configure_libtool.patch'] diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.12-ictce-5.4.0.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.12-ictce-5.4.0.eb index 233b7e31da..777fc010e6 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.12-ictce-5.4.0.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.12-ictce-5.4.0.eb @@ -1,14 +1,14 @@ name = 'HDF5' version = '1.8.12' -homepage = 'http://www.hdfgroup.org/HDF5/' +homepage = 'https://support.hdfgroup.org/HDF5/' description = """HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections.""" toolchain = {'name': 'ictce', 'version': '5.4.0'} toolchainopts = {'optarch': True, 'pic': True, 'usempi': True} -source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src'] +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] patches = [ diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.12-ictce-5.5.0-zlib-1.2.8.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.12-ictce-5.5.0-zlib-1.2.8.eb index bf02342e7c..ba8d085626 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.12-ictce-5.5.0-zlib-1.2.8.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.12-ictce-5.5.0-zlib-1.2.8.eb @@ -2,14 +2,14 @@ name = 'HDF5' version = '1.8.12' versionsuffix = '-zlib-1.2.8' -homepage = 'http://www.hdfgroup.org/HDF5/' +homepage = 'https://support.hdfgroup.org/HDF5/' description = """HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections.""" toolchain = {'name': 'ictce', 'version': '5.5.0'} toolchainopts = {'optarch': True, 'pic': True, 'usempi': True} -source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src'] +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] patches = [ diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.12-ictce-5.5.0.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.12-ictce-5.5.0.eb index 0a10444693..fd08cc083e 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.12-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.12-ictce-5.5.0.eb @@ -1,14 +1,14 @@ name = 'HDF5' version = '1.8.12' -homepage = 'http://www.hdfgroup.org/HDF5/' +homepage = 'https://support.hdfgroup.org/HDF5/' description = """HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections.""" toolchain = {'name': 'ictce', 'version': '5.5.0'} toolchainopts = {'optarch': True, 'pic': True, 'usempi': True} -source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src'] +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] patches = [ diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.12-intel-2016b.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.12-intel-2016b.eb index da7a64fcf9..ba130d5f31 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.12-intel-2016b.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.12-intel-2016b.eb @@ -1,14 +1,14 @@ name = 'HDF5' version = '1.8.12' -homepage = 'http://www.hdfgroup.org/HDF5/' +homepage = 'https://support.hdfgroup.org/HDF5/' description = """HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections.""" toolchain = {'name': 'intel', 'version': '2016b'} toolchainopts = {'pic': True, 'usempi': True} -source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src'] +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] patches = [ diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.13-foss-2014b.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.13-foss-2014b.eb index 2af8e449bf..c5622dfd07 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.13-foss-2014b.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.13-foss-2014b.eb @@ -1,14 +1,14 @@ name = 'HDF5' version = '1.8.13' -homepage = 'http://www.hdfgroup.org/HDF5/' +homepage = 'https://support.hdfgroup.org/HDF5/' description = """HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections.""" toolchain = {'name': 'foss', 'version': '2014b'} toolchainopts = {'optarch': True, 'pic': True, 'usempi': True} -source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src'] +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] patches = ['configure_libtool.patch'] diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.13-foss-2015a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.13-foss-2015a.eb index f79d365b61..f8f32df424 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.13-foss-2015a.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.13-foss-2015a.eb @@ -1,14 +1,14 @@ name = 'HDF5' version = '1.8.13' -homepage = 'http://www.hdfgroup.org/HDF5/' +homepage = 'https://support.hdfgroup.org/HDF5/' description = """HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections.""" toolchain = {'name': 'foss', 'version': '2015a'} toolchainopts = {'optarch': True, 'pic': True, 'usempi': True} -source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src'] +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] patches = [ diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.13-intel-2014b.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.13-intel-2014b.eb index e20cda0940..14daa11265 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.13-intel-2014b.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.13-intel-2014b.eb @@ -1,14 +1,14 @@ name = 'HDF5' version = '1.8.13' -homepage = 'http://www.hdfgroup.org/HDF5/' +homepage = 'https://support.hdfgroup.org/HDF5/' description = """HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections.""" toolchain = {'name': 'intel', 'version': '2014b'} toolchainopts = {'optarch': True, 'pic': True, 'usempi': True} -source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src'] +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] patches = [ diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.13-intel-2015a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.13-intel-2015a.eb index 16f7a03776..901fd44392 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.13-intel-2015a.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.13-intel-2015a.eb @@ -1,14 +1,14 @@ name = 'HDF5' version = '1.8.13' -homepage = 'http://www.hdfgroup.org/HDF5/' +homepage = 'https://support.hdfgroup.org/HDF5/' description = """HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections.""" toolchain = {'name': 'intel', 'version': '2015a'} toolchainopts = {'optarch': True, 'pic': True, 'usempi': True} -source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src'] +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] patches = [ diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.13-intel-2015b.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.13-intel-2015b.eb index a74b48d664..6a1a9188e1 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.13-intel-2015b.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.13-intel-2015b.eb @@ -1,14 +1,14 @@ name = 'HDF5' version = '1.8.13' -homepage = 'http://www.hdfgroup.org/HDF5/' +homepage = 'https://support.hdfgroup.org/HDF5/' description = """HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections.""" toolchain = {'name': 'intel', 'version': '2015b'} toolchainopts = {'optarch': True, 'pic': True, 'usempi': True} -source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src'] +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] patches = [ diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.14-foss-2015a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.14-foss-2015a.eb index 35077bfe35..6720320b04 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.14-foss-2015a.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.14-foss-2015a.eb @@ -2,14 +2,14 @@ name = 'HDF5' version = "1.8.14" -homepage = 'http://www.hdfgroup.org/HDF5/' +homepage = 'https://support.hdfgroup.org/HDF5/' description = """HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections.""" toolchain = {'name': 'foss', 'version': '2015a'} toolchainopts = {'optarch': True, 'pic': True, 'usempi': True} -source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src'] +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] patches = [ diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.14-ictce-7.1.2-serial.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.14-ictce-7.1.2-serial.eb index 8ffb9102ba..8708c7b4dd 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.14-ictce-7.1.2-serial.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.14-ictce-7.1.2-serial.eb @@ -2,14 +2,14 @@ name = 'HDF5' version = '1.8.14' versionsuffix = '-serial' -homepage = 'http://www.hdfgroup.org/HDF5/' +homepage = 'https://support.hdfgroup.org/HDF5/' description = """HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections.""" toolchain = {'name': 'ictce', 'version': '7.1.2'} toolchainopts = {'optarch': True, 'pic': True, 'usempi': False} -source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src'] +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] patches = [ diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.14-ictce-7.1.2.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.14-ictce-7.1.2.eb index 5d8a6788d3..bfef0cbb11 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.14-ictce-7.1.2.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.14-ictce-7.1.2.eb @@ -1,14 +1,14 @@ name = 'HDF5' version = '1.8.14' -homepage = 'http://www.hdfgroup.org/HDF5/' +homepage = 'https://support.hdfgroup.org/HDF5/' description = """HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections.""" toolchain = {'name': 'ictce', 'version': '7.1.2'} toolchainopts = {'optarch': True, 'pic': True, 'usempi': True} -source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src'] +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] patches = [ diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.14-intel-2015a-serial.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.14-intel-2015a-serial.eb index 0db92859a2..5414c97fd0 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.14-intel-2015a-serial.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.14-intel-2015a-serial.eb @@ -2,14 +2,14 @@ name = 'HDF5' version = '1.8.14' versionsuffix = '-serial' -homepage = 'http://www.hdfgroup.org/HDF5/' +homepage = 'https://support.hdfgroup.org/HDF5/' description = """HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections.""" toolchain = {'name': 'intel', 'version': '2015a'} toolchainopts = {'optarch': True, 'pic': True, 'usempi': False} -source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src'] +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] patches = [ diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.14-intel-2015a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.14-intel-2015a.eb index 2b7af38374..8811c59a40 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.14-intel-2015a.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.14-intel-2015a.eb @@ -1,14 +1,14 @@ name = 'HDF5' version = '1.8.14' -homepage = 'http://www.hdfgroup.org/HDF5/' +homepage = 'https://support.hdfgroup.org/HDF5/' description = """HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections.""" toolchain = {'name': 'intel', 'version': '2015a'} toolchainopts = {'optarch': True, 'pic': True, 'usempi': True} -source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src'] +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] patches = [ diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-foss-2015a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-foss-2015a.eb index ef7549e987..88e2ae54b1 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-foss-2015a.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-foss-2015a.eb @@ -1,14 +1,14 @@ name = 'HDF5' version = '1.8.15' -homepage = 'http://www.hdfgroup.org/HDF5/' +homepage = 'https://support.hdfgroup.org/HDF5/' description = """HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections.""" toolchain = {'name': 'foss', 'version': '2015a'} toolchainopts = {'optarch': True, 'pic': True, 'usempi': True} -source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src'] +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] patches = ['configure_libtool.patch'] diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-intel-2015a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-intel-2015a.eb index 9b028b25b8..e5738f0904 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-intel-2015a.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-intel-2015a.eb @@ -1,14 +1,14 @@ name = 'HDF5' version = '1.8.15' -homepage = 'http://www.hdfgroup.org/HDF5/' +homepage = 'https://support.hdfgroup.org/HDF5/' description = """HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections.""" toolchain = {'name': 'intel', 'version': '2015a'} toolchainopts = {'optarch': True, 'pic': True, 'usempi': True} -source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src'] +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] patches = [ diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-intel-2015b.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-intel-2015b.eb index 802e3dd6a1..b35f180383 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-intel-2015b.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-intel-2015b.eb @@ -1,14 +1,14 @@ name = 'HDF5' version = '1.8.15' -homepage = 'http://www.hdfgroup.org/HDF5/' +homepage = 'https://support.hdfgroup.org/HDF5/' description = """HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections.""" toolchain = {'name': 'intel', 'version': '2015b'} toolchainopts = {'optarch': True, 'pic': True, 'usempi': True} -source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src'] +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] patches = [ diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-patch1-foss-2015a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-patch1-foss-2015a.eb index a9ec210198..152a305c88 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-patch1-foss-2015a.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-patch1-foss-2015a.eb @@ -1,14 +1,14 @@ name = 'HDF5' version = '1.8.15-patch1' -homepage = 'http://www.hdfgroup.org/HDF5/' +homepage = 'https://support.hdfgroup.org/HDF5/' description = """HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections.""" toolchain = {'name': 'foss', 'version': '2015a'} toolchainopts = {'optarch': True, 'pic': True, 'usempi': True} -source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src'] +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] patches = ['configure_libtool.patch'] diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-patch1-foss-2015b.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-patch1-foss-2015b.eb index 8b6038c4ee..d234a1dcc1 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-patch1-foss-2015b.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-patch1-foss-2015b.eb @@ -1,14 +1,14 @@ name = 'HDF5' version = '1.8.15-patch1' -homepage = 'http://www.hdfgroup.org/HDF5/' +homepage = 'https://support.hdfgroup.org/HDF5/' description = """HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections.""" toolchain = {'name': 'foss', 'version': '2015b'} toolchainopts = {'optarch': True, 'pic': True, 'usempi': True} -source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src'] +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] patches = ['configure_libtool.patch'] diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-patch1-intel-2015a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-patch1-intel-2015a.eb index ec9b5d3a8a..03fb175bd6 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-patch1-intel-2015a.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-patch1-intel-2015a.eb @@ -1,14 +1,14 @@ name = 'HDF5' version = '1.8.15-patch1' -homepage = 'http://www.hdfgroup.org/HDF5/' +homepage = 'https://support.hdfgroup.org/HDF5/' description = """HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections.""" toolchain = {'name': 'intel', 'version': '2015a'} toolchainopts = {'optarch': True, 'pic': True, 'usempi': True} -source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src'] +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] patches = [ diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-patch1-intel-2015b.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-patch1-intel-2015b.eb index aabe3f8e81..2ddc5c482c 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-patch1-intel-2015b.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-patch1-intel-2015b.eb @@ -1,14 +1,14 @@ name = 'HDF5' version = '1.8.15-patch1' -homepage = 'http://www.hdfgroup.org/HDF5/' +homepage = 'https://support.hdfgroup.org/HDF5/' description = """HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections.""" toolchain = {'name': 'intel', 'version': '2015b'} toolchainopts = {'optarch': True, 'pic': True, 'usempi': True} -source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src'] +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] patches = [ diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-foss-2015a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-foss-2015a.eb index 25e05e8e27..2309adbc85 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-foss-2015a.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-foss-2015a.eb @@ -1,14 +1,14 @@ name = 'HDF5' version = '1.8.16' -homepage = 'http://www.hdfgroup.org/HDF5/' +homepage = 'https://support.hdfgroup.org/HDF5/' description = """HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections.""" toolchain = {'name': 'foss', 'version': '2015a'} toolchainopts = {'optarch': True, 'pic': True, 'usempi': True} -source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src'] +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] patches = ['configure_libtool.patch'] diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-foss-2016a-serial.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-foss-2016a-serial.eb index 2936e9795e..1f315f8f38 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-foss-2016a-serial.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-foss-2016a-serial.eb @@ -2,14 +2,14 @@ name = 'HDF5' version = '1.8.16' versionsuffix = '-serial' -homepage = 'http://www.hdfgroup.org/HDF5/' +homepage = 'https://support.hdfgroup.org/HDF5/' description = """HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections.""" toolchain = {'name': 'foss', 'version': '2016a'} toolchainopts = {'optarch': True, 'pic': True, 'usempi': False} -source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src'] +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] patches = ['configure_libtool.patch'] diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-foss-2016a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-foss-2016a.eb index 7250d32fe5..67235e28b4 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-foss-2016a.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-foss-2016a.eb @@ -1,14 +1,14 @@ name = 'HDF5' version = '1.8.16' -homepage = 'http://www.hdfgroup.org/HDF5/' +homepage = 'https://support.hdfgroup.org/HDF5/' description = """HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections.""" toolchain = {'name': 'foss', 'version': '2016a'} toolchainopts = {'optarch': True, 'pic': True, 'usempi': True} -source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src'] +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] patches = [ diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-gimkl-2.11.5-serial.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-gimkl-2.11.5-serial.eb index 3f80a99e71..ac5b554944 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-gimkl-2.11.5-serial.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-gimkl-2.11.5-serial.eb @@ -2,14 +2,14 @@ name = 'HDF5' version = '1.8.16' versionsuffix = '-serial' -homepage = 'http://www.hdfgroup.org/HDF5/' +homepage = 'https://support.hdfgroup.org/HDF5/' description = """HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections.""" toolchain = {'name': 'gimkl', 'version': '2.11.5'} toolchainopts = {'pic': True} -source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src'] +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] patches = ['configure_libtool.patch'] diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-intel-2015b-serial.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-intel-2015b-serial.eb index 1b0486b830..d28779cc9c 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-intel-2015b-serial.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-intel-2015b-serial.eb @@ -2,14 +2,14 @@ name = 'HDF5' version = '1.8.16' versionsuffix = '-serial' -homepage = 'http://www.hdfgroup.org/HDF5/' +homepage = 'https://support.hdfgroup.org/HDF5/' description = """HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections.""" toolchain = {'name': 'intel', 'version': '2015b'} toolchainopts = {'optarch': True, 'pic': True, 'usempi': False} -source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src'] +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] patches = [ diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-intel-2015b.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-intel-2015b.eb index 8df4b88524..0903315947 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-intel-2015b.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-intel-2015b.eb @@ -1,14 +1,14 @@ name = 'HDF5' version = '1.8.16' -homepage = 'http://www.hdfgroup.org/HDF5/' +homepage = 'https://support.hdfgroup.org/HDF5/' description = """HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections.""" toolchain = {'name': 'intel', 'version': '2015b'} toolchainopts = {'optarch': True, 'pic': True, 'usempi': True} -source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src'] +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] patches = [ diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-intel-2016.02-GCC-4.9.eb index d1c17ce30e..0aa0ce34f3 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-intel-2016.02-GCC-4.9.eb @@ -1,14 +1,14 @@ name = 'HDF5' version = '1.8.16' -homepage = 'http://www.hdfgroup.org/HDF5/' +homepage = 'https://support.hdfgroup.org/HDF5/' description = """HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections.""" toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'} toolchainopts = {'optarch': True, 'pic': True, 'usempi': True} -source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src'] +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] patches = [ diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-intel-2016a-serial.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-intel-2016a-serial.eb index dc2e939bfa..930a707634 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-intel-2016a-serial.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-intel-2016a-serial.eb @@ -2,14 +2,14 @@ name = 'HDF5' version = '1.8.16' versionsuffix = '-serial' -homepage = 'http://www.hdfgroup.org/HDF5/' +homepage = 'https://support.hdfgroup.org/HDF5/' description = """HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections.""" toolchain = {'name': 'intel', 'version': '2016a'} toolchainopts = {'optarch': True, 'pic': True, 'usempi': False} -source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src'] +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] patches = [ diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-intel-2016a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-intel-2016a.eb index dc65dce562..cade57c186 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-intel-2016a.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-intel-2016a.eb @@ -1,14 +1,14 @@ name = 'HDF5' version = '1.8.16' -homepage = 'http://www.hdfgroup.org/HDF5/' +homepage = 'https://support.hdfgroup.org/HDF5/' description = """HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections.""" toolchain = {'name': 'intel', 'version': '2016a'} toolchainopts = {'optarch': True, 'pic': True, 'usempi': True} -source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src'] +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] patches = [ diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-iomkl-2016.07.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-iomkl-2016.07.eb index d61bff1fff..feea5f3d11 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-iomkl-2016.07.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-iomkl-2016.07.eb @@ -1,14 +1,14 @@ name = 'HDF5' version = '1.8.16' -homepage = 'http://www.hdfgroup.org/HDF5/' +homepage = 'https://support.hdfgroup.org/HDF5/' description = """HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections.""" toolchain = {'name': 'iomkl', 'version': '2016.07'} toolchainopts = {'optarch': True, 'pic': True, 'usempi': True} -source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src'] +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] patches = ['configure_libtool.patch'] diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-iomkl-2016.09-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-iomkl-2016.09-GCC-4.9.3-2.25.eb index e3d38f1976..847ddbbde6 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-iomkl-2016.09-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-iomkl-2016.09-GCC-4.9.3-2.25.eb @@ -1,14 +1,14 @@ name = 'HDF5' version = '1.8.16' -homepage = 'http://www.hdfgroup.org/HDF5/' +homepage = 'https://support.hdfgroup.org/HDF5/' description = """HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections.""" toolchain = {'name': 'iomkl', 'version': '2016.09-GCC-4.9.3-2.25'} toolchainopts = {'optarch': True, 'pic': True, 'usempi': True} -source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src'] +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] patches = ['configure_libtool.patch'] diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.17-foss-2016a-serial.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.17-foss-2016a-serial.eb index 1cc3adf6f7..9ed0a9b12d 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.17-foss-2016a-serial.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.17-foss-2016a-serial.eb @@ -2,14 +2,14 @@ name = 'HDF5' version = '1.8.17' versionsuffix = '-serial' -homepage = 'http://www.hdfgroup.org/HDF5/' +homepage = 'https://support.hdfgroup.org/HDF5/' description = """HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections.""" toolchain = {'name': 'foss', 'version': '2016a'} toolchainopts = {'optarch': True, 'pic': True, 'usempi': False} -source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src'] +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] patches = ['configure_libtool.patch'] diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.17-foss-2016a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.17-foss-2016a.eb index 359ef33d9b..7de9eafbba 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.17-foss-2016a.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.17-foss-2016a.eb @@ -1,14 +1,14 @@ name = 'HDF5' version = '1.8.17' -homepage = 'http://www.hdfgroup.org/HDF5/' +homepage = 'https://support.hdfgroup.org/HDF5/' description = """HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections.""" toolchain = {'name': 'foss', 'version': '2016a'} toolchainopts = {'pic': True, 'usempi': True} -source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src'] +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] patches = [ diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.17-foss-2016b.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.17-foss-2016b.eb index 5063dd3bc6..396a16a44d 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.17-foss-2016b.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.17-foss-2016b.eb @@ -1,14 +1,14 @@ name = 'HDF5' version = '1.8.17' -homepage = 'http://www.hdfgroup.org/HDF5/' +homepage = 'https://support.hdfgroup.org/HDF5/' description = """HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections.""" toolchain = {'name': 'foss', 'version': '2016b'} toolchainopts = {'pic': True, 'usempi': True} -source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src'] +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] patches = [ diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.17-intel-2016a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.17-intel-2016a.eb index 7ab0f77fba..a5deac4990 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.17-intel-2016a.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.17-intel-2016a.eb @@ -1,14 +1,14 @@ name = 'HDF5' version = '1.8.17' -homepage = 'http://www.hdfgroup.org/HDF5/' +homepage = 'https://support.hdfgroup.org/HDF5/' description = """HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections.""" toolchain = {'name': 'intel', 'version': '2016a'} toolchainopts = {'pic': True, 'usempi': True} -source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src'] +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] patches = [ diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.17-intel-2016b-serial.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.17-intel-2016b-serial.eb index ded2abcfa1..529a200b16 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.17-intel-2016b-serial.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.17-intel-2016b-serial.eb @@ -2,14 +2,14 @@ name = 'HDF5' version = '1.8.17' versionsuffix = '-serial' -homepage = 'http://www.hdfgroup.org/HDF5/' +homepage = 'https://support.hdfgroup.org/HDF5/' description = """HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections.""" toolchain = {'name': 'intel', 'version': '2016b'} toolchainopts = {'pic': True, 'usempi': False} -source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src'] +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] patches = [ diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.17-intel-2016b.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.17-intel-2016b.eb index d67a77ebd2..24a6c22972 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.17-intel-2016b.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.17-intel-2016b.eb @@ -1,14 +1,14 @@ name = 'HDF5' version = '1.8.17' -homepage = 'http://www.hdfgroup.org/HDF5/' +homepage = 'https://support.hdfgroup.org/HDF5/' description = """HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections.""" toolchain = {'name': 'intel', 'version': '2016b'} toolchainopts = {'pic': True, 'usempi': True} -source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src'] +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] patches = [ diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.18-foss-2016b.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.18-foss-2016b.eb index e6c0e7eab7..f6e11b3e6a 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.18-foss-2016b.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.18-foss-2016b.eb @@ -1,17 +1,14 @@ name = 'HDF5' version = '1.8.18' -homepage = 'http://www.hdfgroup.org/HDF5/' +homepage = 'https://support.hdfgroup.org/HDF5/' description = """HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections.""" toolchain = {'name': 'foss', 'version': '2016b'} toolchainopts = {'pic': True, 'usempi': True} -source_urls = [ - 'https://support.hdfgroup.org/ftp/HDF5/current18/src/', - 'https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(versions)/src/' -] +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] checksums = ['dd2148b740713ca0295442ec683d7b1c'] diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.18-foss-2017a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.18-foss-2017a.eb index 1febe1c832..addd6deb8d 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.18-foss-2017a.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.18-foss-2017a.eb @@ -1,17 +1,14 @@ name = 'HDF5' version = '1.8.18' -homepage = 'http://www.hdfgroup.org/HDF5/' +homepage = 'https://support.hdfgroup.org/HDF5/' description = """HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections.""" toolchain = {'name': 'foss', 'version': '2017a'} toolchainopts = {'pic': True, 'usempi': True} -source_urls = [ - 'https://support.hdfgroup.org/ftp/HDF5/current18/src/', - 'https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(versions)/src/' -] +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] checksums = ['dd2148b740713ca0295442ec683d7b1c'] diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.18-intel-2016b.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.18-intel-2016b.eb index d1efd2d906..1b22bab5d5 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.18-intel-2016b.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.18-intel-2016b.eb @@ -1,17 +1,14 @@ name = 'HDF5' version = '1.8.18' -homepage = 'http://www.hdfgroup.org/HDF5/' +homepage = 'https://support.hdfgroup.org/HDF5/' description = """HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections.""" toolchain = {'name': 'intel', 'version': '2016b'} toolchainopts = {'pic': True, 'usempi': True} -source_urls = [ - 'https://support.hdfgroup.org/ftp/HDF5/current18/src/', - 'https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(versions)/src/' -] +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] checksums = ['dd2148b740713ca0295442ec683d7b1c'] diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.18-intel-2017.01.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.18-intel-2017.01.eb index 2b7452c39b..52424da991 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.18-intel-2017.01.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.18-intel-2017.01.eb @@ -1,17 +1,14 @@ name = 'HDF5' version = '1.8.18' -homepage = 'http://www.hdfgroup.org/HDF5/' +homepage = 'https://support.hdfgroup.org/HDF5/' description = """HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections.""" toolchain = {'name': 'intel', 'version': '2017.01'} toolchainopts = {'pic': True, 'usempi': True} -source_urls = [ - 'https://support.hdfgroup.org/ftp/HDF5/current18/src/', - 'https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(versions)/src/' -] +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] checksums = ['dd2148b740713ca0295442ec683d7b1c'] diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.18-intel-2017a-serial.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.18-intel-2017a-serial.eb index ef054b6cdf..dd0fd05bf2 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.18-intel-2017a-serial.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.18-intel-2017a-serial.eb @@ -2,17 +2,14 @@ name = 'HDF5' version = '1.8.18' versionsuffix = '-serial' -homepage = 'http://www.hdfgroup.org/HDF5/' +homepage = 'https://support.hdfgroup.org/HDF5/' description = """HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections.""" toolchain = {'name': 'intel', 'version': '2017a'} toolchainopts = {'pic': True, 'usempi': False} -source_urls = [ - 'https://support.hdfgroup.org/ftp/HDF5/current18/src/', - 'https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(versions)/src/' -] +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] checksums = ['dd2148b740713ca0295442ec683d7b1c'] diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.18-intel-2017a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.18-intel-2017a.eb index 570e4a8ff2..630ef958f3 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.18-intel-2017a.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.18-intel-2017a.eb @@ -1,17 +1,14 @@ name = 'HDF5' version = '1.8.18' -homepage = 'http://www.hdfgroup.org/HDF5/' +homepage = 'https://support.hdfgroup.org/HDF5/' description = """HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections.""" toolchain = {'name': 'intel', 'version': '2017a'} toolchainopts = {'pic': True, 'usempi': True} -source_urls = [ - 'https://support.hdfgroup.org/ftp/HDF5/current18/src/', - 'https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(versions)/src/' -] +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] checksums = ['dd2148b740713ca0295442ec683d7b1c'] diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.7-goolf-1.4.10.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.7-goolf-1.4.10.eb index b8dd1adc77..3b0999608a 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.7-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.7-goolf-1.4.10.eb @@ -1,14 +1,14 @@ name = 'HDF5' version = '1.8.7' -homepage = 'http://www.hdfgroup.org/HDF5/' +homepage = 'https://support.hdfgroup.org/HDF5/' description = """HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'optarch': True, 'usempi': True, 'pic': True} -source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src'] +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] patches = ['configure_libtool.patch'] diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.7-ictce-5.3.0.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.7-ictce-5.3.0.eb index d33b58408f..efc7ae1f6e 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.7-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.7-ictce-5.3.0.eb @@ -1,14 +1,14 @@ name = 'HDF5' version = '1.8.7' -homepage = 'http://www.hdfgroup.org/HDF5/' +homepage = 'https://support.hdfgroup.org/HDF5/' description = """HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections.""" toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'optarch': True, 'usempi': True, 'pic': True} -source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src'] +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] patches = [ diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.9-goolf-1.4.10.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.9-goolf-1.4.10.eb index 513cb0e22b..ddc5289cb5 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.9-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.9-goolf-1.4.10.eb @@ -1,14 +1,14 @@ name = 'HDF5' version = '1.8.9' -homepage = 'http://www.hdfgroup.org/HDF5/' +homepage = 'https://support.hdfgroup.org/HDF5/' description = """HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'optarch': True, 'usempi': True, 'pic': True} -source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src'] +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] patches = ['configure_libtool.patch'] diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.9-goolf-1.5.16.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.9-goolf-1.5.16.eb index 46dd3d15ad..e77a9b41a1 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.9-goolf-1.5.16.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.9-goolf-1.5.16.eb @@ -1,14 +1,14 @@ name = 'HDF5' version = '1.8.9' -homepage = 'http://www.hdfgroup.org/HDF5/' +homepage = 'https://support.hdfgroup.org/HDF5/' description = """HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections.""" toolchain = {'name': 'goolf', 'version': '1.5.16'} toolchainopts = {'optarch': True, 'usempi': True, 'pic': True} -source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src'] +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] patches = ['configure_libtool.patch'] diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.9-ictce-5.2.0.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.9-ictce-5.2.0.eb index 7cd6cdf595..24dd608c18 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.9-ictce-5.2.0.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.9-ictce-5.2.0.eb @@ -1,15 +1,15 @@ name = 'HDF5' version = '1.8.9' -homepage = 'http://www.hdfgroup.org/HDF5/' +homepage = 'https://support.hdfgroup.org/HDF5/' description = """HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections.""" toolchain = {'name': 'ictce', 'version': '5.2.0'} toolchainopts = {'optarch': True, 'usempi': True, 'pic': True} +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src'] patches = [ 'HDF5_configure_ictce.patch', diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.9-ictce-5.3.0.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.9-ictce-5.3.0.eb index fd4fb4e5c0..202a1ff1e5 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.9-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.9-ictce-5.3.0.eb @@ -1,14 +1,14 @@ name = 'HDF5' version = '1.8.9' -homepage = 'http://www.hdfgroup.org/HDF5/' +homepage = 'https://support.hdfgroup.org/HDF5/' description = """HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections.""" toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'optarch': True, 'usempi': True, 'pic': True} -source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src'] +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] patches = [ diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.9-ictce-5.4.0.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.9-ictce-5.4.0.eb index 4c1c1db157..51723ed590 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.9-ictce-5.4.0.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.9-ictce-5.4.0.eb @@ -1,14 +1,14 @@ name = 'HDF5' version = '1.8.9' -homepage = 'http://www.hdfgroup.org/HDF5/' +homepage = 'https://support.hdfgroup.org/HDF5/' description = """HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections.""" toolchain = {'name': 'ictce', 'version': '5.4.0'} toolchainopts = {'optarch': True, 'usempi': True, 'pic': True} -source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src'] +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] patches = [ diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.9-intel-2014b.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.9-intel-2014b.eb index 24af13ad70..e3dd542387 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.9-intel-2014b.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.9-intel-2014b.eb @@ -1,14 +1,14 @@ name = 'HDF5' version = '1.8.9' -homepage = 'http://www.hdfgroup.org/HDF5/' +homepage = 'https://support.hdfgroup.org/HDF5/' description = """HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections.""" toolchain = {'name': 'intel', 'version': '2014b'} toolchainopts = {'optarch': True, 'usempi': True, 'pic': True} -source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src'] +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] patches = [ -- GitLab From 5aae227867f8c4c0de857c68da96fb79d101e32e Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Tue, 20 Jun 2017 14:48:06 -0500 Subject: [PATCH 0969/1603] adding easyconfigs: ABINIT-8.0.8b-foss-2016b.eb --- .../a/ABINIT/ABINIT-8.0.8b-foss-2016b.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/a/ABINIT/ABINIT-8.0.8b-foss-2016b.eb diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-8.0.8b-foss-2016b.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-8.0.8b-foss-2016b.eb new file mode 100644 index 0000000000..461d6b226e --- /dev/null +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-8.0.8b-foss-2016b.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'ABINIT' +version = '8.0.8b' + +homepage = 'http://www.abinit.org/' +description = """ABINIT is a package whose main program allows one to find the total energy, charge density and + electronic structure of systems made of electrons and nuclei (molecules and periodic solids) within Density Functional + Theory (DFT), using pseudopotentials and a planewave or wavelet basis.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['http://ftp.abinit.org/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['abc9e303bfa7f9f43f95598f87d84d5d'] + +configopts = "--with-mpi-prefix=$EBROOTIMPI/intel64 --with-trio-flavor='etsf_io+netcdf' --with-dft=flavor='libxc' " +configopts += '--with-netcdf-incs="-I$EBROOTNETCDF/include -I$EBROOTNETCDFMINFORTRAN/include" ' +configopts += '--with-netcdf-libs="-L$EBROOTNETCDF/lib -lnetcdf -L$EBROOTNETCDFMINFORTRAN/lib -lnetcdff" ' +configopts += '--with-libxc-incs="-I$EBROOTLIBXC/include" --with-libxc-libs="-L$EBROOTLIBXC/lib -lxc" ' +configopts += 'FCFLAGS="-ffree-line-length-none" ' + +dependencies = [ + ('libxc', '3.0.0'), + ('netCDF', '4.4.1'), + ('netCDF-Fortran', '4.4.4'), +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['abinit', 'aim', 'cut3d', 'conducti', 'mrgddb', 'mrgscr', 'optic']], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'chem' -- GitLab From 4dfab70c387a6de9848001e4cea524714d1ae9cd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 20 Jun 2017 21:56:55 +0200 Subject: [PATCH 0970/1603] adding easyconfigs: Ruby-2.3.4.eb --- easybuild/easyconfigs/r/Ruby/Ruby-2.3.4.eb | 58 ++++++++++++++++++++++ 1 file changed, 58 insertions(+) create mode 100644 easybuild/easyconfigs/r/Ruby/Ruby-2.3.4.eb diff --git a/easybuild/easyconfigs/r/Ruby/Ruby-2.3.4.eb b/easybuild/easyconfigs/r/Ruby/Ruby-2.3.4.eb new file mode 100644 index 0000000000..3149eef3ad --- /dev/null +++ b/easybuild/easyconfigs/r/Ruby/Ruby-2.3.4.eb @@ -0,0 +1,58 @@ +name = 'Ruby' +version = '2.3.4' + +homepage = 'https://www.ruby-lang.org' +description = """Ruby is a dynamic, open source programming language with + a focus on simplicity and productivity. It has an elegant syntax that is + natural to read and easy to write.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://cache.ruby-lang.org/pub/ruby/'] + +ext_options = { + 'source_urls': ['http://rubygems.org/downloads/'], + 'source_tmpl': '%(name)s-%(version)s.gem', +} + +exts_list = [ + ('ffi', '1.9.18', ext_options), + ('childprocess', '0.7.0', ext_options), + ('json', '2.1.0', ext_options), + ('cabin', '0.9.0', ext_options), + ('backports', '3.8.0', ext_options), + ('arr-pm', '0.0.10', ext_options), + ('clamp', '1.1.2', ext_options), + ('multipart-post', '2.0.0', ext_options), + ('faraday', '0.12.1', ext_options), + ('faraday_middleware', '0.11.0.1', ext_options), + ('highline', '1.7.8', ext_options), + ('net-http-pipeline', '1.0.1', ext_options), + ('connection_pool', '2.2.1', ext_options), + ('net-http-persistent', '2.9.4', ext_options), + ('multi_json', '1.12.1', ext_options), + ('public_suffix', '2.0.5', ext_options), + ('addressable', '2.4.0', ext_options), + ('gh', '0.15.1', ext_options), + ('launchy', '2.4.3', ext_options), + ('ethon', '0.10.1', ext_options), + ('typhoeus', '1.1.2', ext_options), + ('websocket', '1.2.4', ext_options), + ('pusher-client', '0.6.2', ext_options), + ('diff-lcs', '1.3', ext_options), + ('rspec-support', '3.6.0', ext_options), + ('rspec-mocks', '3.6.0', ext_options), + ('rspec-expectations', '3.6.0', ext_options), + ('rspec-core', '3.6.0', ext_options), + ('rspec', '3.6.0', ext_options), + ('rack', '2.0.3', ext_options), + ('rack-protection', '2.0.0', ext_options), + ('tilt', '2.0.7', ext_options), + ('mustermann', '1.0.0', ext_options), + ('sinatra', '2.0.0', ext_options), + ('rack-test', '0.6.3', ext_options), + ('bundler', '1.15.1', ext_options), +] + +moduleclass = 'lang' -- GitLab From b6169899ea7e248ba4868b61a594d5d7bb18d43e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 20 Jun 2017 21:57:28 +0200 Subject: [PATCH 0971/1603] adding easyconfigs: Rust-1.18.0-foss-2017a.eb --- .../r/Rust/Rust-1.18.0-foss-2017a.eb | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/r/Rust/Rust-1.18.0-foss-2017a.eb diff --git a/easybuild/easyconfigs/r/Rust/Rust-1.18.0-foss-2017a.eb b/easybuild/easyconfigs/r/Rust/Rust-1.18.0-foss-2017a.eb new file mode 100644 index 0000000000..22f0bbe798 --- /dev/null +++ b/easybuild/easyconfigs/r/Rust/Rust-1.18.0-foss-2017a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'Rust' +version = '1.18.0' + +homepage = 'https://www.rust-lang.org' +description = """Rust is a systems programming language that runs blazingly fast, prevents segfaults, + and guarantees thread safety.""" + +toolchain = {'name': 'foss', 'version': '2017a'} + +source_urls = ['https://static.rust-lang.org/dist/'] +sources = ['rustc-%(version)s-src.tar.gz'] + +builddependencies = [('CMake', '3.8.2')] + +sanity_check_paths = { + 'files': ['bin/rustc', 'bin/rustdoc'], + 'dirs': ['share/doc', 'share/man', 'lib/rustlib'], +} + +moduleclass = 'lang' -- GitLab From 3c32734d5ef41679343539f1526aa5bc6d734801 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 21 Jun 2017 08:38:51 +0200 Subject: [PATCH 0972/1603] adding easyconfigs: CMake-3.8.2-GCCcore-6.3.0.eb --- .../c/CMake/CMake-3.8.2-GCCcore-6.3.0.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.8.2-GCCcore-6.3.0.eb diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.8.2-GCCcore-6.3.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.8.2-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..23aa365a15 --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.8.2-GCCcore-6.3.0.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.8.2' + +homepage = 'http://www.cmake.org' +description = """CMake, the cross-platform, open-source build system. + CMake is a family of tools designed to build, test and package software.""" + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' + +builddependencies = [ + ('binutils', '2.27'), +] + + +dependencies = [ + ('ncurses', '6.0'), + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.1.0c'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From b3a350b8e2d687d3485dc3280668908462b424f7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 21 Jun 2017 10:15:55 +0200 Subject: [PATCH 0973/1603] adding easyconfigs: pydlpoly-20150225-intel-2016b-Python-2.7.12.eb, FFTW-2.1.5-intel-2016b.eb --- .../f/FFTW/FFTW-2.1.5-intel-2016b.eb | 35 +++++++++++++++++ ...poly-20150225-intel-2016b-Python-2.7.12.eb | 39 +++++++++++++++++++ 2 files changed, 74 insertions(+) create mode 100644 easybuild/easyconfigs/f/FFTW/FFTW-2.1.5-intel-2016b.eb create mode 100644 easybuild/easyconfigs/p/pydlpoly/pydlpoly-20150225-intel-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-2.1.5-intel-2016b.eb b/easybuild/easyconfigs/f/FFTW/FFTW-2.1.5-intel-2016b.eb new file mode 100644 index 0000000000..77bea4672e --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW/FFTW-2.1.5-intel-2016b.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'FFTW' +version = '2.1.5' + +homepage = 'http://www.fftw.org' +description = """FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) + in one or more dimensions, of arbitrary input size, and of both real and complex data.""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [homepage] + +patches = ['FFTW-%(version)s_fix-configure-Fortran-linking.patch'] + +common_configopts = "--enable-shared --enable-type-prefix --enable-threads --with-pic" + +configopts = [ + common_configopts + " --enable-float --enable-mpi", + common_configopts + " --enable-mpi", # default as last +] + +sanity_check_paths = { + 'files': ['include/%sfftw%s.h' % (x, y) for x in ['d', 'dr', 's', 'sr'] for y in ['', '_mpi', '_threads']] + + ['lib/lib%sfftw%s.a' % (x, y) for x in ['d', 'dr', 's', 'sr'] for y in ['', '_mpi', '_threads']] + + ['lib/lib%sfftw%s.%s' % (x, y, SHLIB_EXT) for x in ['d', 'dr', 's', 'sr'] + for y in ['', '_mpi', '_threads']], + 'dirs': [], +} +# make sure *_f77 symbols are there (patch is required to avoid --disable-fortran being used automatically) +sanity_check_commands = ["nm %(installdir)s/lib/libdfftw.a | grep _f77"] + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/p/pydlpoly/pydlpoly-20150225-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/pydlpoly/pydlpoly-20150225-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..9e06a0f8d2 --- /dev/null +++ b/easybuild/easyconfigs/p/pydlpoly/pydlpoly-20150225-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,39 @@ +easyblock = 'MakeCp' + +name = 'pydlpoly' +version = '20150225' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://cmc.aci.ruhr-uni-bochum.de/cmc/' +description = """Pydlpoly is a molecular dynamics simulation package which is a modified version of DL-POLY with + a Python language interface.""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'usempi': True, 'pic': True} + +sources = ['%(name)s_250215.tgz'] +checksums = ['cd84a4b563dd16823e22fe6c450b07fd95036e20e0c6b7fc308afdb347241122'] + +dependencies = [ + ('Python', '2.7.12'), # also provides mpi4py, numpy + ('h5py', '2.7.0', versionsuffix), + ('FFTW', '2.1.5'), +] + +start_dir = 'source' + +parallel = 1 +buildopts = 'FC="$FC" LD="$FC -o" LDFLAGS="$FFLAGS" FFLAGS="-c $FFLAGS" LDLIBS="-ldfftw" F2PY_COMP=intelem' + +files_to_copy = ['doc', 'py', 'scripts', 'so'] + +sanity_check_paths = { + 'files': ['so/_pydlpoly.%s' % SHLIB_EXT], + 'dirs': ['py'], +} +sanity_check_commands = ["python -c 'import pydlpoly'"] + +modextrapaths = {'PYTHONPATH': ['py', 'so']} +modextravars = {'PDLPDIR': '%(installdir)s'} + +moduleclass = 'chem' -- GitLab From 91223e02053ee50498fd81041fc24acc35f1c99d Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Mon, 12 Jun 2017 16:20:00 +0200 Subject: [PATCH 0974/1603] install gSOAP --- .../d/davix/davix-0.6.6-intel-2017a.eb | 37 +++++++++++++++++++ .../g/gSOAP/gSOAP-2.8.47-GCCcore-6.3.0.eb | 35 ++++++++++++++++++ .../g/gtest/gtest-1.8.0-GCCcore-6.3.0.eb | 19 ++++++++++ 3 files changed, 91 insertions(+) create mode 100644 easybuild/easyconfigs/d/davix/davix-0.6.6-intel-2017a.eb create mode 100644 easybuild/easyconfigs/g/gSOAP/gSOAP-2.8.47-GCCcore-6.3.0.eb create mode 100644 easybuild/easyconfigs/g/gtest/gtest-1.8.0-GCCcore-6.3.0.eb diff --git a/easybuild/easyconfigs/d/davix/davix-0.6.6-intel-2017a.eb b/easybuild/easyconfigs/d/davix/davix-0.6.6-intel-2017a.eb new file mode 100644 index 0000000000..2ad043d6bd --- /dev/null +++ b/easybuild/easyconfigs/d/davix/davix-0.6.6-intel-2017a.eb @@ -0,0 +1,37 @@ +easyblock = 'CMakeMake' + +name = 'davix' +version = '0.6.6' + +homepage = 'http://dmc.web.cern.ch/projects/davix/home' +description = """The davix project aims to make file management over HTTP-based protocols simple. + The focus is on high-performance remote I/O and data management of large collections of files. + Currently, there is support for the WebDav (link is external), Amazon S3 (link is external), + Microsoft Azure (link is external), and HTTP (link is external) protocols.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['https://github.com/cern-it-sdc-id/davix/archive/'] +sources = ['R_%s.tar.gz' % version.replace('.','_')] + +builddependencies = [ + ('CMake', '3.8.1'), +] + +dependencies = [ + ('libxml2', '2.9.4'), + ('gtest', '1.8.0'), + ('gSOAP', '2.8.47'), + ('Doxygen', '1.8.13'), + ('Boost', '1.63.0', '-Python-2.7.13'), + # ('abi-compliance-checker', ''), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +sanity_check_paths = { + 'files': ['lib/liblib_g2logger.a', 'lib/liblib_activeobject.a'], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/g/gSOAP/gSOAP-2.8.47-GCCcore-6.3.0.eb b/easybuild/easyconfigs/g/gSOAP/gSOAP-2.8.47-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..d5e9165011 --- /dev/null +++ b/easybuild/easyconfigs/g/gSOAP/gSOAP-2.8.47-GCCcore-6.3.0.eb @@ -0,0 +1,35 @@ +easyblock = "ConfigureMake" + +name = 'gSOAP' +version = '2.8.47' + +homepage = 'http://www.cs.fsu.edu/~engelen/soap.html' +description = """The gSOAP toolkit is a C and C++ software development toolkit for + SOAP and REST XML Web services and generic C/C++ XML data bindings. + The toolkit analyzes WSDLs and XML schemas (separately or as a combined set) and maps the XML schema types + and the SOAP/REST XML messaging protocols to easy-to-use and efficient C and C++ code. + It also supports exposing (legacy) C and C++ applications as XML Web services + by auto-generating XML serialization code and WSDL specifications. + Or you can simply use it to automatically convert XML to/from C and C++ data. + The toolkit supports options to generate pure ANSI C or C++ with or without STL.""" + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} + +builddependencies = [ + ('Bison', '3.0.4'), + ('flex', '2.6.3'), +] + +dependencies = [('zlib', '1.2.11')] + +sources = ['%(namelower)s_%(version)s.zip'] +source_urls = [SOURCEFORGE_SOURCE] + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/soapcpp2', 'bin/wsdl2h'] + 'dirs': ['include', 'lib'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/gtest/gtest-1.8.0-GCCcore-6.3.0.eb b/easybuild/easyconfigs/g/gtest/gtest-1.8.0-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..d48012e5d8 --- /dev/null +++ b/easybuild/easyconfigs/g/gtest/gtest-1.8.0-GCCcore-6.3.0.eb @@ -0,0 +1,19 @@ +easyblock = "Tarball" + +name = 'gtest' +version = '1.8.0' + +homepage = 'https://code.google.com/p/googletest/' +description = "Google's framework for writing C++ tests on a variety of platforms" + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} + +sources = [SOURCE_ZIP] +source_urls = ['https://googletest.googlecode.com/files'] + +sanity_check_paths = { + 'files': ['CMakeLists.txt', ], + 'dirs': ['include', 'src'], +} + +moduleclass = 'devel' -- GitLab From b5c6db24f28080f818f251d957c1cd5c896578e3 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Tue, 13 Jun 2017 14:34:05 +0200 Subject: [PATCH 0975/1603] install gtest, gSOAP, davix --- .../easyconfigs/d/davix/davix-0.6.6-intel-2017a.eb | 13 +++++++++++-- .../g/gSOAP/gSOAP-2.8.47-GCCcore-6.3.0.eb | 2 +- .../g/gtest/gtest-1.8.0-GCCcore-6.3.0.eb | 6 +++--- 3 files changed, 15 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/d/davix/davix-0.6.6-intel-2017a.eb b/easybuild/easyconfigs/d/davix/davix-0.6.6-intel-2017a.eb index 2ad043d6bd..e169a1b8ba 100644 --- a/easybuild/easyconfigs/d/davix/davix-0.6.6-intel-2017a.eb +++ b/easybuild/easyconfigs/d/davix/davix-0.6.6-intel-2017a.eb @@ -16,6 +16,7 @@ sources = ['R_%s.tar.gz' % version.replace('.','_')] builddependencies = [ ('CMake', '3.8.1'), + ('LibUUID', '1.0.3'), ] dependencies = [ @@ -30,8 +31,16 @@ dependencies = [ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] sanity_check_paths = { - 'files': ['lib/liblib_g2logger.a', 'lib/liblib_activeobject.a'], - 'dirs': [], + 'files': [ + 'bin/davix-get', + 'bin/davix-http', + 'bin/davix-ls', + 'bin/davix-mkdir', + 'bin/davix-mv', + 'bin/davix-put', + 'bin/davix-rm' + ], + 'dirs': ['include', 'lib64'], } moduleclass = 'tools' diff --git a/easybuild/easyconfigs/g/gSOAP/gSOAP-2.8.47-GCCcore-6.3.0.eb b/easybuild/easyconfigs/g/gSOAP/gSOAP-2.8.47-GCCcore-6.3.0.eb index d5e9165011..386dbdf5e8 100644 --- a/easybuild/easyconfigs/g/gSOAP/gSOAP-2.8.47-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/g/gSOAP/gSOAP-2.8.47-GCCcore-6.3.0.eb @@ -28,7 +28,7 @@ source_urls = [SOURCEFORGE_SOURCE] parallel = 1 sanity_check_paths = { - 'files': ['bin/soapcpp2', 'bin/wsdl2h'] + 'files': ['bin/soapcpp2', 'bin/wsdl2h'], 'dirs': ['include', 'lib'], } diff --git a/easybuild/easyconfigs/g/gtest/gtest-1.8.0-GCCcore-6.3.0.eb b/easybuild/easyconfigs/g/gtest/gtest-1.8.0-GCCcore-6.3.0.eb index d48012e5d8..55b27244e4 100644 --- a/easybuild/easyconfigs/g/gtest/gtest-1.8.0-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/g/gtest/gtest-1.8.0-GCCcore-6.3.0.eb @@ -8,12 +8,12 @@ description = "Google's framework for writing C++ tests on a variety of platform toolchain = {'name': 'GCCcore', 'version': '6.3.0'} -sources = [SOURCE_ZIP] -source_urls = ['https://googletest.googlecode.com/files'] +sources = ['release-%(version)s.tar.gz'] +source_urls = ['https://github.com/google/googletest/archive/'] sanity_check_paths = { 'files': ['CMakeLists.txt', ], - 'dirs': ['include', 'src'], + 'dirs': ['googletest/include', 'googletest/src'], } moduleclass = 'devel' -- GitLab From 357fe53db8337ad167e9c25dae6fe32a5775e6e5 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Tue, 20 Jun 2017 11:02:48 +0200 Subject: [PATCH 0976/1603] delete comment --- easybuild/easyconfigs/d/davix/davix-0.6.6-intel-2017a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/d/davix/davix-0.6.6-intel-2017a.eb b/easybuild/easyconfigs/d/davix/davix-0.6.6-intel-2017a.eb index e169a1b8ba..c35600e22c 100644 --- a/easybuild/easyconfigs/d/davix/davix-0.6.6-intel-2017a.eb +++ b/easybuild/easyconfigs/d/davix/davix-0.6.6-intel-2017a.eb @@ -25,7 +25,6 @@ dependencies = [ ('gSOAP', '2.8.47'), ('Doxygen', '1.8.13'), ('Boost', '1.63.0', '-Python-2.7.13'), - # ('abi-compliance-checker', ''), ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] -- GitLab From ddfc7ba922497ceb27648aa1266a0367a1278159 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Tue, 20 Jun 2017 11:24:36 +0200 Subject: [PATCH 0977/1603] fix build dependencies --- easybuild/easyconfigs/d/davix/davix-0.6.6-intel-2017a.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/d/davix/davix-0.6.6-intel-2017a.eb b/easybuild/easyconfigs/d/davix/davix-0.6.6-intel-2017a.eb index c35600e22c..c0b7fbe385 100644 --- a/easybuild/easyconfigs/d/davix/davix-0.6.6-intel-2017a.eb +++ b/easybuild/easyconfigs/d/davix/davix-0.6.6-intel-2017a.eb @@ -17,13 +17,13 @@ sources = ['R_%s.tar.gz' % version.replace('.','_')] builddependencies = [ ('CMake', '3.8.1'), ('LibUUID', '1.0.3'), + ('gtest', '1.8.0'), + ('Doxygen', '1.8.13'), ] dependencies = [ ('libxml2', '2.9.4'), - ('gtest', '1.8.0'), ('gSOAP', '2.8.47'), - ('Doxygen', '1.8.13'), ('Boost', '1.63.0', '-Python-2.7.13'), ] -- GitLab From feee6dc88d4ab81e7183cc430723b0e104b21531 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Tue, 20 Jun 2017 12:23:33 +0200 Subject: [PATCH 0978/1603] fix style nits --- .../easyconfigs/d/davix/davix-0.6.6-intel-2017a.eb | 10 +--------- .../easyconfigs/g/gSOAP/gSOAP-2.8.47-GCCcore-6.3.0.eb | 6 +++--- 2 files changed, 4 insertions(+), 12 deletions(-) diff --git a/easybuild/easyconfigs/d/davix/davix-0.6.6-intel-2017a.eb b/easybuild/easyconfigs/d/davix/davix-0.6.6-intel-2017a.eb index c0b7fbe385..ff2cf5d69f 100644 --- a/easybuild/easyconfigs/d/davix/davix-0.6.6-intel-2017a.eb +++ b/easybuild/easyconfigs/d/davix/davix-0.6.6-intel-2017a.eb @@ -30,15 +30,7 @@ dependencies = [ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] sanity_check_paths = { - 'files': [ - 'bin/davix-get', - 'bin/davix-http', - 'bin/davix-ls', - 'bin/davix-mkdir', - 'bin/davix-mv', - 'bin/davix-put', - 'bin/davix-rm' - ], + 'files': ['bin/davix-%s' % x for x in ['get', 'http', 'ls', 'mkdir', 'mv', 'put', 'rm']], 'dirs': ['include', 'lib64'], } diff --git a/easybuild/easyconfigs/g/gSOAP/gSOAP-2.8.47-GCCcore-6.3.0.eb b/easybuild/easyconfigs/g/gSOAP/gSOAP-2.8.47-GCCcore-6.3.0.eb index 386dbdf5e8..14c4a424bc 100644 --- a/easybuild/easyconfigs/g/gSOAP/gSOAP-2.8.47-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/g/gSOAP/gSOAP-2.8.47-GCCcore-6.3.0.eb @@ -15,6 +15,9 @@ description = """The gSOAP toolkit is a C and C++ software development toolkit f toolchain = {'name': 'GCCcore', 'version': '6.3.0'} +sources = ['%(namelower)s_%(version)s.zip'] +source_urls = [SOURCEFORGE_SOURCE] + builddependencies = [ ('Bison', '3.0.4'), ('flex', '2.6.3'), @@ -22,9 +25,6 @@ builddependencies = [ dependencies = [('zlib', '1.2.11')] -sources = ['%(namelower)s_%(version)s.zip'] -source_urls = [SOURCEFORGE_SOURCE] - parallel = 1 sanity_check_paths = { -- GitLab From 64f4ebca8138d401b309a33700c15768e00174a8 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Tue, 20 Jun 2017 12:46:03 +0200 Subject: [PATCH 0979/1603] gsoap: fix source_urls and bump version to 2.8.48 --- easybuild/easyconfigs/g/gSOAP/gSOAP-2.8.47-GCCcore-6.3.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/g/gSOAP/gSOAP-2.8.47-GCCcore-6.3.0.eb b/easybuild/easyconfigs/g/gSOAP/gSOAP-2.8.47-GCCcore-6.3.0.eb index 14c4a424bc..1d8dbc1f53 100644 --- a/easybuild/easyconfigs/g/gSOAP/gSOAP-2.8.47-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/g/gSOAP/gSOAP-2.8.47-GCCcore-6.3.0.eb @@ -1,7 +1,7 @@ easyblock = "ConfigureMake" name = 'gSOAP' -version = '2.8.47' +version = '2.8.48' homepage = 'http://www.cs.fsu.edu/~engelen/soap.html' description = """The gSOAP toolkit is a C and C++ software development toolkit for @@ -16,7 +16,7 @@ description = """The gSOAP toolkit is a C and C++ software development toolkit f toolchain = {'name': 'GCCcore', 'version': '6.3.0'} sources = ['%(namelower)s_%(version)s.zip'] -source_urls = [SOURCEFORGE_SOURCE] +source_urls = ['https://downloads.sourceforge.net/project/gsoap%(version_major)s/gsoap-%(version_major_minor)s/'] builddependencies = [ ('Bison', '3.0.4'), -- GitLab From d4a48a1592a999fd51561d3a601ed28181b55339 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Tue, 20 Jun 2017 14:38:54 +0200 Subject: [PATCH 0980/1603] fix gsoap version numbering --- easybuild/easyconfigs/d/davix/davix-0.6.6-intel-2017a.eb | 2 +- ...AP-2.8.47-GCCcore-6.3.0.eb => gSOAP-2.8.48-GCCcore-6.3.0.eb} | 0 2 files changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/g/gSOAP/{gSOAP-2.8.47-GCCcore-6.3.0.eb => gSOAP-2.8.48-GCCcore-6.3.0.eb} (100%) diff --git a/easybuild/easyconfigs/d/davix/davix-0.6.6-intel-2017a.eb b/easybuild/easyconfigs/d/davix/davix-0.6.6-intel-2017a.eb index ff2cf5d69f..d5ca616647 100644 --- a/easybuild/easyconfigs/d/davix/davix-0.6.6-intel-2017a.eb +++ b/easybuild/easyconfigs/d/davix/davix-0.6.6-intel-2017a.eb @@ -23,7 +23,7 @@ builddependencies = [ dependencies = [ ('libxml2', '2.9.4'), - ('gSOAP', '2.8.47'), + ('gSOAP', '2.8.48'), ('Boost', '1.63.0', '-Python-2.7.13'), ] diff --git a/easybuild/easyconfigs/g/gSOAP/gSOAP-2.8.47-GCCcore-6.3.0.eb b/easybuild/easyconfigs/g/gSOAP/gSOAP-2.8.48-GCCcore-6.3.0.eb similarity index 100% rename from easybuild/easyconfigs/g/gSOAP/gSOAP-2.8.47-GCCcore-6.3.0.eb rename to easybuild/easyconfigs/g/gSOAP/gSOAP-2.8.48-GCCcore-6.3.0.eb -- GitLab From f62d25efc2d97006cac424b067d884345270a5c3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 21 Jun 2017 11:48:33 +0200 Subject: [PATCH 0981/1603] adding easyconfigs: DBD-mysql-4.042-intel-2017a-Perl-5.24.1.eb, MariaDB-10.1.24-intel-2017a.eb, Perl-5.24.1-intel-2017a.eb --- ...DBD-mysql-4.042-intel-2017a-Perl-5.24.1.eb | 36 ++++++++++++++++ .../m/MariaDB/MariaDB-10.1.24-intel-2017a.eb | 42 +++++++++++++++++++ .../p/Perl/Perl-5.24.1-intel-2017a.eb | 4 ++ 3 files changed, 82 insertions(+) create mode 100644 easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.042-intel-2017a-Perl-5.24.1.eb create mode 100644 easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.24-intel-2017a.eb diff --git a/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.042-intel-2017a-Perl-5.24.1.eb b/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.042-intel-2017a-Perl-5.24.1.eb new file mode 100644 index 0000000000..0990091ea3 --- /dev/null +++ b/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.042-intel-2017a-Perl-5.24.1.eb @@ -0,0 +1,36 @@ +easyblock = 'PerlModule' + +name = 'DBD-mysql' +version = '4.042' +versionsuffix = '-Perl-%(perlver)s' + +homepage = 'http://search.cpan.org/dist/DBD-mysql/lib/DBD/mysql.pm' +description = """Perl binding for MySQL""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['http://cpan.metacpan.org/authors/id/M/MI/MICHIELB/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Perl', '5.24.1'), + ('MariaDB', '10.1.24'), + ('zlib', '1.2.11'), + # OS dependency should be preferred if the os version is more recent then this version + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1q'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# force static linking of libmysqlclient to dance around problem with unresolved symbols +#configopts = '--libs="-L$EBROOTMARIADB/lib -Wl,-Bstatic -lmariadbclient -Wl,-Bdynamic -lpthread -lz -lrt -lssl -lcrypto"' + +options = {'modulename': 'DBD::mysql'} + +sanity_check_paths = { + 'files': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/DBD/mysql.pm'], + 'dirs': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/DBD/mysql'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.24-intel-2017a.eb b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.24-intel-2017a.eb new file mode 100644 index 0000000000..9869ac1342 --- /dev/null +++ b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.24-intel-2017a.eb @@ -0,0 +1,42 @@ +easyblock = 'CMakeMake' + +name = 'MariaDB' +version = '10.1.24' + +homepage = 'https://mariadb.org/' +description = """MariaDB An enhanced, drop-in replacement for MySQL.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['https://downloads.mariadb.org/f/mariadb-%(version)s/source'] +sources = [SOURCELOWER_TAR_GZ] + +patches = [ + 'MariaDB-10.1.13-link-rt-for-jemalloc.patch', +] + +dependencies = [ + ('zlib', '1.2.11'), + ('ncurses', '6.0'), + ('jemalloc', '4.5.0'), + ('PCRE', '8.40'), + ('XZ', '5.2.3'), + ('Boost', '1.64.0'), + ('libxml2', '2.9.4'), +] + +builddependencies = [('CMake', '3.8.2')] + +separate_build_dir = True + +configopts = "-DWITH_PCRE=system -DWITH_JEMALLOC=yes -DWITH_ZLIB=system -DMYSQL_MAINTAINER_MODE=ON " +configopts += "-DWITH_EMBEDDED_SERVER=ON " # for libmysqld.so & co +configopts += "-DWITHOUT_TOKUDB=ON " # not supported with Intel compilers + +sanity_check_paths = { + 'files': ['bin/mysql', 'bin/mysqld_safe', 'lib/libmysqlclient.%s' % SHLIB_EXT, 'lib/libmysqld.%s' % SHLIB_EXT, + 'scripts/mysql_install_db'], + 'dirs': ['include', 'share'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.24.1-intel-2017a.eb b/easybuild/easyconfigs/p/Perl/Perl-5.24.1-intel-2017a.eb index 7186e3ec91..cc1cd43ca8 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.24.1-intel-2017a.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.24.1-intel-2017a.eb @@ -890,6 +890,10 @@ exts_list = [ 'source_tmpl': 'PDF-API2-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SS/SSIMMS'], }), + ('Devel::CheckLib', '1.11', { + 'source_tmpl': 'Devel-CheckLib-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MATTN'], + }), ] moduleclass = 'lang' -- GitLab From 709e2a7d4d783bdd939c497cd238331c5d320dca Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 21 Jun 2017 13:17:33 +0200 Subject: [PATCH 0982/1603] get rid of tabs --- .../l/LLVM/LLVM-3.7.1-foss-2015a.eb | 2 +- .../MultiQC-0.7-goolf-1.7.20-Python-2.7.11.eb | 25 +++++++++---------- .../MultiQC-0.9-foss-2016b-Python-2.7.12.eb | 24 +++++++++--------- 3 files changed, 25 insertions(+), 26 deletions(-) diff --git a/easybuild/easyconfigs/l/LLVM/LLVM-3.7.1-foss-2015a.eb b/easybuild/easyconfigs/l/LLVM/LLVM-3.7.1-foss-2015a.eb index 031705af89..531f4e4816 100644 --- a/easybuild/easyconfigs/l/LLVM/LLVM-3.7.1-foss-2015a.eb +++ b/easybuild/easyconfigs/l/LLVM/LLVM-3.7.1-foss-2015a.eb @@ -12,7 +12,7 @@ sources = ['%(namelower)s-%(version)s.src.tar.xz'] source_urls = ['http://llvm.org/releases/%(version)s'] builddependencies = [ - ('Python', '2.7.9'), + ('Python', '2.7.9'), ] # No build allowed in source dir diff --git a/easybuild/easyconfigs/m/MultiQC/MultiQC-0.7-goolf-1.7.20-Python-2.7.11.eb b/easybuild/easyconfigs/m/MultiQC/MultiQC-0.7-goolf-1.7.20-Python-2.7.11.eb index 52da5ecd72..e9c753506d 100644 --- a/easybuild/easyconfigs/m/MultiQC/MultiQC-0.7-goolf-1.7.20-Python-2.7.11.eb +++ b/easybuild/easyconfigs/m/MultiQC/MultiQC-0.7-goolf-1.7.20-Python-2.7.11.eb @@ -27,39 +27,38 @@ exts_defaultclass = 'PythonPackage' exts_list = [ ('six', '1.10.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], }), ('pyparsing', '2.1.9', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], }), ('pytz', '2016.6.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pytz/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pytz/'], }), ('cycler', '0.10.0', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cycler/'], + 'source_urls': ['https://pypi.python.org/packages/source/c/cycler/'], }), ('python-dateutil', '2.5.3', { - 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], - 'modulename': 'dateutil', + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], + 'modulename': 'dateutil', }), ('MarkupSafe', '0.23', { - 'source_urls': ['https://pypi.python.org/packages/source/m/markupsafe'], + 'source_urls': ['https://pypi.python.org/packages/source/m/markupsafe'], }), ('click', '6.6', { - 'source_urls': ['https://pypi.python.org/packages/source/c/click/'], + 'source_urls': ['https://pypi.python.org/packages/source/c/click/'], }), ('PyYAML', '3.12', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyyaml'], - 'modulename': 'yaml', + 'source_urls': ['https://pypi.python.org/packages/source/p/pyyaml'], + 'modulename': 'yaml', }), ('simplejson', '3.8.2', { - 'source_urls': ['https://pypi.python.org/packages/source/s/simplejson/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/simplejson/'], }), ('Jinja2', '2.8', { - 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2/'], + 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2/'], }), ('multiqc', version, { - #'source_tmpl': 'v%(version)s.tar.gz', 'source_urls': ['https://pypi.python.org/packages/source/m/multiqc/'], }), ] diff --git a/easybuild/easyconfigs/m/MultiQC/MultiQC-0.9-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/m/MultiQC/MultiQC-0.9-foss-2016b-Python-2.7.12.eb index 4ca3af6861..cb0f244915 100644 --- a/easybuild/easyconfigs/m/MultiQC/MultiQC-0.9-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/m/MultiQC/MultiQC-0.9-foss-2016b-Python-2.7.12.eb @@ -29,36 +29,36 @@ exts_defaultclass = 'PythonPackage' exts_list = [ ('six', '1.10.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], }), ('pyparsing', '2.1.9', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], }), ('pytz', '2016.6.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pytz/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pytz/'], }), ('cycler', '0.10.0', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cycler/'], + 'source_urls': ['https://pypi.python.org/packages/source/c/cycler/'], }), ('python-dateutil', '2.5.3', { - 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], - 'modulename': 'dateutil', + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], + 'modulename': 'dateutil', }), ('MarkupSafe', '0.23', { - 'source_urls': ['https://pypi.python.org/packages/source/m/markupsafe'], + 'source_urls': ['https://pypi.python.org/packages/source/m/markupsafe'], }), ('click', '6.6', { - 'source_urls': ['https://pypi.python.org/packages/source/c/click/'], + 'source_urls': ['https://pypi.python.org/packages/source/c/click/'], }), ('PyYAML', '3.12', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyyaml'], - 'modulename': 'yaml', + 'source_urls': ['https://pypi.python.org/packages/source/p/pyyaml'], + 'modulename': 'yaml', }), ('simplejson', '3.8.2', { - 'source_urls': ['https://pypi.python.org/packages/source/s/simplejson/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/simplejson/'], }), ('Jinja2', '2.8', { - 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2/'], + 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2/'], }), ('multiqc', version, { 'source_urls': ['https://pypi.python.org/packages/source/m/multiqc/'], -- GitLab From 583e3348d4c464baab85cbec638edc4fa9aec02f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 21 Jun 2017 14:32:43 +0200 Subject: [PATCH 0983/1603] clean up commented out configopts in DBD-mysql easyconfig --- .../d/DBD-mysql/DBD-mysql-4.042-intel-2017a-Perl-5.24.1.eb | 3 --- 1 file changed, 3 deletions(-) diff --git a/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.042-intel-2017a-Perl-5.24.1.eb b/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.042-intel-2017a-Perl-5.24.1.eb index 0990091ea3..0db79a7f27 100644 --- a/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.042-intel-2017a-Perl-5.24.1.eb +++ b/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.042-intel-2017a-Perl-5.24.1.eb @@ -23,9 +23,6 @@ dependencies = [ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] -# force static linking of libmysqlclient to dance around problem with unresolved symbols -#configopts = '--libs="-L$EBROOTMARIADB/lib -Wl,-Bstatic -lmariadbclient -Wl,-Bdynamic -lpthread -lz -lrt -lssl -lcrypto"' - options = {'modulename': 'DBD::mysql'} sanity_check_paths = { -- GitLab From 2a26abf2408e73e60b74b538c92ef9c05b2abccf Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Wed, 21 Jun 2017 14:23:19 +0100 Subject: [PATCH 0984/1603] adding easyconfigs: SAMtools-1.5-intel-2017a.eb --- .../s/SAMtools/SAMtools-1.5-intel-2017a.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100755 easybuild/easyconfigs/s/SAMtools/SAMtools-1.5-intel-2017a.eb diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.5-intel-2017a.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.5-intel-2017a.eb new file mode 100755 index 0000000000..07e6c5020c --- /dev/null +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.5-intel-2017a.eb @@ -0,0 +1,37 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Robert Schmidt , Cedric Laczny , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# Modified by: Adam Huffman +# The Francis Crick Institute +# +# Modified for version 1.4 by: Kurt Lust, UAntwerpen +# +## +name = 'SAMtools' +version = '1.5' + +homepage = 'http://www.htslib.org/' +description = """SAM Tools provide various utilities for manipulating alignments in the SAM format, + including sorting, merging, indexing and generating alignments in a per-position format.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s'] +sources = [SOURCELOWER_TAR_BZ2] + +# The htslib component of SAMtools 1.4 uses zlib, bzip2 and lzma compression. +# The latter is currently provided by XZ. +dependencies = [ + ('ncurses', '6.0'), + ('zlib', '1.2.11'), + ('bzip2', '1.0.6'), + ('XZ', '5.2.3'), +] + +moduleclass = 'bio' -- GitLab From ddba7fe2052267fdf848c8c43638803e7b50ba71 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Wed, 21 Jun 2017 15:46:48 +0200 Subject: [PATCH 0985/1603] style fix --- easybuild/easyconfigs/d/davix/davix-0.6.6-intel-2017a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/davix/davix-0.6.6-intel-2017a.eb b/easybuild/easyconfigs/d/davix/davix-0.6.6-intel-2017a.eb index d5ca616647..f4e5dff775 100644 --- a/easybuild/easyconfigs/d/davix/davix-0.6.6-intel-2017a.eb +++ b/easybuild/easyconfigs/d/davix/davix-0.6.6-intel-2017a.eb @@ -12,7 +12,7 @@ description = """The davix project aims to make file management over HTTP-based toolchain = {'name': 'intel', 'version': '2017a'} source_urls = ['https://github.com/cern-it-sdc-id/davix/archive/'] -sources = ['R_%s.tar.gz' % version.replace('.','_')] +sources = ['R_%s.tar.gz' % version.replace('.', '_')] builddependencies = [ ('CMake', '3.8.1'), -- GitLab From b3967ff49c8c53a157588b42c41676a45000b5fb Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 21 Jun 2017 20:40:09 +0200 Subject: [PATCH 0986/1603] more trivial style fixes --- .../b/BCFtools/BCFtools-1.3.1-goolf-1.7.20.eb | 2 +- .../easyconfigs/b/BLAT/BLAT-3.5-intel-2016b.eb | 3 ++- .../Boost/Boost-1.63.0-foss-2017a-Python-2.7.13.eb | 1 - .../easyconfigs/b/Boost/Boost-1.63.0-foss-2017a.eb | 1 - .../b/Bowtie2/Bowtie2-2.2.9-intel-2016b.eb | 2 +- .../b/Bowtie2/Bowtie2-2.3.2-intel-2017a.eb | 2 +- .../b/Bullet/Bullet-2.83.7-foss-2016a.eb | 2 +- ...AL-4.8.1-foss-2015a-GLib-2.48.2-Python-2.7.11.eb | 2 +- .../c/CP2K/CP2K-2.4.0-goolf-1.4.10-ipi.eb | 2 +- .../easyconfigs/c/CP2K/CP2K-2.4.0-goolf-1.4.10.eb | 4 ++-- .../ConnectomeWorkbench-1.2.2.eb | 2 +- ...Cookiecutter-1.4.0-goolf-1.7.20-Python-2.7.11.eb | 4 ++-- .../easyconfigs/d/DBus/DBus-1.10.12-intel-2016b.eb | 2 +- .../d/DCA++/DCA++-1.0-CrayGNU-2015.11-cpu.eb | 4 ++-- .../d/DCA++/DCA++-1.0-CrayGNU-2015.11-cuda.eb | 2 +- .../d/DIAL/DIAL-2011.06.06-foss-2016a.eb | 2 +- ...disambiguate-1.0.0-goolf-1.7.20-Python-2.7.11.eb | 8 ++++---- .../e/ETSF_IO/ETSF_IO-1.0.4-intel-2015b.eb | 2 +- .../EricScript-0.5.5-intel-2017a-R-3.4.0.eb | 2 +- .../e/ea-utils/ea-utils-1.04.807-foss-2016a.eb | 2 +- .../e/ea-utils/ea-utils-1.04.807-foss-2016b.eb | 2 +- .../e/ea-utils/ea-utils-1.04.807-intel-2016b.eb | 2 +- .../f/FFTW/FFTW-3.3.4-intel-2015b-PFFT-20150905.eb | 2 +- easybuild/easyconfigs/f/findhap/findhap-4.eb | 2 +- .../f/freetype/freetype-2.5.5-goolf-1.7.20.eb | 3 ++- .../f/freetype/freetype-2.6.2-goolf-1.7.20.eb | 3 ++- .../easyconfigs/g/GFOLD/GFOLD-1.1.4-goolf-1.7.20.eb | 2 +- .../easyconfigs/g/GFOLD/GFOLD-1.1.4-intel-2016a.eb | 2 +- .../easyconfigs/g/GLib/GLib-2.48.2-foss-2015a.eb | 3 ++- .../easyconfigs/g/Guile/Guile-2.0.11-foss-2016a.eb | 2 +- .../easyconfigs/g/gflags/gflags-2.1.2-foss-2016a.eb | 4 ++-- .../g/grib_api/grib_api-1.21.0-foss-2017a.eb | 1 - .../g/gtkglext/gtkglext-1.2.0-intel-2015b.eb | 2 +- ...2015b-Python-2.7.10-HDF5-1.8.15-patch1-serial.eb | 2 +- .../easyconfigs/i/IGV/IGV-2.3.68-Java-1.7.0_80.eb | 2 +- .../easyconfigs/i/IGV/IGV-2.3.80-Java-1.7.0_80.eb | 2 +- .../i/IGVTools/IGVTools-2.3.68-Java-1.7.0_80.eb | 2 +- .../i/IGVTools/IGVTools-2.3.72-Java-1.7.0_80.eb | 2 +- .../i/IGVTools/IGVTools-2.3.75-Java-1.7.0_80.eb | 2 +- .../easyconfigs/i/IOzone/IOzone-3.434-foss-2016a.eb | 2 +- .../i/igraph/igraph-0.7.1-intel-2016b.eb | 2 +- .../i/impi/impi-2017.1.132-GCC-5.4.0-2.26.eb | 2 +- .../j/JasPer/JasPer-1.900.1-foss-2017a.eb | 1 - .../jModelTest-2.1.10r20160303-Java-1.8.0_92.eb | 2 +- ...est-2.1.9r20160115-goolf-1.4.10-Java-1.7.0_75.eb | 2 +- .../j/jhbuild/jhbuild-3.15.92-GCCcore-4.9.3.eb | 2 +- .../easyconfigs/l/LLVM/LLVM-3.7.1-foss-2015a.eb | 2 +- .../easyconfigs/l/LLVM/LLVM-3.9.1-foss-2017a.eb | 1 - .../easyconfigs/l/LLVM/LLVM-4.0.0-foss-2017a.eb | 1 - .../easyconfigs/l/LSMS/LSMS-3_rev237-foss-2016a.eb | 4 ++-- .../easyconfigs/l/libXi/libXi-1.7.2-goolf-1.4.10.eb | 2 +- .../easyconfigs/l/libXi/libXi-1.7.4-intel-2015b.eb | 2 +- .../l/libreadline/libreadline-6.2-foss-2015a.eb | 8 ++++---- .../easyconfigs/m/METIS/METIS-5.1.0-foss-2017a.eb | 3 +-- .../m/MaSuRCA/MaSuRCA-3.2.2-foss-2016a.eb | 4 ++-- .../easyconfigs/m/Mesa/Mesa-11.2.1-foss-2015a.eb | 2 +- .../m/memkind/memkind-1.5.0-GCCcore-5.4.0.eb | 6 +++--- .../molmod/molmod-1.1-intel-2015b-Python-2.7.10.eb | 2 +- .../molmod/molmod-1.1-intel-2016a-Python-2.7.11.eb | 2 +- .../molmod/molmod-1.1-intel-2016b-Python-2.7.12.eb | 2 +- .../easyconfigs/n/NAMD/NAMD-2.12-foss-2017a-mpi.eb | 2 -- .../NRGLjubljana-2.4.3.23-foss-2016b.eb | 12 ++++++------ .../easyconfigs/n/nettle/nettle-2.6-goolf-1.4.10.eb | 6 ++++-- .../n/nettle/nettle-3.1.1-GNU-4.9.3-2.25.eb | 6 ++++-- .../easyconfigs/n/nettle/nettle-3.1.1-foss-2016a.eb | 6 ++++-- .../n/nettle/nettle-3.1.1-intel-2016a.eb | 6 ++++-- .../n/nettle/nettle-3.2-GCCcore-5.4.0.eb | 6 ++++-- .../easyconfigs/n/nettle/nettle-3.2-foss-2016b.eb | 6 ++++-- .../easyconfigs/n/nettle/nettle-3.2-intel-2016b.eb | 6 ++++-- .../easyconfigs/n/nettle/nettle-3.3-intel-2017a.eb | 6 ++++-- .../o/ORCA/ORCA-4.0.0.2-OpenMPI-2.0.2.eb | 13 ++++++------- .../OSU-Micro-Benchmarks-5.3.2-foss-2017a.eb | 1 - easybuild/easyconfigs/o/OTF2/OTF2-2.0-foss-2017a.eb | 3 +-- .../o/Octopus/Octopus-5.0.0-intel-2015b-mpi.eb | 4 ++-- .../o/OpenFOAM/OpenFOAM-3.0.0-foss-2016a.eb | 2 +- .../o/OpenMPI/OpenMPI-2.0.2-GCC-6.3.0-2.27-opa.eb | 4 +--- .../easyconfigs/p/PEAR/PEAR-0.9.6-goolf-1.4.10.eb | 2 +- .../easyconfigs/p/PEAR/PEAR-0.9.8-foss-2016b.eb | 2 +- .../easyconfigs/p/PEAR/PEAR-0.9.8-intel-2016b.eb | 2 +- .../PETSc-3.7.5-intel-2016b-downloaded-deps.eb | 2 +- .../PRINSEQ-0.20.4-foss-2015b-Perl-5.20.3.eb | 2 +- .../PRINSEQ-0.20.4-goolf-1.4.10-Perl-5.16.3.eb | 2 +- .../easyconfigs/p/PROJ/PROJ-4.8.0-foss-2015b.eb | 2 +- .../easyconfigs/p/PROJ/PROJ-4.9.1-foss-2015a.eb | 2 +- .../easyconfigs/p/Perl/Perl-5.22.0-foss-2015a-mt.eb | 4 ++-- .../easyconfigs/p/Perl/Perl-5.22.0-foss-2015a.eb | 2 +- .../p/Platanus/Platanus-1.2.4-foss-2017a.eb | 4 ++-- .../Pysam/Pysam-0.9.0-goolf-1.7.20-Python-2.7.11.eb | 4 ++-- .../Pysam/Pysam-0.9.1.4-foss-2016b-Python-2.7.12.eb | 4 ++-- .../p/Python/Python-2.7.11-CrayGNU-2015.11.eb | 2 +- .../p/Python/Python-2.7.11-CrayGNU-2016.03.eb | 2 +- .../p/pbbam/pbbam-20170508-intel-2017a.eb | 2 +- .../easyconfigs/p/pigz/pigz-2.3.1-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/r/R/R-3.2.3-foss-2015b.eb | 2 +- easybuild/easyconfigs/r/R/R-3.2.3-foss-2016a.eb | 2 +- easybuild/easyconfigs/r/R/R-3.2.3-foss-2016b.eb | 2 +- .../r/R/R-3.2.3-intel-2016a-libX11-1.6.3.eb | 2 +- easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a.eb | 2 +- .../r/R/R-3.3.3-foss-2016b-X11-20160819.eb | 3 +-- .../r/R/R-3.3.3-intel-2017a-X11-20170314.eb | 3 +-- .../r/RELION/RELION-1.4-intel-2016b-single.eb | 2 +- .../RSeQC-2.6.4-foss-2016b-Python-2.7.12-R-3.3.1.eb | 2 +- .../r/RepastHPC/RepastHPC-2.2.0-foss-2016a.eb | 2 +- .../rootpy/rootpy-0.8.0-foss-2016a-Python-2.7.11.eb | 2 +- .../s/SIONlib/SIONlib-1.7.1-foss-2017a-tools.eb | 1 - .../s/SIONlib/SIONlib-1.7.1-foss-2017a.eb | 1 - .../s/SUMATRA/SUMATRA-1.0.20-foss-2016a.eb | 2 +- easybuild/easyconfigs/s/Sambamba/Sambamba-0.6.6.eb | 2 +- .../easyconfigs/s/SeqAn/SeqAn-2.3.2-foss-2016b.eb | 5 +++-- .../Singularity/Singularity-2.2.1-GCC-6.3.0-2.27.eb | 3 ++- .../easyconfigs/s/Stacks/Stacks-1.40-foss-2016a.eb | 4 ++-- .../easyconfigs/s/Stacks/Stacks-1.42-foss-2016a.eb | 4 ++-- .../easyconfigs/s/Stacks/Stacks-1.44-foss-2016a.eb | 4 ++-- .../easyconfigs/s/Stacks/Stacks-1.45-foss-2016a.eb | 4 ++-- .../easyconfigs/s/Stacks/Stacks-1.46-intel-2017a.eb | 4 ++-- .../SuiteSparse-4.5.5-foss-2017a-METIS-5.1.0.eb | 1 - easybuild/easyconfigs/s/Szip/Szip-2.1-foss-2017a.eb | 1 - .../s/samblaster/samblaster-0.1.24-goolf-1.7.20.eb | 8 ++++---- .../s/segemehl/segemehl-0.2.0-foss-2016b.eb | 4 ++-- easybuild/easyconfigs/s/splitRef/splitRef-0.0.2.eb | 2 +- .../easyconfigs/t/Tcl/Tcl-8.5.19-foss-2017a.eb | 1 - .../VCFtools-0.1.14-goolf-1.4.10-Perl-5.16.3.eb | 6 +++--- .../VCFtools-0.1.14-goolf-1.7.20-Perl-5.22.2.eb | 6 +++--- .../v/VMD/VMD-1.9.3-intel-2016b-Python-2.7.12.eb | 2 +- .../v/Valgrind/Valgrind-3.11.0-foss-2016a.eb | 2 +- .../wkhtmltopdf/wkhtmltopdf-0.12.3-Linux-x86_64.eb | 10 +++++----- easybuild/easyconfigs/x/XZ/XZ-5.2.3-gimkl-2017a.eb | 2 +- .../x/xtrans/xtrans-1.3.5-gimkl-2.11.5.eb | 2 +- .../y/Yade/Yade-1.20.0-foss-2016a-Python-2.7.11.eb | 2 +- .../y/Yade/Yade-1.20.0-intel-2016a-Python-2.7.11.eb | 2 +- ....0.2-rev.90-intel-2015b-QuantumESPRESSO-5.2.1.eb | 2 +- .../easyconfigs/y/Yasm/Yasm-1.3.0-goolf-1.7.20.eb | 2 +- 132 files changed, 196 insertions(+), 195 deletions(-) diff --git a/easybuild/easyconfigs/b/BCFtools/BCFtools-1.3.1-goolf-1.7.20.eb b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.3.1-goolf-1.7.20.eb index 885f9339b0..d1c00e81a6 100644 --- a/easybuild/easyconfigs/b/BCFtools/BCFtools-1.3.1-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.3.1-goolf-1.7.20.eb @@ -26,7 +26,7 @@ buildopts = " USE_GPL=1 GSL_LIBS='-lgsl -lgslcblas'" runtest = 'test' -files_to_copy = [(["bcftools", "plot-vcfstats", "vcfutils.pl"], "bin"), +files_to_copy = [(["bcftools", "plot-vcfstats", "vcfutils.pl"], "bin"), "doc", "plugins", "test", "LICENSE", "README", "AUTHORS"] sanity_check_paths = { diff --git a/easybuild/easyconfigs/b/BLAT/BLAT-3.5-intel-2016b.eb b/easybuild/easyconfigs/b/BLAT/BLAT-3.5-intel-2016b.eb index 48a47daaa1..dfa7db4489 100644 --- a/easybuild/easyconfigs/b/BLAT/BLAT-3.5-intel-2016b.eb +++ b/easybuild/easyconfigs/b/BLAT/BLAT-3.5-intel-2016b.eb @@ -11,7 +11,8 @@ name = 'BLAT' version = '3.5' homepage = 'http://genome.ucsc.edu/FAQ/FAQblat.html' -description = "BLAT on DNA is designed to quickly find sequences of 95% and greater similarity of length 25 bases or more." +description = """BLAT on DNA is designed to quickly find sequences of 95% and greater similarity of length 25 bases + or more.""" toolchain = {'name': 'intel', 'version': '2016b'} diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.63.0-foss-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/b/Boost/Boost-1.63.0-foss-2017a-Python-2.7.13.eb index 49051608e1..5fac3580db 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.63.0-foss-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.63.0-foss-2017a-Python-2.7.13.eb @@ -21,4 +21,3 @@ dependencies = [ boost_mpi = True moduleclass = 'devel' - diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.63.0-foss-2017a.eb b/easybuild/easyconfigs/b/Boost/Boost-1.63.0-foss-2017a.eb index ea4624e01d..09208d29d9 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.63.0-foss-2017a.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.63.0-foss-2017a.eb @@ -21,4 +21,3 @@ configopts = '--without-libraries=python' boost_mpi = True moduleclass = 'devel' - diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9-intel-2016b.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9-intel-2016b.eb index 826bc88a15..ba74ca9337 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9-intel-2016b.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9-intel-2016b.eb @@ -25,6 +25,6 @@ sources = ['%(namelower)s-%(version)s-source.zip'] source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')] # to add script folder to path just uncomment this line -#modextrapaths = {'PATH': 'scripts'} +# modextrapaths = {'PATH': 'scripts'} moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.3.2-intel-2017a.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.3.2-intel-2017a.eb index 98d5525da2..8b78bff172 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.3.2-intel-2017a.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.3.2-intel-2017a.eb @@ -30,6 +30,6 @@ dependencies = [('tbb', '2017_U6')] buildopts = "EXTRA_FLAGS='-wd809'" # to add script folder to path just uncomment this line -#modextrapaths = {'PATH': 'scripts'} +# modextrapaths = {'PATH': 'scripts'} moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/Bullet/Bullet-2.83.7-foss-2016a.eb b/easybuild/easyconfigs/b/Bullet/Bullet-2.83.7-foss-2016a.eb index bcb89c1b4e..e9318b4588 100644 --- a/easybuild/easyconfigs/b/Bullet/Bullet-2.83.7-foss-2016a.eb +++ b/easybuild/easyconfigs/b/Bullet/Bullet-2.83.7-foss-2016a.eb @@ -19,7 +19,7 @@ builddependencies = [('CMake', '3.5.2')] configopts = "-DBUILD_SHARED_LIBS=ON" sanity_check_paths = { - 'files': ['include/bullet/btBullet%sCommon.h' % x for x in ['Collision', 'Dynamics']] + + 'files': ['include/bullet/btBullet%sCommon.h' % x for x in ['Collision', 'Dynamics']] + ['lib/libBullet%s.%s' % (x, SHLIB_EXT) for x in ['Collision', 'Dynamics']], 'dirs': [], } diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.8.1-foss-2015a-GLib-2.48.2-Python-2.7.11.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.8.1-foss-2015a-GLib-2.48.2-Python-2.7.11.eb index 462e46256b..874fac82e5 100644 --- a/easybuild/easyconfigs/c/CGAL/CGAL-4.8.1-foss-2015a-GLib-2.48.2-Python-2.7.11.eb +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.8.1-foss-2015a-GLib-2.48.2-Python-2.7.11.eb @@ -25,7 +25,7 @@ dependencies = [ ('Qt', '4.8.7', versionsuffix), ] -configopts = "-DCMAKE_VERBOSE_MAKEFILE=ON " +configopts = "-DCMAKE_VERBOSE_MAKEFILE=ON " configopts += "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT configopts += "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-2.4.0-goolf-1.4.10-ipi.eb b/easybuild/easyconfigs/c/CP2K/CP2K-2.4.0-goolf-1.4.10-ipi.eb index 7188e62917..0a291108ae 100644 --- a/easybuild/easyconfigs/c/CP2K/CP2K-2.4.0-goolf-1.4.10-ipi.eb +++ b/easybuild/easyconfigs/c/CP2K/CP2K-2.4.0-goolf-1.4.10-ipi.eb @@ -32,6 +32,6 @@ dependencies = [('Libint', '1.1.4')] parallel = 1 # about 100 tests fail -ignore_regtest_fails=True +ignore_regtest_fails = True moduleclass = 'chem' diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-2.4.0-goolf-1.4.10.eb b/easybuild/easyconfigs/c/CP2K/CP2K-2.4.0-goolf-1.4.10.eb index 5c6f21e195..985781685d 100644 --- a/easybuild/easyconfigs/c/CP2K/CP2K-2.4.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/c/CP2K/CP2K-2.4.0-goolf-1.4.10.eb @@ -14,7 +14,7 @@ source_urls = ['http://sourceforge.net/projects/cp2k/files/'] sources = [SOURCELOWER_TAR_BZ2] patches = [ - 'CP2K-%(version)s-fix_compile_date_lastsvn.patch', + 'CP2K-%(version)s-fix_compile_date_lastsvn.patch', 'do_regtest_nocompile.patch' ] @@ -30,6 +30,6 @@ dependencies = [('Libint', '1.1.4')] parallel = 1 # about 100 tests fail -ignore_regtest_fails=True +ignore_regtest_fails = True moduleclass = 'chem' diff --git a/easybuild/easyconfigs/c/ConnectomeWorkbench/ConnectomeWorkbench-1.2.2.eb b/easybuild/easyconfigs/c/ConnectomeWorkbench/ConnectomeWorkbench-1.2.2.eb index fce250c7cf..0cb98a2054 100644 --- a/easybuild/easyconfigs/c/ConnectomeWorkbench/ConnectomeWorkbench-1.2.2.eb +++ b/easybuild/easyconfigs/c/ConnectomeWorkbench/ConnectomeWorkbench-1.2.2.eb @@ -27,7 +27,7 @@ modextrapaths = { } sanity_check_paths = { - 'files': ["bin_rh_linux64/wb_import", "bin_rh_linux64/wb_command", + 'files': ["bin_rh_linux64/wb_import", "bin_rh_linux64/wb_command", "bin_rh_linux64/wb_view"], 'dirs': ["resources"] } diff --git a/easybuild/easyconfigs/c/Cookiecutter/Cookiecutter-1.4.0-goolf-1.7.20-Python-2.7.11.eb b/easybuild/easyconfigs/c/Cookiecutter/Cookiecutter-1.4.0-goolf-1.7.20-Python-2.7.11.eb index 6a2974e5b4..88fa4436a0 100644 --- a/easybuild/easyconfigs/c/Cookiecutter/Cookiecutter-1.4.0-goolf-1.7.20-Python-2.7.11.eb +++ b/easybuild/easyconfigs/c/Cookiecutter/Cookiecutter-1.4.0-goolf-1.7.20-Python-2.7.11.eb @@ -46,10 +46,10 @@ exts_list = [ }), ('binaryornot', '0.4.0', { 'source_urls': ['https://pypi.io/packages/source/b/binaryornot/'], - }), + }), ('Jinja2', '2.8', { 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2/'], - }), + }), ('jinja2-time', '0.2.0', { 'source_urls': ['https://pypi.python.org/packages/source/j/jinja2-time/'], 'modulename': 'jinja2', diff --git a/easybuild/easyconfigs/d/DBus/DBus-1.10.12-intel-2016b.eb b/easybuild/easyconfigs/d/DBus/DBus-1.10.12-intel-2016b.eb index 2a15cb846c..7697871a45 100644 --- a/easybuild/easyconfigs/d/DBus/DBus-1.10.12-intel-2016b.eb +++ b/easybuild/easyconfigs/d/DBus/DBus-1.10.12-intel-2016b.eb @@ -16,7 +16,7 @@ source_urls = ['http://dbus.freedesktop.org/releases/dbus'] sources = [SOURCELOWER_TAR_GZ] sanity_check_paths = { - 'files': ['bin/dbus-%s' % x for x in ['cleanup-sockets', 'daemon', 'launch', 'monitor', 'run-session', + 'files': ['bin/dbus-%s' % x for x in ['cleanup-sockets', 'daemon', 'launch', 'monitor', 'run-session', 'send', 'uuidgen']] + ['lib/libdbus-1.%s' % x for x in ['a', SHLIB_EXT]], 'dirs': ['include', 'share'] diff --git a/easybuild/easyconfigs/d/DCA++/DCA++-1.0-CrayGNU-2015.11-cpu.eb b/easybuild/easyconfigs/d/DCA++/DCA++-1.0-CrayGNU-2015.11-cpu.eb index 86590d12e7..088f873ddb 100644 --- a/easybuild/easyconfigs/d/DCA++/DCA++-1.0-CrayGNU-2015.11-cpu.eb +++ b/easybuild/easyconfigs/d/DCA++/DCA++-1.0-CrayGNU-2015.11-cpu.eb @@ -14,10 +14,10 @@ toolchain = {'name': 'CrayGNU', 'version': '2015.11'} dependencies = [ ('CMake', '3.5.0'), - ('spglib', '1.7.3'), + ('spglib', '1.7.3'), ('NFFT', '3.3.0'), ('GSL', '2.1'), - ('gtest', '1.7.0'), + ('gtest', '1.7.0'), ('cray-hdf5/1.8.13', EXTERNAL_MODULE), ] diff --git a/easybuild/easyconfigs/d/DCA++/DCA++-1.0-CrayGNU-2015.11-cuda.eb b/easybuild/easyconfigs/d/DCA++/DCA++-1.0-CrayGNU-2015.11-cuda.eb index 231148074a..3f3f75acda 100644 --- a/easybuild/easyconfigs/d/DCA++/DCA++-1.0-CrayGNU-2015.11-cuda.eb +++ b/easybuild/easyconfigs/d/DCA++/DCA++-1.0-CrayGNU-2015.11-cuda.eb @@ -14,7 +14,7 @@ toolchain = {'name': 'CrayGNU', 'version': '2015.11'} dependencies = [ ('CMake', '3.5.0'), - ('spglib', '1.7.3'), + ('spglib', '1.7.3'), ('NFFT', '3.3.0'), ('GSL', '2.1'), ('gtest', '1.7.0'), diff --git a/easybuild/easyconfigs/d/DIAL/DIAL-2011.06.06-foss-2016a.eb b/easybuild/easyconfigs/d/DIAL/DIAL-2011.06.06-foss-2016a.eb index 1a6bd6a25d..82b2e17255 100644 --- a/easybuild/easyconfigs/d/DIAL/DIAL-2011.06.06-foss-2016a.eb +++ b/easybuild/easyconfigs/d/DIAL/DIAL-2011.06.06-foss-2016a.eb @@ -21,7 +21,7 @@ dependencies = [ ] binaries = ['assemble', 'assemble1', 'assemble_illumina', 'build_sff_index', 'convertFastqFasta', - 'cull_components', 'DIAL', 'filter', 'filter_clusters', 'fish_clusters', 'make_template', + 'cull_components', 'DIAL', 'filter', 'filter_clusters', 'fish_clusters', 'make_template', 'masker', 'partition', 'remove_clones', 'remove_clusters', 'update', 'update_clusters', 'update_status'] diff --git a/easybuild/easyconfigs/d/disambiguate/disambiguate-1.0.0-goolf-1.7.20-Python-2.7.11.eb b/easybuild/easyconfigs/d/disambiguate/disambiguate-1.0.0-goolf-1.7.20-Python-2.7.11.eb index 7de0a8ea92..8b40d87ea0 100644 --- a/easybuild/easyconfigs/d/disambiguate/disambiguate-1.0.0-goolf-1.7.20-Python-2.7.11.eb +++ b/easybuild/easyconfigs/d/disambiguate/disambiguate-1.0.0-goolf-1.7.20-Python-2.7.11.eb @@ -6,7 +6,7 @@ easyblock = "PythonPackage" name = 'disambiguate' -version = '1.0.0' +version = '1.0.0' versionsuffix = '-Python-%(pyver)s' homepage = "https://github.com/AstraZeneca-NGS/disambiguate" @@ -19,9 +19,9 @@ sources = ["v%(version)s.tar.gz"] dependencies = [ ('Python', '2.7.11'), - ('BamTools', '2.4.0'), - ('zlib', '1.2.8'), - ('Pysam', '0.9.0', versionsuffix), + ('BamTools', '2.4.0'), + ('zlib', '1.2.8'), + ('Pysam', '0.9.0', versionsuffix), ] # this application provides a python implementation and a C++ implementation diff --git a/easybuild/easyconfigs/e/ETSF_IO/ETSF_IO-1.0.4-intel-2015b.eb b/easybuild/easyconfigs/e/ETSF_IO/ETSF_IO-1.0.4-intel-2015b.eb index 0e4a07c55e..7e7f19b2ca 100644 --- a/easybuild/easyconfigs/e/ETSF_IO/ETSF_IO-1.0.4-intel-2015b.eb +++ b/easybuild/easyconfigs/e/ETSF_IO/ETSF_IO-1.0.4-intel-2015b.eb @@ -30,7 +30,7 @@ dependencies = [ ] sanity_check_paths = { - 'files': ["bin/etsf_io"], + 'files': ["bin/etsf_io"], 'dirs': [] } diff --git a/easybuild/easyconfigs/e/EricScript/EricScript-0.5.5-intel-2017a-R-3.4.0.eb b/easybuild/easyconfigs/e/EricScript/EricScript-0.5.5-intel-2017a-R-3.4.0.eb index adaed6879a..222274d259 100644 --- a/easybuild/easyconfigs/e/EricScript/EricScript-0.5.5-intel-2017a-R-3.4.0.eb +++ b/easybuild/easyconfigs/e/EricScript/EricScript-0.5.5-intel-2017a-R-3.4.0.eb @@ -31,4 +31,4 @@ sanity_check_paths = { modextrapaths = {'PATH': ''} -moduleclass = 'bio' +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/e/ea-utils/ea-utils-1.04.807-foss-2016a.eb b/easybuild/easyconfigs/e/ea-utils/ea-utils-1.04.807-foss-2016a.eb index 498218ede9..26cdd728d0 100644 --- a/easybuild/easyconfigs/e/ea-utils/ea-utils-1.04.807-foss-2016a.eb +++ b/easybuild/easyconfigs/e/ea-utils/ea-utils-1.04.807-foss-2016a.eb @@ -32,7 +32,7 @@ dependencies = [ ] files_to_copy = [([ - 'fastq-mcf', 'fastq-multx', 'fastq-join', 'fastq-stats', 'fastq-clipper', + 'fastq-mcf', 'fastq-multx', 'fastq-join', 'fastq-stats', 'fastq-clipper', 'sam-stats', 'varcall', 'randomFQ', 'alc', 'determine-phred'], 'bin' )] diff --git a/easybuild/easyconfigs/e/ea-utils/ea-utils-1.04.807-foss-2016b.eb b/easybuild/easyconfigs/e/ea-utils/ea-utils-1.04.807-foss-2016b.eb index 5bd575648e..8409d2b2d3 100644 --- a/easybuild/easyconfigs/e/ea-utils/ea-utils-1.04.807-foss-2016b.eb +++ b/easybuild/easyconfigs/e/ea-utils/ea-utils-1.04.807-foss-2016b.eb @@ -32,7 +32,7 @@ dependencies = [ ] files_to_copy = [([ - 'fastq-mcf', 'fastq-multx', 'fastq-join', 'fastq-stats', 'fastq-clipper', + 'fastq-mcf', 'fastq-multx', 'fastq-join', 'fastq-stats', 'fastq-clipper', 'sam-stats', 'varcall', 'randomFQ', 'alc', 'determine-phred'], 'bin' )] diff --git a/easybuild/easyconfigs/e/ea-utils/ea-utils-1.04.807-intel-2016b.eb b/easybuild/easyconfigs/e/ea-utils/ea-utils-1.04.807-intel-2016b.eb index a1c32a3e34..1763f70eb3 100644 --- a/easybuild/easyconfigs/e/ea-utils/ea-utils-1.04.807-intel-2016b.eb +++ b/easybuild/easyconfigs/e/ea-utils/ea-utils-1.04.807-intel-2016b.eb @@ -34,7 +34,7 @@ dependencies = [ ] files_to_copy = [([ - 'fastq-mcf', 'fastq-multx', 'fastq-join', 'fastq-stats', 'fastq-clipper', + 'fastq-mcf', 'fastq-multx', 'fastq-join', 'fastq-stats', 'fastq-clipper', 'sam-stats', 'varcall', 'randomFQ', 'alc', 'determine-phred'], 'bin' )] diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-intel-2015b-PFFT-20150905.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-intel-2015b-PFFT-20150905.eb index d127590485..1f513106f6 100644 --- a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-intel-2015b-PFFT-20150905.eb +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-intel-2015b-PFFT-20150905.eb @@ -21,7 +21,7 @@ builddependencies = [ ] # the patch changed a Makefile.am, so we need to call autoreconf -preconfigopts = "autoreconf --verbose --symlink --force && " +preconfigopts = "autoreconf --verbose --symlink --force && " common_configopts = "--enable-threads --enable-openmp --with-pic" diff --git a/easybuild/easyconfigs/f/findhap/findhap-4.eb b/easybuild/easyconfigs/f/findhap/findhap-4.eb index 7622374b66..732e2ab92d 100644 --- a/easybuild/easyconfigs/f/findhap/findhap-4.eb +++ b/easybuild/easyconfigs/f/findhap/findhap-4.eb @@ -19,7 +19,7 @@ modextrapaths = { } modloadmsg = """ -Copy the following file to the directory from which you will be running the executable: +Copy the following file to the directory from which you will be running the executable: $EBROOTFINDHAP/findhap.options Other files in the $EBROOTFINDHAP directory are: diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.5.5-goolf-1.7.20.eb b/easybuild/easyconfigs/f/freetype/freetype-2.5.5-goolf-1.7.20.eb index f26f3a1cf8..415f10d874 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.5.5-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.5.5-goolf-1.7.20.eb @@ -19,7 +19,8 @@ dependencies = [ configopts = '--with-harfbuzz=no' sanity_check_paths = { - 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], + 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, + 'lib/pkgconfig/freetype2.pc'], 'dirs': ['include/freetype2'], } diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.6.2-goolf-1.7.20.eb b/easybuild/easyconfigs/f/freetype/freetype-2.6.2-goolf-1.7.20.eb index fefd237604..e7a7a3593d 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.6.2-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.6.2-goolf-1.7.20.eb @@ -19,7 +19,8 @@ dependencies = [ configopts = '--with-harfbuzz=no' sanity_check_paths = { - 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], + 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, + 'lib/pkgconfig/freetype2.pc'], 'dirs': ['include/freetype2'], } diff --git a/easybuild/easyconfigs/g/GFOLD/GFOLD-1.1.4-goolf-1.7.20.eb b/easybuild/easyconfigs/g/GFOLD/GFOLD-1.1.4-goolf-1.7.20.eb index 8d11408e6b..ae8931f569 100644 --- a/easybuild/easyconfigs/g/GFOLD/GFOLD-1.1.4-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/g/GFOLD/GFOLD-1.1.4-goolf-1.7.20.eb @@ -25,7 +25,7 @@ dependencies = [ files_to_copy = [(['gfold'], 'bin'), 'README', 'doc'] parallel = 1 - + sanity_check_paths = { 'files': ['bin/gfold'], 'dirs': [], diff --git a/easybuild/easyconfigs/g/GFOLD/GFOLD-1.1.4-intel-2016a.eb b/easybuild/easyconfigs/g/GFOLD/GFOLD-1.1.4-intel-2016a.eb index 3b289b47ea..5afa7f55f9 100644 --- a/easybuild/easyconfigs/g/GFOLD/GFOLD-1.1.4-intel-2016a.eb +++ b/easybuild/easyconfigs/g/GFOLD/GFOLD-1.1.4-intel-2016a.eb @@ -25,7 +25,7 @@ dependencies = [ files_to_copy = [(['gfold'], 'bin'), 'README', 'doc'] parallel = 1 - + sanity_check_paths = { 'files': ['bin/gfold'], 'dirs': [], diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.48.2-foss-2015a.eb b/easybuild/easyconfigs/g/GLib/GLib-2.48.2-foss-2015a.eb index 9af7e1beb3..3d7e4ba822 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.48.2-foss-2015a.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.48.2-foss-2015a.eb @@ -21,7 +21,8 @@ dependencies = [ builddependencies = [('Python', '2.7.9')] -configopts = "--disable-maintainer-mode --disable-silent-rules --disable-libelf --enable-static --enable-shared --disable-systemtap --with-pcre=system" +configopts = "--disable-maintainer-mode --disable-silent-rules --disable-libelf --enable-static --enable-shared " +configopts += "--disable-systemtap --with-pcre=system" postinstallcmds = ["sed -i -e 's|#!.*python|#!/usr/bin/env python|' %(installdir)s/bin/*"] diff --git a/easybuild/easyconfigs/g/Guile/Guile-2.0.11-foss-2016a.eb b/easybuild/easyconfigs/g/Guile/Guile-2.0.11-foss-2016a.eb index 94a0abd7af..ec7a8d0587 100644 --- a/easybuild/easyconfigs/g/Guile/Guile-2.0.11-foss-2016a.eb +++ b/easybuild/easyconfigs/g/Guile/Guile-2.0.11-foss-2016a.eb @@ -16,7 +16,7 @@ builddependencies = [('Autotools', '20150215')] dependencies = [ ('libunistring', '0.9.3'), ('libffi', '3.2.1'), - ('gc', '7.4.4'), + ('gc', '7.4.4'), ('GMP', '6.1.0'), ] diff --git a/easybuild/easyconfigs/g/gflags/gflags-2.1.2-foss-2016a.eb b/easybuild/easyconfigs/g/gflags/gflags-2.1.2-foss-2016a.eb index 9a10acf880..5f269fd40d 100644 --- a/easybuild/easyconfigs/g/gflags/gflags-2.1.2-foss-2016a.eb +++ b/easybuild/easyconfigs/g/gflags/gflags-2.1.2-foss-2016a.eb @@ -23,8 +23,8 @@ builddependencies = [ configopts = '-DBUILD_SHARED_LIBS=on -DBUILD_STATIC_LIBS=on' sanity_check_paths = { - 'files': ['bin/gflags_completions.sh'] + - ['lib/%s' % x for x in ['libgflags.%s' % SHLIB_EXT, + 'files': ['bin/gflags_completions.sh'] + + ['lib/%s' % x for x in ['libgflags.%s' % SHLIB_EXT, 'libgflags_nothreads.%s' % SHLIB_EXT, 'libgflags.a', 'libgflags_nothreads.a']] + ['include/gflags/gflags_completions.h'], 'dirs': [], diff --git a/easybuild/easyconfigs/g/grib_api/grib_api-1.21.0-foss-2017a.eb b/easybuild/easyconfigs/g/grib_api/grib_api-1.21.0-foss-2017a.eb index fa7f84d3e3..cd817e4d4a 100644 --- a/easybuild/easyconfigs/g/grib_api/grib_api-1.21.0-foss-2017a.eb +++ b/easybuild/easyconfigs/g/grib_api/grib_api-1.21.0-foss-2017a.eb @@ -22,4 +22,3 @@ configopts = '--with-jasper=$EBROOTJASPER' parallel = 1 moduleclass = 'data' - diff --git a/easybuild/easyconfigs/g/gtkglext/gtkglext-1.2.0-intel-2015b.eb b/easybuild/easyconfigs/g/gtkglext/gtkglext-1.2.0-intel-2015b.eb index 8dc32d3aad..e4de322688 100644 --- a/easybuild/easyconfigs/g/gtkglext/gtkglext-1.2.0-intel-2015b.eb +++ b/easybuild/easyconfigs/g/gtkglext/gtkglext-1.2.0-intel-2015b.eb @@ -21,7 +21,7 @@ dependencies = [ ] sanity_check_paths = { - 'files': ['lib/gtkglext-1.0/include/gdkglext-config.h', + 'files': ['lib/gtkglext-1.0/include/gdkglext-config.h', 'lib/libgdkglext-x11-1.0.a', 'lib/libgdkglext-x11-1.0.%s' % SHLIB_EXT, 'lib/libgtkglext-x11-1.0.a', 'lib/libgtkglext-x11-1.0.%s' % SHLIB_EXT], 'dirs': ['include/gtkglext-1.0/gdk', 'include/gtkglext-1.0/gtk', 'lib/pkgconfig'], diff --git a/easybuild/easyconfigs/h/horton/horton-2.0.0-intel-2015b-Python-2.7.10-HDF5-1.8.15-patch1-serial.eb b/easybuild/easyconfigs/h/horton/horton-2.0.0-intel-2015b-Python-2.7.10-HDF5-1.8.15-patch1-serial.eb index ab045435b2..d0c34c2e67 100644 --- a/easybuild/easyconfigs/h/horton/horton-2.0.0-intel-2015b-Python-2.7.10-HDF5-1.8.15-patch1-serial.eb +++ b/easybuild/easyconfigs/h/horton/horton-2.0.0-intel-2015b-Python-2.7.10-HDF5-1.8.15-patch1-serial.eb @@ -50,4 +50,4 @@ sanity_check_paths = { 'dirs': ['lib/python%s/site-packages/horton' % pyshortver], } -moduleclass = 'chem' +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/i/IGV/IGV-2.3.68-Java-1.7.0_80.eb b/easybuild/easyconfigs/i/IGV/IGV-2.3.68-Java-1.7.0_80.eb index 110b480923..be548b30c0 100644 --- a/easybuild/easyconfigs/i/IGV/IGV-2.3.68-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/i/IGV/IGV-2.3.68-Java-1.7.0_80.eb @@ -24,7 +24,7 @@ versionsuffix = '-%s-%s' % (java, javaver) dependencies = [(java, javaver)] # add the installation dir to PATH -modextrapaths = { +modextrapaths = { 'PATH': '', } diff --git a/easybuild/easyconfigs/i/IGV/IGV-2.3.80-Java-1.7.0_80.eb b/easybuild/easyconfigs/i/IGV/IGV-2.3.80-Java-1.7.0_80.eb index f8dd5d79f2..fb24a4205c 100644 --- a/easybuild/easyconfigs/i/IGV/IGV-2.3.80-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/i/IGV/IGV-2.3.80-Java-1.7.0_80.eb @@ -24,7 +24,7 @@ versionsuffix = '-%s-%s' % (java, javaver) dependencies = [(java, javaver)] # add the installation dir to PATH -modextrapaths = { +modextrapaths = { 'PATH': '', } diff --git a/easybuild/easyconfigs/i/IGVTools/IGVTools-2.3.68-Java-1.7.0_80.eb b/easybuild/easyconfigs/i/IGVTools/IGVTools-2.3.68-Java-1.7.0_80.eb index bc16033a08..5610a087c8 100644 --- a/easybuild/easyconfigs/i/IGVTools/IGVTools-2.3.68-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/i/IGVTools/IGVTools-2.3.68-Java-1.7.0_80.eb @@ -24,7 +24,7 @@ versionsuffix = '-%s-%s' % (java, javaver) dependencies = [(java, javaver)] # add the installation dir to PATH -modextrapaths = { +modextrapaths = { 'PATH': '', } diff --git a/easybuild/easyconfigs/i/IGVTools/IGVTools-2.3.72-Java-1.7.0_80.eb b/easybuild/easyconfigs/i/IGVTools/IGVTools-2.3.72-Java-1.7.0_80.eb index af0616b491..a1e88b7409 100644 --- a/easybuild/easyconfigs/i/IGVTools/IGVTools-2.3.72-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/i/IGVTools/IGVTools-2.3.72-Java-1.7.0_80.eb @@ -26,7 +26,7 @@ versionsuffix = '-%s-%s' % (java, javaver) dependencies = [(java, javaver)] # add the installation dir to PATH -modextrapaths = { +modextrapaths = { 'PATH': '', } diff --git a/easybuild/easyconfigs/i/IGVTools/IGVTools-2.3.75-Java-1.7.0_80.eb b/easybuild/easyconfigs/i/IGVTools/IGVTools-2.3.75-Java-1.7.0_80.eb index d2575fc6ec..6bb0cfc42f 100644 --- a/easybuild/easyconfigs/i/IGVTools/IGVTools-2.3.75-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/i/IGVTools/IGVTools-2.3.75-Java-1.7.0_80.eb @@ -24,7 +24,7 @@ sources = ['%(namelower)s_%(version)s.zip'] dependencies = [('Java', '1.7.0_80')] # add the installation dir to PATH -modextrapaths = { +modextrapaths = { 'PATH': '', } diff --git a/easybuild/easyconfigs/i/IOzone/IOzone-3.434-foss-2016a.eb b/easybuild/easyconfigs/i/IOzone/IOzone-3.434-foss-2016a.eb index 6af67462a3..5427eeed24 100644 --- a/easybuild/easyconfigs/i/IOzone/IOzone-3.434-foss-2016a.eb +++ b/easybuild/easyconfigs/i/IOzone/IOzone-3.434-foss-2016a.eb @@ -21,7 +21,7 @@ files_to_copy = [ (['src/current/%s' % docfile for docfile in ['gengnuplot.sh', 'Generate_Graphs', 'gnu3d.dem']], 'share'), (['docs/iozone.1'], 'share/man/man1'), (['docs/%s' % docfile for docfile in ['IOzone_msword_98.doc', 'IOzone_msword_98.pdf', 'Iozone_ps.gz', - 'Run_rules.doc']], + 'Run_rules.doc']], 'share/doc'), ] diff --git a/easybuild/easyconfigs/i/igraph/igraph-0.7.1-intel-2016b.eb b/easybuild/easyconfigs/i/igraph/igraph-0.7.1-intel-2016b.eb index b0f9d10dbb..0c649171c4 100644 --- a/easybuild/easyconfigs/i/igraph/igraph-0.7.1-intel-2016b.eb +++ b/easybuild/easyconfigs/i/igraph/igraph-0.7.1-intel-2016b.eb @@ -17,7 +17,7 @@ source_urls = ['https://github.com/igraph/igraph/releases/download/%(version)s'] builddependencies = [('Autotools', '20150215')] patches = [ - 'igraph-%(version)s-no-lapack-no-blas.patch', + 'igraph-%(version)s-no-lapack-no-blas.patch', 'igraph-%(version)s-fix-aclocal-version.patch' ] diff --git a/easybuild/easyconfigs/i/impi/impi-2017.1.132-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/impi/impi-2017.1.132-GCC-5.4.0-2.26.eb index 57fd16dd93..4dafa137ca 100644 --- a/easybuild/easyconfigs/i/impi/impi-2017.1.132-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/impi/impi-2017.1.132-GCC-5.4.0-2.26.eb @@ -19,7 +19,7 @@ components = ['intel-mpi', 'intel-psxe', 'intel-imb'] license_file = HOME + '/licenses/intel/license.lic' # Set I_MPI_ variables to point at the appropriate compilers -#set_mpi_wrappers_all = True +# set_mpi_wrappers_all = True postinstallcmds = [ 'ln -s %(installdir)s/lib64/libmpi.so %(installdir)s/lib64/libmpich.so', diff --git a/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-foss-2017a.eb b/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-foss-2017a.eb index 73e404db1c..1d4d9ee543 100644 --- a/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-foss-2017a.eb +++ b/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-foss-2017a.eb @@ -19,4 +19,3 @@ sanity_check_paths = { } moduleclass = 'vis' - diff --git a/easybuild/easyconfigs/j/jModelTest/jModelTest-2.1.10r20160303-Java-1.8.0_92.eb b/easybuild/easyconfigs/j/jModelTest/jModelTest-2.1.10r20160303-Java-1.8.0_92.eb index 4dba96087d..3c4304258a 100644 --- a/easybuild/easyconfigs/j/jModelTest/jModelTest-2.1.10r20160303-Java-1.8.0_92.eb +++ b/easybuild/easyconfigs/j/jModelTest/jModelTest-2.1.10r20160303-Java-1.8.0_92.eb @@ -29,7 +29,7 @@ install_cmd = "cd jmodeltest2-%(version)s && ant -Ddist.dir=%(installdir)s jar" modloadmsg = "To execute jModelTest run: java -jar $EBROOTJMODELTEST/jModelTest.jar\n" sanity_check_paths = { - 'files': ['jModelTest.jar'], + 'files': ['jModelTest.jar'], 'dirs': [], } diff --git a/easybuild/easyconfigs/j/jModelTest/jModelTest-2.1.9r20160115-goolf-1.4.10-Java-1.7.0_75.eb b/easybuild/easyconfigs/j/jModelTest/jModelTest-2.1.9r20160115-goolf-1.4.10-Java-1.7.0_75.eb index 37a4b9dd9a..f01140a3e5 100644 --- a/easybuild/easyconfigs/j/jModelTest/jModelTest-2.1.9r20160115-goolf-1.4.10-Java-1.7.0_75.eb +++ b/easybuild/easyconfigs/j/jModelTest/jModelTest-2.1.9r20160115-goolf-1.4.10-Java-1.7.0_75.eb @@ -29,7 +29,7 @@ install_cmd = "cd jmodeltest2-%(version)s && ant -Ddist.dir=%(installdir)s jar" modloadmsg = "To execute jModelTest run: java -jar $EBROOTJMODELTEST/jModelTest.jar\n" sanity_check_paths = { - 'files': ['jModelTest.jar'], + 'files': ['jModelTest.jar'], 'dirs': [], } diff --git a/easybuild/easyconfigs/j/jhbuild/jhbuild-3.15.92-GCCcore-4.9.3.eb b/easybuild/easyconfigs/j/jhbuild/jhbuild-3.15.92-GCCcore-4.9.3.eb index b2f1cf65eb..401fa1f345 100644 --- a/easybuild/easyconfigs/j/jhbuild/jhbuild-3.15.92-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/j/jhbuild/jhbuild-3.15.92-GCCcore-4.9.3.eb @@ -36,7 +36,7 @@ dependencies = [ # to avoid unnecessary dependencies. This requires us to build in the install dir so that all libs are found. buildininstalldir = True skipsteps = ['configure'] -prebuildopts = './autogen.sh --prefix=%(installdir)s &&' +prebuildopts = './autogen.sh --prefix=%(installdir)s &&' # Make sure there are no "not found" in the sanitycheck output sanity_check_commands = [('! jhbuild', 'sanitycheck| grep not\ found')] diff --git a/easybuild/easyconfigs/l/LLVM/LLVM-3.7.1-foss-2015a.eb b/easybuild/easyconfigs/l/LLVM/LLVM-3.7.1-foss-2015a.eb index 531f4e4816..2b4d52c46c 100644 --- a/easybuild/easyconfigs/l/LLVM/LLVM-3.7.1-foss-2015a.eb +++ b/easybuild/easyconfigs/l/LLVM/LLVM-3.7.1-foss-2015a.eb @@ -20,7 +20,7 @@ preconfigopts = "[ ! -e build ] && mkdir build && cd build &&" configure_cmd_prefix = '../' # For llvmpy / Numba: -configopts = '--enable-optimized --enable-pic --enable-shared' +configopts = '--enable-optimized --enable-pic --enable-shared' prebuildopts = 'cd build && REQUIRES_RTTI=1' preinstallopts = 'cd build &&' diff --git a/easybuild/easyconfigs/l/LLVM/LLVM-3.9.1-foss-2017a.eb b/easybuild/easyconfigs/l/LLVM/LLVM-3.9.1-foss-2017a.eb index 6bffed0098..7666df6063 100644 --- a/easybuild/easyconfigs/l/LLVM/LLVM-3.9.1-foss-2017a.eb +++ b/easybuild/easyconfigs/l/LLVM/LLVM-3.9.1-foss-2017a.eb @@ -41,4 +41,3 @@ sanity_check_paths = { separate_build_dir = True moduleclass = 'compiler' - diff --git a/easybuild/easyconfigs/l/LLVM/LLVM-4.0.0-foss-2017a.eb b/easybuild/easyconfigs/l/LLVM/LLVM-4.0.0-foss-2017a.eb index 5a2a5553d5..d9e41a1460 100644 --- a/easybuild/easyconfigs/l/LLVM/LLVM-4.0.0-foss-2017a.eb +++ b/easybuild/easyconfigs/l/LLVM/LLVM-4.0.0-foss-2017a.eb @@ -41,4 +41,3 @@ sanity_check_paths = { separate_build_dir = True moduleclass = 'compiler' - diff --git a/easybuild/easyconfigs/l/LSMS/LSMS-3_rev237-foss-2016a.eb b/easybuild/easyconfigs/l/LSMS/LSMS-3_rev237-foss-2016a.eb index b39dd8a48b..4e067fb22e 100644 --- a/easybuild/easyconfigs/l/LSMS/LSMS-3_rev237-foss-2016a.eb +++ b/easybuild/easyconfigs/l/LSMS/LSMS-3_rev237-foss-2016a.eb @@ -6,7 +6,7 @@ version = '3_rev237' homepage = 'https://asc.llnl.gov/CORAL-benchmarks/#lsms' description = "LSMS benchmark, part of CORAL suite" -toolchain = {'name': 'foss', 'version': '2016a' } +toolchain = {'name': 'foss', 'version': '2016a'} source_urls = ['https://asc.llnl.gov/CORAL-benchmarks/Science/'] sources = ['%(name)s_%(version)s.tar.bz2'] @@ -27,5 +27,5 @@ sanity_check_paths = { 'files': ['bin/lsms', 'bin/wl-lsms'], 'dirs': [], } - + moduleclass = 'tools' diff --git a/easybuild/easyconfigs/l/libXi/libXi-1.7.2-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libXi/libXi-1.7.2-goolf-1.4.10.eb index b4b7228f14..f715404402 100644 --- a/easybuild/easyconfigs/l/libXi/libXi-1.7.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/libXi/libXi-1.7.2-goolf-1.4.10.eb @@ -20,7 +20,7 @@ dependencies = [ ] sanity_check_paths = { - 'files': ['include/X11/extensions/XInput.h', 'include/X11/extensions/XInput2.h', + 'files': ['include/X11/extensions/XInput.h', 'include/X11/extensions/XInput2.h', 'lib/libXi.%s' % SHLIB_EXT, 'lib/libXi.a'], 'dirs': [], } diff --git a/easybuild/easyconfigs/l/libXi/libXi-1.7.4-intel-2015b.eb b/easybuild/easyconfigs/l/libXi/libXi-1.7.4-intel-2015b.eb index 2316d70175..22b46c1c3e 100644 --- a/easybuild/easyconfigs/l/libXi/libXi-1.7.4-intel-2015b.eb +++ b/easybuild/easyconfigs/l/libXi/libXi-1.7.4-intel-2015b.eb @@ -20,7 +20,7 @@ dependencies = [ ] sanity_check_paths = { - 'files': ['include/X11/extensions/XInput.h', 'include/X11/extensions/XInput2.h', + 'files': ['include/X11/extensions/XInput.h', 'include/X11/extensions/XInput2.h', 'lib/libXi.%s' % SHLIB_EXT, 'lib/libXi.a'], 'dirs': [], } diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-foss-2015a.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-foss-2015a.eb index 45a556ffec..684bf7dc76 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-foss-2015a.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-foss-2015a.eb @@ -18,10 +18,10 @@ source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] sanity_check_paths = { - 'files' : ['lib/libreadline.a', 'lib/libhistory.a'] + - ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', - 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], - 'dirs' : [], + 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + 'dirs': [], } moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/METIS/METIS-5.1.0-foss-2017a.eb b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-foss-2017a.eb index b1648c008c..e2b238572c 100644 --- a/easybuild/easyconfigs/m/METIS/METIS-5.1.0-foss-2017a.eb +++ b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-foss-2017a.eb @@ -15,7 +15,7 @@ source_urls = [ 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/OLD', ] -#We use 32bit for indices and 64bit for content +# we use 32bit for indices and 64bit for content patches = ['METIS-5.1.0-use-doubles.patch'] builddependencies = [('CMake', '3.8.0')] @@ -23,4 +23,3 @@ builddependencies = [('CMake', '3.8.0')] configopts = ['', 'shared=1'] moduleclass = 'math' - diff --git a/easybuild/easyconfigs/m/MaSuRCA/MaSuRCA-3.2.2-foss-2016a.eb b/easybuild/easyconfigs/m/MaSuRCA/MaSuRCA-3.2.2-foss-2016a.eb index 6a0e136d4e..75f0da13ce 100644 --- a/easybuild/easyconfigs/m/MaSuRCA/MaSuRCA-3.2.2-foss-2016a.eb +++ b/easybuild/easyconfigs/m/MaSuRCA/MaSuRCA-3.2.2-foss-2016a.eb @@ -33,8 +33,8 @@ dependencies = [ ('zlib', '1.2.8'), ] -buildopts="install-special" -start_dir="global-1" +buildopts = "install-special" +start_dir = "global-1" sanity_check_paths = { 'files': ['bin/masurca'], diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-11.2.1-foss-2015a.eb b/easybuild/easyconfigs/m/Mesa/Mesa-11.2.1-foss-2015a.eb index 27ac3ec93c..42ded1fee4 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-11.2.1-foss-2015a.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-11.2.1-foss-2015a.eb @@ -34,7 +34,7 @@ dependencies = [ ] # Use the os provided libudev or the EB provided eudev -#osdependencies = ['libudev'] +# osdependencies = ['libudev'] # GLU is not part anymore of Mesa package! configopts = " --disable-osmesa --enable-gallium-osmesa --enable-gallium-llvm --enable-glx --disable-dri" diff --git a/easybuild/easyconfigs/m/memkind/memkind-1.5.0-GCCcore-5.4.0.eb b/easybuild/easyconfigs/m/memkind/memkind-1.5.0-GCCcore-5.4.0.eb index 6a31d17221..3b6604a72e 100644 --- a/easybuild/easyconfigs/m/memkind/memkind-1.5.0-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/m/memkind/memkind-1.5.0-GCCcore-5.4.0.eb @@ -16,12 +16,12 @@ sources = ['v%(version)s.tar.gz'] builddependencies = [ ('binutils', '2.26'), - ('Coreutils', '8.27'), # needed to ensure that ./build_jemalloc.sh works properly - ('Autotools', '20150215'), # needed to ensure that ./build_jemalloc.sh works properly + ('Coreutils', '8.27'), # needed to ensure that ./build_jemalloc.sh works properly + ('Autotools', '20150215'), # needed to ensure that ./build_jemalloc.sh works properly ] dependencies = [ - ('tbb', '2017_U5'), # optional, to enable the tbb heap manager + ('tbb', '2017_U5'), # optional, to enable the tbb heap manager ('numactl', '2.0.11') ] diff --git a/easybuild/easyconfigs/m/molmod/molmod-1.1-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/m/molmod/molmod-1.1-intel-2015b-Python-2.7.10.eb index eb46a80abe..d98ab8d528 100644 --- a/easybuild/easyconfigs/m/molmod/molmod-1.1-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/m/molmod/molmod-1.1-intel-2015b-Python-2.7.10.eb @@ -14,7 +14,7 @@ sources = [SOURCE_TAR_GZ] dependencies = [ ('Python', '2.7.10'), - ('matplotlib', '1.5.0', versionsuffix), + ('matplotlib', '1.5.0', versionsuffix), ] runtest = "export MATPLOTLIBRC=$PWD; echo 'backend: agg' > $MATPLOTLIBRC/matplotlibrc;" diff --git a/easybuild/easyconfigs/m/molmod/molmod-1.1-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/m/molmod/molmod-1.1-intel-2016a-Python-2.7.11.eb index 62f71cc876..c9fec8f432 100644 --- a/easybuild/easyconfigs/m/molmod/molmod-1.1-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/m/molmod/molmod-1.1-intel-2016a-Python-2.7.11.eb @@ -14,7 +14,7 @@ sources = [SOURCE_TAR_GZ] dependencies = [ ('Python', '2.7.11'), - ('matplotlib', '1.5.1', versionsuffix), + ('matplotlib', '1.5.1', versionsuffix), ] runtest = "export MATPLOTLIBRC=$PWD; echo 'backend: agg' > $MATPLOTLIBRC/matplotlibrc;" diff --git a/easybuild/easyconfigs/m/molmod/molmod-1.1-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/m/molmod/molmod-1.1-intel-2016b-Python-2.7.12.eb index 1b74bd9124..a8659a20bf 100644 --- a/easybuild/easyconfigs/m/molmod/molmod-1.1-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/m/molmod/molmod-1.1-intel-2016b-Python-2.7.12.eb @@ -14,7 +14,7 @@ sources = [SOURCE_TAR_GZ] dependencies = [ ('Python', '2.7.12'), - ('matplotlib', '1.5.3', versionsuffix), + ('matplotlib', '1.5.3', versionsuffix), ] runtest = "export MATPLOTLIBRC=$PWD; echo 'backend: agg' > $MATPLOTLIBRC/matplotlibrc;" diff --git a/easybuild/easyconfigs/n/NAMD/NAMD-2.12-foss-2017a-mpi.eb b/easybuild/easyconfigs/n/NAMD/NAMD-2.12-foss-2017a-mpi.eb index 8c793e8447..216d763393 100644 --- a/easybuild/easyconfigs/n/NAMD/NAMD-2.12-foss-2017a-mpi.eb +++ b/easybuild/easyconfigs/n/NAMD/NAMD-2.12-foss-2017a-mpi.eb @@ -22,5 +22,3 @@ osdependencies = ['tcsh'] charm_arch = "mpi-linux-x86_64" moduleclass = 'chem' - - diff --git a/easybuild/easyconfigs/n/NRGLjubljana/NRGLjubljana-2.4.3.23-foss-2016b.eb b/easybuild/easyconfigs/n/NRGLjubljana/NRGLjubljana-2.4.3.23-foss-2016b.eb index 491184693e..e11e467c7e 100644 --- a/easybuild/easyconfigs/n/NRGLjubljana/NRGLjubljana-2.4.3.23-foss-2016b.eb +++ b/easybuild/easyconfigs/n/NRGLjubljana/NRGLjubljana-2.4.3.23-foss-2016b.eb @@ -15,19 +15,19 @@ docurls = 'http://nrgljubljana.ijs.si/examples/' software_license = 'LicenseGPLv3' toolchain = {'name': 'foss', 'version': '2016b'} -toolchainopts = { 'pic': True } +toolchainopts = {'pic': True} -sources = [ '%(namelower)s-%(version)s.tar.gz' ] -source_urls = [ 'http://nrgljubljana.ijs.si/' ] +sources = ['%(namelower)s-%(version)s.tar.gz'] +source_urls = ['http://nrgljubljana.ijs.si/'] configopts = '--with-tools --with-boost-serialization=boost_serialization' configopts += ' CXXFLAGS="-Ddsyev=dsyev_ -Ddsyevr=dsyevr_ -Dzheev=zheev_ -Dzheevr=zheevr_"' configopts += ' LDFLAGS="-lopenblas -L${EBROOTBOOST}/lib"' dependencies = [ - ('GMP', '6.1.2'), - ('GSL', '2.3'), - ('Boost', '1.61.0') + ('GMP', '6.1.2'), + ('GSL', '2.3'), + ('Boost', '1.61.0'), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/n/nettle/nettle-2.6-goolf-1.4.10.eb b/easybuild/easyconfigs/n/nettle/nettle-2.6-goolf-1.4.10.eb index eb26f01e29..8beb3e1e0d 100644 --- a/easybuild/easyconfigs/n/nettle/nettle-2.6-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/n/nettle/nettle-2.6-goolf-1.4.10.eb @@ -15,8 +15,10 @@ dependencies = [('GMP', '5.0.5')] sanity_check_paths = { 'files': ['bin/%s' % x for x in ['nettle-hash', 'nettle-lfib-stream', 'pkcs1-conv', 'sexp-conv']] + - [('lib/libhogweed.a', 'lib64/libhogweed.a'), ('lib/libhogweed.%s' % SHLIB_EXT, 'lib64/libhogweed.%s' % SHLIB_EXT), - ('lib/libnettle.a', 'lib64/libnettle.a'), ('lib/libnettle.%s' % SHLIB_EXT, 'lib64/libnettle.%s' % SHLIB_EXT)], + [('lib/libhogweed.a', 'lib64/libhogweed.a'), + ('lib/libhogweed.%s' % SHLIB_EXT, 'lib64/libhogweed.%s' % SHLIB_EXT), + ('lib/libnettle.a', 'lib64/libnettle.a'), + ('lib/libnettle.%s' % SHLIB_EXT, 'lib64/libnettle.%s' % SHLIB_EXT)], 'dirs': ['include/nettle'], } diff --git a/easybuild/easyconfigs/n/nettle/nettle-3.1.1-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/n/nettle/nettle-3.1.1-GNU-4.9.3-2.25.eb index 27c65b25e8..a611494ef0 100644 --- a/easybuild/easyconfigs/n/nettle/nettle-3.1.1-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/n/nettle/nettle-3.1.1-GNU-4.9.3-2.25.eb @@ -20,8 +20,10 @@ dependencies = [ sanity_check_paths = { 'files': ['bin/%s' % x for x in ['nettle-hash', 'nettle-lfib-stream', 'pkcs1-conv', 'sexp-conv']] + - [('lib/libhogweed.a', 'lib64/libhogweed.a'), ('lib/libhogweed.%s' % SHLIB_EXT, 'lib64/libhogweed.%s' % SHLIB_EXT), - ('lib/libnettle.a', 'lib64/libnettle.a'), ('lib/libnettle.%s' % SHLIB_EXT, 'lib64/libnettle.%s' % SHLIB_EXT)], + [('lib/libhogweed.a', 'lib64/libhogweed.a'), + ('lib/libhogweed.%s' % SHLIB_EXT, 'lib64/libhogweed.%s' % SHLIB_EXT), + ('lib/libnettle.a', 'lib64/libnettle.a'), + ('lib/libnettle.%s' % SHLIB_EXT, 'lib64/libnettle.%s' % SHLIB_EXT)], 'dirs': ['include/nettle'], } diff --git a/easybuild/easyconfigs/n/nettle/nettle-3.1.1-foss-2016a.eb b/easybuild/easyconfigs/n/nettle/nettle-3.1.1-foss-2016a.eb index f658dc22c5..3dfb0c2269 100644 --- a/easybuild/easyconfigs/n/nettle/nettle-3.1.1-foss-2016a.eb +++ b/easybuild/easyconfigs/n/nettle/nettle-3.1.1-foss-2016a.eb @@ -20,8 +20,10 @@ dependencies = [ sanity_check_paths = { 'files': ['bin/%s' % x for x in ['nettle-hash', 'nettle-lfib-stream', 'pkcs1-conv', 'sexp-conv']] + - [('lib/libhogweed.a', 'lib64/libhogweed.a'), ('lib/libhogweed.%s' % SHLIB_EXT, 'lib64/libhogweed.%s' % SHLIB_EXT), - ('lib/libnettle.a', 'lib64/libnettle.a'), ('lib/libnettle.%s' % SHLIB_EXT, 'lib64/libnettle.%s' % SHLIB_EXT)], + [('lib/libhogweed.a', 'lib64/libhogweed.a'), + ('lib/libhogweed.%s' % SHLIB_EXT, 'lib64/libhogweed.%s' % SHLIB_EXT), + ('lib/libnettle.a', 'lib64/libnettle.a'), + ('lib/libnettle.%s' % SHLIB_EXT, 'lib64/libnettle.%s' % SHLIB_EXT)], 'dirs': ['include/nettle'], } diff --git a/easybuild/easyconfigs/n/nettle/nettle-3.1.1-intel-2016a.eb b/easybuild/easyconfigs/n/nettle/nettle-3.1.1-intel-2016a.eb index b0fd192537..a8958f5414 100644 --- a/easybuild/easyconfigs/n/nettle/nettle-3.1.1-intel-2016a.eb +++ b/easybuild/easyconfigs/n/nettle/nettle-3.1.1-intel-2016a.eb @@ -20,8 +20,10 @@ dependencies = [ sanity_check_paths = { 'files': ['bin/%s' % x for x in ['nettle-hash', 'nettle-lfib-stream', 'pkcs1-conv', 'sexp-conv']] + - [('lib/libhogweed.a', 'lib64/libhogweed.a'), ('lib/libhogweed.%s' % SHLIB_EXT, 'lib64/libhogweed.%s' % SHLIB_EXT), - ('lib/libnettle.a', 'lib64/libnettle.a'), ('lib/libnettle.%s' % SHLIB_EXT, 'lib64/libnettle.%s' % SHLIB_EXT)], + [('lib/libhogweed.a', 'lib64/libhogweed.a'), + ('lib/libhogweed.%s' % SHLIB_EXT, 'lib64/libhogweed.%s' % SHLIB_EXT), + ('lib/libnettle.a', 'lib64/libnettle.a'), + ('lib/libnettle.%s' % SHLIB_EXT, 'lib64/libnettle.%s' % SHLIB_EXT)], 'dirs': ['include/nettle'], } diff --git a/easybuild/easyconfigs/n/nettle/nettle-3.2-GCCcore-5.4.0.eb b/easybuild/easyconfigs/n/nettle/nettle-3.2-GCCcore-5.4.0.eb index 295f442406..c818d9c206 100644 --- a/easybuild/easyconfigs/n/nettle/nettle-3.2-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/n/nettle/nettle-3.2-GCCcore-5.4.0.eb @@ -22,8 +22,10 @@ dependencies = [ sanity_check_paths = { 'files': ['bin/%s' % x for x in ['nettle-hash', 'nettle-lfib-stream', 'pkcs1-conv', 'sexp-conv']] + - [('lib/libhogweed.a', 'lib64/libhogweed.a'), ('lib/libhogweed.%s' % SHLIB_EXT, 'lib64/libhogweed.%s' % SHLIB_EXT), - ('lib/libnettle.a', 'lib64/libnettle.a'), ('lib/libnettle.%s' % SHLIB_EXT, 'lib64/libnettle.%s' % SHLIB_EXT)], + [('lib/libhogweed.a', 'lib64/libhogweed.a'), + ('lib/libhogweed.%s' % SHLIB_EXT, 'lib64/libhogweed.%s' % SHLIB_EXT), + ('lib/libnettle.a', 'lib64/libnettle.a'), + ('lib/libnettle.%s' % SHLIB_EXT, 'lib64/libnettle.%s' % SHLIB_EXT)], 'dirs': ['include/nettle'], } diff --git a/easybuild/easyconfigs/n/nettle/nettle-3.2-foss-2016b.eb b/easybuild/easyconfigs/n/nettle/nettle-3.2-foss-2016b.eb index 2f73f07946..9ed2f96361 100644 --- a/easybuild/easyconfigs/n/nettle/nettle-3.2-foss-2016b.eb +++ b/easybuild/easyconfigs/n/nettle/nettle-3.2-foss-2016b.eb @@ -20,8 +20,10 @@ dependencies = [ sanity_check_paths = { 'files': ['bin/%s' % x for x in ['nettle-hash', 'nettle-lfib-stream', 'pkcs1-conv', 'sexp-conv']] + - [('lib/libhogweed.a', 'lib64/libhogweed.a'), ('lib/libhogweed.%s' % SHLIB_EXT, 'lib64/libhogweed.%s' % SHLIB_EXT), - ('lib/libnettle.a', 'lib64/libnettle.a'), ('lib/libnettle.%s' % SHLIB_EXT, 'lib64/libnettle.%s' % SHLIB_EXT)], + [('lib/libhogweed.a', 'lib64/libhogweed.a'), + ('lib/libhogweed.%s' % SHLIB_EXT, 'lib64/libhogweed.%s' % SHLIB_EXT), + ('lib/libnettle.a', 'lib64/libnettle.a'), + ('lib/libnettle.%s' % SHLIB_EXT, 'lib64/libnettle.%s' % SHLIB_EXT)], 'dirs': ['include/nettle'], } diff --git a/easybuild/easyconfigs/n/nettle/nettle-3.2-intel-2016b.eb b/easybuild/easyconfigs/n/nettle/nettle-3.2-intel-2016b.eb index d49da80e3c..9441d6c8c5 100644 --- a/easybuild/easyconfigs/n/nettle/nettle-3.2-intel-2016b.eb +++ b/easybuild/easyconfigs/n/nettle/nettle-3.2-intel-2016b.eb @@ -20,8 +20,10 @@ dependencies = [ sanity_check_paths = { 'files': ['bin/%s' % x for x in ['nettle-hash', 'nettle-lfib-stream', 'pkcs1-conv', 'sexp-conv']] + - [('lib/libhogweed.a', 'lib64/libhogweed.a'), ('lib/libhogweed.%s' % SHLIB_EXT, 'lib64/libhogweed.%s' % SHLIB_EXT), - ('lib/libnettle.a', 'lib64/libnettle.a'), ('lib/libnettle.%s' % SHLIB_EXT, 'lib64/libnettle.%s' % SHLIB_EXT)], + [('lib/libhogweed.a', 'lib64/libhogweed.a'), + ('lib/libhogweed.%s' % SHLIB_EXT, 'lib64/libhogweed.%s' % SHLIB_EXT), + ('lib/libnettle.a', 'lib64/libnettle.a'), + ('lib/libnettle.%s' % SHLIB_EXT, 'lib64/libnettle.%s' % SHLIB_EXT)], 'dirs': ['include/nettle'], } diff --git a/easybuild/easyconfigs/n/nettle/nettle-3.3-intel-2017a.eb b/easybuild/easyconfigs/n/nettle/nettle-3.3-intel-2017a.eb index 9683896ee0..eb6cb21d8f 100644 --- a/easybuild/easyconfigs/n/nettle/nettle-3.3-intel-2017a.eb +++ b/easybuild/easyconfigs/n/nettle/nettle-3.3-intel-2017a.eb @@ -20,8 +20,10 @@ dependencies = [ sanity_check_paths = { 'files': ['bin/%s' % x for x in ['nettle-hash', 'nettle-lfib-stream', 'pkcs1-conv', 'sexp-conv']] + - [('lib/libhogweed.a', 'lib64/libhogweed.a'), ('lib/libhogweed.%s' % SHLIB_EXT, 'lib64/libhogweed.%s' % SHLIB_EXT), - ('lib/libnettle.a', 'lib64/libnettle.a'), ('lib/libnettle.%s' % SHLIB_EXT, 'lib64/libnettle.%s' % SHLIB_EXT)], + [('lib/libhogweed.a', 'lib64/libhogweed.a'), + ('lib/libhogweed.%s' % SHLIB_EXT, 'lib64/libhogweed.%s' % SHLIB_EXT), + ('lib/libnettle.a', 'lib64/libnettle.a'), + ('lib/libnettle.%s' % SHLIB_EXT, 'lib64/libnettle.%s' % SHLIB_EXT)], 'dirs': ['include/nettle'], } diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-4.0.0.2-OpenMPI-2.0.2.eb b/easybuild/easyconfigs/o/ORCA/ORCA-4.0.0.2-OpenMPI-2.0.2.eb index c9312c4044..20a5faa397 100644 --- a/easybuild/easyconfigs/o/ORCA/ORCA-4.0.0.2-OpenMPI-2.0.2.eb +++ b/easybuild/easyconfigs/o/ORCA/ORCA-4.0.0.2-OpenMPI-2.0.2.eb @@ -3,8 +3,8 @@ easyblock = "PackedBinary" name = "ORCA" version = '4.0.0.2' -openmpiversion = '2.0.2' -versionsuffix = '-OpenMPI-%s' % openmpiversion +ompi_ver = '2.0.2' +versionsuffix = '-OpenMPI-%s' % ompi_ver homepage = 'http://cec.mpg.de/forum/' description = """ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum chemistry @@ -16,19 +16,18 @@ description = """ORCA is a flexible, efficient and easy-to-use general purpose t toolchain = {'name': 'dummy', 'version': ''} # Download from https://cec.mpg.de/orcadownload/index.php -sources = ['%%(namelower)s_%s_linux_x86-64_openmpi%s.tbz' % (version.replace('.', '_'), openmpiversion.replace('.', ''))] +sources = ['%%(namelower)s_%s_linux_x86-64_openmpi%s.tbz' % (version.replace('.', '_'), ompi_ver.replace('.', ''))] checksums = ['a5b8ecdd3d004af4bc8190c986f34e11'] -dependencies = [('OpenMPI', openmpiversion, '-GCC-6.3.0-2.27')] +dependencies = [('OpenMPI', ompi_ver, '-GCC-6.3.0-2.27')] sanity_check_paths = { 'files': ['orca_%s%s' % (x, y) for x in ['anoint', 'casscf', 'cis', 'cleanup', 'cpscf', 'eprnmr', 'gtoint', 'mdci', 'mp2', 'mrci', 'pc', - 'rocis', 'scf', 'scfgrad', 'soc'] - for y in ["", "_mpi"]] + + 'rocis', 'scf', 'scfgrad', 'soc'] for y in ['', '_mpi']] + ['orca_%s' % x for x in ['2mkl', 'asa', 'chelpg', 'ciprep', 'eca', 'ecplib', - 'euler', 'fci', 'fitpes', 'gstep', 'loc', 'mapspc', + 'euler', 'fci', 'fitpes', 'gstep', 'loc', 'mapspc', 'md', 'mergefrag', 'ndoint', 'numfreq', 'plot', 'pltvib', 'pop', 'rel', 'vib', 'vpot']] + ['orca'], diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.3.2-foss-2017a.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.3.2-foss-2017a.eb index 3f1b8657b8..009425ac2b 100644 --- a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.3.2-foss-2017a.eb +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.3.2-foss-2017a.eb @@ -22,4 +22,3 @@ sanity_check_paths = { } moduleclass = 'perf' - diff --git a/easybuild/easyconfigs/o/OTF2/OTF2-2.0-foss-2017a.eb b/easybuild/easyconfigs/o/OTF2/OTF2-2.0-foss-2017a.eb index c2ecdc414e..d4318573b4 100644 --- a/easybuild/easyconfigs/o/OTF2/OTF2-2.0-foss-2017a.eb +++ b/easybuild/easyconfigs/o/OTF2/OTF2-2.0-foss-2017a.eb @@ -3,7 +3,7 @@ # Copyright:: Copyright 2013-2016 Juelich Supercomputing Centre, Germany # Authors:: Bernd Mohr # Markus Geimer -## License:: 3-clause BSD +# License:: 3-clause BSD # # This work is based on experiences from the UNITE project # http://apps.fz-juelich.de/unite/ @@ -38,4 +38,3 @@ sanity_check_paths = { } moduleclass = 'perf' - diff --git a/easybuild/easyconfigs/o/Octopus/Octopus-5.0.0-intel-2015b-mpi.eb b/easybuild/easyconfigs/o/Octopus/Octopus-5.0.0-intel-2015b-mpi.eb index 26fbd9394a..88870a022f 100644 --- a/easybuild/easyconfigs/o/Octopus/Octopus-5.0.0-intel-2015b-mpi.eb +++ b/easybuild/easyconfigs/o/Octopus/Octopus-5.0.0-intel-2015b-mpi.eb @@ -41,10 +41,10 @@ configopts += '--with-netcdf-prefix=$EBROOTNETCDFMINFORTRAN ' configopts += '--with-etsf-io-prefix=$EBROOTETSF_IO ' configopts += '--with-pfft-prefix=$EBROOTPFFT --with-mpifftw-prefix=$EBROOTFFTW ' -runtest = 'MPIEXEC=`which mpirun` check' +runtest = 'MPIEXEC=`which mpirun` check' sanity_check_paths = { - 'files': ["bin/octopus_mpi"], + 'files': ["bin/octopus_mpi"], 'dirs': [] } diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-3.0.0-foss-2016a.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-3.0.0-foss-2016a.eb index 7985e4b267..b17352b6a7 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-3.0.0-foss-2016a.eb +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-3.0.0-foss-2016a.eb @@ -21,7 +21,7 @@ patches = [ ('ThirdParty-%(version)s_cleanup.patch', ".."), # patch should not be applied in OpenFOAM subdir ] -dependencies = [ +dependencies = [ ('libreadline', '6.3'), # OpenFOAM requires 64 bit METIS using 32 bit indexes (array indexes) ('METIS', '5.1.0', '-32bitIDX'), diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.2-GCC-6.3.0-2.27-opa.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.2-GCC-6.3.0-2.27-opa.eb index 3413573e74..3736ce11cc 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.2-GCC-6.3.0-2.27-opa.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.2-GCC-6.3.0-2.27-opa.eb @@ -2,7 +2,7 @@ easyblock = 'ConfigureMake' name = 'OpenMPI' version = '2.0.2' -versionsuffix= '-opa' +versionsuffix = '-opa' homepage = 'http://www.open-mpi.org/' description = """The Open MPI Project is an open source MPI-2 implementation.""" @@ -33,5 +33,3 @@ sanity_check_paths = { } moduleclass = 'mpi' - - diff --git a/easybuild/easyconfigs/p/PEAR/PEAR-0.9.6-goolf-1.4.10.eb b/easybuild/easyconfigs/p/PEAR/PEAR-0.9.6-goolf-1.4.10.eb index 5ee2eb89d1..1c4f9ab85d 100644 --- a/easybuild/easyconfigs/p/PEAR/PEAR-0.9.6-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/PEAR/PEAR-0.9.6-goolf-1.4.10.eb @@ -18,7 +18,7 @@ source_urls = ['http://sco.h-its.org/exelixis/web/software/pear/files/'] sources = ['%(namelower)s-%(version)s-src.tar.gz'] dependencies = [ - ('zlib', '1.2.8'), + ('zlib', '1.2.8'), ('bzip2', '1.0.6'), ] diff --git a/easybuild/easyconfigs/p/PEAR/PEAR-0.9.8-foss-2016b.eb b/easybuild/easyconfigs/p/PEAR/PEAR-0.9.8-foss-2016b.eb index 63d0944c28..37c50aa1df 100644 --- a/easybuild/easyconfigs/p/PEAR/PEAR-0.9.8-foss-2016b.eb +++ b/easybuild/easyconfigs/p/PEAR/PEAR-0.9.8-foss-2016b.eb @@ -17,7 +17,7 @@ sources = ['%(namelower)s-%(version)s.tar.gz'] checksums = ['1ab079a2cea61aee816012966b7ccacd'] dependencies = [ - ('zlib', '1.2.8'), + ('zlib', '1.2.8'), ('bzip2', '1.0.6'), ] diff --git a/easybuild/easyconfigs/p/PEAR/PEAR-0.9.8-intel-2016b.eb b/easybuild/easyconfigs/p/PEAR/PEAR-0.9.8-intel-2016b.eb index 33e09a2ad6..fef4a83c9e 100644 --- a/easybuild/easyconfigs/p/PEAR/PEAR-0.9.8-intel-2016b.eb +++ b/easybuild/easyconfigs/p/PEAR/PEAR-0.9.8-intel-2016b.eb @@ -17,7 +17,7 @@ sources = ['%(namelower)s-%(version)s.tar.gz'] checksums = ['1ab079a2cea61aee816012966b7ccacd'] dependencies = [ - ('zlib', '1.2.8'), + ('zlib', '1.2.8'), ('bzip2', '1.0.6'), ] diff --git a/easybuild/easyconfigs/p/PETSc/PETSc-3.7.5-intel-2016b-downloaded-deps.eb b/easybuild/easyconfigs/p/PETSc/PETSc-3.7.5-intel-2016b-downloaded-deps.eb index 87e4b65750..44a7eca4df 100644 --- a/easybuild/easyconfigs/p/PETSc/PETSc-3.7.5-intel-2016b-downloaded-deps.eb +++ b/easybuild/easyconfigs/p/PETSc/PETSc-3.7.5-intel-2016b-downloaded-deps.eb @@ -14,7 +14,7 @@ sources = [SOURCELOWER_TAR_GZ] # (build) dependencies provided through EasyBuild builddependencies = [('CMake', '3.5.2')] -dependencies = [('HDF5','1.8.18')] +dependencies = [('HDF5', '1.8.18')] # external packages that are downloaded with --download-=1 and --download--static=1 download_deps_static = ['hypre', 'metis', 'ml', 'mumps', 'parmetis', 'prometheus', 'ptscotch', 'suitesparse', diff --git a/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-foss-2015b-Perl-5.20.3.eb b/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-foss-2015b-Perl-5.20.3.eb index 261f83dd09..0f000df55c 100644 --- a/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-foss-2015b-Perl-5.20.3.eb +++ b/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-foss-2015b-Perl-5.20.3.eb @@ -108,7 +108,7 @@ modextrapaths = { postinstallcmds = [ "sed -i -e 's|/usr/bin/perl|/usr/bin/env\ perl|' %(installdir)s/*.pl", # fix shebang line "chmod +x %(installdir)s/*.pl" # add execution permission -] +] sanity_check_paths = { 'files': ['prinseq-lite.pl', 'prinseq-graphs.pl', 'prinseq-graphs-noPCA.pl'], diff --git a/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-goolf-1.4.10-Perl-5.16.3.eb b/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-goolf-1.4.10-Perl-5.16.3.eb index f2db549906..8633986686 100644 --- a/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-goolf-1.4.10-Perl-5.16.3.eb +++ b/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-goolf-1.4.10-Perl-5.16.3.eb @@ -106,7 +106,7 @@ modextrapaths = { postinstallcmds = [ "sed -i -e 's|/usr/bin/perl|/usr/bin/env\ perl|' %(installdir)s/*.pl", # fix shebang line "chmod +x %(installdir)s/*.pl" # add execution permission -] +] sanity_check_paths = { 'files': ['prinseq-lite.pl', 'prinseq-graphs.pl', 'prinseq-graphs-noPCA.pl'], diff --git a/easybuild/easyconfigs/p/PROJ/PROJ-4.8.0-foss-2015b.eb b/easybuild/easyconfigs/p/PROJ/PROJ-4.8.0-foss-2015b.eb index 8e0db7e9a1..30f8eb2395 100644 --- a/easybuild/easyconfigs/p/PROJ/PROJ-4.8.0-foss-2015b.eb +++ b/easybuild/easyconfigs/p/PROJ/PROJ-4.8.0-foss-2015b.eb @@ -21,7 +21,7 @@ source_urls = ['http://download.osgeo.org/proj/'] sources = [SOURCELOWER_TAR_GZ] sanity_check_paths = { - 'files': ['bin/cs2cs', 'bin/geod', 'bin/invgeod', 'bin/invproj', + 'files': ['bin/cs2cs', 'bin/geod', 'bin/invgeod', 'bin/invproj', 'bin/nad2bin', 'bin/proj'], 'dirs': [], } diff --git a/easybuild/easyconfigs/p/PROJ/PROJ-4.9.1-foss-2015a.eb b/easybuild/easyconfigs/p/PROJ/PROJ-4.9.1-foss-2015a.eb index ce218bd9f2..4c530e2669 100644 --- a/easybuild/easyconfigs/p/PROJ/PROJ-4.9.1-foss-2015a.eb +++ b/easybuild/easyconfigs/p/PROJ/PROJ-4.9.1-foss-2015a.eb @@ -22,7 +22,7 @@ source_urls = ['http://download.osgeo.org/proj/'] sources = [SOURCELOWER_TAR_GZ] sanity_check_paths = { - 'files': ['bin/cs2cs', 'bin/geod', 'bin/invgeod', 'bin/invproj', + 'files': ['bin/cs2cs', 'bin/geod', 'bin/invgeod', 'bin/invproj', 'bin/nad2bin', 'bin/proj'], 'dirs': [], } diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.22.0-foss-2015a-mt.eb b/easybuild/easyconfigs/p/Perl/Perl-5.22.0-foss-2015a-mt.eb index 3fb8ef382e..7848df036c 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.22.0-foss-2015a-mt.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.22.0-foss-2015a-mt.eb @@ -21,7 +21,7 @@ sources = [SOURCELOWER_TAR_GZ] maxparallel = 1 -#runtest = 'test' +# runtest = 'test' exts_list = [ ('Module::Build', '0.4210', { # std module but recent BioPerl needs a recent version for some reason @@ -260,7 +260,7 @@ exts_list = [ ('Data::Types', '0.09', { 'source_tmpl': 'Data-Types-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DW/DWHEELER/'], - }), + }), ('Exporter::Tiny', '0.042', { 'source_tmpl': 'Exporter-Tiny-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/T/TO/TOBYINK/'], diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.22.0-foss-2015a.eb b/easybuild/easyconfigs/p/Perl/Perl-5.22.0-foss-2015a.eb index 519a5ec0ca..a2edfbd0bd 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.22.0-foss-2015a.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.22.0-foss-2015a.eb @@ -257,7 +257,7 @@ exts_list = [ ('Data::Types', '0.09', { 'source_tmpl': 'Data-Types-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DW/DWHEELER/'], - }), + }), ('Exporter::Tiny', '0.042', { 'source_tmpl': 'Exporter-Tiny-%(version)s.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/T/TO/TOBYINK/'], diff --git a/easybuild/easyconfigs/p/Platanus/Platanus-1.2.4-foss-2017a.eb b/easybuild/easyconfigs/p/Platanus/Platanus-1.2.4-foss-2017a.eb index 47debc3391..b4c1e2fdf5 100644 --- a/easybuild/easyconfigs/p/Platanus/Platanus-1.2.4-foss-2017a.eb +++ b/easybuild/easyconfigs/p/Platanus/Platanus-1.2.4-foss-2017a.eb @@ -1,7 +1,7 @@ easyblock = 'MakeCp' name = 'Platanus' -version = '1.2.4' +version = '1.2.4' homepage = 'http://platanus.bio.titech.ac.jp/' description = """PLATform for Assembling NUcleotide Sequences""" @@ -14,7 +14,7 @@ buildopts = 'CXXFLAGS="$CXXFLAGS -Dnullptr=0 -lm -fpermissive"' source_urls = ['http://platanus.bio.titech.ac.jp/?ddownload=150'] sources = ['%(name)s_v%(version)s.tar.gz'] -files_to_copy = [(["platanus"],'bin'), "README", "LICENSE"] +files_to_copy = [(["platanus"], 'bin'), "README", "LICENSE"] sanity_check_paths = { 'files': ["bin/platanus"], diff --git a/easybuild/easyconfigs/p/Pysam/Pysam-0.9.0-goolf-1.7.20-Python-2.7.11.eb b/easybuild/easyconfigs/p/Pysam/Pysam-0.9.0-goolf-1.7.20-Python-2.7.11.eb index f0889a65b2..160f3b3a15 100644 --- a/easybuild/easyconfigs/p/Pysam/Pysam-0.9.0-goolf-1.7.20-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/Pysam/Pysam-0.9.0-goolf-1.7.20-Python-2.7.11.eb @@ -20,8 +20,8 @@ parallel = 1 dependencies = [ ('Python', '2.7.11'), ('ncurses', '5.9'), - ('zlib', '1.2.8'), - ('cURL', '7.44.0'), + ('zlib', '1.2.8'), + ('cURL', '7.44.0'), ] # this is a bundle of Python packages diff --git a/easybuild/easyconfigs/p/Pysam/Pysam-0.9.1.4-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/Pysam/Pysam-0.9.1.4-foss-2016b-Python-2.7.12.eb index 3deabf6808..e283bd562a 100644 --- a/easybuild/easyconfigs/p/Pysam/Pysam-0.9.1.4-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/p/Pysam/Pysam-0.9.1.4-foss-2016b-Python-2.7.12.eb @@ -23,8 +23,8 @@ parallel = 1 dependencies = [ ('Python', '2.7.12'), ('ncurses', '6.0'), - ('zlib', '1.2.8'), - ('cURL', '7.49.1'), + ('zlib', '1.2.8'), + ('cURL', '7.49.1'), ] # this is a bundle of Python packages diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2015.11.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2015.11.eb index 8a60745ce6..e436c82dbe 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2015.11.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2015.11.eb @@ -27,7 +27,7 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '5.9'), ('SQLite', '3.9.2'), - ('Tk', '8.6.4', '-no-X11'), # this requires a full X11 stack + ('Tk', '8.6.4', '-no-X11'), # this requires a full X11 stack ('GMP', '6.1.0'), ] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2016.03.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2016.03.eb index f9d52e68ec..acbb85722b 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2016.03.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2016.03.eb @@ -27,7 +27,7 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '6.0'), ('SQLite', '3.9.2'), - ('Tk', '8.6.4', '-no-X11'), # this requires a full X11 stack + ('Tk', '8.6.4', '-no-X11'), # this requires a full X11 stack ('GMP', '6.1.0'), ] diff --git a/easybuild/easyconfigs/p/pbbam/pbbam-20170508-intel-2017a.eb b/easybuild/easyconfigs/p/pbbam/pbbam-20170508-intel-2017a.eb index 5e218a3225..cfbcaf72eb 100644 --- a/easybuild/easyconfigs/p/pbbam/pbbam-20170508-intel-2017a.eb +++ b/easybuild/easyconfigs/p/pbbam/pbbam-20170508-intel-2017a.eb @@ -16,7 +16,7 @@ source_urls = [ 'https://github.com/google/googletest/archive/', ] sources = [ - ('%s.tar.gz' % commit, "tar xfvz %s --strip-components=1"), # pbbam + ('%s.tar.gz' % commit, "tar xfvz %s --strip-components=1"), # pbbam 'release-%s.tar.gz' % gtest_ver, # googletest ] diff --git a/easybuild/easyconfigs/p/pigz/pigz-2.3.1-goolf-1.4.10.eb b/easybuild/easyconfigs/p/pigz/pigz-2.3.1-goolf-1.4.10.eb index b6ccc91bd2..9f34b89624 100644 --- a/easybuild/easyconfigs/p/pigz/pigz-2.3.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/pigz/pigz-2.3.1-goolf-1.4.10.eb @@ -18,7 +18,7 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} source_urls = ['https://github.com/madler/pigz/archive/'] sources = ['v%(version)s.tar.gz'] -checksums = ['3a41409da23ff093b61e414d602c5650'] +checksums = ['3a41409da23ff093b61e414d602c5650'] # README recommends zlib 1.2.6 or higher dependencies = [('zlib', '1.2.8')] diff --git a/easybuild/easyconfigs/r/R/R-3.2.3-foss-2015b.eb b/easybuild/easyconfigs/r/R/R-3.2.3-foss-2015b.eb index 95846046fc..193456e409 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.3-foss-2015b.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.3-foss-2015b.eb @@ -166,7 +166,7 @@ exts_list = [ ('mice', '2.25', ext_options), ('urca', '1.2-8', ext_options), ('fracdiff', '1.4-2', ext_options), - ('logistf', '1.21', ext_options), + ('logistf', '1.21', ext_options), ('akima', '0.5-12', ext_options), ('bitops', '1.0-6', ext_options), ('boot', '1.3-17', ext_options), diff --git a/easybuild/easyconfigs/r/R/R-3.2.3-foss-2016a.eb b/easybuild/easyconfigs/r/R/R-3.2.3-foss-2016a.eb index 1389b272dd..48a36233ea 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.3-foss-2016a.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.3-foss-2016a.eb @@ -166,7 +166,7 @@ exts_list = [ ('mice', '2.25', ext_options), ('urca', '1.2-8', ext_options), ('fracdiff', '1.4-2', ext_options), - ('logistf', '1.21', ext_options), + ('logistf', '1.21', ext_options), ('akima', '0.5-12', ext_options), ('bitops', '1.0-6', ext_options), ('boot', '1.3-17', ext_options), diff --git a/easybuild/easyconfigs/r/R/R-3.2.3-foss-2016b.eb b/easybuild/easyconfigs/r/R/R-3.2.3-foss-2016b.eb index 0acfcbd0b3..c866f9a169 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.3-foss-2016b.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.3-foss-2016b.eb @@ -166,7 +166,7 @@ exts_list = [ ('mice', '2.25', ext_options), ('urca', '1.2-8', ext_options), ('fracdiff', '1.4-2', ext_options), - ('logistf', '1.21', ext_options), + ('logistf', '1.21', ext_options), ('akima', '0.5-12', ext_options), ('bitops', '1.0-6', ext_options), ('boot', '1.3-17', ext_options), diff --git a/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a-libX11-1.6.3.eb b/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a-libX11-1.6.3.eb index 39a19900bb..becdf1c504 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a-libX11-1.6.3.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a-libX11-1.6.3.eb @@ -176,7 +176,7 @@ exts_list = [ ('mice', '2.25', ext_options), ('urca', '1.2-8', ext_options), ('fracdiff', '1.4-2', ext_options), - ('logistf', '1.21', ext_options), + ('logistf', '1.21', ext_options), ('akima', '0.5-12', ext_options), ('bitops', '1.0-6', ext_options), ('boot', '1.3-17', ext_options), diff --git a/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a.eb b/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a.eb index ad907eaa04..470ef9623d 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a.eb @@ -166,7 +166,7 @@ exts_list = [ ('mice', '2.25', ext_options), ('urca', '1.2-8', ext_options), ('fracdiff', '1.4-2', ext_options), - ('logistf', '1.21', ext_options), + ('logistf', '1.21', ext_options), ('akima', '0.5-12', ext_options), ('bitops', '1.0-6', ext_options), ('boot', '1.3-17', ext_options), diff --git a/easybuild/easyconfigs/r/R/R-3.3.3-foss-2016b-X11-20160819.eb b/easybuild/easyconfigs/r/R/R-3.3.3-foss-2016b-X11-20160819.eb index 17436647a4..512b0289b6 100644 --- a/easybuild/easyconfigs/r/R/R-3.3.3-foss-2016b-X11-20160819.eb +++ b/easybuild/easyconfigs/r/R/R-3.3.3-foss-2016b-X11-20160819.eb @@ -13,7 +13,7 @@ source_urls = ['http://cran.us.r-project.org/src/base/R-%(version_major)s'] preconfigopts = 'BLAS_LIBS="$LIBBLAS" LAPACK_LIBS="$LIBLAPACK"' configopts = "--with-lapack --with-blas --with-pic --enable-threads --with-x=yes --enable-R-shlib" -#Actually use Tcl/Tk +# actually use Tcl/Tk configopts += ' --with-tcl-config=$EBROOTTCL/lib/tclConfig.sh --with-tk-config=$EBROOTTK/lib/tkConfig.sh ' # Enable graphics capabilities for plotting. configopts += " --with-cairo --with-libpng --with-jpeglib --with-libtiff" @@ -507,4 +507,3 @@ exts_list = [ ] moduleclass = 'lang' - diff --git a/easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170314.eb b/easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170314.eb index dd6b13d0c2..262dd0c121 100644 --- a/easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170314.eb +++ b/easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170314.eb @@ -13,7 +13,7 @@ source_urls = ['http://cran.us.r-project.org/src/base/R-%(version_major)s'] preconfigopts = 'BLAS_LIBS="$LIBBLAS" LAPACK_LIBS="$LIBLAPACK"' configopts = "--with-lapack --with-blas --with-pic --enable-threads --with-x=yes --enable-R-shlib" -#Actually use Tcl/Tk +# actually use Tcl/Tk configopts += ' --with-tcl-config=$EBROOTTCL/lib/tclConfig.sh --with-tk-config=$EBROOTTK/lib/tkConfig.sh ' # Enable graphics capabilities for plotting. configopts += " --with-cairo --with-libpng --with-jpeglib --with-libtiff" @@ -508,4 +508,3 @@ exts_list = [ ] moduleclass = 'lang' - diff --git a/easybuild/easyconfigs/r/RELION/RELION-1.4-intel-2016b-single.eb b/easybuild/easyconfigs/r/RELION/RELION-1.4-intel-2016b-single.eb index add5ffc72c..2998c29cfd 100644 --- a/easybuild/easyconfigs/r/RELION/RELION-1.4-intel-2016b-single.eb +++ b/easybuild/easyconfigs/r/RELION/RELION-1.4-intel-2016b-single.eb @@ -24,7 +24,7 @@ dependencies = [ ] # RELION expects FLTK to be in external/fltk-1.3.0 and we have to add fltk libraries -configopts = '--enable-mpi --enable-float ' +configopts = '--enable-mpi --enable-float ' configopts += 'LIBS="-lfltk -lXcursor -lXfixes -lXext -lXft -lfontconfig -lXinerama -lpthread -lX11" ' configopts += '&& ln -s $EBROOTFLTK/include external/fltk-1.3.0 ' # users expect the maingui binary to be called relion diff --git a/easybuild/easyconfigs/r/RSeQC/RSeQC-2.6.4-foss-2016b-Python-2.7.12-R-3.3.1.eb b/easybuild/easyconfigs/r/RSeQC/RSeQC-2.6.4-foss-2016b-Python-2.7.12-R-3.3.1.eb index f122fed527..8df3ba88af 100644 --- a/easybuild/easyconfigs/r/RSeQC/RSeQC-2.6.4-foss-2016b-Python-2.7.12-R-3.3.1.eb +++ b/easybuild/easyconfigs/r/RSeQC/RSeQC-2.6.4-foss-2016b-Python-2.7.12-R-3.3.1.eb @@ -25,7 +25,7 @@ source_urls = [SOURCEFORGE_SOURCE] dependencies = [ ('R', '3.3.1'), ('Python', '2.7.12'), - ('Pysam', '0.9.1.4', basepyversionsuffix), + ('Pysam', '0.9.1.4', basepyversionsuffix), ] runtest = "python setup.py test" diff --git a/easybuild/easyconfigs/r/RepastHPC/RepastHPC-2.2.0-foss-2016a.eb b/easybuild/easyconfigs/r/RepastHPC/RepastHPC-2.2.0-foss-2016a.eb index fc07069bff..1ed10f0d18 100644 --- a/easybuild/easyconfigs/r/RepastHPC/RepastHPC-2.2.0-foss-2016a.eb +++ b/easybuild/easyconfigs/r/RepastHPC/RepastHPC-2.2.0-foss-2016a.eb @@ -23,7 +23,7 @@ dependencies = [ configopts = '--with-boost=$EBROOTBOOST --with-netcdf=$EBROOTNETCDFMINCPLUSPLUS' sanity_check_paths = { - 'files': ['lib/librelogo-%%(version)s.%s' % SHLIB_EXT, 'lib/librepast_hpc-%%(version)s.%s' % SHLIB_EXT ], + 'files': ['lib/librelogo-%%(version)s.%s' % SHLIB_EXT, 'lib/librepast_hpc-%%(version)s.%s' % SHLIB_EXT], 'dirs': ['bin/rumor', 'bin/zombie', 'include', 'lib'], } diff --git a/easybuild/easyconfigs/r/rootpy/rootpy-0.8.0-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/r/rootpy/rootpy-0.8.0-foss-2016a-Python-2.7.11.eb index efecae95e8..21a990b69b 100644 --- a/easybuild/easyconfigs/r/rootpy/rootpy-0.8.0-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/r/rootpy/rootpy-0.8.0-foss-2016a-Python-2.7.11.eb @@ -20,7 +20,7 @@ sources = ['%(version)s.tar.gz'] dependencies = [ ('Python', '2.7.11'), - ('ROOT','v6.08.02','-Python-%(pyver)s'), + ('ROOT', 'v6.08.02', '-Python-%(pyver)s'), ('matplotlib', '1.5.1', versionsuffix + '-freetype-2.6.3') ] diff --git a/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.1-foss-2017a-tools.eb b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.1-foss-2017a-tools.eb index 7e537ec0fb..1c00d4b38b 100644 --- a/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.1-foss-2017a-tools.eb +++ b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.1-foss-2017a-tools.eb @@ -42,4 +42,3 @@ sanity_check_paths = { } moduleclass = 'lib' - diff --git a/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.1-foss-2017a.eb b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.1-foss-2017a.eb index 46e980be5f..8dd41bb2de 100644 --- a/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.1-foss-2017a.eb +++ b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.1-foss-2017a.eb @@ -36,4 +36,3 @@ sanity_check_paths = { } moduleclass = 'lib' - diff --git a/easybuild/easyconfigs/s/SUMATRA/SUMATRA-1.0.20-foss-2016a.eb b/easybuild/easyconfigs/s/SUMATRA/SUMATRA-1.0.20-foss-2016a.eb index 352f9013ea..a8666f197a 100644 --- a/easybuild/easyconfigs/s/SUMATRA/SUMATRA-1.0.20-foss-2016a.eb +++ b/easybuild/easyconfigs/s/SUMATRA/SUMATRA-1.0.20-foss-2016a.eb @@ -15,7 +15,7 @@ toolchain = {'name': 'foss', 'version': '2016a'} source_urls = ['https://git.metabarcoding.org/obitools/sumatra/uploads/251020bbbd6c6595cb9fce6077e29952/'] sources = ['%(namelower)s_v%(version)s.tar.gz'] -prebuildopts = 'make clean &&' +prebuildopts = 'make clean &&' files_to_copy = [(['sumatra'], 'bin'), 'sumatra_user_manual.pdf'] diff --git a/easybuild/easyconfigs/s/Sambamba/Sambamba-0.6.6.eb b/easybuild/easyconfigs/s/Sambamba/Sambamba-0.6.6.eb index c6c18b59b8..8b68d940d5 100644 --- a/easybuild/easyconfigs/s/Sambamba/Sambamba-0.6.6.eb +++ b/easybuild/easyconfigs/s/Sambamba/Sambamba-0.6.6.eb @@ -18,7 +18,7 @@ toolchain = {'name': 'dummy', 'version': ''} source_urls = ['https://github.com/lomereiter/sambamba/releases/download/v%(version)s/'] sources = ['%(namelower)s_v%(version)s_linux.tar.bz2'] -postinstallcmds = ['cd %(installdir)s && ln -s sambamba_v%(version)s sambamba',] +postinstallcmds = ['cd %(installdir)s && ln -s sambamba_v%(version)s sambamba'] sanity_check_paths = { 'files': ['sambamba_v%(version)s', 'sambamba'], diff --git a/easybuild/easyconfigs/s/SeqAn/SeqAn-2.3.2-foss-2016b.eb b/easybuild/easyconfigs/s/SeqAn/SeqAn-2.3.2-foss-2016b.eb index b89f6044b4..d894a7f03a 100644 --- a/easybuild/easyconfigs/s/SeqAn/SeqAn-2.3.2-foss-2016b.eb +++ b/easybuild/easyconfigs/s/SeqAn/SeqAn-2.3.2-foss-2016b.eb @@ -29,8 +29,9 @@ dependencies = [ separate_build_dir = True sanity_check_paths = { - 'files': ["bin/%s" % x for x in ["gustaf_mate_joining", "mason_materializer", "mason_variator", "rabema_prepare_sam", - "seqan_tcoffee", "s4_join", "samcat", "splazers", "yara_mapper"]], + 'files': ["bin/%s" % x for x in ["gustaf_mate_joining", "mason_materializer", "mason_variator", + "rabema_prepare_sam", "seqan_tcoffee", "s4_join", "samcat", "splazers", + "yara_mapper"]], 'dirs': [], } diff --git a/easybuild/easyconfigs/s/Singularity/Singularity-2.2.1-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/s/Singularity/Singularity-2.2.1-GCC-6.3.0-2.27.eb index 8c36b33253..94de58b731 100644 --- a/easybuild/easyconfigs/s/Singularity/Singularity-2.2.1-GCC-6.3.0-2.27.eb +++ b/easybuild/easyconfigs/s/Singularity/Singularity-2.2.1-GCC-6.3.0-2.27.eb @@ -16,7 +16,8 @@ builddependencies = [('Autotools', '20150215')] preconfigopts = './autogen.sh && ' sanity_check_paths = { - 'files': ['bin/run-singularity', 'bin/singularity', 'etc/singularity/singularity.conf', 'libexec/singularity/sexec-suid'], + 'files': ['bin/run-singularity', 'bin/singularity', 'etc/singularity/singularity.conf', + 'libexec/singularity/sexec-suid'], 'dirs': ['etc', 'libexec/singularity'], } diff --git a/easybuild/easyconfigs/s/Stacks/Stacks-1.40-foss-2016a.eb b/easybuild/easyconfigs/s/Stacks/Stacks-1.40-foss-2016a.eb index 197e799318..cdb98a37f5 100644 --- a/easybuild/easyconfigs/s/Stacks/Stacks-1.40-foss-2016a.eb +++ b/easybuild/easyconfigs/s/Stacks/Stacks-1.40-foss-2016a.eb @@ -15,8 +15,8 @@ source_urls = ['http://catchenlab.life.illinois.edu/stacks/source/'] sources = [SOURCELOWER_TAR_GZ] dependencies = [ - ('zlib', '1.2.8'), - ('SAMtools', '1.3.1'), + ('zlib', '1.2.8'), + ('SAMtools', '1.3.1'), ('sparsehash', '2.0.2'), ] diff --git a/easybuild/easyconfigs/s/Stacks/Stacks-1.42-foss-2016a.eb b/easybuild/easyconfigs/s/Stacks/Stacks-1.42-foss-2016a.eb index e042becab7..bb7e9baadc 100644 --- a/easybuild/easyconfigs/s/Stacks/Stacks-1.42-foss-2016a.eb +++ b/easybuild/easyconfigs/s/Stacks/Stacks-1.42-foss-2016a.eb @@ -15,8 +15,8 @@ source_urls = ['http://catchenlab.life.illinois.edu/stacks/source/'] sources = [SOURCELOWER_TAR_GZ] dependencies = [ - ('zlib', '1.2.8'), - ('SAMtools', '1.3.1'), + ('zlib', '1.2.8'), + ('SAMtools', '1.3.1'), ('sparsehash', '2.0.2'), ] diff --git a/easybuild/easyconfigs/s/Stacks/Stacks-1.44-foss-2016a.eb b/easybuild/easyconfigs/s/Stacks/Stacks-1.44-foss-2016a.eb index 1df7d789c0..f99a6a428f 100644 --- a/easybuild/easyconfigs/s/Stacks/Stacks-1.44-foss-2016a.eb +++ b/easybuild/easyconfigs/s/Stacks/Stacks-1.44-foss-2016a.eb @@ -15,8 +15,8 @@ source_urls = ['http://catchenlab.life.illinois.edu/stacks/source/'] sources = [SOURCELOWER_TAR_GZ] dependencies = [ - ('zlib', '1.2.8'), - ('SAMtools', '1.3.1'), + ('zlib', '1.2.8'), + ('SAMtools', '1.3.1'), ('sparsehash', '2.0.2'), ] diff --git a/easybuild/easyconfigs/s/Stacks/Stacks-1.45-foss-2016a.eb b/easybuild/easyconfigs/s/Stacks/Stacks-1.45-foss-2016a.eb index 4f24751d68..116c79b992 100644 --- a/easybuild/easyconfigs/s/Stacks/Stacks-1.45-foss-2016a.eb +++ b/easybuild/easyconfigs/s/Stacks/Stacks-1.45-foss-2016a.eb @@ -15,8 +15,8 @@ source_urls = ['http://catchenlab.life.illinois.edu/stacks/source/'] sources = [SOURCELOWER_TAR_GZ] dependencies = [ - ('zlib', '1.2.8'), - ('SAMtools', '1.3.1'), + ('zlib', '1.2.8'), + ('SAMtools', '1.3.1'), ('sparsehash', '2.0.2'), ] diff --git a/easybuild/easyconfigs/s/Stacks/Stacks-1.46-intel-2017a.eb b/easybuild/easyconfigs/s/Stacks/Stacks-1.46-intel-2017a.eb index 341b4db710..4509b19211 100644 --- a/easybuild/easyconfigs/s/Stacks/Stacks-1.46-intel-2017a.eb +++ b/easybuild/easyconfigs/s/Stacks/Stacks-1.46-intel-2017a.eb @@ -15,8 +15,8 @@ source_urls = ['http://catchenlab.life.illinois.edu/stacks/source/'] sources = [SOURCELOWER_TAR_GZ] dependencies = [ - ('zlib', '1.2.11'), - ('SAMtools', '1.4'), + ('zlib', '1.2.11'), + ('SAMtools', '1.4'), ('sparsehash', '2.0.3'), ] diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.5-foss-2017a-METIS-5.1.0.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.5-foss-2017a-METIS-5.1.0.eb index 4727d14749..e63d1a798f 100644 --- a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.5-foss-2017a-METIS-5.1.0.eb +++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.5-foss-2017a-METIS-5.1.0.eb @@ -17,4 +17,3 @@ dependencies = [('METIS', metis_ver)] maxparallel = 1 moduleclass = 'numlib' - diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1-foss-2017a.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1-foss-2017a.eb index 9365662b36..7be82daa90 100644 --- a/easybuild/easyconfigs/s/Szip/Szip-2.1-foss-2017a.eb +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1-foss-2017a.eb @@ -21,4 +21,3 @@ sanity_check_paths = { } moduleclass = 'tools' - diff --git a/easybuild/easyconfigs/s/samblaster/samblaster-0.1.24-goolf-1.7.20.eb b/easybuild/easyconfigs/s/samblaster/samblaster-0.1.24-goolf-1.7.20.eb index a99c1c0912..5c35b43fcc 100644 --- a/easybuild/easyconfigs/s/samblaster/samblaster-0.1.24-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/s/samblaster/samblaster-0.1.24-goolf-1.7.20.eb @@ -17,10 +17,10 @@ source_urls = ['https://github.com/GregoryFaust/samblaster/archive/'] sources = ['v.%(version)s.tar.gz'] files_to_copy = [ - (['samblaster'], 'bin/'), - 'README.md', - 'SAMBLASTER_Supplemental.pdf', - 'LICENSE.txt', + (['samblaster'], 'bin/'), + 'README.md', + 'SAMBLASTER_Supplemental.pdf', + 'LICENSE.txt', ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/s/segemehl/segemehl-0.2.0-foss-2016b.eb b/easybuild/easyconfigs/s/segemehl/segemehl-0.2.0-foss-2016b.eb index c7d6d5fcae..3f36bab3c9 100644 --- a/easybuild/easyconfigs/s/segemehl/segemehl-0.2.0-foss-2016b.eb +++ b/easybuild/easyconfigs/s/segemehl/segemehl-0.2.0-foss-2016b.eb @@ -17,7 +17,7 @@ description = """ segemehl is a software to map short sequencer reads to referen toolchain = {'name': 'foss', 'version': '2016b'} source_urls = ['http://www.bioinf.uni-leipzig.de/Software/segemehl/'] -sources = ['%s_%s.tar.gz' % (name, version.replace('.','_'))] +sources = ['%s_%s.tar.gz' % (name, version.replace('.', '_'))] checksums = ['fef4db00ed2742a2bf4131eed674bb08'] @@ -31,7 +31,7 @@ dependencies = [ files_to_copy = [(["lack.x", "segemehl.x", "testrealign.x"], "bin")] sanity_check_paths = { - 'files': ["bin/%s" % x for x in ["lack.x" , "segemehl.x", "testrealign.x"]], + 'files': ["bin/%s" % x for x in ["lack.x", "segemehl.x", "testrealign.x"]], 'dirs': [] } diff --git a/easybuild/easyconfigs/s/splitRef/splitRef-0.0.2.eb b/easybuild/easyconfigs/s/splitRef/splitRef-0.0.2.eb index 585ebb9932..88fc3d4707 100644 --- a/easybuild/easyconfigs/s/splitRef/splitRef-0.0.2.eb +++ b/easybuild/easyconfigs/s/splitRef/splitRef-0.0.2.eb @@ -25,7 +25,7 @@ sanity_check_paths = { } # add folder splitRef_V002 to PATH -modextrapaths = { +modextrapaths = { 'PATH': '%s_V%s' % (name, altver) } diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.5.19-foss-2017a.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.5.19-foss-2017a.eb index 0514b4e682..91e78ce928 100644 --- a/easybuild/easyconfigs/t/Tcl/Tcl-8.5.19-foss-2017a.eb +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.5.19-foss-2017a.eb @@ -24,4 +24,3 @@ runtest = 'test' start_dir = 'unix' moduleclass = 'lang' - diff --git a/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.14-goolf-1.4.10-Perl-5.16.3.eb b/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.14-goolf-1.4.10-Perl-5.16.3.eb index c4c82d2f79..1213968867 100644 --- a/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.14-goolf-1.4.10-Perl-5.16.3.eb +++ b/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.14-goolf-1.4.10-Perl-5.16.3.eb @@ -19,15 +19,15 @@ sources = [SOURCELOWER_TAR_GZ] dependencies = [ ('Perl', '5.16.3'), -] +] sanity_check_paths = { - 'files': ["bin/%s" % x for x in ["vcftools", "fill-fs", "vcf-compare", "vcf-contrast", + 'files': ["bin/%s" % x for x in ["vcftools", "fill-fs", "vcf-compare", "vcf-contrast", "vcf-fix-ploidy", "vcf-merge"]], 'dirs': [], } -modextrapaths = { +modextrapaths = { 'PERL5LIB': 'lib/perl5/site_perl/', } diff --git a/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.14-goolf-1.7.20-Perl-5.22.2.eb b/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.14-goolf-1.7.20-Perl-5.22.2.eb index 6a770e5ef1..0a12c2e817 100644 --- a/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.14-goolf-1.7.20-Perl-5.22.2.eb +++ b/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.14-goolf-1.7.20-Perl-5.22.2.eb @@ -19,15 +19,15 @@ sources = [SOURCELOWER_TAR_GZ] dependencies = [ ('Perl', '5.22.2'), -] +] sanity_check_paths = { - 'files': ["bin/%s" % x for x in ["vcftools", "fill-fs", "vcf-compare", "vcf-contrast", + 'files': ["bin/%s" % x for x in ["vcftools", "fill-fs", "vcf-compare", "vcf-contrast", "vcf-fix-ploidy", "vcf-merge"]], 'dirs': [], } -modextrapaths = { +modextrapaths = { 'PERL5LIB': 'lib/perl5/site_perl/', } diff --git a/easybuild/easyconfigs/v/VMD/VMD-1.9.3-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/v/VMD/VMD-1.9.3-intel-2016b-Python-2.7.12.eb index 3e3df4bec4..54be12bcef 100644 --- a/easybuild/easyconfigs/v/VMD/VMD-1.9.3-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/v/VMD/VMD-1.9.3-intel-2016b-Python-2.7.12.eb @@ -10,7 +10,7 @@ homepage = 'http://www.ks.uiuc.edu/Research/vmd' description = """VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.""" -toolchain= {'name': 'intel' , 'version': '2016b'} +toolchain = {'name': 'intel', 'version': '2016b'} # downloading requires registration sources = ['vmd-%(version)s.src.tar.gz'] diff --git a/easybuild/easyconfigs/v/Valgrind/Valgrind-3.11.0-foss-2016a.eb b/easybuild/easyconfigs/v/Valgrind/Valgrind-3.11.0-foss-2016a.eb index 1582b5a179..63ac2b03b0 100644 --- a/easybuild/easyconfigs/v/Valgrind/Valgrind-3.11.0-foss-2016a.eb +++ b/easybuild/easyconfigs/v/Valgrind/Valgrind-3.11.0-foss-2016a.eb @@ -22,6 +22,6 @@ sanity_check_paths = { 'files': ['bin/%s' % x for x in binaries] + ['lib/valgrind/libmpiwrap-amd64-linux.%s' % SHLIB_EXT], 'dirs': [] -} +} moduleclass = 'debugger' diff --git a/easybuild/easyconfigs/w/wkhtmltopdf/wkhtmltopdf-0.12.3-Linux-x86_64.eb b/easybuild/easyconfigs/w/wkhtmltopdf/wkhtmltopdf-0.12.3-Linux-x86_64.eb index daaefceb38..b0bb280f07 100644 --- a/easybuild/easyconfigs/w/wkhtmltopdf/wkhtmltopdf-0.12.3-Linux-x86_64.eb +++ b/easybuild/easyconfigs/w/wkhtmltopdf/wkhtmltopdf-0.12.3-Linux-x86_64.eb @@ -20,11 +20,11 @@ source_urls = ['http://download.gna.org/wkhtmltopdf/%(version_major_minor)s/%(ve sources = ['wkhtmltox-%(version)s_linux-generic-amd64.tar.xz'] osdependencies = [ - ('zlib', 'zlib1g'), - 'fontconfig', - ('freetype', 'libfreetype6'), - ('libX11', 'libx11-6'), - ('libXext', 'libxext6'), + ('zlib', 'zlib1g'), + 'fontconfig', + ('freetype', 'libfreetype6'), + ('libX11', 'libx11-6'), + ('libXext', 'libxext6'), ('libXrender', 'libxrender1') ] diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.3-gimkl-2017a.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.3-gimkl-2017a.eb index 8d7242f13f..cc9e04a571 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.3-gimkl-2017a.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.3-gimkl-2017a.eb @@ -22,7 +22,7 @@ builddependencies = [ ] # may become useful in non-x86 archs -#configopts = ' --disable-assembler ' +# configopts = ' --disable-assembler ' sanity_check_paths = { 'files': ["bin/xz", "bin/lzmainfo"], diff --git a/easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-gimkl-2.11.5.eb b/easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-gimkl-2.11.5.eb index 4bfb1d13fb..099fcba246 100644 --- a/easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-gimkl-2.11.5.eb @@ -14,7 +14,7 @@ sources = [SOURCE_TAR_GZ] source_urls = [XORG_LIB_SOURCE] sanity_check_paths = { - 'files': ['include/X11/Xtrans/%s' % x for x in ['transport.c', 'Xtrans.c', 'Xtrans.h', 'Xtransint.h', + 'files': ['include/X11/Xtrans/%s' % x for x in ['transport.c', 'Xtrans.c', 'Xtrans.h', 'Xtransint.h', 'Xtranslcl.c', 'Xtranssock.c', 'Xtransutil.c']], 'dirs': [], } diff --git a/easybuild/easyconfigs/y/Yade/Yade-1.20.0-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/y/Yade/Yade-1.20.0-foss-2016a-Python-2.7.11.eb index eeebc684bc..3fd2d83e18 100644 --- a/easybuild/easyconfigs/y/Yade/Yade-1.20.0-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/y/Yade/Yade-1.20.0-foss-2016a-Python-2.7.11.eb @@ -31,7 +31,7 @@ dependencies = [ ('PyGTS', '0.3.1', versionsuffix), ('Python', '2.7.11'), ('Qt', '4.8.7', '-GLib-2.48.0'), - ('SQLite', '3.9.2'), + ('SQLite', '3.9.2'), ('VTK', '6.3.0', versionsuffix), ('zlib', '1.2.8'), ('bzip2', '1.0.6'), diff --git a/easybuild/easyconfigs/y/Yade/Yade-1.20.0-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/y/Yade/Yade-1.20.0-intel-2016a-Python-2.7.11.eb index 4610fe64fd..91273df8f9 100644 --- a/easybuild/easyconfigs/y/Yade/Yade-1.20.0-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/y/Yade/Yade-1.20.0-intel-2016a-Python-2.7.11.eb @@ -31,7 +31,7 @@ dependencies = [ ('PyGTS', '0.3.1', versionsuffix), ('Python', '2.7.11'), ('Qt', '4.8.7', '-GLib-2.48.0'), - ('SQLite', '3.9.2'), + ('SQLite', '3.9.2'), ('VTK', '6.3.0', versionsuffix), ('zlib', '1.2.8'), ('bzip2', '1.0.6'), diff --git a/easybuild/easyconfigs/y/Yambo/Yambo-4.0.2-rev.90-intel-2015b-QuantumESPRESSO-5.2.1.eb b/easybuild/easyconfigs/y/Yambo/Yambo-4.0.2-rev.90-intel-2015b-QuantumESPRESSO-5.2.1.eb index 0c99f457cb..8696368a68 100644 --- a/easybuild/easyconfigs/y/Yambo/Yambo-4.0.2-rev.90-intel-2015b-QuantumESPRESSO-5.2.1.eb +++ b/easybuild/easyconfigs/y/Yambo/Yambo-4.0.2-rev.90-intel-2015b-QuantumESPRESSO-5.2.1.eb @@ -48,6 +48,6 @@ sanity_check_paths = { # is twice in the PATH. Withouth removing the QuantumESPRESSO one, this version of Yambo would be used, # because it is earlier in the PATH modtclfooter = "remove-path PATH $::env(EBROOTQUANTUMESPRESSO)/espresso-%s/YAMBO/bin" % qever -modluafooter = 'remove_path("PATH", os.getenv("EBROOTQUANTUMESPRESSO") .. "/espresso-%s/YAMBO/bin")' % qever +modluafooter = 'remove_path("PATH", os.getenv("EBROOTQUANTUMESPRESSO") .. "/espresso-%s/YAMBO/bin")' % qever moduleclass = 'phys' diff --git a/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-goolf-1.7.20.eb b/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-goolf-1.7.20.eb index 09279b532a..f3f0a1a915 100644 --- a/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-goolf-1.7.20.eb @@ -16,4 +16,4 @@ sanity_check_paths = { 'dirs': [], } -moduleclass = 'lang' +moduleclass = 'lang' -- GitLab From 9bd59ff89be6be1afc70ecb2dedab11c139fd7e0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 21 Jun 2017 21:08:06 +0200 Subject: [PATCH 0987/1603] avoid use of import in ANSYS & MATLAB easyconfigs --- easybuild/easyconfigs/a/ANSYS/ANSYS-15.0.eb | 6 +----- easybuild/easyconfigs/m/MATLAB/MATLAB-2012b.eb | 5 ----- easybuild/easyconfigs/m/MATLAB/MATLAB-2015a.eb | 5 ----- easybuild/easyconfigs/m/MATLAB/MATLAB-2016a.eb | 5 ----- easybuild/easyconfigs/m/MATLAB/MATLAB-2017a.eb | 5 ----- 5 files changed, 1 insertion(+), 25 deletions(-) diff --git a/easybuild/easyconfigs/a/ANSYS/ANSYS-15.0.eb b/easybuild/easyconfigs/a/ANSYS/ANSYS-15.0.eb index 673a19b69d..944ad05e35 100644 --- a/easybuild/easyconfigs/a/ANSYS/ANSYS-15.0.eb +++ b/easybuild/easyconfigs/a/ANSYS/ANSYS-15.0.eb @@ -10,10 +10,6 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} # create a zip file from the 3 install iso files. # make sure all files of the iso's are in the same directory. -sources = ['ANSYS-15.0.zip'] - -import os -license_server = os.getenv('EB_ANSYS_LICENSE_SERVER', 'license.example.com') -license_server_port = os.getenv('EB_ANSYS_LICENSE_SERVER_PORT', '2325:1055') +sources = ['ANSYS-%(version)s.zip'] moduleclass = 'tools' diff --git a/easybuild/easyconfigs/m/MATLAB/MATLAB-2012b.eb b/easybuild/easyconfigs/m/MATLAB/MATLAB-2012b.eb index b0b8036c47..2d79a877de 100644 --- a/easybuild/easyconfigs/m/MATLAB/MATLAB-2012b.eb +++ b/easybuild/easyconfigs/m/MATLAB/MATLAB-2012b.eb @@ -12,9 +12,4 @@ sources = [SOURCELOWER_TAR_GZ] dependencies = [('Java', '1.7.0_10')] -import os -license_server = os.getenv('EB_MATLAB_LICENSE_SERVER', 'license.example.com') -license_server_port = os.getenv('EB_MATLAB_LICENSE_SERVER_PORT', '00000') -key = os.getenv('EB_MATLAB_KEY', '00000-00000-00000-00000-00000-00000-00000-00000-00000-00000') - moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/MATLAB/MATLAB-2015a.eb b/easybuild/easyconfigs/m/MATLAB/MATLAB-2015a.eb index 65e39e1872..068032d310 100644 --- a/easybuild/easyconfigs/m/MATLAB/MATLAB-2015a.eb +++ b/easybuild/easyconfigs/m/MATLAB/MATLAB-2015a.eb @@ -12,9 +12,4 @@ sources = [SOURCELOWER_TAR_GZ] dependencies = [('Java', '1.8.0_45')] -import os -license_server = os.getenv('EB_MATLAB_LICENSE_SERVER', 'license.example.com') -license_server_port = os.getenv('EB_MATLAB_LICENSE_SERVER_PORT', '00000') -key = os.getenv('EB_MATLAB_KEY', '00000-00000-00000-00000-00000-00000-00000-00000-00000-00000') - moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/MATLAB/MATLAB-2016a.eb b/easybuild/easyconfigs/m/MATLAB/MATLAB-2016a.eb index e0113113d0..02024eedff 100644 --- a/easybuild/easyconfigs/m/MATLAB/MATLAB-2016a.eb +++ b/easybuild/easyconfigs/m/MATLAB/MATLAB-2016a.eb @@ -12,9 +12,4 @@ sources = [SOURCELOWER_TAR_GZ] dependencies = [('Java', '1.8.0_92')] -import os -license_server = os.getenv('EB_MATLAB_LICENSE_SERVER', 'license.example.com') -license_server_port = os.getenv('EB_MATLAB_LICENSE_SERVER_PORT', '00000') -key = os.getenv('EB_MATLAB_KEY', '00000-00000-00000-00000-00000-00000-00000-00000-00000-00000') - moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/MATLAB/MATLAB-2017a.eb b/easybuild/easyconfigs/m/MATLAB/MATLAB-2017a.eb index 04d37d4f1e..5aa71b404f 100644 --- a/easybuild/easyconfigs/m/MATLAB/MATLAB-2017a.eb +++ b/easybuild/easyconfigs/m/MATLAB/MATLAB-2017a.eb @@ -14,9 +14,4 @@ sources = [SOURCELOWER_TAR_GZ] dependencies = [('Java', '1.8.0_121')] -import os -license_server = os.getenv('EB_MATLAB_LICENSE_SERVER', 'license.example.com') -license_server_port = os.getenv('EB_MATLAB_LICENSE_SERVER_PORT', '00000') -key = os.getenv('EB_MATLAB_KEY', '00000-00000-00000-00000-00000-00000-00000-00000-00000-00000') - moduleclass = 'math' -- GitLab From 941823b7588db56f33fa954e623f0171cbb863d0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 21 Jun 2017 21:27:48 +0200 Subject: [PATCH 0988/1603] set $OMP_NUM_THREADS during CP2K test step via dedicated easyconfig parameter --- .../easyconfigs/c/CP2K/CP2K-20111205-goolf-1.4.10-psmp.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-20111205-goolf-1.4.10-psmp.eb b/easybuild/easyconfigs/c/CP2K/CP2K-20111205-goolf-1.4.10-psmp.eb index df760b1c15..a4e80549b5 100644 --- a/easybuild/easyconfigs/c/CP2K/CP2K-20111205-goolf-1.4.10-psmp.eb +++ b/easybuild/easyconfigs/c/CP2K/CP2K-20111205-goolf-1.4.10-psmp.eb @@ -37,7 +37,6 @@ maxtasks = 1 # need to set OMP_NUM_THREADS to 1, to avoid failed tests during regression test # without this, 32 tests (out of 2196) fail -import os -os.environ['OMP_NUM_THREADS'] = '1' +omp_num_threads = '1' moduleclass = 'chem' -- GitLab From afe72ba5206fdc3b6d16f8a926c039a11c0222ee Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 21 Jun 2017 21:36:55 +0200 Subject: [PATCH 0989/1603] avoid use of 'import' in BFAST easyconfigs, just strip of 'a' from version --- easybuild/easyconfigs/b/BFAST/BFAST-0.7.0a-goolf-1.4.10.eb | 5 +---- easybuild/easyconfigs/b/BFAST/BFAST-0.7.0a-goolf-1.7.20.eb | 5 +---- easybuild/easyconfigs/b/BFAST/BFAST-0.7.0a-ictce-5.3.0.eb | 5 +---- 3 files changed, 3 insertions(+), 12 deletions(-) diff --git a/easybuild/easyconfigs/b/BFAST/BFAST-0.7.0a-goolf-1.4.10.eb b/easybuild/easyconfigs/b/BFAST/BFAST-0.7.0a-goolf-1.4.10.eb index 372422bd73..048346809a 100644 --- a/easybuild/easyconfigs/b/BFAST/BFAST-0.7.0a-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/BFAST/BFAST-0.7.0a-goolf-1.4.10.eb @@ -24,11 +24,8 @@ description = """BFAST facilitates the fast and accurate mapping of short reads toolchain = {'name': 'goolf', 'version': '1.4.10'} -import string -swdir = version.rstrip(string.lowercase + string.uppercase) -# eg. http://sourceforge.net/projects/bfast/files/bfast/0.7.0/bfast-0.7.0a.tar.gz/download +source_urls = ['http://sourceforge.net/projects/bfast/files/bfast/%s/' % version.rstrip('a'), 'download'] sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://sourceforge.net/projects/bfast/files/bfast/%s/' % swdir, 'download'] dependencies = [('bzip2', '1.0.6')] diff --git a/easybuild/easyconfigs/b/BFAST/BFAST-0.7.0a-goolf-1.7.20.eb b/easybuild/easyconfigs/b/BFAST/BFAST-0.7.0a-goolf-1.7.20.eb index a5c3af2f9a..aec46bb1ff 100644 --- a/easybuild/easyconfigs/b/BFAST/BFAST-0.7.0a-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/b/BFAST/BFAST-0.7.0a-goolf-1.7.20.eb @@ -24,11 +24,8 @@ description = """BFAST facilitates the fast and accurate mapping of short reads toolchain = {'name': 'goolf', 'version': '1.7.20'} -import string -swdir = version.rstrip(string.lowercase + string.uppercase) -# eg. http://sourceforge.net/projects/bfast/files/bfast/0.7.0/bfast-0.7.0a.tar.gz/download +source_urls = ['http://sourceforge.net/projects/bfast/files/bfast/%s/' % version.rstrip('a'), 'download'] sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://sourceforge.net/projects/bfast/files/bfast/%s/' % swdir, 'download'] dependencies = [('bzip2', '1.0.6')] diff --git a/easybuild/easyconfigs/b/BFAST/BFAST-0.7.0a-ictce-5.3.0.eb b/easybuild/easyconfigs/b/BFAST/BFAST-0.7.0a-ictce-5.3.0.eb index b792e697b2..46b0a5ba2d 100644 --- a/easybuild/easyconfigs/b/BFAST/BFAST-0.7.0a-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/b/BFAST/BFAST-0.7.0a-ictce-5.3.0.eb @@ -24,11 +24,8 @@ description = """BFAST facilitates the fast and accurate mapping of short reads toolchain = {'name': 'ictce', 'version': '5.3.0'} -import string -swdir = version.rstrip(string.lowercase + string.uppercase) -# eg. http://sourceforge.net/projects/bfast/files/bfast/0.7.0/bfast-0.7.0a.tar.gz/download +source_urls = ['http://sourceforge.net/projects/bfast/files/bfast/%s/' % version.rstrip('a'), 'download'] sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://sourceforge.net/projects/bfast/files/bfast/%s/' % swdir, 'download'] dependencies = [('bzip2', '1.0.6')] -- GitLab From d98e34825319602ec797e791c905ad7f2de73d9a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 21 Jun 2017 22:19:48 +0200 Subject: [PATCH 0990/1603] avoid hardcoding stripping of 'a' (hat tip @vanzod) --- easybuild/easyconfigs/b/BFAST/BFAST-0.7.0a-goolf-1.4.10.eb | 3 ++- easybuild/easyconfigs/b/BFAST/BFAST-0.7.0a-goolf-1.7.20.eb | 3 ++- easybuild/easyconfigs/b/BFAST/BFAST-0.7.0a-ictce-5.3.0.eb | 3 ++- 3 files changed, 6 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/b/BFAST/BFAST-0.7.0a-goolf-1.4.10.eb b/easybuild/easyconfigs/b/BFAST/BFAST-0.7.0a-goolf-1.4.10.eb index 048346809a..a4739e8c8e 100644 --- a/easybuild/easyconfigs/b/BFAST/BFAST-0.7.0a-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/BFAST/BFAST-0.7.0a-goolf-1.4.10.eb @@ -24,7 +24,8 @@ description = """BFAST facilitates the fast and accurate mapping of short reads toolchain = {'name': 'goolf', 'version': '1.4.10'} -source_urls = ['http://sourceforge.net/projects/bfast/files/bfast/%s/' % version.rstrip('a'), 'download'] +verdir = ''.join(char for char in version if not char.isalpha()) +source_urls = ['http://sourceforge.net/projects/bfast/files/bfast/%s/' % verdir, 'download'] sources = [SOURCELOWER_TAR_GZ] dependencies = [('bzip2', '1.0.6')] diff --git a/easybuild/easyconfigs/b/BFAST/BFAST-0.7.0a-goolf-1.7.20.eb b/easybuild/easyconfigs/b/BFAST/BFAST-0.7.0a-goolf-1.7.20.eb index aec46bb1ff..76e9215e88 100644 --- a/easybuild/easyconfigs/b/BFAST/BFAST-0.7.0a-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/b/BFAST/BFAST-0.7.0a-goolf-1.7.20.eb @@ -24,7 +24,8 @@ description = """BFAST facilitates the fast and accurate mapping of short reads toolchain = {'name': 'goolf', 'version': '1.7.20'} -source_urls = ['http://sourceforge.net/projects/bfast/files/bfast/%s/' % version.rstrip('a'), 'download'] +verdir = ''.join(char for char in version if not char.isalpha()) +source_urls = ['http://sourceforge.net/projects/bfast/files/bfast/%s/' % verdir, 'download'] sources = [SOURCELOWER_TAR_GZ] dependencies = [('bzip2', '1.0.6')] diff --git a/easybuild/easyconfigs/b/BFAST/BFAST-0.7.0a-ictce-5.3.0.eb b/easybuild/easyconfigs/b/BFAST/BFAST-0.7.0a-ictce-5.3.0.eb index 46b0a5ba2d..5bbf580366 100644 --- a/easybuild/easyconfigs/b/BFAST/BFAST-0.7.0a-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/b/BFAST/BFAST-0.7.0a-ictce-5.3.0.eb @@ -24,7 +24,8 @@ description = """BFAST facilitates the fast and accurate mapping of short reads toolchain = {'name': 'ictce', 'version': '5.3.0'} -source_urls = ['http://sourceforge.net/projects/bfast/files/bfast/%s/' % version.rstrip('a'), 'download'] +verdir = ''.join(char for char in version if not char.isalpha()) +source_urls = ['http://sourceforge.net/projects/bfast/files/bfast/%s/' % verdir, 'download'] sources = [SOURCELOWER_TAR_GZ] dependencies = [('bzip2', '1.0.6')] -- GitLab From ba0c1a45283e1c354182ba8ae94273ccf93b812f Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 22 Jun 2017 11:55:15 +0200 Subject: [PATCH 0991/1603] Split of MXNet/0.9.3 with foss/2016b from #4346 The foss one works, the intel one currently doesn't. --- .../MXNet-0.9.3-foss-2016b-Python-2.7.12.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/m/MXNet/MXNet-0.9.3-foss-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/m/MXNet/MXNet-0.9.3-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/m/MXNet/MXNet-0.9.3-foss-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..64f4e6cfd3 --- /dev/null +++ b/easybuild/easyconfigs/m/MXNet/MXNet-0.9.3-foss-2016b-Python-2.7.12.eb @@ -0,0 +1,38 @@ +name = 'MXNet' +version = '0.9.3' +versionsuffix = '-Python-%(pyver)s-R-%(rver)s' + +homepage = 'http://mxnet.io/' +description = """Flexible and Efficient Library for Deep Learning""" + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'cstd': 'c++11', 'opt': True, 'pic': True, 'openmp': True} + +source_urls = ['https://github.com/dmlc/mxnet/archive'] + +# MXNet pulls in a bunch of submodules which don't have releases. +# We download the current HEAD of the repos at the current time (13/03/17) +sources = [ + 'v%(version)s.tar.gz', # MXNet + 'https://github.com/dmlc/ps-lite/archive/6856021ca925c7.tar.gz', # ps-lite + 'https://github.com/dmlc/mshadow/archive/c29ac58320d7b0.tar.gz', # mshadow + 'https://github.com/dmlc/nnvm/archive/0d64855f741e04.tar.gz', # nnvm + 'https://github.com/dmlc/dmlc-core/archive/b32ec4aee65a66.tar.gz', # dmlc-core +] + +checksums = [ + "84971e4a0e2e9db3757623657aa5b9ec", # v0.9.3.tar.gz + "12c96664978c545a7269b93635719b18", # 6856021ca925c7.tar.gz + "3dc48183e123c650707bcf26a9254941", # c29ac58320d7b0.tar.gz + "fb04cb1694f1e66591a31a18bc92b451", # 0d64855f741e04.tar.gz + "da873c881758c0e10ac0928f86568456", # b32ec4aee65a66.tar.gz +] + +dependencies = [ + ('Python', '2.7.12'), + ('graphviz', '0.5.1', '-Python-%(pyver)s'), + ('OpenCV', '3.1.0'), + ('R', '3.3.3', '-X11-20160819'), +] + +moduleclass = 'math' -- GitLab From 353396ee951b088e4b96a313d5dd24078a6adb87 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 22 Jun 2017 12:41:22 +0200 Subject: [PATCH 0992/1603] Fix for style checks --- .../m/MXNet/MXNet-0.9.3-foss-2016b-Python-2.7.12.eb | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/m/MXNet/MXNet-0.9.3-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/m/MXNet/MXNet-0.9.3-foss-2016b-Python-2.7.12.eb index 64f4e6cfd3..ba00fd6f18 100644 --- a/easybuild/easyconfigs/m/MXNet/MXNet-0.9.3-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/m/MXNet/MXNet-0.9.3-foss-2016b-Python-2.7.12.eb @@ -13,11 +13,11 @@ source_urls = ['https://github.com/dmlc/mxnet/archive'] # MXNet pulls in a bunch of submodules which don't have releases. # We download the current HEAD of the repos at the current time (13/03/17) sources = [ - 'v%(version)s.tar.gz', # MXNet - 'https://github.com/dmlc/ps-lite/archive/6856021ca925c7.tar.gz', # ps-lite - 'https://github.com/dmlc/mshadow/archive/c29ac58320d7b0.tar.gz', # mshadow - 'https://github.com/dmlc/nnvm/archive/0d64855f741e04.tar.gz', # nnvm - 'https://github.com/dmlc/dmlc-core/archive/b32ec4aee65a66.tar.gz', # dmlc-core + 'v%(version)s.tar.gz', # MXNet + 'https://github.com/dmlc/ps-lite/archive/6856021ca925c7.tar.gz', # ps-lite + 'https://github.com/dmlc/mshadow/archive/c29ac58320d7b0.tar.gz', # mshadow + 'https://github.com/dmlc/nnvm/archive/0d64855f741e04.tar.gz', # nnvm + 'https://github.com/dmlc/dmlc-core/archive/b32ec4aee65a66.tar.gz', # dmlc-core ] checksums = [ -- GitLab From 8d5e97809793e4aa05bf72c31522b4f039f83341 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 22 Jun 2017 13:35:51 +0200 Subject: [PATCH 0993/1603] rename to make tests happy --- ...-2.7.12.eb => MXNet-0.9.3-foss-2016b-Python-2.7.12-R-3.3.3.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/m/MXNet/{MXNet-0.9.3-foss-2016b-Python-2.7.12.eb => MXNet-0.9.3-foss-2016b-Python-2.7.12-R-3.3.3.eb} (100%) diff --git a/easybuild/easyconfigs/m/MXNet/MXNet-0.9.3-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/m/MXNet/MXNet-0.9.3-foss-2016b-Python-2.7.12-R-3.3.3.eb similarity index 100% rename from easybuild/easyconfigs/m/MXNet/MXNet-0.9.3-foss-2016b-Python-2.7.12.eb rename to easybuild/easyconfigs/m/MXNet/MXNet-0.9.3-foss-2016b-Python-2.7.12-R-3.3.3.eb -- GitLab From 961ef5eff1792e725724043d11a14f57ca75c56b Mon Sep 17 00:00:00 2001 From: Sebastien Varrette Date: Thu, 22 Jun 2017 15:58:13 +0200 Subject: [PATCH 0994/1603] {foss,intel}-2017a versions for LikWid 4.2.0 Signed-off-by: Sebastien Varrette --- .../l/likwid/likwid-4.2.0-foss-2017a.eb | 50 +++++++++++++++++++ .../likwid/likwid-4.2.0-foss-config-mk.patch | 40 +++++++++++++++ .../l/likwid/likwid-4.2.0-intel-2017a.eb | 49 ++++++++++++++++++ .../likwid/likwid-4.2.0-intel-config-mk.patch | 49 ++++++++++++++++++ 4 files changed, 188 insertions(+) create mode 100644 easybuild/easyconfigs/l/likwid/likwid-4.2.0-foss-2017a.eb create mode 100644 easybuild/easyconfigs/l/likwid/likwid-4.2.0-foss-config-mk.patch create mode 100644 easybuild/easyconfigs/l/likwid/likwid-4.2.0-intel-2017a.eb create mode 100644 easybuild/easyconfigs/l/likwid/likwid-4.2.0-intel-config-mk.patch diff --git a/easybuild/easyconfigs/l/likwid/likwid-4.2.0-foss-2017a.eb b/easybuild/easyconfigs/l/likwid/likwid-4.2.0-foss-2017a.eb new file mode 100644 index 0000000000..71712d86cc --- /dev/null +++ b/easybuild/easyconfigs/l/likwid/likwid-4.2.0-foss-2017a.eb @@ -0,0 +1,50 @@ +## +# -*- mode: python; -*- +# EasyBuild reciPY for LikWid -- see https://github.com/RRZE-HPC/likwid +# as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2017 UL HPC -- hpc.uni.lu +# Authors:: UL HPC Team +# License:: MIT/GPL +# +# +easyblock = 'ConfigureMake' + +name = 'likwid' +version = '4.2.0' + +homepage = 'https://github.com/RRZE-HPC/likwid' +description = """Likwid stands for 'Like I knew what I am doing'. Likwid is a +simple to install and use toolsuite of command line applications for performance +oriented programmers. It works for Intel and AMD processors on the Linux +operating system. +""" + +toolchain = {'name': 'foss', 'version': '2017a'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/RRZE-HPC/likwid/archive/'] +sources = ['%(version)s.tar.gz'] + +patches = ['likwid-%(version)s-foss-config-mk.patch'] + +builddependencies = [('binutils', '2.27')] + +skipsteps = ['configure'] +buildopts = 'CC="$CC" CFLAGS="$CFLAGS -std=c99" PREFIX=%(installdir)s' +installopts = 'PREFIX=%(installdir)s' + +sanity_check_paths = { + 'files': ["bin/likwid-memsweeper", "bin/likwid-mpirun", "bin/likwid-perfctr", + "bin/likwid-perfscope", "bin/likwid-pin", "bin/likwid-powermeter", "bin/likwid-topology", + "lib/liblikwidpin.%s" % SHLIB_EXT, "lib/liblikwid.%s" % SHLIB_EXT], + 'dirs': ["man/man1"] +} + +postinstallcmds = [ + 'echo "================================================================================\nIMPORTANT: you will have to manually apply the following changes **as root**:\n sudo chown root:root \$EBROOTLIKWID/sbin/likwid-accessD\n sudo chmod u+s \$EBROOTLIKWID/sbin/likwid-accessD\n ================================================================================"' +] + +maxparallel = 1 + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/likwid/likwid-4.2.0-foss-config-mk.patch b/easybuild/easyconfigs/l/likwid/likwid-4.2.0-foss-config-mk.patch new file mode 100644 index 0000000000..c1de1bdb80 --- /dev/null +++ b/easybuild/easyconfigs/l/likwid/likwid-4.2.0-foss-config-mk.patch @@ -0,0 +1,40 @@ +--- likwid-likwid-4.2.orig/config.mk 2016-12-22 13:22:23.000000000 +0100 ++++ likwid-likwid-4.2/config.mk 2017-06-19 14:36:15.521398000 +0200 +@@ -9,7 +9,7 @@ + COLOR = BLUE#NO SPACE + + # Path were to install likwid +-PREFIX = /usr/local#NO SPACE ++# PREFIX = /usr/local#NO SPACE + + # uncomment to optionally set external lua@5.3: + # default is use internally provide lua +@@ -40,7 +40,7 @@ + # chown installed tools to this user/group + # if you change anything here, make sure that the user/group can access + # the MSR devices and (on Intel) the PCI devices. +-INSTALL_CHOWN = -g root -o root ++INSTALL_CHOWN = + + # For the daemon based secure msr/pci access configure + # the absolute path to the msr daemon executable. +@@ -51,7 +51,7 @@ + # Build the accessDaemon. Have a look in the WIKI for details. + BUILDDAEMON = true#NO SPACE + #Build the setFrequencies tool +-BUILDFREQ = true#NO SPACE ++BUILDFREQ = false#NO SPACE + + # Set the default mode for MSR access. + # This can usually be overriden on the commandline. +@@ -82,8 +82,8 @@ + # a proper config file at CFG_FILE_PATH) + MAX_NUM_THREADS = 263 + MAX_NUM_NODES = 64 +-CFG_FILE_PATH = /etc/likwid.cfg +-TOPO_FILE_PATH = /etc/likwid_topo.cfg ++CFG_FILE_PATH = $(PREFIX)/etc/likwid.cfg ++TOPO_FILE_PATH = $(PREFIX)/etc/likwid_topo.cfg + + # Versioning Information + VERSION = 4 diff --git a/easybuild/easyconfigs/l/likwid/likwid-4.2.0-intel-2017a.eb b/easybuild/easyconfigs/l/likwid/likwid-4.2.0-intel-2017a.eb new file mode 100644 index 0000000000..10441103ad --- /dev/null +++ b/easybuild/easyconfigs/l/likwid/likwid-4.2.0-intel-2017a.eb @@ -0,0 +1,49 @@ +## +# -*- mode: python; -*- +# EasyBuild reciPY for LikWid -- see https://github.com/RRZE-HPC/likwid +# as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2017 UL HPC -- hpc.uni.lu +# Authors:: UL HPC Team +# License:: MIT/GPL +# +# +easyblock = 'ConfigureMake' + +name = 'likwid' +version = '4.2.0' + +homepage = 'https://github.com/RRZE-HPC/likwid' +description = """Likwid stands for 'Like I knew what I am doing'. Likwid is a +simple to install and use toolsuite of command line applications for performance +oriented programmers. It works for Intel and AMD processors on the Linux +operating system.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/RRZE-HPC/likwid/archive/'] +sources = ['%(version)s.tar.gz'] + +patches = ['likwid-%(version)s-intel-config-mk.patch'] + +builddependencies = [('binutils', '2.27')] + +skipsteps = ['configure'] +buildopts = 'CC="$CC" CFLAGS="$CFLAGS -std=c99" PREFIX=%(installdir)s' +installopts = 'PREFIX=%(installdir)s' + +sanity_check_paths = { + 'files': ["bin/likwid-memsweeper", "bin/likwid-mpirun", "bin/likwid-perfctr", + "bin/likwid-perfscope", "bin/likwid-pin", "bin/likwid-powermeter", "bin/likwid-topology", + "lib/liblikwidpin.%s" % SHLIB_EXT, "lib/liblikwid.%s" % SHLIB_EXT], + 'dirs': ["man/man1"] +} + +postinstallcmds = [ + 'echo "================================================================================\nIMPORTANT: you will have to manually apply the following changes **as root**:\n sudo chown root:root \$EBROOTLIKWID/sbin/likwid-accessD\n sudo chmod u+s \$EBROOTLIKWID/sbin/likwid-accessD\n ================================================================================"' +] + +maxparallel = 1 + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/likwid/likwid-4.2.0-intel-config-mk.patch b/easybuild/easyconfigs/l/likwid/likwid-4.2.0-intel-config-mk.patch new file mode 100644 index 0000000000..a7d8fccb54 --- /dev/null +++ b/easybuild/easyconfigs/l/likwid/likwid-4.2.0-intel-config-mk.patch @@ -0,0 +1,49 @@ +--- likwid-likwid-4.2.orig/config.mk 2016-12-22 13:22:23.000000000 +0100 ++++ likwid-likwid-4.2/config.mk 2017-06-22 10:14:28.585696000 +0200 +@@ -1,7 +1,7 @@ + # Please have a look in INSTALL and the WIKI for details on + # configuration options setup steps. + # supported: GCC, CLANG, ICC, MIC (ICC), GCCX86 (for 32bit systems) +-COMPILER = GCC#NO SPACE ++COMPILER = ICC#NO SPACE + + # Define the color of the likwid-pin output + # Can be NONE, BLACK, RED, GREEN, YELLOW, BLUE, +@@ -9,7 +9,7 @@ + COLOR = BLUE#NO SPACE + + # Path were to install likwid +-PREFIX = /usr/local#NO SPACE ++# PREFIX = /usr/local#NO SPACE + + # uncomment to optionally set external lua@5.3: + # default is use internally provide lua +@@ -40,7 +40,7 @@ + # chown installed tools to this user/group + # if you change anything here, make sure that the user/group can access + # the MSR devices and (on Intel) the PCI devices. +-INSTALL_CHOWN = -g root -o root ++INSTALL_CHOWN = + + # For the daemon based secure msr/pci access configure + # the absolute path to the msr daemon executable. +@@ -51,7 +51,7 @@ + # Build the accessDaemon. Have a look in the WIKI for details. + BUILDDAEMON = true#NO SPACE + #Build the setFrequencies tool +-BUILDFREQ = true#NO SPACE ++BUILDFREQ = false#NO SPACE + + # Set the default mode for MSR access. + # This can usually be overriden on the commandline. +@@ -82,8 +82,8 @@ + # a proper config file at CFG_FILE_PATH) + MAX_NUM_THREADS = 263 + MAX_NUM_NODES = 64 +-CFG_FILE_PATH = /etc/likwid.cfg +-TOPO_FILE_PATH = /etc/likwid_topo.cfg ++CFG_FILE_PATH = $(PREFIX)/etc/likwid.cfg ++TOPO_FILE_PATH = $(PREFIX)/etc/likwid_topo.cfg + + # Versioning Information + VERSION = 4 -- GitLab From e7cb3e9fbfc058009fe360524a1b6f4d61ba06cb Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 22 Jun 2017 18:01:37 +0200 Subject: [PATCH 0995/1603] (proposal for) foss/2017b toolchain definition --- .../f/FFTW/FFTW-3.3.6-gompi-2017b.eb | 17 ++++++ easybuild/easyconfigs/f/foss/foss-2017b.eb | 35 ++++++++++++ easybuild/easyconfigs/g/gompi/gompi-2017b.eb | 20 +++++++ .../easyconfigs/h/HPL/HPL-2.2-foss-2017b.eb | 18 ++++++ .../h/hwloc/hwloc-1.11.7-GCC-6.3.0-2.28.eb | 24 ++++++++ ...BLAS-0.2.19-GCC-6.3.0-2.28-LAPACK-3.7.0.eb | 56 +++++++++++++++++++ .../o/OpenMPI/OpenMPI-2.1.1-GCC-6.3.0-2.28.eb | 34 +++++++++++ ...ompi-2017b-OpenBLAS-0.2.19-LAPACK-3.7.0.eb | 25 +++++++++ 8 files changed, 229 insertions(+) create mode 100644 easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-gompi-2017b.eb create mode 100644 easybuild/easyconfigs/f/foss/foss-2017b.eb create mode 100644 easybuild/easyconfigs/g/gompi/gompi-2017b.eb create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.2-foss-2017b.eb create mode 100644 easybuild/easyconfigs/h/hwloc/hwloc-1.11.7-GCC-6.3.0-2.28.eb create mode 100644 easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-GCC-6.3.0-2.28-LAPACK-3.7.0.eb create mode 100644 easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.1-GCC-6.3.0-2.28.eb create mode 100644 easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-2017b-OpenBLAS-0.2.19-LAPACK-3.7.0.eb diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-gompi-2017b.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-gompi-2017b.eb new file mode 100644 index 0000000000..eee27ec554 --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-gompi-2017b.eb @@ -0,0 +1,17 @@ +name = 'FFTW' +version = '3.3.6' + +homepage = 'http://www.fftw.org' +description = """FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) + in one or more dimensions, of arbitrary input size, and of both real and complex data.""" + +toolchain = {'name': 'gompi', 'version': '2017b'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = ['fftw-%(version)s-pl2.tar.gz'] +checksums = ['927e481edbb32575397eb3d62535a856'] + +runtest = 'check' + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/f/foss/foss-2017b.eb b/easybuild/easyconfigs/f/foss/foss-2017b.eb new file mode 100644 index 0000000000..20778cf402 --- /dev/null +++ b/easybuild/easyconfigs/f/foss/foss-2017b.eb @@ -0,0 +1,35 @@ +easyblock = 'Toolchain' + +name = 'foss' +version = '2017b' + +homepage = '(none)' +description = """GNU Compiler Collection (GCC) based compiler toolchain, including + OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +gccver = '6.3.0-2.28' + +blaslib = 'OpenBLAS' +blasver = '0.2.19' +blas = '%s-%s' % (blaslib, blasver) +blassuff = '-LAPACK-3.7.0' + +# toolchain used to build foss dependencies +comp_mpi_tc_name = 'gompi' +comp_mpi_tc = (comp_mpi_tc_name, version) + +# compiler toolchain depencies +# we need GCC and OpenMPI as explicit dependencies instead of gompi toolchain +# because of toolchain preperation functions +# For binutils, stick to http://wiki.osdev.org/Cross-Compiler_Successful_Builds +dependencies = [ + ('GCC', gccver), + ('OpenMPI', '2.1.1', '', ('GCC', gccver)), + (blaslib, blasver, blassuff, ('GCC', gccver)), + ('FFTW', '3.3.6', '', comp_mpi_tc), + ('ScaLAPACK', '2.0.2', '-%s%s' % (blas, blassuff), comp_mpi_tc), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/g/gompi/gompi-2017b.eb b/easybuild/easyconfigs/g/gompi/gompi-2017b.eb new file mode 100644 index 0000000000..ff56275f5c --- /dev/null +++ b/easybuild/easyconfigs/g/gompi/gompi-2017b.eb @@ -0,0 +1,20 @@ +easyblock = "Toolchain" + +name = 'gompi' +version = '2017b' + +homepage = '(none)' +description = """GNU Compiler Collection (GCC) based compiler toolchain, + including OpenMPI for MPI support.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +gccver = '6.3.0-2.28' + +# compiler toolchain dependencies +dependencies = [ + ('GCC', gccver), # includes both GCC 6.3.0 and binutils 2.27 + ('OpenMPI', '2.1.1', '', ('GCC', gccver)), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.2-foss-2017b.eb b/easybuild/easyconfigs/h/HPL/HPL-2.2-foss-2017b.eb new file mode 100644 index 0000000000..7ff64c1745 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.2-foss-2017b.eb @@ -0,0 +1,18 @@ +name = 'HPL' +version = '2.2' + +homepage = 'http://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'foss', 'version': '2017b'} +toolchainopts = {'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] + +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.7-GCC-6.3.0-2.28.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.7-GCC-6.3.0-2.28.eb new file mode 100644 index 0000000000..72dfa36917 --- /dev/null +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.7-GCC-6.3.0-2.28.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'hwloc' +version = '1.11.7' + +homepage = 'http://www.open-mpi.org/projects/hwloc/' +description = """The Portable Hardware Locality (hwloc) software package provides a portable abstraction +(across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including +NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various +system attributes such as cache and memory information as well as the locality of I/O devices such as +network interfaces, InfiniBand HCAs or GPUs. It primarily aims at helping applications with gathering +information about modern computing hardware so as to exploit it accordingly and efficiently.""" + +toolchain = {'name': 'GCC', 'version': '6.3.0-2.28'} + +source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] +sources = [SOURCE_TAR_GZ] +checksums = ['ac16bed9cdd3c63bca1fe1ac3de522a1376b1487c4fc85b7b19592e28fd98e26'] + +dependencies = [('numactl', '2.0.11')] + +configopts = "--enable-libnuma=$EBROOTNUMACTL" + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-GCC-6.3.0-2.28-LAPACK-3.7.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-GCC-6.3.0-2.28-LAPACK-3.7.0.eb new file mode 100644 index 0000000000..a1d7e75e79 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-GCC-6.3.0-2.28-LAPACK-3.7.0.eb @@ -0,0 +1,56 @@ +easyblock = 'ConfigureMake' + +name = 'OpenBLAS' +version = '0.2.19' + +lapackver = '3.7.0' +versionsuffix = '-LAPACK-%s' % lapackver + +homepage = 'http://xianyi.github.com/OpenBLAS/' +description = """OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version.""" + +toolchain = {'name': 'GCC', 'version': '6.3.0-2.28'} + +lapack_src = 'lapack-%s.tgz' % lapackver +large_src = 'large.tgz' +timing_src = 'timing.tgz' + +lapack_unpack_cmd = 'cd %(name)s-%(version)s; rm -rf lapack-netlib;' +lapack_unpack_cmd += 'mkdir lapack-netlib;' +lapack_unpack_cmd += 'tar -C lapack-netlib --strip-components=1 -zxf %s; cd -' + +sources = [ + 'v%(version)s.tar.gz', + (lapack_src, lapack_unpack_cmd), + large_src, + timing_src, +] +source_urls = [ + # order matters, trying to download the LAPACK tarball from GitHub causes trouble + "http://www.netlib.org/lapack/", + "http://www.netlib.org/lapack/timing/", + "https://github.com/xianyi/OpenBLAS/archive/", +] + +patches = [ + (large_src, '.'), + (timing_src, '.'), + 'OpenBLAS-%(version)s_LAPACK-3.7.0-fixes.patch', +] + +skipsteps = ['configure'] + +buildopts = 'BINARY=64 USE_THREAD=1 CC="$CC" FC="$F77" NO_AFFINITY=1' +installopts = "USE_THREAD=1 PREFIX=%(installdir)s" + +# extensive testing can be enabled by uncommenting the line below +# runtest = 'PATH=.:$PATH lapack-timing' + +sanity_check_paths = { + 'files': ['include/cblas.h', 'include/f77blas.h', 'include/lapacke_config.h', 'include/lapacke.h', + 'include/lapacke_mangling.h', 'include/lapacke_utils.h', 'include/openblas_config.h', + 'lib/libopenblas.a', 'lib/libopenblas.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.1-GCC-6.3.0-2.28.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.1-GCC-6.3.0-2.28.eb new file mode 100644 index 0000000000..aba86a17c1 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.1-GCC-6.3.0-2.28.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'OpenMPI' +version = '2.1.1' + +homepage = 'http://www.open-mpi.org/' +description = """The Open MPI Project is an open source MPI-2 implementation.""" + +toolchain = {'name': 'GCC', 'version': '6.3.0-2.28'} + +source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] +sources = [SOURCELOWER_TAR_GZ] + +checksums = ['afe4bef3c4378bc76eea96c623d5aa4c1c98b9e057d281c646e68869292a77dc'] + +dependencies = [('hwloc', '1.11.7')] + +configopts = '--enable-shared --enable-mpi-thread-multiple --with-verbs ' +configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path +configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support +configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading + +# needed for --with-verbs +osdependencies = [('libibverbs-dev', 'libibverbs-devel')] + +libs = ["mpi_mpifh", "mpi", "ompitrace", "open-pal", "open-rte"] +sanity_check_paths = { + 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] + + ["include/%s.h" % x for x in ["mpi-ext", "mpif-config", "mpif", "mpi", "mpi_portable_platform"]], + 'dirs': [], +} + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-2017b-OpenBLAS-0.2.19-LAPACK-3.7.0.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-2017b-OpenBLAS-0.2.19-LAPACK-3.7.0.eb new file mode 100644 index 0000000000..a036bb79cb --- /dev/null +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-2017b-OpenBLAS-0.2.19-LAPACK-3.7.0.eb @@ -0,0 +1,25 @@ +name = 'ScaLAPACK' +version = '2.0.2' + +homepage = 'http://www.netlib.org/scalapack/' +description = """The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines + redesigned for distributed memory MIMD parallel computers.""" + +toolchain = {'name': 'gompi', 'version': '2017b'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = [SOURCELOWER_TGZ] + +blaslib = 'OpenBLAS' +blasver = '0.2.19' +blassuff = '-LAPACK-3.7.0' + +versionsuffix = "-%s-%s%s" % (blaslib, blasver, blassuff) + +dependencies = [(blaslib, blasver, blassuff, ('GCC', '6.3.0-2.28'))] + +# parallel build tends to fail, so disabling it +parallel = 1 + +moduleclass = 'numlib' -- GitLab From 294af8496d6e1cb5d8b75b21959737898179ec95 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Fri, 23 Jun 2017 14:14:23 +0800 Subject: [PATCH 0996/1603] prepare release notes for eb330 --- RELEASE_NOTES | 39 ++++++++++++++++++++++++++++++++++++++- 1 file changed, 38 insertions(+), 1 deletion(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index 4b1afa6117..9d60ed1d8b 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -3,9 +3,46 @@ For more detailed information, please see the git log. These release notes can also be consulted at http://easybuild.readthedocs.org/en/latest/Release_notes.html. -The latest version of easybuild-easyconfig provides 7,036 easyconfig files, for 1,228 different software packages, +The latest version of easybuild-easyconfig provides 7,260 easyconfig files, for 1,256 different software packages, 25 different (compiler) toolchains, 13 software bundles and 1 meta-package. +v3.3.0 (June 23rd 2017) +----------------------- + +feature release +- enable automatic style checks in easyconfig tests (#2506) +- added example easyconfig files for 28 new software packages: + - AUGUSTUS (#4624), Aspera-CLI (#4635), ada (#4594), BUSCO (#4624), Bio-SamTools (#4637), Bpipe (#4590), CNVnator (#4649), + davix (#4755), EricScript (#4594), FUNWAVE-TVD (#4743), gSOAP (#4755), gmpy2 (#4609), LUMPY (#4682), libsndfile (#4628), + lpsolve (#4264), MXNet (#4765), MaSuRCA (#4706), modred (#4729), NRGLjubljana (#4651), OrfM (#4703), + Perl4-CoreLibs (#4670), prodigal (#4468), pydlpoly (#4756), SeqAn (#4603), Spyder (#4627), sharutils (#4745), + Tkinter (#4620), VariantMetaCaller (#4632) +- added additional easyconfigs for various supported software packages, including: + - ABINIT 8.0.8b, ABINIT 8.2.2, ABINIT 8.2.2, ANTLR 2.7.7, AUGUSTUS 3.2.3, Aspera CLI, ada 2.0, arpack ng, BEDOPS 2.4.26.eb, BEDTools 2.26.0, BLAST+ 2.6.0, BUSCO 2.0.1, BWA 0.7.15, Bio SamTools, Bowtie2 2.3.2, Bpipe 0.9.9.2, basemap 1.0.7, buildenv default, bzip2 1.0.6, CDO 1.8.1, CGAL 4.8.1, CMake 3.6.1.eb, CMake 3.8.2, CNVnator 0.3.3, cURL 7.49.1, cURL 7.52.1, DB 6.0.30, DBD mysql, DIAMOND 0.9.6, Doris 4.04beta4, Doris 4.06beta2, Doxygen 1.8.11, davix 0.6.6, EMBOSS 6.6.0, ESMF 6.3.0rp1, EasyBuild 3.2.1.eb, Eigen 3.2.9, EricScript 0.5.5, eudev 3.1.5, expat 2.2.0, expat 2.2.0, FASTA 36.3.5e, FFTW 2.1.5, FFTW 2.1.5, FFmpeg 3.3.1, FLTK 1.3.4, FSL 5.0.10, FUNWAVE TVD, FUNWAVE TVD, flex 2.6.4, fontconfig 2.12.1, freeglut 3.0.0, freetype 2.6.5, GD 2.66, GDAL 2.1.3, GDAL 2.2.0, GDAL 2.2.0, GEOS 3.6.1, GL2PS 1.4.0, GLPK 4.61, GLib 2.48.2, GMP 6.1.1, GMT 5.4.1, GObject Introspection, GraphicsMagick 1.3.25, Guile 1.8.8, gSOAP 2.8.48, gettext 0.19.8, gettext 0.19.8, gimkl 2017a.eb, gimpi 2017a.eb, gmpy2 2.0.8, gnuplot 5.0.6, gperf 3.0.4, gperf 3.0.4, gtest 1.8.0, HTSlib 1.4.1, HarfBuzz 1.3.1, h5py 2.7.0, ImageMagick 7.0.5, imbalanced learn, imkl 2017.1.132, impi 2017.1.132, JasPer 2.0.12, Java 1.8.0_131.eb, Keras 2.0.4, LAME 3.99.5, LLVM 3.7.1, LUMPY 0.2.13, LibTIFF 4.0.7, LibUUID 1.0.3, LittleCMS 2.8, libGLU 9.0.0, libcerf 1.5, libdap 3.18.1, libdrm 2.4.68, libffi 3.2.1, libgd 2.2.4, libgd 2.2.4, libharu 2.3.0, libidn 1.32, libjpeg turbo, libjpeg turbo, libpciaccess 0.13.4, libpng 1.6.24, libpng 1.6.28, libpthread stubs, libreadline 6.2, libreadline 6.3, libreadline 6.3, libsndfile 1.0.28, libtasn1 4.12, libunistring 0.9.6, libxc 3.0.0, libxc 3.0.0, libxml2 2.9.4, libxml2 2.9.4, lpsolve 5.5.2.5, lynx 2.8.9, MATLAB 2017a.eb, MPC 1.0.3, MUMmer 4.0.0beta, MXNet 0.9.3, MaSuRCA 3.2.2, MariaDB 10.1.24, Mesa 11.2.1, makedepend 1.0.5, matplotlib 2.0.2, matplotlib 2.0.2, matplotlib 2.0.2, modred 2.0.2, motif 2.3.7, NAMD 2.12, NASM 2.11.08, NASM 2.12.02.eb, NCL 6.4.0, NCO 4.6.6, NRGLjubljana 2.4.3.23, ncurses 6.0, ne 3.0.1, netCDF C++4, netCDF Fortran, netCDF 4.4.1.1, nettle 3.2, Octave 4.2.1, OrfM 0.6.1, PGI 16.1, PIL 1.1.7, Pango 1.40.5, Perl 5.22.0, Perl 5.22.0, Perl4 CoreLibs, Platanus 1.2.4, PyOpenGL 3.1.1a1, PyQt 4.12, PyQt5 5.8.2, Python 2.7.12, Python 3.5.2, Python 3.5.2, p11 kit, picard 2.2.4, pkg config, prodigal 2.6.2, pydlpoly 20150225, pydlpoly 20150225, Qhull 2015.2, Qt 4.8.7, qrupdate 1.1.2, Ruby 2.3.4.eb, Rust 1.18.0, SAMtools 0.1.17, SAMtools 1.4.1, SAMtools 1.5, SCons 2.5.1, SIP 4.19.2, SQLite 3.13.0, SQLite 3.8.9, STAR 2.5.3a, SWIG 3.0.12, SeqAn 2.3.2, Singularity 2.2.1, SpiceyPy 1.1.1, Spyder 3.1.4, StringTie 1.3.3b, Szip 2.1, scikit learn, segemehl 0.2.0, seqtk 1.2, sharutils 4.15, sleuth 0.29.0, statsmodels 0.8.0, Tcl 8.6.5, Theano 0.9.0, Tk 8.6.5, Tkinter 2.7.13, TopHat 2.1.1, Trim_Galore 0.4.4, tbb 2017.6.196.eb, tbb 2017_U6, VTK 7.1.1, VTune 2017_update3.eb, VariantMetaCaller 1.0, Velvet 1.2.10, X11 20160819, XZ 5.2.2, XZ 5.2.3, xarray 0.9.5, xbitmaps 1.1.1.eb, xprop 1.2.2, YAXT 0.5.1, zlib 1.2.11 +- minor enhancements, including: + - use 'git diff --name-only' and $TRAVIS_COMMIT_RANGE in Travis config to get list of changed files (#4606) + - fix typo in statsmodels source url (/sources/ -> /source/) (#4612) + - branch to current HEAD in Travis config to get relevant list of changed files (#4619) + - add tuneR, seewave, soundecology extensions for R 3.4.0 (+ libsndfile as dep) (#4628) + - also copy README for GapFiller (#4631) + - enable inclusion of version symbol by using --enable-ld-version-script configure option for LibTIFF (#4639) + - add missing /gnu/ ins ftpmirror.gnu.org source_urls, or use GNU_SOURCE where possible (#4653) + - consistently use --with-harfbuzz=no configure option in freetype easyconfigs (#4668) + - add vcfR extension in R 3.4.0 easyconfig (#4680) + - add SHA256 checksums for libpciaccess (#4688) + - ne (nice editor) fix to correct NE_GLOBAL_DIR path (#4698) + - add location to DotLib.pm to $PERL5LIB for SSPACE Basic (#4638) + - use --with-x=yes in R easyconfigs that include X11 as a dependency (#4701) + - remove '4.0' in tbb description (#4707) + - add lib sanity check paths for debian compatibility in nettle (#4722) + - add glmmML & ordinal (+ ucminf) as R extensions (#4747) + - fix source URLs for HDF5 (#4749) + - more (trivial) style fixes (#4761) + - avoid use of import in ANSYS & MATLAB easyconfigs (#4762) + - set $OMP_NUM_THREADS during CP2K test step via dedicated easyconfig parameter (#4763) + - avoid use of 'import' in BFAST easyconfigs, just strip of 'a' from version (#4764) + + v3.2.1 (May 12th 2017) ---------------------- -- GitLab From cf74d5fe885d0cc43d2e45220161ce06542012b8 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Fri, 23 Jun 2017 11:18:56 +0200 Subject: [PATCH 0997/1603] adding easyconfigs: skewer-0.2.2-goolf-1.7.20.eb --- .../s/skewer/skewer-0.2.2-goolf-1.7.20.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/s/skewer/skewer-0.2.2-goolf-1.7.20.eb diff --git a/easybuild/easyconfigs/s/skewer/skewer-0.2.2-goolf-1.7.20.eb b/easybuild/easyconfigs/s/skewer/skewer-0.2.2-goolf-1.7.20.eb new file mode 100644 index 0000000000..4b9e2d6f54 --- /dev/null +++ b/easybuild/easyconfigs/s/skewer/skewer-0.2.2-goolf-1.7.20.eb @@ -0,0 +1,30 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'MakeCp' + +name = 'skewer' +version = '0.2.2' + +homepage = 'http://smithlabresearch.org/software/preseq/' +description = """skewer (transferred from https://sourceforge.net/projects/skewer) implements the + bit-masked k-difference matching algorithm dedicated to the task of adapter trimming and it is + specially designed for processing next-generation sequencing (NGS) paired-end sequences""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +source_urls = ['https://github.com/relipmoc/skewer/archive/'] +sources = ['%(version)s.tar.gz'] + +parallel = 1 + +files_to_copy = [(['skewer'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/skewer'], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From a88bce6fc0a201edd606f587c4b0032e1f28c650 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Lopez Date: Fri, 23 Jun 2017 11:20:58 +0200 Subject: [PATCH 0998/1603] fix buildopts --- easybuild/easyconfigs/s/skewer/skewer-0.2.2-goolf-1.7.20.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/skewer/skewer-0.2.2-goolf-1.7.20.eb b/easybuild/easyconfigs/s/skewer/skewer-0.2.2-goolf-1.7.20.eb index 4b9e2d6f54..abf4cb6e1f 100644 --- a/easybuild/easyconfigs/s/skewer/skewer-0.2.2-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/s/skewer/skewer-0.2.2-goolf-1.7.20.eb @@ -18,7 +18,7 @@ toolchain = {'name': 'goolf', 'version': '1.7.20'} source_urls = ['https://github.com/relipmoc/skewer/archive/'] sources = ['%(version)s.tar.gz'] -parallel = 1 +buildopts = 'CXX="$CXX" CXXFLAGS="-c $CXXFLAGS" LDFLAGS="$CXXFLAGS -pthread"' files_to_copy = [(['skewer'], 'bin')] -- GitLab From 5e2ed91c780fc712ef54d2b6ba1f482c95589a8a Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Fri, 23 Jun 2017 13:09:23 +0200 Subject: [PATCH 0999/1603] Add the docopt module to all Python 2017a easyconfigs --- easybuild/easyconfigs/p/Python/Python-2.7.12-iomkl-2017a.eb | 3 +++ easybuild/easyconfigs/p/Python/Python-2.7.13-foss-2017a.eb | 3 +++ easybuild/easyconfigs/p/Python/Python-2.7.13-intel-2017a.eb | 3 +++ easybuild/easyconfigs/p/Python/Python-3.6.1-intel-2017a.eb | 3 +++ 4 files changed, 12 insertions(+) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.12-iomkl-2017a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.12-iomkl-2017a.eb index eb4f43f9dd..bfb67d268a 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.12-iomkl-2017a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.12-iomkl-2017a.eb @@ -128,6 +128,9 @@ exts_list = [ ('virtualenv', '15.0.2', { 'source_urls': ['https://pypi.python.org/packages/source/v/virtualenv'], }), + ('docopt', '0.6.2', { + 'source_urls': ['https://pypi.python.org/packages/source/d/docopt'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.13-foss-2017a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.13-foss-2017a.eb index 5abe3e3e7d..21d606f252 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.13-foss-2017a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.13-foss-2017a.eb @@ -130,6 +130,9 @@ exts_list = [ ('virtualenv', '15.1.0', { 'source_urls': ['https://pypi.python.org/packages/source/v/virtualenv'], }), + ('docopt', '0.6.2', { + 'source_urls': ['https://pypi.python.org/packages/source/d/docopt'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.13-intel-2017a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.13-intel-2017a.eb index 099f1ae1b2..4ee5f95966 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.13-intel-2017a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.13-intel-2017a.eb @@ -130,6 +130,9 @@ exts_list = [ ('virtualenv', '15.1.0', { 'source_urls': ['https://pypi.python.org/packages/source/v/virtualenv'], }), + ('docopt', '0.6.2', { + 'source_urls': ['https://pypi.python.org/packages/source/d/docopt'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-3.6.1-intel-2017a.eb b/easybuild/easyconfigs/p/Python/Python-3.6.1-intel-2017a.eb index b226f52d51..e17d931cf2 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.6.1-intel-2017a.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.6.1-intel-2017a.eb @@ -122,6 +122,9 @@ exts_list = [ ('virtualenv', '15.1.0', { 'source_urls': ['https://pypi.python.org/packages/source/v/virtualenv'], }), + ('docopt', '0.6.2', { + 'source_urls': ['https://pypi.python.org/packages/source/d/docopt'], + }), ] moduleclass = 'lang' -- GitLab From 142de8b1f27f9072d0533a75da2ef01dff17f941 Mon Sep 17 00:00:00 2001 From: Yann Pouillon Date: Fri, 23 Jun 2017 13:35:23 +0200 Subject: [PATCH 1000/1603] adding easyconfigs: ASE-3.13.0-foss-2016b-Python-2.7.12.eb --- .../ASE-3.13.0-foss-2016b-Python-2.7.12.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/a/ASE/ASE-3.13.0-foss-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.13.0-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/a/ASE/ASE-3.13.0-foss-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..52093a758b --- /dev/null +++ b/easybuild/easyconfigs/a/ASE/ASE-3.13.0-foss-2016b-Python-2.7.12.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'ASE' +version = '3.13.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://wiki.fysik.dtu.dk/ase' +description = """ASE is a python package providing an open source Atomic Simulation Environment + in the Python scripting language.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +checksums = ['e946a0addc5b61e5e2e75857e0f99b89'] + +dependencies = [ + ('Python', '2.7.12'), +] + +sanity_check_paths = { + 'files': ['bin/ase-build', 'bin/ase-db', 'bin/ase-gui', 'bin/ase-info', 'bin/ase-run'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'], +} + +moduleclass = 'chem' + -- GitLab From f1ee7342249f0e4fe516e3024080cd0fdff81de1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 24 Jun 2017 10:59:47 +0200 Subject: [PATCH 1001/1603] stop using deprecated 2-element tuple format in sources, use equivalent dict format instead --- .../a/ABINIT/ABINIT-7.0.3-x86_64_linux_gnu4.5.eb | 6 ++++-- .../a/ABINIT/ABINIT-7.0.5-x86_64_linux_gnu4.5.eb | 6 ++++-- .../a/ABINIT/ABINIT-7.2.1-x86_64_linux_gnu4.5.eb | 6 ++++-- .../a/Aspera-CLI/Aspera-CLI-3.7.2.354.010c3b8.eb | 8 ++++---- easybuild/easyconfigs/a/ack/ack-2.14.eb | 2 +- easybuild/easyconfigs/g/GATE/GATE-6.2-goolf-1.4.10.eb | 5 ++++- easybuild/easyconfigs/g/GATE/GATE-6.2-intel-2015a.eb | 5 ++++- .../g/GATE/GATE-6.2-intel-2016a-Python-2.7.11.eb | 5 ++++- easybuild/easyconfigs/g/GATE/GATE-7.0-intel-2015a.eb | 5 ++++- .../g/GATE/GATE-7.1-intel-2016a-Python-2.7.11.eb | 5 ++++- .../g/GATE/GATE-7.2-intel-2016a-Python-2.7.11.eb | 5 ++++- easybuild/easyconfigs/g/GIMPS/GIMPS-p95v279-GCC-4.8.2.eb | 5 ++++- .../OpenBLAS-0.2.18-GCC-4.9.4-2.25-LAPACK-3.6.0.eb | 2 +- .../OpenBLAS-0.2.18-GCC-5.3.0-2.26-LAPACK-3.6.0.eb | 2 +- .../OpenBLAS-0.2.18-GCC-5.4.0-2.26-LAPACK-3.6.0.eb | 2 +- .../OpenBLAS-0.2.18-GCC-5.4.0-2.26-LAPACK-3.6.1.eb | 2 +- .../OpenBLAS-0.2.18-gompi-2016.07-LAPACK-3.6.1.eb | 2 +- .../OpenBLAS-0.2.19-GCC-5.4.0-2.26-LAPACK-3.7.0.eb | 2 +- .../OpenBLAS-0.2.19-GCC-6.3.0-2.27-LAPACK-3.7.0.eb | 2 +- .../OpenBLAS-0.2.19-gompi-2016.09-LAPACK-3.6.1.eb | 2 +- .../OpenBLAS-0.2.19-gompic-2016.10-LAPACK-3.6.1.eb | 2 +- easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016a.eb | 2 +- easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016b.eb | 2 +- .../easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016a.eb | 2 +- .../easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016b.eb | 2 +- .../easyconfigs/p/pbbam/pbbam-20170508-intel-2017a.eb | 2 +- .../s/SURF/SURF-1.0-goolf-1.4.10-LINUXAMD64.eb | 2 +- .../easyconfigs/s/SURF/SURF-1.0-ictce-5.3.0-LINUXAMD64.eb | 2 +- .../easyconfigs/v/VarScan/VarScan-2.3.6-Java-1.7.0_80.eb | 2 +- 29 files changed, 62 insertions(+), 35 deletions(-) diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.0.3-x86_64_linux_gnu4.5.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.0.3-x86_64_linux_gnu4.5.eb index 9ff4e547c0..0674deea91 100644 --- a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.0.3-x86_64_linux_gnu4.5.eb +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.0.3-x86_64_linux_gnu4.5.eb @@ -22,9 +22,11 @@ description = """Abinit is a plane wave pseudopotential code for doing toolchain = {'name': 'dummy', 'version': 'dummy'} -# eg. http://ftp.abinit.org/abinit-7.0.3_x86_64_linux_gnu4.5.bz2 -sources = [('abinit-%s_%s.bz2' % (version, versionsuffix[1:]), 'tar xfj %s')] source_urls = ['http://ftp.abinit.org/'] +sources = [{ + 'filename': 'abinit-%%(version)s_%s.bz2' % versionsuffix[1:], + 'extract_cmd': "tar xfj %s", +}] sanity_check_paths = { 'files': ["bin/abinit"], diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.0.5-x86_64_linux_gnu4.5.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.0.5-x86_64_linux_gnu4.5.eb index b5b040ce63..f6e72f3fb7 100644 --- a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.0.5-x86_64_linux_gnu4.5.eb +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.0.5-x86_64_linux_gnu4.5.eb @@ -24,9 +24,11 @@ description = """Abinit is a plane wave pseudopotential code for doing toolchain = {'name': 'dummy', 'version': 'dummy'} -# eg. http://ftp.abinit.org/abinit-7.0.5_x86_64_linux_gnu4.5.bz2 -sources = [('abinit-%s_%s.bz2' % (version, versionsuffix[1:]), 'tar xfj %s')] source_urls = ['http://ftp.abinit.org/'] +sources = [{ + 'filename': 'abinit-%%(version)s_%s.bz2' % versionsuffix[1:], + 'extract_cmd': "tar xfj %s", +}] sanity_check_paths = { 'files': ["bin/abinit"], diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.2.1-x86_64_linux_gnu4.5.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.2.1-x86_64_linux_gnu4.5.eb index 051d0927bf..a5a53cf83d 100644 --- a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.2.1-x86_64_linux_gnu4.5.eb +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.2.1-x86_64_linux_gnu4.5.eb @@ -25,9 +25,11 @@ description = """Abinit is a plane wave pseudopotential code for doing toolchain = {'name': 'dummy', 'version': 'dummy'} -# eg. http://ftp.abinit.org/abinit-7.0.5_x86_64_linux_gnu4.5.bz2 -sources = [('abinit-%s_%s.bz2' % (version, versionsuffix[1:]), 'tar xfj %s')] source_urls = ['http://ftp.abinit.org/'] +sources = [{ + 'filename': 'abinit-%%(version)s_%s.bz2' % versionsuffix[1:], + 'extract_cmd': "tar xfj %s", +}] sanity_check_paths = { 'files': ["bin/abinit"], diff --git a/easybuild/easyconfigs/a/Aspera-CLI/Aspera-CLI-3.7.2.354.010c3b8.eb b/easybuild/easyconfigs/a/Aspera-CLI/Aspera-CLI-3.7.2.354.010c3b8.eb index c5b603114d..576043e6dd 100644 --- a/easybuild/easyconfigs/a/Aspera-CLI/Aspera-CLI-3.7.2.354.010c3b8.eb +++ b/easybuild/easyconfigs/a/Aspera-CLI/Aspera-CLI-3.7.2.354.010c3b8.eb @@ -22,10 +22,10 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} # fixed location. Need to include custom extract command to pull # tarball out of install script and pipe to tar. %s in the extraction # command will be replaced by the source filename. -sources = [ - ('%(namelower)s-%(version)s%(versionsuffix)s-linux-64-release.sh', - "sed '1,/^__ARCHIVE_FOLLOWS__$/d' %s | tar -xzpo --strip-components 1 -f -") -] +sources = [{ + 'filename': '%(namelower)s-%(version)s%(versionsuffix)s-linux-64-release.sh', + 'extract_cmd': "sed '1,/^__ARCHIVE_FOLLOWS__$/d' %s | tar -xzpo --strip-components 1 -f -", +}] source_urls = ['http://download.asperasoft.com/download/sw/cli/%(version)s'] checksums = ['02787ca46814fb9ae2de5c706461367e'] diff --git a/easybuild/easyconfigs/a/ack/ack-2.14.eb b/easybuild/easyconfigs/a/ack/ack-2.14.eb index 7f10d7a34e..2fd715d572 100644 --- a/easybuild/easyconfigs/a/ack/ack-2.14.eb +++ b/easybuild/easyconfigs/a/ack/ack-2.14.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = [homepage] # use 'cp' as 'unpack' command -sources = [('ack-%(version)s-single-file', "cp %s ack")] +sources = [{'filename': 'ack-%(version)s-single-file', 'extract_cmd': "cp %s ack"}] cmds_map = [('ack', "chmod a+rx ack")] diff --git a/easybuild/easyconfigs/g/GATE/GATE-6.2-goolf-1.4.10.eb b/easybuild/easyconfigs/g/GATE/GATE-6.2-goolf-1.4.10.eb index 89a8046f2f..a70370fb6a 100644 --- a/easybuild/easyconfigs/g/GATE/GATE-6.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/g/GATE/GATE-6.2-goolf-1.4.10.eb @@ -8,8 +8,11 @@ description = """GATE is an advanced opensource software developed by the intern toolchain = {'name': 'goolf', 'version': '1.4.10'} -sources = [('%%(namelower)s_v%s_tar_gz_15843.gz' % '_'.join(version.split('.')), "tar xfvz %s")] source_urls = ['http://www.opengatecollaboration.org/sites/opengatecollaboration.org/files/gate_release/2012/08/'] +sources = [{ + 'filename': '%%(namelower)s_v%s_tar_gz_15843.gz' % '_'.join(version.split('.')), + 'extract_cmd': "tar xfvz %s", +}] patches = [ 'GATE-%(version)s_Makefile-prefix.patch', diff --git a/easybuild/easyconfigs/g/GATE/GATE-6.2-intel-2015a.eb b/easybuild/easyconfigs/g/GATE/GATE-6.2-intel-2015a.eb index 1a6ef28db9..9cfaecb8e1 100644 --- a/easybuild/easyconfigs/g/GATE/GATE-6.2-intel-2015a.eb +++ b/easybuild/easyconfigs/g/GATE/GATE-6.2-intel-2015a.eb @@ -8,8 +8,11 @@ description = """GATE is an advanced opensource software developed by the intern toolchain = {'name': 'intel', 'version': '2015a'} -sources = [('%%(namelower)s_v%s_tar_gz_15843.gz' % '_'.join(version.split('.')), "tar xfvz %s")] source_urls = ['http://www.opengatecollaboration.org/sites/opengatecollaboration.org/files/gate_release/2012/08/'] +sources = [{ + 'filename': '%%(namelower)s_v%s_tar_gz_15843.gz' % '_'.join(version.split('.')), + 'extract_cmd': "tar xfvz %s", +}] patches = [ 'GATE-%(version)s_Makefile-prefix.patch', diff --git a/easybuild/easyconfigs/g/GATE/GATE-6.2-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/g/GATE/GATE-6.2-intel-2016a-Python-2.7.11.eb index d237afef62..34c0cd8a2e 100644 --- a/easybuild/easyconfigs/g/GATE/GATE-6.2-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/g/GATE/GATE-6.2-intel-2016a-Python-2.7.11.eb @@ -9,8 +9,11 @@ description = """GATE is an advanced opensource software developed by the intern toolchain = {'name': 'intel', 'version': '2016a'} -sources = [('%%(namelower)s_v%s_tar_gz_15843.gz' % '_'.join(version.split('.')), "tar xfvz %s")] source_urls = ['http://www.opengatecollaboration.org/sites/opengatecollaboration.org/files/gate_release/2012/08/'] +sources = [{ + 'filename': '%%(namelower)s_v%s_tar_gz_15843.gz' % '_'.join(version.split('.')), + 'extract_cmd': "tar xfvz %s", +}] patches = [ 'GATE-%(version)s_Makefile-prefix.patch', diff --git a/easybuild/easyconfigs/g/GATE/GATE-7.0-intel-2015a.eb b/easybuild/easyconfigs/g/GATE/GATE-7.0-intel-2015a.eb index 85541021f4..c3235c1acd 100644 --- a/easybuild/easyconfigs/g/GATE/GATE-7.0-intel-2015a.eb +++ b/easybuild/easyconfigs/g/GATE/GATE-7.0-intel-2015a.eb @@ -8,7 +8,10 @@ description = """GATE is an advanced opensource software developed by the intern toolchain = {'name': 'intel', 'version': '2015a'} -sources = [('%(namelower)s_v%(version)s.tar_.gz', "tar xfvz %s")] +sources = [{ + 'filename': '%(namelower)s_v%(version)s.tar_.gz', + 'extract_cmd': "tar xfvz %s", +}] source_urls = ['http://www.opengatecollaboration.org/sites/opengatecollaboration.org/files/'] patches = [ diff --git a/easybuild/easyconfigs/g/GATE/GATE-7.1-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/g/GATE/GATE-7.1-intel-2016a-Python-2.7.11.eb index ddcd9aaa7c..f338b1fb86 100644 --- a/easybuild/easyconfigs/g/GATE/GATE-7.1-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/g/GATE/GATE-7.1-intel-2016a-Python-2.7.11.eb @@ -9,7 +9,10 @@ description = """GATE is an advanced opensource software developed by the intern toolchain = {'name': 'intel', 'version': '2016a'} -sources = [('%(namelower)s_v%(version)s.tar.gz', "tar xfvz %s")] +sources = [{ + 'filename': '%(namelower)s_v%(version)s.tar.gz', + 'extract_cmd': "tar xfvz %s", +}] source_urls = ['http://www.opengatecollaboration.org/sites/opengatecollaboration.org/files/'] patches = [ diff --git a/easybuild/easyconfigs/g/GATE/GATE-7.2-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/g/GATE/GATE-7.2-intel-2016a-Python-2.7.11.eb index 91e8c30f8c..923a13d19f 100644 --- a/easybuild/easyconfigs/g/GATE/GATE-7.2-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/g/GATE/GATE-7.2-intel-2016a-Python-2.7.11.eb @@ -9,7 +9,10 @@ description = """GATE is an advanced opensource software developed by the intern toolchain = {'name': 'intel', 'version': '2016a'} -sources = [('%(namelower)s_v%(version)s.tar.gz', "tar xfvz %s")] +sources = [{ + 'filename': '%(namelower)s_v%(version)s.tar.gz', + 'extract_cmd': "tar xfvz %s", +}] source_urls = ['http://www.opengatecollaboration.org/sites/opengatecollaboration.org/files/'] patches = [ diff --git a/easybuild/easyconfigs/g/GIMPS/GIMPS-p95v279-GCC-4.8.2.eb b/easybuild/easyconfigs/g/GIMPS/GIMPS-p95v279-GCC-4.8.2.eb index b6ac9d8f9f..ebe4c931a7 100644 --- a/easybuild/easyconfigs/g/GIMPS/GIMPS-p95v279-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/g/GIMPS/GIMPS-p95v279-GCC-4.8.2.eb @@ -21,7 +21,10 @@ builddependencies = [('cURL', '7.33.0')] # make sure unzip works, zipped sources may contain some 'corruption', # e.g. "linux64/: ucsize 306 <> csize 0 for STORED entry" -sources = [('%(version)s.source.zip', 'unzip -qq %s || /bin/true')] +sources = [{ + 'filename': '%(version)s.source.zip', + 'extract_cmd': "unzip -qq %s || /bin/true", +}] # e.g. http://www.mersenne.info/gimps/p95v279.source.zip source_urls = ['http://www.mersenne.info/%(namelower)s'] diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-4.9.4-2.25-LAPACK-3.6.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-4.9.4-2.25-LAPACK-3.6.0.eb index 28a8a8d5c5..475ac86396 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-4.9.4-2.25-LAPACK-3.6.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-4.9.4-2.25-LAPACK-3.6.0.eb @@ -21,7 +21,7 @@ lapack_unpack_cmd += 'tar -C lapack-netlib --strip-components=1 -zxf %s; cd -' sources = [ 'v%(version)s.tar.gz', - (lapack_src, lapack_unpack_cmd), + {'filename': lapack_src, 'extract_cmd': lapack_unpack_cmd}, large_src, timing_src, ] diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-5.3.0-2.26-LAPACK-3.6.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-5.3.0-2.26-LAPACK-3.6.0.eb index 92f08781e2..06c39b8261 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-5.3.0-2.26-LAPACK-3.6.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-5.3.0-2.26-LAPACK-3.6.0.eb @@ -21,7 +21,7 @@ lapack_unpack_cmd += 'tar -C lapack-netlib --strip-components=1 -zxf %s; cd -' sources = [ 'v%(version)s.tar.gz', - (lapack_src, lapack_unpack_cmd), + {'filename': lapack_src, 'extract_cmd': lapack_unpack_cmd}, large_src, timing_src, ] diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-5.4.0-2.26-LAPACK-3.6.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-5.4.0-2.26-LAPACK-3.6.0.eb index 0b62a315f7..eaa818e625 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-5.4.0-2.26-LAPACK-3.6.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-5.4.0-2.26-LAPACK-3.6.0.eb @@ -21,7 +21,7 @@ lapack_unpack_cmd += 'tar -C lapack-netlib --strip-components=1 -zxf %s; cd -' sources = [ 'v%(version)s.tar.gz', - (lapack_src, lapack_unpack_cmd), + {'filename': lapack_src, 'extract_cmd': lapack_unpack_cmd}, large_src, timing_src, ] diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-5.4.0-2.26-LAPACK-3.6.1.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-5.4.0-2.26-LAPACK-3.6.1.eb index 85f10c536a..dc7f656e6a 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-5.4.0-2.26-LAPACK-3.6.1.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-5.4.0-2.26-LAPACK-3.6.1.eb @@ -21,7 +21,7 @@ lapack_unpack_cmd += 'tar -C lapack-netlib --strip-components=1 -zxf %s; cd -' sources = [ 'v%(version)s.tar.gz', - (lapack_src, lapack_unpack_cmd), + {'filename': lapack_src, 'extract_cmd': lapack_unpack_cmd}, large_src, timing_src, ] diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-gompi-2016.07-LAPACK-3.6.1.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-gompi-2016.07-LAPACK-3.6.1.eb index 80a706fa33..17a2ecb828 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-gompi-2016.07-LAPACK-3.6.1.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-gompi-2016.07-LAPACK-3.6.1.eb @@ -21,7 +21,7 @@ lapack_unpack_cmd += 'tar -C lapack-netlib --strip-components=1 -zxf %s; cd -' sources = [ 'v%(version)s.tar.gz', - (lapack_src, lapack_unpack_cmd), + {'filename': lapack_src, 'extract_cmd': lapack_unpack_cmd}, large_src, timing_src, ] diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-GCC-5.4.0-2.26-LAPACK-3.7.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-GCC-5.4.0-2.26-LAPACK-3.7.0.eb index 4c55b7dc6c..61372509b2 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-GCC-5.4.0-2.26-LAPACK-3.7.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-GCC-5.4.0-2.26-LAPACK-3.7.0.eb @@ -21,7 +21,7 @@ lapack_unpack_cmd += 'tar -C lapack-netlib --strip-components=1 -zxf %s; cd -' sources = [ 'v%(version)s.tar.gz', - (lapack_src, lapack_unpack_cmd), + {'filename': lapack_src, 'extract_cmd': lapack_unpack_cmd}, large_src, timing_src, ] diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-GCC-6.3.0-2.27-LAPACK-3.7.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-GCC-6.3.0-2.27-LAPACK-3.7.0.eb index 143c9edae7..d9aed5da09 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-GCC-6.3.0-2.27-LAPACK-3.7.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-GCC-6.3.0-2.27-LAPACK-3.7.0.eb @@ -21,7 +21,7 @@ lapack_unpack_cmd += 'tar -C lapack-netlib --strip-components=1 -zxf %s; cd -' sources = [ 'v%(version)s.tar.gz', - (lapack_src, lapack_unpack_cmd), + {'filename': lapack_src, 'extract_cmd': lapack_unpack_cmd}, large_src, timing_src, ] diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-gompi-2016.09-LAPACK-3.6.1.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-gompi-2016.09-LAPACK-3.6.1.eb index 0978b24ced..761f990fdb 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-gompi-2016.09-LAPACK-3.6.1.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-gompi-2016.09-LAPACK-3.6.1.eb @@ -21,7 +21,7 @@ lapack_unpack_cmd += 'tar -C lapack-netlib --strip-components=1 -zxf %s; cd -' sources = [ 'v%(version)s.tar.gz', - (lapack_src, lapack_unpack_cmd), + {'filename': lapack_src, 'extract_cmd': lapack_unpack_cmd}, large_src, timing_src, ] diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-gompic-2016.10-LAPACK-3.6.1.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-gompic-2016.10-LAPACK-3.6.1.eb index 55794b4474..f4055fe601 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-gompic-2016.10-LAPACK-3.6.1.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-gompic-2016.10-LAPACK-3.6.1.eb @@ -21,7 +21,7 @@ lapack_unpack_cmd += 'tar -C lapack-netlib --strip-components=1 -zxf %s; cd -' sources = [ 'v%(version)s.tar.gz', - (lapack_src, lapack_unpack_cmd), + {'filename': lapack_src, 'extract_cmd': lapack_unpack_cmd}, large_src, timing_src, ] diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016a.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016a.eb index 141e1f7cdd..2faed16c6d 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016a.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016a.eb @@ -19,7 +19,7 @@ source_urls = [ sources = [ '%(version)s.zip', - ('ippicv_linux_20151201.tgz', 'cp %s %(builddir)s'), + {'filename': 'ippicv_linux_20151201.tgz', 'extract_cmd': "cp %s %(builddir)s"}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016b.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016b.eb index 1495f695f6..31bcd04d21 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016b.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016b.eb @@ -19,7 +19,7 @@ source_urls = [ sources = [ '%(version)s.zip', - ('ippicv_linux_20151201.tgz', 'cp %s %(builddir)s'), + {'filename': 'ippicv_linux_20151201.tgz', 'extract_cmd': "cp %s %(builddir)s"}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016a.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016a.eb index 23de8de267..7b5c4b2c99 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016a.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016a.eb @@ -19,7 +19,7 @@ source_urls = [ sources = [ '%(version)s.zip', - ('ippicv_linux_20151201.tgz', 'cp %s %(builddir)s'), + {'filename': 'ippicv_linux_20151201.tgz', 'extract_cmd': "cp %s %(builddir)s"}, ] patches = ['OpenCV-%(version)s_with_IPP.patch'] diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016b.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016b.eb index 0b6f2141a7..dadbcc0e05 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016b.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016b.eb @@ -19,7 +19,7 @@ source_urls = [ sources = [ '%(version)s.zip', - ('ippicv_linux_20151201.tgz', 'cp %s %(builddir)s'), + {'filename': 'ippicv_linux_20151201.tgz', 'extract_cmd': "cp %s %(builddir)s"}, ] patches = ['OpenCV-%(version)s_with_IPP.patch'] diff --git a/easybuild/easyconfigs/p/pbbam/pbbam-20170508-intel-2017a.eb b/easybuild/easyconfigs/p/pbbam/pbbam-20170508-intel-2017a.eb index cfbcaf72eb..a724ce7cbe 100644 --- a/easybuild/easyconfigs/p/pbbam/pbbam-20170508-intel-2017a.eb +++ b/easybuild/easyconfigs/p/pbbam/pbbam-20170508-intel-2017a.eb @@ -16,7 +16,7 @@ source_urls = [ 'https://github.com/google/googletest/archive/', ] sources = [ - ('%s.tar.gz' % commit, "tar xfvz %s --strip-components=1"), # pbbam + {'filename': '%s.tar.gz' % commit, 'extract_cmd': "tar xfvz %s --strip-components=1"}, # pbbam 'release-%s.tar.gz' % gtest_ver, # googletest ] diff --git a/easybuild/easyconfigs/s/SURF/SURF-1.0-goolf-1.4.10-LINUXAMD64.eb b/easybuild/easyconfigs/s/SURF/SURF-1.0-goolf-1.4.10-LINUXAMD64.eb index bf5aca8371..29f05e2070 100644 --- a/easybuild/easyconfigs/s/SURF/SURF-1.0-goolf-1.4.10-LINUXAMD64.eb +++ b/easybuild/easyconfigs/s/SURF/SURF-1.0-goolf-1.4.10-LINUXAMD64.eb @@ -14,7 +14,7 @@ description = "A molecular surface solver, which can be used as rendering method toolchain = {'name': 'goolf', 'version': '1.4.10'} source_urls = ['http://www.ks.uiuc.edu/Research/vmd/extsrcs'] -sources = [('%(namelower)s.tar.Z', 'tar -xzf %s')] +sources = [{'filename': '%(namelower)s.tar.Z', 'extract_cmd': "tar -xzf %s"}] builddependencies = [ ('makedepend', '1.0.4'), diff --git a/easybuild/easyconfigs/s/SURF/SURF-1.0-ictce-5.3.0-LINUXAMD64.eb b/easybuild/easyconfigs/s/SURF/SURF-1.0-ictce-5.3.0-LINUXAMD64.eb index c10863bf70..4fb273d1b6 100644 --- a/easybuild/easyconfigs/s/SURF/SURF-1.0-ictce-5.3.0-LINUXAMD64.eb +++ b/easybuild/easyconfigs/s/SURF/SURF-1.0-ictce-5.3.0-LINUXAMD64.eb @@ -14,7 +14,7 @@ description = "A molecular surface solver, which can be used as rendering method toolchain = {'name': 'ictce', 'version': '5.3.0'} source_urls = ['http://www.ks.uiuc.edu/Research/vmd/extsrcs'] -sources = [('%(namelower)s.tar.Z', 'tar -xzf %s')] +sources = [{'filename': '%(namelower)s.tar.Z', 'extract_cmd': "tar -xzf %s"}] builddependencies = [ ('makedepend', '1.0.4'), diff --git a/easybuild/easyconfigs/v/VarScan/VarScan-2.3.6-Java-1.7.0_80.eb b/easybuild/easyconfigs/v/VarScan/VarScan-2.3.6-Java-1.7.0_80.eb index af1032ae7a..88844689a5 100644 --- a/easybuild/easyconfigs/v/VarScan/VarScan-2.3.6-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/v/VarScan/VarScan-2.3.6-Java-1.7.0_80.eb @@ -13,7 +13,7 @@ description = """Variant calling and somatic mutation/CNV detection for next-gen toolchain = {'name': 'dummy', 'version': ''} -sources = [('%(name)s.v%(version)s.jar', 'download')] +sources = ['%(name)s.v%(version)s.jar'] source_urls = ['https://sourceforge.net/projects/varscan/files/'] dependencies = [('Java', '1.7.0_80')] -- GitLab From 9c339304b79ccc16782ae33bec338bfcd3c42d66 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 24 Jun 2017 10:59:19 +0200 Subject: [PATCH 1002/1603] minor tweaks in EasyBuild v3.3.0 release notes --- RELEASE_NOTES | 43 ++++++++++++++++++++++--------------------- 1 file changed, 22 insertions(+), 21 deletions(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index 9d60ed1d8b..a2c55382cb 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -3,44 +3,45 @@ For more detailed information, please see the git log. These release notes can also be consulted at http://easybuild.readthedocs.org/en/latest/Release_notes.html. -The latest version of easybuild-easyconfig provides 7,260 easyconfig files, for 1,256 different software packages, +The latest version of easybuild-easyconfig provides 7,248 easyconfig files, for 1,256 different software packages, 25 different (compiler) toolchains, 13 software bundles and 1 meta-package. -v3.3.0 (June 23rd 2017) +v3.3.0 (June 24th 2017) ----------------------- feature release - enable automatic style checks in easyconfig tests (#2506) - added example easyconfig files for 28 new software packages: - - AUGUSTUS (#4624), Aspera-CLI (#4635), ada (#4594), BUSCO (#4624), Bio-SamTools (#4637), Bpipe (#4590), CNVnator (#4649), - davix (#4755), EricScript (#4594), FUNWAVE-TVD (#4743), gSOAP (#4755), gmpy2 (#4609), LUMPY (#4682), libsndfile (#4628), - lpsolve (#4264), MXNet (#4765), MaSuRCA (#4706), modred (#4729), NRGLjubljana (#4651), OrfM (#4703), - Perl4-CoreLibs (#4670), prodigal (#4468), pydlpoly (#4756), SeqAn (#4603), Spyder (#4627), sharutils (#4745), - Tkinter (#4620), VariantMetaCaller (#4632) + - ada (#4594), Aspera-CLI (#4635), AUGUSTUS (#4624), ada (#4594), Bio-SamTools (#4637), Bpipe (#4590), BUSCO (#4624), + CNVnator (#4649), davix (#4755), EricScript (#4594), FUNWAVE-TVD (#4743), gmpy2 (#4609), gSOAP (#4755), + libsndfile (#4628), lpsolve (#4264), LUMPY (#4682), MaSuRCA (#4706), modred (#4729), MXNet (#4765), + NRGLjubljana (#4651), OrfM (#4703), Perl4-CoreLibs (#4670), prodigal (#4468), pydlpoly (#4756), SeqAn (#4603), + sharutils (#4745), Spyder (#4627), Tkinter (#4620), VariantMetaCaller (#4632) +- added new easyconfigs for existing toolchains: + - gimkl 2017a (#4646) - added additional easyconfigs for various supported software packages, including: - - ABINIT 8.0.8b, ABINIT 8.2.2, ABINIT 8.2.2, ANTLR 2.7.7, AUGUSTUS 3.2.3, Aspera CLI, ada 2.0, arpack ng, BEDOPS 2.4.26.eb, BEDTools 2.26.0, BLAST+ 2.6.0, BUSCO 2.0.1, BWA 0.7.15, Bio SamTools, Bowtie2 2.3.2, Bpipe 0.9.9.2, basemap 1.0.7, buildenv default, bzip2 1.0.6, CDO 1.8.1, CGAL 4.8.1, CMake 3.6.1.eb, CMake 3.8.2, CNVnator 0.3.3, cURL 7.49.1, cURL 7.52.1, DB 6.0.30, DBD mysql, DIAMOND 0.9.6, Doris 4.04beta4, Doris 4.06beta2, Doxygen 1.8.11, davix 0.6.6, EMBOSS 6.6.0, ESMF 6.3.0rp1, EasyBuild 3.2.1.eb, Eigen 3.2.9, EricScript 0.5.5, eudev 3.1.5, expat 2.2.0, expat 2.2.0, FASTA 36.3.5e, FFTW 2.1.5, FFTW 2.1.5, FFmpeg 3.3.1, FLTK 1.3.4, FSL 5.0.10, FUNWAVE TVD, FUNWAVE TVD, flex 2.6.4, fontconfig 2.12.1, freeglut 3.0.0, freetype 2.6.5, GD 2.66, GDAL 2.1.3, GDAL 2.2.0, GDAL 2.2.0, GEOS 3.6.1, GL2PS 1.4.0, GLPK 4.61, GLib 2.48.2, GMP 6.1.1, GMT 5.4.1, GObject Introspection, GraphicsMagick 1.3.25, Guile 1.8.8, gSOAP 2.8.48, gettext 0.19.8, gettext 0.19.8, gimkl 2017a.eb, gimpi 2017a.eb, gmpy2 2.0.8, gnuplot 5.0.6, gperf 3.0.4, gperf 3.0.4, gtest 1.8.0, HTSlib 1.4.1, HarfBuzz 1.3.1, h5py 2.7.0, ImageMagick 7.0.5, imbalanced learn, imkl 2017.1.132, impi 2017.1.132, JasPer 2.0.12, Java 1.8.0_131.eb, Keras 2.0.4, LAME 3.99.5, LLVM 3.7.1, LUMPY 0.2.13, LibTIFF 4.0.7, LibUUID 1.0.3, LittleCMS 2.8, libGLU 9.0.0, libcerf 1.5, libdap 3.18.1, libdrm 2.4.68, libffi 3.2.1, libgd 2.2.4, libgd 2.2.4, libharu 2.3.0, libidn 1.32, libjpeg turbo, libjpeg turbo, libpciaccess 0.13.4, libpng 1.6.24, libpng 1.6.28, libpthread stubs, libreadline 6.2, libreadline 6.3, libreadline 6.3, libsndfile 1.0.28, libtasn1 4.12, libunistring 0.9.6, libxc 3.0.0, libxc 3.0.0, libxml2 2.9.4, libxml2 2.9.4, lpsolve 5.5.2.5, lynx 2.8.9, MATLAB 2017a.eb, MPC 1.0.3, MUMmer 4.0.0beta, MXNet 0.9.3, MaSuRCA 3.2.2, MariaDB 10.1.24, Mesa 11.2.1, makedepend 1.0.5, matplotlib 2.0.2, matplotlib 2.0.2, matplotlib 2.0.2, modred 2.0.2, motif 2.3.7, NAMD 2.12, NASM 2.11.08, NASM 2.12.02.eb, NCL 6.4.0, NCO 4.6.6, NRGLjubljana 2.4.3.23, ncurses 6.0, ne 3.0.1, netCDF C++4, netCDF Fortran, netCDF 4.4.1.1, nettle 3.2, Octave 4.2.1, OrfM 0.6.1, PGI 16.1, PIL 1.1.7, Pango 1.40.5, Perl 5.22.0, Perl 5.22.0, Perl4 CoreLibs, Platanus 1.2.4, PyOpenGL 3.1.1a1, PyQt 4.12, PyQt5 5.8.2, Python 2.7.12, Python 3.5.2, Python 3.5.2, p11 kit, picard 2.2.4, pkg config, prodigal 2.6.2, pydlpoly 20150225, pydlpoly 20150225, Qhull 2015.2, Qt 4.8.7, qrupdate 1.1.2, Ruby 2.3.4.eb, Rust 1.18.0, SAMtools 0.1.17, SAMtools 1.4.1, SAMtools 1.5, SCons 2.5.1, SIP 4.19.2, SQLite 3.13.0, SQLite 3.8.9, STAR 2.5.3a, SWIG 3.0.12, SeqAn 2.3.2, Singularity 2.2.1, SpiceyPy 1.1.1, Spyder 3.1.4, StringTie 1.3.3b, Szip 2.1, scikit learn, segemehl 0.2.0, seqtk 1.2, sharutils 4.15, sleuth 0.29.0, statsmodels 0.8.0, Tcl 8.6.5, Theano 0.9.0, Tk 8.6.5, Tkinter 2.7.13, TopHat 2.1.1, Trim_Galore 0.4.4, tbb 2017.6.196.eb, tbb 2017_U6, VTK 7.1.1, VTune 2017_update3.eb, VariantMetaCaller 1.0, Velvet 1.2.10, X11 20160819, XZ 5.2.2, XZ 5.2.3, xarray 0.9.5, xbitmaps 1.1.1.eb, xprop 1.2.2, YAXT 0.5.1, zlib 1.2.11 + - ABINIT 8.2.2, BLAST+ 2.6.0, Bowtie2 2.3.2, FFmpeg 3.3.1, NCL 6.4.0, Rust 1.18.0, SAMtools 1.5, VTK 7.1.1 - minor enhancements, including: - - use 'git diff --name-only' and $TRAVIS_COMMIT_RANGE in Travis config to get list of changed files (#4606) - - fix typo in statsmodels source url (/sources/ -> /source/) (#4612) - - branch to current HEAD in Travis config to get relevant list of changed files (#4619) - - add tuneR, seewave, soundecology extensions for R 3.4.0 (+ libsndfile as dep) (#4628) + - use 'git diff --name-only' and $TRAVIS_COMMIT_RANGE in Travis config to get list of changed files (#4606, #4619) + - add tuneR, seewave, soundecology, vcfR extensions for R 3.4.0 (+ libsndfile as dep) (#4628, #4680, #4747) - also copy README for GapFiller (#4631) - enable inclusion of version symbol by using --enable-ld-version-script configure option for LibTIFF (#4639) + - add SHA256 checksums for libpciaccess to discriminate from old tarballs that required running autogen.sh (#4688) + - fix NE_GLOBAL_DIR path for ne by also specifying PREFIX in buildopts (#4698) + - more (trivial) style fixes (#4761) + - avoid use of import in ANSYS & MATLAB easyconfigs (#4762) + - set $OMP_NUM_THREADS during CP2K test step via dedicated easyconfig parameter (#4763) + - avoid use of 'import' in BFAST easyconfigs, just strip of 'a' from version (#4764) + - stop using deprecated 2-element tuple format in sources, use equivalent dict format instead (#4774) +- various bug fixes, including: + - fix typo in statsmodels source url (/sources/ -> /source/) (#4612) + - add location to DotLib.pm to $PERL5LIB for SSPACE_Basic (#4638) - add missing /gnu/ ins ftpmirror.gnu.org source_urls, or use GNU_SOURCE where possible (#4653) - consistently use --with-harfbuzz=no configure option in freetype easyconfigs (#4668) - - add vcfR extension in R 3.4.0 easyconfig (#4680) - - add SHA256 checksums for libpciaccess (#4688) - - ne (nice editor) fix to correct NE_GLOBAL_DIR path (#4698) - - add location to DotLib.pm to $PERL5LIB for SSPACE Basic (#4638) - use --with-x=yes in R easyconfigs that include X11 as a dependency (#4701) - remove '4.0' in tbb description (#4707) - add lib sanity check paths for debian compatibility in nettle (#4722) - - add glmmML & ordinal (+ ucminf) as R extensions (#4747) - fix source URLs for HDF5 (#4749) - - more (trivial) style fixes (#4761) - - avoid use of import in ANSYS & MATLAB easyconfigs (#4762) - - set $OMP_NUM_THREADS during CP2K test step via dedicated easyconfig parameter (#4763) - - avoid use of 'import' in BFAST easyconfigs, just strip of 'a' from version (#4764) v3.2.1 (May 12th 2017) -- GitLab From 8f7e530ce1b41980ff827dc46bff43a7c106534c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 25 Jun 2017 11:51:32 +0200 Subject: [PATCH 1003/1603] also include #4770 in EasyBuild v3.3.0 release notes --- RELEASE_NOTES | 1 + 1 file changed, 1 insertion(+) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index a2c55382cb..6775de245c 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -32,6 +32,7 @@ feature release - avoid use of import in ANSYS & MATLAB easyconfigs (#4762) - set $OMP_NUM_THREADS during CP2K test step via dedicated easyconfig parameter (#4763) - avoid use of 'import' in BFAST easyconfigs, just strip of 'a' from version (#4764) + - add the docopt module to all Python 2017a easyconfigs (#4770) - stop using deprecated 2-element tuple format in sources, use equivalent dict format instead (#4774) - various bug fixes, including: - fix typo in statsmodels source url (/sources/ -> /source/) (#4612) -- GitLab From 4ffb4fb69561f7fe69fbc6b339849c92c16002be Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 25 Jun 2017 11:54:00 +0200 Subject: [PATCH 1004/1603] bump version to 3.3.0 --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 85590c2983..2c5a5b79d5 100644 --- a/setup.py +++ b/setup.py @@ -47,7 +47,7 @@ from distutils import log # recent setuptools versions will *TRANSFORM* something like 'X.Y.Zdev' into 'X.Y.Z.dev0', with a warning like # UserWarning: Normalizing '2.4.0dev' to '2.4.0.dev0' # This causes problems further up the dependency chain... -VERSION = '3.3.0.dev0' +VERSION = '3.3.0' API_VERSION = VERSION.split('.')[0] EB_VERSION = '.'.join(VERSION.split('.')[0:2]) -- GitLab From edb13a0170005b7cda6cfca800b72808a29224b8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 25 Jun 2017 20:53:18 +0200 Subject: [PATCH 1005/1603] fix release date for EasyBuild v3.3.0 --- RELEASE_NOTES | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index 6775de245c..31cbc5078b 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -3,10 +3,10 @@ For more detailed information, please see the git log. These release notes can also be consulted at http://easybuild.readthedocs.org/en/latest/Release_notes.html. -The latest version of easybuild-easyconfig provides 7,248 easyconfig files, for 1,256 different software packages, +The latest version of easybuild-easyconfig provides 7,247 easyconfig files, for 1,256 different software packages, 25 different (compiler) toolchains, 13 software bundles and 1 meta-package. -v3.3.0 (June 24th 2017) +v3.3.0 (June 26th 2017) ----------------------- feature release @@ -18,7 +18,7 @@ feature release NRGLjubljana (#4651), OrfM (#4703), Perl4-CoreLibs (#4670), prodigal (#4468), pydlpoly (#4756), SeqAn (#4603), sharutils (#4745), Spyder (#4627), Tkinter (#4620), VariantMetaCaller (#4632) - added new easyconfigs for existing toolchains: - - gimkl 2017a (#4646) + - gimkl/2017a (#4646) - added additional easyconfigs for various supported software packages, including: - ABINIT 8.2.2, BLAST+ 2.6.0, Bowtie2 2.3.2, FFmpeg 3.3.1, NCL 6.4.0, Rust 1.18.0, SAMtools 1.5, VTK 7.1.1 - minor enhancements, including: @@ -41,7 +41,7 @@ feature release - consistently use --with-harfbuzz=no configure option in freetype easyconfigs (#4668) - use --with-x=yes in R easyconfigs that include X11 as a dependency (#4701) - remove '4.0' in tbb description (#4707) - - add lib sanity check paths for debian compatibility in nettle (#4722) + - add lib sanity check paths for Debian compatibility in nettle (#4722) - fix source URLs for HDF5 (#4749) -- GitLab From 746ab0874f0dc8840531cbf5130fbfa7b99f071e Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Mon, 26 Jun 2017 15:54:53 +1200 Subject: [PATCH 1006/1603] New EasyConfig for the X11 bundle with the gimkl-2017a toolchain, plus deps --- .../fontconfig-2.12.1-gimkl-2017a.eb | 22 +++ .../f/freetype/freetype-2.7.1-gimkl-2017a.eb | 26 ++++ .../x/X11/X11-20170129-gimkl-2017a.eb | 135 ++++++++++++++++++ 3 files changed, 183 insertions(+) create mode 100644 easybuild/easyconfigs/f/fontconfig/fontconfig-2.12.1-gimkl-2017a.eb create mode 100644 easybuild/easyconfigs/f/freetype/freetype-2.7.1-gimkl-2017a.eb create mode 100644 easybuild/easyconfigs/x/X11/X11-20170129-gimkl-2017a.eb diff --git a/easybuild/easyconfigs/f/fontconfig/fontconfig-2.12.1-gimkl-2017a.eb b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.12.1-gimkl-2017a.eb new file mode 100644 index 0000000000..5a11636b93 --- /dev/null +++ b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.12.1-gimkl-2017a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'fontconfig' +version = '2.12.1' + +homepage = 'http://www.freedesktop.org/software/fontconfig' +description = """Fontconfig is a library designed to provide system-wide font configuration, customization and +application access.""" + +toolchain = {'name': 'gimkl', 'version': '2017a'} + +source_urls = ['http://www.freedesktop.org/software/fontconfig/release/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('expat', '2.2.0'), + ('freetype', '2.7.1'), +] + +configopts = '--disable-docs ' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.7.1-gimkl-2017a.eb b/easybuild/easyconfigs/f/freetype/freetype-2.7.1-gimkl-2017a.eb new file mode 100644 index 0000000000..ec9a259e85 --- /dev/null +++ b/easybuild/easyconfigs/f/freetype/freetype-2.7.1-gimkl-2017a.eb @@ -0,0 +1,26 @@ +name = 'freetype' +version = "2.7.1" + +homepage = 'http://freetype.org' +description = """FreeType 2 is a software font engine that is designed to be small, efficient, highly customizable, and + portable while capable of producing high-quality output (glyph images). It can be used in graphics libraries, display + servers, font conversion tools, text image generation tools, and many other products as well.""" + +toolchain = {'name': 'gimkl', 'version': '2017a'} + +source_urls = [GNU_SAVANNAH_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('libpng', '1.6.28'), + ('bzip2', '1.0.6'), + ('zlib', '1.2.11'), +] + +sanity_check_paths = { + 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, + 'lib/pkgconfig/freetype2.pc'], + 'dirs': ['include/freetype2'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/x/X11/X11-20170129-gimkl-2017a.eb b/easybuild/easyconfigs/x/X11/X11-20170129-gimkl-2017a.eb new file mode 100644 index 0000000000..71b0754c39 --- /dev/null +++ b/easybuild/easyconfigs/x/X11/X11-20170129-gimkl-2017a.eb @@ -0,0 +1,135 @@ +easyblock = 'Bundle' + +name = 'X11' +version = '20170129' + +homepage = 'https://www.x.org' +description = "The X Window System (X11) is a windowing system for bitmap displays" + +toolchain = {'name': 'gimkl', 'version': '2017a'} + +source_urls = [ + XORG_LIB_SOURCE, + XORG_PROTO_SOURCE, + 'http://xcb.freedesktop.org/dist/', + 'http://xkbcommon.org/download/', + 'http://cgit.freedesktop.org/xorg/util/macros/snapshot', +] + +dependencies = [ + ('bzip2', '1.0.6'), + ('fontconfig', '2.12.1'), # pulls in freetype + ('zlib', '1.2.11'), +] +builddependencies = [ + ('Autotools', '20150215', '', True), + ('Bison', '3.0.4'), + ('gettext', '0.19.8', '', True), + ('pkg-config', '0.29.1'), +] + +default_easyblock = 'ConfigureMake' + +common_specs = { + 'sources': [SOURCE_TAR_GZ], + 'start_dir': '%(name)s-%(version)s', +} +components = [ + ('xorg-macros', '1.19.1', { # 2017-01-29 + 'sources': ['util-macros-%(version)s.tar.gz'], + 'start_dir': 'util-macros-%(version)s', + }), + ('libpthread-stubs', '0.3', common_specs), # 2009-10-14 + ('bigreqsproto', '1.1.2', common_specs), # 2012-03-23 + ('compositeproto', '0.4.2', common_specs), # 2010-10-30 + ('damageproto', '1.2.1', common_specs), # 2010-10-30 + ('dmxproto', '2.3.1', common_specs), # 2011-01-06 + ('dri2proto', '2.8', common_specs), # 2012-07-11 + ('dri3proto', '1.0', common_specs), # 2013-11-01 + ('fixesproto', '5.0', common_specs), # 2011-03-08 + ('fontsproto', '2.1.3', common_specs), # 2014-04-14 + ('glproto', '1.4.17', common_specs), # 2013-12-10 + ('inputproto', '2.3.2', common_specs), # 2016-04-04 + ('kbproto', '1.0.7', common_specs), # 2015-05-01 + ('presentproto', '1.1', common_specs), # 2017-01-26 + ('randrproto', '1.5.0', common_specs), # 2015-05-17 + ('recordproto', '1.14.2', common_specs), # 2012-03-23 + ('renderproto', '0.11.1', common_specs), # 2010-08-10 + ('resourceproto', '1.2.0', common_specs), # 2011-05-28 + ('scrnsaverproto', '1.2.2', common_specs), # 2012-03-23 + ('videoproto', '2.3.3', common_specs), # 2016-03-11 + ('xcmiscproto', '1.2.2', common_specs), # 2012-03-23 + ('xextproto', '7.3.0', common_specs), # 2013-12-27 + ('xf86bigfontproto', '1.2.0', common_specs), # 2009-08-27 + ('xf86dgaproto', '2.1', common_specs), # 2009-10-01 + ('xf86driproto', '2.1.1', common_specs), # 2011-01-06 + ('xf86vidmodeproto', '2.3.1', common_specs), # 2011-01-06 + ('xineramaproto', '1.2.1', common_specs), # 2011-01-06 + ('xproto', '7.0.31', common_specs), # 2016-09-23 + ('libXau', '1.0.8', common_specs), # 2013-05-24 + ('libXdmcp', '1.1.2', common_specs), # 2015-03-21 + ('xcb-proto', '1.12', common_specs), # 2016-05-18 + ('libxcb', '1.12', common_specs), # 2016-05-18 + ('xtrans', '1.3.5', common_specs), # 2014-09-22 + ('libxkbcommon', '0.7.1', { # 2017-01-18 + 'sources': ['libxkbcommon-%(version)s.tar.xz'], + 'start_dir': 'libxkbcommon-%(version)s', + }), + ('libX11', '1.6.4', common_specs), # 2016-10-04 + ('libXext', '1.3.3', common_specs), # 2014-07-24 + ('libFS', '1.0.7', common_specs), # 2015-05-01 + ('libICE', '1.0.9', common_specs), # 2014-06-07 + ('libSM', '1.2.2', common_specs), # 2013-09-08 + ('libXScrnSaver', '1.2.2', common_specs), # 2012-03-08 + ('libXt', '1.1.5', common_specs), # 2015-05-01 + ('libXmu', '1.1.2', common_specs), # 2013-09-08 + ('libXpm', '3.5.12', common_specs), # 2016-12-15 + ('libXaw', '1.0.13', common_specs), # 2015-05-01 + ('libXfixes', '5.0.3', common_specs), # 2016-10-04 + ('libXcomposite', '0.4.4', common_specs), # 2013-01-03 + ('libXrender', '0.9.10', common_specs), # 2016-10-04 + ('libXcursor', '1.1.14', common_specs), # 2013-05-30 + ('libXdamage', '1.1.4', common_specs), # 2013-01-03 + ('libfontenc', '1.1.3', common_specs), # 2015-05-01 + ('libXfont', '1.5.2', common_specs), # 2016-08-31 + ('libXfont2', '2.0.1', common_specs), # 2015-12-11 + ('libXft', '2.3.2', common_specs), # 2014-06-06 + ('libXi', '1.7.9', common_specs), # 2017-01-23 + ('libXinerama', '1.1.3', common_specs), # 2013-05-31 + ('libXrandr', '1.5.1', common_specs), # 2016-10-04 + ('libXres', '1.0.7', common_specs), # 2013-05-31 + ('libXtst', '1.2.3', common_specs), # 2016-10-04 + ('libXv', '1.0.11', common_specs), # 2016-10-04 + ('libXvMC', '1.0.10', common_specs), # 2016-10-04 + ('libXxf86dga', '1.1.4', common_specs), # 2013-05-31 + ('libXxf86vm', '1.1.4', common_specs), # 2015-02-24 + ('libdmx', '1.1.3', common_specs), # 2013-05-28 + ('libpciaccess', '0.13.4', common_specs), # 2015-05-01 + ('libxkbfile', '1.0.9', common_specs), # 2015-05-01 + ('libxshmfence', '1.2', common_specs), # 2015-01-02 + ('xcb-util', '0.4.0', common_specs), # 2014-10-15 + ('xcb-util-image', '0.4.0', common_specs), # 2014-10-15 + ('xcb-util-keysyms', '0.4.0', common_specs), # 2014-10-01 + ('xcb-util-renderutil', '0.3.9', common_specs), # 2014-06-13 + ('xcb-util-wm', '0.4.1', common_specs), # 2014-02-19 + ('xcb-util-cursor', '0.1.3', common_specs), # 2016-05-12 +] + +# Python is required for xcb-proto +allow_system_deps = [ + ('Python', SYS_PYTHON_VERSION), +] +pyshortver = '.'.join(SYS_PYTHON_VERSION.split('.')[0:2]) + +preconfigopts = "if [ ! -f configure ]; then ./autogen.sh; fi && " + +# specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module +full_sanity_check = True + +sanity_check_paths = { + 'files': ['include/X11/Xlib.h', 'include/X11/Xutil.h'], + 'dirs': ['include/GL', 'include/X11', 'include/X11/extensions', 'lib', + 'lib/python%s/site-packages/xcbgen' % pyshortver, 'lib/pkgconfig', 'share/pkgconfig'], +} + +moduleclass = 'vis' -- GitLab From b6fa490e8ed96e8ded075b565a4a99d057492323 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Mon, 26 Jun 2017 16:03:08 +1200 Subject: [PATCH 1007/1603] Easyconfig for pkg-config --- .../pkg-config-0.29.1-gimkl-2017a.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1-gimkl-2017a.eb diff --git a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1-gimkl-2017a.eb b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1-gimkl-2017a.eb new file mode 100644 index 0000000000..b2d6e14f04 --- /dev/null +++ b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1-gimkl-2017a.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'pkg-config' +version = '0.29.1' + +homepage = 'http://www.freedesktop.org/wiki/Software/pkg-config/' +description = """pkg-config is a helper tool used when compiling applications and libraries. It helps you insert the + correct compiler options on the command line so an application can use + gcc -o test test.c `pkg-config --libs --cflags glib-2.0` + for instance, rather than hard-coding values on where to find glib (or other libraries).""" + +toolchain = {'name': 'gimkl', 'version': '2017a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['https://pkg-config.freedesktop.org/releases/'] + +# don't use PAX, it might break. +tar_config_opts = True + +configopts = " --with-internal-glib" + +sanity_check_paths = { + 'files': ['bin/pkg-config'], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From 75aff1d1a4dab442a22a7ecd9012724d5fad66f2 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Mon, 26 Jun 2017 16:06:35 +1200 Subject: [PATCH 1008/1603] Remove comments from start of NASM easyconfig --- easybuild/easyconfigs/n/NASM/NASM-2.12.02.eb | 12 ------------ 1 file changed, 12 deletions(-) diff --git a/easybuild/easyconfigs/n/NASM/NASM-2.12.02.eb b/easybuild/easyconfigs/n/NASM/NASM-2.12.02.eb index b96d1d70fb..3c18189624 100644 --- a/easybuild/easyconfigs/n/NASM/NASM-2.12.02.eb +++ b/easybuild/easyconfigs/n/NASM/NASM-2.12.02.eb @@ -1,15 +1,3 @@ -## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild -# -# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA -# Authors:: Fotis Georgatos -# License:: MIT/GPL -# $Id$ -# -# This work implements a part of the HPCBIOS project and is a component of the policy: -# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-90.html -## - easyblock = 'ConfigureMake' name = 'NASM' -- GitLab From ce0ca7529a7dafccefe307fc9f985f4b5e9a0204 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Mon, 26 Jun 2017 16:14:19 +1200 Subject: [PATCH 1009/1603] Swap order of elements in toolchain directive --- easybuild/easyconfigs/s/Szip/Szip-2.1-gimkl-2017a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1-gimkl-2017a.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1-gimkl-2017a.eb index 4d2a5188f4..be905d9536 100644 --- a/easybuild/easyconfigs/s/Szip/Szip-2.1-gimkl-2017a.eb +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1-gimkl-2017a.eb @@ -6,7 +6,7 @@ version = '2.1' homepage = 'http://www.hdfgroup.org/doc_resource/SZIP/' description = "Szip compression software, providing lossless compression of scientific data" -toolchain = {'version': '2017a', 'name': 'gimkl'} +toolchain = {'name': 'gimkl', 'version': '2017a'} toolchainopts = {'pic': True} source_urls = ['http://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] -- GitLab From 3da0e4a6bc433a079e03b3ec91cea803e838f7cb Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Mon, 26 Jun 2017 16:20:47 +1200 Subject: [PATCH 1010/1603] Don't use dummy toolchains in easyconfigs for general consumption --- easybuild/easyconfigs/b/Bison/Bison-3.0.4-gimkl-2017a.eb | 2 +- easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.13-gimkl-2017a.eb | 2 +- easybuild/easyconfigs/f/flex/flex-2.6.3-gimkl-2017a.eb | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.4-gimkl-2017a.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-gimkl-2017a.eb index 7ef2e128f5..d8b1c076f4 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-3.0.4-gimkl-2017a.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-gimkl-2017a.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'gimkl', 'version': '2017a'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] -builddependencies = [('M4', '1.4.17', '', True)] +builddependencies = [('M4', '1.4.17')] sanity_check_paths = { 'files': ["bin/%s" % x for x in ["bison", "yacc"]] + ["lib/liby.a"], diff --git a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.13-gimkl-2017a.eb b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.13-gimkl-2017a.eb index 5872a02692..9772b7c659 100644 --- a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.13-gimkl-2017a.eb +++ b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.13-gimkl-2017a.eb @@ -11,7 +11,7 @@ sources = ['%(namelower)s-%(version)s.src.tar.gz'] source_urls = ['http://ftp.stack.nl/pub/users/dimitri/'] builddependencies = [ - ('CMake', '3.6.1', '', True), + ('CMake', '3.6.1'), ('flex', '2.6.3'), ('Bison', '3.0.4'), ] diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.3-gimkl-2017a.eb b/easybuild/easyconfigs/f/flex/flex-2.6.3-gimkl-2017a.eb index 6d9bee0a21..69335ad939 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.3-gimkl-2017a.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.3-gimkl-2017a.eb @@ -13,7 +13,7 @@ source_urls = ['https://github.com/westes/flex/releases/download/v%(version)s/'] checksums = ['a5f65570cd9107ec8a8ec88f17b31bb1'] -dependencies = [('M4', '1.4.17', '', True)] +dependencies = [('M4', '1.4.17')] builddependencies = [ ('Bison', '3.0.4'), ('help2man', '1.47.4'), -- GitLab From 2bcce5cecdbb9d0a6624bae1d28ddef1b03918ff Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Mon, 26 Jun 2017 16:26:25 +1200 Subject: [PATCH 1011/1603] New EasyConfig for PCRE 8.40 with the gimkl-2017a toolchain --- .../p/PCRE/PCRE-8.40-gimkl-2017a.eb | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) create mode 100644 easybuild/easyconfigs/p/PCRE/PCRE-8.40-gimkl-2017a.eb diff --git a/easybuild/easyconfigs/p/PCRE/PCRE-8.40-gimkl-2017a.eb b/easybuild/easyconfigs/p/PCRE/PCRE-8.40-gimkl-2017a.eb new file mode 100644 index 0000000000..fedf649f9d --- /dev/null +++ b/easybuild/easyconfigs/p/PCRE/PCRE-8.40-gimkl-2017a.eb @@ -0,0 +1,18 @@ +easyblock = 'ConfigureMake' + +name = 'PCRE' +version = '8.40' + +homepage = 'http://www.pcre.org/' +description = """The PCRE library is a set of functions that implement regular expression pattern matching using + the same syntax and semantics as Perl 5.""" + +toolchain = {'name': 'gimkl', 'version': '2017a'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +configopts = "--with-pic --disable-cpp --enable-utf --enable-unicode-properties" + +moduleclass = 'devel' -- GitLab From 27e2bd0676546c6ef7b0b125f9ae58493ed6dc90 Mon Sep 17 00:00:00 2001 From: Sebastien Varrette Date: Mon, 26 Jun 2017 10:12:07 +0200 Subject: [PATCH 1012/1603] style correction Signed-off-by: Sebastien Varrette --- easybuild/easyconfigs/l/likwid/likwid-4.2.0-foss-2017a.eb | 5 ++++- easybuild/easyconfigs/l/likwid/likwid-4.2.0-intel-2017a.eb | 5 ++++- 2 files changed, 8 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/likwid/likwid-4.2.0-foss-2017a.eb b/easybuild/easyconfigs/l/likwid/likwid-4.2.0-foss-2017a.eb index 71712d86cc..69116819bb 100644 --- a/easybuild/easyconfigs/l/likwid/likwid-4.2.0-foss-2017a.eb +++ b/easybuild/easyconfigs/l/likwid/likwid-4.2.0-foss-2017a.eb @@ -42,7 +42,10 @@ sanity_check_paths = { } postinstallcmds = [ - 'echo "================================================================================\nIMPORTANT: you will have to manually apply the following changes **as root**:\n sudo chown root:root \$EBROOTLIKWID/sbin/likwid-accessD\n sudo chmod u+s \$EBROOTLIKWID/sbin/likwid-accessD\n ================================================================================"' + 'echo "================================================================================"', + 'echo "IMPORTANT: you will have to manually apply the following changes **as root**:"', + 'echo " sudo chown root:root \$EBROOTLIKWID/sbin/likwid-accessD"', + 'echo " sudo chmod u+s \$EBROOTLIKWID/sbin/likwid-accessD"' ] maxparallel = 1 diff --git a/easybuild/easyconfigs/l/likwid/likwid-4.2.0-intel-2017a.eb b/easybuild/easyconfigs/l/likwid/likwid-4.2.0-intel-2017a.eb index 10441103ad..3c4905b6ef 100644 --- a/easybuild/easyconfigs/l/likwid/likwid-4.2.0-intel-2017a.eb +++ b/easybuild/easyconfigs/l/likwid/likwid-4.2.0-intel-2017a.eb @@ -41,7 +41,10 @@ sanity_check_paths = { } postinstallcmds = [ - 'echo "================================================================================\nIMPORTANT: you will have to manually apply the following changes **as root**:\n sudo chown root:root \$EBROOTLIKWID/sbin/likwid-accessD\n sudo chmod u+s \$EBROOTLIKWID/sbin/likwid-accessD\n ================================================================================"' + 'echo "================================================================================"', + 'echo "IMPORTANT: you will have to manually apply the following changes **as root**:"', + 'echo " sudo chown root:root \$EBROOTLIKWID/sbin/likwid-accessD"', + 'echo " sudo chmod u+s \$EBROOTLIKWID/sbin/likwid-accessD"' ] maxparallel = 1 -- GitLab From 53adb260f203daec38e2f4c067784bbb96e96d73 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 26 Jun 2017 10:45:24 +0200 Subject: [PATCH 1013/1603] remove buildopts from HDF5 easyconfigs, taken care of by updated HDF5 easyblock now --- easybuild/easyconfigs/h/HDF5/HDF5-1.10.0-patch1-foss-2016b.eb | 2 -- .../easyconfigs/h/HDF5/HDF5-1.10.0-patch1-goolfc-2016.10.eb | 2 -- easybuild/easyconfigs/h/HDF5/HDF5-1.10.0-patch1-intel-2016b.eb | 2 -- .../easyconfigs/h/HDF5/HDF5-1.10.0-patch1-intel-2017.01.eb | 2 -- easybuild/easyconfigs/h/HDF5/HDF5-1.10.0-patch1-intel-2017a.eb | 2 -- easybuild/easyconfigs/h/HDF5/HDF5-1.10.1-intel-2017a.eb | 2 -- easybuild/easyconfigs/h/HDF5/HDF5-1.8.12-intel-2016b.eb | 2 -- easybuild/easyconfigs/h/HDF5/HDF5-1.8.13-foss-2015a.eb | 2 -- easybuild/easyconfigs/h/HDF5/HDF5-1.8.13-intel-2014b.eb | 2 -- easybuild/easyconfigs/h/HDF5/HDF5-1.8.13-intel-2015a.eb | 2 -- easybuild/easyconfigs/h/HDF5/HDF5-1.8.13-intel-2015b.eb | 2 -- easybuild/easyconfigs/h/HDF5/HDF5-1.8.14-foss-2015a.eb | 3 --- easybuild/easyconfigs/h/HDF5/HDF5-1.8.14-ictce-7.1.2-serial.eb | 2 -- easybuild/easyconfigs/h/HDF5/HDF5-1.8.14-ictce-7.1.2.eb | 2 -- easybuild/easyconfigs/h/HDF5/HDF5-1.8.14-intel-2015a.eb | 2 -- easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-foss-2015a.eb | 2 -- easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-intel-2015a.eb | 2 -- easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-intel-2015b.eb | 2 -- easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-patch1-foss-2015a.eb | 2 -- easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-patch1-foss-2015b.eb | 2 -- easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-patch1-intel-2015a.eb | 2 -- easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-patch1-intel-2015b.eb | 2 -- easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-foss-2015a.eb | 2 -- easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-foss-2016a.eb | 2 -- easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-intel-2015b.eb | 2 -- .../easyconfigs/h/HDF5/HDF5-1.8.16-intel-2016.02-GCC-4.9.eb | 2 -- easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-intel-2016a.eb | 2 -- easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-iomkl-2016.07.eb | 2 -- .../h/HDF5/HDF5-1.8.16-iomkl-2016.09-GCC-4.9.3-2.25.eb | 2 -- easybuild/easyconfigs/h/HDF5/HDF5-1.8.17-foss-2016a.eb | 2 -- easybuild/easyconfigs/h/HDF5/HDF5-1.8.17-foss-2016b.eb | 2 -- easybuild/easyconfigs/h/HDF5/HDF5-1.8.17-intel-2016a.eb | 2 -- easybuild/easyconfigs/h/HDF5/HDF5-1.8.17-intel-2016b-serial.eb | 2 -- easybuild/easyconfigs/h/HDF5/HDF5-1.8.17-intel-2016b.eb | 2 -- easybuild/easyconfigs/h/HDF5/HDF5-1.8.18-foss-2016b.eb | 2 -- easybuild/easyconfigs/h/HDF5/HDF5-1.8.18-foss-2017a.eb | 2 -- easybuild/easyconfigs/h/HDF5/HDF5-1.8.18-intel-2016b.eb | 2 -- easybuild/easyconfigs/h/HDF5/HDF5-1.8.18-intel-2017.01.eb | 2 -- easybuild/easyconfigs/h/HDF5/HDF5-1.8.18-intel-2017a-serial.eb | 2 -- easybuild/easyconfigs/h/HDF5/HDF5-1.8.18-intel-2017a.eb | 2 -- 40 files changed, 81 deletions(-) diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.10.0-patch1-foss-2016b.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.0-patch1-foss-2016b.eb index 11a5ffcadd..78f22f07df 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.10.0-patch1-foss-2016b.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.0-patch1-foss-2016b.eb @@ -12,8 +12,6 @@ source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_ma sources = [SOURCELOWER_TAR_GZ] checksums = ['9180ff0ef8dc2ef3f61bd37a7404f295'] -buildopts = 'CXXFLAGS="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK"' - dependencies = [ ('zlib', '1.2.8'), ('Szip', '2.1'), diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.10.0-patch1-goolfc-2016.10.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.0-patch1-goolfc-2016.10.eb index 761c68b5eb..826740a3fc 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.10.0-patch1-goolfc-2016.10.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.0-patch1-goolfc-2016.10.eb @@ -12,8 +12,6 @@ source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_ma sources = [SOURCELOWER_TAR_GZ] checksums = ['9180ff0ef8dc2ef3f61bd37a7404f295'] -buildopts = 'CXXFLAGS="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK"' - dependencies = [ ('zlib', '1.2.8'), ('Szip', '2.1'), diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.10.0-patch1-intel-2016b.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.0-patch1-intel-2016b.eb index 7253681751..73282dd565 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.10.0-patch1-intel-2016b.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.0-patch1-intel-2016b.eb @@ -12,8 +12,6 @@ source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_ma sources = [SOURCELOWER_TAR_GZ] checksums = ['9180ff0ef8dc2ef3f61bd37a7404f295'] -buildopts = 'CXXFLAGS="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK"' - dependencies = [ ('zlib', '1.2.8'), ('Szip', '2.1'), diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.10.0-patch1-intel-2017.01.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.0-patch1-intel-2017.01.eb index cb5285d7c5..9319a2c2b1 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.10.0-patch1-intel-2017.01.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.0-patch1-intel-2017.01.eb @@ -12,8 +12,6 @@ source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_ma sources = [SOURCELOWER_TAR_GZ] checksums = ['9180ff0ef8dc2ef3f61bd37a7404f295'] -buildopts = 'CXXFLAGS="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK"' - dependencies = [ ('zlib', '1.2.8'), ('Szip', '2.1'), diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.10.0-patch1-intel-2017a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.0-patch1-intel-2017a.eb index 9d04fbcf11..2861eb199d 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.10.0-patch1-intel-2017a.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.0-patch1-intel-2017a.eb @@ -12,8 +12,6 @@ source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_ma sources = [SOURCELOWER_TAR_GZ] checksums = ['9180ff0ef8dc2ef3f61bd37a7404f295'] -buildopts = 'CXXFLAGS="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK"' - dependencies = [ ('zlib', '1.2.11'), ('Szip', '2.1'), diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.10.1-intel-2017a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.1-intel-2017a.eb index 2cb7193188..711b3163cb 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.10.1-intel-2017a.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.1-intel-2017a.eb @@ -12,8 +12,6 @@ source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_ma sources = [SOURCELOWER_TAR_GZ] checksums = ['43a2f9466702fb1db31df98ae6677f15'] -buildopts = 'CXXFLAGS="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK"' - dependencies = [ ('zlib', '1.2.11'), ('Szip', '2.1'), diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.12-intel-2016b.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.12-intel-2016b.eb index ba130d5f31..e8c2b7e7ab 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.12-intel-2016b.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.12-intel-2016b.eb @@ -16,8 +16,6 @@ patches = [ 'configure_libtool.patch', ] -buildopts = 'CXXFLAGS="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK"' - dependencies = [ ('zlib', '1.2.8'), ('Szip', '2.1'), diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.13-foss-2015a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.13-foss-2015a.eb index f8f32df424..b6151ce7c1 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.13-foss-2015a.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.13-foss-2015a.eb @@ -15,8 +15,6 @@ patches = [ 'configure_libtool.patch', ] -buildopts = 'CXXFLAGS="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK"' - dependencies = [ ('zlib', '1.2.8'), ('Szip', '2.1'), diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.13-intel-2014b.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.13-intel-2014b.eb index 14daa11265..440bfaf4da 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.13-intel-2014b.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.13-intel-2014b.eb @@ -16,8 +16,6 @@ patches = [ 'configure_libtool.patch', ] -buildopts = 'CXXFLAGS="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK"' - dependencies = [ ('zlib', '1.2.8'), ('Szip', '2.1'), diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.13-intel-2015a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.13-intel-2015a.eb index 901fd44392..1c2e0ae55d 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.13-intel-2015a.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.13-intel-2015a.eb @@ -16,8 +16,6 @@ patches = [ 'configure_libtool.patch', ] -buildopts = 'CXXFLAGS="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK"' - dependencies = [ ('zlib', '1.2.8'), ('Szip', '2.1'), diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.13-intel-2015b.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.13-intel-2015b.eb index 6a1a9188e1..17df3cb04f 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.13-intel-2015b.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.13-intel-2015b.eb @@ -16,8 +16,6 @@ patches = [ 'configure_libtool.patch', ] -buildopts = 'CXXFLAGS="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK"' - dependencies = [ ('zlib', '1.2.8'), ('Szip', '2.1'), diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.14-foss-2015a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.14-foss-2015a.eb index 6720320b04..d1a99fe666 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.14-foss-2015a.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.14-foss-2015a.eb @@ -1,4 +1,3 @@ -# Built with EasyBuild version 2.2.0dev on 2015-06-16_11-02-41 name = 'HDF5' version = "1.8.14" @@ -16,8 +15,6 @@ patches = [ 'configure_libtool.patch', ] -buildopts = 'CXXFLAGS="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK"' - dependencies = [ ('zlib', '1.2.8'), ('Szip', '2.1'), diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.14-ictce-7.1.2-serial.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.14-ictce-7.1.2-serial.eb index 8708c7b4dd..0fb424c799 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.14-ictce-7.1.2-serial.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.14-ictce-7.1.2-serial.eb @@ -17,8 +17,6 @@ patches = [ 'configure_libtool.patch', ] -buildopts = 'CXXFLAGS="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK"' - dependencies = [ ('zlib', '1.2.8'), ('Szip', '2.1'), diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.14-ictce-7.1.2.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.14-ictce-7.1.2.eb index bfef0cbb11..b97088f0e3 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.14-ictce-7.1.2.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.14-ictce-7.1.2.eb @@ -16,8 +16,6 @@ patches = [ 'configure_libtool.patch', ] -buildopts = 'CXXFLAGS="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK"' - dependencies = [ ('zlib', '1.2.8'), ('Szip', '2.1'), diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.14-intel-2015a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.14-intel-2015a.eb index 8811c59a40..f04a2bfbbc 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.14-intel-2015a.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.14-intel-2015a.eb @@ -16,8 +16,6 @@ patches = [ 'configure_libtool.patch', ] -buildopts = 'CXXFLAGS="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK"' - dependencies = [ ('zlib', '1.2.8'), ('Szip', '2.1'), diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-foss-2015a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-foss-2015a.eb index 88e2ae54b1..cc345601a7 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-foss-2015a.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-foss-2015a.eb @@ -13,8 +13,6 @@ sources = [SOURCELOWER_TAR_GZ] patches = ['configure_libtool.patch'] -buildopts = 'CXXFLAGS="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK"' - dependencies = [ ('zlib', '1.2.8'), ('Szip', '2.1'), diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-intel-2015a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-intel-2015a.eb index e5738f0904..0bfd6778dc 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-intel-2015a.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-intel-2015a.eb @@ -16,8 +16,6 @@ patches = [ 'configure_libtool.patch', ] -buildopts = 'CXXFLAGS="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK"' - dependencies = [ ('zlib', '1.2.8'), ('Szip', '2.1'), diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-intel-2015b.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-intel-2015b.eb index b35f180383..e7b7b4e75d 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-intel-2015b.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-intel-2015b.eb @@ -16,8 +16,6 @@ patches = [ 'configure_libtool.patch', ] -buildopts = 'CXXFLAGS="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK"' - dependencies = [ ('zlib', '1.2.8'), ('Szip', '2.1'), diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-patch1-foss-2015a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-patch1-foss-2015a.eb index 152a305c88..9514ef2c7b 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-patch1-foss-2015a.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-patch1-foss-2015a.eb @@ -13,8 +13,6 @@ sources = [SOURCELOWER_TAR_GZ] patches = ['configure_libtool.patch'] -buildopts = 'CXXFLAGS="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK"' - dependencies = [ ('zlib', '1.2.8'), ('Szip', '2.1'), diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-patch1-foss-2015b.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-patch1-foss-2015b.eb index d234a1dcc1..dde5f4481e 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-patch1-foss-2015b.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-patch1-foss-2015b.eb @@ -13,8 +13,6 @@ sources = [SOURCELOWER_TAR_GZ] patches = ['configure_libtool.patch'] -buildopts = 'CXXFLAGS="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK"' - dependencies = [ ('zlib', '1.2.8'), ('Szip', '2.1'), diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-patch1-intel-2015a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-patch1-intel-2015a.eb index 03fb175bd6..1c3be3c832 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-patch1-intel-2015a.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-patch1-intel-2015a.eb @@ -16,8 +16,6 @@ patches = [ 'configure_libtool.patch', ] -buildopts = 'CXXFLAGS="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK"' - dependencies = [ ('zlib', '1.2.8'), ('Szip', '2.1'), diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-patch1-intel-2015b.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-patch1-intel-2015b.eb index 2ddc5c482c..bcba39eb8f 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-patch1-intel-2015b.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-patch1-intel-2015b.eb @@ -16,8 +16,6 @@ patches = [ 'configure_libtool.patch', ] -buildopts = 'CXXFLAGS="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK"' - dependencies = [ ('zlib', '1.2.8'), ('Szip', '2.1'), diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-foss-2015a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-foss-2015a.eb index 2309adbc85..bdd56e87c1 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-foss-2015a.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-foss-2015a.eb @@ -13,8 +13,6 @@ sources = [SOURCELOWER_TAR_GZ] patches = ['configure_libtool.patch'] -buildopts = 'CXXFLAGS="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK"' - dependencies = [ ('zlib', '1.2.8'), ('Szip', '2.1'), diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-foss-2016a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-foss-2016a.eb index 67235e28b4..d7f79bf614 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-foss-2016a.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-foss-2016a.eb @@ -16,8 +16,6 @@ patches = [ 'configure_libtool.patch', ] -buildopts = 'CXXFLAGS="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK"' - dependencies = [ ('zlib', '1.2.8'), ('Szip', '2.1'), diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-intel-2015b.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-intel-2015b.eb index 0903315947..70e4ec54b7 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-intel-2015b.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-intel-2015b.eb @@ -16,8 +16,6 @@ patches = [ 'configure_libtool.patch', ] -buildopts = 'CXXFLAGS="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK"' - dependencies = [ ('zlib', '1.2.8'), ('Szip', '2.1'), diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-intel-2016.02-GCC-4.9.eb index 0aa0ce34f3..11f989ce67 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-intel-2016.02-GCC-4.9.eb @@ -16,8 +16,6 @@ patches = [ 'configure_libtool.patch', ] -buildopts = 'CXXFLAGS="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK"' - dependencies = [ ('zlib', '1.2.8'), ('Szip', '2.1'), diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-intel-2016a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-intel-2016a.eb index cade57c186..22d10bc205 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-intel-2016a.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-intel-2016a.eb @@ -16,8 +16,6 @@ patches = [ 'configure_libtool.patch', ] -buildopts = 'CXXFLAGS="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK"' - dependencies = [ ('zlib', '1.2.8'), ('Szip', '2.1'), diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-iomkl-2016.07.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-iomkl-2016.07.eb index feea5f3d11..490c43aea3 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-iomkl-2016.07.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-iomkl-2016.07.eb @@ -13,8 +13,6 @@ sources = [SOURCELOWER_TAR_GZ] patches = ['configure_libtool.patch'] -buildopts = 'CXXFLAGS="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK"' - dependencies = [ ('zlib', '1.2.8'), ('Szip', '2.1'), diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-iomkl-2016.09-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-iomkl-2016.09-GCC-4.9.3-2.25.eb index 847ddbbde6..9ace13e3df 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-iomkl-2016.09-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-iomkl-2016.09-GCC-4.9.3-2.25.eb @@ -13,8 +13,6 @@ sources = [SOURCELOWER_TAR_GZ] patches = ['configure_libtool.patch'] -buildopts = 'CXXFLAGS="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK"' - dependencies = [ ('zlib', '1.2.8'), ('Szip', '2.1'), diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.17-foss-2016a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.17-foss-2016a.eb index 7de9eafbba..2a7c9054f4 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.17-foss-2016a.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.17-foss-2016a.eb @@ -15,8 +15,6 @@ patches = [ 'configure_libtool.patch', ] -buildopts = 'CXXFLAGS="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK"' - dependencies = [ ('zlib', '1.2.8'), ('Szip', '2.1'), diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.17-foss-2016b.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.17-foss-2016b.eb index 396a16a44d..365f098c88 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.17-foss-2016b.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.17-foss-2016b.eb @@ -15,8 +15,6 @@ patches = [ 'configure_libtool.patch', ] -buildopts = 'CXXFLAGS="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK"' - dependencies = [ ('zlib', '1.2.8'), ('Szip', '2.1'), diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.17-intel-2016a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.17-intel-2016a.eb index a5deac4990..2dff146ecc 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.17-intel-2016a.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.17-intel-2016a.eb @@ -16,8 +16,6 @@ patches = [ 'configure_libtool.patch', ] -buildopts = 'CXXFLAGS="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK"' - dependencies = [ ('zlib', '1.2.8'), ('Szip', '2.1'), diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.17-intel-2016b-serial.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.17-intel-2016b-serial.eb index 529a200b16..e3b8e084ae 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.17-intel-2016b-serial.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.17-intel-2016b-serial.eb @@ -17,8 +17,6 @@ patches = [ 'configure_libtool.patch', ] -buildopts = 'CXXFLAGS="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK"' - dependencies = [ ('zlib', '1.2.8'), ('Szip', '2.1'), diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.17-intel-2016b.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.17-intel-2016b.eb index 24a6c22972..b513c5e0c7 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.17-intel-2016b.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.17-intel-2016b.eb @@ -16,8 +16,6 @@ patches = [ 'configure_libtool.patch', ] -buildopts = 'CXXFLAGS="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK"' - dependencies = [ ('zlib', '1.2.8'), ('Szip', '2.1'), diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.18-foss-2016b.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.18-foss-2016b.eb index f6e11b3e6a..a6292e12c4 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.18-foss-2016b.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.18-foss-2016b.eb @@ -13,8 +13,6 @@ source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_ma sources = [SOURCELOWER_TAR_GZ] checksums = ['dd2148b740713ca0295442ec683d7b1c'] -buildopts = 'CXXFLAGS="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK"' - dependencies = [ ('zlib', '1.2.8'), ('Szip', '2.1'), diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.18-foss-2017a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.18-foss-2017a.eb index addd6deb8d..fdf33772a9 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.18-foss-2017a.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.18-foss-2017a.eb @@ -13,8 +13,6 @@ source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_ma sources = [SOURCELOWER_TAR_GZ] checksums = ['dd2148b740713ca0295442ec683d7b1c'] -buildopts = 'CXXFLAGS="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK"' - dependencies = [ ('zlib', '1.2.11'), ('Szip', '2.1'), diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.18-intel-2016b.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.18-intel-2016b.eb index 1b22bab5d5..cf96723fc7 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.18-intel-2016b.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.18-intel-2016b.eb @@ -13,8 +13,6 @@ source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_ma sources = [SOURCELOWER_TAR_GZ] checksums = ['dd2148b740713ca0295442ec683d7b1c'] -buildopts = 'CXXFLAGS="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK"' - dependencies = [ ('zlib', '1.2.8'), ('Szip', '2.1'), diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.18-intel-2017.01.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.18-intel-2017.01.eb index 52424da991..5619f021d4 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.18-intel-2017.01.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.18-intel-2017.01.eb @@ -13,8 +13,6 @@ source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_ma sources = [SOURCELOWER_TAR_GZ] checksums = ['dd2148b740713ca0295442ec683d7b1c'] -buildopts = 'CXXFLAGS="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK"' - dependencies = [ ('zlib', '1.2.8'), ('Szip', '2.1'), diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.18-intel-2017a-serial.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.18-intel-2017a-serial.eb index dd0fd05bf2..c33a218cc9 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.18-intel-2017a-serial.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.18-intel-2017a-serial.eb @@ -14,8 +14,6 @@ source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_ma sources = [SOURCELOWER_TAR_GZ] checksums = ['dd2148b740713ca0295442ec683d7b1c'] -buildopts = 'CXXFLAGS="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK"' - dependencies = [ ('zlib', '1.2.11'), ('Szip', '2.1'), diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.18-intel-2017a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.18-intel-2017a.eb index 630ef958f3..861500bc3a 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.18-intel-2017a.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.18-intel-2017a.eb @@ -13,8 +13,6 @@ source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_ma sources = [SOURCELOWER_TAR_GZ] checksums = ['dd2148b740713ca0295442ec683d7b1c'] -buildopts = 'CXXFLAGS="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK"' - dependencies = [ ('zlib', '1.2.11'), ('Szip', '2.1'), -- GitLab From 3bdc067ebd90d148be19a5bc2aa0c959ad8c71ac Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 26 Jun 2017 11:08:04 +0200 Subject: [PATCH 1014/1603] adding easyconfigs: Pillow-4.1.1-intel-2017a-Python-3.6.1.eb, LibTIFF-4.0.8-intel-2017a.eb --- .../l/LibTIFF/LibTIFF-4.0.8-intel-2017a.eb | 35 +++++++++++++++++++ .../Pillow-4.1.1-intel-2017a-Python-3.6.1.eb | 27 ++++++++++++++ 2 files changed, 62 insertions(+) create mode 100644 easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.8-intel-2017a.eb create mode 100644 easybuild/easyconfigs/p/Pillow/Pillow-4.1.1-intel-2017a-Python-3.6.1.eb diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.8-intel-2017a.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.8-intel-2017a.eb new file mode 100644 index 0000000000..445e665d1d --- /dev/null +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.8-intel-2017a.eb @@ -0,0 +1,35 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos , Alan O'Cais (JSC) +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## +easyblock = 'ConfigureMake' + +name = 'LibTIFF' +version = '4.0.8' + +homepage = 'http://www.remotesensing.org/libtiff/' +description = "tiff: Library and tools for reading and writing TIFF data files" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [ + 'http://download.osgeo.org/libtiff/', + 'ftp://ftp.remotesensing.org/pub/libtiff/', +] +sources = ['tiff-%(version)s.tar.gz'] + +configopts = " --enable-ld-version-script " + +sanity_check_paths = { + 'files': ['bin/tiffinfo'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-4.1.1-intel-2017a-Python-3.6.1.eb b/easybuild/easyconfigs/p/Pillow/Pillow-4.1.1-intel-2017a-Python-3.6.1.eb new file mode 100644 index 0000000000..9ff0d2f498 --- /dev/null +++ b/easybuild/easyconfigs/p/Pillow/Pillow-4.1.1-intel-2017a-Python-3.6.1.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'Pillow' +version = '4.1.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://pillow.readthedocs.org/' +description = """Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. + PIL is the Python Imaging Library by Fredrik Lundh and Contributors.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '3.6.1'), + ('libjpeg-turbo', '1.5.1'), + ('libpng', '1.6.28'), + ('zlib', '1.2.11'), + ('LibTIFF', '4.0.8'), + ('freetype', '2.7.1'), +] + +options = {'modulename': 'PIL'} + +moduleclass = 'vis' -- GitLab From 28501e6024f2cc8cce162fbd8a9da5ac29a5a3c0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 26 Jun 2017 11:31:24 +0200 Subject: [PATCH 1015/1603] adding easyconfigs: EasyBuild-3.3.0.eb --- .../e/EasyBuild/EasyBuild-3.3.0.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.3.0.eb diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.3.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.3.0.eb new file mode 100644 index 0000000000..c11a0f20c4 --- /dev/null +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.3.0.eb @@ -0,0 +1,38 @@ +easyblock = 'EB_EasyBuildMeta' + +name = 'EasyBuild' +version = '3.3.0' + +homepage = 'http://hpcugent.github.com/easybuild/' +description = """EasyBuild is a software build and installation framework + written in Python that allows you to install software in a structured, + repeatable and robust way.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = [ + # vsc-install + 'https://pypi.python.org/packages/82/ec/19d85d2bb91b562195d00db9ac82d7529904e7eabc0597720966bf74714f/', + # vsc-base + 'https://pypi.python.org/packages/f7/66/1ff7ecc4a93ba37e063f5bfbe395e95a547b1dec73b017c2724f4475a958/', + # easybuild-framework + 'https://pypi.python.org/packages/b6/8b/383298ddd7718b8455b26719d39c686105ccdba55b66bdd0971ac0a69d70/', + # easybuild-easyblocks + 'https://pypi.python.org/packages/1d/3d/53ea1c02d7a77fcc6c1aa6620a8a6f2e45d3fddf9657919b749c4834b4fb/', + # easybuild-easyconfigs + 'https://pypi.python.org/packages/c8/c0/829c6ddd864f9980c09eb5acec7dc8ece747831f6f3b76852f2796a563fb/', +] +# order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) +sources = [ + 'vsc-install-0.10.26.tar.gz', + 'vsc-base-2.5.8.tar.gz', + 'easybuild-framework-%(version)s.tar.gz', + 'easybuild-easyblocks-%(version)s.tar.gz', + 'easybuild-easyconfigs-%(version)s.tar.gz', +] + +# EasyBuild is a (set of) Python packages, so it depends on Python +# usually, we want to use the system Python, so no actual Python dependency is listed +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +moduleclass = 'tools' -- GitLab From a090242c71d1ea9d38d0ba628e1436a8ad310884 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 26 Jun 2017 11:47:56 +0200 Subject: [PATCH 1016/1603] bump version to 3.3.1.dev0 --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 2c5a5b79d5..6a0698539f 100644 --- a/setup.py +++ b/setup.py @@ -47,7 +47,7 @@ from distutils import log # recent setuptools versions will *TRANSFORM* something like 'X.Y.Zdev' into 'X.Y.Z.dev0', with a warning like # UserWarning: Normalizing '2.4.0dev' to '2.4.0.dev0' # This causes problems further up the dependency chain... -VERSION = '3.3.0' +VERSION = '3.3.1.dev0' API_VERSION = VERSION.split('.')[0] EB_VERSION = '.'.join(VERSION.split('.')[0:2]) -- GitLab From 636479585cc04f247c378192dea2f15e663712f7 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 26 Jun 2017 12:18:35 +0100 Subject: [PATCH 1017/1603] adding easyconfigs: pigz-2.3.3-foss-2016b.eb --- .../p/pigz/pigz-2.3.3-foss-2016b.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100755 easybuild/easyconfigs/p/pigz/pigz-2.3.3-foss-2016b.eb diff --git a/easybuild/easyconfigs/p/pigz/pigz-2.3.3-foss-2016b.eb b/easybuild/easyconfigs/p/pigz/pigz-2.3.3-foss-2016b.eb new file mode 100755 index 0000000000..8790ec7dca --- /dev/null +++ b/easybuild/easyconfigs/p/pigz/pigz-2.3.3-foss-2016b.eb @@ -0,0 +1,40 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = 'MakeCp' + +name = 'pigz' +version = '2.3.3' + +homepage = 'http://zlib.net/pigz/' +description = """ pigz, which stands for parallel implementation of gzip, is a fully + functional replacement for gzip that exploits multiple processors and multiple cores + to the hilt when compressing data. pigz was written by Mark Adler, and uses the zlib + and pthread libraries. """ + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['https://github.com/madler/pigz/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['fb80e8d31498226c99fe8c8b3d19364d'] + +# Patch Makefile so zlib provided by EasyBuild is picked up +patches = ['pigz-2.3.3_Makefile.patch'] + +# README recommends zlib 1.2.6 or higher +dependencies = [('zlib', '1.2.8')] + +buildopts = ' CC=$CC' + +parallel = 1 + +files_to_copy = [(["pigz", "unpigz"], "bin")] + +sanity_check_paths = { + 'files': ["bin/pigz", "bin/unpigz"], + 'dirs': [""], +} + +moduleclass = 'tools' -- GitLab From b9b12caa32774c49bace9f7d0ceca68c6e838ce7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 26 Jun 2017 14:44:42 +0200 Subject: [PATCH 1018/1603] update deps in Pillow 4.1.1 easyconfig to libpng 1.6.29 --- .../p/Pillow/Pillow-4.1.1-intel-2017a-Python-3.6.1.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-4.1.1-intel-2017a-Python-3.6.1.eb b/easybuild/easyconfigs/p/Pillow/Pillow-4.1.1-intel-2017a-Python-3.6.1.eb index 9ff0d2f498..7e73af7e4a 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-4.1.1-intel-2017a-Python-3.6.1.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-4.1.1-intel-2017a-Python-3.6.1.eb @@ -16,10 +16,10 @@ sources = [SOURCE_TAR_GZ] dependencies = [ ('Python', '3.6.1'), ('libjpeg-turbo', '1.5.1'), - ('libpng', '1.6.28'), + ('libpng', '1.6.29'), ('zlib', '1.2.11'), ('LibTIFF', '4.0.8'), - ('freetype', '2.7.1'), + ('freetype', '2.7.1', '-libpng-1.6.29'), ] options = {'modulename': 'PIL'} -- GitLab From 414906407f3a7258177e56dc1b15b0b95fe023af Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 26 Jun 2017 15:00:22 +0200 Subject: [PATCH 1019/1603] adding easyconfigs: Tensorflow-1.2.0-intel-2017a-Python-3.6.1.eb, Keras-2.0.5-intel-2017a-Python-3.6.1.eb --- .../Keras-2.0.5-intel-2017a-Python-3.6.1.eb | 31 ++++++++++++ ...nsorflow-1.2.0-intel-2017a-Python-3.6.1.eb | 48 +++++++++++++++++++ 2 files changed, 79 insertions(+) create mode 100644 easybuild/easyconfigs/k/Keras/Keras-2.0.5-intel-2017a-Python-3.6.1.eb create mode 100755 easybuild/easyconfigs/t/Tensorflow/Tensorflow-1.2.0-intel-2017a-Python-3.6.1.eb diff --git a/easybuild/easyconfigs/k/Keras/Keras-2.0.5-intel-2017a-Python-3.6.1.eb b/easybuild/easyconfigs/k/Keras/Keras-2.0.5-intel-2017a-Python-3.6.1.eb new file mode 100644 index 0000000000..105d38b643 --- /dev/null +++ b/easybuild/easyconfigs/k/Keras/Keras-2.0.5-intel-2017a-Python-3.6.1.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonPackage' + +name = 'Keras' +version = '2.0.5' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://keras.io/' +description = """Keras is a minimalist, highly modular neural networks library, written in Python and +capable of running on top of either TensorFlow or Theano.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '3.6.1'), + ('Theano', '0.9.0', versionsuffix), + ('h5py', '2.7.0', '%(versionsuffix)s'), + ('PyYAML', '3.12', versionsuffix), +] + +# it defaults to Tensorflow +modextravars = {'KERAS_BACKEND': 'theano'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/t/Tensorflow/Tensorflow-1.2.0-intel-2017a-Python-3.6.1.eb b/easybuild/easyconfigs/t/Tensorflow/Tensorflow-1.2.0-intel-2017a-Python-3.6.1.eb new file mode 100755 index 0000000000..b53e9967d6 --- /dev/null +++ b/easybuild/easyconfigs/t/Tensorflow/Tensorflow-1.2.0-intel-2017a-Python-3.6.1.eb @@ -0,0 +1,48 @@ +easyblock = 'Bundle' + +name = 'Tensorflow' +version = '1.2.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://www.tensorflow.org/' +description = "An open-source software library for Machine Intelligence" + +toolchain = {'name': 'intel', 'version': '2017a'} + +pymaj = '3' +pymin = '6' +pyver = pymaj + pymin + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' + +dependencies = [ + ('Python', '%s.%s.1' % (pymaj, pymin)), + ('protobuf-python', '3.3.0', versionsuffix), +] + +exts_list = [ + ('backports.weakref', '1.0rc1', { + 'modulename': 'backports.weakref', + 'source_urls': ['https://pypi.python.org/packages/source/b/backports.weakref'], + }), + ('tensorflow', version, { + 'source_urls': ['https://pypi.python.org/packages/source/t/tensorflow'], + 'source_tmpl': 'tensorflow-%%(version)s-cp%(pyver)s-cp%(pyver)sm-manylinux1_x86_64.whl' % {'pyver': pyver}, + 'checksums': ['a3835274cddd9c5b5a752e39b34c31a2d3d80e0ebcb5488e2dafaf3d614391d1'], + 'use_pip': True, + 'unpack_sources': False, + }), +] + +# specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module +full_sanity_check = True + +sanity_check_paths = { + 'files': ['bin/tensorboard'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +moduleclass = 'lib' -- GitLab From 31b1bb5706b89652d2e446552353f53d117bfc26 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 26 Jun 2017 15:02:34 +0200 Subject: [PATCH 1020/1603] {data}[intel/2017a] scikit-learn v0.18.2 --- ...-intel-2017a-Python-3.6.1-libpng-1.6.29.eb | 44 +++++++++++++++++++ ...t-learn-0.18.2-intel-2017a-Python-3.6.1.eb | 30 +++++++++++++ 2 files changed, 74 insertions(+) create mode 100644 easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.2-intel-2017a-Python-3.6.1-libpng-1.6.29.eb create mode 100755 easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.18.2-intel-2017a-Python-3.6.1.eb diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.2-intel-2017a-Python-3.6.1-libpng-1.6.29.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.2-intel-2017a-Python-3.6.1-libpng-1.6.29.eb new file mode 100644 index 0000000000..bc8e86d8ca --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.2-intel-2017a-Python-3.6.1-libpng-1.6.29.eb @@ -0,0 +1,44 @@ +easyblock = 'Bundle' + +name = 'matplotlib' +version = '2.0.2' +libpng_ver = '1.6.29' +versionsuffix = '-Python-%%(pyver)s-libpng-%s' % libpng_ver + +homepage = 'http://matplotlib.org' +description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of + hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python + and ipython shell, web application servers, and six graphical user interface toolkits.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' + +dependencies = [ + ('Python', '3.6.1'), + ('freetype', '2.7.1', '-libpng-%s' % libpng_ver), +] + +exts_list = [ + ('Cycler', '0.10.0', { + 'modulename': 'cycler', + 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], + 'source_tmpl': 'cycler-%(version)s.tar.gz', + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], + }), +] + +# specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module +full_sanity_check = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.18.2-intel-2017a-Python-3.6.1.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.18.2-intel-2017a-Python-3.6.1.eb new file mode 100755 index 0000000000..680d9601f6 --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.18.2-intel-2017a-Python-3.6.1.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'scikit-learn' +version = '0.18.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://scikit-learn.org/stable/index.html' +description = """Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, +building upon numpy, scipy, and matplotlib. As a machine-learning module, +it provides versatile tools for data mining and analysis in any field of science and engineering. +It strives to be simple and efficient, accessible to everybody, and reusable in various contexts.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '3.6.1'), + ('matplotlib', '2.0.2', versionsuffix + '-libpng-1.6.29'), +] + +options = {'modulename': 'sklearn'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/sklearn'], +} + +moduleclass = 'data' -- GitLab From edfc142e8ef45b89d1da2ebd045f26dc9717a662 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 26 Jun 2017 18:28:31 +0200 Subject: [PATCH 1021/1603] use PYPI_SOURCE as source URL in Tensorflow easyconfigs --- .../t/Tensorflow/Tensorflow-0.12.1-foss-2016b-Python-2.7.12.eb | 2 +- .../t/Tensorflow/Tensorflow-0.12.1-foss-2016b-Python-3.5.2.eb | 2 +- .../t/Tensorflow/Tensorflow-0.12.1-intel-2016b-Python-2.7.12.eb | 2 +- .../t/Tensorflow/Tensorflow-0.12.1-intel-2016b-Python-3.5.2.eb | 2 +- .../t/Tensorflow/Tensorflow-1.0.1-intel-2016b-Python-2.7.12.eb | 2 +- .../t/Tensorflow/Tensorflow-1.0.1-intel-2016b-Python-3.5.2.eb | 2 +- .../t/Tensorflow/Tensorflow-1.1.0-intel-2017a-Python-2.7.13.eb | 2 +- .../t/Tensorflow/Tensorflow-1.1.0-intel-2017a-Python-3.6.1.eb | 2 +- 8 files changed, 8 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/t/Tensorflow/Tensorflow-0.12.1-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/t/Tensorflow/Tensorflow-0.12.1-foss-2016b-Python-2.7.12.eb index b94ca618c9..3dc06f1df1 100755 --- a/easybuild/easyconfigs/t/Tensorflow/Tensorflow-0.12.1-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/t/Tensorflow/Tensorflow-0.12.1-foss-2016b-Python-2.7.12.eb @@ -13,7 +13,7 @@ pymaj = '2' pymin = '7' pymajmin = pymaj + pymin -source_urls = ['https://pypi.python.org/packages/7e/c6/837f4e249aae5c86a632eaaa9779e601eca1487772f8ad75c347bf9e813f/'] +source_urls = [PYPI_SOURCE] sources = [ 'tensorflow-%%(version)s-cp%(pymajmin)s-cp%(pymajmin)smu-manylinux1_x86_64.whl' % {'pymajmin': pymajmin}, ] diff --git a/easybuild/easyconfigs/t/Tensorflow/Tensorflow-0.12.1-foss-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/t/Tensorflow/Tensorflow-0.12.1-foss-2016b-Python-3.5.2.eb index d8b2947422..6dc066128b 100755 --- a/easybuild/easyconfigs/t/Tensorflow/Tensorflow-0.12.1-foss-2016b-Python-3.5.2.eb +++ b/easybuild/easyconfigs/t/Tensorflow/Tensorflow-0.12.1-foss-2016b-Python-3.5.2.eb @@ -13,7 +13,7 @@ pymaj = '3' pymin = '5' pymajmin = pymaj + pymin -source_urls = ['https://pypi.python.org/packages/e5/5c/56e6522fdcd6f8739dcbc4de62e8b0040e141785bb42e5b53a83b0ba3e58/'] +source_urls = [PYPI_SOURCE] sources = [ 'tensorflow-%%(version)s-cp%(pymajmin)s-cp%(pymajmin)sm-manylinux1_x86_64.whl' % {'pymajmin': pymajmin}, ] diff --git a/easybuild/easyconfigs/t/Tensorflow/Tensorflow-0.12.1-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/t/Tensorflow/Tensorflow-0.12.1-intel-2016b-Python-2.7.12.eb index 8ccd735bee..c374b3a8a7 100755 --- a/easybuild/easyconfigs/t/Tensorflow/Tensorflow-0.12.1-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/t/Tensorflow/Tensorflow-0.12.1-intel-2016b-Python-2.7.12.eb @@ -13,7 +13,7 @@ pymaj = '2' pymin = '7' pymajmin = pymaj + pymin -source_urls = ['https://pypi.python.org/packages/7e/c6/837f4e249aae5c86a632eaaa9779e601eca1487772f8ad75c347bf9e813f/'] +source_urls = [PYPI_SOURCE] sources = [ 'tensorflow-%%(version)s-cp%(pymajmin)s-cp%(pymajmin)smu-manylinux1_x86_64.whl' % {'pymajmin': pymajmin}, ] diff --git a/easybuild/easyconfigs/t/Tensorflow/Tensorflow-0.12.1-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/t/Tensorflow/Tensorflow-0.12.1-intel-2016b-Python-3.5.2.eb index 4898d79427..bbe2973b53 100644 --- a/easybuild/easyconfigs/t/Tensorflow/Tensorflow-0.12.1-intel-2016b-Python-3.5.2.eb +++ b/easybuild/easyconfigs/t/Tensorflow/Tensorflow-0.12.1-intel-2016b-Python-3.5.2.eb @@ -13,7 +13,7 @@ pymaj = '3' pymin = '5' pymajmin = pymaj + pymin -source_urls = ['https://pypi.python.org/packages/e5/5c/56e6522fdcd6f8739dcbc4de62e8b0040e141785bb42e5b53a83b0ba3e58/'] +source_urls = [PYPI_SOURCE] sources = [ 'tensorflow-%%(version)s-cp%(pymajmin)s-cp%(pymajmin)sm-manylinux1_x86_64.whl' % {'pymajmin': pymajmin}, ] diff --git a/easybuild/easyconfigs/t/Tensorflow/Tensorflow-1.0.1-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/t/Tensorflow/Tensorflow-1.0.1-intel-2016b-Python-2.7.12.eb index f1c3f15e89..d6e4c6cbb3 100755 --- a/easybuild/easyconfigs/t/Tensorflow/Tensorflow-1.0.1-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/t/Tensorflow/Tensorflow-1.0.1-intel-2016b-Python-2.7.12.eb @@ -13,7 +13,7 @@ pymaj = '2' pymin = '7' pymajmin = pymaj + pymin -source_urls = ['https://pypi.python.org/packages/7e/7c/f398393beab1647be0a5e6974b8a34e4ea2d3cb7bd9e38bd43a657ed27d1/'] +source_urls = [PYPI_SOURCE] sources = [ 'tensorflow-%%(version)s-cp%(pymajmin)s-cp%(pymajmin)smu-manylinux1_x86_64.whl' % {'pymajmin': pymajmin}, ] diff --git a/easybuild/easyconfigs/t/Tensorflow/Tensorflow-1.0.1-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/t/Tensorflow/Tensorflow-1.0.1-intel-2016b-Python-3.5.2.eb index 42b703619c..293d4b8557 100755 --- a/easybuild/easyconfigs/t/Tensorflow/Tensorflow-1.0.1-intel-2016b-Python-3.5.2.eb +++ b/easybuild/easyconfigs/t/Tensorflow/Tensorflow-1.0.1-intel-2016b-Python-3.5.2.eb @@ -13,7 +13,7 @@ pymaj = '3' pymin = '5' pymajmin = pymaj + pymin -source_urls = ['https://pypi.python.org/packages/1f/38/c255432f18005362dd2459e3bff2b2411eb7d02ca09fa20ee1dd1311f69f/'] +source_urls = [PYPI_SOURCE] sources = [ 'tensorflow-%%(version)s-cp%(pymajmin)s-cp%(pymajmin)sm-manylinux1_x86_64.whl' % {'pymajmin': pymajmin}, ] diff --git a/easybuild/easyconfigs/t/Tensorflow/Tensorflow-1.1.0-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/t/Tensorflow/Tensorflow-1.1.0-intel-2017a-Python-2.7.13.eb index a6aec94f18..c3e49d93e0 100755 --- a/easybuild/easyconfigs/t/Tensorflow/Tensorflow-1.1.0-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/t/Tensorflow/Tensorflow-1.1.0-intel-2017a-Python-2.7.13.eb @@ -13,7 +13,7 @@ pymaj = '2' pymin = '7' pymajmin = pymaj + pymin -source_urls = ['https://pypi.python.org/packages/8a/73/74c610decd5e0a1fd7f441a32e3561d21c28ced98fd6d3d9d5c70dbf92ce/'] +source_urls = [PYPI_SOURCE] sources = [ 'tensorflow-%%(version)s-cp%(pymajmin)s-cp%(pymajmin)smu-manylinux1_x86_64.whl' % {'pymajmin': pymajmin}, ] diff --git a/easybuild/easyconfigs/t/Tensorflow/Tensorflow-1.1.0-intel-2017a-Python-3.6.1.eb b/easybuild/easyconfigs/t/Tensorflow/Tensorflow-1.1.0-intel-2017a-Python-3.6.1.eb index f134b5be2b..1dd71b4078 100755 --- a/easybuild/easyconfigs/t/Tensorflow/Tensorflow-1.1.0-intel-2017a-Python-3.6.1.eb +++ b/easybuild/easyconfigs/t/Tensorflow/Tensorflow-1.1.0-intel-2017a-Python-3.6.1.eb @@ -13,7 +13,7 @@ pymaj = '3' pymin = '6' pymajmin = pymaj + pymin -source_urls = ['https://pypi.python.org/packages/cd/e4/b2a8bcd1fa689489050386ec70c5c547e4a75d06f2cc2b55f45463cd092c/'] +source_urls = [PYPI_SOURCE] sources = [ 'tensorflow-%%(version)s-cp%(pymajmin)s-cp%(pymajmin)sm-manylinux1_x86_64.whl' % {'pymajmin': pymajmin}, ] -- GitLab From c679889fdfab359099b7e2dc0ab2c4e34fa528ee Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 26 Jun 2017 19:04:17 +0200 Subject: [PATCH 1022/1603] rename intel/2017.05 to intel/2017b, stick to GCC 6.3.0 as a base --- ...HPL-2.2-intel-2017.05.eb => HPL-2.2-intel-2017b.eb} | 2 +- ...-7.1.0-2.28.eb => icc-2017.4.196-GCC-6.3.0-2.28.eb} | 2 +- ...0-2.28.eb => iccifort-2017.4.196-GCC-6.3.0-2.28.eb} | 2 +- ....1.0-2.28.eb => ifort-2017.4.196-GCC-6.3.0-2.28.eb} | 2 +- ...{iimpi-2017.05-GCC-7.1.0-2.28.eb => iimpi-2017b.eb} | 10 +++++----- ...CC-7.1.0-2.28.eb => imkl-2017.3.196-iimpi-2017b.eb} | 2 +- ...i-2017.3.196-iccifort-2017.4.196-GCC-6.3.0-2.28.eb} | 2 +- .../i/intel/{intel-2017.05.eb => intel-2017b.eb} | 6 +++--- 8 files changed, 14 insertions(+), 14 deletions(-) rename easybuild/easyconfigs/h/HPL/{HPL-2.2-intel-2017.05.eb => HPL-2.2-intel-2017b.eb} (92%) rename easybuild/easyconfigs/i/icc/{icc-2017.4.196-GCC-7.1.0-2.28.eb => icc-2017.4.196-GCC-6.3.0-2.28.eb} (98%) rename easybuild/easyconfigs/i/iccifort/{iccifort-2017.4.196-GCC-7.1.0-2.28.eb => iccifort-2017.4.196-GCC-6.3.0-2.28.eb} (93%) rename easybuild/easyconfigs/i/ifort/{ifort-2017.4.196-GCC-7.1.0-2.28.eb => ifort-2017.4.196-GCC-6.3.0-2.28.eb} (98%) rename easybuild/easyconfigs/i/iimpi/{iimpi-2017.05-GCC-7.1.0-2.28.eb => iimpi-2017b.eb} (65%) rename easybuild/easyconfigs/i/imkl/{imkl-2017.3.196-iimpi-2017.05-GCC-7.1.0-2.28.eb => imkl-2017.3.196-iimpi-2017b.eb} (95%) rename easybuild/easyconfigs/i/impi/{impi-2017.3.196-iccifort-2017.4.196-GCC-7.1.0-2.28.eb => impi-2017.3.196-iccifort-2017.4.196-GCC-6.3.0-2.28.eb} (95%) rename easybuild/easyconfigs/i/intel/{intel-2017.05.eb => intel-2017b.eb} (86%) diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.2-intel-2017.05.eb b/easybuild/easyconfigs/h/HPL/HPL-2.2-intel-2017b.eb similarity index 92% rename from easybuild/easyconfigs/h/HPL/HPL-2.2-intel-2017.05.eb rename to easybuild/easyconfigs/h/HPL/HPL-2.2-intel-2017b.eb index f649fc1c6c..32a513858c 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.2-intel-2017.05.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.2-intel-2017b.eb @@ -6,7 +6,7 @@ description = """HPL is a software package that solves a (random) dense linear s arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the High Performance Computing Linpack Benchmark.""" -toolchain = {'name': 'intel', 'version': '2017.05'} +toolchain = {'name': 'intel', 'version': '2017b'} toolchainopts = {'usempi': True} sources = [SOURCELOWER_TAR_GZ] diff --git a/easybuild/easyconfigs/i/icc/icc-2017.4.196-GCC-7.1.0-2.28.eb b/easybuild/easyconfigs/i/icc/icc-2017.4.196-GCC-6.3.0-2.28.eb similarity index 98% rename from easybuild/easyconfigs/i/icc/icc-2017.4.196-GCC-7.1.0-2.28.eb rename to easybuild/easyconfigs/i/icc/icc-2017.4.196-GCC-6.3.0-2.28.eb index 75482e87cf..c3b0319dcb 100644 --- a/easybuild/easyconfigs/i/icc/icc-2017.4.196-GCC-7.1.0-2.28.eb +++ b/easybuild/easyconfigs/i/icc/icc-2017.4.196-GCC-6.3.0-2.28.eb @@ -12,7 +12,7 @@ sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_compose checksums = ['6b9b57dada0ec68e394866ec0a8b162c9233de18a7a6dd2dcc956d335e06acbc'] -gccver = '7.1.0' +gccver = '6.3.0' binutilsver = '2.28' versionsuffix = '-GCC-%s-%s' % (gccver, binutilsver) diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2017.4.196-GCC-7.1.0-2.28.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2017.4.196-GCC-6.3.0-2.28.eb similarity index 93% rename from easybuild/easyconfigs/i/iccifort/iccifort-2017.4.196-GCC-7.1.0-2.28.eb rename to easybuild/easyconfigs/i/iccifort/iccifort-2017.4.196-GCC-6.3.0-2.28.eb index 20175f1539..1fbc0afc0a 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2017.4.196-GCC-7.1.0-2.28.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2017.4.196-GCC-6.3.0-2.28.eb @@ -3,7 +3,7 @@ easyblock = 'Toolchain' name = 'iccifort' version = '2017.4.196' -versionsuffix = '-GCC-7.1.0-2.28' +versionsuffix = '-GCC-6.3.0-2.28' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = """Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and diff --git a/easybuild/easyconfigs/i/ifort/ifort-2017.4.196-GCC-7.1.0-2.28.eb b/easybuild/easyconfigs/i/ifort/ifort-2017.4.196-GCC-6.3.0-2.28.eb similarity index 98% rename from easybuild/easyconfigs/i/ifort/ifort-2017.4.196-GCC-7.1.0-2.28.eb rename to easybuild/easyconfigs/i/ifort/ifort-2017.4.196-GCC-6.3.0-2.28.eb index 0ad62b89f5..8f6eacf9f8 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2017.4.196-GCC-7.1.0-2.28.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2017.4.196-GCC-6.3.0-2.28.eb @@ -15,7 +15,7 @@ checksums = ['0b6a222e015f776600b12b17c19506249c9e7691a8d287f44cd40a66ca9ac749'] # remove dependency on intel-mpi-rt-mic patches = ['ifort_2017_no_mpi_mic_dependency.patch'] -gccver = '7.1.0' +gccver = '6.3.0' binutilsver = '2.28' versionsuffix = '-GCC-%s-%s' % (gccver, binutilsver) diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-2017.05-GCC-7.1.0-2.28.eb b/easybuild/easyconfigs/i/iimpi/iimpi-2017b.eb similarity index 65% rename from easybuild/easyconfigs/i/iimpi/iimpi-2017.05-GCC-7.1.0-2.28.eb rename to easybuild/easyconfigs/i/iimpi/iimpi-2017b.eb index ff25b839db..8d59809f4c 100644 --- a/easybuild/easyconfigs/i/iimpi/iimpi-2017.05-GCC-7.1.0-2.28.eb +++ b/easybuild/easyconfigs/i/iimpi/iimpi-2017b.eb @@ -2,8 +2,7 @@ easyblock = "Toolchain" name = 'iimpi' -version = '2017.05' -versionsuffix = '-GCC-7.1.0-2.28' +version = '2017b' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = """Intel C/C++ and Fortran compilers, alongside Intel MPI.""" @@ -11,10 +10,11 @@ description = """Intel C/C++ and Fortran compilers, alongside Intel MPI.""" toolchain = {'name': 'dummy', 'version': 'dummy'} compver = '2017.4.196' +suff = '-GCC-6.3.0-2.28' dependencies = [ - ('icc', compver, versionsuffix), - ('ifort', compver, versionsuffix), - ('impi', '2017.3.196', '', ('iccifort', '%s%s' % (compver, versionsuffix))), + ('icc', compver, suff), + ('ifort', compver, suff), + ('impi', '2017.3.196', '', ('iccifort', '%s%s' % (compver, suff))), ] moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/imkl/imkl-2017.3.196-iimpi-2017.05-GCC-7.1.0-2.28.eb b/easybuild/easyconfigs/i/imkl/imkl-2017.3.196-iimpi-2017b.eb similarity index 95% rename from easybuild/easyconfigs/i/imkl/imkl-2017.3.196-iimpi-2017.05-GCC-7.1.0-2.28.eb rename to easybuild/easyconfigs/i/imkl/imkl-2017.3.196-iimpi-2017b.eb index 2793cfba56..4d773b67ad 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2017.3.196-iimpi-2017.05-GCC-7.1.0-2.28.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2017.3.196-iimpi-2017b.eb @@ -9,7 +9,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, applications that require maximum performance. Core math functions include BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.""" -toolchain = {'name': 'iimpi', 'version': '2017.05-GCC-7.1.0-2.28'} +toolchain = {'name': 'iimpi', 'version': '2017b'} sources = ['l_mkl_%(version)s.tgz'] checksums = ['fd7295870fa164d6138c9818304f25f2bb263c814a6c6539c9fe4e104055f1ca'] diff --git a/easybuild/easyconfigs/i/impi/impi-2017.3.196-iccifort-2017.4.196-GCC-7.1.0-2.28.eb b/easybuild/easyconfigs/i/impi/impi-2017.3.196-iccifort-2017.4.196-GCC-6.3.0-2.28.eb similarity index 95% rename from easybuild/easyconfigs/i/impi/impi-2017.3.196-iccifort-2017.4.196-GCC-7.1.0-2.28.eb rename to easybuild/easyconfigs/i/impi/impi-2017.3.196-iccifort-2017.4.196-GCC-6.3.0-2.28.eb index 75d92e43ef..473cd8b786 100644 --- a/easybuild/easyconfigs/i/impi/impi-2017.3.196-iccifort-2017.4.196-GCC-7.1.0-2.28.eb +++ b/easybuild/easyconfigs/i/impi/impi-2017.3.196-iccifort-2017.4.196-GCC-6.3.0-2.28.eb @@ -8,7 +8,7 @@ description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric messag passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for Linux OS implements the Message Passing Interface, version 2 (MPI-2) specification.""" -toolchain = {'name': 'iccifort', 'version': '2017.4.196-GCC-7.1.0-2.28'} +toolchain = {'name': 'iccifort', 'version': '2017.4.196-GCC-6.3.0-2.28'} sources = ['l_mpi_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/intel/intel-2017.05.eb b/easybuild/easyconfigs/i/intel/intel-2017b.eb similarity index 86% rename from easybuild/easyconfigs/i/intel/intel-2017.05.eb rename to easybuild/easyconfigs/i/intel/intel-2017b.eb index 6e68b4ba70..aecf829181 100644 --- a/easybuild/easyconfigs/i/intel/intel-2017.05.eb +++ b/easybuild/easyconfigs/i/intel/intel-2017b.eb @@ -1,7 +1,7 @@ easyblock = 'Toolchain' name = 'intel' -version = '2017.05' +version = '2017b' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & @@ -10,7 +10,7 @@ description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and toolchain = {'name': 'dummy', 'version': 'dummy'} compver = '2017.4.196' -gccver = '7.1.0' +gccver = '6.3.0' binutilsver = '2.28' gccsuff = '-GCC-%s-%s' % (gccver, binutilsver) dependencies = [ @@ -19,7 +19,7 @@ dependencies = [ ('icc', compver, gccsuff), ('ifort', compver, gccsuff), ('impi', '2017.3.196', '', ('iccifort', '%s%s' % (compver, gccsuff))), - ('imkl', '2017.3.196', '', ('iimpi', version + gccsuff)), + ('imkl', '2017.3.196', '', ('iimpi', version)), ] moduleclass = 'toolchain' -- GitLab From 4df0c777484c5d495616eabae7e19bdebcc8efd3 Mon Sep 17 00:00:00 2001 From: Yann Pouillon Date: Tue, 27 Jun 2017 10:39:37 +0200 Subject: [PATCH 1023/1603] Removed trailing blank lines as requested --- .../easyconfigs/a/ASE/ASE-3.13.0-foss-2016b-Python-2.7.12.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.13.0-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/a/ASE/ASE-3.13.0-foss-2016b-Python-2.7.12.eb index 52093a758b..4228f89c2f 100644 --- a/easybuild/easyconfigs/a/ASE/ASE-3.13.0-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/a/ASE/ASE-3.13.0-foss-2016b-Python-2.7.12.eb @@ -25,4 +25,3 @@ sanity_check_paths = { } moduleclass = 'chem' - -- GitLab From 43f181fa53e7e1f9750613a977c6348a51770e4c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 27 Jun 2017 11:31:36 +0200 Subject: [PATCH 1024/1603] {math}[intel/2017a] numpy 1.13.0 --- .../numpy-1.13.0-intel-2017a-Python-2.7.13.eb | 26 ++++++ .../n/numpy/numpy-1.13.0_fix-intel.patch | 83 +++++++++++++++++++ 2 files changed, 109 insertions(+) create mode 100644 easybuild/easyconfigs/n/numpy/numpy-1.13.0-intel-2017a-Python-2.7.13.eb create mode 100644 easybuild/easyconfigs/n/numpy/numpy-1.13.0_fix-intel.patch diff --git a/easybuild/easyconfigs/n/numpy/numpy-1.13.0-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/n/numpy/numpy-1.13.0-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..d0c0134be7 --- /dev/null +++ b/easybuild/easyconfigs/n/numpy/numpy-1.13.0-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,26 @@ +name = 'numpy' +version = '1.13.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.numpy.org' +description = """NumPy is the fundamental package for scientific computing with Python. It contains among other things: + a powerful N-dimensional array object, sophisticated (broadcasting) functions, tools for integrating C/C++ and Fortran + code, useful linear algebra, Fourier transform, and random number capabilities. Besides its obvious scientific uses, + NumPy can also be used as an efficient multi-dimensional container of generic data. Arbitrary data-types can be + defined. This allows NumPy to seamlessly and speedily integrate with a wide variety of databases.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_ZIP] + +patches = [ + 'numpy-1.12.0-mkl.patch', + 'numpy-%(version)s_fix-intel.patch', +] + +dependencies = [ + ('Python', '2.7.13'), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/n/numpy/numpy-1.13.0_fix-intel.patch b/easybuild/easyconfigs/n/numpy/numpy-1.13.0_fix-intel.patch new file mode 100644 index 0000000000..ea2a355828 --- /dev/null +++ b/easybuild/easyconfigs/n/numpy/numpy-1.13.0_fix-intel.patch @@ -0,0 +1,83 @@ +see https://github.com/numpy/numpy/issues/9278 and https://github.com/numpy/numpy/pull/9285 +diff --git a/numpy/distutils/ccompiler.py b/numpy/distutils/ccompiler.py +index 93ef4587c26..bbc3923bd6d 100644 +--- a/numpy/distutils/ccompiler.py ++++ b/numpy/distutils/ccompiler.py +@@ -80,6 +80,7 @@ def _needs_build(obj, cc_args, extra_postargs, pp_opts): + + return False + ++ + def replace_method(klass, method_name, func): + if sys.version_info[0] < 3: + m = types.MethodType(func, None, klass) +@@ -88,6 +89,25 @@ def replace_method(klass, method_name, func): + m = lambda self, *args, **kw: func(self, *args, **kw) + setattr(klass, method_name, m) + ++ ++###################################################################### ++## Method that subclasses may redefine. But don't call this method, ++## it i private to CCompiler class and may return unexpected ++## results if used elsewhere. So, you have been warned.. ++ ++def CCompiler_find_executables(self): ++ """ ++ Does nothing here, but is called by the get_version method and can be ++ overridden by subclasses. In particular it is redefined in the `FCompiler` ++ class where more documentation can be found. ++ ++ """ ++ pass ++ ++ ++replace_method(CCompiler, 'find_executables', CCompiler_find_executables) ++ ++ + # Using customized CCompiler.spawn. + def CCompiler_spawn(self, cmd, display=None): + """ +diff --git a/numpy/distutils/fcompiler/intel.py b/numpy/distutils/fcompiler/intel.py +index eb6150201c2..4dee8492f9b 100644 +--- a/numpy/distutils/fcompiler/intel.py ++++ b/numpy/distutils/fcompiler/intel.py +@@ -57,7 +57,7 @@ def get_flags(self): + + def get_flags_opt(self): # Scipy test failures with -O2 + v = self.get_version() +- mpopt = 'openmp' if v and int(v.split('.')[0]) < 15 else 'qopenmp' ++ mpopt = 'openmp' if v and v < '15' else 'qopenmp' + return ['-xhost -fp-model strict -O1 -{}'.format(mpopt)] + + def get_flags_arch(self): +@@ -123,7 +123,7 @@ def get_flags(self): + + def get_flags_opt(self): # Scipy test failures with -O2 + v = self.get_version() +- mpopt = 'openmp' if v and int(v.split('.')[0]) < 15 else 'qopenmp' ++ mpopt = 'openmp' if v and v < '15' else 'qopenmp' + return ['-fp-model strict -O1 -{}'.format(mpopt)] + + def get_flags_arch(self): +diff --git a/numpy/distutils/intelccompiler.py b/numpy/distutils/intelccompiler.py +index 3b7756b598c..3386775ee56 100644 +--- a/numpy/distutils/intelccompiler.py ++++ b/numpy/distutils/intelccompiler.py +@@ -19,7 +19,7 @@ def __init__(self, verbose=0, dry_run=0, force=0): + UnixCCompiler.__init__(self, verbose, dry_run, force) + + v = self.get_version() +- mpopt = 'openmp' if v and int(v.split('.')[0]) < 15 else 'qopenmp' ++ mpopt = 'openmp' if v and v < '15' else 'qopenmp' + self.cc_exe = ('icc -fPIC -fp-model strict -O3 ' + '-fomit-frame-pointer -{}').format(mpopt) + compiler = self.cc_exe +@@ -59,7 +59,7 @@ def __init__(self, verbose=0, dry_run=0, force=0): + UnixCCompiler.__init__(self, verbose, dry_run, force) + + v = self.get_version() +- mpopt = 'openmp' if v and int(v.split('.')[0]) < 15 else 'qopenmp' ++ mpopt = 'openmp' if v and v < '15' else 'qopenmp' + self.cc_exe = ('icc -m64 -fPIC -fp-model strict -O3 ' + '-fomit-frame-pointer -{}').format(mpopt) + compiler = self.cc_exe -- GitLab From 166c15ac70dc57c777ab5145b36526779176664e Mon Sep 17 00:00:00 2001 From: Sebastien Varrette Date: Tue, 27 Jun 2017 11:40:54 +0200 Subject: [PATCH 1025/1603] reuse common default patch Signed-off-by: Sebastien Varrette --- easybuild/easyconfigs/l/likwid/likwid-4.2.0-foss-2017a.eb | 2 +- easybuild/easyconfigs/l/likwid/likwid-4.2.0-intel-2017a.eb | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/l/likwid/likwid-4.2.0-foss-2017a.eb b/easybuild/easyconfigs/l/likwid/likwid-4.2.0-foss-2017a.eb index 69116819bb..6fabae1ced 100644 --- a/easybuild/easyconfigs/l/likwid/likwid-4.2.0-foss-2017a.eb +++ b/easybuild/easyconfigs/l/likwid/likwid-4.2.0-foss-2017a.eb @@ -26,7 +26,7 @@ toolchainopts = {'pic': True} source_urls = ['https://github.com/RRZE-HPC/likwid/archive/'] sources = ['%(version)s.tar.gz'] -patches = ['likwid-%(version)s-foss-config-mk.patch'] +patches = ['likwid-%(version)s-config-mk.patch'] builddependencies = [('binutils', '2.27')] diff --git a/easybuild/easyconfigs/l/likwid/likwid-4.2.0-intel-2017a.eb b/easybuild/easyconfigs/l/likwid/likwid-4.2.0-intel-2017a.eb index 3c4905b6ef..c694c1cfac 100644 --- a/easybuild/easyconfigs/l/likwid/likwid-4.2.0-intel-2017a.eb +++ b/easybuild/easyconfigs/l/likwid/likwid-4.2.0-intel-2017a.eb @@ -25,12 +25,12 @@ toolchainopts = {'pic': True} source_urls = ['https://github.com/RRZE-HPC/likwid/archive/'] sources = ['%(version)s.tar.gz'] -patches = ['likwid-%(version)s-intel-config-mk.patch'] +patches = ['likwid-%(version)s-config-mk.patch'] builddependencies = [('binutils', '2.27')] skipsteps = ['configure'] -buildopts = 'CC="$CC" CFLAGS="$CFLAGS -std=c99" PREFIX=%(installdir)s' +buildopts = 'COMPILER="ICC" CC="$CC" CFLAGS="$CFLAGS -std=c99" PREFIX=%(installdir)s' installopts = 'PREFIX=%(installdir)s' sanity_check_paths = { -- GitLab From d1e4eec86e7e686c44091c8cf8f8184b00d73dd0 Mon Sep 17 00:00:00 2001 From: Sebastien Varrette Date: Tue, 27 Jun 2017 12:00:51 +0200 Subject: [PATCH 1026/1603] remove useless (additional) patch files Signed-off-by: Sebastien Varrette --- .../likwid/likwid-4.2.0-foss-config-mk.patch | 40 --------------- .../likwid/likwid-4.2.0-intel-config-mk.patch | 49 ------------------- 2 files changed, 89 deletions(-) delete mode 100644 easybuild/easyconfigs/l/likwid/likwid-4.2.0-foss-config-mk.patch delete mode 100644 easybuild/easyconfigs/l/likwid/likwid-4.2.0-intel-config-mk.patch diff --git a/easybuild/easyconfigs/l/likwid/likwid-4.2.0-foss-config-mk.patch b/easybuild/easyconfigs/l/likwid/likwid-4.2.0-foss-config-mk.patch deleted file mode 100644 index c1de1bdb80..0000000000 --- a/easybuild/easyconfigs/l/likwid/likwid-4.2.0-foss-config-mk.patch +++ /dev/null @@ -1,40 +0,0 @@ ---- likwid-likwid-4.2.orig/config.mk 2016-12-22 13:22:23.000000000 +0100 -+++ likwid-likwid-4.2/config.mk 2017-06-19 14:36:15.521398000 +0200 -@@ -9,7 +9,7 @@ - COLOR = BLUE#NO SPACE - - # Path were to install likwid --PREFIX = /usr/local#NO SPACE -+# PREFIX = /usr/local#NO SPACE - - # uncomment to optionally set external lua@5.3: - # default is use internally provide lua -@@ -40,7 +40,7 @@ - # chown installed tools to this user/group - # if you change anything here, make sure that the user/group can access - # the MSR devices and (on Intel) the PCI devices. --INSTALL_CHOWN = -g root -o root -+INSTALL_CHOWN = - - # For the daemon based secure msr/pci access configure - # the absolute path to the msr daemon executable. -@@ -51,7 +51,7 @@ - # Build the accessDaemon. Have a look in the WIKI for details. - BUILDDAEMON = true#NO SPACE - #Build the setFrequencies tool --BUILDFREQ = true#NO SPACE -+BUILDFREQ = false#NO SPACE - - # Set the default mode for MSR access. - # This can usually be overriden on the commandline. -@@ -82,8 +82,8 @@ - # a proper config file at CFG_FILE_PATH) - MAX_NUM_THREADS = 263 - MAX_NUM_NODES = 64 --CFG_FILE_PATH = /etc/likwid.cfg --TOPO_FILE_PATH = /etc/likwid_topo.cfg -+CFG_FILE_PATH = $(PREFIX)/etc/likwid.cfg -+TOPO_FILE_PATH = $(PREFIX)/etc/likwid_topo.cfg - - # Versioning Information - VERSION = 4 diff --git a/easybuild/easyconfigs/l/likwid/likwid-4.2.0-intel-config-mk.patch b/easybuild/easyconfigs/l/likwid/likwid-4.2.0-intel-config-mk.patch deleted file mode 100644 index a7d8fccb54..0000000000 --- a/easybuild/easyconfigs/l/likwid/likwid-4.2.0-intel-config-mk.patch +++ /dev/null @@ -1,49 +0,0 @@ ---- likwid-likwid-4.2.orig/config.mk 2016-12-22 13:22:23.000000000 +0100 -+++ likwid-likwid-4.2/config.mk 2017-06-22 10:14:28.585696000 +0200 -@@ -1,7 +1,7 @@ - # Please have a look in INSTALL and the WIKI for details on - # configuration options setup steps. - # supported: GCC, CLANG, ICC, MIC (ICC), GCCX86 (for 32bit systems) --COMPILER = GCC#NO SPACE -+COMPILER = ICC#NO SPACE - - # Define the color of the likwid-pin output - # Can be NONE, BLACK, RED, GREEN, YELLOW, BLUE, -@@ -9,7 +9,7 @@ - COLOR = BLUE#NO SPACE - - # Path were to install likwid --PREFIX = /usr/local#NO SPACE -+# PREFIX = /usr/local#NO SPACE - - # uncomment to optionally set external lua@5.3: - # default is use internally provide lua -@@ -40,7 +40,7 @@ - # chown installed tools to this user/group - # if you change anything here, make sure that the user/group can access - # the MSR devices and (on Intel) the PCI devices. --INSTALL_CHOWN = -g root -o root -+INSTALL_CHOWN = - - # For the daemon based secure msr/pci access configure - # the absolute path to the msr daemon executable. -@@ -51,7 +51,7 @@ - # Build the accessDaemon. Have a look in the WIKI for details. - BUILDDAEMON = true#NO SPACE - #Build the setFrequencies tool --BUILDFREQ = true#NO SPACE -+BUILDFREQ = false#NO SPACE - - # Set the default mode for MSR access. - # This can usually be overriden on the commandline. -@@ -82,8 +82,8 @@ - # a proper config file at CFG_FILE_PATH) - MAX_NUM_THREADS = 263 - MAX_NUM_NODES = 64 --CFG_FILE_PATH = /etc/likwid.cfg --TOPO_FILE_PATH = /etc/likwid_topo.cfg -+CFG_FILE_PATH = $(PREFIX)/etc/likwid.cfg -+TOPO_FILE_PATH = $(PREFIX)/etc/likwid_topo.cfg - - # Versioning Information - VERSION = 4 -- GitLab From 1de635693283fc62ca4cdeebd7d7610b5e76e6bb Mon Sep 17 00:00:00 2001 From: Yann Pouillon Date: Tue, 27 Jun 2017 17:50:20 +0200 Subject: [PATCH 1027/1603] adding easyconfigs: git-2.13.1-foss-2016b.eb --- .../g/git/git-2.13.1-foss-2016b.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/g/git/git-2.13.1-foss-2016b.eb diff --git a/easybuild/easyconfigs/g/git/git-2.13.1-foss-2016b.eb b/easybuild/easyconfigs/g/git/git-2.13.1-foss-2016b.eb new file mode 100644 index 0000000000..76cf3e7957 --- /dev/null +++ b/easybuild/easyconfigs/g/git/git-2.13.1-foss-2016b.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'git' +version = '2.13.1' + +homepage = 'http://git-scm.com/' +description = """Git is a free and open source distributed version control system designed +to handle everything from small to very large projects with speed and efficiency.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +sources = ['v%(version)s.tar.gz'] +source_urls = ['https://github.com/git/git/archive'] +checksums = ['c0e3fe359f715cb7dfc3ac63fa6e733a'] + +dependencies = [ + ('cURL', '7.49.1'), + ('expat', '2.2.0'), + ('gettext', '0.19.8'), + ('Perl', '5.24.0', '-bare'), +] + +preconfigopts = 'make configure && ' + +# Work around git build system bug. If LIBS contains -lpthread, then configure +# will not append -lpthread to LDFLAGS, but Makefile ignores LIBS. +configopts = "--with-perl=${EBROOTPERL}/bin/perl --enable-pthreads='-lpthread'" + +sanity_check_paths = { + 'files': ['bin/git'], + 'dirs': [], +} + +moduleclass = 'tools' -- GitLab From 49338c243f00474333351dbfc88ef3d2da81f811 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Wed, 28 Jun 2017 09:52:03 +0200 Subject: [PATCH 1028/1603] Add Circos for foss-2016b Add needed Perl modules --- .../Circos-0.69-5-foss-2016b-Perl-5.24.0.eb | 35 +++++++++++++++++++ .../p/Perl/Perl-5.24.0-foss-2016b.eb | 8 +++++ 2 files changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/c/Circos/Circos-0.69-5-foss-2016b-Perl-5.24.0.eb diff --git a/easybuild/easyconfigs/c/Circos/Circos-0.69-5-foss-2016b-Perl-5.24.0.eb b/easybuild/easyconfigs/c/Circos/Circos-0.69-5-foss-2016b-Perl-5.24.0.eb new file mode 100644 index 0000000000..893126e7c3 --- /dev/null +++ b/easybuild/easyconfigs/c/Circos/Circos-0.69-5-foss-2016b-Perl-5.24.0.eb @@ -0,0 +1,35 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild + +easyblock = 'Tarball' + +name = 'Circos' +version = '0.69-5' +versionsuffix = '-Perl-%(perlver)s' + +homepage = 'http://www.circos.ca/' +description = """Circos is a software package for visualizing data and information. + It visualizes data in a circular layout - this makes Circos ideal for exploring + relationships between objects or positions.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['http://circos.ca/distribution/'] +sources = [SOURCELOWER_TGZ] + +checksums = ['49b4c467ba871fa416013c47d69db9e6'] + +dependencies = [ + ('Perl', '5.24.0'), + ('GD', '2.66', versionsuffix), +] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': ['lib/%(name)s'], +} + +modextrapaths = {'PERL5LIB': 'lib'} + +sanity_check_commands = [('perl', '-e "use Circos"')] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.24.0-foss-2016b.eb b/easybuild/easyconfigs/p/Perl/Perl-5.24.0-foss-2016b.eb index 3f4c7638c7..41e1a64944 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.24.0-foss-2016b.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.24.0-foss-2016b.eb @@ -887,6 +887,14 @@ exts_list = [ 'source_tmpl': 'PDF-API2-2.031.tar.gz', 'source_urls': ['http://search.cpan.org/CPAN/authors/id/S/SS/SSIMMS/'], }), + ('SVG', '2.77', { + 'source_tmpl': 'SVG-2.77.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/M/MA/MANWAR/'], + }), + ('Statistics::Basic', '1.6611', { + 'source_tmpl': 'Statistics-Basic-1.6611.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/J/JE/JETTERO/'], + }), ] moduleclass = 'lang' -- GitLab From d5b4bb5815373058062096d3d4a107bd6b6e21b1 Mon Sep 17 00:00:00 2001 From: Sebastien Varrette Date: Wed, 28 Jun 2017 11:00:38 +0200 Subject: [PATCH 1029/1603] remove useless dependency on binutils Signed-off-by: Sebastien Varrette --- easybuild/easyconfigs/l/likwid/likwid-4.2.0-foss-2017a.eb | 2 -- easybuild/easyconfigs/l/likwid/likwid-4.2.0-intel-2017a.eb | 2 -- 2 files changed, 4 deletions(-) diff --git a/easybuild/easyconfigs/l/likwid/likwid-4.2.0-foss-2017a.eb b/easybuild/easyconfigs/l/likwid/likwid-4.2.0-foss-2017a.eb index 6fabae1ced..ebb2f3de9b 100644 --- a/easybuild/easyconfigs/l/likwid/likwid-4.2.0-foss-2017a.eb +++ b/easybuild/easyconfigs/l/likwid/likwid-4.2.0-foss-2017a.eb @@ -28,8 +28,6 @@ sources = ['%(version)s.tar.gz'] patches = ['likwid-%(version)s-config-mk.patch'] -builddependencies = [('binutils', '2.27')] - skipsteps = ['configure'] buildopts = 'CC="$CC" CFLAGS="$CFLAGS -std=c99" PREFIX=%(installdir)s' installopts = 'PREFIX=%(installdir)s' diff --git a/easybuild/easyconfigs/l/likwid/likwid-4.2.0-intel-2017a.eb b/easybuild/easyconfigs/l/likwid/likwid-4.2.0-intel-2017a.eb index c694c1cfac..b38fb421b8 100644 --- a/easybuild/easyconfigs/l/likwid/likwid-4.2.0-intel-2017a.eb +++ b/easybuild/easyconfigs/l/likwid/likwid-4.2.0-intel-2017a.eb @@ -27,8 +27,6 @@ sources = ['%(version)s.tar.gz'] patches = ['likwid-%(version)s-config-mk.patch'] -builddependencies = [('binutils', '2.27')] - skipsteps = ['configure'] buildopts = 'COMPILER="ICC" CC="$CC" CFLAGS="$CFLAGS -std=c99" PREFIX=%(installdir)s' installopts = 'PREFIX=%(installdir)s' -- GitLab From 18f8a84dae2dfb3bcb42a177369d9ec305d9ca28 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Wed, 28 Jun 2017 11:29:25 +0200 Subject: [PATCH 1030/1603] adding easyconfigs: skewer-0.2.2-goolf-1.7.20.eb --- easybuild/easyconfigs/s/skewer/skewer-0.2.2-goolf-1.7.20.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/skewer/skewer-0.2.2-goolf-1.7.20.eb b/easybuild/easyconfigs/s/skewer/skewer-0.2.2-goolf-1.7.20.eb index abf4cb6e1f..89547eb928 100644 --- a/easybuild/easyconfigs/s/skewer/skewer-0.2.2-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/s/skewer/skewer-0.2.2-goolf-1.7.20.eb @@ -8,7 +8,7 @@ easyblock = 'MakeCp' name = 'skewer' version = '0.2.2' -homepage = 'http://smithlabresearch.org/software/preseq/' +homepage = 'https://github.com/relipmoc/skewer' description = """skewer (transferred from https://sourceforge.net/projects/skewer) implements the bit-masked k-difference matching algorithm dedicated to the task of adapter trimming and it is specially designed for processing next-generation sequencing (NGS) paired-end sequences""" -- GitLab From 6b46855e1cf91182be3ba1cbd805ef75585a7bb4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 28 Jun 2017 13:17:30 +0200 Subject: [PATCH 1031/1603] bump GCC to 6.4.0 for foss/2017b --- easybuild/easyconfigs/f/foss/foss-2017b.eb | 2 +- easybuild/easyconfigs/g/gompi/gompi-2017b.eb | 4 ++-- ...2.28.eb => hwloc-1.11.7-GCC-6.4.0-2.28.eb} | 2 +- .../numactl/numactl-2.0.11-GCC-6.4.0-2.28.eb | 23 +++++++++++++++++++ ...LAS-0.2.19-GCC-6.4.0-2.28-LAPACK-3.7.0.eb} | 2 +- ....28.eb => OpenMPI-2.1.1-GCC-6.4.0-2.28.eb} | 2 +- ...ompi-2017b-OpenBLAS-0.2.19-LAPACK-3.7.0.eb | 2 +- 7 files changed, 30 insertions(+), 7 deletions(-) rename easybuild/easyconfigs/h/hwloc/{hwloc-1.11.7-GCC-6.3.0-2.28.eb => hwloc-1.11.7-GCC-6.4.0-2.28.eb} (95%) create mode 100644 easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCC-6.4.0-2.28.eb rename easybuild/easyconfigs/o/OpenBLAS/{OpenBLAS-0.2.19-GCC-6.3.0-2.28-LAPACK-3.7.0.eb => OpenBLAS-0.2.19-GCC-6.4.0-2.28-LAPACK-3.7.0.eb} (96%) rename easybuild/easyconfigs/o/OpenMPI/{OpenMPI-2.1.1-GCC-6.3.0-2.28.eb => OpenMPI-2.1.1-GCC-6.4.0-2.28.eb} (95%) diff --git a/easybuild/easyconfigs/f/foss/foss-2017b.eb b/easybuild/easyconfigs/f/foss/foss-2017b.eb index 20778cf402..5ce20b722f 100644 --- a/easybuild/easyconfigs/f/foss/foss-2017b.eb +++ b/easybuild/easyconfigs/f/foss/foss-2017b.eb @@ -9,7 +9,7 @@ description = """GNU Compiler Collection (GCC) based compiler toolchain, includi toolchain = {'name': 'dummy', 'version': 'dummy'} -gccver = '6.3.0-2.28' +gccver = '6.4.0-2.28' blaslib = 'OpenBLAS' blasver = '0.2.19' diff --git a/easybuild/easyconfigs/g/gompi/gompi-2017b.eb b/easybuild/easyconfigs/g/gompi/gompi-2017b.eb index ff56275f5c..acba6f51d9 100644 --- a/easybuild/easyconfigs/g/gompi/gompi-2017b.eb +++ b/easybuild/easyconfigs/g/gompi/gompi-2017b.eb @@ -9,11 +9,11 @@ description = """GNU Compiler Collection (GCC) based compiler toolchain, toolchain = {'name': 'dummy', 'version': 'dummy'} -gccver = '6.3.0-2.28' +gccver = '6.4.0-2.28' # compiler toolchain dependencies dependencies = [ - ('GCC', gccver), # includes both GCC 6.3.0 and binutils 2.27 + ('GCC', gccver), # includes both GCC and binutils ('OpenMPI', '2.1.1', '', ('GCC', gccver)), ] diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.7-GCC-6.3.0-2.28.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.7-GCC-6.4.0-2.28.eb similarity index 95% rename from easybuild/easyconfigs/h/hwloc/hwloc-1.11.7-GCC-6.3.0-2.28.eb rename to easybuild/easyconfigs/h/hwloc/hwloc-1.11.7-GCC-6.4.0-2.28.eb index 72dfa36917..b5be4b59bc 100644 --- a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.7-GCC-6.3.0-2.28.eb +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.7-GCC-6.4.0-2.28.eb @@ -11,7 +11,7 @@ system attributes such as cache and memory information as well as the locality o network interfaces, InfiniBand HCAs or GPUs. It primarily aims at helping applications with gathering information about modern computing hardware so as to exploit it accordingly and efficiently.""" -toolchain = {'name': 'GCC', 'version': '6.3.0-2.28'} +toolchain = {'name': 'GCC', 'version': '6.4.0-2.28'} source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCC-6.4.0-2.28.eb new file mode 100644 index 0000000000..521df8ded9 --- /dev/null +++ b/easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCC-6.4.0-2.28.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'numactl' +version = '2.0.11' + +homepage = 'http://oss.sgi.com/projects/libnuma/' +description = """The numactl program allows you to run your application program on specific cpu's and memory nodes. +It does this by supplying a NUMA memory policy to the operating system before running your program. +The libnuma library provides convenient ways for you to add NUMA memory policies into your own program.""" + +toolchain = {'name': 'GCC', 'version': '6.4.0-2.28'} + +source_urls = ['ftp://oss.sgi.com/www/projects/libnuma/download/'] +sources = [SOURCE_TAR_GZ] + +checksums = ['d3bc88b7ddb9f06d60898f4816ae9127'] + +sanity_check_paths = { + 'files': ['bin/numactl', 'bin/numastat', 'lib/libnuma.%s' % SHLIB_EXT, 'lib/libnuma.a'], + 'dirs': ['share/man', 'include'] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-GCC-6.3.0-2.28-LAPACK-3.7.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-GCC-6.4.0-2.28-LAPACK-3.7.0.eb similarity index 96% rename from easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-GCC-6.3.0-2.28-LAPACK-3.7.0.eb rename to easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-GCC-6.4.0-2.28-LAPACK-3.7.0.eb index a1d7e75e79..21faaaf7ab 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-GCC-6.3.0-2.28-LAPACK-3.7.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-GCC-6.4.0-2.28-LAPACK-3.7.0.eb @@ -9,7 +9,7 @@ versionsuffix = '-LAPACK-%s' % lapackver homepage = 'http://xianyi.github.com/OpenBLAS/' description = """OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version.""" -toolchain = {'name': 'GCC', 'version': '6.3.0-2.28'} +toolchain = {'name': 'GCC', 'version': '6.4.0-2.28'} lapack_src = 'lapack-%s.tgz' % lapackver large_src = 'large.tgz' diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.1-GCC-6.3.0-2.28.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.1-GCC-6.4.0-2.28.eb similarity index 95% rename from easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.1-GCC-6.3.0-2.28.eb rename to easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.1-GCC-6.4.0-2.28.eb index aba86a17c1..c55bade938 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.1-GCC-6.3.0-2.28.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.1-GCC-6.4.0-2.28.eb @@ -6,7 +6,7 @@ version = '2.1.1' homepage = 'http://www.open-mpi.org/' description = """The Open MPI Project is an open source MPI-2 implementation.""" -toolchain = {'name': 'GCC', 'version': '6.3.0-2.28'} +toolchain = {'name': 'GCC', 'version': '6.4.0-2.28'} source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-2017b-OpenBLAS-0.2.19-LAPACK-3.7.0.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-2017b-OpenBLAS-0.2.19-LAPACK-3.7.0.eb index a036bb79cb..84d34e0f8a 100644 --- a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-2017b-OpenBLAS-0.2.19-LAPACK-3.7.0.eb +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-2017b-OpenBLAS-0.2.19-LAPACK-3.7.0.eb @@ -17,7 +17,7 @@ blassuff = '-LAPACK-3.7.0' versionsuffix = "-%s-%s%s" % (blaslib, blasver, blassuff) -dependencies = [(blaslib, blasver, blassuff, ('GCC', '6.3.0-2.28'))] +dependencies = [(blaslib, blasver, blassuff, ('GCC', '6.4.0-2.28'))] # parallel build tends to fail, so disabling it parallel = 1 -- GitLab From fd94badd5568b746667408e86c3a8827b46beb07 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 28 Jun 2017 13:53:42 +0200 Subject: [PATCH 1032/1603] {math}[intel/2017a] molmod 1.1 w/ Python 2.7.13 --- .../molmod-1.1-intel-2017a-Python-2.7.13.eb | 32 +++++++++++++++++++ .../molmod-1.1_ignore-errors-np-det.patch | 16 ++++++++++ 2 files changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/m/molmod/molmod-1.1-intel-2017a-Python-2.7.13.eb create mode 100644 easybuild/easyconfigs/m/molmod/molmod-1.1_ignore-errors-np-det.patch diff --git a/easybuild/easyconfigs/m/molmod/molmod-1.1-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/m/molmod/molmod-1.1-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..1ac9bf5546 --- /dev/null +++ b/easybuild/easyconfigs/m/molmod/molmod-1.1-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonPackage' + +name = 'molmod' +version = '1.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://molmod.github.io/molmod/' +description = "MolMod is a Python library with many compoments that are useful to write molecular modeling programs." + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['https://github.com/molmod/molmod/releases/download/v%(version)s'] +sources = [SOURCE_TAR_GZ] +patches = ['molmod-%(version)s_ignore-errors-np-det.patch'] + +dependencies = [ + ('Python', '2.7.13'), + ('matplotlib', '2.0.2', versionsuffix), +] + +runtest = "export MATPLOTLIBRC=$PWD; echo 'backend: agg' > $MATPLOTLIBRC/matplotlibrc;" +runtest += "python setup.py build_ext -i; nosetests -v" + +# fix permissions issue on files in share/molmod subdir +postinstallcmds = ['chmod -R o+r %(installdir)s/share/molmod'] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/molmod'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/molmod/molmod-1.1_ignore-errors-np-det.patch b/easybuild/easyconfigs/m/molmod/molmod-1.1_ignore-errors-np-det.patch new file mode 100644 index 0000000000..6dfb4ce31c --- /dev/null +++ b/easybuild/easyconfigs/m/molmod/molmod-1.1_ignore-errors-np-det.patch @@ -0,0 +1,16 @@ +fix for incompatibility between recent Intel MKL versions and numpy +see https://github.com/numpy/numpy/issues/8529 +--- molmod/transformations.py.orig 2017-06-28 11:04:49.405580197 +0200 ++++ molmod/transformations.py 2017-06-28 11:04:12.324857787 +0200 +@@ -469,8 +469,9 @@ + W[0] = 1 + W[1] = 1 + W[2] = 1 +- if numpy.linalg.det(A) < 0: +- W[2] = -1 ++ with numpy.errstate(invalid='ignore'): ++ if numpy.linalg.det(A) < 0: ++ W[2] = -1 + r = numpy.dot(Vt.transpose()*W, U.transpose()) + return Complete(r, numpy.dot(r, -mb) + ma) + -- GitLab From c96a1a8fc6bd7967383d663655698dba1f1a18e8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 28 Jun 2017 16:52:46 +0200 Subject: [PATCH 1033/1603] adding easyconfigs: yaff-1.1.2-intel-2017a-Python-2.7.13.eb --- .../yaff-1.1.2-intel-2017a-Python-2.7.13.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/y/yaff/yaff-1.1.2-intel-2017a-Python-2.7.13.eb diff --git a/easybuild/easyconfigs/y/yaff/yaff-1.1.2-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/y/yaff/yaff-1.1.2-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..70745662fc --- /dev/null +++ b/easybuild/easyconfigs/y/yaff/yaff-1.1.2-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'yaff' +version = '1.1.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://molmod.github.io/yaff/' +description = """Yaff stands for 'Yet another force field'. It is a pythonic force-field code.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['https://github.com/molmod/yaff/releases/download/%(version)s'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.13'), + ('h5py', '2.7.0', versionsuffix), + ('molmod', '1.1', '-Python-%(pyver)s'), +] + +options = {'modulename': name} +runtest = "export MATPLOTLIBRC=$PWD; echo 'backend: agg' > $MATPLOTLIBRC/matplotlibrc; " +runtest += "python setup.py build_ext -i; nosetests --verbosity=10" + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s'], +} + +moduleclass = 'chem' -- GitLab From 46ef26e8beed7864b850b7a25969f4d32e4c2fad Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 28 Jun 2017 17:04:50 +0200 Subject: [PATCH 1034/1603] GCC 6.4.0 + binutils 2.28 (base for */2017b toolchains) [WIP] --- .../b/Bison/Bison-3.0.4-GCCcore-6.4.0.eb | 28 ++++++++++ .../b/binutils/binutils-2.28-GCCcore-6.4.0.eb | 21 +++++++ .../f/flex/flex-2.6.4-GCCcore-6.4.0.eb | 24 ++++++++ easybuild/easyconfigs/g/GCC/GCC-6.4.0-2.28.eb | 25 +++++++++ .../easyconfigs/g/GCCcore/GCCcore-6.4.0.eb | 56 +++++++++++++++++++ .../help2man/help2man-1.47.4-GCCcore-6.4.0.eb | 25 +++++++++ .../m/M4/M4-1.4.18-GCCcore-6.4.0.eb | 29 ++++++++++ .../z/zlib/zlib-1.2.11-GCCcore-6.4.0.eb | 26 +++++++++ 8 files changed, 234 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-6.4.0.eb create mode 100644 easybuild/easyconfigs/b/binutils/binutils-2.28-GCCcore-6.4.0.eb create mode 100644 easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-6.4.0.eb create mode 100644 easybuild/easyconfigs/g/GCC/GCC-6.4.0-2.28.eb create mode 100644 easybuild/easyconfigs/g/GCCcore/GCCcore-6.4.0.eb create mode 100644 easybuild/easyconfigs/h/help2man/help2man-1.47.4-GCCcore-6.4.0.eb create mode 100644 easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-6.4.0.eb create mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-6.4.0.eb diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-6.4.0.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-6.4.0.eb new file mode 100644 index 0000000000..2623578bc5 --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-6.4.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'Bison' +version = '3.0.4' + +homepage = 'http://www.gnu.org/software/bison' +description = """Bison is a general-purpose parser generator that converts an annotated context-free grammar + into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] +checksums = ['b67fd2daae7a64b5ba862c66c07c1addb9e6b1b05c5f2049392cfd8a2172952e'] + +builddependencies = [ + ('M4', '1.4.18'), + # use same binutils version that was used when building GCCcore toolchain + ('binutils', '2.28', '', True), +] + + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['bison', 'yacc']] + ['lib/liby.a'], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.28-GCCcore-6.4.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.28-GCCcore-6.4.0.eb new file mode 100644 index 0000000000..b22b7d16ba --- /dev/null +++ b/easybuild/easyconfigs/b/binutils/binutils-2.28-GCCcore-6.4.0.eb @@ -0,0 +1,21 @@ +name = 'binutils' +version = '2.28' + +homepage = 'http://directory.fsf.org/project/binutils/' +description = "binutils: GNU binary utilities" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} + +sources = [SOURCE_TAR_GZ] +source_urls = [GNU_SOURCE] + +builddependencies = [ + ('flex', '2.6.4'), + ('Bison', '3.0.4'), + # zlib required, but being linked in statically, so not a runtime dep + ('zlib', '1.2.11'), + # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils + ('binutils', version, '', True) +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-6.4.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-6.4.0.eb new file mode 100644 index 0000000000..55845823d8 --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-6.4.0.eb @@ -0,0 +1,24 @@ +name = 'flex' +version = '2.6.4' + +homepage = 'http://flex.sourceforge.net/' +description = """Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, + sometimes called a tokenizer, is a program which recognizes lexical patterns in text.""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['https://github.com/westes/flex/releases/download/v%(version)s/'] + +checksums = ['e87aae032bf07c26f85ac0ed3250998c37621d95f8bd748b31f15b33c45ee995'] + +dependencies = [('M4', '1.4.18')] +builddependencies = [ + ('Bison', '3.0.4'), + ('help2man', '1.47.4'), + # use same binutils version that was used when building GCC toolchain + ('binutils', '2.28', '', True), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/g/GCC/GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/g/GCC/GCC-6.4.0-2.28.eb new file mode 100644 index 0000000000..6d830c0286 --- /dev/null +++ b/easybuild/easyconfigs/g/GCC/GCC-6.4.0-2.28.eb @@ -0,0 +1,25 @@ +easyblock = 'Bundle' + +name = 'GCC' +version = '6.4.0' + +binutilsver = '2.28' +versionsuffix = '-%s' % binutilsver + +homepage = 'http://gcc.gnu.org/' +description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, + as well as libraries for these languages (libstdc++, libgcj,...).""" + +toolchain = {'name': 'dummy', 'version': ''} + +dependencies = [ + ('GCCcore', version), + # binutils built on top of GCCcore, which was built on top of (dummy-built) binutils + ('binutils', binutilsver, '', ('GCCcore', version)), +] + +altroot = 'GCCcore' +altversion = 'GCCcore' + +# this bundle serves as a compiler-only toolchain, so it should be marked as compiler (important for HMNS) +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-6.4.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-6.4.0.eb new file mode 100644 index 0000000000..9dbb7d3700 --- /dev/null +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-6.4.0.eb @@ -0,0 +1,56 @@ +easyblock = 'EB_GCC' + +name = 'GCCcore' +version = '6.4.0' + +homepage = 'http://gcc.gnu.org/' +description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, + as well as libraries for these languages (libstdc++, libgcj,...).""" + +toolchain = {'name': 'dummy', 'version': ''} + +mpfr_version = '3.1.5' + +source_urls = [ + 'http://ftpmirror.gnu.org/gnu/gcc/gcc-%(version)s', # GCC auto-resolving HTTP mirror + 'http://ftpmirror.gnu.org/gnu/gmp', # idem for GMP + 'http://ftpmirror.gnu.org/gnu/mpfr', # idem for MPFR + 'http://www.multiprecision.org/mpc/download', # MPC official + 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies + 'http://gcc.cybermirror.org/infrastructure/', # HTTP mirror for GCC dependencies + 'http://isl.gforge.inria.fr/', # original HTTP source for ISL +] + +sources = [ + 'gcc-%(version)s-RC-20170628.tar.gz', # FIXME 'gcc-%(version)s.tar.bz2', + 'gmp-6.1.2.tar.bz2', + 'mpfr-%s.tar.bz2' % mpfr_version, + 'mpc-1.0.3.tar.gz', + 'isl-0.16.1.tar.bz2', +] + +builddependencies = [ + ('M4', '1.4.18'), + ('binutils', '2.28'), +] + +patches = [ + ('mpfr-%s-allpatches-20170606.patch' % mpfr_version, '../mpfr-%s' % mpfr_version), + 'GCCcore-6.2.0-fix-find-isl.patch', +] + +checksums = [ + '005e58fb723efb3bf51dac5db8a5edf7c66ea2e7ddb6de6ed02dbb74fcc31f80', # gcc-6.4.0.tar.bz2 + '5275bb04f4863a13516b2f39392ac5e272f5e1bb8057b18aec1c9b79d73d8fb2', # gmp-6.1.2.tar.bz2 + 'ca498c1c7a74dd37a576f353312d1e68d490978de4395fa28f1cbd46a364e658', # mpfr-3.1.5.tar.gz + '617decc6ea09889fb08ede330917a00b16809b8db88c29c31bfbb49cbf88ecc3', # mpc-1.0.3.tar.gz + '412538bb65c799ac98e17e8cfcdacbb257a57362acfaaff254b0fcae970126d2', # isl-0.16.1.tar.bz2 + '137108952139486755e8c1bee30314ffa9233cc05cddfd848aa85503a6fea9d7', # mpfr-3.1.5-allpatches-20170606.patch + '5ad909606d17d851c6ad629b4fddb6c1621844218b8d139fed18c502a7696c68', # GCCcore-6.2.0-fix-find-isl.patch +] + +languages = ['c', 'c++', 'fortran'] + +withisl = True + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/h/help2man/help2man-1.47.4-GCCcore-6.4.0.eb b/easybuild/easyconfigs/h/help2man/help2man-1.47.4-GCCcore-6.4.0.eb new file mode 100644 index 0000000000..192cdb14fe --- /dev/null +++ b/easybuild/easyconfigs/h/help2man/help2man-1.47.4-GCCcore-6.4.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'help2man' +version = '1.47.4' + +homepage = 'https://www.gnu.org/software/help2man/' +description = """help2man produces simple manual pages from the '--help' and '--version' output of other commands.""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_XZ] +checksums = ['d4ecf697d13f14dd1a78c5995f06459bff706fd1ce593d1c02d81667c0207753'] + +builddependencies = [ + # use same binutils version that was used when building GCC toolchain + ('binutils', '2.28', '', True), +] + +sanity_check_paths = { + 'files': ['bin/help2man'], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-6.4.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-6.4.0.eb new file mode 100644 index 0000000000..2a832cbb83 --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-6.4.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'M4' +version = '1.4.18' + +homepage = 'http://www.gnu.org/software/m4/m4.html' +description = """GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible + although it has some extensions (for example, handling more than 9 positional parameters to macros). + GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc.""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] +checksums = ['ab2633921a5cd38e48797bf5521ad259bdc4b979078034a3b790d7fec5493fab'] + +# use same binutils version that was used when building GCC toolchain +builddependencies = [('binutils', '2.28', '', True)] + +# '-fgnu89-inline' is required to avoid linking errors with older glibc's, +# see https://github.com/hpcugent/easybuild-easyconfigs/issues/529 +configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" + +sanity_check_paths = { + 'files': ["bin/m4"], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-6.4.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-6.4.0.eb new file mode 100644 index 0000000000..a520a02364 --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-6.4.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'zlib' +version = '1.2.11' + +homepage = 'http://www.zlib.net/' +description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is, + not covered by any patents -- lossless data-compression library for use on virtually any + computer hardware and operating system.""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} +toolchainopts = {'pic': True} + +source_urls = ['http://zlib.net/fossils'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['c3e5e9fdd5004dcb542feda5ee4f0ff0744628baf8ed2dd5d66f8ca1197cb1a1'] + +# use same binutils version that was used when building GCC toolchain +builddependencies = [('binutils', '2.28', '', True)] + +sanity_check_paths = { + 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' -- GitLab From 72064f85e6399f8c905b70301fd8f0cf0bf5b050 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 28 Jun 2017 17:11:17 +0200 Subject: [PATCH 1035/1603] bump to GCC 6.4.0 as base for intel/2017b --- ...4.196-GCC-6.3.0-2.28.eb => icc-2017.4.196-GCC-6.4.0-2.28.eb} | 2 +- ...-GCC-6.3.0-2.28.eb => iccifort-2017.4.196-GCC-6.4.0-2.28.eb} | 2 +- ...196-GCC-6.3.0-2.28.eb => ifort-2017.4.196-GCC-6.4.0-2.28.eb} | 2 +- easybuild/easyconfigs/i/iimpi/iimpi-2017b.eb | 2 +- ...eb => impi-2017.3.196-iccifort-2017.4.196-GCC-6.4.0-2.28.eb} | 2 +- easybuild/easyconfigs/i/intel/intel-2017b.eb | 2 +- 6 files changed, 6 insertions(+), 6 deletions(-) rename easybuild/easyconfigs/i/icc/{icc-2017.4.196-GCC-6.3.0-2.28.eb => icc-2017.4.196-GCC-6.4.0-2.28.eb} (98%) rename easybuild/easyconfigs/i/iccifort/{iccifort-2017.4.196-GCC-6.3.0-2.28.eb => iccifort-2017.4.196-GCC-6.4.0-2.28.eb} (93%) rename easybuild/easyconfigs/i/ifort/{ifort-2017.4.196-GCC-6.3.0-2.28.eb => ifort-2017.4.196-GCC-6.4.0-2.28.eb} (98%) rename easybuild/easyconfigs/i/impi/{impi-2017.3.196-iccifort-2017.4.196-GCC-6.3.0-2.28.eb => impi-2017.3.196-iccifort-2017.4.196-GCC-6.4.0-2.28.eb} (95%) diff --git a/easybuild/easyconfigs/i/icc/icc-2017.4.196-GCC-6.3.0-2.28.eb b/easybuild/easyconfigs/i/icc/icc-2017.4.196-GCC-6.4.0-2.28.eb similarity index 98% rename from easybuild/easyconfigs/i/icc/icc-2017.4.196-GCC-6.3.0-2.28.eb rename to easybuild/easyconfigs/i/icc/icc-2017.4.196-GCC-6.4.0-2.28.eb index c3b0319dcb..05acc34697 100644 --- a/easybuild/easyconfigs/i/icc/icc-2017.4.196-GCC-6.3.0-2.28.eb +++ b/easybuild/easyconfigs/i/icc/icc-2017.4.196-GCC-6.4.0-2.28.eb @@ -12,7 +12,7 @@ sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_compose checksums = ['6b9b57dada0ec68e394866ec0a8b162c9233de18a7a6dd2dcc956d335e06acbc'] -gccver = '6.3.0' +gccver = '6.4.0' binutilsver = '2.28' versionsuffix = '-GCC-%s-%s' % (gccver, binutilsver) diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2017.4.196-GCC-6.3.0-2.28.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2017.4.196-GCC-6.4.0-2.28.eb similarity index 93% rename from easybuild/easyconfigs/i/iccifort/iccifort-2017.4.196-GCC-6.3.0-2.28.eb rename to easybuild/easyconfigs/i/iccifort/iccifort-2017.4.196-GCC-6.4.0-2.28.eb index 1fbc0afc0a..a3c7d6585e 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2017.4.196-GCC-6.3.0-2.28.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2017.4.196-GCC-6.4.0-2.28.eb @@ -3,7 +3,7 @@ easyblock = 'Toolchain' name = 'iccifort' version = '2017.4.196' -versionsuffix = '-GCC-6.3.0-2.28' +versionsuffix = '-GCC-6.4.0-2.28' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = """Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and diff --git a/easybuild/easyconfigs/i/ifort/ifort-2017.4.196-GCC-6.3.0-2.28.eb b/easybuild/easyconfigs/i/ifort/ifort-2017.4.196-GCC-6.4.0-2.28.eb similarity index 98% rename from easybuild/easyconfigs/i/ifort/ifort-2017.4.196-GCC-6.3.0-2.28.eb rename to easybuild/easyconfigs/i/ifort/ifort-2017.4.196-GCC-6.4.0-2.28.eb index 8f6eacf9f8..b3b151820c 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2017.4.196-GCC-6.3.0-2.28.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2017.4.196-GCC-6.4.0-2.28.eb @@ -15,7 +15,7 @@ checksums = ['0b6a222e015f776600b12b17c19506249c9e7691a8d287f44cd40a66ca9ac749'] # remove dependency on intel-mpi-rt-mic patches = ['ifort_2017_no_mpi_mic_dependency.patch'] -gccver = '6.3.0' +gccver = '6.4.0' binutilsver = '2.28' versionsuffix = '-GCC-%s-%s' % (gccver, binutilsver) diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-2017b.eb b/easybuild/easyconfigs/i/iimpi/iimpi-2017b.eb index 8d59809f4c..53c7c29886 100644 --- a/easybuild/easyconfigs/i/iimpi/iimpi-2017b.eb +++ b/easybuild/easyconfigs/i/iimpi/iimpi-2017b.eb @@ -10,7 +10,7 @@ description = """Intel C/C++ and Fortran compilers, alongside Intel MPI.""" toolchain = {'name': 'dummy', 'version': 'dummy'} compver = '2017.4.196' -suff = '-GCC-6.3.0-2.28' +suff = '-GCC-6.4.0-2.28' dependencies = [ ('icc', compver, suff), ('ifort', compver, suff), diff --git a/easybuild/easyconfigs/i/impi/impi-2017.3.196-iccifort-2017.4.196-GCC-6.3.0-2.28.eb b/easybuild/easyconfigs/i/impi/impi-2017.3.196-iccifort-2017.4.196-GCC-6.4.0-2.28.eb similarity index 95% rename from easybuild/easyconfigs/i/impi/impi-2017.3.196-iccifort-2017.4.196-GCC-6.3.0-2.28.eb rename to easybuild/easyconfigs/i/impi/impi-2017.3.196-iccifort-2017.4.196-GCC-6.4.0-2.28.eb index 473cd8b786..2e46f8a579 100644 --- a/easybuild/easyconfigs/i/impi/impi-2017.3.196-iccifort-2017.4.196-GCC-6.3.0-2.28.eb +++ b/easybuild/easyconfigs/i/impi/impi-2017.3.196-iccifort-2017.4.196-GCC-6.4.0-2.28.eb @@ -8,7 +8,7 @@ description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric messag passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for Linux OS implements the Message Passing Interface, version 2 (MPI-2) specification.""" -toolchain = {'name': 'iccifort', 'version': '2017.4.196-GCC-6.3.0-2.28'} +toolchain = {'name': 'iccifort', 'version': '2017.4.196-GCC-6.4.0-2.28'} sources = ['l_mpi_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/intel/intel-2017b.eb b/easybuild/easyconfigs/i/intel/intel-2017b.eb index aecf829181..79c32a59cd 100644 --- a/easybuild/easyconfigs/i/intel/intel-2017b.eb +++ b/easybuild/easyconfigs/i/intel/intel-2017b.eb @@ -10,7 +10,7 @@ description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and toolchain = {'name': 'dummy', 'version': 'dummy'} compver = '2017.4.196' -gccver = '6.3.0' +gccver = '6.4.0' binutilsver = '2.28' gccsuff = '-GCC-%s-%s' % (gccver, binutilsver) dependencies = [ -- GitLab From d57f214ac0ae76167f605a38b6729f9e585ad8bc Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 28 Jun 2017 17:11:53 +0200 Subject: [PATCH 1036/1603] don't be too verbose in yaff 1.1.2 tests --- .../easyconfigs/y/yaff/yaff-1.1.2-intel-2017a-Python-2.7.13.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/y/yaff/yaff-1.1.2-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/y/yaff/yaff-1.1.2-intel-2017a-Python-2.7.13.eb index 70745662fc..a76854e99b 100644 --- a/easybuild/easyconfigs/y/yaff/yaff-1.1.2-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/y/yaff/yaff-1.1.2-intel-2017a-Python-2.7.13.eb @@ -20,7 +20,7 @@ dependencies = [ options = {'modulename': name} runtest = "export MATPLOTLIBRC=$PWD; echo 'backend: agg' > $MATPLOTLIBRC/matplotlibrc; " -runtest += "python setup.py build_ext -i; nosetests --verbosity=10" +runtest += "python setup.py build_ext -i; nosetests -v" sanity_check_paths = { 'files': [], -- GitLab From 8c470ec536ff0550061cda52e48e119b6be97d6f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 28 Jun 2017 17:18:31 +0200 Subject: [PATCH 1037/1603] add missing MPFR patch used in GCCcore 6.4.0 easyconfig --- .../mpfr-3.1.5-allpatches-20170606.patch | 689 ++++++++++++++++++ 1 file changed, 689 insertions(+) create mode 100644 easybuild/easyconfigs/g/GCCcore/mpfr-3.1.5-allpatches-20170606.patch diff --git a/easybuild/easyconfigs/g/GCCcore/mpfr-3.1.5-allpatches-20170606.patch b/easybuild/easyconfigs/g/GCCcore/mpfr-3.1.5-allpatches-20170606.patch new file mode 100644 index 0000000000..f25a39e542 --- /dev/null +++ b/easybuild/easyconfigs/g/GCCcore/mpfr-3.1.5-allpatches-20170606.patch @@ -0,0 +1,689 @@ +# MPFR v3.1.5 patch dated 2017-06-06 +# downloaded via https://gforge.inria.fr/frs/?group_id=136 +diff -Naurd mpfr-3.1.5-a/PATCHES mpfr-3.1.5-b/PATCHES +--- mpfr-3.1.5-a/PATCHES 2016-12-15 08:35:46.476430238 +0000 ++++ mpfr-3.1.5-b/PATCHES 2016-12-15 08:35:46.544430346 +0000 +@@ -0,0 +1 @@ ++vasprintf +diff -Naurd mpfr-3.1.5-a/VERSION mpfr-3.1.5-b/VERSION +--- mpfr-3.1.5-a/VERSION 2016-09-27 07:58:14.000000000 +0000 ++++ mpfr-3.1.5-b/VERSION 2016-12-15 08:35:46.544430346 +0000 +@@ -1 +1 @@ +-3.1.5 ++3.1.5-p1 +diff -Naurd mpfr-3.1.5-a/src/mpfr.h mpfr-3.1.5-b/src/mpfr.h +--- mpfr-3.1.5-a/src/mpfr.h 2016-09-27 07:58:15.000000000 +0000 ++++ mpfr-3.1.5-b/src/mpfr.h 2016-12-15 08:35:46.540430340 +0000 +@@ -27,7 +27,7 @@ + #define MPFR_VERSION_MAJOR 3 + #define MPFR_VERSION_MINOR 1 + #define MPFR_VERSION_PATCHLEVEL 5 +-#define MPFR_VERSION_STRING "3.1.5" ++#define MPFR_VERSION_STRING "3.1.5-p1" + + /* Macros dealing with MPFR VERSION */ + #define MPFR_VERSION_NUM(a,b,c) (((a) << 16L) | ((b) << 8) | (c)) +diff -Naurd mpfr-3.1.5-a/src/vasprintf.c mpfr-3.1.5-b/src/vasprintf.c +--- mpfr-3.1.5-a/src/vasprintf.c 2016-09-27 07:58:15.000000000 +0000 ++++ mpfr-3.1.5-b/src/vasprintf.c 2016-12-15 08:35:46.520430308 +0000 +@@ -1593,7 +1593,7 @@ + } + else if (spec.spec == 'f' || spec.spec == 'F') + { +- if (spec.prec == -1) ++ if (spec.prec < 0) + spec.prec = 6; + if (regular_fg (np, p, spec, NULL) == -1) + goto error; +diff -Naurd mpfr-3.1.5-a/src/version.c mpfr-3.1.5-b/src/version.c +--- mpfr-3.1.5-a/src/version.c 2016-09-27 07:58:15.000000000 +0000 ++++ mpfr-3.1.5-b/src/version.c 2016-12-15 08:35:46.544430346 +0000 +@@ -25,5 +25,5 @@ + const char * + mpfr_get_version (void) + { +- return "3.1.5"; ++ return "3.1.5-p1"; + } +diff -Naurd mpfr-3.1.5-a/tests/tsprintf.c mpfr-3.1.5-b/tests/tsprintf.c +--- mpfr-3.1.5-a/tests/tsprintf.c 2016-09-27 07:58:14.000000000 +0000 ++++ mpfr-3.1.5-b/tests/tsprintf.c 2016-12-15 08:35:46.520430308 +0000 +@@ -1251,6 +1251,25 @@ + check_emin_aux (MPFR_EMIN_MIN); + } + ++static void ++test20161214 (void) ++{ ++ mpfr_t x; ++ char buf[32]; ++ const char s[] = "0x0.fffffffffffff8p+1024"; ++ int r; ++ ++ mpfr_init2 (x, 64); ++ mpfr_set_str (x, s, 16, MPFR_RNDN); ++ r = mpfr_snprintf (buf, 32, "%.*RDf", -2, x); ++ MPFR_ASSERTN(r == 316); ++ r = mpfr_snprintf (buf, 32, "%.*RDf", INT_MIN + 1, x); ++ MPFR_ASSERTN(r == 316); ++ r = mpfr_snprintf (buf, 32, "%.*RDf", INT_MIN, x); ++ MPFR_ASSERTN(r == 316); ++ mpfr_clear (x); ++} ++ + int + main (int argc, char **argv) + { +@@ -1271,6 +1290,7 @@ + mixed (); + check_emax (); + check_emin (); ++ test20161214 (); + + #if defined(HAVE_LOCALE_H) && defined(HAVE_SETLOCALE) + #if MPFR_LCONV_DPTS +diff -Naurd mpfr-3.1.5-a/PATCHES mpfr-3.1.5-b/PATCHES +--- mpfr-3.1.5-a/PATCHES 2016-12-19 22:11:17.022676737 +0000 ++++ mpfr-3.1.5-b/PATCHES 2016-12-19 22:11:17.094676820 +0000 +@@ -0,0 +1 @@ ++strtofr +diff -Naurd mpfr-3.1.5-a/VERSION mpfr-3.1.5-b/VERSION +--- mpfr-3.1.5-a/VERSION 2016-12-15 08:35:46.544430346 +0000 ++++ mpfr-3.1.5-b/VERSION 2016-12-19 22:11:17.094676820 +0000 +@@ -1 +1 @@ +-3.1.5-p1 ++3.1.5-p2 +diff -Naurd mpfr-3.1.5-a/src/mpfr.h mpfr-3.1.5-b/src/mpfr.h +--- mpfr-3.1.5-a/src/mpfr.h 2016-12-15 08:35:46.540430340 +0000 ++++ mpfr-3.1.5-b/src/mpfr.h 2016-12-19 22:11:17.090676815 +0000 +@@ -27,7 +27,7 @@ + #define MPFR_VERSION_MAJOR 3 + #define MPFR_VERSION_MINOR 1 + #define MPFR_VERSION_PATCHLEVEL 5 +-#define MPFR_VERSION_STRING "3.1.5-p1" ++#define MPFR_VERSION_STRING "3.1.5-p2" + + /* Macros dealing with MPFR VERSION */ + #define MPFR_VERSION_NUM(a,b,c) (((a) << 16L) | ((b) << 8) | (c)) +diff -Naurd mpfr-3.1.5-a/src/strtofr.c mpfr-3.1.5-b/src/strtofr.c +--- mpfr-3.1.5-a/src/strtofr.c 2016-09-27 07:58:15.000000000 +0000 ++++ mpfr-3.1.5-b/src/strtofr.c 2016-12-19 22:11:17.066676788 +0000 +@@ -743,11 +743,14 @@ + of the pstr_size most significant digits of pstr->mant, with + equality in case exact is non-zero. */ + +- /* test if rounding is possible, and if so exit the loop */ +- if (exact || mpfr_can_round_raw (result, ysize, +- (pstr->negative) ? -1 : 1, +- ysize_bits - err - 1, +- MPFR_RNDN, rnd, MPFR_PREC(x))) ++ /* test if rounding is possible, and if so exit the loop. ++ Note: we also need to be able to determine the correct ternary value, ++ thus we use the MPFR_PREC(x) + (rnd == MPFR_RNDN) trick. ++ For example if result = xxx...xxx111...111 and rnd = RNDN, ++ then we know the correct rounding is xxx...xx(x+1), but we cannot know ++ the correct ternary value. */ ++ if (exact || mpfr_round_p (result, ysize, ysize_bits - err - 1, ++ MPFR_PREC(x) + (rnd == MPFR_RNDN))) + break; + + next_loop: +diff -Naurd mpfr-3.1.5-a/src/version.c mpfr-3.1.5-b/src/version.c +--- mpfr-3.1.5-a/src/version.c 2016-12-15 08:35:46.544430346 +0000 ++++ mpfr-3.1.5-b/src/version.c 2016-12-19 22:11:17.094676820 +0000 +@@ -25,5 +25,5 @@ + const char * + mpfr_get_version (void) + { +- return "3.1.5-p1"; ++ return "3.1.5-p2"; + } +diff -Naurd mpfr-3.1.5-a/tests/tstrtofr.c mpfr-3.1.5-b/tests/tstrtofr.c +--- mpfr-3.1.5-a/tests/tstrtofr.c 2016-09-27 07:58:14.000000000 +0000 ++++ mpfr-3.1.5-b/tests/tstrtofr.c 2016-12-19 22:11:17.066676788 +0000 +@@ -1191,6 +1191,24 @@ + mpfr_clears (e, x1, x2, (mpfr_ptr) 0); + } + ++/* Note: the number is 5^47/2^9. */ ++static void ++bug20161217 (void) ++{ ++ mpfr_t fp, z; ++ static const char * num = "0.1387778780781445675529539585113525390625e31"; ++ int inex; ++ ++ mpfr_init2 (fp, 110); ++ mpfr_init2 (z, 110); ++ inex = mpfr_strtofr (fp, num, NULL, 10, MPFR_RNDN); ++ MPFR_ASSERTN(inex == 0); ++ mpfr_set_str_binary (z, "10001100001000010011110110011101101001010000001011011110010001010100010100100110111101000010001011001100001101E-9"); ++ MPFR_ASSERTN(mpfr_equal_p (fp, z)); ++ mpfr_clear (fp); ++ mpfr_clear (z); ++} ++ + int + main (int argc, char *argv[]) + { +@@ -1205,6 +1223,7 @@ + test20100310 (); + bug20120814 (); + bug20120829 (); ++ bug20161217 (); + + tests_end_mpfr (); + return 0; +diff -Naurd mpfr-3.1.5-a/PATCHES mpfr-3.1.5-b/PATCHES +--- mpfr-3.1.5-a/PATCHES 2017-06-06 19:21:17.580843571 +0000 ++++ mpfr-3.1.5-b/PATCHES 2017-06-06 19:21:17.604843293 +0000 +@@ -0,0 +1 @@ ++ret-macro +diff -Naurd mpfr-3.1.5-a/VERSION mpfr-3.1.5-b/VERSION +--- mpfr-3.1.5-a/VERSION 2016-12-19 22:11:17.094676820 +0000 ++++ mpfr-3.1.5-b/VERSION 2017-06-06 19:21:17.604843293 +0000 +@@ -1 +1 @@ +-3.1.5-p2 ++3.1.5-p3 +diff -Naurd mpfr-3.1.5-a/src/mpfr-impl.h mpfr-3.1.5-b/src/mpfr-impl.h +--- mpfr-3.1.5-a/src/mpfr-impl.h 2016-09-27 07:58:15.000000000 +0000 ++++ mpfr-3.1.5-b/src/mpfr-impl.h 2017-06-06 19:21:17.592843433 +0000 +@@ -873,7 +873,7 @@ + following two macros, unless the flag comes from another function + returning the ternary inexact value */ + #define MPFR_RET(I) return \ +- (I) ? ((__gmpfr_flags |= MPFR_FLAGS_INEXACT), (I)) : 0 ++ (I) != 0 ? ((__gmpfr_flags |= MPFR_FLAGS_INEXACT), (I)) : 0 + #define MPFR_RET_NAN return (__gmpfr_flags |= MPFR_FLAGS_NAN), 0 + + #define MPFR_SET_ERANGE() (__gmpfr_flags |= MPFR_FLAGS_ERANGE) +diff -Naurd mpfr-3.1.5-a/src/mpfr.h mpfr-3.1.5-b/src/mpfr.h +--- mpfr-3.1.5-a/src/mpfr.h 2016-12-19 22:11:17.090676815 +0000 ++++ mpfr-3.1.5-b/src/mpfr.h 2017-06-06 19:21:17.600843340 +0000 +@@ -27,7 +27,7 @@ + #define MPFR_VERSION_MAJOR 3 + #define MPFR_VERSION_MINOR 1 + #define MPFR_VERSION_PATCHLEVEL 5 +-#define MPFR_VERSION_STRING "3.1.5-p2" ++#define MPFR_VERSION_STRING "3.1.5-p3" + + /* Macros dealing with MPFR VERSION */ + #define MPFR_VERSION_NUM(a,b,c) (((a) << 16L) | ((b) << 8) | (c)) +diff -Naurd mpfr-3.1.5-a/src/version.c mpfr-3.1.5-b/src/version.c +--- mpfr-3.1.5-a/src/version.c 2016-12-19 22:11:17.094676820 +0000 ++++ mpfr-3.1.5-b/src/version.c 2017-06-06 19:21:17.604843293 +0000 +@@ -25,5 +25,5 @@ + const char * + mpfr_get_version (void) + { +- return "3.1.5-p2"; ++ return "3.1.5-p3"; + } +diff -Naurd mpfr-3.1.5-a/PATCHES mpfr-3.1.5-b/PATCHES +--- mpfr-3.1.5-a/PATCHES 2017-06-06 19:50:30.708438500 +0000 ++++ mpfr-3.1.5-b/PATCHES 2017-06-06 19:50:30.736438175 +0000 +@@ -0,0 +1 @@ ++tests-buffer-size +diff -Naurd mpfr-3.1.5-a/VERSION mpfr-3.1.5-b/VERSION +--- mpfr-3.1.5-a/VERSION 2017-06-06 19:21:17.604843293 +0000 ++++ mpfr-3.1.5-b/VERSION 2017-06-06 19:50:30.736438175 +0000 +@@ -1 +1 @@ +-3.1.5-p3 ++3.1.5-p4 +diff -Naurd mpfr-3.1.5-a/src/mpfr.h mpfr-3.1.5-b/src/mpfr.h +--- mpfr-3.1.5-a/src/mpfr.h 2017-06-06 19:21:17.600843340 +0000 ++++ mpfr-3.1.5-b/src/mpfr.h 2017-06-06 19:50:30.732438221 +0000 +@@ -27,7 +27,7 @@ + #define MPFR_VERSION_MAJOR 3 + #define MPFR_VERSION_MINOR 1 + #define MPFR_VERSION_PATCHLEVEL 5 +-#define MPFR_VERSION_STRING "3.1.5-p3" ++#define MPFR_VERSION_STRING "3.1.5-p4" + + /* Macros dealing with MPFR VERSION */ + #define MPFR_VERSION_NUM(a,b,c) (((a) << 16L) | ((b) << 8) | (c)) +diff -Naurd mpfr-3.1.5-a/src/version.c mpfr-3.1.5-b/src/version.c +--- mpfr-3.1.5-a/src/version.c 2017-06-06 19:21:17.604843293 +0000 ++++ mpfr-3.1.5-b/src/version.c 2017-06-06 19:50:30.736438175 +0000 +@@ -25,5 +25,5 @@ + const char * + mpfr_get_version (void) + { +- return "3.1.5-p3"; ++ return "3.1.5-p4"; + } +diff -Naurd mpfr-3.1.5-a/tests/tl2b.c mpfr-3.1.5-b/tests/tl2b.c +--- mpfr-3.1.5-a/tests/tl2b.c 2016-09-27 07:58:14.000000000 +0000 ++++ mpfr-3.1.5-b/tests/tl2b.c 2017-06-06 19:50:30.724438314 +0000 +@@ -83,7 +83,7 @@ + mpfr_srcptr t; + int beta, i; + int error = 0; +- char buffer[30]; ++ char buffer[256]; /* larger than needed, for maintainability */ + + for (beta = 2; beta <= BASE_MAX; beta++) + { +diff -Naurd mpfr-3.1.5-a/tests/tpow_all.c mpfr-3.1.5-b/tests/tpow_all.c +--- mpfr-3.1.5-a/tests/tpow_all.c 2016-09-27 07:58:14.000000000 +0000 ++++ mpfr-3.1.5-b/tests/tpow_all.c 2017-06-06 19:50:30.724438314 +0000 +@@ -498,7 +498,7 @@ + for (i = 0; i <= 12; i++) + { + unsigned int flags = 0; +- char sy[16]; ++ char sy[256]; /* larger than needed, for maintainability */ + + /* Test 2^(emin - i/4). + * --> Underflow iff i > 4. +diff -Naurd mpfr-3.1.5-a/PATCHES mpfr-3.1.5-b/PATCHES +--- mpfr-3.1.5-a/PATCHES 2017-06-06 19:57:01.947910247 +0000 ++++ mpfr-3.1.5-b/PATCHES 2017-06-06 19:57:01.971909970 +0000 +@@ -0,0 +1 @@ ++vasprintf-overflow-check +diff -Naurd mpfr-3.1.5-a/VERSION mpfr-3.1.5-b/VERSION +--- mpfr-3.1.5-a/VERSION 2017-06-06 19:50:30.736438175 +0000 ++++ mpfr-3.1.5-b/VERSION 2017-06-06 19:57:01.971909970 +0000 +@@ -1 +1 @@ +-3.1.5-p4 ++3.1.5-p5 +diff -Naurd mpfr-3.1.5-a/src/mpfr.h mpfr-3.1.5-b/src/mpfr.h +--- mpfr-3.1.5-a/src/mpfr.h 2017-06-06 19:50:30.732438221 +0000 ++++ mpfr-3.1.5-b/src/mpfr.h 2017-06-06 19:57:01.971909970 +0000 +@@ -27,7 +27,7 @@ + #define MPFR_VERSION_MAJOR 3 + #define MPFR_VERSION_MINOR 1 + #define MPFR_VERSION_PATCHLEVEL 5 +-#define MPFR_VERSION_STRING "3.1.5-p4" ++#define MPFR_VERSION_STRING "3.1.5-p5" + + /* Macros dealing with MPFR VERSION */ + #define MPFR_VERSION_NUM(a,b,c) (((a) << 16L) | ((b) << 8) | (c)) +diff -Naurd mpfr-3.1.5-a/src/vasprintf.c mpfr-3.1.5-b/src/vasprintf.c +--- mpfr-3.1.5-a/src/vasprintf.c 2016-12-15 08:35:46.520430308 +0000 ++++ mpfr-3.1.5-b/src/vasprintf.c 2017-06-06 19:57:01.963910062 +0000 +@@ -1452,7 +1452,7 @@ + struct printf_spec spec) + { + char *str; +- long total; ++ unsigned int total; /* can hold the sum of two non-negative int's + 1 */ + int uppercase; + + /* WARNING: left justification means right space padding */ +@@ -1645,43 +1645,43 @@ + + /* compute the number of characters to be written verifying it is not too + much */ ++ ++#define INCR_TOTAL(v) \ ++ do { \ ++ MPFR_ASSERTD ((v) >= 0); \ ++ if (MPFR_UNLIKELY ((v) > INT_MAX)) \ ++ goto error; \ ++ total += (v); \ ++ if (MPFR_UNLIKELY (total > INT_MAX)) \ ++ goto error; \ ++ } while (0) ++ + total = np->sign ? 1 : 0; +- total += np->prefix_size; +- total += np->ip_size; +- if (MPFR_UNLIKELY (total < 0 || total > INT_MAX)) +- goto error; +- total += np->ip_trailing_zeros; +- if (MPFR_UNLIKELY (total < 0 || total > INT_MAX)) +- goto error; ++ INCR_TOTAL (np->prefix_size); ++ INCR_TOTAL (np->ip_size); ++ INCR_TOTAL (np->ip_trailing_zeros); ++ MPFR_ASSERTD (np->ip_size + np->ip_trailing_zeros >= 1); + if (np->thousands_sep) + /* ' flag, style f and the thousands separator in current locale is not + reduced to the null character */ +- total += (np->ip_size + np->ip_trailing_zeros) / 3; +- if (MPFR_UNLIKELY (total < 0 || total > INT_MAX)) +- goto error; ++ INCR_TOTAL ((np->ip_size + np->ip_trailing_zeros - 1) / 3); + if (np->point) + ++total; +- total += np->fp_leading_zeros; +- if (MPFR_UNLIKELY (total < 0 || total > INT_MAX)) +- goto error; +- total += np->fp_size; +- if (MPFR_UNLIKELY (total < 0 || total > INT_MAX)) +- goto error; +- total += np->fp_trailing_zeros; +- if (MPFR_UNLIKELY (total < 0 || total > INT_MAX)) +- goto error; +- total += np->exp_size; +- if (MPFR_UNLIKELY (total < 0 || total > INT_MAX)) +- goto error; ++ INCR_TOTAL (np->fp_leading_zeros); ++ INCR_TOTAL (np->fp_size); ++ INCR_TOTAL (np->fp_trailing_zeros); ++ INCR_TOTAL (np->exp_size); + + if (spec.width > total) + /* pad with spaces or zeros depending on np->pad_type */ + { + np->pad_size = spec.width - total; + total += np->pad_size; /* here total == spec.width, +- so 0 < total < INT_MAX */ ++ so 0 < total <= INT_MAX */ ++ MPFR_ASSERTD (total == spec.width); + } + ++ MPFR_ASSERTD (total > 0 && total <= INT_MAX); + return total; + + error: +diff -Naurd mpfr-3.1.5-a/src/version.c mpfr-3.1.5-b/src/version.c +--- mpfr-3.1.5-a/src/version.c 2017-06-06 19:50:30.736438175 +0000 ++++ mpfr-3.1.5-b/src/version.c 2017-06-06 19:57:01.971909970 +0000 +@@ -25,5 +25,5 @@ + const char * + mpfr_get_version (void) + { +- return "3.1.5-p4"; ++ return "3.1.5-p5"; + } +diff -Naurd mpfr-3.1.5-a/PATCHES mpfr-3.1.5-b/PATCHES +--- mpfr-3.1.5-a/PATCHES 2017-06-06 20:17:02.489704106 +0000 ++++ mpfr-3.1.5-b/PATCHES 2017-06-06 20:17:02.513703814 +0000 +@@ -0,0 +1 @@ ++printf-errno +diff -Naurd mpfr-3.1.5-a/VERSION mpfr-3.1.5-b/VERSION +--- mpfr-3.1.5-a/VERSION 2017-06-06 19:57:01.971909970 +0000 ++++ mpfr-3.1.5-b/VERSION 2017-06-06 20:17:02.513703814 +0000 +@@ -1 +1 @@ +-3.1.5-p5 ++3.1.5-p6 +diff -Naurd mpfr-3.1.5-a/src/mpfr.h mpfr-3.1.5-b/src/mpfr.h +--- mpfr-3.1.5-a/src/mpfr.h 2017-06-06 19:57:01.971909970 +0000 ++++ mpfr-3.1.5-b/src/mpfr.h 2017-06-06 20:17:02.513703814 +0000 +@@ -27,7 +27,7 @@ + #define MPFR_VERSION_MAJOR 3 + #define MPFR_VERSION_MINOR 1 + #define MPFR_VERSION_PATCHLEVEL 5 +-#define MPFR_VERSION_STRING "3.1.5-p5" ++#define MPFR_VERSION_STRING "3.1.5-p6" + + /* Macros dealing with MPFR VERSION */ + #define MPFR_VERSION_NUM(a,b,c) (((a) << 16L) | ((b) << 8) | (c)) +diff -Naurd mpfr-3.1.5-a/src/printf.c mpfr-3.1.5-b/src/printf.c +--- mpfr-3.1.5-a/src/printf.c 2016-09-27 07:58:15.000000000 +0000 ++++ mpfr-3.1.5-b/src/printf.c 2017-06-06 20:17:02.501703960 +0000 +@@ -40,7 +40,6 @@ + # endif /* HAVE___VA_COPY */ + #endif /* HAVE_VA_COPY */ + +-#include + #include "mpfr-impl.h" + + #ifdef _MPFR_H_HAVE_FILE +diff -Naurd mpfr-3.1.5-a/src/vasprintf.c mpfr-3.1.5-b/src/vasprintf.c +--- mpfr-3.1.5-a/src/vasprintf.c 2017-06-06 19:57:01.963910062 +0000 ++++ mpfr-3.1.5-b/src/vasprintf.c 2017-06-06 20:17:02.501703960 +0000 +@@ -52,6 +52,8 @@ + #include /* for ptrdiff_t */ + #endif + ++#include ++ + #define MPFR_NEED_LONGLONG_H + #include "mpfr-intmax.h" + #include "mpfr-impl.h" +diff -Naurd mpfr-3.1.5-a/src/version.c mpfr-3.1.5-b/src/version.c +--- mpfr-3.1.5-a/src/version.c 2017-06-06 19:57:01.971909970 +0000 ++++ mpfr-3.1.5-b/src/version.c 2017-06-06 20:17:02.513703814 +0000 +@@ -25,5 +25,5 @@ + const char * + mpfr_get_version (void) + { +- return "3.1.5-p5"; ++ return "3.1.5-p6"; + } +diff -Naurd mpfr-3.1.5-a/tests/tprintf.c mpfr-3.1.5-b/tests/tprintf.c +--- mpfr-3.1.5-a/tests/tprintf.c 2016-09-27 07:58:14.000000000 +0000 ++++ mpfr-3.1.5-b/tests/tprintf.c 2017-06-06 20:17:02.501703960 +0000 +@@ -26,6 +26,7 @@ + #include + #include + #include ++#include + + #include "mpfr-intmax.h" + #include "mpfr-test.h" +@@ -109,6 +110,33 @@ + } + + static void ++check_vprintf_overflow (const char *fmt, ...) ++{ ++ va_list ap; ++ int r, e; ++ ++ va_start (ap, fmt); ++ errno = 0; ++ r = mpfr_vprintf (fmt, ap); ++ e = errno; ++ va_end (ap); ++ ++ if (r != -1 ++#ifdef EOVERFLOW ++ || e != EOVERFLOW ++#endif ++ ) ++ { ++ putchar ('\n'); ++ fprintf (stderr, "Error in mpfr_vprintf(\"%s\", ...)\n" ++ "Got r = %d, errno = %d\n", fmt, r, e); ++ exit (1); ++ } ++ ++ putchar ('\n'); ++} ++ ++static void + check_invalid_format (void) + { + int i = 0; +@@ -167,8 +195,8 @@ + mpfr_set_ui (x, 1, MPFR_RNDN); + mpfr_nextabove (x); + +- check_vprintf_failure ("%Rb", x); +- check_vprintf_failure ("%RA %RA %Ra %Ra", x, x, x, x); ++ check_vprintf_overflow ("%Rb", x); ++ check_vprintf_overflow ("%RA %RA %Ra %Ra", x, x, x, x); + + mpfr_clear (x); + } +diff -Naurd mpfr-3.1.5-a/PATCHES mpfr-3.1.5-b/PATCHES +--- mpfr-3.1.5-a/PATCHES 2017-06-06 20:24:00.580702002 +0000 ++++ mpfr-3.1.5-b/PATCHES 2017-06-06 20:24:00.604701719 +0000 +@@ -0,0 +1 @@ ++tsprintf-setlocale +diff -Naurd mpfr-3.1.5-a/VERSION mpfr-3.1.5-b/VERSION +--- mpfr-3.1.5-a/VERSION 2017-06-06 20:17:02.513703814 +0000 ++++ mpfr-3.1.5-b/VERSION 2017-06-06 20:24:00.604701719 +0000 +@@ -1 +1 @@ +-3.1.5-p6 ++3.1.5-p7 +diff -Naurd mpfr-3.1.5-a/src/mpfr.h mpfr-3.1.5-b/src/mpfr.h +--- mpfr-3.1.5-a/src/mpfr.h 2017-06-06 20:17:02.513703814 +0000 ++++ mpfr-3.1.5-b/src/mpfr.h 2017-06-06 20:24:00.604701719 +0000 +@@ -27,7 +27,7 @@ + #define MPFR_VERSION_MAJOR 3 + #define MPFR_VERSION_MINOR 1 + #define MPFR_VERSION_PATCHLEVEL 5 +-#define MPFR_VERSION_STRING "3.1.5-p6" ++#define MPFR_VERSION_STRING "3.1.5-p7" + + /* Macros dealing with MPFR VERSION */ + #define MPFR_VERSION_NUM(a,b,c) (((a) << 16L) | ((b) << 8) | (c)) +diff -Naurd mpfr-3.1.5-a/src/version.c mpfr-3.1.5-b/src/version.c +--- mpfr-3.1.5-a/src/version.c 2017-06-06 20:17:02.513703814 +0000 ++++ mpfr-3.1.5-b/src/version.c 2017-06-06 20:24:00.604701719 +0000 +@@ -25,5 +25,5 @@ + const char * + mpfr_get_version (void) + { +- return "3.1.5-p6"; ++ return "3.1.5-p7"; + } +diff -Naurd mpfr-3.1.5-a/tests/tsprintf.c mpfr-3.1.5-b/tests/tsprintf.c +--- mpfr-3.1.5-a/tests/tsprintf.c 2016-12-15 08:35:46.520430308 +0000 ++++ mpfr-3.1.5-b/tests/tsprintf.c 2017-06-06 20:24:00.596701813 +0000 +@@ -1273,13 +1273,12 @@ + int + main (int argc, char **argv) + { +- char *locale; + + tests_start_mpfr (); + + #if defined(HAVE_LOCALE_H) && defined(HAVE_SETLOCALE) + /* currently, we just check with 'C' locale */ +- locale = setlocale (LC_ALL, "C"); ++ setlocale (LC_ALL, "C"); + #endif + + bug20111102 (); +@@ -1297,7 +1296,7 @@ + locale_da_DK (); + /* Avoid a warning by doing the setlocale outside of this #if */ + #endif +- setlocale (LC_ALL, locale); ++ setlocale (LC_ALL, "C"); + #endif + + if (getenv ("MPFR_CHECK_LIBC_PRINTF")) +diff -Naurd mpfr-3.1.5-a/PATCHES mpfr-3.1.5-b/PATCHES +--- mpfr-3.1.5-a/PATCHES 2017-06-06 20:31:35.919341495 +0000 ++++ mpfr-3.1.5-b/PATCHES 2017-06-06 20:31:35.943341213 +0000 +@@ -0,0 +1 @@ ++mpf-compat-signed +diff -Naurd mpfr-3.1.5-a/VERSION mpfr-3.1.5-b/VERSION +--- mpfr-3.1.5-a/VERSION 2017-06-06 20:24:00.604701719 +0000 ++++ mpfr-3.1.5-b/VERSION 2017-06-06 20:31:35.943341213 +0000 +@@ -1 +1 @@ +-3.1.5-p7 ++3.1.5-p8 +diff -Naurd mpfr-3.1.5-a/src/mpf2mpfr.h mpfr-3.1.5-b/src/mpf2mpfr.h +--- mpfr-3.1.5-a/src/mpf2mpfr.h 2016-09-27 07:58:15.000000000 +0000 ++++ mpfr-3.1.5-b/src/mpf2mpfr.h 2017-06-06 20:31:35.931341353 +0000 +@@ -93,15 +93,15 @@ + #undef mpf_div_2exp + #define mpf_div_2exp(x,y,z) mpfr_div_2exp(x,y,z,MPFR_DEFAULT_RND) + #undef mpf_fits_slong_p +-#define mpf_fits_slong_p(x) mpfr_fits_ulong_p(x,MPFR_DEFAULT_RND) ++#define mpf_fits_slong_p(x) mpfr_fits_slong_p(x,MPFR_DEFAULT_RND) + #undef mpf_fits_ulong_p + #define mpf_fits_ulong_p(x) mpfr_fits_ulong_p(x,MPFR_DEFAULT_RND) + #undef mpf_fits_sint_p +-#define mpf_fits_sint_p(x) mpfr_fits_uint_p(x,MPFR_DEFAULT_RND) ++#define mpf_fits_sint_p(x) mpfr_fits_sint_p(x,MPFR_DEFAULT_RND) + #undef mpf_fits_uint_p + #define mpf_fits_uint_p(x) mpfr_fits_uint_p(x,MPFR_DEFAULT_RND) + #undef mpf_fits_sshort_p +-#define mpf_fits_sshort_p(x) mpfr_fits_ushort_p(x,MPFR_DEFAULT_RND) ++#define mpf_fits_sshort_p(x) mpfr_fits_sshort_p(x,MPFR_DEFAULT_RND) + #undef mpf_fits_ushort_p + #define mpf_fits_ushort_p(x) mpfr_fits_ushort_p(x,MPFR_DEFAULT_RND) + #undef mpf_get_str +@@ -113,7 +113,7 @@ + #undef mpf_get_ui + #define mpf_get_ui(x) mpfr_get_ui(x,MPFR_DEFAULT_RND) + #undef mpf_get_si +-#define mpf_get_si(x) mpfr_get_ui(x,MPFR_DEFAULT_RND) ++#define mpf_get_si(x) mpfr_get_si(x,MPFR_DEFAULT_RND) + #undef mpf_inp_str + #define mpf_inp_str(x,y,z) mpfr_inp_str(x,y,z,MPFR_DEFAULT_RND) + #undef mpf_set_str +diff -Naurd mpfr-3.1.5-a/src/mpfr-impl.h mpfr-3.1.5-b/src/mpfr-impl.h +--- mpfr-3.1.5-a/src/mpfr-impl.h 2017-06-06 19:21:17.592843433 +0000 ++++ mpfr-3.1.5-b/src/mpfr-impl.h 2017-06-06 20:31:35.931341353 +0000 +@@ -342,11 +342,15 @@ + #define MPFR_FLAGS_DIVBY0 32 + #define MPFR_FLAGS_ALL 63 + +-/* Replace some common functions for direct access to the global vars */ +-#define mpfr_get_emin() (__gmpfr_emin + 0) +-#define mpfr_get_emax() (__gmpfr_emax + 0) +-#define mpfr_get_default_rounding_mode() (__gmpfr_default_rounding_mode + 0) +-#define mpfr_get_default_prec() (__gmpfr_default_fp_bit_precision + 0) ++/* Replace some common functions for direct access to the global vars. ++ The casts prevent these macros from being used as a lvalue (and this ++ method makes sure that the expressions have the correct type). */ ++#define mpfr_get_emin() ((mpfr_exp_t) __gmpfr_emin) ++#define mpfr_get_emax() ((mpfr_exp_t) __gmpfr_emax) ++#define mpfr_get_default_rounding_mode() \ ++ ((mpfr_rnd_t) __gmpfr_default_rounding_mode) ++#define mpfr_get_default_prec() \ ++ ((mpfr_prec_t) __gmpfr_default_fp_bit_precision) + + #define mpfr_clear_flags() \ + ((void) (__gmpfr_flags = 0)) +diff -Naurd mpfr-3.1.5-a/src/mpfr.h mpfr-3.1.5-b/src/mpfr.h +--- mpfr-3.1.5-a/src/mpfr.h 2017-06-06 20:24:00.604701719 +0000 ++++ mpfr-3.1.5-b/src/mpfr.h 2017-06-06 20:31:35.939341259 +0000 +@@ -27,7 +27,7 @@ + #define MPFR_VERSION_MAJOR 3 + #define MPFR_VERSION_MINOR 1 + #define MPFR_VERSION_PATCHLEVEL 5 +-#define MPFR_VERSION_STRING "3.1.5-p7" ++#define MPFR_VERSION_STRING "3.1.5-p8" + + /* Macros dealing with MPFR VERSION */ + #define MPFR_VERSION_NUM(a,b,c) (((a) << 16L) | ((b) << 8) | (c)) +diff -Naurd mpfr-3.1.5-a/src/version.c mpfr-3.1.5-b/src/version.c +--- mpfr-3.1.5-a/src/version.c 2017-06-06 20:24:00.604701719 +0000 ++++ mpfr-3.1.5-b/src/version.c 2017-06-06 20:31:35.943341213 +0000 +@@ -25,5 +25,5 @@ + const char * + mpfr_get_version (void) + { +- return "3.1.5-p7"; ++ return "3.1.5-p8"; + } +diff -Naurd mpfr-3.1.5-a/tests/mpf_compat.h mpfr-3.1.5-b/tests/mpf_compat.h +--- mpfr-3.1.5-a/tests/mpf_compat.h 2016-09-27 07:58:14.000000000 +0000 ++++ mpfr-3.1.5-b/tests/mpf_compat.h 2017-06-06 20:31:35.931341353 +0000 +@@ -20,16 +20,10 @@ + http://www.gnu.org/licenses/ or write to the Free Software Foundation, Inc., + 51 Franklin St, Fifth Floor, Boston, MA 02110-1301, USA. */ + +-#if defined (__cplusplus) +-#include +-#else +-#include +-#endif + #include +-#include + +-#include "gmp.h" +-#include "mpfr.h" ++#include "mpfr-impl.h" ++ + #ifdef MPFR + #include "mpf2mpfr.h" + #endif +@@ -228,6 +222,16 @@ + exit (1); + } + ++ /* non-regression tests for bugs fixed in revision 11565 */ ++ mpf_set_si (x, -1); ++ MPFR_ASSERTN(mpf_fits_ulong_p (x) == 0); ++ MPFR_ASSERTN(mpf_fits_slong_p (x) != 0); ++ MPFR_ASSERTN(mpf_fits_uint_p (x) == 0); ++ MPFR_ASSERTN(mpf_fits_sint_p (x) != 0); ++ MPFR_ASSERTN(mpf_fits_ushort_p (x) == 0); ++ MPFR_ASSERTN(mpf_fits_sshort_p (x) != 0); ++ MPFR_ASSERTN(mpf_get_si (x) == -1); ++ + /* clear all variables */ + mpf_clear (y); + mpf_clear (x); -- GitLab From 890286487e7834e47b98ab9b54a8eafa15640431 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Thu, 29 Jun 2017 07:33:47 +0200 Subject: [PATCH 1038/1603] Add SVG and Statistics::Basic to recent Perl --- easybuild/easyconfigs/p/Perl/Perl-5.22.1-foss-2016a.eb | 8 ++++++++ easybuild/easyconfigs/p/Perl/Perl-5.22.1-foss-2016b.eb | 8 ++++++++ easybuild/easyconfigs/p/Perl/Perl-5.22.1-intel-2016a.eb | 8 ++++++++ easybuild/easyconfigs/p/Perl/Perl-5.22.2-goolf-1.7.20.eb | 8 ++++++++ easybuild/easyconfigs/p/Perl/Perl-5.22.2-intel-2016a.eb | 8 ++++++++ .../easyconfigs/p/Perl/Perl-5.24.0-GCC-5.4.0-2.26.eb | 8 ++++++++ easybuild/easyconfigs/p/Perl/Perl-5.24.0-GCCcore-4.9.3.eb | 8 ++++++++ easybuild/easyconfigs/p/Perl/Perl-5.24.0-intel-2016b.eb | 8 ++++++++ easybuild/easyconfigs/p/Perl/Perl-5.24.1-intel-2017a.eb | 8 ++++++++ 9 files changed, 72 insertions(+) diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.22.1-foss-2016a.eb b/easybuild/easyconfigs/p/Perl/Perl-5.22.1-foss-2016a.eb index f1ad7853f0..da492710dc 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.22.1-foss-2016a.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.22.1-foss-2016a.eb @@ -880,6 +880,14 @@ exts_list = [ 'source_tmpl': 'MailTools-2.14.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARKOV'], }), + ('SVG', '2.77', { + 'source_tmpl': 'SVG-2.77.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/M/MA/MANWAR/'], + }), + ('Statistics::Basic', '1.6611', { + 'source_tmpl': 'Statistics-Basic-1.6611.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/J/JE/JETTERO/'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.22.1-foss-2016b.eb b/easybuild/easyconfigs/p/Perl/Perl-5.22.1-foss-2016b.eb index 873d35ef8a..40d7dcb64d 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.22.1-foss-2016b.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.22.1-foss-2016b.eb @@ -880,6 +880,14 @@ exts_list = [ 'source_tmpl': 'MailTools-2.14.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARKOV'], }), + ('SVG', '2.77', { + 'source_tmpl': 'SVG-2.77.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/M/MA/MANWAR/'], + }), + ('Statistics::Basic', '1.6611', { + 'source_tmpl': 'Statistics-Basic-1.6611.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/J/JE/JETTERO/'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.22.1-intel-2016a.eb b/easybuild/easyconfigs/p/Perl/Perl-5.22.1-intel-2016a.eb index b58ce50af4..84b07d8df7 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.22.1-intel-2016a.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.22.1-intel-2016a.eb @@ -881,6 +881,14 @@ exts_list = [ 'source_tmpl': 'MailTools-2.14.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARKOV'], }), + ('SVG', '2.77', { + 'source_tmpl': 'SVG-2.77.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/M/MA/MANWAR/'], + }), + ('Statistics::Basic', '1.6611', { + 'source_tmpl': 'Statistics-Basic-1.6611.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/J/JE/JETTERO/'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.22.2-goolf-1.7.20.eb b/easybuild/easyconfigs/p/Perl/Perl-5.22.2-goolf-1.7.20.eb index 2a1f8007bb..f1a40e88cc 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.22.2-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.22.2-goolf-1.7.20.eb @@ -879,6 +879,14 @@ exts_list = [ 'source_tmpl': 'MailTools-2.18.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARKOV'], }), + ('SVG', '2.77', { + 'source_tmpl': 'SVG-2.77.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/M/MA/MANWAR/'], + }), + ('Statistics::Basic', '1.6611', { + 'source_tmpl': 'Statistics-Basic-1.6611.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/J/JE/JETTERO/'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.22.2-intel-2016a.eb b/easybuild/easyconfigs/p/Perl/Perl-5.22.2-intel-2016a.eb index c8a4524d45..972556dd95 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.22.2-intel-2016a.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.22.2-intel-2016a.eb @@ -880,6 +880,14 @@ exts_list = [ 'source_tmpl': 'MailTools-2.18.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARKOV'], }), + ('SVG', '2.77', { + 'source_tmpl': 'SVG-2.77.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/M/MA/MANWAR/'], + }), + ('Statistics::Basic', '1.6611', { + 'source_tmpl': 'Statistics-Basic-1.6611.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/J/JE/JETTERO/'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.24.0-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/p/Perl/Perl-5.24.0-GCC-5.4.0-2.26.eb index f39c5f51b0..ff9b04399d 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.24.0-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.24.0-GCC-5.4.0-2.26.eb @@ -887,6 +887,14 @@ exts_list = [ 'source_tmpl': 'PDF-API2-2.031.tar.gz', 'source_urls': ['http://search.cpan.org/CPAN/authors/id/S/SS/SSIMMS/'], }), + ('SVG', '2.77', { + 'source_tmpl': 'SVG-2.77.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/M/MA/MANWAR/'], + }), + ('Statistics::Basic', '1.6611', { + 'source_tmpl': 'Statistics-Basic-1.6611.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/J/JE/JETTERO/'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.24.0-GCCcore-4.9.3.eb b/easybuild/easyconfigs/p/Perl/Perl-5.24.0-GCCcore-4.9.3.eb index 47164262e3..62d5ecc186 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.24.0-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.24.0-GCCcore-4.9.3.eb @@ -889,6 +889,14 @@ exts_list = [ 'source_tmpl': 'PDF-API2-2.031.tar.gz', 'source_urls': ['http://search.cpan.org/CPAN/authors/id/S/SS/SSIMMS/'], }), + ('SVG', '2.77', { + 'source_tmpl': 'SVG-2.77.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/M/MA/MANWAR/'], + }), + ('Statistics::Basic', '1.6611', { + 'source_tmpl': 'Statistics-Basic-1.6611.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/J/JE/JETTERO/'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.24.0-intel-2016b.eb b/easybuild/easyconfigs/p/Perl/Perl-5.24.0-intel-2016b.eb index 8fd86e040f..da2611b723 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.24.0-intel-2016b.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.24.0-intel-2016b.eb @@ -888,6 +888,14 @@ exts_list = [ 'source_tmpl': 'PDF-API2-2.031.tar.gz', 'source_urls': ['http://search.cpan.org/CPAN/authors/id/S/SS/SSIMMS/'], }), + ('SVG', '2.77', { + 'source_tmpl': 'SVG-2.77.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/M/MA/MANWAR/'], + }), + ('Statistics::Basic', '1.6611', { + 'source_tmpl': 'Statistics-Basic-1.6611.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/J/JE/JETTERO/'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.24.1-intel-2017a.eb b/easybuild/easyconfigs/p/Perl/Perl-5.24.1-intel-2017a.eb index cc1cd43ca8..4dc5dd9a5c 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.24.1-intel-2017a.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.24.1-intel-2017a.eb @@ -894,6 +894,14 @@ exts_list = [ 'source_tmpl': 'Devel-CheckLib-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MATTN'], }), + ('SVG', '2.77', { + 'source_tmpl': 'SVG-2.77.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/M/MA/MANWAR/'], + }), + ('Statistics::Basic', '1.6611', { + 'source_tmpl': 'Statistics-Basic-1.6611.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/J/JE/JETTERO/'], + }), ] moduleclass = 'lang' -- GitLab From 5b04767e8556f1834f54addf2d86480cdd5ffd39 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 29 Jun 2017 12:22:47 +0200 Subject: [PATCH 1039/1603] adding easyconfigs: ABAQUS-2017-hotfix-1721.eb --- .../a/ABAQUS/ABAQUS-2017-hotfix-1721.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/a/ABAQUS/ABAQUS-2017-hotfix-1721.eb diff --git a/easybuild/easyconfigs/a/ABAQUS/ABAQUS-2017-hotfix-1721.eb b/easybuild/easyconfigs/a/ABAQUS/ABAQUS-2017-hotfix-1721.eb new file mode 100644 index 0000000000..c0357522cc --- /dev/null +++ b/easybuild/easyconfigs/a/ABAQUS/ABAQUS-2017-hotfix-1721.eb @@ -0,0 +1,24 @@ +name = 'ABAQUS' +version = '2017' +hotfix = '1721' +versionsuffix = '-hotfix-%s' % hotfix + +homepage = 'http://www.simulia.com/products/abaqus_fea.html' +description = """Finite Element Analysis software for modeling, visualization and best-in-class implicit and explicit + dynamics FEA.""" + +toolchain = {'name': 'dummy', 'version': ''} + +sources = [ + '%(version)s.AM_SIM_Abaqus_Extend.AllOS.1-6.tar', + '%(version)s.AM_SIM_Abaqus_Extend.AllOS.2-6.tar', + '%(version)s.AM_SIM_Abaqus_Extend.AllOS.3-6.tar', + '%(version)s.AM_SIM_Abaqus_Extend.AllOS.4-6.tar', + '%(version)s.AM_SIM_Abaqus_Extend.AllOS.5-6.tar', + '%(version)s.AM_SIM_Abaqus_Extend.AllOS.6-6.tar', + # hotfixes + '%%(version)s.FP.CFA.%s.Part_3DEXP_SimulationServices.Linux64.tar' % hotfix, + '%%(version)s.FP.CFA.%s.Part_SIMULIA_Abaqus_CAE.Linux64.tar' % hotfix, +] + +moduleclass = 'cae' -- GitLab From cb667e0a0f27f4d659780bbc2c67064a46453538 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 29 Jun 2017 17:34:55 +0200 Subject: [PATCH 1040/1603] {bio}[intel/2017a] NCBI-Toolkit 18.0.0 --- .../l/libxslt/libxslt-1.1.29-intel-2017a.eb | 24 ++++++++++ .../NCBI-Toolkit-18.0.0-intel-2017a.eb | 46 +++++++++++++++++++ ...NCBI-Toolkit-18.0.0_fix-make-install.patch | 14 ++++++ 3 files changed, 84 insertions(+) create mode 100644 easybuild/easyconfigs/l/libxslt/libxslt-1.1.29-intel-2017a.eb create mode 100644 easybuild/easyconfigs/n/NCBI-Toolkit/NCBI-Toolkit-18.0.0-intel-2017a.eb create mode 100644 easybuild/easyconfigs/n/NCBI-Toolkit/NCBI-Toolkit-18.0.0_fix-make-install.patch diff --git a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.29-intel-2017a.eb b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.29-intel-2017a.eb new file mode 100644 index 0000000000..03b3d4547e --- /dev/null +++ b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.29-intel-2017a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'libxslt' +version = '1.1.29' + +homepage = 'http://xmlsoft.org/' +description = """Libxslt is the XSLT C library developed for the GNOME project + (but usable outside of the Gnome platform).""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] + +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('zlib', '1.2.11'), + ('libxml2', '2.9.4'), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/NCBI-Toolkit/NCBI-Toolkit-18.0.0-intel-2017a.eb b/easybuild/easyconfigs/n/NCBI-Toolkit/NCBI-Toolkit-18.0.0-intel-2017a.eb new file mode 100644 index 0000000000..c29b279f64 --- /dev/null +++ b/easybuild/easyconfigs/n/NCBI-Toolkit/NCBI-Toolkit-18.0.0-intel-2017a.eb @@ -0,0 +1,46 @@ +easyblock = 'ConfigureMake' + +name = 'NCBI-Toolkit' +version = '18.0.0' + +homepage = 'http://ncbi.github.io/cxx-toolkit/' +description = """The NCBI Toolkit is a collection of utilities developed for the + production and distribution of GenBank, Entrez, BLAST, and related services + by the National Center for Biotechnology Information.""" +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [ + 'ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools++/CURRENT', + 'ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools++/ARCHIVE/2017/Jan_10_2017/', +] +sources = ['ncbi_cxx--%s.tar.gz' % '_'.join(version.split('.'))] +patches = ['NCBI-Toolkit-%(version)s_fix-make-install.patch'] +checksums = [ + 'f9c47db64e5e31fcb8fdebb165c3eb895cb1668e419f4b917414aadf70f1bdf5', # ncbi_cxx--18_0_0.tar.gz + 'c3e0fe8dcf5bd95c9efd9dcf3613bb053a16597eb40d4c23b8f1f7ae5e19951a', # NCBI-Toolkit-18.0.0_fix-make-install.patch +] + +dependencies = [ + ('Boost', '1.58.0'), + ('SAMtools', '1.4.1'), + ('HTSlib', '1.4.1'), + ('Python', '2.7.13'), + ('libxslt', '1.1.29'), +] + +preconfigopts = 'export CFLAGS="$CFLAGS -wd3377" && export CXXFLAGS="$CXXFLAGS -wd3377" && ' +preconfigopts += 'export LIBS="$LIBS -lstdc++" && ' +configopts = '--with-boost=$EBROOTBOOST --with-python=$EBROOTPYTHON ' +configopts += '--with-libxml=$EBROOTLIBXML2 --with-libxslt=$EBROOTLIBXSLT ' +configopts += '--with-dll --with-bin-release --with-mt ' +configopts += '--without-debug --without-ccache' + +buildopts = 'SAMTOOLS=$EBROOTSAMTOOLS SAMTOOLS_INCLUDE="-I$EBROOTSAMTOOLS/include/bam -I$EBROOTHTSLIB/include" ' +buildopts += 'SAMTOOLS_LIBS="-L$EBROOTSAMTOOLS/lib -lbam -L$EBROOTHTSLIB/lib -lhts"' + +sanity_check_paths = { + 'files': ['bin/blastn', 'bin/blastp', 'bin/blastx', 'bin/table2asn'], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/n/NCBI-Toolkit/NCBI-Toolkit-18.0.0_fix-make-install.patch b/easybuild/easyconfigs/n/NCBI-Toolkit/NCBI-Toolkit-18.0.0_fix-make-install.patch new file mode 100644 index 0000000000..e02333d788 --- /dev/null +++ b/easybuild/easyconfigs/n/NCBI-Toolkit/NCBI-Toolkit-18.0.0_fix-make-install.patch @@ -0,0 +1,14 @@ +fix for "omitting directory" error on installing of 'inc/common' during 'make install' +author: Kenneth Hoste (HPC-UGent) +--- ncbi_cxx--18_0_0/src/build-system/Makefile.in.top.orig 2017-06-29 14:51:43.855712613 +0200 ++++ ncbi_cxx--18_0_0/src/build-system/Makefile.in.top 2017-06-29 14:54:47.876416764 +0200 +@@ -51,7 +51,8 @@ + done + cd $(includedir0) && find * -name CVS -prune -o -print |\ + cpio -pd $(pincludedir) +- $(INSTALL) -m 644 $(incdir)/* $(pincludedir) ++ $(INSTALL) -m 644 $(incdir)/*.h $(pincludedir) ++ $(INSTALL) -m 644 $(incdir)/common/* $(pincludedir)/common + ## set up appropriate build and status directories somewhere under $(libdir)? + + install-gbench: -- GitLab From 0002d42891421489d1eb537097499a5d843b0467 Mon Sep 17 00:00:00 2001 From: Anuj Sharm Date: Fri, 30 Jun 2017 01:09:19 +0100 Subject: [PATCH 1041/1603] adding easyconfig: OpenCoarrays-1.9.0-gompi-2017a.eb --- .../OpenCoarrays-1.9.0-gompi-2017a.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenCoarrays/OpenCoarrays-1.9.0-gompi-2017a.eb diff --git a/easybuild/easyconfigs/o/OpenCoarrays/OpenCoarrays-1.9.0-gompi-2017a.eb b/easybuild/easyconfigs/o/OpenCoarrays/OpenCoarrays-1.9.0-gompi-2017a.eb new file mode 100644 index 0000000000..03a9dacdd6 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenCoarrays/OpenCoarrays-1.9.0-gompi-2017a.eb @@ -0,0 +1,30 @@ +easyblock = 'CMakeMake' + +name = 'OpenCoarrays' +version = '1.9.0' + +homepage = 'https://github.com/sourceryinstitute/opencoarrays' +description = """OpenCoarrays is an open-source software project that supports +the coarray Fortran (CAF) parallel programming features of the Fortran 2008 +standard and several features proposed for Fortran 2015 in the draft Technical +Specification TS 18508 Additional Parallel Features in Fortran.""" + +toolchain = {'name': 'gompi', 'version': '2017a'} +toolchainopts = {'pic': True} + +source_urls = ['%s/releases/download/%s' % (homepage, version)] + +sources = [SOURCE_TAR_GZ] + +separate_build_dir = True + +sanity_check_paths = { + 'files': ['lib/%s' % x for x in ['libcaf_mpi.a']] + + ['include/%s' % x for x in ['opencoarrays.mod']] + + ['bin/%s' % x for x in ['caf', 'cafrun']], + 'dirs': ['bin'] + + ['include'] + + ['lib'] +} + +moduleclass = 'mpi' -- GitLab From b300e5226ae59ad14bd477c0ae840f712d5b12f9 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Fri, 30 Jun 2017 16:46:16 +1200 Subject: [PATCH 1042/1603] Remove extra commands now in EasyBlock --- easybuild/easyconfigs/h/HDF5/HDF5-1.8.18-gimkl-2017a.eb | 7 ------- 1 file changed, 7 deletions(-) diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.18-gimkl-2017a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.18-gimkl-2017a.eb index 57cd66e064..b35a90f186 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.18-gimkl-2017a.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.18-gimkl-2017a.eb @@ -16,16 +16,9 @@ source_urls = [ sources = [SOURCELOWER_TAR_GZ] checksums = ['dd2148b740713ca0295442ec683d7b1c'] -buildopts = 'CXXFLAGS="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK"' - dependencies = [ ('zlib', '1.2.11'), ('Szip', '2.1'), ] -# Needed for h5py in Python (at least sometimes) -modextravars = { - 'HDF5_DIR': '%(installdir)s', -} - moduleclass = 'data' -- GitLab From 8b97fccb20c68a77931953f6c76e36b520c0ed03 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 30 Jun 2017 08:57:31 +0200 Subject: [PATCH 1043/1603] add missing easyconfig for Boost 1.58.0 dependency to NCBI-Toolkit 18.0.0 --- .../b/Boost/Boost-1.58.0-intel-2017a.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.58.0-intel-2017a.eb diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.58.0-intel-2017a.eb b/easybuild/easyconfigs/b/Boost/Boost-1.58.0-intel-2017a.eb new file mode 100644 index 0000000000..13f1c926c3 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.58.0-intel-2017a.eb @@ -0,0 +1,23 @@ +name = 'Boost' +version = '1.58.0' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.11'), +] + +configopts = '--without-libraries=python' + +# also build boost_mpi +boost_mpi = True + +moduleclass = 'devel' -- GitLab From 2e2e34427a9220ef4cfb6792cd3dce40026c0ac6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 30 Jun 2017 10:16:14 +0200 Subject: [PATCH 1044/1603] sync/fix source_urls & homepage in HDF5 easyconfig --- easybuild/easyconfigs/h/HDF5/HDF5-1.8.18-gimkl-2017a.eb | 7 ++----- 1 file changed, 2 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.18-gimkl-2017a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.18-gimkl-2017a.eb index b35a90f186..11630b75f7 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.18-gimkl-2017a.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.18-gimkl-2017a.eb @@ -1,17 +1,14 @@ name = 'HDF5' version = '1.8.18' -homepage = 'http://www.hdfgroup.org/HDF5/' +homepage = 'https://support.hdfgroup.org/HDF5/' description = """HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections.""" toolchain = {'name': 'gimkl', 'version': '2017a'} toolchainopts = {'pic': True, 'usempi': True} -source_urls = [ - 'https://support.hdfgroup.org/ftp/HDF5/current18/src/', - 'https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(versions)/src/' -] +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] checksums = ['dd2148b740713ca0295442ec683d7b1c'] -- GitLab From 8d143f0527f960f527c046f32215366b43b3313f Mon Sep 17 00:00:00 2001 From: Anuj Sharm Date: Sat, 1 Jul 2017 13:53:20 +0100 Subject: [PATCH 1045/1603] adding easyconfig: OpenCoarrays-1.9.0-gompi-2017a.eb Included the style changes and added the CMake dependency --- .../o/OpenCoarrays/OpenCoarrays-1.9.0-gompi-2017a.eb | 12 +++++------- 1 file changed, 5 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenCoarrays/OpenCoarrays-1.9.0-gompi-2017a.eb b/easybuild/easyconfigs/o/OpenCoarrays/OpenCoarrays-1.9.0-gompi-2017a.eb index 03a9dacdd6..19bc16c65e 100644 --- a/easybuild/easyconfigs/o/OpenCoarrays/OpenCoarrays-1.9.0-gompi-2017a.eb +++ b/easybuild/easyconfigs/o/OpenCoarrays/OpenCoarrays-1.9.0-gompi-2017a.eb @@ -12,19 +12,17 @@ Specification TS 18508 Additional Parallel Features in Fortran.""" toolchain = {'name': 'gompi', 'version': '2017a'} toolchainopts = {'pic': True} -source_urls = ['%s/releases/download/%s' % (homepage, version)] +source_urls = ['https://github.com/sourceryinstitute/opencoarrays/releases/download/%(version)s'] sources = [SOURCE_TAR_GZ] separate_build_dir = True +builddependencies = [('CMake', '3.8.2')] + sanity_check_paths = { - 'files': ['lib/%s' % x for x in ['libcaf_mpi.a']] + - ['include/%s' % x for x in ['opencoarrays.mod']] + - ['bin/%s' % x for x in ['caf', 'cafrun']], - 'dirs': ['bin'] + - ['include'] + - ['lib'] + 'files': ['bin/caf', 'bin/cafrun', 'include/opencoarrays.mod', 'lib/libcaf_mpi.a'], + 'dirs': [], } moduleclass = 'mpi' -- GitLab From 0859a3b1aec1aca96597f50feab5aa6d543cb0b0 Mon Sep 17 00:00:00 2001 From: Anuj Sharm Date: Sat, 1 Jul 2017 14:24:53 +0100 Subject: [PATCH 1046/1603] adding easyconfig: OpenCoarrays-1.9.0-gompi-2017a.eb Fixed trailing whitespace --- .../o/OpenCoarrays/OpenCoarrays-1.9.0-gompi-2017a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OpenCoarrays/OpenCoarrays-1.9.0-gompi-2017a.eb b/easybuild/easyconfigs/o/OpenCoarrays/OpenCoarrays-1.9.0-gompi-2017a.eb index 19bc16c65e..fe75320f74 100644 --- a/easybuild/easyconfigs/o/OpenCoarrays/OpenCoarrays-1.9.0-gompi-2017a.eb +++ b/easybuild/easyconfigs/o/OpenCoarrays/OpenCoarrays-1.9.0-gompi-2017a.eb @@ -22,7 +22,7 @@ builddependencies = [('CMake', '3.8.2')] sanity_check_paths = { 'files': ['bin/caf', 'bin/cafrun', 'include/opencoarrays.mod', 'lib/libcaf_mpi.a'], - 'dirs': [], + 'dirs': [], } moduleclass = 'mpi' -- GitLab From 8e054be4f1803c1e117246ba929ca24522665ad3 Mon Sep 17 00:00:00 2001 From: Anuj Sharm Date: Sat, 1 Jul 2017 22:47:02 +0100 Subject: [PATCH 1047/1603] adding easyconfig: OpenCoarrays-1.9.0-gompi-2017a.eb Updated sanity check --- .../o/OpenCoarrays/OpenCoarrays-1.9.0-gompi-2017a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OpenCoarrays/OpenCoarrays-1.9.0-gompi-2017a.eb b/easybuild/easyconfigs/o/OpenCoarrays/OpenCoarrays-1.9.0-gompi-2017a.eb index fe75320f74..c1b457179d 100644 --- a/easybuild/easyconfigs/o/OpenCoarrays/OpenCoarrays-1.9.0-gompi-2017a.eb +++ b/easybuild/easyconfigs/o/OpenCoarrays/OpenCoarrays-1.9.0-gompi-2017a.eb @@ -21,7 +21,7 @@ separate_build_dir = True builddependencies = [('CMake', '3.8.2')] sanity_check_paths = { - 'files': ['bin/caf', 'bin/cafrun', 'include/opencoarrays.mod', 'lib/libcaf_mpi.a'], + 'files': ['bin/caf', 'bin/cafrun', 'include/opencoarrays.mod', ('lib/libcaf_mpi.a', 'lib64/libcaf_mpi.a')], 'dirs': [], } -- GitLab From 67be0389f4ed57b5db1f6e6a060278a9b13733e7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 3 Jul 2017 11:22:18 +0200 Subject: [PATCH 1048/1603] add missing DB dependency for NCBI-Toolkit --- .../easyconfigs/d/DB/DB-6.2.23-intel-2017a.eb | 18 ++++++++++++++++++ .../NCBI-Toolkit-18.0.0-intel-2017a.eb | 1 + 2 files changed, 19 insertions(+) create mode 100644 easybuild/easyconfigs/d/DB/DB-6.2.23-intel-2017a.eb diff --git a/easybuild/easyconfigs/d/DB/DB-6.2.23-intel-2017a.eb b/easybuild/easyconfigs/d/DB/DB-6.2.23-intel-2017a.eb new file mode 100644 index 0000000000..e519c86c5f --- /dev/null +++ b/easybuild/easyconfigs/d/DB/DB-6.2.23-intel-2017a.eb @@ -0,0 +1,18 @@ +name = 'DB' +version = '6.2.23' + +homepage = 'http://www.oracle.com/technetwork/products/berkeleydb' +description = """Berkeley DB enables the development of custom data management solutions, + without the overhead traditionally associated with such custom projects.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +# download via http://www.oracle.com/technetwork/products/berkeleydb/downloads/, requires registration +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': ['include/db.h', 'lib/libdb.a', 'lib/libdb.%s' % SHLIB_EXT], + 'dirs': ['bin'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/n/NCBI-Toolkit/NCBI-Toolkit-18.0.0-intel-2017a.eb b/easybuild/easyconfigs/n/NCBI-Toolkit/NCBI-Toolkit-18.0.0-intel-2017a.eb index c29b279f64..4d14bced16 100644 --- a/easybuild/easyconfigs/n/NCBI-Toolkit/NCBI-Toolkit-18.0.0-intel-2017a.eb +++ b/easybuild/easyconfigs/n/NCBI-Toolkit/NCBI-Toolkit-18.0.0-intel-2017a.eb @@ -26,6 +26,7 @@ dependencies = [ ('HTSlib', '1.4.1'), ('Python', '2.7.13'), ('libxslt', '1.1.29'), + ('DB', '6.2.23'), ] preconfigopts = 'export CFLAGS="$CFLAGS -wd3377" && export CXXFLAGS="$CXXFLAGS -wd3377" && ' -- GitLab From c386dbc57f9a1a337a39c4ea517f351495cab8e8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 3 Jul 2017 12:05:22 +0200 Subject: [PATCH 1049/1603] include joblib as extension in recent Python easyconfigs --- easybuild/easyconfigs/p/Python/Python-2.7.13-foss-2017a.eb | 3 +++ easybuild/easyconfigs/p/Python/Python-2.7.13-intel-2017a.eb | 3 +++ easybuild/easyconfigs/p/Python/Python-3.6.1-intel-2017a.eb | 3 +++ 3 files changed, 9 insertions(+) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.13-foss-2017a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.13-foss-2017a.eb index 21d606f252..836a809f6b 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.13-foss-2017a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.13-foss-2017a.eb @@ -133,6 +133,9 @@ exts_list = [ ('docopt', '0.6.2', { 'source_urls': ['https://pypi.python.org/packages/source/d/docopt'], }), + ('joblib', '0.11', { + 'source_urls': ['https://pypi.python.org/packages/source/j/joblib'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.13-intel-2017a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.13-intel-2017a.eb index 4ee5f95966..0bc26ff7b9 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.13-intel-2017a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.13-intel-2017a.eb @@ -133,6 +133,9 @@ exts_list = [ ('docopt', '0.6.2', { 'source_urls': ['https://pypi.python.org/packages/source/d/docopt'], }), + ('joblib', '0.11', { + 'source_urls': ['https://pypi.python.org/packages/source/j/joblib'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-3.6.1-intel-2017a.eb b/easybuild/easyconfigs/p/Python/Python-3.6.1-intel-2017a.eb index e17d931cf2..9157c902c6 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.6.1-intel-2017a.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.6.1-intel-2017a.eb @@ -125,6 +125,9 @@ exts_list = [ ('docopt', '0.6.2', { 'source_urls': ['https://pypi.python.org/packages/source/d/docopt'], }), + ('joblib', '0.11', { + 'source_urls': ['https://pypi.python.org/packages/source/j/joblib'], + }), ] moduleclass = 'lang' -- GitLab From 4cbb6857506998e5771547214cf8257d36719629 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 3 Jul 2017 15:53:28 +0200 Subject: [PATCH 1050/1603] bump DB to 6.2.32 as dep for NCBI-Toolkit --- .../DB/{DB-6.2.23-intel-2017a.eb => DB-6.2.32-intel-2017a.eb} | 3 ++- .../n/NCBI-Toolkit/NCBI-Toolkit-18.0.0-intel-2017a.eb | 2 +- 2 files changed, 3 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/d/DB/{DB-6.2.23-intel-2017a.eb => DB-6.2.32-intel-2017a.eb} (85%) diff --git a/easybuild/easyconfigs/d/DB/DB-6.2.23-intel-2017a.eb b/easybuild/easyconfigs/d/DB/DB-6.2.32-intel-2017a.eb similarity index 85% rename from easybuild/easyconfigs/d/DB/DB-6.2.23-intel-2017a.eb rename to easybuild/easyconfigs/d/DB/DB-6.2.32-intel-2017a.eb index e519c86c5f..0eb67b8e2c 100644 --- a/easybuild/easyconfigs/d/DB/DB-6.2.23-intel-2017a.eb +++ b/easybuild/easyconfigs/d/DB/DB-6.2.32-intel-2017a.eb @@ -1,5 +1,5 @@ name = 'DB' -version = '6.2.23' +version = '6.2.32' homepage = 'http://www.oracle.com/technetwork/products/berkeleydb' description = """Berkeley DB enables the development of custom data management solutions, @@ -9,6 +9,7 @@ toolchain = {'name': 'intel', 'version': '2017a'} # download via http://www.oracle.com/technetwork/products/berkeleydb/downloads/, requires registration sources = [SOURCELOWER_TAR_GZ] +checksums = ['a9c5e2b004a5777aa03510cfe5cd766a4a3b777713406b02809c17c8e0e7a8fb'] sanity_check_paths = { 'files': ['include/db.h', 'lib/libdb.a', 'lib/libdb.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/n/NCBI-Toolkit/NCBI-Toolkit-18.0.0-intel-2017a.eb b/easybuild/easyconfigs/n/NCBI-Toolkit/NCBI-Toolkit-18.0.0-intel-2017a.eb index 4d14bced16..708e64725c 100644 --- a/easybuild/easyconfigs/n/NCBI-Toolkit/NCBI-Toolkit-18.0.0-intel-2017a.eb +++ b/easybuild/easyconfigs/n/NCBI-Toolkit/NCBI-Toolkit-18.0.0-intel-2017a.eb @@ -26,7 +26,7 @@ dependencies = [ ('HTSlib', '1.4.1'), ('Python', '2.7.13'), ('libxslt', '1.1.29'), - ('DB', '6.2.23'), + ('DB', '6.2.32'), ] preconfigopts = 'export CFLAGS="$CFLAGS -wd3377" && export CXXFLAGS="$CXXFLAGS -wd3377" && ' -- GitLab From b92163eaf6d685c063c40ce7a9214beb282cb373 Mon Sep 17 00:00:00 2001 From: Damian Alvarez Date: Mon, 3 Jul 2017 16:53:49 +0200 Subject: [PATCH 1051/1603] Changed moduleclass in mpi4py to better reflect what it is and to don't get HMNS confused --- .../m/mpi4py/mpi4py-1.3-goolf-1.4.10-Python-2.7.3.eb | 2 +- .../m/mpi4py/mpi4py-1.3-goolf-1.4.10-Python-3.2.3.eb | 2 +- .../easyconfigs/m/mpi4py/mpi4py-1.3-ictce-5.3.0-Python-2.7.3.eb | 2 +- .../easyconfigs/m/mpi4py/mpi4py-1.3-ictce-5.5.0-Python-2.7.5.eb | 2 +- .../mpi4py-1.3.1-intel-2015b-Python-2.7.10-timed-pingpong.eb | 2 +- .../m/mpi4py/mpi4py-1.3.1-intel-2015b-Python-2.7.10.eb | 2 +- .../mpi4py-1.3.1-intel-2015b-Python-2.7.11-timed-pingpong.eb | 2 +- .../mpi4py-1.3.1-intel-2016a-Python-2.7.11-timed-pingpong.eb | 2 +- .../mpi4py-1.3.1-intel-2016b-Python-2.7.12-timed-pingpong.eb | 2 +- .../m/mpi4py/mpi4py-2.0.0-intel-2015b-Python-2.7.10.eb | 2 +- .../m/mpi4py/mpi4py-2.0.0-intel-2016b-Python-2.7.12.eb | 2 +- 11 files changed, 11 insertions(+), 11 deletions(-) diff --git a/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-goolf-1.4.10-Python-2.7.3.eb index e5d94c2ee2..b3cad4430c 100644 --- a/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-goolf-1.4.10-Python-2.7.3.eb @@ -26,4 +26,4 @@ sanity_check_paths = { 'dirs': ['lib/python%s/site-packages/mpi4py' % pyshortver], } -moduleclass = 'mpi' +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-goolf-1.4.10-Python-3.2.3.eb b/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-goolf-1.4.10-Python-3.2.3.eb index 4e871b0231..b04c0fc199 100644 --- a/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-goolf-1.4.10-Python-3.2.3.eb +++ b/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-goolf-1.4.10-Python-3.2.3.eb @@ -27,4 +27,4 @@ sanity_check_paths = { 'dirs': ['lib/python%s/site-packages/mpi4py' % pyshortver], } -moduleclass = 'mpi' +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-ictce-5.3.0-Python-2.7.3.eb index 14d09f706a..9d22c53e8f 100644 --- a/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-ictce-5.3.0-Python-2.7.3.eb @@ -24,4 +24,4 @@ sanity_check_paths = { 'dirs': ['lib/python%s/site-packages/mpi4py' % pyshortver], } -moduleclass = 'mpi' +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-ictce-5.5.0-Python-2.7.5.eb b/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-ictce-5.5.0-Python-2.7.5.eb index 96628ba336..7f116835fa 100644 --- a/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-ictce-5.5.0-Python-2.7.5.eb +++ b/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-ictce-5.5.0-Python-2.7.5.eb @@ -24,4 +24,4 @@ sanity_check_paths = { 'dirs': ['lib/python%s/site-packages/mpi4py' % pyshortver], } -moduleclass = 'mpi' +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3.1-intel-2015b-Python-2.7.10-timed-pingpong.eb b/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3.1-intel-2015b-Python-2.7.10-timed-pingpong.eb index e8592db2a2..88c6067f4d 100644 --- a/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3.1-intel-2015b-Python-2.7.10-timed-pingpong.eb +++ b/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3.1-intel-2015b-Python-2.7.10-timed-pingpong.eb @@ -34,4 +34,4 @@ sanity_check_commands = [ ('python', '-c "from mpi4py.MPI import Comm; import sys; sys.exit((1, 0)[\'PingpongRS\' in dir(Comm)])"'), ] -moduleclass = 'mpi' +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3.1-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3.1-intel-2015b-Python-2.7.10.eb index 9ee5130156..5e3a747282 100644 --- a/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3.1-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3.1-intel-2015b-Python-2.7.10.eb @@ -23,4 +23,4 @@ sanity_check_paths = { 'dirs': ['lib/python%s/site-packages/mpi4py' % py_maj_min], } -moduleclass = 'mpi' +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3.1-intel-2015b-Python-2.7.11-timed-pingpong.eb b/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3.1-intel-2015b-Python-2.7.11-timed-pingpong.eb index 8f22d6b607..633d85b7c2 100644 --- a/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3.1-intel-2015b-Python-2.7.11-timed-pingpong.eb +++ b/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3.1-intel-2015b-Python-2.7.11-timed-pingpong.eb @@ -31,4 +31,4 @@ sanity_check_commands = [ ('python', '-c "from mpi4py.MPI import Comm; import sys; sys.exit((1, 0)[\'PingpongRS\' in dir(Comm)])"'), ] -moduleclass = 'mpi' +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3.1-intel-2016a-Python-2.7.11-timed-pingpong.eb b/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3.1-intel-2016a-Python-2.7.11-timed-pingpong.eb index 654b6f59ec..01ec7adf94 100644 --- a/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3.1-intel-2016a-Python-2.7.11-timed-pingpong.eb +++ b/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3.1-intel-2016a-Python-2.7.11-timed-pingpong.eb @@ -31,4 +31,4 @@ sanity_check_commands = [ ('python', '-c "from mpi4py.MPI import Comm; import sys; sys.exit((1, 0)[\'PingpongRS\' in dir(Comm)])"'), ] -moduleclass = 'mpi' +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3.1-intel-2016b-Python-2.7.12-timed-pingpong.eb b/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3.1-intel-2016b-Python-2.7.12-timed-pingpong.eb index e2e1da4cf2..94ab105eff 100644 --- a/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3.1-intel-2016b-Python-2.7.12-timed-pingpong.eb +++ b/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3.1-intel-2016b-Python-2.7.12-timed-pingpong.eb @@ -31,4 +31,4 @@ sanity_check_commands = [ ('python', '-c "from mpi4py.MPI import Comm; import sys; sys.exit((1, 0)[\'PingpongRS\' in dir(Comm)])"'), ] -moduleclass = 'mpi' +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/mpi4py/mpi4py-2.0.0-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/m/mpi4py/mpi4py-2.0.0-intel-2015b-Python-2.7.10.eb index 0bec59079b..934953ce0a 100644 --- a/easybuild/easyconfigs/m/mpi4py/mpi4py-2.0.0-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/m/mpi4py/mpi4py-2.0.0-intel-2015b-Python-2.7.10.eb @@ -23,4 +23,4 @@ sanity_check_paths = { 'dirs': ['lib/python%s/site-packages/mpi4py' % py_maj_min], } -moduleclass = 'mpi' +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/mpi4py/mpi4py-2.0.0-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/m/mpi4py/mpi4py-2.0.0-intel-2016b-Python-2.7.12.eb index eade0fd4f9..a1f0fb7dc3 100644 --- a/easybuild/easyconfigs/m/mpi4py/mpi4py-2.0.0-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/m/mpi4py/mpi4py-2.0.0-intel-2016b-Python-2.7.12.eb @@ -20,4 +20,4 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages/mpi4py'], } -moduleclass = 'mpi' +moduleclass = 'lib' -- GitLab From 3575bf8c5e804881aaf4efab3092a4a19098e361 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 3 Jul 2017 17:23:19 +0200 Subject: [PATCH 1052/1603] adding easyconfigs: vsc-mympirun-4.0.0.eb, vsc-install-0.10.26.eb --- .../v/vsc-install/vsc-install-0.10.26.eb | 23 +++++++++++++ .../v/vsc-mympirun/vsc-mympirun-4.0.0.eb | 33 +++++++++++++++++++ 2 files changed, 56 insertions(+) create mode 100644 easybuild/easyconfigs/v/vsc-install/vsc-install-0.10.26.eb create mode 100755 easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-4.0.0.eb diff --git a/easybuild/easyconfigs/v/vsc-install/vsc-install-0.10.26.eb b/easybuild/easyconfigs/v/vsc-install/vsc-install-0.10.26.eb new file mode 100644 index 0000000000..66693d8845 --- /dev/null +++ b/easybuild/easyconfigs/v/vsc-install/vsc-install-0.10.26.eb @@ -0,0 +1,23 @@ +easyblock = 'PythonPackage' + +name = 'vsc-install' +version = '0.10.26' + +homepage = 'http://hpcugent.github.com/vsc-install/' +description = """Shared setuptools functions and classes for python libraries developed by UGent's HPC group""" + +# purposely built with system compilers & Python +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = [SOURCE_TAR_GZ] +source_urls = [PYPI_SOURCE] + +options = {'modulename': 'vsc.install'} + +pyshortver = '.'.join(SYS_PYTHON_VERSION.split('.')[:2]) +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages' % pyshortver], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-4.0.0.eb b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-4.0.0.eb new file mode 100755 index 0000000000..2a97ab5dab --- /dev/null +++ b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-4.0.0.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonPackage' + +name = 'vsc-mympirun' +version = '4.0.0' + +homepage = 'https://github.com/hpcugent/vsc-mympirun' +description = """VSC-tools is a set of Python libraries and scripts that are commonly used within HPC-UGent.""" + +# we build this to work with every python version +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +builddependencies = [('vsc-install', '0.10.26')] +dependencies = [('vsc-base', '2.5.8')] + +osdependencies = ['python-setuptools'] + +# we ship something in bin/fake +modextrapaths = {'PATH': 'bin/fake'} + +# don't check for import of vsc.mympirun, since that may fail if vsc-base is picked up from the OS +options = {'modulename': 'vsc'} + +pyshortver = '.'.join(SYS_PYTHON_VERSION.split('.')[:2]) +sanity_check_paths = { + 'files': ['bin/mympirun', 'bin/mympisanity'], + 'dirs': ['bin/fake', 'lib/python%s/site-packages' % pyshortver], +} +sanity_check_commands = ["mympirun --help"] + +moduleclass = 'tools' -- GitLab From 1c6664d0bde4cf74f27096d9934c40037330d870 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Mon, 3 Jul 2017 15:15:01 +0200 Subject: [PATCH 1053/1603] Add kallisto for foss-2016b --- .../h/HDF5/HDF5-1.8.18-foss-2016b-serial.eb | 26 ++++++++++++++ .../k/kallisto/kallisto-0.43.1-foss-2016b.eb | 34 +++++++++++++++++++ 2 files changed, 60 insertions(+) create mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.8.18-foss-2016b-serial.eb create mode 100644 easybuild/easyconfigs/k/kallisto/kallisto-0.43.1-foss-2016b.eb diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.18-foss-2016b-serial.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.18-foss-2016b-serial.eb new file mode 100644 index 0000000000..5144aa0dac --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.18-foss-2016b-serial.eb @@ -0,0 +1,26 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild + +name = 'HDF5' +version = '1.8.18' +versionsuffix = '-serial' + +homepage = 'https://support.hdfgroup.org/HDF5/' +description = """HDF5 is a unique technology suite that makes possible the management of + extremely large and complex data collections.""" + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'pic': True, 'usempi': False} + +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] + +checksums = ['cdb195ad8d9e6782acf24b2488061289f615628c2ccda8457b0a0c3fb7a8a063'] + +buildopts = 'CXXFLAGS="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK"' + +dependencies = [ + ('zlib', '1.2.8'), + ('Szip', '2.1'), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/k/kallisto/kallisto-0.43.1-foss-2016b.eb b/easybuild/easyconfigs/k/kallisto/kallisto-0.43.1-foss-2016b.eb new file mode 100644 index 0000000000..c79b5734ff --- /dev/null +++ b/easybuild/easyconfigs/k/kallisto/kallisto-0.43.1-foss-2016b.eb @@ -0,0 +1,34 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild + +easyblock = 'CMakeMake' + +name = 'kallisto' +version = '0.43.1' + +homepage = 'http://pachterlab.github.io/kallisto/' +description = """kallisto is a program for quantifying abundances of transcripts from RNA-Seq data, or more generally + of target sequences using high-throughput sequencing reads.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['https://github.com/pachterlab/kallisto/archive/'] +sources = ['v%(version)s.tar.gz'] + +checksums = ['7baef1b3b67bcf81dc7c604db2ef30f5520b48d532bf28ec26331cb60ce69400'] + +builddependencies = [ + ('CMake', '3.7.2') +] + +dependencies = [ + ('HDF5', '1.8.18', '-serial') +] + +separate_build_dir = True + +sanity_check_paths = { + 'files': ['bin/kallisto'], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From 6d2f05e1d387c53d6c2d8d9e4566c9551c64494e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 4 Jul 2017 11:23:48 +0200 Subject: [PATCH 1054/1603] adding easyconfigs: FLUENT-18.1.eb --- easybuild/easyconfigs/f/FLUENT/FLUENT-18.1.eb | 14 ++++++++++++++ 1 file changed, 14 insertions(+) create mode 100644 easybuild/easyconfigs/f/FLUENT/FLUENT-18.1.eb diff --git a/easybuild/easyconfigs/f/FLUENT/FLUENT-18.1.eb b/easybuild/easyconfigs/f/FLUENT/FLUENT-18.1.eb new file mode 100644 index 0000000000..adedc0b444 --- /dev/null +++ b/easybuild/easyconfigs/f/FLUENT/FLUENT-18.1.eb @@ -0,0 +1,14 @@ +name = 'FLUENT' +version = '18.1' + +homepage = 'http://www.ansys.com/Products/Simulation+Technology/Fluid+Dynamics/Fluid+Dynamics+Products/ANSYS+Fluent' +description = """ANSYS FLUENT software contains the broad physical modeling capabilities needed +to model flow, turbulence, heat transfer, and reactions for industrial applications ranging from +air flow over an aircraft wing to combustion in a furnace, from bubble columns to oil platforms, +from blood flow to semiconductor manufacturing, and from clean room design to wastewater treatment plants.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['FLUIDSTRUCTURES_%(version_major)s%(version_minor)s_LINX64.tar'] + +moduleclass = 'cae' -- GitLab From 62d549469c9ddb821d7cef0524510a9346dee22b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Tue, 4 Jul 2017 12:47:00 +0200 Subject: [PATCH 1055/1603] Add requested changes Switched to HDF5-1.8.18-foss-2016b. Added toolchainopts usempi and pic. Put single dependencies on one line. --- .../h/HDF5/HDF5-1.8.18-foss-2016b-serial.eb | 26 ------------------- .../k/kallisto/kallisto-0.43.1-foss-2016b.eb | 9 +++---- 2 files changed, 3 insertions(+), 32 deletions(-) delete mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.8.18-foss-2016b-serial.eb diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.18-foss-2016b-serial.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.18-foss-2016b-serial.eb deleted file mode 100644 index 5144aa0dac..0000000000 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.18-foss-2016b-serial.eb +++ /dev/null @@ -1,26 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild - -name = 'HDF5' -version = '1.8.18' -versionsuffix = '-serial' - -homepage = 'https://support.hdfgroup.org/HDF5/' -description = """HDF5 is a unique technology suite that makes possible the management of - extremely large and complex data collections.""" - -toolchain = {'name': 'foss', 'version': '2016b'} -toolchainopts = {'pic': True, 'usempi': False} - -source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] -sources = [SOURCELOWER_TAR_GZ] - -checksums = ['cdb195ad8d9e6782acf24b2488061289f615628c2ccda8457b0a0c3fb7a8a063'] - -buildopts = 'CXXFLAGS="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK"' - -dependencies = [ - ('zlib', '1.2.8'), - ('Szip', '2.1'), -] - -moduleclass = 'data' diff --git a/easybuild/easyconfigs/k/kallisto/kallisto-0.43.1-foss-2016b.eb b/easybuild/easyconfigs/k/kallisto/kallisto-0.43.1-foss-2016b.eb index c79b5734ff..9d74f7a398 100644 --- a/easybuild/easyconfigs/k/kallisto/kallisto-0.43.1-foss-2016b.eb +++ b/easybuild/easyconfigs/k/kallisto/kallisto-0.43.1-foss-2016b.eb @@ -10,19 +10,16 @@ description = """kallisto is a program for quantifying abundances of transcripts of target sequences using high-throughput sequencing reads.""" toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'pic': True, 'usempi': True} source_urls = ['https://github.com/pachterlab/kallisto/archive/'] sources = ['v%(version)s.tar.gz'] checksums = ['7baef1b3b67bcf81dc7c604db2ef30f5520b48d532bf28ec26331cb60ce69400'] -builddependencies = [ - ('CMake', '3.7.2') -] +builddependencies = [('CMake', '3.7.2')] -dependencies = [ - ('HDF5', '1.8.18', '-serial') -] +dependencies = [('HDF5', '1.8.18')] separate_build_dir = True -- GitLab From 2bd0cc121d598b5219e4924be2d17046238e6a4a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 4 Jul 2017 13:23:30 +0200 Subject: [PATCH 1056/1603] use released version of GCC 6.4.0 --- easybuild/easyconfigs/g/GCCcore/GCCcore-6.4.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-6.4.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-6.4.0.eb index 9dbb7d3700..8c17a18894 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-6.4.0.eb @@ -22,7 +22,7 @@ source_urls = [ ] sources = [ - 'gcc-%(version)s-RC-20170628.tar.gz', # FIXME 'gcc-%(version)s.tar.bz2', + 'gcc-%(version)s.tar.gz', 'gmp-6.1.2.tar.bz2', 'mpfr-%s.tar.bz2' % mpfr_version, 'mpc-1.0.3.tar.gz', @@ -40,7 +40,7 @@ patches = [ ] checksums = [ - '005e58fb723efb3bf51dac5db8a5edf7c66ea2e7ddb6de6ed02dbb74fcc31f80', # gcc-6.4.0.tar.bz2 + '4715f02413f8a91d02d967521c084990c99ce1a671b8a450a80fbd4245f4b728', # gcc-6.4.0.tar.gz '5275bb04f4863a13516b2f39392ac5e272f5e1bb8057b18aec1c9b79d73d8fb2', # gmp-6.1.2.tar.bz2 'ca498c1c7a74dd37a576f353312d1e68d490978de4395fa28f1cbd46a364e658', # mpfr-3.1.5.tar.gz '617decc6ea09889fb08ede330917a00b16809b8db88c29c31bfbb49cbf88ecc3', # mpc-1.0.3.tar.gz -- GitLab From b19681c8d8faf724a4e0c2e20dfc55c17b6a9929 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Tue, 4 Jul 2017 14:44:34 +0200 Subject: [PATCH 1057/1603] Add Salmon for foss-2016b with dependencies --- .../j/Jellyfish/Jellyfish-2.2.6-foss-2016b.eb | 32 +++++++++++++++ .../Salmon-0.8.2-foss-2016b-Python-2.7.12.eb | 41 +++++++++++++++++++ .../Salmon/Salmon-0.8.2_CMAKE_CXX_FLAGS.patch | 12 ++++++ 3 files changed, 85 insertions(+) create mode 100644 easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.2.6-foss-2016b.eb create mode 100644 easybuild/easyconfigs/s/Salmon/Salmon-0.8.2-foss-2016b-Python-2.7.12.eb create mode 100644 easybuild/easyconfigs/s/Salmon/Salmon-0.8.2_CMAKE_CXX_FLAGS.patch diff --git a/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.2.6-foss-2016b.eb b/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.2.6-foss-2016b.eb new file mode 100644 index 0000000000..ff9fe9e8d2 --- /dev/null +++ b/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.2.6-foss-2016b.eb @@ -0,0 +1,32 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild + +easyblock = 'ConfigureMake' + +name = 'Jellyfish' +version = '2.2.6' + +homepage = 'http://www.genome.umd.edu/jellyfish.html' +description = """ Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['https://github.com/gmarcais/Jellyfish/releases/download/v%(version)s'] +sources = [SOURCELOWER_TAR_GZ] + +checksums = ['4532fb003a0494f6473bb97d52467904f631b94f7f9afb0d45b398f6c413692e'] + +parallel = 1 + +# The tests for the Bloom filter are statistical tests and can randomly fail, they actually don't make a lot of sense +runtest = "check GTEST_FILTER=-'*Bloom*'" + +postinstallcmds = ["cp config.h %(installdir)s/include/%(namelower)s-%(version)s/%(namelower)s/"] + +sanity_check_paths = { + 'files': ['bin/jellyfish'], + 'dirs': [] +} + +modextrapaths = {'CPATH': 'include/%(namelower)s-%(version)s'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/Salmon/Salmon-0.8.2-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/s/Salmon/Salmon-0.8.2-foss-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..0eaeb53856 --- /dev/null +++ b/easybuild/easyconfigs/s/Salmon/Salmon-0.8.2-foss-2016b-Python-2.7.12.eb @@ -0,0 +1,41 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild + +easyblock = 'CMakeMake' + +name = 'Salmon' +version = '0.8.2' + +homepage = 'https://github.com/COMBINE-lab/salmon' +description = """Salmon is a wicked-fast program to produce a highly-accurate, + transcript-level quantification estimates from RNA-seq data.""" + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'pic': True, 'openmp': True} + +sources = ['v%(version)s.tar.gz'] +source_urls = ['https://github.com/COMBINE-lab/salmon/archive/'] + +checksums = ['299168e873e71e9b07d63a84ae0b0c41b0876d1ad1d434b326a5be2dce7c4b91'] + +patches = ['Salmon-%(version)s_CMAKE_CXX_FLAGS.patch'] + +python = 'Python' +pyver = '2.7.12' +versionsuffix = '-%s-%s' % (python, pyver) + +builddependencies = [('CMake', '3.7.2')] + +dependencies = [ + ('Boost', '1.63.0', versionsuffix), + ('tbb', '2017_U5'), + ('Jellyfish', '2.2.6'), +] + +sanity_check_paths = { + 'files': ['bin/salmon'], + 'dirs': [] +} + +parallel = 1 + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/Salmon/Salmon-0.8.2_CMAKE_CXX_FLAGS.patch b/easybuild/easyconfigs/s/Salmon/Salmon-0.8.2_CMAKE_CXX_FLAGS.patch new file mode 100644 index 0000000000..396046c304 --- /dev/null +++ b/easybuild/easyconfigs/s/Salmon/Salmon-0.8.2_CMAKE_CXX_FLAGS.patch @@ -0,0 +1,12 @@ +* don't hardcode $CMAKE_CXX_FLAGS +--- salmon-0.8.2/CMakeLists.txt.orig 2017-07-03 13:31:00.000000000 +0200 ++++ salmon-0.8.2/CMakeLists.txt 2017-07-03 13:49:34.000000000 +0200 +@@ -32,7 +32,7 @@ + + ## Set the standard required compile flags + # Nov 18th --- removed -DHAVE_CONFIG_H +-set (CMAKE_CXX_FLAGS "-pthread -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DRAPMAP_SALMON_SUPPORT -DHAVE_ANSI_TERM -DHAVE_SSTREAM -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -std=c++11 -Wreturn-type -Werror=return-type") ++set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -L$ENV{EBROOTJELLYFISH}/lib -ljellyfish-2.0 -pthread -DRAPMAP_SALMON_SUPPORT -DHAVE_ANSI_TERM -DHAVE_SSTREAM -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -std=c++11 -Wreturn-type -Werror=return-type") + + ## + # OSX is strange (some might say, stupid in this regard). Deal with it's quirkines here. -- GitLab From 8e2b4f1bac30fd06d4e9c346cfc3dad6a01af863 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Tue, 4 Jul 2017 16:16:27 +0200 Subject: [PATCH 1058/1603] Easyconfig for FastME 2.1.5. with foss 2016a --- .../f/FastME/FastME-2.1.5-foss-2016a.eb | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) create mode 100644 easybuild/easyconfigs/f/FastME/FastME-2.1.5-foss-2016a.eb diff --git a/easybuild/easyconfigs/f/FastME/FastME-2.1.5-foss-2016a.eb b/easybuild/easyconfigs/f/FastME/FastME-2.1.5-foss-2016a.eb new file mode 100644 index 0000000000..e2f94ba178 --- /dev/null +++ b/easybuild/easyconfigs/f/FastME/FastME-2.1.5-foss-2016a.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'FastME' +version = '2.1.5' + +homepage = 'http://www.atgc-montpellier.fr/fastme/' +description = """FastME: a comprehensive, accurate and fast distance-based phylogeny inference program.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://www.atgc-montpellier.fr/download/sources/fastme/'] +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': ['bin/fastme'], + 'dirs': [] +} + +moduleclass = 'bio' -- GitLab From 47b25139d47479665894c37184c3670edf781600 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Wed, 5 Jul 2017 07:48:44 +0200 Subject: [PATCH 1059/1603] Add dependency tbb --- .../easyconfigs/t/tbb/tbb-2017_U5-foss-2016b.eb | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) create mode 100644 easybuild/easyconfigs/t/tbb/tbb-2017_U5-foss-2016b.eb diff --git a/easybuild/easyconfigs/t/tbb/tbb-2017_U5-foss-2016b.eb b/easybuild/easyconfigs/t/tbb/tbb-2017_U5-foss-2016b.eb new file mode 100644 index 0000000000..17d6caf922 --- /dev/null +++ b/easybuild/easyconfigs/t/tbb/tbb-2017_U5-foss-2016b.eb @@ -0,0 +1,17 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild + +name = 'tbb' +version = '2017_U5' + +homepage = 'https://01.org/tbb/' +description = """Intel(R) Threading Building Blocks (Intel(R) TBB) lets you easily write parallel C++ programs that + take full advantage of multicore performance, that are portable, composable and have future-proof scalability.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['https://github.com/01org/tbb/archive/'] +sources = ['%(version)s.tar.gz'] + +checksums = ['780baf0ad520f23b54dd20dc97bf5aae4bc562019e0a70f53bfc4c1afec6e545'] + +moduleclass = 'lib' -- GitLab From 623780a3037913c17a05ff27dc35daef8f9182e0 Mon Sep 17 00:00:00 2001 From: zao Date: Wed, 5 Jul 2017 09:54:44 +0200 Subject: [PATCH 1060/1603] Fix bug in ubsan.c that prevents GCC 7.1 from building GCC 6.3 --- .../g/GCCcore/GCCcore-6.3.0-fix-ubsan.patch | 12 ++++++++++++ easybuild/easyconfigs/g/GCCcore/GCCcore-6.3.0.eb | 1 + 2 files changed, 13 insertions(+) create mode 100644 easybuild/easyconfigs/g/GCCcore/GCCcore-6.3.0-fix-ubsan.patch diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-6.3.0-fix-ubsan.patch b/easybuild/easyconfigs/g/GCCcore/GCCcore-6.3.0-fix-ubsan.patch new file mode 100644 index 0000000000..8b5e6acbfb --- /dev/null +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-6.3.0-fix-ubsan.patch @@ -0,0 +1,12 @@ +diff -ru gcc-6.3.0-orig/gcc/ubsan.c gcc-6.3.0/gcc/ubsan.c +--- gcc-6.3.0-orig/gcc/ubsan.c 2016-12-07 23:39:29.000000000 +0100 ++++ gcc-6.3.0/gcc/ubsan.c 2017-07-05 08:57:03.297566616 +0200 +@@ -1471,7 +1471,7 @@ + + expanded_location xloc = expand_location (loc); + if (xloc.file == NULL || strncmp (xloc.file, "\1", 2) == 0 +- || xloc.file == '\0' || xloc.file[0] == '\xff' ++ || xloc.file[0] == '\0' || xloc.file[0] == '\xff' + || xloc.file[1] == '\xff') + return false; + diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-6.3.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-6.3.0.eb index 603d43dcde..b95420541e 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-6.3.0.eb @@ -37,6 +37,7 @@ builddependencies = [ patches = [ ('mpfr-%s-allpatches-20161215.patch' % mpfr_version, '../mpfr-%s' % mpfr_version), 'GCCcore-6.2.0-fix-find-isl.patch', + 'GCCcore-6.3.0-fix-ubsan.patch', ] checksums = [ -- GitLab From a1c4e3f18a7bccbcfca3112a36b5be50f3d8cd3a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Wed, 5 Jul 2017 07:58:15 +0200 Subject: [PATCH 1061/1603] Move Python versionsuffix up --- .../s/Salmon/Salmon-0.8.2-foss-2016b-Python-2.7.12.eb | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/s/Salmon/Salmon-0.8.2-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/s/Salmon/Salmon-0.8.2-foss-2016b-Python-2.7.12.eb index 0eaeb53856..3b07e6d2d4 100644 --- a/easybuild/easyconfigs/s/Salmon/Salmon-0.8.2-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/s/Salmon/Salmon-0.8.2-foss-2016b-Python-2.7.12.eb @@ -4,6 +4,7 @@ easyblock = 'CMakeMake' name = 'Salmon' version = '0.8.2' +versionsuffix = '-Python-2.7.12' homepage = 'https://github.com/COMBINE-lab/salmon' description = """Salmon is a wicked-fast program to produce a highly-accurate, @@ -19,10 +20,6 @@ checksums = ['299168e873e71e9b07d63a84ae0b0c41b0876d1ad1d434b326a5be2dce7c4b91'] patches = ['Salmon-%(version)s_CMAKE_CXX_FLAGS.patch'] -python = 'Python' -pyver = '2.7.12' -versionsuffix = '-%s-%s' % (python, pyver) - builddependencies = [('CMake', '3.7.2')] dependencies = [ -- GitLab From 1029301d3b150a028e78c311aab8db916cd41c1b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Wed, 5 Jul 2017 10:22:23 +0200 Subject: [PATCH 1062/1603] Patch for compiler flags and Jellyfish --- .../Salmon-0.8.2-foss-2016b-Python-2.7.12.eb | 2 +- .../Salmon/Salmon-0.8.2_CMAKE_CXX_FLAGS.patch | 12 --- ...Salmon-0.8.2_skip-included-Jellyfish.patch | 99 +++++++++++++++++++ 3 files changed, 100 insertions(+), 13 deletions(-) delete mode 100644 easybuild/easyconfigs/s/Salmon/Salmon-0.8.2_CMAKE_CXX_FLAGS.patch create mode 100644 easybuild/easyconfigs/s/Salmon/Salmon-0.8.2_skip-included-Jellyfish.patch diff --git a/easybuild/easyconfigs/s/Salmon/Salmon-0.8.2-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/s/Salmon/Salmon-0.8.2-foss-2016b-Python-2.7.12.eb index 3b07e6d2d4..6ff3af6070 100644 --- a/easybuild/easyconfigs/s/Salmon/Salmon-0.8.2-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/s/Salmon/Salmon-0.8.2-foss-2016b-Python-2.7.12.eb @@ -18,7 +18,7 @@ source_urls = ['https://github.com/COMBINE-lab/salmon/archive/'] checksums = ['299168e873e71e9b07d63a84ae0b0c41b0876d1ad1d434b326a5be2dce7c4b91'] -patches = ['Salmon-%(version)s_CMAKE_CXX_FLAGS.patch'] +patches = ['Salmon-%(version)s_skip-included-Jellyfish.patch'] builddependencies = [('CMake', '3.7.2')] diff --git a/easybuild/easyconfigs/s/Salmon/Salmon-0.8.2_CMAKE_CXX_FLAGS.patch b/easybuild/easyconfigs/s/Salmon/Salmon-0.8.2_CMAKE_CXX_FLAGS.patch deleted file mode 100644 index 396046c304..0000000000 --- a/easybuild/easyconfigs/s/Salmon/Salmon-0.8.2_CMAKE_CXX_FLAGS.patch +++ /dev/null @@ -1,12 +0,0 @@ -* don't hardcode $CMAKE_CXX_FLAGS ---- salmon-0.8.2/CMakeLists.txt.orig 2017-07-03 13:31:00.000000000 +0200 -+++ salmon-0.8.2/CMakeLists.txt 2017-07-03 13:49:34.000000000 +0200 -@@ -32,7 +32,7 @@ - - ## Set the standard required compile flags - # Nov 18th --- removed -DHAVE_CONFIG_H --set (CMAKE_CXX_FLAGS "-pthread -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DRAPMAP_SALMON_SUPPORT -DHAVE_ANSI_TERM -DHAVE_SSTREAM -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -std=c++11 -Wreturn-type -Werror=return-type") -+set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -L$ENV{EBROOTJELLYFISH}/lib -ljellyfish-2.0 -pthread -DRAPMAP_SALMON_SUPPORT -DHAVE_ANSI_TERM -DHAVE_SSTREAM -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -std=c++11 -Wreturn-type -Werror=return-type") - - ## - # OSX is strange (some might say, stupid in this regard). Deal with it's quirkines here. diff --git a/easybuild/easyconfigs/s/Salmon/Salmon-0.8.2_skip-included-Jellyfish.patch b/easybuild/easyconfigs/s/Salmon/Salmon-0.8.2_skip-included-Jellyfish.patch new file mode 100644 index 0000000000..cc8f3208b9 --- /dev/null +++ b/easybuild/easyconfigs/s/Salmon/Salmon-0.8.2_skip-included-Jellyfish.patch @@ -0,0 +1,99 @@ +* skip downloading and building of Jellyfish, since it's provided via EasyBuild already +* don't hardcode $CMAKE_CXX_FLAGS +author: Paul Jähne +--- CMakeLists.txt.orig 2017-07-05 08:07:10.000000000 +0200 ++++ CMakeLists.txt 2017-07-05 08:15:13.000000000 +0200 +@@ -32,7 +32,7 @@ + + ## Set the standard required compile flags + # Nov 18th --- removed -DHAVE_CONFIG_H +-set (CMAKE_CXX_FLAGS "-pthread -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DRAPMAP_SALMON_SUPPORT -DHAVE_ANSI_TERM -DHAVE_SSTREAM -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -std=c++11 -Wreturn-type -Werror=return-type") ++set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -L$ENV{EBROOTJELLYFISH}/lib -ljellyfish-2.0 -pthread -DRAPMAP_SALMON_SUPPORT -DHAVE_ANSI_TERM -DHAVE_SSTREAM -Wall -Wno-reorder -Wno-unused-variable -std=c++11 -Wreturn-type -Werror=return-type") + + ## + # OSX is strange (some might say, stupid in this regard). Deal with it's quirkines here. +@@ -459,33 +459,6 @@ + BUILD_IN_SOURCE TRUE + ) + +-find_package(Jellyfish 2.2.6) +- +-if (NOT JELLYFISH_FOUND) +-message("Build system will fetch and build Jellyfish") +-message("==================================================================") +-ExternalProject_Add(libjellyfish +- DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external +- ## +- #URL https://github.com/gmarcais/Jellyfish/releases/download/v2.2.6/jellyfish-2.2.6.tar.gz +- #DOWNLOAD_NAME jellyfish-2.2.6.tgz +- #URL_HASH SHA1=53819a57ea8ffae26e3f917babf978f8215ef117 +- #TLS_VERIFY FALSE +- ## +- DOWNLOAD_COMMAND curl -k -L https://github.com/gmarcais/Jellyfish/releases/download/v2.2.6/jellyfish-2.2.6.tar.gz -o jellyfish-2.2.6.tgz && +- ${SHASUM} 4532fb003a0494f6473bb97d52467904f631b94f7f9afb0d45b398f6c413692e jellyfish-2.2.6.tgz && +- rm -fr jellyfish-2.2.6 && +- tar -xzvf jellyfish-2.2.6.tgz +- SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/jellyfish-2.2.6 +- INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install +- CONFIGURE_COMMAND ${CMAKE_CURRENT_SOURCE_DIR}/external/jellyfish-2.2.6/configure --prefix= CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER} CXXFLAGS=${JELLYFISH_CXX_FLAGS} +- BUILD_COMMAND ${MAKE} CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER} CXXFLAGS=${JELLYFISH_CXX_FLAGS} +- BUILD_IN_SOURCE 1 +- INSTALL_COMMAND make ${QUIET_MAKE} install +-) +-set (FETCHED_JELLYFISH TRUE) +-endif() +- + ## Try and find TBB first + find_package(TBB 4.4 COMPONENTS tbb tbbmalloc tbbmalloc_proxy ) + +--- src/CMakeLists.txt.orig 2017-07-05 09:12:35.000000000 +0200 ++++ src/CMakeLists.txt 2017-07-05 09:18:12.000000000 +0200 +@@ -4,7 +4,6 @@ + ${GAT_SOURCE_DIR}/external + ${GAT_SOURCE_DIR}/external/cereal/include + ${GAT_SOURCE_DIR}/external/install/include +-${GAT_SOURCE_DIR}/external/install/include/jellyfish-2.2.6 + ${GAT_SOURCE_DIR}/external/install/include/bwa + ${ZLIB_INCLUDE_DIR} + ${TBB_INCLUDE_DIRS} +@@ -12,12 +11,6 @@ + ${GAT_SOURCE_DIR}/external/install/include/rapmap + ) + +-if (JELLYFISH_FOUND) +- include_directories(${JELLYFISH_INCLUDE_DIR}) +-else() +- include_directories(${GAT_SOURCE_DIR}/external/install/include/jellyfish-2.2.6) +-endif() +- + set ( SALMON_MAIN_SRCS + QSufSort.c + is.c +@@ -135,7 +128,6 @@ + ${ZLIB_LIBRARY} + ${SUFFARRAY_LIB} + ${SUFFARRAY64_LIB} +- ${GAT_SOURCE_DIR}/external/install/lib/libjellyfish-2.0.a + ${GAT_SOURCE_DIR}/external/install/lib/libbwa.a + m + ${LIBLZMA_LIBRARIES} +@@ -160,11 +152,6 @@ + add_dependencies(salmon libboost) + endif() + +-if (${FETCHED_JELLYFISH}) +- add_dependencies(salmon_core libjellyfish) +- add_dependencies(salmon libjellyfish) +-endif() +- + if (${FETCHED_TBB}) + add_dependencies(salmon_core libtbb) + add_dependencies(salmon libtbb) +@@ -193,7 +180,6 @@ + ${ZLIB_LIBRARY} + ${SUFFARRAY_LIB} + ${SUFFARRAY64_LIB} +- ${GAT_SOURCE_DIR}/external/install/lib/libjellyfish-2.0.a + ${GAT_SOURCE_DIR}/external/install/lib/libbwa.a + m + ${LIBLZMA_LIBRARIES} -- GitLab From 9e2358699f0c2f57d5f16769d88a663340302bd8 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Wed, 5 Jul 2017 14:14:29 +0200 Subject: [PATCH 1063/1603] Remove parallel option --- .../s/Salmon/Salmon-0.8.2-foss-2016b-Python-2.7.12.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/s/Salmon/Salmon-0.8.2-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/s/Salmon/Salmon-0.8.2-foss-2016b-Python-2.7.12.eb index 6ff3af6070..54ff0aac82 100644 --- a/easybuild/easyconfigs/s/Salmon/Salmon-0.8.2-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/s/Salmon/Salmon-0.8.2-foss-2016b-Python-2.7.12.eb @@ -33,6 +33,4 @@ sanity_check_paths = { 'dirs': [] } -parallel = 1 - moduleclass = 'bio' -- GitLab From da07ca4793fe822b96a9387bfadcdb34f1dff7b7 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Wed, 5 Jul 2017 15:04:39 +0200 Subject: [PATCH 1064/1603] Use name variables --- .../s/Salmon/Salmon-0.8.2-foss-2016b-Python-2.7.12.eb | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/s/Salmon/Salmon-0.8.2-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/s/Salmon/Salmon-0.8.2-foss-2016b-Python-2.7.12.eb index 54ff0aac82..a171f04582 100644 --- a/easybuild/easyconfigs/s/Salmon/Salmon-0.8.2-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/s/Salmon/Salmon-0.8.2-foss-2016b-Python-2.7.12.eb @@ -6,7 +6,7 @@ name = 'Salmon' version = '0.8.2' versionsuffix = '-Python-2.7.12' -homepage = 'https://github.com/COMBINE-lab/salmon' +homepage = 'https://github.com/COMBINE-lab/%(namelower)s' description = """Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq data.""" @@ -14,11 +14,11 @@ toolchain = {'name': 'foss', 'version': '2016b'} toolchainopts = {'pic': True, 'openmp': True} sources = ['v%(version)s.tar.gz'] -source_urls = ['https://github.com/COMBINE-lab/salmon/archive/'] +source_urls = ['https://github.com/COMBINE-lab/%(namelower)s/archive/'] checksums = ['299168e873e71e9b07d63a84ae0b0c41b0876d1ad1d434b326a5be2dce7c4b91'] -patches = ['Salmon-%(version)s_skip-included-Jellyfish.patch'] +patches = ['%(name)s-%(version)s_skip-included-Jellyfish.patch'] builddependencies = [('CMake', '3.7.2')] @@ -29,7 +29,7 @@ dependencies = [ ] sanity_check_paths = { - 'files': ['bin/salmon'], + 'files': ['bin/%(namelower)s'], 'dirs': [] } -- GitLab From aa629cffa92f94cb41641fb0028d03482e2fb12d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 4 Jul 2017 21:49:37 +0200 Subject: [PATCH 1065/1603] get rid of references to 'hpcugent' organisation after move to github.com/easybuilders --- CONTRIBUTING.md | 12 ++++++------ README.rst | 18 +++++++++--------- RELEASE_NOTES | 6 +++--- easybuild/easyconfigs/TEMPLATE.eb | 2 +- ...S-1.3.4-goalf-1.1.0-no-OFED-Python-2.7.3.eb | 2 +- .../ABySS-1.3.4-ictce-4.0.6-Python-2.7.3.eb | 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.../StringTie/StringTie-1.2.2-goolf-1.4.10.eb | 2 +- .../s/StringTie/StringTie-1.3.0-intel-2016b.eb | 2 +- .../s/StringTie/StringTie-1.3.3-intel-2017a.eb | 2 +- .../s/StringTie/StringTie-1.3.3b-foss-2016b.eb | 2 +- .../s/Subread/Subread-1.5.0-p1-foss-2015b.eb | 2 +- .../s/Subread/Subread-1.5.0-p1-foss-2016a.eb | 2 +- .../s/Subread/Subread-1.5.0-p1-foss-2016b.eb | 2 +- .../samblaster-0.1.24-goolf-1.7.20.eb | 2 +- .../s/segemehl/segemehl-0.1.7-goolf-1.4.10.eb | 2 +- .../s/segemehl/segemehl-0.2.0-foss-2016b.eb | 2 +- .../s/segemehl/segemehl-0.2.0-goolf-1.4.10.eb | 2 +- .../sickle-1.210-goolf-1.4.10-bab15f7.eb | 2 +- .../s/skewer/skewer-0.2.2-goolf-1.7.20.eb | 2 +- .../easyconfigs/s/splitRef/splitRef-0.0.2.eb | 2 +- .../s/sratoolkit/sratoolkit-2.5.7.eb | 2 +- .../s/stress/stress-1.0.4-goolf-1.7.20.eb | 2 +- ...synchronicity-1.1.9.1-foss-2015b-R-3.2.3.eb | 2 +- .../t/TAU/TAU-2.22.2-goolf-1.5.14.eb | 2 +- easybuild/easyconfigs/t/TCC/TCC-0.9.26.eb | 2 +- .../TREE-PUZZLE-5.2-goolf-1.4.10.eb | 2 +- .../easyconfigs/t/Tar/Tar-1.26-goolf-1.4.10.eb | 2 +- .../easyconfigs/t/Tar/Tar-1.26-ictce-5.3.0.eb | 2 +- .../Tesla-Deployment-Kit-5.319.43.eb | 2 +- .../t/TopHat/TopHat-2.0.10-ictce-5.5.0.eb | 2 +- .../t/TopHat/TopHat-2.0.13-goolf-1.7.20.eb | 2 +- .../t/TopHat/TopHat-2.0.14-goolf-1.7.20.eb | 2 +- .../t/TopHat/TopHat-2.0.4-goolf-1.4.10.eb | 2 +- ...-2.0.8-goolf-1.4.10-biodeps-1.6-extended.eb | 2 +- ...t-2.0.8-ictce-5.3.0-biodeps-1.6-extended.eb | 2 +- .../t/TopHat/TopHat-2.0.8-ictce-5.3.0.eb | 2 +- .../t/TopHat/TopHat-2.1.0-intel-2015b.eb | 2 +- .../t/TopHat/TopHat-2.1.1-foss-2015b.eb | 2 +- .../t/TopHat/TopHat-2.1.1-foss-2016a.eb | 2 +- .../t/TopHat/TopHat-2.1.1-intel-2017a.eb | 2 +- .../TotalView-8.11.0-0-linux-x86-64.eb | 2 +- .../TotalView-8.11.0-2-linux-x86-64.eb | 2 +- .../TotalView-8.12.0-0-linux-x86-64.eb | 2 +- .../Trimmomatic-0.32-Java-1.7.0_80.eb | 2 +- .../t/Trinity/Trinity-2.0.4-goolf-1.4.10.eb | 2 +- .../t/Trinity/Trinity-2.0.6-goolf-1.4.10.eb | 2 +- .../t/Trinity/Trinity-2.2.0-foss-2016a.eb | 2 +- .../t/tabix/tabix-0.2.6-goolf-1.4.10.eb | 2 +- .../t/tabix/tabix-0.2.6-intel-2014b.eb | 2 +- .../t/tabix/tabix-0.2.6-intel-2016b.eb | 2 +- .../t/tcsh/tcsh-6.18.01-CrayGNU-2015.06.eb | 2 +- .../t/tcsh/tcsh-6.18.01-CrayGNU-2015.11.eb | 2 +- .../t/tcsh/tcsh-6.18.01-CrayIntel-2015.11.eb | 2 +- .../t/tcsh/tcsh-6.18.01-foss-2015a.eb | 2 +- .../t/tcsh/tcsh-6.18.01-goolf-1.4.10.eb | 2 +- .../t/tcsh/tcsh-6.18.01-goolf-1.5.14.eb | 2 +- .../t/tcsh/tcsh-6.18.01-ictce-5.3.0.eb | 2 +- .../t/tcsh/tcsh-6.18.01-intel-2014b.eb | 2 +- .../t/tcsh/tcsh-6.18.01-intel-2015a.eb | 2 +- .../t/tcsh/tcsh-6.19.00-intel-2015a.eb | 2 +- .../t/tcsh/tcsh-6.19.00-intel-2016a.eb | 2 +- .../t/tcsh/tcsh-6.20.00-GCCcore-5.4.0.eb | 2 +- .../u/UDUNITS/UDUNITS-2.1.24-goolf-1.4.10.eb | 2 +- .../u/UDUNITS/UDUNITS-2.1.24-ictce-5.2.0.eb | 2 +- .../u/UDUNITS/UDUNITS-2.1.24-ictce-5.3.0.eb | 2 +- .../u/UDUNITS/UDUNITS-2.1.24-ictce-5.4.0.eb | 2 +- .../u/UDUNITS/UDUNITS-2.1.24-intel-2014b.eb | 2 +- .../u/UDUNITS/UDUNITS-2.2.19-intel-2015a.eb | 2 +- .../u/UDUNITS/UDUNITS-2.2.19-intel-2015b.eb | 2 +- .../u/UDUNITS/UDUNITS-2.2.20-foss-2016a.eb | 2 +- .../u/UDUNITS/UDUNITS-2.2.20-intel-2016b.eb | 2 +- .../u/UDUNITS/UDUNITS-2.2.24-intel-2017a.eb | 2 +- ...VCFtools-0.1.11-goolf-1.4.10-Perl-5.16.3.eb | 2 +- .../VCFtools-0.1.11-ictce-5.5.0-Perl-5.16.3.eb | 2 +- ...VCFtools-0.1.12-goolf-1.4.10-Perl-5.16.3.eb | 2 +- .../VCFtools-0.1.14-foss-2015b-Perl-5.20.3.eb | 2 +- .../VCFtools-0.1.14-foss-2016a-Perl-5.22.1.eb | 2 +- ...VCFtools-0.1.14-goolf-1.4.10-Perl-5.16.3.eb | 2 +- ...VCFtools-0.1.14-goolf-1.7.20-Perl-5.22.2.eb | 2 +- .../VCFtools-0.1.14-intel-2016a-Perl-5.22.1.eb | 2 +- easybuild/easyconfigs/v/VEGAS/VEGAS-0.8.27.eb | 2 +- .../VMD/VMD-1.9.3-intel-2016b-Python-2.7.12.eb | 2 +- .../v/VTK/VTK-5.10.1-goolf-1.4.10.eb | 2 +- .../v/VTK/VTK-5.10.1-ictce-5.3.0.eb | 2 +- .../VTK/VTK-6.3.0-foss-2016b-Python-2.7.12.eb | 2 +- .../VTK/VTK-6.3.0-intel-2015b-Python-2.7.11.eb | 2 +- .../VTK/VTK-6.3.0-intel-2016a-Python-2.7.11.eb | 2 +- .../VTK/VTK-6.3.0-intel-2016b-Python-2.7.12.eb | 2 +- .../VTK/VTK-7.0.0-intel-2016b-Python-2.7.12.eb | 2 +- .../VTK/VTK-7.1.0-intel-2016b-Python-2.7.12.eb | 2 +- .../VTK/VTK-7.1.1-intel-2017a-Python-2.7.13.eb | 2 +- .../v/Valgrind/Valgrind-3.8.1-goolf-1.4.10.eb | 2 +- .../easyconfigs/v/Vampir/Vampir-8.4.1-demo.eb | 2 +- easybuild/easyconfigs/v/Vampir/Vampir-8.4.1.eb | 2 +- .../VampirServer-8.4.1-gompi-2015a.eb | 2 +- .../VampirTrace-5.14.4-goolf-1.5.14.eb | 2 +- .../v/VarScan/VarScan-2.3.6-Java-1.7.0_80.eb | 2 +- .../v/VarScan/VarScan-2.4.1-Java-1.7.0_80.eb | 2 +- .../v/Velvet/Velvet-1.2.07-goolf-1.4.10.eb | 2 +- .../v/Velvet/Velvet-1.2.07-ictce-5.3.0.eb | 2 +- .../v/Velvet/Velvet-1.2.09-goolf-1.4.10.eb | 2 +- .../v/Velvet/Velvet-1.2.09-ictce-5.3.0.eb | 2 +- .../Velvet-1.2.10-goolf-1.4.10-mt-kmer_31.eb | 2 +- .../Velvet-1.2.10-goolf-1.4.10-mt-kmer_57.eb | 2 +- .../Velvet-1.2.10-goolf-1.4.10-mt-kmer_63.eb | 2 +- ...2.10-intel-2015b-mt-kmer_100-Perl-5.20.3.eb | 2 +- .../Velvet-1.2.10-intel-2015b-mt-kmer_100.eb | 2 +- ....2.10-intel-2015b-mt-kmer_31-Perl-5.20.3.eb | 2 +- .../Velvet-1.2.10-intel-2015b-mt-kmer_31.eb | 2 +- .../Velvet-1.2.10-intel-2017a-mt-kmer_37.eb | 2 +- .../ViennaRNA/ViennaRNA-2.0.7-goolf-1.4.10.eb | 2 +- .../v/ViennaRNA/ViennaRNA-2.0.7-ictce-5.3.0.eb | 2 +- .../v/ViennaRNA/ViennaRNA-2.1.6-ictce-5.5.0.eb | 2 +- .../v/ViennaRNA/ViennaRNA-2.2.3-intel-2016b.eb | 2 +- .../v/ViennaRNA/ViennaRNA-2.3.4-foss-2016b.eb | 2 +- .../v/ViennaRNA/ViennaRNA-2.3.5-intel-2017a.eb | 2 +- .../easyconfigs/v/Vim/Vim-7.4-goolf-1.4.10.eb | 2 +- .../v/Vim/Vim-8.0-foss-2016a-Python-2.7.11.eb | 2 +- .../Viper-1.0.0-goolf-1.4.10-Python-2.7.3.eb | 2 +- .../Viper-1.0.0-ictce-5.3.0-Python-2.7.3.eb | 2 +- .../v/vsc-mympirun/vsc-mympirun-3.2.1.eb | 2 +- .../easyconfigs/v/vt/vt-0.577-goolf-1.7.20.eb | 2 +- .../w/WEKA/WEKA-3.6.12-Java-1.7.0_80.eb | 2 +- .../w/WEKA/WEKA-3.7.0-Java-1.7.0_80.eb | 2 +- .../w/WHAM/WHAM-2.0.9-goolf-1.4.10.eb | 2 +- .../w/WHAM/WHAM-2.0.9-ictce-6.2.5.eb | 2 +- ...i2beamer-0.9.5-goolf-1.4.10-Python-2.7.3.eb | 2 +- ...ki2beamer-0.9.5-ictce-5.3.0-Python-2.7.3.eb | 2 +- .../wkhtmltopdf-0.12.3-Linux-x86_64.eb | 2 +- .../wxPropertyGrid-1.4.15-GCC-4.7.3.eb | 2 +- .../wxPropertyGrid-1.4.15-GCC-4.9.2.eb | 2 +- .../x/XZ/XZ-5.2.2_compat-libs.patch | 2 +- .../YAML-Syck-1.27-goolf-1.4.10-Perl-5.16.3.eb | 2 +- .../YAML-Syck-1.27-ictce-5.3.0-Perl-5.16.3.eb | 2 +- .../y/Yasm/Yasm-1.2.0-goolf-1.4.10.eb | 2 +- .../y/Yasm/Yasm-1.2.0-ictce-5.3.0.eb | 2 +- .../y/Yasm/Yasm-1.3.0-foss-2015a.eb | 2 +- .../y/Yasm/Yasm-1.3.0-foss-2016a.eb | 2 +- .../y/Yasm/Yasm-1.3.0-foss-2016b.eb | 2 +- .../y/Yasm/Yasm-1.3.0-foss-2017a.eb | 2 +- .../y/Yasm/Yasm-1.3.0-gimkl-2.11.5.eb | 2 +- .../y/Yasm/Yasm-1.3.0-gimkl-2017a.eb | 2 +- .../y/Yasm/Yasm-1.3.0-intel-2015b.eb | 2 +- .../y/Yasm/Yasm-1.3.0-intel-2016a.eb | 2 +- .../y/Yasm/Yasm-1.3.0-intel-2016b.eb | 2 +- .../y/Yasm/Yasm-1.3.0-intel-2017a.eb | 2 +- .../easyconfigs/z/ZPAQ/ZPAQ-7.00-GCC-4.8.2.eb | 2 +- .../z/zsync/zsync-0.6.2-goolf-1.4.10.eb | 2 +- .../z/zsync/zsync-0.6.2-ictce-5.3.0.eb | 2 +- setup.py | 4 ++-- test/__init__.py | 2 +- test/easyconfigs/easyconfigs.py | 2 +- test/easyconfigs/styletests.py | 2 +- test/easyconfigs/suite.py | 2 +- 1499 files changed, 1515 insertions(+), 1515 deletions(-) diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index fe82903a6c..920072b756 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -5,7 +5,7 @@ We'd love you to contribute back to EasyBuild, and here's how you can do it: the ### Fork easybuild-easyconfigs -First, you'll need to fork [easybuild-easyconfigs on GitHub](http://github.com/hpcugent/easybuild-easyconfigs). +First, you'll need to fork [easybuild-easyconfigs on GitHub](https://github.com/easybuilders/easybuild-easyconfigs). If you do not have a (free) GitHub account yet, you'll need to get one. @@ -25,10 +25,10 @@ Pull the _develop_ branch from the main easybuild-easyconfigs repository: ```bash cd easybuild -git remote add github_hpcugent git@github.com:hpcugent/easybuild-easyconfigs.git +git remote add github_easybuilders git@github.com:easybuilders/easybuild-easyconfigs.git git branch develop git checkout develop -git pull github_hpcugent develop +git pull github_easybuilders develop ``` ### Keep develop up-to-date @@ -39,7 +39,7 @@ Make sure you update it every time you create a feature branch (see below): ```bash git checkout develop -git pull github_hpcugent develop +git pull github_easybuilders develop ``` @@ -49,7 +49,7 @@ git pull github_hpcugent develop ### Pick a branch name Please try and follow these guidelines when picking a branch name: - * use the number of the issue as a prefix for your branch name, e.g. `86_` for issue [#86](https://github.com/hpcugent/easybuild-framework/issues/86) + * use the number of the issue as a prefix for your branch name, e.g. `86_` for issue [#86](https://github.com/easybuilders/easybuild-framework/issues/86) * append a short but descriptive branch name, in which words are joined by underscores, e.g. `86_encoding_scheme` ### Create branch @@ -113,7 +113,7 @@ If you're contributing code to an existing issue you can also convert the issue GITHUBUSER=your_username && PASSWD=your_password && BRANCH=branch_name && ISSUE=issue_number && \ curl --user "$GITHUBUSER:$PASSWD" --request POST \ --data "{\"issue\": \"$ISSUE\", \"head\": \"$GITHUBUSER:$BRANCH\", \"base\": \"develop\"}" \ -https://api.github.com/repos/hpcugent/easybuild-easyconfigs/pulls +https://api.github.com/repos/easybuilders/easybuild-easyconfigs/pulls ``` This is currently only supported by github from the command line and not via the web interface. You might also want to look into [hub](https://github.com/defunkt/hub) for more command line features. diff --git a/README.rst b/README.rst index b6fcf302e9..ff6d26a0ab 100644 --- a/README.rst +++ b/README.rst @@ -1,7 +1,7 @@ -.. image:: http://hpcugent.github.io/easybuild/images/easybuild_logo_small.png +.. image:: http://easybuilders.github.io/easybuild/images/easybuild_logo_small.png :align: center -`EasyBuild `_ is a software build +`EasyBuild `_ is a software build and installation framework that allows you to manage (scientific) software on High Performance Computing (HPC) systems in an efficient way. @@ -15,7 +15,7 @@ The EasyBuild documentation is available at http://easybuild.readthedocs.org/. The easybuild-easyconfigs package is hosted on GitHub, along with an issue tracker for bug reports and feature requests, see -http://github.com/hpcugent/easybuild-easyconfigs. +https://github.com/easybuilders/easybuild-easyconfigs. Related Python packages: @@ -23,23 +23,23 @@ Related Python packages: * the EasyBuild framework, which includes the ``easybuild.framework`` and ``easybuild.tools`` Python packages that provide general support for building and installing software - * GitHub repository: http://github.com/hpcugent/easybuild-framework + * GitHub repository: https://github.com/easybuilders/easybuild-framework * PyPi: https://pypi.python.org/pypi/easybuild-framework * **easybuild-easyblocks** * a collection of easyblocks that implement support for building and installing (groups of) software packages - * GitHub repository: http://github.com/hpcugent/easybuild-easyblocks + * GitHub repository: https://github.com/easybuilders/easybuild-easyblocks * package on PyPi: https://pypi.python.org/pypi/easybuild-easyblocks *Build status overview:* * **master** branch: - .. image:: https://travis-ci.org/hpcugent/easybuild-easyconfigs.svg?branch=master - :target: https://travis-ci.org/hpcugent/easybuild-easyconfigs/branches + .. image:: https://travis-ci.org/easybuilders/easybuild-easyconfigs.svg?branch=master + :target: https://travis-ci.org/easybuilders/easybuild-easyconfigs/branches * **develop** branch: - .. image:: https://travis-ci.org/hpcugent/easybuild-easyconfigs.svg?branch=develop - :target: https://travis-ci.org/hpcugent/easybuild-easyconfigs/branches + .. image:: https://travis-ci.org/easybuilders/easybuild-easyconfigs.svg?branch=develop + :target: https://travis-ci.org/easybuilders/easybuild-easyconfigs/branches diff --git a/RELEASE_NOTES b/RELEASE_NOTES index 31cbc5078b..1dcd904d75 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -749,7 +749,7 @@ feature + bugfix release Xmipp (#1489) - added easyconfigs for new (Cray-specific) toolchains (#1538): CrayGNU, CrayIntel, CrayCCE - initially supported software (using CrayGNU toolchains): CP2K, GROMACS, HPL, Python + numpy/scipy, WRF (#1558) - - see also https://github.com/hpcugent/easybuild/wiki/EasyBuild-on-Cray + - see also https://github.com/easybuilders/easybuild/wiki/EasyBuild-on-Cray - added new easyconfigs for existing toolchains: goolf/1.5.16, intel/2014.06 - added additional easyconfigs for various supported software packages: version updates, different toolchains, ... including GCC v5.1.0, OpenFOAM v2.3.1, R v3.1.3 and v3.2.0, PETSc/SLEPc v3.5.3, WIEN2k v14.1 @@ -789,7 +789,7 @@ feature + bugfix release - various other enhancements, including: - don't define $LDSHARED in zlib easyconfigs (#1350) - this fixes the long-standing "no version information available" issue with zlib - - see also https://github.com/hpcugent/easybuild-framework/issues/108 + - see also https://github.com/easybuilders/easybuild-framework/issues/108 - add unit test to check that all extra_options keys are defined in EasyConfig instance (#1378) - add source MD5 checksums in all GCC easyconfigs (#1391) - speeding up the unit tests by avoiding rereading of same easyconfig file (#1432) @@ -800,7 +800,7 @@ feature + bugfix release - revert version of Libint dependency to 1.1.4 in CP2K v2.5.1 easyconfig (#1144) - added Java dependencies to EMBOSS easyconfigs (#1167) - don't list 'lto' as a language in GCC easyconfigs (#1286) - - related to the fixes in the GCC easyblock, see hpcugent/easybuild-easyblocks#535 + - related to the fixes in the GCC easyblock, see easybuilders/easybuild-easyblocks#535 - rename libint2 easyconfigs as Libint v2 easyconfigs (#1287) - fix mpi4py source_urls in Python easyconfigs (#1306) - consistently use CLooG 0.18.0 for GCC 4.8 series (#1392) diff --git a/easybuild/easyconfigs/TEMPLATE.eb b/easybuild/easyconfigs/TEMPLATE.eb index 69759ec8da..06218cade8 100644 --- a/easybuild/easyconfigs/TEMPLATE.eb +++ b/easybuild/easyconfigs/TEMPLATE.eb @@ -1,5 +1,5 @@ # Note: -# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild # It was auto-generated based on a template easyconfig, so it should be used with care. easyblock = 'ConfigureMake' diff --git a/easybuild/easyconfigs/__archive__/a/ABySS/ABySS-1.3.4-goalf-1.1.0-no-OFED-Python-2.7.3.eb b/easybuild/easyconfigs/__archive__/a/ABySS/ABySS-1.3.4-goalf-1.1.0-no-OFED-Python-2.7.3.eb index c096f680fa..630226b1ef 100644 --- a/easybuild/easyconfigs/__archive__/a/ABySS/ABySS-1.3.4-goalf-1.1.0-no-OFED-Python-2.7.3.eb +++ b/easybuild/easyconfigs/__archive__/a/ABySS/ABySS-1.3.4-goalf-1.1.0-no-OFED-Python-2.7.3.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/a/ABySS/ABySS-1.3.4-ictce-4.0.6-Python-2.7.3.eb b/easybuild/easyconfigs/__archive__/a/ABySS/ABySS-1.3.4-ictce-4.0.6-Python-2.7.3.eb index 935dda4340..0b631d51e0 100644 --- a/easybuild/easyconfigs/__archive__/a/ABySS/ABySS-1.3.4-ictce-4.0.6-Python-2.7.3.eb +++ b/easybuild/easyconfigs/__archive__/a/ABySS/ABySS-1.3.4-ictce-4.0.6-Python-2.7.3.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/a/AMOS/AMOS-3.1.0-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/a/AMOS/AMOS-3.1.0-goalf-1.1.0-no-OFED.eb index 42399e1539..9a991355c4 100644 --- a/easybuild/easyconfigs/__archive__/a/AMOS/AMOS-3.1.0-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/__archive__/a/AMOS/AMOS-3.1.0-goalf-1.1.0-no-OFED.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Cedric Laczny , Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/a/AMOS/AMOS-3.1.0-ictce-4.0.6.eb b/easybuild/easyconfigs/__archive__/a/AMOS/AMOS-3.1.0-ictce-4.0.6.eb index 02a64a2c6f..3e655ad07e 100644 --- a/easybuild/easyconfigs/__archive__/a/AMOS/AMOS-3.1.0-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/__archive__/a/AMOS/AMOS-3.1.0-ictce-4.0.6.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Cedric Laczny , Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/a/Automake/Automake-1.13.4-ictce-4.1.13.eb b/easybuild/easyconfigs/__archive__/a/Automake/Automake-1.13.4-ictce-4.1.13.eb index df3ffc4bcb..07865181a7 100644 --- a/easybuild/easyconfigs/__archive__/a/Automake/Automake-1.13.4-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/__archive__/a/Automake/Automake-1.13.4-ictce-4.1.13.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/a/Automake/Automake-1.14-gcccuda-2.6.10.eb b/easybuild/easyconfigs/__archive__/a/Automake/Automake-1.14-gcccuda-2.6.10.eb index 732b039251..947d1eff62 100644 --- a/easybuild/easyconfigs/__archive__/a/Automake/Automake-1.14-gcccuda-2.6.10.eb +++ b/easybuild/easyconfigs/__archive__/a/Automake/Automake-1.14-gcccuda-2.6.10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/a/a2ps/a2ps-4.14-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/a/a2ps/a2ps-4.14-goalf-1.1.0-no-OFED.eb index 916fcd7e48..ed2242bd75 100644 --- a/easybuild/easyconfigs/__archive__/a/a2ps/a2ps-4.14-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/__archive__/a/a2ps/a2ps-4.14-goalf-1.1.0-no-OFED.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/a/a2ps/a2ps-4.14-ictce-4.0.6.eb b/easybuild/easyconfigs/__archive__/a/a2ps/a2ps-4.14-ictce-4.0.6.eb index 74f9dffca6..1b91de7220 100644 --- a/easybuild/easyconfigs/__archive__/a/a2ps/a2ps-4.14-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/__archive__/a/a2ps/a2ps-4.14-ictce-4.0.6.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/a/aria2/aria2-1.15.1-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/a/aria2/aria2-1.15.1-goalf-1.1.0-no-OFED.eb index 118bf6fc3b..93ba30e57e 100644 --- a/easybuild/easyconfigs/__archive__/a/aria2/aria2-1.15.1-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/__archive__/a/aria2/aria2-1.15.1-goalf-1.1.0-no-OFED.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/a/aria2/aria2-1.15.1-ictce-4.0.6.eb b/easybuild/easyconfigs/__archive__/a/aria2/aria2-1.15.1-ictce-4.0.6.eb index b6ba853506..56e2941ef6 100644 --- a/easybuild/easyconfigs/__archive__/a/aria2/aria2-1.15.1-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/__archive__/a/aria2/aria2-1.15.1-ictce-4.0.6.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/b/BEEF/BEEF-0.1.1-r16-iomkl-4.6.13.eb b/easybuild/easyconfigs/__archive__/b/BEEF/BEEF-0.1.1-r16-iomkl-4.6.13.eb index ea0ea19754..e76944242b 100644 --- a/easybuild/easyconfigs/__archive__/b/BEEF/BEEF-0.1.1-r16-iomkl-4.6.13.eb +++ b/easybuild/easyconfigs/__archive__/b/BEEF/BEEF-0.1.1-r16-iomkl-4.6.13.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Benjamin P. Roberts # New Zealand eScience Infrastructure # The University of Auckland, Auckland, New Zealand diff --git a/easybuild/easyconfigs/__archive__/b/BFAST/BFAST-0.7.0a-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/b/BFAST/BFAST-0.7.0a-goalf-1.1.0-no-OFED.eb index a3b2575da6..1c4e2656e2 100644 --- a/easybuild/easyconfigs/__archive__/b/BFAST/BFAST-0.7.0a-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/__archive__/b/BFAST/BFAST-0.7.0a-goalf-1.1.0-no-OFED.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/b/BFAST/BFAST-0.7.0a-ictce-4.0.6.eb b/easybuild/easyconfigs/__archive__/b/BFAST/BFAST-0.7.0a-ictce-4.0.6.eb index 06a9cd2e7e..ec20c6b63d 100644 --- a/easybuild/easyconfigs/__archive__/b/BFAST/BFAST-0.7.0a-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/__archive__/b/BFAST/BFAST-0.7.0a-ictce-4.0.6.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/b/BLAST+/BLAST+-2.2.27-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/b/BLAST+/BLAST+-2.2.27-goalf-1.1.0-no-OFED.eb index 3d76340994..3e1f898b70 100644 --- a/easybuild/easyconfigs/__archive__/b/BLAST+/BLAST+-2.2.27-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/__archive__/b/BLAST+/BLAST+-2.2.27-goalf-1.1.0-no-OFED.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/b/BLAST+/BLAST+-2.2.27-ictce-4.0.6.eb b/easybuild/easyconfigs/__archive__/b/BLAST+/BLAST+-2.2.27-ictce-4.0.6.eb index 5d3bf84644..04156efea5 100644 --- a/easybuild/easyconfigs/__archive__/b/BLAST+/BLAST+-2.2.27-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/__archive__/b/BLAST+/BLAST+-2.2.27-ictce-4.0.6.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/b/BLAST+/BLAST+-2.2.28-ictce-4.1.13.eb b/easybuild/easyconfigs/__archive__/b/BLAST+/BLAST+-2.2.28-ictce-4.1.13.eb index 9a1f3c0269..fe0372bd55 100644 --- a/easybuild/easyconfigs/__archive__/b/BLAST+/BLAST+-2.2.28-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/__archive__/b/BLAST+/BLAST+-2.2.28-ictce-4.1.13.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos , Kenneth Hoste (UGent) diff --git a/easybuild/easyconfigs/__archive__/b/BWA/BWA-0.6.2-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/b/BWA/BWA-0.6.2-goalf-1.1.0-no-OFED.eb index 5bb0458964..9e6c729189 100644 --- a/easybuild/easyconfigs/__archive__/b/BWA/BWA-0.6.2-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/__archive__/b/BWA/BWA-0.6.2-goalf-1.1.0-no-OFED.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Cedric Laczny , Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/b/BWA/BWA-0.6.2-ictce-4.0.6.eb b/easybuild/easyconfigs/__archive__/b/BWA/BWA-0.6.2-ictce-4.0.6.eb index 9ff15e2434..e6c61cba4a 100644 --- a/easybuild/easyconfigs/__archive__/b/BWA/BWA-0.6.2-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/__archive__/b/BWA/BWA-0.6.2-ictce-4.0.6.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Cedric Laczny , Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/b/BWA/BWA-0.7.4-ictce-4.1.13.eb b/easybuild/easyconfigs/__archive__/b/BWA/BWA-0.7.4-ictce-4.1.13.eb index 000b5950bd..500bfbfd84 100644 --- a/easybuild/easyconfigs/__archive__/b/BWA/BWA-0.7.4-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/__archive__/b/BWA/BWA-0.7.4-ictce-4.1.13.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Cyprus Institute / CaSToRC, Uni.Lu/LCSB, NTUA # Authors:: George Tsouloupas , Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/b/BamTools/BamTools-2.2.3-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/b/BamTools/BamTools-2.2.3-goalf-1.1.0-no-OFED.eb index 7d0f3c7ae3..cea77237c3 100644 --- a/easybuild/easyconfigs/__archive__/b/BamTools/BamTools-2.2.3-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/__archive__/b/BamTools/BamTools-2.2.3-goalf-1.1.0-no-OFED.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2013 The Cyprus Institute # Authors:: Andreas Panteli , George Tsouloupas diff --git a/easybuild/easyconfigs/__archive__/b/Bash/Bash-4.2-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/b/Bash/Bash-4.2-goalf-1.1.0-no-OFED.eb index 57dbb97a1a..104c33d233 100644 --- a/easybuild/easyconfigs/__archive__/b/Bash/Bash-4.2-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/__archive__/b/Bash/Bash-4.2-goalf-1.1.0-no-OFED.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2013 University of Luxembourg/Computer Science and Communications Research Unit # Authors:: Valentin Plugaru diff --git a/easybuild/easyconfigs/__archive__/b/Bonnie++/Bonnie++-1.03e-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/b/Bonnie++/Bonnie++-1.03e-goalf-1.1.0-no-OFED.eb index 8bcb1abedd..cd15f91b8a 100644 --- a/easybuild/easyconfigs/__archive__/b/Bonnie++/Bonnie++-1.03e-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/__archive__/b/Bonnie++/Bonnie++-1.03e-goalf-1.1.0-no-OFED.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/b/Bonnie++/Bonnie++-1.03e-ictce-4.0.6.eb b/easybuild/easyconfigs/__archive__/b/Bonnie++/Bonnie++-1.03e-ictce-4.0.6.eb index f4e01e36bd..df3e2919cb 100644 --- a/easybuild/easyconfigs/__archive__/b/Bonnie++/Bonnie++-1.03e-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/__archive__/b/Bonnie++/Bonnie++-1.03e-ictce-4.0.6.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/b/Bowtie2/Bowtie2-2.0.2-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/b/Bowtie2/Bowtie2-2.0.2-goalf-1.1.0-no-OFED.eb index 99061a9473..c7d6d38625 100644 --- a/easybuild/easyconfigs/__archive__/b/Bowtie2/Bowtie2-2.0.2-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/__archive__/b/Bowtie2/Bowtie2-2.0.2-goalf-1.1.0-no-OFED.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Cedric Laczny , Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/b/Bowtie2/Bowtie2-2.0.2-ictce-4.0.6.eb b/easybuild/easyconfigs/__archive__/b/Bowtie2/Bowtie2-2.0.2-ictce-4.0.6.eb index 15a2db61d2..30756c2e9e 100644 --- a/easybuild/easyconfigs/__archive__/b/Bowtie2/Bowtie2-2.0.2-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/__archive__/b/Bowtie2/Bowtie2-2.0.2-ictce-4.0.6.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Cedric Laczny , Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/b/bbFTP/bbFTP-3.2.0-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/b/bbFTP/bbFTP-3.2.0-goalf-1.1.0-no-OFED.eb index e14fa5b01a..6cca8c54a5 100644 --- a/easybuild/easyconfigs/__archive__/b/bbFTP/bbFTP-3.2.0-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/__archive__/b/bbFTP/bbFTP-3.2.0-goalf-1.1.0-no-OFED.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/b/bbftpPRO/bbftpPRO-9.3.1-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/b/bbftpPRO/bbftpPRO-9.3.1-goalf-1.1.0-no-OFED.eb index eae65e841f..48b977fff3 100644 --- a/easybuild/easyconfigs/__archive__/b/bbftpPRO/bbftpPRO-9.3.1-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/__archive__/b/bbftpPRO/bbftpPRO-9.3.1-goalf-1.1.0-no-OFED.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/b/binutils/binutils-2.22-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/b/binutils/binutils-2.22-goalf-1.1.0-no-OFED.eb index af12b0472e..9c5bb1d47d 100644 --- a/easybuild/easyconfigs/__archive__/b/binutils/binutils-2.22-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/__archive__/b/binutils/binutils-2.22-goalf-1.1.0-no-OFED.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/b/binutils/binutils-2.22-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/__archive__/b/binutils/binutils-2.22-gompi-1.4.12-no-OFED.eb index 8035182b62..1b73cc3ce3 100644 --- a/easybuild/easyconfigs/__archive__/b/binutils/binutils-2.22-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/__archive__/b/binutils/binutils-2.22-gompi-1.4.12-no-OFED.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/c/Chapel/Chapel-1.6.0-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/c/Chapel/Chapel-1.6.0-goalf-1.1.0-no-OFED.eb index 8def4493c5..a151dccdce 100644 --- a/easybuild/easyconfigs/__archive__/c/Chapel/Chapel-1.6.0-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/__archive__/c/Chapel/Chapel-1.6.0-goalf-1.1.0-no-OFED.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/c/ClustalW2/ClustalW2-2.1-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/c/ClustalW2/ClustalW2-2.1-goalf-1.1.0-no-OFED.eb index 0649ad44a0..802e525ec8 100644 --- a/easybuild/easyconfigs/__archive__/c/ClustalW2/ClustalW2-2.1-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/__archive__/c/ClustalW2/ClustalW2-2.1-goalf-1.1.0-no-OFED.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Cedric Laczny , Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/c/ClustalW2/ClustalW2-2.1-ictce-4.0.6.eb b/easybuild/easyconfigs/__archive__/c/ClustalW2/ClustalW2-2.1-ictce-4.0.6.eb index cad6e2ddab..740b066bb4 100644 --- a/easybuild/easyconfigs/__archive__/c/ClustalW2/ClustalW2-2.1-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/__archive__/c/ClustalW2/ClustalW2-2.1-ictce-4.0.6.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Cedric Laczny , Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/c/Corkscrew/Corkscrew-2.0-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/c/Corkscrew/Corkscrew-2.0-goalf-1.1.0-no-OFED.eb index a41c761aaf..743a5cbdf2 100644 --- a/easybuild/easyconfigs/__archive__/c/Corkscrew/Corkscrew-2.0-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/__archive__/c/Corkscrew/Corkscrew-2.0-goalf-1.1.0-no-OFED.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/c/Corkscrew/Corkscrew-2.0-ictce-4.0.6.eb b/easybuild/easyconfigs/__archive__/c/Corkscrew/Corkscrew-2.0-ictce-4.0.6.eb index ebeb826b66..0d9f914641 100644 --- a/easybuild/easyconfigs/__archive__/c/Corkscrew/Corkscrew-2.0-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/__archive__/c/Corkscrew/Corkscrew-2.0-ictce-4.0.6.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/c/Cube/Cube-3.4.3-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/__archive__/c/Cube/Cube-3.4.3-gompi-1.4.12-no-OFED.eb index 94eaf15f8d..619d4f0b69 100644 --- a/easybuild/easyconfigs/__archive__/c/Cube/Cube-3.4.3-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/__archive__/c/Cube/Cube-3.4.3-gompi-1.4.12-no-OFED.eb @@ -1,5 +1,5 @@ ## -# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2013-2015 Juelich Supercomputing Centre, Germany # Authors:: Bernd Mohr diff --git a/easybuild/easyconfigs/__archive__/c/Cube/Cube-4.2-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/__archive__/c/Cube/Cube-4.2-gompi-1.4.12-no-OFED.eb index df627c9d7b..dbfd632ffa 100644 --- a/easybuild/easyconfigs/__archive__/c/Cube/Cube-4.2-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/__archive__/c/Cube/Cube-4.2-gompi-1.4.12-no-OFED.eb @@ -1,5 +1,5 @@ ## -# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2013-2015 Juelich Supercomputing Centre, Germany # Authors:: Bernd Mohr diff --git a/easybuild/easyconfigs/__archive__/c/Cube/Cube-4.3-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/__archive__/c/Cube/Cube-4.3-gompi-1.4.12-no-OFED.eb index ced2f5b555..6998de4138 100644 --- a/easybuild/easyconfigs/__archive__/c/Cube/Cube-4.3-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/__archive__/c/Cube/Cube-4.3-gompi-1.4.12-no-OFED.eb @@ -1,5 +1,5 @@ ## -# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2013-2015 Juelich Supercomputing Centre, Germany # Authors:: Bernd Mohr diff --git a/easybuild/easyconfigs/__archive__/c/Cufflinks/Cufflinks-2.0.2-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/c/Cufflinks/Cufflinks-2.0.2-goalf-1.1.0-no-OFED.eb index 2ef873d2da..c6c9980db5 100644 --- a/easybuild/easyconfigs/__archive__/c/Cufflinks/Cufflinks-2.0.2-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/__archive__/c/Cufflinks/Cufflinks-2.0.2-goalf-1.1.0-no-OFED.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Cedric Laczny , Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/c/ccache/ccache-3.1.9-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/c/ccache/ccache-3.1.9-goalf-1.1.0-no-OFED.eb index bbabdb92a5..501b2e5aee 100644 --- a/easybuild/easyconfigs/__archive__/c/ccache/ccache-3.1.9-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/__archive__/c/ccache/ccache-3.1.9-goalf-1.1.0-no-OFED.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/c/ccache/ccache-3.1.9-ictce-4.0.6.eb b/easybuild/easyconfigs/__archive__/c/ccache/ccache-3.1.9-ictce-4.0.6.eb index 3011b90d17..801de9dbad 100644 --- a/easybuild/easyconfigs/__archive__/c/ccache/ccache-3.1.9-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/__archive__/c/ccache/ccache-3.1.9-ictce-4.0.6.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/c/cflow/cflow-1.4-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/c/cflow/cflow-1.4-goalf-1.1.0-no-OFED.eb index 98800f3677..ae2a54ac33 100644 --- a/easybuild/easyconfigs/__archive__/c/cflow/cflow-1.4-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/__archive__/c/cflow/cflow-1.4-goalf-1.1.0-no-OFED.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/c/cflow/cflow-1.4-ictce-4.0.6.eb b/easybuild/easyconfigs/__archive__/c/cflow/cflow-1.4-ictce-4.0.6.eb index a3e495b0c6..b26666270b 100644 --- a/easybuild/easyconfigs/__archive__/c/cflow/cflow-1.4-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/__archive__/c/cflow/cflow-1.4-ictce-4.0.6.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/c/cgdb/cgdb-0.6.5-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/c/cgdb/cgdb-0.6.5-goalf-1.1.0-no-OFED.eb index 2112acc096..10dd43c52c 100644 --- a/easybuild/easyconfigs/__archive__/c/cgdb/cgdb-0.6.5-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/__archive__/c/cgdb/cgdb-0.6.5-goalf-1.1.0-no-OFED.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/c/cgdb/cgdb-0.6.5-ictce-4.0.6.eb b/easybuild/easyconfigs/__archive__/c/cgdb/cgdb-0.6.5-ictce-4.0.6.eb index 3cff32f247..e8c4aaf751 100644 --- a/easybuild/easyconfigs/__archive__/c/cgdb/cgdb-0.6.5-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/__archive__/c/cgdb/cgdb-0.6.5-ictce-4.0.6.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/e/ELinks/ELinks-0.12pre5-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/e/ELinks/ELinks-0.12pre5-goalf-1.1.0-no-OFED.eb index 6e775a095b..8bc52abe18 100644 --- a/easybuild/easyconfigs/__archive__/e/ELinks/ELinks-0.12pre5-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/__archive__/e/ELinks/ELinks-0.12pre5-goalf-1.1.0-no-OFED.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/e/ELinks/ELinks-0.12pre5-ictce-4.0.6.eb b/easybuild/easyconfigs/__archive__/e/ELinks/ELinks-0.12pre5-ictce-4.0.6.eb index 413650f9a5..c712b873ca 100644 --- a/easybuild/easyconfigs/__archive__/e/ELinks/ELinks-0.12pre5-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/__archive__/e/ELinks/ELinks-0.12pre5-ictce-4.0.6.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/e/ESPResSo/ESPResSo-3.1.1-goalf-1.1.0-no-OFED-parallel.eb b/easybuild/easyconfigs/__archive__/e/ESPResSo/ESPResSo-3.1.1-goalf-1.1.0-no-OFED-parallel.eb index 5ef397df32..e5a7971a87 100644 --- a/easybuild/easyconfigs/__archive__/e/ESPResSo/ESPResSo-3.1.1-goalf-1.1.0-no-OFED-parallel.eb +++ b/easybuild/easyconfigs/__archive__/e/ESPResSo/ESPResSo-3.1.1-goalf-1.1.0-no-OFED-parallel.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Josh Berryman , Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/e/ESPResSo/ESPResSo-3.1.1-goalf-1.1.0-no-OFED-serial.eb b/easybuild/easyconfigs/__archive__/e/ESPResSo/ESPResSo-3.1.1-goalf-1.1.0-no-OFED-serial.eb index dc0eba6edb..b7c119348c 100644 --- a/easybuild/easyconfigs/__archive__/e/ESPResSo/ESPResSo-3.1.1-goalf-1.1.0-no-OFED-serial.eb +++ b/easybuild/easyconfigs/__archive__/e/ESPResSo/ESPResSo-3.1.1-goalf-1.1.0-no-OFED-serial.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Josh Berryman , Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/e/ESPResSo/ESPResSo-3.1.1-ictce-4.0.6-parallel.eb b/easybuild/easyconfigs/__archive__/e/ESPResSo/ESPResSo-3.1.1-ictce-4.0.6-parallel.eb index 5b960cc12d..89786fb93c 100644 --- a/easybuild/easyconfigs/__archive__/e/ESPResSo/ESPResSo-3.1.1-ictce-4.0.6-parallel.eb +++ b/easybuild/easyconfigs/__archive__/e/ESPResSo/ESPResSo-3.1.1-ictce-4.0.6-parallel.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Josh Berryman , Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/e/ESPResSo/ESPResSo-3.1.1-ictce-4.0.6-serial.eb b/easybuild/easyconfigs/__archive__/e/ESPResSo/ESPResSo-3.1.1-ictce-4.0.6-serial.eb index 21dd493eb1..6b6b2358f8 100644 --- a/easybuild/easyconfigs/__archive__/e/ESPResSo/ESPResSo-3.1.1-ictce-4.0.6-serial.eb +++ b/easybuild/easyconfigs/__archive__/e/ESPResSo/ESPResSo-3.1.1-ictce-4.0.6-serial.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Josh Berryman , Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/e/Eigen/Eigen-3.1.1-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/e/Eigen/Eigen-3.1.1-goalf-1.1.0-no-OFED.eb index 3cc61b8643..37f1ee9f61 100644 --- a/easybuild/easyconfigs/__archive__/e/Eigen/Eigen-3.1.1-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/__archive__/e/Eigen/Eigen-3.1.1-goalf-1.1.0-no-OFED.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Cedric Laczny , Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/e/Eigen/Eigen-3.1.1-ictce-4.0.6.eb b/easybuild/easyconfigs/__archive__/e/Eigen/Eigen-3.1.1-ictce-4.0.6.eb index ad92c7352d..77d246ec69 100644 --- a/easybuild/easyconfigs/__archive__/e/Eigen/Eigen-3.1.1-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/__archive__/e/Eigen/Eigen-3.1.1-ictce-4.0.6.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Cedric Laczny , Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/e/Eigen/Eigen-3.1.4-goalf-1.5.12-no-OFED.eb b/easybuild/easyconfigs/__archive__/e/Eigen/Eigen-3.1.4-goalf-1.5.12-no-OFED.eb index 0db2cb2232..61116f3e1b 100644 --- a/easybuild/easyconfigs/__archive__/e/Eigen/Eigen-3.1.4-goalf-1.5.12-no-OFED.eb +++ b/easybuild/easyconfigs/__archive__/e/Eigen/Eigen-3.1.4-goalf-1.5.12-no-OFED.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Cedric Laczny , Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/e/Eigen/Eigen-3.1.4-ictce-4.1.13.eb b/easybuild/easyconfigs/__archive__/e/Eigen/Eigen-3.1.4-ictce-4.1.13.eb index 8868b07c82..81a4069801 100644 --- a/easybuild/easyconfigs/__archive__/e/Eigen/Eigen-3.1.4-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/__archive__/e/Eigen/Eigen-3.1.4-ictce-4.1.13.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Cedric Laczny , Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/e/Extrae/Extrae-2.4.1-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/__archive__/e/Extrae/Extrae-2.4.1-gompi-1.4.12-no-OFED.eb index b3d4b5ae5a..1a891e9ce7 100644 --- a/easybuild/easyconfigs/__archive__/e/Extrae/Extrae-2.4.1-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/__archive__/e/Extrae/Extrae-2.4.1-gompi-1.4.12-no-OFED.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild # Copyright:: Copyright 2013 Juelich Supercomputing Centre, Germany # Authors:: Bernd Mohr # License:: New BSD diff --git a/easybuild/easyconfigs/__archive__/f/FASTX-Toolkit/FASTX-Toolkit-0.0.13.2-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/f/FASTX-Toolkit/FASTX-Toolkit-0.0.13.2-goalf-1.1.0-no-OFED.eb index 4bda1588f1..f2354a3ca7 100644 --- a/easybuild/easyconfigs/__archive__/f/FASTX-Toolkit/FASTX-Toolkit-0.0.13.2-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/__archive__/f/FASTX-Toolkit/FASTX-Toolkit-0.0.13.2-goalf-1.1.0-no-OFED.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Cedric Laczny , Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/f/FASTX-Toolkit/FASTX-Toolkit-0.0.13.2-ictce-4.0.6.eb b/easybuild/easyconfigs/__archive__/f/FASTX-Toolkit/FASTX-Toolkit-0.0.13.2-ictce-4.0.6.eb index b9a9acd1bf..cb71a068e5 100644 --- a/easybuild/easyconfigs/__archive__/f/FASTX-Toolkit/FASTX-Toolkit-0.0.13.2-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/__archive__/f/FASTX-Toolkit/FASTX-Toolkit-0.0.13.2-ictce-4.0.6.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Cedric Laczny , Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/g/GDB/GDB-7.5.1-cgmpolf-1.1.6.eb b/easybuild/easyconfigs/__archive__/g/GDB/GDB-7.5.1-cgmpolf-1.1.6.eb index 2278befdce..e8870f1aa5 100644 --- a/easybuild/easyconfigs/__archive__/g/GDB/GDB-7.5.1-cgmpolf-1.1.6.eb +++ b/easybuild/easyconfigs/__archive__/g/GDB/GDB-7.5.1-cgmpolf-1.1.6.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/g/GDB/GDB-7.5.1-cgmvolf-1.1.12rc1.eb b/easybuild/easyconfigs/__archive__/g/GDB/GDB-7.5.1-cgmvolf-1.1.12rc1.eb index 7e35ed60fd..a54cdbf4ed 100644 --- a/easybuild/easyconfigs/__archive__/g/GDB/GDB-7.5.1-cgmvolf-1.1.12rc1.eb +++ b/easybuild/easyconfigs/__archive__/g/GDB/GDB-7.5.1-cgmvolf-1.1.12rc1.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/g/GDB/GDB-7.5.1-cgmvolf-1.2.7.eb b/easybuild/easyconfigs/__archive__/g/GDB/GDB-7.5.1-cgmvolf-1.2.7.eb index 5c2723f3cc..ef6bba63f9 100644 --- a/easybuild/easyconfigs/__archive__/g/GDB/GDB-7.5.1-cgmvolf-1.2.7.eb +++ b/easybuild/easyconfigs/__archive__/g/GDB/GDB-7.5.1-cgmvolf-1.2.7.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/g/GDB/GDB-7.5.1-cgoolf-1.1.7.eb b/easybuild/easyconfigs/__archive__/g/GDB/GDB-7.5.1-cgoolf-1.1.7.eb index a55ddb3780..4b7bc2353a 100644 --- a/easybuild/easyconfigs/__archive__/g/GDB/GDB-7.5.1-cgoolf-1.1.7.eb +++ b/easybuild/easyconfigs/__archive__/g/GDB/GDB-7.5.1-cgoolf-1.1.7.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/g/GDB/GDB-7.5.1-gmvolf-1.7.12.eb b/easybuild/easyconfigs/__archive__/g/GDB/GDB-7.5.1-gmvolf-1.7.12.eb index 5cb326d9c8..b4a874e646 100644 --- a/easybuild/easyconfigs/__archive__/g/GDB/GDB-7.5.1-gmvolf-1.7.12.eb +++ b/easybuild/easyconfigs/__archive__/g/GDB/GDB-7.5.1-gmvolf-1.7.12.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild recipy as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild recipy as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/g/GDB/GDB-7.5.1-gmvolf-1.7.12rc1.eb b/easybuild/easyconfigs/__archive__/g/GDB/GDB-7.5.1-gmvolf-1.7.12rc1.eb index 9a83935f73..6732b1f516 100644 --- a/easybuild/easyconfigs/__archive__/g/GDB/GDB-7.5.1-gmvolf-1.7.12rc1.eb +++ b/easybuild/easyconfigs/__archive__/g/GDB/GDB-7.5.1-gmvolf-1.7.12rc1.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild recipy as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild recipy as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/g/GDB/GDB-7.5.1-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/g/GDB/GDB-7.5.1-goalf-1.1.0-no-OFED.eb index e69629310c..5e909d69c1 100644 --- a/easybuild/easyconfigs/__archive__/g/GDB/GDB-7.5.1-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/__archive__/g/GDB/GDB-7.5.1-goalf-1.1.0-no-OFED.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/g/GROMACS/GROMACS-4.6.1-goolfc-1.3.12-hybrid.eb b/easybuild/easyconfigs/__archive__/g/GROMACS/GROMACS-4.6.1-goolfc-1.3.12-hybrid.eb index 10de39383d..c93754ab31 100644 --- a/easybuild/easyconfigs/__archive__/g/GROMACS/GROMACS-4.6.1-goolfc-1.3.12-hybrid.eb +++ b/easybuild/easyconfigs/__archive__/g/GROMACS/GROMACS-4.6.1-goolfc-1.3.12-hybrid.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA, Cyprus Institute / CaSToRC, Ghent University # Authors:: Wiktor Jurkowski , Fotis Georgatos , \ diff --git a/easybuild/easyconfigs/__archive__/g/GROMACS/GROMACS-4.6.1-goolfc-1.3.12-mt.eb b/easybuild/easyconfigs/__archive__/g/GROMACS/GROMACS-4.6.1-goolfc-1.3.12-mt.eb index 7d4a515bd7..01e29400b7 100644 --- a/easybuild/easyconfigs/__archive__/g/GROMACS/GROMACS-4.6.1-goolfc-1.3.12-mt.eb +++ b/easybuild/easyconfigs/__archive__/g/GROMACS/GROMACS-4.6.1-goolfc-1.3.12-mt.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA, Cyprus Institute / CaSToRC, Ghent University # Authors:: Wiktor Jurkowski , Fotis Georgatos , \ diff --git a/easybuild/easyconfigs/__archive__/g/GROMACS/GROMACS-4.6.5-gmpolf-1.4.8-hybrid.eb b/easybuild/easyconfigs/__archive__/g/GROMACS/GROMACS-4.6.5-gmpolf-1.4.8-hybrid.eb index c6a01d5cb9..b62bee2ccc 100644 --- a/easybuild/easyconfigs/__archive__/g/GROMACS/GROMACS-4.6.5-gmpolf-1.4.8-hybrid.eb +++ b/easybuild/easyconfigs/__archive__/g/GROMACS/GROMACS-4.6.5-gmpolf-1.4.8-hybrid.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA, Cyprus Institute / CaSToRC, Ghent University # Authors:: Wiktor Jurkowski , Fotis Georgatos , \ diff --git a/easybuild/easyconfigs/__archive__/g/GROMACS/GROMACS-4.6.5-gmpolf-1.4.8-mt.eb b/easybuild/easyconfigs/__archive__/g/GROMACS/GROMACS-4.6.5-gmpolf-1.4.8-mt.eb index f47fc727b1..9ad41b86cd 100644 --- a/easybuild/easyconfigs/__archive__/g/GROMACS/GROMACS-4.6.5-gmpolf-1.4.8-mt.eb +++ b/easybuild/easyconfigs/__archive__/g/GROMACS/GROMACS-4.6.5-gmpolf-1.4.8-mt.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA, Cyprus Institute / CaSToRC, Ghent University # Authors:: Wiktor Jurkowski , Fotis Georgatos , \ diff --git a/easybuild/easyconfigs/__archive__/g/GROMACS/GROMACS-4.6.5-gmvolf-1.7.12-hybrid.eb b/easybuild/easyconfigs/__archive__/g/GROMACS/GROMACS-4.6.5-gmvolf-1.7.12-hybrid.eb index c1dc7fabd0..6cff17d466 100644 --- a/easybuild/easyconfigs/__archive__/g/GROMACS/GROMACS-4.6.5-gmvolf-1.7.12-hybrid.eb +++ b/easybuild/easyconfigs/__archive__/g/GROMACS/GROMACS-4.6.5-gmvolf-1.7.12-hybrid.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA, Cyprus Institute / CaSToRC, Ghent University # Authors:: Wiktor Jurkowski , Fotis Georgatos , \ diff --git a/easybuild/easyconfigs/__archive__/g/GROMACS/GROMACS-4.6.5-gmvolf-1.7.12-mt.eb b/easybuild/easyconfigs/__archive__/g/GROMACS/GROMACS-4.6.5-gmvolf-1.7.12-mt.eb index aa2709aff9..8a0d1877e1 100644 --- a/easybuild/easyconfigs/__archive__/g/GROMACS/GROMACS-4.6.5-gmvolf-1.7.12-mt.eb +++ b/easybuild/easyconfigs/__archive__/g/GROMACS/GROMACS-4.6.5-gmvolf-1.7.12-mt.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA, Cyprus Institute / CaSToRC, Ghent University # Authors:: Wiktor Jurkowski , Fotis Georgatos , \ diff --git a/easybuild/easyconfigs/__archive__/g/GROMACS/GROMACS-4.6.5-goalf-1.1.0-no-OFED-hybrid.eb b/easybuild/easyconfigs/__archive__/g/GROMACS/GROMACS-4.6.5-goalf-1.1.0-no-OFED-hybrid.eb index 6a5829cb21..8ea94fe3e3 100644 --- a/easybuild/easyconfigs/__archive__/g/GROMACS/GROMACS-4.6.5-goalf-1.1.0-no-OFED-hybrid.eb +++ b/easybuild/easyconfigs/__archive__/g/GROMACS/GROMACS-4.6.5-goalf-1.1.0-no-OFED-hybrid.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA, Cyprus Institute / CaSToRC, Ghent University # Authors:: Wiktor Jurkowski , Fotis Georgatos , \ diff --git a/easybuild/easyconfigs/__archive__/g/GROMACS/GROMACS-4.6.5-goalf-1.1.0-no-OFED-mt.eb b/easybuild/easyconfigs/__archive__/g/GROMACS/GROMACS-4.6.5-goalf-1.1.0-no-OFED-mt.eb index 897f8573da..5d65ed4da5 100644 --- a/easybuild/easyconfigs/__archive__/g/GROMACS/GROMACS-4.6.5-goalf-1.1.0-no-OFED-mt.eb +++ b/easybuild/easyconfigs/__archive__/g/GROMACS/GROMACS-4.6.5-goalf-1.1.0-no-OFED-mt.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA, Cyprus Institute / CaSToRC, Ghent University # Authors:: Wiktor Jurkowski , Fotis Georgatos , \ diff --git a/easybuild/easyconfigs/__archive__/g/GROMACS/GROMACS-4.6.5-goolfc-2.6.10-hybrid.eb b/easybuild/easyconfigs/__archive__/g/GROMACS/GROMACS-4.6.5-goolfc-2.6.10-hybrid.eb index 1de33cf464..88e2d9aa12 100644 --- a/easybuild/easyconfigs/__archive__/g/GROMACS/GROMACS-4.6.5-goolfc-2.6.10-hybrid.eb +++ b/easybuild/easyconfigs/__archive__/g/GROMACS/GROMACS-4.6.5-goolfc-2.6.10-hybrid.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA, Cyprus Institute / CaSToRC, Ghent University # Authors:: Wiktor Jurkowski , Fotis Georgatos , \ diff --git a/easybuild/easyconfigs/__archive__/g/GROMACS/GROMACS-4.6.5-goolfc-2.6.10-mt.eb b/easybuild/easyconfigs/__archive__/g/GROMACS/GROMACS-4.6.5-goolfc-2.6.10-mt.eb index 367a63d0a3..b7e5aa7eff 100644 --- a/easybuild/easyconfigs/__archive__/g/GROMACS/GROMACS-4.6.5-goolfc-2.6.10-mt.eb +++ b/easybuild/easyconfigs/__archive__/g/GROMACS/GROMACS-4.6.5-goolfc-2.6.10-mt.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA, Cyprus Institute / CaSToRC, Ghent University # Authors:: Wiktor Jurkowski , Fotis Georgatos , \ diff --git a/easybuild/easyconfigs/__archive__/g/GTI/GTI-1.2.0-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/__archive__/g/GTI/GTI-1.2.0-gompi-1.4.12-no-OFED.eb index 3d384db2d6..926c752629 100644 --- a/easybuild/easyconfigs/__archive__/g/GTI/GTI-1.2.0-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/__archive__/g/GTI/GTI-1.2.0-gompi-1.4.12-no-OFED.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild # Copyright:: Copyright 2013 Juelich Supercomputing Centre, Germany # Authors:: Bernd Mohr # License:: New BSD diff --git a/easybuild/easyconfigs/__archive__/g/git/git-1.7.12-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/g/git/git-1.7.12-goalf-1.1.0-no-OFED.eb index 6e6602e1ac..e5256d2d34 100644 --- a/easybuild/easyconfigs/__archive__/g/git/git-1.7.12-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/__archive__/g/git/git-1.7.12-goalf-1.1.0-no-OFED.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/g/git/git-1.7.12-ictce-4.0.6.eb b/easybuild/easyconfigs/__archive__/g/git/git-1.7.12-ictce-4.0.6.eb index 08b113a1e9..2fbf7d9d74 100644 --- a/easybuild/easyconfigs/__archive__/g/git/git-1.7.12-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/__archive__/g/git/git-1.7.12-ictce-4.0.6.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/g/git/git-1.8.2-cgmpolf-1.1.6.eb b/easybuild/easyconfigs/__archive__/g/git/git-1.8.2-cgmpolf-1.1.6.eb index 6a6c3a3ab6..ccc2af2068 100644 --- a/easybuild/easyconfigs/__archive__/g/git/git-1.8.2-cgmpolf-1.1.6.eb +++ b/easybuild/easyconfigs/__archive__/g/git/git-1.8.2-cgmpolf-1.1.6.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/g/git/git-1.8.2-cgmvolf-1.1.12rc1.eb b/easybuild/easyconfigs/__archive__/g/git/git-1.8.2-cgmvolf-1.1.12rc1.eb index 031cdf8a76..5b33fd1e3d 100644 --- a/easybuild/easyconfigs/__archive__/g/git/git-1.8.2-cgmvolf-1.1.12rc1.eb +++ b/easybuild/easyconfigs/__archive__/g/git/git-1.8.2-cgmvolf-1.1.12rc1.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/g/git/git-1.8.2-cgmvolf-1.2.7.eb b/easybuild/easyconfigs/__archive__/g/git/git-1.8.2-cgmvolf-1.2.7.eb index 0400716225..9a65ddf609 100644 --- a/easybuild/easyconfigs/__archive__/g/git/git-1.8.2-cgmvolf-1.2.7.eb +++ b/easybuild/easyconfigs/__archive__/g/git/git-1.8.2-cgmvolf-1.2.7.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/g/git/git-1.8.2-cgoolf-1.1.7.eb b/easybuild/easyconfigs/__archive__/g/git/git-1.8.2-cgoolf-1.1.7.eb index f5e0842b35..dd164a4f2a 100644 --- a/easybuild/easyconfigs/__archive__/g/git/git-1.8.2-cgoolf-1.1.7.eb +++ b/easybuild/easyconfigs/__archive__/g/git/git-1.8.2-cgoolf-1.1.7.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/g/git/git-1.8.2-gmvolf-1.7.12.eb b/easybuild/easyconfigs/__archive__/g/git/git-1.8.2-gmvolf-1.7.12.eb index 544929857c..e54476f0a4 100644 --- a/easybuild/easyconfigs/__archive__/g/git/git-1.8.2-gmvolf-1.7.12.eb +++ b/easybuild/easyconfigs/__archive__/g/git/git-1.8.2-gmvolf-1.7.12.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/g/git/git-1.8.2-gmvolf-1.7.12rc1.eb b/easybuild/easyconfigs/__archive__/g/git/git-1.8.2-gmvolf-1.7.12rc1.eb index 89c596b617..38680f091d 100644 --- a/easybuild/easyconfigs/__archive__/g/git/git-1.8.2-gmvolf-1.7.12rc1.eb +++ b/easybuild/easyconfigs/__archive__/g/git/git-1.8.2-gmvolf-1.7.12rc1.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/g/gnuplot/gnuplot-4.6.0-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/g/gnuplot/gnuplot-4.6.0-goalf-1.1.0-no-OFED.eb index bd0bbb0ca0..b91d8d2d53 100644 --- a/easybuild/easyconfigs/__archive__/g/gnuplot/gnuplot-4.6.0-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/__archive__/g/gnuplot/gnuplot-4.6.0-goalf-1.1.0-no-OFED.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/g/gnuplot/gnuplot-4.6.0-ictce-4.0.6.eb b/easybuild/easyconfigs/__archive__/g/gnuplot/gnuplot-4.6.0-ictce-4.0.6.eb index 23b0d23f05..aeae930afd 100644 --- a/easybuild/easyconfigs/__archive__/g/gnuplot/gnuplot-4.6.0-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/__archive__/g/gnuplot/gnuplot-4.6.0-ictce-4.0.6.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/g/gzip/gzip-1.5-cgoolf-1.1.7.eb b/easybuild/easyconfigs/__archive__/g/gzip/gzip-1.5-cgoolf-1.1.7.eb index 96eb4d4a94..d31a140295 100644 --- a/easybuild/easyconfigs/__archive__/g/gzip/gzip-1.5-cgoolf-1.1.7.eb +++ b/easybuild/easyconfigs/__archive__/g/gzip/gzip-1.5-cgoolf-1.1.7.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright (c) 2012-2013 Cyprus Institute / CaSToRC # Authors:: Thekla Loizou diff --git a/easybuild/easyconfigs/__archive__/g/gzip/gzip-1.5-gmpolf-1.4.8.eb b/easybuild/easyconfigs/__archive__/g/gzip/gzip-1.5-gmpolf-1.4.8.eb index 627ddf488d..0748c110a0 100644 --- a/easybuild/easyconfigs/__archive__/g/gzip/gzip-1.5-gmpolf-1.4.8.eb +++ b/easybuild/easyconfigs/__archive__/g/gzip/gzip-1.5-gmpolf-1.4.8.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright (c) 2012-2013 Cyprus Institute / CaSToRC # Authors:: Thekla Loizou diff --git a/easybuild/easyconfigs/__archive__/g/gzip/gzip-1.5-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/g/gzip/gzip-1.5-goalf-1.1.0-no-OFED.eb index 282fc7aa9f..7e61a60bf2 100644 --- a/easybuild/easyconfigs/__archive__/g/gzip/gzip-1.5-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/__archive__/g/gzip/gzip-1.5-goalf-1.1.0-no-OFED.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright (c) 2012-2013 Cyprus Institute / CaSToRC # Authors:: Thekla Loizou diff --git a/easybuild/easyconfigs/__archive__/g/gzip/gzip-1.5-ictce-4.0.6.eb b/easybuild/easyconfigs/__archive__/g/gzip/gzip-1.5-ictce-4.0.6.eb index 2072304457..65b9cc7f01 100644 --- a/easybuild/easyconfigs/__archive__/g/gzip/gzip-1.5-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/__archive__/g/gzip/gzip-1.5-ictce-4.0.6.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright (c) 2012-2013 Cyprus Institute / CaSToRC # Authors:: Thekla Loizou diff --git a/easybuild/easyconfigs/__archive__/g/gzip/gzip-1.5-ictce-4.1.13.eb b/easybuild/easyconfigs/__archive__/g/gzip/gzip-1.5-ictce-4.1.13.eb index 34e650a014..6e06ea391d 100644 --- a/easybuild/easyconfigs/__archive__/g/gzip/gzip-1.5-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/__archive__/g/gzip/gzip-1.5-ictce-4.1.13.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright (c) 2012-2013 Cyprus Institute / CaSToRC # Authors:: Thekla Loizou diff --git a/easybuild/easyconfigs/__archive__/g/gzip/gzip-1.6-goolf-1.5.14-no-OFED.eb b/easybuild/easyconfigs/__archive__/g/gzip/gzip-1.6-goolf-1.5.14-no-OFED.eb index e4663d467a..34796e201d 100644 --- a/easybuild/easyconfigs/__archive__/g/gzip/gzip-1.6-goolf-1.5.14-no-OFED.eb +++ b/easybuild/easyconfigs/__archive__/g/gzip/gzip-1.6-goolf-1.5.14-no-OFED.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright (c) 2012-2013 Cyprus Institute / CaSToRC # Authors:: Thekla Loizou diff --git a/easybuild/easyconfigs/__archive__/h/HH-suite/HH-suite-2.0.16-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/h/HH-suite/HH-suite-2.0.16-goalf-1.1.0-no-OFED.eb index 9bc25a5071..ee1aee5e77 100644 --- a/easybuild/easyconfigs/__archive__/h/HH-suite/HH-suite-2.0.16-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/__archive__/h/HH-suite/HH-suite-2.0.16-goalf-1.1.0-no-OFED.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild recipy as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild recipy as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/h/HMMER/HMMER-3.0-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/h/HMMER/HMMER-3.0-goalf-1.1.0-no-OFED.eb index c14d1e9c4c..e4f9f9f405 100644 --- a/easybuild/easyconfigs/__archive__/h/HMMER/HMMER-3.0-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/__archive__/h/HMMER/HMMER-3.0-goalf-1.1.0-no-OFED.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/h/HMMER/HMMER-3.0-ictce-4.0.6.eb b/easybuild/easyconfigs/__archive__/h/HMMER/HMMER-3.0-ictce-4.0.6.eb index 882be30c22..d640899214 100644 --- a/easybuild/easyconfigs/__archive__/h/HMMER/HMMER-3.0-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/__archive__/h/HMMER/HMMER-3.0-ictce-4.0.6.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/h/HPCBIOS_Math/HPCBIOS_Math-20130829-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/h/HPCBIOS_Math/HPCBIOS_Math-20130829-goalf-1.1.0-no-OFED.eb index e86ac02683..8976d6c40b 100644 --- a/easybuild/easyconfigs/__archive__/h/HPCBIOS_Math/HPCBIOS_Math-20130829-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/__archive__/h/HPCBIOS_Math/HPCBIOS_Math-20130829-goalf-1.1.0-no-OFED.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/i/Infernal/Infernal-1.1-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/i/Infernal/Infernal-1.1-goalf-1.1.0-no-OFED.eb index 67c9b4b47c..a1dacdc98c 100644 --- a/easybuild/easyconfigs/__archive__/i/Infernal/Infernal-1.1-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/__archive__/i/Infernal/Infernal-1.1-goalf-1.1.0-no-OFED.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Cedric Laczny , Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/i/Infernal/Infernal-1.1-ictce-4.0.6.eb b/easybuild/easyconfigs/__archive__/i/Infernal/Infernal-1.1-ictce-4.0.6.eb index aa9857ce93..7031201322 100644 --- a/easybuild/easyconfigs/__archive__/i/Infernal/Infernal-1.1-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/__archive__/i/Infernal/Infernal-1.1-ictce-4.0.6.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Cedric Laczny , Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/i/Infernal/Infernal-1.1rc1-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/i/Infernal/Infernal-1.1rc1-goalf-1.1.0-no-OFED.eb index 807ce3ee01..6165515b54 100644 --- a/easybuild/easyconfigs/__archive__/i/Infernal/Infernal-1.1rc1-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/__archive__/i/Infernal/Infernal-1.1rc1-goalf-1.1.0-no-OFED.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Cedric Laczny , Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/i/Infernal/Infernal-1.1rc1-ictce-4.0.6.eb b/easybuild/easyconfigs/__archive__/i/Infernal/Infernal-1.1rc1-ictce-4.0.6.eb index 3fb03037b9..2c5ec1ce14 100644 --- a/easybuild/easyconfigs/__archive__/i/Infernal/Infernal-1.1rc1-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/__archive__/i/Infernal/Infernal-1.1rc1-ictce-4.0.6.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Cedric Laczny , Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/i/Iperf/Iperf-2.0.5-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/i/Iperf/Iperf-2.0.5-goalf-1.1.0-no-OFED.eb index 974a5d000e..66d6e15438 100644 --- a/easybuild/easyconfigs/__archive__/i/Iperf/Iperf-2.0.5-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/__archive__/i/Iperf/Iperf-2.0.5-goalf-1.1.0-no-OFED.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/i/Iperf/Iperf-2.0.5-ictce-4.0.6.eb b/easybuild/easyconfigs/__archive__/i/Iperf/Iperf-2.0.5-ictce-4.0.6.eb index c6a180825f..6c38105a14 100644 --- a/easybuild/easyconfigs/__archive__/i/Iperf/Iperf-2.0.5-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/__archive__/i/Iperf/Iperf-2.0.5-ictce-4.0.6.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/l/LWM2/LWM2-1.1-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/__archive__/l/LWM2/LWM2-1.1-gompi-1.4.12-no-OFED.eb index dec9b30b4f..07e343af8a 100644 --- a/easybuild/easyconfigs/__archive__/l/LWM2/LWM2-1.1-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/__archive__/l/LWM2/LWM2-1.1-gompi-1.4.12-no-OFED.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild # Copyright:: Copyright 2013 Juelich Supercomputing Centre, Germany # Authors:: Bernd Mohr # License:: New BSD diff --git a/easybuild/easyconfigs/__archive__/l/LZO/LZO-2.06-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/l/LZO/LZO-2.06-goalf-1.1.0-no-OFED.eb index 94a0908fdc..7ebc542f5e 100644 --- a/easybuild/easyconfigs/__archive__/l/LZO/LZO-2.06-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/__archive__/l/LZO/LZO-2.06-goalf-1.1.0-no-OFED.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/l/LZO/LZO-2.06-ictce-4.0.6.eb b/easybuild/easyconfigs/__archive__/l/LZO/LZO-2.06-ictce-4.0.6.eb index 3dc6b8939e..5080a2c53c 100644 --- a/easybuild/easyconfigs/__archive__/l/LZO/LZO-2.06-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/__archive__/l/LZO/LZO-2.06-ictce-4.0.6.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/l/LZO/LZO-2.06-ictce-5.1.1.eb b/easybuild/easyconfigs/__archive__/l/LZO/LZO-2.06-ictce-5.1.1.eb index 91bc730999..4460cae67c 100644 --- a/easybuild/easyconfigs/__archive__/l/LZO/LZO-2.06-ictce-5.1.1.eb +++ b/easybuild/easyconfigs/__archive__/l/LZO/LZO-2.06-ictce-5.1.1.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/l/LibTIFF/LibTIFF-4.0.3-ictce-4.1.13.eb b/easybuild/easyconfigs/__archive__/l/LibTIFF/LibTIFF-4.0.3-ictce-4.1.13.eb index 3fa3aba61e..f332d73c30 100644 --- a/easybuild/easyconfigs/__archive__/l/LibTIFF/LibTIFF-4.0.3-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/__archive__/l/LibTIFF/LibTIFF-4.0.3-ictce-4.1.13.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/l/lftp/lftp-4.4.1-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/l/lftp/lftp-4.4.1-goalf-1.1.0-no-OFED.eb index cca49e12bf..9f675f07bf 100644 --- a/easybuild/easyconfigs/__archive__/l/lftp/lftp-4.4.1-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/__archive__/l/lftp/lftp-4.4.1-goalf-1.1.0-no-OFED.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/l/libgtextutils/libgtextutils-0.6.1-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/l/libgtextutils/libgtextutils-0.6.1-goalf-1.1.0-no-OFED.eb index 6aabc3ac11..f9f4cbfcd6 100644 --- a/easybuild/easyconfigs/__archive__/l/libgtextutils/libgtextutils-0.6.1-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/__archive__/l/libgtextutils/libgtextutils-0.6.1-goalf-1.1.0-no-OFED.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Cedric Laczny , Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/l/libgtextutils/libgtextutils-0.6.1-ictce-4.0.6.eb b/easybuild/easyconfigs/__archive__/l/libgtextutils/libgtextutils-0.6.1-ictce-4.0.6.eb index ded8654240..4f58924c62 100644 --- a/easybuild/easyconfigs/__archive__/l/libgtextutils/libgtextutils-0.6.1-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/__archive__/l/libgtextutils/libgtextutils-0.6.1-ictce-4.0.6.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Cedric Laczny , Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/l/libharu/libharu-2.2.0-ictce-4.1.13.eb b/easybuild/easyconfigs/__archive__/l/libharu/libharu-2.2.0-ictce-4.1.13.eb index 26e45a4b96..f2db5e1bd1 100644 --- a/easybuild/easyconfigs/__archive__/l/libharu/libharu-2.2.0-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/__archive__/l/libharu/libharu-2.2.0-ictce-4.1.13.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Cyprus Institute / CaSToRC, Uni.Lu/LCSB, NTUA # Authors:: George Tsouloupas , Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/l/libunwind/libunwind-1.1-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/__archive__/l/libunwind/libunwind-1.1-gompi-1.4.12-no-OFED.eb index cdac53c708..bba047b19e 100644 --- a/easybuild/easyconfigs/__archive__/l/libunwind/libunwind-1.1-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/__archive__/l/libunwind/libunwind-1.1-gompi-1.4.12-no-OFED.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild # Copyright:: Copyright 2013 Juelich Supercomputing Centre, Germany # Authors:: Bernd Mohr # License:: New BSD diff --git a/easybuild/easyconfigs/__archive__/l/libyaml/libyaml-0.1.4-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/l/libyaml/libyaml-0.1.4-goalf-1.1.0-no-OFED.eb index 3a53284403..efb2f812e3 100644 --- a/easybuild/easyconfigs/__archive__/l/libyaml/libyaml-0.1.4-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/__archive__/l/libyaml/libyaml-0.1.4-goalf-1.1.0-no-OFED.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Nils Christian diff --git a/easybuild/easyconfigs/__archive__/m/M4/M4-1.4.17-intel-para-2014.12.eb b/easybuild/easyconfigs/__archive__/m/M4/M4-1.4.17-intel-para-2014.12.eb index cda9d848b7..63fd93faa8 100644 --- a/easybuild/easyconfigs/__archive__/m/M4/M4-1.4.17-intel-para-2014.12.eb +++ b/easybuild/easyconfigs/__archive__/m/M4/M4-1.4.17-intel-para-2014.12.eb @@ -14,7 +14,7 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] # '-fgnu89-inline' is required to avoid linking errors with older glibc's, -# see https://github.com/hpcugent/easybuild-easyconfigs/issues/529 +# see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { diff --git a/easybuild/easyconfigs/__archive__/m/MCL/MCL-12.135-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/m/MCL/MCL-12.135-goalf-1.1.0-no-OFED.eb index e322ccb0af..d5b537170a 100644 --- a/easybuild/easyconfigs/__archive__/m/MCL/MCL-12.135-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/__archive__/m/MCL/MCL-12.135-goalf-1.1.0-no-OFED.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/m/MCL/MCL-12.135-ictce-4.0.6.eb b/easybuild/easyconfigs/__archive__/m/MCL/MCL-12.135-ictce-4.0.6.eb index 232ec42670..3f99722ada 100644 --- a/easybuild/easyconfigs/__archive__/m/MCL/MCL-12.135-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/__archive__/m/MCL/MCL-12.135-ictce-4.0.6.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/m/MCL/MCL-12.135-ictce-4.1.13.eb b/easybuild/easyconfigs/__archive__/m/MCL/MCL-12.135-ictce-4.1.13.eb index 3edc17b8e9..5c54eded48 100644 --- a/easybuild/easyconfigs/__archive__/m/MCL/MCL-12.135-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/__archive__/m/MCL/MCL-12.135-ictce-4.1.13.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/m/MEME/MEME-4.8.0-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/m/MEME/MEME-4.8.0-goalf-1.1.0-no-OFED.eb index 4a37b2243d..822a714f43 100644 --- a/easybuild/easyconfigs/__archive__/m/MEME/MEME-4.8.0-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/__archive__/m/MEME/MEME-4.8.0-goalf-1.1.0-no-OFED.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/m/MEME/MEME-4.8.0-ictce-4.0.6.eb b/easybuild/easyconfigs/__archive__/m/MEME/MEME-4.8.0-ictce-4.0.6.eb index 2079802769..0ee39c9be9 100644 --- a/easybuild/easyconfigs/__archive__/m/MEME/MEME-4.8.0-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/__archive__/m/MEME/MEME-4.8.0-ictce-4.0.6.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/m/MUMmer/MUMmer-3.23-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/m/MUMmer/MUMmer-3.23-goalf-1.1.0-no-OFED.eb index df55442b24..e52c131955 100644 --- a/easybuild/easyconfigs/__archive__/m/MUMmer/MUMmer-3.23-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/__archive__/m/MUMmer/MUMmer-3.23-goalf-1.1.0-no-OFED.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Cedric Laczny , Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/m/MUMmer/MUMmer-3.23-ictce-4.0.6.eb b/easybuild/easyconfigs/__archive__/m/MUMmer/MUMmer-3.23-ictce-4.0.6.eb index b12e9042ad..e1bfaff6af 100644 --- a/easybuild/easyconfigs/__archive__/m/MUMmer/MUMmer-3.23-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/__archive__/m/MUMmer/MUMmer-3.23-ictce-4.0.6.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Cedric Laczny , Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/m/MUMmer/MUMmer-3.23-ictce-4.1.13-Perl-5.16.3.eb b/easybuild/easyconfigs/__archive__/m/MUMmer/MUMmer-3.23-ictce-4.1.13-Perl-5.16.3.eb index 578f64de52..6402f3b4f0 100644 --- a/easybuild/easyconfigs/__archive__/m/MUMmer/MUMmer-3.23-ictce-4.1.13-Perl-5.16.3.eb +++ b/easybuild/easyconfigs/__archive__/m/MUMmer/MUMmer-3.23-ictce-4.1.13-Perl-5.16.3.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Cedric Laczny , Fotis Georgatos , Kenneth Hoste diff --git a/easybuild/easyconfigs/__archive__/m/MUST/MUST-1.2.0-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/__archive__/m/MUST/MUST-1.2.0-gompi-1.4.12-no-OFED.eb index cd0624726e..355411d625 100644 --- a/easybuild/easyconfigs/__archive__/m/MUST/MUST-1.2.0-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/__archive__/m/MUST/MUST-1.2.0-gompi-1.4.12-no-OFED.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild # Copyright:: Copyright 2013 Juelich Supercomputing Centre, Germany # Authors:: Bernd Mohr # License:: New BSD diff --git a/easybuild/easyconfigs/__archive__/m/MetaVelvet/MetaVelvet-1.2.01-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/m/MetaVelvet/MetaVelvet-1.2.01-goalf-1.1.0-no-OFED.eb index a43b075cea..2f8eece7c4 100644 --- a/easybuild/easyconfigs/__archive__/m/MetaVelvet/MetaVelvet-1.2.01-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/__archive__/m/MetaVelvet/MetaVelvet-1.2.01-goalf-1.1.0-no-OFED.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Cedric Laczny , Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/m/MetaVelvet/MetaVelvet-1.2.01-ictce-4.0.6.eb b/easybuild/easyconfigs/__archive__/m/MetaVelvet/MetaVelvet-1.2.01-ictce-4.0.6.eb index aa9f2cf5ec..d2bcadda2e 100644 --- a/easybuild/easyconfigs/__archive__/m/MetaVelvet/MetaVelvet-1.2.01-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/__archive__/m/MetaVelvet/MetaVelvet-1.2.01-ictce-4.0.6.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Cedric Laczny , Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/m/mc/mc-4.6.1-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/m/mc/mc-4.6.1-goalf-1.1.0-no-OFED.eb index a05d906924..730be02be3 100644 --- a/easybuild/easyconfigs/__archive__/m/mc/mc-4.6.1-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/__archive__/m/mc/mc-4.6.1-goalf-1.1.0-no-OFED.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/m/mc/mc-4.6.1-ictce-4.0.6.eb b/easybuild/easyconfigs/__archive__/m/mc/mc-4.6.1-ictce-4.0.6.eb index 9830f37904..3fd39ef56e 100644 --- a/easybuild/easyconfigs/__archive__/m/mc/mc-4.6.1-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/__archive__/m/mc/mc-4.6.1-ictce-4.0.6.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/m/mpiBLAST/mpiBLAST-1.6.0-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/m/mpiBLAST/mpiBLAST-1.6.0-goalf-1.1.0-no-OFED.eb index b4ca6871ed..e5f4cf2404 100644 --- a/easybuild/easyconfigs/__archive__/m/mpiBLAST/mpiBLAST-1.6.0-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/__archive__/m/mpiBLAST/mpiBLAST-1.6.0-goalf-1.1.0-no-OFED.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos , Kenneth Hoste diff --git a/easybuild/easyconfigs/__archive__/m/mpiBLAST/mpiBLAST-1.6.0-ictce-4.0.6.eb b/easybuild/easyconfigs/__archive__/m/mpiBLAST/mpiBLAST-1.6.0-ictce-4.0.6.eb index f14049a15f..0f7c4a1cb5 100644 --- a/easybuild/easyconfigs/__archive__/m/mpiBLAST/mpiBLAST-1.6.0-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/__archive__/m/mpiBLAST/mpiBLAST-1.6.0-ictce-4.0.6.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos , Kenneth Hoste diff --git a/easybuild/easyconfigs/__archive__/n/NASM/NASM-2.07-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/n/NASM/NASM-2.07-goalf-1.1.0-no-OFED.eb index ce0c799863..8c8c8d6b64 100644 --- a/easybuild/easyconfigs/__archive__/n/NASM/NASM-2.07-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/__archive__/n/NASM/NASM-2.07-goalf-1.1.0-no-OFED.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/n/NASM/NASM-2.07-ictce-4.0.6.eb b/easybuild/easyconfigs/__archive__/n/NASM/NASM-2.07-ictce-4.0.6.eb index 261d1e65aa..05b4d75cdb 100644 --- a/easybuild/easyconfigs/__archive__/n/NASM/NASM-2.07-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/__archive__/n/NASM/NASM-2.07-ictce-4.0.6.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/n/NASM/NASM-2.07-ictce-4.1.13.eb b/easybuild/easyconfigs/__archive__/n/NASM/NASM-2.07-ictce-4.1.13.eb index ec4bc1b519..f62ff8c098 100644 --- a/easybuild/easyconfigs/__archive__/n/NASM/NASM-2.07-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/__archive__/n/NASM/NASM-2.07-ictce-4.1.13.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/n/NASM/NASM-2.11.05-ictce-6.3.5.eb b/easybuild/easyconfigs/__archive__/n/NASM/NASM-2.11.05-ictce-6.3.5.eb index 8210b35b66..d98adb2215 100644 --- a/easybuild/easyconfigs/__archive__/n/NASM/NASM-2.11.05-ictce-6.3.5.eb +++ b/easybuild/easyconfigs/__archive__/n/NASM/NASM-2.11.05-ictce-6.3.5.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/n/NCBI-Toolkit/NCBI-Toolkit-9.0.0-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/n/NCBI-Toolkit/NCBI-Toolkit-9.0.0-goalf-1.1.0-no-OFED.eb index c4688cb405..aaef538e3a 100644 --- a/easybuild/easyconfigs/__archive__/n/NCBI-Toolkit/NCBI-Toolkit-9.0.0-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/__archive__/n/NCBI-Toolkit/NCBI-Toolkit-9.0.0-goalf-1.1.0-no-OFED.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos , Kenneth Hoste diff --git a/easybuild/easyconfigs/__archive__/n/NCBI-Toolkit/NCBI-Toolkit-9.0.0-ictce-4.0.6.eb b/easybuild/easyconfigs/__archive__/n/NCBI-Toolkit/NCBI-Toolkit-9.0.0-ictce-4.0.6.eb index 7d8e37d42d..81777b4947 100644 --- a/easybuild/easyconfigs/__archive__/n/NCBI-Toolkit/NCBI-Toolkit-9.0.0-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/__archive__/n/NCBI-Toolkit/NCBI-Toolkit-9.0.0-ictce-4.0.6.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos , Kenneth Hoste diff --git a/easybuild/easyconfigs/__archive__/n/nano/nano-2.2.6-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/n/nano/nano-2.2.6-goalf-1.1.0-no-OFED.eb index 07e2cab7c0..ea62784fb7 100644 --- a/easybuild/easyconfigs/__archive__/n/nano/nano-2.2.6-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/__archive__/n/nano/nano-2.2.6-goalf-1.1.0-no-OFED.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/n/nano/nano-2.2.6-ictce-4.0.6.eb b/easybuild/easyconfigs/__archive__/n/nano/nano-2.2.6-ictce-4.0.6.eb index 2a997d6bdf..6edb4f983c 100644 --- a/easybuild/easyconfigs/__archive__/n/nano/nano-2.2.6-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/__archive__/n/nano/nano-2.2.6-ictce-4.0.6.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/o/OPARI2/OPARI2-1.0.7-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/__archive__/o/OPARI2/OPARI2-1.0.7-gompi-1.4.12-no-OFED.eb index 0361dfc86a..6ba1cb4abd 100644 --- a/easybuild/easyconfigs/__archive__/o/OPARI2/OPARI2-1.0.7-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/__archive__/o/OPARI2/OPARI2-1.0.7-gompi-1.4.12-no-OFED.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild # Copyright:: Copyright 2013 Juelich Supercomputing Centre, Germany # Authors:: Bernd Mohr # License:: New BSD diff --git a/easybuild/easyconfigs/__archive__/o/OPARI2/OPARI2-1.1.1-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/__archive__/o/OPARI2/OPARI2-1.1.1-gompi-1.4.12-no-OFED.eb index 45442d4279..14ec77b8ce 100644 --- a/easybuild/easyconfigs/__archive__/o/OPARI2/OPARI2-1.1.1-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/__archive__/o/OPARI2/OPARI2-1.1.1-gompi-1.4.12-no-OFED.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild # Copyright:: Copyright 2013 Juelich Supercomputing Centre, Germany # Authors:: Bernd Mohr # License:: New BSD diff --git a/easybuild/easyconfigs/__archive__/o/OTF/OTF-1.12.4-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/__archive__/o/OTF/OTF-1.12.4-gompi-1.4.12-no-OFED.eb index e12b8e7289..e14fc7614e 100644 --- a/easybuild/easyconfigs/__archive__/o/OTF/OTF-1.12.4-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/__archive__/o/OTF/OTF-1.12.4-gompi-1.4.12-no-OFED.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild # Copyright:: Copyright 2013 Juelich Supercomputing Centre, Germany # Authors:: Bernd Mohr # License:: New BSD diff --git a/easybuild/easyconfigs/__archive__/o/OTF2/OTF2-1.2.1-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/__archive__/o/OTF2/OTF2-1.2.1-gompi-1.4.12-no-OFED.eb index 88c6562214..ec87a9a0a1 100644 --- a/easybuild/easyconfigs/__archive__/o/OTF2/OTF2-1.2.1-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/__archive__/o/OTF2/OTF2-1.2.1-gompi-1.4.12-no-OFED.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild # Copyright:: Copyright 2013 Juelich Supercomputing Centre, Germany # Authors:: Bernd Mohr # License:: New BSD diff --git a/easybuild/easyconfigs/__archive__/p/PAPI/PAPI-5.0.1-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/p/PAPI/PAPI-5.0.1-goalf-1.1.0-no-OFED.eb index 4cd82eaeb6..e509bee068 100644 --- a/easybuild/easyconfigs/__archive__/p/PAPI/PAPI-5.0.1-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/__archive__/p/PAPI/PAPI-5.0.1-goalf-1.1.0-no-OFED.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/p/PAPI/PAPI-5.0.1-ictce-4.0.6.eb b/easybuild/easyconfigs/__archive__/p/PAPI/PAPI-5.0.1-ictce-4.0.6.eb index 7a5c98d762..767ac0cf8a 100644 --- a/easybuild/easyconfigs/__archive__/p/PAPI/PAPI-5.0.1-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/__archive__/p/PAPI/PAPI-5.0.1-ictce-4.0.6.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/p/PAPI/PAPI-5.2.0-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/__archive__/p/PAPI/PAPI-5.2.0-gompi-1.4.12-no-OFED.eb index c8c6b3d569..34593b5431 100644 --- a/easybuild/easyconfigs/__archive__/p/PAPI/PAPI-5.2.0-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/__archive__/p/PAPI/PAPI-5.2.0-gompi-1.4.12-no-OFED.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/p/PDT/PDT-3.19-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/__archive__/p/PDT/PDT-3.19-gompi-1.4.12-no-OFED.eb index eef9a27cd7..9c604d4a85 100644 --- a/easybuild/easyconfigs/__archive__/p/PDT/PDT-3.19-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/__archive__/p/PDT/PDT-3.19-gompi-1.4.12-no-OFED.eb @@ -1,5 +1,5 @@ ## -# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2013-2015 Juelich Supercomputing Centre, Germany # Authors:: Bernd Mohr diff --git a/easybuild/easyconfigs/__archive__/p/PLINK/PLINK-1.07-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/p/PLINK/PLINK-1.07-goalf-1.1.0-no-OFED.eb index 71cade10ff..852c7755e0 100644 --- a/easybuild/easyconfigs/__archive__/p/PLINK/PLINK-1.07-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/__archive__/p/PLINK/PLINK-1.07-goalf-1.1.0-no-OFED.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2013 The Cyprus Institute # Authors:: Thekla Loizou , Andreas Panteli , diff --git a/easybuild/easyconfigs/__archive__/p/PnMPI/PnMPI-1.2.0-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/__archive__/p/PnMPI/PnMPI-1.2.0-gompi-1.4.12-no-OFED.eb index 909fa6783b..63102afdba 100644 --- a/easybuild/easyconfigs/__archive__/p/PnMPI/PnMPI-1.2.0-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/__archive__/p/PnMPI/PnMPI-1.2.0-gompi-1.4.12-no-OFED.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild # Copyright:: Copyright 2013 Juelich Supercomputing Centre, Germany # Authors:: Bernd Mohr # License:: New BSD diff --git a/easybuild/easyconfigs/__archive__/p/parallel/parallel-20130122-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/p/parallel/parallel-20130122-goalf-1.1.0-no-OFED.eb index 3804c6ccaa..55ce03a711 100644 --- a/easybuild/easyconfigs/__archive__/p/parallel/parallel-20130122-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/__archive__/p/parallel/parallel-20130122-goalf-1.1.0-no-OFED.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/p/parallel/parallel-20130122-ictce-4.0.6.eb b/easybuild/easyconfigs/__archive__/p/parallel/parallel-20130122-ictce-4.0.6.eb index 94c10ffced..fb701cf2e0 100644 --- a/easybuild/easyconfigs/__archive__/p/parallel/parallel-20130122-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/__archive__/p/parallel/parallel-20130122-ictce-4.0.6.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/r/RNAz/RNAz-2.1-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/r/RNAz/RNAz-2.1-goalf-1.1.0-no-OFED.eb index 5f373bcc46..d87f890d0f 100644 --- a/easybuild/easyconfigs/__archive__/r/RNAz/RNAz-2.1-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/__archive__/r/RNAz/RNAz-2.1-goalf-1.1.0-no-OFED.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Cedric Laczny , Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/r/RNAz/RNAz-2.1-ictce-4.0.6.eb b/easybuild/easyconfigs/__archive__/r/RNAz/RNAz-2.1-ictce-4.0.6.eb index 71400b6f39..27678245ba 100644 --- a/easybuild/easyconfigs/__archive__/r/RNAz/RNAz-2.1-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/__archive__/r/RNAz/RNAz-2.1-ictce-4.0.6.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Cedric Laczny , Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/s/SAMtools/SAMtools-0.1.18-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/s/SAMtools/SAMtools-0.1.18-goalf-1.1.0-no-OFED.eb index 495ee12fa8..2d7908e75a 100644 --- a/easybuild/easyconfigs/__archive__/s/SAMtools/SAMtools-0.1.18-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/__archive__/s/SAMtools/SAMtools-0.1.18-goalf-1.1.0-no-OFED.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Cedric Laczny , Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/s/SAMtools/SAMtools-0.1.18-ictce-4.0.6.eb b/easybuild/easyconfigs/__archive__/s/SAMtools/SAMtools-0.1.18-ictce-4.0.6.eb index b9570c368a..3a8baa0737 100644 --- a/easybuild/easyconfigs/__archive__/s/SAMtools/SAMtools-0.1.18-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/__archive__/s/SAMtools/SAMtools-0.1.18-ictce-4.0.6.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Cedric Laczny , Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/s/SOAPdenovo/SOAPdenovo-1.05-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/s/SOAPdenovo/SOAPdenovo-1.05-goalf-1.1.0-no-OFED.eb index 8da8e28b17..336f9b970c 100644 --- a/easybuild/easyconfigs/__archive__/s/SOAPdenovo/SOAPdenovo-1.05-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/__archive__/s/SOAPdenovo/SOAPdenovo-1.05-goalf-1.1.0-no-OFED.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Cedric Laczny , Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/s/SOAPdenovo/SOAPdenovo-1.05-ictce-4.0.6.eb b/easybuild/easyconfigs/__archive__/s/SOAPdenovo/SOAPdenovo-1.05-ictce-4.0.6.eb index 3fda9e525f..9210bc4b2a 100644 --- a/easybuild/easyconfigs/__archive__/s/SOAPdenovo/SOAPdenovo-1.05-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/__archive__/s/SOAPdenovo/SOAPdenovo-1.05-ictce-4.0.6.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Cedric Laczny , Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/s/Scalasca/Scalasca-1.4.3-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/__archive__/s/Scalasca/Scalasca-1.4.3-gompi-1.4.12-no-OFED.eb index 26b61def41..b264014712 100644 --- a/easybuild/easyconfigs/__archive__/s/Scalasca/Scalasca-1.4.3-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/__archive__/s/Scalasca/Scalasca-1.4.3-gompi-1.4.12-no-OFED.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild # Copyright:: Copyright 2013 Juelich Supercomputing Centre, Germany # Authors:: Bernd Mohr # License:: New BSD diff --git a/easybuild/easyconfigs/__archive__/s/Scalasca/Scalasca-2.0-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/__archive__/s/Scalasca/Scalasca-2.0-gompi-1.4.12-no-OFED.eb index b4c09a0c49..a6bb75721d 100644 --- a/easybuild/easyconfigs/__archive__/s/Scalasca/Scalasca-2.0-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/__archive__/s/Scalasca/Scalasca-2.0-gompi-1.4.12-no-OFED.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild # Copyright:: Copyright 2013 Juelich Supercomputing Centre, Germany # Authors:: Bernd Mohr # License:: New BSD diff --git a/easybuild/easyconfigs/__archive__/s/Score-P/Score-P-1.2.1-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/__archive__/s/Score-P/Score-P-1.2.1-gompi-1.4.12-no-OFED.eb index 4c327fa96c..dbfcd3190c 100644 --- a/easybuild/easyconfigs/__archive__/s/Score-P/Score-P-1.2.1-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/__archive__/s/Score-P/Score-P-1.2.1-gompi-1.4.12-no-OFED.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild # Copyright:: Copyright 2013 Juelich Supercomputing Centre, Germany # Authors:: Bernd Mohr # License:: New BSD diff --git a/easybuild/easyconfigs/__archive__/s/Stow/Stow-1.3.3-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/s/Stow/Stow-1.3.3-goalf-1.1.0-no-OFED.eb index 0d2c3773f8..7d558ac71a 100644 --- a/easybuild/easyconfigs/__archive__/s/Stow/Stow-1.3.3-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/__archive__/s/Stow/Stow-1.3.3-goalf-1.1.0-no-OFED.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/s/Stow/Stow-1.3.3-ictce-4.0.6.eb b/easybuild/easyconfigs/__archive__/s/Stow/Stow-1.3.3-ictce-4.0.6.eb index e7734dc526..4b640a501f 100644 --- a/easybuild/easyconfigs/__archive__/s/Stow/Stow-1.3.3-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/__archive__/s/Stow/Stow-1.3.3-ictce-4.0.6.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/t/TAU/TAU-2.22.2-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/__archive__/t/TAU/TAU-2.22.2-gompi-1.4.12-no-OFED.eb index b8a2739b01..ccfd573f79 100644 --- a/easybuild/easyconfigs/__archive__/t/TAU/TAU-2.22.2-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/__archive__/t/TAU/TAU-2.22.2-gompi-1.4.12-no-OFED.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild # Copyright:: Copyright 2013 Juelich Supercomputing Centre, Germany # Authors:: Bernd Mohr # License:: New BSD diff --git a/easybuild/easyconfigs/__archive__/t/Tar/Tar-1.26-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/t/Tar/Tar-1.26-goalf-1.1.0-no-OFED.eb index 9c40f2197e..70a6e42479 100644 --- a/easybuild/easyconfigs/__archive__/t/Tar/Tar-1.26-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/__archive__/t/Tar/Tar-1.26-goalf-1.1.0-no-OFED.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright (c) 2012-2013 Cyprus Institute / CaSToRC # Authors:: Thekla Loizou diff --git a/easybuild/easyconfigs/__archive__/t/Tar/Tar-1.26-ictce-4.0.6.eb b/easybuild/easyconfigs/__archive__/t/Tar/Tar-1.26-ictce-4.0.6.eb index 79b6f833d1..76bcf79055 100644 --- a/easybuild/easyconfigs/__archive__/t/Tar/Tar-1.26-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/__archive__/t/Tar/Tar-1.26-ictce-4.0.6.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright (c) 2012-2013 Cyprus Institute / CaSToRC # Authors:: Thekla Loizou diff --git a/easybuild/easyconfigs/__archive__/t/TopHat/TopHat-2.0.4-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/t/TopHat/TopHat-2.0.4-goalf-1.1.0-no-OFED.eb index 2ba3b07819..9eecf23237 100644 --- a/easybuild/easyconfigs/__archive__/t/TopHat/TopHat-2.0.4-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/__archive__/t/TopHat/TopHat-2.0.4-goalf-1.1.0-no-OFED.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Cedric Laczny , Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/t/TopHat/TopHat-2.0.8-ictce-4.0.6.eb b/easybuild/easyconfigs/__archive__/t/TopHat/TopHat-2.0.8-ictce-4.0.6.eb index 76567e2542..dcf1959131 100644 --- a/easybuild/easyconfigs/__archive__/t/TopHat/TopHat-2.0.8-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/__archive__/t/TopHat/TopHat-2.0.8-ictce-4.0.6.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Cedric Laczny , Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/t/tcsh/tcsh-6.18.01-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/t/tcsh/tcsh-6.18.01-goalf-1.1.0-no-OFED.eb index 66720a2d37..81bacb467e 100644 --- a/easybuild/easyconfigs/__archive__/t/tcsh/tcsh-6.18.01-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/__archive__/t/tcsh/tcsh-6.18.01-goalf-1.1.0-no-OFED.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2013 University of Luxembourg/Computer Science and Communications Research Unit # Authors:: Valentin Plugaru diff --git a/easybuild/easyconfigs/__archive__/t/tcsh/tcsh-6.18.01-ictce-3.2.2.u3.eb b/easybuild/easyconfigs/__archive__/t/tcsh/tcsh-6.18.01-ictce-3.2.2.u3.eb index e8fe446e8b..dae024dd09 100644 --- a/easybuild/easyconfigs/__archive__/t/tcsh/tcsh-6.18.01-ictce-3.2.2.u3.eb +++ b/easybuild/easyconfigs/__archive__/t/tcsh/tcsh-6.18.01-ictce-3.2.2.u3.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2013 University of Luxembourg/Computer Science and Communications Research Unit # Authors:: Valentin Plugaru diff --git a/easybuild/easyconfigs/__archive__/t/tcsh/tcsh-6.18.01-ictce-4.1.13.eb b/easybuild/easyconfigs/__archive__/t/tcsh/tcsh-6.18.01-ictce-4.1.13.eb index 42dc94a346..b878f2b439 100644 --- a/easybuild/easyconfigs/__archive__/t/tcsh/tcsh-6.18.01-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/__archive__/t/tcsh/tcsh-6.18.01-ictce-4.1.13.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2013 University of Luxembourg/Computer Science and Communications Research Unit # Authors:: Valentin Plugaru diff --git a/easybuild/easyconfigs/__archive__/t/tcsh/tcsh-6.18.01-iqacml-3.7.3.eb b/easybuild/easyconfigs/__archive__/t/tcsh/tcsh-6.18.01-iqacml-3.7.3.eb index 37494982ed..a65b416429 100644 --- a/easybuild/easyconfigs/__archive__/t/tcsh/tcsh-6.18.01-iqacml-3.7.3.eb +++ b/easybuild/easyconfigs/__archive__/t/tcsh/tcsh-6.18.01-iqacml-3.7.3.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2013 University of Luxembourg/Computer Science and Communications Research Unit # Authors:: Valentin Plugaru diff --git a/easybuild/easyconfigs/__archive__/u/UDUNITS/UDUNITS-2.1.24-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/u/UDUNITS/UDUNITS-2.1.24-goalf-1.1.0-no-OFED.eb index a52aa694fc..bfa34ecda1 100644 --- a/easybuild/easyconfigs/__archive__/u/UDUNITS/UDUNITS-2.1.24-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/__archive__/u/UDUNITS/UDUNITS-2.1.24-goalf-1.1.0-no-OFED.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2013 University of Luxembourg, Ghent University # Authors:: Fotis Georgatos , Kenneth Hoste (Ghent University) diff --git a/easybuild/easyconfigs/__archive__/u/UDUNITS/UDUNITS-2.1.24-ictce-3.2.2.u3.eb b/easybuild/easyconfigs/__archive__/u/UDUNITS/UDUNITS-2.1.24-ictce-3.2.2.u3.eb index b9d1c0a574..5c9413974d 100644 --- a/easybuild/easyconfigs/__archive__/u/UDUNITS/UDUNITS-2.1.24-ictce-3.2.2.u3.eb +++ b/easybuild/easyconfigs/__archive__/u/UDUNITS/UDUNITS-2.1.24-ictce-3.2.2.u3.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2013 University of Luxembourg, Ghent University # Authors:: Fotis Georgatos , Kenneth Hoste (Ghent University) diff --git a/easybuild/easyconfigs/__archive__/u/UDUNITS/UDUNITS-2.1.24-ictce-4.0.6.eb b/easybuild/easyconfigs/__archive__/u/UDUNITS/UDUNITS-2.1.24-ictce-4.0.6.eb index 7a9b90a956..a61ec089a4 100644 --- a/easybuild/easyconfigs/__archive__/u/UDUNITS/UDUNITS-2.1.24-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/__archive__/u/UDUNITS/UDUNITS-2.1.24-ictce-4.0.6.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2013 University of Luxembourg, Ghent University # Authors:: Fotis Georgatos , Kenneth Hoste (Ghent University) diff --git a/easybuild/easyconfigs/__archive__/u/UDUNITS/UDUNITS-2.1.24-ictce-4.1.13.eb b/easybuild/easyconfigs/__archive__/u/UDUNITS/UDUNITS-2.1.24-ictce-4.1.13.eb index f166af2248..09c2b01c03 100644 --- a/easybuild/easyconfigs/__archive__/u/UDUNITS/UDUNITS-2.1.24-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/__archive__/u/UDUNITS/UDUNITS-2.1.24-ictce-4.1.13.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2013 University of Luxembourg, Ghent University # Authors:: Fotis Georgatos , Kenneth Hoste (Ghent University) diff --git a/easybuild/easyconfigs/__archive__/u/UDUNITS/UDUNITS-2.1.24-iqacml-3.7.3.eb b/easybuild/easyconfigs/__archive__/u/UDUNITS/UDUNITS-2.1.24-iqacml-3.7.3.eb index 193e10df49..b2201ef04e 100644 --- a/easybuild/easyconfigs/__archive__/u/UDUNITS/UDUNITS-2.1.24-iqacml-3.7.3.eb +++ b/easybuild/easyconfigs/__archive__/u/UDUNITS/UDUNITS-2.1.24-iqacml-3.7.3.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2013 University of Luxembourg, Ghent University # Authors:: Fotis Georgatos , Kenneth Hoste (Ghent University) diff --git a/easybuild/easyconfigs/__archive__/v/VTK/VTK-5.10.1-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/v/VTK/VTK-5.10.1-goalf-1.1.0-no-OFED.eb index d0373056bb..34a7df2c71 100644 --- a/easybuild/easyconfigs/__archive__/v/VTK/VTK-5.10.1-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/__archive__/v/VTK/VTK-5.10.1-goalf-1.1.0-no-OFED.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/v/VTK/VTK-5.10.1-ictce-4.0.6.eb b/easybuild/easyconfigs/__archive__/v/VTK/VTK-5.10.1-ictce-4.0.6.eb index 2a354f444a..64d04fb6e5 100644 --- a/easybuild/easyconfigs/__archive__/v/VTK/VTK-5.10.1-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/__archive__/v/VTK/VTK-5.10.1-ictce-4.0.6.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/v/VTK/VTK-6.0.0-ictce-4.1.13-Python-2.7.3.eb b/easybuild/easyconfigs/__archive__/v/VTK/VTK-6.0.0-ictce-4.1.13-Python-2.7.3.eb index fb24b1b64c..02603d970f 100644 --- a/easybuild/easyconfigs/__archive__/v/VTK/VTK-6.0.0-ictce-4.1.13-Python-2.7.3.eb +++ b/easybuild/easyconfigs/__archive__/v/VTK/VTK-6.0.0-ictce-4.1.13-Python-2.7.3.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/v/Valgrind/Valgrind-3.8.1-cgmpolf-1.1.6.eb b/easybuild/easyconfigs/__archive__/v/Valgrind/Valgrind-3.8.1-cgmpolf-1.1.6.eb index 831d945988..f5fe5e11ed 100644 --- a/easybuild/easyconfigs/__archive__/v/Valgrind/Valgrind-3.8.1-cgmpolf-1.1.6.eb +++ b/easybuild/easyconfigs/__archive__/v/Valgrind/Valgrind-3.8.1-cgmpolf-1.1.6.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/v/Valgrind/Valgrind-3.8.1-cgmvolf-1.1.12rc1.eb b/easybuild/easyconfigs/__archive__/v/Valgrind/Valgrind-3.8.1-cgmvolf-1.1.12rc1.eb index 4ef81eed36..1f1889615e 100644 --- a/easybuild/easyconfigs/__archive__/v/Valgrind/Valgrind-3.8.1-cgmvolf-1.1.12rc1.eb +++ b/easybuild/easyconfigs/__archive__/v/Valgrind/Valgrind-3.8.1-cgmvolf-1.1.12rc1.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/v/Valgrind/Valgrind-3.8.1-cgmvolf-1.2.7.eb b/easybuild/easyconfigs/__archive__/v/Valgrind/Valgrind-3.8.1-cgmvolf-1.2.7.eb index 07d51ab2d9..cc1196047f 100644 --- a/easybuild/easyconfigs/__archive__/v/Valgrind/Valgrind-3.8.1-cgmvolf-1.2.7.eb +++ b/easybuild/easyconfigs/__archive__/v/Valgrind/Valgrind-3.8.1-cgmvolf-1.2.7.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/v/Valgrind/Valgrind-3.8.1-cgoolf-1.1.7.eb b/easybuild/easyconfigs/__archive__/v/Valgrind/Valgrind-3.8.1-cgoolf-1.1.7.eb index b01834e9d7..a9f0386228 100644 --- a/easybuild/easyconfigs/__archive__/v/Valgrind/Valgrind-3.8.1-cgoolf-1.1.7.eb +++ b/easybuild/easyconfigs/__archive__/v/Valgrind/Valgrind-3.8.1-cgoolf-1.1.7.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/v/Valgrind/Valgrind-3.8.1-gmvolf-1.7.12.eb b/easybuild/easyconfigs/__archive__/v/Valgrind/Valgrind-3.8.1-gmvolf-1.7.12.eb index 9b14309ef1..1243dcfcb8 100644 --- a/easybuild/easyconfigs/__archive__/v/Valgrind/Valgrind-3.8.1-gmvolf-1.7.12.eb +++ b/easybuild/easyconfigs/__archive__/v/Valgrind/Valgrind-3.8.1-gmvolf-1.7.12.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/v/Valgrind/Valgrind-3.8.1-gmvolf-1.7.12rc1.eb b/easybuild/easyconfigs/__archive__/v/Valgrind/Valgrind-3.8.1-gmvolf-1.7.12rc1.eb index 6b6c92bf80..32ef6ee8bd 100644 --- a/easybuild/easyconfigs/__archive__/v/Valgrind/Valgrind-3.8.1-gmvolf-1.7.12rc1.eb +++ b/easybuild/easyconfigs/__archive__/v/Valgrind/Valgrind-3.8.1-gmvolf-1.7.12rc1.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/v/Valgrind/Valgrind-3.8.1-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/v/Valgrind/Valgrind-3.8.1-goalf-1.1.0-no-OFED.eb index 87fdb08561..fd8cedb7a9 100644 --- a/easybuild/easyconfigs/__archive__/v/Valgrind/Valgrind-3.8.1-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/__archive__/v/Valgrind/Valgrind-3.8.1-goalf-1.1.0-no-OFED.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/v/Valgrind/Valgrind-3.9.0-goalf-1.5.12-no-OFED.eb b/easybuild/easyconfigs/__archive__/v/Valgrind/Valgrind-3.9.0-goalf-1.5.12-no-OFED.eb index 3a3d16b550..4f5a351349 100644 --- a/easybuild/easyconfigs/__archive__/v/Valgrind/Valgrind-3.9.0-goalf-1.5.12-no-OFED.eb +++ b/easybuild/easyconfigs/__archive__/v/Valgrind/Valgrind-3.9.0-goalf-1.5.12-no-OFED.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA, Ghent University # Authors:: Fotis Georgatos , Ward Poelmans diff --git a/easybuild/easyconfigs/__archive__/v/VampirTrace/VampirTrace-5.14.4-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/__archive__/v/VampirTrace/VampirTrace-5.14.4-gompi-1.4.12-no-OFED.eb index 02bc1f21cc..4f6d2fd3db 100644 --- a/easybuild/easyconfigs/__archive__/v/VampirTrace/VampirTrace-5.14.4-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/__archive__/v/VampirTrace/VampirTrace-5.14.4-gompi-1.4.12-no-OFED.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild # Copyright:: Copyright 2013 Juelich Supercomputing Centre, Germany # Authors:: Bernd Mohr # License:: New BSD diff --git a/easybuild/easyconfigs/__archive__/v/Velvet/Velvet-1.2.07-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/v/Velvet/Velvet-1.2.07-goalf-1.1.0-no-OFED.eb index 898d4cda78..9c6279fddf 100644 --- a/easybuild/easyconfigs/__archive__/v/Velvet/Velvet-1.2.07-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/__archive__/v/Velvet/Velvet-1.2.07-goalf-1.1.0-no-OFED.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Cedric Laczny , Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/v/Velvet/Velvet-1.2.07-ictce-4.0.6.eb b/easybuild/easyconfigs/__archive__/v/Velvet/Velvet-1.2.07-ictce-4.0.6.eb index 96163b744c..3179b97658 100644 --- a/easybuild/easyconfigs/__archive__/v/Velvet/Velvet-1.2.07-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/__archive__/v/Velvet/Velvet-1.2.07-ictce-4.0.6.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Cedric Laczny , Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/v/ViennaRNA/ViennaRNA-2.0.7-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/v/ViennaRNA/ViennaRNA-2.0.7-goalf-1.1.0-no-OFED.eb index 795671412f..e2b533028e 100644 --- a/easybuild/easyconfigs/__archive__/v/ViennaRNA/ViennaRNA-2.0.7-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/__archive__/v/ViennaRNA/ViennaRNA-2.0.7-goalf-1.1.0-no-OFED.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Cedric Laczny , Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/v/ViennaRNA/ViennaRNA-2.0.7-ictce-4.0.6.eb b/easybuild/easyconfigs/__archive__/v/ViennaRNA/ViennaRNA-2.0.7-ictce-4.0.6.eb index b7723d7af3..c767b5e210 100644 --- a/easybuild/easyconfigs/__archive__/v/ViennaRNA/ViennaRNA-2.0.7-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/__archive__/v/ViennaRNA/ViennaRNA-2.0.7-ictce-4.0.6.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Cedric Laczny , Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/v/Viper/Viper-1.0.0-goalf-1.1.0-no-OFED-Python-2.7.3.eb b/easybuild/easyconfigs/__archive__/v/Viper/Viper-1.0.0-goalf-1.1.0-no-OFED-Python-2.7.3.eb index 66555db5aa..19e0844ca8 100644 --- a/easybuild/easyconfigs/__archive__/v/Viper/Viper-1.0.0-goalf-1.1.0-no-OFED-Python-2.7.3.eb +++ b/easybuild/easyconfigs/__archive__/v/Viper/Viper-1.0.0-goalf-1.1.0-no-OFED-Python-2.7.3.eb @@ -22,7 +22,7 @@ versionsuffix = "-%s-%s" % (python, pythonversion) dependencies = [(python, pythonversion)] # hack, 'import viper' fails because VTK and numpy dependencies are missing -# see https://github.com/hpcugent/easybuild-easyconfigs/issues/100 +# see https://github.com/easybuilders/easybuild-easyconfigs/issues/100 options = {'modulename': 'os'} sanity_check_paths = { diff --git a/easybuild/easyconfigs/__archive__/v/Viper/Viper-1.0.0-ictce-4.0.6-Python-2.7.3.eb b/easybuild/easyconfigs/__archive__/v/Viper/Viper-1.0.0-ictce-4.0.6-Python-2.7.3.eb index 031d7e98f1..0800e6ccb7 100644 --- a/easybuild/easyconfigs/__archive__/v/Viper/Viper-1.0.0-ictce-4.0.6-Python-2.7.3.eb +++ b/easybuild/easyconfigs/__archive__/v/Viper/Viper-1.0.0-ictce-4.0.6-Python-2.7.3.eb @@ -22,7 +22,7 @@ versionsuffix = "-%s-%s" % (python, pythonversion) dependencies = [(python, pythonversion)] # hack, 'import viper' fails because VTK and numpy dependencies are missing -# see https://github.com/hpcugent/easybuild-easyconfigs/issues/100 +# see https://github.com/easybuilders/easybuild-easyconfigs/issues/100 options = {'modulename': 'os'} sanity_check_paths = { diff --git a/easybuild/easyconfigs/__archive__/w/wiki2beamer/wiki2beamer-0.9.5-goalf-1.1.0-no-OFED-Python-2.7.3.eb b/easybuild/easyconfigs/__archive__/w/wiki2beamer/wiki2beamer-0.9.5-goalf-1.1.0-no-OFED-Python-2.7.3.eb index e43780a277..daf144962d 100644 --- a/easybuild/easyconfigs/__archive__/w/wiki2beamer/wiki2beamer-0.9.5-goalf-1.1.0-no-OFED-Python-2.7.3.eb +++ b/easybuild/easyconfigs/__archive__/w/wiki2beamer/wiki2beamer-0.9.5-goalf-1.1.0-no-OFED-Python-2.7.3.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Cedric Laczny , Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/y/YAML-Syck/YAML-Syck-1.27-ictce-4.1.13-Perl-5.16.3.eb b/easybuild/easyconfigs/__archive__/y/YAML-Syck/YAML-Syck-1.27-ictce-4.1.13-Perl-5.16.3.eb index 5efafeb0f0..405a8b5fde 100644 --- a/easybuild/easyconfigs/__archive__/y/YAML-Syck/YAML-Syck-1.27-ictce-4.1.13-Perl-5.16.3.eb +++ b/easybuild/easyconfigs/__archive__/y/YAML-Syck/YAML-Syck-1.27-ictce-4.1.13-Perl-5.16.3.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2013 Uni.Lu/LCSB # Authors:: Nils Christian diff --git a/easybuild/easyconfigs/__archive__/y/Yasm/Yasm-1.2.0-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/y/Yasm/Yasm-1.2.0-goalf-1.1.0-no-OFED.eb index e2bfa1c5fb..56100a1cb5 100644 --- a/easybuild/easyconfigs/__archive__/y/Yasm/Yasm-1.2.0-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/__archive__/y/Yasm/Yasm-1.2.0-goalf-1.1.0-no-OFED.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/y/Yasm/Yasm-1.2.0-ictce-4.0.6.eb b/easybuild/easyconfigs/__archive__/y/Yasm/Yasm-1.2.0-ictce-4.0.6.eb index 5b66cf87a7..70d7963092 100644 --- a/easybuild/easyconfigs/__archive__/y/Yasm/Yasm-1.2.0-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/__archive__/y/Yasm/Yasm-1.2.0-ictce-4.0.6.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/z/zsync/zsync-0.6.2-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/z/zsync/zsync-0.6.2-goalf-1.1.0-no-OFED.eb index b70a682d96..c293d54a8c 100644 --- a/easybuild/easyconfigs/__archive__/z/zsync/zsync-0.6.2-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/__archive__/z/zsync/zsync-0.6.2-goalf-1.1.0-no-OFED.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/__archive__/z/zsync/zsync-0.6.2-ictce-4.0.6.eb b/easybuild/easyconfigs/__archive__/z/zsync/zsync-0.6.2-ictce-4.0.6.eb index 9a77005cb5..0719af199a 100644 --- a/easybuild/easyconfigs/__archive__/z/zsync/zsync-0.6.2-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/__archive__/z/zsync/zsync-0.6.2-ictce-4.0.6.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.0.3-x86_64_linux_gnu4.5.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.0.3-x86_64_linux_gnu4.5.eb index 0674deea91..4802aa3c15 100644 --- a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.0.3-x86_64_linux_gnu4.5.eb +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.0.3-x86_64_linux_gnu4.5.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.0.5-x86_64_linux_gnu4.5.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.0.5-x86_64_linux_gnu4.5.eb index f6e72f3fb7..bb745faa33 100644 --- a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.0.5-x86_64_linux_gnu4.5.eb +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.0.5-x86_64_linux_gnu4.5.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.2.1-x86_64_linux_gnu4.5.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.2.1-x86_64_linux_gnu4.5.eb index a5a53cf83d..1d942af521 100644 --- a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.2.1-x86_64_linux_gnu4.5.eb +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.2.1-x86_64_linux_gnu4.5.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.4.3-goolf-1.4.10-ETSF_IO-1.0.4.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.4.3-goolf-1.4.10-ETSF_IO-1.0.4.eb index f598583eb7..30945704b7 100644 --- a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.4.3-goolf-1.4.10-ETSF_IO-1.0.4.eb +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.4.3-goolf-1.4.10-ETSF_IO-1.0.4.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2013-2014 The Cyprus Institute # Authors:: Thekla Loizou diff --git a/easybuild/easyconfigs/a/ABySS/ABySS-1.3.4-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/a/ABySS/ABySS-1.3.4-goolf-1.4.10-Python-2.7.3.eb index 6d7dc91575..e205e2d8ac 100644 --- a/easybuild/easyconfigs/a/ABySS/ABySS-1.3.4-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/a/ABySS/ABySS-1.3.4-goolf-1.4.10-Python-2.7.3.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/a/ABySS/ABySS-1.3.4-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/a/ABySS/ABySS-1.3.4-ictce-5.3.0-Python-2.7.3.eb index f7709440c3..5a1d132b7c 100644 --- a/easybuild/easyconfigs/a/ABySS/ABySS-1.3.4-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/a/ABySS/ABySS-1.3.4-ictce-5.3.0-Python-2.7.3.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/a/ABySS/ABySS-1.3.6-goolf-1.4.10-Python-2.7.5.eb b/easybuild/easyconfigs/a/ABySS/ABySS-1.3.6-goolf-1.4.10-Python-2.7.5.eb index 93b76ef8be..4ebae49b2a 100644 --- a/easybuild/easyconfigs/a/ABySS/ABySS-1.3.6-goolf-1.4.10-Python-2.7.5.eb +++ b/easybuild/easyconfigs/a/ABySS/ABySS-1.3.6-goolf-1.4.10-Python-2.7.5.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/a/ABySS/ABySS-1.3.7-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/a/ABySS/ABySS-1.3.7-intel-2015a-Python-2.7.9.eb index 6b5c1c6d52..a55aa9d2cf 100644 --- a/easybuild/easyconfigs/a/ABySS/ABySS-1.3.7-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/a/ABySS/ABySS-1.3.7-intel-2015a-Python-2.7.9.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/a/ABySS/ABySS-1.5.2-goolf-1.4.10.eb b/easybuild/easyconfigs/a/ABySS/ABySS-1.5.2-goolf-1.4.10.eb index c055778c8e..5995eab527 100644 --- a/easybuild/easyconfigs/a/ABySS/ABySS-1.5.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/a/ABySS/ABySS-1.5.2-goolf-1.4.10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Maxime Schmitt , Fotis Georgatos diff --git a/easybuild/easyconfigs/a/ABySS/ABySS-1.9.0-foss-2016a.eb b/easybuild/easyconfigs/a/ABySS/ABySS-1.9.0-foss-2016a.eb index aa09a6e789..5bd2d17aaf 100644 --- a/easybuild/easyconfigs/a/ABySS/ABySS-1.9.0-foss-2016a.eb +++ b/easybuild/easyconfigs/a/ABySS/ABySS-1.9.0-foss-2016a.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Maxime Schmitt , Fotis Georgatos diff --git a/easybuild/easyconfigs/a/AFNI/AFNI-linux_openmp_64-goolf-1.5.14-20141023.eb b/easybuild/easyconfigs/a/AFNI/AFNI-linux_openmp_64-goolf-1.5.14-20141023.eb index c680dc7f26..d880a919fb 100644 --- a/easybuild/easyconfigs/a/AFNI/AFNI-linux_openmp_64-goolf-1.5.14-20141023.eb +++ b/easybuild/easyconfigs/a/AFNI/AFNI-linux_openmp_64-goolf-1.5.14-20141023.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Bart Verleye # Center for eResearch, Auckland easyblock = 'PackedBinary' diff --git a/easybuild/easyconfigs/a/AFNI/AFNI-linux_openmp_64-intel-2015a-20141023.eb b/easybuild/easyconfigs/a/AFNI/AFNI-linux_openmp_64-intel-2015a-20141023.eb index f082a4fbeb..686bb45434 100644 --- a/easybuild/easyconfigs/a/AFNI/AFNI-linux_openmp_64-intel-2015a-20141023.eb +++ b/easybuild/easyconfigs/a/AFNI/AFNI-linux_openmp_64-intel-2015a-20141023.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Bart Verleye # Center for eResearch, Auckland easyblock = 'PackedBinary' diff --git a/easybuild/easyconfigs/a/ALLPATHS-LG/ALLPATHS-LG-46968-goolf-1.4.10.eb b/easybuild/easyconfigs/a/ALLPATHS-LG/ALLPATHS-LG-46968-goolf-1.4.10.eb index 6fb42921f6..33c6b93585 100644 --- a/easybuild/easyconfigs/a/ALLPATHS-LG/ALLPATHS-LG-46968-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/a/ALLPATHS-LG/ALLPATHS-LG-46968-goolf-1.4.10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2013 The Cyprus Institute # Authors:: Andreas Panteli , Thekla Loizou , diff --git a/easybuild/easyconfigs/a/ALLPATHS-LG/ALLPATHS-LG-52488-foss-2016a.eb b/easybuild/easyconfigs/a/ALLPATHS-LG/ALLPATHS-LG-52488-foss-2016a.eb index 0227efebd7..27afe82b2d 100755 --- a/easybuild/easyconfigs/a/ALLPATHS-LG/ALLPATHS-LG-52488-foss-2016a.eb +++ b/easybuild/easyconfigs/a/ALLPATHS-LG/ALLPATHS-LG-52488-foss-2016a.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2013 The Cyprus Institute # Authors:: Andreas Panteli , Thekla Loizou , diff --git a/easybuild/easyconfigs/a/AMOS/AMOS-3.1.0-goolf-1.4.10.eb b/easybuild/easyconfigs/a/AMOS/AMOS-3.1.0-goolf-1.4.10.eb index e1a0148b75..440bc7a909 100644 --- a/easybuild/easyconfigs/a/AMOS/AMOS-3.1.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/a/AMOS/AMOS-3.1.0-goolf-1.4.10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Cedric Laczny , Fotis Georgatos diff --git a/easybuild/easyconfigs/a/AMOS/AMOS-3.1.0-ictce-5.3.0.eb b/easybuild/easyconfigs/a/AMOS/AMOS-3.1.0-ictce-5.3.0.eb index 7fce76229e..d767191d1b 100644 --- a/easybuild/easyconfigs/a/AMOS/AMOS-3.1.0-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/a/AMOS/AMOS-3.1.0-ictce-5.3.0.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Cedric Laczny , Fotis Georgatos diff --git a/easybuild/easyconfigs/a/APBS/APBS-1.4-linux-static-x86_64.eb b/easybuild/easyconfigs/a/APBS/APBS-1.4-linux-static-x86_64.eb index 730a5cb604..53c4769900 100644 --- a/easybuild/easyconfigs/a/APBS/APBS-1.4-linux-static-x86_64.eb +++ b/easybuild/easyconfigs/a/APBS/APBS-1.4-linux-static-x86_64.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/a/ASHS/ASHS-rev103_20140612.eb b/easybuild/easyconfigs/a/ASHS/ASHS-rev103_20140612.eb index a251f6e6b4..86e01377a6 100644 --- a/easybuild/easyconfigs/a/ASHS/ASHS-rev103_20140612.eb +++ b/easybuild/easyconfigs/a/ASHS/ASHS-rev103_20140612.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Ravi Tripathi # Email: ravi89@uab.edu diff --git a/easybuild/easyconfigs/a/AdapterRemoval/AdapterRemoval-2.2.0-foss-2016b.eb b/easybuild/easyconfigs/a/AdapterRemoval/AdapterRemoval-2.2.0-foss-2016b.eb index 738b03c0ca..50e7938a22 100644 --- a/easybuild/easyconfigs/a/AdapterRemoval/AdapterRemoval-2.2.0-foss-2016b.eb +++ b/easybuild/easyconfigs/a/AdapterRemoval/AdapterRemoval-2.2.0-foss-2016b.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild easyblock = 'MakeCp' diff --git a/easybuild/easyconfigs/a/Aspera-CLI/Aspera-CLI-3.7.2.354.010c3b8.eb b/easybuild/easyconfigs/a/Aspera-CLI/Aspera-CLI-3.7.2.354.010c3b8.eb index 576043e6dd..4f0e52ebff 100644 --- a/easybuild/easyconfigs/a/Aspera-CLI/Aspera-CLI-3.7.2.354.010c3b8.eb +++ b/easybuild/easyconfigs/a/Aspera-CLI/Aspera-CLI-3.7.2.354.010c3b8.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild # Author: Daniel D. Kinnamon # Division of Human Genetics # The Ohio State University Wexner Medical Center diff --git a/easybuild/easyconfigs/a/AutoDock_Vina/AutoDock_Vina-1.1.2_linux_x86.eb b/easybuild/easyconfigs/a/AutoDock_Vina/AutoDock_Vina-1.1.2_linux_x86.eb index 98f8c2275a..e4f561f624 100644 --- a/easybuild/easyconfigs/a/AutoDock_Vina/AutoDock_Vina-1.1.2_linux_x86.eb +++ b/easybuild/easyconfigs/a/AutoDock_Vina/AutoDock_Vina-1.1.2_linux_x86.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.13.4-goolf-1.4.10.eb b/easybuild/easyconfigs/a/Automake/Automake-1.13.4-goolf-1.4.10.eb index 11720186ff..d45cd6848d 100644 --- a/easybuild/easyconfigs/a/Automake/Automake-1.13.4-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/a/Automake/Automake-1.13.4-goolf-1.4.10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.13.4-ictce-5.3.0.eb b/easybuild/easyconfigs/a/Automake/Automake-1.13.4-ictce-5.3.0.eb index b9e7f68389..31955d8aed 100644 --- a/easybuild/easyconfigs/a/Automake/Automake-1.13.4-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/a/Automake/Automake-1.13.4-ictce-5.3.0.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.13.4-ictce-5.5.0.eb b/easybuild/easyconfigs/a/Automake/Automake-1.13.4-ictce-5.5.0.eb index 5661ddb517..30d9cf6f3a 100644 --- a/easybuild/easyconfigs/a/Automake/Automake-1.13.4-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/a/Automake/Automake-1.13.4-ictce-5.5.0.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Authors:: Alan O'Cais # $Id$ diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.14-GCC-4.8.2.eb b/easybuild/easyconfigs/a/Automake/Automake-1.14-GCC-4.8.2.eb index bec66dfd3d..07a0d34525 100644 --- a/easybuild/easyconfigs/a/Automake/Automake-1.14-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/a/Automake/Automake-1.14-GCC-4.8.2.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.14-ictce-5.3.0.eb b/easybuild/easyconfigs/a/Automake/Automake-1.14-ictce-5.3.0.eb index 2e5a33ea9b..28155619ee 100644 --- a/easybuild/easyconfigs/a/Automake/Automake-1.14-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/a/Automake/Automake-1.14-ictce-5.3.0.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.14-ictce-5.5.0.eb b/easybuild/easyconfigs/a/Automake/Automake-1.14-ictce-5.5.0.eb index 1ef76d9727..eb44e9f250 100644 --- a/easybuild/easyconfigs/a/Automake/Automake-1.14-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/a/Automake/Automake-1.14-ictce-5.5.0.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.14-intel-2016a.eb b/easybuild/easyconfigs/a/Automake/Automake-1.14-intel-2016a.eb index a1f5954bb7..f6806921ee 100644 --- a/easybuild/easyconfigs/a/Automake/Automake-1.14-intel-2016a.eb +++ b/easybuild/easyconfigs/a/Automake/Automake-1.14-intel-2016a.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.14.1-GCC-4.8.2.eb b/easybuild/easyconfigs/a/Automake/Automake-1.14.1-GCC-4.8.2.eb index 3a06e84989..8374474780 100644 --- a/easybuild/easyconfigs/a/Automake/Automake-1.14.1-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/a/Automake/Automake-1.14.1-GCC-4.8.2.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.15-GCC-4.7.2.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15-GCC-4.7.2.eb index 05705b029e..9beb6f5545 100644 --- a/easybuild/easyconfigs/a/Automake/Automake-1.15-GCC-4.7.2.eb +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15-GCC-4.7.2.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.15-GCC-4.8.4.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15-GCC-4.8.4.eb index bf119a1eaf..661344dafe 100644 --- a/easybuild/easyconfigs/a/Automake/Automake-1.15-GCC-4.8.4.eb +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15-GCC-4.8.4.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.15-GCC-4.9.2.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15-GCC-4.9.2.eb index b24d010c0a..5839e4ae64 100644 --- a/easybuild/easyconfigs/a/Automake/Automake-1.15-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15-GCC-4.9.2.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.15-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15-GCC-4.9.3-2.25.eb index a37c1d9e3b..e5248806a5 100644 --- a/easybuild/easyconfigs/a/Automake/Automake-1.15-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15-GCC-4.9.3-2.25.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.15-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15-GCC-5.4.0-2.26.eb index e42ff28556..de29b041a3 100644 --- a/easybuild/easyconfigs/a/Automake/Automake-1.15-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15-GCC-5.4.0-2.26.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.15-GCCcore-4.9.3.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15-GCCcore-4.9.3.eb index 5927ea856a..b5a5bec1bd 100644 --- a/easybuild/easyconfigs/a/Automake/Automake-1.15-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15-GCCcore-4.9.3.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.15-GCCcore-5.4.0.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15-GCCcore-5.4.0.eb index 0d4c530534..1e6da1f343 100644 --- a/easybuild/easyconfigs/a/Automake/Automake-1.15-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15-GCCcore-5.4.0.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.15-GCCcore-6.3.0.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15-GCCcore-6.3.0.eb index 304170650f..e7a39e24d8 100644 --- a/easybuild/easyconfigs/a/Automake/Automake-1.15-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15-GCCcore-6.3.0.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.15-GNU-4.9.2-2.25.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15-GNU-4.9.2-2.25.eb index f0e456c431..766349c4fd 100644 --- a/easybuild/easyconfigs/a/Automake/Automake-1.15-GNU-4.9.2-2.25.eb +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15-GNU-4.9.2-2.25.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.15-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15-GNU-4.9.3-2.25.eb index 1c089451d8..d97b8a59c7 100644 --- a/easybuild/easyconfigs/a/Automake/Automake-1.15-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15-GNU-4.9.3-2.25.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.15-GNU-5.1.0-2.25.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15-GNU-5.1.0-2.25.eb index 1d63ee839d..7cce783015 100644 --- a/easybuild/easyconfigs/a/Automake/Automake-1.15-GNU-5.1.0-2.25.eb +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15-GNU-5.1.0-2.25.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.15-foss-2015a.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15-foss-2015a.eb index 7303c3d70e..0c1ee484bc 100644 --- a/easybuild/easyconfigs/a/Automake/Automake-1.15-foss-2015a.eb +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15-foss-2015a.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.15-foss-2015b.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15-foss-2015b.eb index 543e7a0ba7..d06c3b5cb6 100644 --- a/easybuild/easyconfigs/a/Automake/Automake-1.15-foss-2015b.eb +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15-foss-2015b.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.15-foss-2016.04.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15-foss-2016.04.eb index 40213b047b..21d3b4aab0 100644 --- a/easybuild/easyconfigs/a/Automake/Automake-1.15-foss-2016.04.eb +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15-foss-2016.04.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.15-foss-2016a.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15-foss-2016a.eb index f73c4759ee..65fc481bf4 100644 --- a/easybuild/easyconfigs/a/Automake/Automake-1.15-foss-2016a.eb +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15-foss-2016a.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.15-foss-2016b.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15-foss-2016b.eb index 5c1e645dea..c72d3ad8d7 100644 --- a/easybuild/easyconfigs/a/Automake/Automake-1.15-foss-2016b.eb +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15-foss-2016b.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.15-gimkl-2.11.5.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15-gimkl-2.11.5.eb index d521a6ebe2..49bcde6b70 100644 --- a/easybuild/easyconfigs/a/Automake/Automake-1.15-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15-gimkl-2.11.5.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.15-ictce-5.3.0.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15-ictce-5.3.0.eb index cc76e86a61..3b84dabf7b 100644 --- a/easybuild/easyconfigs/a/Automake/Automake-1.15-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15-ictce-5.3.0.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.15-ictce-5.5.0.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15-ictce-5.5.0.eb index 25677b6f64..a8793fcf5f 100644 --- a/easybuild/easyconfigs/a/Automake/Automake-1.15-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15-ictce-5.5.0.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.15-intel-2015a.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15-intel-2015a.eb index 3a528809f4..a3cddb527c 100644 --- a/easybuild/easyconfigs/a/Automake/Automake-1.15-intel-2015a.eb +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15-intel-2015a.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.15-intel-2015b.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15-intel-2015b.eb index 8a059d28e6..67f074a5f9 100644 --- a/easybuild/easyconfigs/a/Automake/Automake-1.15-intel-2015b.eb +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15-intel-2015b.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.15-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15-intel-2016.02-GCC-4.9.eb index 84750fffa9..c7071ba16e 100644 --- a/easybuild/easyconfigs/a/Automake/Automake-1.15-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15-intel-2016.02-GCC-4.9.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.15-intel-2016a.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15-intel-2016a.eb index 06fbc9d74b..6ece7398d5 100644 --- a/easybuild/easyconfigs/a/Automake/Automake-1.15-intel-2016a.eb +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15-intel-2016a.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.15-intel-2016b.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15-intel-2016b.eb index 2a6c180878..d3009f88e2 100644 --- a/easybuild/easyconfigs/a/Automake/Automake-1.15-intel-2016b.eb +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15-intel-2016b.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.15-iomkl-2016.07.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15-iomkl-2016.07.eb index d787cbd50b..88bed3e485 100644 --- a/easybuild/easyconfigs/a/Automake/Automake-1.15-iomkl-2016.07.eb +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15-iomkl-2016.07.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.15-iomkl-2016.09-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15-iomkl-2016.09-GCC-4.9.3-2.25.eb index c8260533e6..97cf835b9b 100644 --- a/easybuild/easyconfigs/a/Automake/Automake-1.15-iomkl-2016.09-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15-iomkl-2016.09-GCC-4.9.3-2.25.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.15.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15.eb index 155ccd39aa..49b03cdda9 100644 --- a/easybuild/easyconfigs/a/Automake/Automake-1.15.eb +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/a/a2ps/a2ps-4.14-goolf-1.4.10.eb b/easybuild/easyconfigs/a/a2ps/a2ps-4.14-goolf-1.4.10.eb index 97e5c8330b..43ebff1094 100644 --- a/easybuild/easyconfigs/a/a2ps/a2ps-4.14-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/a/a2ps/a2ps-4.14-goolf-1.4.10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/a/a2ps/a2ps-4.14-ictce-5.3.0.eb b/easybuild/easyconfigs/a/a2ps/a2ps-4.14-ictce-5.3.0.eb index efd5845e70..7c34cc881b 100644 --- a/easybuild/easyconfigs/a/a2ps/a2ps-4.14-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/a/a2ps/a2ps-4.14-ictce-5.3.0.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/a/annovar/annovar-2016Feb01-foss-2016a-Perl-5.22.1.eb b/easybuild/easyconfigs/a/annovar/annovar-2016Feb01-foss-2016a-Perl-5.22.1.eb index e14e022891..92edb6bb67 100644 --- a/easybuild/easyconfigs/a/annovar/annovar-2016Feb01-foss-2016a-Perl-5.22.1.eb +++ b/easybuild/easyconfigs/a/annovar/annovar-2016Feb01-foss-2016a-Perl-5.22.1.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Modified by Adam Huffman # The Francis Crick Institute diff --git a/easybuild/easyconfigs/a/argtable/argtable-2.13-foss-2015b.eb b/easybuild/easyconfigs/a/argtable/argtable-2.13-foss-2015b.eb index 251023a5bd..92c65de8d1 100644 --- a/easybuild/easyconfigs/a/argtable/argtable-2.13-foss-2015b.eb +++ b/easybuild/easyconfigs/a/argtable/argtable-2.13-foss-2015b.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/a/argtable/argtable-2.13-foss-2016b.eb b/easybuild/easyconfigs/a/argtable/argtable-2.13-foss-2016b.eb index ec3422f109..2eb391926f 100644 --- a/easybuild/easyconfigs/a/argtable/argtable-2.13-foss-2016b.eb +++ b/easybuild/easyconfigs/a/argtable/argtable-2.13-foss-2016b.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/a/argtable/argtable-2.13-goolf-1.4.10.eb b/easybuild/easyconfigs/a/argtable/argtable-2.13-goolf-1.4.10.eb index 5b65e6e0a5..aa880de8ec 100644 --- a/easybuild/easyconfigs/a/argtable/argtable-2.13-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/a/argtable/argtable-2.13-goolf-1.4.10.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/a/aria2/aria2-1.15.1-goolf-1.4.10.eb b/easybuild/easyconfigs/a/aria2/aria2-1.15.1-goolf-1.4.10.eb index 7d1302187b..b870897d26 100644 --- a/easybuild/easyconfigs/a/aria2/aria2-1.15.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/a/aria2/aria2-1.15.1-goolf-1.4.10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/a/aria2/aria2-1.15.1-ictce-5.3.0.eb b/easybuild/easyconfigs/a/aria2/aria2-1.15.1-ictce-5.3.0.eb index f4d08974f2..5cbd7bb040 100644 --- a/easybuild/easyconfigs/a/aria2/aria2-1.15.1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/a/aria2/aria2-1.15.1-ictce-5.3.0.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/b/BCFtools/BCFtools-1.1-goolf-1.4.10.eb b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.1-goolf-1.4.10.eb index b307dca6af..b404abc90b 100644 --- a/easybuild/easyconfigs/b/BCFtools/BCFtools-1.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.1-goolf-1.4.10.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/b/BCFtools/BCFtools-1.3.1-goolf-1.7.20.eb b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.3.1-goolf-1.7.20.eb index d1c00e81a6..e0f7223e0f 100644 --- a/easybuild/easyconfigs/b/BCFtools/BCFtools-1.3.1-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.3.1-goolf-1.7.20.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # sciCORE - University of Basel # SIB Swiss Institute of Bioinformatics diff --git a/easybuild/easyconfigs/b/BEDOPS/BEDOPS-2.4.1-GCC-4.8.4.eb b/easybuild/easyconfigs/b/BEDOPS/BEDOPS-2.4.1-GCC-4.8.4.eb index 4ed43caefd..4efc6b0c7d 100644 --- a/easybuild/easyconfigs/b/BEDOPS/BEDOPS-2.4.1-GCC-4.8.4.eb +++ b/easybuild/easyconfigs/b/BEDOPS/BEDOPS-2.4.1-GCC-4.8.4.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/b/BEDOPS/BEDOPS-2.4.2-GCC-4.8.2.eb b/easybuild/easyconfigs/b/BEDOPS/BEDOPS-2.4.2-GCC-4.8.2.eb index ffd5f8b8e6..dc4740370e 100644 --- a/easybuild/easyconfigs/b/BEDOPS/BEDOPS-2.4.2-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/b/BEDOPS/BEDOPS-2.4.2-GCC-4.8.2.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez, Wiktor Jurkowski # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/b/BEDOPS/BEDOPS-2.4.26.eb b/easybuild/easyconfigs/b/BEDOPS/BEDOPS-2.4.26.eb index b96f53227b..8a52cdc728 100644 --- a/easybuild/easyconfigs/b/BEDOPS/BEDOPS-2.4.26.eb +++ b/easybuild/easyconfigs/b/BEDOPS/BEDOPS-2.4.26.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild easyblock = 'Tarball' diff --git a/easybuild/easyconfigs/b/BEEF/BEEF-0.1.1-r16-intel-2015a.eb b/easybuild/easyconfigs/b/BEEF/BEEF-0.1.1-r16-intel-2015a.eb index 0f53e3f3c3..ffdd4549c8 100644 --- a/easybuild/easyconfigs/b/BEEF/BEEF-0.1.1-r16-intel-2015a.eb +++ b/easybuild/easyconfigs/b/BEEF/BEEF-0.1.1-r16-intel-2015a.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Benjamin P. Roberts # New Zealand eScience Infrastructure # The University of Auckland, Auckland, New Zealand diff --git a/easybuild/easyconfigs/b/BFAST/BFAST-0.7.0a-goolf-1.4.10.eb b/easybuild/easyconfigs/b/BFAST/BFAST-0.7.0a-goolf-1.4.10.eb index a4739e8c8e..c18f95594e 100644 --- a/easybuild/easyconfigs/b/BFAST/BFAST-0.7.0a-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/BFAST/BFAST-0.7.0a-goolf-1.4.10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/b/BFAST/BFAST-0.7.0a-goolf-1.7.20.eb b/easybuild/easyconfigs/b/BFAST/BFAST-0.7.0a-goolf-1.7.20.eb index 76e9215e88..f6de18a805 100644 --- a/easybuild/easyconfigs/b/BFAST/BFAST-0.7.0a-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/b/BFAST/BFAST-0.7.0a-goolf-1.7.20.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/b/BFAST/BFAST-0.7.0a-ictce-5.3.0.eb b/easybuild/easyconfigs/b/BFAST/BFAST-0.7.0a-ictce-5.3.0.eb index 5bbf580366..14232999d6 100644 --- a/easybuild/easyconfigs/b/BFAST/BFAST-0.7.0a-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/b/BFAST/BFAST-0.7.0a-ictce-5.3.0.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/b/BH/BH-1.60.0-1-foss-2015b-R-3.2.3.eb b/easybuild/easyconfigs/b/BH/BH-1.60.0-1-foss-2015b-R-3.2.3.eb index 16cdd37dda..c0f5cd84bc 100644 --- a/easybuild/easyconfigs/b/BH/BH-1.60.0-1-foss-2015b-R-3.2.3.eb +++ b/easybuild/easyconfigs/b/BH/BH-1.60.0-1-foss-2015b-R-3.2.3.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Author: Adam Huffman # The Francis Crick Institute diff --git a/easybuild/easyconfigs/b/BLASR/BLASR-2.1-goolf-1.4.10.eb b/easybuild/easyconfigs/b/BLASR/BLASR-2.1-goolf-1.4.10.eb index 1461dc4f22..a65d17b813 100644 --- a/easybuild/easyconfigs/b/BLASR/BLASR-2.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/BLASR/BLASR-2.1-goolf-1.4.10.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/b/BLASR/BLASR-2.2-intel-2016b.eb b/easybuild/easyconfigs/b/BLASR/BLASR-2.2-intel-2016b.eb index d31c4ec289..eaea479586 100644 --- a/easybuild/easyconfigs/b/BLASR/BLASR-2.2-intel-2016b.eb +++ b/easybuild/easyconfigs/b/BLASR/BLASR-2.2-intel-2016b.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.27-goolf-1.4.10.eb b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.27-goolf-1.4.10.eb index d441a3b6be..94be2abbf8 100644 --- a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.27-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.27-goolf-1.4.10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.28-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.28-goolf-1.4.10-Python-2.7.3.eb index f3f69270a5..b6365defe3 100644 --- a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.28-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.28-goolf-1.4.10-Python-2.7.3.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos , Kenneth Hoste (UGent) diff --git a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.28-goolf-1.4.10.eb b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.28-goolf-1.4.10.eb index 0da49b06b6..4d988cb0cd 100644 --- a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.28-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.28-goolf-1.4.10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos , Kenneth Hoste (UGent) diff --git a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.28-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.28-ictce-5.3.0-Python-2.7.3.eb index a4329e5cf5..2fb0a6aeec 100644 --- a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.28-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.28-ictce-5.3.0-Python-2.7.3.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos , Kenneth Hoste (UGent) diff --git a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.28-ictce-5.3.0.eb b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.28-ictce-5.3.0.eb index a55a29ffe4..c4c54549a4 100644 --- a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.28-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.28-ictce-5.3.0.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos , Kenneth Hoste (UGent) diff --git a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.30-foss-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.30-foss-2015a-Python-2.7.9.eb index 8c97b6b7aa..3c11c9414b 100644 --- a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.30-foss-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.30-foss-2015a-Python-2.7.9.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2013 University of Luxembourg/Luxembourg Centre for Systems Biomedicine # Authors:: Fotis Georgatos , Kenneth Hoste (UGent) diff --git a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.30-goolf-1.4.10.eb b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.30-goolf-1.4.10.eb index 5daf7c4b33..60d5401e1e 100644 --- a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.30-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.30-goolf-1.4.10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2013 University of Luxembourg/Luxembourg Centre for Systems Biomedicine # Authors:: Fotis Georgatos , Kenneth Hoste (UGent) diff --git a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.30-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.30-intel-2015a-Python-2.7.9.eb index 87e25ede69..6c427e6894 100644 --- a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.30-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.30-intel-2015a-Python-2.7.9.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos , Kenneth Hoste (UGent) diff --git a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.31-foss-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.31-foss-2015b-Python-2.7.10.eb index a64fc6a528..a02e6a5b24 100644 --- a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.31-foss-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.31-foss-2015b-Python-2.7.10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos , Kenneth Hoste (UGent) diff --git a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.31-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.31-intel-2015a-Python-2.7.10.eb index e09b9fd298..85d9b0cc0d 100644 --- a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.31-intel-2015a-Python-2.7.10.eb +++ b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.31-intel-2015a-Python-2.7.10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos , Kenneth Hoste (UGent) diff --git a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.31-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.31-intel-2015b-Python-2.7.10.eb index a150b8d6d9..6dc430a123 100644 --- a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.31-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.31-intel-2015b-Python-2.7.10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos , Kenneth Hoste (UGent) diff --git a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.3.0-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.3.0-foss-2016a-Python-2.7.11.eb index c7b71288fa..866b25a202 100644 --- a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.3.0-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.3.0-foss-2016a-Python-2.7.11.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos , Kenneth Hoste (UGent) diff --git a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.6.0-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.6.0-intel-2017a-Python-2.7.13.eb index 37ae5901c6..654ef1d919 100644 --- a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.6.0-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.6.0-intel-2017a-Python-2.7.13.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos , Kenneth Hoste (UGent) diff --git a/easybuild/easyconfigs/b/BLAST/BLAST-2.2.26-Linux_x86_64.eb b/easybuild/easyconfigs/b/BLAST/BLAST-2.2.26-Linux_x86_64.eb index 5befdd3e11..98748d456d 100644 --- a/easybuild/easyconfigs/b/BLAST/BLAST-2.2.26-Linux_x86_64.eb +++ b/easybuild/easyconfigs/b/BLAST/BLAST-2.2.26-Linux_x86_64.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/b/BLAT/BLAT-3.5-goolf-1.4.10.eb b/easybuild/easyconfigs/b/BLAT/BLAT-3.5-goolf-1.4.10.eb index eb88b061dd..083100e335 100644 --- a/easybuild/easyconfigs/b/BLAT/BLAT-3.5-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/BLAT/BLAT-3.5-goolf-1.4.10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2013 The Cyprus Institute # Authors:: Andreas Panteli , Thekla Loizou diff --git a/easybuild/easyconfigs/b/BLAT/BLAT-3.5-ictce-5.5.0-libpng-1.6.9.eb b/easybuild/easyconfigs/b/BLAT/BLAT-3.5-ictce-5.5.0-libpng-1.6.9.eb index 0222da1546..df2e50f7ef 100644 --- a/easybuild/easyconfigs/b/BLAT/BLAT-3.5-ictce-5.5.0-libpng-1.6.9.eb +++ b/easybuild/easyconfigs/b/BLAT/BLAT-3.5-ictce-5.5.0-libpng-1.6.9.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2013 The Cyprus Institute # Authors:: Andreas Panteli , Thekla Loizou diff --git a/easybuild/easyconfigs/b/BLAT/BLAT-3.5-ictce-5.5.0.eb b/easybuild/easyconfigs/b/BLAT/BLAT-3.5-ictce-5.5.0.eb index 955ee61e30..c62cc8c37c 100644 --- a/easybuild/easyconfigs/b/BLAT/BLAT-3.5-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/b/BLAT/BLAT-3.5-ictce-5.5.0.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2013 The Cyprus Institute # Authors:: Andreas Panteli , Thekla Loizou diff --git a/easybuild/easyconfigs/b/BLAT/BLAT-3.5-intel-2016b.eb b/easybuild/easyconfigs/b/BLAT/BLAT-3.5-intel-2016b.eb index dfa7db4489..73121f1b93 100644 --- a/easybuild/easyconfigs/b/BLAT/BLAT-3.5-intel-2016b.eb +++ b/easybuild/easyconfigs/b/BLAT/BLAT-3.5-intel-2016b.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2013 The Cyprus Institute # Authors:: Andreas Panteli , Thekla Loizou diff --git a/easybuild/easyconfigs/b/BLAT/BLAT-3.5-intel-2017a.eb b/easybuild/easyconfigs/b/BLAT/BLAT-3.5-intel-2017a.eb index 7e57ded042..6ccbd52bf5 100644 --- a/easybuild/easyconfigs/b/BLAT/BLAT-3.5-intel-2017a.eb +++ b/easybuild/easyconfigs/b/BLAT/BLAT-3.5-intel-2017a.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2013 The Cyprus Institute # Authors:: Andreas Panteli , Thekla Loizou diff --git a/easybuild/easyconfigs/b/BWA/BWA-0.6.2-goolf-1.4.10.eb b/easybuild/easyconfigs/b/BWA/BWA-0.6.2-goolf-1.4.10.eb index 88e63bb1ae..8ffe52e8b4 100644 --- a/easybuild/easyconfigs/b/BWA/BWA-0.6.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/BWA/BWA-0.6.2-goolf-1.4.10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Cedric Laczny , Fotis Georgatos diff --git a/easybuild/easyconfigs/b/BWA/BWA-0.6.2-ictce-5.3.0.eb b/easybuild/easyconfigs/b/BWA/BWA-0.6.2-ictce-5.3.0.eb index bd449ad58f..347e942fa7 100644 --- a/easybuild/easyconfigs/b/BWA/BWA-0.6.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/b/BWA/BWA-0.6.2-ictce-5.3.0.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Cedric Laczny , Fotis Georgatos diff --git a/easybuild/easyconfigs/b/BWA/BWA-0.7.13-foss-2015b.eb b/easybuild/easyconfigs/b/BWA/BWA-0.7.13-foss-2015b.eb index 2018ca59b4..bc277b6746 100644 --- a/easybuild/easyconfigs/b/BWA/BWA-0.7.13-foss-2015b.eb +++ b/easybuild/easyconfigs/b/BWA/BWA-0.7.13-foss-2015b.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Cyprus Institute / CaSToRC, Uni.Lu/LCSB, NTUA # Authors:: George Tsouloupas , Fotis Georgatos diff --git a/easybuild/easyconfigs/b/BWA/BWA-0.7.13-foss-2016a.eb b/easybuild/easyconfigs/b/BWA/BWA-0.7.13-foss-2016a.eb index 419aba7bab..5701149cf0 100644 --- a/easybuild/easyconfigs/b/BWA/BWA-0.7.13-foss-2016a.eb +++ b/easybuild/easyconfigs/b/BWA/BWA-0.7.13-foss-2016a.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Cyprus Institute / CaSToRC, Uni.Lu/LCSB, NTUA # Authors:: George Tsouloupas , Fotis Georgatos diff --git a/easybuild/easyconfigs/b/BWA/BWA-0.7.13-goolf-1.4.10.eb b/easybuild/easyconfigs/b/BWA/BWA-0.7.13-goolf-1.4.10.eb index 2dbdeeb980..8727436b5f 100644 --- a/easybuild/easyconfigs/b/BWA/BWA-0.7.13-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/BWA/BWA-0.7.13-goolf-1.4.10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Cyprus Institute / CaSToRC, Uni.Lu/LCSB, NTUA # Authors:: George Tsouloupas , Fotis Georgatos , diff --git a/easybuild/easyconfigs/b/BWA/BWA-0.7.13-intel-2016a.eb b/easybuild/easyconfigs/b/BWA/BWA-0.7.13-intel-2016a.eb index f4774cbbbe..17ac0a8257 100644 --- a/easybuild/easyconfigs/b/BWA/BWA-0.7.13-intel-2016a.eb +++ b/easybuild/easyconfigs/b/BWA/BWA-0.7.13-intel-2016a.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Cyprus Institute / CaSToRC, Uni.Lu/LCSB, NTUA # Authors:: George Tsouloupas , Fotis Georgatos diff --git a/easybuild/easyconfigs/b/BWA/BWA-0.7.15-foss-2016a.eb b/easybuild/easyconfigs/b/BWA/BWA-0.7.15-foss-2016a.eb index 88e524cd9d..44614302d1 100644 --- a/easybuild/easyconfigs/b/BWA/BWA-0.7.15-foss-2016a.eb +++ b/easybuild/easyconfigs/b/BWA/BWA-0.7.15-foss-2016a.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Cyprus Institute / CaSToRC, Uni.Lu/LCSB, NTUA # Authors:: George Tsouloupas , Fotis Georgatos diff --git a/easybuild/easyconfigs/b/BWA/BWA-0.7.15-intel-2016b.eb b/easybuild/easyconfigs/b/BWA/BWA-0.7.15-intel-2016b.eb index 62b042ace9..e96ea32189 100644 --- a/easybuild/easyconfigs/b/BWA/BWA-0.7.15-intel-2016b.eb +++ b/easybuild/easyconfigs/b/BWA/BWA-0.7.15-intel-2016b.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Cyprus Institute / CaSToRC, Uni.Lu/LCSB, NTUA # Authors:: George Tsouloupas , Fotis Georgatos diff --git a/easybuild/easyconfigs/b/BWA/BWA-0.7.15-intel-2017a.eb b/easybuild/easyconfigs/b/BWA/BWA-0.7.15-intel-2017a.eb index 04f7fad391..587cba3307 100644 --- a/easybuild/easyconfigs/b/BWA/BWA-0.7.15-intel-2017a.eb +++ b/easybuild/easyconfigs/b/BWA/BWA-0.7.15-intel-2017a.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Cyprus Institute / CaSToRC, Uni.Lu/LCSB, NTUA # Authors:: George Tsouloupas , Fotis Georgatos diff --git a/easybuild/easyconfigs/b/BWA/BWA-0.7.4-goolf-1.4.10.eb b/easybuild/easyconfigs/b/BWA/BWA-0.7.4-goolf-1.4.10.eb index 6c6c1aff71..440154e3c4 100644 --- a/easybuild/easyconfigs/b/BWA/BWA-0.7.4-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/BWA/BWA-0.7.4-goolf-1.4.10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Cyprus Institute / CaSToRC, Uni.Lu/LCSB, NTUA # Authors:: George Tsouloupas , Fotis Georgatos diff --git a/easybuild/easyconfigs/b/BWA/BWA-0.7.4-ictce-5.3.0.eb b/easybuild/easyconfigs/b/BWA/BWA-0.7.4-ictce-5.3.0.eb index 66de8f1a86..d9ece5f8bc 100644 --- a/easybuild/easyconfigs/b/BWA/BWA-0.7.4-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/b/BWA/BWA-0.7.4-ictce-5.3.0.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Cyprus Institute / CaSToRC, Uni.Lu/LCSB, NTUA # Authors:: George Tsouloupas , Fotis Georgatos diff --git a/easybuild/easyconfigs/b/BWA/BWA-0.7.5a-goolf-1.4.10.eb b/easybuild/easyconfigs/b/BWA/BWA-0.7.5a-goolf-1.4.10.eb index 860efca9e4..de76a6f003 100644 --- a/easybuild/easyconfigs/b/BWA/BWA-0.7.5a-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/BWA/BWA-0.7.5a-goolf-1.4.10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Cyprus Institute / CaSToRC, Uni.Lu/LCSB, NTUA # Authors:: George Tsouloupas , Fotis Georgatos diff --git a/easybuild/easyconfigs/b/BXH_XCEDE_TOOLS/BXH_XCEDE_TOOLS-1.11.1.eb b/easybuild/easyconfigs/b/BXH_XCEDE_TOOLS/BXH_XCEDE_TOOLS-1.11.1.eb index c0802f9ddd..1584cea297 100644 --- a/easybuild/easyconfigs/b/BXH_XCEDE_TOOLS/BXH_XCEDE_TOOLS-1.11.1.eb +++ b/easybuild/easyconfigs/b/BXH_XCEDE_TOOLS/BXH_XCEDE_TOOLS-1.11.1.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Ravi Tripathi # Email: ravi89@uab.edu diff --git a/easybuild/easyconfigs/b/BamTools/BamTools-2.2.3-goolf-1.4.10.eb b/easybuild/easyconfigs/b/BamTools/BamTools-2.2.3-goolf-1.4.10.eb index 3c60714d7f..b2223051af 100644 --- a/easybuild/easyconfigs/b/BamTools/BamTools-2.2.3-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/BamTools/BamTools-2.2.3-goolf-1.4.10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2013 The Cyprus Institute # Authors:: Andreas Panteli , George Tsouloupas diff --git a/easybuild/easyconfigs/b/BamTools/BamTools-2.2.3-ictce-5.3.0.eb b/easybuild/easyconfigs/b/BamTools/BamTools-2.2.3-ictce-5.3.0.eb index 7fbeba0c2d..8ff8d44b31 100644 --- a/easybuild/easyconfigs/b/BamTools/BamTools-2.2.3-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/b/BamTools/BamTools-2.2.3-ictce-5.3.0.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2013 The Cyprus Institute # Authors:: Andreas Panteli , George Tsouloupas diff --git a/easybuild/easyconfigs/b/BamTools/BamTools-2.4.0-foss-2015b.eb b/easybuild/easyconfigs/b/BamTools/BamTools-2.4.0-foss-2015b.eb index 9e9c2961a5..4cba6a6b0e 100644 --- a/easybuild/easyconfigs/b/BamTools/BamTools-2.4.0-foss-2015b.eb +++ b/easybuild/easyconfigs/b/BamTools/BamTools-2.4.0-foss-2015b.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2013 The Cyprus Institute # Authors:: Andreas Panteli , George Tsouloupas diff --git a/easybuild/easyconfigs/b/BamTools/BamTools-2.4.0-foss-2016b.eb b/easybuild/easyconfigs/b/BamTools/BamTools-2.4.0-foss-2016b.eb index b1a2aa0cf6..9f0e3941f0 100644 --- a/easybuild/easyconfigs/b/BamTools/BamTools-2.4.0-foss-2016b.eb +++ b/easybuild/easyconfigs/b/BamTools/BamTools-2.4.0-foss-2016b.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2013 The Cyprus Institute # Authors:: Andreas Panteli , George Tsouloupas diff --git a/easybuild/easyconfigs/b/BamUtil/BamUtil-1.0.13-foss-2015b.eb b/easybuild/easyconfigs/b/BamUtil/BamUtil-1.0.13-foss-2015b.eb index bbca7a748e..f601bc63da 100644 --- a/easybuild/easyconfigs/b/BamUtil/BamUtil-1.0.13-foss-2015b.eb +++ b/easybuild/easyconfigs/b/BamUtil/BamUtil-1.0.13-foss-2015b.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Author: Adam Huffman # adam.huffman@crick.ac.uk diff --git a/easybuild/easyconfigs/b/BamUtil/BamUtil-1.0.13-intel-2016b.eb b/easybuild/easyconfigs/b/BamUtil/BamUtil-1.0.13-intel-2016b.eb index ceadf51bc5..65f9d502aa 100644 --- a/easybuild/easyconfigs/b/BamUtil/BamUtil-1.0.13-intel-2016b.eb +++ b/easybuild/easyconfigs/b/BamUtil/BamUtil-1.0.13-intel-2016b.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Author: Adam Huffman # adam.huffman@crick.ac.uk diff --git a/easybuild/easyconfigs/b/Bash/Bash-4.2-goolf-1.4.10.eb b/easybuild/easyconfigs/b/Bash/Bash-4.2-goolf-1.4.10.eb index 7cf887ea82..528d89262c 100644 --- a/easybuild/easyconfigs/b/Bash/Bash-4.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/Bash/Bash-4.2-goolf-1.4.10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2013 University of Luxembourg/Computer Science and Communications Research Unit # Authors:: Valentin Plugaru diff --git a/easybuild/easyconfigs/b/Bash/Bash-4.2-ictce-5.3.0.eb b/easybuild/easyconfigs/b/Bash/Bash-4.2-ictce-5.3.0.eb index b45858d56f..8432304838 100644 --- a/easybuild/easyconfigs/b/Bash/Bash-4.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/b/Bash/Bash-4.2-ictce-5.3.0.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2013 University of Luxembourg/Computer Science and Communications Research Unit # Authors:: Valentin Plugaru diff --git a/easybuild/easyconfigs/b/Bash/Bash-4.3-GCC-4.9.2.eb b/easybuild/easyconfigs/b/Bash/Bash-4.3-GCC-4.9.2.eb index 3d11d3fad4..c6c7915da3 100644 --- a/easybuild/easyconfigs/b/Bash/Bash-4.3-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/b/Bash/Bash-4.3-GCC-4.9.2.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild ## # Copyright:: Copyright 2012-2013 University of Luxembourg/Computer Science and Communications Research Unit # Authors:: Valentin Plugaru diff --git a/easybuild/easyconfigs/b/BayPass/BayPass-2.1-goolf-1.7.20.eb b/easybuild/easyconfigs/b/BayPass/BayPass-2.1-goolf-1.7.20.eb index 65f14b74d8..25bcd12143 100644 --- a/easybuild/easyconfigs/b/BayPass/BayPass-2.1-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/b/BayPass/BayPass-2.1-goolf-1.7.20.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # sciCORE - University of Basel # SIB Swiss Institute of Bioinformatics diff --git a/easybuild/easyconfigs/b/BayeScEnv/BayeScEnv-1.1-foss-2016a.eb b/easybuild/easyconfigs/b/BayeScEnv/BayeScEnv-1.1-foss-2016a.eb index 25707a1810..e2b2f40c7e 100644 --- a/easybuild/easyconfigs/b/BayeScEnv/BayeScEnv-1.1-foss-2016a.eb +++ b/easybuild/easyconfigs/b/BayeScEnv/BayeScEnv-1.1-foss-2016a.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # sciCORE - University of Basel # SIB Swiss Institute of Bioinformatics diff --git a/easybuild/easyconfigs/b/BayeScEnv/BayeScEnv-1.1-goolf-1.4.10.eb b/easybuild/easyconfigs/b/BayeScEnv/BayeScEnv-1.1-goolf-1.4.10.eb index a0b996743d..336a764164 100644 --- a/easybuild/easyconfigs/b/BayeScEnv/BayeScEnv-1.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/BayeScEnv/BayeScEnv-1.1-goolf-1.4.10.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # sciCORE - University of Basel # SIB Swiss Institute of Bioinformatics diff --git a/easybuild/easyconfigs/b/BayeScan/BayeScan-2.1-foss-2016a.eb b/easybuild/easyconfigs/b/BayeScan/BayeScan-2.1-foss-2016a.eb index ebd814c54e..f1ea19dfa0 100644 --- a/easybuild/easyconfigs/b/BayeScan/BayeScan-2.1-foss-2016a.eb +++ b/easybuild/easyconfigs/b/BayeScan/BayeScan-2.1-foss-2016a.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # sciCORE - University of Basel # SIB Swiss Institute of Bioinformatics diff --git a/easybuild/easyconfigs/b/BayeScan/BayeScan-2.1-goolf-1.4.10.eb b/easybuild/easyconfigs/b/BayeScan/BayeScan-2.1-goolf-1.4.10.eb index 2902acfde6..3a8d229257 100644 --- a/easybuild/easyconfigs/b/BayeScan/BayeScan-2.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/BayeScan/BayeScan-2.1-goolf-1.4.10.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # sciCORE - University of Basel # SIB Swiss Institute of Bioinformatics diff --git a/easybuild/easyconfigs/b/BayesTraits/BayesTraits-1.0-linux32.eb b/easybuild/easyconfigs/b/BayesTraits/BayesTraits-1.0-linux32.eb index 8d561cd81b..d034b7c154 100644 --- a/easybuild/easyconfigs/b/BayesTraits/BayesTraits-1.0-linux32.eb +++ b/easybuild/easyconfigs/b/BayesTraits/BayesTraits-1.0-linux32.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/b/BayesTraits/BayesTraits-2.0-Beta-Linux64.eb b/easybuild/easyconfigs/b/BayesTraits/BayesTraits-2.0-Beta-Linux64.eb index 29cb55f251..a7199d6201 100644 --- a/easybuild/easyconfigs/b/BayesTraits/BayesTraits-2.0-Beta-Linux64.eb +++ b/easybuild/easyconfigs/b/BayesTraits/BayesTraits-2.0-Beta-Linux64.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/b/Beast/Beast-1.8.4.eb b/easybuild/easyconfigs/b/Beast/Beast-1.8.4.eb index 283940594d..c94bcc0b40 100644 --- a/easybuild/easyconfigs/b/Beast/Beast-1.8.4.eb +++ b/easybuild/easyconfigs/b/Beast/Beast-1.8.4.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/b/Beast/Beast-2.1.3.eb b/easybuild/easyconfigs/b/Beast/Beast-2.1.3.eb index f28387fbee..512e98ad2a 100644 --- a/easybuild/easyconfigs/b/Beast/Beast-2.1.3.eb +++ b/easybuild/easyconfigs/b/Beast/Beast-2.1.3.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/b/Beast/Beast-2.4.0-foss-2016a.eb b/easybuild/easyconfigs/b/Beast/Beast-2.4.0-foss-2016a.eb index 484da63909..1e44caf2ee 100644 --- a/easybuild/easyconfigs/b/Beast/Beast-2.4.0-foss-2016a.eb +++ b/easybuild/easyconfigs/b/Beast/Beast-2.4.0-foss-2016a.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/b/Biopython/Biopython-1.61-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/b/Biopython/Biopython-1.61-goolf-1.4.10-Python-2.7.3.eb index 26ff0e4f6a..5462b9b74f 100644 --- a/easybuild/easyconfigs/b/Biopython/Biopython-1.61-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/b/Biopython/Biopython-1.61-goolf-1.4.10-Python-2.7.3.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2013 The Cyprus Institute # Authors:: Andreas Panteli , Thekla Loizou , diff --git a/easybuild/easyconfigs/b/Biopython/Biopython-1.61-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/b/Biopython/Biopython-1.61-ictce-5.3.0-Python-2.7.3.eb index 462ab92f17..bb428926a0 100644 --- a/easybuild/easyconfigs/b/Biopython/Biopython-1.61-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/b/Biopython/Biopython-1.61-ictce-5.3.0-Python-2.7.3.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2013 The Cyprus Institute # Authors:: Andreas Panteli , Thekla Loizou , diff --git a/easybuild/easyconfigs/b/Biopython/Biopython-1.65-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/b/Biopython/Biopython-1.65-foss-2016a-Python-2.7.11.eb index c5aa94f58c..cc4c98123e 100644 --- a/easybuild/easyconfigs/b/Biopython/Biopython-1.65-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/b/Biopython/Biopython-1.65-foss-2016a-Python-2.7.11.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2013 The Cyprus Institute # Authors:: Andreas Panteli , Thekla Loizou , diff --git a/easybuild/easyconfigs/b/Biopython/Biopython-1.68-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/b/Biopython/Biopython-1.68-foss-2016b-Python-2.7.12.eb index f5a410bf23..74455b1860 100644 --- a/easybuild/easyconfigs/b/Biopython/Biopython-1.68-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/b/Biopython/Biopython-1.68-foss-2016b-Python-2.7.12.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2013 The Cyprus Institute # Authors:: Andreas Panteli , Thekla Loizou , diff --git a/easybuild/easyconfigs/b/Biopython/Biopython-1.68-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/b/Biopython/Biopython-1.68-intel-2016b-Python-2.7.12.eb index 762f84f558..7f7a694462 100644 --- a/easybuild/easyconfigs/b/Biopython/Biopython-1.68-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/b/Biopython/Biopython-1.68-intel-2016b-Python-2.7.12.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2013 The Cyprus Institute # Authors:: Andreas Panteli , Thekla Loizou , diff --git a/easybuild/easyconfigs/b/Biopython/Biopython-1.68-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/b/Biopython/Biopython-1.68-intel-2016b-Python-3.5.2.eb index 36d03b946c..cb2c07fb7f 100644 --- a/easybuild/easyconfigs/b/Biopython/Biopython-1.68-intel-2016b-Python-3.5.2.eb +++ b/easybuild/easyconfigs/b/Biopython/Biopython-1.68-intel-2016b-Python-3.5.2.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2013 The Cyprus Institute # Authors:: Andreas Panteli , Thekla Loizou , diff --git a/easybuild/easyconfigs/b/Bismark/Bismark-0.10.1-goolf-1.4.10.eb b/easybuild/easyconfigs/b/Bismark/Bismark-0.10.1-goolf-1.4.10.eb index ee96cc0a43..d6a0d16ca9 100644 --- a/easybuild/easyconfigs/b/Bismark/Bismark-0.10.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/Bismark/Bismark-0.10.1-goolf-1.4.10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2013-2014 The Cyprus Institute # Authors:: Thekla Loizou diff --git a/easybuild/easyconfigs/b/BitSeq/BitSeq-0.7.0-goolf-1.4.10.eb b/easybuild/easyconfigs/b/BitSeq/BitSeq-0.7.0-goolf-1.4.10.eb index 5a270ebc00..49a48ad18f 100644 --- a/easybuild/easyconfigs/b/BitSeq/BitSeq-0.7.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/BitSeq/BitSeq-0.7.0-goolf-1.4.10.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/b/Bonnie++/Bonnie++-1.03e-goolf-1.4.10.eb b/easybuild/easyconfigs/b/Bonnie++/Bonnie++-1.03e-goolf-1.4.10.eb index fd432782eb..63fcc66046 100644 --- a/easybuild/easyconfigs/b/Bonnie++/Bonnie++-1.03e-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/Bonnie++/Bonnie++-1.03e-goolf-1.4.10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/b/Bonnie++/Bonnie++-1.03e-ictce-5.3.0.eb b/easybuild/easyconfigs/b/Bonnie++/Bonnie++-1.03e-ictce-5.3.0.eb index c663871a9c..cce4aa524a 100644 --- a/easybuild/easyconfigs/b/Bonnie++/Bonnie++-1.03e-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/b/Bonnie++/Bonnie++-1.03e-ictce-5.3.0.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/b/Bonnie++/Bonnie++-1.97-foss-2016a.eb b/easybuild/easyconfigs/b/Bonnie++/Bonnie++-1.97-foss-2016a.eb index f63a76fa69..b9cf727486 100644 --- a/easybuild/easyconfigs/b/Bonnie++/Bonnie++-1.97-foss-2016a.eb +++ b/easybuild/easyconfigs/b/Bonnie++/Bonnie++-1.97-foss-2016a.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.2-goolf-1.4.10.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.2-goolf-1.4.10.eb index f334c5a116..696fee331f 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.2-goolf-1.4.10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Cedric Laczny , Fotis Georgatos diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.2-ictce-5.3.0.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.2-ictce-5.3.0.eb index fa8a4e145b..c6f9f99e38 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.2-ictce-5.3.0.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Cedric Laczny , Fotis Georgatos diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.5-goolf-1.4.10.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.5-goolf-1.4.10.eb index a81247d559..5f0e98a15a 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.5-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.5-goolf-1.4.10.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.6-goolf-1.4.10.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.6-goolf-1.4.10.eb index 00cfc5cb06..45020b3fa7 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.6-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.6-goolf-1.4.10.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.1.0-goolf-1.4.10.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.1.0-goolf-1.4.10.eb index 8f006d9054..151407252c 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.1.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.1.0-goolf-1.4.10.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.1.0-ictce-5.5.0.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.1.0-ictce-5.5.0.eb index de611ce79f..ed9036db9f 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.1.0-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.1.0-ictce-5.5.0.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Cedric Laczny , Fotis Georgatos diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.0-goolf-1.4.10.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.0-goolf-1.4.10.eb index 9dc4955f2b..f453956b9e 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.0-goolf-1.4.10.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.2-goolf-1.4.10.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.2-goolf-1.4.10.eb index 535fcdd94e..d67420cc10 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.2-goolf-1.4.10.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.4-goolf-1.4.10.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.4-goolf-1.4.10.eb index 8e2370c316..726d063f44 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.4-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.4-goolf-1.4.10.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.5-goolf-1.7.20.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.5-goolf-1.7.20.eb index b011315af8..91e64b60c7 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.5-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.5-goolf-1.7.20.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.5-intel-2015a.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.5-intel-2015a.eb index 4dca70247f..7849523909 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.5-intel-2015a.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.5-intel-2015a.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.6-foss-2015b.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.6-foss-2015b.eb index 6cd8cef8b8..379fb19b0a 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.6-foss-2015b.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.6-foss-2015b.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.6-intel-2015b.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.6-intel-2015b.eb index 5c6e44e1e9..37dd9eeb5e 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.6-intel-2015b.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.6-intel-2015b.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.7-foss-2015b.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.7-foss-2015b.eb index 7cd080fdb1..e3549fe5dc 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.7-foss-2015b.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.7-foss-2015b.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.8-foss-2015b.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.8-foss-2015b.eb index e6c1bebf90..c461c553d1 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.8-foss-2015b.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.8-foss-2015b.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.8-foss-2016a.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.8-foss-2016a.eb index 4982ab4d19..35ea0c2d17 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.8-foss-2016a.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.8-foss-2016a.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9-foss-2016a.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9-foss-2016a.eb index cf2e82b71c..2e3a3b0513 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9-foss-2016a.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9-foss-2016a.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9-goolf-1.7.20.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9-goolf-1.7.20.eb index 637e625710..728208e851 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9-goolf-1.7.20.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9-intel-2016b.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9-intel-2016b.eb index ba74ca9337..cadc838afb 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9-intel-2016b.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9-intel-2016b.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.3.2-intel-2017a.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.3.2-intel-2017a.eb index 8b78bff172..875117f165 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.3.2-intel-2017a.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.3.2-intel-2017a.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/b/bam-readcount/bam-readcount-0.7.4-foss-2015b.eb b/easybuild/easyconfigs/b/bam-readcount/bam-readcount-0.7.4-foss-2015b.eb index 9f5b2f295c..2bde81198c 100644 --- a/easybuild/easyconfigs/b/bam-readcount/bam-readcount-0.7.4-foss-2015b.eb +++ b/easybuild/easyconfigs/b/bam-readcount/bam-readcount-0.7.4-foss-2015b.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Adam Huffman # The Francis Crick Institute easyblock = 'CMakeMake' diff --git a/easybuild/easyconfigs/b/bam2fastq/bam2fastq-1.1.0-goolf-1.4.10.eb b/easybuild/easyconfigs/b/bam2fastq/bam2fastq-1.1.0-goolf-1.4.10.eb index c86e6e0a3b..17f4948e3d 100644 --- a/easybuild/easyconfigs/b/bam2fastq/bam2fastq-1.1.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/bam2fastq/bam2fastq-1.1.0-goolf-1.4.10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Cyprus Institute / CaSToRC, Uni.Lu/LCSB, NTUA # Authors:: George Tsouloupas , Fotis Georgatos , Kenneth Hoste (UGent) diff --git a/easybuild/easyconfigs/b/bam2fastq/bam2fastq-1.1.0-ictce-5.3.0.eb b/easybuild/easyconfigs/b/bam2fastq/bam2fastq-1.1.0-ictce-5.3.0.eb index 4398ec5150..6826ce4726 100644 --- a/easybuild/easyconfigs/b/bam2fastq/bam2fastq-1.1.0-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/b/bam2fastq/bam2fastq-1.1.0-ictce-5.3.0.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Cyprus Institute / CaSToRC, Uni.Lu/LCSB, NTUA # Authors:: George Tsouloupas , Fotis Georgatos , Kenneth Hoste (UGent) diff --git a/easybuild/easyconfigs/b/bbFTP/bbFTP-3.2.0-goolf-1.4.10.eb b/easybuild/easyconfigs/b/bbFTP/bbFTP-3.2.0-goolf-1.4.10.eb index b334202a6e..b5a8101154 100644 --- a/easybuild/easyconfigs/b/bbFTP/bbFTP-3.2.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/bbFTP/bbFTP-3.2.0-goolf-1.4.10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/b/bbFTP/bbFTP-3.2.1-intel-2016a.eb b/easybuild/easyconfigs/b/bbFTP/bbFTP-3.2.1-intel-2016a.eb index 3c955962eb..4eba5f7b79 100644 --- a/easybuild/easyconfigs/b/bbFTP/bbFTP-3.2.1-intel-2016a.eb +++ b/easybuild/easyconfigs/b/bbFTP/bbFTP-3.2.1-intel-2016a.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/b/bbcp/bbcp-12.01.30.00.0-amd64_linux26.eb b/easybuild/easyconfigs/b/bbcp/bbcp-12.01.30.00.0-amd64_linux26.eb index 738e6ce0b1..4779d17ea8 100644 --- a/easybuild/easyconfigs/b/bbcp/bbcp-12.01.30.00.0-amd64_linux26.eb +++ b/easybuild/easyconfigs/b/bbcp/bbcp-12.01.30.00.0-amd64_linux26.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/b/bbftpPRO/bbftpPRO-9.3.1-goolf-1.4.10.eb b/easybuild/easyconfigs/b/bbftpPRO/bbftpPRO-9.3.1-goolf-1.4.10.eb index 29c92454a6..fe465ff81c 100644 --- a/easybuild/easyconfigs/b/bbftpPRO/bbftpPRO-9.3.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/bbftpPRO/bbftpPRO-9.3.1-goolf-1.4.10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/b/bbftpPRO/bbftpPRO-9.3.1-ictce-5.3.0.eb b/easybuild/easyconfigs/b/bbftpPRO/bbftpPRO-9.3.1-ictce-5.3.0.eb index 21a811ccbf..45d006c6b1 100644 --- a/easybuild/easyconfigs/b/bbftpPRO/bbftpPRO-9.3.1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/b/bbftpPRO/bbftpPRO-9.3.1-ictce-5.3.0.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/b/bc/bc-1.06.95-GCC-4.8.2.eb b/easybuild/easyconfigs/b/bc/bc-1.06.95-GCC-4.8.2.eb index 3755390098..a2bbef0236 100644 --- a/easybuild/easyconfigs/b/bc/bc-1.06.95-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/b/bc/bc-1.06.95-GCC-4.8.2.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # ## diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.22-goolf-1.4.10.eb b/easybuild/easyconfigs/b/binutils/binutils-2.22-goolf-1.4.10.eb index de87300f7c..1c728da8c0 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.22-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.22-goolf-1.4.10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.22-goolf-1.5.14.eb b/easybuild/easyconfigs/b/binutils/binutils-2.22-goolf-1.5.14.eb index d989a00acf..b9f1d711c1 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.22-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.22-goolf-1.5.14.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2013 University of Luxembourg/Luxembourg Centre for Systems Biomedicine # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/b/biodeps/biodeps-1.6-goolf-1.4.10-extended.eb b/easybuild/easyconfigs/b/biodeps/biodeps-1.6-goolf-1.4.10-extended.eb index 428ecbe9cf..847f035741 100644 --- a/easybuild/easyconfigs/b/biodeps/biodeps-1.6-goolf-1.4.10-extended.eb +++ b/easybuild/easyconfigs/b/biodeps/biodeps-1.6-goolf-1.4.10-extended.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/b/biodeps/biodeps-1.6-goolf-1.4.10.eb b/easybuild/easyconfigs/b/biodeps/biodeps-1.6-goolf-1.4.10.eb index 6fcc534d72..c2a6853c15 100644 --- a/easybuild/easyconfigs/b/biodeps/biodeps-1.6-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/biodeps/biodeps-1.6-goolf-1.4.10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/b/biodeps/biodeps-1.6-ictce-5.3.0-extended.eb b/easybuild/easyconfigs/b/biodeps/biodeps-1.6-ictce-5.3.0-extended.eb index 34a00add44..3354b93931 100644 --- a/easybuild/easyconfigs/b/biodeps/biodeps-1.6-ictce-5.3.0-extended.eb +++ b/easybuild/easyconfigs/b/biodeps/biodeps-1.6-ictce-5.3.0-extended.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/b/biodeps/biodeps-1.6-ictce-5.3.0.eb b/easybuild/easyconfigs/b/biodeps/biodeps-1.6-ictce-5.3.0.eb index 1091497ff7..02f177a07b 100644 --- a/easybuild/easyconfigs/b/biodeps/biodeps-1.6-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/b/biodeps/biodeps-1.6-ictce-5.3.0.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/b/bwakit/bwakit-0.7.15_x64-linux.eb b/easybuild/easyconfigs/b/bwakit/bwakit-0.7.15_x64-linux.eb index 25c4049311..d9d9591bf7 100644 --- a/easybuild/easyconfigs/b/bwakit/bwakit-0.7.15_x64-linux.eb +++ b/easybuild/easyconfigs/b/bwakit/bwakit-0.7.15_x64-linux.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # sciCORE - University of Basel # SIB Swiss Institute of Bioinformatics diff --git a/easybuild/easyconfigs/c/CAP3/CAP3-20071221-intel-x86.eb b/easybuild/easyconfigs/c/CAP3/CAP3-20071221-intel-x86.eb index 98b5be9cc7..de682d1d50 100644 --- a/easybuild/easyconfigs/c/CAP3/CAP3-20071221-intel-x86.eb +++ b/easybuild/easyconfigs/c/CAP3/CAP3-20071221-intel-x86.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/c/CAP3/CAP3-20071221-intel-x86_64.eb b/easybuild/easyconfigs/c/CAP3/CAP3-20071221-intel-x86_64.eb index a459a2b2ae..ceeb82f27d 100644 --- a/easybuild/easyconfigs/c/CAP3/CAP3-20071221-intel-x86_64.eb +++ b/easybuild/easyconfigs/c/CAP3/CAP3-20071221-intel-x86_64.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/c/CAP3/CAP3-20071221-opteron.eb b/easybuild/easyconfigs/c/CAP3/CAP3-20071221-opteron.eb index 574d59a93d..4747b56abd 100644 --- a/easybuild/easyconfigs/c/CAP3/CAP3-20071221-opteron.eb +++ b/easybuild/easyconfigs/c/CAP3/CAP3-20071221-opteron.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.5.4-ictce-5.3.0-2011-03-07.eb b/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.5.4-ictce-5.3.0-2011-03-07.eb index e4650118de..9879063135 100644 --- a/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.5.4-ictce-5.3.0-2011-03-07.eb +++ b/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.5.4-ictce-5.3.0-2011-03-07.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2013 The Cyprus Institute # Authors:: Andreas Panteli , George Tsouloupas diff --git a/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.6.1-foss-2015b-2012-08-27.eb b/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.6.1-foss-2015b-2012-08-27.eb index 2fdb2ffa3d..6304e11440 100644 --- a/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.6.1-foss-2015b-2012-08-27.eb +++ b/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.6.1-foss-2015b-2012-08-27.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.6.1-goolf-1.4.10-2012-08-27.eb b/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.6.1-goolf-1.4.10-2012-08-27.eb index c3e01a8650..1d1c993287 100644 --- a/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.6.1-goolf-1.4.10-2012-08-27.eb +++ b/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.6.1-goolf-1.4.10-2012-08-27.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.6.1-ictce-5.5.0-2012-08-27.eb b/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.6.1-ictce-5.5.0-2012-08-27.eb index 5563d4c561..81ac44439d 100644 --- a/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.6.1-ictce-5.5.0-2012-08-27.eb +++ b/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.6.1-ictce-5.5.0-2012-08-27.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.6.4-GNU-4.9.3-2.25-2015-0603.eb b/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.6.4-GNU-4.9.3-2.25-2015-0603.eb index 268e532192..9c71be8290 100644 --- a/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.6.4-GNU-4.9.3-2.25-2015-0603.eb +++ b/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.6.4-GNU-4.9.3-2.25-2015-0603.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.6.4-foss-2015b-2015-0603.eb b/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.6.4-foss-2015b-2015-0603.eb index 832db33507..a251b7271b 100644 --- a/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.6.4-foss-2015b-2015-0603.eb +++ b/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.6.4-foss-2015b-2015-0603.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.6.6-foss-2016b.eb b/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.6.6-foss-2016b.eb index 741d95b545..47badeab0f 100644 --- a/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.6.6-foss-2016b.eb +++ b/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.6.6-foss-2016b.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild easyblock = 'MakeCp' diff --git a/easybuild/easyconfigs/c/CEM/CEM-0.9.1-goolf-1.4.10.eb b/easybuild/easyconfigs/c/CEM/CEM-0.9.1-goolf-1.4.10.eb index 6709e17801..3a72410974 100644 --- a/easybuild/easyconfigs/c/CEM/CEM-0.9.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/c/CEM/CEM-0.9.1-goolf-1.4.10.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/c/CHASE/CHASE-20130626.eb b/easybuild/easyconfigs/c/CHASE/CHASE-20130626.eb index 83fba54e75..a951a89a48 100644 --- a/easybuild/easyconfigs/c/CHASE/CHASE-20130626.eb +++ b/easybuild/easyconfigs/c/CHASE/CHASE-20130626.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Ravi Tripathi # Email: ravi89@uab.edu diff --git a/easybuild/easyconfigs/c/CONTRAfold/CONTRAfold-2.02-goolf-1.4.10.eb b/easybuild/easyconfigs/c/CONTRAfold/CONTRAfold-2.02-goolf-1.4.10.eb index 7f2755eaba..0ede673dd5 100644 --- a/easybuild/easyconfigs/c/CONTRAfold/CONTRAfold-2.02-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/c/CONTRAfold/CONTRAfold-2.02-goolf-1.4.10.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/c/CONTRAlign/CONTRAlign-2.01-goolf-1.4.10-proteins.eb b/easybuild/easyconfigs/c/CONTRAlign/CONTRAlign-2.01-goolf-1.4.10-proteins.eb index b60083b2b2..b276c15679 100644 --- a/easybuild/easyconfigs/c/CONTRAlign/CONTRAlign-2.01-goolf-1.4.10-proteins.eb +++ b/easybuild/easyconfigs/c/CONTRAlign/CONTRAlign-2.01-goolf-1.4.10-proteins.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # sciCORE - University of Basel # SIB Swiss Institute of Bioinformatics diff --git a/easybuild/easyconfigs/c/CONTRAlign/CONTRAlign-2.01-goolf-1.4.10-rna.eb b/easybuild/easyconfigs/c/CONTRAlign/CONTRAlign-2.01-goolf-1.4.10-rna.eb index 41ffea3e50..67bfcf476e 100644 --- a/easybuild/easyconfigs/c/CONTRAlign/CONTRAlign-2.01-goolf-1.4.10-rna.eb +++ b/easybuild/easyconfigs/c/CONTRAlign/CONTRAlign-2.01-goolf-1.4.10-rna.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # sciCORE - University of Basel # SIB Swiss Institute of Bioinformatics diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-5.0.35-1.eb b/easybuild/easyconfigs/c/CUDA/CUDA-5.0.35-1.eb index 8997152413..c2e6b4b406 100644 --- a/easybuild/easyconfigs/c/CUDA/CUDA-5.0.35-1.eb +++ b/easybuild/easyconfigs/c/CUDA/CUDA-5.0.35-1.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Cyprus Institute / CaSToRC, Uni.Lu/LCSB, NTUA, Ghent University # Authors:: George Tsouloupas , Fotis Georgatos , Kenneth Hoste diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-5.0.35-GCC-4.6.4-1.eb b/easybuild/easyconfigs/c/CUDA/CUDA-5.0.35-GCC-4.6.4-1.eb index 194a2991a9..266db17b73 100644 --- a/easybuild/easyconfigs/c/CUDA/CUDA-5.0.35-GCC-4.6.4-1.eb +++ b/easybuild/easyconfigs/c/CUDA/CUDA-5.0.35-GCC-4.6.4-1.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Cyprus Institute / CaSToRC, Uni.Lu/LCSB, NTUA, Ghent University # Authors:: George Tsouloupas , Fotis Georgatos , Kenneth Hoste diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-5.5.22-GCC-4.7.2.eb b/easybuild/easyconfigs/c/CUDA/CUDA-5.5.22-GCC-4.7.2.eb index 437ebc2ce7..3213a31732 100644 --- a/easybuild/easyconfigs/c/CUDA/CUDA-5.5.22-GCC-4.7.2.eb +++ b/easybuild/easyconfigs/c/CUDA/CUDA-5.5.22-GCC-4.7.2.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Cyprus Institute / CaSToRC, Uni.Lu/LCSB, NTUA, Ghent University # Authors:: George Tsouloupas , Fotis Georgatos , Kenneth Hoste diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-5.5.22-GCC-4.8.2.eb b/easybuild/easyconfigs/c/CUDA/CUDA-5.5.22-GCC-4.8.2.eb index 63bd33a5ba..41fb7a42e9 100644 --- a/easybuild/easyconfigs/c/CUDA/CUDA-5.5.22-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/c/CUDA/CUDA-5.5.22-GCC-4.8.2.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Cyprus Institute / CaSToRC, Uni.Lu/LCSB, NTUA, Ghent University # Authors:: George Tsouloupas , Fotis Georgatos , Kenneth Hoste diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-5.5.22.eb b/easybuild/easyconfigs/c/CUDA/CUDA-5.5.22.eb index c2fec1c504..bf2df9790e 100644 --- a/easybuild/easyconfigs/c/CUDA/CUDA-5.5.22.eb +++ b/easybuild/easyconfigs/c/CUDA/CUDA-5.5.22.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Cyprus Institute / CaSToRC, Uni.Lu/LCSB, NTUA, Ghent University # Authors:: George Tsouloupas , Fotis Georgatos , Kenneth Hoste diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-6.0.37.eb b/easybuild/easyconfigs/c/CUDA/CUDA-6.0.37.eb index 76cb0b94f9..009755e0fb 100644 --- a/easybuild/easyconfigs/c/CUDA/CUDA-6.0.37.eb +++ b/easybuild/easyconfigs/c/CUDA/CUDA-6.0.37.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2013 Cyprus Institute / CaSToRC, University of Luxembourg / LCSB, Ghent University # Authors:: George Tsouloupas , Fotis Georgatos , Kenneth Hoste diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-6.5.14.eb b/easybuild/easyconfigs/c/CUDA/CUDA-6.5.14.eb index 920ee4c4fa..d2a841d669 100644 --- a/easybuild/easyconfigs/c/CUDA/CUDA-6.5.14.eb +++ b/easybuild/easyconfigs/c/CUDA/CUDA-6.5.14.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2013 Cyprus Institute / CaSToRC, University of Luxembourg / LCSB, Ghent University # Authors:: George Tsouloupas , Fotis Georgatos , Kenneth Hoste diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-7.5.18-GCC-4.9.4-2.25.eb b/easybuild/easyconfigs/c/CUDA/CUDA-7.5.18-GCC-4.9.4-2.25.eb index eecde07096..e931619230 100644 --- a/easybuild/easyconfigs/c/CUDA/CUDA-7.5.18-GCC-4.9.4-2.25.eb +++ b/easybuild/easyconfigs/c/CUDA/CUDA-7.5.18-GCC-4.9.4-2.25.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2016 Cyprus Institute / CaSToRC, Uni.Lu/LCSB, NTUA, Ghent University, Microway # Authors:: George Tsouloupas , Fotis Georgatos , Kenneth Hoste, Eliot Eshelman diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-7.5.18-iccifort-2015.3.187-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/c/CUDA/CUDA-7.5.18-iccifort-2015.3.187-GNU-4.9.3-2.25.eb index 45b63f0380..b9b41e5dca 100644 --- a/easybuild/easyconfigs/c/CUDA/CUDA-7.5.18-iccifort-2015.3.187-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/c/CUDA/CUDA-7.5.18-iccifort-2015.3.187-GNU-4.9.3-2.25.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2013 Cyprus Institute / CaSToRC, University of Luxembourg / LCSB, Ghent University, # Forschungszentrum Juelich diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-7.5.18-iccifort-2016.3.210-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/c/CUDA/CUDA-7.5.18-iccifort-2016.3.210-GCC-4.9.3-2.25.eb index 72651d5b54..0752dc6cc8 100644 --- a/easybuild/easyconfigs/c/CUDA/CUDA-7.5.18-iccifort-2016.3.210-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/c/CUDA/CUDA-7.5.18-iccifort-2016.3.210-GCC-4.9.3-2.25.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2013 Cyprus Institute / CaSToRC, University of Luxembourg / LCSB, Ghent University, # Forschungszentrum Juelich diff --git a/easybuild/easyconfigs/c/CVS/CVS-1.11.23-GCC-4.8.2.eb b/easybuild/easyconfigs/c/CVS/CVS-1.11.23-GCC-4.8.2.eb index b8b9c80a8d..d6aba60dab 100644 --- a/easybuild/easyconfigs/c/CVS/CVS-1.11.23-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/c/CVS/CVS-1.11.23-GCC-4.8.2.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # ## diff --git a/easybuild/easyconfigs/c/CVS/CVS-1.11.23-GCCcore-4.9.3.eb b/easybuild/easyconfigs/c/CVS/CVS-1.11.23-GCCcore-4.9.3.eb index e9bbed8bb4..b4f49365df 100644 --- a/easybuild/easyconfigs/c/CVS/CVS-1.11.23-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/c/CVS/CVS-1.11.23-GCCcore-4.9.3.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # ## diff --git a/easybuild/easyconfigs/c/ChIP-Seq/ChIP-Seq-1.5-1-goolf-1.4.10.eb b/easybuild/easyconfigs/c/ChIP-Seq/ChIP-Seq-1.5-1-goolf-1.4.10.eb index b0d7e2e41b..0b19390665 100644 --- a/easybuild/easyconfigs/c/ChIP-Seq/ChIP-Seq-1.5-1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/c/ChIP-Seq/ChIP-Seq-1.5-1-goolf-1.4.10.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # sciCORE - University of Basel # SIB Swiss Institute of Bioinformatics diff --git a/easybuild/easyconfigs/c/ChIP-Seq/ChIP-Seq-1.5-1-goolf-1.7.20.eb b/easybuild/easyconfigs/c/ChIP-Seq/ChIP-Seq-1.5-1-goolf-1.7.20.eb index 54bfcde59b..8e66ed510b 100644 --- a/easybuild/easyconfigs/c/ChIP-Seq/ChIP-Seq-1.5-1-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/c/ChIP-Seq/ChIP-Seq-1.5-1-goolf-1.7.20.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # sciCORE - University of Basel # SIB Swiss Institute of Bioinformatics diff --git a/easybuild/easyconfigs/c/Chapel/Chapel-1.10.0-goolf-1.4.10.eb b/easybuild/easyconfigs/c/Chapel/Chapel-1.10.0-goolf-1.4.10.eb index d78acf92e2..2131f933b4 100644 --- a/easybuild/easyconfigs/c/Chapel/Chapel-1.10.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/c/Chapel/Chapel-1.10.0-goolf-1.4.10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2014, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/c/Chapel/Chapel-1.10.0-goolf-1.6.10.eb b/easybuild/easyconfigs/c/Chapel/Chapel-1.10.0-goolf-1.6.10.eb index e0ea8f21ce..e1386c970b 100644 --- a/easybuild/easyconfigs/c/Chapel/Chapel-1.10.0-goolf-1.6.10.eb +++ b/easybuild/easyconfigs/c/Chapel/Chapel-1.10.0-goolf-1.6.10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2014, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/c/Chapel/Chapel-1.6.0-goolf-1.4.10.eb b/easybuild/easyconfigs/c/Chapel/Chapel-1.6.0-goolf-1.4.10.eb index a1aed2106e..a5282bdd2a 100644 --- a/easybuild/easyconfigs/c/Chapel/Chapel-1.6.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/c/Chapel/Chapel-1.6.0-goolf-1.4.10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/c/Chapel/Chapel-1.7.0-goolf-1.4.10.eb b/easybuild/easyconfigs/c/Chapel/Chapel-1.7.0-goolf-1.4.10.eb index 0d583d38e1..a293117d13 100644 --- a/easybuild/easyconfigs/c/Chapel/Chapel-1.7.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/c/Chapel/Chapel-1.7.0-goolf-1.4.10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/c/Chapel/Chapel-1.8.0-goolf-1.4.10.eb b/easybuild/easyconfigs/c/Chapel/Chapel-1.8.0-goolf-1.4.10.eb index 9a54bec5f4..b85bbceaf9 100644 --- a/easybuild/easyconfigs/c/Chapel/Chapel-1.8.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/c/Chapel/Chapel-1.8.0-goolf-1.4.10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/c/Chapel/Chapel-1.8.0-goolf-1.6.10.eb b/easybuild/easyconfigs/c/Chapel/Chapel-1.8.0-goolf-1.6.10.eb index 9f53c75fb2..e6d5a956d7 100644 --- a/easybuild/easyconfigs/c/Chapel/Chapel-1.8.0-goolf-1.6.10.eb +++ b/easybuild/easyconfigs/c/Chapel/Chapel-1.8.0-goolf-1.6.10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/c/Chapel/Chapel-1.9.0-goolf-1.4.10.eb b/easybuild/easyconfigs/c/Chapel/Chapel-1.9.0-goolf-1.4.10.eb index 45906bfb00..9d6afe2d98 100644 --- a/easybuild/easyconfigs/c/Chapel/Chapel-1.9.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/c/Chapel/Chapel-1.9.0-goolf-1.4.10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2014, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/c/Chapel/Chapel-1.9.0-goolf-1.5.14.eb b/easybuild/easyconfigs/c/Chapel/Chapel-1.9.0-goolf-1.5.14.eb index 80c79f1859..3f3cf69376 100644 --- a/easybuild/easyconfigs/c/Chapel/Chapel-1.9.0-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/c/Chapel/Chapel-1.9.0-goolf-1.5.14.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Authors:: Jordi Blasco (NeSI) # License:: MIT/GPL diff --git a/easybuild/easyconfigs/c/Chapel/Chapel-1.9.0-goolf-1.6.10.eb b/easybuild/easyconfigs/c/Chapel/Chapel-1.9.0-goolf-1.6.10.eb index 289cbf479a..af2eb91036 100644 --- a/easybuild/easyconfigs/c/Chapel/Chapel-1.9.0-goolf-1.6.10.eb +++ b/easybuild/easyconfigs/c/Chapel/Chapel-1.9.0-goolf-1.6.10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2014, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/c/Check/Check-0.9.12-goolf-1.4.10.eb b/easybuild/easyconfigs/c/Check/Check-0.9.12-goolf-1.4.10.eb index 665f1371cb..1a131a403b 100644 --- a/easybuild/easyconfigs/c/Check/Check-0.9.12-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/c/Check/Check-0.9.12-goolf-1.4.10.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/c/Chimera/Chimera-1.10-linux_x86_64.eb b/easybuild/easyconfigs/c/Chimera/Chimera-1.10-linux_x86_64.eb index d050aae52b..509561f076 100644 --- a/easybuild/easyconfigs/c/Chimera/Chimera-1.10-linux_x86_64.eb +++ b/easybuild/easyconfigs/c/Chimera/Chimera-1.10-linux_x86_64.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/c/Circos/Circos-0.69-5-foss-2016b-Perl-5.24.0.eb b/easybuild/easyconfigs/c/Circos/Circos-0.69-5-foss-2016b-Perl-5.24.0.eb index 893126e7c3..319ec0d55c 100644 --- a/easybuild/easyconfigs/c/Circos/Circos-0.69-5-foss-2016b-Perl-5.24.0.eb +++ b/easybuild/easyconfigs/c/Circos/Circos-0.69-5-foss-2016b-Perl-5.24.0.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild easyblock = 'Tarball' diff --git a/easybuild/easyconfigs/c/Clang/Clang-3.2-GCC-4.7.3.eb b/easybuild/easyconfigs/c/Clang/Clang-3.2-GCC-4.7.3.eb index 05ffad5f40..183e2860f5 100644 --- a/easybuild/easyconfigs/c/Clang/Clang-3.2-GCC-4.7.3.eb +++ b/easybuild/easyconfigs/c/Clang/Clang-3.2-GCC-4.7.3.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2013 Dmitri Gribenko # Authors:: Dmitri Gribenko diff --git a/easybuild/easyconfigs/c/Clang/Clang-3.3-GCC-4.8.1.eb b/easybuild/easyconfigs/c/Clang/Clang-3.3-GCC-4.8.1.eb index 66ca5a1bc4..066a79dfcb 100644 --- a/easybuild/easyconfigs/c/Clang/Clang-3.3-GCC-4.8.1.eb +++ b/easybuild/easyconfigs/c/Clang/Clang-3.3-GCC-4.8.1.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2013 Dmitri Gribenko, Ward Poelmans # Authors:: Dmitri Gribenko diff --git a/easybuild/easyconfigs/c/Clang/Clang-3.4-GCC-4.8.2.eb b/easybuild/easyconfigs/c/Clang/Clang-3.4-GCC-4.8.2.eb index 5a1fdbfc0b..3c76811582 100644 --- a/easybuild/easyconfigs/c/Clang/Clang-3.4-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/c/Clang/Clang-3.4-GCC-4.8.2.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2013 Dmitri Gribenko, Ward Poelmans # Authors:: Dmitri Gribenko diff --git a/easybuild/easyconfigs/c/Clang/Clang-3.4.1-GCC-4.8.2.eb b/easybuild/easyconfigs/c/Clang/Clang-3.4.1-GCC-4.8.2.eb index 12a16f8dd5..987ff2c9ae 100644 --- a/easybuild/easyconfigs/c/Clang/Clang-3.4.1-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/c/Clang/Clang-3.4.1-GCC-4.8.2.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2013 Dmitri Gribenko, Ward Poelmans # Authors:: Dmitri Gribenko diff --git a/easybuild/easyconfigs/c/Clang/Clang-3.4.2-GCC-4.8.2.eb b/easybuild/easyconfigs/c/Clang/Clang-3.4.2-GCC-4.8.2.eb index f425fcd86e..d228769b61 100644 --- a/easybuild/easyconfigs/c/Clang/Clang-3.4.2-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/c/Clang/Clang-3.4.2-GCC-4.8.2.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2014 Dmitri Gribenko, Ward Poelmans # Authors:: Dmitri Gribenko diff --git a/easybuild/easyconfigs/c/Clang/Clang-3.6.0-GCC-4.9.2.eb b/easybuild/easyconfigs/c/Clang/Clang-3.6.0-GCC-4.9.2.eb index 9d5881c525..3478797af3 100644 --- a/easybuild/easyconfigs/c/Clang/Clang-3.6.0-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/c/Clang/Clang-3.6.0-GCC-4.9.2.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2013 Dmitri Gribenko, Ward Poelmans # Authors:: Dmitri Gribenko diff --git a/easybuild/easyconfigs/c/Clang/Clang-3.6.1-GCC-4.9.2.eb b/easybuild/easyconfigs/c/Clang/Clang-3.6.1-GCC-4.9.2.eb index bb31f282f6..e83e5346d7 100644 --- a/easybuild/easyconfigs/c/Clang/Clang-3.6.1-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/c/Clang/Clang-3.6.1-GCC-4.9.2.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2013 Dmitri Gribenko, Ward Poelmans # Authors:: Dmitri Gribenko diff --git a/easybuild/easyconfigs/c/Clang/Clang-3.7.0-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/c/Clang/Clang-3.7.0-GNU-4.9.3-2.25.eb index a76712524b..d79fb1dcca 100644 --- a/easybuild/easyconfigs/c/Clang/Clang-3.7.0-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/c/Clang/Clang-3.7.0-GNU-4.9.3-2.25.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2013-2015 Dmitri Gribenko, Ward Poelmans # Authors:: Dmitri Gribenko diff --git a/easybuild/easyconfigs/c/Clang/Clang-3.7.1-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/c/Clang/Clang-3.7.1-GCC-4.9.3-2.25.eb index ee437ef2f2..961f0eb891 100644 --- a/easybuild/easyconfigs/c/Clang/Clang-3.7.1-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/c/Clang/Clang-3.7.1-GCC-4.9.3-2.25.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2013-2015 Dmitri Gribenko, Ward Poelmans # Authors:: Dmitri Gribenko diff --git a/easybuild/easyconfigs/c/Clang/Clang-3.7.1-foss-2016a.eb b/easybuild/easyconfigs/c/Clang/Clang-3.7.1-foss-2016a.eb index 9037365bc8..99e144ac87 100644 --- a/easybuild/easyconfigs/c/Clang/Clang-3.7.1-foss-2016a.eb +++ b/easybuild/easyconfigs/c/Clang/Clang-3.7.1-foss-2016a.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2013-2015 Dmitri Gribenko, Ward Poelmans # Authors:: Dmitri Gribenko diff --git a/easybuild/easyconfigs/c/Clang/Clang-3.8.0-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/c/Clang/Clang-3.8.0-GCC-4.9.3-2.25.eb index 23fe1ddcc9..d2ce11eb6a 100644 --- a/easybuild/easyconfigs/c/Clang/Clang-3.8.0-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/c/Clang/Clang-3.8.0-GCC-4.9.3-2.25.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2013-2015 Dmitri Gribenko, Ward Poelmans # Authors:: Dmitri Gribenko diff --git a/easybuild/easyconfigs/c/Clang/Clang-3.8.1-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/c/Clang/Clang-3.8.1-GCC-5.4.0-2.26.eb index 3c6cb72c88..f8e1c1318f 100644 --- a/easybuild/easyconfigs/c/Clang/Clang-3.8.1-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/c/Clang/Clang-3.8.1-GCC-5.4.0-2.26.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2013-2015 Dmitri Gribenko, Ward Poelmans # Authors:: Dmitri Gribenko diff --git a/easybuild/easyconfigs/c/Clang/Clang-3.8.1-foss-2016b.eb b/easybuild/easyconfigs/c/Clang/Clang-3.8.1-foss-2016b.eb index bc4ee73735..16b0d65003 100644 --- a/easybuild/easyconfigs/c/Clang/Clang-3.8.1-foss-2016b.eb +++ b/easybuild/easyconfigs/c/Clang/Clang-3.8.1-foss-2016b.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2013-2015 Dmitri Gribenko, Ward Poelmans # Authors:: Dmitri Gribenko diff --git a/easybuild/easyconfigs/c/Clustal-Omega/Clustal-Omega-1.2.0-foss-2015b.eb b/easybuild/easyconfigs/c/Clustal-Omega/Clustal-Omega-1.2.0-foss-2015b.eb index 2ddcf2b93a..444a714932 100644 --- a/easybuild/easyconfigs/c/Clustal-Omega/Clustal-Omega-1.2.0-foss-2015b.eb +++ b/easybuild/easyconfigs/c/Clustal-Omega/Clustal-Omega-1.2.0-foss-2015b.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/c/Clustal-Omega/Clustal-Omega-1.2.0-foss-2016b.eb b/easybuild/easyconfigs/c/Clustal-Omega/Clustal-Omega-1.2.0-foss-2016b.eb index 06226cf0b0..4b16e09c52 100644 --- a/easybuild/easyconfigs/c/Clustal-Omega/Clustal-Omega-1.2.0-foss-2016b.eb +++ b/easybuild/easyconfigs/c/Clustal-Omega/Clustal-Omega-1.2.0-foss-2016b.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/c/Clustal-Omega/Clustal-Omega-1.2.0-goolf-1.4.10.eb b/easybuild/easyconfigs/c/Clustal-Omega/Clustal-Omega-1.2.0-goolf-1.4.10.eb index 4286aeb066..333cd83483 100644 --- a/easybuild/easyconfigs/c/Clustal-Omega/Clustal-Omega-1.2.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/c/Clustal-Omega/Clustal-Omega-1.2.0-goolf-1.4.10.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/c/ClustalW2/ClustalW2-2.1-foss-2015b.eb b/easybuild/easyconfigs/c/ClustalW2/ClustalW2-2.1-foss-2015b.eb index 2c61c0adb7..d60a1926b6 100644 --- a/easybuild/easyconfigs/c/ClustalW2/ClustalW2-2.1-foss-2015b.eb +++ b/easybuild/easyconfigs/c/ClustalW2/ClustalW2-2.1-foss-2015b.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Cedric Laczny , Fotis Georgatos diff --git a/easybuild/easyconfigs/c/ClustalW2/ClustalW2-2.1-foss-2016b.eb b/easybuild/easyconfigs/c/ClustalW2/ClustalW2-2.1-foss-2016b.eb index 2a03b23888..dd5edaff52 100644 --- a/easybuild/easyconfigs/c/ClustalW2/ClustalW2-2.1-foss-2016b.eb +++ b/easybuild/easyconfigs/c/ClustalW2/ClustalW2-2.1-foss-2016b.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Cedric Laczny , Fotis Georgatos diff --git a/easybuild/easyconfigs/c/ClustalW2/ClustalW2-2.1-goolf-1.4.10.eb b/easybuild/easyconfigs/c/ClustalW2/ClustalW2-2.1-goolf-1.4.10.eb index de52a79a13..2e81136477 100644 --- a/easybuild/easyconfigs/c/ClustalW2/ClustalW2-2.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/c/ClustalW2/ClustalW2-2.1-goolf-1.4.10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Cedric Laczny , Fotis Georgatos diff --git a/easybuild/easyconfigs/c/ClustalW2/ClustalW2-2.1-ictce-5.3.0.eb b/easybuild/easyconfigs/c/ClustalW2/ClustalW2-2.1-ictce-5.3.0.eb index 068dfd89ce..5e25ce08f3 100644 --- a/easybuild/easyconfigs/c/ClustalW2/ClustalW2-2.1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/c/ClustalW2/ClustalW2-2.1-ictce-5.3.0.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Cedric Laczny , Fotis Georgatos diff --git a/easybuild/easyconfigs/c/ConnectomeWorkbench/ConnectomeWorkbench-1.2.2.eb b/easybuild/easyconfigs/c/ConnectomeWorkbench/ConnectomeWorkbench-1.2.2.eb index 0cb98a2054..1b697a0fc2 100644 --- a/easybuild/easyconfigs/c/ConnectomeWorkbench/ConnectomeWorkbench-1.2.2.eb +++ b/easybuild/easyconfigs/c/ConnectomeWorkbench/ConnectomeWorkbench-1.2.2.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Ravi Tripathi # Email: ravi89@uab.edu diff --git a/easybuild/easyconfigs/c/Cookiecutter/Cookiecutter-1.4.0-goolf-1.7.20-Python-2.7.11.eb b/easybuild/easyconfigs/c/Cookiecutter/Cookiecutter-1.4.0-goolf-1.7.20-Python-2.7.11.eb index 88fa4436a0..df729ad2ff 100644 --- a/easybuild/easyconfigs/c/Cookiecutter/Cookiecutter-1.4.0-goolf-1.7.20-Python-2.7.11.eb +++ b/easybuild/easyconfigs/c/Cookiecutter/Cookiecutter-1.4.0-goolf-1.7.20-Python-2.7.11.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # sciCORE - University of Basel # SIB Swiss Institute of Bioinformatics diff --git a/easybuild/easyconfigs/c/Coot/Coot-0.8.1-binary-Linux-x86_64-rhel-6-python-gtk2.eb b/easybuild/easyconfigs/c/Coot/Coot-0.8.1-binary-Linux-x86_64-rhel-6-python-gtk2.eb index 1386d5329d..c89dad88b7 100644 --- a/easybuild/easyconfigs/c/Coot/Coot-0.8.1-binary-Linux-x86_64-rhel-6-python-gtk2.eb +++ b/easybuild/easyconfigs/c/Coot/Coot-0.8.1-binary-Linux-x86_64-rhel-6-python-gtk2.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Adam Mazur # Research IT # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/c/Corkscrew/Corkscrew-2.0-goolf-1.4.10.eb b/easybuild/easyconfigs/c/Corkscrew/Corkscrew-2.0-goolf-1.4.10.eb index 8e4f18d89d..82fce2b21b 100644 --- a/easybuild/easyconfigs/c/Corkscrew/Corkscrew-2.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/c/Corkscrew/Corkscrew-2.0-goolf-1.4.10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/c/Corkscrew/Corkscrew-2.0-ictce-5.3.0.eb b/easybuild/easyconfigs/c/Corkscrew/Corkscrew-2.0-ictce-5.3.0.eb index 0afa91c77f..68607c8fb2 100644 --- a/easybuild/easyconfigs/c/Corkscrew/Corkscrew-2.0-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/c/Corkscrew/Corkscrew-2.0-ictce-5.3.0.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/c/Cube/Cube-4.2-goolf-1.5.14.eb b/easybuild/easyconfigs/c/Cube/Cube-4.2-goolf-1.5.14.eb index 94f4a3ca61..4ad949c668 100644 --- a/easybuild/easyconfigs/c/Cube/Cube-4.2-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/c/Cube/Cube-4.2-goolf-1.5.14.eb @@ -1,5 +1,5 @@ ## -# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2013-2015 Juelich Supercomputing Centre, Germany # Authors:: Bernd Mohr diff --git a/easybuild/easyconfigs/c/Cube/Cube-4.2.3-goolf-1.5.14.eb b/easybuild/easyconfigs/c/Cube/Cube-4.2.3-goolf-1.5.14.eb index ad5e3d68d5..d6ae37f211 100644 --- a/easybuild/easyconfigs/c/Cube/Cube-4.2.3-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/c/Cube/Cube-4.2.3-goolf-1.5.14.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild # Authors:: Jordi Blasco # License:: New BSD # diff --git a/easybuild/easyconfigs/c/Cube/Cube-4.3-foss-2015a.eb b/easybuild/easyconfigs/c/Cube/Cube-4.3-foss-2015a.eb index 5763a26ed1..b4f629e071 100644 --- a/easybuild/easyconfigs/c/Cube/Cube-4.3-foss-2015a.eb +++ b/easybuild/easyconfigs/c/Cube/Cube-4.3-foss-2015a.eb @@ -1,5 +1,5 @@ ## -# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2013-2015 Juelich Supercomputing Centre, Germany # Authors:: Bernd Mohr diff --git a/easybuild/easyconfigs/c/Cube/Cube-4.3.2-foss-2015a.eb b/easybuild/easyconfigs/c/Cube/Cube-4.3.2-foss-2015a.eb index c274b99b8c..259be54087 100644 --- a/easybuild/easyconfigs/c/Cube/Cube-4.3.2-foss-2015a.eb +++ b/easybuild/easyconfigs/c/Cube/Cube-4.3.2-foss-2015a.eb @@ -1,5 +1,5 @@ ## -# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2013-2015 Juelich Supercomputing Centre, Germany # Authors:: Bernd Mohr diff --git a/easybuild/easyconfigs/c/Cube/Cube-4.3.4-foss-2016a.eb b/easybuild/easyconfigs/c/Cube/Cube-4.3.4-foss-2016a.eb index 2ac3b5a935..44788c8041 100644 --- a/easybuild/easyconfigs/c/Cube/Cube-4.3.4-foss-2016a.eb +++ b/easybuild/easyconfigs/c/Cube/Cube-4.3.4-foss-2016a.eb @@ -1,5 +1,5 @@ ## -# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2013-2016 Juelich Supercomputing Centre, Germany # Authors:: Bernd Mohr diff --git a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-1.3.0-goolf-1.4.10.eb b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-1.3.0-goolf-1.4.10.eb index 7b8dca8554..7e5d556bb7 100644 --- a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-1.3.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-1.3.0-goolf-1.4.10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Cedric Laczny , Fotis Georgatos diff --git a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.0.2-goolf-1.4.10.eb b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.0.2-goolf-1.4.10.eb index 25b9208f0e..4c2199c2b2 100644 --- a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.0.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.0.2-goolf-1.4.10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Cedric Laczny , Fotis Georgatos diff --git a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.0.2-ictce-5.3.0.eb b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.0.2-ictce-5.3.0.eb index 9c37cd717b..0aa76e0d7c 100644 --- a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.0.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.0.2-ictce-5.3.0.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Cedric Laczny , Fotis Georgatos diff --git a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.1.1-ictce-5.5.0.eb b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.1.1-ictce-5.5.0.eb index 6751cec530..0afef46d29 100644 --- a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.1.1-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.1.1-ictce-5.5.0.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Cedric Laczny , Fotis Georgatos diff --git a/easybuild/easyconfigs/c/ccache/ccache-3.1.9-goolf-1.4.10.eb b/easybuild/easyconfigs/c/ccache/ccache-3.1.9-goolf-1.4.10.eb index 3bf08594da..97cad490a6 100644 --- a/easybuild/easyconfigs/c/ccache/ccache-3.1.9-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/c/ccache/ccache-3.1.9-goolf-1.4.10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/c/ccache/ccache-3.1.9-ictce-5.3.0.eb b/easybuild/easyconfigs/c/ccache/ccache-3.1.9-ictce-5.3.0.eb index 84c3e7baf8..98555a7a7a 100644 --- a/easybuild/easyconfigs/c/ccache/ccache-3.1.9-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/c/ccache/ccache-3.1.9-ictce-5.3.0.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/c/ccache/ccache-3.2.5.eb b/easybuild/easyconfigs/c/ccache/ccache-3.2.5.eb index 3880874512..1db87d3057 100644 --- a/easybuild/easyconfigs/c/ccache/ccache-3.2.5.eb +++ b/easybuild/easyconfigs/c/ccache/ccache-3.2.5.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/c/ccache/ccache-3.3.1.eb b/easybuild/easyconfigs/c/ccache/ccache-3.3.1.eb index 66a9fe225a..f857d10d3a 100644 --- a/easybuild/easyconfigs/c/ccache/ccache-3.3.1.eb +++ b/easybuild/easyconfigs/c/ccache/ccache-3.3.1.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/c/ccache/ccache-3.3.3.eb b/easybuild/easyconfigs/c/ccache/ccache-3.3.3.eb index f3c8b6240f..66d52c698c 100644 --- a/easybuild/easyconfigs/c/ccache/ccache-3.3.3.eb +++ b/easybuild/easyconfigs/c/ccache/ccache-3.3.3.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/c/cflow/cflow-1.4-goolf-1.4.10.eb b/easybuild/easyconfigs/c/cflow/cflow-1.4-goolf-1.4.10.eb index bb9da36f80..a04ee2f9d7 100644 --- a/easybuild/easyconfigs/c/cflow/cflow-1.4-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/c/cflow/cflow-1.4-goolf-1.4.10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/c/cflow/cflow-1.4-ictce-5.3.0.eb b/easybuild/easyconfigs/c/cflow/cflow-1.4-ictce-5.3.0.eb index 107d08647f..30c2c7c615 100644 --- a/easybuild/easyconfigs/c/cflow/cflow-1.4-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/c/cflow/cflow-1.4-ictce-5.3.0.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/c/cgdb/cgdb-0.6.5-goolf-1.4.10.eb b/easybuild/easyconfigs/c/cgdb/cgdb-0.6.5-goolf-1.4.10.eb index 9684225cb7..2c027621e8 100644 --- a/easybuild/easyconfigs/c/cgdb/cgdb-0.6.5-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/c/cgdb/cgdb-0.6.5-goolf-1.4.10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/c/cgdb/cgdb-0.6.5-ictce-5.3.0.eb b/easybuild/easyconfigs/c/cgdb/cgdb-0.6.5-ictce-5.3.0.eb index eb6eb8ffbf..fe9db26324 100644 --- a/easybuild/easyconfigs/c/cgdb/cgdb-0.6.5-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/c/cgdb/cgdb-0.6.5-ictce-5.3.0.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/c/ctffind/ctffind-4.0.17-intel-2015b.eb b/easybuild/easyconfigs/c/ctffind/ctffind-4.0.17-intel-2015b.eb index 60152e7602..f6b9d86aa2 100644 --- a/easybuild/easyconfigs/c/ctffind/ctffind-4.0.17-intel-2015b.eb +++ b/easybuild/easyconfigs/c/ctffind/ctffind-4.0.17-intel-2015b.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # sciCORE - University of Basel # SIB Swiss Institute of Bioinformatics diff --git a/easybuild/easyconfigs/c/cuDNN/cuDNN-4.0.eb b/easybuild/easyconfigs/c/cuDNN/cuDNN-4.0.eb index 5bcd0e1aa3..ccc5cdbff9 100644 --- a/easybuild/easyconfigs/c/cuDNN/cuDNN-4.0.eb +++ b/easybuild/easyconfigs/c/cuDNN/cuDNN-4.0.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Author: Stephane Thiell ## diff --git a/easybuild/easyconfigs/c/cuDNN/cuDNN-5.0-CUDA-7.5.18.eb b/easybuild/easyconfigs/c/cuDNN/cuDNN-5.0-CUDA-7.5.18.eb index aaab290dcf..1c8da2633c 100644 --- a/easybuild/easyconfigs/c/cuDNN/cuDNN-5.0-CUDA-7.5.18.eb +++ b/easybuild/easyconfigs/c/cuDNN/cuDNN-5.0-CUDA-7.5.18.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Author: Stephane Thiell ## diff --git a/easybuild/easyconfigs/c/cuDNN/cuDNN-5.0-rc.eb b/easybuild/easyconfigs/c/cuDNN/cuDNN-5.0-rc.eb index 536c2f33c6..97236ec5ff 100644 --- a/easybuild/easyconfigs/c/cuDNN/cuDNN-5.0-rc.eb +++ b/easybuild/easyconfigs/c/cuDNN/cuDNN-5.0-rc.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Author: Stephane Thiell ## diff --git a/easybuild/easyconfigs/c/cuDNN/cuDNN-5.1-CUDA-8.0.44.eb b/easybuild/easyconfigs/c/cuDNN/cuDNN-5.1-CUDA-8.0.44.eb index 08976a1f68..655063d179 100644 --- a/easybuild/easyconfigs/c/cuDNN/cuDNN-5.1-CUDA-8.0.44.eb +++ b/easybuild/easyconfigs/c/cuDNN/cuDNN-5.1-CUDA-8.0.44.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Author: Stephane Thiell ## diff --git a/easybuild/easyconfigs/c/cuDNN/cuDNN-6.0-CUDA-8.0.61.eb b/easybuild/easyconfigs/c/cuDNN/cuDNN-6.0-CUDA-8.0.61.eb index 942648ea47..29bbebe51b 100644 --- a/easybuild/easyconfigs/c/cuDNN/cuDNN-6.0-CUDA-8.0.61.eb +++ b/easybuild/easyconfigs/c/cuDNN/cuDNN-6.0-CUDA-8.0.61.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Author: Stephane Thiell ## diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.3-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.3-goolf-1.4.10-Python-2.7.3.eb index d487d344f6..15b0a97b3b 100644 --- a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.3-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.3-goolf-1.4.10-Python-2.7.3.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics (SIB) # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.3-goolf-1.4.10-Python-2.7.5.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.3-goolf-1.4.10-Python-2.7.5.eb index aceb217de4..78181eace3 100644 --- a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.3-goolf-1.4.10-Python-2.7.5.eb +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.3-goolf-1.4.10-Python-2.7.5.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics (SIB) # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.4.1-foss-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.4.1-foss-2014b-Python-2.7.8.eb index 9d2802684e..2eb271b2cb 100644 --- a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.4.1-foss-2014b-Python-2.7.8.eb +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.4.1-foss-2014b-Python-2.7.8.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics (SIB) # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.4.1-goolf-1.4.10-Python-2.7.5.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.4.1-goolf-1.4.10-Python-2.7.5.eb index a4f5169761..0a914d43dd 100644 --- a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.4.1-goolf-1.4.10-Python-2.7.5.eb +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.4.1-goolf-1.4.10-Python-2.7.5.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics (SIB) # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.5-foss-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.5-foss-2014b-Python-2.7.8.eb index edcade8044..b5fa67bd28 100644 --- a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.5-foss-2014b-Python-2.7.8.eb +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.5-foss-2014b-Python-2.7.8.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics (SIB) # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.6-foss-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.6-foss-2014b-Python-2.7.8.eb index 6d660f5bc5..9fd455ea4e 100644 --- a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.6-foss-2014b-Python-2.7.8.eb +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.6-foss-2014b-Python-2.7.8.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics (SIB) # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.7-foss-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.7-foss-2014b-Python-2.7.8.eb index 7e135e5021..8fd82f9c4c 100644 --- a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.7-foss-2014b-Python-2.7.8.eb +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.7-foss-2014b-Python-2.7.8.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics (SIB) # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.7.1-foss-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.7.1-foss-2014b-Python-2.7.8.eb index ccfea59372..4eaa0d8f1e 100644 --- a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.7.1-foss-2014b-Python-2.7.8.eb +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.7.1-foss-2014b-Python-2.7.8.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics (SIB) # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.8.1-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.8.1-intel-2015a-Python-2.7.9.eb index 8898d1ce85..1f2a8db354 100644 --- a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.8.1-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.8.1-intel-2015a-Python-2.7.9.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics (SIB) # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.9.1-foss-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.9.1-foss-2015b-Python-2.7.10.eb index 6c74a88bb4..2508964d7f 100644 --- a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.9.1-foss-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.9.1-foss-2015b-Python-2.7.10.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics (SIB) # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.9.1-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.9.1-foss-2016a-Python-2.7.11.eb index 99d5dfa45c..65f2550e40 100644 --- a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.9.1-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.9.1-foss-2016a-Python-2.7.11.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics (SIB) # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.9.1-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.9.1-foss-2016b-Python-2.7.12.eb index 63398f9cb0..9397e22d2b 100644 --- a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.9.1-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.9.1-foss-2016b-Python-2.7.12.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics (SIB) # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/d/DIALIGN-TX/DIALIGN-TX-1.0.2-goolf-1.4.10.eb b/easybuild/easyconfigs/d/DIALIGN-TX/DIALIGN-TX-1.0.2-goolf-1.4.10.eb index f6fd6246c4..bb425b52f0 100644 --- a/easybuild/easyconfigs/d/DIALIGN-TX/DIALIGN-TX-1.0.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/d/DIALIGN-TX/DIALIGN-TX-1.0.2-goolf-1.4.10.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/d/DIAMOND/DIAMOND-0.8.35-goolf-1.7.20.eb b/easybuild/easyconfigs/d/DIAMOND/DIAMOND-0.8.35-goolf-1.7.20.eb index 19f96d592f..2c2bb31863 100644 --- a/easybuild/easyconfigs/d/DIAMOND/DIAMOND-0.8.35-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/d/DIAMOND/DIAMOND-0.8.35-goolf-1.7.20.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # sciCORE - University of Basel # SIB Swiss Institute of Bioinformatics diff --git a/easybuild/easyconfigs/d/DIAMOND/DIAMOND-0.9.6-goolf-1.7.20.eb b/easybuild/easyconfigs/d/DIAMOND/DIAMOND-0.9.6-goolf-1.7.20.eb index bc285581b6..3d1b5aebca 100644 --- a/easybuild/easyconfigs/d/DIAMOND/DIAMOND-0.9.6-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/d/DIAMOND/DIAMOND-0.9.6-goolf-1.7.20.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # sciCORE - University of Basel # SIB Swiss Institute of Bioinformatics diff --git a/easybuild/easyconfigs/d/DMTCP/DMTCP-2.4.5.eb b/easybuild/easyconfigs/d/DMTCP/DMTCP-2.4.5.eb index 04e4fd7a51..27c3a7d1ef 100644 --- a/easybuild/easyconfigs/d/DMTCP/DMTCP-2.4.5.eb +++ b/easybuild/easyconfigs/d/DMTCP/DMTCP-2.4.5.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Ravi Tripathi # Email: ravi89@uab.edu diff --git a/easybuild/easyconfigs/d/DMTCP/DMTCP-2.5.0-foss-2016a.eb b/easybuild/easyconfigs/d/DMTCP/DMTCP-2.5.0-foss-2016a.eb index 1687e9b44d..f7a7f714c1 100644 --- a/easybuild/easyconfigs/d/DMTCP/DMTCP-2.5.0-foss-2016a.eb +++ b/easybuild/easyconfigs/d/DMTCP/DMTCP-2.5.0-foss-2016a.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Ravi Tripathi # Email: ravi89@uab.edu diff --git a/easybuild/easyconfigs/d/DSRC/DSRC-2.0rc-linux-64-bit.eb b/easybuild/easyconfigs/d/DSRC/DSRC-2.0rc-linux-64-bit.eb index 76c48d1e81..2a945fa40d 100644 --- a/easybuild/easyconfigs/d/DSRC/DSRC-2.0rc-linux-64-bit.eb +++ b/easybuild/easyconfigs/d/DSRC/DSRC-2.0rc-linux-64-bit.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2015 NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/d/DendroPy/DendroPy-3.12.0-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/d/DendroPy/DendroPy-3.12.0-goolf-1.4.10-Python-2.7.3.eb index 7d7b15088e..000354596f 100644 --- a/easybuild/easyconfigs/d/DendroPy/DendroPy-3.12.0-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/d/DendroPy/DendroPy-3.12.0-goolf-1.4.10-Python-2.7.3.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2013-2014 The Cyprus Institute # Authors:: Thekla Loizou diff --git a/easybuild/easyconfigs/d/DicomBrowser/DicomBrowser-1.7.0b5-Java-1.7.0_80.eb b/easybuild/easyconfigs/d/DicomBrowser/DicomBrowser-1.7.0b5-Java-1.7.0_80.eb index 5106c4165f..e27f766c81 100644 --- a/easybuild/easyconfigs/d/DicomBrowser/DicomBrowser-1.7.0b5-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/d/DicomBrowser/DicomBrowser-1.7.0b5-Java-1.7.0_80.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # sciCORE - University of Basel # SIB Swiss Institute of Bioinformatics diff --git a/easybuild/easyconfigs/d/Diffutils/Diffutils-3.2-goolf-1.4.10.eb b/easybuild/easyconfigs/d/Diffutils/Diffutils-3.2-goolf-1.4.10.eb index cfed427bb7..730559ad83 100644 --- a/easybuild/easyconfigs/d/Diffutils/Diffutils-3.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/d/Diffutils/Diffutils-3.2-goolf-1.4.10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/d/Diffutils/Diffutils-3.2-ictce-5.3.0.eb b/easybuild/easyconfigs/d/Diffutils/Diffutils-3.2-ictce-5.3.0.eb index 9021d61ff6..94063017d3 100644 --- a/easybuild/easyconfigs/d/Diffutils/Diffutils-3.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/d/Diffutils/Diffutils-3.2-ictce-5.3.0.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/d/Diffutils/Diffutils-3.3-GCC-4.8.2.eb b/easybuild/easyconfigs/d/Diffutils/Diffutils-3.3-GCC-4.8.2.eb index 03dd2d88f6..a48cfb999d 100644 --- a/easybuild/easyconfigs/d/Diffutils/Diffutils-3.3-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/d/Diffutils/Diffutils-3.3-GCC-4.8.2.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/d/disambiguate/disambiguate-1.0.0-goolf-1.7.20-Python-2.7.11.eb b/easybuild/easyconfigs/d/disambiguate/disambiguate-1.0.0-goolf-1.7.20-Python-2.7.11.eb index 8b40d87ea0..3f7a8cf8e8 100644 --- a/easybuild/easyconfigs/d/disambiguate/disambiguate-1.0.0-goolf-1.7.20-Python-2.7.11.eb +++ b/easybuild/easyconfigs/d/disambiguate/disambiguate-1.0.0-goolf-1.7.20-Python-2.7.11.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # sciCORE - University of Basel # SIB Swiss Institute of Bioinformatics diff --git a/easybuild/easyconfigs/d/drFAST/drFAST-1.0.0.0-goolf-1.4.10.eb b/easybuild/easyconfigs/d/drFAST/drFAST-1.0.0.0-goolf-1.4.10.eb index 3d7e8e50d6..b4f4f41636 100644 --- a/easybuild/easyconfigs/d/drFAST/drFAST-1.0.0.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/d/drFAST/drFAST-1.0.0.0-goolf-1.4.10.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # sciCORE - University of Basel # SIB Swiss Institute of Bioinformatics diff --git a/easybuild/easyconfigs/d/drFAST/drFAST-1.0.0.0-ictce-6.2.5.eb b/easybuild/easyconfigs/d/drFAST/drFAST-1.0.0.0-ictce-6.2.5.eb index 33794a918d..60fff5c063 100644 --- a/easybuild/easyconfigs/d/drFAST/drFAST-1.0.0.0-ictce-6.2.5.eb +++ b/easybuild/easyconfigs/d/drFAST/drFAST-1.0.0.0-ictce-6.2.5.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # sciCORE - University of Basel # SIB Swiss Institute of Bioinformatics diff --git a/easybuild/easyconfigs/e/EIGENSOFT/EIGENSOFT-6.0.1-foss-2016a.eb b/easybuild/easyconfigs/e/EIGENSOFT/EIGENSOFT-6.0.1-foss-2016a.eb index c1c0d70437..15ad25d3e8 100644 --- a/easybuild/easyconfigs/e/EIGENSOFT/EIGENSOFT-6.0.1-foss-2016a.eb +++ b/easybuild/easyconfigs/e/EIGENSOFT/EIGENSOFT-6.0.1-foss-2016a.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # sciCORE - University of Basel # SIB Swiss Institute of Bioinformatics diff --git a/easybuild/easyconfigs/e/EIGENSOFT/EIGENSOFT-6.1.1-foss-2016a.eb b/easybuild/easyconfigs/e/EIGENSOFT/EIGENSOFT-6.1.1-foss-2016a.eb index 198de40465..7dd70ec70b 100644 --- a/easybuild/easyconfigs/e/EIGENSOFT/EIGENSOFT-6.1.1-foss-2016a.eb +++ b/easybuild/easyconfigs/e/EIGENSOFT/EIGENSOFT-6.1.1-foss-2016a.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # sciCORE - University of Basel # SIB Swiss Institute of Bioinformatics diff --git a/easybuild/easyconfigs/e/EIGENSOFT/EIGENSOFT-6.1.1-goolf-1.7.20.eb b/easybuild/easyconfigs/e/EIGENSOFT/EIGENSOFT-6.1.1-goolf-1.7.20.eb index a429626ec5..1b6aee4f0e 100644 --- a/easybuild/easyconfigs/e/EIGENSOFT/EIGENSOFT-6.1.1-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/e/EIGENSOFT/EIGENSOFT-6.1.1-goolf-1.7.20.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # sciCORE - University of Basel # SIB Swiss Institute of Bioinformatics diff --git a/easybuild/easyconfigs/e/EIGENSOFT/EIGENSOFT-6.1.4-foss-2016b.eb b/easybuild/easyconfigs/e/EIGENSOFT/EIGENSOFT-6.1.4-foss-2016b.eb index 5b6b65198e..13e8afdb7f 100644 --- a/easybuild/easyconfigs/e/EIGENSOFT/EIGENSOFT-6.1.4-foss-2016b.eb +++ b/easybuild/easyconfigs/e/EIGENSOFT/EIGENSOFT-6.1.4-foss-2016b.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # sciCORE - University of Basel # SIB Swiss Institute of Bioinformatics diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2013.11-ictce-5.3.0.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2013.11-ictce-5.3.0.eb index c9a900612f..b23777f71c 100644 --- a/easybuild/easyconfigs/e/ELPA/ELPA-2013.11-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2013.11-ictce-5.3.0.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Authors:: Inge Gutheil , Alan O'Cais # License:: MIT/GPL diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2013.11-ictce-5.5.0.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2013.11-ictce-5.5.0.eb index 9783862078..05d749936e 100644 --- a/easybuild/easyconfigs/e/ELPA/ELPA-2013.11-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2013.11-ictce-5.5.0.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Authors:: Inge Gutheil , Alan O'Cais # License:: MIT/GPL diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2016.05.004-intel-2016b.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2016.05.004-intel-2016b.eb index b188df034a..6168179ce8 100644 --- a/easybuild/easyconfigs/e/ELPA/ELPA-2016.05.004-intel-2016b.eb +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2016.05.004-intel-2016b.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Authors:: Inge Gutheil , Alan O'Cais # License:: MIT/GPL diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2016.05.004-intel-2017a.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2016.05.004-intel-2017a.eb index 75d318f670..ee72d9cdc5 100644 --- a/easybuild/easyconfigs/e/ELPA/ELPA-2016.05.004-intel-2017a.eb +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2016.05.004-intel-2017a.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Authors:: Inge Gutheil , Alan O'Cais # License:: MIT/GPL diff --git a/easybuild/easyconfigs/e/ELPH/ELPH-1.0.1-goolf-1.4.10.eb b/easybuild/easyconfigs/e/ELPH/ELPH-1.0.1-goolf-1.4.10.eb index 8ac9aea768..5f261e1c14 100644 --- a/easybuild/easyconfigs/e/ELPH/ELPH-1.0.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/e/ELPH/ELPH-1.0.1-goolf-1.4.10.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/e/ELPH/ELPH-1.0.1-ictce-6.2.5.eb b/easybuild/easyconfigs/e/ELPH/ELPH-1.0.1-ictce-6.2.5.eb index ba2c506ee5..71841b9321 100644 --- a/easybuild/easyconfigs/e/ELPH/ELPH-1.0.1-ictce-6.2.5.eb +++ b/easybuild/easyconfigs/e/ELPH/ELPH-1.0.1-ictce-6.2.5.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/e/ELinks/ELinks-0.12pre5-goolf-1.4.10.eb b/easybuild/easyconfigs/e/ELinks/ELinks-0.12pre5-goolf-1.4.10.eb index ee65cc074e..c8cce9a3c7 100644 --- a/easybuild/easyconfigs/e/ELinks/ELinks-0.12pre5-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/e/ELinks/ELinks-0.12pre5-goolf-1.4.10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/e/ELinks/ELinks-0.12pre5-ictce-5.3.0.eb b/easybuild/easyconfigs/e/ELinks/ELinks-0.12pre5-ictce-5.3.0.eb index 176ffcb6bd..0c4dfa07a3 100644 --- a/easybuild/easyconfigs/e/ELinks/ELinks-0.12pre5-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/e/ELinks/ELinks-0.12pre5-ictce-5.3.0.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/e/ESPResSo/ESPResSo-3.1.1-goolf-1.4.10-parallel.eb b/easybuild/easyconfigs/e/ESPResSo/ESPResSo-3.1.1-goolf-1.4.10-parallel.eb index 209b0e8d81..f31aca4bb2 100644 --- a/easybuild/easyconfigs/e/ESPResSo/ESPResSo-3.1.1-goolf-1.4.10-parallel.eb +++ b/easybuild/easyconfigs/e/ESPResSo/ESPResSo-3.1.1-goolf-1.4.10-parallel.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Josh Berryman , Fotis Georgatos diff --git a/easybuild/easyconfigs/e/ESPResSo/ESPResSo-3.1.1-goolf-1.4.10-serial.eb b/easybuild/easyconfigs/e/ESPResSo/ESPResSo-3.1.1-goolf-1.4.10-serial.eb index 80ab0978a1..250bf7f6ef 100644 --- a/easybuild/easyconfigs/e/ESPResSo/ESPResSo-3.1.1-goolf-1.4.10-serial.eb +++ b/easybuild/easyconfigs/e/ESPResSo/ESPResSo-3.1.1-goolf-1.4.10-serial.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Josh Berryman , Fotis Georgatos diff --git a/easybuild/easyconfigs/e/ESPResSo/ESPResSo-3.1.1-ictce-5.3.0-parallel.eb b/easybuild/easyconfigs/e/ESPResSo/ESPResSo-3.1.1-ictce-5.3.0-parallel.eb index 9ad3efca4c..16a651c9b3 100644 --- a/easybuild/easyconfigs/e/ESPResSo/ESPResSo-3.1.1-ictce-5.3.0-parallel.eb +++ b/easybuild/easyconfigs/e/ESPResSo/ESPResSo-3.1.1-ictce-5.3.0-parallel.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Josh Berryman , Fotis Georgatos diff --git a/easybuild/easyconfigs/e/ESPResSo/ESPResSo-3.1.1-ictce-5.3.0-serial.eb b/easybuild/easyconfigs/e/ESPResSo/ESPResSo-3.1.1-ictce-5.3.0-serial.eb index 525e2ebf3e..be9504c095 100644 --- a/easybuild/easyconfigs/e/ESPResSo/ESPResSo-3.1.1-ictce-5.3.0-serial.eb +++ b/easybuild/easyconfigs/e/ESPResSo/ESPResSo-3.1.1-ictce-5.3.0-serial.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Josh Berryman , Fotis Georgatos diff --git a/easybuild/easyconfigs/e/ETSF_IO/ETSF_IO-1.0.4-goolf-1.4.10.eb b/easybuild/easyconfigs/e/ETSF_IO/ETSF_IO-1.0.4-goolf-1.4.10.eb index 17f0b9d160..cfe2dfd1da 100644 --- a/easybuild/easyconfigs/e/ETSF_IO/ETSF_IO-1.0.4-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/e/ETSF_IO/ETSF_IO-1.0.4-goolf-1.4.10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2013-2014 The Cyprus Institute # Authors:: Thekla Loizou diff --git a/easybuild/easyconfigs/e/ETSF_IO/ETSF_IO-1.0.4-intel-2015b.eb b/easybuild/easyconfigs/e/ETSF_IO/ETSF_IO-1.0.4-intel-2015b.eb index 7e7f19b2ca..502c0c493a 100644 --- a/easybuild/easyconfigs/e/ETSF_IO/ETSF_IO-1.0.4-intel-2015b.eb +++ b/easybuild/easyconfigs/e/ETSF_IO/ETSF_IO-1.0.4-intel-2015b.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2013-2014 The Cyprus Institute # Authors:: Thekla Loizou diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.0.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.0.0.eb index 6a13fbccbd..819bcfdba2 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.0.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.0.0.eb @@ -3,7 +3,7 @@ easyblock = 'EB_EasyBuildMeta' name = 'EasyBuild' version = '1.0.0' -homepage = 'http://hpcugent.github.com/easybuild/' +homepage = 'http://easybuilders.github.io/easybuild' description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.0.1.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.0.1.eb index 1fc508215c..c22351c6de 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.0.1.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.0.1.eb @@ -3,7 +3,7 @@ easyblock = 'EB_EasyBuildMeta' name = 'EasyBuild' version = '1.0.1' -homepage = 'http://hpcugent.github.com/easybuild/' +homepage = 'http://easybuilders.github.io/easybuild' description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.0.2.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.0.2.eb index aefe4f3461..10e52177b1 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.0.2.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.0.2.eb @@ -3,7 +3,7 @@ easyblock = 'EB_EasyBuildMeta' name = 'EasyBuild' version = '1.0.2' -homepage = 'http://hpcugent.github.com/easybuild/' +homepage = 'http://easybuilders.github.io/easybuild' description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.1.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.1.0.eb index aec17460aa..b86dfbf810 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.1.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.1.0.eb @@ -3,7 +3,7 @@ easyblock = 'EB_EasyBuildMeta' name = 'EasyBuild' version = '1.1.0' -homepage = 'http://hpcugent.github.com/easybuild/' +homepage = 'http://easybuilders.github.io/easybuild' description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.10.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.10.0.eb index 12381b6467..a6804f4f58 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.10.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.10.0.eb @@ -3,7 +3,7 @@ easyblock = 'EB_EasyBuildMeta' name = 'EasyBuild' version = '1.10.0' -homepage = 'http://hpcugent.github.com/easybuild/' +homepage = 'http://easybuilders.github.io/easybuild' description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.11.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.11.0.eb index a8ef6b164a..23833e2836 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.11.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.11.0.eb @@ -3,7 +3,7 @@ easyblock = 'EB_EasyBuildMeta' name = 'EasyBuild' version = '1.11.0' -homepage = 'http://hpcugent.github.com/easybuild/' +homepage = 'http://easybuilders.github.io/easybuild' description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.11.1.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.11.1.eb index d2df7f1988..47f1a751e4 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.11.1.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.11.1.eb @@ -3,7 +3,7 @@ easyblock = 'EB_EasyBuildMeta' name = 'EasyBuild' version = '1.11.1' -homepage = 'http://hpcugent.github.com/easybuild/' +homepage = 'http://easybuilders.github.io/easybuild' description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.12.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.12.0.eb index 345d210d28..e4a27cb487 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.12.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.12.0.eb @@ -3,7 +3,7 @@ easyblock = 'EB_EasyBuildMeta' name = 'EasyBuild' version = '1.12.0' -homepage = 'http://hpcugent.github.com/easybuild/' +homepage = 'http://easybuilders.github.io/easybuild' description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.12.1.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.12.1.eb index 97720876b9..eb82e53707 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.12.1.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.12.1.eb @@ -3,7 +3,7 @@ easyblock = 'EB_EasyBuildMeta' name = 'EasyBuild' version = '1.12.1' -homepage = 'http://hpcugent.github.com/easybuild/' +homepage = 'http://easybuilders.github.io/easybuild' description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.13.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.13.0.eb index 0b5ba14c24..5455bc671c 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.13.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.13.0.eb @@ -3,7 +3,7 @@ easyblock = 'EB_EasyBuildMeta' name = 'EasyBuild' version = '1.13.0' -homepage = 'http://hpcugent.github.com/easybuild/' +homepage = 'http://easybuilders.github.io/easybuild' description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.14.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.14.0.eb index 0176f2b558..bf7bef23ba 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.14.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.14.0.eb @@ -3,7 +3,7 @@ easyblock = 'EB_EasyBuildMeta' name = 'EasyBuild' version = '1.14.0' -homepage = 'http://hpcugent.github.com/easybuild/' +homepage = 'http://easybuilders.github.io/easybuild' description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.15.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.15.0.eb index 3ae286c658..bc94abbd43 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.15.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.15.0.eb @@ -3,7 +3,7 @@ easyblock = 'EB_EasyBuildMeta' name = 'EasyBuild' version = "1.15.0" -homepage = 'http://hpcugent.github.com/easybuild/' +homepage = 'http://easybuilders.github.io/easybuild' description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.15.1.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.15.1.eb index b4fb5e015c..567d84626d 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.15.1.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.15.1.eb @@ -3,7 +3,7 @@ easyblock = 'EB_EasyBuildMeta' name = 'EasyBuild' version = "1.15.1" -homepage = 'http://hpcugent.github.com/easybuild/' +homepage = 'http://easybuilders.github.io/easybuild' description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.15.2.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.15.2.eb index 9025d6b24b..dc940ff5f3 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.15.2.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.15.2.eb @@ -3,7 +3,7 @@ easyblock = 'EB_EasyBuildMeta' name = 'EasyBuild' version = "1.15.2" -homepage = 'http://hpcugent.github.com/easybuild/' +homepage = 'http://easybuilders.github.io/easybuild' description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.16.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.16.0.eb index 2ac7d84426..07b994c134 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.16.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.16.0.eb @@ -3,7 +3,7 @@ easyblock = 'EB_EasyBuildMeta' name = 'EasyBuild' version = "1.16.0" -homepage = 'http://hpcugent.github.com/easybuild/' +homepage = 'http://easybuilders.github.io/easybuild' description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.16.1.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.16.1.eb index a7a958a3ca..063c0cae95 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.16.1.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.16.1.eb @@ -3,7 +3,7 @@ easyblock = 'EB_EasyBuildMeta' name = 'EasyBuild' version = "1.16.1" -homepage = 'http://hpcugent.github.com/easybuild/' +homepage = 'http://easybuilders.github.io/easybuild' description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.16.2.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.16.2.eb index 26fbe953cd..ca54ce2b48 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.16.2.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.16.2.eb @@ -3,7 +3,7 @@ easyblock = 'EB_EasyBuildMeta' name = 'EasyBuild' version = "1.16.2" -homepage = 'http://hpcugent.github.com/easybuild/' +homepage = 'http://easybuilders.github.io/easybuild' description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.2.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.2.0.eb index 84e658abed..5ab2ef518b 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.2.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.2.0.eb @@ -3,7 +3,7 @@ easyblock = 'EB_EasyBuildMeta' name = 'EasyBuild' version = '1.2.0' -homepage = 'http://hpcugent.github.com/easybuild/' +homepage = 'http://easybuilders.github.io/easybuild' description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.3.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.3.0.eb index 62ec508192..74208a9b9f 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.3.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.3.0.eb @@ -3,7 +3,7 @@ easyblock = 'EB_EasyBuildMeta' name = 'EasyBuild' version = '1.3.0' -homepage = 'http://hpcugent.github.com/easybuild/' +homepage = 'http://easybuilders.github.io/easybuild' description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.4.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.4.0.eb index f56094b5c0..cf1ab671cb 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.4.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.4.0.eb @@ -3,7 +3,7 @@ easyblock = 'EB_EasyBuildMeta' name = 'EasyBuild' version = '1.4.0' -homepage = 'http://hpcugent.github.com/easybuild/' +homepage = 'http://easybuilders.github.io/easybuild' description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.5.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.5.0.eb index df9a262ab2..395394e677 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.5.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.5.0.eb @@ -3,7 +3,7 @@ easyblock = 'EB_EasyBuildMeta' name = 'EasyBuild' version = '1.5.0' -homepage = 'http://hpcugent.github.com/easybuild/' +homepage = 'http://easybuilders.github.io/easybuild' description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.6.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.6.0.eb index 9082a71a46..673b37a447 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.6.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.6.0.eb @@ -3,7 +3,7 @@ easyblock = 'EB_EasyBuildMeta' name = 'EasyBuild' version = '1.6.0' -homepage = 'http://hpcugent.github.com/easybuild/' +homepage = 'http://easybuilders.github.io/easybuild' description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.7.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.7.0.eb index a2164fa02d..d63e41ec85 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.7.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.7.0.eb @@ -3,7 +3,7 @@ easyblock = 'EB_EasyBuildMeta' name = 'EasyBuild' version = '1.7.0' -homepage = 'http://hpcugent.github.com/easybuild/' +homepage = 'http://easybuilders.github.io/easybuild' description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.8.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.8.0.eb index 8fa4a0a750..f5a9269b1f 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.8.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.8.0.eb @@ -3,7 +3,7 @@ easyblock = 'EB_EasyBuildMeta' name = 'EasyBuild' version = '1.8.0' -homepage = 'http://hpcugent.github.com/easybuild/' +homepage = 'http://easybuilders.github.io/easybuild' description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.8.1.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.8.1.eb index 1774b8976c..e18328251e 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.8.1.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.8.1.eb @@ -3,7 +3,7 @@ easyblock = 'EB_EasyBuildMeta' name = 'EasyBuild' version = '1.8.1' -homepage = 'http://hpcugent.github.com/easybuild/' +homepage = 'http://easybuilders.github.io/easybuild' description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.8.2.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.8.2.eb index d990801ac2..76df856dd7 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.8.2.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.8.2.eb @@ -3,7 +3,7 @@ easyblock = 'EB_EasyBuildMeta' name = 'EasyBuild' version = '1.8.2' -homepage = 'http://hpcugent.github.com/easybuild/' +homepage = 'http://easybuilders.github.io/easybuild' description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.9.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.9.0.eb index 97801124aa..d2e8a2944e 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.9.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.9.0.eb @@ -3,7 +3,7 @@ easyblock = 'EB_EasyBuildMeta' name = 'EasyBuild' version = '1.9.0' -homepage = 'http://hpcugent.github.com/easybuild/' +homepage = 'http://easybuilders.github.io/easybuild' description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.0.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.0.0.eb index 81d586f625..24720fca1c 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.0.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.0.0.eb @@ -3,7 +3,7 @@ easyblock = 'EB_EasyBuildMeta' name = 'EasyBuild' version = "2.0.0" -homepage = 'http://hpcugent.github.com/easybuild/' +homepage = 'http://easybuilders.github.io/easybuild' description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.1.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.1.0.eb index cb8c19e606..4a7b7be82f 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.1.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.1.0.eb @@ -3,7 +3,7 @@ easyblock = 'EB_EasyBuildMeta' name = 'EasyBuild' version = '2.1.0' -homepage = 'http://hpcugent.github.com/easybuild/' +homepage = 'http://easybuilders.github.io/easybuild' description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.1.1.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.1.1.eb index 632563276e..84afda8b48 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.1.1.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.1.1.eb @@ -3,7 +3,7 @@ easyblock = 'EB_EasyBuildMeta' name = 'EasyBuild' version = '2.1.1' -homepage = 'http://hpcugent.github.com/easybuild/' +homepage = 'http://easybuilders.github.io/easybuild' description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.2.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.2.0.eb index 116950af4b..ce7e5bf141 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.2.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.2.0.eb @@ -3,7 +3,7 @@ easyblock = 'EB_EasyBuildMeta' name = 'EasyBuild' version = '2.2.0' -homepage = 'http://hpcugent.github.com/easybuild/' +homepage = 'http://easybuilders.github.io/easybuild' description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.3.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.3.0.eb index 6080ef8f0c..31548a1769 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.3.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.3.0.eb @@ -3,7 +3,7 @@ easyblock = 'EB_EasyBuildMeta' name = 'EasyBuild' version = '2.3.0' -homepage = 'http://hpcugent.github.com/easybuild/' +homepage = 'http://easybuilders.github.io/easybuild' description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.4.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.4.0.eb index bc8d7c8dd5..d7fe564a73 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.4.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.4.0.eb @@ -3,7 +3,7 @@ easyblock = 'EB_EasyBuildMeta' name = 'EasyBuild' version = '2.4.0' -homepage = 'http://hpcugent.github.com/easybuild/' +homepage = 'http://easybuilders.github.io/easybuild' description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.5.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.5.0.eb index 37d212b334..89f2840b11 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.5.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.5.0.eb @@ -3,7 +3,7 @@ easyblock = 'EB_EasyBuildMeta' name = 'EasyBuild' version = '2.5.0' -homepage = 'http://hpcugent.github.com/easybuild/' +homepage = 'http://easybuilders.github.io/easybuild' description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.6.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.6.0.eb index 01e4502a09..5d5435bb7f 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.6.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.6.0.eb @@ -3,7 +3,7 @@ easyblock = 'EB_EasyBuildMeta' name = 'EasyBuild' version = '2.6.0' -homepage = 'http://hpcugent.github.com/easybuild/' +homepage = 'http://easybuilders.github.io/easybuild' description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.7.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.7.0.eb index 1ca29896e8..b09425b770 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.7.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.7.0.eb @@ -3,7 +3,7 @@ easyblock = 'EB_EasyBuildMeta' name = 'EasyBuild' version = '2.7.0' -homepage = 'http://hpcugent.github.com/easybuild/' +homepage = 'http://easybuilders.github.io/easybuild' description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.8.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.8.0.eb index 07bb77b453..2e50e9c4e7 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.8.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.8.0.eb @@ -3,7 +3,7 @@ easyblock = 'EB_EasyBuildMeta' name = 'EasyBuild' version = '2.8.0' -homepage = 'http://hpcugent.github.com/easybuild/' +homepage = 'http://easybuilders.github.io/easybuild' description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.8.1.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.8.1.eb index f166a5d587..d8d510a78c 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.8.1.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.8.1.eb @@ -3,7 +3,7 @@ easyblock = 'EB_EasyBuildMeta' name = 'EasyBuild' version = '2.8.1' -homepage = 'http://hpcugent.github.com/easybuild/' +homepage = 'http://easybuilders.github.io/easybuild' description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.8.2.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.8.2.eb index b0edd36c96..2c33962b07 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.8.2.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.8.2.eb @@ -3,7 +3,7 @@ easyblock = 'EB_EasyBuildMeta' name = 'EasyBuild' version = '2.8.2' -homepage = 'http://hpcugent.github.com/easybuild/' +homepage = 'http://easybuilders.github.io/easybuild' description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.9.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.9.0.eb index 09a04b73a8..7ab918d84c 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.9.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.9.0.eb @@ -3,7 +3,7 @@ easyblock = 'EB_EasyBuildMeta' name = 'EasyBuild' version = '2.9.0' -homepage = 'http://hpcugent.github.com/easybuild/' +homepage = 'http://easybuilders.github.io/easybuild' description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.0.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.0.0.eb index a77b43aaad..c9a8f9fb2a 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.0.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.0.0.eb @@ -3,7 +3,7 @@ easyblock = 'EB_EasyBuildMeta' name = 'EasyBuild' version = '3.0.0' -homepage = 'http://hpcugent.github.com/easybuild/' +homepage = 'http://easybuilders.github.io/easybuild' description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.0.1.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.0.1.eb index 3d9fd92508..7fcaac8436 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.0.1.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.0.1.eb @@ -3,7 +3,7 @@ easyblock = 'EB_EasyBuildMeta' name = 'EasyBuild' version = '3.0.1' -homepage = 'http://hpcugent.github.com/easybuild/' +homepage = 'http://easybuilders.github.io/easybuild' description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.0.2.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.0.2.eb index 708295ab3c..ab22452b62 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.0.2.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.0.2.eb @@ -3,7 +3,7 @@ easyblock = 'EB_EasyBuildMeta' name = 'EasyBuild' version = '3.0.2' -homepage = 'http://hpcugent.github.com/easybuild/' +homepage = 'http://easybuilders.github.io/easybuild' description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.1.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.1.0.eb index 606f9a318d..7961017185 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.1.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.1.0.eb @@ -3,7 +3,7 @@ easyblock = 'EB_EasyBuildMeta' name = 'EasyBuild' version = '3.1.0' -homepage = 'http://hpcugent.github.com/easybuild/' +homepage = 'http://easybuilders.github.io/easybuild' description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.1.1.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.1.1.eb index 2dbc7fa9ba..bb9b2572df 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.1.1.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.1.1.eb @@ -3,7 +3,7 @@ easyblock = 'EB_EasyBuildMeta' name = 'EasyBuild' version = '3.1.1' -homepage = 'http://hpcugent.github.com/easybuild/' +homepage = 'http://easybuilders.github.io/easybuild' description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.1.2.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.1.2.eb index eaadea3b41..7bf19cc08b 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.1.2.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.1.2.eb @@ -3,7 +3,7 @@ easyblock = 'EB_EasyBuildMeta' name = 'EasyBuild' version = '3.1.2' -homepage = 'http://hpcugent.github.com/easybuild/' +homepage = 'http://easybuilders.github.io/easybuild' description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.2.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.2.0.eb index d84e16eaba..97d13804f9 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.2.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.2.0.eb @@ -3,7 +3,7 @@ easyblock = 'EB_EasyBuildMeta' name = 'EasyBuild' version = '3.2.0' -homepage = 'http://hpcugent.github.com/easybuild/' +homepage = 'http://easybuilders.github.io/easybuild' description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.2.1.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.2.1.eb index dfebb15dea..ee42c1d6b9 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.2.1.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.2.1.eb @@ -3,7 +3,7 @@ easyblock = 'EB_EasyBuildMeta' name = 'EasyBuild' version = '3.2.1' -homepage = 'http://hpcugent.github.com/easybuild/' +homepage = 'http://easybuilders.github.io/easybuild' description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.3.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.3.0.eb index c11a0f20c4..5d4ea9ca97 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.3.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.3.0.eb @@ -3,7 +3,7 @@ easyblock = 'EB_EasyBuildMeta' name = 'EasyBuild' version = '3.3.0' -homepage = 'http://hpcugent.github.com/easybuild/' +homepage = 'http://easybuilders.github.io/easybuild' description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.1.1-goolf-1.4.10.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.1.1-goolf-1.4.10.eb index f64ca17dc1..03e5ae3142 100644 --- a/easybuild/easyconfigs/e/Eigen/Eigen-3.1.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.1.1-goolf-1.4.10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Cedric Laczny , Fotis Georgatos diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.1.1-ictce-5.3.0.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.1.1-ictce-5.3.0.eb index c2159638f2..29c0f0a24e 100644 --- a/easybuild/easyconfigs/e/Eigen/Eigen-3.1.1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.1.1-ictce-5.3.0.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Cedric Laczny , Fotis Georgatos diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.1.4-goolf-1.4.10.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.1.4-goolf-1.4.10.eb index ad65bdfc92..52df5baa8d 100644 --- a/easybuild/easyconfigs/e/Eigen/Eigen-3.1.4-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.1.4-goolf-1.4.10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Cedric Laczny , Fotis Georgatos diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.1.4-ictce-5.3.0.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.1.4-ictce-5.3.0.eb index 0a2271f035..0fec576ce6 100644 --- a/easybuild/easyconfigs/e/Eigen/Eigen-3.1.4-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.1.4-ictce-5.3.0.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Cedric Laczny , Fotis Georgatos diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.1.4-ictce-5.5.0.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.1.4-ictce-5.5.0.eb index 0dd48816d2..70ef04ea87 100644 --- a/easybuild/easyconfigs/e/Eigen/Eigen-3.1.4-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.1.4-ictce-5.5.0.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Cedric Laczny , Fotis Georgatos diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.0-ictce-5.5.0.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.0-ictce-5.5.0.eb index 9e7b9cf60d..7831be18f5 100644 --- a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.0-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.0-ictce-5.5.0.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Cedric Laczny , Fotis Georgatos diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.2-goolf-1.5.14.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.2-goolf-1.5.14.eb index 7cbefdf8ab..1e4a8f49a5 100644 --- a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.2-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.2-goolf-1.5.14.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Cedric Laczny , Fotis Georgatos diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.2-ictce-7.1.2.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.2-ictce-7.1.2.eb index 81edc7d68b..f1219c065a 100644 --- a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.2-ictce-7.1.2.eb +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.2-ictce-7.1.2.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Cedric Laczny , Fotis Georgatos diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.2-intel-2014b.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.2-intel-2014b.eb index b3c186165b..16de65cee4 100644 --- a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.2-intel-2014b.eb +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.2-intel-2014b.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Cedric Laczny , Fotis Georgatos diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.6-goolf-1.7.20.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.6-goolf-1.7.20.eb index 59832233f0..2ac82d539a 100644 --- a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.6-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.6-goolf-1.7.20.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Cedric Laczny , Fotis Georgatos diff --git a/easybuild/easyconfigs/e/ErlangOTP/ErlangOTP-R16B02-goolf-1.4.10-no-Java.eb b/easybuild/easyconfigs/e/ErlangOTP/ErlangOTP-R16B02-goolf-1.4.10-no-Java.eb index 1e6432cb6d..32b4b7697d 100644 --- a/easybuild/easyconfigs/e/ErlangOTP/ErlangOTP-R16B02-goolf-1.4.10-no-Java.eb +++ b/easybuild/easyconfigs/e/ErlangOTP/ErlangOTP-R16B02-goolf-1.4.10-no-Java.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/e/Exonerate/Exonerate-2.2.0-foss-2015b.eb b/easybuild/easyconfigs/e/Exonerate/Exonerate-2.2.0-foss-2015b.eb index 6a9d4b5398..84c6277a5a 100644 --- a/easybuild/easyconfigs/e/Exonerate/Exonerate-2.2.0-foss-2015b.eb +++ b/easybuild/easyconfigs/e/Exonerate/Exonerate-2.2.0-foss-2015b.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/e/Exonerate/Exonerate-2.2.0-goolf-1.4.10.eb b/easybuild/easyconfigs/e/Exonerate/Exonerate-2.2.0-goolf-1.4.10.eb index 7f862017dd..db59680faa 100644 --- a/easybuild/easyconfigs/e/Exonerate/Exonerate-2.2.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/e/Exonerate/Exonerate-2.2.0-goolf-1.4.10.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/e/Exonerate/Exonerate-2.2.0-ictce-5.3.0.eb b/easybuild/easyconfigs/e/Exonerate/Exonerate-2.2.0-ictce-5.3.0.eb index 899422100c..19e0931e00 100644 --- a/easybuild/easyconfigs/e/Exonerate/Exonerate-2.2.0-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/e/Exonerate/Exonerate-2.2.0-ictce-5.3.0.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/e/Exonerate/Exonerate-2.4.0-foss-2015b.eb b/easybuild/easyconfigs/e/Exonerate/Exonerate-2.4.0-foss-2015b.eb index 524d427c0e..89c9d6f1ca 100644 --- a/easybuild/easyconfigs/e/Exonerate/Exonerate-2.4.0-foss-2015b.eb +++ b/easybuild/easyconfigs/e/Exonerate/Exonerate-2.4.0-foss-2015b.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/e/Exonerate/Exonerate-2.4.0-foss-2016a.eb b/easybuild/easyconfigs/e/Exonerate/Exonerate-2.4.0-foss-2016a.eb index 0cfe11f239..9d263392d3 100644 --- a/easybuild/easyconfigs/e/Exonerate/Exonerate-2.4.0-foss-2016a.eb +++ b/easybuild/easyconfigs/e/Exonerate/Exonerate-2.4.0-foss-2016a.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/e/Exonerate/Exonerate-2.4.0-foss-2016b.eb b/easybuild/easyconfigs/e/Exonerate/Exonerate-2.4.0-foss-2016b.eb index f186cddd62..afcb38952d 100644 --- a/easybuild/easyconfigs/e/Exonerate/Exonerate-2.4.0-foss-2016b.eb +++ b/easybuild/easyconfigs/e/Exonerate/Exonerate-2.4.0-foss-2016b.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/e/Extrae/Extrae-3.0.1-foss-2015a.eb b/easybuild/easyconfigs/e/Extrae/Extrae-3.0.1-foss-2015a.eb index 4e0f98d635..a37c5f2e77 100644 --- a/easybuild/easyconfigs/e/Extrae/Extrae-3.0.1-foss-2015a.eb +++ b/easybuild/easyconfigs/e/Extrae/Extrae-3.0.1-foss-2015a.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild # Copyright:: Copyright 2013 Juelich Supercomputing Centre, Germany # Authors:: Bernd Mohr # License:: New BSD diff --git a/easybuild/easyconfigs/e/eXpress/eXpress-1.5.1-goolf-1.4.10.eb b/easybuild/easyconfigs/e/eXpress/eXpress-1.5.1-goolf-1.4.10.eb index 037dcd8185..94c1eb603b 100644 --- a/easybuild/easyconfigs/e/eXpress/eXpress-1.5.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/e/eXpress/eXpress-1.5.1-goolf-1.4.10.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/f/FASTA/FASTA-36.3.5e-foss-2016b.eb b/easybuild/easyconfigs/f/FASTA/FASTA-36.3.5e-foss-2016b.eb index 93fe9bd8a4..9ecdd700fb 100644 --- a/easybuild/easyconfigs/f/FASTA/FASTA-36.3.5e-foss-2016b.eb +++ b/easybuild/easyconfigs/f/FASTA/FASTA-36.3.5e-foss-2016b.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild easyblock = 'MakeCp' diff --git a/easybuild/easyconfigs/f/FASTA/FASTA-36.3.5e-goolf-1.4.10.eb b/easybuild/easyconfigs/f/FASTA/FASTA-36.3.5e-goolf-1.4.10.eb index cb997fa593..7738a65d8c 100644 --- a/easybuild/easyconfigs/f/FASTA/FASTA-36.3.5e-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/f/FASTA/FASTA-36.3.5e-goolf-1.4.10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2013 The Cyprus Institute # Authors:: Andreas Panteli , Thekla Loizou , diff --git a/easybuild/easyconfigs/f/FASTA/FASTA-36.3.5e-ictce-5.3.0.eb b/easybuild/easyconfigs/f/FASTA/FASTA-36.3.5e-ictce-5.3.0.eb index 31a89c0085..723f27db16 100644 --- a/easybuild/easyconfigs/f/FASTA/FASTA-36.3.5e-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/f/FASTA/FASTA-36.3.5e-ictce-5.3.0.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2013 The Cyprus Institute # Authors:: Andreas Panteli , Thekla Loizou , diff --git a/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.13.2-goolf-1.4.10.eb b/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.13.2-goolf-1.4.10.eb index 3b0992eef6..0c2b26660e 100644 --- a/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.13.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.13.2-goolf-1.4.10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Cedric Laczny , Fotis Georgatos diff --git a/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.13.2-ictce-5.3.0.eb b/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.13.2-ictce-5.3.0.eb index 1f15e35214..8736954b97 100644 --- a/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.13.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.13.2-ictce-5.3.0.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Cedric Laczny , Fotis Georgatos diff --git a/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-foss-2015b.eb b/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-foss-2015b.eb index 000e1a89b7..6b26b56f8f 100644 --- a/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-foss-2015b.eb +++ b/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-foss-2015b.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Cedric Laczny , Fotis Georgatos diff --git a/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-foss-2016a.eb b/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-foss-2016a.eb index a69a7b9e2f..0b62a9167c 100644 --- a/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-foss-2016a.eb +++ b/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-foss-2016a.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Cedric Laczny , Fotis Georgatos diff --git a/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-foss-2016b.eb b/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-foss-2016b.eb index ef4b99cd73..c8f2a2e194 100644 --- a/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-foss-2016b.eb +++ b/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-foss-2016b.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Cedric Laczny , Fotis Georgatos diff --git a/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-goolf-1.4.10.eb b/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-goolf-1.4.10.eb index 1b0419e8b8..2455f164d6 100644 --- a/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-goolf-1.4.10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Cedric Laczny , Fotis Georgatos diff --git a/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-intel-2015a.eb b/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-intel-2015a.eb index 88eedbe248..bfe6932967 100644 --- a/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-intel-2015a.eb +++ b/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-intel-2015a.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Cedric Laczny , Fotis Georgatos diff --git a/easybuild/easyconfigs/f/FFLAS-FFPACK/FFLAS-FFPACK-2.2.0-foss-2016a.eb b/easybuild/easyconfigs/f/FFLAS-FFPACK/FFLAS-FFPACK-2.2.0-foss-2016a.eb index da99f9d5b8..d03b85f906 100644 --- a/easybuild/easyconfigs/f/FFLAS-FFPACK/FFLAS-FFPACK-2.2.0-foss-2016a.eb +++ b/easybuild/easyconfigs/f/FFLAS-FFPACK/FFLAS-FFPACK-2.2.0-foss-2016a.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild recipe; see https://github.com/hpcugent/easybuild +# This file is an EasyBuild recipe; see https://github.com/easybuilders/easybuild # # Copyright:: Copyright (c) 2016 Riccardo Murri # Authors:: Riccardo Murri diff --git a/easybuild/easyconfigs/f/FLAC/FLAC-1.3.1-foss-2015a.eb b/easybuild/easyconfigs/f/FLAC/FLAC-1.3.1-foss-2015a.eb index 76be36ffc6..81cb92955e 100644 --- a/easybuild/easyconfigs/f/FLAC/FLAC-1.3.1-foss-2015a.eb +++ b/easybuild/easyconfigs/f/FLAC/FLAC-1.3.1-foss-2015a.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Author: Stephane Thiell ### diff --git a/easybuild/easyconfigs/f/FSA/FSA-1.15.8-goolf-1.4.10.eb b/easybuild/easyconfigs/f/FSA/FSA-1.15.8-goolf-1.4.10.eb index 0f49be8035..7e45a7cbdc 100644 --- a/easybuild/easyconfigs/f/FSA/FSA-1.15.8-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/f/FSA/FSA-1.15.8-goolf-1.4.10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/NTUA, Swiss Institute of Bioinformatics # Authors:: Fotis Georgatos , Pablo Escobar Lopez diff --git a/easybuild/easyconfigs/f/FSA/FSA-1.15.8-ictce-5.3.0.eb b/easybuild/easyconfigs/f/FSA/FSA-1.15.8-ictce-5.3.0.eb index 27159a0ac8..c0b720f5c0 100644 --- a/easybuild/easyconfigs/f/FSA/FSA-1.15.8-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/f/FSA/FSA-1.15.8-ictce-5.3.0.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/NTUA, Swiss Institute of Bioinformatics # Authors:: Fotis Georgatos , Pablo Escobar Lopez diff --git a/easybuild/easyconfigs/f/FastQC/FastQC-0.10.1-Java-1.7.0_80.eb b/easybuild/easyconfigs/f/FastQC/FastQC-0.10.1-Java-1.7.0_80.eb index 5441477664..602621d4aa 100644 --- a/easybuild/easyconfigs/f/FastQC/FastQC-0.10.1-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/f/FastQC/FastQC-0.10.1-Java-1.7.0_80.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2013 The Cyprus Institute # Authors:: Andreas Panteli , Thekla Loizou diff --git a/easybuild/easyconfigs/f/Firefox/Firefox-44.0.2.eb b/easybuild/easyconfigs/f/Firefox/Firefox-44.0.2.eb index 1788c8a21a..5f3c9ec326 100644 --- a/easybuild/easyconfigs/f/Firefox/Firefox-44.0.2.eb +++ b/easybuild/easyconfigs/f/Firefox/Firefox-44.0.2.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # sciCORE - University of Basel # SIB Swiss Institute of Bioinformatics diff --git a/easybuild/easyconfigs/f/fastPHASE/fastPHASE-1.4.8.eb b/easybuild/easyconfigs/f/fastPHASE/fastPHASE-1.4.8.eb index 189d668ffd..f17bac6c21 100644 --- a/easybuild/easyconfigs/f/fastPHASE/fastPHASE-1.4.8.eb +++ b/easybuild/easyconfigs/f/fastPHASE/fastPHASE-1.4.8.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Ravi Tripathi # Email: ravi89@uab.edu diff --git a/easybuild/easyconfigs/f/fastQValidator/fastQValidator-0.1.1a-20151214-goolf-1.7.20-aadc6f9.eb b/easybuild/easyconfigs/f/fastQValidator/fastQValidator-0.1.1a-20151214-goolf-1.7.20-aadc6f9.eb index 5e8c01ab2d..fa8db6dbc2 100644 --- a/easybuild/easyconfigs/f/fastQValidator/fastQValidator-0.1.1a-20151214-goolf-1.7.20-aadc6f9.eb +++ b/easybuild/easyconfigs/f/fastQValidator/fastQValidator-0.1.1a-20151214-goolf-1.7.20-aadc6f9.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # sciCORE - University of Basel # SIB Swiss Institute of Bioinformatics diff --git a/easybuild/easyconfigs/f/fastqz/fastqz-1.5-GCC-4.8.2.eb b/easybuild/easyconfigs/f/fastqz/fastqz-1.5-GCC-4.8.2.eb index 4af4d1b872..2f83116b78 100644 --- a/easybuild/easyconfigs/f/fastqz/fastqz-1.5-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/f/fastqz/fastqz-1.5-GCC-4.8.2.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2015 NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/f/file/file-5.17-GCC-4.8.2.eb b/easybuild/easyconfigs/f/file/file-5.17-GCC-4.8.2.eb index bca5d69508..6d15ec35c6 100644 --- a/easybuild/easyconfigs/f/file/file-5.17-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/f/file/file-5.17-GCC-4.8.2.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # ## diff --git a/easybuild/easyconfigs/f/file/file-5.25-intel-2016a.eb b/easybuild/easyconfigs/f/file/file-5.25-intel-2016a.eb index 61f8e29397..2cd84ee8fc 100644 --- a/easybuild/easyconfigs/f/file/file-5.25-intel-2016a.eb +++ b/easybuild/easyconfigs/f/file/file-5.25-intel-2016a.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # ## diff --git a/easybuild/easyconfigs/f/file/file-5.28-foss-2016b.eb b/easybuild/easyconfigs/f/file/file-5.28-foss-2016b.eb index 51d81cd710..23357248bb 100644 --- a/easybuild/easyconfigs/f/file/file-5.28-foss-2016b.eb +++ b/easybuild/easyconfigs/f/file/file-5.28-foss-2016b.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # ## diff --git a/easybuild/easyconfigs/f/file/file-5.30-intel-2017a.eb b/easybuild/easyconfigs/f/file/file-5.30-intel-2017a.eb index cab481c6f4..92682e458a 100644 --- a/easybuild/easyconfigs/f/file/file-5.30-intel-2017a.eb +++ b/easybuild/easyconfigs/f/file/file-5.30-intel-2017a.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # ## diff --git a/easybuild/easyconfigs/f/findutils/findutils-4.2.33-goolf-1.4.10.eb b/easybuild/easyconfigs/f/findutils/findutils-4.2.33-goolf-1.4.10.eb index 6b2e49e08a..56642aa7ab 100644 --- a/easybuild/easyconfigs/f/findutils/findutils-4.2.33-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/f/findutils/findutils-4.2.33-goolf-1.4.10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/f/findutils/findutils-4.2.33-ictce-5.3.0.eb b/easybuild/easyconfigs/f/findutils/findutils-4.2.33-ictce-5.3.0.eb index ea5abc6927..34097eba86 100644 --- a/easybuild/easyconfigs/f/findutils/findutils-4.2.33-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/f/findutils/findutils-4.2.33-ictce-5.3.0.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/f/findutils/findutils-4.4.2-GCC-4.8.2.eb b/easybuild/easyconfigs/f/findutils/findutils-4.4.2-GCC-4.8.2.eb index bd925b7e0f..b9beaeb6db 100644 --- a/easybuild/easyconfigs/f/findutils/findutils-4.4.2-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/f/findutils/findutils-4.4.2-GCC-4.8.2.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/f/fqzcomp/fqzcomp-4.6-GCC-4.8.2.eb b/easybuild/easyconfigs/f/fqzcomp/fqzcomp-4.6-GCC-4.8.2.eb index c4cf3f3ff7..35005a8b95 100644 --- a/easybuild/easyconfigs/f/fqzcomp/fqzcomp-4.6-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/f/fqzcomp/fqzcomp-4.6-GCC-4.8.2.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2015 NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/g/GATK/GATK-2.5-2-Java-1.7.0_10.eb b/easybuild/easyconfigs/g/GATK/GATK-2.5-2-Java-1.7.0_10.eb index 6afbdb7b4c..b64688b618 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-2.5-2-Java-1.7.0_10.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-2.5-2-Java-1.7.0_10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Cyprus Institute / CaSToRC, Uni.Lu/LCSB, NTUA # Authors:: George Tsouloupas , Fotis Georgatos , Kenneth Hoste (UGent) diff --git a/easybuild/easyconfigs/g/GATK/GATK-2.6-5-Java-1.7.0_10.eb b/easybuild/easyconfigs/g/GATK/GATK-2.6-5-Java-1.7.0_10.eb index 921621187e..1b89f6c6ec 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-2.6-5-Java-1.7.0_10.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-2.6-5-Java-1.7.0_10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Cyprus Institute / CaSToRC, Uni.Lu/LCSB, NTUA # Authors:: George Tsouloupas , Fotis Georgatos , Kenneth Hoste (UGent) diff --git a/easybuild/easyconfigs/g/GATK/GATK-2.7-4-Java-1.7.0_10.eb b/easybuild/easyconfigs/g/GATK/GATK-2.7-4-Java-1.7.0_10.eb index 7e9f79abb8..1969cdc702 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-2.7-4-Java-1.7.0_10.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-2.7-4-Java-1.7.0_10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Cyprus Institute / CaSToRC, Uni.Lu/LCSB, NTUA # Authors:: George Tsouloupas , Fotis Georgatos , Kenneth Hoste (UGent) diff --git a/easybuild/easyconfigs/g/GATK/GATK-2.8-1-Java-1.7.0_10.eb b/easybuild/easyconfigs/g/GATK/GATK-2.8-1-Java-1.7.0_10.eb index 959d6f681a..df931a819c 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-2.8-1-Java-1.7.0_10.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-2.8-1-Java-1.7.0_10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Cyprus Institute / CaSToRC, Uni.Lu/LCSB, NTUA # Authors:: George Tsouloupas , Fotis Georgatos , Kenneth Hoste (UGent) diff --git a/easybuild/easyconfigs/g/GATK/GATK-3.0-0-Java-1.7.0_10.eb b/easybuild/easyconfigs/g/GATK/GATK-3.0-0-Java-1.7.0_10.eb index a6fc22eedf..afaf5a587a 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-3.0-0-Java-1.7.0_10.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-3.0-0-Java-1.7.0_10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2013-2014 Cyprus Institute # Authors:: Thekla Loizou diff --git a/easybuild/easyconfigs/g/GATK/GATK-3.3-0-Java-1.7.0_21.eb b/easybuild/easyconfigs/g/GATK/GATK-3.3-0-Java-1.7.0_21.eb index bae4a90d91..fd5122e871 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-3.3-0-Java-1.7.0_21.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-3.3-0-Java-1.7.0_21.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2013 Cyprus Institute / CaSToRC, University of Luxembourg / LCSB # Authors:: George Tsouloupas , Fotis Georgatos , diff --git a/easybuild/easyconfigs/g/GATK/GATK-3.3-0-Java-1.7.0_80.eb b/easybuild/easyconfigs/g/GATK/GATK-3.3-0-Java-1.7.0_80.eb index 88a772e2f8..f3b21831fe 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-3.3-0-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-3.3-0-Java-1.7.0_80.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2013 Cyprus Institute / CaSToRC, University of Luxembourg / LCSB # Authors:: George Tsouloupas , Fotis Georgatos , diff --git a/easybuild/easyconfigs/g/GATK/GATK-3.3-0-Java-1.8.0_66.eb b/easybuild/easyconfigs/g/GATK/GATK-3.3-0-Java-1.8.0_66.eb index d0d5a239b6..8dd25ea92a 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-3.3-0-Java-1.8.0_66.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-3.3-0-Java-1.8.0_66.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2013 Cyprus Institute / CaSToRC, University of Luxembourg / LCSB # Authors:: George Tsouloupas , Fotis Georgatos , diff --git a/easybuild/easyconfigs/g/GATK/GATK-3.5-Java-1.8.0_66.eb b/easybuild/easyconfigs/g/GATK/GATK-3.5-Java-1.8.0_66.eb index b6d45b10ea..598a86e9b2 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-3.5-Java-1.8.0_66.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-3.5-Java-1.8.0_66.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2013 Cyprus Institute / CaSToRC, University of Luxembourg / LCSB # Authors:: George Tsouloupas , Fotis Georgatos , diff --git a/easybuild/easyconfigs/g/GATK/GATK-3.5-Java-1.8.0_74.eb b/easybuild/easyconfigs/g/GATK/GATK-3.5-Java-1.8.0_74.eb index 935f73ec90..06ec8c03a7 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-3.5-Java-1.8.0_74.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-3.5-Java-1.8.0_74.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2013 Cyprus Institute / CaSToRC, University of Luxembourg / LCSB # Authors:: George Tsouloupas , Fotis Georgatos , diff --git a/easybuild/easyconfigs/g/GATK/GATK-3.6-Java-1.8.0_92.eb b/easybuild/easyconfigs/g/GATK/GATK-3.6-Java-1.8.0_92.eb index 6ed0f40863..bd6fea5ef5 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-3.6-Java-1.8.0_92.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-3.6-Java-1.8.0_92.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2013 Cyprus Institute / CaSToRC, University of Luxembourg / LCSB # Authors:: George Tsouloupas , Fotis Georgatos , diff --git a/easybuild/easyconfigs/g/GATK/GATK-3.7-Java-1.8.0_112.eb b/easybuild/easyconfigs/g/GATK/GATK-3.7-Java-1.8.0_112.eb index afc148cb14..bc0c66d4fe 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-3.7-Java-1.8.0_112.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-3.7-Java-1.8.0_112.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2013 Cyprus Institute / CaSToRC, University of Luxembourg / LCSB # Authors:: George Tsouloupas , Fotis Georgatos , diff --git a/easybuild/easyconfigs/g/GCC/GCC-system.eb b/easybuild/easyconfigs/g/GCC/GCC-system.eb index b24177d713..cff7cc3f07 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-system.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-system.eb @@ -1,5 +1,5 @@ ## -# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2015 Juelich Supercomputing Centre, Germany # Authors:: Bernd Mohr diff --git a/easybuild/easyconfigs/g/GD/GD-2.66-foss-2016b-Perl-5.24.0.eb b/easybuild/easyconfigs/g/GD/GD-2.66-foss-2016b-Perl-5.24.0.eb index 88f756e1ce..73a29b2ebe 100644 --- a/easybuild/easyconfigs/g/GD/GD-2.66-foss-2016b-Perl-5.24.0.eb +++ b/easybuild/easyconfigs/g/GD/GD-2.66-foss-2016b-Perl-5.24.0.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild easyblock = 'PerlModule' diff --git a/easybuild/easyconfigs/g/GDB/GDB-7.5.1-goolf-1.4.10.eb b/easybuild/easyconfigs/g/GDB/GDB-7.5.1-goolf-1.4.10.eb index 633ee3c7d8..03c1be68ac 100644 --- a/easybuild/easyconfigs/g/GDB/GDB-7.5.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/g/GDB/GDB-7.5.1-goolf-1.4.10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/g/GEM-library/GEM-library-20130406-045632_pre-release-3_Linux-x86_64.eb b/easybuild/easyconfigs/g/GEM-library/GEM-library-20130406-045632_pre-release-3_Linux-x86_64.eb index b7ffec63fe..62ae81e4f0 100644 --- a/easybuild/easyconfigs/g/GEM-library/GEM-library-20130406-045632_pre-release-3_Linux-x86_64.eb +++ b/easybuild/easyconfigs/g/GEM-library/GEM-library-20130406-045632_pre-release-3_Linux-x86_64.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/g/GEMSTAT/GEMSTAT-1.0-goolf-1.4.10.eb b/easybuild/easyconfigs/g/GEMSTAT/GEMSTAT-1.0-goolf-1.4.10.eb index 71eda7f181..4bfe15af38 100644 --- a/easybuild/easyconfigs/g/GEMSTAT/GEMSTAT-1.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/g/GEMSTAT/GEMSTAT-1.0-goolf-1.4.10.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/g/GFOLD/GFOLD-1.1.4-goolf-1.7.20.eb b/easybuild/easyconfigs/g/GFOLD/GFOLD-1.1.4-goolf-1.7.20.eb index ae8931f569..f2c4bc1afd 100644 --- a/easybuild/easyconfigs/g/GFOLD/GFOLD-1.1.4-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/g/GFOLD/GFOLD-1.1.4-goolf-1.7.20.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # sciCORE - University of Basel # SIB Swiss Institute of Bioinformatics diff --git a/easybuild/easyconfigs/g/GFOLD/GFOLD-1.1.4-intel-2016a.eb b/easybuild/easyconfigs/g/GFOLD/GFOLD-1.1.4-intel-2016a.eb index 5afa7f55f9..4f13bddcdc 100644 --- a/easybuild/easyconfigs/g/GFOLD/GFOLD-1.1.4-intel-2016a.eb +++ b/easybuild/easyconfigs/g/GFOLD/GFOLD-1.1.4-intel-2016a.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # sciCORE - University of Basel # SIB Swiss Institute of Bioinformatics diff --git a/easybuild/easyconfigs/g/GIMPS/GIMPS-p95v279-GCC-4.8.2.eb b/easybuild/easyconfigs/g/GIMPS/GIMPS-p95v279-GCC-4.8.2.eb index ebe4c931a7..0260a39483 100644 --- a/easybuild/easyconfigs/g/GIMPS/GIMPS-p95v279-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/g/GIMPS/GIMPS-p95v279-GCC-4.8.2.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/g/GIMPS/GIMPS-p95v279.linux64.eb b/easybuild/easyconfigs/g/GIMPS/GIMPS-p95v279.linux64.eb index 55fa61353f..271972fd7f 100644 --- a/easybuild/easyconfigs/g/GIMPS/GIMPS-p95v279.linux64.eb +++ b/easybuild/easyconfigs/g/GIMPS/GIMPS-p95v279.linux64.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/g/GLIMMER/GLIMMER-3.02b-goolf-1.4.10.eb b/easybuild/easyconfigs/g/GLIMMER/GLIMMER-3.02b-goolf-1.4.10.eb index 8ad521809b..9224bccf7f 100644 --- a/easybuild/easyconfigs/g/GLIMMER/GLIMMER-3.02b-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/g/GLIMMER/GLIMMER-3.02b-goolf-1.4.10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2013 The Cyprus Institute # Authors:: Andreas Panteli , Thekla Loizou diff --git a/easybuild/easyconfigs/g/GLIMMER/GLIMMER-3.02b-ictce-5.3.0.eb b/easybuild/easyconfigs/g/GLIMMER/GLIMMER-3.02b-ictce-5.3.0.eb index e4aa1f5c2e..90a24de0cf 100644 --- a/easybuild/easyconfigs/g/GLIMMER/GLIMMER-3.02b-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/g/GLIMMER/GLIMMER-3.02b-ictce-5.3.0.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2013 The Cyprus Institute # Authors:: Andreas Panteli , Thekla Loizou diff --git a/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2014-01-21-goolf-1.4.10.eb b/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2014-01-21-goolf-1.4.10.eb index d00a71f2d8..4da7b9cac0 100644 --- a/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2014-01-21-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2014-01-21-goolf-1.4.10.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2014-06-10-goolf-1.4.10.eb b/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2014-06-10-goolf-1.4.10.eb index 3994be6bc4..01026712de 100644 --- a/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2014-06-10-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2014-06-10-goolf-1.4.10.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2015-12-31.v2-foss-2015b.eb b/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2015-12-31.v2-foss-2015b.eb index abea13b1ce..48d2d898a5 100644 --- a/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2015-12-31.v2-foss-2015b.eb +++ b/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2015-12-31.v2-foss-2015b.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2016-05-01-foss-2016a.eb b/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2016-05-01-foss-2016a.eb index f2525337c6..a93eff9b9b 100644 --- a/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2016-05-01-foss-2016a.eb +++ b/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2016-05-01-foss-2016a.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2016-11-07-foss-2016b.eb b/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2016-11-07-foss-2016b.eb index 6b8d559ccc..7af870d276 100644 --- a/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2016-11-07-foss-2016b.eb +++ b/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2016-11-07-foss-2016b.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2016-foss-2016b-hybrid.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2016-foss-2016b-hybrid.eb index f72c224d32..cf07fe6921 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2016-foss-2016b-hybrid.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2016-foss-2016b-hybrid.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2016 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, # Ghent University / The Francis Crick Institute diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2016-foss-2016b-mt.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2016-foss-2016b-mt.eb index 1a85f392c7..4b007038bb 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2016-foss-2016b-mt.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2016-foss-2016b-mt.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2016 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, # Ghent University / The Francis Crick Institute diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.1-foss-2017a-PLUMED.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.1-foss-2017a-PLUMED.eb index 9fc85b8f3e..392a977903 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.1-foss-2017a-PLUMED.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.1-foss-2017a-PLUMED.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2016 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, # Ghent University / The Francis Crick Institute diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.2-foss-2017a.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.2-foss-2017a.eb index 8ad8f765c7..b2f4ae93aa 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.2-foss-2017a.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.2-foss-2017a.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2016 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, # Ghent University / The Francis Crick Institute diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.3-foss-2017a.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.3-foss-2017a.eb index c3f26a2915..42fbccf907 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.3-foss-2017a.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.3-foss-2017a.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2016 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, # Ghent University / The Francis Crick Institute diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.3-intel-2017a.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.3-intel-2017a.eb index edcd456df0..c0b9b8febe 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.3-intel-2017a.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.3-intel-2017a.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2016 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, # Ghent University / The Francis Crick Institute diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-3.3.3-goolf-1.5.14.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-3.3.3-goolf-1.5.14.eb index 6cbe4c8289..fbece4acc1 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-3.3.3-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-3.3.3-goolf-1.5.14.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA, Cyprus Institute / CaSToRC, Ghent University # Authors:: Wiktor Jurkowski , Fotis Georgatos , \ diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.1-goolf-1.4.10-hybrid.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.1-goolf-1.4.10-hybrid.eb index 85881f3e38..483e81edc4 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.1-goolf-1.4.10-hybrid.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.1-goolf-1.4.10-hybrid.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA, Cyprus Institute / CaSToRC, Ghent University # Authors:: Wiktor Jurkowski , Fotis Georgatos , \ diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.1-goolf-1.4.10-mt.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.1-goolf-1.4.10-mt.eb index 8dac71d952..f8e9652452 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.1-goolf-1.4.10-mt.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.1-goolf-1.4.10-mt.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA, Cyprus Institute / CaSToRC, Ghent University # Authors:: Wiktor Jurkowski , Fotis Georgatos , \ diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.1-ictce-5.3.0-hybrid.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.1-ictce-5.3.0-hybrid.eb index 11decefff1..e046619790 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.1-ictce-5.3.0-hybrid.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.1-ictce-5.3.0-hybrid.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA, Cyprus Institute / CaSToRC, Ghent University # Authors:: Wiktor Jurkowski , Fotis Georgatos , \ diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.1-ictce-5.3.0-mt.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.1-ictce-5.3.0-mt.eb index 7bc4e4ad92..2336d79f1f 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.1-ictce-5.3.0-mt.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.1-ictce-5.3.0-mt.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA, Cyprus Institute / CaSToRC, Ghent University # Authors:: Wiktor Jurkowski , Fotis Georgatos , \ diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-goolf-1.4.10-hybrid.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-goolf-1.4.10-hybrid.eb index eaada284fd..cf451c2390 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-goolf-1.4.10-hybrid.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-goolf-1.4.10-hybrid.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA, Cyprus Institute / CaSToRC, Ghent University # Authors:: Wiktor Jurkowski , Fotis Georgatos , \ diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-goolf-1.4.10-mt.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-goolf-1.4.10-mt.eb index 95002c6f56..21de51a948 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-goolf-1.4.10-mt.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-goolf-1.4.10-mt.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA, Cyprus Institute / CaSToRC, Ghent University # Authors:: Wiktor Jurkowski , Fotis Georgatos , \ diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-ictce-5.5.0-hybrid.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-ictce-5.5.0-hybrid.eb index 4e7a111b3a..6060f72245 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-ictce-5.5.0-hybrid.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-ictce-5.5.0-hybrid.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA, Cyprus Institute / CaSToRC, Ghent University # Authors:: Wiktor Jurkowski , Fotis Georgatos , \ diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-ictce-5.5.0-mt.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-ictce-5.5.0-mt.eb index 1d36cf5099..ae821baece 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-ictce-5.5.0-mt.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-ictce-5.5.0-mt.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA, Cyprus Institute / CaSToRC, Ghent University # Authors:: Wiktor Jurkowski , Fotis Georgatos , \ diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-2015.06-mpi.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-2015.06-mpi.eb index adf36de398..48b16c52ff 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-2015.06-mpi.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-2015.06-mpi.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2013 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, Ghent University # Authors:: Wiktor Jurkowski , Fotis Georgatos , \ diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-2015.11-mpi.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-2015.11-mpi.eb index f52ab6e342..0456808f10 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-2015.11-mpi.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-2015.11-mpi.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2013 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, Ghent University # Authors:: Wiktor Jurkowski , Fotis Georgatos , \ diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayIntel-2015.11-mpi.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayIntel-2015.11-mpi.eb index 3f046b2129..cce424c9ba 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayIntel-2015.11-mpi.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayIntel-2015.11-mpi.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2013 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, Ghent University # Authors:: Wiktor Jurkowski , Fotis Georgatos , \ diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.2-ictce-7.1.2-mt.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.2-ictce-7.1.2-mt.eb index b6b649c1ec..db4bdb854c 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.2-ictce-7.1.2-mt.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.2-ictce-7.1.2-mt.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2013 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, Ghent University # Authors:: Wiktor Jurkowski , Fotis Georgatos , \ diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.4-intel-2015a-hybrid.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.4-intel-2015a-hybrid.eb index 0914af5ffd..fc540e8f19 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.4-intel-2015a-hybrid.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.4-intel-2015a-hybrid.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2013 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, Ghent University # Authors:: Wiktor Jurkowski , Fotis Georgatos , \ diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.4-intel-2015a-mt.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.4-intel-2015a-mt.eb index f0da8f6053..dab6da36ba 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.4-intel-2015a-mt.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.4-intel-2015a-mt.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2013 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, Ghent University # Authors:: Wiktor Jurkowski , Fotis Georgatos , \ diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.5-intel-2015a-hybrid.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.5-intel-2015a-hybrid.eb index c7e0273a3e..1e5465d878 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.5-intel-2015a-hybrid.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.5-intel-2015a-hybrid.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2013 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, Ghent University # Authors:: Wiktor Jurkowski , Fotis Georgatos , \ diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.7-intel-2015a-hybrid.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.7-intel-2015a-hybrid.eb index 69bf5a5d40..a45d822382 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.7-intel-2015a-hybrid.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.7-intel-2015a-hybrid.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2013 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, Ghent University # Authors:: Wiktor Jurkowski , Fotis Georgatos , \ diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-5.1.1-intel-2015b-hybrid.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.1.1-intel-2015b-hybrid.eb index 327b471426..9fd003a18d 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-5.1.1-intel-2015b-hybrid.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.1.1-intel-2015b-hybrid.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2013 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, Ghent University # Authors:: Wiktor Jurkowski , Fotis Georgatos , \ diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-5.1.2-foss-2015b-hybrid.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.1.2-foss-2015b-hybrid.eb index db2a991381..100f817f32 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-5.1.2-foss-2015b-hybrid.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.1.2-foss-2015b-hybrid.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2013 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, Ghent University # Authors:: Wiktor Jurkowski , Fotis Georgatos , \ diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-5.1.2-foss-2016a-hybrid.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.1.2-foss-2016a-hybrid.eb index e699b7dd9b..0f65d23d03 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-5.1.2-foss-2016a-hybrid.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.1.2-foss-2016a-hybrid.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2013 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, Ghent University # Authors:: Wiktor Jurkowski , Fotis Georgatos , \ diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-5.1.2-foss-2016a-mt.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.1.2-foss-2016a-mt.eb index 3c8fdff8cf..9c98d6f546 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-5.1.2-foss-2016a-mt.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.1.2-foss-2016a-mt.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2013 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, Ghent University # Authors:: Wiktor Jurkowski , Fotis Georgatos , \ diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-5.1.2-goolf-1.7.20-mt.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.1.2-goolf-1.7.20-mt.eb index 5f20cd92b4..7292972b00 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-5.1.2-goolf-1.7.20-mt.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.1.2-goolf-1.7.20-mt.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2013 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, Ghent University # Authors:: Wiktor Jurkowski , Fotis Georgatos , \ diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-5.1.2-intel-2016a-hybrid-dp.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.1.2-intel-2016a-hybrid-dp.eb index e85182e185..922df0412b 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-5.1.2-intel-2016a-hybrid-dp.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.1.2-intel-2016a-hybrid-dp.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2013 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, Ghent University # Authors:: Wiktor Jurkowski , Fotis Georgatos , \ diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-5.1.2-intel-2016a-hybrid.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.1.2-intel-2016a-hybrid.eb index 1d0b356a9e..6db4e0caa3 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-5.1.2-intel-2016a-hybrid.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.1.2-intel-2016a-hybrid.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2013 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, Ghent University # Authors:: Wiktor Jurkowski , Fotis Georgatos , \ diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-5.1.4-foss-2016b-hybrid.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.1.4-foss-2016b-hybrid.eb index 2e153e4c27..ed0de02f0d 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-5.1.4-foss-2016b-hybrid.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.1.4-foss-2016b-hybrid.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2013 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, Ghent University # Authors:: Wiktor Jurkowski , Fotis Georgatos , \ diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-5.1.4-foss-2016b-mt.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.1.4-foss-2016b-mt.eb index ab660ee955..a3faf14469 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-5.1.4-foss-2016b-mt.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.1.4-foss-2016b-mt.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2013 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, Ghent University # Authors:: Wiktor Jurkowski , Fotis Georgatos , \ diff --git a/easybuild/easyconfigs/g/GROMOS++/GROMOS++-1.0.2211-goolf-1.5.14-openmp.eb b/easybuild/easyconfigs/g/GROMOS++/GROMOS++-1.0.2211-goolf-1.5.14-openmp.eb index cd7029cdae..14cf03acd4 100644 --- a/easybuild/easyconfigs/g/GROMOS++/GROMOS++-1.0.2211-goolf-1.5.14-openmp.eb +++ b/easybuild/easyconfigs/g/GROMOS++/GROMOS++-1.0.2211-goolf-1.5.14-openmp.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Benjamin P. Roberts # New Zealand eScience Infrastructure # The University of Auckland, Auckland, New Zealand diff --git a/easybuild/easyconfigs/g/GROMOS++/GROMOS++-1.0.2211-goolf-1.5.14-serial.eb b/easybuild/easyconfigs/g/GROMOS++/GROMOS++-1.0.2211-goolf-1.5.14-serial.eb index 2b1345c99b..372e30a64a 100644 --- a/easybuild/easyconfigs/g/GROMOS++/GROMOS++-1.0.2211-goolf-1.5.14-serial.eb +++ b/easybuild/easyconfigs/g/GROMOS++/GROMOS++-1.0.2211-goolf-1.5.14-serial.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Benjamin P. Roberts # New Zealand eScience Infrastructure # The University of Auckland, Auckland, New Zealand diff --git a/easybuild/easyconfigs/g/GTI/GTI-1.2.0-goolf-1.5.14.eb b/easybuild/easyconfigs/g/GTI/GTI-1.2.0-goolf-1.5.14.eb index d2f8ea38ad..a06a2799fd 100644 --- a/easybuild/easyconfigs/g/GTI/GTI-1.2.0-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/g/GTI/GTI-1.2.0-goolf-1.5.14.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild # Copyright:: Copyright 2013 Juelich Supercomputing Centre, Germany # Authors:: Bernd Mohr # License:: New BSD diff --git a/easybuild/easyconfigs/g/GTOOL/GTOOL-0.7.5.eb b/easybuild/easyconfigs/g/GTOOL/GTOOL-0.7.5.eb index 69e22e6cab..df06c73009 100644 --- a/easybuild/easyconfigs/g/GTOOL/GTOOL-0.7.5.eb +++ b/easybuild/easyconfigs/g/GTOOL/GTOOL-0.7.5.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Ravi Tripathi # Email: ravi89@uab.edu diff --git a/easybuild/easyconfigs/g/Givaro/Givaro-4.0.1-foss-2016a.eb b/easybuild/easyconfigs/g/Givaro/Givaro-4.0.1-foss-2016a.eb index 22ad6d392a..b56c68075d 100644 --- a/easybuild/easyconfigs/g/Givaro/Givaro-4.0.1-foss-2016a.eb +++ b/easybuild/easyconfigs/g/Givaro/Givaro-4.0.1-foss-2016a.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild recipe; see https://github.com/hpcugent/easybuild +# This file is an EasyBuild recipe; see https://github.com/easybuilders/easybuild # # Copyright:: Copyright (c) 2016 Riccardo Murri # Authors:: Riccardo Murri diff --git a/easybuild/easyconfigs/g/gawk/gawk-4.0.2-goolf-1.4.10.eb b/easybuild/easyconfigs/g/gawk/gawk-4.0.2-goolf-1.4.10.eb index 39b5e35917..b1ff3e1fdc 100644 --- a/easybuild/easyconfigs/g/gawk/gawk-4.0.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/g/gawk/gawk-4.0.2-goolf-1.4.10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/g/gawk/gawk-4.0.2-ictce-5.3.0.eb b/easybuild/easyconfigs/g/gawk/gawk-4.0.2-ictce-5.3.0.eb index 75c54349b6..a78d2827af 100644 --- a/easybuild/easyconfigs/g/gawk/gawk-4.0.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/g/gawk/gawk-4.0.2-ictce-5.3.0.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/g/gencore_variant_detection/gencore_variant_detection-1.0.eb b/easybuild/easyconfigs/g/gencore_variant_detection/gencore_variant_detection-1.0.eb index f4f2214acc..ff69d49387 100644 --- a/easybuild/easyconfigs/g/gencore_variant_detection/gencore_variant_detection-1.0.eb +++ b/easybuild/easyconfigs/g/gencore_variant_detection/gencore_variant_detection-1.0.eb @@ -1,5 +1,5 @@ ## -# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2013-2015 Juelich Supercomputing Centre, Germany # Authors:: Bernd Mohr diff --git a/easybuild/easyconfigs/g/git-lfs/git-lfs-1.1.1.eb b/easybuild/easyconfigs/g/git-lfs/git-lfs-1.1.1.eb index c16d2b51eb..449b40c4aa 100755 --- a/easybuild/easyconfigs/g/git-lfs/git-lfs-1.1.1.eb +++ b/easybuild/easyconfigs/g/git-lfs/git-lfs-1.1.1.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # sciCORE - University of Basel # SIB Swiss Institute of Bioinformatics diff --git a/easybuild/easyconfigs/g/git/git-1.7.12-goolf-1.4.10.eb b/easybuild/easyconfigs/g/git/git-1.7.12-goolf-1.4.10.eb index 7f241b6884..68edf4aa52 100644 --- a/easybuild/easyconfigs/g/git/git-1.7.12-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/g/git/git-1.7.12-goolf-1.4.10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/g/git/git-1.7.12-ictce-5.3.0.eb b/easybuild/easyconfigs/g/git/git-1.7.12-ictce-5.3.0.eb index 316219216f..3fc62cda33 100644 --- a/easybuild/easyconfigs/g/git/git-1.7.12-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/g/git/git-1.7.12-ictce-5.3.0.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/g/git/git-1.8.2-goolf-1.4.10.eb b/easybuild/easyconfigs/g/git/git-1.8.2-goolf-1.4.10.eb index 12ddedc547..98ff106f5e 100644 --- a/easybuild/easyconfigs/g/git/git-1.8.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/g/git/git-1.8.2-goolf-1.4.10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/g/git/git-1.8.3.1-goolf-1.4.10.eb b/easybuild/easyconfigs/g/git/git-1.8.3.1-goolf-1.4.10.eb index 343da7e2bc..9d558fa920 100644 --- a/easybuild/easyconfigs/g/git/git-1.8.3.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/g/git/git-1.8.3.1-goolf-1.4.10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/g/git/git-1.8.5.6-GCC-4.9.2.eb b/easybuild/easyconfigs/g/git/git-1.8.5.6-GCC-4.9.2.eb index 7360f033fe..6ac9c8056e 100644 --- a/easybuild/easyconfigs/g/git/git-1.8.5.6-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/g/git/git-1.8.5.6-GCC-4.9.2.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/g/git/git-2.2.2-GCC-4.9.2.eb b/easybuild/easyconfigs/g/git/git-2.2.2-GCC-4.9.2.eb index 1da07f9d58..9d36d6d2e5 100644 --- a/easybuild/easyconfigs/g/git/git-2.2.2-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/g/git/git-2.2.2-GCC-4.9.2.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/g/git/git-2.4.1-GCC-4.9.2.eb b/easybuild/easyconfigs/g/git/git-2.4.1-GCC-4.9.2.eb index ec7ac4488b..e2b308a370 100644 --- a/easybuild/easyconfigs/g/git/git-2.4.1-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/g/git/git-2.4.1-GCC-4.9.2.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/g/gnuplot/gnuplot-4.6.0-goolf-1.4.10.eb b/easybuild/easyconfigs/g/gnuplot/gnuplot-4.6.0-goolf-1.4.10.eb index 3d45dffc3f..b7a8f51ec8 100644 --- a/easybuild/easyconfigs/g/gnuplot/gnuplot-4.6.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/g/gnuplot/gnuplot-4.6.0-goolf-1.4.10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/g/gnuplot/gnuplot-4.6.0-ictce-5.3.0.eb b/easybuild/easyconfigs/g/gnuplot/gnuplot-4.6.0-ictce-5.3.0.eb index b95685cff8..30a93a0ae6 100644 --- a/easybuild/easyconfigs/g/gnuplot/gnuplot-4.6.0-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/g/gnuplot/gnuplot-4.6.0-ictce-5.3.0.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/g/gnuplot/gnuplot-4.6.6-intel-2014b.eb b/easybuild/easyconfigs/g/gnuplot/gnuplot-4.6.6-intel-2014b.eb index 7112a25a66..175322b4a7 100644 --- a/easybuild/easyconfigs/g/gnuplot/gnuplot-4.6.6-intel-2014b.eb +++ b/easybuild/easyconfigs/g/gnuplot/gnuplot-4.6.6-intel-2014b.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/g/gnuplot/gnuplot-5.0.0-intel-2014b.eb b/easybuild/easyconfigs/g/gnuplot/gnuplot-5.0.0-intel-2014b.eb index e30d4a22d3..98df4333c5 100644 --- a/easybuild/easyconfigs/g/gnuplot/gnuplot-5.0.0-intel-2014b.eb +++ b/easybuild/easyconfigs/g/gnuplot/gnuplot-5.0.0-intel-2014b.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2013 University of Luxembourg/Luxembourg Centre for Systems Biomedicine # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/g/gnuplot/gnuplot-5.0.0-intel-2015a.eb b/easybuild/easyconfigs/g/gnuplot/gnuplot-5.0.0-intel-2015a.eb index 8f7d80279e..711098e083 100644 --- a/easybuild/easyconfigs/g/gnuplot/gnuplot-5.0.0-intel-2015a.eb +++ b/easybuild/easyconfigs/g/gnuplot/gnuplot-5.0.0-intel-2015a.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2013 University of Luxembourg/Luxembourg Centre for Systems Biomedicine # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/g/gnuplot/gnuplot-5.0.1-intel-2015b.eb b/easybuild/easyconfigs/g/gnuplot/gnuplot-5.0.1-intel-2015b.eb index 5903cd754c..622c222c99 100644 --- a/easybuild/easyconfigs/g/gnuplot/gnuplot-5.0.1-intel-2015b.eb +++ b/easybuild/easyconfigs/g/gnuplot/gnuplot-5.0.1-intel-2015b.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2013 University of Luxembourg/Luxembourg Centre for Systems Biomedicine # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/g/gnuplot/gnuplot-5.0.3-foss-2016a.eb b/easybuild/easyconfigs/g/gnuplot/gnuplot-5.0.3-foss-2016a.eb index 7e42e00e67..abc501af50 100644 --- a/easybuild/easyconfigs/g/gnuplot/gnuplot-5.0.3-foss-2016a.eb +++ b/easybuild/easyconfigs/g/gnuplot/gnuplot-5.0.3-foss-2016a.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2013 University of Luxembourg/Luxembourg Centre for Systems Biomedicine # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/g/gnuplot/gnuplot-5.0.3-intel-2016a.eb b/easybuild/easyconfigs/g/gnuplot/gnuplot-5.0.3-intel-2016a.eb index 131131cfee..e83b27fbe1 100644 --- a/easybuild/easyconfigs/g/gnuplot/gnuplot-5.0.3-intel-2016a.eb +++ b/easybuild/easyconfigs/g/gnuplot/gnuplot-5.0.3-intel-2016a.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2013 University of Luxembourg/Luxembourg Centre for Systems Biomedicine # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/g/gnuplot/gnuplot-5.0.5-foss-2016b.eb b/easybuild/easyconfigs/g/gnuplot/gnuplot-5.0.5-foss-2016b.eb index 20416b1946..09840a3a2e 100755 --- a/easybuild/easyconfigs/g/gnuplot/gnuplot-5.0.5-foss-2016b.eb +++ b/easybuild/easyconfigs/g/gnuplot/gnuplot-5.0.5-foss-2016b.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2013 University of Luxembourg/Luxembourg Centre for Systems Biomedicine # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/g/gnuplot/gnuplot-5.0.5-intel-2016b.eb b/easybuild/easyconfigs/g/gnuplot/gnuplot-5.0.5-intel-2016b.eb index 1181859b40..500cd9df29 100644 --- a/easybuild/easyconfigs/g/gnuplot/gnuplot-5.0.5-intel-2016b.eb +++ b/easybuild/easyconfigs/g/gnuplot/gnuplot-5.0.5-intel-2016b.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2013 University of Luxembourg/Luxembourg Centre for Systems Biomedicine # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/g/gnuplot/gnuplot-5.0.6-intel-2017a.eb b/easybuild/easyconfigs/g/gnuplot/gnuplot-5.0.6-intel-2017a.eb index 22b8ccefa5..7b2974dbf3 100644 --- a/easybuild/easyconfigs/g/gnuplot/gnuplot-5.0.6-intel-2017a.eb +++ b/easybuild/easyconfigs/g/gnuplot/gnuplot-5.0.6-intel-2017a.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2013 University of Luxembourg/Luxembourg Centre for Systems Biomedicine # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/g/grabix/grabix-0.1.6-goolf-1.7.20.eb b/easybuild/easyconfigs/g/grabix/grabix-0.1.6-goolf-1.7.20.eb index 1bf0222ad3..a16b047807 100644 --- a/easybuild/easyconfigs/g/grabix/grabix-0.1.6-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/g/grabix/grabix-0.1.6-goolf-1.7.20.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # sciCORE - University of Basel # SIB Swiss Institute of Bioinformatics diff --git a/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-mpi.eb b/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-mpi.eb index 3020c00623..bffc1db371 100644 --- a/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-mpi.eb +++ b/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-mpi.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Benjamin P. Roberts # New Zealand eScience Infrastructure # The University of Auckland, Auckland, New Zealand diff --git a/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-openmp.eb b/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-openmp.eb index 8cae45f338..d14dd7b8c3 100644 --- a/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-openmp.eb +++ b/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-openmp.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Benjamin P. Roberts # New Zealand eScience Infrastructure # The University of Auckland, Auckland, New Zealand diff --git a/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-serial.eb b/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-serial.eb index 075812f642..3f1f59fa95 100644 --- a/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-serial.eb +++ b/easybuild/easyconfigs/g/gromosXX/gromosXX-1.0.1737-goolf-1.5.14-serial.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Benjamin P. Roberts # New Zealand eScience Infrastructure # The University of Auckland, Auckland, New Zealand diff --git a/easybuild/easyconfigs/g/gzip/gzip-1.5-goolf-1.4.10.eb b/easybuild/easyconfigs/g/gzip/gzip-1.5-goolf-1.4.10.eb index 04f2007013..346229a60d 100644 --- a/easybuild/easyconfigs/g/gzip/gzip-1.5-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/g/gzip/gzip-1.5-goolf-1.4.10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright (c) 2012-2013 Cyprus Institute / CaSToRC # Authors:: Thekla Loizou diff --git a/easybuild/easyconfigs/g/gzip/gzip-1.5-ictce-5.3.0.eb b/easybuild/easyconfigs/g/gzip/gzip-1.5-ictce-5.3.0.eb index 677ec0c4a6..0282f12e45 100644 --- a/easybuild/easyconfigs/g/gzip/gzip-1.5-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/g/gzip/gzip-1.5-ictce-5.3.0.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild recipy as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild recipy as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright (c) 2012-2013 Cyprus Institute / CaSToRC # Author:: Thekla Loizou diff --git a/easybuild/easyconfigs/g/gzip/gzip-1.6-goolf-1.5.14.eb b/easybuild/easyconfigs/g/gzip/gzip-1.6-goolf-1.5.14.eb index 87a654b58c..356edf5aad 100644 --- a/easybuild/easyconfigs/g/gzip/gzip-1.6-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/g/gzip/gzip-1.6-goolf-1.5.14.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright (c) 2012-2013 Cyprus Institute / CaSToRC # Authors:: Thekla Loizou diff --git a/easybuild/easyconfigs/g/gzip/gzip-1.6-goolf-1.6.10.eb b/easybuild/easyconfigs/g/gzip/gzip-1.6-goolf-1.6.10.eb index 86cfca091f..fdb8e4ad69 100644 --- a/easybuild/easyconfigs/g/gzip/gzip-1.6-goolf-1.6.10.eb +++ b/easybuild/easyconfigs/g/gzip/gzip-1.6-goolf-1.6.10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright (c) 2012-2013 Cyprus Institute / CaSToRC # Authors:: Thekla Loizou diff --git a/easybuild/easyconfigs/g/gzip/gzip-1.6-ictce-5.3.0.eb b/easybuild/easyconfigs/g/gzip/gzip-1.6-ictce-5.3.0.eb index 443c4e034e..006952caba 100644 --- a/easybuild/easyconfigs/g/gzip/gzip-1.6-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/g/gzip/gzip-1.6-ictce-5.3.0.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright (c) 2012-2013 Cyprus Institute / CaSToRC # Authors:: Thekla Loizou diff --git a/easybuild/easyconfigs/g/gzip/gzip-1.6-ictce-5.5.0.eb b/easybuild/easyconfigs/g/gzip/gzip-1.6-ictce-5.5.0.eb index ce75649419..24f9247f5e 100644 --- a/easybuild/easyconfigs/g/gzip/gzip-1.6-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/g/gzip/gzip-1.6-ictce-5.5.0.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright (c) 2012-2013 Cyprus Institute / CaSToRC # Authors:: Thekla Loizou diff --git a/easybuild/easyconfigs/g/gzip/gzip-1.6-ictce-6.2.5.eb b/easybuild/easyconfigs/g/gzip/gzip-1.6-ictce-6.2.5.eb index 0b795ea36c..9c01e1b2fa 100644 --- a/easybuild/easyconfigs/g/gzip/gzip-1.6-ictce-6.2.5.eb +++ b/easybuild/easyconfigs/g/gzip/gzip-1.6-ictce-6.2.5.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright (c) 2012-2013 Cyprus Institute / CaSToRC # Authors:: Thekla Loizou diff --git a/easybuild/easyconfigs/h/HAPGEN2/HAPGEN2-2.2.0.eb b/easybuild/easyconfigs/h/HAPGEN2/HAPGEN2-2.2.0.eb index 9874a034c6..9ce0955413 100644 --- a/easybuild/easyconfigs/h/HAPGEN2/HAPGEN2-2.2.0.eb +++ b/easybuild/easyconfigs/h/HAPGEN2/HAPGEN2-2.2.0.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Ravi Tripathi # Email: ravi89@uab.edu diff --git a/easybuild/easyconfigs/h/HH-suite/HH-suite-2.0.16-goolf-1.4.10.eb b/easybuild/easyconfigs/h/HH-suite/HH-suite-2.0.16-goolf-1.4.10.eb index 562e595557..d814155d48 100644 --- a/easybuild/easyconfigs/h/HH-suite/HH-suite-2.0.16-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/h/HH-suite/HH-suite-2.0.16-goolf-1.4.10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild recipy as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild recipy as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/h/HMMER/HMMER-3.0-goolf-1.4.10.eb b/easybuild/easyconfigs/h/HMMER/HMMER-3.0-goolf-1.4.10.eb index ee8ba62195..575f1cb3a1 100644 --- a/easybuild/easyconfigs/h/HMMER/HMMER-3.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/h/HMMER/HMMER-3.0-goolf-1.4.10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/h/HMMER/HMMER-3.0-ictce-5.3.0.eb b/easybuild/easyconfigs/h/HMMER/HMMER-3.0-ictce-5.3.0.eb index ee8eae3fa7..58666bd91f 100644 --- a/easybuild/easyconfigs/h/HMMER/HMMER-3.0-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/h/HMMER/HMMER-3.0-ictce-5.3.0.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/h/HMMER/HMMER-3.1b1-goolf-1.4.10.eb b/easybuild/easyconfigs/h/HMMER/HMMER-3.1b1-goolf-1.4.10.eb index c4861d5fc5..180372ef32 100644 --- a/easybuild/easyconfigs/h/HMMER/HMMER-3.1b1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/h/HMMER/HMMER-3.1b1-goolf-1.4.10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Nils Christian , Fotis Georgatos diff --git a/easybuild/easyconfigs/h/HMMER/HMMER-3.1b1-ictce-5.3.0.eb b/easybuild/easyconfigs/h/HMMER/HMMER-3.1b1-ictce-5.3.0.eb index de6a298e59..46ef675ae2 100644 --- a/easybuild/easyconfigs/h/HMMER/HMMER-3.1b1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/h/HMMER/HMMER-3.1b1-ictce-5.3.0.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Nils Christian , Fotis Georgatos diff --git a/easybuild/easyconfigs/h/HMMER/HMMER-3.1b1-ictce-6.2.5.eb b/easybuild/easyconfigs/h/HMMER/HMMER-3.1b1-ictce-6.2.5.eb index 2a1f6d334f..9368f8b014 100644 --- a/easybuild/easyconfigs/h/HMMER/HMMER-3.1b1-ictce-6.2.5.eb +++ b/easybuild/easyconfigs/h/HMMER/HMMER-3.1b1-ictce-6.2.5.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Nils Christian , Fotis Georgatos diff --git a/easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-foss-2016a.eb b/easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-foss-2016a.eb index aed3e32ba8..cad1b86e44 100644 --- a/easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-foss-2016a.eb +++ b/easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-foss-2016a.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Nils Christian , Fotis Georgatos diff --git a/easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-intel-2015a.eb b/easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-intel-2015a.eb index 66c915507d..eb4bc8d61f 100644 --- a/easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-intel-2015a.eb +++ b/easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-intel-2015a.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Nils Christian , Fotis Georgatos diff --git a/easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-intel-2017a.eb b/easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-intel-2017a.eb index 3ca7456fc5..16913ef0f2 100644 --- a/easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-intel-2017a.eb +++ b/easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-intel-2017a.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Nils Christian , Fotis Georgatos diff --git a/easybuild/easyconfigs/h/HPCBIOS_Bioinfo/HPCBIOS_Bioinfo-20130829-goolf-1.4.10.eb b/easybuild/easyconfigs/h/HPCBIOS_Bioinfo/HPCBIOS_Bioinfo-20130829-goolf-1.4.10.eb index 05c50b39b9..36c9dbdcc4 100644 --- a/easybuild/easyconfigs/h/HPCBIOS_Bioinfo/HPCBIOS_Bioinfo-20130829-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/h/HPCBIOS_Bioinfo/HPCBIOS_Bioinfo-20130829-goolf-1.4.10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/h/HPCBIOS_Bioinfo/HPCBIOS_Bioinfo-20130829-ictce-5.3.0.eb b/easybuild/easyconfigs/h/HPCBIOS_Bioinfo/HPCBIOS_Bioinfo-20130829-ictce-5.3.0.eb index a420531cae..2a8073ec74 100644 --- a/easybuild/easyconfigs/h/HPCBIOS_Bioinfo/HPCBIOS_Bioinfo-20130829-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/h/HPCBIOS_Bioinfo/HPCBIOS_Bioinfo-20130829-ictce-5.3.0.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/h/HPCBIOS_Debuggers/HPCBIOS_Debuggers-20130829-goolf-1.4.10.eb b/easybuild/easyconfigs/h/HPCBIOS_Debuggers/HPCBIOS_Debuggers-20130829-goolf-1.4.10.eb index 259d3f70b6..1b8304beca 100644 --- a/easybuild/easyconfigs/h/HPCBIOS_Debuggers/HPCBIOS_Debuggers-20130829-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/h/HPCBIOS_Debuggers/HPCBIOS_Debuggers-20130829-goolf-1.4.10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/h/HPCBIOS_LifeSciences/HPCBIOS_LifeSciences-20130829-goolf-1.4.10.eb b/easybuild/easyconfigs/h/HPCBIOS_LifeSciences/HPCBIOS_LifeSciences-20130829-goolf-1.4.10.eb index ac9bda6d5d..f65efedca6 100644 --- a/easybuild/easyconfigs/h/HPCBIOS_LifeSciences/HPCBIOS_LifeSciences-20130829-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/h/HPCBIOS_LifeSciences/HPCBIOS_LifeSciences-20130829-goolf-1.4.10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/h/HPCBIOS_LifeSciences/HPCBIOS_LifeSciences-20130829-ictce-5.3.0.eb b/easybuild/easyconfigs/h/HPCBIOS_LifeSciences/HPCBIOS_LifeSciences-20130829-ictce-5.3.0.eb index a4a4c517a0..c6d311c611 100644 --- a/easybuild/easyconfigs/h/HPCBIOS_LifeSciences/HPCBIOS_LifeSciences-20130829-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/h/HPCBIOS_LifeSciences/HPCBIOS_LifeSciences-20130829-ictce-5.3.0.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/h/HPCBIOS_Math/HPCBIOS_Math-20130829-goolf-1.4.10.eb b/easybuild/easyconfigs/h/HPCBIOS_Math/HPCBIOS_Math-20130829-goolf-1.4.10.eb index db4a026864..3147429e4f 100644 --- a/easybuild/easyconfigs/h/HPCBIOS_Math/HPCBIOS_Math-20130829-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/h/HPCBIOS_Math/HPCBIOS_Math-20130829-goolf-1.4.10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/h/HPCBIOS_Math/HPCBIOS_Math-20130829-ictce-5.3.0.eb b/easybuild/easyconfigs/h/HPCBIOS_Math/HPCBIOS_Math-20130829-ictce-5.3.0.eb index 53cb50514f..a497fa7b0e 100644 --- a/easybuild/easyconfigs/h/HPCBIOS_Math/HPCBIOS_Math-20130829-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/h/HPCBIOS_Math/HPCBIOS_Math-20130829-ictce-5.3.0.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/h/HPCBIOS_Profilers/HPCBIOS_Profilers-20130829-goolf-1.4.10.eb b/easybuild/easyconfigs/h/HPCBIOS_Profilers/HPCBIOS_Profilers-20130829-goolf-1.4.10.eb index 7f92d9a951..a39dfd9547 100644 --- a/easybuild/easyconfigs/h/HPCBIOS_Profilers/HPCBIOS_Profilers-20130829-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/h/HPCBIOS_Profilers/HPCBIOS_Profilers-20130829-goolf-1.4.10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/h/HTSlib/HTSlib-1.1-goolf-1.4.10.eb b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.1-goolf-1.4.10.eb index 2f2abef4e6..0f044b4961 100644 --- a/easybuild/easyconfigs/h/HTSlib/HTSlib-1.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.1-goolf-1.4.10.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/h/HTSlib/HTSlib-1.2.1-foss-2015a.eb b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.2.1-foss-2015a.eb index 36facf37a3..ffc593fc72 100644 --- a/easybuild/easyconfigs/h/HTSlib/HTSlib-1.2.1-foss-2015a.eb +++ b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.2.1-foss-2015a.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/h/HTSlib/HTSlib-1.2.1-goolf-1.7.20.eb b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.2.1-goolf-1.7.20.eb index 7f25a2acfb..510a0b491a 100644 --- a/easybuild/easyconfigs/h/HTSlib/HTSlib-1.2.1-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.2.1-goolf-1.7.20.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/h/HTSlib/HTSlib-1.2.1-intel-2015a.eb b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.2.1-intel-2015a.eb index 258f48d92e..5770c1df40 100644 --- a/easybuild/easyconfigs/h/HTSlib/HTSlib-1.2.1-intel-2015a.eb +++ b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.2.1-intel-2015a.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/h/HTSlib/HTSlib-1.2.1-intel-2015b.eb b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.2.1-intel-2015b.eb index 8c0f7d5ac6..bc2b40e77d 100644 --- a/easybuild/easyconfigs/h/HTSlib/HTSlib-1.2.1-intel-2015b.eb +++ b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.2.1-intel-2015b.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/h/HTSlib/HTSlib-1.3-foss-2016a.eb b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.3-foss-2016a.eb index 93d7d3c6df..aa4b195ecd 100644 --- a/easybuild/easyconfigs/h/HTSlib/HTSlib-1.3-foss-2016a.eb +++ b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.3-foss-2016a.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/h/HTSlib/HTSlib-1.3-intel-2016a.eb b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.3-intel-2016a.eb index 7b22333e99..3cf499fca6 100644 --- a/easybuild/easyconfigs/h/HTSlib/HTSlib-1.3-intel-2016a.eb +++ b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.3-intel-2016a.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/h/HTSlib/HTSlib-1.3.1-foss-2016a.eb b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.3.1-foss-2016a.eb index a935ba2870..77e076361b 100644 --- a/easybuild/easyconfigs/h/HTSlib/HTSlib-1.3.1-foss-2016a.eb +++ b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.3.1-foss-2016a.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # sciCORE - University of Basel # SIB Swiss Institute of Bioinformatics diff --git a/easybuild/easyconfigs/h/HTSlib/HTSlib-1.3.1-foss-2016b.eb b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.3.1-foss-2016b.eb index 71dc997206..76292f8b71 100644 --- a/easybuild/easyconfigs/h/HTSlib/HTSlib-1.3.1-foss-2016b.eb +++ b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.3.1-foss-2016b.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # sciCORE - University of Basel # SIB Swiss Institute of Bioinformatics diff --git a/easybuild/easyconfigs/h/HTSlib/HTSlib-1.3.1-goolf-1.7.20.eb b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.3.1-goolf-1.7.20.eb index f75133a502..890b17a7bb 100644 --- a/easybuild/easyconfigs/h/HTSlib/HTSlib-1.3.1-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.3.1-goolf-1.7.20.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # sciCORE - University of Basel # SIB Swiss Institute of Bioinformatics diff --git a/easybuild/easyconfigs/h/HTSlib/HTSlib-1.3.1-intel-2016b.eb b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.3.1-intel-2016b.eb index 38ae993dca..beb21e0706 100644 --- a/easybuild/easyconfigs/h/HTSlib/HTSlib-1.3.1-intel-2016b.eb +++ b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.3.1-intel-2016b.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # sciCORE - University of Basel # SIB Swiss Institute of Bioinformatics diff --git a/easybuild/easyconfigs/h/HTSlib/HTSlib-1.3.2-intel-2016b.eb b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.3.2-intel-2016b.eb index b0528a8f0c..d8508a8bed 100644 --- a/easybuild/easyconfigs/h/HTSlib/HTSlib-1.3.2-intel-2016b.eb +++ b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.3.2-intel-2016b.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/h/HTSlib/HTSlib-1.4-foss-2016b.eb b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.4-foss-2016b.eb index 9bdb215d4c..6efdbf1487 100644 --- a/easybuild/easyconfigs/h/HTSlib/HTSlib-1.4-foss-2016b.eb +++ b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.4-foss-2016b.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/h/HTSlib/HTSlib-1.4-intel-2016b.eb b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.4-intel-2016b.eb index 5c5a91710c..6836878b7b 100644 --- a/easybuild/easyconfigs/h/HTSlib/HTSlib-1.4-intel-2016b.eb +++ b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.4-intel-2016b.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/h/HTSlib/HTSlib-1.4.1-intel-2017a.eb b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.4.1-intel-2017a.eb index 03cac8f884..a8c2560f6d 100644 --- a/easybuild/easyconfigs/h/HTSlib/HTSlib-1.4.1-intel-2017a.eb +++ b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.4.1-intel-2017a.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/h/HTSlib/HTSlib-20160107-intel-2017a-PacBio.eb b/easybuild/easyconfigs/h/HTSlib/HTSlib-20160107-intel-2017a-PacBio.eb index e9e046ddd8..332b887d49 100644 --- a/easybuild/easyconfigs/h/HTSlib/HTSlib-20160107-intel-2017a-PacBio.eb +++ b/easybuild/easyconfigs/h/HTSlib/HTSlib-20160107-intel-2017a-PacBio.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/i/IDBA-UD/IDBA-UD-1.1.1-goolf-1.4.10.eb b/easybuild/easyconfigs/i/IDBA-UD/IDBA-UD-1.1.1-goolf-1.4.10.eb index 70a1e78b61..fe1544cd62 100644 --- a/easybuild/easyconfigs/i/IDBA-UD/IDBA-UD-1.1.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/i/IDBA-UD/IDBA-UD-1.1.1-goolf-1.4.10.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/i/IGV/IGV-2.3.68-Java-1.7.0_80.eb b/easybuild/easyconfigs/i/IGV/IGV-2.3.68-Java-1.7.0_80.eb index be548b30c0..ee79473cdf 100644 --- a/easybuild/easyconfigs/i/IGV/IGV-2.3.68-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/i/IGV/IGV-2.3.68-Java-1.7.0_80.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # sciCORE - University of Basel # SIB Swiss Institute of Bioinformatics diff --git a/easybuild/easyconfigs/i/IGV/IGV-2.3.80-Java-1.7.0_80.eb b/easybuild/easyconfigs/i/IGV/IGV-2.3.80-Java-1.7.0_80.eb index fb24a4205c..c819155a71 100644 --- a/easybuild/easyconfigs/i/IGV/IGV-2.3.80-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/i/IGV/IGV-2.3.80-Java-1.7.0_80.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # sciCORE - University of Basel # SIB Swiss Institute of Bioinformatics diff --git a/easybuild/easyconfigs/i/IGVTools/IGVTools-2.3.68-Java-1.7.0_80.eb b/easybuild/easyconfigs/i/IGVTools/IGVTools-2.3.68-Java-1.7.0_80.eb index 5610a087c8..cea60ec233 100644 --- a/easybuild/easyconfigs/i/IGVTools/IGVTools-2.3.68-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/i/IGVTools/IGVTools-2.3.68-Java-1.7.0_80.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # sciCORE - University of Basel # SIB Swiss Institute of Bioinformatics diff --git a/easybuild/easyconfigs/i/IGVTools/IGVTools-2.3.72-Java-1.7.0_80.eb b/easybuild/easyconfigs/i/IGVTools/IGVTools-2.3.72-Java-1.7.0_80.eb index a1e88b7409..789c813666 100644 --- a/easybuild/easyconfigs/i/IGVTools/IGVTools-2.3.72-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/i/IGVTools/IGVTools-2.3.72-Java-1.7.0_80.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # sciCORE - University of Basel # SIB Swiss Institute of Bioinformatics diff --git a/easybuild/easyconfigs/i/IGVTools/IGVTools-2.3.75-Java-1.7.0_80.eb b/easybuild/easyconfigs/i/IGVTools/IGVTools-2.3.75-Java-1.7.0_80.eb index 6bb0cfc42f..d8d59137d0 100644 --- a/easybuild/easyconfigs/i/IGVTools/IGVTools-2.3.75-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/i/IGVTools/IGVTools-2.3.75-Java-1.7.0_80.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # sciCORE - University of Basel # SIB Swiss Institute of Bioinformatics diff --git a/easybuild/easyconfigs/i/IMOD/IMOD-4.7.15_RHEL6-64_CUDA6.0.eb b/easybuild/easyconfigs/i/IMOD/IMOD-4.7.15_RHEL6-64_CUDA6.0.eb index 2cca42e4db..51f4a9d25b 100644 --- a/easybuild/easyconfigs/i/IMOD/IMOD-4.7.15_RHEL6-64_CUDA6.0.eb +++ b/easybuild/easyconfigs/i/IMOD/IMOD-4.7.15_RHEL6-64_CUDA6.0.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # authors: # * Pablo Escobar Lopez (sciCORE - University of Basel - SIB Swiss Institute of Bioinformatics) # * Benjamin Roberts (Landcare Research NZ Ltd) diff --git a/easybuild/easyconfigs/i/IMPUTE2/IMPUTE2-2.3.0_x86_64_dynamic.eb b/easybuild/easyconfigs/i/IMPUTE2/IMPUTE2-2.3.0_x86_64_dynamic.eb index 03ab71fb09..5e16612e00 100644 --- a/easybuild/easyconfigs/i/IMPUTE2/IMPUTE2-2.3.0_x86_64_dynamic.eb +++ b/easybuild/easyconfigs/i/IMPUTE2/IMPUTE2-2.3.0_x86_64_dynamic.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/i/IMPUTE2/IMPUTE2-2.3.0_x86_64_static.eb b/easybuild/easyconfigs/i/IMPUTE2/IMPUTE2-2.3.0_x86_64_static.eb index ba5278c540..3bbb6f11e4 100644 --- a/easybuild/easyconfigs/i/IMPUTE2/IMPUTE2-2.3.0_x86_64_static.eb +++ b/easybuild/easyconfigs/i/IMPUTE2/IMPUTE2-2.3.0_x86_64_static.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/i/IMPUTE2/IMPUTE2-2.3.2_x86_64_dynamic.eb b/easybuild/easyconfigs/i/IMPUTE2/IMPUTE2-2.3.2_x86_64_dynamic.eb index 4a7086b810..a3ccfb16ac 100644 --- a/easybuild/easyconfigs/i/IMPUTE2/IMPUTE2-2.3.2_x86_64_dynamic.eb +++ b/easybuild/easyconfigs/i/IMPUTE2/IMPUTE2-2.3.2_x86_64_dynamic.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/i/IMPUTE2/IMPUTE2-2.3.2_x86_64_static.eb b/easybuild/easyconfigs/i/IMPUTE2/IMPUTE2-2.3.2_x86_64_static.eb index 2f68d383ff..d7a1d00fa6 100644 --- a/easybuild/easyconfigs/i/IMPUTE2/IMPUTE2-2.3.2_x86_64_static.eb +++ b/easybuild/easyconfigs/i/IMPUTE2/IMPUTE2-2.3.2_x86_64_static.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/i/IOR/IOR-2.10.3-goolf-1.4.10-mpiio.eb b/easybuild/easyconfigs/i/IOR/IOR-2.10.3-goolf-1.4.10-mpiio.eb index da34c32da1..369a2092f8 100644 --- a/easybuild/easyconfigs/i/IOR/IOR-2.10.3-goolf-1.4.10-mpiio.eb +++ b/easybuild/easyconfigs/i/IOR/IOR-2.10.3-goolf-1.4.10-mpiio.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/i/IOR/IOR-2.10.3-intel-2014b-mpiio.eb b/easybuild/easyconfigs/i/IOR/IOR-2.10.3-intel-2014b-mpiio.eb index 7502a94f71..4cabeebb51 100644 --- a/easybuild/easyconfigs/i/IOR/IOR-2.10.3-intel-2014b-mpiio.eb +++ b/easybuild/easyconfigs/i/IOR/IOR-2.10.3-intel-2014b-mpiio.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/i/IOR/IOR-3.0.1-foss-2016a-mpiio.eb b/easybuild/easyconfigs/i/IOR/IOR-3.0.1-foss-2016a-mpiio.eb index 66d029ece5..ab6a7103ce 100644 --- a/easybuild/easyconfigs/i/IOR/IOR-3.0.1-foss-2016a-mpiio.eb +++ b/easybuild/easyconfigs/i/IOR/IOR-3.0.1-foss-2016a-mpiio.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/i/IPython/IPython-4.1.0-goolf-1.4.10-Python-2.7.5.eb b/easybuild/easyconfigs/i/IPython/IPython-4.1.0-goolf-1.4.10-Python-2.7.5.eb index cc3235c707..d40e59455e 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-4.1.0-goolf-1.4.10-Python-2.7.5.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-4.1.0-goolf-1.4.10-Python-2.7.5.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # sciCORE - University of Basel # SIB Swiss Institute of Bioinformatics diff --git a/easybuild/easyconfigs/i/IPython/IPython-4.2.0-goolf-1.7.20-Python-2.7.11.eb b/easybuild/easyconfigs/i/IPython/IPython-4.2.0-goolf-1.7.20-Python-2.7.11.eb index e5a53f115d..4d411ebcda 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-4.2.0-goolf-1.7.20-Python-2.7.11.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-4.2.0-goolf-1.7.20-Python-2.7.11.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # sciCORE - University of Basel # SIB Swiss Institute of Bioinformatics diff --git a/easybuild/easyconfigs/i/IPython/IPython-4.2.0-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/i/IPython/IPython-4.2.0-intel-2016a-Python-2.7.11.eb index ec8e81a4ce..86ef6979c5 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-4.2.0-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-4.2.0-intel-2016a-Python-2.7.11.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # sciCORE - University of Basel # SIB Swiss Institute of Bioinformatics diff --git a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.2-9-intel-2016a.eb b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.2-9-intel-2016a.eb index 17c246342c..5a4fee9bff 100644 --- a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.2-9-intel-2016a.eb +++ b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.2-9-intel-2016a.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Ravi Tripathi # Email: ravi89@uab.edu diff --git a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.3-1-intel-2016b.eb b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.3-1-intel-2016b.eb index 7e4fd1539e..9453d2738a 100644 --- a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.3-1-intel-2016b.eb +++ b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.3-1-intel-2016b.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Ravi Tripathi # Email: ravi89@uab.edu diff --git a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.5-10-foss-2016b.eb b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.5-10-foss-2016b.eb index 495de72aba..11c3dbd676 100644 --- a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.5-10-foss-2016b.eb +++ b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.5-10-foss-2016b.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Ravi Tripathi # Email: ravi89@uab.edu diff --git a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.5-4-intel-2017a.eb b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.5-4-intel-2017a.eb index b01509be3a..1d846a28fe 100644 --- a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.5-4-intel-2017a.eb +++ b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.5-4-intel-2017a.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Ravi Tripathi # Email: ravi89@uab.edu diff --git a/easybuild/easyconfigs/i/Infernal/Infernal-1.1-goolf-1.4.10.eb b/easybuild/easyconfigs/i/Infernal/Infernal-1.1-goolf-1.4.10.eb index 033191a3d9..430a419631 100644 --- a/easybuild/easyconfigs/i/Infernal/Infernal-1.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/i/Infernal/Infernal-1.1-goolf-1.4.10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Cedric Laczny , Fotis Georgatos diff --git a/easybuild/easyconfigs/i/Infernal/Infernal-1.1-ictce-5.3.0.eb b/easybuild/easyconfigs/i/Infernal/Infernal-1.1-ictce-5.3.0.eb index e7debfe98f..76f0bd86d1 100644 --- a/easybuild/easyconfigs/i/Infernal/Infernal-1.1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/i/Infernal/Infernal-1.1-ictce-5.3.0.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Cedric Laczny , Fotis Georgatos diff --git a/easybuild/easyconfigs/i/Infernal/Infernal-1.1rc1-goolf-1.4.10.eb b/easybuild/easyconfigs/i/Infernal/Infernal-1.1rc1-goolf-1.4.10.eb index 5171c8b613..a1c6278078 100644 --- a/easybuild/easyconfigs/i/Infernal/Infernal-1.1rc1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/i/Infernal/Infernal-1.1rc1-goolf-1.4.10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Cedric Laczny , Fotis Georgatos diff --git a/easybuild/easyconfigs/i/Infernal/Infernal-1.1rc1-ictce-5.3.0.eb b/easybuild/easyconfigs/i/Infernal/Infernal-1.1rc1-ictce-5.3.0.eb index a1476edd29..303ad1f1b5 100644 --- a/easybuild/easyconfigs/i/Infernal/Infernal-1.1rc1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/i/Infernal/Infernal-1.1rc1-ictce-5.3.0.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Cedric Laczny , Fotis Georgatos diff --git a/easybuild/easyconfigs/i/Iperf/Iperf-2.0.5-goolf-1.4.10.eb b/easybuild/easyconfigs/i/Iperf/Iperf-2.0.5-goolf-1.4.10.eb index 68b608ac4b..045ed0c649 100644 --- a/easybuild/easyconfigs/i/Iperf/Iperf-2.0.5-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/i/Iperf/Iperf-2.0.5-goolf-1.4.10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/i/Iperf/Iperf-2.0.5-ictce-5.3.0.eb b/easybuild/easyconfigs/i/Iperf/Iperf-2.0.5-ictce-5.3.0.eb index 3bbd50af7c..5206bec3f8 100644 --- a/easybuild/easyconfigs/i/Iperf/Iperf-2.0.5-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/i/Iperf/Iperf-2.0.5-ictce-5.3.0.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/i/IsoInfer/IsoInfer-0.9.1-goolf-1.4.10.eb b/easybuild/easyconfigs/i/IsoInfer/IsoInfer-0.9.1-goolf-1.4.10.eb index 5f71030257..237e4fd6ac 100644 --- a/easybuild/easyconfigs/i/IsoInfer/IsoInfer-0.9.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/i/IsoInfer/IsoInfer-0.9.1-goolf-1.4.10.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Authors: Kenneth Hoste (UGent), Pablo Escobar Lopez (Unibas) easyblock = 'MakeCp' diff --git a/easybuild/easyconfigs/i/IsoInfer/IsoInfer-0.9.1-ictce-6.2.5.eb b/easybuild/easyconfigs/i/IsoInfer/IsoInfer-0.9.1-ictce-6.2.5.eb index 10342bedf0..1e7adc8498 100644 --- a/easybuild/easyconfigs/i/IsoInfer/IsoInfer-0.9.1-ictce-6.2.5.eb +++ b/easybuild/easyconfigs/i/IsoInfer/IsoInfer-0.9.1-ictce-6.2.5.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Authors: Kenneth Hoste (UGent), Pablo Escobar Lopez (Unibas) easyblock = 'MakeCp' diff --git a/easybuild/easyconfigs/i/icc/icc-2016.0.109-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/icc/icc-2016.0.109-GCC-4.9.3-2.25.eb index f15a97cd30..96e09e4442 100644 --- a/easybuild/easyconfigs/i/icc/icc-2016.0.109-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/icc/icc-2016.0.109-GCC-4.9.3-2.25.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ name = 'icc' version = '2016.0.109' diff --git a/easybuild/easyconfigs/i/icc/icc-2016.0.109.eb b/easybuild/easyconfigs/i/icc/icc-2016.0.109.eb index 18895dbe61..6f3261b9b3 100644 --- a/easybuild/easyconfigs/i/icc/icc-2016.0.109.eb +++ b/easybuild/easyconfigs/i/icc/icc-2016.0.109.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ name = 'icc' version = '2016.0.109' diff --git a/easybuild/easyconfigs/i/icc/icc-2016.1.150-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/icc/icc-2016.1.150-GCC-4.9.3-2.25.eb index d375c69cbb..64e0d33ac6 100644 --- a/easybuild/easyconfigs/i/icc/icc-2016.1.150-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/icc/icc-2016.1.150-GCC-4.9.3-2.25.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ name = 'icc' version = '2016.1.150' diff --git a/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-4.9.3-2.25.eb index 4d0d75afae..721567e03f 100644 --- a/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-4.9.3-2.25.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ name = 'icc' version = '2016.2.181' diff --git a/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-5.3.0-2.26.eb index 5c1c6d97c5..0cbfad31f7 100644 --- a/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-5.3.0-2.26.eb +++ b/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-5.3.0-2.26.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ name = 'icc' version = '2016.2.181' diff --git a/easybuild/easyconfigs/i/icc/icc-2016.3.210-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/icc/icc-2016.3.210-GCC-4.9.3-2.25.eb index 4511a57a9e..2895d405cf 100644 --- a/easybuild/easyconfigs/i/icc/icc-2016.3.210-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/icc/icc-2016.3.210-GCC-4.9.3-2.25.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ name = 'icc' version = '2016.3.210' diff --git a/easybuild/easyconfigs/i/icc/icc-2016.3.210-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/icc/icc-2016.3.210-GCC-5.3.0-2.26.eb index 2192bcc506..15866eea89 100644 --- a/easybuild/easyconfigs/i/icc/icc-2016.3.210-GCC-5.3.0-2.26.eb +++ b/easybuild/easyconfigs/i/icc/icc-2016.3.210-GCC-5.3.0-2.26.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ name = 'icc' version = '2016.3.210' diff --git a/easybuild/easyconfigs/i/icc/icc-2016.3.210-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/icc/icc-2016.3.210-GCC-5.4.0-2.26.eb index 9ce84e0f30..dc7b23e0a2 100644 --- a/easybuild/easyconfigs/i/icc/icc-2016.3.210-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/icc/icc-2016.3.210-GCC-5.4.0-2.26.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ name = 'icc' version = '2016.3.210' diff --git a/easybuild/easyconfigs/i/icc/icc-2017.0.098-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/icc/icc-2017.0.098-GCC-5.4.0-2.26.eb index d1cc307109..06ec2ed952 100644 --- a/easybuild/easyconfigs/i/icc/icc-2017.0.098-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/icc/icc-2017.0.098-GCC-5.4.0-2.26.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ name = 'icc' version = '2017.0.098' diff --git a/easybuild/easyconfigs/i/icc/icc-2017.1.132-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/icc/icc-2017.1.132-GCC-5.4.0-2.26.eb index 924f53625d..126b6eb3e0 100644 --- a/easybuild/easyconfigs/i/icc/icc-2017.1.132-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/icc/icc-2017.1.132-GCC-5.4.0-2.26.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ name = 'icc' version = '2017.1.132' diff --git a/easybuild/easyconfigs/i/icc/icc-2017.1.132-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/i/icc/icc-2017.1.132-GCC-6.3.0-2.27.eb index 39745a0399..bada3a0811 100644 --- a/easybuild/easyconfigs/i/icc/icc-2017.1.132-GCC-6.3.0-2.27.eb +++ b/easybuild/easyconfigs/i/icc/icc-2017.1.132-GCC-6.3.0-2.27.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ name = 'icc' version = '2017.1.132' diff --git a/easybuild/easyconfigs/i/icc/icc-2017.2.174-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/i/icc/icc-2017.2.174-GCC-6.3.0-2.27.eb index cd7f8184fe..6d8d739d3b 100644 --- a/easybuild/easyconfigs/i/icc/icc-2017.2.174-GCC-6.3.0-2.27.eb +++ b/easybuild/easyconfigs/i/icc/icc-2017.2.174-GCC-6.3.0-2.27.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ name = 'icc' version = '2017.2.174' diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2016.0.109-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2016.0.109-GCC-4.9.3-2.25.eb index d51e11b541..4af351f8fe 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2016.0.109-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2016.0.109-GCC-4.9.3-2.25.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ easyblock = "Toolchain" name = 'iccifort' diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2016.0.109.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2016.0.109.eb index f03bb37944..6753c1145f 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2016.0.109.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2016.0.109.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ easyblock = "Toolchain" name = 'iccifort' diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2016.1.150-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2016.1.150-GCC-4.9.3-2.25.eb index 8bf45db5e6..923d9700ec 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2016.1.150-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2016.1.150-GCC-4.9.3-2.25.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ easyblock = "Toolchain" name = 'iccifort' diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2016.2.181-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2016.2.181-GCC-4.9.3-2.25.eb index 7fc5fd1e8f..b3ced2b66f 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2016.2.181-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2016.2.181-GCC-4.9.3-2.25.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ easyblock = "Toolchain" name = 'iccifort' diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2016.2.181-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2016.2.181-GCC-5.3.0-2.26.eb index 0b2036c9e0..f7d7ee5159 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2016.2.181-GCC-5.3.0-2.26.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2016.2.181-GCC-5.3.0-2.26.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ easyblock = "Toolchain" name = 'iccifort' diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2016.3.210-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2016.3.210-GCC-4.9.3-2.25.eb index f961d74a1f..fcdd6710aa 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2016.3.210-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2016.3.210-GCC-4.9.3-2.25.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ easyblock = "Toolchain" name = 'iccifort' diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2016.3.210-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2016.3.210-GCC-5.3.0-2.26.eb index f89991b41e..d7cafce265 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2016.3.210-GCC-5.3.0-2.26.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2016.3.210-GCC-5.3.0-2.26.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ easyblock = "Toolchain" name = 'iccifort' diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2016.3.210-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2016.3.210-GCC-5.4.0-2.26.eb index 52e91145c6..41183af553 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2016.3.210-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2016.3.210-GCC-5.4.0-2.26.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ easyblock = "Toolchain" name = 'iccifort' diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2017.0.098-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2017.0.098-GCC-5.4.0-2.26.eb index e2ed764a7b..e047e9f7b3 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2017.0.098-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2017.0.098-GCC-5.4.0-2.26.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ easyblock = "Toolchain" name = 'iccifort' diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2017.1.132-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2017.1.132-GCC-5.4.0-2.26.eb index 6e347be3a2..de0d741a72 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2017.1.132-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2017.1.132-GCC-5.4.0-2.26.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ easyblock = "Toolchain" name = 'iccifort' diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2017.1.132-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2017.1.132-GCC-6.3.0-2.27.eb index ea60f74334..3ec7427089 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2017.1.132-GCC-6.3.0-2.27.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2017.1.132-GCC-6.3.0-2.27.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ easyblock = "Toolchain" name = 'iccifort' diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2017.2.174-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2017.2.174-GCC-6.3.0-2.27.eb index d622580adc..87ed0a937d 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2017.2.174-GCC-6.3.0-2.27.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2017.2.174-GCC-6.3.0-2.27.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ easyblock = 'Toolchain' name = 'iccifort' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2016.0.109-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/ifort/ifort-2016.0.109-GCC-4.9.3-2.25.eb index a32fd8278a..255161f320 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2016.0.109-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2016.0.109-GCC-4.9.3-2.25.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ name = 'ifort' version = '2016.0.109' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2016.0.109.eb b/easybuild/easyconfigs/i/ifort/ifort-2016.0.109.eb index b40428eab7..479cec077d 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2016.0.109.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2016.0.109.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ name = 'ifort' version = '2016.0.109' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2016.1.150-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/ifort/ifort-2016.1.150-GCC-4.9.3-2.25.eb index fdfcf853b6..a01ea21032 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2016.1.150-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2016.1.150-GCC-4.9.3-2.25.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ name = 'ifort' version = '2016.1.150' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-4.9.3-2.25.eb index 39dd006552..4a5a9da050 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-4.9.3-2.25.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ name = 'ifort' version = '2016.2.181' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-5.3.0-2.26.eb index 952e908d84..61a7a9cb99 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-5.3.0-2.26.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-5.3.0-2.26.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ name = 'ifort' version = '2016.2.181' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-4.9.3-2.25.eb index 624fe2510b..67930d3ffb 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-4.9.3-2.25.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ name = 'ifort' version = '2016.3.210' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-5.3.0-2.26.eb index 148dc06764..189b6b9916 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-5.3.0-2.26.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-5.3.0-2.26.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ name = 'ifort' version = '2016.3.210' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-5.4.0-2.26.eb index 48e857188b..bbc290ac69 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-5.4.0-2.26.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ name = 'ifort' version = '2016.3.210' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2017.0.098-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/ifort/ifort-2017.0.098-GCC-5.4.0-2.26.eb index 26de8ad254..994e8bb45e 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2017.0.098-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2017.0.098-GCC-5.4.0-2.26.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ name = 'ifort' version = '2017.0.098' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2017.1.132-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/ifort/ifort-2017.1.132-GCC-5.4.0-2.26.eb index c275933f9d..d03607c38d 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2017.1.132-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2017.1.132-GCC-5.4.0-2.26.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ name = 'ifort' version = '2017.1.132' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2017.1.132-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/i/ifort/ifort-2017.1.132-GCC-6.3.0-2.27.eb index 746cfd78bf..11f2e31d72 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2017.1.132-GCC-6.3.0-2.27.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2017.1.132-GCC-6.3.0-2.27.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ name = 'ifort' version = '2017.1.132' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2017.2.174-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/i/ifort/ifort-2017.2.174-GCC-6.3.0-2.27.eb index c4b671b697..7d3dc3b6f7 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2017.2.174-GCC-6.3.0-2.27.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2017.2.174-GCC-6.3.0-2.27.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ name = 'ifort' version = '2017.2.174' diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-2016.00-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/iimpi/iimpi-2016.00-GCC-4.9.3-2.25.eb index 73e504fad6..57a86a76d8 100644 --- a/easybuild/easyconfigs/i/iimpi/iimpi-2016.00-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/iimpi/iimpi-2016.00-GCC-4.9.3-2.25.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ easyblock = "Toolchain" name = 'iimpi' diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-2016.01-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/iimpi/iimpi-2016.01-GCC-4.9.3-2.25.eb index 5df1cad542..8e46199a8e 100644 --- a/easybuild/easyconfigs/i/iimpi/iimpi-2016.01-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/iimpi/iimpi-2016.01-GCC-4.9.3-2.25.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ easyblock = "Toolchain" name = 'iimpi' diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-2016.02-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/iimpi/iimpi-2016.02-GCC-4.9.3-2.25.eb index 3d1b981714..3c4734b17b 100644 --- a/easybuild/easyconfigs/i/iimpi/iimpi-2016.02-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/iimpi/iimpi-2016.02-GCC-4.9.3-2.25.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ easyblock = "Toolchain" name = 'iimpi' diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-2016.02-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/iimpi/iimpi-2016.02-GCC-5.3.0-2.26.eb index 9e93414ff1..9c1506b2e4 100644 --- a/easybuild/easyconfigs/i/iimpi/iimpi-2016.02-GCC-5.3.0-2.26.eb +++ b/easybuild/easyconfigs/i/iimpi/iimpi-2016.02-GCC-5.3.0-2.26.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ easyblock = "Toolchain" name = 'iimpi' diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-2016.03-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/iimpi/iimpi-2016.03-GCC-4.9.3-2.25.eb index f4a56beef1..e3b3a17989 100644 --- a/easybuild/easyconfigs/i/iimpi/iimpi-2016.03-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/iimpi/iimpi-2016.03-GCC-4.9.3-2.25.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ easyblock = "Toolchain" name = 'iimpi' diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-2016.03-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/iimpi/iimpi-2016.03-GCC-5.3.0-2.26.eb index 8e5a35ceef..2b5ee4fd1b 100644 --- a/easybuild/easyconfigs/i/iimpi/iimpi-2016.03-GCC-5.3.0-2.26.eb +++ b/easybuild/easyconfigs/i/iimpi/iimpi-2016.03-GCC-5.3.0-2.26.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ easyblock = "Toolchain" name = 'iimpi' diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-2016.03-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/iimpi/iimpi-2016.03-GCC-5.4.0-2.26.eb index 8ee7c61e95..3fa553dc7b 100644 --- a/easybuild/easyconfigs/i/iimpi/iimpi-2016.03-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/iimpi/iimpi-2016.03-GCC-5.4.0-2.26.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ easyblock = "Toolchain" name = 'iimpi' diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-2016b.eb b/easybuild/easyconfigs/i/iimpi/iimpi-2016b.eb index 0af3e3a3ab..5db059f41d 100644 --- a/easybuild/easyconfigs/i/iimpi/iimpi-2016b.eb +++ b/easybuild/easyconfigs/i/iimpi/iimpi-2016b.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ easyblock = "Toolchain" name = 'iimpi' diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-2017.00-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/iimpi/iimpi-2017.00-GCC-5.4.0-2.26.eb index 1af95a3473..d6118a326e 100644 --- a/easybuild/easyconfigs/i/iimpi/iimpi-2017.00-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/iimpi/iimpi-2017.00-GCC-5.4.0-2.26.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ easyblock = "Toolchain" name = 'iimpi' diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-2017.01-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/iimpi/iimpi-2017.01-GCC-5.4.0-2.26.eb index 97332c6ea3..1807df2103 100644 --- a/easybuild/easyconfigs/i/iimpi/iimpi-2017.01-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/iimpi/iimpi-2017.01-GCC-5.4.0-2.26.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ easyblock = "Toolchain" name = 'iimpi' diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-2017.02-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/i/iimpi/iimpi-2017.02-GCC-6.3.0-2.27.eb index b0f86b1096..96132c62bd 100644 --- a/easybuild/easyconfigs/i/iimpi/iimpi-2017.02-GCC-6.3.0-2.27.eb +++ b/easybuild/easyconfigs/i/iimpi/iimpi-2017.02-GCC-6.3.0-2.27.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ easyblock = "Toolchain" name = 'iimpi' diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-2017a.eb b/easybuild/easyconfigs/i/iimpi/iimpi-2017a.eb index c272ff0803..daa347a40e 100644 --- a/easybuild/easyconfigs/i/iimpi/iimpi-2017a.eb +++ b/easybuild/easyconfigs/i/iimpi/iimpi-2017a.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ easyblock = "Toolchain" name = 'iimpi' diff --git a/easybuild/easyconfigs/i/iimpic/iimpic-2016.10.eb b/easybuild/easyconfigs/i/iimpic/iimpic-2016.10.eb index 33bf002bbf..b1196702a9 100644 --- a/easybuild/easyconfigs/i/iimpic/iimpic-2016.10.eb +++ b/easybuild/easyconfigs/i/iimpic/iimpic-2016.10.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ easyblock = "Toolchain" name = 'iimpic' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.0.109-iimpi-2016.00-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.0.109-iimpi-2016.00-GCC-4.9.3-2.25.eb index a928de1ca4..c67f0e36d5 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.3.0.109-iimpi-2016.00-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.0.109-iimpi-2016.00-GCC-4.9.3-2.25.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ name = 'imkl' version = '11.3.0.109' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.1.150-iimpi-2016.01-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.1.150-iimpi-2016.01-GCC-4.9.3-2.25.eb index 49c3e5d75b..5f46cfbdc5 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.3.1.150-iimpi-2016.01-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.1.150-iimpi-2016.01-GCC-4.9.3-2.25.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ name = 'imkl' version = '11.3.1.150' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-4.9.3-2.25.eb index 91dcce3df9..41939dc99b 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-4.9.3-2.25.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ name = 'imkl' version = '11.3.2.181' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-5.3.0-2.26.eb index d1edf0b015..9ec0acc472 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-5.3.0-2.26.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-5.3.0-2.26.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ name = 'imkl' version = '11.3.2.181' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-pompi-2016.03.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-pompi-2016.03.eb index ac3a95728c..f85a4efd37 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-pompi-2016.03.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-pompi-2016.03.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ name = 'imkl' version = '11.3.2.181' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpi-2016.03-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpi-2016.03-GCC-4.9.3-2.25.eb index 0a5bb0e3ee..710968ace7 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpi-2016.03-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpi-2016.03-GCC-4.9.3-2.25.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ name = 'imkl' version = '11.3.3.210' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpi-2016.03-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpi-2016.03-GCC-5.3.0-2.26.eb index 09806746b2..8418178c3b 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpi-2016.03-GCC-5.3.0-2.26.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpi-2016.03-GCC-5.3.0-2.26.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ name = 'imkl' version = '11.3.3.210' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpi-2016.03-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpi-2016.03-GCC-5.4.0-2.26.eb index 490c4fbf42..bf72302fc9 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpi-2016.03-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpi-2016.03-GCC-5.4.0-2.26.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ name = 'imkl' version = '11.3.3.210' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpi-2016b.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpi-2016b.eb index cce72ce10a..c3af772fef 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpi-2016b.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpi-2016b.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ name = 'imkl' version = '11.3.3.210' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpic-2016.10.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpic-2016.10.eb index 601460577a..d5a808222b 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpic-2016.10.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpic-2016.10.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ name = 'imkl' version = '11.3.3.210' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-pompi-2016.04.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-pompi-2016.04.eb index ab281bf6b1..a138ed11d0 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-pompi-2016.04.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-pompi-2016.04.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ name = 'imkl' version = '11.3.3.210' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-pompi-2016.09.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-pompi-2016.09.eb index ea94f4aa6a..5981bc06f0 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-pompi-2016.09.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-pompi-2016.09.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ name = 'imkl' version = '11.3.3.210' diff --git a/easybuild/easyconfigs/i/imkl/imkl-2017.0.098-iimpi-2017.00-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/imkl/imkl-2017.0.098-iimpi-2017.00-GCC-5.4.0-2.26.eb index 341dbab7ed..2ec64feae2 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2017.0.098-iimpi-2017.00-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2017.0.098-iimpi-2017.00-GCC-5.4.0-2.26.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ name = 'imkl' version = '2017.0.098' diff --git a/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-iimpi-2017.01-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-iimpi-2017.01-GCC-5.4.0-2.26.eb index be8b68226a..105db4b7f3 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-iimpi-2017.01-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-iimpi-2017.01-GCC-5.4.0-2.26.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ name = 'imkl' version = '2017.1.132' diff --git a/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-iimpi-2017a.eb b/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-iimpi-2017a.eb index e28e5314fa..bbf353b48c 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-iimpi-2017a.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-iimpi-2017a.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ name = 'imkl' version = '2017.1.132' diff --git a/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-iompi-2017.01.eb b/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-iompi-2017.01.eb index 1f68711972..dc78fc3b80 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-iompi-2017.01.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-iompi-2017.01.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ name = 'imkl' version = '2017.1.132' diff --git a/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-iompi-2017a.eb b/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-iompi-2017a.eb index 38909739c9..324695a571 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-iompi-2017a.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-iompi-2017a.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ name = 'imkl' version = '2017.1.132' diff --git a/easybuild/easyconfigs/i/imkl/imkl-2017.2.174-iimpi-2017.02-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/i/imkl/imkl-2017.2.174-iimpi-2017.02-GCC-6.3.0-2.27.eb index 62ed829038..5c4c02adc2 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2017.2.174-iimpi-2017.02-GCC-6.3.0-2.27.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2017.2.174-iimpi-2017.02-GCC-6.3.0-2.27.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ name = 'imkl' version = '2017.2.174' diff --git a/easybuild/easyconfigs/i/impi/impi-2017.0.098-iccifort-2017.0.098-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/impi/impi-2017.0.098-iccifort-2017.0.098-GCC-5.4.0-2.26.eb index 3457aacbc5..35a62bb371 100644 --- a/easybuild/easyconfigs/i/impi/impi-2017.0.098-iccifort-2017.0.098-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/impi/impi-2017.0.098-iccifort-2017.0.098-GCC-5.4.0-2.26.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ name = 'impi' version = '2017.0.098' diff --git a/easybuild/easyconfigs/i/impi/impi-2017.1.132-iccifort-2017.1.132-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/impi/impi-2017.1.132-iccifort-2017.1.132-GCC-5.4.0-2.26.eb index aa746359e2..7c55fcf3e3 100644 --- a/easybuild/easyconfigs/i/impi/impi-2017.1.132-iccifort-2017.1.132-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/impi/impi-2017.1.132-iccifort-2017.1.132-GCC-5.4.0-2.26.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ name = 'impi' version = '2017.1.132' diff --git a/easybuild/easyconfigs/i/impi/impi-2017.1.132-iccifort-2017.1.132-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/i/impi/impi-2017.1.132-iccifort-2017.1.132-GCC-6.3.0-2.27.eb index 48a890bbcf..4222d6a26a 100644 --- a/easybuild/easyconfigs/i/impi/impi-2017.1.132-iccifort-2017.1.132-GCC-6.3.0-2.27.eb +++ b/easybuild/easyconfigs/i/impi/impi-2017.1.132-iccifort-2017.1.132-GCC-6.3.0-2.27.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ name = 'impi' version = '2017.1.132' diff --git a/easybuild/easyconfigs/i/impi/impi-2017.2.174-iccifort-2017.2.174-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/i/impi/impi-2017.2.174-iccifort-2017.2.174-GCC-6.3.0-2.27.eb index 2d925e4ac1..fbace1b7ac 100644 --- a/easybuild/easyconfigs/i/impi/impi-2017.2.174-iccifort-2017.2.174-GCC-6.3.0-2.27.eb +++ b/easybuild/easyconfigs/i/impi/impi-2017.2.174-iccifort-2017.2.174-GCC-6.3.0-2.27.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ name = 'impi' version = '2017.2.174' diff --git a/easybuild/easyconfigs/i/impi/impi-5.1.1.109-iccifort-2016.0.109-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/impi/impi-5.1.1.109-iccifort-2016.0.109-GCC-4.9.3-2.25.eb index 2a54c28eb8..72c0998995 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.1.1.109-iccifort-2016.0.109-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.1.1.109-iccifort-2016.0.109-GCC-4.9.3-2.25.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ name = 'impi' version = '5.1.1.109' diff --git a/easybuild/easyconfigs/i/impi/impi-5.1.2.150-iccifort-2016.1.150-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/impi/impi-5.1.2.150-iccifort-2016.1.150-GCC-4.9.3-2.25.eb index 71b0e15d81..eddf864db7 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.1.2.150-iccifort-2016.1.150-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.1.2.150-iccifort-2016.1.150-GCC-4.9.3-2.25.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ name = 'impi' version = '5.1.2.150' diff --git a/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-4.9.3-2.25.eb index 8f1eb713c5..b779e3185b 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-4.9.3-2.25.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ name = 'impi' version = '5.1.3.181' diff --git a/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-5.3.0-2.26.eb index 72d570c9ae..b05f10add0 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-5.3.0-2.26.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-5.3.0-2.26.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ name = 'impi' version = '5.1.3.181' diff --git a/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.3.210-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.3.210-GCC-4.9.3-2.25.eb index 212b21a522..a8d2a5e21e 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.3.210-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.3.210-GCC-4.9.3-2.25.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ name = 'impi' version = '5.1.3.181' diff --git a/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.3.210-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.3.210-GCC-5.3.0-2.26.eb index 783cda572d..2886d91689 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.3.210-GCC-5.3.0-2.26.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.3.210-GCC-5.3.0-2.26.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ name = 'impi' version = '5.1.3.181' diff --git a/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.3.210-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.3.210-GCC-5.4.0-2.26.eb index 420224789e..da9923db0a 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.3.210-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.3.210-GCC-5.4.0-2.26.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ name = 'impi' version = '5.1.3.181' diff --git a/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifortcuda-2016.10.eb b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifortcuda-2016.10.eb index b61daed0c1..2da07ac2d4 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifortcuda-2016.10.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifortcuda-2016.10.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ name = 'impi' version = '5.1.3.181' diff --git a/easybuild/easyconfigs/i/intel/intel-2016.00.eb b/easybuild/easyconfigs/i/intel/intel-2016.00.eb index 2f03a7cc46..f4149f4027 100644 --- a/easybuild/easyconfigs/i/intel/intel-2016.00.eb +++ b/easybuild/easyconfigs/i/intel/intel-2016.00.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ easyblock = "Toolchain" name = 'intel' diff --git a/easybuild/easyconfigs/i/intel/intel-2016.01.eb b/easybuild/easyconfigs/i/intel/intel-2016.01.eb index 7c51ee2938..1f12eaea94 100644 --- a/easybuild/easyconfigs/i/intel/intel-2016.01.eb +++ b/easybuild/easyconfigs/i/intel/intel-2016.01.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ easyblock = "Toolchain" name = 'intel' diff --git a/easybuild/easyconfigs/i/iompi/iompi-2017.01.eb b/easybuild/easyconfigs/i/iompi/iompi-2017.01.eb index 9c2c6b52a5..b648d9709a 100644 --- a/easybuild/easyconfigs/i/iompi/iompi-2017.01.eb +++ b/easybuild/easyconfigs/i/iompi/iompi-2017.01.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ easyblock = "Toolchain" name = 'iompi' diff --git a/easybuild/easyconfigs/i/iompi/iompi-2017a.eb b/easybuild/easyconfigs/i/iompi/iompi-2017a.eb index 571b319a14..c74e1212e9 100644 --- a/easybuild/easyconfigs/i/iompi/iompi-2017a.eb +++ b/easybuild/easyconfigs/i/iompi/iompi-2017a.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ easyblock = "Toolchain" name = 'iompi' diff --git a/easybuild/easyconfigs/j/JAGS/JAGS-3.4.0-goolf-1.4.10.eb b/easybuild/easyconfigs/j/JAGS/JAGS-3.4.0-goolf-1.4.10.eb index d0c1108872..076891eb84 100644 --- a/easybuild/easyconfigs/j/JAGS/JAGS-3.4.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/j/JAGS/JAGS-3.4.0-goolf-1.4.10.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/j/JAGS/JAGS-3.4.0-ictce-6.2.5.eb b/easybuild/easyconfigs/j/JAGS/JAGS-3.4.0-ictce-6.2.5.eb index 9e1ed006d5..adaf15166d 100644 --- a/easybuild/easyconfigs/j/JAGS/JAGS-3.4.0-ictce-6.2.5.eb +++ b/easybuild/easyconfigs/j/JAGS/JAGS-3.4.0-ictce-6.2.5.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/j/JAGS/JAGS-3.4.0-intel-2014b.eb b/easybuild/easyconfigs/j/JAGS/JAGS-3.4.0-intel-2014b.eb index 76755f474c..38931e456f 100644 --- a/easybuild/easyconfigs/j/JAGS/JAGS-3.4.0-intel-2014b.eb +++ b/easybuild/easyconfigs/j/JAGS/JAGS-3.4.0-intel-2014b.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/j/JAGS/JAGS-4.2.0-foss-2016a.eb b/easybuild/easyconfigs/j/JAGS/JAGS-4.2.0-foss-2016a.eb index b168dd347e..9d8a457376 100644 --- a/easybuild/easyconfigs/j/JAGS/JAGS-4.2.0-foss-2016a.eb +++ b/easybuild/easyconfigs/j/JAGS/JAGS-4.2.0-foss-2016a.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/j/JAGS/JAGS-4.2.0-intel-2016a.eb b/easybuild/easyconfigs/j/JAGS/JAGS-4.2.0-intel-2016a.eb index 1474dde18b..ff82e5fae9 100644 --- a/easybuild/easyconfigs/j/JAGS/JAGS-4.2.0-intel-2016a.eb +++ b/easybuild/easyconfigs/j/JAGS/JAGS-4.2.0-intel-2016a.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/j/Jellyfish/Jellyfish-1.1.11-foss-2016a.eb b/easybuild/easyconfigs/j/Jellyfish/Jellyfish-1.1.11-foss-2016a.eb index 8e2a518511..6ff63e83c0 100644 --- a/easybuild/easyconfigs/j/Jellyfish/Jellyfish-1.1.11-foss-2016a.eb +++ b/easybuild/easyconfigs/j/Jellyfish/Jellyfish-1.1.11-foss-2016a.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/j/Jellyfish/Jellyfish-1.1.11-foss-2016b.eb b/easybuild/easyconfigs/j/Jellyfish/Jellyfish-1.1.11-foss-2016b.eb index 6acf8320e7..a27ec31e26 100644 --- a/easybuild/easyconfigs/j/Jellyfish/Jellyfish-1.1.11-foss-2016b.eb +++ b/easybuild/easyconfigs/j/Jellyfish/Jellyfish-1.1.11-foss-2016b.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.1.3-foss-2014b.eb b/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.1.3-foss-2014b.eb index bd77b8e773..6db319bc18 100644 --- a/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.1.3-foss-2014b.eb +++ b/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.1.3-foss-2014b.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.1.3-goolf-1.4.10.eb b/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.1.3-goolf-1.4.10.eb index e874c05030..948d483703 100644 --- a/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.1.3-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.1.3-goolf-1.4.10.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.2.3-intel-2015b.eb b/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.2.3-intel-2015b.eb index 5e170ee4c5..c33284a909 100644 --- a/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.2.3-intel-2015b.eb +++ b/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.2.3-intel-2015b.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.2.4-foss-2015b.eb b/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.2.4-foss-2015b.eb index ff49f091da..9c8c977462 100644 --- a/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.2.4-foss-2015b.eb +++ b/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.2.4-foss-2015b.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.2.4-intel-2015b.eb b/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.2.4-intel-2015b.eb index 01b9cb403d..d8949f35fa 100644 --- a/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.2.4-intel-2015b.eb +++ b/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.2.4-intel-2015b.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.2.6-goolf-1.7.20.eb b/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.2.6-goolf-1.7.20.eb index 09aa380fc6..1696c554aa 100644 --- a/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.2.6-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.2.6-goolf-1.7.20.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # sciCORE - University of Basel # SIB Swiss Institute of Bioinformatics diff --git a/easybuild/easyconfigs/j/jModelTest/jModelTest-2.1.10r20160303-Java-1.8.0_92.eb b/easybuild/easyconfigs/j/jModelTest/jModelTest-2.1.10r20160303-Java-1.8.0_92.eb index 3c4304258a..e619e71cb4 100644 --- a/easybuild/easyconfigs/j/jModelTest/jModelTest-2.1.10r20160303-Java-1.8.0_92.eb +++ b/easybuild/easyconfigs/j/jModelTest/jModelTest-2.1.10r20160303-Java-1.8.0_92.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # sciCORE - University of Basel # SIB Swiss Institute of Bioinformatics diff --git a/easybuild/easyconfigs/j/jModelTest/jModelTest-2.1.9r20160115-goolf-1.4.10-Java-1.7.0_75.eb b/easybuild/easyconfigs/j/jModelTest/jModelTest-2.1.9r20160115-goolf-1.4.10-Java-1.7.0_75.eb index f01140a3e5..dafa45afa9 100644 --- a/easybuild/easyconfigs/j/jModelTest/jModelTest-2.1.9r20160115-goolf-1.4.10-Java-1.7.0_75.eb +++ b/easybuild/easyconfigs/j/jModelTest/jModelTest-2.1.9r20160115-goolf-1.4.10-Java-1.7.0_75.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # sciCORE - University of Basel # SIB Swiss Institute of Bioinformatics diff --git a/easybuild/easyconfigs/k/kallisto/kallisto-0.43.1-foss-2016b.eb b/easybuild/easyconfigs/k/kallisto/kallisto-0.43.1-foss-2016b.eb index 9d74f7a398..54e8f3a226 100644 --- a/easybuild/easyconfigs/k/kallisto/kallisto-0.43.1-foss-2016b.eb +++ b/easybuild/easyconfigs/k/kallisto/kallisto-0.43.1-foss-2016b.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild easyblock = 'CMakeMake' diff --git a/easybuild/easyconfigs/k/khmer/khmer-1.1-goolf-1.4.10-Python-2.7.5.eb b/easybuild/easyconfigs/k/khmer/khmer-1.1-goolf-1.4.10-Python-2.7.5.eb index a821aa77f2..2d87b632b4 100644 --- a/easybuild/easyconfigs/k/khmer/khmer-1.1-goolf-1.4.10-Python-2.7.5.eb +++ b/easybuild/easyconfigs/k/khmer/khmer-1.1-goolf-1.4.10-Python-2.7.5.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/k/khmer/khmer-1.4.1-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/k/khmer/khmer-1.4.1-foss-2016b-Python-2.7.12.eb index 68addbe817..5e1eea59c2 100644 --- a/easybuild/easyconfigs/k/khmer/khmer-1.4.1-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/k/khmer/khmer-1.4.1-foss-2016b-Python-2.7.12.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/l/LAME/LAME-3.99.5-foss-2015a.eb b/easybuild/easyconfigs/l/LAME/LAME-3.99.5-foss-2015a.eb index a1da0d2c90..d087299b3c 100644 --- a/easybuild/easyconfigs/l/LAME/LAME-3.99.5-foss-2015a.eb +++ b/easybuild/easyconfigs/l/LAME/LAME-3.99.5-foss-2015a.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Author: Stephane Thiell ### diff --git a/easybuild/easyconfigs/l/LAME/LAME-3.99.5-foss-2016b.eb b/easybuild/easyconfigs/l/LAME/LAME-3.99.5-foss-2016b.eb index 042510cf2a..f61518de91 100644 --- a/easybuild/easyconfigs/l/LAME/LAME-3.99.5-foss-2016b.eb +++ b/easybuild/easyconfigs/l/LAME/LAME-3.99.5-foss-2016b.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Author: Stephane Thiell ### diff --git a/easybuild/easyconfigs/l/LASTZ/LASTZ-1.02.00-goolf-1.7.20.eb b/easybuild/easyconfigs/l/LASTZ/LASTZ-1.02.00-goolf-1.7.20.eb index d7a88ce495..64d822c449 100644 --- a/easybuild/easyconfigs/l/LASTZ/LASTZ-1.02.00-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/l/LASTZ/LASTZ-1.02.00-goolf-1.7.20.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # sciCORE - University of Basel # SIB Swiss Institute of Bioinformatics diff --git a/easybuild/easyconfigs/l/LWM2/LWM2-1.1-ictce-5.3.0.eb b/easybuild/easyconfigs/l/LWM2/LWM2-1.1-ictce-5.3.0.eb index 18cafee304..fa8505d85c 100644 --- a/easybuild/easyconfigs/l/LWM2/LWM2-1.1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/l/LWM2/LWM2-1.1-ictce-5.3.0.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild # Copyright:: Copyright 2013 Juelich Supercomputing Centre, Germany # Authors:: Bernd Mohr # License:: New BSD diff --git a/easybuild/easyconfigs/l/LZO/LZO-2.06-goolf-1.4.10.eb b/easybuild/easyconfigs/l/LZO/LZO-2.06-goolf-1.4.10.eb index 82b1a9bd7b..47a560f2cc 100644 --- a/easybuild/easyconfigs/l/LZO/LZO-2.06-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/LZO/LZO-2.06-goolf-1.4.10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/l/LZO/LZO-2.06-ictce-5.3.0.eb b/easybuild/easyconfigs/l/LZO/LZO-2.06-ictce-5.3.0.eb index 5b7a6a1f5c..8aa4e392fe 100644 --- a/easybuild/easyconfigs/l/LZO/LZO-2.06-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/l/LZO/LZO-2.06-ictce-5.3.0.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/l/LZO/LZO-2.09-intel-2016b.eb b/easybuild/easyconfigs/l/LZO/LZO-2.09-intel-2016b.eb index 6e7ff8a596..9e716ad72c 100644 --- a/easybuild/easyconfigs/l/LZO/LZO-2.09-intel-2016b.eb +++ b/easybuild/easyconfigs/l/LZO/LZO-2.09-intel-2016b.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/l/LZO/LZO-2.10-intel-2017a.eb b/easybuild/easyconfigs/l/LZO/LZO-2.10-intel-2017a.eb index 801057a84f..161e209f29 100644 --- a/easybuild/easyconfigs/l/LZO/LZO-2.10-intel-2017a.eb +++ b/easybuild/easyconfigs/l/LZO/LZO-2.10-intel-2017a.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/l/LeadIT/LeadIT-2.1.9.eb b/easybuild/easyconfigs/l/LeadIT/LeadIT-2.1.9.eb index 27a91f92c0..4232098544 100644 --- a/easybuild/easyconfigs/l/LeadIT/LeadIT-2.1.9.eb +++ b/easybuild/easyconfigs/l/LeadIT/LeadIT-2.1.9.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Ravi Tripathi # Email: ravi89@uab.edu diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-goolf-1.4.10.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-goolf-1.4.10.eb index b741841310..73513a342d 100644 --- a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-goolf-1.4.10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-ictce-5.3.0.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-ictce-5.3.0.eb index 3b637dfd68..c9a462f4f4 100644 --- a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-ictce-5.3.0.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-intel-2014.06.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-intel-2014.06.eb index 2d0643c0a8..a27f793005 100644 --- a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-intel-2014.06.eb +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-intel-2014.06.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-intel-2014b.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-intel-2014b.eb index 42a3e46a06..8db6c03653 100644 --- a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-intel-2014b.eb +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-intel-2014b.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-intel-2015a.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-intel-2015a.eb index a080abfe8e..c0287c6b3a 100644 --- a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-intel-2015a.eb +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-intel-2015a.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-intel-2015b.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-intel-2015b.eb index 769d5c3bf4..4efb1e7e06 100644 --- a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-intel-2015b.eb +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-intel-2015b.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.4-foss-2015a.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.4-foss-2015a.eb index 9fdf349e0c..c4f46971bf 100644 --- a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.4-foss-2015a.eb +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.4-foss-2015a.eb @@ -1,6 +1,6 @@ # Built with EasyBuild version 2.2.0dev on 2015-06-16_10-51-42 ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.4-intel-2015a.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.4-intel-2015a.eb index caf97944ef..01eb7c0c93 100644 --- a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.4-intel-2015a.eb +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.4-intel-2015a.eb @@ -1,6 +1,6 @@ # Built with EasyBuild version 2.2.0dev on 2015-06-16_10-51-42 ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.4beta-foss-2015a.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.4beta-foss-2015a.eb index a7ec21003e..4b2b2093c4 100644 --- a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.4beta-foss-2015a.eb +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.4beta-foss-2015a.eb @@ -1,6 +1,6 @@ # Built with EasyBuild version 2.2.0dev on 2015-06-16_10-51-42 ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.4beta-intel-2015a.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.4beta-intel-2015a.eb index 2ebd87d4b6..3dc8674fdf 100644 --- a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.4beta-intel-2015a.eb +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.4beta-intel-2015a.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-foss-2015a.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-foss-2015a.eb index 259a9d8bc6..382c881a95 100644 --- a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-foss-2015a.eb +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-foss-2015a.eb @@ -1,6 +1,6 @@ # Built with EasyBuild version 2.2.0dev on 2015-06-16_10-51-42 ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-foss-2016a.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-foss-2016a.eb index f513557a05..76688580b9 100644 --- a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-foss-2016a.eb +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-foss-2016a.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos , Alan O'Cais (JSC) diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-foss-2016b.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-foss-2016b.eb index a7365c221f..a98972105e 100644 --- a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-foss-2016b.eb +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-foss-2016b.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos , Alan O'Cais (JSC) diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-intel-2016a.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-intel-2016a.eb index b666f47dc2..fda1e3ceb5 100644 --- a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-intel-2016a.eb +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-intel-2016a.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos , Alan O'Cais (JSC) diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-intel-2016b.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-intel-2016b.eb index 9281e4ddc9..cb758aec72 100644 --- a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-intel-2016b.eb +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-intel-2016b.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos , Alan O'Cais (JSC) diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.7-foss-2016b.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.7-foss-2016b.eb index e74567cf30..49f589e6d4 100644 --- a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.7-foss-2016b.eb +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.7-foss-2016b.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos , Alan O'Cais (JSC) diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.7-intel-2017a.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.7-intel-2017a.eb index 073c1b3d60..bc88218600 100644 --- a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.7-intel-2017a.eb +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.7-intel-2017a.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos , Alan O'Cais (JSC) diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.8-intel-2017a.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.8-intel-2017a.eb index 445e665d1d..c1c395504c 100644 --- a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.8-intel-2017a.eb +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.8-intel-2017a.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos , Alan O'Cais (JSC) diff --git a/easybuild/easyconfigs/l/LinBox/LinBox-1.4.0-foss-2016a.eb b/easybuild/easyconfigs/l/LinBox/LinBox-1.4.0-foss-2016a.eb index f0951b2b35..32aac5dd56 100644 --- a/easybuild/easyconfigs/l/LinBox/LinBox-1.4.0-foss-2016a.eb +++ b/easybuild/easyconfigs/l/LinBox/LinBox-1.4.0-foss-2016a.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild recipe; see https://github.com/hpcugent/easybuild +# This file is an EasyBuild recipe; see https://github.com/easybuilders/easybuild # # Copyright:: Copyright (c) 2016 Riccardo Murri # Authors:: Riccardo Murri diff --git a/easybuild/easyconfigs/l/lbzip2/lbzip2-2.5-goolf-1.7.20.eb b/easybuild/easyconfigs/l/lbzip2/lbzip2-2.5-goolf-1.7.20.eb index 5abfa7b4da..cb155b9c9f 100644 --- a/easybuild/easyconfigs/l/lbzip2/lbzip2-2.5-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/l/lbzip2/lbzip2-2.5-goolf-1.7.20.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # sciCORE - University of Basel # SIB Swiss Institute of Bioinformatics diff --git a/easybuild/easyconfigs/l/less/less-458-GCC-4.8.2.eb b/easybuild/easyconfigs/l/less/less-458-GCC-4.8.2.eb index 3ee23b3ce7..3870f8d203 100644 --- a/easybuild/easyconfigs/l/less/less-458-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/l/less/less-458-GCC-4.8.2.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # ## diff --git a/easybuild/easyconfigs/l/lftp/lftp-4.4.1-goolf-1.4.10.eb b/easybuild/easyconfigs/l/lftp/lftp-4.4.1-goolf-1.4.10.eb index d1eb5179b8..d656d8a7e2 100644 --- a/easybuild/easyconfigs/l/lftp/lftp-4.4.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/lftp/lftp-4.4.1-goolf-1.4.10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/l/lftp/lftp-4.6.4-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/l/lftp/lftp-4.6.4-GNU-4.9.3-2.25.eb index f9975e31e2..0e5f0b7f04 100644 --- a/easybuild/easyconfigs/l/lftp/lftp-4.6.4-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/l/lftp/lftp-4.6.4-GNU-4.9.3-2.25.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/l/libgd/libgd-2.2.4-foss-2016b.eb b/easybuild/easyconfigs/l/libgd/libgd-2.2.4-foss-2016b.eb index 5856a57c8d..c1f0033e09 100644 --- a/easybuild/easyconfigs/l/libgd/libgd-2.2.4-foss-2016b.eb +++ b/easybuild/easyconfigs/l/libgd/libgd-2.2.4-foss-2016b.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild easyblock = 'ConfigureMake' diff --git a/easybuild/easyconfigs/l/libgtextutils/libgtextutils-0.6.1-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libgtextutils/libgtextutils-0.6.1-goolf-1.4.10.eb index 2f55afa678..9a49b39337 100644 --- a/easybuild/easyconfigs/l/libgtextutils/libgtextutils-0.6.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/libgtextutils/libgtextutils-0.6.1-goolf-1.4.10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Cedric Laczny , Fotis Georgatos diff --git a/easybuild/easyconfigs/l/libgtextutils/libgtextutils-0.6.1-goolf-1.7.20.eb b/easybuild/easyconfigs/l/libgtextutils/libgtextutils-0.6.1-goolf-1.7.20.eb index 1b5c00b84c..e53635c2b0 100644 --- a/easybuild/easyconfigs/l/libgtextutils/libgtextutils-0.6.1-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/l/libgtextutils/libgtextutils-0.6.1-goolf-1.7.20.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Cedric Laczny , Fotis Georgatos diff --git a/easybuild/easyconfigs/l/libgtextutils/libgtextutils-0.6.1-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libgtextutils/libgtextutils-0.6.1-ictce-5.3.0.eb index 7ff4a544d3..29770eb9ac 100644 --- a/easybuild/easyconfigs/l/libgtextutils/libgtextutils-0.6.1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/l/libgtextutils/libgtextutils-0.6.1-ictce-5.3.0.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Cedric Laczny , Fotis Georgatos diff --git a/easybuild/easyconfigs/l/libgtextutils/libgtextutils-0.6.1-intel-2015a.eb b/easybuild/easyconfigs/l/libgtextutils/libgtextutils-0.6.1-intel-2015a.eb index a911adbdf6..b6e7c90fb8 100644 --- a/easybuild/easyconfigs/l/libgtextutils/libgtextutils-0.6.1-intel-2015a.eb +++ b/easybuild/easyconfigs/l/libgtextutils/libgtextutils-0.6.1-intel-2015a.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Cedric Laczny , Fotis Georgatos diff --git a/easybuild/easyconfigs/l/libgtextutils/libgtextutils-0.7-foss-2015b.eb b/easybuild/easyconfigs/l/libgtextutils/libgtextutils-0.7-foss-2015b.eb index 733d12d5e4..6f04e6d6a8 100644 --- a/easybuild/easyconfigs/l/libgtextutils/libgtextutils-0.7-foss-2015b.eb +++ b/easybuild/easyconfigs/l/libgtextutils/libgtextutils-0.7-foss-2015b.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Cedric Laczny , Fotis Georgatos diff --git a/easybuild/easyconfigs/l/libgtextutils/libgtextutils-0.7-foss-2016a.eb b/easybuild/easyconfigs/l/libgtextutils/libgtextutils-0.7-foss-2016a.eb index c1b5b27e46..21f520c0e6 100644 --- a/easybuild/easyconfigs/l/libgtextutils/libgtextutils-0.7-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libgtextutils/libgtextutils-0.7-foss-2016a.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Cedric Laczny , Fotis Georgatos diff --git a/easybuild/easyconfigs/l/libgtextutils/libgtextutils-0.7-foss-2016b.eb b/easybuild/easyconfigs/l/libgtextutils/libgtextutils-0.7-foss-2016b.eb index 0c761422aa..416434ef6e 100644 --- a/easybuild/easyconfigs/l/libgtextutils/libgtextutils-0.7-foss-2016b.eb +++ b/easybuild/easyconfigs/l/libgtextutils/libgtextutils-0.7-foss-2016b.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Cedric Laczny , Fotis Georgatos diff --git a/easybuild/easyconfigs/l/libharu/libharu-2.2.0-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libharu/libharu-2.2.0-goolf-1.4.10.eb index ede4708977..34834f9883 100644 --- a/easybuild/easyconfigs/l/libharu/libharu-2.2.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/libharu/libharu-2.2.0-goolf-1.4.10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Cyprus Institute / CaSToRC, Uni.Lu/LCSB, NTUA # Authors:: George Tsouloupas , Fotis Georgatos diff --git a/easybuild/easyconfigs/l/libharu/libharu-2.2.0-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libharu/libharu-2.2.0-ictce-5.3.0.eb index 29d1902d63..c6e5039403 100644 --- a/easybuild/easyconfigs/l/libharu/libharu-2.2.0-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/l/libharu/libharu-2.2.0-ictce-5.3.0.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Cyprus Institute / CaSToRC, Uni.Lu/LCSB, NTUA # Authors:: George Tsouloupas , Fotis Georgatos diff --git a/easybuild/easyconfigs/l/libharu/libharu-2.3.0-foss-2016a.eb b/easybuild/easyconfigs/l/libharu/libharu-2.3.0-foss-2016a.eb index f150abd20c..6400af43d6 100644 --- a/easybuild/easyconfigs/l/libharu/libharu-2.3.0-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libharu/libharu-2.3.0-foss-2016a.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Cyprus Institute / CaSToRC, Uni.Lu/LCSB, NTUA # Authors:: George Tsouloupas , Fotis Georgatos diff --git a/easybuild/easyconfigs/l/libharu/libharu-2.3.0-foss-2016b.eb b/easybuild/easyconfigs/l/libharu/libharu-2.3.0-foss-2016b.eb index 2b4825fe33..041fd7f660 100644 --- a/easybuild/easyconfigs/l/libharu/libharu-2.3.0-foss-2016b.eb +++ b/easybuild/easyconfigs/l/libharu/libharu-2.3.0-foss-2016b.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Cyprus Institute / CaSToRC, Uni.Lu/LCSB, NTUA # Authors:: George Tsouloupas , Fotis Georgatos diff --git a/easybuild/easyconfigs/l/libharu/libharu-2.3.0-intel-2017a.eb b/easybuild/easyconfigs/l/libharu/libharu-2.3.0-intel-2017a.eb index b87a22de76..144f1b9687 100644 --- a/easybuild/easyconfigs/l/libharu/libharu-2.3.0-intel-2017a.eb +++ b/easybuild/easyconfigs/l/libharu/libharu-2.3.0-intel-2017a.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Cyprus Institute / CaSToRC, Uni.Lu/LCSB, NTUA # Authors:: George Tsouloupas , Fotis Georgatos diff --git a/easybuild/easyconfigs/l/libungif/libungif-4.1.4-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libungif/libungif-4.1.4-goolf-1.4.10.eb index 4ae4db7879..b8af039cc7 100644 --- a/easybuild/easyconfigs/l/libungif/libungif-4.1.4-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/libungif/libungif-4.1.4-goolf-1.4.10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/l/libungif/libungif-4.1.4-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libungif/libungif-4.1.4-ictce-5.3.0.eb index 51b4352aa5..e851a2e134 100644 --- a/easybuild/easyconfigs/l/libungif/libungif-4.1.4-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/l/libungif/libungif-4.1.4-ictce-5.3.0.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/l/libyaml/libyaml-0.1.4-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libyaml/libyaml-0.1.4-goolf-1.4.10.eb index 1383948289..b13bc6b78f 100644 --- a/easybuild/easyconfigs/l/libyaml/libyaml-0.1.4-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/libyaml/libyaml-0.1.4-goolf-1.4.10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Nils Christian diff --git a/easybuild/easyconfigs/l/libyaml/libyaml-0.1.4-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libyaml/libyaml-0.1.4-ictce-5.3.0.eb index ff0da7e033..f14a7e7513 100644 --- a/easybuild/easyconfigs/l/libyaml/libyaml-0.1.4-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/l/libyaml/libyaml-0.1.4-ictce-5.3.0.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Nils Christian diff --git a/easybuild/easyconfigs/l/libyaml/libyaml-0.1.6-intel-2015a.eb b/easybuild/easyconfigs/l/libyaml/libyaml-0.1.6-intel-2015a.eb index 2a9749a581..17d86127bf 100644 --- a/easybuild/easyconfigs/l/libyaml/libyaml-0.1.6-intel-2015a.eb +++ b/easybuild/easyconfigs/l/libyaml/libyaml-0.1.6-intel-2015a.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Nils Christian diff --git a/easybuild/easyconfigs/l/libyaml/libyaml-0.1.6-intel-2015b.eb b/easybuild/easyconfigs/l/libyaml/libyaml-0.1.6-intel-2015b.eb index cf285fb5ec..0af648ec22 100644 --- a/easybuild/easyconfigs/l/libyaml/libyaml-0.1.6-intel-2015b.eb +++ b/easybuild/easyconfigs/l/libyaml/libyaml-0.1.6-intel-2015b.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Nils Christian diff --git a/easybuild/easyconfigs/l/libyaml/libyaml-0.1.6-intel-2016a.eb b/easybuild/easyconfigs/l/libyaml/libyaml-0.1.6-intel-2016a.eb index c715793903..bb08d2990a 100644 --- a/easybuild/easyconfigs/l/libyaml/libyaml-0.1.6-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libyaml/libyaml-0.1.6-intel-2016a.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Nils Christian diff --git a/easybuild/easyconfigs/l/libyaml/libyaml-0.1.6-intel-2016b.eb b/easybuild/easyconfigs/l/libyaml/libyaml-0.1.6-intel-2016b.eb index e7ae73819e..83ca6c3ec6 100644 --- a/easybuild/easyconfigs/l/libyaml/libyaml-0.1.6-intel-2016b.eb +++ b/easybuild/easyconfigs/l/libyaml/libyaml-0.1.6-intel-2016b.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Nils Christian diff --git a/easybuild/easyconfigs/l/libyaml/libyaml-0.1.7.eb b/easybuild/easyconfigs/l/libyaml/libyaml-0.1.7.eb index 44f94ecc3d..c04077ae4e 100644 --- a/easybuild/easyconfigs/l/libyaml/libyaml-0.1.7.eb +++ b/easybuild/easyconfigs/l/libyaml/libyaml-0.1.7.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Nils Christian diff --git a/easybuild/easyconfigs/l/likwid/likwid-4.2.0-foss-2017a.eb b/easybuild/easyconfigs/l/likwid/likwid-4.2.0-foss-2017a.eb index ebb2f3de9b..1d91bac04d 100644 --- a/easybuild/easyconfigs/l/likwid/likwid-4.2.0-foss-2017a.eb +++ b/easybuild/easyconfigs/l/likwid/likwid-4.2.0-foss-2017a.eb @@ -1,7 +1,7 @@ ## # -*- mode: python; -*- # EasyBuild reciPY for LikWid -- see https://github.com/RRZE-HPC/likwid -# as per https://github.com/hpcugent/easybuild +# as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2017 UL HPC -- hpc.uni.lu # Authors:: UL HPC Team diff --git a/easybuild/easyconfigs/l/likwid/likwid-4.2.0-intel-2017a.eb b/easybuild/easyconfigs/l/likwid/likwid-4.2.0-intel-2017a.eb index b38fb421b8..5558b79e5f 100644 --- a/easybuild/easyconfigs/l/likwid/likwid-4.2.0-intel-2017a.eb +++ b/easybuild/easyconfigs/l/likwid/likwid-4.2.0-intel-2017a.eb @@ -1,7 +1,7 @@ ## # -*- mode: python; -*- # EasyBuild reciPY for LikWid -- see https://github.com/RRZE-HPC/likwid -# as per https://github.com/hpcugent/easybuild +# as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2017 UL HPC -- hpc.uni.lu # Authors:: UL HPC Team diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-2015.06.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-2015.06.eb index 54365e5c12..4811e3333a 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-2015.06.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-2015.06.eb @@ -14,7 +14,7 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] # '-fgnu89-inline' is required to avoid linking errors with older glibc's, -# see https://github.com/hpcugent/easybuild-easyconfigs/issues/529 +# see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-2015.11.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-2015.11.eb index 41431f6ed6..08c0165d80 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-2015.11.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-2015.11.eb @@ -14,7 +14,7 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] # '-fgnu89-inline' is required to avoid linking errors with older glibc's, -# see https://github.com/hpcugent/easybuild-easyconfigs/issues/529 +# see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.7.2.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.7.2.eb index 91d64e5bd3..dfbd2123ff 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.7.2.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.7.2.eb @@ -14,7 +14,7 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] # '-fgnu89-inline' is required to avoid linking errors with older glibc's, -# see https://github.com/hpcugent/easybuild-easyconfigs/issues/529 +# see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.8.2.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.8.2.eb index cb0daa392f..0c6c8895af 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.8.2.eb @@ -14,7 +14,7 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] # '-fgnu89-inline' is required to avoid linking errors with older glibc's, -# see https://github.com/hpcugent/easybuild-easyconfigs/issues/529 +# see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.8.4.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.8.4.eb index e59131c48f..4f5b6c32ba 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.8.4.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.8.4.eb @@ -14,7 +14,7 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] # '-fgnu89-inline' is required to avoid linking errors with older glibc's, -# see https://github.com/hpcugent/easybuild-easyconfigs/issues/529 +# see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.2-binutils-2.25.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.2-binutils-2.25.eb index c9b8ae162c..09ed58a2b9 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.2-binutils-2.25.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.2-binutils-2.25.eb @@ -17,7 +17,7 @@ source_urls = [GNU_SOURCE] builddependencies = [('binutils', '2.25', '', True)] # '-fgnu89-inline' is required to avoid linking errors with older glibc's, -# see https://github.com/hpcugent/easybuild-easyconfigs/issues/529 +# see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.2.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.2.eb index d52dd469f6..91e9fc5026 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.2.eb @@ -14,7 +14,7 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] # '-fgnu89-inline' is required to avoid linking errors with older glibc's, -# see https://github.com/hpcugent/easybuild-easyconfigs/issues/529 +# see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.3-2.25.eb index 5658dda837..18abbd3731 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.3-2.25.eb @@ -14,7 +14,7 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] # '-fgnu89-inline' is required to avoid linking errors with older glibc's, -# see https://github.com/hpcugent/easybuild-easyconfigs/issues/529 +# see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.3-binutils-2.25.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.3-binutils-2.25.eb index 006446b9f0..675ca2e5f8 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.3-binutils-2.25.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.3-binutils-2.25.eb @@ -17,7 +17,7 @@ source_urls = [GNU_SOURCE] builddependencies = [('binutils', '2.25', '', True)] # '-fgnu89-inline' is required to avoid linking errors with older glibc's, -# see https://github.com/hpcugent/easybuild-easyconfigs/issues/529 +# see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.3.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.3.eb index e7a4d305fe..49ea4854d5 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.3.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.3.eb @@ -14,7 +14,7 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] # '-fgnu89-inline' is required to avoid linking errors with older glibc's, -# see https://github.com/hpcugent/easybuild-easyconfigs/issues/529 +# see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-5.1.0-binutils-2.25.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-5.1.0-binutils-2.25.eb index 6e2de92ed5..b86be0771d 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-5.1.0-binutils-2.25.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-5.1.0-binutils-2.25.eb @@ -17,7 +17,7 @@ source_urls = [GNU_SOURCE] builddependencies = [('binutils', '2.25', '', True)] # '-fgnu89-inline' is required to avoid linking errors with older glibc's, -# see https://github.com/hpcugent/easybuild-easyconfigs/issues/529 +# see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-5.4.0-2.26.eb index ab63650383..cf9325ba99 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-5.4.0-2.26.eb @@ -14,7 +14,7 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] # '-fgnu89-inline' is required to avoid linking errors with older glibc's, -# see https://github.com/hpcugent/easybuild-easyconfigs/issues/529 +# see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-4.9.2.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-4.9.2.eb index 4a7f47d9bc..7c607c059e 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-4.9.2.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-4.9.2.eb @@ -17,7 +17,7 @@ source_urls = [GNU_SOURCE] builddependencies = [('binutils', '2.25', '', True)] # '-fgnu89-inline' is required to avoid linking errors with older glibc's, -# see https://github.com/hpcugent/easybuild-easyconfigs/issues/529 +# see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 configopts = "--enable-cxx CPPFLAGS='-fgnu89-inline'" sanity_check_paths = { diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-4.9.3.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-4.9.3.eb index 72fbf1541b..25039d6e39 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-4.9.3.eb @@ -17,7 +17,7 @@ source_urls = [GNU_SOURCE] builddependencies = [('binutils', '2.25', '', True)] # '-fgnu89-inline' is required to avoid linking errors with older glibc's, -# see https://github.com/hpcugent/easybuild-easyconfigs/issues/529 +# see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 configopts = "--enable-cxx CPPFLAGS='-fgnu89-inline'" sanity_check_paths = { diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-4.9.4.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-4.9.4.eb index 83effb6682..697ed59231 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-4.9.4.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-4.9.4.eb @@ -17,7 +17,7 @@ source_urls = [GNU_SOURCE] builddependencies = [('binutils', '2.25', '', True)] # '-fgnu89-inline' is required to avoid linking errors with older glibc's, -# see https://github.com/hpcugent/easybuild-easyconfigs/issues/529 +# see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 configopts = "--enable-cxx CPPFLAGS='-fgnu89-inline'" sanity_check_paths = { diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-5.3.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-5.3.0.eb index d508b59ac7..9fd2f629f9 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-5.3.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-5.3.0.eb @@ -17,7 +17,7 @@ source_urls = [GNU_SOURCE] builddependencies = [('binutils', '2.26', '', True)] # '-fgnu89-inline' is required to avoid linking errors with older glibc's, -# see https://github.com/hpcugent/easybuild-easyconfigs/issues/529 +# see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-5.4.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-5.4.0.eb index 702e859518..3ea2d5a8a5 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-5.4.0.eb @@ -17,7 +17,7 @@ source_urls = [GNU_SOURCE] builddependencies = [('binutils', '2.26', '', True)] # '-fgnu89-inline' is required to avoid linking errors with older glibc's, -# see https://github.com/hpcugent/easybuild-easyconfigs/issues/529 +# see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-6.1.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-6.1.0.eb index 87ca206fb4..dfbcc45466 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-6.1.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-6.1.0.eb @@ -17,7 +17,7 @@ source_urls = [GNU_SOURCE] builddependencies = [('binutils', '2.27', '', True)] # '-fgnu89-inline' is required to avoid linking errors with older glibc's, -# see https://github.com/hpcugent/easybuild-easyconfigs/issues/529 +# see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-6.2.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-6.2.0.eb index 9a89ad1fbd..a888ba53c1 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-6.2.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-6.2.0.eb @@ -17,7 +17,7 @@ source_urls = [GNU_SOURCE] builddependencies = [('binutils', '2.27', '', True)] # '-fgnu89-inline' is required to avoid linking errors with older glibc's, -# see https://github.com/hpcugent/easybuild-easyconfigs/issues/529 +# see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GNU-4.9.2-2.25.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GNU-4.9.2-2.25.eb index 9fd3840472..e74ca76bb2 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GNU-4.9.2-2.25.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GNU-4.9.2-2.25.eb @@ -14,7 +14,7 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] # '-fgnu89-inline' is required to avoid linking errors with older glibc's, -# see https://github.com/hpcugent/easybuild-easyconfigs/issues/529 +# see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GNU-4.9.3-2.25.eb index 222b4603e6..89d12d3ecc 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GNU-4.9.3-2.25.eb @@ -14,7 +14,7 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] # '-fgnu89-inline' is required to avoid linking errors with older glibc's, -# see https://github.com/hpcugent/easybuild-easyconfigs/issues/529 +# see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GNU-5.1.0-2.25.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GNU-5.1.0-2.25.eb index 8d48b94390..b8a22e8dd1 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GNU-5.1.0-2.25.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GNU-5.1.0-2.25.eb @@ -14,7 +14,7 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] # '-fgnu89-inline' is required to avoid linking errors with older glibc's, -# see https://github.com/hpcugent/easybuild-easyconfigs/issues/529 +# see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2014b.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2014b.eb index 4190871d6e..9f81198d34 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2014b.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2014b.eb @@ -14,7 +14,7 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] # '-fgnu89-inline' is required to avoid linking errors with older glibc's, -# see https://github.com/hpcugent/easybuild-easyconfigs/issues/529 +# see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2015.05.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2015.05.eb index a244ff7f0d..abf727c78d 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2015.05.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2015.05.eb @@ -14,7 +14,7 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] # '-fgnu89-inline' is required to avoid linking errors with older glibc's, -# see https://github.com/hpcugent/easybuild-easyconfigs/issues/529 +# see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2015a.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2015a.eb index 6b8e25d1d4..8a2f6a69b7 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2015a.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2015a.eb @@ -14,7 +14,7 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] # '-fgnu89-inline' is required to avoid linking errors with older glibc's, -# see https://github.com/hpcugent/easybuild-easyconfigs/issues/529 +# see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2015b.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2015b.eb index 414bbac849..c94c57b0c9 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2015b.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2015b.eb @@ -14,7 +14,7 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] # '-fgnu89-inline' is required to avoid linking errors with older glibc's, -# see https://github.com/hpcugent/easybuild-easyconfigs/issues/529 +# see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2016.04.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2016.04.eb index e93393c961..ac1d3f2336 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2016.04.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2016.04.eb @@ -14,7 +14,7 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] # '-fgnu89-inline' is required to avoid linking errors with older glibc's, -# see https://github.com/hpcugent/easybuild-easyconfigs/issues/529 +# see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2016a.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2016a.eb index 32fe2f7b78..d6580cb3e9 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2016a.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2016a.eb @@ -14,7 +14,7 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] # '-fgnu89-inline' is required to avoid linking errors with older glibc's, -# see https://github.com/hpcugent/easybuild-easyconfigs/issues/529 +# see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 configopts = "--enable-cxx CPPFLAGS='-fgnu89-inline'" sanity_check_paths = { diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2016b.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2016b.eb index 3d6737ba08..7121f7d172 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2016b.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2016b.eb @@ -14,7 +14,7 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] # '-fgnu89-inline' is required to avoid linking errors with older glibc's, -# see https://github.com/hpcugent/easybuild-easyconfigs/issues/529 +# see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-gimkl-2.11.5.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-gimkl-2.11.5.eb index 04ba474daf..75de298f7a 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-gimkl-2.11.5.eb @@ -14,7 +14,7 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] # '-fgnu89-inline' is required to avoid linking errors with older glibc's, -# see https://github.com/hpcugent/easybuild-easyconfigs/issues/529 +# see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-ictce-5.4.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-ictce-5.4.0.eb index ca3c0c7b6c..0157f04741 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-ictce-5.4.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-ictce-5.4.0.eb @@ -14,7 +14,7 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] # '-fgnu89-inline' is required to avoid linking errors with older glibc's, -# see https://github.com/hpcugent/easybuild-easyconfigs/issues/529 +# see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-ictce-5.5.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-ictce-5.5.0.eb index e8ed91309a..740881ec34 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-ictce-5.5.0.eb @@ -14,7 +14,7 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] # '-fgnu89-inline' is required to avoid linking errors with older glibc's, -# see https://github.com/hpcugent/easybuild-easyconfigs/issues/529 +# see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-ictce-7.1.2.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-ictce-7.1.2.eb index a896f05992..e141025d05 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-ictce-7.1.2.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-ictce-7.1.2.eb @@ -14,7 +14,7 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] # '-fgnu89-inline' is required to avoid linking errors with older glibc's, -# see https://github.com/hpcugent/easybuild-easyconfigs/issues/529 +# see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2014b.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2014b.eb index bd224278e8..39930debab 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2014b.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2014b.eb @@ -14,7 +14,7 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] # '-fgnu89-inline' is required to avoid linking errors with older glibc's, -# see https://github.com/hpcugent/easybuild-easyconfigs/issues/529 +# see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2015a.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2015a.eb index 942e49510c..0f8a70041c 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2015a.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2015a.eb @@ -14,7 +14,7 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] # '-fgnu89-inline' is required to avoid linking errors with older glibc's, -# see https://github.com/hpcugent/easybuild-easyconfigs/issues/529 +# see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2015b.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2015b.eb index dbdac66931..0f22f64f82 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2015b.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2015b.eb @@ -14,7 +14,7 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] # '-fgnu89-inline' is required to avoid linking errors with older glibc's, -# see https://github.com/hpcugent/easybuild-easyconfigs/issues/529 +# see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2016.02-GCC-4.9.eb index 683e8274c8..aba40b2a53 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2016.02-GCC-4.9.eb @@ -14,7 +14,7 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] # '-fgnu89-inline' is required to avoid linking errors with older glibc's, -# see https://github.com/hpcugent/easybuild-easyconfigs/issues/529 +# see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2016a.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2016a.eb index 2b9dd5a6b8..308aa5a579 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2016a.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2016a.eb @@ -14,7 +14,7 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] # '-fgnu89-inline' is required to avoid linking errors with older glibc's, -# see https://github.com/hpcugent/easybuild-easyconfigs/issues/529 +# see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2016b.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2016b.eb index d339ed79b8..4da8a15bac 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2016b.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2016b.eb @@ -14,7 +14,7 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] # '-fgnu89-inline' is required to avoid linking errors with older glibc's, -# see https://github.com/hpcugent/easybuild-easyconfigs/issues/529 +# see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17.eb index 159d8d0173..92afdc0086 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17.eb @@ -16,7 +16,7 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] # '-fgnu89-inline' is required to avoid linking errors with older glibc's, -# see https://github.com/hpcugent/easybuild-easyconfigs/issues/529 +# see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.4.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.4.0.eb index c1c1439bf3..34356fc1a7 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.4.0.eb @@ -17,7 +17,7 @@ source_urls = [GNU_SOURCE] builddependencies = [('binutils', '2.26', '', True)] # '-fgnu89-inline' is required to avoid linking errors with older glibc's, -# see https://github.com/hpcugent/easybuild-easyconfigs/issues/529 +# see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-6.3.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-6.3.0.eb index ffbaa7a77a..ae199e4d28 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-6.3.0.eb @@ -17,7 +17,7 @@ source_urls = [GNU_SOURCE] builddependencies = [('binutils', '2.27', '', True)] # '-fgnu89-inline' is required to avoid linking errors with older glibc's, -# see https://github.com/hpcugent/easybuild-easyconfigs/issues/529 +# see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.1.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.1.0.eb index 18394615f9..0c20559e8b 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.1.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.1.0.eb @@ -17,7 +17,7 @@ source_urls = [GNU_SOURCE] builddependencies = [('binutils', '2.28', '', True)] # '-fgnu89-inline' is required to avoid linking errors with older glibc's, -# see https://github.com/hpcugent/easybuild-easyconfigs/issues/529 +# see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18.eb index f186b0ad85..bce719edb0 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18.eb @@ -16,7 +16,7 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] # '-fgnu89-inline' is required to avoid linking errors with older glibc's, -# see https://github.com/hpcugent/easybuild-easyconfigs/issues/529 +# see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { diff --git a/easybuild/easyconfigs/m/MACH/MACH-1.0.18.eb b/easybuild/easyconfigs/m/MACH/MACH-1.0.18.eb index b2fe855c56..708d54f146 100644 --- a/easybuild/easyconfigs/m/MACH/MACH-1.0.18.eb +++ b/easybuild/easyconfigs/m/MACH/MACH-1.0.18.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Ravi Tripathi # Email: ravi89@uab.edu diff --git a/easybuild/easyconfigs/m/MACS/MACS-1.4.2-1-goolf-1.4.10-Python-2.7.5.eb b/easybuild/easyconfigs/m/MACS/MACS-1.4.2-1-goolf-1.4.10-Python-2.7.5.eb index fe54887474..a1e0594673 100644 --- a/easybuild/easyconfigs/m/MACS/MACS-1.4.2-1-goolf-1.4.10-Python-2.7.5.eb +++ b/easybuild/easyconfigs/m/MACS/MACS-1.4.2-1-goolf-1.4.10-Python-2.7.5.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics (SIB) # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/m/MACS2/MACS2-2.1.0.20150731-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/m/MACS2/MACS2-2.1.0.20150731-goolf-1.4.10-Python-2.7.3.eb index 74d5a36f68..d1dc14f1ec 100644 --- a/easybuild/easyconfigs/m/MACS2/MACS2-2.1.0.20150731-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/m/MACS2/MACS2-2.1.0.20150731-goolf-1.4.10-Python-2.7.3.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright (c) 2015 Virginia Bioinformatics Institute at Virginia Tech # Authors:: Dominik L. Borkowski diff --git a/easybuild/easyconfigs/m/MAFFT/MAFFT-7.130-goolf-1.4.10-with-extensions.eb b/easybuild/easyconfigs/m/MAFFT/MAFFT-7.130-goolf-1.4.10-with-extensions.eb index 66ff95669d..301e024b2e 100644 --- a/easybuild/easyconfigs/m/MAFFT/MAFFT-7.130-goolf-1.4.10-with-extensions.eb +++ b/easybuild/easyconfigs/m/MAFFT/MAFFT-7.130-goolf-1.4.10-with-extensions.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/m/MAFFT/MAFFT-7.130-ictce-5.3.0-with-extensions.eb b/easybuild/easyconfigs/m/MAFFT/MAFFT-7.130-ictce-5.3.0-with-extensions.eb index 6bf747d607..de247f7e05 100644 --- a/easybuild/easyconfigs/m/MAFFT/MAFFT-7.130-ictce-5.3.0-with-extensions.eb +++ b/easybuild/easyconfigs/m/MAFFT/MAFFT-7.130-ictce-5.3.0-with-extensions.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/m/MAFFT/MAFFT-7.305-foss-2016b-with-extensions.eb b/easybuild/easyconfigs/m/MAFFT/MAFFT-7.305-foss-2016b-with-extensions.eb index 725469edc9..420ca72862 100644 --- a/easybuild/easyconfigs/m/MAFFT/MAFFT-7.305-foss-2016b-with-extensions.eb +++ b/easybuild/easyconfigs/m/MAFFT/MAFFT-7.305-foss-2016b-with-extensions.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/m/MATIO/MATIO-1.5.2-goolf-1.4.10.eb b/easybuild/easyconfigs/m/MATIO/MATIO-1.5.2-goolf-1.4.10.eb index 013f802b61..fb42e73bb6 100644 --- a/easybuild/easyconfigs/m/MATIO/MATIO-1.5.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/m/MATIO/MATIO-1.5.2-goolf-1.4.10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2014-2015 The Cyprus Institute # Authors:: Thekla Loizou diff --git a/easybuild/easyconfigs/m/MATIO/MATIO-1.5.2-intel-2015b.eb b/easybuild/easyconfigs/m/MATIO/MATIO-1.5.2-intel-2015b.eb index 05e18b2e8b..92679ceb39 100644 --- a/easybuild/easyconfigs/m/MATIO/MATIO-1.5.2-intel-2015b.eb +++ b/easybuild/easyconfigs/m/MATIO/MATIO-1.5.2-intel-2015b.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2014-2015 The Cyprus Institute # Authors:: Thekla Loizou diff --git a/easybuild/easyconfigs/m/MCL/MCL-12.135-goolf-1.4.10.eb b/easybuild/easyconfigs/m/MCL/MCL-12.135-goolf-1.4.10.eb index b1a95f4031..79f149914d 100644 --- a/easybuild/easyconfigs/m/MCL/MCL-12.135-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/m/MCL/MCL-12.135-goolf-1.4.10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/m/MCL/MCL-12.135-ictce-5.3.0.eb b/easybuild/easyconfigs/m/MCL/MCL-12.135-ictce-5.3.0.eb index 0619f29465..8922cbe4f1 100644 --- a/easybuild/easyconfigs/m/MCL/MCL-12.135-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/m/MCL/MCL-12.135-ictce-5.3.0.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/m/MEGACC/MEGACC-7.0.18-1.eb b/easybuild/easyconfigs/m/MEGACC/MEGACC-7.0.18-1.eb index a3ab3c4257..82d928f902 100644 --- a/easybuild/easyconfigs/m/MEGACC/MEGACC-7.0.18-1.eb +++ b/easybuild/easyconfigs/m/MEGACC/MEGACC-7.0.18-1.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2016, UNIGE # Authors:: Yann Sagon diff --git a/easybuild/easyconfigs/m/MEME/MEME-4.8.0-goolf-1.4.10.eb b/easybuild/easyconfigs/m/MEME/MEME-4.8.0-goolf-1.4.10.eb index 2b1ca4f4f3..a51d0ef450 100644 --- a/easybuild/easyconfigs/m/MEME/MEME-4.8.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/m/MEME/MEME-4.8.0-goolf-1.4.10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/m/MEME/MEME-4.8.0-ictce-5.3.0.eb b/easybuild/easyconfigs/m/MEME/MEME-4.8.0-ictce-5.3.0.eb index 8c5d271d61..71e10b9d12 100644 --- a/easybuild/easyconfigs/m/MEME/MEME-4.8.0-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/m/MEME/MEME-4.8.0-ictce-5.3.0.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/m/MM-align/MM-align-20130815-goolf-1.4.10.eb b/easybuild/easyconfigs/m/MM-align/MM-align-20130815-goolf-1.4.10.eb index 6c78bbddaf..11cadedbcf 100644 --- a/easybuild/easyconfigs/m/MM-align/MM-align-20130815-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/m/MM-align/MM-align-20130815-goolf-1.4.10.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # sciCORE - University of Basel # SIB Swiss Institute of Bioinformatics diff --git a/easybuild/easyconfigs/m/MMSEQ/MMSEQ-1.0.8-linux64-static.eb b/easybuild/easyconfigs/m/MMSEQ/MMSEQ-1.0.8-linux64-static.eb index 9077537b1d..c3c02301be 100644 --- a/easybuild/easyconfigs/m/MMSEQ/MMSEQ-1.0.8-linux64-static.eb +++ b/easybuild/easyconfigs/m/MMSEQ/MMSEQ-1.0.8-linux64-static.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/m/MOSAIK/MOSAIK-2.2.28-goolf-1.4.10-20140425-24cf06.eb b/easybuild/easyconfigs/m/MOSAIK/MOSAIK-2.2.28-goolf-1.4.10-20140425-24cf06.eb index a98288f900..8006954711 100644 --- a/easybuild/easyconfigs/m/MOSAIK/MOSAIK-2.2.28-goolf-1.4.10-20140425-24cf06.eb +++ b/easybuild/easyconfigs/m/MOSAIK/MOSAIK-2.2.28-goolf-1.4.10-20140425-24cf06.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # sciCORE - University of Basel # SIB Swiss Institute of Bioinformatics diff --git a/easybuild/easyconfigs/m/MOSAIK/MOSAIK-2.2.28-ictce-6.2.5-20140425-24cf06.eb b/easybuild/easyconfigs/m/MOSAIK/MOSAIK-2.2.28-ictce-6.2.5-20140425-24cf06.eb index 3ce4130b75..054ec92efa 100644 --- a/easybuild/easyconfigs/m/MOSAIK/MOSAIK-2.2.28-ictce-6.2.5-20140425-24cf06.eb +++ b/easybuild/easyconfigs/m/MOSAIK/MOSAIK-2.2.28-ictce-6.2.5-20140425-24cf06.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # sciCORE - University of Basel # SIB Swiss Institute of Bioinformatics diff --git a/easybuild/easyconfigs/m/MPJ-Express/MPJ-Express-0.44-foss-2016a-Java-1.8.0_92.eb b/easybuild/easyconfigs/m/MPJ-Express/MPJ-Express-0.44-foss-2016a-Java-1.8.0_92.eb index 6e3b23ba3c..d8d121944a 100644 --- a/easybuild/easyconfigs/m/MPJ-Express/MPJ-Express-0.44-foss-2016a-Java-1.8.0_92.eb +++ b/easybuild/easyconfigs/m/MPJ-Express/MPJ-Express-0.44-foss-2016a-Java-1.8.0_92.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # sciCORE - University of Basel # SIB Swiss Institute of Bioinformatics diff --git a/easybuild/easyconfigs/m/MPJ-Express/MPJ-Express-0.44-goolf-1.4.10-Java-1.7.0_75.eb b/easybuild/easyconfigs/m/MPJ-Express/MPJ-Express-0.44-goolf-1.4.10-Java-1.7.0_75.eb index 8577e3deb4..e553dd3905 100644 --- a/easybuild/easyconfigs/m/MPJ-Express/MPJ-Express-0.44-goolf-1.4.10-Java-1.7.0_75.eb +++ b/easybuild/easyconfigs/m/MPJ-Express/MPJ-Express-0.44-goolf-1.4.10-Java-1.7.0_75.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # sciCORE - University of Basel # SIB Swiss Institute of Bioinformatics diff --git a/easybuild/easyconfigs/m/MRIcron/MRIcron-20150601.eb b/easybuild/easyconfigs/m/MRIcron/MRIcron-20150601.eb index 9830a06815..733f6228b4 100644 --- a/easybuild/easyconfigs/m/MRIcron/MRIcron-20150601.eb +++ b/easybuild/easyconfigs/m/MRIcron/MRIcron-20150601.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Ravi Tripathi # Email: ravi89@uab.edu diff --git a/easybuild/easyconfigs/m/MUMmer/MUMmer-3.23-foss-2016b.eb b/easybuild/easyconfigs/m/MUMmer/MUMmer-3.23-foss-2016b.eb index 279406579d..d8f8b6c576 100644 --- a/easybuild/easyconfigs/m/MUMmer/MUMmer-3.23-foss-2016b.eb +++ b/easybuild/easyconfigs/m/MUMmer/MUMmer-3.23-foss-2016b.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Cedric Laczny , Fotis Georgatos diff --git a/easybuild/easyconfigs/m/MUMmer/MUMmer-3.23-goolf-1.4.10-Perl-5.16.3.eb b/easybuild/easyconfigs/m/MUMmer/MUMmer-3.23-goolf-1.4.10-Perl-5.16.3.eb index c1b84b6840..1c9331d3a6 100644 --- a/easybuild/easyconfigs/m/MUMmer/MUMmer-3.23-goolf-1.4.10-Perl-5.16.3.eb +++ b/easybuild/easyconfigs/m/MUMmer/MUMmer-3.23-goolf-1.4.10-Perl-5.16.3.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Cedric Laczny , Fotis Georgatos , Kenneth Hoste diff --git a/easybuild/easyconfigs/m/MUMmer/MUMmer-3.23-goolf-1.4.10.eb b/easybuild/easyconfigs/m/MUMmer/MUMmer-3.23-goolf-1.4.10.eb index 7f6b9e72b5..c14d1b405f 100644 --- a/easybuild/easyconfigs/m/MUMmer/MUMmer-3.23-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/m/MUMmer/MUMmer-3.23-goolf-1.4.10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Cedric Laczny , Fotis Georgatos diff --git a/easybuild/easyconfigs/m/MUMmer/MUMmer-3.23-ictce-5.3.0-Perl-5.16.3.eb b/easybuild/easyconfigs/m/MUMmer/MUMmer-3.23-ictce-5.3.0-Perl-5.16.3.eb index 89fe1f89da..5f3eab90e4 100644 --- a/easybuild/easyconfigs/m/MUMmer/MUMmer-3.23-ictce-5.3.0-Perl-5.16.3.eb +++ b/easybuild/easyconfigs/m/MUMmer/MUMmer-3.23-ictce-5.3.0-Perl-5.16.3.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Cedric Laczny , Fotis Georgatos , Kenneth Hoste diff --git a/easybuild/easyconfigs/m/MUMmer/MUMmer-3.23-ictce-5.3.0.eb b/easybuild/easyconfigs/m/MUMmer/MUMmer-3.23-ictce-5.3.0.eb index 2a22c67912..e8c2cf7793 100644 --- a/easybuild/easyconfigs/m/MUMmer/MUMmer-3.23-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/m/MUMmer/MUMmer-3.23-ictce-5.3.0.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Cedric Laczny , Fotis Georgatos diff --git a/easybuild/easyconfigs/m/MUMmer/MUMmer-4.0.0beta-goolf-1.7.20.eb b/easybuild/easyconfigs/m/MUMmer/MUMmer-4.0.0beta-goolf-1.7.20.eb index 8471838376..df73ec7490 100644 --- a/easybuild/easyconfigs/m/MUMmer/MUMmer-4.0.0beta-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/m/MUMmer/MUMmer-4.0.0beta-goolf-1.7.20.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # sciCORE - University of Basel # SIB Swiss Institute of Bioinformatics diff --git a/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.31-foss-2016a.eb b/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.31-foss-2016a.eb index 026425a12b..0107cb4698 100644 --- a/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.31-foss-2016a.eb +++ b/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.31-foss-2016a.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.31-goolf-1.4.10.eb b/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.31-goolf-1.4.10.eb index f41c1f7758..57e72b59d6 100644 --- a/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.31-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.31-goolf-1.4.10.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.31-i86linux64.eb b/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.31-i86linux64.eb index eb4529c9fa..839544e3dd 100644 --- a/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.31-i86linux64.eb +++ b/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.31-i86linux64.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos , Andreas Panteli , diff --git a/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.31-ictce-5.5.0.eb b/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.31-ictce-5.5.0.eb index 2998cc688a..6ff84960dd 100644 --- a/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.31-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.31-ictce-5.5.0.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.31-intel-2016a.eb b/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.31-intel-2016a.eb index 467b83b6ce..03afecade9 100644 --- a/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.31-intel-2016a.eb +++ b/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.31-intel-2016a.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/m/MUST/MUST-1.2.0-goolf-1.5.14.eb b/easybuild/easyconfigs/m/MUST/MUST-1.2.0-goolf-1.5.14.eb index a3e8ea9b64..d1011fd9c1 100644 --- a/easybuild/easyconfigs/m/MUST/MUST-1.2.0-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/m/MUST/MUST-1.2.0-goolf-1.5.14.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild # Copyright:: Copyright 2013 Juelich Supercomputing Centre, Germany # Authors:: Bernd Mohr # License:: New BSD diff --git a/easybuild/easyconfigs/m/MUSTANG/MUSTANG-3.2.1-goolf-1.4.10.eb b/easybuild/easyconfigs/m/MUSTANG/MUSTANG-3.2.1-goolf-1.4.10.eb index 9ce401d07a..39ec3bd32a 100644 --- a/easybuild/easyconfigs/m/MUSTANG/MUSTANG-3.2.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/m/MUSTANG/MUSTANG-3.2.1-goolf-1.4.10.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/m/MView/MView-1.57-goolf-1.4.10-Perl-5.16.3.eb b/easybuild/easyconfigs/m/MView/MView-1.57-goolf-1.4.10-Perl-5.16.3.eb index 973e13d894..086df1b66a 100644 --- a/easybuild/easyconfigs/m/MView/MView-1.57-goolf-1.4.10-Perl-5.16.3.eb +++ b/easybuild/easyconfigs/m/MView/MView-1.57-goolf-1.4.10-Perl-5.16.3.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # sciCORE - University of Basel # SIB Swiss Institute of Bioinformatics diff --git a/easybuild/easyconfigs/m/MaCH/MaCH-1.0.18.c-goolf-1.4.10.eb b/easybuild/easyconfigs/m/MaCH/MaCH-1.0.18.c-goolf-1.4.10.eb index b454981b04..9a34deab14 100644 --- a/easybuild/easyconfigs/m/MaCH/MaCH-1.0.18.c-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/m/MaCH/MaCH-1.0.18.c-goolf-1.4.10.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/m/MaCH/MaCH-1.0.18.c-ictce-6.2.5.eb b/easybuild/easyconfigs/m/MaCH/MaCH-1.0.18.c-ictce-6.2.5.eb index e008b133f5..6c4e322386 100644 --- a/easybuild/easyconfigs/m/MaCH/MaCH-1.0.18.c-ictce-6.2.5.eb +++ b/easybuild/easyconfigs/m/MaCH/MaCH-1.0.18.c-ictce-6.2.5.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/m/MaSuRCA/MaSuRCA-3.2.2-foss-2016a.eb b/easybuild/easyconfigs/m/MaSuRCA/MaSuRCA-3.2.2-foss-2016a.eb index 75f0da13ce..08c7be2718 100644 --- a/easybuild/easyconfigs/m/MaSuRCA/MaSuRCA-3.2.2-foss-2016a.eb +++ b/easybuild/easyconfigs/m/MaSuRCA/MaSuRCA-3.2.2-foss-2016a.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2017 University of Geneva # Authors:: Yann Sagon diff --git a/easybuild/easyconfigs/m/Maq/Maq-0.7.0.eb b/easybuild/easyconfigs/m/Maq/Maq-0.7.0.eb index 8357cd6199..b268eeb163 100644 --- a/easybuild/easyconfigs/m/Maq/Maq-0.7.0.eb +++ b/easybuild/easyconfigs/m/Maq/Maq-0.7.0.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Ravi Tripathi # Email: ravi89@uab.edu diff --git a/easybuild/easyconfigs/m/Mawk/Mawk-1.3.4-goolf-1.4.10-20150503.eb b/easybuild/easyconfigs/m/Mawk/Mawk-1.3.4-goolf-1.4.10-20150503.eb index 5b5a91c678..752b5a4a61 100644 --- a/easybuild/easyconfigs/m/Mawk/Mawk-1.3.4-goolf-1.4.10-20150503.eb +++ b/easybuild/easyconfigs/m/Mawk/Mawk-1.3.4-goolf-1.4.10-20150503.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # sciCORE - University of Basel # SIB Swiss Institute of Bioinformatics diff --git a/easybuild/easyconfigs/m/MetaVelvet/MetaVelvet-1.2.01-goolf-1.4.10.eb b/easybuild/easyconfigs/m/MetaVelvet/MetaVelvet-1.2.01-goolf-1.4.10.eb index 3887c3f2e8..2fa6bdbab4 100644 --- a/easybuild/easyconfigs/m/MetaVelvet/MetaVelvet-1.2.01-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/m/MetaVelvet/MetaVelvet-1.2.01-goolf-1.4.10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Cedric Laczny , Fotis Georgatos diff --git a/easybuild/easyconfigs/m/MetaVelvet/MetaVelvet-1.2.01-ictce-5.3.0.eb b/easybuild/easyconfigs/m/MetaVelvet/MetaVelvet-1.2.01-ictce-5.3.0.eb index 98f80aa50e..ec9153655e 100644 --- a/easybuild/easyconfigs/m/MetaVelvet/MetaVelvet-1.2.01-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/m/MetaVelvet/MetaVelvet-1.2.01-ictce-5.3.0.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Cedric Laczny , Fotis Georgatos diff --git a/easybuild/easyconfigs/m/MethPipe/MethPipe-3.0.1-goolf-1.4.10.eb b/easybuild/easyconfigs/m/MethPipe/MethPipe-3.0.1-goolf-1.4.10.eb index 3af2bae350..db06302aba 100644 --- a/easybuild/easyconfigs/m/MethPipe/MethPipe-3.0.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/m/MethPipe/MethPipe-3.0.1-goolf-1.4.10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2013-2014 The Cyprus Institute # Authors:: Thekla Loizou diff --git a/easybuild/easyconfigs/m/MethPipe/MethPipe-3.0.1-intel-2014b.eb b/easybuild/easyconfigs/m/MethPipe/MethPipe-3.0.1-intel-2014b.eb index 3f4fca5919..644456e884 100644 --- a/easybuild/easyconfigs/m/MethPipe/MethPipe-3.0.1-intel-2014b.eb +++ b/easybuild/easyconfigs/m/MethPipe/MethPipe-3.0.1-intel-2014b.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2013-2014 The Cyprus Institute # Authors:: Thekla Loizou diff --git a/easybuild/easyconfigs/m/Minia/Minia-2.0.7-goolf-1.7.20.eb b/easybuild/easyconfigs/m/Minia/Minia-2.0.7-goolf-1.7.20.eb index 947de950b4..8577f2b939 100644 --- a/easybuild/easyconfigs/m/Minia/Minia-2.0.7-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/m/Minia/Minia-2.0.7-goolf-1.7.20.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # sciCORE - University of Basel # SIB Swiss Institute of Bioinformatics diff --git a/easybuild/easyconfigs/m/Minimac/Minimac-20140110-goolf-1.4.10.eb b/easybuild/easyconfigs/m/Minimac/Minimac-20140110-goolf-1.4.10.eb index c110a85228..653db9e11e 100644 --- a/easybuild/easyconfigs/m/Minimac/Minimac-20140110-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/m/Minimac/Minimac-20140110-goolf-1.4.10.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/m/Minimac2/Minimac2-2014.9.15-goolf-1.7.20.eb b/easybuild/easyconfigs/m/Minimac2/Minimac2-2014.9.15-goolf-1.7.20.eb index c6a015a815..262f951ba0 100644 --- a/easybuild/easyconfigs/m/Minimac2/Minimac2-2014.9.15-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/m/Minimac2/Minimac2-2014.9.15-goolf-1.7.20.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # sciCORE - University of Basel # SIB Swiss Institute of Bioinformatics diff --git a/easybuild/easyconfigs/m/Modeller/Modeller-9.13-goolf-1.4.10-Python-2.7.5.eb b/easybuild/easyconfigs/m/Modeller/Modeller-9.13-goolf-1.4.10-Python-2.7.5.eb index 4beaf4d721..f59e41f393 100644 --- a/easybuild/easyconfigs/m/Modeller/Modeller-9.13-goolf-1.4.10-Python-2.7.5.eb +++ b/easybuild/easyconfigs/m/Modeller/Modeller-9.13-goolf-1.4.10-Python-2.7.5.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/m/MotEvo/MotEvo-1.02-goolf-1.4.10.eb b/easybuild/easyconfigs/m/MotEvo/MotEvo-1.02-goolf-1.4.10.eb index 5da93a4bfe..f84995643d 100644 --- a/easybuild/easyconfigs/m/MotEvo/MotEvo-1.02-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/m/MotEvo/MotEvo-1.02-goolf-1.4.10.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/m/MuTect/MuTect-1.1.4-Java-1.7.0_76.eb b/easybuild/easyconfigs/m/MuTect/MuTect-1.1.4-Java-1.7.0_76.eb index aa90066de8..025271c90b 100644 --- a/easybuild/easyconfigs/m/MuTect/MuTect-1.1.4-Java-1.7.0_76.eb +++ b/easybuild/easyconfigs/m/MuTect/MuTect-1.1.4-Java-1.7.0_76.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/m/MuTect/MuTect-1.1.4-Java-1.7.0_80.eb b/easybuild/easyconfigs/m/MuTect/MuTect-1.1.4-Java-1.7.0_80.eb index 4774c63625..46a5db5d00 100644 --- a/easybuild/easyconfigs/m/MuTect/MuTect-1.1.4-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/m/MuTect/MuTect-1.1.4-Java-1.7.0_80.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/m/MuTect/MuTect-1.1.7-Java-1.7.0_80.eb b/easybuild/easyconfigs/m/MuTect/MuTect-1.1.7-Java-1.7.0_80.eb index c8d608145e..e09b7d7128 100644 --- a/easybuild/easyconfigs/m/MuTect/MuTect-1.1.7-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/m/MuTect/MuTect-1.1.7-Java-1.7.0_80.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/m/MultiQC/MultiQC-0.7-goolf-1.7.20-Python-2.7.11.eb b/easybuild/easyconfigs/m/MultiQC/MultiQC-0.7-goolf-1.7.20-Python-2.7.11.eb index e9c753506d..433ec7e3b7 100644 --- a/easybuild/easyconfigs/m/MultiQC/MultiQC-0.7-goolf-1.7.20-Python-2.7.11.eb +++ b/easybuild/easyconfigs/m/MultiQC/MultiQC-0.7-goolf-1.7.20-Python-2.7.11.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # sciCORE - University of Basel # SIB Swiss Institute of Bioinformatics diff --git a/easybuild/easyconfigs/m/MultiQC/MultiQC-0.9-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/m/MultiQC/MultiQC-0.9-foss-2016b-Python-2.7.12.eb index cb0f244915..0be8df4a6a 100644 --- a/easybuild/easyconfigs/m/MultiQC/MultiQC-0.9-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/m/MultiQC/MultiQC-0.9-foss-2016b-Python-2.7.12.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Adam Huffman # The Francis Crick Institute # Elements derived from work by Pablo Escobar diff --git a/easybuild/easyconfigs/m/make/make-3.82-GCC-4.8.2.eb b/easybuild/easyconfigs/m/make/make-3.82-GCC-4.8.2.eb index ef981bb4df..fccc02c38a 100644 --- a/easybuild/easyconfigs/m/make/make-3.82-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/m/make/make-3.82-GCC-4.8.2.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild recipy as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild recipy as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/m/make/make-3.82-goolf-1.4.10.eb b/easybuild/easyconfigs/m/make/make-3.82-goolf-1.4.10.eb index e13659096e..e6d5d57368 100644 --- a/easybuild/easyconfigs/m/make/make-3.82-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/m/make/make-3.82-goolf-1.4.10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild recipy as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild recipy as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/m/make/make-3.82-ictce-5.3.0.eb b/easybuild/easyconfigs/m/make/make-3.82-ictce-5.3.0.eb index 7ab215e130..9b88858f90 100644 --- a/easybuild/easyconfigs/m/make/make-3.82-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/m/make/make-3.82-ictce-5.3.0.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild recipy as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild recipy as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/m/make/make-3.82-ictce-5.5.0.eb b/easybuild/easyconfigs/m/make/make-3.82-ictce-5.5.0.eb index 256925f8ab..649ae523d5 100644 --- a/easybuild/easyconfigs/m/make/make-3.82-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/m/make/make-3.82-ictce-5.5.0.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild recipy as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild recipy as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/m/make/make-4.1-GCC-4.9.2.eb b/easybuild/easyconfigs/m/make/make-4.1-GCC-4.9.2.eb index bff321b4b2..7ca6f969a4 100644 --- a/easybuild/easyconfigs/m/make/make-4.1-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/m/make/make-4.1-GCC-4.9.2.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild recipy as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild recipy as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/m/mc/mc-4.6.1-goolf-1.4.10.eb b/easybuild/easyconfigs/m/mc/mc-4.6.1-goolf-1.4.10.eb index 87c8b17b1f..a27e4ffe9f 100644 --- a/easybuild/easyconfigs/m/mc/mc-4.6.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/m/mc/mc-4.6.1-goolf-1.4.10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/m/mc/mc-4.6.1-ictce-5.3.0.eb b/easybuild/easyconfigs/m/mc/mc-4.6.1-ictce-5.3.0.eb index 7047839f2d..fcd0c73edf 100644 --- a/easybuild/easyconfigs/m/mc/mc-4.6.1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/m/mc/mc-4.6.1-ictce-5.3.0.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/m/mc/mc-4.8.13-GCC-4.9.2.eb b/easybuild/easyconfigs/m/mc/mc-4.8.13-GCC-4.9.2.eb index 96e39f3ada..a78726d466 100644 --- a/easybuild/easyconfigs/m/mc/mc-4.8.13-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/m/mc/mc-4.8.13-GCC-4.9.2.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/m/mdtest/mdtest-1.7.1-goolf-1.4.10.eb b/easybuild/easyconfigs/m/mdtest/mdtest-1.7.1-goolf-1.4.10.eb index 13a13c28d8..6682ecef20 100644 --- a/easybuild/easyconfigs/m/mdtest/mdtest-1.7.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/m/mdtest/mdtest-1.7.1-goolf-1.4.10.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/m/mdtest/mdtest-1.7.1-ictce-6.2.5.eb b/easybuild/easyconfigs/m/mdtest/mdtest-1.7.1-ictce-6.2.5.eb index fdcf4609af..4002011eea 100644 --- a/easybuild/easyconfigs/m/mdtest/mdtest-1.7.1-ictce-6.2.5.eb +++ b/easybuild/easyconfigs/m/mdtest/mdtest-1.7.1-ictce-6.2.5.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/m/mdtest/mdtest-1.9.3-goolf-1.4.10.eb b/easybuild/easyconfigs/m/mdtest/mdtest-1.9.3-goolf-1.4.10.eb index 6a4c7c8893..59b48a2d38 100644 --- a/easybuild/easyconfigs/m/mdtest/mdtest-1.9.3-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/m/mdtest/mdtest-1.9.3-goolf-1.4.10.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/m/mdtest/mdtest-1.9.3-ictce-6.2.5.eb b/easybuild/easyconfigs/m/mdtest/mdtest-1.9.3-ictce-6.2.5.eb index 31e12db3cc..ef13aa622d 100644 --- a/easybuild/easyconfigs/m/mdtest/mdtest-1.9.3-ictce-6.2.5.eb +++ b/easybuild/easyconfigs/m/mdtest/mdtest-1.9.3-ictce-6.2.5.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/m/mpiBLAST/mpiBLAST-1.6.0-goolf-1.4.10.eb b/easybuild/easyconfigs/m/mpiBLAST/mpiBLAST-1.6.0-goolf-1.4.10.eb index 273a8c9d5f..598a5a64ee 100644 --- a/easybuild/easyconfigs/m/mpiBLAST/mpiBLAST-1.6.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/m/mpiBLAST/mpiBLAST-1.6.0-goolf-1.4.10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/m/mpiBLAST/mpiBLAST-1.6.0-ictce-5.2.0.eb b/easybuild/easyconfigs/m/mpiBLAST/mpiBLAST-1.6.0-ictce-5.2.0.eb index 1bb43bc486..1c9d77935a 100644 --- a/easybuild/easyconfigs/m/mpiBLAST/mpiBLAST-1.6.0-ictce-5.2.0.eb +++ b/easybuild/easyconfigs/m/mpiBLAST/mpiBLAST-1.6.0-ictce-5.2.0.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos , Kenneth Hoste diff --git a/easybuild/easyconfigs/m/mpiBLAST/mpiBLAST-1.6.0-ictce-5.3.0.eb b/easybuild/easyconfigs/m/mpiBLAST/mpiBLAST-1.6.0-ictce-5.3.0.eb index 58c91d09bc..80d940898f 100644 --- a/easybuild/easyconfigs/m/mpiBLAST/mpiBLAST-1.6.0-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/m/mpiBLAST/mpiBLAST-1.6.0-ictce-5.3.0.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos , Kenneth Hoste diff --git a/easybuild/easyconfigs/m/mpmath/mpmath-0.19-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/m/mpmath/mpmath-0.19-foss-2016a-Python-2.7.11.eb index 6602e3fb19..f8f47b4abc 100644 --- a/easybuild/easyconfigs/m/mpmath/mpmath-0.19-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/m/mpmath/mpmath-0.19-foss-2016a-Python-2.7.11.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Author: Adam Huffman # adam.huffman@crick.ac.uk diff --git a/easybuild/easyconfigs/m/mpmath/mpmath-0.19-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/m/mpmath/mpmath-0.19-intel-2016a-Python-2.7.11.eb index 56a88f540c..e9f53eb87d 100644 --- a/easybuild/easyconfigs/m/mpmath/mpmath-0.19-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/m/mpmath/mpmath-0.19-intel-2016a-Python-2.7.11.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Author: Adam Huffman # adam.huffman@crick.ac.uk diff --git a/easybuild/easyconfigs/m/mrFAST/mrFAST-2.6.0.1-goolf-1.4.10.eb b/easybuild/easyconfigs/m/mrFAST/mrFAST-2.6.0.1-goolf-1.4.10.eb index fb05915a84..b2be7d9ff5 100644 --- a/easybuild/easyconfigs/m/mrFAST/mrFAST-2.6.0.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/m/mrFAST/mrFAST-2.6.0.1-goolf-1.4.10.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # sciCORE - University of Basel # SIB Swiss Institute of Bioinformatics diff --git a/easybuild/easyconfigs/m/mrFAST/mrFAST-2.6.0.1-ictce-6.2.5.eb b/easybuild/easyconfigs/m/mrFAST/mrFAST-2.6.0.1-ictce-6.2.5.eb index 1bc0838af6..d385b5af30 100644 --- a/easybuild/easyconfigs/m/mrFAST/mrFAST-2.6.0.1-ictce-6.2.5.eb +++ b/easybuild/easyconfigs/m/mrFAST/mrFAST-2.6.0.1-ictce-6.2.5.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # sciCORE - University of Basel # SIB Swiss Institute of Bioinformatics diff --git a/easybuild/easyconfigs/m/mrsFAST/mrsFAST-2.6.0.4-goolf-1.4.10.eb b/easybuild/easyconfigs/m/mrsFAST/mrsFAST-2.6.0.4-goolf-1.4.10.eb index e58c648eee..f6a3fa5bda 100644 --- a/easybuild/easyconfigs/m/mrsFAST/mrsFAST-2.6.0.4-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/m/mrsFAST/mrsFAST-2.6.0.4-goolf-1.4.10.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # sciCORE - University of Basel # SIB Swiss Institute of Bioinformatics diff --git a/easybuild/easyconfigs/m/mrsFAST/mrsFAST-2.6.0.4-ictce-6.2.5.eb b/easybuild/easyconfigs/m/mrsFAST/mrsFAST-2.6.0.4-ictce-6.2.5.eb index 933177a5af..12a460e953 100644 --- a/easybuild/easyconfigs/m/mrsFAST/mrsFAST-2.6.0.4-ictce-6.2.5.eb +++ b/easybuild/easyconfigs/m/mrsFAST/mrsFAST-2.6.0.4-ictce-6.2.5.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # sciCORE - University of Basel # SIB Swiss Institute of Bioinformatics diff --git a/easybuild/easyconfigs/n/NASM/NASM-2.07-goolf-1.4.10.eb b/easybuild/easyconfigs/n/NASM/NASM-2.07-goolf-1.4.10.eb index d17113cb06..ef1067a4f7 100644 --- a/easybuild/easyconfigs/n/NASM/NASM-2.07-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/n/NASM/NASM-2.07-goolf-1.4.10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/n/NASM/NASM-2.07-ictce-5.3.0.eb b/easybuild/easyconfigs/n/NASM/NASM-2.07-ictce-5.3.0.eb index 6c053969c2..09bfc070e6 100644 --- a/easybuild/easyconfigs/n/NASM/NASM-2.07-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/n/NASM/NASM-2.07-ictce-5.3.0.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/n/NASM/NASM-2.07-ictce-5.5.0.eb b/easybuild/easyconfigs/n/NASM/NASM-2.07-ictce-5.5.0.eb index f361a2932f..2631c95531 100644 --- a/easybuild/easyconfigs/n/NASM/NASM-2.07-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/n/NASM/NASM-2.07-ictce-5.5.0.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/n/NASM/NASM-2.07-intel-2014b.eb b/easybuild/easyconfigs/n/NASM/NASM-2.07-intel-2014b.eb index 777c4695fd..9995450154 100644 --- a/easybuild/easyconfigs/n/NASM/NASM-2.07-intel-2014b.eb +++ b/easybuild/easyconfigs/n/NASM/NASM-2.07-intel-2014b.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/n/NASM/NASM-2.11.05-goolf-1.7.20.eb b/easybuild/easyconfigs/n/NASM/NASM-2.11.05-goolf-1.7.20.eb index 61250ef0ab..3f9dfdbbef 100644 --- a/easybuild/easyconfigs/n/NASM/NASM-2.11.05-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/n/NASM/NASM-2.11.05-goolf-1.7.20.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/n/NASM/NASM-2.11.05-ictce-6.2.5.eb b/easybuild/easyconfigs/n/NASM/NASM-2.11.05-ictce-6.2.5.eb index d0c5c529db..73698fba89 100644 --- a/easybuild/easyconfigs/n/NASM/NASM-2.11.05-ictce-6.2.5.eb +++ b/easybuild/easyconfigs/n/NASM/NASM-2.11.05-ictce-6.2.5.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/n/NASM/NASM-2.11.05-intel-2014.06.eb b/easybuild/easyconfigs/n/NASM/NASM-2.11.05-intel-2014.06.eb index 8eacf467e7..cabd7636da 100644 --- a/easybuild/easyconfigs/n/NASM/NASM-2.11.05-intel-2014.06.eb +++ b/easybuild/easyconfigs/n/NASM/NASM-2.11.05-intel-2014.06.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/n/NASM/NASM-2.11.05-intel-2014b.eb b/easybuild/easyconfigs/n/NASM/NASM-2.11.05-intel-2014b.eb index 940cf3e83b..1dc98bc56e 100644 --- a/easybuild/easyconfigs/n/NASM/NASM-2.11.05-intel-2014b.eb +++ b/easybuild/easyconfigs/n/NASM/NASM-2.11.05-intel-2014b.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/n/NASM/NASM-2.11.05-intel-2015a.eb b/easybuild/easyconfigs/n/NASM/NASM-2.11.05-intel-2015a.eb index 9bf8366459..470433544b 100644 --- a/easybuild/easyconfigs/n/NASM/NASM-2.11.05-intel-2015a.eb +++ b/easybuild/easyconfigs/n/NASM/NASM-2.11.05-intel-2015a.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/n/NASM/NASM-2.11.06-foss-2015a.eb b/easybuild/easyconfigs/n/NASM/NASM-2.11.06-foss-2015a.eb index a9ff827237..1040eaec79 100644 --- a/easybuild/easyconfigs/n/NASM/NASM-2.11.06-foss-2015a.eb +++ b/easybuild/easyconfigs/n/NASM/NASM-2.11.06-foss-2015a.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/n/NASM/NASM-2.11.06-goolf-1.5.14.eb b/easybuild/easyconfigs/n/NASM/NASM-2.11.06-goolf-1.5.14.eb index e4df9a5cd4..701ac12d5c 100644 --- a/easybuild/easyconfigs/n/NASM/NASM-2.11.06-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/n/NASM/NASM-2.11.06-goolf-1.5.14.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/n/NASM/NASM-2.11.06-goolf-1.7.20.eb b/easybuild/easyconfigs/n/NASM/NASM-2.11.06-goolf-1.7.20.eb index 8ece8f5082..3cb349ff14 100644 --- a/easybuild/easyconfigs/n/NASM/NASM-2.11.06-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/n/NASM/NASM-2.11.06-goolf-1.7.20.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/n/NASM/NASM-2.11.06-intel-2015a.eb b/easybuild/easyconfigs/n/NASM/NASM-2.11.06-intel-2015a.eb index 058a25ffb3..0742f88efd 100644 --- a/easybuild/easyconfigs/n/NASM/NASM-2.11.06-intel-2015a.eb +++ b/easybuild/easyconfigs/n/NASM/NASM-2.11.06-intel-2015a.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/n/NASM/NASM-2.11.06-intel-2015b.eb b/easybuild/easyconfigs/n/NASM/NASM-2.11.06-intel-2015b.eb index f174be96fd..98cd4d01ec 100644 --- a/easybuild/easyconfigs/n/NASM/NASM-2.11.06-intel-2015b.eb +++ b/easybuild/easyconfigs/n/NASM/NASM-2.11.06-intel-2015b.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/n/NASM/NASM-2.11.08-foss-2015a.eb b/easybuild/easyconfigs/n/NASM/NASM-2.11.08-foss-2015a.eb index 54389e3415..4bec0e9960 100644 --- a/easybuild/easyconfigs/n/NASM/NASM-2.11.08-foss-2015a.eb +++ b/easybuild/easyconfigs/n/NASM/NASM-2.11.08-foss-2015a.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/n/NASM/NASM-2.11.08-foss-2015b.eb b/easybuild/easyconfigs/n/NASM/NASM-2.11.08-foss-2015b.eb index bcb04e7841..f467619905 100644 --- a/easybuild/easyconfigs/n/NASM/NASM-2.11.08-foss-2015b.eb +++ b/easybuild/easyconfigs/n/NASM/NASM-2.11.08-foss-2015b.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/n/NASM/NASM-2.11.08-foss-2016a.eb b/easybuild/easyconfigs/n/NASM/NASM-2.11.08-foss-2016a.eb index 691495f52f..0067d98017 100644 --- a/easybuild/easyconfigs/n/NASM/NASM-2.11.08-foss-2016a.eb +++ b/easybuild/easyconfigs/n/NASM/NASM-2.11.08-foss-2016a.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/n/NASM/NASM-2.11.08-foss-2016b.eb b/easybuild/easyconfigs/n/NASM/NASM-2.11.08-foss-2016b.eb index 72c77d6685..1930c1a1fc 100644 --- a/easybuild/easyconfigs/n/NASM/NASM-2.11.08-foss-2016b.eb +++ b/easybuild/easyconfigs/n/NASM/NASM-2.11.08-foss-2016b.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/n/NASM/NASM-2.11.08-gimkl-2.11.5.eb b/easybuild/easyconfigs/n/NASM/NASM-2.11.08-gimkl-2.11.5.eb index 60a507ddb8..ca8a738432 100644 --- a/easybuild/easyconfigs/n/NASM/NASM-2.11.08-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/n/NASM/NASM-2.11.08-gimkl-2.11.5.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/n/NASM/NASM-2.11.08-goolf-1.4.10.eb b/easybuild/easyconfigs/n/NASM/NASM-2.11.08-goolf-1.4.10.eb index 617fb03523..072b3e15a7 100644 --- a/easybuild/easyconfigs/n/NASM/NASM-2.11.08-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/n/NASM/NASM-2.11.08-goolf-1.4.10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/n/NASM/NASM-2.11.08-intel-2015a.eb b/easybuild/easyconfigs/n/NASM/NASM-2.11.08-intel-2015a.eb index 77ceaa2d9a..2730435062 100644 --- a/easybuild/easyconfigs/n/NASM/NASM-2.11.08-intel-2015a.eb +++ b/easybuild/easyconfigs/n/NASM/NASM-2.11.08-intel-2015a.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/n/NASM/NASM-2.11.08-intel-2015b.eb b/easybuild/easyconfigs/n/NASM/NASM-2.11.08-intel-2015b.eb index 92d511ac9c..742f32c7b6 100644 --- a/easybuild/easyconfigs/n/NASM/NASM-2.11.08-intel-2015b.eb +++ b/easybuild/easyconfigs/n/NASM/NASM-2.11.08-intel-2015b.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/n/NASM/NASM-2.11.08-intel-2016a.eb b/easybuild/easyconfigs/n/NASM/NASM-2.11.08-intel-2016a.eb index 7fa10b2782..99068e7f7b 100644 --- a/easybuild/easyconfigs/n/NASM/NASM-2.11.08-intel-2016a.eb +++ b/easybuild/easyconfigs/n/NASM/NASM-2.11.08-intel-2016a.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/n/NASM/NASM-2.12.01-foss-2016a.eb b/easybuild/easyconfigs/n/NASM/NASM-2.12.01-foss-2016a.eb index 3097f4cb0e..727f9c3f6c 100644 --- a/easybuild/easyconfigs/n/NASM/NASM-2.12.01-foss-2016a.eb +++ b/easybuild/easyconfigs/n/NASM/NASM-2.12.01-foss-2016a.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/n/NASM/NASM-2.12.01-intel-2016a.eb b/easybuild/easyconfigs/n/NASM/NASM-2.12.01-intel-2016a.eb index dc884fc260..f733c9124c 100644 --- a/easybuild/easyconfigs/n/NASM/NASM-2.12.01-intel-2016a.eb +++ b/easybuild/easyconfigs/n/NASM/NASM-2.12.01-intel-2016a.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/n/NASM/NASM-2.12.02-foss-2016a.eb b/easybuild/easyconfigs/n/NASM/NASM-2.12.02-foss-2016a.eb index 0ef2b03e67..0a75781a62 100644 --- a/easybuild/easyconfigs/n/NASM/NASM-2.12.02-foss-2016a.eb +++ b/easybuild/easyconfigs/n/NASM/NASM-2.12.02-foss-2016a.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/n/NASM/NASM-2.12.02-foss-2016b.eb b/easybuild/easyconfigs/n/NASM/NASM-2.12.02-foss-2016b.eb index 1c877d7045..35000996fb 100644 --- a/easybuild/easyconfigs/n/NASM/NASM-2.12.02-foss-2016b.eb +++ b/easybuild/easyconfigs/n/NASM/NASM-2.12.02-foss-2016b.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/n/NASM/NASM-2.12.02-intel-2016b.eb b/easybuild/easyconfigs/n/NASM/NASM-2.12.02-intel-2016b.eb index daeffdca98..5428307bd7 100644 --- a/easybuild/easyconfigs/n/NASM/NASM-2.12.02-intel-2016b.eb +++ b/easybuild/easyconfigs/n/NASM/NASM-2.12.02-intel-2016b.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/n/NASM/NASM-2.12.02-intel-2017a.eb b/easybuild/easyconfigs/n/NASM/NASM-2.12.02-intel-2017a.eb index a4d8935beb..b15496c3c9 100644 --- a/easybuild/easyconfigs/n/NASM/NASM-2.12.02-intel-2017a.eb +++ b/easybuild/easyconfigs/n/NASM/NASM-2.12.02-intel-2017a.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/n/NCBI-Toolkit/NCBI-Toolkit-9.0.0-goolf-1.4.10.eb b/easybuild/easyconfigs/n/NCBI-Toolkit/NCBI-Toolkit-9.0.0-goolf-1.4.10.eb index b11e19a831..af111599e9 100644 --- a/easybuild/easyconfigs/n/NCBI-Toolkit/NCBI-Toolkit-9.0.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/n/NCBI-Toolkit/NCBI-Toolkit-9.0.0-goolf-1.4.10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/n/NLopt/NLopt-2.4.2-goolf-1.4.10.eb b/easybuild/easyconfigs/n/NLopt/NLopt-2.4.2-goolf-1.4.10.eb index abf5bbc277..37e86398d4 100644 --- a/easybuild/easyconfigs/n/NLopt/NLopt-2.4.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/n/NLopt/NLopt-2.4.2-goolf-1.4.10.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/n/NLopt/NLopt-2.4.2-intel-2017a.eb b/easybuild/easyconfigs/n/NLopt/NLopt-2.4.2-intel-2017a.eb index 607bdc3f75..e7dbf65423 100644 --- a/easybuild/easyconfigs/n/NLopt/NLopt-2.4.2-intel-2017a.eb +++ b/easybuild/easyconfigs/n/NLopt/NLopt-2.4.2-intel-2017a.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/n/nano/nano-2.2.6-goolf-1.4.10.eb b/easybuild/easyconfigs/n/nano/nano-2.2.6-goolf-1.4.10.eb index b4bf60ef3c..c8e5168447 100644 --- a/easybuild/easyconfigs/n/nano/nano-2.2.6-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/n/nano/nano-2.2.6-goolf-1.4.10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/n/nano/nano-2.2.6-ictce-5.3.0.eb b/easybuild/easyconfigs/n/nano/nano-2.2.6-ictce-5.3.0.eb index 1ff272d5d5..efcd1039a6 100644 --- a/easybuild/easyconfigs/n/nano/nano-2.2.6-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/n/nano/nano-2.2.6-ictce-5.3.0.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/n/ncview/ncview-2.1.2-goolf-1.4.10.eb b/easybuild/easyconfigs/n/ncview/ncview-2.1.2-goolf-1.4.10.eb index 01beb09931..b07eebeedb 100644 --- a/easybuild/easyconfigs/n/ncview/ncview-2.1.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/n/ncview/ncview-2.1.2-goolf-1.4.10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2014 The Cyprus Institute # Authors:: Thekla Loizou diff --git a/easybuild/easyconfigs/n/ncview/ncview-2.1.2-ictce-5.3.0.eb b/easybuild/easyconfigs/n/ncview/ncview-2.1.2-ictce-5.3.0.eb index 26ed84e0ca..39826e3412 100644 --- a/easybuild/easyconfigs/n/ncview/ncview-2.1.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/n/ncview/ncview-2.1.2-ictce-5.3.0.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2014 The Cyprus Institute # Authors:: Thekla Loizou diff --git a/easybuild/easyconfigs/n/ncview/ncview-2.1.7-intel-2016b.eb b/easybuild/easyconfigs/n/ncview/ncview-2.1.7-intel-2016b.eb index 5320b4aa4c..fc4eee291e 100644 --- a/easybuild/easyconfigs/n/ncview/ncview-2.1.7-intel-2016b.eb +++ b/easybuild/easyconfigs/n/ncview/ncview-2.1.7-intel-2016b.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2014 The Cyprus Institute # Authors:: Thekla Loizou diff --git a/easybuild/easyconfigs/o/OCaml/OCaml-4.01.0-goolf-1.4.10.eb b/easybuild/easyconfigs/o/OCaml/OCaml-4.01.0-goolf-1.4.10.eb index 0a78e38ade..fcdbb10aad 100644 --- a/easybuild/easyconfigs/o/OCaml/OCaml-4.01.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/o/OCaml/OCaml-4.01.0-goolf-1.4.10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/o/OCaml/OCaml-4.01.0-ictce-5.5.0.eb b/easybuild/easyconfigs/o/OCaml/OCaml-4.01.0-ictce-5.5.0.eb index eb591f01b3..c1e9a74c6f 100644 --- a/easybuild/easyconfigs/o/OCaml/OCaml-4.01.0-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/o/OCaml/OCaml-4.01.0-ictce-5.5.0.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/o/OCaml/OCaml-4.02.3-foss-2015a.eb b/easybuild/easyconfigs/o/OCaml/OCaml-4.02.3-foss-2015a.eb index 12dba48bf0..a71841771b 100644 --- a/easybuild/easyconfigs/o/OCaml/OCaml-4.02.3-foss-2015a.eb +++ b/easybuild/easyconfigs/o/OCaml/OCaml-4.02.3-foss-2015a.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/o/OCaml/OCaml-4.02.3-foss-2016a.eb b/easybuild/easyconfigs/o/OCaml/OCaml-4.02.3-foss-2016a.eb index ee452fb08e..5a93a730dc 100644 --- a/easybuild/easyconfigs/o/OCaml/OCaml-4.02.3-foss-2016a.eb +++ b/easybuild/easyconfigs/o/OCaml/OCaml-4.02.3-foss-2016a.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/o/OPARI2/OPARI2-1.1.1-goolf-1.5.14.eb b/easybuild/easyconfigs/o/OPARI2/OPARI2-1.1.1-goolf-1.5.14.eb index d50dab2154..cbd3a83974 100644 --- a/easybuild/easyconfigs/o/OPARI2/OPARI2-1.1.1-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/o/OPARI2/OPARI2-1.1.1-goolf-1.5.14.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild # Copyright:: Copyright 2013 Juelich Supercomputing Centre, Germany # Authors:: Bernd Mohr # License:: New BSD diff --git a/easybuild/easyconfigs/o/OPARI2/OPARI2-1.1.2-foss-2015a.eb b/easybuild/easyconfigs/o/OPARI2/OPARI2-1.1.2-foss-2015a.eb index 6a2ab2df29..c6cc202fed 100644 --- a/easybuild/easyconfigs/o/OPARI2/OPARI2-1.1.2-foss-2015a.eb +++ b/easybuild/easyconfigs/o/OPARI2/OPARI2-1.1.2-foss-2015a.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild # Copyright:: Copyright 2013 Juelich Supercomputing Centre, Germany # Authors:: Bernd Mohr # License:: New BSD diff --git a/easybuild/easyconfigs/o/OPARI2/OPARI2-1.1.2-goolf-1.5.14.eb b/easybuild/easyconfigs/o/OPARI2/OPARI2-1.1.2-goolf-1.5.14.eb index 34e2fdbcea..c859d761df 100644 --- a/easybuild/easyconfigs/o/OPARI2/OPARI2-1.1.2-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/o/OPARI2/OPARI2-1.1.2-goolf-1.5.14.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild # Authors:: Jordi Blasco # License:: New BSD # diff --git a/easybuild/easyconfigs/o/OPARI2/OPARI2-2.0-foss-2016a.eb b/easybuild/easyconfigs/o/OPARI2/OPARI2-2.0-foss-2016a.eb index 2f3c2cf421..4c1cdfb922 100644 --- a/easybuild/easyconfigs/o/OPARI2/OPARI2-2.0-foss-2016a.eb +++ b/easybuild/easyconfigs/o/OPARI2/OPARI2-2.0-foss-2016a.eb @@ -1,5 +1,5 @@ ## -# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2013-2016 Juelich Supercomputing Centre, Germany # Authors:: Bernd Mohr diff --git a/easybuild/easyconfigs/o/OTF/OTF-1.12.4-goolf-1.5.14.eb b/easybuild/easyconfigs/o/OTF/OTF-1.12.4-goolf-1.5.14.eb index 831526692c..2b97f66bf4 100644 --- a/easybuild/easyconfigs/o/OTF/OTF-1.12.4-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/o/OTF/OTF-1.12.4-goolf-1.5.14.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild # Copyright:: Copyright 2013 Juelich Supercomputing Centre, Germany # Authors:: Bernd Mohr # License:: New BSD diff --git a/easybuild/easyconfigs/o/OTF/OTF-1.12.4-ictce-5.3.0.eb b/easybuild/easyconfigs/o/OTF/OTF-1.12.4-ictce-5.3.0.eb index 3d6eb22e24..47ba7c137c 100644 --- a/easybuild/easyconfigs/o/OTF/OTF-1.12.4-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/o/OTF/OTF-1.12.4-ictce-5.3.0.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild # Copyright:: Copyright 2013 Juelich Supercomputing Centre, Germany # Authors:: Bernd Mohr # License:: New BSD diff --git a/easybuild/easyconfigs/o/OTF2/OTF2-1.2.1-goolf-1.5.14.eb b/easybuild/easyconfigs/o/OTF2/OTF2-1.2.1-goolf-1.5.14.eb index 60c9ce8691..6e57763759 100644 --- a/easybuild/easyconfigs/o/OTF2/OTF2-1.2.1-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/o/OTF2/OTF2-1.2.1-goolf-1.5.14.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild # Copyright:: Copyright 2013 Juelich Supercomputing Centre, Germany # Authors:: Bernd Mohr # License:: New BSD diff --git a/easybuild/easyconfigs/o/OTF2/OTF2-1.2.1-ictce-5.3.0.eb b/easybuild/easyconfigs/o/OTF2/OTF2-1.2.1-ictce-5.3.0.eb index 341f324efb..b3e56a6986 100644 --- a/easybuild/easyconfigs/o/OTF2/OTF2-1.2.1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/o/OTF2/OTF2-1.2.1-ictce-5.3.0.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild # Copyright:: Copyright 2013 Juelich Supercomputing Centre, Germany # Authors:: Bernd Mohr # License:: New BSD diff --git a/easybuild/easyconfigs/o/OTF2/OTF2-1.5.1-foss-2015a.eb b/easybuild/easyconfigs/o/OTF2/OTF2-1.5.1-foss-2015a.eb index 4f583c01b1..d76e3051fb 100644 --- a/easybuild/easyconfigs/o/OTF2/OTF2-1.5.1-foss-2015a.eb +++ b/easybuild/easyconfigs/o/OTF2/OTF2-1.5.1-foss-2015a.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild # Copyright:: Copyright 2013 Juelich Supercomputing Centre, Germany # Authors:: Bernd Mohr # License:: New BSD diff --git a/easybuild/easyconfigs/o/OTF2/OTF2-2.0-foss-2016a.eb b/easybuild/easyconfigs/o/OTF2/OTF2-2.0-foss-2016a.eb index 3b724d990f..2e24f54ef8 100644 --- a/easybuild/easyconfigs/o/OTF2/OTF2-2.0-foss-2016a.eb +++ b/easybuild/easyconfigs/o/OTF2/OTF2-2.0-foss-2016a.eb @@ -1,5 +1,5 @@ ## -# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild # Copyright:: Copyright 2013-2016 Juelich Supercomputing Centre, Germany # Authors:: Bernd Mohr # Markus Geimer diff --git a/easybuild/easyconfigs/o/OTF2/OTF2-2.0-foss-2017a.eb b/easybuild/easyconfigs/o/OTF2/OTF2-2.0-foss-2017a.eb index d4318573b4..41a3d0f3c9 100644 --- a/easybuild/easyconfigs/o/OTF2/OTF2-2.0-foss-2017a.eb +++ b/easybuild/easyconfigs/o/OTF2/OTF2-2.0-foss-2017a.eb @@ -1,5 +1,5 @@ ## -# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild # Copyright:: Copyright 2013-2016 Juelich Supercomputing Centre, Germany # Authors:: Bernd Mohr # Markus Geimer diff --git a/easybuild/easyconfigs/o/Oases/Oases-0.2.08-foss-2016b.eb b/easybuild/easyconfigs/o/Oases/Oases-0.2.08-foss-2016b.eb index 335f79d16b..7bcec339f4 100644 --- a/easybuild/easyconfigs/o/Oases/Oases-0.2.08-foss-2016b.eb +++ b/easybuild/easyconfigs/o/Oases/Oases-0.2.08-foss-2016b.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2013 The Cyprus Institute # Authors:: Andreas Panteli , Fotis Georgatos diff --git a/easybuild/easyconfigs/o/Oases/Oases-0.2.08-goolf-1.4.10.eb b/easybuild/easyconfigs/o/Oases/Oases-0.2.08-goolf-1.4.10.eb index d34174340c..d26e10aab3 100644 --- a/easybuild/easyconfigs/o/Oases/Oases-0.2.08-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/o/Oases/Oases-0.2.08-goolf-1.4.10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2013 The Cyprus Institute # Authors:: Andreas Panteli , Fotis Georgatos diff --git a/easybuild/easyconfigs/o/Oases/Oases-0.2.08-ictce-5.3.0.eb b/easybuild/easyconfigs/o/Oases/Oases-0.2.08-ictce-5.3.0.eb index c408bf08bd..51d2029f8b 100644 --- a/easybuild/easyconfigs/o/Oases/Oases-0.2.08-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/o/Oases/Oases-0.2.08-ictce-5.3.0.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2013 The Cyprus Institute # Authors:: Andreas Panteli , Fotis Georgatos diff --git a/easybuild/easyconfigs/o/Oases/Oases-0.2.08-intel-2015a.eb b/easybuild/easyconfigs/o/Oases/Oases-0.2.08-intel-2015a.eb index ed69d393e3..fa31b8119c 100644 --- a/easybuild/easyconfigs/o/Oases/Oases-0.2.08-intel-2015a.eb +++ b/easybuild/easyconfigs/o/Oases/Oases-0.2.08-intel-2015a.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2013 The Cyprus Institute # Authors:: Andreas Panteli , Fotis Georgatos diff --git a/easybuild/easyconfigs/o/OpenMM/OpenMM-6.1-goolf-1.4.10-Python-2.7.5.eb b/easybuild/easyconfigs/o/OpenMM/OpenMM-6.1-goolf-1.4.10-Python-2.7.5.eb index 33c2f06dff..547084c491 100644 --- a/easybuild/easyconfigs/o/OpenMM/OpenMM-6.1-goolf-1.4.10-Python-2.7.5.eb +++ b/easybuild/easyconfigs/o/OpenMM/OpenMM-6.1-goolf-1.4.10-Python-2.7.5.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # sciCORE - University of Basel # SIB Swiss Institute of Bioinformatics diff --git a/easybuild/easyconfigs/o/OptiX/OptiX-3.8.0-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/o/OptiX/OptiX-3.8.0-GNU-4.9.3-2.25.eb index 69dec5c347..bb8c2ce071 100644 --- a/easybuild/easyconfigs/o/OptiX/OptiX-3.8.0-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/o/OptiX/OptiX-3.8.0-GNU-4.9.3-2.25.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Authors:: Stephane Thiell ## easyblock = 'Binary' diff --git a/easybuild/easyconfigs/o/OptiX/OptiX-3.9.0-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/o/OptiX/OptiX-3.9.0-GNU-4.9.3-2.25.eb index 7960265e87..28cec1fdb8 100644 --- a/easybuild/easyconfigs/o/OptiX/OptiX-3.9.0-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/o/OptiX/OptiX-3.9.0-GNU-4.9.3-2.25.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Authors:: Stephane Thiell ## easyblock = 'Binary' diff --git a/easybuild/easyconfigs/o/o2scl/o2scl-0.913-goolf-1.4.10.eb b/easybuild/easyconfigs/o/o2scl/o2scl-0.913-goolf-1.4.10.eb index 665ae52c04..ce8b6a310c 100644 --- a/easybuild/easyconfigs/o/o2scl/o2scl-0.913-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/o/o2scl/o2scl-0.913-goolf-1.4.10.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics (SIB) # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/p/PAML/PAML-4.7-goolf-1.4.10.eb b/easybuild/easyconfigs/p/PAML/PAML-4.7-goolf-1.4.10.eb index a3f69b41df..4ce9f6acc1 100644 --- a/easybuild/easyconfigs/p/PAML/PAML-4.7-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/PAML/PAML-4.7-goolf-1.4.10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Cyprus Institute / CaSToRC, Uni.Lu/LCSB, NTUA # Authors:: George Tsouloupas , Fotis Georgatos , Kenneth Hoste (UGent) diff --git a/easybuild/easyconfigs/p/PAML/PAML-4.7-ictce-5.3.0.eb b/easybuild/easyconfigs/p/PAML/PAML-4.7-ictce-5.3.0.eb index 5d277564d7..663098d7ea 100644 --- a/easybuild/easyconfigs/p/PAML/PAML-4.7-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/p/PAML/PAML-4.7-ictce-5.3.0.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Cyprus Institute / CaSToRC, Uni.Lu/LCSB, NTUA # Authors:: George Tsouloupas , Fotis Georgatos , Kenneth Hoste (UGent) diff --git a/easybuild/easyconfigs/p/PAPI/PAPI-5.0.1-goolf-1.4.10.eb b/easybuild/easyconfigs/p/PAPI/PAPI-5.0.1-goolf-1.4.10.eb index 6ad4131d3d..abf2f2f348 100644 --- a/easybuild/easyconfigs/p/PAPI/PAPI-5.0.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/PAPI/PAPI-5.0.1-goolf-1.4.10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/p/PAPI/PAPI-5.0.1-ictce-5.3.0.eb b/easybuild/easyconfigs/p/PAPI/PAPI-5.0.1-ictce-5.3.0.eb index 7dfa97e510..5fdc97ba25 100644 --- a/easybuild/easyconfigs/p/PAPI/PAPI-5.0.1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/p/PAPI/PAPI-5.0.1-ictce-5.3.0.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/p/PAPI/PAPI-5.2.0-goolf-1.5.14.eb b/easybuild/easyconfigs/p/PAPI/PAPI-5.2.0-goolf-1.5.14.eb index d485c2eb57..5520734983 100644 --- a/easybuild/easyconfigs/p/PAPI/PAPI-5.2.0-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/p/PAPI/PAPI-5.2.0-goolf-1.5.14.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2013 University of Luxembourg/Luxembourg Centre for Systems Biomedicine # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/p/PAPI/PAPI-5.2.0-ictce-5.3.0.eb b/easybuild/easyconfigs/p/PAPI/PAPI-5.2.0-ictce-5.3.0.eb index c548c0f167..beb87afa42 100644 --- a/easybuild/easyconfigs/p/PAPI/PAPI-5.2.0-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/p/PAPI/PAPI-5.2.0-ictce-5.3.0.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/p/PAPI/PAPI-5.4.0-foss-2015a.eb b/easybuild/easyconfigs/p/PAPI/PAPI-5.4.0-foss-2015a.eb index cbf18980bc..591c1a1cfb 100644 --- a/easybuild/easyconfigs/p/PAPI/PAPI-5.4.0-foss-2015a.eb +++ b/easybuild/easyconfigs/p/PAPI/PAPI-5.4.0-foss-2015a.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/p/PAPI/PAPI-5.4.1-foss-2015a.eb b/easybuild/easyconfigs/p/PAPI/PAPI-5.4.1-foss-2015a.eb index b5babf4529..aedb5208f2 100644 --- a/easybuild/easyconfigs/p/PAPI/PAPI-5.4.1-foss-2015a.eb +++ b/easybuild/easyconfigs/p/PAPI/PAPI-5.4.1-foss-2015a.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/p/PAPI/PAPI-5.4.3-foss-2016a.eb b/easybuild/easyconfigs/p/PAPI/PAPI-5.4.3-foss-2016a.eb index e76514b4cc..3aaed28371 100644 --- a/easybuild/easyconfigs/p/PAPI/PAPI-5.4.3-foss-2016a.eb +++ b/easybuild/easyconfigs/p/PAPI/PAPI-5.4.3-foss-2016a.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/p/PBZIP2/PBZIP2-1.1.8-goolf-1.4.10.eb b/easybuild/easyconfigs/p/PBZIP2/PBZIP2-1.1.8-goolf-1.4.10.eb index e1ffffe615..b212b2e2ef 100644 --- a/easybuild/easyconfigs/p/PBZIP2/PBZIP2-1.1.8-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/PBZIP2/PBZIP2-1.1.8-goolf-1.4.10.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/p/PBZIP2/PBZIP2-1.1.8-ictce-6.2.5.eb b/easybuild/easyconfigs/p/PBZIP2/PBZIP2-1.1.8-ictce-6.2.5.eb index 795cc4f409..a0d4aaa3ee 100644 --- a/easybuild/easyconfigs/p/PBZIP2/PBZIP2-1.1.8-ictce-6.2.5.eb +++ b/easybuild/easyconfigs/p/PBZIP2/PBZIP2-1.1.8-ictce-6.2.5.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/p/PCC/PCC-20131024.eb b/easybuild/easyconfigs/p/PCC/PCC-20131024.eb index 4ba60f4784..ed87db5729 100644 --- a/easybuild/easyconfigs/p/PCC/PCC-20131024.eb +++ b/easybuild/easyconfigs/p/PCC/PCC-20131024.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/p/PDT/PDT-3.19-goolf-1.5.14.eb b/easybuild/easyconfigs/p/PDT/PDT-3.19-goolf-1.5.14.eb index 48f0570291..e3744fc95a 100644 --- a/easybuild/easyconfigs/p/PDT/PDT-3.19-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/p/PDT/PDT-3.19-goolf-1.5.14.eb @@ -1,5 +1,5 @@ ## -# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2013-2015 Juelich Supercomputing Centre, Germany # Authors:: Bernd Mohr diff --git a/easybuild/easyconfigs/p/PDT/PDT-3.19-ictce-5.3.0.eb b/easybuild/easyconfigs/p/PDT/PDT-3.19-ictce-5.3.0.eb index f50e7519a2..381266ea15 100644 --- a/easybuild/easyconfigs/p/PDT/PDT-3.19-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/p/PDT/PDT-3.19-ictce-5.3.0.eb @@ -1,5 +1,5 @@ ## -# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2013-2015 Juelich Supercomputing Centre, Germany # Authors:: Bernd Mohr diff --git a/easybuild/easyconfigs/p/PDT/PDT-3.20-foss-2015a.eb b/easybuild/easyconfigs/p/PDT/PDT-3.20-foss-2015a.eb index 4acb86b021..17487e1283 100644 --- a/easybuild/easyconfigs/p/PDT/PDT-3.20-foss-2015a.eb +++ b/easybuild/easyconfigs/p/PDT/PDT-3.20-foss-2015a.eb @@ -1,5 +1,5 @@ ## -# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2013-2015 Juelich Supercomputing Centre, Germany # Authors:: Bernd Mohr diff --git a/easybuild/easyconfigs/p/PDT/PDT-3.20-goolf-1.5.14.eb b/easybuild/easyconfigs/p/PDT/PDT-3.20-goolf-1.5.14.eb index bb1e979e80..ca20f00b88 100644 --- a/easybuild/easyconfigs/p/PDT/PDT-3.20-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/p/PDT/PDT-3.20-goolf-1.5.14.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild # Authors:: Jordi Blasco # License:: New BSD # diff --git a/easybuild/easyconfigs/p/PDT/PDT-3.22-foss-2016a.eb b/easybuild/easyconfigs/p/PDT/PDT-3.22-foss-2016a.eb index c1c3137a73..7f1635e8a8 100644 --- a/easybuild/easyconfigs/p/PDT/PDT-3.22-foss-2016a.eb +++ b/easybuild/easyconfigs/p/PDT/PDT-3.22-foss-2016a.eb @@ -1,5 +1,5 @@ ## -# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2013-2016 Juelich Supercomputing Centre, Germany # Authors:: Bernd Mohr diff --git a/easybuild/easyconfigs/p/PEAR/PEAR-0.9.6-goolf-1.4.10.eb b/easybuild/easyconfigs/p/PEAR/PEAR-0.9.6-goolf-1.4.10.eb index 1c4f9ab85d..31449b54e7 100644 --- a/easybuild/easyconfigs/p/PEAR/PEAR-0.9.6-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/PEAR/PEAR-0.9.6-goolf-1.4.10.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # sciCORE - University of Basel # SIB Swiss Institute of Bioinformatics diff --git a/easybuild/easyconfigs/p/PEAR/PEAR-0.9.8-foss-2016b.eb b/easybuild/easyconfigs/p/PEAR/PEAR-0.9.8-foss-2016b.eb index 37c50aa1df..8aa84dce9f 100644 --- a/easybuild/easyconfigs/p/PEAR/PEAR-0.9.8-foss-2016b.eb +++ b/easybuild/easyconfigs/p/PEAR/PEAR-0.9.8-foss-2016b.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild easyblock = 'ConfigureMake' diff --git a/easybuild/easyconfigs/p/PEAR/PEAR-0.9.8-intel-2016b.eb b/easybuild/easyconfigs/p/PEAR/PEAR-0.9.8-intel-2016b.eb index fef4a83c9e..3ec9dad849 100644 --- a/easybuild/easyconfigs/p/PEAR/PEAR-0.9.8-intel-2016b.eb +++ b/easybuild/easyconfigs/p/PEAR/PEAR-0.9.8-intel-2016b.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild easyblock = 'ConfigureMake' diff --git a/easybuild/easyconfigs/p/PGDSpider/PGDSpider-2.1.0.3-Java-1.7.0_80.eb b/easybuild/easyconfigs/p/PGDSpider/PGDSpider-2.1.0.3-Java-1.7.0_80.eb index 32e6adc9b7..6c18c7665d 100644 --- a/easybuild/easyconfigs/p/PGDSpider/PGDSpider-2.1.0.3-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/p/PGDSpider/PGDSpider-2.1.0.3-Java-1.7.0_80.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # sciCORE - University of Basel # SIB Swiss Institute of Bioinformatics diff --git a/easybuild/easyconfigs/p/PHASE/PHASE-2.1.1.eb b/easybuild/easyconfigs/p/PHASE/PHASE-2.1.1.eb index 9a71ee57a7..d018f814f2 100644 --- a/easybuild/easyconfigs/p/PHASE/PHASE-2.1.1.eb +++ b/easybuild/easyconfigs/p/PHASE/PHASE-2.1.1.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Ravi Tripathi # Email: ravi89@uab.edu diff --git a/easybuild/easyconfigs/p/PLINK/PLINK-1.07-foss-2015b.eb b/easybuild/easyconfigs/p/PLINK/PLINK-1.07-foss-2015b.eb index 3dbf1f6dcc..7d60edd787 100644 --- a/easybuild/easyconfigs/p/PLINK/PLINK-1.07-foss-2015b.eb +++ b/easybuild/easyconfigs/p/PLINK/PLINK-1.07-foss-2015b.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/p/PLINK/PLINK-1.07-foss-2016a.eb b/easybuild/easyconfigs/p/PLINK/PLINK-1.07-foss-2016a.eb index 3a9a5a29e9..5b4efc33f6 100644 --- a/easybuild/easyconfigs/p/PLINK/PLINK-1.07-foss-2016a.eb +++ b/easybuild/easyconfigs/p/PLINK/PLINK-1.07-foss-2016a.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/p/PLINK/PLINK-1.07-foss-2016b.eb b/easybuild/easyconfigs/p/PLINK/PLINK-1.07-foss-2016b.eb index 8d5a6d2eb6..26b293a777 100644 --- a/easybuild/easyconfigs/p/PLINK/PLINK-1.07-foss-2016b.eb +++ b/easybuild/easyconfigs/p/PLINK/PLINK-1.07-foss-2016b.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/p/PLINK/PLINK-1.07-ictce-5.3.0.eb b/easybuild/easyconfigs/p/PLINK/PLINK-1.07-ictce-5.3.0.eb index 136c6e53e0..1c0a984949 100644 --- a/easybuild/easyconfigs/p/PLINK/PLINK-1.07-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/p/PLINK/PLINK-1.07-ictce-5.3.0.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2013 The Cyprus Institute # Authors:: Thekla Loizou , Andreas Panteli , diff --git a/easybuild/easyconfigs/p/PLINK/PLINK-1.07-ictce-6.2.5.eb b/easybuild/easyconfigs/p/PLINK/PLINK-1.07-ictce-6.2.5.eb index 0a3b48db5b..c6adbf0428 100644 --- a/easybuild/easyconfigs/p/PLINK/PLINK-1.07-ictce-6.2.5.eb +++ b/easybuild/easyconfigs/p/PLINK/PLINK-1.07-ictce-6.2.5.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/p/PLINKSEQ/PLINKSEQ-0.10-goolf-1.7.20.eb b/easybuild/easyconfigs/p/PLINKSEQ/PLINKSEQ-0.10-goolf-1.7.20.eb index 1ed4041bd8..de9f5cdd55 100644 --- a/easybuild/easyconfigs/p/PLINKSEQ/PLINKSEQ-0.10-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/p/PLINKSEQ/PLINKSEQ-0.10-goolf-1.7.20.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/p/POV-Ray/POV-Ray-3.7.0.0-intel-2016b.eb b/easybuild/easyconfigs/p/POV-Ray/POV-Ray-3.7.0.0-intel-2016b.eb index b01bff9fa6..95b77ff16a 100644 --- a/easybuild/easyconfigs/p/POV-Ray/POV-Ray-3.7.0.0-intel-2016b.eb +++ b/easybuild/easyconfigs/p/POV-Ray/POV-Ray-3.7.0.0-intel-2016b.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/p/PRACE/PRACE-20130605-goolf-1.4.10.eb b/easybuild/easyconfigs/p/PRACE/PRACE-20130605-goolf-1.4.10.eb index 1cdadae78c..ba3147aeda 100644 --- a/easybuild/easyconfigs/p/PRACE/PRACE-20130605-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/PRACE/PRACE-20130605-goolf-1.4.10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/p/PRACE/PRACE-20130605-ictce-5.3.0.eb b/easybuild/easyconfigs/p/PRACE/PRACE-20130605-ictce-5.3.0.eb index 6807550e34..e1d9097357 100644 --- a/easybuild/easyconfigs/p/PRACE/PRACE-20130605-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/p/PRACE/PRACE-20130605-ictce-5.3.0.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/p/PRANK/PRANK-130820-goolf-1.4.10.eb b/easybuild/easyconfigs/p/PRANK/PRANK-130820-goolf-1.4.10.eb index 59d3a92f69..d91b5c16d2 100644 --- a/easybuild/easyconfigs/p/PRANK/PRANK-130820-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/PRANK/PRANK-130820-goolf-1.4.10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/p/PRANK/PRANK-130820-ictce-5.3.0.eb b/easybuild/easyconfigs/p/PRANK/PRANK-130820-ictce-5.3.0.eb index cc4ff83fdd..e37d705eb5 100644 --- a/easybuild/easyconfigs/p/PRANK/PRANK-130820-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/p/PRANK/PRANK-130820-ictce-5.3.0.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/p/PRANK/PRANK-140110-goolf-1.4.10.eb b/easybuild/easyconfigs/p/PRANK/PRANK-140110-goolf-1.4.10.eb index 463e126a1a..e5306a0264 100644 --- a/easybuild/easyconfigs/p/PRANK/PRANK-140110-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/PRANK/PRANK-140110-goolf-1.4.10.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-foss-2015b-Perl-5.20.3.eb b/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-foss-2015b-Perl-5.20.3.eb index 0f000df55c..a8599a4532 100644 --- a/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-foss-2015b-Perl-5.20.3.eb +++ b/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-foss-2015b-Perl-5.20.3.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # sciCORE - University of Basel # SIB Swiss Institute of Bioinformatics diff --git a/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-goolf-1.4.10-Perl-5.16.3.eb b/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-goolf-1.4.10-Perl-5.16.3.eb index 8633986686..b72be2600b 100644 --- a/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-goolf-1.4.10-Perl-5.16.3.eb +++ b/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-goolf-1.4.10-Perl-5.16.3.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # sciCORE - University of Basel # SIB Swiss Institute of Bioinformatics diff --git a/easybuild/easyconfigs/p/PROJ/PROJ-4.8.0-foss-2015b.eb b/easybuild/easyconfigs/p/PROJ/PROJ-4.8.0-foss-2015b.eb index 30f8eb2395..00f55ae5a3 100644 --- a/easybuild/easyconfigs/p/PROJ/PROJ-4.8.0-foss-2015b.eb +++ b/easybuild/easyconfigs/p/PROJ/PROJ-4.8.0-foss-2015b.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2014-2015 The Cyprus Institute # Authors:: Thekla Loizou diff --git a/easybuild/easyconfigs/p/PROJ/PROJ-4.8.0-goolf-1.4.10.eb b/easybuild/easyconfigs/p/PROJ/PROJ-4.8.0-goolf-1.4.10.eb index 34a1760e0e..f7686d4769 100644 --- a/easybuild/easyconfigs/p/PROJ/PROJ-4.8.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/PROJ/PROJ-4.8.0-goolf-1.4.10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2014-2015 The Cyprus Institute # Authors:: Thekla Loizou diff --git a/easybuild/easyconfigs/p/PROJ/PROJ-4.8.0-ictce-5.3.0.eb b/easybuild/easyconfigs/p/PROJ/PROJ-4.8.0-ictce-5.3.0.eb index 968d0aa66a..76fc53fbf0 100644 --- a/easybuild/easyconfigs/p/PROJ/PROJ-4.8.0-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/p/PROJ/PROJ-4.8.0-ictce-5.3.0.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2014-2015 The Cyprus Institute # Authors:: Thekla Loizou diff --git a/easybuild/easyconfigs/p/PROJ/PROJ-4.9.1-foss-2015a.eb b/easybuild/easyconfigs/p/PROJ/PROJ-4.9.1-foss-2015a.eb index 4c530e2669..200a9f51d1 100644 --- a/easybuild/easyconfigs/p/PROJ/PROJ-4.9.1-foss-2015a.eb +++ b/easybuild/easyconfigs/p/PROJ/PROJ-4.9.1-foss-2015a.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2014-2015 The Cyprus Institute # Authors:: Thekla Loizou diff --git a/easybuild/easyconfigs/p/PROJ/PROJ-4.9.2-foss-2016a.eb b/easybuild/easyconfigs/p/PROJ/PROJ-4.9.2-foss-2016a.eb index 8073931ffc..3cf2db1934 100644 --- a/easybuild/easyconfigs/p/PROJ/PROJ-4.9.2-foss-2016a.eb +++ b/easybuild/easyconfigs/p/PROJ/PROJ-4.9.2-foss-2016a.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2014-2015 The Cyprus Institute # Authors:: Thekla Loizou diff --git a/easybuild/easyconfigs/p/PROJ/PROJ-4.9.2-foss-2016b.eb b/easybuild/easyconfigs/p/PROJ/PROJ-4.9.2-foss-2016b.eb index 324f2cd7f8..f00ad2c895 100644 --- a/easybuild/easyconfigs/p/PROJ/PROJ-4.9.2-foss-2016b.eb +++ b/easybuild/easyconfigs/p/PROJ/PROJ-4.9.2-foss-2016b.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2014-2015 The Cyprus Institute # Authors:: Thekla Loizou diff --git a/easybuild/easyconfigs/p/PROJ/PROJ-4.9.2-intel-2016a.eb b/easybuild/easyconfigs/p/PROJ/PROJ-4.9.2-intel-2016a.eb index 67b8275d1e..6f79ab820c 100644 --- a/easybuild/easyconfigs/p/PROJ/PROJ-4.9.2-intel-2016a.eb +++ b/easybuild/easyconfigs/p/PROJ/PROJ-4.9.2-intel-2016a.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2014-2015 The Cyprus Institute # Authors:: Thekla Loizou diff --git a/easybuild/easyconfigs/p/PROJ/PROJ-4.9.2-intel-2016b.eb b/easybuild/easyconfigs/p/PROJ/PROJ-4.9.2-intel-2016b.eb index bcb1e2a0d1..9de59c679b 100644 --- a/easybuild/easyconfigs/p/PROJ/PROJ-4.9.2-intel-2016b.eb +++ b/easybuild/easyconfigs/p/PROJ/PROJ-4.9.2-intel-2016b.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2014-2015 The Cyprus Institute # Authors:: Thekla Loizou diff --git a/easybuild/easyconfigs/p/PROJ/PROJ-4.9.3-foss-2016b.eb b/easybuild/easyconfigs/p/PROJ/PROJ-4.9.3-foss-2016b.eb index 7b1bb021f3..f1ed8cc4b8 100644 --- a/easybuild/easyconfigs/p/PROJ/PROJ-4.9.3-foss-2016b.eb +++ b/easybuild/easyconfigs/p/PROJ/PROJ-4.9.3-foss-2016b.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2014-2015 The Cyprus Institute # Authors:: Thekla Loizou diff --git a/easybuild/easyconfigs/p/PROJ/PROJ-4.9.3-intel-2016b.eb b/easybuild/easyconfigs/p/PROJ/PROJ-4.9.3-intel-2016b.eb index 0bd9d6514d..cfe024f452 100644 --- a/easybuild/easyconfigs/p/PROJ/PROJ-4.9.3-intel-2016b.eb +++ b/easybuild/easyconfigs/p/PROJ/PROJ-4.9.3-intel-2016b.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2014-2015 The Cyprus Institute # Authors:: Thekla Loizou diff --git a/easybuild/easyconfigs/p/PROJ/PROJ-4.9.3-intel-2017a.eb b/easybuild/easyconfigs/p/PROJ/PROJ-4.9.3-intel-2017a.eb index 07a9a99e42..b01ce62b7f 100644 --- a/easybuild/easyconfigs/p/PROJ/PROJ-4.9.3-intel-2017a.eb +++ b/easybuild/easyconfigs/p/PROJ/PROJ-4.9.3-intel-2017a.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2014-2015 The Cyprus Institute # Authors:: Thekla Loizou diff --git a/easybuild/easyconfigs/p/Parallel-ForkManager/Parallel-ForkManager-1.06-goolf-1.4.10-Perl-5.16.3.eb b/easybuild/easyconfigs/p/Parallel-ForkManager/Parallel-ForkManager-1.06-goolf-1.4.10-Perl-5.16.3.eb index 973a23b9d2..6cdd113ef0 100644 --- a/easybuild/easyconfigs/p/Parallel-ForkManager/Parallel-ForkManager-1.06-goolf-1.4.10-Perl-5.16.3.eb +++ b/easybuild/easyconfigs/p/Parallel-ForkManager/Parallel-ForkManager-1.06-goolf-1.4.10-Perl-5.16.3.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2013 The Cyprus Institute # Authors:: Andreas Panteli diff --git a/easybuild/easyconfigs/p/Paraver/Paraver-4.4.5-GCC-4.7.3.eb b/easybuild/easyconfigs/p/Paraver/Paraver-4.4.5-GCC-4.7.3.eb index aabbb0dc24..8a33b15619 100644 --- a/easybuild/easyconfigs/p/Paraver/Paraver-4.4.5-GCC-4.7.3.eb +++ b/easybuild/easyconfigs/p/Paraver/Paraver-4.4.5-GCC-4.7.3.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild # Copyright:: Copyright 2013 Juelich Supercomputing Centre, Germany # Authors:: Bernd Mohr # License:: New BSD diff --git a/easybuild/easyconfigs/p/Paraver/Paraver-4.5.6-foss-2015a.eb b/easybuild/easyconfigs/p/Paraver/Paraver-4.5.6-foss-2015a.eb index f5a5940d0d..6e4a28d4a2 100644 --- a/easybuild/easyconfigs/p/Paraver/Paraver-4.5.6-foss-2015a.eb +++ b/easybuild/easyconfigs/p/Paraver/Paraver-4.5.6-foss-2015a.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild # Copyright:: Copyright 2013 Juelich Supercomputing Centre, Germany # Authors:: Bernd Mohr # License:: New BSD diff --git a/easybuild/easyconfigs/p/PeakSeq/PeakSeq-1.3-goolf-1.4.10.eb b/easybuild/easyconfigs/p/PeakSeq/PeakSeq-1.3-goolf-1.4.10.eb index beddc1be80..cb8631f828 100644 --- a/easybuild/easyconfigs/p/PeakSeq/PeakSeq-1.3-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/PeakSeq/PeakSeq-1.3-goolf-1.4.10.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/p/PhyML/PhyML-20120412-goolf-1.4.10.eb b/easybuild/easyconfigs/p/PhyML/PhyML-20120412-goolf-1.4.10.eb index 2ee0e32243..dfae3001aa 100644 --- a/easybuild/easyconfigs/p/PhyML/PhyML-20120412-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/PhyML/PhyML-20120412-goolf-1.4.10.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/p/PhyML/PhyML-20131016-goolf-1.4.10devel.eb b/easybuild/easyconfigs/p/PhyML/PhyML-20131016-goolf-1.4.10devel.eb index 3c4e95c7ce..f0201e1312 100644 --- a/easybuild/easyconfigs/p/PhyML/PhyML-20131016-goolf-1.4.10devel.eb +++ b/easybuild/easyconfigs/p/PhyML/PhyML-20131016-goolf-1.4.10devel.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/p/Pindel/Pindel-0.2.5a7-goolf-1.4.10.eb b/easybuild/easyconfigs/p/Pindel/Pindel-0.2.5a7-goolf-1.4.10.eb index bca12c0034..a1bd0d68a7 100644 --- a/easybuild/easyconfigs/p/Pindel/Pindel-0.2.5a7-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/Pindel/Pindel-0.2.5a7-goolf-1.4.10.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/p/Pindel/Pindel-0.2.5b8-foss-2016b.eb b/easybuild/easyconfigs/p/Pindel/Pindel-0.2.5b8-foss-2016b.eb index 9f45199e95..7c9fc74d13 100644 --- a/easybuild/easyconfigs/p/Pindel/Pindel-0.2.5b8-foss-2016b.eb +++ b/easybuild/easyconfigs/p/Pindel/Pindel-0.2.5b8-foss-2016b.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/p/Platanus/Platanus-1.2.4-goolf-1.7.20.eb b/easybuild/easyconfigs/p/Platanus/Platanus-1.2.4-goolf-1.7.20.eb index fb465f5c89..f30e2624cc 100644 --- a/easybuild/easyconfigs/p/Platanus/Platanus-1.2.4-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/p/Platanus/Platanus-1.2.4-goolf-1.7.20.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # sciCORE - University of Basel # SIB Swiss Institute of Bioinformatics diff --git a/easybuild/easyconfigs/p/Pmw/Pmw-1.3.3-goolf-1.4.10-Python-2.7.5.eb b/easybuild/easyconfigs/p/Pmw/Pmw-1.3.3-goolf-1.4.10-Python-2.7.5.eb index c8749eca4a..105ca94d20 100644 --- a/easybuild/easyconfigs/p/Pmw/Pmw-1.3.3-goolf-1.4.10-Python-2.7.5.eb +++ b/easybuild/easyconfigs/p/Pmw/Pmw-1.3.3-goolf-1.4.10-Python-2.7.5.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Adam Mazur # Research IT # Biozentrum, University of Basel diff --git a/easybuild/easyconfigs/p/PnMPI/PnMPI-1.2.0-goolf-1.5.14.eb b/easybuild/easyconfigs/p/PnMPI/PnMPI-1.2.0-goolf-1.5.14.eb index 30ff748dc8..008ed299aa 100644 --- a/easybuild/easyconfigs/p/PnMPI/PnMPI-1.2.0-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/p/PnMPI/PnMPI-1.2.0-goolf-1.5.14.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild # Copyright:: Copyright 2013 Juelich Supercomputing Centre, Germany # Authors:: Bernd Mohr # License:: New BSD diff --git a/easybuild/easyconfigs/p/PyQt/PyQt-4.11.3-goolf-1.5.14-Python-2.7.9.eb b/easybuild/easyconfigs/p/PyQt/PyQt-4.11.3-goolf-1.5.14-Python-2.7.9.eb index 51aeabb7ca..36bbf7c9f6 100644 --- a/easybuild/easyconfigs/p/PyQt/PyQt-4.11.3-goolf-1.5.14-Python-2.7.9.eb +++ b/easybuild/easyconfigs/p/PyQt/PyQt-4.11.3-goolf-1.5.14-Python-2.7.9.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Bart Verleye # Center for eResearch, Auckland easyblock = 'ConfigureMakePythonPackage' diff --git a/easybuild/easyconfigs/p/PyQt/PyQt-4.11.3-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/p/PyQt/PyQt-4.11.3-intel-2015a-Python-2.7.9.eb index 328b12d5a9..af29a1b6dd 100644 --- a/easybuild/easyconfigs/p/PyQt/PyQt-4.11.3-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/p/PyQt/PyQt-4.11.3-intel-2015a-Python-2.7.9.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Bart Verleye # Center for eResearch, Auckland easyblock = 'ConfigureMakePythonPackage' diff --git a/easybuild/easyconfigs/p/PyQt/PyQt-4.11.4-foss-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/p/PyQt/PyQt-4.11.4-foss-2015a-Python-2.7.9.eb index 992e13df88..0bee14ad36 100644 --- a/easybuild/easyconfigs/p/PyQt/PyQt-4.11.4-foss-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/p/PyQt/PyQt-4.11.4-foss-2015a-Python-2.7.9.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Bart Verleye # Center for eResearch, Auckland easyblock = 'ConfigureMakePythonPackage' diff --git a/easybuild/easyconfigs/p/PyQt/PyQt-4.11.4-intel-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/p/PyQt/PyQt-4.11.4-intel-2014b-Python-2.7.8.eb index 0d39a830f0..a32f597303 100644 --- a/easybuild/easyconfigs/p/PyQt/PyQt-4.11.4-intel-2014b-Python-2.7.8.eb +++ b/easybuild/easyconfigs/p/PyQt/PyQt-4.11.4-intel-2014b-Python-2.7.8.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Bart Verleye # Center for eResearch, Auckland easyblock = 'ConfigureMakePythonPackage' diff --git a/easybuild/easyconfigs/p/PyQt/PyQt-4.11.4-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/p/PyQt/PyQt-4.11.4-intel-2015a-Python-2.7.9.eb index f40c0f4c4b..aa50b0c60d 100644 --- a/easybuild/easyconfigs/p/PyQt/PyQt-4.11.4-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/p/PyQt/PyQt-4.11.4-intel-2015a-Python-2.7.9.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Bart Verleye # Center for eResearch, Auckland easyblock = 'ConfigureMakePythonPackage' diff --git a/easybuild/easyconfigs/p/PyQt/PyQt-4.11.4-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/PyQt/PyQt-4.11.4-intel-2016a-Python-2.7.11.eb index a3811f7d21..afceaf85fc 100644 --- a/easybuild/easyconfigs/p/PyQt/PyQt-4.11.4-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/PyQt/PyQt-4.11.4-intel-2016a-Python-2.7.11.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Bart Verleye # Center for eResearch, Auckland easyblock = 'ConfigureMakePythonPackage' diff --git a/easybuild/easyconfigs/p/PyQt/PyQt-4.11.4-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/PyQt/PyQt-4.11.4-intel-2016b-Python-2.7.12.eb index b495a5ba45..a3cbafa68a 100644 --- a/easybuild/easyconfigs/p/PyQt/PyQt-4.11.4-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/p/PyQt/PyQt-4.11.4-intel-2016b-Python-2.7.12.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Bart Verleye # Center for eResearch, Auckland easyblock = 'ConfigureMakePythonPackage' diff --git a/easybuild/easyconfigs/p/PyQt/PyQt-4.12-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/PyQt/PyQt-4.12-foss-2016b-Python-2.7.12.eb index f8e50daad2..52a8b8d0db 100644 --- a/easybuild/easyconfigs/p/PyQt/PyQt-4.12-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/p/PyQt/PyQt-4.12-foss-2016b-Python-2.7.12.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Bart Verleye # Center for eResearch, Auckland easyblock = 'ConfigureMakePythonPackage' diff --git a/easybuild/easyconfigs/p/PyQt/PyQt-4.12-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/PyQt/PyQt-4.12-intel-2016b-Python-2.7.12.eb index 8afd4b1225..95b12ce511 100644 --- a/easybuild/easyconfigs/p/PyQt/PyQt-4.12-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/p/PyQt/PyQt-4.12-intel-2016b-Python-2.7.12.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Bart Verleye # Center for eResearch, Auckland easyblock = 'ConfigureMakePythonPackage' diff --git a/easybuild/easyconfigs/p/PyQt/PyQt-4.12-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/p/PyQt/PyQt-4.12-intel-2017a-Python-2.7.13.eb index d5c9f991a7..12cb80c0d5 100644 --- a/easybuild/easyconfigs/p/PyQt/PyQt-4.12-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/p/PyQt/PyQt-4.12-intel-2017a-Python-2.7.13.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Bart Verleye # Center for eResearch, Auckland easyblock = 'ConfigureMakePythonPackage' diff --git a/easybuild/easyconfigs/p/Pysam/Pysam-0.10.0-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/Pysam/Pysam-0.10.0-intel-2016b-Python-2.7.12.eb index 624f14ed18..ef54c7fce2 100644 --- a/easybuild/easyconfigs/p/Pysam/Pysam-0.10.0-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/p/Pysam/Pysam-0.10.0-intel-2016b-Python-2.7.12.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # sciCORE - University of Basel # SIB Swiss Institute of Bioinformatics diff --git a/easybuild/easyconfigs/p/Pysam/Pysam-0.9.0-goolf-1.7.20-Python-2.7.11.eb b/easybuild/easyconfigs/p/Pysam/Pysam-0.9.0-goolf-1.7.20-Python-2.7.11.eb index 160f3b3a15..829a039d16 100644 --- a/easybuild/easyconfigs/p/Pysam/Pysam-0.9.0-goolf-1.7.20-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/Pysam/Pysam-0.9.0-goolf-1.7.20-Python-2.7.11.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # sciCORE - University of Basel # SIB Swiss Institute of Bioinformatics diff --git a/easybuild/easyconfigs/p/Pysam/Pysam-0.9.1.4-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/Pysam/Pysam-0.9.1.4-foss-2016b-Python-2.7.12.eb index e283bd562a..93e0a90956 100644 --- a/easybuild/easyconfigs/p/Pysam/Pysam-0.9.1.4-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/p/Pysam/Pysam-0.9.1.4-foss-2016b-Python-2.7.12.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # sciCORE - University of Basel # SIB Swiss Institute of Bioinformatics diff --git a/easybuild/easyconfigs/p/pBWA/pBWA-0.5.9_1.21009-goolf-1.4.10.eb b/easybuild/easyconfigs/p/pBWA/pBWA-0.5.9_1.21009-goolf-1.4.10.eb index f8e2358b4a..4538b1fdca 100644 --- a/easybuild/easyconfigs/p/pBWA/pBWA-0.5.9_1.21009-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/pBWA/pBWA-0.5.9_1.21009-goolf-1.4.10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2013-2014 Cyprus Institute # Authors:: Thekla Loizou diff --git a/easybuild/easyconfigs/p/parallel/parallel-20130122-goolf-1.4.10.eb b/easybuild/easyconfigs/p/parallel/parallel-20130122-goolf-1.4.10.eb index 3810b2de94..3fc50c7310 100644 --- a/easybuild/easyconfigs/p/parallel/parallel-20130122-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/parallel/parallel-20130122-goolf-1.4.10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/p/parallel/parallel-20130122-ictce-5.3.0.eb b/easybuild/easyconfigs/p/parallel/parallel-20130122-ictce-5.3.0.eb index fc4fbe41bc..62379f0f87 100644 --- a/easybuild/easyconfigs/p/parallel/parallel-20130122-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/p/parallel/parallel-20130122-ictce-5.3.0.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/p/perl-app-cpanminus/perl-app-cpanminus-1.7039.eb b/easybuild/easyconfigs/p/perl-app-cpanminus/perl-app-cpanminus-1.7039.eb index cc1d205d40..2b1fc2a612 100644 --- a/easybuild/easyconfigs/p/perl-app-cpanminus/perl-app-cpanminus-1.7039.eb +++ b/easybuild/easyconfigs/p/perl-app-cpanminus/perl-app-cpanminus-1.7039.eb @@ -1,5 +1,5 @@ ## -# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2013-2015 Juelich Supercomputing Centre, Germany # Authors:: Bernd Mohr diff --git a/easybuild/easyconfigs/p/picard/picard-2.1.0.eb b/easybuild/easyconfigs/p/picard/picard-2.1.0.eb index 702287f8f6..9cc6b0c56a 100644 --- a/easybuild/easyconfigs/p/picard/picard-2.1.0.eb +++ b/easybuild/easyconfigs/p/picard/picard-2.1.0.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Adam Huffman # The Francis Crick Institute diff --git a/easybuild/easyconfigs/p/pigz/pigz-2.3.1-goolf-1.4.10.eb b/easybuild/easyconfigs/p/pigz/pigz-2.3.1-goolf-1.4.10.eb index 9f34b89624..513a7c2b79 100644 --- a/easybuild/easyconfigs/p/pigz/pigz-2.3.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/pigz/pigz-2.3.1-goolf-1.4.10.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/p/pigz/pigz-2.3.1-ictce-6.2.5.eb b/easybuild/easyconfigs/p/pigz/pigz-2.3.1-ictce-6.2.5.eb index e3e7f189b1..594f9b1a27 100644 --- a/easybuild/easyconfigs/p/pigz/pigz-2.3.1-ictce-6.2.5.eb +++ b/easybuild/easyconfigs/p/pigz/pigz-2.3.1-ictce-6.2.5.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/p/pigz/pigz-2.3.3-foss-2015b.eb b/easybuild/easyconfigs/p/pigz/pigz-2.3.3-foss-2015b.eb index a50f50774e..6bf9fd86a2 100644 --- a/easybuild/easyconfigs/p/pigz/pigz-2.3.3-foss-2015b.eb +++ b/easybuild/easyconfigs/p/pigz/pigz-2.3.3-foss-2015b.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/p/pigz/pigz-2.3.3-foss-2016b.eb b/easybuild/easyconfigs/p/pigz/pigz-2.3.3-foss-2016b.eb index 8790ec7dca..0a2b15f59b 100755 --- a/easybuild/easyconfigs/p/pigz/pigz-2.3.3-foss-2016b.eb +++ b/easybuild/easyconfigs/p/pigz/pigz-2.3.3-foss-2016b.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/q/QIIME/QIIME-1.9.1.eb b/easybuild/easyconfigs/q/QIIME/QIIME-1.9.1.eb index 4b9209b380..b1a1d1feb4 100644 --- a/easybuild/easyconfigs/q/QIIME/QIIME-1.9.1.eb +++ b/easybuild/easyconfigs/q/QIIME/QIIME-1.9.1.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # sciCORE - University of Basel # SIB Swiss Institute of Bioinformatics diff --git a/easybuild/easyconfigs/q/QuadProg++/QuadProg++-1.2.1-goolf-1.4.10.eb b/easybuild/easyconfigs/q/QuadProg++/QuadProg++-1.2.1-goolf-1.4.10.eb index 16a64ab3be..0a472e9d66 100644 --- a/easybuild/easyconfigs/q/QuadProg++/QuadProg++-1.2.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/q/QuadProg++/QuadProg++-1.2.1-goolf-1.4.10.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/q/QuadProg++/QuadProg++-1.2.1-ictce-6.2.5.eb b/easybuild/easyconfigs/q/QuadProg++/QuadProg++-1.2.1-ictce-6.2.5.eb index 8514e49d95..d677851e09 100644 --- a/easybuild/easyconfigs/q/QuadProg++/QuadProg++-1.2.1-ictce-6.2.5.eb +++ b/easybuild/easyconfigs/q/QuadProg++/QuadProg++-1.2.1-ictce-6.2.5.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/q/Quip/Quip-1.1.8-GCC-4.8.2.eb b/easybuild/easyconfigs/q/Quip/Quip-1.1.8-GCC-4.8.2.eb index e4973548b5..91fe68d23d 100644 --- a/easybuild/easyconfigs/q/Quip/Quip-1.1.8-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/q/Quip/Quip-1.1.8-GCC-4.8.2.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2015 NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/q/qtop/qtop-53-1.eb b/easybuild/easyconfigs/q/qtop/qtop-53-1.eb index 1e12105e71..5c02ce39e5 100644 --- a/easybuild/easyconfigs/q/qtop/qtop-53-1.eb +++ b/easybuild/easyconfigs/q/qtop/qtop-53-1.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/r/RAxML/RAxML-8.1.1-goolf-1.4.10-mpi-avx.eb b/easybuild/easyconfigs/r/RAxML/RAxML-8.1.1-goolf-1.4.10-mpi-avx.eb index d7d22ad5ae..7f1a2331ac 100644 --- a/easybuild/easyconfigs/r/RAxML/RAxML-8.1.1-goolf-1.4.10-mpi-avx.eb +++ b/easybuild/easyconfigs/r/RAxML/RAxML-8.1.1-goolf-1.4.10-mpi-avx.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/r/RAxML/RAxML-8.1.1-goolf-1.4.10-mpi-sse3.eb b/easybuild/easyconfigs/r/RAxML/RAxML-8.1.1-goolf-1.4.10-mpi-sse3.eb index dd4462802c..80e5bb60d4 100644 --- a/easybuild/easyconfigs/r/RAxML/RAxML-8.1.1-goolf-1.4.10-mpi-sse3.eb +++ b/easybuild/easyconfigs/r/RAxML/RAxML-8.1.1-goolf-1.4.10-mpi-sse3.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/r/RAxML/RAxML-8.1.1-goolf-1.4.10-mt-avx.eb b/easybuild/easyconfigs/r/RAxML/RAxML-8.1.1-goolf-1.4.10-mt-avx.eb index d55bca8237..7542264fa7 100644 --- a/easybuild/easyconfigs/r/RAxML/RAxML-8.1.1-goolf-1.4.10-mt-avx.eb +++ b/easybuild/easyconfigs/r/RAxML/RAxML-8.1.1-goolf-1.4.10-mt-avx.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/r/RAxML/RAxML-8.1.1-goolf-1.4.10-mt-sse3.eb b/easybuild/easyconfigs/r/RAxML/RAxML-8.1.1-goolf-1.4.10-mt-sse3.eb index 859f2adbb7..eac6deabda 100644 --- a/easybuild/easyconfigs/r/RAxML/RAxML-8.1.1-goolf-1.4.10-mt-sse3.eb +++ b/easybuild/easyconfigs/r/RAxML/RAxML-8.1.1-goolf-1.4.10-mt-sse3.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/r/RCS/RCS-5.7-goolf-1.4.10.eb b/easybuild/easyconfigs/r/RCS/RCS-5.7-goolf-1.4.10.eb index 1fd62ac72d..525c7dcda5 100644 --- a/easybuild/easyconfigs/r/RCS/RCS-5.7-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/r/RCS/RCS-5.7-goolf-1.4.10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/r/RCS/RCS-5.7-ictce-5.3.0.eb b/easybuild/easyconfigs/r/RCS/RCS-5.7-ictce-5.3.0.eb index ff4020095b..60eaccfc47 100644 --- a/easybuild/easyconfigs/r/RCS/RCS-5.7-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/r/RCS/RCS-5.7-ictce-5.3.0.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/r/RNAz/RNAz-2.1-foss-2016b.eb b/easybuild/easyconfigs/r/RNAz/RNAz-2.1-foss-2016b.eb index 4ff67a0efb..642eea5ef8 100644 --- a/easybuild/easyconfigs/r/RNAz/RNAz-2.1-foss-2016b.eb +++ b/easybuild/easyconfigs/r/RNAz/RNAz-2.1-foss-2016b.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild easyblock = 'ConfigureMake' diff --git a/easybuild/easyconfigs/r/RNAz/RNAz-2.1-goolf-1.4.10.eb b/easybuild/easyconfigs/r/RNAz/RNAz-2.1-goolf-1.4.10.eb index 2155ac1e76..83c1690c1c 100644 --- a/easybuild/easyconfigs/r/RNAz/RNAz-2.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/r/RNAz/RNAz-2.1-goolf-1.4.10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Cedric Laczny , Fotis Georgatos diff --git a/easybuild/easyconfigs/r/RNAz/RNAz-2.1-ictce-5.3.0.eb b/easybuild/easyconfigs/r/RNAz/RNAz-2.1-ictce-5.3.0.eb index 03f3c66bab..23460531f8 100644 --- a/easybuild/easyconfigs/r/RNAz/RNAz-2.1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/r/RNAz/RNAz-2.1-ictce-5.3.0.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Cedric Laczny , Fotis Georgatos diff --git a/easybuild/easyconfigs/r/RSEQtools/RSEQtools-0.6-goolf-1.4.10.eb b/easybuild/easyconfigs/r/RSEQtools/RSEQtools-0.6-goolf-1.4.10.eb index d0bbd7da76..2500753cc5 100644 --- a/easybuild/easyconfigs/r/RSEQtools/RSEQtools-0.6-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/r/RSEQtools/RSEQtools-0.6-goolf-1.4.10.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/r/RSeQC/RSeQC-2.6.3-foss-2015b-Python-2.7.10-R-3.2.3.eb b/easybuild/easyconfigs/r/RSeQC/RSeQC-2.6.3-foss-2015b-Python-2.7.10-R-3.2.3.eb index d3a31d723c..2d60c20928 100644 --- a/easybuild/easyconfigs/r/RSeQC/RSeQC-2.6.3-foss-2015b-Python-2.7.10-R-3.2.3.eb +++ b/easybuild/easyconfigs/r/RSeQC/RSeQC-2.6.3-foss-2015b-Python-2.7.10-R-3.2.3.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Adam Huffman # The Francis Crick Institute diff --git a/easybuild/easyconfigs/r/RSeQC/RSeQC-2.6.4-foss-2016b-Python-2.7.12-R-3.3.1.eb b/easybuild/easyconfigs/r/RSeQC/RSeQC-2.6.4-foss-2016b-Python-2.7.12-R-3.3.1.eb index 8df3ba88af..0e7c072381 100644 --- a/easybuild/easyconfigs/r/RSeQC/RSeQC-2.6.4-foss-2016b-Python-2.7.12-R-3.3.1.eb +++ b/easybuild/easyconfigs/r/RSeQC/RSeQC-2.6.4-foss-2016b-Python-2.7.12-R-3.3.1.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Adam Huffman # The Francis Crick Institute diff --git a/easybuild/easyconfigs/r/Reads2snp/Reads2snp-2.0.eb b/easybuild/easyconfigs/r/Reads2snp/Reads2snp-2.0.eb index 462568a58d..99b121a0e8 100644 --- a/easybuild/easyconfigs/r/Reads2snp/Reads2snp-2.0.eb +++ b/easybuild/easyconfigs/r/Reads2snp/Reads2snp-2.0.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # sciCORE - University of Basel # SIB Swiss Institute of Bioinformatics diff --git a/easybuild/easyconfigs/r/rCUDA/rCUDA-4.0.1_linux_64_Ubuntu10.04.eb b/easybuild/easyconfigs/r/rCUDA/rCUDA-4.0.1_linux_64_Ubuntu10.04.eb index 764e0a5654..a2dd96fcb9 100644 --- a/easybuild/easyconfigs/r/rCUDA/rCUDA-4.0.1_linux_64_Ubuntu10.04.eb +++ b/easybuild/easyconfigs/r/rCUDA/rCUDA-4.0.1_linux_64_Ubuntu10.04.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/r/rCUDA/rCUDA-5.0_linux_64_scientificLinux6.eb b/easybuild/easyconfigs/r/rCUDA/rCUDA-5.0_linux_64_scientificLinux6.eb index 67667d2f43..0e88376e1b 100644 --- a/easybuild/easyconfigs/r/rCUDA/rCUDA-5.0_linux_64_scientificLinux6.eb +++ b/easybuild/easyconfigs/r/rCUDA/rCUDA-5.0_linux_64_scientificLinux6.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/r/rSeq/rSeq-0.2.0-goolf-1.4.10.eb b/easybuild/easyconfigs/r/rSeq/rSeq-0.2.0-goolf-1.4.10.eb index 515ad4d74a..de39a6a664 100644 --- a/easybuild/easyconfigs/r/rSeq/rSeq-0.2.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/r/rSeq/rSeq-0.2.0-goolf-1.4.10.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/r/rainbow/rainbow-2.0.4-goolf-1.4.10.eb b/easybuild/easyconfigs/r/rainbow/rainbow-2.0.4-goolf-1.4.10.eb index ebe8bfa5d5..cbe0f89b48 100644 --- a/easybuild/easyconfigs/r/rainbow/rainbow-2.0.4-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/r/rainbow/rainbow-2.0.4-goolf-1.4.10.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # sciCORE - University of Basel # SIB Swiss Institute of Bioinformatics diff --git a/easybuild/easyconfigs/r/rpmrebuild/rpmrebuild-2.11.eb b/easybuild/easyconfigs/r/rpmrebuild/rpmrebuild-2.11.eb index 5b2154b146..7752f26f31 100644 --- a/easybuild/easyconfigs/r/rpmrebuild/rpmrebuild-2.11.eb +++ b/easybuild/easyconfigs/r/rpmrebuild/rpmrebuild-2.11.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2016 Forschungszentrum Juelich GmbH # Authors:: Damian Alvarez diff --git a/easybuild/easyconfigs/s/SAGE/SAGE-6.3.eb b/easybuild/easyconfigs/s/SAGE/SAGE-6.3.eb index 3c539b01d1..e6e619d7ae 100644 --- a/easybuild/easyconfigs/s/SAGE/SAGE-6.3.eb +++ b/easybuild/easyconfigs/s/SAGE/SAGE-6.3.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Ravi Tripathi # Email: ravi89@uab.edu diff --git a/easybuild/easyconfigs/s/SAGE/SAGE-6.4.eb b/easybuild/easyconfigs/s/SAGE/SAGE-6.4.eb index f518617128..44c08dffd3 100644 --- a/easybuild/easyconfigs/s/SAGE/SAGE-6.4.eb +++ b/easybuild/easyconfigs/s/SAGE/SAGE-6.4.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Ravi Tripathi # Email: ravi89@uab.edu diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.18-goolf-1.4.10.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.18-goolf-1.4.10.eb index 073affc93b..41c9a41b52 100644 --- a/easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.18-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.18-goolf-1.4.10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Cedric Laczny , Fotis Georgatos diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.18-ictce-5.3.0.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.18-ictce-5.3.0.eb index 5b8825becb..cb95f09db1 100644 --- a/easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.18-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.18-ictce-5.3.0.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Cedric Laczny , Fotis Georgatos diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.19-goolf-1.4.10.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.19-goolf-1.4.10.eb index e632ad1cd5..c3c62371e3 100644 --- a/easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.19-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.19-goolf-1.4.10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Cedric Laczny , Fotis Georgatos diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.19-ictce-5.5.0.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.19-ictce-5.5.0.eb index d1a3148379..4feaa86295 100644 --- a/easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.19-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.19-ictce-5.5.0.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Cedric Laczny , Fotis Georgatos diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.1-foss-2014b.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.1-foss-2014b.eb index 37118ac1e1..fe530c9987 100644 --- a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.1-foss-2014b.eb +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.1-foss-2014b.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Robert Schmidt , Cedric Laczny , Fotis Georgatos diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.1-goolf-1.4.10.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.1-goolf-1.4.10.eb index ffeec869d8..6d55792df5 100644 --- a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.1-goolf-1.4.10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Cedric Laczny , Fotis Georgatos diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.1-intel-2014b.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.1-intel-2014b.eb index f6766acbd2..143b4f0e11 100644 --- a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.1-intel-2014b.eb +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.1-intel-2014b.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Cedric Laczny , Fotis Georgatos diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.1-intel-2015a.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.1-intel-2015a.eb index 805874583a..ec9e8200a5 100644 --- a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.1-intel-2015a.eb +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.1-intel-2015a.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Cedric Laczny , Fotis Georgatos diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.2-foss-2015a-HTSlib-1.2.1.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.2-foss-2015a-HTSlib-1.2.1.eb index 3835083700..e36e28d9bb 100644 --- a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.2-foss-2015a-HTSlib-1.2.1.eb +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.2-foss-2015a-HTSlib-1.2.1.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Robert Schmidt , Cedric Laczny , Fotis Georgatos diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.2-foss-2015a.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.2-foss-2015a.eb index be9360b7e5..a99016b990 100644 --- a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.2-foss-2015a.eb +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.2-foss-2015a.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Robert Schmidt , Cedric Laczny , Fotis Georgatos diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.2-foss-2015b.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.2-foss-2015b.eb index 598ba6e51e..e1dd81f160 100644 --- a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.2-foss-2015b.eb +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.2-foss-2015b.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Robert Schmidt , Cedric Laczny , Fotis Georgatos diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.2-goolf-1.4.10.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.2-goolf-1.4.10.eb index 97a147d8ec..b93365bdd7 100644 --- a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.2-goolf-1.4.10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Robert Schmidt , Cedric Laczny , Fotis Georgatos diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.2-goolf-1.7.20.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.2-goolf-1.7.20.eb index e3ff7301d8..ce7c10f8f2 100644 --- a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.2-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.2-goolf-1.7.20.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Robert Schmidt , Cedric Laczny , Fotis Georgatos diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.2-intel-2015a-HTSlib-1.2.1.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.2-intel-2015a-HTSlib-1.2.1.eb index 2896876819..09d30b179c 100644 --- a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.2-intel-2015a-HTSlib-1.2.1.eb +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.2-intel-2015a-HTSlib-1.2.1.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Robert Schmidt , Cedric Laczny , Fotis Georgatos diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.2-intel-2015b-HTSlib-1.2.1.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.2-intel-2015b-HTSlib-1.2.1.eb index 739c632246..303f3a583d 100644 --- a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.2-intel-2015b-HTSlib-1.2.1.eb +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.2-intel-2015b-HTSlib-1.2.1.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Robert Schmidt , Cedric Laczny , Fotis Georgatos diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3-foss-2015b.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3-foss-2015b.eb index 4ff251eb73..63b113948c 100644 --- a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3-foss-2015b.eb +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3-foss-2015b.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Robert Schmidt , Cedric Laczny , Fotis Georgatos diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3-foss-2016a.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3-foss-2016a.eb index 96d3b95f0f..40b271c59e 100644 --- a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3-foss-2016a.eb +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3-foss-2016a.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Robert Schmidt , Cedric Laczny , Fotis Georgatos diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3-intel-2016a.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3-intel-2016a.eb index d869d21007..20c0daa2e9 100644 --- a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3-intel-2016a.eb +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3-intel-2016a.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Robert Schmidt , Cedric Laczny , Fotis Georgatos diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1-foss-2015b.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1-foss-2015b.eb index a7026c36d0..af67f0ad29 100644 --- a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1-foss-2015b.eb +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1-foss-2015b.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Robert Schmidt , Cedric Laczny , Fotis Georgatos diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1-foss-2016a.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1-foss-2016a.eb index 7fa65122da..1fcd04d5c5 100644 --- a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1-foss-2016a.eb +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1-foss-2016a.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Robert Schmidt , Cedric Laczny , Fotis Georgatos diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1-intel-2016a.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1-intel-2016a.eb index 91ca187c34..8a9d0ec272 100644 --- a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1-intel-2016a.eb +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1-intel-2016a.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Robert Schmidt , Cedric Laczny , Fotis Georgatos diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1-intel-2016b-HTSlib-1.3.2.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1-intel-2016b-HTSlib-1.3.2.eb index cf342e2224..aaae3bc65c 100644 --- a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1-intel-2016b-HTSlib-1.3.2.eb +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1-intel-2016b-HTSlib-1.3.2.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Robert Schmidt , Cedric Laczny , Fotis Georgatos diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1-intel-2016b.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1-intel-2016b.eb index ad73efb9d9..1d3b8759e6 100644 --- a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1-intel-2016b.eb +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1-intel-2016b.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Robert Schmidt , Cedric Laczny , Fotis Georgatos diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-foss-2016b.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-foss-2016b.eb index 340f9547b8..becb1e33df 100644 --- a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-foss-2016b.eb +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-foss-2016b.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Robert Schmidt , Cedric Laczny , Fotis Georgatos diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-goolf-1.4.10.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-goolf-1.4.10.eb index f620000661..a590f0e5c5 100644 --- a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-goolf-1.4.10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Robert Schmidt , Cedric Laczny , Fotis Georgatos diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-intel-2016b.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-intel-2016b.eb index 3167310f24..5fc351ad68 100644 --- a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-intel-2016b.eb +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-intel-2016b.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Robert Schmidt , Cedric Laczny , Fotis Georgatos diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-intel-2017a.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-intel-2017a.eb index 86a737bc61..a9362a745f 100644 --- a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-intel-2017a.eb +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-intel-2017a.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Robert Schmidt , Cedric Laczny , Fotis Georgatos diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4.1-intel-2017a.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4.1-intel-2017a.eb index cd48ea8cde..1cb0955d19 100644 --- a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4.1-intel-2017a.eb +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4.1-intel-2017a.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Robert Schmidt , Cedric Laczny , Fotis Georgatos diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.5-intel-2017a.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.5-intel-2017a.eb index 07e6c5020c..ae85c24427 100755 --- a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.5-intel-2017a.eb +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.5-intel-2017a.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Robert Schmidt , Cedric Laczny , Fotis Georgatos diff --git a/easybuild/easyconfigs/s/SCALCE/SCALCE-2.7-GCC-4.8.2.eb b/easybuild/easyconfigs/s/SCALCE/SCALCE-2.7-GCC-4.8.2.eb index d732b448eb..ec8b73d725 100644 --- a/easybuild/easyconfigs/s/SCALCE/SCALCE-2.7-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/s/SCALCE/SCALCE-2.7-GCC-4.8.2.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2015 NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/s/SCANMS/SCANMS-2.02-goolf-1.4.10-Perl-5.16.3.eb b/easybuild/easyconfigs/s/SCANMS/SCANMS-2.02-goolf-1.4.10-Perl-5.16.3.eb index 88fe827b03..607082a502 100644 --- a/easybuild/easyconfigs/s/SCANMS/SCANMS-2.02-goolf-1.4.10-Perl-5.16.3.eb +++ b/easybuild/easyconfigs/s/SCANMS/SCANMS-2.02-goolf-1.4.10-Perl-5.16.3.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/s/SDCC/SDCC-3.3.0.eb b/easybuild/easyconfigs/s/SDCC/SDCC-3.3.0.eb index cd91fac4e4..1d6583cd4c 100644 --- a/easybuild/easyconfigs/s/SDCC/SDCC-3.3.0.eb +++ b/easybuild/easyconfigs/s/SDCC/SDCC-3.3.0.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/s/SDL2/SDL2-2.0.4-intel-2016b.eb b/easybuild/easyconfigs/s/SDL2/SDL2-2.0.4-intel-2016b.eb index 9d089f04eb..e43bffbbb4 100644 --- a/easybuild/easyconfigs/s/SDL2/SDL2-2.0.4-intel-2016b.eb +++ b/easybuild/easyconfigs/s/SDL2/SDL2-2.0.4-intel-2016b.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/s/SHAPEIT/SHAPEIT-2.r837.GLIBCv2.12.eb b/easybuild/easyconfigs/s/SHAPEIT/SHAPEIT-2.r837.GLIBCv2.12.eb index f2424bbea4..8b988dc0fd 100644 --- a/easybuild/easyconfigs/s/SHAPEIT/SHAPEIT-2.r837.GLIBCv2.12.eb +++ b/easybuild/easyconfigs/s/SHAPEIT/SHAPEIT-2.r837.GLIBCv2.12.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Ravi Tripathi # Email: ravi89@uab.edu diff --git a/easybuild/easyconfigs/s/SIBELia/SIBELia-3.0.4-goolf-1.4.10.eb b/easybuild/easyconfigs/s/SIBELia/SIBELia-3.0.4-goolf-1.4.10.eb index 5c52477972..08978cbb4b 100644 --- a/easybuild/easyconfigs/s/SIBELia/SIBELia-3.0.4-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/s/SIBELia/SIBELia-3.0.4-goolf-1.4.10.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/s/SIONlib/SIONlib-1.6.1-foss-2016a-tools.eb b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.6.1-foss-2016a-tools.eb index e773779617..89441506e0 100644 --- a/easybuild/easyconfigs/s/SIONlib/SIONlib-1.6.1-foss-2016a-tools.eb +++ b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.6.1-foss-2016a-tools.eb @@ -1,5 +1,5 @@ ## -# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2016 Juelich Supercomputing Centre, Germany # Authors:: Markus Geimer diff --git a/easybuild/easyconfigs/s/SIONlib/SIONlib-1.6.1-foss-2016a.eb b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.6.1-foss-2016a.eb index a093e042cb..ca3d9eb8ab 100644 --- a/easybuild/easyconfigs/s/SIONlib/SIONlib-1.6.1-foss-2016a.eb +++ b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.6.1-foss-2016a.eb @@ -1,5 +1,5 @@ ## -# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2016 Juelich Supercomputing Centre, Germany # Authors:: Markus Geimer diff --git a/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.1-foss-2017a-tools.eb b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.1-foss-2017a-tools.eb index 1c00d4b38b..d9d11099a3 100644 --- a/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.1-foss-2017a-tools.eb +++ b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.1-foss-2017a-tools.eb @@ -1,5 +1,5 @@ ## -# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2016 Juelich Supercomputing Centre, Germany # Authors:: Markus Geimer diff --git a/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.1-foss-2017a.eb b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.1-foss-2017a.eb index 8dd41bb2de..37b3f1f4e7 100644 --- a/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.1-foss-2017a.eb +++ b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.1-foss-2017a.eb @@ -1,5 +1,5 @@ ## -# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2016 Juelich Supercomputing Centre, Germany # Authors:: Markus Geimer diff --git a/easybuild/easyconfigs/s/SIP/SIP-4.16.4-goolf-1.5.14-Python-2.7.9.eb b/easybuild/easyconfigs/s/SIP/SIP-4.16.4-goolf-1.5.14-Python-2.7.9.eb index 49346a9d1c..9053298580 100644 --- a/easybuild/easyconfigs/s/SIP/SIP-4.16.4-goolf-1.5.14-Python-2.7.9.eb +++ b/easybuild/easyconfigs/s/SIP/SIP-4.16.4-goolf-1.5.14-Python-2.7.9.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Bart Verleye # Center for eResearch, Auckland easyblock = 'ConfigureMakePythonPackage' diff --git a/easybuild/easyconfigs/s/SIP/SIP-4.16.4-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/s/SIP/SIP-4.16.4-intel-2015a-Python-2.7.9.eb index e61810f5fd..c121f5bccb 100644 --- a/easybuild/easyconfigs/s/SIP/SIP-4.16.4-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/s/SIP/SIP-4.16.4-intel-2015a-Python-2.7.9.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Bart Verleye # Center for eResearch, Auckland easyblock = 'ConfigureMakePythonPackage' diff --git a/easybuild/easyconfigs/s/SIP/SIP-4.16.8-foss-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/s/SIP/SIP-4.16.8-foss-2015a-Python-2.7.9.eb index eed3ec9cee..472bc669ce 100644 --- a/easybuild/easyconfigs/s/SIP/SIP-4.16.8-foss-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/s/SIP/SIP-4.16.8-foss-2015a-Python-2.7.9.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Bart Verleye # Center for eResearch, Auckland easyblock = 'ConfigureMakePythonPackage' diff --git a/easybuild/easyconfigs/s/SIP/SIP-4.16.8-intel-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/s/SIP/SIP-4.16.8-intel-2014b-Python-2.7.8.eb index 517317038b..4370af06f2 100644 --- a/easybuild/easyconfigs/s/SIP/SIP-4.16.8-intel-2014b-Python-2.7.8.eb +++ b/easybuild/easyconfigs/s/SIP/SIP-4.16.8-intel-2014b-Python-2.7.8.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Bart Verleye # Center for eResearch, Auckland easyblock = 'ConfigureMakePythonPackage' diff --git a/easybuild/easyconfigs/s/SIP/SIP-4.16.8-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/s/SIP/SIP-4.16.8-intel-2015a-Python-2.7.9.eb index b2e1479cba..fc5e6d4e1f 100644 --- a/easybuild/easyconfigs/s/SIP/SIP-4.16.8-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/s/SIP/SIP-4.16.8-intel-2015a-Python-2.7.9.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Bart Verleye # Center for eResearch, Auckland easyblock = 'ConfigureMakePythonPackage' diff --git a/easybuild/easyconfigs/s/SIP/SIP-4.18-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/s/SIP/SIP-4.18-foss-2016a-Python-2.7.11.eb index 0ac8c1861d..8d523f3226 100644 --- a/easybuild/easyconfigs/s/SIP/SIP-4.18-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/s/SIP/SIP-4.18-foss-2016a-Python-2.7.11.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Bart Verleye # Center for eResearch, Auckland easyblock = 'ConfigureMakePythonPackage' diff --git a/easybuild/easyconfigs/s/SIP/SIP-4.18-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/s/SIP/SIP-4.18-intel-2016a-Python-2.7.11.eb index b3dda16325..09c013815d 100644 --- a/easybuild/easyconfigs/s/SIP/SIP-4.18-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/s/SIP/SIP-4.18-intel-2016a-Python-2.7.11.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Bart Verleye # Center for eResearch, Auckland easyblock = 'ConfigureMakePythonPackage' diff --git a/easybuild/easyconfigs/s/SIP/SIP-4.18.1-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/s/SIP/SIP-4.18.1-foss-2016a-Python-2.7.11.eb index dbc48b8044..a247773edd 100644 --- a/easybuild/easyconfigs/s/SIP/SIP-4.18.1-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/s/SIP/SIP-4.18.1-foss-2016a-Python-2.7.11.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Bart Verleye # Center for eResearch, Auckland easyblock = 'ConfigureMakePythonPackage' diff --git a/easybuild/easyconfigs/s/SIP/SIP-4.18.1-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/s/SIP/SIP-4.18.1-intel-2016b-Python-2.7.12.eb index 57997a86bf..f0abfcf40e 100644 --- a/easybuild/easyconfigs/s/SIP/SIP-4.18.1-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/s/SIP/SIP-4.18.1-intel-2016b-Python-2.7.12.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Bart Verleye # Center for eResearch, Auckland easyblock = 'ConfigureMakePythonPackage' diff --git a/easybuild/easyconfigs/s/SIP/SIP-4.19-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/s/SIP/SIP-4.19-foss-2016b-Python-2.7.12.eb index be020214d2..9f50c74569 100644 --- a/easybuild/easyconfigs/s/SIP/SIP-4.19-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/s/SIP/SIP-4.19-foss-2016b-Python-2.7.12.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Bart Verleye # Center for eResearch, Auckland easyblock = 'ConfigureMakePythonPackage' diff --git a/easybuild/easyconfigs/s/SIP/SIP-4.19-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/s/SIP/SIP-4.19-intel-2016b-Python-2.7.12.eb index 9f5fa19c24..2e69e76a1a 100644 --- a/easybuild/easyconfigs/s/SIP/SIP-4.19-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/s/SIP/SIP-4.19-intel-2016b-Python-2.7.12.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Bart Verleye # Center for eResearch, Auckland easyblock = 'ConfigureMakePythonPackage' diff --git a/easybuild/easyconfigs/s/SIP/SIP-4.19.2-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/s/SIP/SIP-4.19.2-intel-2017a-Python-2.7.13.eb index c113a20dd9..cea8cbea9c 100644 --- a/easybuild/easyconfigs/s/SIP/SIP-4.19.2-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/s/SIP/SIP-4.19.2-intel-2017a-Python-2.7.13.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Bart Verleye # Center for eResearch, Auckland easyblock = 'ConfigureMakePythonPackage' diff --git a/easybuild/easyconfigs/s/SMALT/SMALT-0.7.5-goolf-1.4.10.eb b/easybuild/easyconfigs/s/SMALT/SMALT-0.7.5-goolf-1.4.10.eb index ed0395223c..07bc8cff7a 100644 --- a/easybuild/easyconfigs/s/SMALT/SMALT-0.7.5-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/s/SMALT/SMALT-0.7.5-goolf-1.4.10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/s/SMALT/SMALT-0.7.5-ictce-5.3.0.eb b/easybuild/easyconfigs/s/SMALT/SMALT-0.7.5-ictce-5.3.0.eb index 16d05cf341..7d14bea6a9 100644 --- a/easybuild/easyconfigs/s/SMALT/SMALT-0.7.5-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/s/SMALT/SMALT-0.7.5-ictce-5.3.0.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/s/SOAPaligner/SOAPaligner-2.21_Linux-x86_64.eb b/easybuild/easyconfigs/s/SOAPaligner/SOAPaligner-2.21_Linux-x86_64.eb index 67f7cd27da..8734a7daed 100644 --- a/easybuild/easyconfigs/s/SOAPaligner/SOAPaligner-2.21_Linux-x86_64.eb +++ b/easybuild/easyconfigs/s/SOAPaligner/SOAPaligner-2.21_Linux-x86_64.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/s/SOAPdenovo/SOAPdenovo-1.05-goolf-1.4.10.eb b/easybuild/easyconfigs/s/SOAPdenovo/SOAPdenovo-1.05-goolf-1.4.10.eb index 05651770f2..f288d7f917 100644 --- a/easybuild/easyconfigs/s/SOAPdenovo/SOAPdenovo-1.05-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/s/SOAPdenovo/SOAPdenovo-1.05-goolf-1.4.10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Cedric Laczny , Fotis Georgatos diff --git a/easybuild/easyconfigs/s/SOAPdenovo/SOAPdenovo-1.05-ictce-5.3.0.eb b/easybuild/easyconfigs/s/SOAPdenovo/SOAPdenovo-1.05-ictce-5.3.0.eb index 0ce4a98f03..762c7d68fd 100644 --- a/easybuild/easyconfigs/s/SOAPdenovo/SOAPdenovo-1.05-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/s/SOAPdenovo/SOAPdenovo-1.05-ictce-5.3.0.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Cedric Laczny , Fotis Georgatos diff --git a/easybuild/easyconfigs/s/SPAdes/SPAdes-3.0.0-goolf-1.4.10.eb b/easybuild/easyconfigs/s/SPAdes/SPAdes-3.0.0-goolf-1.4.10.eb index ab6bd52347..672b4b6174 100644 --- a/easybuild/easyconfigs/s/SPAdes/SPAdes-3.0.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/s/SPAdes/SPAdes-3.0.0-goolf-1.4.10.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/s/SPAdes/SPAdes-3.1.0-goolf-1.4.10.eb b/easybuild/easyconfigs/s/SPAdes/SPAdes-3.1.0-goolf-1.4.10.eb index 5eb12170f6..36652b20f0 100644 --- a/easybuild/easyconfigs/s/SPAdes/SPAdes-3.1.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/s/SPAdes/SPAdes-3.1.0-goolf-1.4.10.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/s/SPAdes/SPAdes-3.10.1-foss-2016b.eb b/easybuild/easyconfigs/s/SPAdes/SPAdes-3.10.1-foss-2016b.eb index 6e5c9aeb32..5d56e586a2 100644 --- a/easybuild/easyconfigs/s/SPAdes/SPAdes-3.10.1-foss-2016b.eb +++ b/easybuild/easyconfigs/s/SPAdes/SPAdes-3.10.1-foss-2016b.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # sciCORE - University of Basel # SIB Swiss Institute of Bioinformatics diff --git a/easybuild/easyconfigs/s/SPAdes/SPAdes-3.6.2-goolf-1.4.10.eb b/easybuild/easyconfigs/s/SPAdes/SPAdes-3.6.2-goolf-1.4.10.eb index b8ae8d0ad8..50ca4cd509 100644 --- a/easybuild/easyconfigs/s/SPAdes/SPAdes-3.6.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/s/SPAdes/SPAdes-3.6.2-goolf-1.4.10.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # sciCORE - University of Basel # SIB Swiss Institute of Bioinformatics diff --git a/easybuild/easyconfigs/s/SPAdes/SPAdes-3.6.2-goolf-1.7.20.eb b/easybuild/easyconfigs/s/SPAdes/SPAdes-3.6.2-goolf-1.7.20.eb index df712d6830..46422756f7 100644 --- a/easybuild/easyconfigs/s/SPAdes/SPAdes-3.6.2-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/s/SPAdes/SPAdes-3.6.2-goolf-1.7.20.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # sciCORE - University of Basel # SIB Swiss Institute of Bioinformatics diff --git a/easybuild/easyconfigs/s/SPAdes/SPAdes-3.9.0-foss-2016a.eb b/easybuild/easyconfigs/s/SPAdes/SPAdes-3.9.0-foss-2016a.eb index af3845c60d..52377a3fe1 100644 --- a/easybuild/easyconfigs/s/SPAdes/SPAdes-3.9.0-foss-2016a.eb +++ b/easybuild/easyconfigs/s/SPAdes/SPAdes-3.9.0-foss-2016a.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # sciCORE - University of Basel # SIB Swiss Institute of Bioinformatics diff --git a/easybuild/easyconfigs/s/SPAdes/SPAdes-3.9.0-foss-2016b.eb b/easybuild/easyconfigs/s/SPAdes/SPAdes-3.9.0-foss-2016b.eb index a92f27ffac..00831a4e1c 100644 --- a/easybuild/easyconfigs/s/SPAdes/SPAdes-3.9.0-foss-2016b.eb +++ b/easybuild/easyconfigs/s/SPAdes/SPAdes-3.9.0-foss-2016b.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # sciCORE - University of Basel # SIB Swiss Institute of Bioinformatics diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.10.0-foss-2015a.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.10.0-foss-2015a.eb index c435d47a74..17f00411a9 100644 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.10.0-foss-2015a.eb +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.10.0-foss-2015a.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.13.0-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.13.0-GCC-4.9.3-2.25.eb index 212dfd1d75..16c91c0d28 100644 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.13.0-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.13.0-GCC-4.9.3-2.25.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.13.0-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.13.0-GCC-5.4.0-2.26.eb index c8632b48d5..1d32b0c2a3 100644 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.13.0-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.13.0-GCC-5.4.0-2.26.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.13.0-GCCcore-6.3.0.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.13.0-GCCcore-6.3.0.eb index f7ba78e654..f9639f1cf8 100644 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.13.0-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.13.0-GCCcore-6.3.0.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.13.0-foss-2016.04.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.13.0-foss-2016.04.eb index ee0989cdf4..e48edbbcf7 100644 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.13.0-foss-2016.04.eb +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.13.0-foss-2016.04.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.13.0-foss-2016a.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.13.0-foss-2016a.eb index ec5703f27d..2bfe96771a 100644 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.13.0-foss-2016a.eb +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.13.0-foss-2016a.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.13.0-foss-2016b.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.13.0-foss-2016b.eb index 1c9912537c..c95b85d4e3 100644 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.13.0-foss-2016b.eb +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.13.0-foss-2016b.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.13.0-iccifort-2016.3.210-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.13.0-iccifort-2016.3.210-GCC-5.4.0-2.26.eb index de897a790e..6e1bb042c8 100644 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.13.0-iccifort-2016.3.210-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.13.0-iccifort-2016.3.210-GCC-5.4.0-2.26.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.13.0-intel-2016b.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.13.0-intel-2016b.eb index e6b0322891..701c924942 100644 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.13.0-intel-2016b.eb +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.13.0-intel-2016b.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.14.1-GCCcore-4.9.3.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.14.1-GCCcore-4.9.3.eb index cb84023340..55a1ec7a89 100644 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.14.1-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.14.1-GCCcore-4.9.3.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.17.0-GCCcore-6.3.0.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.17.0-GCCcore-6.3.0.eb index 41b5a58bd2..d5d4a80684 100644 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.17.0-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.17.0-GCCcore-6.3.0.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.7.17-goolf-1.4.10.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.7.17-goolf-1.4.10.eb index e74d6f7a39..f3308cf41c 100644 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.7.17-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.7.17-goolf-1.4.10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.7.17-ictce-5.3.0.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.7.17-ictce-5.3.0.eb index 30d45082a1..e3447aee6b 100644 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.7.17-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.7.17-ictce-5.3.0.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.1-goolf-1.4.10.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.1-goolf-1.4.10.eb index c08623a5a5..f65ec4dae6 100644 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.1-goolf-1.4.10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.1-ictce-5.3.0.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.1-ictce-5.3.0.eb index 05b5ca95c1..80c5606194 100644 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.1-ictce-5.3.0.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-GCC-4.9.3-2.25.eb index 15a228e4cf..2a4b96094a 100644 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-GCC-4.9.3-2.25.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-GNU-4.9.3-2.25.eb index 87526d7754..8ce08d273d 100644 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-GNU-4.9.3-2.25.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-foss-2015a.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-foss-2015a.eb index 0e3d5b0943..9fe38bf12a 100644 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-foss-2015a.eb +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-foss-2015a.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-foss-2015b.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-foss-2015b.eb index 3cdb5e9a31..5a806bef03 100644 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-foss-2015b.eb +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-foss-2015b.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-gimkl-2.11.5.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-gimkl-2.11.5.eb index c9bee3d1d5..0d4572d689 100644 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-gimkl-2.11.5.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-goolf-1.4.10.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-goolf-1.4.10.eb index 2b1f98a6ac..e01c868906 100644 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-goolf-1.4.10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-goolf-1.7.20.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-goolf-1.7.20.eb index 86716967ff..7fb046898e 100644 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-goolf-1.7.20.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-intel-2015a.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-intel-2015a.eb index 70270519d3..8738842f40 100644 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-intel-2015a.eb +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-intel-2015a.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-intel-2015b.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-intel-2015b.eb index 5c38e72b1a..94e236ef73 100644 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-intel-2015b.eb +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-intel-2015b.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.4.1-goolf-1.4.10.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.4.1-goolf-1.4.10.eb index 0a07713fbb..db742635b8 100644 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.4.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.4.1-goolf-1.4.10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2013 University of Luxembourg/Luxembourg Centre for Systems Biomedicine # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.5-goolf-1.4.10.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.5-goolf-1.4.10.eb index 72f8da9d34..6cd5fb9e4f 100644 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.5-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.5-goolf-1.4.10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.6-ictce-5.5.0.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.6-ictce-5.5.0.eb index ac855e7cba..883edbcbca 100644 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.6-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.6-ictce-5.5.0.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.6-intel-2014b.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.6-intel-2014b.eb index f0ed15f86c..00aa9db433 100644 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.6-intel-2014b.eb +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.6-intel-2014b.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-GCC-4.8.4.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-GCC-4.8.4.eb index 27cd84d7ec..77933d168b 100644 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-GCC-4.8.4.eb +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-GCC-4.8.4.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-GCC-4.9.2.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-GCC-4.9.2.eb index ed00f7b981..53c285b780 100644 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-GCC-4.9.2.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-foss-2015.05.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-foss-2015.05.eb index 5e77859d07..bc6c9dd40e 100644 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-foss-2015.05.eb +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-foss-2015.05.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-foss-2015a.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-foss-2015a.eb index a8d05d1f18..2916ae6c7e 100644 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-foss-2015a.eb +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-foss-2015a.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-foss-2015b.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-foss-2015b.eb index b3cfb08afd..fb622bfe69 100644 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-foss-2015b.eb +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-foss-2015b.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-gompi-1.5.16.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-gompi-1.5.16.eb index d4af19e4fa..55e1cd7d9f 100644 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-gompi-1.5.16.eb +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-gompi-1.5.16.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-goolf-1.5.14.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-goolf-1.5.14.eb index 763de183e3..31dbee8c48 100644 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-goolf-1.5.14.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-goolf-1.5.16.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-goolf-1.5.16.eb index 6946daaee7..c93baeda44 100644 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-goolf-1.5.16.eb +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-goolf-1.5.16.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-goolf-1.7.20.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-goolf-1.7.20.eb index ee10abf948..53e7f6572d 100644 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-goolf-1.7.20.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-intel-2015a.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-intel-2015a.eb index f5e96601f1..3dcf095ade 100644 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-intel-2015a.eb +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-intel-2015a.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.9-foss-2015a.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.9-foss-2015a.eb index 8c66a0ef4c..dd707477c9 100644 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.9-foss-2015a.eb +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.9-foss-2015a.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2013 University of Luxembourg/Luxembourg Centre for Systems Biomedicine # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-CrayGNU-2015.11.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-CrayGNU-2015.11.eb index 408f74829a..9084d936c8 100644 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-CrayGNU-2015.11.eb +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-CrayGNU-2015.11.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-CrayGNU-2016.03.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-CrayGNU-2016.03.eb index 5c92bc8136..2eb44c755d 100644 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-CrayGNU-2016.03.eb +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-CrayGNU-2016.03.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-GCC-4.9.3-2.25.eb index 5c86155323..bb425e87a7 100644 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-GCC-4.9.3-2.25.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-foss-2016a.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-foss-2016a.eb index 8902612f46..f7d80fd057 100644 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-foss-2016a.eb +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-foss-2016a.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-gimkl-2.11.5.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-gimkl-2.11.5.eb index 4b9cea2422..55a3d892fc 100644 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-gimkl-2.11.5.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-goolf-1.7.20.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-goolf-1.7.20.eb index d75861cbb6..b694c4fcaa 100644 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-goolf-1.7.20.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-intel-2015b.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-intel-2015b.eb index 177a74a0fb..28138bf968 100644 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-intel-2015b.eb +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-intel-2015b.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-intel-2016.02-GCC-4.9.eb index 885ab346a9..ecce43f756 100644 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-intel-2016.02-GCC-4.9.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-intel-2016a.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-intel-2016a.eb index 46583c5246..21da189572 100644 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-intel-2016a.eb +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-intel-2016a.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-iomkl-2016.07.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-iomkl-2016.07.eb index c1a72bbbe4..fb1547876e 100644 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-iomkl-2016.07.eb +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-iomkl-2016.07.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-iomkl-2016.09-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-iomkl-2016.09-GCC-4.9.3-2.25.eb index 68f9f01974..3de2d7ff50 100644 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-iomkl-2016.09-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-iomkl-2016.09-GCC-4.9.3-2.25.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-2.3.5-centos_linux64.eb b/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-2.3.5-centos_linux64.eb index fc325c12fd..cfbdcb45e7 100644 --- a/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-2.3.5-centos_linux64.eb +++ b/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-2.3.5-centos_linux64.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-2.5.4-1-centos_linux64.eb b/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-2.5.4-1-centos_linux64.eb index 54156d4303..263ce2d19f 100644 --- a/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-2.5.4-1-centos_linux64.eb +++ b/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-2.5.4-1-centos_linux64.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/s/SSAHA2/SSAHA2-2.5.5-i686.eb b/easybuild/easyconfigs/s/SSAHA2/SSAHA2-2.5.5-i686.eb index 0e8750aa56..c7d58c5217 100644 --- a/easybuild/easyconfigs/s/SSAHA2/SSAHA2-2.5.5-i686.eb +++ b/easybuild/easyconfigs/s/SSAHA2/SSAHA2-2.5.5-i686.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/s/SSAHA2/SSAHA2-2.5.5-x86_64.eb b/easybuild/easyconfigs/s/SSAHA2/SSAHA2-2.5.5-x86_64.eb index ea1f495c8a..24b10cedf9 100644 --- a/easybuild/easyconfigs/s/SSAHA2/SSAHA2-2.5.5-x86_64.eb +++ b/easybuild/easyconfigs/s/SSAHA2/SSAHA2-2.5.5-x86_64.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/s/STAR-Fusion/STAR-Fusion-0.6.0-goolf-1.4.10-Perl-5.16.3.eb b/easybuild/easyconfigs/s/STAR-Fusion/STAR-Fusion-0.6.0-goolf-1.4.10-Perl-5.16.3.eb index c87beb9409..4b19365503 100644 --- a/easybuild/easyconfigs/s/STAR-Fusion/STAR-Fusion-0.6.0-goolf-1.4.10-Perl-5.16.3.eb +++ b/easybuild/easyconfigs/s/STAR-Fusion/STAR-Fusion-0.6.0-goolf-1.4.10-Perl-5.16.3.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # sciCORE - University of Basel # SIB Swiss Institute of Bioinformatics diff --git a/easybuild/easyconfigs/s/STAR/STAR-2.3.0e-goolf-1.4.10.eb b/easybuild/easyconfigs/s/STAR/STAR-2.3.0e-goolf-1.4.10.eb index c819f307db..851afee495 100644 --- a/easybuild/easyconfigs/s/STAR/STAR-2.3.0e-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/s/STAR/STAR-2.3.0e-goolf-1.4.10.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/s/STAR/STAR-2.5.0a-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/s/STAR/STAR-2.5.0a-GNU-4.9.3-2.25.eb index 04188b3f1a..c464f7f180 100644 --- a/easybuild/easyconfigs/s/STAR/STAR-2.5.0a-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/s/STAR/STAR-2.5.0a-GNU-4.9.3-2.25.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # sciCORE - University of Basel # SIB Swiss Institute of Bioinformatics diff --git a/easybuild/easyconfigs/s/STAR/STAR-2.5.0a-goolf-1.4.10.eb b/easybuild/easyconfigs/s/STAR/STAR-2.5.0a-goolf-1.4.10.eb index 457ab933f7..3b0c1e3f28 100644 --- a/easybuild/easyconfigs/s/STAR/STAR-2.5.0a-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/s/STAR/STAR-2.5.0a-goolf-1.4.10.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # sciCORE - University of Basel # SIB Swiss Institute of Bioinformatics diff --git a/easybuild/easyconfigs/s/STAR/STAR-2.5.1b-foss-2015b.eb b/easybuild/easyconfigs/s/STAR/STAR-2.5.1b-foss-2015b.eb index b4f28e006e..ce729a34b0 100644 --- a/easybuild/easyconfigs/s/STAR/STAR-2.5.1b-foss-2015b.eb +++ b/easybuild/easyconfigs/s/STAR/STAR-2.5.1b-foss-2015b.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # sciCORE - University of Basel # SIB Swiss Institute of Bioinformatics diff --git a/easybuild/easyconfigs/s/STAR/STAR-2.5.1b-goolf-1.4.10.eb b/easybuild/easyconfigs/s/STAR/STAR-2.5.1b-goolf-1.4.10.eb index acf5436cbe..6147b68e4b 100644 --- a/easybuild/easyconfigs/s/STAR/STAR-2.5.1b-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/s/STAR/STAR-2.5.1b-goolf-1.4.10.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # sciCORE - University of Basel # SIB Swiss Institute of Bioinformatics diff --git a/easybuild/easyconfigs/s/STAR/STAR-2.5.2a-foss-2016a.eb b/easybuild/easyconfigs/s/STAR/STAR-2.5.2a-foss-2016a.eb index 43cc47b2aa..47cc2f8fb8 100644 --- a/easybuild/easyconfigs/s/STAR/STAR-2.5.2a-foss-2016a.eb +++ b/easybuild/easyconfigs/s/STAR/STAR-2.5.2a-foss-2016a.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # sciCORE - University of Basel # SIB Swiss Institute of Bioinformatics diff --git a/easybuild/easyconfigs/s/STAR/STAR-2.5.2a-goolf-1.7.20.eb b/easybuild/easyconfigs/s/STAR/STAR-2.5.2a-goolf-1.7.20.eb index d8c6f0be04..6655aaf699 100644 --- a/easybuild/easyconfigs/s/STAR/STAR-2.5.2a-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/s/STAR/STAR-2.5.2a-goolf-1.7.20.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # sciCORE - University of Basel # SIB Swiss Institute of Bioinformatics diff --git a/easybuild/easyconfigs/s/STAR/STAR-2.5.2b-intel-2016b.eb b/easybuild/easyconfigs/s/STAR/STAR-2.5.2b-intel-2016b.eb index 05c3e56c2f..fdff081070 100644 --- a/easybuild/easyconfigs/s/STAR/STAR-2.5.2b-intel-2016b.eb +++ b/easybuild/easyconfigs/s/STAR/STAR-2.5.2b-intel-2016b.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # sciCORE - University of Basel # SIB Swiss Institute of Bioinformatics diff --git a/easybuild/easyconfigs/s/STAR/STAR-2.5.3a-intel-2017a.eb b/easybuild/easyconfigs/s/STAR/STAR-2.5.3a-intel-2017a.eb index 7bb56d5efd..02ac65a9a0 100644 --- a/easybuild/easyconfigs/s/STAR/STAR-2.5.3a-intel-2017a.eb +++ b/easybuild/easyconfigs/s/STAR/STAR-2.5.3a-intel-2017a.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # sciCORE - University of Basel # SIB Swiss Institute of Bioinformatics diff --git a/easybuild/easyconfigs/s/Sambamba/Sambamba-0.6.6.eb b/easybuild/easyconfigs/s/Sambamba/Sambamba-0.6.6.eb index 8b68d940d5..aaa111b447 100644 --- a/easybuild/easyconfigs/s/Sambamba/Sambamba-0.6.6.eb +++ b/easybuild/easyconfigs/s/Sambamba/Sambamba-0.6.6.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # sciCORE - University of Basel # SIB Swiss Institute of Bioinformatics diff --git a/easybuild/easyconfigs/s/Scalasca/Scalasca-2.2-foss-2015a.eb b/easybuild/easyconfigs/s/Scalasca/Scalasca-2.2-foss-2015a.eb index 55d127b2f7..9c891ad200 100644 --- a/easybuild/easyconfigs/s/Scalasca/Scalasca-2.2-foss-2015a.eb +++ b/easybuild/easyconfigs/s/Scalasca/Scalasca-2.2-foss-2015a.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild # Copyright:: Copyright 2013 Juelich Supercomputing Centre, Germany # Authors:: Bernd Mohr # License:: New BSD diff --git a/easybuild/easyconfigs/s/Scalasca/Scalasca-2.3-foss-2016a.eb b/easybuild/easyconfigs/s/Scalasca/Scalasca-2.3-foss-2016a.eb index 250c8ea829..f768f2c53c 100644 --- a/easybuild/easyconfigs/s/Scalasca/Scalasca-2.3-foss-2016a.eb +++ b/easybuild/easyconfigs/s/Scalasca/Scalasca-2.3-foss-2016a.eb @@ -1,5 +1,5 @@ ## -# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild # Copyright:: Copyright 2013-2016 Juelich Supercomputing Centre, Germany # Authors:: Bernd Mohr # Markus Geimer diff --git a/easybuild/easyconfigs/s/Score-P/Score-P-1.2.1-goolf-1.5.14.eb b/easybuild/easyconfigs/s/Score-P/Score-P-1.2.1-goolf-1.5.14.eb index df0333c95e..26a76a0f44 100644 --- a/easybuild/easyconfigs/s/Score-P/Score-P-1.2.1-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/s/Score-P/Score-P-1.2.1-goolf-1.5.14.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild # Copyright:: Copyright 2013 Juelich Supercomputing Centre, Germany # Authors:: Bernd Mohr # License:: New BSD diff --git a/easybuild/easyconfigs/s/Score-P/Score-P-1.2.3-goolf-1.5.14.eb b/easybuild/easyconfigs/s/Score-P/Score-P-1.2.3-goolf-1.5.14.eb index 137bacee9c..3f22891997 100644 --- a/easybuild/easyconfigs/s/Score-P/Score-P-1.2.3-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/s/Score-P/Score-P-1.2.3-goolf-1.5.14.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild # Authors:: Jordi Blasco # License:: New BSD # diff --git a/easybuild/easyconfigs/s/Score-P/Score-P-1.4-foss-2015a.eb b/easybuild/easyconfigs/s/Score-P/Score-P-1.4-foss-2015a.eb index 91b0941367..c70a882623 100644 --- a/easybuild/easyconfigs/s/Score-P/Score-P-1.4-foss-2015a.eb +++ b/easybuild/easyconfigs/s/Score-P/Score-P-1.4-foss-2015a.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild # Copyright:: Copyright 2013 Juelich Supercomputing Centre, Germany # Authors:: Bernd Mohr # License:: New BSD diff --git a/easybuild/easyconfigs/s/Score-P/Score-P-2.0.1-foss-2016a.eb b/easybuild/easyconfigs/s/Score-P/Score-P-2.0.1-foss-2016a.eb index 5df9e5efff..65fe9f43f3 100644 --- a/easybuild/easyconfigs/s/Score-P/Score-P-2.0.1-foss-2016a.eb +++ b/easybuild/easyconfigs/s/Score-P/Score-P-2.0.1-foss-2016a.eb @@ -1,5 +1,5 @@ ## -# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild # Copyright:: Copyright 2013-2016 Juelich Supercomputing Centre, Germany # Authors:: Bernd Mohr # Markus Geimer diff --git a/easybuild/easyconfigs/s/Seaborn/Seaborn-0.6.0-goolf-1.4.10-Python-2.7.5.eb b/easybuild/easyconfigs/s/Seaborn/Seaborn-0.6.0-goolf-1.4.10-Python-2.7.5.eb index 8a86868303..31c53447fc 100644 --- a/easybuild/easyconfigs/s/Seaborn/Seaborn-0.6.0-goolf-1.4.10-Python-2.7.5.eb +++ b/easybuild/easyconfigs/s/Seaborn/Seaborn-0.6.0-goolf-1.4.10-Python-2.7.5.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics (SIB) # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/s/Seaborn/Seaborn-0.6.0-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/s/Seaborn/Seaborn-0.6.0-intel-2015b-Python-2.7.10.eb index a2b58989a1..1cbfd0027a 100644 --- a/easybuild/easyconfigs/s/Seaborn/Seaborn-0.6.0-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/s/Seaborn/Seaborn-0.6.0-intel-2015b-Python-2.7.10.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics (SIB) # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/s/Seaborn/Seaborn-0.7.1-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/s/Seaborn/Seaborn-0.7.1-intel-2016b-Python-2.7.12.eb index c0dc9e45f8..e80e2daca5 100644 --- a/easybuild/easyconfigs/s/Seaborn/Seaborn-0.7.1-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/s/Seaborn/Seaborn-0.7.1-intel-2016b-Python-2.7.12.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics (SIB) # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/s/SelEstim/SelEstim-1.1.4-Linux-64bits.eb b/easybuild/easyconfigs/s/SelEstim/SelEstim-1.1.4-Linux-64bits.eb index 1b943d4062..a54e53ac82 100644 --- a/easybuild/easyconfigs/s/SelEstim/SelEstim-1.1.4-Linux-64bits.eb +++ b/easybuild/easyconfigs/s/SelEstim/SelEstim-1.1.4-Linux-64bits.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # sciCORE - University of Basel # SIB Swiss Institute of Bioinformatics diff --git a/easybuild/easyconfigs/s/SeqAn/SeqAn-2.3.2-foss-2016b.eb b/easybuild/easyconfigs/s/SeqAn/SeqAn-2.3.2-foss-2016b.eb index d894a7f03a..1d596bb25f 100644 --- a/easybuild/easyconfigs/s/SeqAn/SeqAn-2.3.2-foss-2016b.eb +++ b/easybuild/easyconfigs/s/SeqAn/SeqAn-2.3.2-foss-2016b.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # sciCORE - University of Basel # SIB Swiss Institute of Bioinformatics diff --git a/easybuild/easyconfigs/s/SeqPrep/SeqPrep-1.2-goolf-1.7.20.eb b/easybuild/easyconfigs/s/SeqPrep/SeqPrep-1.2-goolf-1.7.20.eb index 86ba1ed78f..5baf4c3200 100644 --- a/easybuild/easyconfigs/s/SeqPrep/SeqPrep-1.2-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/s/SeqPrep/SeqPrep-1.2-goolf-1.7.20.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # sciCORE - University of Basel # SIB Swiss Institute of Bioinformatics diff --git a/easybuild/easyconfigs/s/Seqmagick/Seqmagick-0.6.1-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/s/Seqmagick/Seqmagick-0.6.1-foss-2016a-Python-2.7.11.eb index ae2145d3df..e171a32650 100644 --- a/easybuild/easyconfigs/s/Seqmagick/Seqmagick-0.6.1-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/s/Seqmagick/Seqmagick-0.6.1-foss-2016a-Python-2.7.11.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2016 University of Geneva Switzerland # Authors:: Yann Sagon diff --git a/easybuild/easyconfigs/s/SoX/SoX-14.4.2-foss-2015a.eb b/easybuild/easyconfigs/s/SoX/SoX-14.4.2-foss-2015a.eb index a71ba0bca6..08b010527a 100644 --- a/easybuild/easyconfigs/s/SoX/SoX-14.4.2-foss-2015a.eb +++ b/easybuild/easyconfigs/s/SoX/SoX-14.4.2-foss-2015a.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Author: Stephane Thiell ### diff --git a/easybuild/easyconfigs/s/SolexaQA++/SolexaQA++-3.1.5-foss-2016b.eb b/easybuild/easyconfigs/s/SolexaQA++/SolexaQA++-3.1.5-foss-2016b.eb index bb975b50f8..ba655d3a43 100644 --- a/easybuild/easyconfigs/s/SolexaQA++/SolexaQA++-3.1.5-foss-2016b.eb +++ b/easybuild/easyconfigs/s/SolexaQA++/SolexaQA++-3.1.5-foss-2016b.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Adam Huffman # The Francis Crick Institute easyblock = 'MakeCp' diff --git a/easybuild/easyconfigs/s/SortMeRNA/SortMeRNA-2.1-foss-2016a.eb b/easybuild/easyconfigs/s/SortMeRNA/SortMeRNA-2.1-foss-2016a.eb index 6af29bdb8b..4a5290e878 100644 --- a/easybuild/easyconfigs/s/SortMeRNA/SortMeRNA-2.1-foss-2016a.eb +++ b/easybuild/easyconfigs/s/SortMeRNA/SortMeRNA-2.1-foss-2016a.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Cedric Laczny , Fotis Georgatos diff --git a/easybuild/easyconfigs/s/Stow/Stow-1.3.3-goolf-1.4.10.eb b/easybuild/easyconfigs/s/Stow/Stow-1.3.3-goolf-1.4.10.eb index df639eb5dc..ab80ccc5bd 100644 --- a/easybuild/easyconfigs/s/Stow/Stow-1.3.3-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/s/Stow/Stow-1.3.3-goolf-1.4.10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/s/Stow/Stow-1.3.3-ictce-5.3.0.eb b/easybuild/easyconfigs/s/Stow/Stow-1.3.3-ictce-5.3.0.eb index 43fedd4e90..4a0685460a 100644 --- a/easybuild/easyconfigs/s/Stow/Stow-1.3.3-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/s/Stow/Stow-1.3.3-ictce-5.3.0.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/s/StringTie/StringTie-1.2.2-goolf-1.4.10.eb b/easybuild/easyconfigs/s/StringTie/StringTie-1.2.2-goolf-1.4.10.eb index f2c6a5db74..0d9f6439b2 100644 --- a/easybuild/easyconfigs/s/StringTie/StringTie-1.2.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/s/StringTie/StringTie-1.2.2-goolf-1.4.10.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # sciCORE - University of Basel # SIB Swiss Institute of Bioinformatics diff --git a/easybuild/easyconfigs/s/StringTie/StringTie-1.3.0-intel-2016b.eb b/easybuild/easyconfigs/s/StringTie/StringTie-1.3.0-intel-2016b.eb index 69634c30e6..6f1084f664 100644 --- a/easybuild/easyconfigs/s/StringTie/StringTie-1.3.0-intel-2016b.eb +++ b/easybuild/easyconfigs/s/StringTie/StringTie-1.3.0-intel-2016b.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # sciCORE - University of Basel # SIB Swiss Institute of Bioinformatics diff --git a/easybuild/easyconfigs/s/StringTie/StringTie-1.3.3-intel-2017a.eb b/easybuild/easyconfigs/s/StringTie/StringTie-1.3.3-intel-2017a.eb index 2476496f2d..0d4e070e86 100644 --- a/easybuild/easyconfigs/s/StringTie/StringTie-1.3.3-intel-2017a.eb +++ b/easybuild/easyconfigs/s/StringTie/StringTie-1.3.3-intel-2017a.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # sciCORE - University of Basel # SIB Swiss Institute of Bioinformatics diff --git a/easybuild/easyconfigs/s/StringTie/StringTie-1.3.3b-foss-2016b.eb b/easybuild/easyconfigs/s/StringTie/StringTie-1.3.3b-foss-2016b.eb index d1eb27f7fe..3924753a79 100644 --- a/easybuild/easyconfigs/s/StringTie/StringTie-1.3.3b-foss-2016b.eb +++ b/easybuild/easyconfigs/s/StringTie/StringTie-1.3.3b-foss-2016b.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild easyblock = 'MakeCp' diff --git a/easybuild/easyconfigs/s/Subread/Subread-1.5.0-p1-foss-2015b.eb b/easybuild/easyconfigs/s/Subread/Subread-1.5.0-p1-foss-2015b.eb index 612c514399..ca748e8873 100644 --- a/easybuild/easyconfigs/s/Subread/Subread-1.5.0-p1-foss-2015b.eb +++ b/easybuild/easyconfigs/s/Subread/Subread-1.5.0-p1-foss-2015b.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Adam Huffman # The Francis Crick Institute easyblock = 'MakeCp' diff --git a/easybuild/easyconfigs/s/Subread/Subread-1.5.0-p1-foss-2016a.eb b/easybuild/easyconfigs/s/Subread/Subread-1.5.0-p1-foss-2016a.eb index e525a015c8..3ea35d4e6e 100644 --- a/easybuild/easyconfigs/s/Subread/Subread-1.5.0-p1-foss-2016a.eb +++ b/easybuild/easyconfigs/s/Subread/Subread-1.5.0-p1-foss-2016a.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Adam Huffman # The Francis Crick Institute easyblock = 'MakeCp' diff --git a/easybuild/easyconfigs/s/Subread/Subread-1.5.0-p1-foss-2016b.eb b/easybuild/easyconfigs/s/Subread/Subread-1.5.0-p1-foss-2016b.eb index ecdac2f7d2..baebc0d989 100644 --- a/easybuild/easyconfigs/s/Subread/Subread-1.5.0-p1-foss-2016b.eb +++ b/easybuild/easyconfigs/s/Subread/Subread-1.5.0-p1-foss-2016b.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Adam Huffman # The Francis Crick Institute easyblock = 'MakeCp' diff --git a/easybuild/easyconfigs/s/samblaster/samblaster-0.1.24-goolf-1.7.20.eb b/easybuild/easyconfigs/s/samblaster/samblaster-0.1.24-goolf-1.7.20.eb index 5c35b43fcc..3f53f0997a 100644 --- a/easybuild/easyconfigs/s/samblaster/samblaster-0.1.24-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/s/samblaster/samblaster-0.1.24-goolf-1.7.20.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # sciCORE - University of Basel # SIB Swiss Institute of Bioinformatics diff --git a/easybuild/easyconfigs/s/segemehl/segemehl-0.1.7-goolf-1.4.10.eb b/easybuild/easyconfigs/s/segemehl/segemehl-0.1.7-goolf-1.4.10.eb index 0c7b7b159e..beef8b39ec 100644 --- a/easybuild/easyconfigs/s/segemehl/segemehl-0.1.7-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/s/segemehl/segemehl-0.1.7-goolf-1.4.10.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/s/segemehl/segemehl-0.2.0-foss-2016b.eb b/easybuild/easyconfigs/s/segemehl/segemehl-0.2.0-foss-2016b.eb index 3f36bab3c9..09a2f081e9 100644 --- a/easybuild/easyconfigs/s/segemehl/segemehl-0.2.0-foss-2016b.eb +++ b/easybuild/easyconfigs/s/segemehl/segemehl-0.2.0-foss-2016b.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild easyblock = 'MakeCp' diff --git a/easybuild/easyconfigs/s/segemehl/segemehl-0.2.0-goolf-1.4.10.eb b/easybuild/easyconfigs/s/segemehl/segemehl-0.2.0-goolf-1.4.10.eb index a9245a0b76..beeb661537 100644 --- a/easybuild/easyconfigs/s/segemehl/segemehl-0.2.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/s/segemehl/segemehl-0.2.0-goolf-1.4.10.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # sciCORE - University of Basel # SIB Swiss Institute of Bioinformatics diff --git a/easybuild/easyconfigs/s/sickle/sickle-1.210-goolf-1.4.10-bab15f7.eb b/easybuild/easyconfigs/s/sickle/sickle-1.210-goolf-1.4.10-bab15f7.eb index a2500b9e04..bc93dbaa1d 100644 --- a/easybuild/easyconfigs/s/sickle/sickle-1.210-goolf-1.4.10-bab15f7.eb +++ b/easybuild/easyconfigs/s/sickle/sickle-1.210-goolf-1.4.10-bab15f7.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/s/skewer/skewer-0.2.2-goolf-1.7.20.eb b/easybuild/easyconfigs/s/skewer/skewer-0.2.2-goolf-1.7.20.eb index 89547eb928..51eeeb8491 100644 --- a/easybuild/easyconfigs/s/skewer/skewer-0.2.2-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/s/skewer/skewer-0.2.2-goolf-1.7.20.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # sciCORE - University of Basel # SIB Swiss Institute of Bioinformatics diff --git a/easybuild/easyconfigs/s/splitRef/splitRef-0.0.2.eb b/easybuild/easyconfigs/s/splitRef/splitRef-0.0.2.eb index 88fc3d4707..306703a33f 100644 --- a/easybuild/easyconfigs/s/splitRef/splitRef-0.0.2.eb +++ b/easybuild/easyconfigs/s/splitRef/splitRef-0.0.2.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # sciCORE - University of Basel # SIB Swiss Institute of Bioinformatics diff --git a/easybuild/easyconfigs/s/sratoolkit/sratoolkit-2.5.7.eb b/easybuild/easyconfigs/s/sratoolkit/sratoolkit-2.5.7.eb index b3d358e4a3..adcf73dd1b 100644 --- a/easybuild/easyconfigs/s/sratoolkit/sratoolkit-2.5.7.eb +++ b/easybuild/easyconfigs/s/sratoolkit/sratoolkit-2.5.7.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Author: Adam Huffman # adam.huffman@crick.ac.uk diff --git a/easybuild/easyconfigs/s/stress/stress-1.0.4-goolf-1.7.20.eb b/easybuild/easyconfigs/s/stress/stress-1.0.4-goolf-1.7.20.eb index e91ebd2437..004ae31693 100644 --- a/easybuild/easyconfigs/s/stress/stress-1.0.4-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/s/stress/stress-1.0.4-goolf-1.7.20.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # sciCORE - University of Basel # SIB Swiss Institute of Bioinformatics diff --git a/easybuild/easyconfigs/s/synchronicity/synchronicity-1.1.9.1-foss-2015b-R-3.2.3.eb b/easybuild/easyconfigs/s/synchronicity/synchronicity-1.1.9.1-foss-2015b-R-3.2.3.eb index f056af2b4f..56b9997a88 100644 --- a/easybuild/easyconfigs/s/synchronicity/synchronicity-1.1.9.1-foss-2015b-R-3.2.3.eb +++ b/easybuild/easyconfigs/s/synchronicity/synchronicity-1.1.9.1-foss-2015b-R-3.2.3.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Author: Adam Huffman # The Francis Crick Institute diff --git a/easybuild/easyconfigs/t/TAU/TAU-2.22.2-goolf-1.5.14.eb b/easybuild/easyconfigs/t/TAU/TAU-2.22.2-goolf-1.5.14.eb index 72a246892c..211ff82a35 100644 --- a/easybuild/easyconfigs/t/TAU/TAU-2.22.2-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/t/TAU/TAU-2.22.2-goolf-1.5.14.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild # Copyright:: Copyright 2013 Juelich Supercomputing Centre, Germany # Authors:: Bernd Mohr # License:: New BSD diff --git a/easybuild/easyconfigs/t/TCC/TCC-0.9.26.eb b/easybuild/easyconfigs/t/TCC/TCC-0.9.26.eb index c502d5385e..e97300a69c 100644 --- a/easybuild/easyconfigs/t/TCC/TCC-0.9.26.eb +++ b/easybuild/easyconfigs/t/TCC/TCC-0.9.26.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/t/TREE-PUZZLE/TREE-PUZZLE-5.2-goolf-1.4.10.eb b/easybuild/easyconfigs/t/TREE-PUZZLE/TREE-PUZZLE-5.2-goolf-1.4.10.eb index c6409b2a07..3ffa16eea4 100644 --- a/easybuild/easyconfigs/t/TREE-PUZZLE/TREE-PUZZLE-5.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/t/TREE-PUZZLE/TREE-PUZZLE-5.2-goolf-1.4.10.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/t/Tar/Tar-1.26-goolf-1.4.10.eb b/easybuild/easyconfigs/t/Tar/Tar-1.26-goolf-1.4.10.eb index 69b3b4ca40..d39813bb2e 100644 --- a/easybuild/easyconfigs/t/Tar/Tar-1.26-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/t/Tar/Tar-1.26-goolf-1.4.10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright (c) 2012-2013 Cyprus Institute / CaSToRC # Authors:: Thekla Loizou diff --git a/easybuild/easyconfigs/t/Tar/Tar-1.26-ictce-5.3.0.eb b/easybuild/easyconfigs/t/Tar/Tar-1.26-ictce-5.3.0.eb index 20133db903..7791f62bfc 100644 --- a/easybuild/easyconfigs/t/Tar/Tar-1.26-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/t/Tar/Tar-1.26-ictce-5.3.0.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild recipy as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild recipy as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright (c) 2012-2013 Cyprus Institute / CaSToRC # Author:: Thekla Loizou diff --git a/easybuild/easyconfigs/t/Tesla-Deployment-Kit/Tesla-Deployment-Kit-5.319.43.eb b/easybuild/easyconfigs/t/Tesla-Deployment-Kit/Tesla-Deployment-Kit-5.319.43.eb index af40f4958d..e759c8ef98 100644 --- a/easybuild/easyconfigs/t/Tesla-Deployment-Kit/Tesla-Deployment-Kit-5.319.43.eb +++ b/easybuild/easyconfigs/t/Tesla-Deployment-Kit/Tesla-Deployment-Kit-5.319.43.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/t/TopHat/TopHat-2.0.10-ictce-5.5.0.eb b/easybuild/easyconfigs/t/TopHat/TopHat-2.0.10-ictce-5.5.0.eb index 063b42af9e..febb5f6fbb 100644 --- a/easybuild/easyconfigs/t/TopHat/TopHat-2.0.10-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/t/TopHat/TopHat-2.0.10-ictce-5.5.0.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Cedric Laczny , Fotis Georgatos , Jens Timmerman diff --git a/easybuild/easyconfigs/t/TopHat/TopHat-2.0.13-goolf-1.7.20.eb b/easybuild/easyconfigs/t/TopHat/TopHat-2.0.13-goolf-1.7.20.eb index d99d70b100..43d3b55138 100644 --- a/easybuild/easyconfigs/t/TopHat/TopHat-2.0.13-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/t/TopHat/TopHat-2.0.13-goolf-1.7.20.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/t/TopHat/TopHat-2.0.14-goolf-1.7.20.eb b/easybuild/easyconfigs/t/TopHat/TopHat-2.0.14-goolf-1.7.20.eb index 6743572399..63c44a4d0f 100644 --- a/easybuild/easyconfigs/t/TopHat/TopHat-2.0.14-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/t/TopHat/TopHat-2.0.14-goolf-1.7.20.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/t/TopHat/TopHat-2.0.4-goolf-1.4.10.eb b/easybuild/easyconfigs/t/TopHat/TopHat-2.0.4-goolf-1.4.10.eb index 0136815261..22225c98c3 100644 --- a/easybuild/easyconfigs/t/TopHat/TopHat-2.0.4-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/t/TopHat/TopHat-2.0.4-goolf-1.4.10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Cedric Laczny , Fotis Georgatos diff --git a/easybuild/easyconfigs/t/TopHat/TopHat-2.0.8-goolf-1.4.10-biodeps-1.6-extended.eb b/easybuild/easyconfigs/t/TopHat/TopHat-2.0.8-goolf-1.4.10-biodeps-1.6-extended.eb index dff35b1d3f..c3104a01d2 100644 --- a/easybuild/easyconfigs/t/TopHat/TopHat-2.0.8-goolf-1.4.10-biodeps-1.6-extended.eb +++ b/easybuild/easyconfigs/t/TopHat/TopHat-2.0.8-goolf-1.4.10-biodeps-1.6-extended.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Cedric Laczny , Fotis Georgatos diff --git a/easybuild/easyconfigs/t/TopHat/TopHat-2.0.8-ictce-5.3.0-biodeps-1.6-extended.eb b/easybuild/easyconfigs/t/TopHat/TopHat-2.0.8-ictce-5.3.0-biodeps-1.6-extended.eb index 5890c30330..30a6d4d9a9 100644 --- a/easybuild/easyconfigs/t/TopHat/TopHat-2.0.8-ictce-5.3.0-biodeps-1.6-extended.eb +++ b/easybuild/easyconfigs/t/TopHat/TopHat-2.0.8-ictce-5.3.0-biodeps-1.6-extended.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Cedric Laczny , Fotis Georgatos diff --git a/easybuild/easyconfigs/t/TopHat/TopHat-2.0.8-ictce-5.3.0.eb b/easybuild/easyconfigs/t/TopHat/TopHat-2.0.8-ictce-5.3.0.eb index 60dbbd04a5..900fa70d9e 100644 --- a/easybuild/easyconfigs/t/TopHat/TopHat-2.0.8-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/t/TopHat/TopHat-2.0.8-ictce-5.3.0.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Cedric Laczny , Fotis Georgatos , Jens Timmerman diff --git a/easybuild/easyconfigs/t/TopHat/TopHat-2.1.0-intel-2015b.eb b/easybuild/easyconfigs/t/TopHat/TopHat-2.1.0-intel-2015b.eb index f7aede356f..41077a3e98 100644 --- a/easybuild/easyconfigs/t/TopHat/TopHat-2.1.0-intel-2015b.eb +++ b/easybuild/easyconfigs/t/TopHat/TopHat-2.1.0-intel-2015b.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/t/TopHat/TopHat-2.1.1-foss-2015b.eb b/easybuild/easyconfigs/t/TopHat/TopHat-2.1.1-foss-2015b.eb index 3bdcb05552..2dd3fe0d6e 100644 --- a/easybuild/easyconfigs/t/TopHat/TopHat-2.1.1-foss-2015b.eb +++ b/easybuild/easyconfigs/t/TopHat/TopHat-2.1.1-foss-2015b.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/t/TopHat/TopHat-2.1.1-foss-2016a.eb b/easybuild/easyconfigs/t/TopHat/TopHat-2.1.1-foss-2016a.eb index bf3b1885b2..e3d8f194e2 100644 --- a/easybuild/easyconfigs/t/TopHat/TopHat-2.1.1-foss-2016a.eb +++ b/easybuild/easyconfigs/t/TopHat/TopHat-2.1.1-foss-2016a.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/t/TopHat/TopHat-2.1.1-intel-2017a.eb b/easybuild/easyconfigs/t/TopHat/TopHat-2.1.1-intel-2017a.eb index f3be80ad62..f3a9590faf 100644 --- a/easybuild/easyconfigs/t/TopHat/TopHat-2.1.1-intel-2017a.eb +++ b/easybuild/easyconfigs/t/TopHat/TopHat-2.1.1-intel-2017a.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/t/TotalView/TotalView-8.11.0-0-linux-x86-64.eb b/easybuild/easyconfigs/t/TotalView/TotalView-8.11.0-0-linux-x86-64.eb index edea937fc8..2994b54774 100644 --- a/easybuild/easyconfigs/t/TotalView/TotalView-8.11.0-0-linux-x86-64.eb +++ b/easybuild/easyconfigs/t/TotalView/TotalView-8.11.0-0-linux-x86-64.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/t/TotalView/TotalView-8.11.0-2-linux-x86-64.eb b/easybuild/easyconfigs/t/TotalView/TotalView-8.11.0-2-linux-x86-64.eb index 7af5c3b6cd..b17b02345e 100644 --- a/easybuild/easyconfigs/t/TotalView/TotalView-8.11.0-2-linux-x86-64.eb +++ b/easybuild/easyconfigs/t/TotalView/TotalView-8.11.0-2-linux-x86-64.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild recipy as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild recipy as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/t/TotalView/TotalView-8.12.0-0-linux-x86-64.eb b/easybuild/easyconfigs/t/TotalView/TotalView-8.12.0-0-linux-x86-64.eb index 69f8803b05..2a37a8ab13 100644 --- a/easybuild/easyconfigs/t/TotalView/TotalView-8.12.0-0-linux-x86-64.eb +++ b/easybuild/easyconfigs/t/TotalView/TotalView-8.12.0-0-linux-x86-64.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild recipy as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild recipy as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/t/Trimmomatic/Trimmomatic-0.32-Java-1.7.0_80.eb b/easybuild/easyconfigs/t/Trimmomatic/Trimmomatic-0.32-Java-1.7.0_80.eb index 091f914cb3..bcb8cdfed4 100644 --- a/easybuild/easyconfigs/t/Trimmomatic/Trimmomatic-0.32-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/t/Trimmomatic/Trimmomatic-0.32-Java-1.7.0_80.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/t/Trinity/Trinity-2.0.4-goolf-1.4.10.eb b/easybuild/easyconfigs/t/Trinity/Trinity-2.0.4-goolf-1.4.10.eb index 1f448f04b9..821333d6ef 100644 --- a/easybuild/easyconfigs/t/Trinity/Trinity-2.0.4-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/t/Trinity/Trinity-2.0.4-goolf-1.4.10.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/t/Trinity/Trinity-2.0.6-goolf-1.4.10.eb b/easybuild/easyconfigs/t/Trinity/Trinity-2.0.6-goolf-1.4.10.eb index 30e64b353f..014e8ca411 100644 --- a/easybuild/easyconfigs/t/Trinity/Trinity-2.0.6-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/t/Trinity/Trinity-2.0.6-goolf-1.4.10.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/t/Trinity/Trinity-2.2.0-foss-2016a.eb b/easybuild/easyconfigs/t/Trinity/Trinity-2.2.0-foss-2016a.eb index 181142b3db..b4e2affc99 100644 --- a/easybuild/easyconfigs/t/Trinity/Trinity-2.2.0-foss-2016a.eb +++ b/easybuild/easyconfigs/t/Trinity/Trinity-2.2.0-foss-2016a.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/t/tabix/tabix-0.2.6-goolf-1.4.10.eb b/easybuild/easyconfigs/t/tabix/tabix-0.2.6-goolf-1.4.10.eb index e138adfe4c..6169c8b9f9 100644 --- a/easybuild/easyconfigs/t/tabix/tabix-0.2.6-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/t/tabix/tabix-0.2.6-goolf-1.4.10.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/t/tabix/tabix-0.2.6-intel-2014b.eb b/easybuild/easyconfigs/t/tabix/tabix-0.2.6-intel-2014b.eb index af291cd25c..beb5e691d0 100644 --- a/easybuild/easyconfigs/t/tabix/tabix-0.2.6-intel-2014b.eb +++ b/easybuild/easyconfigs/t/tabix/tabix-0.2.6-intel-2014b.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/t/tabix/tabix-0.2.6-intel-2016b.eb b/easybuild/easyconfigs/t/tabix/tabix-0.2.6-intel-2016b.eb index ef8197538d..6524a38488 100644 --- a/easybuild/easyconfigs/t/tabix/tabix-0.2.6-intel-2016b.eb +++ b/easybuild/easyconfigs/t/tabix/tabix-0.2.6-intel-2016b.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayGNU-2015.06.eb b/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayGNU-2015.06.eb index bf01430fff..09047308c7 100644 --- a/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayGNU-2015.06.eb +++ b/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayGNU-2015.06.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2013 University of Luxembourg/Computer Science and Communications Research Unit # Authors:: Valentin Plugaru diff --git a/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayGNU-2015.11.eb b/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayGNU-2015.11.eb index 57a30b1d87..b79551e930 100644 --- a/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayGNU-2015.11.eb +++ b/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayGNU-2015.11.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2013 University of Luxembourg/Computer Science and Communications Research Unit # Authors:: Valentin Plugaru diff --git a/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayIntel-2015.11.eb b/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayIntel-2015.11.eb index 558feb7579..79fccb1726 100644 --- a/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayIntel-2015.11.eb +++ b/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayIntel-2015.11.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2013 University of Luxembourg/Computer Science and Communications Research Unit # Authors:: Valentin Plugaru diff --git a/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-foss-2015a.eb b/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-foss-2015a.eb index 4b5f7237ff..20e7328d6b 100644 --- a/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-foss-2015a.eb +++ b/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-foss-2015a.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2013 University of Luxembourg/Computer Science and Communications Research Unit # Authors:: Valentin Plugaru diff --git a/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-goolf-1.4.10.eb b/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-goolf-1.4.10.eb index a414135707..a3d8189e6b 100644 --- a/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-goolf-1.4.10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2013 University of Luxembourg/Computer Science and Communications Research Unit # Authors:: Valentin Plugaru diff --git a/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-goolf-1.5.14.eb b/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-goolf-1.5.14.eb index 5e7647f183..2997563ac9 100644 --- a/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-goolf-1.5.14.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2013 University of Luxembourg/Computer Science and Communications Research Unit # Authors:: Valentin Plugaru diff --git a/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-ictce-5.3.0.eb b/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-ictce-5.3.0.eb index 432a9ad37d..7adcf86b00 100644 --- a/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-ictce-5.3.0.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2013 University of Luxembourg/Computer Science and Communications Research Unit # Authors:: Valentin Plugaru diff --git a/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-intel-2014b.eb b/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-intel-2014b.eb index 648d6836c1..4cfdeaa84c 100644 --- a/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-intel-2014b.eb +++ b/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-intel-2014b.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2013 University of Luxembourg/Computer Science and Communications Research Unit # Authors:: Valentin Plugaru diff --git a/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-intel-2015a.eb b/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-intel-2015a.eb index 747d099188..ba0c2dc9f5 100644 --- a/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-intel-2015a.eb +++ b/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-intel-2015a.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2013 University of Luxembourg/Computer Science and Communications Research Unit # Authors:: Valentin Plugaru diff --git a/easybuild/easyconfigs/t/tcsh/tcsh-6.19.00-intel-2015a.eb b/easybuild/easyconfigs/t/tcsh/tcsh-6.19.00-intel-2015a.eb index ef7cef982f..a1e7c5f53c 100644 --- a/easybuild/easyconfigs/t/tcsh/tcsh-6.19.00-intel-2015a.eb +++ b/easybuild/easyconfigs/t/tcsh/tcsh-6.19.00-intel-2015a.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2013 University of Luxembourg/Computer Science and Communications Research Unit # Authors:: Valentin Plugaru diff --git a/easybuild/easyconfigs/t/tcsh/tcsh-6.19.00-intel-2016a.eb b/easybuild/easyconfigs/t/tcsh/tcsh-6.19.00-intel-2016a.eb index 4a02bab4b4..3f9f04e15c 100644 --- a/easybuild/easyconfigs/t/tcsh/tcsh-6.19.00-intel-2016a.eb +++ b/easybuild/easyconfigs/t/tcsh/tcsh-6.19.00-intel-2016a.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2013 University of Luxembourg/Computer Science and Communications Research Unit # Authors:: Valentin Plugaru diff --git a/easybuild/easyconfigs/t/tcsh/tcsh-6.20.00-GCCcore-5.4.0.eb b/easybuild/easyconfigs/t/tcsh/tcsh-6.20.00-GCCcore-5.4.0.eb index 1413bb1d34..7522e28d25 100644 --- a/easybuild/easyconfigs/t/tcsh/tcsh-6.20.00-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/t/tcsh/tcsh-6.20.00-GCCcore-5.4.0.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2013 University of Luxembourg/Computer Science and Communications Research Unit # Authors:: Valentin Plugaru diff --git a/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.1.24-goolf-1.4.10.eb b/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.1.24-goolf-1.4.10.eb index 72d80a88dd..2ab471b817 100644 --- a/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.1.24-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.1.24-goolf-1.4.10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2013 University of Luxembourg, Ghent University # Authors:: Fotis Georgatos , Kenneth Hoste (Ghent University) diff --git a/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.1.24-ictce-5.2.0.eb b/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.1.24-ictce-5.2.0.eb index 6769cda969..638cd3928b 100644 --- a/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.1.24-ictce-5.2.0.eb +++ b/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.1.24-ictce-5.2.0.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2013 University of Luxembourg, Ghent University # Authors:: Fotis Georgatos , Kenneth Hoste (Ghent University) diff --git a/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.1.24-ictce-5.3.0.eb b/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.1.24-ictce-5.3.0.eb index 13138db3b0..bec670c6aa 100644 --- a/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.1.24-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.1.24-ictce-5.3.0.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2013 University of Luxembourg, Ghent University # Authors:: Fotis Georgatos , Kenneth Hoste (Ghent University) diff --git a/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.1.24-ictce-5.4.0.eb b/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.1.24-ictce-5.4.0.eb index 39dc1241a0..6aff879dc7 100644 --- a/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.1.24-ictce-5.4.0.eb +++ b/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.1.24-ictce-5.4.0.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2013 University of Luxembourg, Ghent University # Authors:: Fotis Georgatos , Kenneth Hoste (Ghent University) diff --git a/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.1.24-intel-2014b.eb b/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.1.24-intel-2014b.eb index e773e384b2..432d91c019 100644 --- a/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.1.24-intel-2014b.eb +++ b/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.1.24-intel-2014b.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2013 University of Luxembourg, Ghent University # Authors:: Fotis Georgatos , Kenneth Hoste (Ghent University) diff --git a/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.19-intel-2015a.eb b/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.19-intel-2015a.eb index 964a50f27f..4cb77bfe4a 100644 --- a/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.19-intel-2015a.eb +++ b/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.19-intel-2015a.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2013 University of Luxembourg, Ghent University # Authors:: Fotis Georgatos , Kenneth Hoste (Ghent University) diff --git a/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.19-intel-2015b.eb b/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.19-intel-2015b.eb index efdb4ae86f..b02471d463 100644 --- a/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.19-intel-2015b.eb +++ b/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.19-intel-2015b.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2013 University of Luxembourg, Ghent University # Authors:: Fotis Georgatos , Kenneth Hoste (Ghent University) diff --git a/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.20-foss-2016a.eb b/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.20-foss-2016a.eb index a1f9ee01f4..72be70a029 100644 --- a/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.20-foss-2016a.eb +++ b/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.20-foss-2016a.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2013 University of Luxembourg, Ghent University # Authors:: Fotis Georgatos , Kenneth Hoste (Ghent University) diff --git a/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.20-intel-2016b.eb b/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.20-intel-2016b.eb index ae9bb8dae3..318c851243 100644 --- a/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.20-intel-2016b.eb +++ b/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.20-intel-2016b.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2013 University of Luxembourg, Ghent University # Authors:: Fotis Georgatos , Kenneth Hoste (Ghent University) diff --git a/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.24-intel-2017a.eb b/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.24-intel-2017a.eb index 0e89a4b4d6..70717c12c1 100644 --- a/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.24-intel-2017a.eb +++ b/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.24-intel-2017a.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2013 University of Luxembourg, Ghent University # Authors:: Fotis Georgatos , Kenneth Hoste (Ghent University) diff --git a/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.11-goolf-1.4.10-Perl-5.16.3.eb b/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.11-goolf-1.4.10-Perl-5.16.3.eb index 47c30351f2..fbb9094225 100644 --- a/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.11-goolf-1.4.10-Perl-5.16.3.eb +++ b/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.11-goolf-1.4.10-Perl-5.16.3.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.11-ictce-5.5.0-Perl-5.16.3.eb b/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.11-ictce-5.5.0-Perl-5.16.3.eb index 1350a7b674..d9afc1fbcd 100644 --- a/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.11-ictce-5.5.0-Perl-5.16.3.eb +++ b/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.11-ictce-5.5.0-Perl-5.16.3.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.12-goolf-1.4.10-Perl-5.16.3.eb b/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.12-goolf-1.4.10-Perl-5.16.3.eb index 26093f8c38..9ba6154d14 100644 --- a/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.12-goolf-1.4.10-Perl-5.16.3.eb +++ b/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.12-goolf-1.4.10-Perl-5.16.3.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.14-foss-2015b-Perl-5.20.3.eb b/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.14-foss-2015b-Perl-5.20.3.eb index 9d1e642f25..c64bd42cd9 100644 --- a/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.14-foss-2015b-Perl-5.20.3.eb +++ b/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.14-foss-2015b-Perl-5.20.3.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.14-foss-2016a-Perl-5.22.1.eb b/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.14-foss-2016a-Perl-5.22.1.eb index c7db740277..a5698a5603 100644 --- a/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.14-foss-2016a-Perl-5.22.1.eb +++ b/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.14-foss-2016a-Perl-5.22.1.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.14-goolf-1.4.10-Perl-5.16.3.eb b/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.14-goolf-1.4.10-Perl-5.16.3.eb index 1213968867..46e460924a 100644 --- a/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.14-goolf-1.4.10-Perl-5.16.3.eb +++ b/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.14-goolf-1.4.10-Perl-5.16.3.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # sciCORE - University of Basel # SIB Swiss Institute of Bioinformatics diff --git a/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.14-goolf-1.7.20-Perl-5.22.2.eb b/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.14-goolf-1.7.20-Perl-5.22.2.eb index 0a12c2e817..d984b53e5f 100644 --- a/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.14-goolf-1.7.20-Perl-5.22.2.eb +++ b/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.14-goolf-1.7.20-Perl-5.22.2.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # sciCORE - University of Basel # SIB Swiss Institute of Bioinformatics diff --git a/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.14-intel-2016a-Perl-5.22.1.eb b/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.14-intel-2016a-Perl-5.22.1.eb index 9f1d001bfa..08f1cb8b26 100644 --- a/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.14-intel-2016a-Perl-5.22.1.eb +++ b/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.14-intel-2016a-Perl-5.22.1.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/v/VEGAS/VEGAS-0.8.27.eb b/easybuild/easyconfigs/v/VEGAS/VEGAS-0.8.27.eb index 367fff5696..ecaa08a980 100644 --- a/easybuild/easyconfigs/v/VEGAS/VEGAS-0.8.27.eb +++ b/easybuild/easyconfigs/v/VEGAS/VEGAS-0.8.27.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Ravi Tripathi # Email: ravi89@uab.edu diff --git a/easybuild/easyconfigs/v/VMD/VMD-1.9.3-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/v/VMD/VMD-1.9.3-intel-2016b-Python-2.7.12.eb index 54be12bcef..2f45c3f95b 100644 --- a/easybuild/easyconfigs/v/VMD/VMD-1.9.3-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/v/VMD/VMD-1.9.3-intel-2016b-Python-2.7.12.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Authors:: Stephane Thiell ## name = 'VMD' diff --git a/easybuild/easyconfigs/v/VTK/VTK-5.10.1-goolf-1.4.10.eb b/easybuild/easyconfigs/v/VTK/VTK-5.10.1-goolf-1.4.10.eb index 8849734f1b..93686e2ec1 100644 --- a/easybuild/easyconfigs/v/VTK/VTK-5.10.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/v/VTK/VTK-5.10.1-goolf-1.4.10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/v/VTK/VTK-5.10.1-ictce-5.3.0.eb b/easybuild/easyconfigs/v/VTK/VTK-5.10.1-ictce-5.3.0.eb index 45d8b25c17..9bb845d1ba 100644 --- a/easybuild/easyconfigs/v/VTK/VTK-5.10.1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/v/VTK/VTK-5.10.1-ictce-5.3.0.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/v/VTK/VTK-6.3.0-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/v/VTK/VTK-6.3.0-foss-2016b-Python-2.7.12.eb index 71edba0d68..053267f953 100644 --- a/easybuild/easyconfigs/v/VTK/VTK-6.3.0-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/v/VTK/VTK-6.3.0-foss-2016b-Python-2.7.12.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/v/VTK/VTK-6.3.0-intel-2015b-Python-2.7.11.eb b/easybuild/easyconfigs/v/VTK/VTK-6.3.0-intel-2015b-Python-2.7.11.eb index 94b031902b..4bb971d12b 100644 --- a/easybuild/easyconfigs/v/VTK/VTK-6.3.0-intel-2015b-Python-2.7.11.eb +++ b/easybuild/easyconfigs/v/VTK/VTK-6.3.0-intel-2015b-Python-2.7.11.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/v/VTK/VTK-6.3.0-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/v/VTK/VTK-6.3.0-intel-2016a-Python-2.7.11.eb index e549b2e963..8128b35ee7 100644 --- a/easybuild/easyconfigs/v/VTK/VTK-6.3.0-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/v/VTK/VTK-6.3.0-intel-2016a-Python-2.7.11.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/v/VTK/VTK-6.3.0-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/v/VTK/VTK-6.3.0-intel-2016b-Python-2.7.12.eb index d63c30f413..164e61a3e9 100644 --- a/easybuild/easyconfigs/v/VTK/VTK-6.3.0-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/v/VTK/VTK-6.3.0-intel-2016b-Python-2.7.12.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/v/VTK/VTK-7.0.0-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/v/VTK/VTK-7.0.0-intel-2016b-Python-2.7.12.eb index ce85c69cbd..ed12cc491a 100644 --- a/easybuild/easyconfigs/v/VTK/VTK-7.0.0-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/v/VTK/VTK-7.0.0-intel-2016b-Python-2.7.12.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/v/VTK/VTK-7.1.0-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/v/VTK/VTK-7.1.0-intel-2016b-Python-2.7.12.eb index ff2f4a0f63..748919048a 100644 --- a/easybuild/easyconfigs/v/VTK/VTK-7.1.0-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/v/VTK/VTK-7.1.0-intel-2016b-Python-2.7.12.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/v/VTK/VTK-7.1.1-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/v/VTK/VTK-7.1.1-intel-2017a-Python-2.7.13.eb index e0221778a4..dffb09bfb6 100644 --- a/easybuild/easyconfigs/v/VTK/VTK-7.1.1-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/v/VTK/VTK-7.1.1-intel-2017a-Python-2.7.13.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/v/Valgrind/Valgrind-3.8.1-goolf-1.4.10.eb b/easybuild/easyconfigs/v/Valgrind/Valgrind-3.8.1-goolf-1.4.10.eb index 577f4846d8..f191980d63 100644 --- a/easybuild/easyconfigs/v/Valgrind/Valgrind-3.8.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/v/Valgrind/Valgrind-3.8.1-goolf-1.4.10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-demo.eb b/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-demo.eb index 85c8901493..920b6b2d14 100644 --- a/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-demo.eb +++ b/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-demo.eb @@ -1,5 +1,5 @@ ## -# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2013-2015 Juelich Supercomputing Centre, Germany # Authors:: Bernd Mohr diff --git a/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1.eb b/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1.eb index a25a9d20e8..d365513d88 100644 --- a/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1.eb +++ b/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1.eb @@ -1,5 +1,5 @@ ## -# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2013-2015 Juelich Supercomputing Centre, Germany # Authors:: Bernd Mohr diff --git a/easybuild/easyconfigs/v/VampirServer/VampirServer-8.4.1-gompi-2015a.eb b/easybuild/easyconfigs/v/VampirServer/VampirServer-8.4.1-gompi-2015a.eb index 6a97299365..17cc603f5a 100644 --- a/easybuild/easyconfigs/v/VampirServer/VampirServer-8.4.1-gompi-2015a.eb +++ b/easybuild/easyconfigs/v/VampirServer/VampirServer-8.4.1-gompi-2015a.eb @@ -1,5 +1,5 @@ ## -# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2013-2015 Juelich Supercomputing Centre, Germany # Authors:: Bernd Mohr diff --git a/easybuild/easyconfigs/v/VampirTrace/VampirTrace-5.14.4-goolf-1.5.14.eb b/easybuild/easyconfigs/v/VampirTrace/VampirTrace-5.14.4-goolf-1.5.14.eb index 8c1fc2104f..55d368233c 100644 --- a/easybuild/easyconfigs/v/VampirTrace/VampirTrace-5.14.4-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/v/VampirTrace/VampirTrace-5.14.4-goolf-1.5.14.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild # Copyright:: Copyright 2013 Juelich Supercomputing Centre, Germany # Authors:: Bernd Mohr # License:: New BSD diff --git a/easybuild/easyconfigs/v/VarScan/VarScan-2.3.6-Java-1.7.0_80.eb b/easybuild/easyconfigs/v/VarScan/VarScan-2.3.6-Java-1.7.0_80.eb index 88844689a5..afd1980045 100644 --- a/easybuild/easyconfigs/v/VarScan/VarScan-2.3.6-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/v/VarScan/VarScan-2.3.6-Java-1.7.0_80.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Adam Huffman # The Francis Crick Institute diff --git a/easybuild/easyconfigs/v/VarScan/VarScan-2.4.1-Java-1.7.0_80.eb b/easybuild/easyconfigs/v/VarScan/VarScan-2.4.1-Java-1.7.0_80.eb index dd6c6f31b0..b1573bf27c 100644 --- a/easybuild/easyconfigs/v/VarScan/VarScan-2.4.1-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/v/VarScan/VarScan-2.4.1-Java-1.7.0_80.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Adam Huffman, based on initial work by Jordi Blasco # The Francis Crick Institute diff --git a/easybuild/easyconfigs/v/Velvet/Velvet-1.2.07-goolf-1.4.10.eb b/easybuild/easyconfigs/v/Velvet/Velvet-1.2.07-goolf-1.4.10.eb index 8e5bf1c81c..1a83b16bd6 100644 --- a/easybuild/easyconfigs/v/Velvet/Velvet-1.2.07-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/v/Velvet/Velvet-1.2.07-goolf-1.4.10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Cedric Laczny , Fotis Georgatos diff --git a/easybuild/easyconfigs/v/Velvet/Velvet-1.2.07-ictce-5.3.0.eb b/easybuild/easyconfigs/v/Velvet/Velvet-1.2.07-ictce-5.3.0.eb index 7fff5ef5b5..fab2964040 100644 --- a/easybuild/easyconfigs/v/Velvet/Velvet-1.2.07-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/v/Velvet/Velvet-1.2.07-ictce-5.3.0.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Cedric Laczny , Fotis Georgatos diff --git a/easybuild/easyconfigs/v/Velvet/Velvet-1.2.09-goolf-1.4.10.eb b/easybuild/easyconfigs/v/Velvet/Velvet-1.2.09-goolf-1.4.10.eb index e2ba08da33..310c71d1cf 100644 --- a/easybuild/easyconfigs/v/Velvet/Velvet-1.2.09-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/v/Velvet/Velvet-1.2.09-goolf-1.4.10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2013 The Cyprus Institute # Authors:: Thekla Loizou , Andreas Panteli diff --git a/easybuild/easyconfigs/v/Velvet/Velvet-1.2.09-ictce-5.3.0.eb b/easybuild/easyconfigs/v/Velvet/Velvet-1.2.09-ictce-5.3.0.eb index 24b79e8841..df2799a1c3 100644 --- a/easybuild/easyconfigs/v/Velvet/Velvet-1.2.09-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/v/Velvet/Velvet-1.2.09-ictce-5.3.0.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Thekla Loizou , Andreas Panteli diff --git a/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-goolf-1.4.10-mt-kmer_31.eb b/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-goolf-1.4.10-mt-kmer_31.eb index 7c27a7683f..99932f6b56 100644 --- a/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-goolf-1.4.10-mt-kmer_31.eb +++ b/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-goolf-1.4.10-mt-kmer_31.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2013 The Cyprus Institute # Authors:: Thekla Loizou , Andreas Panteli diff --git a/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-goolf-1.4.10-mt-kmer_57.eb b/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-goolf-1.4.10-mt-kmer_57.eb index 8457ee4903..41695b9d6e 100644 --- a/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-goolf-1.4.10-mt-kmer_57.eb +++ b/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-goolf-1.4.10-mt-kmer_57.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2013 The Cyprus Institute # Authors:: Thekla Loizou , Andreas Panteli diff --git a/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-goolf-1.4.10-mt-kmer_63.eb b/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-goolf-1.4.10-mt-kmer_63.eb index ad56fb1790..e2cb044179 100644 --- a/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-goolf-1.4.10-mt-kmer_63.eb +++ b/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-goolf-1.4.10-mt-kmer_63.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2013 The Cyprus Institute # Authors:: Thekla Loizou , Andreas Panteli diff --git a/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2015b-mt-kmer_100-Perl-5.20.3.eb b/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2015b-mt-kmer_100-Perl-5.20.3.eb index d05f4f9c7a..0c9debe597 100644 --- a/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2015b-mt-kmer_100-Perl-5.20.3.eb +++ b/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2015b-mt-kmer_100-Perl-5.20.3.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA, 2012-2013 The Cyprus Institute # Authors:: Cedric Laczny , Fotis Georgatos , diff --git a/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2015b-mt-kmer_100.eb b/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2015b-mt-kmer_100.eb index 52c0ab85db..7fc70475a3 100644 --- a/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2015b-mt-kmer_100.eb +++ b/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2015b-mt-kmer_100.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA, 2012-2013 The Cyprus Institute # Authors:: Cedric Laczny , Fotis Georgatos , diff --git a/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2015b-mt-kmer_31-Perl-5.20.3.eb b/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2015b-mt-kmer_31-Perl-5.20.3.eb index fe2df81ad0..8ee19aee56 100644 --- a/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2015b-mt-kmer_31-Perl-5.20.3.eb +++ b/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2015b-mt-kmer_31-Perl-5.20.3.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA, 2012-2013 The Cyprus Institute # Authors:: Cedric Laczny , Fotis Georgatos , diff --git a/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2015b-mt-kmer_31.eb b/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2015b-mt-kmer_31.eb index c23584dddd..fe1e76769e 100644 --- a/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2015b-mt-kmer_31.eb +++ b/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2015b-mt-kmer_31.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA, 2012-2013 The Cyprus Institute # Authors:: Cedric Laczny , Fotis Georgatos , diff --git a/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2017a-mt-kmer_37.eb b/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2017a-mt-kmer_37.eb index 19b58c6e52..8e2cfba9b5 100644 --- a/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2017a-mt-kmer_37.eb +++ b/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2017a-mt-kmer_37.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA, 2012-2013 The Cyprus Institute # Authors:: Cedric Laczny , Fotis Georgatos , diff --git a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-goolf-1.4.10.eb b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-goolf-1.4.10.eb index 45a8cbb1a5..924f3ce2cc 100644 --- a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-goolf-1.4.10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Cedric Laczny , Fotis Georgatos diff --git a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-ictce-5.3.0.eb b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-ictce-5.3.0.eb index fafae9335e..cf8e038130 100644 --- a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-ictce-5.3.0.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Cedric Laczny , Fotis Georgatos diff --git a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.1.6-ictce-5.5.0.eb b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.1.6-ictce-5.5.0.eb index 29c51c1030..b1d2ca1c12 100644 --- a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.1.6-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.1.6-ictce-5.5.0.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Cedric Laczny , Fotis Georgatos diff --git a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.2.3-intel-2016b.eb b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.2.3-intel-2016b.eb index 3214395e25..dc5c973772 100644 --- a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.2.3-intel-2016b.eb +++ b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.2.3-intel-2016b.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Cedric Laczny , Fotis Georgatos diff --git a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.3.4-foss-2016b.eb b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.3.4-foss-2016b.eb index ec625ff6c6..4f26e4b2b5 100644 --- a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.3.4-foss-2016b.eb +++ b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.3.4-foss-2016b.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild easyblock = 'ConfigureMake' diff --git a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.3.5-intel-2017a.eb b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.3.5-intel-2017a.eb index fc2a6f62b8..1232bbbdcc 100644 --- a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.3.5-intel-2017a.eb +++ b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.3.5-intel-2017a.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Cedric Laczny , Fotis Georgatos diff --git a/easybuild/easyconfigs/v/Vim/Vim-7.4-goolf-1.4.10.eb b/easybuild/easyconfigs/v/Vim/Vim-7.4-goolf-1.4.10.eb index 824152274f..9e67a4c535 100644 --- a/easybuild/easyconfigs/v/Vim/Vim-7.4-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/v/Vim/Vim-7.4-goolf-1.4.10.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/v/Vim/Vim-8.0-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/v/Vim/Vim-8.0-foss-2016a-Python-2.7.11.eb index 674a6d44d5..f0f30967f2 100644 --- a/easybuild/easyconfigs/v/Vim/Vim-8.0-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/v/Vim/Vim-8.0-foss-2016a-Python-2.7.11.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/v/Viper/Viper-1.0.0-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/v/Viper/Viper-1.0.0-goolf-1.4.10-Python-2.7.3.eb index 120e8225ae..51976a2e40 100644 --- a/easybuild/easyconfigs/v/Viper/Viper-1.0.0-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/v/Viper/Viper-1.0.0-goolf-1.4.10-Python-2.7.3.eb @@ -22,7 +22,7 @@ versionsuffix = "-%s-%s" % (python, pythonversion) dependencies = [(python, pythonversion)] # hack, 'import viper' fails because VTK and numpy dependencies are missing -# see https://github.com/hpcugent/easybuild-easyconfigs/issues/100 +# see https://github.com/easybuilders/easybuild-easyconfigs/issues/100 options = {'modulename': 'os'} sanity_check_paths = { diff --git a/easybuild/easyconfigs/v/Viper/Viper-1.0.0-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/v/Viper/Viper-1.0.0-ictce-5.3.0-Python-2.7.3.eb index 5c807c96fb..5d302a4553 100644 --- a/easybuild/easyconfigs/v/Viper/Viper-1.0.0-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/v/Viper/Viper-1.0.0-ictce-5.3.0-Python-2.7.3.eb @@ -23,7 +23,7 @@ versionsuffix = "-%s-%s" % (python, pythonversion) dependencies = [(python, pythonversion)] # hack, 'import viper' fails because VTK and numpy dependencies are missing -# see https://github.com/hpcugent/easybuild-easyconfigs/issues/100 +# see https://github.com/easybuilders/easybuild-easyconfigs/issues/100 options = {'modulename': 'os'} sanity_check_paths = { diff --git a/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-3.2.1.eb b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-3.2.1.eb index 368c166390..1243b5ec82 100644 --- a/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-3.2.1.eb +++ b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-3.2.1.eb @@ -3,7 +3,7 @@ easyblock = 'VersionIndependentPythonPackage' name = 'vsc-mympirun' version = '3.2.1' -homepage = 'http://github.com/hpcugent/vsc-mympirun/' +homepage = 'https://github.com/hpcugent/vsc-mympirun/' description = """VSC-tools is a set of Python libraries and scripts that are commonly used within HPC-UGent.""" # we build this to work with every python version diff --git a/easybuild/easyconfigs/v/vt/vt-0.577-goolf-1.7.20.eb b/easybuild/easyconfigs/v/vt/vt-0.577-goolf-1.7.20.eb index f8de4a4721..9bf6597cd2 100644 --- a/easybuild/easyconfigs/v/vt/vt-0.577-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/v/vt/vt-0.577-goolf-1.7.20.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # sciCORE - University of Basel # SIB Swiss Institute of Bioinformatics diff --git a/easybuild/easyconfigs/w/WEKA/WEKA-3.6.12-Java-1.7.0_80.eb b/easybuild/easyconfigs/w/WEKA/WEKA-3.6.12-Java-1.7.0_80.eb index c6a5e3fa14..94ae40e0cd 100644 --- a/easybuild/easyconfigs/w/WEKA/WEKA-3.6.12-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/w/WEKA/WEKA-3.6.12-Java-1.7.0_80.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/w/WEKA/WEKA-3.7.0-Java-1.7.0_80.eb b/easybuild/easyconfigs/w/WEKA/WEKA-3.7.0-Java-1.7.0_80.eb index 96ac9d6530..a06d973254 100644 --- a/easybuild/easyconfigs/w/WEKA/WEKA-3.7.0-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/w/WEKA/WEKA-3.7.0-Java-1.7.0_80.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/w/WHAM/WHAM-2.0.9-goolf-1.4.10.eb b/easybuild/easyconfigs/w/WHAM/WHAM-2.0.9-goolf-1.4.10.eb index e27e4f7760..e4cd7e32e8 100644 --- a/easybuild/easyconfigs/w/WHAM/WHAM-2.0.9-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/w/WHAM/WHAM-2.0.9-goolf-1.4.10.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/w/WHAM/WHAM-2.0.9-ictce-6.2.5.eb b/easybuild/easyconfigs/w/WHAM/WHAM-2.0.9-ictce-6.2.5.eb index cb26524e7f..e26d3170c2 100644 --- a/easybuild/easyconfigs/w/WHAM/WHAM-2.0.9-ictce-6.2.5.eb +++ b/easybuild/easyconfigs/w/WHAM/WHAM-2.0.9-ictce-6.2.5.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel diff --git a/easybuild/easyconfigs/w/wiki2beamer/wiki2beamer-0.9.5-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/w/wiki2beamer/wiki2beamer-0.9.5-goolf-1.4.10-Python-2.7.3.eb index 71553532b1..fe7a81ee6d 100644 --- a/easybuild/easyconfigs/w/wiki2beamer/wiki2beamer-0.9.5-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/w/wiki2beamer/wiki2beamer-0.9.5-goolf-1.4.10-Python-2.7.3.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/w/wiki2beamer/wiki2beamer-0.9.5-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/w/wiki2beamer/wiki2beamer-0.9.5-ictce-5.3.0-Python-2.7.3.eb index b2e2623f1f..e5c33bcbbd 100644 --- a/easybuild/easyconfigs/w/wiki2beamer/wiki2beamer-0.9.5-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/w/wiki2beamer/wiki2beamer-0.9.5-ictce-5.3.0-Python-2.7.3.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Cedric Laczny , Fotis Georgatos diff --git a/easybuild/easyconfigs/w/wkhtmltopdf/wkhtmltopdf-0.12.3-Linux-x86_64.eb b/easybuild/easyconfigs/w/wkhtmltopdf/wkhtmltopdf-0.12.3-Linux-x86_64.eb index b0bb280f07..dfff31c3a7 100644 --- a/easybuild/easyconfigs/w/wkhtmltopdf/wkhtmltopdf-0.12.3-Linux-x86_64.eb +++ b/easybuild/easyconfigs/w/wkhtmltopdf/wkhtmltopdf-0.12.3-Linux-x86_64.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # sciCORE - University of Basel # SIB Swiss Institute of Bioinformatics diff --git a/easybuild/easyconfigs/w/wxPropertyGrid/wxPropertyGrid-1.4.15-GCC-4.7.3.eb b/easybuild/easyconfigs/w/wxPropertyGrid/wxPropertyGrid-1.4.15-GCC-4.7.3.eb index 93c328cff6..ff437b5dba 100644 --- a/easybuild/easyconfigs/w/wxPropertyGrid/wxPropertyGrid-1.4.15-GCC-4.7.3.eb +++ b/easybuild/easyconfigs/w/wxPropertyGrid/wxPropertyGrid-1.4.15-GCC-4.7.3.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild # Copyright:: Copyright 2013 Juelich Supercomputing Centre, Germany # Authors:: Bernd Mohr # License:: New BSD diff --git a/easybuild/easyconfigs/w/wxPropertyGrid/wxPropertyGrid-1.4.15-GCC-4.9.2.eb b/easybuild/easyconfigs/w/wxPropertyGrid/wxPropertyGrid-1.4.15-GCC-4.9.2.eb index ccad95cd1d..7f314736fb 100644 --- a/easybuild/easyconfigs/w/wxPropertyGrid/wxPropertyGrid-1.4.15-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/w/wxPropertyGrid/wxPropertyGrid-1.4.15-GCC-4.9.2.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild # Copyright:: Copyright 2013 Juelich Supercomputing Centre, Germany # Authors:: Bernd Mohr # License:: New BSD diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.2_compat-libs.patch b/easybuild/easyconfigs/x/XZ/XZ-5.2.2_compat-libs.patch index 3090e4e0ea..03b241cdc6 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.2_compat-libs.patch +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.2_compat-libs.patch @@ -1,5 +1,5 @@ include two 5.1.2aplha symbols that were included in XZ 5.1.2alpha which are required by the 'rpm' command on CentOS 7.x -see also https://github.com/hpcugent/easybuild-easyconfigs/issues/4036 +see also https://github.com/easybuilders/easybuild-easyconfigs/issues/4036 original patch: xz-5.2.2-compat-libs.patch, cfr. https://git.centos.org/patch/rpms!xz.git/3f035cee1da9f864609885e5ef2a1be77cd37eee --- src/liblzma/liblzma.map.orig 2015-09-29 12:57:36.000000000 +0200 diff --git a/easybuild/easyconfigs/y/YAML-Syck/YAML-Syck-1.27-goolf-1.4.10-Perl-5.16.3.eb b/easybuild/easyconfigs/y/YAML-Syck/YAML-Syck-1.27-goolf-1.4.10-Perl-5.16.3.eb index 8cae54960c..634b4f040d 100644 --- a/easybuild/easyconfigs/y/YAML-Syck/YAML-Syck-1.27-goolf-1.4.10-Perl-5.16.3.eb +++ b/easybuild/easyconfigs/y/YAML-Syck/YAML-Syck-1.27-goolf-1.4.10-Perl-5.16.3.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2013 Uni.Lu/LCSB # Authors:: Nils Christian diff --git a/easybuild/easyconfigs/y/YAML-Syck/YAML-Syck-1.27-ictce-5.3.0-Perl-5.16.3.eb b/easybuild/easyconfigs/y/YAML-Syck/YAML-Syck-1.27-ictce-5.3.0-Perl-5.16.3.eb index 19442cc19e..a9b0150761 100644 --- a/easybuild/easyconfigs/y/YAML-Syck/YAML-Syck-1.27-ictce-5.3.0-Perl-5.16.3.eb +++ b/easybuild/easyconfigs/y/YAML-Syck/YAML-Syck-1.27-ictce-5.3.0-Perl-5.16.3.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2013 Uni.Lu/LCSB # Authors:: Nils Christian diff --git a/easybuild/easyconfigs/y/Yasm/Yasm-1.2.0-goolf-1.4.10.eb b/easybuild/easyconfigs/y/Yasm/Yasm-1.2.0-goolf-1.4.10.eb index 6ed4579c34..4a89685079 100644 --- a/easybuild/easyconfigs/y/Yasm/Yasm-1.2.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/y/Yasm/Yasm-1.2.0-goolf-1.4.10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/y/Yasm/Yasm-1.2.0-ictce-5.3.0.eb b/easybuild/easyconfigs/y/Yasm/Yasm-1.2.0-ictce-5.3.0.eb index a98dbc5915..a67685c36b 100644 --- a/easybuild/easyconfigs/y/Yasm/Yasm-1.2.0-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/y/Yasm/Yasm-1.2.0-ictce-5.3.0.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-foss-2015a.eb b/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-foss-2015a.eb index 90c83cfb4e..83c2304c3f 100644 --- a/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-foss-2015a.eb +++ b/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-foss-2015a.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-foss-2016a.eb b/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-foss-2016a.eb index fd9ab5e210..5d91905b00 100644 --- a/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-foss-2016a.eb +++ b/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-foss-2016a.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-foss-2016b.eb b/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-foss-2016b.eb index d40e39150a..2b3b53fc13 100644 --- a/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-foss-2016b.eb +++ b/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-foss-2016b.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-foss-2017a.eb b/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-foss-2017a.eb index bae739cbfa..884d55d98d 100644 --- a/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-foss-2017a.eb +++ b/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-foss-2017a.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-gimkl-2.11.5.eb b/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-gimkl-2.11.5.eb index b2b7c412d9..54da1bfc1c 100644 --- a/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-gimkl-2.11.5.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-gimkl-2017a.eb b/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-gimkl-2017a.eb index 78f408a971..190f07dd2b 100644 --- a/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-gimkl-2017a.eb +++ b/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-gimkl-2017a.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-intel-2015b.eb b/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-intel-2015b.eb index af77be599d..053cfe39f7 100644 --- a/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-intel-2015b.eb +++ b/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-intel-2015b.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-intel-2016a.eb b/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-intel-2016a.eb index b5dae68924..31172f8c40 100644 --- a/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-intel-2016a.eb +++ b/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-intel-2016a.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-intel-2016b.eb b/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-intel-2016b.eb index bd4bc5d66f..a838254d15 100644 --- a/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-intel-2016b.eb +++ b/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-intel-2016b.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-intel-2017a.eb b/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-intel-2017a.eb index f0db7e8256..89a5a1ab38 100644 --- a/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-intel-2017a.eb +++ b/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-intel-2017a.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/z/ZPAQ/ZPAQ-7.00-GCC-4.8.2.eb b/easybuild/easyconfigs/z/ZPAQ/ZPAQ-7.00-GCC-4.8.2.eb index 6b82f0fc24..66f5997d8e 100644 --- a/easybuild/easyconfigs/z/ZPAQ/ZPAQ-7.00-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/z/ZPAQ/ZPAQ-7.00-GCC-4.8.2.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2015 NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/z/zsync/zsync-0.6.2-goolf-1.4.10.eb b/easybuild/easyconfigs/z/zsync/zsync-0.6.2-goolf-1.4.10.eb index d756317c6c..aeebd7e248 100644 --- a/easybuild/easyconfigs/z/zsync/zsync-0.6.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/z/zsync/zsync-0.6.2-goolf-1.4.10.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/easybuild/easyconfigs/z/zsync/zsync-0.6.2-ictce-5.3.0.eb b/easybuild/easyconfigs/z/zsync/zsync-0.6.2-ictce-5.3.0.eb index 960ac2460a..f13e061e4e 100644 --- a/easybuild/easyconfigs/z/zsync/zsync-0.6.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/z/zsync/zsync-0.6.2-ictce-5.3.0.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos diff --git a/setup.py b/setup.py index 6a0698539f..af2eb6baaf 100644 --- a/setup.py +++ b/setup.py @@ -8,7 +8,7 @@ # Flemish Research Foundation (FWO) (http://www.fwo.be/en) # and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en). # -# http://github.com/hpcugent/easybuild +# https://github.com/easybuilders/easybuild # # EasyBuild is free software: you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by @@ -109,7 +109,7 @@ that specify the build parameters for software packages (version, compiler toolc versions, etc.).""", license = "GPLv2", keywords = "software build building installation installing compilation HPC scientific", - url = "http://hpcugent.github.com/easybuild", + url = "http://easybuilders.github.io/easybuild/", data_files = get_data_files(), long_description = read("README.rst"), classifiers = [ diff --git a/test/__init__.py b/test/__init__.py index e44e0c6e58..4c16c11e57 100644 --- a/test/__init__.py +++ b/test/__init__.py @@ -8,7 +8,7 @@ # Flemish Research Foundation (FWO) (http://www.fwo.be/en) # and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en). # -# http://github.com/hpcugent/easybuild +# https://github.com/easybuilders/easybuild # # EasyBuild is free software: you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 993e9395ba..6e9ae84a7b 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -8,7 +8,7 @@ # Flemish Research Foundation (FWO) (http://www.fwo.be/en) # and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en). # -# http://github.com/hpcugent/easybuild +# https://github.com/easybuilders/easybuild # # EasyBuild is free software: you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by diff --git a/test/easyconfigs/styletests.py b/test/easyconfigs/styletests.py index 2ea259071e..7baae28007 100644 --- a/test/easyconfigs/styletests.py +++ b/test/easyconfigs/styletests.py @@ -8,7 +8,7 @@ # the Hercules foundation (http://www.herculesstichting.be/in_English) # and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en). # -# http://github.com/hpcugent/easybuild +# https://github.com/easybuilders/easybuild # # EasyBuild is free software: you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by diff --git a/test/easyconfigs/suite.py b/test/easyconfigs/suite.py index 56d7f05b41..a8806bf1ae 100644 --- a/test/easyconfigs/suite.py +++ b/test/easyconfigs/suite.py @@ -9,7 +9,7 @@ # Flemish Research Foundation (FWO) (http://www.fwo.be/en) # and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en). # -# http://github.com/hpcugent/easybuild +# https://github.com/easybuilders/easybuild # # EasyBuild is free software: you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by -- GitLab From 016235a044cf8a0fb906ad27bfe398d2bf69b33d Mon Sep 17 00:00:00 2001 From: zao Date: Wed, 5 Jul 2017 19:02:50 +0200 Subject: [PATCH 1066/1603] Credit upstream, use %(version)s format --- easybuild/easyconfigs/g/GCCcore/GCCcore-6.3.0-fix-ubsan.patch | 3 +++ easybuild/easyconfigs/g/GCCcore/GCCcore-6.3.0.eb | 2 +- 2 files changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-6.3.0-fix-ubsan.patch b/easybuild/easyconfigs/g/GCCcore/GCCcore-6.3.0-fix-ubsan.patch index 8b5e6acbfb..494ae7c00e 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-6.3.0-fix-ubsan.patch +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-6.3.0-fix-ubsan.patch @@ -1,3 +1,6 @@ +# GCC 7 errors on comparing a pointer and an integer, code means to test +# first byte. This is fixed in 6.4.0 and onward by SVN revision 239971. +# Upstream credit: Kirill Yukhin diff -ru gcc-6.3.0-orig/gcc/ubsan.c gcc-6.3.0/gcc/ubsan.c --- gcc-6.3.0-orig/gcc/ubsan.c 2016-12-07 23:39:29.000000000 +0100 +++ gcc-6.3.0/gcc/ubsan.c 2017-07-05 08:57:03.297566616 +0200 diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-6.3.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-6.3.0.eb index b95420541e..7c5c5cfbf2 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-6.3.0.eb @@ -37,7 +37,7 @@ builddependencies = [ patches = [ ('mpfr-%s-allpatches-20161215.patch' % mpfr_version, '../mpfr-%s' % mpfr_version), 'GCCcore-6.2.0-fix-find-isl.patch', - 'GCCcore-6.3.0-fix-ubsan.patch', + 'GCCcore-%(version)s-fix-ubsan.patch', ] checksums = [ -- GitLab From 588b5b4167171cc967bd9299600b007c07b999d3 Mon Sep 17 00:00:00 2001 From: zao Date: Wed, 5 Jul 2017 20:34:07 +0200 Subject: [PATCH 1067/1603] Generalize ubsan patch for earlier 6.x releases --- easybuild/easyconfigs/g/GCCcore/GCCcore-6.1.0.eb | 1 + easybuild/easyconfigs/g/GCCcore/GCCcore-6.2.0.eb | 1 + easybuild/easyconfigs/g/GCCcore/GCCcore-6.3.0.eb | 2 +- ...CCcore-6.3.0-fix-ubsan.patch => GCCcore-6.x-fix-ubsan.patch} | 1 + 4 files changed, 4 insertions(+), 1 deletion(-) rename easybuild/easyconfigs/g/GCCcore/{GCCcore-6.3.0-fix-ubsan.patch => GCCcore-6.x-fix-ubsan.patch} (97%) diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-6.1.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-6.1.0.eb index b3173aaf56..0423a2a006 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-6.1.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-6.1.0.eb @@ -38,6 +38,7 @@ builddependencies = [ patches = [ ('mpfr-%s-allpatches-20160804.patch' % mpfr_version, '../mpfr-%s' % mpfr_version), ('%s-%s_fix-find-isl.patch' % (name, version)), + 'GCCcore-6.x-fix-ubsan.patch', ] checksums = [ diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-6.2.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-6.2.0.eb index 8bf2b22931..2ac9bf8b09 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-6.2.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-6.2.0.eb @@ -37,6 +37,7 @@ builddependencies = [ patches = [ ('mpfr-%s-allpatches-20160804.patch' % mpfr_version, '../mpfr-%s' % mpfr_version), '%(name)s-%(version)s-fix-find-isl.patch', + 'GCCcore-6.x-fix-ubsan.patch', ] checksums = [ diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-6.3.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-6.3.0.eb index 7c5c5cfbf2..96befaf7f0 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-6.3.0.eb @@ -37,7 +37,7 @@ builddependencies = [ patches = [ ('mpfr-%s-allpatches-20161215.patch' % mpfr_version, '../mpfr-%s' % mpfr_version), 'GCCcore-6.2.0-fix-find-isl.patch', - 'GCCcore-%(version)s-fix-ubsan.patch', + 'GCCcore-6.x-fix-ubsan.patch', ] checksums = [ diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-6.3.0-fix-ubsan.patch b/easybuild/easyconfigs/g/GCCcore/GCCcore-6.x-fix-ubsan.patch similarity index 97% rename from easybuild/easyconfigs/g/GCCcore/GCCcore-6.3.0-fix-ubsan.patch rename to easybuild/easyconfigs/g/GCCcore/GCCcore-6.x-fix-ubsan.patch index 494ae7c00e..1c8e22152a 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-6.3.0-fix-ubsan.patch +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-6.x-fix-ubsan.patch @@ -1,5 +1,6 @@ # GCC 7 errors on comparing a pointer and an integer, code means to test # first byte. This is fixed in 6.4.0 and onward by SVN revision 239971. +# Affects 6.1-6.3. # Upstream credit: Kirill Yukhin diff -ru gcc-6.3.0-orig/gcc/ubsan.c gcc-6.3.0/gcc/ubsan.c --- gcc-6.3.0-orig/gcc/ubsan.c 2016-12-07 23:39:29.000000000 +0100 -- GitLab From 6c51593a0c5e2a2f21afdb672b185c0a337eec27 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 5 Jul 2017 21:30:22 +0200 Subject: [PATCH 1068/1603] add SHA256 checksum in binutils-2.28-GCCcore-6.4.0.eb --- easybuild/easyconfigs/b/binutils/binutils-2.28-GCCcore-6.4.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.28-GCCcore-6.4.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.28-GCCcore-6.4.0.eb index b22b7d16ba..b6486c7dfb 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.28-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.28-GCCcore-6.4.0.eb @@ -8,6 +8,7 @@ toolchain = {'name': 'GCCcore', 'version': '6.4.0'} sources = [SOURCE_TAR_GZ] source_urls = [GNU_SOURCE] +checksums = ['cd717966fc761d840d451dbd58d44e1e5b92949d2073d75b73fccb476d772fcf'] builddependencies = [ ('flex', '2.6.4'), -- GitLab From ddec90ce3c0d1175651948bcd4aeed77b26edf2f Mon Sep 17 00:00:00 2001 From: "Nathan S. Watson-Haigh" Date: Thu, 6 Jul 2017 11:35:25 +0930 Subject: [PATCH 1069/1603] Added easyconfig for ngmlr-0.2.6-foss-2015b --- .../n/ngmlr/ngmlr-0.2.6-foss-2015b.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/n/ngmlr/ngmlr-0.2.6-foss-2015b.eb diff --git a/easybuild/easyconfigs/n/ngmlr/ngmlr-0.2.6-foss-2015b.eb b/easybuild/easyconfigs/n/ngmlr/ngmlr-0.2.6-foss-2015b.eb new file mode 100644 index 0000000000..a5b9e6ff70 --- /dev/null +++ b/easybuild/easyconfigs/n/ngmlr/ngmlr-0.2.6-foss-2015b.eb @@ -0,0 +1,26 @@ +easyblock = 'CMakeMake' + +name = 'ngmlr' +version = '0.2.6' + +homepage = 'https://github.com/philres/ngmlr' +description = """Ngmlr is a long-read mapper designed to align PacBilo or Oxford Nanopore to a + reference genome with a focus on reads that span structural variations.""" + +toolchain = {'name': 'foss', 'version': '2015b'} + +sources = ['v%(version)s.tar.gz'] +source_urls = ['https://github.com/philres/ngmlr/archive'] + +builddependencies = [('CMake', '3.4.1')] + +dependencies = [ + ('zlib', '1.2.8'), +] + +sanity_check_paths = { + 'files': ['bin/ngmlr'], + 'dirs': [''] +} + +moduleclass = 'bio' -- GitLab From b7e29f64c2f8e97990239584aaee5887910ccdae Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 6 Jul 2017 08:34:49 +0200 Subject: [PATCH 1070/1603] replace wiki link with readthedocs link --- RELEASE_NOTES | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index 1dcd904d75..904813d080 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -749,7 +749,7 @@ feature + bugfix release Xmipp (#1489) - added easyconfigs for new (Cray-specific) toolchains (#1538): CrayGNU, CrayIntel, CrayCCE - initially supported software (using CrayGNU toolchains): CP2K, GROMACS, HPL, Python + numpy/scipy, WRF (#1558) - - see also https://github.com/easybuilders/easybuild/wiki/EasyBuild-on-Cray + - see also http://easybuild.readthedocs.io/en/latest/Cray-support.html - added new easyconfigs for existing toolchains: goolf/1.5.16, intel/2014.06 - added additional easyconfigs for various supported software packages: version updates, different toolchains, ... including GCC v5.1.0, OpenFOAM v2.3.1, R v3.1.3 and v3.2.0, PETSc/SLEPc v3.5.3, WIEN2k v14.1 -- GitLab From aff9c11faf9f40979971076197f79b1ad23b72c7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 6 Jul 2017 08:51:20 +0200 Subject: [PATCH 1071/1603] consistently use https:// for EasyBuild website URL --- README.rst | 2 +- easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.0.0.eb | 2 +- easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.0.1.eb | 2 +- easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.0.2.eb | 2 +- easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.1.0.eb | 2 +- easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.10.0.eb | 2 +- easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.11.0.eb | 2 +- easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.11.1.eb | 2 +- easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.12.0.eb | 2 +- easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.12.1.eb | 2 +- easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.13.0.eb | 2 +- easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.14.0.eb | 2 +- easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.15.0.eb | 2 +- easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.15.1.eb | 2 +- easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.15.2.eb | 2 +- easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.16.0.eb | 2 +- easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.16.1.eb | 2 +- easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.16.2.eb | 2 +- easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.2.0.eb | 2 +- easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.3.0.eb | 2 +- easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.4.0.eb | 2 +- easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.5.0.eb | 2 +- easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.6.0.eb | 2 +- easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.7.0.eb | 2 +- easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.8.0.eb | 2 +- easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.8.1.eb | 2 +- easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.8.2.eb | 2 +- easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.9.0.eb | 2 +- easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.0.0.eb | 2 +- easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.1.0.eb | 2 +- easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.1.1.eb | 2 +- easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.2.0.eb | 2 +- easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.3.0.eb | 2 +- easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.4.0.eb | 2 +- easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.5.0.eb | 2 +- easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.6.0.eb | 2 +- easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.7.0.eb | 2 +- easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.8.0.eb | 2 +- easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.8.1.eb | 2 +- easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.8.2.eb | 2 +- easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.9.0.eb | 2 +- easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.0.0.eb | 2 +- easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.0.1.eb | 2 +- easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.0.2.eb | 2 +- easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.1.0.eb | 2 +- easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.1.1.eb | 2 +- easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.1.2.eb | 2 +- easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.2.0.eb | 2 +- easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.2.1.eb | 2 +- easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.3.0.eb | 2 +- easybuild/easyconfigs/i/icc/icc-2016.0.109-GCC-4.9.3-2.25.eb | 2 +- easybuild/easyconfigs/i/icc/icc-2016.0.109.eb | 2 +- easybuild/easyconfigs/i/icc/icc-2016.1.150-GCC-4.9.3-2.25.eb | 2 +- easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-4.9.3-2.25.eb | 2 +- easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-5.3.0-2.26.eb | 2 +- easybuild/easyconfigs/i/icc/icc-2016.3.210-GCC-4.9.3-2.25.eb | 2 +- easybuild/easyconfigs/i/icc/icc-2016.3.210-GCC-5.3.0-2.26.eb | 2 +- easybuild/easyconfigs/i/icc/icc-2016.3.210-GCC-5.4.0-2.26.eb | 2 +- easybuild/easyconfigs/i/icc/icc-2017.0.098-GCC-5.4.0-2.26.eb | 2 +- easybuild/easyconfigs/i/icc/icc-2017.1.132-GCC-5.4.0-2.26.eb | 2 +- easybuild/easyconfigs/i/icc/icc-2017.1.132-GCC-6.3.0-2.27.eb | 2 +- easybuild/easyconfigs/i/icc/icc-2017.2.174-GCC-6.3.0-2.27.eb | 2 +- .../i/iccifort/iccifort-2016.0.109-GCC-4.9.3-2.25.eb | 2 +- easybuild/easyconfigs/i/iccifort/iccifort-2016.0.109.eb | 2 +- .../i/iccifort/iccifort-2016.1.150-GCC-4.9.3-2.25.eb | 2 +- .../i/iccifort/iccifort-2016.2.181-GCC-4.9.3-2.25.eb | 2 +- .../i/iccifort/iccifort-2016.2.181-GCC-5.3.0-2.26.eb | 2 +- .../i/iccifort/iccifort-2016.3.210-GCC-4.9.3-2.25.eb | 2 +- .../i/iccifort/iccifort-2016.3.210-GCC-5.3.0-2.26.eb | 2 +- .../i/iccifort/iccifort-2016.3.210-GCC-5.4.0-2.26.eb | 2 +- .../i/iccifort/iccifort-2017.0.098-GCC-5.4.0-2.26.eb | 2 +- .../i/iccifort/iccifort-2017.1.132-GCC-5.4.0-2.26.eb | 2 +- .../i/iccifort/iccifort-2017.1.132-GCC-6.3.0-2.27.eb | 2 +- .../i/iccifort/iccifort-2017.2.174-GCC-6.3.0-2.27.eb | 2 +- .../easyconfigs/i/ifort/ifort-2016.0.109-GCC-4.9.3-2.25.eb | 2 +- easybuild/easyconfigs/i/ifort/ifort-2016.0.109.eb | 2 +- .../easyconfigs/i/ifort/ifort-2016.1.150-GCC-4.9.3-2.25.eb | 2 +- .../easyconfigs/i/ifort/ifort-2016.2.181-GCC-4.9.3-2.25.eb | 2 +- .../easyconfigs/i/ifort/ifort-2016.2.181-GCC-5.3.0-2.26.eb | 2 +- .../easyconfigs/i/ifort/ifort-2016.3.210-GCC-4.9.3-2.25.eb | 2 +- .../easyconfigs/i/ifort/ifort-2016.3.210-GCC-5.3.0-2.26.eb | 2 +- .../easyconfigs/i/ifort/ifort-2016.3.210-GCC-5.4.0-2.26.eb | 2 +- .../easyconfigs/i/ifort/ifort-2017.0.098-GCC-5.4.0-2.26.eb | 2 +- .../easyconfigs/i/ifort/ifort-2017.1.132-GCC-5.4.0-2.26.eb | 2 +- .../easyconfigs/i/ifort/ifort-2017.1.132-GCC-6.3.0-2.27.eb | 2 +- .../easyconfigs/i/ifort/ifort-2017.2.174-GCC-6.3.0-2.27.eb | 2 +- easybuild/easyconfigs/i/iimpi/iimpi-2016.00-GCC-4.9.3-2.25.eb | 2 +- easybuild/easyconfigs/i/iimpi/iimpi-2016.01-GCC-4.9.3-2.25.eb | 2 +- easybuild/easyconfigs/i/iimpi/iimpi-2016.02-GCC-4.9.3-2.25.eb | 2 +- easybuild/easyconfigs/i/iimpi/iimpi-2016.02-GCC-5.3.0-2.26.eb | 2 +- easybuild/easyconfigs/i/iimpi/iimpi-2016.03-GCC-4.9.3-2.25.eb | 2 +- easybuild/easyconfigs/i/iimpi/iimpi-2016.03-GCC-5.3.0-2.26.eb | 2 +- easybuild/easyconfigs/i/iimpi/iimpi-2016.03-GCC-5.4.0-2.26.eb | 2 +- easybuild/easyconfigs/i/iimpi/iimpi-2016b.eb | 2 +- easybuild/easyconfigs/i/iimpi/iimpi-2017.00-GCC-5.4.0-2.26.eb | 2 +- easybuild/easyconfigs/i/iimpi/iimpi-2017.01-GCC-5.4.0-2.26.eb | 2 +- easybuild/easyconfigs/i/iimpi/iimpi-2017.02-GCC-6.3.0-2.27.eb | 2 +- easybuild/easyconfigs/i/iimpi/iimpi-2017a.eb | 2 +- easybuild/easyconfigs/i/iimpic/iimpic-2016.10.eb | 2 +- .../i/imkl/imkl-11.3.0.109-iimpi-2016.00-GCC-4.9.3-2.25.eb | 2 +- .../i/imkl/imkl-11.3.1.150-iimpi-2016.01-GCC-4.9.3-2.25.eb | 2 +- .../i/imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-4.9.3-2.25.eb | 2 +- .../i/imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-5.3.0-2.26.eb | 2 +- easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-pompi-2016.03.eb | 2 +- .../i/imkl/imkl-11.3.3.210-iimpi-2016.03-GCC-4.9.3-2.25.eb | 2 +- .../i/imkl/imkl-11.3.3.210-iimpi-2016.03-GCC-5.3.0-2.26.eb | 2 +- .../i/imkl/imkl-11.3.3.210-iimpi-2016.03-GCC-5.4.0-2.26.eb | 2 +- easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpi-2016b.eb | 2 +- easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpic-2016.10.eb | 2 +- easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-pompi-2016.04.eb | 2 +- easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-pompi-2016.09.eb | 2 +- .../i/imkl/imkl-2017.0.098-iimpi-2017.00-GCC-5.4.0-2.26.eb | 2 +- .../i/imkl/imkl-2017.1.132-iimpi-2017.01-GCC-5.4.0-2.26.eb | 2 +- easybuild/easyconfigs/i/imkl/imkl-2017.1.132-iimpi-2017a.eb | 2 +- easybuild/easyconfigs/i/imkl/imkl-2017.1.132-iompi-2017.01.eb | 2 +- easybuild/easyconfigs/i/imkl/imkl-2017.1.132-iompi-2017a.eb | 2 +- .../i/imkl/imkl-2017.2.174-iimpi-2017.02-GCC-6.3.0-2.27.eb | 2 +- .../impi/impi-2017.0.098-iccifort-2017.0.098-GCC-5.4.0-2.26.eb | 2 +- .../impi/impi-2017.1.132-iccifort-2017.1.132-GCC-5.4.0-2.26.eb | 2 +- .../impi/impi-2017.1.132-iccifort-2017.1.132-GCC-6.3.0-2.27.eb | 2 +- .../impi/impi-2017.2.174-iccifort-2017.2.174-GCC-6.3.0-2.27.eb | 2 +- .../i/impi/impi-5.1.1.109-iccifort-2016.0.109-GCC-4.9.3-2.25.eb | 2 +- .../i/impi/impi-5.1.2.150-iccifort-2016.1.150-GCC-4.9.3-2.25.eb | 2 +- .../i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-4.9.3-2.25.eb | 2 +- .../i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-5.3.0-2.26.eb | 2 +- .../i/impi/impi-5.1.3.181-iccifort-2016.3.210-GCC-4.9.3-2.25.eb | 2 +- .../i/impi/impi-5.1.3.181-iccifort-2016.3.210-GCC-5.3.0-2.26.eb | 2 +- .../i/impi/impi-5.1.3.181-iccifort-2016.3.210-GCC-5.4.0-2.26.eb | 2 +- .../easyconfigs/i/impi/impi-5.1.3.181-iccifortcuda-2016.10.eb | 2 +- easybuild/easyconfigs/i/intel/intel-2016.00.eb | 2 +- easybuild/easyconfigs/i/intel/intel-2016.01.eb | 2 +- easybuild/easyconfigs/i/iompi/iompi-2017.01.eb | 2 +- easybuild/easyconfigs/i/iompi/iompi-2017a.eb | 2 +- setup.py | 2 +- 134 files changed, 134 insertions(+), 134 deletions(-) diff --git a/README.rst b/README.rst index ff6d26a0ab..be42964380 100644 --- a/README.rst +++ b/README.rst @@ -1,4 +1,4 @@ -.. image:: http://easybuilders.github.io/easybuild/images/easybuild_logo_small.png +.. image:: https://easybuilders.github.io/easybuild/images/easybuild_logo_small.png :align: center `EasyBuild `_ is a software build diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.0.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.0.0.eb index 819bcfdba2..9b67e77290 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.0.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.0.0.eb @@ -3,7 +3,7 @@ easyblock = 'EB_EasyBuildMeta' name = 'EasyBuild' version = '1.0.0' -homepage = 'http://easybuilders.github.io/easybuild' +homepage = 'https://easybuilders.github.io/easybuild' description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.0.1.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.0.1.eb index c22351c6de..f6e48794a2 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.0.1.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.0.1.eb @@ -3,7 +3,7 @@ easyblock = 'EB_EasyBuildMeta' name = 'EasyBuild' version = '1.0.1' -homepage = 'http://easybuilders.github.io/easybuild' +homepage = 'https://easybuilders.github.io/easybuild' description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.0.2.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.0.2.eb index 10e52177b1..f65e4d33b7 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.0.2.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.0.2.eb @@ -3,7 +3,7 @@ easyblock = 'EB_EasyBuildMeta' name = 'EasyBuild' version = '1.0.2' -homepage = 'http://easybuilders.github.io/easybuild' +homepage = 'https://easybuilders.github.io/easybuild' description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.1.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.1.0.eb index b86dfbf810..b404084816 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.1.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.1.0.eb @@ -3,7 +3,7 @@ easyblock = 'EB_EasyBuildMeta' name = 'EasyBuild' version = '1.1.0' -homepage = 'http://easybuilders.github.io/easybuild' +homepage = 'https://easybuilders.github.io/easybuild' description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.10.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.10.0.eb index a6804f4f58..6d0b6bbd58 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.10.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.10.0.eb @@ -3,7 +3,7 @@ easyblock = 'EB_EasyBuildMeta' name = 'EasyBuild' version = '1.10.0' -homepage = 'http://easybuilders.github.io/easybuild' +homepage = 'https://easybuilders.github.io/easybuild' description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.11.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.11.0.eb index 23833e2836..09d7412e21 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.11.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.11.0.eb @@ -3,7 +3,7 @@ easyblock = 'EB_EasyBuildMeta' name = 'EasyBuild' version = '1.11.0' -homepage = 'http://easybuilders.github.io/easybuild' +homepage = 'https://easybuilders.github.io/easybuild' description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.11.1.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.11.1.eb index 47f1a751e4..3e0b477551 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.11.1.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.11.1.eb @@ -3,7 +3,7 @@ easyblock = 'EB_EasyBuildMeta' name = 'EasyBuild' version = '1.11.1' -homepage = 'http://easybuilders.github.io/easybuild' +homepage = 'https://easybuilders.github.io/easybuild' description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.12.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.12.0.eb index e4a27cb487..fda0eaa230 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.12.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.12.0.eb @@ -3,7 +3,7 @@ easyblock = 'EB_EasyBuildMeta' name = 'EasyBuild' version = '1.12.0' -homepage = 'http://easybuilders.github.io/easybuild' +homepage = 'https://easybuilders.github.io/easybuild' description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.12.1.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.12.1.eb index eb82e53707..e8bc170959 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.12.1.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.12.1.eb @@ -3,7 +3,7 @@ easyblock = 'EB_EasyBuildMeta' name = 'EasyBuild' version = '1.12.1' -homepage = 'http://easybuilders.github.io/easybuild' +homepage = 'https://easybuilders.github.io/easybuild' description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.13.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.13.0.eb index 5455bc671c..148881ec17 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.13.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.13.0.eb @@ -3,7 +3,7 @@ easyblock = 'EB_EasyBuildMeta' name = 'EasyBuild' version = '1.13.0' -homepage = 'http://easybuilders.github.io/easybuild' +homepage = 'https://easybuilders.github.io/easybuild' description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.14.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.14.0.eb index bf7bef23ba..a573ff7efb 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.14.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.14.0.eb @@ -3,7 +3,7 @@ easyblock = 'EB_EasyBuildMeta' name = 'EasyBuild' version = '1.14.0' -homepage = 'http://easybuilders.github.io/easybuild' +homepage = 'https://easybuilders.github.io/easybuild' description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.15.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.15.0.eb index bc94abbd43..017904a16a 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.15.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.15.0.eb @@ -3,7 +3,7 @@ easyblock = 'EB_EasyBuildMeta' name = 'EasyBuild' version = "1.15.0" -homepage = 'http://easybuilders.github.io/easybuild' +homepage = 'https://easybuilders.github.io/easybuild' description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.15.1.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.15.1.eb index 567d84626d..4b605cc474 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.15.1.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.15.1.eb @@ -3,7 +3,7 @@ easyblock = 'EB_EasyBuildMeta' name = 'EasyBuild' version = "1.15.1" -homepage = 'http://easybuilders.github.io/easybuild' +homepage = 'https://easybuilders.github.io/easybuild' description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.15.2.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.15.2.eb index dc940ff5f3..71ca7c902d 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.15.2.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.15.2.eb @@ -3,7 +3,7 @@ easyblock = 'EB_EasyBuildMeta' name = 'EasyBuild' version = "1.15.2" -homepage = 'http://easybuilders.github.io/easybuild' +homepage = 'https://easybuilders.github.io/easybuild' description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.16.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.16.0.eb index 07b994c134..d694c3a975 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.16.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.16.0.eb @@ -3,7 +3,7 @@ easyblock = 'EB_EasyBuildMeta' name = 'EasyBuild' version = "1.16.0" -homepage = 'http://easybuilders.github.io/easybuild' +homepage = 'https://easybuilders.github.io/easybuild' description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.16.1.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.16.1.eb index 063c0cae95..777f78e3ad 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.16.1.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.16.1.eb @@ -3,7 +3,7 @@ easyblock = 'EB_EasyBuildMeta' name = 'EasyBuild' version = "1.16.1" -homepage = 'http://easybuilders.github.io/easybuild' +homepage = 'https://easybuilders.github.io/easybuild' description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.16.2.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.16.2.eb index ca54ce2b48..5c38c0a983 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.16.2.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.16.2.eb @@ -3,7 +3,7 @@ easyblock = 'EB_EasyBuildMeta' name = 'EasyBuild' version = "1.16.2" -homepage = 'http://easybuilders.github.io/easybuild' +homepage = 'https://easybuilders.github.io/easybuild' description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.2.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.2.0.eb index 5ab2ef518b..ee0fb34daf 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.2.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.2.0.eb @@ -3,7 +3,7 @@ easyblock = 'EB_EasyBuildMeta' name = 'EasyBuild' version = '1.2.0' -homepage = 'http://easybuilders.github.io/easybuild' +homepage = 'https://easybuilders.github.io/easybuild' description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.3.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.3.0.eb index 74208a9b9f..0249a90b8d 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.3.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.3.0.eb @@ -3,7 +3,7 @@ easyblock = 'EB_EasyBuildMeta' name = 'EasyBuild' version = '1.3.0' -homepage = 'http://easybuilders.github.io/easybuild' +homepage = 'https://easybuilders.github.io/easybuild' description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.4.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.4.0.eb index cf1ab671cb..58e8279a68 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.4.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.4.0.eb @@ -3,7 +3,7 @@ easyblock = 'EB_EasyBuildMeta' name = 'EasyBuild' version = '1.4.0' -homepage = 'http://easybuilders.github.io/easybuild' +homepage = 'https://easybuilders.github.io/easybuild' description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.5.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.5.0.eb index 395394e677..1b589199e1 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.5.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.5.0.eb @@ -3,7 +3,7 @@ easyblock = 'EB_EasyBuildMeta' name = 'EasyBuild' version = '1.5.0' -homepage = 'http://easybuilders.github.io/easybuild' +homepage = 'https://easybuilders.github.io/easybuild' description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.6.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.6.0.eb index 673b37a447..95539b250f 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.6.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.6.0.eb @@ -3,7 +3,7 @@ easyblock = 'EB_EasyBuildMeta' name = 'EasyBuild' version = '1.6.0' -homepage = 'http://easybuilders.github.io/easybuild' +homepage = 'https://easybuilders.github.io/easybuild' description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.7.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.7.0.eb index d63e41ec85..3caeb8de82 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.7.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.7.0.eb @@ -3,7 +3,7 @@ easyblock = 'EB_EasyBuildMeta' name = 'EasyBuild' version = '1.7.0' -homepage = 'http://easybuilders.github.io/easybuild' +homepage = 'https://easybuilders.github.io/easybuild' description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.8.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.8.0.eb index f5a9269b1f..63848ea26b 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.8.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.8.0.eb @@ -3,7 +3,7 @@ easyblock = 'EB_EasyBuildMeta' name = 'EasyBuild' version = '1.8.0' -homepage = 'http://easybuilders.github.io/easybuild' +homepage = 'https://easybuilders.github.io/easybuild' description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.8.1.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.8.1.eb index e18328251e..a99feae3bc 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.8.1.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.8.1.eb @@ -3,7 +3,7 @@ easyblock = 'EB_EasyBuildMeta' name = 'EasyBuild' version = '1.8.1' -homepage = 'http://easybuilders.github.io/easybuild' +homepage = 'https://easybuilders.github.io/easybuild' description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.8.2.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.8.2.eb index 76df856dd7..f835d8df77 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.8.2.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.8.2.eb @@ -3,7 +3,7 @@ easyblock = 'EB_EasyBuildMeta' name = 'EasyBuild' version = '1.8.2' -homepage = 'http://easybuilders.github.io/easybuild' +homepage = 'https://easybuilders.github.io/easybuild' description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.9.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.9.0.eb index d2e8a2944e..74d11b79a1 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.9.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.9.0.eb @@ -3,7 +3,7 @@ easyblock = 'EB_EasyBuildMeta' name = 'EasyBuild' version = '1.9.0' -homepage = 'http://easybuilders.github.io/easybuild' +homepage = 'https://easybuilders.github.io/easybuild' description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.0.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.0.0.eb index 24720fca1c..2fb2c7bbce 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.0.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.0.0.eb @@ -3,7 +3,7 @@ easyblock = 'EB_EasyBuildMeta' name = 'EasyBuild' version = "2.0.0" -homepage = 'http://easybuilders.github.io/easybuild' +homepage = 'https://easybuilders.github.io/easybuild' description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.1.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.1.0.eb index 4a7b7be82f..b20ff4070b 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.1.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.1.0.eb @@ -3,7 +3,7 @@ easyblock = 'EB_EasyBuildMeta' name = 'EasyBuild' version = '2.1.0' -homepage = 'http://easybuilders.github.io/easybuild' +homepage = 'https://easybuilders.github.io/easybuild' description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.1.1.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.1.1.eb index 84afda8b48..1f6796bb5a 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.1.1.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.1.1.eb @@ -3,7 +3,7 @@ easyblock = 'EB_EasyBuildMeta' name = 'EasyBuild' version = '2.1.1' -homepage = 'http://easybuilders.github.io/easybuild' +homepage = 'https://easybuilders.github.io/easybuild' description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.2.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.2.0.eb index ce7e5bf141..e49097cb3f 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.2.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.2.0.eb @@ -3,7 +3,7 @@ easyblock = 'EB_EasyBuildMeta' name = 'EasyBuild' version = '2.2.0' -homepage = 'http://easybuilders.github.io/easybuild' +homepage = 'https://easybuilders.github.io/easybuild' description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.3.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.3.0.eb index 31548a1769..3e1199f516 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.3.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.3.0.eb @@ -3,7 +3,7 @@ easyblock = 'EB_EasyBuildMeta' name = 'EasyBuild' version = '2.3.0' -homepage = 'http://easybuilders.github.io/easybuild' +homepage = 'https://easybuilders.github.io/easybuild' description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.4.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.4.0.eb index d7fe564a73..0f1a2dfaa8 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.4.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.4.0.eb @@ -3,7 +3,7 @@ easyblock = 'EB_EasyBuildMeta' name = 'EasyBuild' version = '2.4.0' -homepage = 'http://easybuilders.github.io/easybuild' +homepage = 'https://easybuilders.github.io/easybuild' description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.5.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.5.0.eb index 89f2840b11..d04e3a4e31 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.5.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.5.0.eb @@ -3,7 +3,7 @@ easyblock = 'EB_EasyBuildMeta' name = 'EasyBuild' version = '2.5.0' -homepage = 'http://easybuilders.github.io/easybuild' +homepage = 'https://easybuilders.github.io/easybuild' description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.6.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.6.0.eb index 5d5435bb7f..c7485aea5f 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.6.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.6.0.eb @@ -3,7 +3,7 @@ easyblock = 'EB_EasyBuildMeta' name = 'EasyBuild' version = '2.6.0' -homepage = 'http://easybuilders.github.io/easybuild' +homepage = 'https://easybuilders.github.io/easybuild' description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.7.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.7.0.eb index b09425b770..fcefd77778 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.7.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.7.0.eb @@ -3,7 +3,7 @@ easyblock = 'EB_EasyBuildMeta' name = 'EasyBuild' version = '2.7.0' -homepage = 'http://easybuilders.github.io/easybuild' +homepage = 'https://easybuilders.github.io/easybuild' description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.8.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.8.0.eb index 2e50e9c4e7..ee8f725ccc 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.8.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.8.0.eb @@ -3,7 +3,7 @@ easyblock = 'EB_EasyBuildMeta' name = 'EasyBuild' version = '2.8.0' -homepage = 'http://easybuilders.github.io/easybuild' +homepage = 'https://easybuilders.github.io/easybuild' description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.8.1.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.8.1.eb index d8d510a78c..5785d7ac7a 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.8.1.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.8.1.eb @@ -3,7 +3,7 @@ easyblock = 'EB_EasyBuildMeta' name = 'EasyBuild' version = '2.8.1' -homepage = 'http://easybuilders.github.io/easybuild' +homepage = 'https://easybuilders.github.io/easybuild' description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.8.2.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.8.2.eb index 2c33962b07..ef3430f3de 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.8.2.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.8.2.eb @@ -3,7 +3,7 @@ easyblock = 'EB_EasyBuildMeta' name = 'EasyBuild' version = '2.8.2' -homepage = 'http://easybuilders.github.io/easybuild' +homepage = 'https://easybuilders.github.io/easybuild' description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.9.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.9.0.eb index 7ab918d84c..1660b8e4a1 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.9.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.9.0.eb @@ -3,7 +3,7 @@ easyblock = 'EB_EasyBuildMeta' name = 'EasyBuild' version = '2.9.0' -homepage = 'http://easybuilders.github.io/easybuild' +homepage = 'https://easybuilders.github.io/easybuild' description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.0.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.0.0.eb index c9a8f9fb2a..70b18de510 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.0.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.0.0.eb @@ -3,7 +3,7 @@ easyblock = 'EB_EasyBuildMeta' name = 'EasyBuild' version = '3.0.0' -homepage = 'http://easybuilders.github.io/easybuild' +homepage = 'https://easybuilders.github.io/easybuild' description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.0.1.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.0.1.eb index 7fcaac8436..f26a42f001 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.0.1.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.0.1.eb @@ -3,7 +3,7 @@ easyblock = 'EB_EasyBuildMeta' name = 'EasyBuild' version = '3.0.1' -homepage = 'http://easybuilders.github.io/easybuild' +homepage = 'https://easybuilders.github.io/easybuild' description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.0.2.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.0.2.eb index ab22452b62..f26040b3c7 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.0.2.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.0.2.eb @@ -3,7 +3,7 @@ easyblock = 'EB_EasyBuildMeta' name = 'EasyBuild' version = '3.0.2' -homepage = 'http://easybuilders.github.io/easybuild' +homepage = 'https://easybuilders.github.io/easybuild' description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.1.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.1.0.eb index 7961017185..e385b6fbbe 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.1.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.1.0.eb @@ -3,7 +3,7 @@ easyblock = 'EB_EasyBuildMeta' name = 'EasyBuild' version = '3.1.0' -homepage = 'http://easybuilders.github.io/easybuild' +homepage = 'https://easybuilders.github.io/easybuild' description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.1.1.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.1.1.eb index bb9b2572df..94e497613d 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.1.1.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.1.1.eb @@ -3,7 +3,7 @@ easyblock = 'EB_EasyBuildMeta' name = 'EasyBuild' version = '3.1.1' -homepage = 'http://easybuilders.github.io/easybuild' +homepage = 'https://easybuilders.github.io/easybuild' description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.1.2.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.1.2.eb index 7bf19cc08b..ce2ab0cb59 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.1.2.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.1.2.eb @@ -3,7 +3,7 @@ easyblock = 'EB_EasyBuildMeta' name = 'EasyBuild' version = '3.1.2' -homepage = 'http://easybuilders.github.io/easybuild' +homepage = 'https://easybuilders.github.io/easybuild' description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.2.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.2.0.eb index 97d13804f9..3ee48d069a 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.2.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.2.0.eb @@ -3,7 +3,7 @@ easyblock = 'EB_EasyBuildMeta' name = 'EasyBuild' version = '3.2.0' -homepage = 'http://easybuilders.github.io/easybuild' +homepage = 'https://easybuilders.github.io/easybuild' description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.2.1.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.2.1.eb index ee42c1d6b9..176c9217f3 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.2.1.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.2.1.eb @@ -3,7 +3,7 @@ easyblock = 'EB_EasyBuildMeta' name = 'EasyBuild' version = '3.2.1' -homepage = 'http://easybuilders.github.io/easybuild' +homepage = 'https://easybuilders.github.io/easybuild' description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.3.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.3.0.eb index 5d4ea9ca97..5f1753bce3 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.3.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.3.0.eb @@ -3,7 +3,7 @@ easyblock = 'EB_EasyBuildMeta' name = 'EasyBuild' version = '3.3.0' -homepage = 'http://easybuilders.github.io/easybuild' +homepage = 'https://easybuilders.github.io/easybuild' description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" diff --git a/easybuild/easyconfigs/i/icc/icc-2016.0.109-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/icc/icc-2016.0.109-GCC-4.9.3-2.25.eb index 96e09e4442..3fe029f3bd 100644 --- a/easybuild/easyconfigs/i/icc/icc-2016.0.109-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/icc/icc-2016.0.109-GCC-4.9.3-2.25.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ +# This is an easyconfig file for EasyBuild, see https://easybuilders.github.io/easybuild/ name = 'icc' version = '2016.0.109' diff --git a/easybuild/easyconfigs/i/icc/icc-2016.0.109.eb b/easybuild/easyconfigs/i/icc/icc-2016.0.109.eb index 6f3261b9b3..5ca90df672 100644 --- a/easybuild/easyconfigs/i/icc/icc-2016.0.109.eb +++ b/easybuild/easyconfigs/i/icc/icc-2016.0.109.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ +# This is an easyconfig file for EasyBuild, see https://easybuilders.github.io/easybuild/ name = 'icc' version = '2016.0.109' diff --git a/easybuild/easyconfigs/i/icc/icc-2016.1.150-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/icc/icc-2016.1.150-GCC-4.9.3-2.25.eb index 64e0d33ac6..acee6423cd 100644 --- a/easybuild/easyconfigs/i/icc/icc-2016.1.150-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/icc/icc-2016.1.150-GCC-4.9.3-2.25.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ +# This is an easyconfig file for EasyBuild, see https://easybuilders.github.io/easybuild/ name = 'icc' version = '2016.1.150' diff --git a/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-4.9.3-2.25.eb index 721567e03f..c51aeed69f 100644 --- a/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-4.9.3-2.25.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ +# This is an easyconfig file for EasyBuild, see https://easybuilders.github.io/easybuild/ name = 'icc' version = '2016.2.181' diff --git a/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-5.3.0-2.26.eb index 0cbfad31f7..9efd4f304a 100644 --- a/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-5.3.0-2.26.eb +++ b/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-5.3.0-2.26.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ +# This is an easyconfig file for EasyBuild, see https://easybuilders.github.io/easybuild/ name = 'icc' version = '2016.2.181' diff --git a/easybuild/easyconfigs/i/icc/icc-2016.3.210-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/icc/icc-2016.3.210-GCC-4.9.3-2.25.eb index 2895d405cf..c834d93024 100644 --- a/easybuild/easyconfigs/i/icc/icc-2016.3.210-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/icc/icc-2016.3.210-GCC-4.9.3-2.25.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ +# This is an easyconfig file for EasyBuild, see https://easybuilders.github.io/easybuild/ name = 'icc' version = '2016.3.210' diff --git a/easybuild/easyconfigs/i/icc/icc-2016.3.210-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/icc/icc-2016.3.210-GCC-5.3.0-2.26.eb index 15866eea89..100faf7343 100644 --- a/easybuild/easyconfigs/i/icc/icc-2016.3.210-GCC-5.3.0-2.26.eb +++ b/easybuild/easyconfigs/i/icc/icc-2016.3.210-GCC-5.3.0-2.26.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ +# This is an easyconfig file for EasyBuild, see https://easybuilders.github.io/easybuild/ name = 'icc' version = '2016.3.210' diff --git a/easybuild/easyconfigs/i/icc/icc-2016.3.210-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/icc/icc-2016.3.210-GCC-5.4.0-2.26.eb index dc7b23e0a2..0e2464f373 100644 --- a/easybuild/easyconfigs/i/icc/icc-2016.3.210-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/icc/icc-2016.3.210-GCC-5.4.0-2.26.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ +# This is an easyconfig file for EasyBuild, see https://easybuilders.github.io/easybuild/ name = 'icc' version = '2016.3.210' diff --git a/easybuild/easyconfigs/i/icc/icc-2017.0.098-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/icc/icc-2017.0.098-GCC-5.4.0-2.26.eb index 06ec2ed952..41ed689a72 100644 --- a/easybuild/easyconfigs/i/icc/icc-2017.0.098-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/icc/icc-2017.0.098-GCC-5.4.0-2.26.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ +# This is an easyconfig file for EasyBuild, see https://easybuilders.github.io/easybuild/ name = 'icc' version = '2017.0.098' diff --git a/easybuild/easyconfigs/i/icc/icc-2017.1.132-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/icc/icc-2017.1.132-GCC-5.4.0-2.26.eb index 126b6eb3e0..77118ae45d 100644 --- a/easybuild/easyconfigs/i/icc/icc-2017.1.132-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/icc/icc-2017.1.132-GCC-5.4.0-2.26.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ +# This is an easyconfig file for EasyBuild, see https://easybuilders.github.io/easybuild/ name = 'icc' version = '2017.1.132' diff --git a/easybuild/easyconfigs/i/icc/icc-2017.1.132-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/i/icc/icc-2017.1.132-GCC-6.3.0-2.27.eb index bada3a0811..362d477441 100644 --- a/easybuild/easyconfigs/i/icc/icc-2017.1.132-GCC-6.3.0-2.27.eb +++ b/easybuild/easyconfigs/i/icc/icc-2017.1.132-GCC-6.3.0-2.27.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ +# This is an easyconfig file for EasyBuild, see https://easybuilders.github.io/easybuild/ name = 'icc' version = '2017.1.132' diff --git a/easybuild/easyconfigs/i/icc/icc-2017.2.174-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/i/icc/icc-2017.2.174-GCC-6.3.0-2.27.eb index 6d8d739d3b..55411b8971 100644 --- a/easybuild/easyconfigs/i/icc/icc-2017.2.174-GCC-6.3.0-2.27.eb +++ b/easybuild/easyconfigs/i/icc/icc-2017.2.174-GCC-6.3.0-2.27.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ +# This is an easyconfig file for EasyBuild, see https://easybuilders.github.io/easybuild/ name = 'icc' version = '2017.2.174' diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2016.0.109-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2016.0.109-GCC-4.9.3-2.25.eb index 4af351f8fe..fe66dc2742 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2016.0.109-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2016.0.109-GCC-4.9.3-2.25.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ +# This is an easyconfig file for EasyBuild, see https://easybuilders.github.io/easybuild/ easyblock = "Toolchain" name = 'iccifort' diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2016.0.109.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2016.0.109.eb index 6753c1145f..4bb42ab041 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2016.0.109.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2016.0.109.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ +# This is an easyconfig file for EasyBuild, see https://easybuilders.github.io/easybuild/ easyblock = "Toolchain" name = 'iccifort' diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2016.1.150-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2016.1.150-GCC-4.9.3-2.25.eb index 923d9700ec..cc24a9ab54 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2016.1.150-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2016.1.150-GCC-4.9.3-2.25.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ +# This is an easyconfig file for EasyBuild, see https://easybuilders.github.io/easybuild/ easyblock = "Toolchain" name = 'iccifort' diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2016.2.181-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2016.2.181-GCC-4.9.3-2.25.eb index b3ced2b66f..297fe04854 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2016.2.181-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2016.2.181-GCC-4.9.3-2.25.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ +# This is an easyconfig file for EasyBuild, see https://easybuilders.github.io/easybuild/ easyblock = "Toolchain" name = 'iccifort' diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2016.2.181-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2016.2.181-GCC-5.3.0-2.26.eb index f7d7ee5159..f2c485ee20 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2016.2.181-GCC-5.3.0-2.26.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2016.2.181-GCC-5.3.0-2.26.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ +# This is an easyconfig file for EasyBuild, see https://easybuilders.github.io/easybuild/ easyblock = "Toolchain" name = 'iccifort' diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2016.3.210-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2016.3.210-GCC-4.9.3-2.25.eb index fcdd6710aa..3683fdab6e 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2016.3.210-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2016.3.210-GCC-4.9.3-2.25.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ +# This is an easyconfig file for EasyBuild, see https://easybuilders.github.io/easybuild/ easyblock = "Toolchain" name = 'iccifort' diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2016.3.210-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2016.3.210-GCC-5.3.0-2.26.eb index d7cafce265..0401f8025e 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2016.3.210-GCC-5.3.0-2.26.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2016.3.210-GCC-5.3.0-2.26.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ +# This is an easyconfig file for EasyBuild, see https://easybuilders.github.io/easybuild/ easyblock = "Toolchain" name = 'iccifort' diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2016.3.210-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2016.3.210-GCC-5.4.0-2.26.eb index 41183af553..fdf3a88aa5 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2016.3.210-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2016.3.210-GCC-5.4.0-2.26.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ +# This is an easyconfig file for EasyBuild, see https://easybuilders.github.io/easybuild/ easyblock = "Toolchain" name = 'iccifort' diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2017.0.098-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2017.0.098-GCC-5.4.0-2.26.eb index e047e9f7b3..a77c406ff7 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2017.0.098-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2017.0.098-GCC-5.4.0-2.26.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ +# This is an easyconfig file for EasyBuild, see https://easybuilders.github.io/easybuild/ easyblock = "Toolchain" name = 'iccifort' diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2017.1.132-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2017.1.132-GCC-5.4.0-2.26.eb index de0d741a72..3fc87e0a0a 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2017.1.132-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2017.1.132-GCC-5.4.0-2.26.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ +# This is an easyconfig file for EasyBuild, see https://easybuilders.github.io/easybuild/ easyblock = "Toolchain" name = 'iccifort' diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2017.1.132-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2017.1.132-GCC-6.3.0-2.27.eb index 3ec7427089..d4e78567c7 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2017.1.132-GCC-6.3.0-2.27.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2017.1.132-GCC-6.3.0-2.27.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ +# This is an easyconfig file for EasyBuild, see https://easybuilders.github.io/easybuild/ easyblock = "Toolchain" name = 'iccifort' diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2017.2.174-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2017.2.174-GCC-6.3.0-2.27.eb index 87ed0a937d..577b228300 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2017.2.174-GCC-6.3.0-2.27.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2017.2.174-GCC-6.3.0-2.27.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ +# This is an easyconfig file for EasyBuild, see https://easybuilders.github.io/easybuild/ easyblock = 'Toolchain' name = 'iccifort' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2016.0.109-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/ifort/ifort-2016.0.109-GCC-4.9.3-2.25.eb index 255161f320..aabb1cd11e 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2016.0.109-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2016.0.109-GCC-4.9.3-2.25.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ +# This is an easyconfig file for EasyBuild, see https://easybuilders.github.io/easybuild/ name = 'ifort' version = '2016.0.109' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2016.0.109.eb b/easybuild/easyconfigs/i/ifort/ifort-2016.0.109.eb index 479cec077d..d138aad0c3 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2016.0.109.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2016.0.109.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ +# This is an easyconfig file for EasyBuild, see https://easybuilders.github.io/easybuild/ name = 'ifort' version = '2016.0.109' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2016.1.150-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/ifort/ifort-2016.1.150-GCC-4.9.3-2.25.eb index a01ea21032..9b68272441 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2016.1.150-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2016.1.150-GCC-4.9.3-2.25.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ +# This is an easyconfig file for EasyBuild, see https://easybuilders.github.io/easybuild/ name = 'ifort' version = '2016.1.150' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-4.9.3-2.25.eb index 4a5a9da050..ece99a7387 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-4.9.3-2.25.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ +# This is an easyconfig file for EasyBuild, see https://easybuilders.github.io/easybuild/ name = 'ifort' version = '2016.2.181' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-5.3.0-2.26.eb index 61a7a9cb99..5bba923e8f 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-5.3.0-2.26.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-5.3.0-2.26.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ +# This is an easyconfig file for EasyBuild, see https://easybuilders.github.io/easybuild/ name = 'ifort' version = '2016.2.181' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-4.9.3-2.25.eb index 67930d3ffb..856da5d488 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-4.9.3-2.25.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ +# This is an easyconfig file for EasyBuild, see https://easybuilders.github.io/easybuild/ name = 'ifort' version = '2016.3.210' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-5.3.0-2.26.eb index 189b6b9916..1204efb964 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-5.3.0-2.26.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-5.3.0-2.26.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ +# This is an easyconfig file for EasyBuild, see https://easybuilders.github.io/easybuild/ name = 'ifort' version = '2016.3.210' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-5.4.0-2.26.eb index bbc290ac69..52c45d2af4 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-5.4.0-2.26.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ +# This is an easyconfig file for EasyBuild, see https://easybuilders.github.io/easybuild/ name = 'ifort' version = '2016.3.210' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2017.0.098-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/ifort/ifort-2017.0.098-GCC-5.4.0-2.26.eb index 994e8bb45e..b49a02c89a 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2017.0.098-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2017.0.098-GCC-5.4.0-2.26.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ +# This is an easyconfig file for EasyBuild, see https://easybuilders.github.io/easybuild/ name = 'ifort' version = '2017.0.098' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2017.1.132-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/ifort/ifort-2017.1.132-GCC-5.4.0-2.26.eb index d03607c38d..8f58c81952 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2017.1.132-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2017.1.132-GCC-5.4.0-2.26.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ +# This is an easyconfig file for EasyBuild, see https://easybuilders.github.io/easybuild/ name = 'ifort' version = '2017.1.132' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2017.1.132-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/i/ifort/ifort-2017.1.132-GCC-6.3.0-2.27.eb index 11f2e31d72..215324831e 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2017.1.132-GCC-6.3.0-2.27.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2017.1.132-GCC-6.3.0-2.27.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ +# This is an easyconfig file for EasyBuild, see https://easybuilders.github.io/easybuild/ name = 'ifort' version = '2017.1.132' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2017.2.174-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/i/ifort/ifort-2017.2.174-GCC-6.3.0-2.27.eb index 7d3dc3b6f7..1d5cac3fad 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2017.2.174-GCC-6.3.0-2.27.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2017.2.174-GCC-6.3.0-2.27.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ +# This is an easyconfig file for EasyBuild, see https://easybuilders.github.io/easybuild/ name = 'ifort' version = '2017.2.174' diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-2016.00-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/iimpi/iimpi-2016.00-GCC-4.9.3-2.25.eb index 57a86a76d8..44c8e6ecaa 100644 --- a/easybuild/easyconfigs/i/iimpi/iimpi-2016.00-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/iimpi/iimpi-2016.00-GCC-4.9.3-2.25.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ +# This is an easyconfig file for EasyBuild, see https://easybuilders.github.io/easybuild/ easyblock = "Toolchain" name = 'iimpi' diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-2016.01-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/iimpi/iimpi-2016.01-GCC-4.9.3-2.25.eb index 8e46199a8e..476d9acb2b 100644 --- a/easybuild/easyconfigs/i/iimpi/iimpi-2016.01-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/iimpi/iimpi-2016.01-GCC-4.9.3-2.25.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ +# This is an easyconfig file for EasyBuild, see https://easybuilders.github.io/easybuild/ easyblock = "Toolchain" name = 'iimpi' diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-2016.02-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/iimpi/iimpi-2016.02-GCC-4.9.3-2.25.eb index 3c4734b17b..7878168e2e 100644 --- a/easybuild/easyconfigs/i/iimpi/iimpi-2016.02-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/iimpi/iimpi-2016.02-GCC-4.9.3-2.25.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ +# This is an easyconfig file for EasyBuild, see https://easybuilders.github.io/easybuild/ easyblock = "Toolchain" name = 'iimpi' diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-2016.02-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/iimpi/iimpi-2016.02-GCC-5.3.0-2.26.eb index 9c1506b2e4..9510f7e46a 100644 --- a/easybuild/easyconfigs/i/iimpi/iimpi-2016.02-GCC-5.3.0-2.26.eb +++ b/easybuild/easyconfigs/i/iimpi/iimpi-2016.02-GCC-5.3.0-2.26.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ +# This is an easyconfig file for EasyBuild, see https://easybuilders.github.io/easybuild/ easyblock = "Toolchain" name = 'iimpi' diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-2016.03-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/iimpi/iimpi-2016.03-GCC-4.9.3-2.25.eb index e3b3a17989..08b9b3f507 100644 --- a/easybuild/easyconfigs/i/iimpi/iimpi-2016.03-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/iimpi/iimpi-2016.03-GCC-4.9.3-2.25.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ +# This is an easyconfig file for EasyBuild, see https://easybuilders.github.io/easybuild/ easyblock = "Toolchain" name = 'iimpi' diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-2016.03-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/iimpi/iimpi-2016.03-GCC-5.3.0-2.26.eb index 2b5ee4fd1b..a8596d5825 100644 --- a/easybuild/easyconfigs/i/iimpi/iimpi-2016.03-GCC-5.3.0-2.26.eb +++ b/easybuild/easyconfigs/i/iimpi/iimpi-2016.03-GCC-5.3.0-2.26.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ +# This is an easyconfig file for EasyBuild, see https://easybuilders.github.io/easybuild/ easyblock = "Toolchain" name = 'iimpi' diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-2016.03-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/iimpi/iimpi-2016.03-GCC-5.4.0-2.26.eb index 3fa553dc7b..7ac8a1f5c1 100644 --- a/easybuild/easyconfigs/i/iimpi/iimpi-2016.03-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/iimpi/iimpi-2016.03-GCC-5.4.0-2.26.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ +# This is an easyconfig file for EasyBuild, see https://easybuilders.github.io/easybuild/ easyblock = "Toolchain" name = 'iimpi' diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-2016b.eb b/easybuild/easyconfigs/i/iimpi/iimpi-2016b.eb index 5db059f41d..4df51c9895 100644 --- a/easybuild/easyconfigs/i/iimpi/iimpi-2016b.eb +++ b/easybuild/easyconfigs/i/iimpi/iimpi-2016b.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ +# This is an easyconfig file for EasyBuild, see https://easybuilders.github.io/easybuild/ easyblock = "Toolchain" name = 'iimpi' diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-2017.00-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/iimpi/iimpi-2017.00-GCC-5.4.0-2.26.eb index d6118a326e..843a2fdb37 100644 --- a/easybuild/easyconfigs/i/iimpi/iimpi-2017.00-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/iimpi/iimpi-2017.00-GCC-5.4.0-2.26.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ +# This is an easyconfig file for EasyBuild, see https://easybuilders.github.io/easybuild/ easyblock = "Toolchain" name = 'iimpi' diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-2017.01-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/iimpi/iimpi-2017.01-GCC-5.4.0-2.26.eb index 1807df2103..cfdd91b0bf 100644 --- a/easybuild/easyconfigs/i/iimpi/iimpi-2017.01-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/iimpi/iimpi-2017.01-GCC-5.4.0-2.26.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ +# This is an easyconfig file for EasyBuild, see https://easybuilders.github.io/easybuild/ easyblock = "Toolchain" name = 'iimpi' diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-2017.02-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/i/iimpi/iimpi-2017.02-GCC-6.3.0-2.27.eb index 96132c62bd..65c861bb3f 100644 --- a/easybuild/easyconfigs/i/iimpi/iimpi-2017.02-GCC-6.3.0-2.27.eb +++ b/easybuild/easyconfigs/i/iimpi/iimpi-2017.02-GCC-6.3.0-2.27.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ +# This is an easyconfig file for EasyBuild, see https://easybuilders.github.io/easybuild/ easyblock = "Toolchain" name = 'iimpi' diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-2017a.eb b/easybuild/easyconfigs/i/iimpi/iimpi-2017a.eb index daa347a40e..14c6d0426d 100644 --- a/easybuild/easyconfigs/i/iimpi/iimpi-2017a.eb +++ b/easybuild/easyconfigs/i/iimpi/iimpi-2017a.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ +# This is an easyconfig file for EasyBuild, see https://easybuilders.github.io/easybuild/ easyblock = "Toolchain" name = 'iimpi' diff --git a/easybuild/easyconfigs/i/iimpic/iimpic-2016.10.eb b/easybuild/easyconfigs/i/iimpic/iimpic-2016.10.eb index b1196702a9..568c34ad3f 100644 --- a/easybuild/easyconfigs/i/iimpic/iimpic-2016.10.eb +++ b/easybuild/easyconfigs/i/iimpic/iimpic-2016.10.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ +# This is an easyconfig file for EasyBuild, see https://easybuilders.github.io/easybuild/ easyblock = "Toolchain" name = 'iimpic' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.0.109-iimpi-2016.00-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.0.109-iimpi-2016.00-GCC-4.9.3-2.25.eb index c67f0e36d5..d58ab5dfd6 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.3.0.109-iimpi-2016.00-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.0.109-iimpi-2016.00-GCC-4.9.3-2.25.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ +# This is an easyconfig file for EasyBuild, see https://easybuilders.github.io/easybuild/ name = 'imkl' version = '11.3.0.109' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.1.150-iimpi-2016.01-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.1.150-iimpi-2016.01-GCC-4.9.3-2.25.eb index 5f46cfbdc5..440d1741c0 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.3.1.150-iimpi-2016.01-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.1.150-iimpi-2016.01-GCC-4.9.3-2.25.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ +# This is an easyconfig file for EasyBuild, see https://easybuilders.github.io/easybuild/ name = 'imkl' version = '11.3.1.150' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-4.9.3-2.25.eb index 41939dc99b..ecf070b29c 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-4.9.3-2.25.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ +# This is an easyconfig file for EasyBuild, see https://easybuilders.github.io/easybuild/ name = 'imkl' version = '11.3.2.181' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-5.3.0-2.26.eb index 9ec0acc472..49091028d6 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-5.3.0-2.26.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-iimpi-2016.02-GCC-5.3.0-2.26.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ +# This is an easyconfig file for EasyBuild, see https://easybuilders.github.io/easybuild/ name = 'imkl' version = '11.3.2.181' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-pompi-2016.03.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-pompi-2016.03.eb index f85a4efd37..d468fef58a 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-pompi-2016.03.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.2.181-pompi-2016.03.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ +# This is an easyconfig file for EasyBuild, see https://easybuilders.github.io/easybuild/ name = 'imkl' version = '11.3.2.181' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpi-2016.03-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpi-2016.03-GCC-4.9.3-2.25.eb index 710968ace7..229575d9aa 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpi-2016.03-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpi-2016.03-GCC-4.9.3-2.25.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ +# This is an easyconfig file for EasyBuild, see https://easybuilders.github.io/easybuild/ name = 'imkl' version = '11.3.3.210' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpi-2016.03-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpi-2016.03-GCC-5.3.0-2.26.eb index 8418178c3b..5cf1169219 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpi-2016.03-GCC-5.3.0-2.26.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpi-2016.03-GCC-5.3.0-2.26.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ +# This is an easyconfig file for EasyBuild, see https://easybuilders.github.io/easybuild/ name = 'imkl' version = '11.3.3.210' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpi-2016.03-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpi-2016.03-GCC-5.4.0-2.26.eb index bf72302fc9..59e82c5910 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpi-2016.03-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpi-2016.03-GCC-5.4.0-2.26.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ +# This is an easyconfig file for EasyBuild, see https://easybuilders.github.io/easybuild/ name = 'imkl' version = '11.3.3.210' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpi-2016b.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpi-2016b.eb index c3af772fef..71ce462a11 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpi-2016b.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpi-2016b.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ +# This is an easyconfig file for EasyBuild, see https://easybuilders.github.io/easybuild/ name = 'imkl' version = '11.3.3.210' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpic-2016.10.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpic-2016.10.eb index d5a808222b..78c54328f4 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpic-2016.10.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpic-2016.10.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ +# This is an easyconfig file for EasyBuild, see https://easybuilders.github.io/easybuild/ name = 'imkl' version = '11.3.3.210' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-pompi-2016.04.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-pompi-2016.04.eb index a138ed11d0..c5041e44d7 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-pompi-2016.04.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-pompi-2016.04.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ +# This is an easyconfig file for EasyBuild, see https://easybuilders.github.io/easybuild/ name = 'imkl' version = '11.3.3.210' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-pompi-2016.09.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-pompi-2016.09.eb index 5981bc06f0..76e951f9af 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-pompi-2016.09.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-pompi-2016.09.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ +# This is an easyconfig file for EasyBuild, see https://easybuilders.github.io/easybuild/ name = 'imkl' version = '11.3.3.210' diff --git a/easybuild/easyconfigs/i/imkl/imkl-2017.0.098-iimpi-2017.00-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/imkl/imkl-2017.0.098-iimpi-2017.00-GCC-5.4.0-2.26.eb index 2ec64feae2..5fdaf87f4c 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2017.0.098-iimpi-2017.00-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2017.0.098-iimpi-2017.00-GCC-5.4.0-2.26.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ +# This is an easyconfig file for EasyBuild, see https://easybuilders.github.io/easybuild/ name = 'imkl' version = '2017.0.098' diff --git a/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-iimpi-2017.01-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-iimpi-2017.01-GCC-5.4.0-2.26.eb index 105db4b7f3..8f2a455c2d 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-iimpi-2017.01-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-iimpi-2017.01-GCC-5.4.0-2.26.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ +# This is an easyconfig file for EasyBuild, see https://easybuilders.github.io/easybuild/ name = 'imkl' version = '2017.1.132' diff --git a/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-iimpi-2017a.eb b/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-iimpi-2017a.eb index bbf353b48c..1b5c22920c 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-iimpi-2017a.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-iimpi-2017a.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ +# This is an easyconfig file for EasyBuild, see https://easybuilders.github.io/easybuild/ name = 'imkl' version = '2017.1.132' diff --git a/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-iompi-2017.01.eb b/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-iompi-2017.01.eb index dc78fc3b80..470e9458e0 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-iompi-2017.01.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-iompi-2017.01.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ +# This is an easyconfig file for EasyBuild, see https://easybuilders.github.io/easybuild/ name = 'imkl' version = '2017.1.132' diff --git a/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-iompi-2017a.eb b/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-iompi-2017a.eb index 324695a571..a6925bd1bb 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-iompi-2017a.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2017.1.132-iompi-2017a.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ +# This is an easyconfig file for EasyBuild, see https://easybuilders.github.io/easybuild/ name = 'imkl' version = '2017.1.132' diff --git a/easybuild/easyconfigs/i/imkl/imkl-2017.2.174-iimpi-2017.02-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/i/imkl/imkl-2017.2.174-iimpi-2017.02-GCC-6.3.0-2.27.eb index 5c4c02adc2..96112a1923 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2017.2.174-iimpi-2017.02-GCC-6.3.0-2.27.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2017.2.174-iimpi-2017.02-GCC-6.3.0-2.27.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ +# This is an easyconfig file for EasyBuild, see https://easybuilders.github.io/easybuild/ name = 'imkl' version = '2017.2.174' diff --git a/easybuild/easyconfigs/i/impi/impi-2017.0.098-iccifort-2017.0.098-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/impi/impi-2017.0.098-iccifort-2017.0.098-GCC-5.4.0-2.26.eb index 35a62bb371..39fce39091 100644 --- a/easybuild/easyconfigs/i/impi/impi-2017.0.098-iccifort-2017.0.098-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/impi/impi-2017.0.098-iccifort-2017.0.098-GCC-5.4.0-2.26.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ +# This is an easyconfig file for EasyBuild, see https://easybuilders.github.io/easybuild/ name = 'impi' version = '2017.0.098' diff --git a/easybuild/easyconfigs/i/impi/impi-2017.1.132-iccifort-2017.1.132-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/impi/impi-2017.1.132-iccifort-2017.1.132-GCC-5.4.0-2.26.eb index 7c55fcf3e3..a8fce42a53 100644 --- a/easybuild/easyconfigs/i/impi/impi-2017.1.132-iccifort-2017.1.132-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/impi/impi-2017.1.132-iccifort-2017.1.132-GCC-5.4.0-2.26.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ +# This is an easyconfig file for EasyBuild, see https://easybuilders.github.io/easybuild/ name = 'impi' version = '2017.1.132' diff --git a/easybuild/easyconfigs/i/impi/impi-2017.1.132-iccifort-2017.1.132-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/i/impi/impi-2017.1.132-iccifort-2017.1.132-GCC-6.3.0-2.27.eb index 4222d6a26a..9f5485d56c 100644 --- a/easybuild/easyconfigs/i/impi/impi-2017.1.132-iccifort-2017.1.132-GCC-6.3.0-2.27.eb +++ b/easybuild/easyconfigs/i/impi/impi-2017.1.132-iccifort-2017.1.132-GCC-6.3.0-2.27.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ +# This is an easyconfig file for EasyBuild, see https://easybuilders.github.io/easybuild/ name = 'impi' version = '2017.1.132' diff --git a/easybuild/easyconfigs/i/impi/impi-2017.2.174-iccifort-2017.2.174-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/i/impi/impi-2017.2.174-iccifort-2017.2.174-GCC-6.3.0-2.27.eb index fbace1b7ac..fc92127950 100644 --- a/easybuild/easyconfigs/i/impi/impi-2017.2.174-iccifort-2017.2.174-GCC-6.3.0-2.27.eb +++ b/easybuild/easyconfigs/i/impi/impi-2017.2.174-iccifort-2017.2.174-GCC-6.3.0-2.27.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ +# This is an easyconfig file for EasyBuild, see https://easybuilders.github.io/easybuild/ name = 'impi' version = '2017.2.174' diff --git a/easybuild/easyconfigs/i/impi/impi-5.1.1.109-iccifort-2016.0.109-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/impi/impi-5.1.1.109-iccifort-2016.0.109-GCC-4.9.3-2.25.eb index 72c0998995..d09b33f679 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.1.1.109-iccifort-2016.0.109-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.1.1.109-iccifort-2016.0.109-GCC-4.9.3-2.25.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ +# This is an easyconfig file for EasyBuild, see https://easybuilders.github.io/easybuild/ name = 'impi' version = '5.1.1.109' diff --git a/easybuild/easyconfigs/i/impi/impi-5.1.2.150-iccifort-2016.1.150-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/impi/impi-5.1.2.150-iccifort-2016.1.150-GCC-4.9.3-2.25.eb index eddf864db7..137847dcf7 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.1.2.150-iccifort-2016.1.150-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.1.2.150-iccifort-2016.1.150-GCC-4.9.3-2.25.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ +# This is an easyconfig file for EasyBuild, see https://easybuilders.github.io/easybuild/ name = 'impi' version = '5.1.2.150' diff --git a/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-4.9.3-2.25.eb index b779e3185b..08aa97c8f6 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-4.9.3-2.25.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ +# This is an easyconfig file for EasyBuild, see https://easybuilders.github.io/easybuild/ name = 'impi' version = '5.1.3.181' diff --git a/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-5.3.0-2.26.eb index b05f10add0..a1e94bdfa1 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-5.3.0-2.26.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.2.181-GCC-5.3.0-2.26.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ +# This is an easyconfig file for EasyBuild, see https://easybuilders.github.io/easybuild/ name = 'impi' version = '5.1.3.181' diff --git a/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.3.210-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.3.210-GCC-4.9.3-2.25.eb index a8d2a5e21e..3d597f449e 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.3.210-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.3.210-GCC-4.9.3-2.25.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ +# This is an easyconfig file for EasyBuild, see https://easybuilders.github.io/easybuild/ name = 'impi' version = '5.1.3.181' diff --git a/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.3.210-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.3.210-GCC-5.3.0-2.26.eb index 2886d91689..121e9258f2 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.3.210-GCC-5.3.0-2.26.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.3.210-GCC-5.3.0-2.26.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ +# This is an easyconfig file for EasyBuild, see https://easybuilders.github.io/easybuild/ name = 'impi' version = '5.1.3.181' diff --git a/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.3.210-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.3.210-GCC-5.4.0-2.26.eb index da9923db0a..e74cd02b1b 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.3.210-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.3.210-GCC-5.4.0-2.26.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ +# This is an easyconfig file for EasyBuild, see https://easybuilders.github.io/easybuild/ name = 'impi' version = '5.1.3.181' diff --git a/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifortcuda-2016.10.eb b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifortcuda-2016.10.eb index 2da07ac2d4..f3e312361a 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifortcuda-2016.10.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifortcuda-2016.10.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ +# This is an easyconfig file for EasyBuild, see https://easybuilders.github.io/easybuild/ name = 'impi' version = '5.1.3.181' diff --git a/easybuild/easyconfigs/i/intel/intel-2016.00.eb b/easybuild/easyconfigs/i/intel/intel-2016.00.eb index f4149f4027..5010692164 100644 --- a/easybuild/easyconfigs/i/intel/intel-2016.00.eb +++ b/easybuild/easyconfigs/i/intel/intel-2016.00.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ +# This is an easyconfig file for EasyBuild, see https://easybuilders.github.io/easybuild/ easyblock = "Toolchain" name = 'intel' diff --git a/easybuild/easyconfigs/i/intel/intel-2016.01.eb b/easybuild/easyconfigs/i/intel/intel-2016.01.eb index 1f12eaea94..bbcac55ebc 100644 --- a/easybuild/easyconfigs/i/intel/intel-2016.01.eb +++ b/easybuild/easyconfigs/i/intel/intel-2016.01.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ +# This is an easyconfig file for EasyBuild, see https://easybuilders.github.io/easybuild/ easyblock = "Toolchain" name = 'intel' diff --git a/easybuild/easyconfigs/i/iompi/iompi-2017.01.eb b/easybuild/easyconfigs/i/iompi/iompi-2017.01.eb index b648d9709a..cf97e1f426 100644 --- a/easybuild/easyconfigs/i/iompi/iompi-2017.01.eb +++ b/easybuild/easyconfigs/i/iompi/iompi-2017.01.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ +# This is an easyconfig file for EasyBuild, see https://easybuilders.github.io/easybuild/ easyblock = "Toolchain" name = 'iompi' diff --git a/easybuild/easyconfigs/i/iompi/iompi-2017a.eb b/easybuild/easyconfigs/i/iompi/iompi-2017a.eb index c74e1212e9..f5e1679c27 100644 --- a/easybuild/easyconfigs/i/iompi/iompi-2017a.eb +++ b/easybuild/easyconfigs/i/iompi/iompi-2017a.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild/ +# This is an easyconfig file for EasyBuild, see https://easybuilders.github.io/easybuild/ easyblock = "Toolchain" name = 'iompi' diff --git a/setup.py b/setup.py index af2eb6baaf..2ea811fb80 100644 --- a/setup.py +++ b/setup.py @@ -109,7 +109,7 @@ that specify the build parameters for software packages (version, compiler toolc versions, etc.).""", license = "GPLv2", keywords = "software build building installation installing compilation HPC scientific", - url = "http://easybuilders.github.io/easybuild/", + url = "https://easybuilders.github.io/easybuild/", data_files = get_data_files(), long_description = read("README.rst"), classifiers = [ -- GitLab From 24d6f4422383581d26a3d4c05fde35089356040f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 6 Jul 2017 09:14:33 +0200 Subject: [PATCH 1072/1603] remove reference to 'hpcugent' in M4 easyconfig --- easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-6.4.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-6.4.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-6.4.0.eb index 2a832cbb83..2aef3d06c6 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-6.4.0.eb @@ -18,7 +18,7 @@ checksums = ['ab2633921a5cd38e48797bf5521ad259bdc4b979078034a3b790d7fec5493fab'] builddependencies = [('binutils', '2.28', '', True)] # '-fgnu89-inline' is required to avoid linking errors with older glibc's, -# see https://github.com/hpcugent/easybuild-easyconfigs/issues/529 +# see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { -- GitLab From 64d67db1ecd019e8c6de4d68c90d257949cb76f1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 6 Jul 2017 09:14:46 +0200 Subject: [PATCH 1073/1603] check for old GitHUb EasyBuild URLs in easyconfig tests --- test/easyconfigs/easyconfigs.py | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 6e9ae84a7b..2dac08069f 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -240,6 +240,15 @@ def template_easyconfig_test(self, spec): error_msg = "Found use of '$root', not compatible with modules in Lua syntax, use '%%(installdir)s' instead: %s" self.assertFalse(res, error_msg % res) + # make sure old GitHub urls for EasyBuild that include 'hpcugent' are no longer used + old_urls = [ + 'github.com/hpcugent/easybuild', + 'hpcugent.github.com/easybuild', + 'hpcugent.github.io/easybuild', + ] + for old_url in old_urls: + self.assertFalse(old_url in ec.rawtxt, "Old URL '%s' not found in %s" % (old_url, spec)) + # make sure all patch files are available specdir = os.path.dirname(spec) specfn = os.path.basename(spec) -- GitLab From 5070365c634903f95e91f1367a7dd6cf00ac2c38 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 6 Jul 2017 10:51:08 +0200 Subject: [PATCH 1074/1603] adding easyconfigs: yaff-1.1.3-intel-2017a-Python-2.7.13.eb --- .../yaff-1.1.3-intel-2017a-Python-2.7.13.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/y/yaff/yaff-1.1.3-intel-2017a-Python-2.7.13.eb diff --git a/easybuild/easyconfigs/y/yaff/yaff-1.1.3-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/y/yaff/yaff-1.1.3-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..16b4d6c331 --- /dev/null +++ b/easybuild/easyconfigs/y/yaff/yaff-1.1.3-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonPackage' + +name = 'yaff' +version = '1.1.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://molmod.github.io/yaff/' +description = """Yaff stands for 'Yet another force field'. It is a pythonic force-field code.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['https://github.com/molmod/yaff/releases/download/%(version)s'] +sources = [SOURCE_TAR_GZ] +checksums = ['1e4ce10c19ed4338cb8ddee63beecadee4ecefcf1c12be90312ce29a6cbae116'] + +dependencies = [ + ('Python', '2.7.13'), + ('h5py', '2.7.0', versionsuffix), + ('molmod', '1.1', '-Python-%(pyver)s'), +] + +options = {'modulename': name} +runtest = "export MATPLOTLIBRC=$PWD; echo 'backend: agg' > $MATPLOTLIBRC/matplotlibrc; " +runtest += "python setup.py build_ext -i; nosetests -v" + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s'], +} + +moduleclass = 'chem' -- GitLab From 0363b0fcf8b4fa4981b0d272c3a031f64c280518 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 6 Jul 2017 12:43:32 +0200 Subject: [PATCH 1075/1603] adding easyconfigs: geopy-1.11.0-intel-2017a.eb --- .../g/geopy/geopy-1.11.0-intel-2017a.eb | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/g/geopy/geopy-1.11.0-intel-2017a.eb diff --git a/easybuild/easyconfigs/g/geopy/geopy-1.11.0-intel-2017a.eb b/easybuild/easyconfigs/g/geopy/geopy-1.11.0-intel-2017a.eb new file mode 100644 index 0000000000..d8e1943c56 --- /dev/null +++ b/easybuild/easyconfigs/g/geopy/geopy-1.11.0-intel-2017a.eb @@ -0,0 +1,21 @@ +easyblock = 'PythonPackage' + +name = 'geopy' +version = '1.11.0' + +homepage = 'https://github.com/geopy/geopy' +description = "geopy is a Python 2 and 3 client for several popular geocoding web services." + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [('Python', '3.6.1')] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'lib' -- GitLab From a8411994093907b47826e22dcf1235a029b04099 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 6 Jul 2017 13:02:56 +0200 Subject: [PATCH 1076/1603] add missing versionsuffix to geopy easyconfig --- ...0-intel-2017a.eb => geopy-1.11.0-intel-2017a-Python-3.6.1.eb} | 1 + 1 file changed, 1 insertion(+) rename easybuild/easyconfigs/g/geopy/{geopy-1.11.0-intel-2017a.eb => geopy-1.11.0-intel-2017a-Python-3.6.1.eb} (92%) diff --git a/easybuild/easyconfigs/g/geopy/geopy-1.11.0-intel-2017a.eb b/easybuild/easyconfigs/g/geopy/geopy-1.11.0-intel-2017a-Python-3.6.1.eb similarity index 92% rename from easybuild/easyconfigs/g/geopy/geopy-1.11.0-intel-2017a.eb rename to easybuild/easyconfigs/g/geopy/geopy-1.11.0-intel-2017a-Python-3.6.1.eb index d8e1943c56..4b03e02aee 100644 --- a/easybuild/easyconfigs/g/geopy/geopy-1.11.0-intel-2017a.eb +++ b/easybuild/easyconfigs/g/geopy/geopy-1.11.0-intel-2017a-Python-3.6.1.eb @@ -2,6 +2,7 @@ easyblock = 'PythonPackage' name = 'geopy' version = '1.11.0' +versionsuffix = '-Python-%(pyver)s' homepage = 'https://github.com/geopy/geopy' description = "geopy is a Python 2 and 3 client for several popular geocoding web services." -- GitLab From a94c3c6691da037d785341e19c5377e077b362b1 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Thu, 6 Jul 2017 13:33:24 +0200 Subject: [PATCH 1077/1603] Update EasyBuild URL --- easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.2.6-foss-2016b.eb | 2 +- .../s/Salmon/Salmon-0.8.2-foss-2016b-Python-2.7.12.eb | 2 +- easybuild/easyconfigs/t/tbb/tbb-2017_U5-foss-2016b.eb | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.2.6-foss-2016b.eb b/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.2.6-foss-2016b.eb index ff9fe9e8d2..d5a896eea2 100644 --- a/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.2.6-foss-2016b.eb +++ b/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.2.6-foss-2016b.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild easyblock = 'ConfigureMake' diff --git a/easybuild/easyconfigs/s/Salmon/Salmon-0.8.2-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/s/Salmon/Salmon-0.8.2-foss-2016b-Python-2.7.12.eb index a171f04582..1ef3760d15 100644 --- a/easybuild/easyconfigs/s/Salmon/Salmon-0.8.2-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/s/Salmon/Salmon-0.8.2-foss-2016b-Python-2.7.12.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild easyblock = 'CMakeMake' diff --git a/easybuild/easyconfigs/t/tbb/tbb-2017_U5-foss-2016b.eb b/easybuild/easyconfigs/t/tbb/tbb-2017_U5-foss-2016b.eb index 17d6caf922..c187512784 100644 --- a/easybuild/easyconfigs/t/tbb/tbb-2017_U5-foss-2016b.eb +++ b/easybuild/easyconfigs/t/tbb/tbb-2017_U5-foss-2016b.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild name = 'tbb' version = '2017_U5' -- GitLab From 070007f419368b29cbbeec96ab8549b4f0629b1e Mon Sep 17 00:00:00 2001 From: Shahzeb Siddiqui Date: Thu, 6 Jul 2017 15:49:43 -0400 Subject: [PATCH 1078/1603] adding Bowtiew with GCCcore 5.4.0 --- .../b/Bowtie/Bowtie-1.1.2-GCCcore-5.4.0.eb | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2-GCCcore-5.4.0.eb diff --git a/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2-GCCcore-5.4.0.eb b/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2-GCCcore-5.4.0.eb new file mode 100644 index 0000000000..f12c5655a0 --- /dev/null +++ b/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2-GCCcore-5.4.0.eb @@ -0,0 +1,18 @@ +# Modified from existing version by: +# Robert Schmidt +# Ottawa Hospital Research Institute - Bioinformatics Team +name = 'Bowtie' +version = '1.1.2' + +homepage = 'http://bowtie-bio.sourceforge.net/index.shtml' +description = """Bowtie is an ultrafast, memory-efficient short read aligner. +It aligns short DNA sequences (reads) to the human genome. +""" + +toolchain = {'name': 'GCCcore', 'version': '5.4.0'} +toolchainopts = {'pic': True} + +sources = ['%(namelower)s-%(version)s-src.zip'] +source_urls = ['http://download.sourceforge.net/bowtie-bio/'] + +moduleclass = 'bio' -- GitLab From d02a28e898c32b15e69f03e684ccd17f6c1c5c0e Mon Sep 17 00:00:00 2001 From: Shahzeb Siddiqui Date: Thu, 6 Jul 2017 15:53:16 -0400 Subject: [PATCH 1079/1603] adding BWA for GCCcore 5.4.0 --- .../b/BWA/BWA-0.7.15-GCCcore-5.4.0.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/b/BWA/BWA-0.7.15-GCCcore-5.4.0.eb diff --git a/easybuild/easyconfigs/b/BWA/BWA-0.7.15-GCCcore-5.4.0.eb b/easybuild/easyconfigs/b/BWA/BWA-0.7.15-GCCcore-5.4.0.eb new file mode 100644 index 0000000000..ffaa2a351d --- /dev/null +++ b/easybuild/easyconfigs/b/BWA/BWA-0.7.15-GCCcore-5.4.0.eb @@ -0,0 +1,26 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Cyprus Institute / CaSToRC, Uni.Lu/LCSB, NTUA +# Authors:: George Tsouloupas , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + +name = 'BWA' +version = '0.7.15' + +homepage = 'http://bio-bwa.sourceforge.net/' +description = """Burrows-Wheeler Aligner (BWA) is an efficient program that aligns + relatively short nucleotide sequences against a long reference sequence such as the human genome.""" + +toolchain = {'name': 'GCCcore', 'version': '5.4.0'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = [('http://sourceforge.net/projects/bio-bwa/files/', 'download')] + +moduleclass = 'bio' -- GitLab From f64b4029c4d5f9271c40c771c690b86a6ec64857 Mon Sep 17 00:00:00 2001 From: Shahzeb Siddiqui Date: Thu, 6 Jul 2017 16:40:25 -0400 Subject: [PATCH 1080/1603] making changes requested in PR https://github.com/easybuilders/easybuild-easyconfigs/pull/4822 --- easybuild/easyconfigs/b/BWA/BWA-0.7.15-GCCcore-5.4.0.eb | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/b/BWA/BWA-0.7.15-GCCcore-5.4.0.eb b/easybuild/easyconfigs/b/BWA/BWA-0.7.15-GCCcore-5.4.0.eb index ffaa2a351d..726ee69664 100644 --- a/easybuild/easyconfigs/b/BWA/BWA-0.7.15-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/b/BWA/BWA-0.7.15-GCCcore-5.4.0.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Cyprus Institute / CaSToRC, Uni.Lu/LCSB, NTUA # Authors:: George Tsouloupas , Fotis Georgatos @@ -18,9 +18,9 @@ description = """Burrows-Wheeler Aligner (BWA) is an efficient program that alig relatively short nucleotide sequences against a long reference sequence such as the human genome.""" toolchain = {'name': 'GCCcore', 'version': '5.4.0'} -toolchainopts = {'optarch': True, 'pic': True} +toolchainopts = {'pic': True} -sources = [SOURCELOWER_TAR_BZ2] -source_urls = [('http://sourceforge.net/projects/bio-bwa/files/', 'download')] +sources = ['v%(version)s.tar.gz'] +source_urls = ['https://github.com/lh3/%(name)s/archive/'] moduleclass = 'bio' -- GitLab From 09f8c3ed6e282441d5177ee82c7770add890a395 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Fri, 7 Jul 2017 09:08:57 +0200 Subject: [PATCH 1081/1603] Add Boost 1.54.0 for foss-2016b --- .../Boost-1.54.0-foss-2016b-Python-2.7.12.eb | 31 +++++++++++++++++++ .../b/Boost/Boost-1.54.0_fix-allocator.patch | 13 ++++++++ .../Boost-1.54.0_fix-int64_t-support.patch | 16 ++++++++++ ...oost-1.54.0_fix-make_tuple-namespace.patch | 22 +++++++++++++ 4 files changed, 82 insertions(+) create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.54.0-foss-2016b-Python-2.7.12.eb create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.54.0_fix-allocator.patch create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.54.0_fix-int64_t-support.patch create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.54.0_fix-make_tuple-namespace.patch diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.54.0-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/b/Boost/Boost-1.54.0-foss-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..f2dba0b8a4 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.54.0-foss-2016b-Python-2.7.12.eb @@ -0,0 +1,31 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +name = 'Boost' +version = '1.54.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.boost.org/' +description = "Boost provides free peer-reviewed portable C++ source libraries." + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'usempi': True, 'pic': True, 'cstd': 'c++0x'} + +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] +source_urls = ['https://sourceforge.net/projects/%(namelower)s/files/%(namelower)s/%(version)s'] + +patches = [ + '%(name)s-%(version)s_fix-allocator.patch', + '%(name)s-%(version)s_fix-int64_t-support.patch', + '%(name)s-%(version)s_fix-make_tuple-namespace.patch', +] + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('Python', '2.7.12'), +] + +# also build boost_mpi +boost_mpi = True + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.54.0_fix-allocator.patch b/easybuild/easyconfigs/b/Boost/Boost-1.54.0_fix-allocator.patch new file mode 100644 index 0000000000..d8417cd358 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.54.0_fix-allocator.patch @@ -0,0 +1,13 @@ +* fix build error: No best alternative for libs/coroutine/build/allocator_sources +author: Paul Jähne +--- libs/coroutine/build/Jamfile.v2 ++++ libs/coroutine/build/Jamfile.v2 +@@ -40,7 +40,7 @@ + : detail/standard_stack_allocator_posix.cpp + ; + +-explicit yield_sources ; ++explicit allocator_sources ; + + lib boost_coroutine + : allocator_sources diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.54.0_fix-int64_t-support.patch b/easybuild/easyconfigs/b/Boost/Boost-1.54.0_fix-int64_t-support.patch new file mode 100644 index 0000000000..3f717263bf --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.54.0_fix-int64_t-support.patch @@ -0,0 +1,16 @@ +* fix build error: int64_t support +author: Paul Jähne +--- boost/cstdint.hpp ++++ boost/cstdint.hpp +@@ -41,7 +41,10 @@ + // so we disable use of stdint.h when GLIBC does not define __GLIBC_HAVE_LONG_LONG. + // See https://svn.boost.org/trac/boost/ticket/3548 and http://sources.redhat.com/bugzilla/show_bug.cgi?id=10990 + // +-#if defined(BOOST_HAS_STDINT_H) && (!defined(__GLIBC__) || defined(__GLIBC_HAVE_LONG_LONG)) ++#if defined(BOOST_HAS_STDINT_H) \ ++ && (!defined(__GLIBC__) \ ++ || defined(__GLIBC_HAVE_LONG_LONG) \ ++ || (defined(__GLIBC__) && ((__GLIBC__ > 2) || ((__GLIBC__ == 2) && (__GLIBC_MINOR__ >= 17))))) + + // The following #include is an implementation artifact; not part of interface. + # ifdef __hpux diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.54.0_fix-make_tuple-namespace.patch b/easybuild/easyconfigs/b/Boost/Boost-1.54.0_fix-make_tuple-namespace.patch new file mode 100644 index 0000000000..42226a8183 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.54.0_fix-make_tuple-namespace.patch @@ -0,0 +1,22 @@ +* fix build error: could not convert 'std::make_tuple(_Elements&& ...) +author: Paul Jähne +--- libs/mpi/src/python/py_nonblocking.cpp ++++ libs/mpi/src/python/py_nonblocking.cpp +@@ -118,7 +118,7 @@ + pair result = + wait_any(requests.begin(), requests.end()); + +- return make_tuple( ++ return boost::python::make_tuple( + result.second->get_value_or_none(), + result.first, + distance(requests.begin(), result.second)); +@@ -134,7 +134,7 @@ + test_any(requests.begin(), requests.end()); + + if (result) +- return make_tuple( ++ return boost::python::make_tuple( + result->second->get_value_or_none(), + result->first, + distance(requests.begin(), result->second)); -- GitLab From 39932ee7b377ebe2d3a0ba170a0368a00de0d57b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Fri, 7 Jul 2017 09:20:36 +0200 Subject: [PATCH 1082/1603] Add Sailfish for foss-2016b with dependencies --- .../g/g2log/g2log-1.0-foss-2016b.eb | 33 ++++++++++ ...ailfish-0.10.1-foss-2016b-Python-2.7.12.eb | 40 ++++++++++++ ...lfish-0.10.1_skip-included-Jellyfish.patch | 64 +++++++++++++++++++ 3 files changed, 137 insertions(+) create mode 100644 easybuild/easyconfigs/g/g2log/g2log-1.0-foss-2016b.eb create mode 100644 easybuild/easyconfigs/s/Sailfish/Sailfish-0.10.1-foss-2016b-Python-2.7.12.eb create mode 100644 easybuild/easyconfigs/s/Sailfish/Sailfish-0.10.1_skip-included-Jellyfish.patch diff --git a/easybuild/easyconfigs/g/g2log/g2log-1.0-foss-2016b.eb b/easybuild/easyconfigs/g/g2log/g2log-1.0-foss-2016b.eb new file mode 100644 index 0000000000..d656235b6c --- /dev/null +++ b/easybuild/easyconfigs/g/g2log/g2log-1.0-foss-2016b.eb @@ -0,0 +1,33 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'CMakeMake' + +name = 'g2log' +version = '1.0' + +homepage = 'https://sites.google.com/site/kjellhedstrom2//g2log-efficient-background-io-processign-with-c11' +description = """g2log, efficient asynchronous logger using C++11""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['https://bitbucket.org/KjellKod/g2log/get/'] +sources = ['version-%(version)s.tar.gz'] + +checksums = ['2cd2d9cfa0cf71c80a546cde1a25f19f6b7fddf610f7cbb30a67bb81dadb7026'] + +preconfigopts = 'unzip ../3rdParty/gtest/gtest-1.6.0__stripped.zip -d ../3rdParty/gtest/ &&' +preinstallopts = 'mkdir %(installdir)s/lib && cp lib*.a %(installdir)s/lib ||' + +builddependencies = [ + ('CMake', '3.7.2'), +] + +start_dir = 'g2log' +parallel = 1 + +sanity_check_paths = { + 'files': ['lib/liblib_g2logger.a', 'lib/liblib_activeobject.a'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/Sailfish/Sailfish-0.10.1-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/s/Sailfish/Sailfish-0.10.1-foss-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..0b7cab53e1 --- /dev/null +++ b/easybuild/easyconfigs/s/Sailfish/Sailfish-0.10.1-foss-2016b-Python-2.7.12.eb @@ -0,0 +1,40 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'CMakeMake' + +name = 'Sailfish' +version = '0.10.1' +versionsuffix = '-Python-2.7.12' + +homepage = 'http://www.cs.cmu.edu/~ckingsf/software/%(namelower)s/' +description = """Sailfish is a software tool that implements a novel, alignment-free algorithm for the estimation of + isoform abundances directly from a set of reference sequences and RNA-seq reads. """ + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/kingsfordgroup/%(namelower)s/archive/'] +sources = ['v%(version)s.tar.gz'] + +checksums = ['a0d6d944382f2e07ffbfd0371132588e2f22bb846ecfc3d3435ff3d81b30d6c6'] + +patches = ['%(name)s-%(version)s_skip-included-Jellyfish.patch'] + +builddependencies = [('CMake', '3.7.2')] + +dependencies = [ + ('Boost', '1.63.0', versionsuffix), + ('tbb', '2017_U5'), + ('Jellyfish', '2.2.6'), + ('g2log', '1.0'), +] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': [] +} + +# build fails otherwise +parallel = 1 + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/Sailfish/Sailfish-0.10.1_skip-included-Jellyfish.patch b/easybuild/easyconfigs/s/Sailfish/Sailfish-0.10.1_skip-included-Jellyfish.patch new file mode 100644 index 0000000000..6f8d75e098 --- /dev/null +++ b/easybuild/easyconfigs/s/Sailfish/Sailfish-0.10.1_skip-included-Jellyfish.patch @@ -0,0 +1,64 @@ +* skip downloading and building of Jellyfish, since it's provided via EasyBuild already +* don't hardcode $CMAKE_CXX_FLAGS +author: Paul Jähne +--- CMakeLists.txt ++++ CMakeLists.txt +@@ -25,7 +25,7 @@ + + ## Set the standard required compile flags + # Nov 18th --- removed -DHAVE_CONFIG_H +-set (CMAKE_CXX_FLAGS "-pthread -funroll-loops -fPIC -fomit-frame-pointer -Ofast -DHAVE_ANSI_TERM -DHAVE_SSTREAM -DRAPMAP_SALMON_SUPPORT -Wall -std=c++11 -Wreturn-type -Werror=return-type") ++set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -L$ENV{EBROOTJELLYFISH}/lib -ljellyfish-2.0 -pthread -DHAVE_ANSI_TERM -DHAVE_SSTREAM -DRAPMAP_SALMON_SUPPORT -Wall -std=c++11 -Wreturn-type -Werror=return-type") + + ## + # OSX is strange (some might say, stupid in this regard). Deal with it's quirkines here. +@@ -287,23 +287,6 @@ + set(SUFFARRAY_INCLUDE_DIRS ${CMAKE_CURRENT_SOURCE_DIR}/external/install/include) + + +-message("Build system will fetch and build Jellyfish") +-message("==================================================================") +-ExternalProject_Add(libjellyfish +- DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external +- DOWNLOAD_COMMAND curl -k -L https://github.com/gmarcais/Jellyfish/releases/download/v2.2.3/jellyfish-2.2.3.tar.gz -o jellyfish-2.2.3.tgz && +- rm -fr jellyfish-2.2.3 && +- tar -xzvf jellyfish-2.2.3.tgz +- SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/jellyfish-2.2.3 +- INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install +- CONFIGURE_COMMAND ${CMAKE_CURRENT_SOURCE_DIR}/external/jellyfish-2.2.3/configure --prefix= CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER} CXXFLAGS=${JELLYFISH_CXX_FLAGS} +- BUILD_COMMAND ${MAKE} CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER} CXXFLAGS=${JELLYFISH_CXX_FLAGS} +- BUILD_IN_SOURCE 1 +- INSTALL_COMMAND make install && +- cp config.h /include/jellyfish-2.2.3/jellyfish/ && +- cp config.h /include/ +-) +- + find_package(TBB) + ## + # +--- src/CMakeLists.txt ++++ src/CMakeLists.txt +@@ -43,7 +43,6 @@ + ${GAT_SOURCE_DIR}/external/cereal/include + ${GAT_SOURCE_DIR}/external/install/include + ${GAT_SOURCE_DIR}/external/install/include/rapmap +-${GAT_SOURCE_DIR}/external/install/include/jellyfish-2.2.3 + ${ZLIB_INCLUDE_DIR} + ${TBB_INCLUDE_DIRS} + ${Boost_INCLUDE_DIRS} +@@ -97,7 +96,6 @@ + ${ZLIB_LIBRARY} + ${SUFFARRAY_LIB} + ${SUFFARRAY64_LIB} +- ${GAT_SOURCE_DIR}/external/install/lib/libjellyfish-2.0.a + m + ${TBB_LIBRARIES} + ${LIBSAILFISH_LINKER_FLAGS} +@@ -115,7 +113,6 @@ + ${ZLIB_LIBRARY} + ${SUFFARRAY_LIB} + ${SUFFARRAY64_LIB} +- ${GAT_SOURCE_DIR}/external/install/lib/libjellyfish-2.0.a + m + ${TBB_LIBRARIES} + ${LIBSAILFISH_LINKER_FLAGS} -- GitLab From 364705bb737cb8efecb12254ddb8328f74da3b3d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 7 Jul 2017 15:40:19 +0200 Subject: [PATCH 1083/1603] add Rtsne as extension to R 3.4.0 --- .../r/R/R-3.4.0-intel-2017a-X11-20170314.eb | 1 + .../r/R/Rtsne-0.13_icpc-wd308.patch | 20 +++++++++++++++++++ 2 files changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/r/R/Rtsne-0.13_icpc-wd308.patch diff --git a/easybuild/easyconfigs/r/R/R-3.4.0-intel-2017a-X11-20170314.eb b/easybuild/easyconfigs/r/R/R-3.4.0-intel-2017a-X11-20170314.eb index 5616a94b6a..78bdaaa928 100644 --- a/easybuild/easyconfigs/r/R/R-3.4.0-intel-2017a-X11-20170314.eb +++ b/easybuild/easyconfigs/r/R/R-3.4.0-intel-2017a-X11-20170314.eb @@ -527,6 +527,7 @@ exts_list = [ ('glmmML', '1.0.2', ext_options), ('ucminf', '1.1-4', ext_options), ('ordinal', '2015.6-28', ext_options), + ('Rtsne', '0.13', dict(ext_options.items() + [('patches', ['Rtsne-0.13_icpc-wd308.patch'])])), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/Rtsne-0.13_icpc-wd308.patch b/easybuild/easyconfigs/r/R/Rtsne-0.13_icpc-wd308.patch new file mode 100644 index 0000000000..f1c22fbba2 --- /dev/null +++ b/easybuild/easyconfigs/r/R/Rtsne-0.13_icpc-wd308.patch @@ -0,0 +1,20 @@ +--- Rtsne.orig/src/Makevars 2017-04-14 17:51:58.000000000 +0200 ++++ Rtsne/src/Makevars 2017-07-07 15:29:41.426358000 +0200 +@@ -25,4 +25,5 @@ + ## done by a number of packages, but recommended only for more advanced users + ## comfortable with autoconf and its related tools. + +- ++# disable Intel C++ compiler (icpc) warning/error #308, to avoid 'member "std::complex::_M_value" is inaccessible' ++PKG_CXXFLAGS = -wd308 +--- Rtsne.orig/MD5 2017-04-14 18:38:37.000000000 +0200 ++++ Rtsne/MD5 2017-07-07 15:29:58.247065000 +0200 +@@ -6,7 +6,7 @@ + 7af8fde3597798501e00bdc337d8f03e *README.md + 42ae2f3c4872e03c5e401d949a86cad9 *inst/CITATION + 065bed604fc3d4be094fea9fbf7f162e *man/Rtsne.Rd +-fcd429500be5e9251157f001145e8a8b *src/Makevars ++5ed55ce6fb49190f62c48ff8ce8705a1 *src/Makevars + e9a378d06e68a325926bf92e779f280e *src/Makevars.win + 5d991038a3c68e7232302c837179c26d *src/RcppExports.cpp + 3740407bdc49d16ee9a7a8d5ee96a327 *src/Rtsne.cpp -- GitLab From aa4b988517a8c6f143af91b990c1cc3a0c85a567 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 7 Jul 2017 15:42:58 +0200 Subject: [PATCH 1084/1603] adding easyconfigs: Seurat-1.4.0-intel-2017a-R-3.4.0.eb --- .../Seurat-1.4.0-intel-2017a-R-3.4.0.eb | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/s/Seurat/Seurat-1.4.0-intel-2017a-R-3.4.0.eb diff --git a/easybuild/easyconfigs/s/Seurat/Seurat-1.4.0-intel-2017a-R-3.4.0.eb b/easybuild/easyconfigs/s/Seurat/Seurat-1.4.0-intel-2017a-R-3.4.0.eb new file mode 100644 index 0000000000..7db49d1db5 --- /dev/null +++ b/easybuild/easyconfigs/s/Seurat/Seurat-1.4.0-intel-2017a-R-3.4.0.eb @@ -0,0 +1,22 @@ +easyblock = 'RPackage' + +name = 'Seurat' +version = '1.4.0' +versionsuffix = '-R-%(rver)s' + +homepage = 'http://satijalab.org/seurat' +description = "Seurat is an R package designed for QC, analysis, and exploration of single cell RNA-seq data." + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['https://github.com/satijalab/seurat/releases/download/v%(version_major_minor)s.0/'] +sources = ['%(name)s_%(version)s.tgz'] + +dependencies = [('R', '3.4.0', '-X11-20170314')] + +sanity_check_paths = { + 'files': [], + 'dirs': [name], +} + +moduleclass = 'bio' -- GitLab From 86575128430ae51b7d7d79940826d9937455e220 Mon Sep 17 00:00:00 2001 From: jrbosch Date: Fri, 7 Jul 2017 10:40:02 -0400 Subject: [PATCH 1085/1603] use the new URL in the header - https://github.com/easybuilders/easybuild --- .../b/Biopython/Biopython-1.68-foss-2016b-Python-3.5.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/Biopython/Biopython-1.68-foss-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/b/Biopython/Biopython-1.68-foss-2016b-Python-3.5.2.eb index 82e737e6cf..dc0119ae93 100644 --- a/easybuild/easyconfigs/b/Biopython/Biopython-1.68-foss-2016b-Python-3.5.2.eb +++ b/easybuild/easyconfigs/b/Biopython/Biopython-1.68-foss-2016b-Python-3.5.2.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2013 The Cyprus Institute # Authors:: Andreas Panteli , Thekla Loizou , -- GitLab From 028cae5ca68d431ccf9482757d3a208613f3b74e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 7 Jul 2017 16:50:50 +0200 Subject: [PATCH 1086/1603] add comments to patch for Rtsne --- easybuild/easyconfigs/r/R/Rtsne-0.13_icpc-wd308.patch | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R/Rtsne-0.13_icpc-wd308.patch b/easybuild/easyconfigs/r/R/Rtsne-0.13_icpc-wd308.patch index f1c22fbba2..6c76f3883e 100644 --- a/easybuild/easyconfigs/r/R/Rtsne-0.13_icpc-wd308.patch +++ b/easybuild/easyconfigs/r/R/Rtsne-0.13_icpc-wd308.patch @@ -1,4 +1,6 @@ ---- Rtsne.orig/src/Makevars 2017-04-14 17:51:58.000000000 +0200 +add -wd308 compiler option to avoid compiler warning #308 being treated as an error +author: Kenneth Hoste (HPC-UGent) +-- Rtsne.orig/src/Makevars 2017-04-14 17:51:58.000000000 +0200 +++ Rtsne/src/Makevars 2017-07-07 15:29:41.426358000 +0200 @@ -25,4 +25,5 @@ ## done by a number of packages, but recommended only for more advanced users -- GitLab From 5062b06e6694b73d1609e4f8af885a9bf2217718 Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Fri, 7 Jul 2017 14:51:17 -0500 Subject: [PATCH 1087/1603] adding easyconfigs: GCC-6.4.0-2.28.eb --- .../b/Bison/Bison-3.0.4-GCCcore-6.4.0.eb | 13 ++++---- easybuild/easyconfigs/b/Bison/Bison-3.0.4.eb | 19 ++++++++---- .../b/binutils/binutils-2.28-GCCcore-6.4.0.eb | 8 +++-- .../easyconfigs/b/binutils/binutils-2.28.eb | 8 +++-- .../f/flex/flex-2.6.4-GCCcore-6.4.0.eb | 16 ++++++---- easybuild/easyconfigs/f/flex/flex-2.6.4.eb | 30 +++++++++++++++++++ easybuild/easyconfigs/g/GCC/GCC-6.4.0-2.28.eb | 14 ++++++--- .../easyconfigs/g/GCCcore/GCCcore-6.4.0.eb | 18 ++++++----- .../help2man/help2man-1.47.4-GCCcore-6.4.0.eb | 8 +++-- .../easyconfigs/h/help2man/help2man-1.47.4.eb | 9 ++++-- .../m/M4/M4-1.4.18-GCCcore-6.4.0.eb | 20 ++++++++----- easybuild/easyconfigs/m/M4/M4-1.4.18.eb | 17 ++++++----- .../z/zlib/zlib-1.2.11-GCCcore-6.4.0.eb | 20 ++++++++----- easybuild/easyconfigs/z/zlib/zlib-1.2.11.eb | 18 +++++++---- 14 files changed, 156 insertions(+), 62 deletions(-) create mode 100644 easybuild/easyconfigs/f/flex/flex-2.6.4.eb diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-6.4.0.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-6.4.0.eb index 2623578bc5..8a3bfe8164 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-6.4.0.eb @@ -4,13 +4,17 @@ name = 'Bison' version = '3.0.4' homepage = 'http://www.gnu.org/software/bison' -description = """Bison is a general-purpose parser generator that converts an annotated context-free grammar - into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.""" + +description = """ + Bison is a general-purpose parser generator that converts an annotated + context-free grammar into a deterministic LR or generalized LR (GLR) parser + employing LALR(1) parser tables. +""" toolchain = {'name': 'GCCcore', 'version': '6.4.0'} -sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] checksums = ['b67fd2daae7a64b5ba862c66c07c1addb9e6b1b05c5f2049392cfd8a2172952e'] builddependencies = [ @@ -19,10 +23,9 @@ builddependencies = [ ('binutils', '2.28', '', True), ] - sanity_check_paths = { + 'dirs': ['bin', 'lib'], 'files': ['bin/%s' % x for x in ['bison', 'yacc']] + ['lib/liby.a'], - 'dirs': [], } moduleclass = 'lang' diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.4.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.4.eb index 7828372bd5..ea20c01d4d 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-3.0.4.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.4.eb @@ -4,19 +4,26 @@ name = 'Bison' version = '3.0.4' homepage = 'http://www.gnu.org/software/bison' -description = """Bison is a general-purpose parser generator that converts an annotated context-free grammar -into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.""" + +description = """ + Bison is a general-purpose parser generator that converts an annotated + context-free grammar into a deterministic LR or generalized LR (GLR) parser + employing LALR(1) parser tables. +""" toolchain = {'name': 'dummy', 'version': ''} -sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['b67fd2daae7a64b5ba862c66c07c1addb9e6b1b05c5f2049392cfd8a2172952e'] -builddependencies = [('M4', '1.4.17')] +builddependencies = [ + ('M4', '1.4.18'), +] sanity_check_paths = { - 'files': ["bin/%s" % x for x in ["bison", "yacc"]] + ["lib/liby.a"], - 'dirs': [], + 'dirs': ['bin', 'lib'], + 'files': ['bin/%s' % x for x in ['bison', 'yacc']] + ['lib/liby.a'], } moduleclass = 'lang' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.28-GCCcore-6.4.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.28-GCCcore-6.4.0.eb index b6486c7dfb..cb761e0729 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.28-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.28-GCCcore-6.4.0.eb @@ -1,13 +1,16 @@ +easyblock = 'EB_binutils' + name = 'binutils' version = '2.28' homepage = 'http://directory.fsf.org/project/binutils/' + description = "binutils: GNU binary utilities" toolchain = {'name': 'GCCcore', 'version': '6.4.0'} -sources = [SOURCE_TAR_GZ] source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] checksums = ['cd717966fc761d840d451dbd58d44e1e5b92949d2073d75b73fccb476d772fcf'] builddependencies = [ @@ -15,7 +18,8 @@ builddependencies = [ ('Bison', '3.0.4'), # zlib required, but being linked in statically, so not a runtime dep ('zlib', '1.2.11'), - # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils + # use same binutils version that was used when building GCC toolchain, + # to 'bootstrap' this binutils ('binutils', version, '', True) ] diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.28.eb b/easybuild/easyconfigs/b/binutils/binutils-2.28.eb index 7681d5cc1f..a3ca8d487e 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.28.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.28.eb @@ -1,16 +1,20 @@ +easyblock = 'EB_binutils' + name = 'binutils' version = '2.28' homepage = 'http://directory.fsf.org/project/binutils/' + description = "binutils: GNU binary utilities" toolchain = {'name': 'dummy', 'version': ''} -sources = [SOURCE_TAR_GZ] source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['cd717966fc761d840d451dbd58d44e1e5b92949d2073d75b73fccb476d772fcf'] builddependencies = [ - ('flex', '2.6.3'), + ('flex', '2.6.4'), ('Bison', '3.0.4'), # zlib required, but being linked in statically, so not a runtime dep ('zlib', '1.2.11'), diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-6.4.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-6.4.0.eb index 55845823d8..37b5152374 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-6.4.0.eb @@ -2,18 +2,20 @@ name = 'flex' version = '2.6.4' homepage = 'http://flex.sourceforge.net/' -description = """Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, - sometimes called a tokenizer, is a program which recognizes lexical patterns in text.""" + +description = """ + Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, + sometimes called a tokenizer, is a program which recognizes lexical patterns + in text. +""" toolchain = {'name': 'GCCcore', 'version': '6.4.0'} toolchainopts = {'pic': True} -sources = [SOURCELOWER_TAR_GZ] source_urls = ['https://github.com/westes/flex/releases/download/v%(version)s/'] - +sources = [SOURCELOWER_TAR_GZ] checksums = ['e87aae032bf07c26f85ac0ed3250998c37621d95f8bd748b31f15b33c45ee995'] -dependencies = [('M4', '1.4.18')] builddependencies = [ ('Bison', '3.0.4'), ('help2man', '1.47.4'), @@ -21,4 +23,8 @@ builddependencies = [ ('binutils', '2.28', '', True), ] +dependencies = [ + ('M4', '1.4.18'), +] + moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.4.eb b/easybuild/easyconfigs/f/flex/flex-2.6.4.eb new file mode 100644 index 0000000000..d85380798d --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.6.4.eb @@ -0,0 +1,30 @@ +easyblock = 'EB_flex' + +name = 'flex' +version = '2.6.4' + +homepage = 'http://flex.sourceforge.net/' + +description = """ + Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, + sometimes called a tokenizer, is a program which recognizes lexical patterns + in text. +""" + +toolchain = {'name': 'dummy', 'version': ''} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/westes/flex/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['e87aae032bf07c26f85ac0ed3250998c37621d95f8bd748b31f15b33c45ee995'] + +builddependencies = [ + ('Bison', '3.0.4'), + ('help2man', '1.47.4'), +] + +dependencies = [ + ('M4', '1.4.18'), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/g/GCC/GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/g/GCC/GCC-6.4.0-2.28.eb index 6d830c0286..f5f6e4e49d 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-6.4.0-2.28.eb @@ -7,19 +7,25 @@ binutilsver = '2.28' versionsuffix = '-%s' % binutilsver homepage = 'http://gcc.gnu.org/' -description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, - as well as libraries for these languages (libstdc++, libgcj,...).""" + +description = """ + The GNU Compiler Collection includes front ends for C, C++, Objective-C, + Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, + libgcj,...). [NOTE: This module does not include Objective-C, Java or Ada] +""" toolchain = {'name': 'dummy', 'version': ''} dependencies = [ ('GCCcore', version), - # binutils built on top of GCCcore, which was built on top of (dummy-built) binutils + # binutils built on top of GCCcore, which was built + # on top of (dummy-built) binutils ('binutils', binutilsver, '', ('GCCcore', version)), ] altroot = 'GCCcore' altversion = 'GCCcore' -# this bundle serves as a compiler-only toolchain, so it should be marked as compiler (important for HMNS) +# this bundle serves as a compiler-only toolchain, +# so it should be marked as compiler (important for HMNS) moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-6.4.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-6.4.0.eb index 8c17a18894..37077d5dbf 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-6.4.0.eb @@ -4,8 +4,12 @@ name = 'GCCcore' version = '6.4.0' homepage = 'http://gcc.gnu.org/' -description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, - as well as libraries for these languages (libstdc++, libgcj,...).""" + +description = """ + The GNU Compiler Collection includes front ends for C, C++, Objective-C, + Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, + libgcj,...). [NOTE: This module does not include Objective-C, Java or Ada] +""" toolchain = {'name': 'dummy', 'version': ''} @@ -40,11 +44,11 @@ patches = [ ] checksums = [ - '4715f02413f8a91d02d967521c084990c99ce1a671b8a450a80fbd4245f4b728', # gcc-6.4.0.tar.gz - '5275bb04f4863a13516b2f39392ac5e272f5e1bb8057b18aec1c9b79d73d8fb2', # gmp-6.1.2.tar.bz2 - 'ca498c1c7a74dd37a576f353312d1e68d490978de4395fa28f1cbd46a364e658', # mpfr-3.1.5.tar.gz - '617decc6ea09889fb08ede330917a00b16809b8db88c29c31bfbb49cbf88ecc3', # mpc-1.0.3.tar.gz - '412538bb65c799ac98e17e8cfcdacbb257a57362acfaaff254b0fcae970126d2', # isl-0.16.1.tar.bz2 + '4715f02413f8a91d02d967521c084990c99ce1a671b8a450a80fbd4245f4b728', # gcc-6.4.0.tar.gz + '5275bb04f4863a13516b2f39392ac5e272f5e1bb8057b18aec1c9b79d73d8fb2', # gmp-6.1.2.tar.bz2 + 'ca498c1c7a74dd37a576f353312d1e68d490978de4395fa28f1cbd46a364e658', # mpfr-3.1.5.tar.gz + '617decc6ea09889fb08ede330917a00b16809b8db88c29c31bfbb49cbf88ecc3', # mpc-1.0.3.tar.gz + '412538bb65c799ac98e17e8cfcdacbb257a57362acfaaff254b0fcae970126d2', # isl-0.16.1.tar.bz2 '137108952139486755e8c1bee30314ffa9233cc05cddfd848aa85503a6fea9d7', # mpfr-3.1.5-allpatches-20170606.patch '5ad909606d17d851c6ad629b4fddb6c1621844218b8d139fed18c502a7696c68', # GCCcore-6.2.0-fix-find-isl.patch ] diff --git a/easybuild/easyconfigs/h/help2man/help2man-1.47.4-GCCcore-6.4.0.eb b/easybuild/easyconfigs/h/help2man/help2man-1.47.4-GCCcore-6.4.0.eb index 192cdb14fe..2993c21bd9 100644 --- a/easybuild/easyconfigs/h/help2man/help2man-1.47.4-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/h/help2man/help2man-1.47.4-GCCcore-6.4.0.eb @@ -4,7 +4,11 @@ name = 'help2man' version = '1.47.4' homepage = 'https://www.gnu.org/software/help2man/' -description = """help2man produces simple manual pages from the '--help' and '--version' output of other commands.""" + +description = """ + help2man produces simple manual pages from the '--help' and '--version' + output of other commands. +""" toolchain = {'name': 'GCCcore', 'version': '6.4.0'} @@ -18,8 +22,8 @@ builddependencies = [ ] sanity_check_paths = { + 'dirs': ['bin'], 'files': ['bin/help2man'], - 'dirs': [], } moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/help2man/help2man-1.47.4.eb b/easybuild/easyconfigs/h/help2man/help2man-1.47.4.eb index 292de661e9..a06e019c8b 100644 --- a/easybuild/easyconfigs/h/help2man/help2man-1.47.4.eb +++ b/easybuild/easyconfigs/h/help2man/help2man-1.47.4.eb @@ -4,16 +4,21 @@ name = 'help2man' version = '1.47.4' homepage = 'https://www.gnu.org/software/help2man/' -description = """help2man produces simple manual pages from the '--help' and '--version' output of other commands.""" + +description = """ + help2man produces simple manual pages from the '--help' and '--version' + output of other commands. +""" toolchain = {'name': 'dummy', 'version': ''} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_XZ] +checksums = ['d4ecf697d13f14dd1a78c5995f06459bff706fd1ce593d1c02d81667c0207753'] sanity_check_paths = { + 'dirs': ['bin'], 'files': ['bin/help2man'], - 'dirs': [], } moduleclass = 'tools' diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-6.4.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-6.4.0.eb index 2aef3d06c6..0aaa327fd6 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-6.4.0.eb @@ -4,26 +4,32 @@ name = 'M4' version = '1.4.18' homepage = 'http://www.gnu.org/software/m4/m4.html' -description = """GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible - although it has some extensions (for example, handling more than 9 positional parameters to macros). - GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc.""" + +description = """ + GNU M4 is an implementation of the traditional Unix macro processor. It is + mostly SVR4 compatible although it has some extensions (for example, handling + more than 9 positional parameters to macros). GNU M4 also has built-in + functions for including files, running shell commands, doing arithmetic, etc. +""" toolchain = {'name': 'GCCcore', 'version': '6.4.0'} -sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] checksums = ['ab2633921a5cd38e48797bf5521ad259bdc4b979078034a3b790d7fec5493fab'] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.28', '', True)] +builddependencies = [ + ('binutils', '2.28', '', True), +] # '-fgnu89-inline' is required to avoid linking errors with older glibc's, # see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { - 'files': ["bin/m4"], - 'dirs': [], + 'dirs': ['bin'], + 'files': ['bin/m4'], } moduleclass = 'devel' diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18.eb index bce719edb0..5d4ba8a946 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18.eb @@ -4,24 +4,27 @@ name = 'M4' version = '1.4.18' homepage = 'http://www.gnu.org/software/m4/m4.html' -description = """GNU M4 is an implementation of the traditional Unix macro processor. - It is mostly SVR4 compatible although it has some extensions - (for example, handling more than 9 positional parameters to macros). - GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc. + +description = """ + GNU M4 is an implementation of the traditional Unix macro processor. It is + mostly SVR4 compatible although it has some extensions (for example, handling + more than 9 positional parameters to macros). GNU M4 also has built-in + functions for including files, running shell commands, doing arithmetic, etc. """ toolchain = {'name': 'dummy', 'version': 'dummy'} -sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['ab2633921a5cd38e48797bf5521ad259bdc4b979078034a3b790d7fec5493fab'] # '-fgnu89-inline' is required to avoid linking errors with older glibc's, # see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { - 'files': ["bin/m4"], - 'dirs': [], + 'dirs': ['bin'], + 'files': ['bin/m4'], } moduleclass = 'devel' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-6.4.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-6.4.0.eb index a520a02364..dfe62b551a 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-6.4.0.eb @@ -4,23 +4,29 @@ name = 'zlib' version = '1.2.11' homepage = 'http://www.zlib.net/' -description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is, - not covered by any patents -- lossless data-compression library for use on virtually any - computer hardware and operating system.""" + +description = """ + zlib is designed to be a free, general-purpose, legally unencumbered -- that + is, not covered by any patents -- lossless data-compression library for use + on virtually any computer hardware and operating system. +""" toolchain = {'name': 'GCCcore', 'version': '6.4.0'} toolchainopts = {'pic': True} -source_urls = ['http://zlib.net/fossils'] +source_urls = ['http://zlib.net/fossils/'] sources = [SOURCELOWER_TAR_GZ] checksums = ['c3e5e9fdd5004dcb542feda5ee4f0ff0744628baf8ed2dd5d66f8ca1197cb1a1'] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.28', '', True)] +builddependencies = [ + ('binutils', '2.28', '', True), +] sanity_check_paths = { - 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], - 'dirs': [], + 'dirs': ['include', 'lib'], + 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', + 'lib/libz.%s' % SHLIB_EXT], } moduleclass = 'lib' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.11.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.11.eb index b74939ef09..b582c747ed 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.11.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.11.eb @@ -4,23 +4,29 @@ name = 'zlib' version = '1.2.11' homepage = 'http://www.zlib.net/' -description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is, - not covered by any patents -- lossless data-compression library for use on virtually any - computer hardware and operating system.""" + +description = """ + zlib is designed to be a free, general-purpose, legally unencumbered -- that + is, not covered by any patents -- lossless data-compression library for use + on virtually any computer hardware and operating system. +""" toolchain = {'name': 'dummy', 'version': 'dummy'} toolchainopts = {'pic': True} source_urls = ['http://zlib.net/fossils/'] sources = [SOURCELOWER_TAR_GZ] +checksums = ['c3e5e9fdd5004dcb542feda5ee4f0ff0744628baf8ed2dd5d66f8ca1197cb1a1'] # need to take care of $CFLAGS ourselves with dummy toolchain -# we need to add -fPIC, but should also include -O* option to avoid compiling with -O0 (default for GCC) +# we need to add -fPIC, but should also include -O* option to avoid +# compiling with -O0 (default for GCC) buildopts = 'CFLAGS="-O2 -fPIC"' sanity_check_paths = { - 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], - 'dirs': [], + 'dirs': ['include', 'lib'], + 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', + 'lib/libz.%s' % SHLIB_EXT], } moduleclass = 'lib' -- GitLab From e450ad265a7d5c46daf2780b7c049695a1b99b3e Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Sat, 8 Jul 2017 10:49:07 -0500 Subject: [PATCH 1088/1603] bowing to authority and will ask the whys later --- .../b/Bison/Bison-3.0.4-GCCcore-6.4.0.eb | 2 +- easybuild/easyconfigs/b/Bison/Bison-3.0.4.eb | 4 ++-- .../easyconfigs/b/binutils/binutils-2.28.eb | 2 +- easybuild/easyconfigs/f/flex/flex-2.6.3.eb | 17 +++++++++++++---- .../h/help2man/help2man-1.47.4-GCCcore-6.4.0.eb | 2 +- .../easyconfigs/h/help2man/help2man-1.47.4.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.17.eb | 15 +++++++++------ .../easyconfigs/m/M4/M4-1.4.18-GCCcore-6.4.0.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.18.eb | 2 +- .../z/zlib/zlib-1.2.11-GCCcore-6.4.0.eb | 2 +- easybuild/easyconfigs/z/zlib/zlib-1.2.11.eb | 2 +- 11 files changed, 32 insertions(+), 20 deletions(-) diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-6.4.0.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-6.4.0.eb index 8a3bfe8164..00833a66e3 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-6.4.0.eb @@ -24,8 +24,8 @@ builddependencies = [ ] sanity_check_paths = { - 'dirs': ['bin', 'lib'], 'files': ['bin/%s' % x for x in ['bison', 'yacc']] + ['lib/liby.a'], + 'dirs': [], } moduleclass = 'lang' diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.4.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.4.eb index ea20c01d4d..fc43bdc45f 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-3.0.4.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.4.eb @@ -18,12 +18,12 @@ sources = [SOURCELOWER_TAR_GZ] checksums = ['b67fd2daae7a64b5ba862c66c07c1addb9e6b1b05c5f2049392cfd8a2172952e'] builddependencies = [ - ('M4', '1.4.18'), + ('M4', '1.4.17'), ] sanity_check_paths = { - 'dirs': ['bin', 'lib'], 'files': ['bin/%s' % x for x in ['bison', 'yacc']] + ['lib/liby.a'], + 'dirs': [], } moduleclass = 'lang' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.28.eb b/easybuild/easyconfigs/b/binutils/binutils-2.28.eb index a3ca8d487e..873588d2d7 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.28.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.28.eb @@ -14,7 +14,7 @@ sources = [SOURCE_TAR_GZ] checksums = ['cd717966fc761d840d451dbd58d44e1e5b92949d2073d75b73fccb476d772fcf'] builddependencies = [ - ('flex', '2.6.4'), + ('flex', '2.6.3'), ('Bison', '3.0.4'), # zlib required, but being linked in statically, so not a runtime dep ('zlib', '1.2.11'), diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.3.eb b/easybuild/easyconfigs/f/flex/flex-2.6.3.eb index 568be27f41..9161055702 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.3.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.3.eb @@ -1,22 +1,31 @@ +easyblock = 'EB_flex' + name = 'flex' version = '2.6.3' homepage = 'http://flex.sourceforge.net/' -description = """Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, - sometimes called a tokenizer, is a program which recognizes lexical patterns in text.""" + +description = """ + Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, + sometimes called a tokenizer, is a program which recognizes lexical patterns + in text. +""" toolchain = {'name': 'dummy', 'version': ''} toolchainopts = {'pic': True} -sources = [SOURCELOWER_TAR_GZ] source_urls = ['https://github.com/westes/flex/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] checksums = ['a5f65570cd9107ec8a8ec88f17b31bb1'] -dependencies = [('M4', '1.4.18')] builddependencies = [ ('Bison', '3.0.4'), ('help2man', '1.47.4'), ] +dependencies = [ + ('M4', '1.4.18'), +] + moduleclass = 'lang' diff --git a/easybuild/easyconfigs/h/help2man/help2man-1.47.4-GCCcore-6.4.0.eb b/easybuild/easyconfigs/h/help2man/help2man-1.47.4-GCCcore-6.4.0.eb index 2993c21bd9..c354ad3369 100644 --- a/easybuild/easyconfigs/h/help2man/help2man-1.47.4-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/h/help2man/help2man-1.47.4-GCCcore-6.4.0.eb @@ -22,8 +22,8 @@ builddependencies = [ ] sanity_check_paths = { - 'dirs': ['bin'], 'files': ['bin/help2man'], + 'dirs': [], } moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/help2man/help2man-1.47.4.eb b/easybuild/easyconfigs/h/help2man/help2man-1.47.4.eb index a06e019c8b..9dded57c01 100644 --- a/easybuild/easyconfigs/h/help2man/help2man-1.47.4.eb +++ b/easybuild/easyconfigs/h/help2man/help2man-1.47.4.eb @@ -17,8 +17,8 @@ sources = [SOURCE_TAR_XZ] checksums = ['d4ecf697d13f14dd1a78c5995f06459bff706fd1ce593d1c02d81667c0207753'] sanity_check_paths = { - 'dirs': ['bin'], 'files': ['bin/help2man'], + 'dirs': [], } moduleclass = 'tools' diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17.eb index 92afdc0086..0ac466ffad 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17.eb @@ -4,23 +4,26 @@ name = 'M4' version = '1.4.17' homepage = 'http://www.gnu.org/software/m4/m4.html' -description = """GNU M4 is an implementation of the traditional Unix macro processor. - It is mostly SVR4 compatible although it has some extensions - (for example, handling more than 9 positional parameters to macros). - GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc. + +description = """ + GNU M4 is an implementation of the traditional Unix macro processor. It is + mostly SVR4 compatible although it has some extensions (for example, handling + more than 9 positional parameters to macros). GNU M4 also has built-in + functions for including files, running shell commands, doing arithmetic, etc. """ toolchain = {'name': 'dummy', 'version': 'dummy'} -sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['3ce725133ee552b8b4baca7837fb772940b25e81b2a9dc92537aeaf733538c9e'] # '-fgnu89-inline' is required to avoid linking errors with older glibc's, # see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { - 'files': ["bin/m4"], + 'files': ['bin/m4'], 'dirs': [], } diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-6.4.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-6.4.0.eb index 0aaa327fd6..a71de342f1 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-6.4.0.eb @@ -28,8 +28,8 @@ builddependencies = [ configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { - 'dirs': ['bin'], 'files': ['bin/m4'], + 'dirs': [], } moduleclass = 'devel' diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18.eb index 5d4ba8a946..ac19a0bf0a 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18.eb @@ -23,8 +23,8 @@ checksums = ['ab2633921a5cd38e48797bf5521ad259bdc4b979078034a3b790d7fec5493fab'] configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" sanity_check_paths = { - 'dirs': ['bin'], 'files': ['bin/m4'], + 'dirs': [], } moduleclass = 'devel' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-6.4.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-6.4.0.eb index dfe62b551a..acbff073f4 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-6.4.0.eb @@ -24,9 +24,9 @@ builddependencies = [ ] sanity_check_paths = { - 'dirs': ['include', 'lib'], 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], + 'dirs': [], } moduleclass = 'lib' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.11.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.11.eb index b582c747ed..d8f38e9cad 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.11.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.11.eb @@ -24,9 +24,9 @@ checksums = ['c3e5e9fdd5004dcb542feda5ee4f0ff0744628baf8ed2dd5d66f8ca1197cb1a1'] buildopts = 'CFLAGS="-O2 -fPIC"' sanity_check_paths = { - 'dirs': ['include', 'lib'], 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], + 'dirs': [], } moduleclass = 'lib' -- GitLab From ce776755097cde226b848c01874e180eda20183b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 8 Jul 2017 19:23:56 +0200 Subject: [PATCH 1089/1603] fix reference to github.com/hpcugent in GROMACS easyconfig --- .../easyconfigs/g/GROMACS/GROMACS-2016.3-goolfc-2017.01.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.3-goolfc-2017.01.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.3-goolfc-2017.01.eb index 24d9e0afe2..070615703c 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.3-goolfc-2017.01.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.3-goolfc-2017.01.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2016 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, # Ghent University / The Francis Crick Institute -- GitLab From 953a508d0f013c50dc8b9eebcadcfa0e65fcab95 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 8 Jul 2017 19:44:44 +0200 Subject: [PATCH 1090/1603] notify EasyBuild maintainers of failing tests --- .travis.yml | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/.travis.yml b/.travis.yml index cab5b8a8be..d0416aad91 100644 --- a/.travis.yml +++ b/.travis.yml @@ -49,3 +49,11 @@ script: - cd $HOME - export PYTHONPATH=$TRAVIS_BUILD_DIR - python -O -m test.easyconfigs.suite +# EasyBuild maintainers should get notified when tests in master/develop fail; +# no notifications are sent for pull requests +notifications: + email: + recipients: + - easybuild-maintainers@lists.ugent.be + on_success: change + on_failure: always -- GitLab From 6348765f06cc4e0199fe66cb609ecdda63ccb226 Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Sun, 9 Jul 2017 05:17:30 -0500 Subject: [PATCH 1091/1603] EBv2.0 didn't go far enough on explict easyblocks :) --- easybuild/easyconfigs/b/binutils/binutils-2.28-GCCcore-6.4.0.eb | 2 -- easybuild/easyconfigs/b/binutils/binutils-2.28.eb | 2 -- easybuild/easyconfigs/f/flex/flex-2.6.4.eb | 2 -- 3 files changed, 6 deletions(-) diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.28-GCCcore-6.4.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.28-GCCcore-6.4.0.eb index cb761e0729..4281a9f323 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.28-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.28-GCCcore-6.4.0.eb @@ -1,5 +1,3 @@ -easyblock = 'EB_binutils' - name = 'binutils' version = '2.28' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.28.eb b/easybuild/easyconfigs/b/binutils/binutils-2.28.eb index 873588d2d7..a50c4f25ca 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.28.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.28.eb @@ -1,5 +1,3 @@ -easyblock = 'EB_binutils' - name = 'binutils' version = '2.28' diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.4.eb b/easybuild/easyconfigs/f/flex/flex-2.6.4.eb index d85380798d..7ef4743c46 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.4.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.4.eb @@ -1,5 +1,3 @@ -easyblock = 'EB_flex' - name = 'flex' version = '2.6.4' -- GitLab From 4b9b3864ad8a5ca4555d59e423019165aad94c98 Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Sun, 9 Jul 2017 05:36:26 -0500 Subject: [PATCH 1092/1603] missed one --- easybuild/easyconfigs/f/flex/flex-2.6.3.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.3.eb b/easybuild/easyconfigs/f/flex/flex-2.6.3.eb index 9161055702..f920a0f965 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.3.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.3.eb @@ -1,5 +1,3 @@ -easyblock = 'EB_flex' - name = 'flex' version = '2.6.3' -- GitLab From f9ee63dd1023732f31de530aef9cea79496677cb Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 9 Jul 2017 19:01:46 +0200 Subject: [PATCH 1093/1603] Revert "notify EasyBuild maintainers of failing tests" This reverts commit 953a508d0f013c50dc8b9eebcadcfa0e65fcab95. --- .travis.yml | 8 -------- 1 file changed, 8 deletions(-) diff --git a/.travis.yml b/.travis.yml index d0416aad91..cab5b8a8be 100644 --- a/.travis.yml +++ b/.travis.yml @@ -49,11 +49,3 @@ script: - cd $HOME - export PYTHONPATH=$TRAVIS_BUILD_DIR - python -O -m test.easyconfigs.suite -# EasyBuild maintainers should get notified when tests in master/develop fail; -# no notifications are sent for pull requests -notifications: - email: - recipients: - - easybuild-maintainers@lists.ugent.be - on_success: change - on_failure: always -- GitLab From 7a71cee4fa329d1504b027bd441d30828e551959 Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Sun, 9 Jul 2017 16:28:03 -0500 Subject: [PATCH 1094/1603] adding easyconfigs: libsigsegv-2.11-GCC-6.4.0-2.28.eb, libsigsegv-2.11-GCCcore-6.4.0.eb --- .../libsigsegv-2.11-GCC-6.4.0-2.28.eb | 24 ++++++++++++++++ .../libsigsegv-2.11-GCCcore-6.4.0.eb | 28 +++++++++++++++++++ 2 files changed, 52 insertions(+) create mode 100644 easybuild/easyconfigs/l/libsigsegv/libsigsegv-2.11-GCC-6.4.0-2.28.eb create mode 100644 easybuild/easyconfigs/l/libsigsegv/libsigsegv-2.11-GCCcore-6.4.0.eb diff --git a/easybuild/easyconfigs/l/libsigsegv/libsigsegv-2.11-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/l/libsigsegv/libsigsegv-2.11-GCC-6.4.0-2.28.eb new file mode 100644 index 0000000000..dfc2614481 --- /dev/null +++ b/easybuild/easyconfigs/l/libsigsegv/libsigsegv-2.11-GCC-6.4.0-2.28.eb @@ -0,0 +1,24 @@ +# Authors:: Jack Perdue - TAMU HPRC - http://hprc.tamu.edu + +easyblock = 'ConfigureMake' + +name = 'libsigsegv' +version = '2.11' + +homepage = 'https://www.gnu.org/software/libsigsegv/' + +description = """ + GNU libsigsegv is a library for handling page faults in user mode. +""" + +toolchain = {'name': 'GCC', 'version': '6.4.0-2.28'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'dirs': ['include', 'lib'], + 'files': ['include/sigsegv.h', 'lib/libsigsegv.a', 'lib/libsigsegv.la'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libsigsegv/libsigsegv-2.11-GCCcore-6.4.0.eb b/easybuild/easyconfigs/l/libsigsegv/libsigsegv-2.11-GCCcore-6.4.0.eb new file mode 100644 index 0000000000..cdeb207cc1 --- /dev/null +++ b/easybuild/easyconfigs/l/libsigsegv/libsigsegv-2.11-GCCcore-6.4.0.eb @@ -0,0 +1,28 @@ +# Authors:: Jack Perdue - TAMU HPRC - http://hprc.tamu.edu + +easyblock = 'ConfigureMake' + +name = 'libsigsegv' +version = '2.11' + +homepage = 'https://www.gnu.org/software/libsigsegv/' + +description = """ + GNU libsigsegv is a library for handling page faults in user mode. +""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +builddependencies = [ + ('binutils', '2.28'), +] + +sanity_check_paths = { + 'dirs': ['include', 'lib'], + 'files': ['include/sigsegv.h', 'lib/libsigsegv.a', 'lib/libsigsegv.la'], +} + +moduleclass = 'lib' -- GitLab From bfc7a51f6291e138bf7f0e9c711b1201e1c5a74e Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Mon, 10 Jul 2017 00:03:05 +0200 Subject: [PATCH 1095/1603] added easyconfig for miniconda --- .../easyconfigs/m/Miniconda/Miniconda-4.3.21.eb | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) create mode 100644 easybuild/easyconfigs/m/Miniconda/Miniconda-4.3.21.eb diff --git a/easybuild/easyconfigs/m/Miniconda/Miniconda-4.3.21.eb b/easybuild/easyconfigs/m/Miniconda/Miniconda-4.3.21.eb new file mode 100644 index 0000000000..a5ae211a5c --- /dev/null +++ b/easybuild/easyconfigs/m/Miniconda/Miniconda-4.3.21.eb @@ -0,0 +1,17 @@ +easyblock = 'EB_Anaconda' + +name = 'Miniconda2' +version = '4.3.21' + +homepage = 'https://www.continuum.io/anaconda-overview' +description = """Built to complement the rich, open source Python community, +the Anaconda platform provides an enterprise-ready data analytics platform +that empowers companies to adopt a modern open data science analytics architecture. +""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['https://repo.continuum.io/miniconda/'] +sources = ['%(name)s-%(version)s-Linux-x86_64.sh'] + +moduleclass = 'lang' -- GitLab From 17ea4f57e70ff40e221a71fd094d6ce2bd0c4dab Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Sun, 9 Jul 2017 17:04:23 -0500 Subject: [PATCH 1096/1603] alter sanity_check_paths to match the sanity standards of EB (which may or may not be entirely sane) --- .../easyconfigs/l/libsigsegv/libsigsegv-2.11-GCC-6.4.0-2.28.eb | 2 +- .../easyconfigs/l/libsigsegv/libsigsegv-2.11-GCCcore-6.4.0.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/libsigsegv/libsigsegv-2.11-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/l/libsigsegv/libsigsegv-2.11-GCC-6.4.0-2.28.eb index dfc2614481..716653df4c 100644 --- a/easybuild/easyconfigs/l/libsigsegv/libsigsegv-2.11-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/l/libsigsegv/libsigsegv-2.11-GCC-6.4.0-2.28.eb @@ -17,8 +17,8 @@ source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] sanity_check_paths = { - 'dirs': ['include', 'lib'], 'files': ['include/sigsegv.h', 'lib/libsigsegv.a', 'lib/libsigsegv.la'], + 'dirs': [], } moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libsigsegv/libsigsegv-2.11-GCCcore-6.4.0.eb b/easybuild/easyconfigs/l/libsigsegv/libsigsegv-2.11-GCCcore-6.4.0.eb index cdeb207cc1..519b35b032 100644 --- a/easybuild/easyconfigs/l/libsigsegv/libsigsegv-2.11-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/l/libsigsegv/libsigsegv-2.11-GCCcore-6.4.0.eb @@ -21,8 +21,8 @@ builddependencies = [ ] sanity_check_paths = { - 'dirs': ['include', 'lib'], 'files': ['include/sigsegv.h', 'lib/libsigsegv.a', 'lib/libsigsegv.la'], + 'dirs': [], } moduleclass = 'lib' -- GitLab From 4208b46a31a003336870a20378e1d9d683c58508 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Mon, 10 Jul 2017 00:09:26 +0200 Subject: [PATCH 1097/1603] added miniconda easyconfig --- .../easyconfigs/m/Miniconda/Miniconda-4.3.21.eb | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) create mode 100644 easybuild/easyconfigs/m/Miniconda/Miniconda-4.3.21.eb diff --git a/easybuild/easyconfigs/m/Miniconda/Miniconda-4.3.21.eb b/easybuild/easyconfigs/m/Miniconda/Miniconda-4.3.21.eb new file mode 100644 index 0000000000..a5ae211a5c --- /dev/null +++ b/easybuild/easyconfigs/m/Miniconda/Miniconda-4.3.21.eb @@ -0,0 +1,17 @@ +easyblock = 'EB_Anaconda' + +name = 'Miniconda2' +version = '4.3.21' + +homepage = 'https://www.continuum.io/anaconda-overview' +description = """Built to complement the rich, open source Python community, +the Anaconda platform provides an enterprise-ready data analytics platform +that empowers companies to adopt a modern open data science analytics architecture. +""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['https://repo.continuum.io/miniconda/'] +sources = ['%(name)s-%(version)s-Linux-x86_64.sh'] + +moduleclass = 'lang' -- GitLab From a845d52a42c29d6f32c8f3d18b57f2ced7fae8e4 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Mon, 10 Jul 2017 14:35:38 +0800 Subject: [PATCH 1098/1603] prepare release notes for eb331 --- RELEASE_NOTES | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index 904813d080..ef2fd1b52d 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -6,6 +6,29 @@ These release notes can also be consulted at http://easybuild.readthedocs.org/en The latest version of easybuild-easyconfig provides 7,247 easyconfig files, for 1,256 different software packages, 25 different (compiler) toolchains, 13 software bundles and 1 meta-package. +v3.3.1 (July 12th 2017) +----------------------- + +bugfix/update release +- added example easyconfig files for 5 new software packages: + - FastME (#4811), geopy (#4821), ngmlr (#4818), OpenCoarrays (#4799), Seurat (#4832) +- added additional easyconfigs for various supported software packages, including: + - ABAQUS 2017, ASE 3.13.0, BWA 0.7.15, Biopython 1.68, Bison 3.0.4, Bison 3.0.4, Boost 1.54.0, Boost 1.58.0, Bowtie 1.1.2, binutils 2.28, Circos 0.69, DB 6.2.32, Doxygen 1.8.13, FFmpeg 3.2.4, FLUENT 18.1.eb, flex 2.6.3, flex 2.6.4, fontconfig 2.12.1, freetype 2.7.1, GCC 6.4.0, GCCcore 6.4.0.eb, GROMACS 2016.3, g2log 1.0, git 2.13.1, HDF5 1.8.18, help2man 1.47.4, help2man 1.47.4, Jellyfish 2.2.6, Keras 2.0.5, kallisto 0.43.1, LibTIFF 4.0.8, libxslt 1.1.29, likwid 4.2.0, likwid 4.2.0, M4 1.4.18, matplotlib 2.0.2, molmod 1.1, NCBI Toolkit, numpy 1.13.0, PCRE 8.40, Pillow 4.1.1, pigz 2.3.3, pkg config, Sailfish 0.10.1, Salmon 0.8.2, Szip 2.1, scikit learn, skewer 0.2.2, Tensorflow 1.2.0, tbb 2017_U5, vsc install, vsc mympirun, X11 20170129, x264 20170406, Yasm 1.3.0, yaff 1.1.2, yaff 1.1.3, zlib 1.2.11 +- minor enhancements, including: + - add SVG and Statistics::Basic to recent Perl versions (#4796) + - remove buildopts from HDF5 easyconfigs, taken care of by updated HDF5 easyblock now (#4779) + - include joblib as extension in recent Python easyconfigs (#4805) + - changed moduleclass in mpi4py to better reflect what it is and to not confuse HMNS (#4807) + - get rid of references to 'hpcugent' organisation after move to github.com/easybuilders (#4815) + - add Rtsne as extension to R 3.4.0 (#4831) + - fix reference to github.com/hpcugent in GROMACS easyconfig (#4837) +- various bug fixes, including: + - use PYPI_SOURCE as source URL in Tensorflow easyconfigs (#4786) + - fix homepage for skewer (#4791) + - sync/fix source_urls & homepage in HDF5 easyconfig (#4800) + - fix ubsan error blocking build of GCCcore 6.1.0, 6.2.0, 6.3.0 with system GCC 7.1 (#4813) + + v3.3.0 (June 26th 2017) ----------------------- -- GitLab From 2d3d85367eb920e815580d9bc3471faa843ddd75 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 10 Jul 2017 18:26:39 +0100 Subject: [PATCH 1099/1603] adding easyconfigs: VERSE-0.1.5-foss-2016b.eb --- .../v/VERSE/VERSE-0.1.5-foss-2016b.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100755 easybuild/easyconfigs/v/VERSE/VERSE-0.1.5-foss-2016b.eb diff --git a/easybuild/easyconfigs/v/VERSE/VERSE-0.1.5-foss-2016b.eb b/easybuild/easyconfigs/v/VERSE/VERSE-0.1.5-foss-2016b.eb new file mode 100755 index 0000000000..3b817ea0e5 --- /dev/null +++ b/easybuild/easyconfigs/v/VERSE/VERSE-0.1.5-foss-2016b.eb @@ -0,0 +1,29 @@ +# This file is an EasyBuild reciPY, as per https://github.com/easybuilders/easybuild +# Adam Huffman +# The Francis Crick Institute +easyblock = 'MakeCp' + +name = 'VERSE' +version = '0.1.5' + +homepage = 'https://github.com/qinzhu/VERSE' +description = """A versatile and efficient RNA-Seq read counting tool""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +# No proper release tarballs +sources = ['master.zip'] +source_urls = ['https://github.com/qinzhu/VERSE/archive'] + +buildopts = ' -f Makefile.Linux' + +start_dir = 'src' + +files_to_copy = [(['%(namelower)s'], 'bin'), 'LICENSE', 'readme.txt', 'update_log.txt', '%(namelower)s_manual.html', 'testdata' ] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s', 'readme.txt'], + 'dirs': ['testdata'] +} + +moduleclass = 'bio' -- GitLab From 87b0b30ed563af0f87fff02e0f4dff831967325a Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 10 Jul 2017 19:07:29 +0100 Subject: [PATCH 1100/1603] Fix PEP8 errors --- easybuild/easyconfigs/v/VERSE/VERSE-0.1.5-foss-2016b.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/v/VERSE/VERSE-0.1.5-foss-2016b.eb b/easybuild/easyconfigs/v/VERSE/VERSE-0.1.5-foss-2016b.eb index 3b817ea0e5..fdecec7eee 100755 --- a/easybuild/easyconfigs/v/VERSE/VERSE-0.1.5-foss-2016b.eb +++ b/easybuild/easyconfigs/v/VERSE/VERSE-0.1.5-foss-2016b.eb @@ -19,7 +19,8 @@ buildopts = ' -f Makefile.Linux' start_dir = 'src' -files_to_copy = [(['%(namelower)s'], 'bin'), 'LICENSE', 'readme.txt', 'update_log.txt', '%(namelower)s_manual.html', 'testdata' ] +files_to_copy = [(['%(namelower)s'], 'bin'), 'LICENSE', 'readme.txt', 'update_log.txt', + '%(namelower)s_manual.html', 'testdata'] sanity_check_paths = { 'files': ['bin/%(namelower)s', 'readme.txt'], -- GitLab From 3cc0f5cc9a301affc02ec7bef261fd459f4fd502 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Mon, 10 Jul 2017 20:31:56 +0200 Subject: [PATCH 1101/1603] renamed miniconda2 easyconfig --- .../Miniconda-4.3.21.eb => Miniconda2/Miniconda2-4.3.21.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/m/{Miniconda/Miniconda-4.3.21.eb => Miniconda2/Miniconda2-4.3.21.eb} (100%) diff --git a/easybuild/easyconfigs/m/Miniconda/Miniconda-4.3.21.eb b/easybuild/easyconfigs/m/Miniconda2/Miniconda2-4.3.21.eb similarity index 100% rename from easybuild/easyconfigs/m/Miniconda/Miniconda-4.3.21.eb rename to easybuild/easyconfigs/m/Miniconda2/Miniconda2-4.3.21.eb -- GitLab From 29836ba5d091e5ede388c15ba0c1b1a7de11b1a7 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Mon, 10 Jul 2017 20:34:31 +0200 Subject: [PATCH 1102/1603] removed miniconda easyconfig with wrong name --- .../easyconfigs/m/Miniconda/Miniconda-4.3.21.eb | 17 ----------------- 1 file changed, 17 deletions(-) delete mode 100644 easybuild/easyconfigs/m/Miniconda/Miniconda-4.3.21.eb diff --git a/easybuild/easyconfigs/m/Miniconda/Miniconda-4.3.21.eb b/easybuild/easyconfigs/m/Miniconda/Miniconda-4.3.21.eb deleted file mode 100644 index a5ae211a5c..0000000000 --- a/easybuild/easyconfigs/m/Miniconda/Miniconda-4.3.21.eb +++ /dev/null @@ -1,17 +0,0 @@ -easyblock = 'EB_Anaconda' - -name = 'Miniconda2' -version = '4.3.21' - -homepage = 'https://www.continuum.io/anaconda-overview' -description = """Built to complement the rich, open source Python community, -the Anaconda platform provides an enterprise-ready data analytics platform -that empowers companies to adopt a modern open data science analytics architecture. -""" - -toolchain = {'name': 'dummy', 'version': 'dummy'} - -source_urls = ['https://repo.continuum.io/miniconda/'] -sources = ['%(name)s-%(version)s-Linux-x86_64.sh'] - -moduleclass = 'lang' -- GitLab From 9bfcb388b655a8973de34a2f66eb01a16fca55a9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 10 Jul 2017 21:26:21 +0200 Subject: [PATCH 1103/1603] minor cleanup in EasyBuild v3.3.1 release notes + include #4841 --- RELEASE_NOTES | 11 +++++------ 1 file changed, 5 insertions(+), 6 deletions(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index ef2fd1b52d..e766c8da3c 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -3,25 +3,24 @@ For more detailed information, please see the git log. These release notes can also be consulted at http://easybuild.readthedocs.org/en/latest/Release_notes.html. -The latest version of easybuild-easyconfig provides 7,247 easyconfig files, for 1,256 different software packages, +The latest version of easybuild-easyconfig provides 7,313 easyconfig files, for 1,262 different software packages, 25 different (compiler) toolchains, 13 software bundles and 1 meta-package. v3.3.1 (July 12th 2017) ----------------------- bugfix/update release -- added example easyconfig files for 5 new software packages: - - FastME (#4811), geopy (#4821), ngmlr (#4818), OpenCoarrays (#4799), Seurat (#4832) +- added example easyconfig files for 6 new software packages: + - FastME (#4811), geopy (#4821), Miniconda2 (#4841), ngmlr (#4818), OpenCoarrays (#4799), Seurat (#4832) - added additional easyconfigs for various supported software packages, including: - - ABAQUS 2017, ASE 3.13.0, BWA 0.7.15, Biopython 1.68, Bison 3.0.4, Bison 3.0.4, Boost 1.54.0, Boost 1.58.0, Bowtie 1.1.2, binutils 2.28, Circos 0.69, DB 6.2.32, Doxygen 1.8.13, FFmpeg 3.2.4, FLUENT 18.1.eb, flex 2.6.3, flex 2.6.4, fontconfig 2.12.1, freetype 2.7.1, GCC 6.4.0, GCCcore 6.4.0.eb, GROMACS 2016.3, g2log 1.0, git 2.13.1, HDF5 1.8.18, help2man 1.47.4, help2man 1.47.4, Jellyfish 2.2.6, Keras 2.0.5, kallisto 0.43.1, LibTIFF 4.0.8, libxslt 1.1.29, likwid 4.2.0, likwid 4.2.0, M4 1.4.18, matplotlib 2.0.2, molmod 1.1, NCBI Toolkit, numpy 1.13.0, PCRE 8.40, Pillow 4.1.1, pigz 2.3.3, pkg config, Sailfish 0.10.1, Salmon 0.8.2, Szip 2.1, scikit learn, skewer 0.2.2, Tensorflow 1.2.0, tbb 2017_U5, vsc install, vsc mympirun, X11 20170129, x264 20170406, Yasm 1.3.0, yaff 1.1.2, yaff 1.1.3, zlib 1.2.11 + - ABAQUS 2017, GCC(core) 6.4.0, Keras 2.0.5, NCBI-Toolkit 18.0.0, numpy 1.13.0, Tensorflow 1.2.0 - minor enhancements, including: - add SVG and Statistics::Basic to recent Perl versions (#4796) - remove buildopts from HDF5 easyconfigs, taken care of by updated HDF5 easyblock now (#4779) - include joblib as extension in recent Python easyconfigs (#4805) - changed moduleclass in mpi4py to better reflect what it is and to not confuse HMNS (#4807) - - get rid of references to 'hpcugent' organisation after move to github.com/easybuilders (#4815) + - get rid of references to 'hpcugent' organisation after move to github.com/easybuilders (#4815, #4837) - add Rtsne as extension to R 3.4.0 (#4831) - - fix reference to github.com/hpcugent in GROMACS easyconfig (#4837) - various bug fixes, including: - use PYPI_SOURCE as source URL in Tensorflow easyconfigs (#4786) - fix homepage for skewer (#4791) -- GitLab From 78ed6a695d355f7dd58fe091bfcf9cdc5b6141d3 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Tue, 11 Jul 2017 07:14:15 +0100 Subject: [PATCH 1104/1603] Use new source file renaming --- easybuild/easyconfigs/v/VERSE/VERSE-0.1.5-foss-2016b.eb | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/v/VERSE/VERSE-0.1.5-foss-2016b.eb b/easybuild/easyconfigs/v/VERSE/VERSE-0.1.5-foss-2016b.eb index fdecec7eee..87ff075002 100755 --- a/easybuild/easyconfigs/v/VERSE/VERSE-0.1.5-foss-2016b.eb +++ b/easybuild/easyconfigs/v/VERSE/VERSE-0.1.5-foss-2016b.eb @@ -11,8 +11,11 @@ description = """A versatile and efficient RNA-Seq read counting tool""" toolchain = {'name': 'foss', 'version': '2016b'} -# No proper release tarballs -sources = ['master.zip'] +sources = [{ + 'filename': '%(name)s-%(version)s.zip', + 'download_filename': 'master.zip', # No proper release tarballs +}] + source_urls = ['https://github.com/qinzhu/VERSE/archive'] buildopts = ' -f Makefile.Linux' -- GitLab From 366b862195676cc04ba10a87acd0ff1da78de2f3 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Tue, 11 Jul 2017 07:47:22 +0100 Subject: [PATCH 1105/1603] adding easyconfigs: picard-2.6.0-Java-1.8.0_131.eb, picard-2.10.0-Java-1.8.0_131.eb --- .../p/picard/picard-2.10.0-Java-1.8.0_131.eb | 38 +++++++++++++++++++ .../p/picard/picard-2.6.0-Java-1.8.0_131.eb | 37 ++++++++++++++++++ 2 files changed, 75 insertions(+) create mode 100755 easybuild/easyconfigs/p/picard/picard-2.10.0-Java-1.8.0_131.eb create mode 100755 easybuild/easyconfigs/p/picard/picard-2.6.0-Java-1.8.0_131.eb diff --git a/easybuild/easyconfigs/p/picard/picard-2.10.0-Java-1.8.0_131.eb b/easybuild/easyconfigs/p/picard/picard-2.10.0-Java-1.8.0_131.eb new file mode 100755 index 0000000000..170d1a3b37 --- /dev/null +++ b/easybuild/easyconfigs/p/picard/picard-2.10.0-Java-1.8.0_131.eb @@ -0,0 +1,38 @@ +## +# This is a contribution from Phoenix HPC Service, The University of Adelaide, Australia +# Homepage: https://www.adelaide.edu.au/phoenix/ +# +# Copyright:: adelaide.edu.au/phoenix +# Authors:: Robert Qiao , Exe Escobedo +# License:: MIT +# +# 2.10.0: +# Adam Huffman +# The Francis Crick Institute +# +## + +easyblock = 'JAR' + +name = 'picard' +version = '2.10.0' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'http://sourceforge.net/projects/picard' +description = """A set of tools (in Java) for working with next generation sequencing data in the BAM format.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['https://github.com/broadinstitute/picard/releases/download/%(version)s'] +sources = ['%(name)s.jar'] + +dependencies = [('Java', '1.8.0_131')] + +sanity_check_paths = { + 'files': ['picard.jar'], + 'dirs': [], +} + +modloadmsg = "To execute picard run: java -jar $EBROOTPICARD/%(name)s.jar" + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/picard/picard-2.6.0-Java-1.8.0_131.eb b/easybuild/easyconfigs/p/picard/picard-2.6.0-Java-1.8.0_131.eb new file mode 100755 index 0000000000..281b0c7c59 --- /dev/null +++ b/easybuild/easyconfigs/p/picard/picard-2.6.0-Java-1.8.0_131.eb @@ -0,0 +1,37 @@ +## +# This is a contribution from Phoenix HPC Service, The University of Adelaide, Australia +# Homepage: https://www.adelaide.edu.au/phoenix/ +# +# Copyright:: adelaide.edu.au/phoenix +# Authors:: Robert Qiao , Exe Escobedo +# License:: MIT +# +# 2.6.0: +# Adam Huffman +# The Francis Crick Institute +## + +easyblock = 'JAR' + +name = 'picard' +version = '2.6.0' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'http://sourceforge.net/projects/picard' +description = """A set of tools (in Java) for working with next generation sequencing data in the BAM format.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['https://github.com/broadinstitute/picard/releases/download/%(version)s'] +sources = ['%(name)s.jar'] + +dependencies = [('Java', '1.8.0_131')] + +sanity_check_paths = { + 'files': ['picard.jar'], + 'dirs': [], +} + +modloadmsg = "To execute picard run: java -jar $EBROOTPICARD/%(name)s.jar" + +moduleclass = 'bio' -- GitLab From 83cd7fdd0a059db8e4cdea873ca5d9c80e8d20d9 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Tue, 11 Jul 2017 07:49:45 +0100 Subject: [PATCH 1106/1603] Another PEP8-compliance fix --- easybuild/easyconfigs/v/VERSE/VERSE-0.1.5-foss-2016b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/v/VERSE/VERSE-0.1.5-foss-2016b.eb b/easybuild/easyconfigs/v/VERSE/VERSE-0.1.5-foss-2016b.eb index 87ff075002..6ef907ef1e 100755 --- a/easybuild/easyconfigs/v/VERSE/VERSE-0.1.5-foss-2016b.eb +++ b/easybuild/easyconfigs/v/VERSE/VERSE-0.1.5-foss-2016b.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'foss', 'version': '2016b'} sources = [{ 'filename': '%(name)s-%(version)s.zip', - 'download_filename': 'master.zip', # No proper release tarballs + 'download_filename': 'master.zip', # No proper release tarballs }] source_urls = ['https://github.com/qinzhu/VERSE/archive'] -- GitLab From e60d49ca3987eed4bb64b123f80b2ab5742dd59d Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Tue, 11 Jul 2017 07:43:50 -0500 Subject: [PATCH 1107/1603] adding easyconfigs: libpng-1.6.30-GCCcore-6.4.0.eb --- .../l/libpng/libpng-1.6.30-GCCcore-6.4.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/l/libpng/libpng-1.6.30-GCCcore-6.4.0.eb diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.30-GCCcore-6.4.0.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.30-GCCcore-6.4.0.eb new file mode 100644 index 0000000000..6dc219faec --- /dev/null +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.30-GCCcore-6.4.0.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'libpng' +version = '1.6.30' + +homepage = 'http://www.libpng.org/pub/png/libpng.html' + +description = "libpng is the official PNG reference library" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +builddependencies = [ + ('binutils', '2.28'), +] + +dependencies = [ + ('zlib', '1.2.11'), +] + +majminver = ''.join(version.split('.')[:2]) + +sanity_check_paths = { + 'files': ['include/pngconf.h', 'include/png.h', 'include/pnglibconf.h', + 'lib/libpng.a', 'lib/libpng.%s' % SHLIB_EXT, + 'lib/libpng%s.a' % majminver, + 'lib/libpng%s.%s' % (majminver, SHLIB_EXT)], + 'dirs': ['bin', 'include/libpng%s' % majminver, 'share/man'], +} + +moduleclass = 'lib' -- GitLab From 5e90010e50d437f233423b51301f745c334d4c05 Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Tue, 11 Jul 2017 07:48:20 -0500 Subject: [PATCH 1108/1603] adding easyconfigs: bzip2-1.0.6-GCCcore-6.4.0.eb --- .../b/bzip2/bzip2-1.0.6-GCCcore-6.4.0.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCCcore-6.4.0.eb diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCCcore-6.4.0.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCCcore-6.4.0.eb new file mode 100644 index 0000000000..37301419e8 --- /dev/null +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCCcore-6.4.0.eb @@ -0,0 +1,23 @@ +name = 'bzip2' +version = '1.0.6' + +homepage = 'http://www.bzip.org/' + +description = """ + bzip2 is a freely available, patent free, high-quality data compressor. It + typically compresses files to within 10% to 15% of the best available + techniques (the PPM family of statistical compressors), whilst being around + twice as fast at compression and six times faster at decompression. +""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.bzip.org/%(version)s'] +sources = [SOURCE_TAR_GZ] + +builddependencies = [ + ('binutils', '2.28'), +] + +moduleclass = 'tools' -- GitLab From 3a808479c0d17fcab5b3177a4d6af23f21871522 Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Tue, 11 Jul 2017 08:22:04 -0500 Subject: [PATCH 1109/1603] adding easyconfigs: NASM-2.13.01-GCCcore-6.4.0.eb --- .../n/NASM/NASM-2.13.01-GCCcore-6.4.0.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/n/NASM/NASM-2.13.01-GCCcore-6.4.0.eb diff --git a/easybuild/easyconfigs/n/NASM/NASM-2.13.01-GCCcore-6.4.0.eb b/easybuild/easyconfigs/n/NASM/NASM-2.13.01-GCCcore-6.4.0.eb new file mode 100644 index 0000000000..cbacaeb62b --- /dev/null +++ b/easybuild/easyconfigs/n/NASM/NASM-2.13.01-GCCcore-6.4.0.eb @@ -0,0 +1,37 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-90.html +## + +easyblock = 'ConfigureMake' + +name = 'NASM' +version = '2.13.01' + +homepage = 'http://www.nasm.us/' + +description = """NASM: General-purpose x86 assembler""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.nasm.us/pub/nasm/releasebuilds/%(version)s'] +sources = [SOURCELOWER_TAR_BZ2] + +builddependencies = [ + ('binutils', '2.28'), +] + +sanity_check_paths = { + 'files': ['bin/nasm'], + 'dirs': [], +} + +moduleclass = 'lang' -- GitLab From 46c4d09406a8917b77a4f961249daf08e4259bb8 Mon Sep 17 00:00:00 2001 From: Maxime Boissonneault Date: Tue, 11 Jul 2017 13:29:10 +0000 Subject: [PATCH 1110/1603] added easyconfig for Armadillo 7.950.1 --- ...dillo-7.950.1-intel-2016b-Python-2.7.12.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/a/Armadillo/Armadillo-7.950.1-intel-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/a/Armadillo/Armadillo-7.950.1-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/a/Armadillo/Armadillo-7.950.1-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..ca56813122 --- /dev/null +++ b/easybuild/easyconfigs/a/Armadillo/Armadillo-7.950.1-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,23 @@ +name = 'Armadillo' +version = '7.950.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://arma.sourceforge.net/' +description = """Armadillo is an open-source C++ linear algebra library (matrix maths) aiming towards + a good balance between speed and ease of use. Integer, floating point and complex numbers are supported, + as well as a subset of trigonometric and statistics functions.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +sources = [SOURCELOWER_TAR_XZ] +source_urls = ['http://sourceforge.net/projects/arma/files'] + +dependencies = [ + ('Boost', '1.63.0', versionsuffix), + ('arpack-ng', '3.4.0'), + ('Python', '2.7.12'), +] + +builddependencies = [('CMake', '3.7.2')] + +moduleclass = 'numlib' -- GitLab From aaa1e4096193c5d6668ab36b55d0b1f7b4572f05 Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Tue, 11 Jul 2017 08:31:28 -0500 Subject: [PATCH 1111/1603] adding easyconfigs: libffcall-1.13-GCCcore-6.4.0.eb --- .../libffcall/libffcall-1.13-GCCcore-6.4.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/l/libffcall/libffcall-1.13-GCCcore-6.4.0.eb diff --git a/easybuild/easyconfigs/l/libffcall/libffcall-1.13-GCCcore-6.4.0.eb b/easybuild/easyconfigs/l/libffcall/libffcall-1.13-GCCcore-6.4.0.eb new file mode 100644 index 0000000000..703f985fd0 --- /dev/null +++ b/easybuild/easyconfigs/l/libffcall/libffcall-1.13-GCCcore-6.4.0.eb @@ -0,0 +1,34 @@ +# Authors:: Jack Perdue - TAMU HPRC - http://hprc.tamu.edu + +easyblock = 'ConfigureMake' + +name = 'libffcall' +version = '1.13' + +homepage = 'https://www.gnu.org/software/libffcall/' + +description = """ + GNU Libffcall is a collection of four libraries which can be used to build + foreign function call interfaces in embedded interpreters +""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} +toolchainopts = {'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] + +builddependencies = [ + ('binutils', '2.28'), +] + +sanity_check_paths = { + 'files': ['include/avcall.h', 'include/callback.h', 'include/trampoline.h', + 'include/vacall.h', 'lib/libavcall.a', 'lib/libcallback.a', + 'lib/libtrampoline.a', 'lib/libvacall.a'], + 'dirs': [], +} + +parallel = 1 + +moduleclass = 'lib' -- GitLab From cd73627e185e1aec1edbb1986f6dd7d86f92b11f Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Tue, 11 Jul 2017 08:34:11 -0500 Subject: [PATCH 1112/1603] adding easyconfigs: muParser-2.2.5-GCCcore-6.4.0.eb --- .../muParser/muParser-2.2.5-GCCcore-6.4.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/m/muParser/muParser-2.2.5-GCCcore-6.4.0.eb diff --git a/easybuild/easyconfigs/m/muParser/muParser-2.2.5-GCCcore-6.4.0.eb b/easybuild/easyconfigs/m/muParser/muParser-2.2.5-GCCcore-6.4.0.eb new file mode 100644 index 0000000000..754dbd44a4 --- /dev/null +++ b/easybuild/easyconfigs/m/muParser/muParser-2.2.5-GCCcore-6.4.0.eb @@ -0,0 +1,34 @@ +# Author:: Jack Perdue - TAMU HPRC - http://hprc.tamu.edu + +easyblock = 'ConfigureMake' + +name = 'muParser' +version = '2.2.5' + +homepage = 'http://beltoforion.de/article.php?a=muparser' + +description = """ + muParser is an extensible high performance math expression parser library + written in C++. It works by transforming a mathematical expression into + bytecode and precalculating constant parts of the expression. +""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} +toolchainopts = {'pic': True} + +# https://github.com/beltoforion/muparser/archive/v2.2.5.tar.gz +source_urls = ['https://github.com/beltoforion/muparser/archive/'] +sources = [SOURCELOWER_TAR_GZ] + +builddependencies = [ + ('binutils', '2.28'), +] + +sanity_check_paths = { + 'files': ['include/muParser.h', 'lib/libmuparser.so'], + 'dirs': [], +} + +parallel = 1 + +moduleclass = 'math' -- GitLab From 073e3eddd651925b53c7ab6408bdd7d7b2b91a8d Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Tue, 11 Jul 2017 08:36:47 -0500 Subject: [PATCH 1113/1603] adding easyconfigs: ncompress-4.2.4.4-GCCcore-6.4.0.eb --- .../ncompress-4.2.4.4-GCCcore-6.4.0.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/n/ncompress/ncompress-4.2.4.4-GCCcore-6.4.0.eb diff --git a/easybuild/easyconfigs/n/ncompress/ncompress-4.2.4.4-GCCcore-6.4.0.eb b/easybuild/easyconfigs/n/ncompress/ncompress-4.2.4.4-GCCcore-6.4.0.eb new file mode 100644 index 0000000000..a000487503 --- /dev/null +++ b/easybuild/easyconfigs/n/ncompress/ncompress-4.2.4.4-GCCcore-6.4.0.eb @@ -0,0 +1,40 @@ +# Authors:: Jack Perdue - TAMU HPRC - http://hprc.tamu.edu + +easyblock = 'ConfigureMake' + +name = 'ncompress' +version = '4.2.4.4' + +homepage = 'http://ncompress.sourceforge.net/' + +description = """ + Compress is a fast, simple LZW file compressor. Compress does not have the + highest compression rate, but it is one of the fastest programs to compress + data. Compress is the defacto standard in the UNIX community for compressing + files. +""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} + +# https://github.com/vapier/ncompress/archive/v4.2.4.4.tar.gz +source_urls = ['https://github.com/vapier/ncompress/archive/'] +sources = ['%(name)s-%(version)s.tar.gz'] + +builddependencies = [ + ('binutils', '2.28'), +] + +skipsteps = ['configure'] + +installopts = """\ + DESTDIR=%(installdir)s\ + BINDIR=/bin\ + MANDIR=/man/man1\ +""" + +sanity_check_paths = { + 'files': ['bin/compress', 'man/man1/compress.1'], + 'dirs': [] +} + +moduleclass = 'tools' -- GitLab From fc97836f7b8459c9671013836940d6a2954b61d5 Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Tue, 11 Jul 2017 08:56:10 -0500 Subject: [PATCH 1114/1603] adding easyconfigs: Szip-2.1.1-GCCcore-6.4.0.eb --- .../s/Szip/Szip-2.1.1-GCCcore-6.4.0.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-6.4.0.eb diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-6.4.0.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-6.4.0.eb new file mode 100644 index 0000000000..8df5fac01e --- /dev/null +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-6.4.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'Szip' +version = '2.1.1' + +homepage = 'http://www.hdfgroup.org/doc_resource/SZIP/' + +description = """ + Szip compression software, providing lossless compression of scientific data +""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['897dda94e1d4bf88c91adeaad88c07b468b18eaf2d6125c47acac57e540904a9'] + +builddependencies = [ + ('binutils', '2.28'), +] + +sanity_check_paths = { + 'files': ["lib/libsz.a", "lib/libsz.%s" % SHLIB_EXT] + + ["include/%s" % x for x in + ["ricehdf.h", "szip_adpt.h", "szlib.h"]], + 'dirs': [], +} + +moduleclass = 'tools' -- GitLab From a3f7cbfe1588fc83d5c81f8a5f9ca3d070a20b59 Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Tue, 11 Jul 2017 09:19:49 -0500 Subject: [PATCH 1115/1603] adding easyconfigs: Yasm-1.3.0-GCCcore-6.4.0.eb --- .../y/Yasm/Yasm-1.3.0-GCCcore-6.4.0.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-GCCcore-6.4.0.eb diff --git a/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-GCCcore-6.4.0.eb b/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-GCCcore-6.4.0.eb new file mode 100644 index 0000000000..53ab4485ce --- /dev/null +++ b/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-GCCcore-6.4.0.eb @@ -0,0 +1,39 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of +# the policy: # http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-90.html +## + +easyblock = 'ConfigureMake' + +name = 'Yasm' +version = '1.3.0' + +homepage = 'http://www.tortall.net/projects/yasm/' + +description = """ + Yasm: Complete rewrite of the NASM assembler with BSD license +""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} + +source_urls = ['http://www.tortall.net/projects/yasm/releases/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['3dce6601b495f5b3d45b59f7d2492a340ee7e84b5beca17e48f862502bd5603f'] + +builddependencies = [ + ('binutils', '2.28'), +] + +sanity_check_paths = { + 'files': ['bin/yasm'], + 'dirs': [], +} + +moduleclass = 'lang' -- GitLab From 3f5989b58bb78f9c77780e824c08a14e337c239c Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Tue, 11 Jul 2017 09:34:11 -0500 Subject: [PATCH 1116/1603] adding easyconfigs: PAPI-5.5.1-GCCcore-6.4.0.eb --- .../p/PAPI/PAPI-5.5.1-GCCcore-6.4.0.eb | 55 +++++++++++++++++++ 1 file changed, 55 insertions(+) create mode 100644 easybuild/easyconfigs/p/PAPI/PAPI-5.5.1-GCCcore-6.4.0.eb diff --git a/easybuild/easyconfigs/p/PAPI/PAPI-5.5.1-GCCcore-6.4.0.eb b/easybuild/easyconfigs/p/PAPI/PAPI-5.5.1-GCCcore-6.4.0.eb new file mode 100644 index 0000000000..af271fc244 --- /dev/null +++ b/easybuild/easyconfigs/p/PAPI/PAPI-5.5.1-GCCcore-6.4.0.eb @@ -0,0 +1,55 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_07-02.html +## + +easyblock = 'ConfigureMake' + +name = 'PAPI' +version = '5.5.1' + +homepage = 'http://icl.cs.utk.edu/projects/papi/' + +description = """ + PAPI provides the tool designer and application engineer with a consistent + interface and methodology for use of the performance counter hardware found + in most major microprocessors. PAPI enables software engineers to see, in near + real time, the relation between software performance and processor events. + In addition Component PAPI provides access to a collection of components + that expose performance measurement opportunites across the hardware and + software stack. +""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} + +source_urls = ['http://icl.cs.utk.edu/projects/papi/downloads/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['49dc2c2323f6164c4a7e81b799ed690ee73158671205e71501f849391dd2c2d4'] + +builddependencies = [ + ('binutils', '2.28'), +] + +start_dir = 'src' + +parallel = 1 + +runtest = 'fulltest' + +sanity_check_paths = { + 'files': ["bin/papi_%s" % x + for x in ["avail", "clockres", "command_line", "component_avail", + "cost", "decode", "error_codes", "event_chooser", + "mem_info", "multiplex_cost", "native_avail", + "version", "xml_event_info"]], + 'dirs': [], +} + +moduleclass = 'perf' -- GitLab From bb27b5a3e822fdec0721b82bd4737390d7b32e42 Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Tue, 11 Jul 2017 09:40:56 -0500 Subject: [PATCH 1117/1603] adding easyconfigs: Mesquite-2.3.0-GCCcore-6.4.0.eb --- .../m/Mesquite/Mesquite-2.3.0-GCCcore-6.4.0.eb | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) create mode 100644 easybuild/easyconfigs/m/Mesquite/Mesquite-2.3.0-GCCcore-6.4.0.eb diff --git a/easybuild/easyconfigs/m/Mesquite/Mesquite-2.3.0-GCCcore-6.4.0.eb b/easybuild/easyconfigs/m/Mesquite/Mesquite-2.3.0-GCCcore-6.4.0.eb new file mode 100644 index 0000000000..f3e3eb3a99 --- /dev/null +++ b/easybuild/easyconfigs/m/Mesquite/Mesquite-2.3.0-GCCcore-6.4.0.eb @@ -0,0 +1,16 @@ +easyblock = 'ConfigureMake' + +name = 'Mesquite' +version = '2.3.0' + +homepage = 'https://software.sandia.gov/mesquite/' + +description = """Mesh-Quality Improvement Library""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://software.sandia.gov/mesquite/'] +sources = [SOURCELOWER_TAR_GZ] + +moduleclass = 'math' -- GitLab From 8f152b333af45d8cdd4ca52905e0fa23eec4b6ee Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Tue, 11 Jul 2017 09:52:06 -0500 Subject: [PATCH 1118/1603] adding easyconfigs: ncurses-6.0-GCCcore-6.4.0.eb --- .../n/ncurses/ncurses-6.0-GCCcore-6.4.0.eb | 47 +++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 easybuild/easyconfigs/n/ncurses/ncurses-6.0-GCCcore-6.4.0.eb diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.0-GCCcore-6.4.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-GCCcore-6.4.0.eb new file mode 100644 index 0000000000..c4eefc78a1 --- /dev/null +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-GCCcore-6.4.0.eb @@ -0,0 +1,47 @@ +easyblock = 'ConfigureMake' + +name = 'ncurses' +version = '6.0' + +homepage = 'http://www.gnu.org/software/ncurses/' + +description = """ + The Ncurses (new curses) library is a free software emulation of curses in + System V Release 4.0, and more. It uses Terminfo format, supports pads and + color and multiple highlights and forms characters and function-key mapping, + and has all the other SYSV-curses enhancements over BSD Curses. +""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} +toolchainopts = {'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] + +patches = ['ncurses-%(version)s_gcc-5.patch'] + +builddependencies = [ + ('binutils', '2.28'), +] + +configopts = [ + # default build + '--with-shared --enable-overwrite', + # the UTF-8 enabled version (ncursesw) + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", + "infotocap", + "ncurses%(version_major)s-config", + "reset", "tabs", "tic", "toe", "tput", + "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.%s' % (x, y, SHLIB_EXT) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + +moduleclass = 'devel' -- GitLab From 55fc01112c068288dd96838d05f814c184407745 Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Tue, 11 Jul 2017 10:58:56 -0500 Subject: [PATCH 1119/1603] adding easyconfigs: LibUUID-1.0.3-GCCcore-6.4.0.eb --- .../l/LibUUID/LibUUID-1.0.3-GCCcore-6.4.0.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/l/LibUUID/LibUUID-1.0.3-GCCcore-6.4.0.eb diff --git a/easybuild/easyconfigs/l/LibUUID/LibUUID-1.0.3-GCCcore-6.4.0.eb b/easybuild/easyconfigs/l/LibUUID/LibUUID-1.0.3-GCCcore-6.4.0.eb new file mode 100644 index 0000000000..9ba6bc305a --- /dev/null +++ b/easybuild/easyconfigs/l/LibUUID/LibUUID-1.0.3-GCCcore-6.4.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'LibUUID' +version = '1.0.3' + +homepage = 'http://sourceforge.net/projects/libuuid/' + +description = """Portable uuid C library""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['46af3275291091009ad7f1b899de3d0cea0252737550e7919d17237997db5644'] + +builddependencies = [ + ('binutils', '2.28'), +] + +sanity_check_paths = { + 'files': ['include/uuid/uuid.h', 'lib/libuuid.a', + 'lib/libuuid.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' -- GitLab From b6268ae8e8f642023981351a9d5da2f629f5e75d Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Tue, 11 Jul 2017 11:07:35 -0500 Subject: [PATCH 1120/1603] adding easyconfigs: libtool-2.4.6-GCCcore-6.4.0.eb --- .../l/libtool/libtool-2.4.6-GCCcore-6.4.0.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-6.4.0.eb diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-6.4.0.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-6.4.0.eb new file mode 100644 index 0000000000..2f6e8100a5 --- /dev/null +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-6.4.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'libtool' +version = '2.4.6' + +homepage = 'http://www.gnu.org/software/libtool' + +description = """ + GNU libtool is a generic library support script. Libtool hides the complexity + of using shared libraries behind a consistent, portable interface. +""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +builddependencies = [ + ('binutils', '2.28'), +] + +dependencies = [ + ('M4', '1.4.18'), +] + +moduleclass = 'lib' -- GitLab From 5accbaa8a2259be104cb9497c3b3838f0abf27f2 Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Tue, 11 Jul 2017 11:20:14 -0500 Subject: [PATCH 1121/1603] adding easyconfigs: expat-2.2.1-GCCcore-6.4.0.eb --- .../e/expat/expat-2.2.1-GCCcore-6.4.0.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/e/expat/expat-2.2.1-GCCcore-6.4.0.eb diff --git a/easybuild/easyconfigs/e/expat/expat-2.2.1-GCCcore-6.4.0.eb b/easybuild/easyconfigs/e/expat/expat-2.2.1-GCCcore-6.4.0.eb new file mode 100644 index 0000000000..87f8150c28 --- /dev/null +++ b/easybuild/easyconfigs/e/expat/expat-2.2.1-GCCcore-6.4.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'expat' +version = '2.2.1' + +homepage = 'http://expat.sourceforge.net/' + +description = """ + Expat is an XML parser library written in C. It is a stream-oriented parser + in which an application registers handlers for things the parser might find + in the XML document (like start tags) +""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['1868cadae4c82a018e361e2b2091de103cd820aaacb0d6cfa49bd2cd83978885'] + +builddependencies = [ + ('binutils', '2.28'), +] + +moduleclass = 'tools' -- GitLab From d8a7b01534d97da3a402edd8b1770c54bc10344f Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Tue, 11 Jul 2017 11:26:55 -0500 Subject: [PATCH 1122/1603] adding easyconfigs: gzip-1.8-GCCcore-6.4.0.eb --- .../g/gzip/gzip-1.8-GCCcore-6.4.0.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/g/gzip/gzip-1.8-GCCcore-6.4.0.eb diff --git a/easybuild/easyconfigs/g/gzip/gzip-1.8-GCCcore-6.4.0.eb b/easybuild/easyconfigs/g/gzip/gzip-1.8-GCCcore-6.4.0.eb new file mode 100644 index 0000000000..fc8158dc1a --- /dev/null +++ b/easybuild/easyconfigs/g/gzip/gzip-1.8-GCCcore-6.4.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'gzip' +version = '1.8' + +homepage = 'http://www.gnu.org/software/gzip/' + +description = """ + gzip (GNU zip) is a popular data compression program as + a replacement for compress +""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] + +sanity_check_paths = { + 'files': ["bin/gunzip", "bin/gzip", "bin/uncompress"], + 'dirs': [], +} + +sanity_check_commands = [True, ('gzip', '--version')] + +moduleclass = 'tools' -- GitLab From 7c6ea8e8415790bcaea6a254d1b307ac121233fa Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Tue, 11 Jul 2017 12:06:41 -0500 Subject: [PATCH 1123/1603] adding easyconfigs: libspatialindex-1.8.5-GCCcore-6.4.0.eb --- .../libspatialindex-1.8.5-GCCcore-6.4.0.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/l/libspatialindex/libspatialindex-1.8.5-GCCcore-6.4.0.eb diff --git a/easybuild/easyconfigs/l/libspatialindex/libspatialindex-1.8.5-GCCcore-6.4.0.eb b/easybuild/easyconfigs/l/libspatialindex/libspatialindex-1.8.5-GCCcore-6.4.0.eb new file mode 100644 index 0000000000..127c1cea1b --- /dev/null +++ b/easybuild/easyconfigs/l/libspatialindex/libspatialindex-1.8.5-GCCcore-6.4.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'libspatialindex' +version = '1.8.5' + +homepage = 'http://libspatialindex.github.io' + +description = """ + C++ implementation of R*-tree, an MVR-tree and a TPR-tree with C API +""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} +toolchainopts = {'pic': True} + +source_urls = ['http://download.osgeo.org/libspatialindex/'] +sources = ['spatialindex-src-%(version)s.tar.gz'] +checksums = ['7caa46a2cb9b40960f7bc82c3de60fa14f8f3e000b02561b36cbf2cfe6a9bfef'] + +builddependencies = [ + ('binutils', '2.28'), +] + +sanity_check_paths = { + 'files': ['lib/libspatialindex.a', 'lib/libspatialindex.%s' % SHLIB_EXT], + 'dirs': ['include/spatialindex'], +} + +moduleclass = 'lib' -- GitLab From 0ba557815ac618e6ac298b05b2f055a11db78c90 Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Tue, 11 Jul 2017 12:23:26 -0500 Subject: [PATCH 1124/1603] adding easyconfigs: DB-6.2.32-GCCcore-6.4.0.eb --- .../d/DB/DB-6.2.32-GCCcore-6.4.0.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/d/DB/DB-6.2.32-GCCcore-6.4.0.eb diff --git a/easybuild/easyconfigs/d/DB/DB-6.2.32-GCCcore-6.4.0.eb b/easybuild/easyconfigs/d/DB/DB-6.2.32-GCCcore-6.4.0.eb new file mode 100644 index 0000000000..076d25e019 --- /dev/null +++ b/easybuild/easyconfigs/d/DB/DB-6.2.32-GCCcore-6.4.0.eb @@ -0,0 +1,26 @@ +name = 'DB' +version = '6.2.32' + +homepage = 'http://www.oracle.com/technetwork/products/berkeleydb' + +description = """ + Berkeley DB enables the development of custom data management solutions, + without the overhead traditionally associated with such custom projects. +""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} + +# download via http://www.oracle.com/technetwork/products/berkeleydb/downloads/, requires registration +sources = [SOURCELOWER_TAR_GZ] +checksums = ['a9c5e2b004a5777aa03510cfe5cd766a4a3b777713406b02809c17c8e0e7a8fb'] + +builddependencies = [ + ('binutils', '2.28'), +] + +sanity_check_paths = { + 'files': ["include/db.h"], + 'dirs': [], +} + +moduleclass = 'tools' -- GitLab From 7ea16f5cb288d60db25eaa6b8d28f10ea6044216 Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Tue, 11 Jul 2017 12:38:32 -0500 Subject: [PATCH 1125/1603] adding easyconfigs: libsodium-1.0.12-GCCcore-6.4.0.eb --- .../libsodium-1.0.12-GCCcore-6.4.0.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/l/libsodium/libsodium-1.0.12-GCCcore-6.4.0.eb diff --git a/easybuild/easyconfigs/l/libsodium/libsodium-1.0.12-GCCcore-6.4.0.eb b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.12-GCCcore-6.4.0.eb new file mode 100644 index 0000000000..927f15bb68 --- /dev/null +++ b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.12-GCCcore-6.4.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'libsodium' +version = '1.0.12' + +homepage = 'http://doc.libsodium.org/' + +description = """ + Sodium is a modern, easy-to-use software library for encryption, decryption, + signatures, password hashing and more. +""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://download.libsodium.org/libsodium/releases/'] +sources = [SOURCE_TAR_GZ] +checksums = ['b8648f1bb3a54b0251cf4ffa4f0d76ded13977d4fa7517d988f4c902dd8e2f95'] + +builddependencies = [ + ('binutils', '2.28'), +] + +sanity_check_paths = { + 'files': ['include/sodium.h', 'lib/libsodium.so', 'lib/libsodium.a'], + 'dirs': ['include/sodium', 'lib/pkgconfig'], +} + +moduleclass = 'lib' -- GitLab From 37572be522de100feaf2d3ea1c4540839b511e64 Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Tue, 11 Jul 2017 12:51:11 -0500 Subject: [PATCH 1126/1603] adding easyconfigs: GSL-2.4-GCCcore-6.4.0.eb --- .../g/GSL/GSL-2.4-GCCcore-6.4.0.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/g/GSL/GSL-2.4-GCCcore-6.4.0.eb diff --git a/easybuild/easyconfigs/g/GSL/GSL-2.4-GCCcore-6.4.0.eb b/easybuild/easyconfigs/g/GSL/GSL-2.4-GCCcore-6.4.0.eb new file mode 100644 index 0000000000..4ea2f3d1a3 --- /dev/null +++ b/easybuild/easyconfigs/g/GSL/GSL-2.4-GCCcore-6.4.0.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'GSL' +version = '2.4' + +homepage = 'http://www.gnu.org/software/gsl/' + +description = """ + The GNU Scientific Library (GSL) is a numerical library for C and C++ + programmers. The library provides a wide range of mathematical routines + such as random number generators, special functions and least-squares fitting. +""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} +toolchainopts = {'unroll': True, 'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +builddependencies = [ + ('binutils', '2.28'), +] + +moduleclass = 'numlib' -- GitLab From 4bbb276adc2e4cf86ae6400165dde5b08591d787 Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Tue, 11 Jul 2017 13:04:18 -0500 Subject: [PATCH 1127/1603] adding easyconfigs: Autoconf-2.69-GCCcore-6.4.0.eb --- .../a/Autoconf/Autoconf-2.69-GCCcore-6.4.0.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-6.4.0.eb diff --git a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-6.4.0.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-6.4.0.eb new file mode 100644 index 0000000000..6574fccdb0 --- /dev/null +++ b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-6.4.0.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'Autoconf' +version = '2.69' + +homepage = 'http://www.gnu.org/software/autoconf/' + +description = """ + Autoconf is an extensible package of M4 macros that produce shell scripts + to automatically configure software source code packages. These scripts can + adapt the packages to many kinds of UNIX-like systems without manual user + intervention. Autoconf creates a configuration script for a package from a + template file that lists the operating system features that the package can + use, in the form of M4 macro calls. +""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +builddependencies = [ + ('binutils', '2.28'), +] + +dependencies = [ + ('M4', '1.4.18'), +] + +sanity_check_paths = { + 'files': ["bin/%s" % x + for x in ["autoconf", "autoheader", "autom4te", "autoreconf", + "autoscan", "autoupdate", "ifnames"]], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From 188586bb59e096d70b4ebd5d1af9953b28b3d285 Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Tue, 11 Jul 2017 15:01:26 -0500 Subject: [PATCH 1128/1603] adding easyconfigs: pixman-0.34.0-GCCcore-6.4.0.eb --- .../p/pixman/pixman-0.34.0-GCCcore-6.4.0.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/p/pixman/pixman-0.34.0-GCCcore-6.4.0.eb diff --git a/easybuild/easyconfigs/p/pixman/pixman-0.34.0-GCCcore-6.4.0.eb b/easybuild/easyconfigs/p/pixman/pixman-0.34.0-GCCcore-6.4.0.eb new file mode 100644 index 0000000000..5f58c9f25c --- /dev/null +++ b/easybuild/easyconfigs/p/pixman/pixman-0.34.0-GCCcore-6.4.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = "pixman" +version = '0.34.0' + +homepage = 'http://www.pixman.org/' + +description = """ + Pixman is a low-level software library for pixel manipulation, providing + features such as image compositing and trapezoid rasterization. Important + users of pixman are the cairo graphics library and the X server. +""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} + +source_urls = ['http://cairographics.org/releases/'] +sources = [SOURCE_TAR_GZ] + +builddependencies = [ + ('binutils', '2.28'), +] + +sanity_check_paths = { + 'files': ['lib/libpixman-1.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'vis' -- GitLab From 6cf827bacd4ec898d8b2743ec19f623e3e1848a3 Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Tue, 11 Jul 2017 15:13:14 -0500 Subject: [PATCH 1129/1603] adding easyconfigs: byacc-20170709-GCCcore-6.4.0.eb --- .../b/byacc/byacc-20170709-GCCcore-6.4.0.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/b/byacc/byacc-20170709-GCCcore-6.4.0.eb diff --git a/easybuild/easyconfigs/b/byacc/byacc-20170709-GCCcore-6.4.0.eb b/easybuild/easyconfigs/b/byacc/byacc-20170709-GCCcore-6.4.0.eb new file mode 100644 index 0000000000..64ac3adea0 --- /dev/null +++ b/easybuild/easyconfigs/b/byacc/byacc-20170709-GCCcore-6.4.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'byacc' +version = '20170709' + +homepage = 'http://invisible-island.net/byacc/byacc.html' + +description = """ + Berkeley Yacc (byacc) is generally conceded to be the best yacc variant + available. In contrast to bison, it is written to avoid dependencies + upon a particular compiler. +""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} + +source_urls = ['ftp://invisible-island.net/byacc'] +sources = [SOURCELOWER_TGZ] +checksums = ['27cf801985dc6082b8732522588a7b64377dd3df841d584ba6150bc86d78d9eb'] + +builddependencies = [ + ('binutils', '2.28'), +] + +sanity_check_paths = { + 'files': ["bin/yacc"], + 'dirs': [] +} + +moduleclass = 'lang' -- GitLab From 8f8ffe4780cb744445ba2ba888633d3e6cb55912 Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Tue, 11 Jul 2017 15:44:49 -0500 Subject: [PATCH 1130/1603] adding easyconfigs: libpthread-stubs-0.4-GCCcore-6.4.0.eb --- .../libpthread-stubs-0.4-GCCcore-6.4.0.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.4-GCCcore-6.4.0.eb diff --git a/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.4-GCCcore-6.4.0.eb b/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.4-GCCcore-6.4.0.eb new file mode 100644 index 0000000000..f65b67ddd6 --- /dev/null +++ b/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.4-GCCcore-6.4.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'libpthread-stubs' +version = '0.4' + +homepage = 'http://xcb.freedesktop.org/' + +description = """ + The X protocol C-language Binding (XCB) is a replacement for Xlib featuring + a small footprint, latency hiding, direct access to the protocol, improved + threading support, and extensibility. +""" + +source_urls = ['http://xcb.freedesktop.org/dist/'] +sources = [SOURCELOWER_TAR_GZ] + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} +toolchainopts = {'pic': True} + +builddependencies = [ + ('binutils','2.28'), +] + +sanity_check_paths = { + 'files': ['lib/pkgconfig/pthread-stubs.pc'], + 'dirs': [], +} + +moduleclass = 'lib' -- GitLab From e1dab4351bcf8ad75383439ada951bc392c0a81d Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Tue, 11 Jul 2017 22:39:26 +0100 Subject: [PATCH 1131/1603] Update to new upstream release and add checksum --- .../p/picard/picard-2.10.1-Java-1.8.0_131.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100755 easybuild/easyconfigs/p/picard/picard-2.10.1-Java-1.8.0_131.eb diff --git a/easybuild/easyconfigs/p/picard/picard-2.10.1-Java-1.8.0_131.eb b/easybuild/easyconfigs/p/picard/picard-2.10.1-Java-1.8.0_131.eb new file mode 100755 index 0000000000..3495cd4e50 --- /dev/null +++ b/easybuild/easyconfigs/p/picard/picard-2.10.1-Java-1.8.0_131.eb @@ -0,0 +1,40 @@ +## +# This is a contribution from Phoenix HPC Service, The University of Adelaide, Australia +# Homepage: https://www.adelaide.edu.au/phoenix/ +# +# Copyright:: adelaide.edu.au/phoenix +# Authors:: Robert Qiao , Exe Escobedo +# License:: MIT +# +# 2.10.1: +# Adam Huffman +# The Francis Crick Institute +# +## + +easyblock = 'JAR' + +name = 'picard' +version = '2.10.1' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'http://sourceforge.net/projects/picard' +description = """A set of tools (in Java) for working with next generation sequencing data in the BAM format.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['https://github.com/broadinstitute/picard/releases/download/%(version)s'] +sources = ['%(name)s.jar'] + +dependencies = [('Java', '1.8.0_131')] + +checksums = [('sha256', 'e256d5e43656b7d8be454201a7056dce543fe9cbeb30329a0d8c22d28e655775')] + +sanity_check_paths = { + 'files': ['picard.jar'], + 'dirs': [], +} + +modloadmsg = "To execute picard run: java -jar $EBROOTPICARD/%(name)s.jar" + +moduleclass = 'bio' -- GitLab From 4b7723372aa2d45bd891f8e2faed54b2a2a44362 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Tue, 11 Jul 2017 22:41:12 +0100 Subject: [PATCH 1132/1603] Add checksum --- easybuild/easyconfigs/p/picard/picard-2.6.0-Java-1.8.0_131.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/p/picard/picard-2.6.0-Java-1.8.0_131.eb b/easybuild/easyconfigs/p/picard/picard-2.6.0-Java-1.8.0_131.eb index 281b0c7c59..a7676529fe 100755 --- a/easybuild/easyconfigs/p/picard/picard-2.6.0-Java-1.8.0_131.eb +++ b/easybuild/easyconfigs/p/picard/picard-2.6.0-Java-1.8.0_131.eb @@ -27,6 +27,8 @@ sources = ['%(name)s.jar'] dependencies = [('Java', '1.8.0_131')] +checksums = [('sha256', '671d9e86e6bf0c28ee007aea55d07e2456ae3a57016491b50aab0fd2fd0e493b')] + sanity_check_paths = { 'files': ['picard.jar'], 'dirs': [], -- GitLab From d239678acd341d12ef9780007d7273d6fd89c874 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Tue, 11 Jul 2017 23:03:45 +0100 Subject: [PATCH 1133/1603] Move checksum --- .../easyconfigs/p/picard/picard-2.10.1-Java-1.8.0_131.eb | 4 ++-- easybuild/easyconfigs/p/picard/picard-2.6.0-Java-1.8.0_131.eb | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/p/picard/picard-2.10.1-Java-1.8.0_131.eb b/easybuild/easyconfigs/p/picard/picard-2.10.1-Java-1.8.0_131.eb index 3495cd4e50..e69580f5e4 100755 --- a/easybuild/easyconfigs/p/picard/picard-2.10.1-Java-1.8.0_131.eb +++ b/easybuild/easyconfigs/p/picard/picard-2.10.1-Java-1.8.0_131.eb @@ -26,10 +26,10 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = ['https://github.com/broadinstitute/picard/releases/download/%(version)s'] sources = ['%(name)s.jar'] -dependencies = [('Java', '1.8.0_131')] - checksums = [('sha256', 'e256d5e43656b7d8be454201a7056dce543fe9cbeb30329a0d8c22d28e655775')] +dependencies = [('Java', '1.8.0_131')] + sanity_check_paths = { 'files': ['picard.jar'], 'dirs': [], diff --git a/easybuild/easyconfigs/p/picard/picard-2.6.0-Java-1.8.0_131.eb b/easybuild/easyconfigs/p/picard/picard-2.6.0-Java-1.8.0_131.eb index a7676529fe..674512ad38 100755 --- a/easybuild/easyconfigs/p/picard/picard-2.6.0-Java-1.8.0_131.eb +++ b/easybuild/easyconfigs/p/picard/picard-2.6.0-Java-1.8.0_131.eb @@ -25,10 +25,10 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = ['https://github.com/broadinstitute/picard/releases/download/%(version)s'] sources = ['%(name)s.jar'] -dependencies = [('Java', '1.8.0_131')] - checksums = [('sha256', '671d9e86e6bf0c28ee007aea55d07e2456ae3a57016491b50aab0fd2fd0e493b')] +dependencies = [('Java', '1.8.0_131')] + sanity_check_paths = { 'files': ['picard.jar'], 'dirs': [], -- GitLab From fecac8b65510995ed52737dc0c2c0176476f322a Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Tue, 11 Jul 2017 23:15:23 +0100 Subject: [PATCH 1134/1603] Remove obsolete 2.10.0 --- .../p/picard/picard-2.10.0-Java-1.8.0_131.eb | 38 ------------------- 1 file changed, 38 deletions(-) delete mode 100755 easybuild/easyconfigs/p/picard/picard-2.10.0-Java-1.8.0_131.eb diff --git a/easybuild/easyconfigs/p/picard/picard-2.10.0-Java-1.8.0_131.eb b/easybuild/easyconfigs/p/picard/picard-2.10.0-Java-1.8.0_131.eb deleted file mode 100755 index 170d1a3b37..0000000000 --- a/easybuild/easyconfigs/p/picard/picard-2.10.0-Java-1.8.0_131.eb +++ /dev/null @@ -1,38 +0,0 @@ -## -# This is a contribution from Phoenix HPC Service, The University of Adelaide, Australia -# Homepage: https://www.adelaide.edu.au/phoenix/ -# -# Copyright:: adelaide.edu.au/phoenix -# Authors:: Robert Qiao , Exe Escobedo -# License:: MIT -# -# 2.10.0: -# Adam Huffman -# The Francis Crick Institute -# -## - -easyblock = 'JAR' - -name = 'picard' -version = '2.10.0' -versionsuffix = '-Java-%(javaver)s' - -homepage = 'http://sourceforge.net/projects/picard' -description = """A set of tools (in Java) for working with next generation sequencing data in the BAM format.""" - -toolchain = {'name': 'dummy', 'version': 'dummy'} - -source_urls = ['https://github.com/broadinstitute/picard/releases/download/%(version)s'] -sources = ['%(name)s.jar'] - -dependencies = [('Java', '1.8.0_131')] - -sanity_check_paths = { - 'files': ['picard.jar'], - 'dirs': [], -} - -modloadmsg = "To execute picard run: java -jar $EBROOTPICARD/%(name)s.jar" - -moduleclass = 'bio' -- GitLab From 2b094023d93f00574d96d9510acb47608bd983b7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 12 Jul 2017 07:34:59 +0200 Subject: [PATCH 1135/1603] bump version to 3.3.1 --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 2ea811fb80..8b55846bb7 100644 --- a/setup.py +++ b/setup.py @@ -47,7 +47,7 @@ from distutils import log # recent setuptools versions will *TRANSFORM* something like 'X.Y.Zdev' into 'X.Y.Z.dev0', with a warning like # UserWarning: Normalizing '2.4.0dev' to '2.4.0.dev0' # This causes problems further up the dependency chain... -VERSION = '3.3.1.dev0' +VERSION = '3.3.1' API_VERSION = VERSION.split('.')[0] EB_VERSION = '.'.join(VERSION.split('.')[0:2]) -- GitLab From df48ba2c1ea46aad632f7067bd3d47b18162ba35 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 12 Jul 2017 11:14:16 +0200 Subject: [PATCH 1136/1603] adding easyconfigs: cadaver-0.23.3-intel-2017a.eb --- .../c/cadaver/cadaver-0.23.3-intel-2017a.eb | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) create mode 100644 easybuild/easyconfigs/c/cadaver/cadaver-0.23.3-intel-2017a.eb diff --git a/easybuild/easyconfigs/c/cadaver/cadaver-0.23.3-intel-2017a.eb b/easybuild/easyconfigs/c/cadaver/cadaver-0.23.3-intel-2017a.eb new file mode 100644 index 0000000000..0d2c3a61b1 --- /dev/null +++ b/easybuild/easyconfigs/c/cadaver/cadaver-0.23.3-intel-2017a.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'cadaver' +version = '0.23.3' + +homepage = 'http://www.webdav.org/cadaver/' +description = "cadaver is a command-line WebDAV client for Unix." + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['http://www.webdav.org/cadaver/'] +sources = [SOURCE_TAR_GZ] + +sanity_check_paths = { + 'files': ['bin/cadaver'], + 'dirs': ['share/man'], +} + +moduleclass = 'tools' -- GitLab From e711a75ad462f1bbfbd5d1adb7c0fd8dfca98250 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 12 Jul 2017 11:48:37 +0200 Subject: [PATCH 1137/1603] bump version to 3.4.0.dev0 --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 8b55846bb7..2d468796a8 100644 --- a/setup.py +++ b/setup.py @@ -47,7 +47,7 @@ from distutils import log # recent setuptools versions will *TRANSFORM* something like 'X.Y.Zdev' into 'X.Y.Z.dev0', with a warning like # UserWarning: Normalizing '2.4.0dev' to '2.4.0.dev0' # This causes problems further up the dependency chain... -VERSION = '3.3.1' +VERSION = '3.4.0.dev0' API_VERSION = VERSION.split('.')[0] EB_VERSION = '.'.join(VERSION.split('.')[0:2]) -- GitLab From 599c37fec698a971c7996f79c65b0d138e671436 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 12 Jul 2017 13:42:56 +0200 Subject: [PATCH 1138/1603] adding easyconfigs: EasyBuild-3.3.1.eb --- .../e/EasyBuild/EasyBuild-3.3.1.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.3.1.eb diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.3.1.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.3.1.eb new file mode 100644 index 0000000000..38ca592d16 --- /dev/null +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.3.1.eb @@ -0,0 +1,38 @@ +easyblock = 'EB_EasyBuildMeta' + +name = 'EasyBuild' +version = '3.3.1' + +homepage = 'https://easybuilders.github.io/easybuild' +description = """EasyBuild is a software build and installation framework + written in Python that allows you to install software in a structured, + repeatable and robust way.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = [ + # vsc-install + 'https://pypi.python.org/packages/82/ec/19d85d2bb91b562195d00db9ac82d7529904e7eabc0597720966bf74714f/', + # vsc-base + 'https://pypi.python.org/packages/f7/66/1ff7ecc4a93ba37e063f5bfbe395e95a547b1dec73b017c2724f4475a958/', + # easybuild-framework + 'https://pypi.python.org/packages/5b/1e/26bcb7c4407a68b22bd545014bf5536c4f3c4b196bc0467b008d848008da', + # easybuild-easyblocks + 'https://pypi.python.org/packages/7c/03/0ca88b299508689eea650652f5188f9f03d8fc3001670ad37885e71b6e4f', + # easybuild-easyconfigs + 'https://pypi.python.org/packages/57/d0/d5683dbb6aca7dfd2f39f38be9f11252177012ef894dfdf2b19e70eddf44', +] +# order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) +sources = [ + 'vsc-install-0.10.26.tar.gz', + 'vsc-base-2.5.8.tar.gz', + 'easybuild-framework-%(version)s.tar.gz', + 'easybuild-easyblocks-%(version)s.tar.gz', + 'easybuild-easyconfigs-%(version)s.tar.gz', +] + +# EasyBuild is a (set of) Python packages, so it depends on Python +# usually, we want to use the system Python, so no actual Python dependency is listed +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +moduleclass = 'tools' -- GitLab From 875c1ba5366326e387cf54f6c77ec96d93942e3b Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Wed, 12 Jul 2017 12:53:37 +0100 Subject: [PATCH 1139/1603] adding easyconfigs: cadaver-0.23.3-intel-2017a.eb --- easybuild/easyconfigs/c/cadaver/cadaver-0.23.3-intel-2017a.eb | 2 ++ 1 file changed, 2 insertions(+) mode change 100644 => 100755 easybuild/easyconfigs/c/cadaver/cadaver-0.23.3-intel-2017a.eb diff --git a/easybuild/easyconfigs/c/cadaver/cadaver-0.23.3-intel-2017a.eb b/easybuild/easyconfigs/c/cadaver/cadaver-0.23.3-intel-2017a.eb old mode 100644 new mode 100755 index 0d2c3a61b1..860d309726 --- a/easybuild/easyconfigs/c/cadaver/cadaver-0.23.3-intel-2017a.eb +++ b/easybuild/easyconfigs/c/cadaver/cadaver-0.23.3-intel-2017a.eb @@ -11,6 +11,8 @@ toolchain = {'name': 'intel', 'version': '2017a'} source_urls = ['http://www.webdav.org/cadaver/'] sources = [SOURCE_TAR_GZ] +checksums = ['fd4ce68a3230ba459a92bcb747fc6afa91e46d803c1d5ffe964b661793c13fca'] + sanity_check_paths = { 'files': ['bin/cadaver'], 'dirs': ['share/man'], -- GitLab From 46f7cd85922fb164216b84d8115c8fcad6660cef Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Wed, 12 Jul 2017 08:31:54 -0500 Subject: [PATCH 1140/1603] add checksum --- easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCCcore-6.4.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCCcore-6.4.0.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCCcore-6.4.0.eb index 37301419e8..e4b34a6f11 100644 --- a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCCcore-6.4.0.eb @@ -12,6 +12,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '6.4.0'} toolchainopts = {'pic': True} +checksums = ['a2848f34fcd5d6cf47def00461fcb528a0484d8edef8208d6d2e2909dc61d9cd'] source_urls = ['http://www.bzip.org/%(version)s'] sources = [SOURCE_TAR_GZ] -- GitLab From 689e8f8ffef0dad21b24ae37b1579021ccd4eb2f Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Wed, 12 Jul 2017 08:40:25 -0500 Subject: [PATCH 1141/1603] edits and add checksum --- easybuild/easyconfigs/n/NASM/NASM-2.13.01-GCCcore-6.4.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/n/NASM/NASM-2.13.01-GCCcore-6.4.0.eb b/easybuild/easyconfigs/n/NASM/NASM-2.13.01-GCCcore-6.4.0.eb index cbacaeb62b..a992c888d4 100644 --- a/easybuild/easyconfigs/n/NASM/NASM-2.13.01-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/n/NASM/NASM-2.13.01-GCCcore-6.4.0.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos @@ -20,10 +20,10 @@ homepage = 'http://www.nasm.us/' description = """NASM: General-purpose x86 assembler""" toolchain = {'name': 'GCCcore', 'version': '6.4.0'} -toolchainopts = {'pic': True} source_urls = ['http://www.nasm.us/pub/nasm/releasebuilds/%(version)s'] sources = [SOURCELOWER_TAR_BZ2] +checksums = ['08f97baf0a7f892128c6413cfa93b69dc5825fbbd06c70928aea028835d198fa'] builddependencies = [ ('binutils', '2.28'), -- GitLab From fc9c539ca126e84f40090aacb5af08b7b426d4c1 Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Wed, 12 Jul 2017 08:47:23 -0500 Subject: [PATCH 1142/1603] add checksum --- .../easyconfigs/l/libffcall/libffcall-1.13-GCCcore-6.4.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/l/libffcall/libffcall-1.13-GCCcore-6.4.0.eb b/easybuild/easyconfigs/l/libffcall/libffcall-1.13-GCCcore-6.4.0.eb index 703f985fd0..336a7eca3d 100644 --- a/easybuild/easyconfigs/l/libffcall/libffcall-1.13-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/l/libffcall/libffcall-1.13-GCCcore-6.4.0.eb @@ -17,6 +17,7 @@ toolchainopts = {'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +checksums = ['1707ce707dbbf57f1bbe9aa56929c0da866046b0d5a26eb0d96d9f0bb29bbce7'] builddependencies = [ ('binutils', '2.28'), -- GitLab From 9c79e99bf7928d6f9c786e9f09fcabdda70306f4 Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Wed, 12 Jul 2017 09:22:20 -0500 Subject: [PATCH 1143/1603] edits and add checksum --- .../m/muParser/muParser-2.2.5-GCCcore-6.4.0.eb | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/m/muParser/muParser-2.2.5-GCCcore-6.4.0.eb b/easybuild/easyconfigs/m/muParser/muParser-2.2.5-GCCcore-6.4.0.eb index 754dbd44a4..915de6c6ce 100644 --- a/easybuild/easyconfigs/m/muParser/muParser-2.2.5-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/m/muParser/muParser-2.2.5-GCCcore-6.4.0.eb @@ -1,5 +1,3 @@ -# Author:: Jack Perdue - TAMU HPRC - http://hprc.tamu.edu - easyblock = 'ConfigureMake' name = 'muParser' @@ -19,16 +17,17 @@ toolchainopts = {'pic': True} # https://github.com/beltoforion/muparser/archive/v2.2.5.tar.gz source_urls = ['https://github.com/beltoforion/muparser/archive/'] sources = [SOURCELOWER_TAR_GZ] +checksums = ['0666ef55da72c3e356ca85b6a0084d56b05dd740c3c21d26d372085aa2c6e708'] builddependencies = [ ('binutils', '2.28'), ] +configopts = "--disable-samples --enable-shared" + sanity_check_paths = { - 'files': ['include/muParser.h', 'lib/libmuparser.so'], + 'files': ['include/muParser.h', 'lib/libmuparser.%s' %SHLIB_EXT], 'dirs': [], } -parallel = 1 - moduleclass = 'math' -- GitLab From 71980e5c4b2c186d0e7066e4af0f649a5903d654 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Wed, 12 Jul 2017 15:31:10 +0100 Subject: [PATCH 1144/1603] Create versioned source file and move to unversioned for the runtime copy --- .../easyconfigs/p/picard/picard-2.10.1-Java-1.8.0_131.eb | 9 +++++++-- .../easyconfigs/p/picard/picard-2.6.0-Java-1.8.0_131.eb | 9 ++++++++- 2 files changed, 15 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/p/picard/picard-2.10.1-Java-1.8.0_131.eb b/easybuild/easyconfigs/p/picard/picard-2.10.1-Java-1.8.0_131.eb index e69580f5e4..ab38eef7a5 100755 --- a/easybuild/easyconfigs/p/picard/picard-2.10.1-Java-1.8.0_131.eb +++ b/easybuild/easyconfigs/p/picard/picard-2.10.1-Java-1.8.0_131.eb @@ -24,9 +24,14 @@ description = """A set of tools (in Java) for working with next generation seque toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = ['https://github.com/broadinstitute/picard/releases/download/%(version)s'] -sources = ['%(name)s.jar'] +sources = [{ + 'filename': '%(name)s-%(version)s.jar', + 'download_filename': '%(name)s.jar', +}] -checksums = [('sha256', 'e256d5e43656b7d8be454201a7056dce543fe9cbeb30329a0d8c22d28e655775')] +checksums = ['ace0de725f7dbf3a1f621ac146e205b41bc872a0bdc700cf687124740fb60412'] + +postinstallcmds = [' mv %(installdir)s/%(name)s-%(version)s.jar %(installdir)s/%(name)s.jar'] dependencies = [('Java', '1.8.0_131')] diff --git a/easybuild/easyconfigs/p/picard/picard-2.6.0-Java-1.8.0_131.eb b/easybuild/easyconfigs/p/picard/picard-2.6.0-Java-1.8.0_131.eb index 674512ad38..f2d7251544 100755 --- a/easybuild/easyconfigs/p/picard/picard-2.6.0-Java-1.8.0_131.eb +++ b/easybuild/easyconfigs/p/picard/picard-2.6.0-Java-1.8.0_131.eb @@ -25,7 +25,14 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = ['https://github.com/broadinstitute/picard/releases/download/%(version)s'] sources = ['%(name)s.jar'] -checksums = [('sha256', '671d9e86e6bf0c28ee007aea55d07e2456ae3a57016491b50aab0fd2fd0e493b')] +sources = [{ + 'filename': '%(name)s-%(version)s.jar', + 'download_filename': '%(name)s.jar', +}] + +checksums = ['671d9e86e6bf0c28ee007aea55d07e2456ae3a57016491b50aab0fd2fd0e493b'] + +postinstallcmds = [' mv %(installdir)s/%(name)s-%(version)s.jar %(installdir)s/%(name)s.jar'] dependencies = [('Java', '1.8.0_131')] -- GitLab From e94c16366aef8249db878d49e4f349b58f71d230 Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Wed, 12 Jul 2017 09:32:05 -0500 Subject: [PATCH 1145/1603] cleanup and add checksum --- .../easyconfigs/n/ncompress/ncompress-4.2.4.4-GCCcore-6.4.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/ncompress/ncompress-4.2.4.4-GCCcore-6.4.0.eb b/easybuild/easyconfigs/n/ncompress/ncompress-4.2.4.4-GCCcore-6.4.0.eb index a000487503..a9b3d371a0 100644 --- a/easybuild/easyconfigs/n/ncompress/ncompress-4.2.4.4-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/n/ncompress/ncompress-4.2.4.4-GCCcore-6.4.0.eb @@ -16,9 +16,9 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '6.4.0'} -# https://github.com/vapier/ncompress/archive/v4.2.4.4.tar.gz source_urls = ['https://github.com/vapier/ncompress/archive/'] sources = ['%(name)s-%(version)s.tar.gz'] +checksums = ['2670439935e7639c3a767087da99810e45bc3997d0638b3094396043571e5aec'] builddependencies = [ ('binutils', '2.28'), -- GitLab From 7e945a3421406121e5ac9c9aebe16a05b34bab91 Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Wed, 12 Jul 2017 09:40:17 -0500 Subject: [PATCH 1146/1603] cleanup --- easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-6.4.0.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-6.4.0.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-6.4.0.eb index 8df5fac01e..98b8e0cf48 100644 --- a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-6.4.0.eb @@ -22,8 +22,7 @@ builddependencies = [ sanity_check_paths = { 'files': ["lib/libsz.a", "lib/libsz.%s" % SHLIB_EXT] + - ["include/%s" % x for x in - ["ricehdf.h", "szip_adpt.h", "szlib.h"]], + ["include/%s" % x for x in ["ricehdf.h", "szip_adpt.h", "szlib.h"]], 'dirs': [], } -- GitLab From 58cd5d05e7226cfd0e5099b955e1b8d2ffdc8742 Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Wed, 12 Jul 2017 09:55:49 -0500 Subject: [PATCH 1147/1603] cleanup --- easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-GCCcore-6.4.0.eb | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-GCCcore-6.4.0.eb b/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-GCCcore-6.4.0.eb index 53ab4485ce..691d1170d5 100644 --- a/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-GCCcore-6.4.0.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos @@ -17,9 +17,7 @@ version = '1.3.0' homepage = 'http://www.tortall.net/projects/yasm/' -description = """ - Yasm: Complete rewrite of the NASM assembler with BSD license -""" +description = """Yasm: Complete rewrite of the NASM assembler with BSD license""" toolchain = {'name': 'GCCcore', 'version': '6.4.0'} -- GitLab From 05ef2db0b1b76c5635076e836d28897e3707a661 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 12 Jul 2017 17:06:54 +0200 Subject: [PATCH 1148/1603] adding easyconfigs: vsc-mympirun-4.0.1.eb --- .../v/vsc-mympirun/vsc-mympirun-4.0.1.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100755 easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-4.0.1.eb diff --git a/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-4.0.1.eb b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-4.0.1.eb new file mode 100755 index 0000000000..5e6aaec33a --- /dev/null +++ b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-4.0.1.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'vsc-mympirun' +version = '4.0.1' + +homepage = 'https://github.com/hpcugent/vsc-mympirun' +description = """VSC-tools is a set of Python libraries and scripts that are commonly used within HPC-UGent.""" + +# we build this to work with every python version +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['b5b08e6291a68802d29c344d5807e4c2a1945375055b57c819721151775789f0'] + +builddependencies = [('vsc-install', '0.10.26')] +dependencies = [('vsc-base', '2.5.8')] + +osdependencies = ['python-setuptools'] + +# we ship something in bin/fake +modextrapaths = {'PATH': 'bin/fake'} + +# don't check for import of vsc.mympirun, since that may fail if vsc-base is picked up from the OS +options = {'modulename': 'vsc'} + +pyshortver = '.'.join(SYS_PYTHON_VERSION.split('.')[:2]) +sanity_check_paths = { + 'files': ['bin/mympirun', 'bin/mympisanity'], + 'dirs': ['bin/fake', 'lib/python%s/site-packages' % pyshortver], +} +sanity_check_commands = ["mympirun --help"] + +moduleclass = 'tools' -- GitLab From d4fd3ae511ea33e8783fbd386892b051e1f036fa Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 12 Jul 2017 17:49:08 +0200 Subject: [PATCH 1149/1603] use single-line description in setup.py --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 2d468796a8..49f7189df7 100644 --- a/setup.py +++ b/setup.py @@ -104,7 +104,7 @@ setup( version = VERSION, author = "EasyBuild community", author_email = "easybuild@lists.ugent.be", - description = """Easyconfig files are simple build specification files for EasyBuild, + description = """Easyconfig files are simple build specification files for EasyBuild, \ that specify the build parameters for software packages (version, compiler toolchain, dependency \ versions, etc.).""", license = "GPLv2", -- GitLab From 05b56fd157e1f8c3189657a4d6a4200209730694 Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Wed, 12 Jul 2017 11:04:51 -0500 Subject: [PATCH 1150/1603] update EB URL --- easybuild/easyconfigs/p/PAPI/PAPI-5.5.1-GCCcore-6.4.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PAPI/PAPI-5.5.1-GCCcore-6.4.0.eb b/easybuild/easyconfigs/p/PAPI/PAPI-5.5.1-GCCcore-6.4.0.eb index af271fc244..19d05f8452 100644 --- a/easybuild/easyconfigs/p/PAPI/PAPI-5.5.1-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/p/PAPI/PAPI-5.5.1-GCCcore-6.4.0.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Fotis Georgatos -- GitLab From 8e039123b500e97895da8deda4fcb9f9ea635c96 Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Wed, 12 Jul 2017 11:12:22 -0500 Subject: [PATCH 1151/1603] add checksum --- easybuild/easyconfigs/m/Mesquite/Mesquite-2.3.0-GCCcore-6.4.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/m/Mesquite/Mesquite-2.3.0-GCCcore-6.4.0.eb b/easybuild/easyconfigs/m/Mesquite/Mesquite-2.3.0-GCCcore-6.4.0.eb index f3e3eb3a99..b48cf2aa8f 100644 --- a/easybuild/easyconfigs/m/Mesquite/Mesquite-2.3.0-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/m/Mesquite/Mesquite-2.3.0-GCCcore-6.4.0.eb @@ -12,5 +12,6 @@ toolchainopts = {'pic': True} source_urls = ['https://software.sandia.gov/mesquite/'] sources = [SOURCELOWER_TAR_GZ] +checksums = ['4ab4ceadfa596e16c00dbb0e8b830a9112fa1b73291ca07633ec379a39b8bb28'] moduleclass = 'math' -- GitLab From 9afe523875f44516cafb53bd3a0dc7fd07a2e09d Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Wed, 12 Jul 2017 11:16:17 -0500 Subject: [PATCH 1152/1603] add checksum --- easybuild/easyconfigs/n/ncurses/ncurses-6.0-GCCcore-6.4.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.0-GCCcore-6.4.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-GCCcore-6.4.0.eb index c4eefc78a1..0ee6b52eeb 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-6.0-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-GCCcore-6.4.0.eb @@ -17,6 +17,7 @@ toolchainopts = {'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +checksums = ['f551c24b30ce8bfb6e96d9f59b42fbea30fa3a6123384172f9e7284bcf647260'] patches = ['ncurses-%(version)s_gcc-5.patch'] -- GitLab From d3d0cc6b9d59519fbe578324b2fec65b0fcb8ab4 Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Wed, 12 Jul 2017 11:24:42 -0500 Subject: [PATCH 1153/1603] add checksum --- easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-6.4.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-6.4.0.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-6.4.0.eb index 2f6e8100a5..bc5c6cb40c 100644 --- a/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-6.4.0.eb @@ -14,6 +14,7 @@ toolchain = {'name': 'GCCcore', 'version': '6.4.0'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] +checksums = ['e3bd4d5d3d025a36c21dd6af7ea818a2afcd4dfc1ea5a17b39d7854bcd0c06e3'] builddependencies = [ ('binutils', '2.28'), -- GitLab From edaed19af3fb64227be2ab9ae3c25faa21c396b2 Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Wed, 12 Jul 2017 11:38:42 -0500 Subject: [PATCH 1154/1603] add checksum --- easybuild/easyconfigs/g/gzip/gzip-1.8-GCCcore-6.4.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/g/gzip/gzip-1.8-GCCcore-6.4.0.eb b/easybuild/easyconfigs/g/gzip/gzip-1.8-GCCcore-6.4.0.eb index fc8158dc1a..fcd38e2364 100644 --- a/easybuild/easyconfigs/g/gzip/gzip-1.8-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/g/gzip/gzip-1.8-GCCcore-6.4.0.eb @@ -14,6 +14,7 @@ toolchain = {'name': 'GCCcore', 'version': '6.4.0'} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +checksums = ['1ff7aedb3d66a0d73f442f6261e4b3860df6fd6c94025c2cb31a202c9c60fe0e'] sanity_check_paths = { 'files': ["bin/gunzip", "bin/gzip", "bin/uncompress"], -- GitLab From 1180e84291b36a4c4ed76fc16f6e05316e8a728d Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Wed, 12 Jul 2017 12:03:04 -0500 Subject: [PATCH 1155/1603] maintain sanity --- easybuild/easyconfigs/d/DB/DB-6.2.32-GCCcore-6.4.0.eb | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/d/DB/DB-6.2.32-GCCcore-6.4.0.eb b/easybuild/easyconfigs/d/DB/DB-6.2.32-GCCcore-6.4.0.eb index 076d25e019..7182e6afe1 100644 --- a/easybuild/easyconfigs/d/DB/DB-6.2.32-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/d/DB/DB-6.2.32-GCCcore-6.4.0.eb @@ -10,7 +10,8 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '6.4.0'} -# download via http://www.oracle.com/technetwork/products/berkeleydb/downloads/, requires registration +# download via http://www.oracle.com/technetwork/products/berkeleydb/downloads/, +# requires registration sources = [SOURCELOWER_TAR_GZ] checksums = ['a9c5e2b004a5777aa03510cfe5cd766a4a3b777713406b02809c17c8e0e7a8fb'] @@ -19,7 +20,8 @@ builddependencies = [ ] sanity_check_paths = { - 'files': ["include/db.h"], + 'files': ['bin/db_archive', 'include/db.h', 'lib/libdb.a', + 'lib/libdb.%s' % SHLIB_EXT], 'dirs': [], } -- GitLab From 844a1c5a147387eccf4ebb7784e3ec3e57cec5a7 Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Wed, 12 Jul 2017 12:24:59 -0500 Subject: [PATCH 1156/1603] add checksum --- easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-6.4.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-6.4.0.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-6.4.0.eb index 6574fccdb0..741c36b430 100644 --- a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-6.4.0.eb @@ -18,6 +18,7 @@ toolchain = {'name': 'GCCcore', 'version': '6.4.0'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] +checksums = ['954bd69b391edc12d6a4a51a2dd1476543da5c6bbf05a95b59dc0dd6fd4c2969'] builddependencies = [ ('binutils', '2.28'), -- GitLab From 0ca4803546c93bd4c41a90b7d1019a88e3e1a439 Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Wed, 12 Jul 2017 12:44:19 -0500 Subject: [PATCH 1157/1603] add checksum --- easybuild/easyconfigs/p/pixman/pixman-0.34.0-GCCcore-6.4.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/p/pixman/pixman-0.34.0-GCCcore-6.4.0.eb b/easybuild/easyconfigs/p/pixman/pixman-0.34.0-GCCcore-6.4.0.eb index 5f58c9f25c..9fb2609138 100644 --- a/easybuild/easyconfigs/p/pixman/pixman-0.34.0-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/p/pixman/pixman-0.34.0-GCCcore-6.4.0.eb @@ -15,6 +15,7 @@ toolchain = {'name': 'GCCcore', 'version': '6.4.0'} source_urls = ['http://cairographics.org/releases/'] sources = [SOURCE_TAR_GZ] +checksums = ['21b6b249b51c6800dc9553b65106e1e37d0e25df942c90531d4c3997aa20a88e'] builddependencies = [ ('binutils', '2.28'), -- GitLab From f7dcd08e2054af6d6aceb8c1b616fd9cef0a4245 Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Wed, 12 Jul 2017 12:48:21 -0500 Subject: [PATCH 1158/1603] add checksum --- .../l/libpthread-stubs/libpthread-stubs-0.4-GCCcore-6.4.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.4-GCCcore-6.4.0.eb b/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.4-GCCcore-6.4.0.eb index f65b67ddd6..f5302ea370 100644 --- a/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.4-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.4-GCCcore-6.4.0.eb @@ -18,7 +18,7 @@ toolchain = {'name': 'GCCcore', 'version': '6.4.0'} toolchainopts = {'pic': True} builddependencies = [ - ('binutils','2.28'), + ('binutils', '2.28'), ] sanity_check_paths = { -- GitLab From 62a3d90a39970bec28bfb2c07b8349b17fe990d2 Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Wed, 12 Jul 2017 12:53:49 -0500 Subject: [PATCH 1159/1603] really this time, add checksums --- .../l/libpthread-stubs/libpthread-stubs-0.4-GCCcore-6.4.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.4-GCCcore-6.4.0.eb b/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.4-GCCcore-6.4.0.eb index f5302ea370..64f2cd1602 100644 --- a/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.4-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.4-GCCcore-6.4.0.eb @@ -13,6 +13,7 @@ description = """ source_urls = ['http://xcb.freedesktop.org/dist/'] sources = [SOURCELOWER_TAR_GZ] +checksums = ['50d5686b79019ccea08bcbd7b02fe5a40634abcfd4146b6e75c6420cc170e9d9'] toolchain = {'name': 'GCCcore', 'version': '6.4.0'} toolchainopts = {'pic': True} -- GitLab From 7821ecb9619ef1e35b1424d26aa71770380cb5f5 Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Wed, 12 Jul 2017 22:47:03 -0500 Subject: [PATCH 1160/1603] pigz and patch --- .../p/pigz/pigz-2.3.4-GCCcore-6.4.0.eb | 42 +++++++++++++++++++ .../p/pigz/pigz-2.3.4_Makefile.patch | 17 ++++++++ 2 files changed, 59 insertions(+) create mode 100644 easybuild/easyconfigs/p/pigz/pigz-2.3.4-GCCcore-6.4.0.eb create mode 100644 easybuild/easyconfigs/p/pigz/pigz-2.3.4_Makefile.patch diff --git a/easybuild/easyconfigs/p/pigz/pigz-2.3.4-GCCcore-6.4.0.eb b/easybuild/easyconfigs/p/pigz/pigz-2.3.4-GCCcore-6.4.0.eb new file mode 100644 index 0000000000..4b0af18f75 --- /dev/null +++ b/easybuild/easyconfigs/p/pigz/pigz-2.3.4-GCCcore-6.4.0.eb @@ -0,0 +1,42 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = 'MakeCp' + +name = 'pigz' +version = '2.3.4' + +homepage = 'http://zlib.net/pigz/' + +description = """ + pigz, which stands for parallel implementation of gzip, is a fully + functional replacement for gzip that exploits multiple processors and multiple + cores to the hilt when compressing data. pigz was written by Mark Adler, and + uses the zlib and pthread libraries. +""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} + +source_urls = ['http://zlib.net/pigz/'] +sources = [SOURCE_TAR_GZ] +checksums = ['6f031fa40bc15b1d80d502ff91f83ba14f4b079e886bfb83221374f7bf5c8f9a'] + +# Patch Makefile so zlib provided by EasyBuild is picked up +patches = ['%(name)s-%(version)s_Makefile.patch'] + +dependencies = [ + ('zlib', '1.2.11'), +] + +parallel = 1 + +files_to_copy = [(["pigz", "unpigz"], "bin")] + +sanity_check_paths = { + 'files': ['bin/pigz', 'bin/unpigz'], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/pigz/pigz-2.3.4_Makefile.patch b/easybuild/easyconfigs/p/pigz/pigz-2.3.4_Makefile.patch new file mode 100644 index 0000000000..05008c1033 --- /dev/null +++ b/easybuild/easyconfigs/p/pigz/pigz-2.3.4_Makefile.patch @@ -0,0 +1,17 @@ +--- Makefile.orig 2017-07-12 22:16:56.931252958 -0500 ++++ Makefile 2017-07-12 22:25:34.472386094 -0500 +@@ -1,12 +1,11 @@ +-CC=cc +-CFLAGS=-O3 -Wall -Wextra ++ZLIB=-L$(EBROOTZLIB)/lib + LDFLAGS= + LIBS=-lm -lpthread -lz + ZOPFLI=zopfli/src/zopfli/ + # use gcc and gmake on Solaris + + pigz: pigz.o yarn.o try.o ${ZOPFLI}deflate.o ${ZOPFLI}blocksplitter.o ${ZOPFLI}tree.o ${ZOPFLI}lz77.o ${ZOPFLI}cache.o ${ZOPFLI}hash.o ${ZOPFLI}util.o ${ZOPFLI}squeeze.o ${ZOPFLI}katajainen.o +- $(CC) $(LDFLAGS) -o pigz $^ $(LIBS) ++ $(CC) $(LDFLAGS) -o pigz $^ $(ZLIB) $(LIBS) + ln -f pigz unpigz + + pigz.o: pigz.c yarn.h try.h ${ZOPFLI}deflate.h ${ZOPFLI}util.h -- GitLab From a75d1e7c0c30290cf695b666cc90fa51bd7b13cc Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Wed, 12 Jul 2017 23:19:26 -0500 Subject: [PATCH 1161/1603] fix URL fail --- easybuild/easyconfigs/p/pigz/pigz-2.3.4-GCCcore-6.4.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/pigz/pigz-2.3.4-GCCcore-6.4.0.eb b/easybuild/easyconfigs/p/pigz/pigz-2.3.4-GCCcore-6.4.0.eb index 4b0af18f75..0042955a0b 100644 --- a/easybuild/easyconfigs/p/pigz/pigz-2.3.4-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/p/pigz/pigz-2.3.4-GCCcore-6.4.0.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel -- GitLab From 3dce9cfcebc9337afd45f218818a45ad1ecee22e Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Wed, 12 Jul 2017 23:24:54 -0500 Subject: [PATCH 1162/1603] adding easyconfigs: CMake-3.8.2-GCCcore-6.4.0.eb --- .../c/CMake/CMake-3.8.2-GCCcore-6.4.0.eb | 38 +++++++++++++++ .../n/ncurses/ncurses-6.0-GCCcore-6.4.0.eb | 48 +++++++++++++++++++ 2 files changed, 86 insertions(+) create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.8.2-GCCcore-6.4.0.eb create mode 100644 easybuild/easyconfigs/n/ncurses/ncurses-6.0-GCCcore-6.4.0.eb diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.8.2-GCCcore-6.4.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.8.2-GCCcore-6.4.0.eb new file mode 100644 index 0000000000..84630972bf --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.8.2-GCCcore-6.4.0.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.8.2' + +homepage = 'http://www.cmake.org' + +description = """ + CMake, the cross-platform, open-source build system. CMake is a family of + tools designed to build, test and package software. +""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['da3072794eb4c09f2d782fcee043847b99bb4cf8d4573978d9b2024214d6e92d'] + +configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' + +builddependencies = [ + ('binutils', '2.28'), +] + +dependencies = [ + ('ncurses', '6.0'), +] + +osdependencies = [ + ('openssl-devel', 'libssl-dev', 'libopenssl-devel'), +] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.0-GCCcore-6.4.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-GCCcore-6.4.0.eb new file mode 100644 index 0000000000..0ee6b52eeb --- /dev/null +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-GCCcore-6.4.0.eb @@ -0,0 +1,48 @@ +easyblock = 'ConfigureMake' + +name = 'ncurses' +version = '6.0' + +homepage = 'http://www.gnu.org/software/ncurses/' + +description = """ + The Ncurses (new curses) library is a free software emulation of curses in + System V Release 4.0, and more. It uses Terminfo format, supports pads and + color and multiple highlights and forms characters and function-key mapping, + and has all the other SYSV-curses enhancements over BSD Curses. +""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} +toolchainopts = {'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['f551c24b30ce8bfb6e96d9f59b42fbea30fa3a6123384172f9e7284bcf647260'] + +patches = ['ncurses-%(version)s_gcc-5.patch'] + +builddependencies = [ + ('binutils', '2.28'), +] + +configopts = [ + # default build + '--with-shared --enable-overwrite', + # the UTF-8 enabled version (ncursesw) + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", + "infotocap", + "ncurses%(version_major)s-config", + "reset", "tabs", "tic", "toe", "tput", + "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.%s' % (x, y, SHLIB_EXT) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + +moduleclass = 'devel' -- GitLab From 95d04f57d80eba01f7ee9bc9f96abd6d8b364cfc Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Thu, 13 Jul 2017 00:29:53 -0500 Subject: [PATCH 1163/1603] add binutils --- .../easyconfigs/m/Mesquite/Mesquite-2.3.0-GCCcore-6.4.0.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/m/Mesquite/Mesquite-2.3.0-GCCcore-6.4.0.eb b/easybuild/easyconfigs/m/Mesquite/Mesquite-2.3.0-GCCcore-6.4.0.eb index b48cf2aa8f..bf18a3528d 100644 --- a/easybuild/easyconfigs/m/Mesquite/Mesquite-2.3.0-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/m/Mesquite/Mesquite-2.3.0-GCCcore-6.4.0.eb @@ -14,4 +14,8 @@ source_urls = ['https://software.sandia.gov/mesquite/'] sources = [SOURCELOWER_TAR_GZ] checksums = ['4ab4ceadfa596e16c00dbb0e8b830a9112fa1b73291ca07633ec379a39b8bb28'] +builddependencies = [ + ('binutils', '2.28'), +] + moduleclass = 'math' -- GitLab From 267b906f2b2dd9a648d0b44e8d8689798c416dbf Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Thu, 13 Jul 2017 01:10:28 -0500 Subject: [PATCH 1164/1603] adding easyconfigs: gc-7.6.0-GCCcore-6.4.0.eb --- .../g/gc/gc-7.6.0-GCCcore-6.4.0.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/g/gc/gc-7.6.0-GCCcore-6.4.0.eb diff --git a/easybuild/easyconfigs/g/gc/gc-7.6.0-GCCcore-6.4.0.eb b/easybuild/easyconfigs/g/gc/gc-7.6.0-GCCcore-6.4.0.eb new file mode 100644 index 0000000000..aa7d33f680 --- /dev/null +++ b/easybuild/easyconfigs/g/gc/gc-7.6.0-GCCcore-6.4.0.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'gc' +version = '7.6.0' + +homepage = 'http://hboehm.info/gc/' + +description = """ + The Boehm-Demers-Weiser conservative garbage collector can be used as a + garbage collecting replacement for C malloc or C++ new. +""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} + +source_urls = [ + 'http://hboehm.info/gc/gc_source/', + 'https://github.com/ivmai/libatomic_ops/releases/download/v7.4.6/', +] +sources = [ + SOURCE_TAR_GZ, + 'libatomic_ops-7.4.6.tar.gz', +] +checksums = [ + 'a14a28b1129be90e55cd6f71127ffc5594e1091d5d54131528c24cd0c03b7d90', + '96e88ba450ae5fa10aa8e94e6b151a63ffbe47f8069574bd12da22ae80c686db', +] + +builddependencies = [ + ('binutils', '2.28'), +] + +preconfigopts = 'ln -s %(builddir)s/libatomic_ops*/ libatomic_ops && ' + +sanity_check_paths = { + 'files': ['include/gc.h', 'lib/libcord.a', 'lib/libcord.%s' % SHLIB_EXT, + 'lib/libgc.a', 'lib/libgc.%s' % SHLIB_EXT], + 'dirs': ['include/gc', 'share'], +} + +moduleclass = 'lib' -- GitLab From 04e4a0bc1bcbb8612c080143bccce49073a8160f Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Thu, 13 Jul 2017 01:42:05 -0500 Subject: [PATCH 1165/1603] adding easyconfigs: cURL-7.54.1-GCCcore-6.4.0.eb --- .../c/cURL/cURL-7.54.1-GCCcore-6.4.0.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/c/cURL/cURL-7.54.1-GCCcore-6.4.0.eb diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.54.1-GCCcore-6.4.0.eb b/easybuild/easyconfigs/c/cURL/cURL-7.54.1-GCCcore-6.4.0.eb new file mode 100644 index 0000000000..0c330ab8c8 --- /dev/null +++ b/easybuild/easyconfigs/c/cURL/cURL-7.54.1-GCCcore-6.4.0.eb @@ -0,0 +1,45 @@ +easyblock = 'ConfigureMake' + +name = 'cURL' +version = '7.54.1' + +homepage = 'http://curl.haxx.se' + +description = """ + libcurl is a free and easy-to-use client-side URL transfer library, + supporting DICT, FILE, FTP, FTPS, Gopher, HTTP, HTTPS, IMAP, IMAPS, LDAP, + LDAPS, POP3, POP3S, RTMP, RTSP, SCP, SFTP, SMTP, SMTPS, Telnet and TFTP. + libcurl supports SSL certificates, HTTP POST, HTTP PUT, FTP uploading, HTTP + form based upload, proxies, cookies, user+password authentication (Basic, + Digest, NTLM, Negotiate, Kerberos), file transfer resume, http proxy tunneling + and more. +""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} + +source_urls = ['http://curl.haxx.se/download/'] +sources = [SOURCELOWER_TAR_GZ] + +osdependencies = [ + ('libssh2-devel'), + ('openssl-devel', 'libssl-dev', 'libopenssl-devel'), +] + +builddependencies = [ + ('binutils', '2.28'), +] + +dependencies = [ + ('zlib', '1.2.11'), +] + +configopts = '--with-libssh2 --with-zlib' + +modextravars = {'CURL_INCLUDES': '%(installdir)s/include'} + +sanity_check_paths = { + 'files': ['bin/curl', 'lib/libcurl.a', 'lib/libcurl.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'tools' -- GitLab From 18c0ed1bc962eddef6fabf77445c1db9ec47ac63 Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Thu, 13 Jul 2017 02:13:46 -0500 Subject: [PATCH 1166/1603] adding easyconfigs: libreadline-7.0-GCCcore-6.4.0.eb --- .../libreadline-7.0-GCCcore-6.4.0.eb | 43 +++++++++++++++++ .../n/ncurses/ncurses-6.0-GCCcore-6.4.0.eb | 48 +++++++++++++++++++ 2 files changed, 91 insertions(+) create mode 100644 easybuild/easyconfigs/l/libreadline/libreadline-7.0-GCCcore-6.4.0.eb create mode 100644 easybuild/easyconfigs/n/ncurses/ncurses-6.0-GCCcore-6.4.0.eb diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-7.0-GCCcore-6.4.0.eb b/easybuild/easyconfigs/l/libreadline/libreadline-7.0-GCCcore-6.4.0.eb new file mode 100644 index 0000000000..b26a32205d --- /dev/null +++ b/easybuild/easyconfigs/l/libreadline/libreadline-7.0-GCCcore-6.4.0.eb @@ -0,0 +1,43 @@ +easyblock = 'ConfigureMake' + +name = 'libreadline' +version = '7.0' + +homepage = 'http://cnswww.cns.cwru.edu/php/chet/readline/rltop.html' + +description = """ + The GNU Readline library provides a set of functions for use by applications + that allow users to edit command lines as they are typed in. Both Emacs and + vi editing modes are available. The Readline library includes additional + functions to maintain a list of previously-entered command lines, to recall + and perhaps reedit those lines, and perform csh-like history expansion on + previous commands. +""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} +toolchainopts = {'pic': True} + +source_urls = ['http://ftp.gnu.org/gnu/readline'] +sources = ['readline-%(version)s.tar.gz'] +checksums = ['750d437185286f40a369e1e4f4764eda932b9459b5ec9a731628393dd3d32334'] + +builddependencies = [ + ('binutils', '2.28'), +] + +dependencies = [ + ('ncurses', '6.0'), +] + +# for the termcap symbols, use EB ncurses +preconfigopts = "env LDFLAGS='-lncurses'" + +sanity_check_paths = { + 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + + ['include/readline/%s' % x + for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', + 'rlconf.h', 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.0-GCCcore-6.4.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-GCCcore-6.4.0.eb new file mode 100644 index 0000000000..0ee6b52eeb --- /dev/null +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-GCCcore-6.4.0.eb @@ -0,0 +1,48 @@ +easyblock = 'ConfigureMake' + +name = 'ncurses' +version = '6.0' + +homepage = 'http://www.gnu.org/software/ncurses/' + +description = """ + The Ncurses (new curses) library is a free software emulation of curses in + System V Release 4.0, and more. It uses Terminfo format, supports pads and + color and multiple highlights and forms characters and function-key mapping, + and has all the other SYSV-curses enhancements over BSD Curses. +""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} +toolchainopts = {'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['f551c24b30ce8bfb6e96d9f59b42fbea30fa3a6123384172f9e7284bcf647260'] + +patches = ['ncurses-%(version)s_gcc-5.patch'] + +builddependencies = [ + ('binutils', '2.28'), +] + +configopts = [ + # default build + '--with-shared --enable-overwrite', + # the UTF-8 enabled version (ncursesw) + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", + "infotocap", + "ncurses%(version_major)s-config", + "reset", "tabs", "tic", "toe", "tput", + "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.%s' % (x, y, SHLIB_EXT) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + +moduleclass = 'devel' -- GitLab From 9b25022eb3400b38202d3a31baea829ec1f3f01f Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Thu, 13 Jul 2017 02:25:59 -0500 Subject: [PATCH 1167/1603] toss SSH --- easybuild/easyconfigs/c/cURL/cURL-7.54.1-GCCcore-6.4.0.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.54.1-GCCcore-6.4.0.eb b/easybuild/easyconfigs/c/cURL/cURL-7.54.1-GCCcore-6.4.0.eb index 0c330ab8c8..cc57b35bc9 100644 --- a/easybuild/easyconfigs/c/cURL/cURL-7.54.1-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/c/cURL/cURL-7.54.1-GCCcore-6.4.0.eb @@ -21,7 +21,6 @@ source_urls = ['http://curl.haxx.se/download/'] sources = [SOURCELOWER_TAR_GZ] osdependencies = [ - ('libssh2-devel'), ('openssl-devel', 'libssl-dev', 'libopenssl-devel'), ] @@ -33,7 +32,7 @@ dependencies = [ ('zlib', '1.2.11'), ] -configopts = '--with-libssh2 --with-zlib' +configopts = '--with-zlib' modextravars = {'CURL_INCLUDES': '%(installdir)s/include'} -- GitLab From 41d89ea5d2185498b6eb326f416e368a3f63fd72 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 13 Jul 2017 11:27:34 +0200 Subject: [PATCH 1168/1603] fix version and source for Seurat (use sources, not binary release), add extensions required by Seurat in R 3.4.0 easyconfig --- .../easyconfigs/r/R/R-3.4.0-intel-2017a-X11-20170314.eb | 7 +++++++ ...R-3.4.0.eb => Seurat-1.4.0.16-intel-2017a-R-3.4.0.eb} | 9 ++++++--- 2 files changed, 13 insertions(+), 3 deletions(-) rename easybuild/easyconfigs/s/Seurat/{Seurat-1.4.0-intel-2017a-R-3.4.0.eb => Seurat-1.4.0.16-intel-2017a-R-3.4.0.eb} (70%) diff --git a/easybuild/easyconfigs/r/R/R-3.4.0-intel-2017a-X11-20170314.eb b/easybuild/easyconfigs/r/R/R-3.4.0-intel-2017a-X11-20170314.eb index 78bdaaa928..10a1470cb3 100644 --- a/easybuild/easyconfigs/r/R/R-3.4.0-intel-2017a-X11-20170314.eb +++ b/easybuild/easyconfigs/r/R/R-3.4.0-intel-2017a-X11-20170314.eb @@ -528,6 +528,13 @@ exts_list = [ ('ucminf', '1.1-4', ext_options), ('ordinal', '2015.6-28', ext_options), ('Rtsne', '0.13', dict(ext_options.items() + [('patches', ['Rtsne-0.13_icpc-wd308.patch'])])), + ('cowplot', '0.7.0', ext_options), + ('tsne', '0.1-3', ext_options), + ('pbapply', '1.3-3', ext_options), + ('RcppProgress', '0.3', ext_options), + ('sn', '1.5-0', ext_options), + ('tclust', '1.2-7', ext_options), + ('ranger', '0.8.0', ext_options), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/s/Seurat/Seurat-1.4.0-intel-2017a-R-3.4.0.eb b/easybuild/easyconfigs/s/Seurat/Seurat-1.4.0.16-intel-2017a-R-3.4.0.eb similarity index 70% rename from easybuild/easyconfigs/s/Seurat/Seurat-1.4.0-intel-2017a-R-3.4.0.eb rename to easybuild/easyconfigs/s/Seurat/Seurat-1.4.0.16-intel-2017a-R-3.4.0.eb index 7db49d1db5..47751ee440 100644 --- a/easybuild/easyconfigs/s/Seurat/Seurat-1.4.0-intel-2017a-R-3.4.0.eb +++ b/easybuild/easyconfigs/s/Seurat/Seurat-1.4.0.16-intel-2017a-R-3.4.0.eb @@ -1,7 +1,7 @@ easyblock = 'RPackage' name = 'Seurat' -version = '1.4.0' +version = '1.4.0.16' versionsuffix = '-R-%(rver)s' homepage = 'http://satijalab.org/seurat' @@ -9,8 +9,11 @@ description = "Seurat is an R package designed for QC, analysis, and exploration toolchain = {'name': 'intel', 'version': '2017a'} -source_urls = ['https://github.com/satijalab/seurat/releases/download/v%(version_major_minor)s.0/'] -sources = ['%(name)s_%(version)s.tgz'] +source_urls = ['https://github.com/satijalab/seurat/archive/'] +sources = [{ + 'filename': SOURCE_TAR_GZ, + 'download_filename': '3bd092a.tar.gz', +}] dependencies = [('R', '3.4.0', '-X11-20170314')] -- GitLab From 3ccc82892883980470a421457ecc24b1baa85773 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Thu, 13 Jul 2017 18:12:18 +0800 Subject: [PATCH 1169/1603] adding easyconfigs: Siesta-4.0.1-intel-2017a.eb, Siesta-4.1-b3-intel-2017a.eb --- .../s/Siesta/Siesta-4.0.1-intel-2017a.eb | 17 +++++++++++++++++ .../s/Siesta/Siesta-4.1-b3-intel-2017a.eb | 18 ++++++++++++++++++ 2 files changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/s/Siesta/Siesta-4.0.1-intel-2017a.eb create mode 100644 easybuild/easyconfigs/s/Siesta/Siesta-4.1-b3-intel-2017a.eb diff --git a/easybuild/easyconfigs/s/Siesta/Siesta-4.0.1-intel-2017a.eb b/easybuild/easyconfigs/s/Siesta/Siesta-4.0.1-intel-2017a.eb new file mode 100644 index 0000000000..a7acc195e9 --- /dev/null +++ b/easybuild/easyconfigs/s/Siesta/Siesta-4.0.1-intel-2017a.eb @@ -0,0 +1,17 @@ +name = 'Siesta' +version = '4.0.1' + +homepage = 'http://departments.icmab.es/leem/siesta' +description = """SIESTA is both a method and its computer program implementation, to perform efficient electronic + structure calculations and ab initio molecular dynamics simulations of molecules and solids.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['https://launchpad.net/siesta/%(version_major_minor)s/%(version)s/+download'] +checksums = ['bfb9e4335ae1d1639a749ce7e679e739fdead5ee5766b5356ea1d259a6b1e6d1'] + +dependencies = [('netCDF-Fortran', '4.4.4')] + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/s/Siesta/Siesta-4.1-b3-intel-2017a.eb b/easybuild/easyconfigs/s/Siesta/Siesta-4.1-b3-intel-2017a.eb new file mode 100644 index 0000000000..44fa8757f7 --- /dev/null +++ b/easybuild/easyconfigs/s/Siesta/Siesta-4.1-b3-intel-2017a.eb @@ -0,0 +1,18 @@ +name = 'Siesta' +version = '4.1-b3' + +homepage = 'http://departments.icmab.es/leem/siesta' +description = """SIESTA is both a method and its computer program implementation, to perform efficient electronic + structure calculations and ab initio molecular dynamics simulations of molecules and solids.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +vl = version.split('-') +source_urls = ['https://launchpad.net/siesta/%s/%%(version)s/+download' % vl[0]] +checksums = ['f51970f34ee9b6b9de7fb77f722dde4e10817bafe7315716502eaa22bb96a090'] + +dependencies = [('netCDF-Fortran', '4.4.4')] + +moduleclass = 'phys' -- GitLab From 7b16d355b6c4d0a420f1c6f659a5d766888ce7b8 Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Thu, 13 Jul 2017 10:01:06 -0500 Subject: [PATCH 1170/1603] cope with GitHubs weird download URLs --- .../easyconfigs/m/muParser/muParser-2.2.5-GCCcore-6.4.0.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/muParser/muParser-2.2.5-GCCcore-6.4.0.eb b/easybuild/easyconfigs/m/muParser/muParser-2.2.5-GCCcore-6.4.0.eb index 915de6c6ce..0995bc4f02 100644 --- a/easybuild/easyconfigs/m/muParser/muParser-2.2.5-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/m/muParser/muParser-2.2.5-GCCcore-6.4.0.eb @@ -14,9 +14,8 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '6.4.0'} toolchainopts = {'pic': True} -# https://github.com/beltoforion/muparser/archive/v2.2.5.tar.gz source_urls = ['https://github.com/beltoforion/muparser/archive/'] -sources = [SOURCELOWER_TAR_GZ] +sources = ['v%(version)s.tar.gz'] checksums = ['0666ef55da72c3e356ca85b6a0084d56b05dd740c3c21d26d372085aa2c6e708'] builddependencies = [ -- GitLab From d305a60010159db45b8453342954513b23bbcf76 Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Thu, 13 Jul 2017 10:17:28 -0500 Subject: [PATCH 1171/1603] toolchain before sources --- .../libpthread-stubs/libpthread-stubs-0.4-GCCcore-6.4.0.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.4-GCCcore-6.4.0.eb b/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.4-GCCcore-6.4.0.eb index 64f2cd1602..60da643bb8 100644 --- a/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.4-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.4-GCCcore-6.4.0.eb @@ -11,13 +11,13 @@ description = """ threading support, and extensibility. """ +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} +toolchainopts = {'pic': True} + source_urls = ['http://xcb.freedesktop.org/dist/'] sources = [SOURCELOWER_TAR_GZ] checksums = ['50d5686b79019ccea08bcbd7b02fe5a40634abcfd4146b6e75c6420cc170e9d9'] -toolchain = {'name': 'GCCcore', 'version': '6.4.0'} -toolchainopts = {'pic': True} - builddependencies = [ ('binutils', '2.28'), ] -- GitLab From 0fd588c772be9a3d3a4093b2e195e5c1365b7682 Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Thu, 13 Jul 2017 10:32:48 -0500 Subject: [PATCH 1172/1603] readd OpenSSH comments --- easybuild/easyconfigs/c/CMake/CMake-3.8.2-GCCcore-6.4.0.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.8.2-GCCcore-6.4.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.8.2-GCCcore-6.4.0.eb index 84630972bf..80d38b2735 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.8.2-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.8.2-GCCcore-6.4.0.eb @@ -24,6 +24,9 @@ builddependencies = [ dependencies = [ ('ncurses', '6.0'), + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.1.0c'), ] osdependencies = [ -- GitLab From 63df373aa095c2327818f5935e59a34967344581 Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Thu, 13 Jul 2017 10:34:13 -0500 Subject: [PATCH 1173/1603] readd OpenSSH comments --- easybuild/easyconfigs/c/cURL/cURL-7.54.1-GCCcore-6.4.0.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.54.1-GCCcore-6.4.0.eb b/easybuild/easyconfigs/c/cURL/cURL-7.54.1-GCCcore-6.4.0.eb index cc57b35bc9..7b0a7c7ffb 100644 --- a/easybuild/easyconfigs/c/cURL/cURL-7.54.1-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/c/cURL/cURL-7.54.1-GCCcore-6.4.0.eb @@ -29,10 +29,14 @@ builddependencies = [ ] dependencies = [ + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + #('OpenSSL', '1.1.0e') ('zlib', '1.2.11'), ] configopts = '--with-zlib' +#configopts += '--with-ssl=$EBROOTOPENSSL' modextravars = {'CURL_INCLUDES': '%(installdir)s/include'} -- GitLab From 24e782112dbf9a8ccc746b8e7df034916fcc4913 Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Thu, 13 Jul 2017 10:45:05 -0500 Subject: [PATCH 1174/1603] cleanups --- .../n/ncompress/ncompress-4.2.4.4-GCCcore-6.4.0.eb | 11 +++++------ 1 file changed, 5 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/n/ncompress/ncompress-4.2.4.4-GCCcore-6.4.0.eb b/easybuild/easyconfigs/n/ncompress/ncompress-4.2.4.4-GCCcore-6.4.0.eb index a9b3d371a0..51e898837e 100644 --- a/easybuild/easyconfigs/n/ncompress/ncompress-4.2.4.4-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/n/ncompress/ncompress-4.2.4.4-GCCcore-6.4.0.eb @@ -17,7 +17,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '6.4.0'} source_urls = ['https://github.com/vapier/ncompress/archive/'] -sources = ['%(name)s-%(version)s.tar.gz'] +sources = ['v%(version)s.tar.gz'] checksums = ['2670439935e7639c3a767087da99810e45bc3997d0638b3094396043571e5aec'] builddependencies = [ @@ -26,11 +26,10 @@ builddependencies = [ skipsteps = ['configure'] -installopts = """\ - DESTDIR=%(installdir)s\ - BINDIR=/bin\ - MANDIR=/man/man1\ -""" +installopts = '' +installopts += 'DESTDIR=%(installdir)s ' +installopts += 'BINDIR=/bin ' +installopts += 'MANDIR=/man/man1 ' sanity_check_paths = { 'files': ['bin/compress', 'man/man1/compress.1'], -- GitLab From c2a87864118cbb19386b9d174dd083c964454143 Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Thu, 13 Jul 2017 11:24:40 -0500 Subject: [PATCH 1175/1603] adding easyconfigs: Automake-1.15.1-GCCcore-6.4.0.eb --- .../Automake/Automake-1.15.1-GCCcore-6.4.0.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/a/Automake/Automake-1.15.1-GCCcore-6.4.0.eb diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.15.1-GCCcore-6.4.0.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15.1-GCCcore-6.4.0.eb new file mode 100644 index 0000000000..8aa27a8cf4 --- /dev/null +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15.1-GCCcore-6.4.0.eb @@ -0,0 +1,41 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## + +easyblock = 'ConfigureMake' + +name = 'Automake' +version = "1.15.1" + +homepage = 'http://www.gnu.org/software/automake/automake.html' + +description = "Automake: GNU Standards-compliant Makefile generator" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['988e32527abe052307d21c8ca000aa238b914df363a617e38f4fb89f5abf6260'] + +builddependencies = [ + ('binutils', '2.28'), +] + +dependencies = [ + ('Autoconf', '2.69'), +] + +sanity_check_paths = { + 'files': ['bin/automake', 'bin/aclocal'], + 'dirs': [] +} + +moduleclass = 'devel' -- GitLab From c2597c8882c5c2d8b17128d2ad42902cdc80a06f Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Thu, 13 Jul 2017 11:36:40 -0500 Subject: [PATCH 1176/1603] missed a pep8 warning --- .../easyconfigs/m/muParser/muParser-2.2.5-GCCcore-6.4.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/muParser/muParser-2.2.5-GCCcore-6.4.0.eb b/easybuild/easyconfigs/m/muParser/muParser-2.2.5-GCCcore-6.4.0.eb index 0995bc4f02..d54dab67db 100644 --- a/easybuild/easyconfigs/m/muParser/muParser-2.2.5-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/m/muParser/muParser-2.2.5-GCCcore-6.4.0.eb @@ -25,7 +25,7 @@ builddependencies = [ configopts = "--disable-samples --enable-shared" sanity_check_paths = { - 'files': ['include/muParser.h', 'lib/libmuparser.%s' %SHLIB_EXT], + 'files': ['include/muParser.h', 'lib/libmuparser.%s' % SHLIB_EXT], 'dirs': [], } -- GitLab From 149c41a2088b8cbabb7216b37139af6ab294ff77 Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Thu, 13 Jul 2017 11:46:27 -0500 Subject: [PATCH 1177/1603] style fixes --- easybuild/easyconfigs/c/cURL/cURL-7.54.1-GCCcore-6.4.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.54.1-GCCcore-6.4.0.eb b/easybuild/easyconfigs/c/cURL/cURL-7.54.1-GCCcore-6.4.0.eb index 7b0a7c7ffb..852ba24f5c 100644 --- a/easybuild/easyconfigs/c/cURL/cURL-7.54.1-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/c/cURL/cURL-7.54.1-GCCcore-6.4.0.eb @@ -31,12 +31,12 @@ builddependencies = [ dependencies = [ # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons - #('OpenSSL', '1.1.0e') + # ('OpenSSL', '1.1.0e') ('zlib', '1.2.11'), ] configopts = '--with-zlib' -#configopts += '--with-ssl=$EBROOTOPENSSL' +# configopts += '--with-ssl=$EBROOTOPENSSL' modextravars = {'CURL_INCLUDES': '%(installdir)s/include'} -- GitLab From af138eeb23b861ab94d4a65af1f44332d7f1ff5a Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Thu, 13 Jul 2017 12:05:25 -0500 Subject: [PATCH 1178/1603] depends on PR #4859 and #4890 --- .../Automake/Automake-1.15.1-GCCcore-6.4.0.eb | 41 +++++++++++++++++++ .../Autotools-20170619-GCCcore-6.4.0.eb | 24 +++++++++++ .../l/libtool/libtool-2.4.6-GCCcore-6.4.0.eb | 27 ++++++++++++ 3 files changed, 92 insertions(+) create mode 100644 easybuild/easyconfigs/a/Automake/Automake-1.15.1-GCCcore-6.4.0.eb create mode 100644 easybuild/easyconfigs/a/Autotools/Autotools-20170619-GCCcore-6.4.0.eb create mode 100644 easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-6.4.0.eb diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.15.1-GCCcore-6.4.0.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15.1-GCCcore-6.4.0.eb new file mode 100644 index 0000000000..8aa27a8cf4 --- /dev/null +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15.1-GCCcore-6.4.0.eb @@ -0,0 +1,41 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## + +easyblock = 'ConfigureMake' + +name = 'Automake' +version = "1.15.1" + +homepage = 'http://www.gnu.org/software/automake/automake.html' + +description = "Automake: GNU Standards-compliant Makefile generator" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['988e32527abe052307d21c8ca000aa238b914df363a617e38f4fb89f5abf6260'] + +builddependencies = [ + ('binutils', '2.28'), +] + +dependencies = [ + ('Autoconf', '2.69'), +] + +sanity_check_paths = { + 'files': ['bin/automake', 'bin/aclocal'], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/a/Autotools/Autotools-20170619-GCCcore-6.4.0.eb b/easybuild/easyconfigs/a/Autotools/Autotools-20170619-GCCcore-6.4.0.eb new file mode 100644 index 0000000000..34009edd83 --- /dev/null +++ b/easybuild/easyconfigs/a/Autotools/Autotools-20170619-GCCcore-6.4.0.eb @@ -0,0 +1,24 @@ +easyblock = 'Bundle' + +name = 'Autotools' +version = '20170619' # date of the most recent change + +homepage = 'http://autotools.io' + +description = """ + This bundle collect the standard GNU build tools: Autoconf, Automake + and libtool +""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} + +dependencies = [ + ('Autoconf', '2.69'), # 20120424 + ('Automake', '1.15.1'), # 20170619 + ('libtool', '2.4.6'), # 20150215 +] + +# Pure bundle -- no need to specify 'binutils' used when building GCCcore +# toolchain as build dependency + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-6.4.0.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-6.4.0.eb new file mode 100644 index 0000000000..bc5c6cb40c --- /dev/null +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-6.4.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'libtool' +version = '2.4.6' + +homepage = 'http://www.gnu.org/software/libtool' + +description = """ + GNU libtool is a generic library support script. Libtool hides the complexity + of using shared libraries behind a consistent, portable interface. +""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['e3bd4d5d3d025a36c21dd6af7ea818a2afcd4dfc1ea5a17b39d7854bcd0c06e3'] + +builddependencies = [ + ('binutils', '2.28'), +] + +dependencies = [ + ('M4', '1.4.18'), +] + +moduleclass = 'lib' -- GitLab From b1da9f1a5aac34c92ebdb9abeb6f4a5f962d9c7b Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Thu, 13 Jul 2017 12:15:39 -0500 Subject: [PATCH 1179/1603] adding easyconfigs: FreeXL-1.0.2-GCCcore-6.4.0.eb --- .../f/FreeXL/FreeXL-1.0.2-GCCcore-6.4.0.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.2-GCCcore-6.4.0.eb diff --git a/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.2-GCCcore-6.4.0.eb b/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.2-GCCcore-6.4.0.eb new file mode 100644 index 0000000000..a4542ae867 --- /dev/null +++ b/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.2-GCCcore-6.4.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'FreeXL' +version = '1.0.2' + +homepage = 'https://www.gaia-gis.it/fossil/freexl/index' + +description = """ + FreeXL is an open source library to extract valid data from within an + Excel (.xls) spreadsheet. +""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.gaia-gis.it/gaia-sins/freexl-sources/'] +sources = [SOURCELOWER_TAR_GZ] + +builddependencies = [ + ('binutils', '2.28'), + ('CMake', '3.8.2'), +] + +sanity_check_paths = { + 'files': ['lib/libfreexl.a'], + 'dirs': [] + } + +moduleclass = 'lib' -- GitLab From 007bf7400d443aafe5d4c469f41b9481f58ef7ca Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Thu, 13 Jul 2017 12:21:16 -0500 Subject: [PATCH 1180/1603] add checksum --- easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.2-GCCcore-6.4.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.2-GCCcore-6.4.0.eb b/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.2-GCCcore-6.4.0.eb index a4542ae867..cdc2b4f4bc 100644 --- a/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.2-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.2-GCCcore-6.4.0.eb @@ -15,6 +15,7 @@ toolchainopts = {'pic': True} source_urls = ['http://www.gaia-gis.it/gaia-sins/freexl-sources/'] sources = [SOURCELOWER_TAR_GZ] +checksums = ['b39a4814a0f53f5e09a9192c41e3e51bd658843f770399023a963eb064f6409d'] builddependencies = [ ('binutils', '2.28'), -- GitLab From 1fe36def8814cc53df44843e98282de9d2bf6981 Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Thu, 13 Jul 2017 12:33:28 -0500 Subject: [PATCH 1181/1603] adding easyconfigs: PCRE-8.41-GCCcore-6.4.0.eb --- .../p/PCRE/PCRE-8.41-GCCcore-6.4.0.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/p/PCRE/PCRE-8.41-GCCcore-6.4.0.eb diff --git a/easybuild/easyconfigs/p/PCRE/PCRE-8.41-GCCcore-6.4.0.eb b/easybuild/easyconfigs/p/PCRE/PCRE-8.41-GCCcore-6.4.0.eb new file mode 100644 index 0000000000..0beae5c4cc --- /dev/null +++ b/easybuild/easyconfigs/p/PCRE/PCRE-8.41-GCCcore-6.4.0.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'PCRE' +version = '8.41' + +homepage = 'http://www.pcre.org/' + +description = """ + The PCRE library is a set of functions that implement regular expression + pattern matching using the same syntax and semantics as Perl 5. +""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['244838e1f1d14f7e2fa7681b857b3a8566b74215f28133f14a8f5e59241b682c'] + +builddependencies = [ + ('binutils', '2.28'), +] + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.11'), +] + +configopts = """\ + --enable-utf\ + --enable-unicode-properties\ + --enable-pcre16\ + --enable-pcre32\ +""" + +moduleclass = 'devel' -- GitLab From 3cbe316f1efe5a3e7d4e77d5a7993c5e8d47c713 Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Thu, 13 Jul 2017 12:58:00 -0500 Subject: [PATCH 1182/1603] adding easyconfigs: fontconfig-2.12.1-GCCcore-6.4.0.eb --- .../fontconfig-2.12.1-GCCcore-6.4.0.eb | 31 +++++++++++++++ .../f/freetype/freetype-2.8-GCCcore-6.4.0.eb | 39 +++++++++++++++++++ 2 files changed, 70 insertions(+) create mode 100644 easybuild/easyconfigs/f/fontconfig/fontconfig-2.12.1-GCCcore-6.4.0.eb create mode 100644 easybuild/easyconfigs/f/freetype/freetype-2.8-GCCcore-6.4.0.eb diff --git a/easybuild/easyconfigs/f/fontconfig/fontconfig-2.12.1-GCCcore-6.4.0.eb b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.12.1-GCCcore-6.4.0.eb new file mode 100644 index 0000000000..985994992e --- /dev/null +++ b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.12.1-GCCcore-6.4.0.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'fontconfig' +version = '2.12.1' + +homepage = 'http://www.freedesktop.org/software/fontconfig' + +description = """ + Fontconfig is a library designed to provide system-wide font configuration, + customization and application access. +""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.freedesktop.org/software/fontconfig/release/'] +sources = [SOURCE_TAR_GZ] +checksums = ['a9f42d03949f948a3a4f762287dbc16e53a927c91a07ee64207ebd90a9e5e292'] + +builddependencies = [ + ('binutils', '2.28'), +] + +dependencies = [ + ('expat', '2.2.1'), + ('freetype', '2.8'), +] + +configopts = '--disable-docs ' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.8-GCCcore-6.4.0.eb b/easybuild/easyconfigs/f/freetype/freetype-2.8-GCCcore-6.4.0.eb new file mode 100644 index 0000000000..683ea59e3d --- /dev/null +++ b/easybuild/easyconfigs/f/freetype/freetype-2.8-GCCcore-6.4.0.eb @@ -0,0 +1,39 @@ +name = 'freetype' +version = '2.8' + +homepage = 'http://freetype.org' + +description = """ + FreeType 2 is a software font engine that is designed to be small, efficient, + highly customizable, and portable while capable of producing high-quality + output (glyph images). It can be used in graphics libraries, display servers, + font conversion tools, text image generation tools, and many other products + as well. +""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} +toolchainopts = {'pic': True} + +source_urls = [GNU_SAVANNAH_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['33a28fabac471891d0523033e99c0005b95e5618dc8ffa7fa47f9dadcacb1c9b'] + +builddependencies = [ + ('binutils', '2.28'), +] + +dependencies = [ + ('bzip2', '1.0.6'), + ('libpng', '1.6.30'), + ('zlib', '1.2.11'), +] + +configopts = '--with-harfbuzz=no' + +sanity_check_paths = { + 'files': ['bin/freetype-config', 'lib/libfreetype.a', + 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], + 'dirs': ['include/freetype2'], +} + +moduleclass = 'vis' -- GitLab From b5771c2fc23bb69e43e097b0af1b387cdc3e3fc6 Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Thu, 13 Jul 2017 14:10:18 -0500 Subject: [PATCH 1183/1603] adding easyconfigs: HDF-4.2.13-GCCcore-6.4.0.eb --- .../h/HDF/HDF-4.2.13-GCCcore-6.4.0.eb | 43 +++++++++++++++++++ .../libjpeg-turbo-1.5.2-GCCcore-6.4.0.eb | 41 ++++++++++++++++++ .../s/Szip/Szip-2.1.1-GCCcore-6.4.0.eb | 29 +++++++++++++ 3 files changed, 113 insertions(+) create mode 100644 easybuild/easyconfigs/h/HDF/HDF-4.2.13-GCCcore-6.4.0.eb create mode 100644 easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.5.2-GCCcore-6.4.0.eb create mode 100644 easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-6.4.0.eb diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.13-GCCcore-6.4.0.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.13-GCCcore-6.4.0.eb new file mode 100644 index 0000000000..f1b4395af4 --- /dev/null +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.13-GCCcore-6.4.0.eb @@ -0,0 +1,43 @@ +easyblock = 'ConfigureMake' + +name = 'HDF' +version = '4.2.13' + +homepage = 'http://www.hdfgroup.org/products/hdf4/' + +description = """ + HDF (also known as HDF4) is a library and multi-object file format for + storing and managing data between machines. +""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] +checksums = ['be9813c1dc3712c2df977d4960e1f13f20f447dfa8c3ce53331d610c1f470483'] + +builddependencies = [ + ('binutils', '2.28'), + ('Bison', '3.0.4'), + ('flex', '2.6.4'), +] + +dependencies = [ + ('libjpeg-turbo', '1.5.2'), + ('Szip', '2.1.1'), + ('zlib', '1.2.11'), +] + +configopts = '' +configopts += '--with-szlib=$EBROOTSZIP ' +configopts += '--includedir=%(installdir)s/include/%(namelower)s ' + +modextrapaths = {'CPATH': 'include/hdf'} + +sanity_check_paths = { + 'files': ['lib/libdf.a', 'lib/libhdf4.settings', 'lib/libmfhdf.a'], + 'dirs': ['bin', 'include/hdf'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.5.2-GCCcore-6.4.0.eb b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.5.2-GCCcore-6.4.0.eb new file mode 100644 index 0000000000..8d3ce16df6 --- /dev/null +++ b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.5.2-GCCcore-6.4.0.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'libjpeg-turbo' +version = '1.5.2' + +homepage = 'http://sourceforge.net/projects/libjpeg-turbo/' + +description = """ + libjpeg-turbo is a fork of the original IJG libjpeg which uses SIMD to + accelerate baseline JPEG compression and decompression. libjpeg is a library + that implements JPEG image encoding, decoding and transcoding. +""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['9098943b270388727ae61de82adec73cf9f0dbb240b3bc8b172595ebf405b528'] + +builddependencies = [ + ('binutils', '2.28'), +] + +dependencies = [ + ('NASM', '2.13.01'), +] + +configopts = "--with-jpeg8" + +runtest = "test" + +sanity_check_paths = { + 'files': ['bin/cjpeg', 'bin/djpeg', 'bin/jpegtran', 'bin/rdjpgcom', + 'bin/tjbench', 'bin/wrjpgcom', 'lib/libjpeg.a', + 'lib/libjpeg.%s' % SHLIB_EXT, 'lib/libturbojpeg.a', + 'lib/libturbojpeg.%s' % SHLIB_EXT], + 'dirs': ['include', 'share'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-6.4.0.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-6.4.0.eb new file mode 100644 index 0000000000..98b8e0cf48 --- /dev/null +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-6.4.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'Szip' +version = '2.1.1' + +homepage = 'http://www.hdfgroup.org/doc_resource/SZIP/' + +description = """ + Szip compression software, providing lossless compression of scientific data +""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['897dda94e1d4bf88c91adeaad88c07b468b18eaf2d6125c47acac57e540904a9'] + +builddependencies = [ + ('binutils', '2.28'), +] + +sanity_check_paths = { + 'files': ["lib/libsz.a", "lib/libsz.%s" % SHLIB_EXT] + + ["include/%s" % x for x in ["ricehdf.h", "szip_adpt.h", "szlib.h"]], + 'dirs': [], +} + +moduleclass = 'tools' -- GitLab From e56d0c1885a545622e7aa95f33c3e4a6051d1eaf Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Thu, 13 Jul 2017 14:35:09 -0500 Subject: [PATCH 1184/1603] indentation fix --- easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.2-GCCcore-6.4.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.2-GCCcore-6.4.0.eb b/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.2-GCCcore-6.4.0.eb index cdc2b4f4bc..f0015556cc 100644 --- a/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.2-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.2-GCCcore-6.4.0.eb @@ -25,6 +25,6 @@ builddependencies = [ sanity_check_paths = { 'files': ['lib/libfreexl.a'], 'dirs': [] - } +} moduleclass = 'lib' -- GitLab From 056a9a561de34df0584dde15a2eb1436e68fe77e Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Thu, 13 Jul 2017 14:39:00 -0500 Subject: [PATCH 1185/1603] adding easyconfigs: GMP-6.1.2-GCCcore-6.4.0.eb --- .../g/GMP/GMP-6.1.2-GCCcore-6.4.0.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/g/GMP/GMP-6.1.2-GCCcore-6.4.0.eb diff --git a/easybuild/easyconfigs/g/GMP/GMP-6.1.2-GCCcore-6.4.0.eb b/easybuild/easyconfigs/g/GMP/GMP-6.1.2-GCCcore-6.4.0.eb new file mode 100644 index 0000000000..579e3410d3 --- /dev/null +++ b/easybuild/easyconfigs/g/GMP/GMP-6.1.2-GCCcore-6.4.0.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'GMP' +version = '6.1.2' + +homepage = 'http://gmplib.org/' + +description = """ + GMP is a free library for arbitrary precision arithmetic, operating on signed + integers, rational numbers, and floating point numbers. +""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} +toolchainopts = {'pic': True, 'precise': True} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://ftp.gnu.org/gnu/gmp'] +checksums = ['5275bb04f4863a13516b2f39392ac5e272f5e1bb8057b18aec1c9b79d73d8fb2'] + +builddependencies = [ + ('Autotools', '20170619'), + ('binutils', '2.28'), +] + +# enable C++ interface +configopts = '--enable-cxx' + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libgmp.%s' % SHLIB_EXT, 'include/gmp.h'], + 'dirs': [], +} + +moduleclass = 'math' -- GitLab From c8f0fbf6ebc21b3cbc4d024516e1aa8f50585e99 Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Thu, 13 Jul 2017 15:18:26 -0500 Subject: [PATCH 1186/1603] adding easyconfigs: JasPer-2.0.12-GCCcore-6.4.0.eb --- .../j/JasPer/JasPer-2.0.12-GCCcore-6.4.0.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/j/JasPer/JasPer-2.0.12-GCCcore-6.4.0.eb diff --git a/easybuild/easyconfigs/j/JasPer/JasPer-2.0.12-GCCcore-6.4.0.eb b/easybuild/easyconfigs/j/JasPer/JasPer-2.0.12-GCCcore-6.4.0.eb new file mode 100644 index 0000000000..b2d812f323 --- /dev/null +++ b/easybuild/easyconfigs/j/JasPer/JasPer-2.0.12-GCCcore-6.4.0.eb @@ -0,0 +1,35 @@ +easyblock = 'CMakeMake' + +name = 'JasPer' +version = '2.0.12' + +homepage = 'http://www.ece.uvic.ca/~frodo/jasper/' + +description = """ + The JasPer Project is an open-source initiative to provide a free + software-based reference implementation of the codec specified in + the JPEG-2000 Part-1 standard. +""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.ece.uvic.ca/~frodo/jasper/software/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['5b24faf5ed38670d6286e45ab7516b26458d05e7929b435afe569176765f4dda'] + +builddependencies = [ + ('binutils', '2.28'), + ('CMake', '3.8.2'), +] + +separate_build_dir = True + +configopts = '-DJAS_ENABLE_DOC=OFF ' + +sanity_check_paths = { + 'files': ['bin/jasper', 'lib64/libjasper.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'vis' -- GitLab From c46a9ba250b09cd33a2cd137c667d0a6d398ed99 Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Thu, 13 Jul 2017 15:48:08 -0500 Subject: [PATCH 1187/1603] adding easyconfigs: Voro++-0.4.6-GCCcore-6.4.0.eb --- .../v/Voro++/Voro++-0.4.6-GCCcore-6.4.0.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/v/Voro++/Voro++-0.4.6-GCCcore-6.4.0.eb diff --git a/easybuild/easyconfigs/v/Voro++/Voro++-0.4.6-GCCcore-6.4.0.eb b/easybuild/easyconfigs/v/Voro++/Voro++-0.4.6-GCCcore-6.4.0.eb new file mode 100644 index 0000000000..9d8d8d4d19 --- /dev/null +++ b/easybuild/easyconfigs/v/Voro++/Voro++-0.4.6-GCCcore-6.4.0.eb @@ -0,0 +1,45 @@ +easyblock = 'ConfigureMake' + +name = 'Voro++' +version = '0.4.6' + +homepage = 'http://math.lbl.gov/voro++/' + +description = """ + Voro++ is a software library for carrying out three-dimensional computations + of the Voronoi tessellation. A distinguishing feature of the Voro++ library is + that it carries out cell-based calculations, computing the Voronoi cell for + each particle individually. It is particularly well-suited for applications + that rely on cell-based statistics, where features of Voronoi cells (eg. + volume, centroid, number of faces) can be used to analyze a system of + particles. +""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} +toolchainopts = {'pic': True} + +source_urls = ['http://math.lbl.gov/voro++/download/dir/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['ef7970071ee2ce3800daa8723649ca069dc4c71cc25f0f7d22552387f3ea437e'] + +builddependencies = [ + ('binutils', '2.28'), +] + +# No configure +skipsteps = ['configure'] + +# Override CXX and CFLAGS variables from Makefile +buildopts = 'CXX="$CXX" CFLAGS="$CXXFLAGS"' + +# Override PREFIX variable from Makefile +installopts = 'PREFIX=%(installdir)s' + +sanity_check_paths = { + 'files': ['bin/voro++', 'lib/libvoro++.a', 'include/voro++/voro++.hh'], + 'dirs': [], +} + +modextrapaths = {'CPATH': 'include/voro++'} + +moduleclass = 'math' -- GitLab From ed582f7e7b5e3294f76d9656704b99740ec65c12 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Fri, 14 Jul 2017 14:31:09 -0500 Subject: [PATCH 1188/1603] Adding required zlib dependency --- .../u/util-linux/util-linux-2.29.2-intel-2017a.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/u/util-linux/util-linux-2.29.2-intel-2017a.eb b/easybuild/easyconfigs/u/util-linux/util-linux-2.29.2-intel-2017a.eb index 3495ebee0c..b794436556 100644 --- a/easybuild/easyconfigs/u/util-linux/util-linux-2.29.2-intel-2017a.eb +++ b/easybuild/easyconfigs/u/util-linux/util-linux-2.29.2-intel-2017a.eb @@ -23,7 +23,10 @@ configopts += "--with-bashcompletiondir='${prefix}/share/bash-completion/complet # disable building Python bindings (since we don't include Python as a dep) configopts += "--without-python " -dependencies = [('ncurses', '6.0')] +dependencies = [ + ('ncurses', '6.0'), + ('zlib', '1.2.11'), +] sanity_check_paths = { 'files': ['lib/lib%s.a' % x for x in ['blkid', 'mount', 'uuid']], -- GitLab From 459ecc488f3c15192c74f6b7d73f58f74810d485 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Mon, 17 Jul 2017 07:38:34 +0200 Subject: [PATCH 1189/1603] Add BLAST+ 2.6.0 for foss-2016b --- .../BLAST+-2.6.0-foss-2016b-Python-2.7.12.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/b/BLAST+/BLAST+-2.6.0-foss-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.6.0-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.6.0-foss-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..ecc6133475 --- /dev/null +++ b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.6.0-foss-2016b-Python-2.7.12.eb @@ -0,0 +1,41 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'ConfigureMake' + +name = 'BLAST+' +version = '2.6.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://blast.ncbi.nlm.nih.gov/' +description = """Basic Local Alignment Search Tool, or BLAST, is an algorithm + for comparing primary biological sequence information, such as the amino-acid + sequences of different proteins or the nucleotides of DNA sequences.""" + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'cstd': 'c++14'} + +sources = ['ncbi-blast-%(version)s+-src.tar.gz'] +source_urls = ['http://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/%(version)s/'] +patches = ['BLAST+-%(version)s_fix-make-install.patch'] + +dependencies = [ + ('zlib', '1.2.8'), + ('bzip2', '1.0.6'), + ('PCRE', '8.39'), + ('Python', '2.7.12'), + ('Boost', '1.63.0', versionsuffix), + ('GMP', '6.1.1'), + ('libpng', '1.6.26'), + ('libjpeg-turbo', '1.5.0'), +] + +configopts = "--with-64 --with-z=$EBROOTZLIB --with-bz2=$EBROOTBZIP2 --with-pcre=$EBROOTPCRE " +configopts += "--with-python=$EBROOTPYTHON --with-boost=$EBROOTBOOST --with-gmp=$EBROOTGMP " +configopts += "--with-png=$EBROOTLIBPNG --with-jpeg=$EBROOTLIBJPEGMINTURBO " + +sanity_check_paths = { + 'files': ['bin/blastn', 'bin/blastp', 'bin/blastx'], + 'dirs': [] +} + +moduleclass = 'bio' -- GitLab From 6c0b5310022d0c040ebd19c85c62e81bbc81bc98 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Mon, 17 Jul 2017 07:44:18 +0200 Subject: [PATCH 1190/1603] Add bcl2fastq2 2.19.1 for foss-2016b --- ...2fastq2-2.19.1-foss-2016b-Python-2.7.12.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.19.1-foss-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.19.1-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.19.1-foss-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..bbe3f9e5a8 --- /dev/null +++ b/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.19.1-foss-2016b-Python-2.7.12.eb @@ -0,0 +1,35 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'ConfigureMake' + +name = 'bcl2fastq2' +version = '2.19.1' +versionsuffix = '-Python-2.7.12' + +homepage = 'https://support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software.html' +description = """bcl2fastq Conversion Software both demultiplexes data and converts BCL files generated by + Illumina sequencing systems to standard FASTQ file formats for downstream analysis.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['ftp://webdata2:webdata2@ussd-ftp.illumina.com/downloads/software/bcl2fastq/'] +sources = [{ + 'filename': '%(name)s-v%(version)s-tar.zip', + 'extract_cmd': 'unzip -p %s | tar -xzvf -', # source file is a .zip that contains a .tar.gz +}] + +checksums = ['cf13580f2c1ebcc3642b4d98a02ad01e41a44e644db7d31730f9767b25521806'] + +start_dir = 'src' +configopts = '--force-builddir' + +dependencies = [ + ('Boost', '1.54.0', versionsuffix), +] + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': ['lib'] +} + +moduleclass = 'bio' -- GitLab From 90fa9bb8a1ae4cb00351d23451286a9c60c76a58 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Mon, 17 Jul 2017 08:51:43 +0200 Subject: [PATCH 1191/1603] Add requested changes Use pyver variable and explicitly add Python as dependency. Use two spaces for inline comment. --- .../bcl2fastq2/bcl2fastq2-2.19.1-foss-2016b-Python-2.7.12.eb | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.19.1-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.19.1-foss-2016b-Python-2.7.12.eb index bbe3f9e5a8..9f550972a5 100644 --- a/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.19.1-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.19.1-foss-2016b-Python-2.7.12.eb @@ -4,7 +4,7 @@ easyblock = 'ConfigureMake' name = 'bcl2fastq2' version = '2.19.1' -versionsuffix = '-Python-2.7.12' +versionsuffix = '-Python-%(pyver)s' homepage = 'https://support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software.html' description = """bcl2fastq Conversion Software both demultiplexes data and converts BCL files generated by @@ -15,7 +15,7 @@ toolchain = {'name': 'foss', 'version': '2016b'} source_urls = ['ftp://webdata2:webdata2@ussd-ftp.illumina.com/downloads/software/bcl2fastq/'] sources = [{ 'filename': '%(name)s-v%(version)s-tar.zip', - 'extract_cmd': 'unzip -p %s | tar -xzvf -', # source file is a .zip that contains a .tar.gz + 'extract_cmd': 'unzip -p %s | tar -xzvf -', # source file is a .zip that contains a .tar.gz }] checksums = ['cf13580f2c1ebcc3642b4d98a02ad01e41a44e644db7d31730f9767b25521806'] @@ -25,6 +25,7 @@ configopts = '--force-builddir' dependencies = [ ('Boost', '1.54.0', versionsuffix), + ('Python', '2.7.12'), ] sanity_check_paths = { -- GitLab From e3002d7b5e25ff400c668cef51a14803365c1aba Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Mon, 17 Jul 2017 08:54:21 +0200 Subject: [PATCH 1192/1603] Fix sanity check Executable name is bcl2fastq not bcl2fastq2. --- .../b/bcl2fastq2/bcl2fastq2-2.19.1-foss-2016b-Python-2.7.12.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.19.1-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.19.1-foss-2016b-Python-2.7.12.eb index 9f550972a5..eb24e2f5ed 100644 --- a/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.19.1-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.19.1-foss-2016b-Python-2.7.12.eb @@ -29,7 +29,7 @@ dependencies = [ ] sanity_check_paths = { - 'files': ['bin/%(name)s'], + 'files': ['bin/bcl2fastq'], 'dirs': ['lib'] } -- GitLab From be75232725b621228d075facb0d644180985e9c7 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Mon, 17 Jul 2017 10:48:27 +0200 Subject: [PATCH 1193/1603] fix typo. Use modextrapaths instead of modextravars --- .../o/OpenMM/OpenMM-6.1-goolf-1.4.10-Python-2.7.5.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OpenMM/OpenMM-6.1-goolf-1.4.10-Python-2.7.5.eb b/easybuild/easyconfigs/o/OpenMM/OpenMM-6.1-goolf-1.4.10-Python-2.7.5.eb index 547084c491..1644d773d3 100644 --- a/easybuild/easyconfigs/o/OpenMM/OpenMM-6.1-goolf-1.4.10-Python-2.7.5.eb +++ b/easybuild/easyconfigs/o/OpenMM/OpenMM-6.1-goolf-1.4.10-Python-2.7.5.eb @@ -45,7 +45,7 @@ modextrapaths = { 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', } -modextravars = { +modextrapaths = { 'OPENMM_INCLUDE_PATH': 'include', 'OPENMM_LIB_PATH': 'lib', } -- GitLab From affa6cb03c5917cbbdb701abb25e8200f8d53791 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Mon, 17 Jul 2017 11:01:26 +0200 Subject: [PATCH 1194/1603] put all modextrapaths together --- .../o/OpenMM/OpenMM-6.1-goolf-1.4.10-Python-2.7.5.eb | 3 --- 1 file changed, 3 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenMM/OpenMM-6.1-goolf-1.4.10-Python-2.7.5.eb b/easybuild/easyconfigs/o/OpenMM/OpenMM-6.1-goolf-1.4.10-Python-2.7.5.eb index 1644d773d3..c0eaaaab71 100644 --- a/easybuild/easyconfigs/o/OpenMM/OpenMM-6.1-goolf-1.4.10-Python-2.7.5.eb +++ b/easybuild/easyconfigs/o/OpenMM/OpenMM-6.1-goolf-1.4.10-Python-2.7.5.eb @@ -43,9 +43,6 @@ sanity_check_paths = { modextrapaths = { 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', -} - -modextrapaths = { 'OPENMM_INCLUDE_PATH': 'include', 'OPENMM_LIB_PATH': 'lib', } -- GitLab From dcfcb3c73374b0d7ae67af20e58bc1f9bf12c383 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Tue, 18 Jul 2017 07:10:57 +0200 Subject: [PATCH 1195/1603] Add SHA256 checksum --- .../b/BLAST+/BLAST+-2.6.0-foss-2016b-Python-2.7.12.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.6.0-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.6.0-foss-2016b-Python-2.7.12.eb index ecc6133475..0942e32de1 100644 --- a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.6.0-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.6.0-foss-2016b-Python-2.7.12.eb @@ -16,6 +16,9 @@ toolchainopts = {'cstd': 'c++14'} sources = ['ncbi-blast-%(version)s+-src.tar.gz'] source_urls = ['http://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/%(version)s/'] + +checksums = ['0510e1d607d0fb4389eca50d434d5a0be787423b6850b3a4f315abc2ef19c996'] + patches = ['BLAST+-%(version)s_fix-make-install.patch'] dependencies = [ -- GitLab From 16e89fc20d32bb91ea24b217d6866b173bbed635 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Tue, 18 Jul 2017 10:01:56 +0200 Subject: [PATCH 1196/1603] Add Bowtie2 2.3.2 for foss-2016b --- .../b/Bowtie2/Bowtie2-2.3.2-foss-2016b.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.3.2-foss-2016b.eb diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.3.2-foss-2016b.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.3.2-foss-2016b.eb new file mode 100644 index 0000000000..5f6d0b56d6 --- /dev/null +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.3.2-foss-2016b.eb @@ -0,0 +1,26 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +name = 'Bowtie2' +version = '2.3.2' + +homepage = 'http://bowtie-bio.sourceforge.net/bowtie2/index.shtml' +description = """ Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads + to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s + of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. + Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, + its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.""" + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'pic': True} + +sources = ['%(namelower)s-%(version)s-source.zip'] +source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')] + +checksums = ['ef0fe6d712eb3f9fbd784a5772547a28859a71eb6c455ef670b0f11a56cc73f7'] + +dependencies = [('tbb', '2017_U5')] + +# to add script folder to path just uncomment this line +# modextrapaths = {'PATH': 'scripts'} + +moduleclass = 'bio' -- GitLab From 2afd8b882e9dd970968cb241ee1901a69606a5ed Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Tue, 18 Jul 2017 09:59:43 +0200 Subject: [PATCH 1197/1603] Add Bowtie 1.2.1.1 for foss-2016b --- .../b/Bowtie/Bowtie-1.2.1.1-foss-2016b.eb | 20 +++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bowtie/Bowtie-1.2.1.1-foss-2016b.eb diff --git a/easybuild/easyconfigs/b/Bowtie/Bowtie-1.2.1.1-foss-2016b.eb b/easybuild/easyconfigs/b/Bowtie/Bowtie-1.2.1.1-foss-2016b.eb new file mode 100644 index 0000000000..8e5cbc7d40 --- /dev/null +++ b/easybuild/easyconfigs/b/Bowtie/Bowtie-1.2.1.1-foss-2016b.eb @@ -0,0 +1,20 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +name = 'Bowtie' +version = '1.2.1.1' + +homepage = 'http://bowtie-bio.sourceforge.net/index.shtml' +description = """Bowtie is an ultrafast, memory-efficient short read aligner. + It aligns short DNA sequences (reads) to the human genome.""" + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'pic': True} + +sources = ['%(namelower)s-%(version)s-src.zip'] +source_urls = ['http://download.sourceforge.net/bowtie-bio/'] + +checksums = ['71d708c957380e115ba420a96ac5f8456c6a61760a5f4dbe06305df6a42131d8'] + +dependencies = [('tbb', '2017_U5')] + +moduleclass = 'bio' -- GitLab From f6306c149824717463c6a05f9a769177a3903d6e Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Tue, 18 Jul 2017 07:00:21 -0500 Subject: [PATCH 1198/1603] maintain sanity --- .../easyconfigs/l/libtool/libtool-2.4.6-GCCcore-6.4.0.eb | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-6.4.0.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-6.4.0.eb index bc5c6cb40c..93cdcb700f 100644 --- a/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-6.4.0.eb @@ -24,4 +24,9 @@ dependencies = [ ('M4', '1.4.18'), ] +sanity_check_paths = { + 'files': ['bin/libtool', 'bin/libtoolize', 'lib/libltdl.%s' % SHLIB_EXT], + 'dirs': ['include/libltdl', 'share/libtool/loaders', 'share/man/man1'], +} + moduleclass = 'lib' -- GitLab From 2d46898043deb387804b017ddf809f38df0d20f4 Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Tue, 18 Jul 2017 07:23:07 -0500 Subject: [PATCH 1199/1603] maintain sanity --- easybuild/easyconfigs/p/PCRE/PCRE-8.41-GCCcore-6.4.0.eb | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/p/PCRE/PCRE-8.41-GCCcore-6.4.0.eb b/easybuild/easyconfigs/p/PCRE/PCRE-8.41-GCCcore-6.4.0.eb index 0beae5c4cc..197001b9a8 100644 --- a/easybuild/easyconfigs/p/PCRE/PCRE-8.41-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/p/PCRE/PCRE-8.41-GCCcore-6.4.0.eb @@ -33,4 +33,10 @@ configopts = """\ --enable-pcre32\ """ +sanity_check_paths = { + 'files': ['bin/pcre-config', 'include/pcre.h', + 'share/man/man3/pcre.3', 'lib/libpcre32.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig', 'share/doc/pcre/html', 'share/man/man1'], +} + moduleclass = 'devel' -- GitLab From 2016d8b4c31d9beffacbc0338bab36c2a0d07247 Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Tue, 18 Jul 2017 07:48:25 -0500 Subject: [PATCH 1200/1603] adding easyconfigs: Tcl-8.6.6-GCCcore-6.4.0.eb --- .../t/Tcl/Tcl-8.6.6-GCCcore-6.4.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/t/Tcl/Tcl-8.6.6-GCCcore-6.4.0.eb diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.6-GCCcore-6.4.0.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.6-GCCcore-6.4.0.eb new file mode 100644 index 0000000000..a74036c985 --- /dev/null +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.6-GCCcore-6.4.0.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'Tcl' +version = '8.6.6' + +homepage = 'http://www.tcl.tk/' + +description = """ + Tcl (Tool Command Language) is a very powerful but easy to learn dynamic + programming language, suitable for a very wide range of uses, including web + and desktop applications, networking, administration, testing and many more. +""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] +checksums = ['a265409781e4b3edcc4ef822533071b34c3dc6790b893963809b9fe221befe07'] + +builddependencies = [ + ('binutils', '2.28'), +] + +dependencies = [ + ('zlib', '1.2.11'), +] + +configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' + +runtest = 'test' + +start_dir = 'unix' + +moduleclass = 'lang' -- GitLab From e630f55224a1938297732855ec50eba38c517c96 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Wed, 19 Jul 2017 07:37:49 +0200 Subject: [PATCH 1201/1603] Add sanity check --- .../easyconfigs/b/Bowtie/Bowtie-1.2.1.1-foss-2016b.eb | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/easybuild/easyconfigs/b/Bowtie/Bowtie-1.2.1.1-foss-2016b.eb b/easybuild/easyconfigs/b/Bowtie/Bowtie-1.2.1.1-foss-2016b.eb index 8e5cbc7d40..ceafd39df5 100644 --- a/easybuild/easyconfigs/b/Bowtie/Bowtie-1.2.1.1-foss-2016b.eb +++ b/easybuild/easyconfigs/b/Bowtie/Bowtie-1.2.1.1-foss-2016b.eb @@ -17,4 +17,11 @@ checksums = ['71d708c957380e115ba420a96ac5f8456c6a61760a5f4dbe06305df6a42131d8'] dependencies = [('tbb', '2017_U5')] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['bowtie', 'bowtie-align-l', 'bowtie-align-s', 'bowtie-build', 'bowtie-build-l', 'bowtie-build-s', 'bowtie-inspect', 'bowtie-inspect-l', 'bowtie-inspect-s']], + 'dirs': [] +} + +sanity_check_commands = [('bowtie', '--version')] + moduleclass = 'bio' -- GitLab From 9693231280b707f8da0792c9912aef823f772f6e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Wed, 19 Jul 2017 07:39:12 +0200 Subject: [PATCH 1202/1603] Add sanity check --- .../easyconfigs/b/Bowtie2/Bowtie2-2.3.2-foss-2016b.eb | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.3.2-foss-2016b.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.3.2-foss-2016b.eb index 5f6d0b56d6..2258f2b213 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.3.2-foss-2016b.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.3.2-foss-2016b.eb @@ -20,6 +20,13 @@ checksums = ['ef0fe6d712eb3f9fbd784a5772547a28859a71eb6c455ef670b0f11a56cc73f7'] dependencies = [('tbb', '2017_U5')] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['bowtie2', 'bowtie2-align-l', 'bowtie2-align-s', 'bowtie2-build', 'bowtie2-build-l', 'bowtie2-build-s', 'bowtie2-inspect', 'bowtie2-inspect-l', 'bowtie2-inspect-s']], + 'dirs': [] +} + +sanity_check_commands = [('bowtie2', '--version')] + # to add script folder to path just uncomment this line # modextrapaths = {'PATH': 'scripts'} -- GitLab From 2ea485b45b24e27d4e9ae8ce5f76085d01dafbed Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Wed, 19 Jul 2017 08:05:32 +0200 Subject: [PATCH 1203/1603] Fix line length --- easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.3.2-foss-2016b.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.3.2-foss-2016b.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.3.2-foss-2016b.eb index 2258f2b213..03a5dea73d 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.3.2-foss-2016b.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.3.2-foss-2016b.eb @@ -21,7 +21,9 @@ checksums = ['ef0fe6d712eb3f9fbd784a5772547a28859a71eb6c455ef670b0f11a56cc73f7'] dependencies = [('tbb', '2017_U5')] sanity_check_paths = { - 'files': ['bin/%s' % x for x in ['bowtie2', 'bowtie2-align-l', 'bowtie2-align-s', 'bowtie2-build', 'bowtie2-build-l', 'bowtie2-build-s', 'bowtie2-inspect', 'bowtie2-inspect-l', 'bowtie2-inspect-s']], + 'files': ['bin/%s' % x for x in ['bowtie2', 'bowtie2-align-l', 'bowtie2-align-s', 'bowtie2-build', + 'bowtie2-build-l', 'bowtie2-build-s', 'bowtie2-inspect', 'bowtie2-inspect-l', + 'bowtie2-inspect-s']], 'dirs': [] } -- GitLab From 700d746e651ab98fed83705df9c1c5904977241d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Wed, 19 Jul 2017 08:07:20 +0200 Subject: [PATCH 1204/1603] Fix line length --- easybuild/easyconfigs/b/Bowtie/Bowtie-1.2.1.1-foss-2016b.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/Bowtie/Bowtie-1.2.1.1-foss-2016b.eb b/easybuild/easyconfigs/b/Bowtie/Bowtie-1.2.1.1-foss-2016b.eb index ceafd39df5..28f4c0d027 100644 --- a/easybuild/easyconfigs/b/Bowtie/Bowtie-1.2.1.1-foss-2016b.eb +++ b/easybuild/easyconfigs/b/Bowtie/Bowtie-1.2.1.1-foss-2016b.eb @@ -18,7 +18,8 @@ checksums = ['71d708c957380e115ba420a96ac5f8456c6a61760a5f4dbe06305df6a42131d8'] dependencies = [('tbb', '2017_U5')] sanity_check_paths = { - 'files': ['bin/%s' % x for x in ['bowtie', 'bowtie-align-l', 'bowtie-align-s', 'bowtie-build', 'bowtie-build-l', 'bowtie-build-s', 'bowtie-inspect', 'bowtie-inspect-l', 'bowtie-inspect-s']], + 'files': ['bin/%s' % x for x in ['bowtie', 'bowtie-align-l', 'bowtie-align-s', 'bowtie-build', 'bowtie-build-l', + 'bowtie-build-s', 'bowtie-inspect', 'bowtie-inspect-l', 'bowtie-inspect-s']], 'dirs': [] } -- GitLab From 1c3daacb0de6ba160c554a291522809a40740742 Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Wed, 19 Jul 2017 08:39:50 -0500 Subject: [PATCH 1205/1603] maintain sanity --- easybuild/easyconfigs/t/Tcl/Tcl-8.6.6-GCCcore-6.4.0.eb | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.6-GCCcore-6.4.0.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.6-GCCcore-6.4.0.eb index a74036c985..cffeed4270 100644 --- a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.6-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.6-GCCcore-6.4.0.eb @@ -31,4 +31,12 @@ runtest = 'test' start_dir = 'unix' +sanity_check_paths = { + 'files': ['bin/tclsh%(version_major)s.%(version_minor)s', 'include/tcl.h', + 'lib/libtcl%%(version_major)s.%%(version_minor)s.%s' % SHLIB_EXT, + 'lib/tclConfig.sh', 'man/man1/tclsh.1'], + 'dirs': ['share'], +} + + moduleclass = 'lang' -- GitLab From e77ec006d9dba2842069315d0bdc557e5650aca9 Mon Sep 17 00:00:00 2001 From: Oliver Stueker Date: Wed, 19 Jul 2017 16:37:36 -0230 Subject: [PATCH 1206/1603] GAMESS-US Apr 20 2017 R1 configs, patches --- .../GAMESS-US-20170420-R1-foss-2016b.eb | 39 ++++++++++++++ ...MESS-US-20170420-R1-intel-2016b-sockets.eb | 39 ++++++++++++++ .../GAMESS-US-20170420-R1-intel-2016b.eb | 38 ++++++++++++++ .../GAMESS-US-20170420-R1_recent-gcc.patch | 52 +++++++++++++++++++ ...20-R1_rungms_fix_PPN_not_initialized.patch | 10 ++++ 5 files changed, 178 insertions(+) create mode 100644 easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20170420-R1-foss-2016b.eb create mode 100644 easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20170420-R1-intel-2016b-sockets.eb create mode 100644 easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20170420-R1-intel-2016b.eb create mode 100644 easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20170420-R1_recent-gcc.patch create mode 100644 easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20170420-R1_rungms_fix_PPN_not_initialized.patch diff --git a/easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20170420-R1-foss-2016b.eb b/easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20170420-R1-foss-2016b.eb new file mode 100644 index 0000000000..a18cd469bd --- /dev/null +++ b/easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20170420-R1-foss-2016b.eb @@ -0,0 +1,39 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2017 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, +# Ghent University / The Francis Crick Institute +# +# Authors:: +# * Kenneth Hoste +# * Ward Poelmans +# * Oliver Stueker +# License:: MIT/GPL +## +name = 'GAMESS-US' +version = '20170420-R1' + +homepage = 'http://www.msg.chem.iastate.edu/gamess/index.html' +description = """ The General Atomic and Molecular Electronic Structure System (GAMESS) + is a general ab initio quantum chemistry package. """ + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'usempi': True} + +# manually download via http://www.msg.chem.iastate.edu/gamess/download.html (requires registration) +# rename gamess-current.tar.gz by changing 'current' to the proper version +sources = ['gamess-%(version)s.tar.gz'] +checksums = ['e9fa2e725ccbd69f4d996ab68bb65ff2'] + +patches = [ + 'GAMESS-US_rungms-slurm.patch', + 'GAMESS-US-20170420-R1_rungms_fix_PPN_not_initialized.patch', + 'GAMESS-US-20170420-R1_recent-gcc.patch', +] + +# increase these numbers if your system is bigger in terms of cores-per-node or number of nodes +# it's OK if these values are larger than what your system provides +maxcpus = '1000' +maxnodes = '100000' + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20170420-R1-intel-2016b-sockets.eb b/easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20170420-R1-intel-2016b-sockets.eb new file mode 100644 index 0000000000..d2d82e8fab --- /dev/null +++ b/easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20170420-R1-intel-2016b-sockets.eb @@ -0,0 +1,39 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2017 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, +# Ghent University / The Francis Crick Institute +# +# Authors:: +# * Kenneth Hoste +# * Ward Poelmans +# * Oliver Stueker +# License:: MIT/GPL +## +name = 'GAMESS-US' +version = '20170420-R1' + +homepage = 'http://www.msg.chem.iastate.edu/gamess/index.html' +description = """ The General Atomic and Molecular Electronic Structure System (GAMESS) + is a general ab initio quantum chemistry package. """ + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'usempi': False} +ddi_comm = 'sockets' + +# manually download via http://www.msg.chem.iastate.edu/gamess/download.html (requires registration) +# rename gamess-current.tar.gz by changing 'current' to the proper version +sources = ['gamess-%(version)s.tar.gz'] +checksums = ['e9fa2e725ccbd69f4d996ab68bb65ff2'] + +patches = [ + 'GAMESS-US_rungms-slurm.patch', + 'GAMESS-US-20170420-R1_rungms_fix_PPN_not_initialized.patch', +] + +# increase these numbers if your system is bigger in terms of cores-per-node or number of nodes +# it's OK if these values are larger than what your system provides +maxcpus = '1000' +maxnodes = '100000' + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20170420-R1-intel-2016b.eb b/easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20170420-R1-intel-2016b.eb new file mode 100644 index 0000000000..7a10fdb215 --- /dev/null +++ b/easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20170420-R1-intel-2016b.eb @@ -0,0 +1,38 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2017 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, +# Ghent University / The Francis Crick Institute +# +# Authors:: +# * Kenneth Hoste +# * Ward Poelmans +# * Oliver Stueker +# License:: MIT/GPL +## +name = 'GAMESS-US' +version = '20170420-R1' + +homepage = 'http://www.msg.chem.iastate.edu/gamess/index.html' +description = """ The General Atomic and Molecular Electronic Structure System (GAMESS) + is a general ab initio quantum chemistry package. """ + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'usempi': True} + +# manually download via http://www.msg.chem.iastate.edu/gamess/download.html (requires registration) +# rename gamess-current.tar.gz by changing 'current' to the proper version +sources = ['gamess-%(version)s.tar.gz'] +checksums = ['e9fa2e725ccbd69f4d996ab68bb65ff2'] + +patches = [ + 'GAMESS-US_rungms-slurm.patch', + 'GAMESS-US-20170420-R1_rungms_fix_PPN_not_initialized.patch', +] + +# increase these numbers if your system is bigger in terms of cores-per-node or number of nodes +# it's OK if these values are larger than what your system provides +maxcpus = '1000' +maxnodes = '100000' + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20170420-R1_recent-gcc.patch b/easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20170420-R1_recent-gcc.patch new file mode 100644 index 0000000000..3287498882 --- /dev/null +++ b/easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20170420-R1_recent-gcc.patch @@ -0,0 +1,52 @@ +--- config.orig 2017-07-18 19:34:32.056678893 +0000 ++++ config 2017-07-18 19:48:37.701737302 +0000 +@@ -410,6 +410,7 @@ + case 5.1: + case 5.2: + case 5.3: ++ case 5.4: + echo " Good, the newest gfortrans can compile REAL*16 data type." + breaksw + default: +@@ -810,6 +811,7 @@ + case 5.1: + case 5.2: + case 5.3: ++ case 5.4: + echo " Good, the newest gfortrans can compile REAL*16 data type." + breaksw + default: +--- comp.orig 2017-07-19 11:55:05.490262037 +0000 ++++ comp 2017-07-19 11:52:47.986565565 +0000 +@@ -1593,6 +1593,7 @@ + case 5.1: + case 5.2: + case 5.3: ++ case 5.4: + if ($MODULE == cosmo) set OPT='-O0' + if ($MODULE == dcscf) set OPT='-O0' + if ($MODULE == tddgrd) set OPT='-O0' +@@ -1823,6 +1824,7 @@ + case 5.1: + case 5.2: + case 5.3: ++ case 5.4: + if ($MODULE == cosmo) set OPT='-O0' # same issue as seen in 4.6 + if ($MODULE == dcscf) set OPT='-O0' # exam44, continues from 4.7 + if ($MODULE == tddgrd) set OPT='-O0' # exam41, continues from 4.6 +@@ -2074,6 +2076,7 @@ + case 5.1: + case 5.2: + case 5.3: ++ case 5.4: + if ($MODULE == cosmo) set OPT='-O0' + if ($MODULE == dcscf) set OPT='-O0' + if ($MODULE == tddgrd) set OPT='-O0' +@@ -2191,6 +2194,7 @@ + case 5.1: + case 5.2: + case 5.3: ++ case 5.4: + if ($MODULE == cosmo) set OPT='-O0' + if ($MODULE == dcscf) set OPT='-O0' + if ($MODULE == tddgrd) set OPT='-O0' diff --git a/easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20170420-R1_rungms_fix_PPN_not_initialized.patch b/easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20170420-R1_rungms_fix_PPN_not_initialized.patch new file mode 100644 index 0000000000..0e6126bbf3 --- /dev/null +++ b/easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20170420-R1_rungms_fix_PPN_not_initialized.patch @@ -0,0 +1,10 @@ +--- rungms.orig 2017-07-19 16:53:29.325530604 +0000 ++++ rungms 2017-07-19 16:55:39.627358245 +0000 +@@ -538,6 +538,7 @@ + # all nodes are presumed to have equal numbers of cores. + # + set PPN=$4 ++ if (null$PPN == null) set PPN=1 # make sure PPN is initialized + # + # Allow for compute process and data servers (one pair per core) + # note that NCPUS = #cores, and NPROCS = #MPI processes -- GitLab From 56179a8e735a06a8dc9af0d06d683a4ac8f971d8 Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Wed, 19 Jul 2017 18:47:59 -0500 Subject: [PATCH 1207/1603] adding easyconfigs: SQLite-3.19.3-GCCcore-6.4.0.eb --- .../s/SQLite/SQLite-3.19.3-GCCcore-6.4.0.eb | 49 +++++++++++++++++++ .../t/Tcl/Tcl-8.6.6-GCCcore-6.4.0.eb | 42 ++++++++++++++++ 2 files changed, 91 insertions(+) create mode 100644 easybuild/easyconfigs/s/SQLite/SQLite-3.19.3-GCCcore-6.4.0.eb create mode 100644 easybuild/easyconfigs/t/Tcl/Tcl-8.6.6-GCCcore-6.4.0.eb diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.19.3-GCCcore-6.4.0.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.19.3-GCCcore-6.4.0.eb new file mode 100644 index 0000000000..9d9a1ef2eb --- /dev/null +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.19.3-GCCcore-6.4.0.eb @@ -0,0 +1,49 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the +# policy: http://hpcbios.readthedocs.org/en/latest/ +## + +easyblock = 'ConfigureMake' + +name = 'SQLite' +version = '3.19.3' + +homepage = 'http://www.sqlite.org/' + +description = 'SQLite: SQL Database Engine in a C Library' + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} +toolchainopts = {'pic': True} + +# eg. http://www.sqlite.org/2017/sqlite-autoconf-3190300.tar.gz +source_urls = ['http://www.sqlite.org/2017/'] +version_str = '%%(version_major)s%s00' % ''.join('%02d' % + int(x) for x in version.split('.')[1:]) +sources = ['sqlite-autoconf-%s.tar.gz' % version_str] +checksums = ['06129c03dced9f87733a8cba408871bd60673b8f93b920ba8d815efab0a06301'] + +builddependencies = [ + ('binutils', '2.28'), +] + +dependencies = [ + ('libreadline', '7.0'), + ('Tcl', '8.6.6'), +] + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', + 'lib/libsqlite3.a', 'lib/libsqlite3.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.6-GCCcore-6.4.0.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.6-GCCcore-6.4.0.eb new file mode 100644 index 0000000000..cffeed4270 --- /dev/null +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.6-GCCcore-6.4.0.eb @@ -0,0 +1,42 @@ +easyblock = 'ConfigureMake' + +name = 'Tcl' +version = '8.6.6' + +homepage = 'http://www.tcl.tk/' + +description = """ + Tcl (Tool Command Language) is a very powerful but easy to learn dynamic + programming language, suitable for a very wide range of uses, including web + and desktop applications, networking, administration, testing and many more. +""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] +checksums = ['a265409781e4b3edcc4ef822533071b34c3dc6790b893963809b9fe221befe07'] + +builddependencies = [ + ('binutils', '2.28'), +] + +dependencies = [ + ('zlib', '1.2.11'), +] + +configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' + +runtest = 'test' + +start_dir = 'unix' + +sanity_check_paths = { + 'files': ['bin/tclsh%(version_major)s.%(version_minor)s', 'include/tcl.h', + 'lib/libtcl%%(version_major)s.%%(version_minor)s.%s' % SHLIB_EXT, + 'lib/tclConfig.sh', 'man/man1/tclsh.1'], + 'dirs': ['share'], +} + + +moduleclass = 'lang' -- GitLab From 34014ba01b2606d1dd77782c9f5d426cccfca08f Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Wed, 19 Jul 2017 19:37:20 -0500 Subject: [PATCH 1208/1603] adding easyconfigs: PyYAML-3.12-GCCcore-6.4.0-Python-2.7.13-bare.eb --- .../l/libyaml/libyaml-0.1.6-GCCcore-6.4.0.eb | 34 ++++++++++++ ...L-3.12-GCCcore-6.4.0-Python-2.7.13-bare.eb | 38 +++++++++++++ .../Python-2.7.13-GCCcore-6.4.0-bare.eb | 53 +++++++++++++++++++ .../s/SQLite/SQLite-3.19.3-GCCcore-6.4.0.eb | 49 +++++++++++++++++ .../t/Tcl/Tcl-8.6.6-GCCcore-6.4.0.eb | 42 +++++++++++++++ 5 files changed, 216 insertions(+) create mode 100644 easybuild/easyconfigs/l/libyaml/libyaml-0.1.6-GCCcore-6.4.0.eb create mode 100644 easybuild/easyconfigs/p/PyYAML/PyYAML-3.12-GCCcore-6.4.0-Python-2.7.13-bare.eb create mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.13-GCCcore-6.4.0-bare.eb create mode 100644 easybuild/easyconfigs/s/SQLite/SQLite-3.19.3-GCCcore-6.4.0.eb create mode 100644 easybuild/easyconfigs/t/Tcl/Tcl-8.6.6-GCCcore-6.4.0.eb diff --git a/easybuild/easyconfigs/l/libyaml/libyaml-0.1.6-GCCcore-6.4.0.eb b/easybuild/easyconfigs/l/libyaml/libyaml-0.1.6-GCCcore-6.4.0.eb new file mode 100644 index 0000000000..156fcf6ef5 --- /dev/null +++ b/easybuild/easyconfigs/l/libyaml/libyaml-0.1.6-GCCcore-6.4.0.eb @@ -0,0 +1,34 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Nils Christian +# License:: MIT/GPL +# $Id$ +## + +easyblock = 'ConfigureMake' + +name = 'libyaml' +version = '0.1.6' + +homepage = 'http://pyyaml.org/wiki/LibYAML' + +description = """LibYAML is a YAML parser and emitter written in C.""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} + +source_urls = ['http://pyyaml.org/download/libyaml/'] +sources = ['yaml-%(version)s.tar.gz'] +checksums = ['7da6971b4bd08a986dd2a61353bc422362bd0edcc67d7ebaac68c95f74182749'] + +builddependencies = [ + ('binutils', '2.28'), +] + +sanity_check_paths = { + 'files': ["include/yaml.h", "lib/libyaml.a", "lib/libyaml.%s" % SHLIB_EXT], + 'dirs': ["lib/pkgconfig"] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12-GCCcore-6.4.0-Python-2.7.13-bare.eb b/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12-GCCcore-6.4.0-Python-2.7.13-bare.eb new file mode 100644 index 0000000000..eb4c534d26 --- /dev/null +++ b/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12-GCCcore-6.4.0-Python-2.7.13-bare.eb @@ -0,0 +1,38 @@ +easyblock = 'PythonPackage' + +name = 'PyYAML' +version = '3.12' +pyver = '2.7.13' +pyshortver = '2.7' +pysubver = '-bare' +versionsuffix = '-Python-%s%s' % (pyver, pysubver) + +homepage = 'https://pypi.python.org/pypi/PyYAML/' + +description = """ + PyYAML is a YAML parser and emitter for the Python programming language. +""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['592766c6303207a20efc445587778322d7f73b161bd994f227adaa341ba212ab'] + +builddependencies = [ + ('binutils', '2.28'), + ('Python', pyver, pysubver), +] + +dependencies = [ + ('libyaml', '0.1.6'), +] + +options = {'modulename': 'yaml'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages' % pyshortver], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.13-GCCcore-6.4.0-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.13-GCCcore-6.4.0-bare.eb new file mode 100644 index 0000000000..42f2730022 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.13-GCCcore-6.4.0-bare.eb @@ -0,0 +1,53 @@ +name = 'Python' +version = '2.7.13' +versionsuffix = '-bare' + +homepage = 'http://python.org/' + +description = """ + Python is a programming language that lets you work more quickly and + integrate your systems more effectively. + +Note: This module is meant to provide a builddependency for other Python + modules while using EasyBuild's --minimaltoolchain option. Modules + built with it will require the full Python later +""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +builddependencies = [ + ('binutils', '2.28'), +] + +dependencies = [ + ('bzip2', '1.0.6'), + ('libreadline', '7.0'), + ('ncurses', '6.0'), + ('SQLite', '3.19.3'), + ('zlib', '1.2.11'), +] + +osdependencies = [ + # rely upon distribution for timely security updates + ('openssl-devel', 'libssl-dev', 'libopenssl-devel'), +] + +# We hide this by default since users should not use it in production, +# high-performance Python should be delivered at compiler level with +# a default extension set +#hidden = True + +# bare installation: only known module deps for GCCcore tools included +exts_list = [] + +# Until such time that EasyBuild accepts 'rpath' as a toolchainopt... +# add RPATH so this can be as a builddependency later +prebuildopts = """ + sed -e 's:Modules/python.o \\\\:-Wl,-rpath=%(installdir)s/lib Modules/python.o \\\\:' -i.eb Makefile +""" + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.19.3-GCCcore-6.4.0.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.19.3-GCCcore-6.4.0.eb new file mode 100644 index 0000000000..9d9a1ef2eb --- /dev/null +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.19.3-GCCcore-6.4.0.eb @@ -0,0 +1,49 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the +# policy: http://hpcbios.readthedocs.org/en/latest/ +## + +easyblock = 'ConfigureMake' + +name = 'SQLite' +version = '3.19.3' + +homepage = 'http://www.sqlite.org/' + +description = 'SQLite: SQL Database Engine in a C Library' + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} +toolchainopts = {'pic': True} + +# eg. http://www.sqlite.org/2017/sqlite-autoconf-3190300.tar.gz +source_urls = ['http://www.sqlite.org/2017/'] +version_str = '%%(version_major)s%s00' % ''.join('%02d' % + int(x) for x in version.split('.')[1:]) +sources = ['sqlite-autoconf-%s.tar.gz' % version_str] +checksums = ['06129c03dced9f87733a8cba408871bd60673b8f93b920ba8d815efab0a06301'] + +builddependencies = [ + ('binutils', '2.28'), +] + +dependencies = [ + ('libreadline', '7.0'), + ('Tcl', '8.6.6'), +] + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', + 'lib/libsqlite3.a', 'lib/libsqlite3.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.6-GCCcore-6.4.0.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.6-GCCcore-6.4.0.eb new file mode 100644 index 0000000000..cffeed4270 --- /dev/null +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.6-GCCcore-6.4.0.eb @@ -0,0 +1,42 @@ +easyblock = 'ConfigureMake' + +name = 'Tcl' +version = '8.6.6' + +homepage = 'http://www.tcl.tk/' + +description = """ + Tcl (Tool Command Language) is a very powerful but easy to learn dynamic + programming language, suitable for a very wide range of uses, including web + and desktop applications, networking, administration, testing and many more. +""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] +checksums = ['a265409781e4b3edcc4ef822533071b34c3dc6790b893963809b9fe221befe07'] + +builddependencies = [ + ('binutils', '2.28'), +] + +dependencies = [ + ('zlib', '1.2.11'), +] + +configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' + +runtest = 'test' + +start_dir = 'unix' + +sanity_check_paths = { + 'files': ['bin/tclsh%(version_major)s.%(version_minor)s', 'include/tcl.h', + 'lib/libtcl%%(version_major)s.%%(version_minor)s.%s' % SHLIB_EXT, + 'lib/tclConfig.sh', 'man/man1/tclsh.1'], + 'dirs': ['share'], +} + + +moduleclass = 'lang' -- GitLab From afd8369b9930976bfe3178f5f15bfdfa64ab4bed Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Wed, 19 Jul 2017 19:54:41 -0500 Subject: [PATCH 1209/1603] adding easyconfigs: setuptools-36.2.0-GCCcore-6.4.0-Python-2.7.13-bare.eb --- .../Python-2.7.13-GCCcore-6.4.0-bare.eb | 53 +++++++++++++++++++ .../s/SQLite/SQLite-3.19.3-GCCcore-6.4.0.eb | 49 +++++++++++++++++ ...36.2.0-GCCcore-6.4.0-Python-2.7.13-bare.eb | 32 +++++++++++ .../t/Tcl/Tcl-8.6.6-GCCcore-6.4.0.eb | 42 +++++++++++++++ 4 files changed, 176 insertions(+) create mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.13-GCCcore-6.4.0-bare.eb create mode 100644 easybuild/easyconfigs/s/SQLite/SQLite-3.19.3-GCCcore-6.4.0.eb create mode 100644 easybuild/easyconfigs/s/setuptools/setuptools-36.2.0-GCCcore-6.4.0-Python-2.7.13-bare.eb create mode 100644 easybuild/easyconfigs/t/Tcl/Tcl-8.6.6-GCCcore-6.4.0.eb diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.13-GCCcore-6.4.0-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.13-GCCcore-6.4.0-bare.eb new file mode 100644 index 0000000000..42f2730022 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.13-GCCcore-6.4.0-bare.eb @@ -0,0 +1,53 @@ +name = 'Python' +version = '2.7.13' +versionsuffix = '-bare' + +homepage = 'http://python.org/' + +description = """ + Python is a programming language that lets you work more quickly and + integrate your systems more effectively. + +Note: This module is meant to provide a builddependency for other Python + modules while using EasyBuild's --minimaltoolchain option. Modules + built with it will require the full Python later +""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +builddependencies = [ + ('binutils', '2.28'), +] + +dependencies = [ + ('bzip2', '1.0.6'), + ('libreadline', '7.0'), + ('ncurses', '6.0'), + ('SQLite', '3.19.3'), + ('zlib', '1.2.11'), +] + +osdependencies = [ + # rely upon distribution for timely security updates + ('openssl-devel', 'libssl-dev', 'libopenssl-devel'), +] + +# We hide this by default since users should not use it in production, +# high-performance Python should be delivered at compiler level with +# a default extension set +#hidden = True + +# bare installation: only known module deps for GCCcore tools included +exts_list = [] + +# Until such time that EasyBuild accepts 'rpath' as a toolchainopt... +# add RPATH so this can be as a builddependency later +prebuildopts = """ + sed -e 's:Modules/python.o \\\\:-Wl,-rpath=%(installdir)s/lib Modules/python.o \\\\:' -i.eb Makefile +""" + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.19.3-GCCcore-6.4.0.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.19.3-GCCcore-6.4.0.eb new file mode 100644 index 0000000000..9d9a1ef2eb --- /dev/null +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.19.3-GCCcore-6.4.0.eb @@ -0,0 +1,49 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the +# policy: http://hpcbios.readthedocs.org/en/latest/ +## + +easyblock = 'ConfigureMake' + +name = 'SQLite' +version = '3.19.3' + +homepage = 'http://www.sqlite.org/' + +description = 'SQLite: SQL Database Engine in a C Library' + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} +toolchainopts = {'pic': True} + +# eg. http://www.sqlite.org/2017/sqlite-autoconf-3190300.tar.gz +source_urls = ['http://www.sqlite.org/2017/'] +version_str = '%%(version_major)s%s00' % ''.join('%02d' % + int(x) for x in version.split('.')[1:]) +sources = ['sqlite-autoconf-%s.tar.gz' % version_str] +checksums = ['06129c03dced9f87733a8cba408871bd60673b8f93b920ba8d815efab0a06301'] + +builddependencies = [ + ('binutils', '2.28'), +] + +dependencies = [ + ('libreadline', '7.0'), + ('Tcl', '8.6.6'), +] + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', + 'lib/libsqlite3.a', 'lib/libsqlite3.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/setuptools/setuptools-36.2.0-GCCcore-6.4.0-Python-2.7.13-bare.eb b/easybuild/easyconfigs/s/setuptools/setuptools-36.2.0-GCCcore-6.4.0-Python-2.7.13-bare.eb new file mode 100644 index 0000000000..6c0e83e5dc --- /dev/null +++ b/easybuild/easyconfigs/s/setuptools/setuptools-36.2.0-GCCcore-6.4.0-Python-2.7.13-bare.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonPackage' + +name = 'setuptools' +version = '36.2.0' +pyver = '2.7.13' +pyshortver = '2.7' +pysubver = '-bare' +versionsuffix = '-Python-%s%s' % (pyver, pysubver) + +homepage = 'http://pypi.python.org/pypi/setuptools/' + +description = """ + Download, build, install, upgrade, and uninstall Python packages -- easily! +""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_ZIP] + +builddependencies = [ + ('Python', pyver, pysubver), +] + +pylibdir = "lib/python%s/site-packages/%s" % (pyshortver, name) +sanity_check_paths = { + 'files': ["bin/easy_install", "%s-%s-py%s.egg" % + (pylibdir, version, pyshortver)], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.6-GCCcore-6.4.0.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.6-GCCcore-6.4.0.eb new file mode 100644 index 0000000000..cffeed4270 --- /dev/null +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.6-GCCcore-6.4.0.eb @@ -0,0 +1,42 @@ +easyblock = 'ConfigureMake' + +name = 'Tcl' +version = '8.6.6' + +homepage = 'http://www.tcl.tk/' + +description = """ + Tcl (Tool Command Language) is a very powerful but easy to learn dynamic + programming language, suitable for a very wide range of uses, including web + and desktop applications, networking, administration, testing and many more. +""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] +checksums = ['a265409781e4b3edcc4ef822533071b34c3dc6790b893963809b9fe221befe07'] + +builddependencies = [ + ('binutils', '2.28'), +] + +dependencies = [ + ('zlib', '1.2.11'), +] + +configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' + +runtest = 'test' + +start_dir = 'unix' + +sanity_check_paths = { + 'files': ['bin/tclsh%(version_major)s.%(version_minor)s', 'include/tcl.h', + 'lib/libtcl%%(version_major)s.%%(version_minor)s.%s' % SHLIB_EXT, + 'lib/tclConfig.sh', 'man/man1/tclsh.1'], + 'dirs': ['share'], +} + + +moduleclass = 'lang' -- GitLab From cc31c73e147ea9d13d35ab0af9080bae73301a33 Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Wed, 19 Jul 2017 20:04:10 -0500 Subject: [PATCH 1210/1603] add checksum --- .../setuptools-36.2.0-GCCcore-6.4.0-Python-2.7.13-bare.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/s/setuptools/setuptools-36.2.0-GCCcore-6.4.0-Python-2.7.13-bare.eb b/easybuild/easyconfigs/s/setuptools/setuptools-36.2.0-GCCcore-6.4.0-Python-2.7.13-bare.eb index 6c0e83e5dc..9b5a4054e1 100644 --- a/easybuild/easyconfigs/s/setuptools/setuptools-36.2.0-GCCcore-6.4.0-Python-2.7.13-bare.eb +++ b/easybuild/easyconfigs/s/setuptools/setuptools-36.2.0-GCCcore-6.4.0-Python-2.7.13-bare.eb @@ -17,6 +17,7 @@ toolchain = {'name': 'GCCcore', 'version': '6.4.0'} source_urls = [PYPI_SOURCE] sources = [SOURCE_ZIP] +checksums = ['4c2bda3829c9dbbe9c2b33d89c4b1cb6d45813615ab8e248ad352e3697a96d81'] builddependencies = [ ('Python', pyver, pysubver), -- GitLab From d8d78be361b0d88101593befe669901993a6c468 Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Wed, 19 Jul 2017 20:20:27 -0500 Subject: [PATCH 1211/1603] adding easyconfigs: six-1.10.0-GCCcore-6.4.0-Python-2.7.13-bare.eb --- .../Python-2.7.13-GCCcore-6.4.0-bare.eb | 53 +++++++++++++++++++ .../s/SQLite/SQLite-3.19.3-GCCcore-6.4.0.eb | 49 +++++++++++++++++ ...1.10.0-GCCcore-6.4.0-Python-2.7.13-bare.eb | 31 +++++++++++ .../t/Tcl/Tcl-8.6.6-GCCcore-6.4.0.eb | 42 +++++++++++++++ 4 files changed, 175 insertions(+) create mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.13-GCCcore-6.4.0-bare.eb create mode 100644 easybuild/easyconfigs/s/SQLite/SQLite-3.19.3-GCCcore-6.4.0.eb create mode 100644 easybuild/easyconfigs/s/six/six-1.10.0-GCCcore-6.4.0-Python-2.7.13-bare.eb create mode 100644 easybuild/easyconfigs/t/Tcl/Tcl-8.6.6-GCCcore-6.4.0.eb diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.13-GCCcore-6.4.0-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.13-GCCcore-6.4.0-bare.eb new file mode 100644 index 0000000000..42f2730022 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.13-GCCcore-6.4.0-bare.eb @@ -0,0 +1,53 @@ +name = 'Python' +version = '2.7.13' +versionsuffix = '-bare' + +homepage = 'http://python.org/' + +description = """ + Python is a programming language that lets you work more quickly and + integrate your systems more effectively. + +Note: This module is meant to provide a builddependency for other Python + modules while using EasyBuild's --minimaltoolchain option. Modules + built with it will require the full Python later +""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +builddependencies = [ + ('binutils', '2.28'), +] + +dependencies = [ + ('bzip2', '1.0.6'), + ('libreadline', '7.0'), + ('ncurses', '6.0'), + ('SQLite', '3.19.3'), + ('zlib', '1.2.11'), +] + +osdependencies = [ + # rely upon distribution for timely security updates + ('openssl-devel', 'libssl-dev', 'libopenssl-devel'), +] + +# We hide this by default since users should not use it in production, +# high-performance Python should be delivered at compiler level with +# a default extension set +#hidden = True + +# bare installation: only known module deps for GCCcore tools included +exts_list = [] + +# Until such time that EasyBuild accepts 'rpath' as a toolchainopt... +# add RPATH so this can be as a builddependency later +prebuildopts = """ + sed -e 's:Modules/python.o \\\\:-Wl,-rpath=%(installdir)s/lib Modules/python.o \\\\:' -i.eb Makefile +""" + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.19.3-GCCcore-6.4.0.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.19.3-GCCcore-6.4.0.eb new file mode 100644 index 0000000000..9d9a1ef2eb --- /dev/null +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.19.3-GCCcore-6.4.0.eb @@ -0,0 +1,49 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the +# policy: http://hpcbios.readthedocs.org/en/latest/ +## + +easyblock = 'ConfigureMake' + +name = 'SQLite' +version = '3.19.3' + +homepage = 'http://www.sqlite.org/' + +description = 'SQLite: SQL Database Engine in a C Library' + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} +toolchainopts = {'pic': True} + +# eg. http://www.sqlite.org/2017/sqlite-autoconf-3190300.tar.gz +source_urls = ['http://www.sqlite.org/2017/'] +version_str = '%%(version_major)s%s00' % ''.join('%02d' % + int(x) for x in version.split('.')[1:]) +sources = ['sqlite-autoconf-%s.tar.gz' % version_str] +checksums = ['06129c03dced9f87733a8cba408871bd60673b8f93b920ba8d815efab0a06301'] + +builddependencies = [ + ('binutils', '2.28'), +] + +dependencies = [ + ('libreadline', '7.0'), + ('Tcl', '8.6.6'), +] + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', + 'lib/libsqlite3.a', 'lib/libsqlite3.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/six/six-1.10.0-GCCcore-6.4.0-Python-2.7.13-bare.eb b/easybuild/easyconfigs/s/six/six-1.10.0-GCCcore-6.4.0-Python-2.7.13-bare.eb new file mode 100644 index 0000000000..f5345426c3 --- /dev/null +++ b/easybuild/easyconfigs/s/six/six-1.10.0-GCCcore-6.4.0-Python-2.7.13-bare.eb @@ -0,0 +1,31 @@ +# Author:: Jack Perdue - TAMU HPRC - http://sc.tamu.edu + +easyblock = 'PythonPackage' + +name = 'six' +version = '1.10.0' +pyver = '2.7.13' +pyshortver = '2.7' +pysubver = '-bare' +versionsuffix = '-Python-%s%s' % (pyver, pysubver) + +homepage = 'https://pypi.python.org/pypi/six/1.10.0' + +description = "Python 2 and 3 compatibility utilities" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} + +sources = [SOURCE_TAR_GZ] +source_urls = [PYPI_LOWER_SOURCE] +checksums = ['105f8d68616f8248e24bf0e9372ef04d3cc10104f1980f54d57b2ce73a5ad56a'] + +builddependencies = [ + ('Python', pyver, pysubver), +] + +sanity_check_paths = { + 'files': ['lib/python%s/site-packages/%%(name)s.py' % pyshortver], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.6-GCCcore-6.4.0.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.6-GCCcore-6.4.0.eb new file mode 100644 index 0000000000..cffeed4270 --- /dev/null +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.6-GCCcore-6.4.0.eb @@ -0,0 +1,42 @@ +easyblock = 'ConfigureMake' + +name = 'Tcl' +version = '8.6.6' + +homepage = 'http://www.tcl.tk/' + +description = """ + Tcl (Tool Command Language) is a very powerful but easy to learn dynamic + programming language, suitable for a very wide range of uses, including web + and desktop applications, networking, administration, testing and many more. +""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] +checksums = ['a265409781e4b3edcc4ef822533071b34c3dc6790b893963809b9fe221befe07'] + +builddependencies = [ + ('binutils', '2.28'), +] + +dependencies = [ + ('zlib', '1.2.11'), +] + +configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' + +runtest = 'test' + +start_dir = 'unix' + +sanity_check_paths = { + 'files': ['bin/tclsh%(version_major)s.%(version_minor)s', 'include/tcl.h', + 'lib/libtcl%%(version_major)s.%%(version_minor)s.%s' % SHLIB_EXT, + 'lib/tclConfig.sh', 'man/man1/tclsh.1'], + 'dirs': ['share'], +} + + +moduleclass = 'lang' -- GitLab From 189003600e9f8ae77a05fbb0c471d0178fce96a5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Thu, 20 Jul 2017 14:15:59 +0200 Subject: [PATCH 1212/1603] Add attributions --- .../easyconfigs/b/Bowtie2/Bowtie2-2.3.2-foss-2016b.eb | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.3.2-foss-2016b.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.3.2-foss-2016b.eb index 03a5dea73d..bea5f1dfd7 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.3.2-foss-2016b.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.3.2-foss-2016b.eb @@ -1,4 +1,13 @@ # This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# Modified by: Robert Schmidt +# Ottawa Hospital Research Institute - Bioinformatics Team +# Modified by: Adam Huffman +# The Francis Crick Institute +# Modified by: Kurt Lust, UAntwerp +# Modified by: Paul Jähne name = 'Bowtie2' version = '2.3.2' -- GitLab From 8345476b3737f24120a99075def0b85bcbabc516 Mon Sep 17 00:00:00 2001 From: Oliver Stueker Date: Thu, 20 Jul 2017 11:13:07 -0230 Subject: [PATCH 1213/1603] GAMESS-US add versionsuffix to pass styletests --- .../g/GAMESS-US/GAMESS-US-20170420-R1-intel-2016b-sockets.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20170420-R1-intel-2016b-sockets.eb b/easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20170420-R1-intel-2016b-sockets.eb index d2d82e8fab..756354fcc7 100644 --- a/easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20170420-R1-intel-2016b-sockets.eb +++ b/easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20170420-R1-intel-2016b-sockets.eb @@ -12,6 +12,7 @@ ## name = 'GAMESS-US' version = '20170420-R1' +versionsuffix = '-sockets' homepage = 'http://www.msg.chem.iastate.edu/gamess/index.html' description = """ The General Atomic and Molecular Electronic Structure System (GAMESS) -- GitLab From 8399263869d34a464185fd3a09c183138f89204c Mon Sep 17 00:00:00 2001 From: Oliver Stueker Date: Thu, 20 Jul 2017 11:29:38 -0230 Subject: [PATCH 1214/1603] GAMESS-US minor style fixes --- .../g/GAMESS-US/GAMESS-US-20170420-R1-foss-2016b.eb | 6 +++--- .../GAMESS-US/GAMESS-US-20170420-R1-intel-2016b-sockets.eb | 4 ++-- .../g/GAMESS-US/GAMESS-US-20170420-R1-intel-2016b.eb | 4 ++-- 3 files changed, 7 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20170420-R1-foss-2016b.eb b/easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20170420-R1-foss-2016b.eb index a18cd469bd..3d445caa7f 100644 --- a/easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20170420-R1-foss-2016b.eb +++ b/easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20170420-R1-foss-2016b.eb @@ -26,9 +26,9 @@ sources = ['gamess-%(version)s.tar.gz'] checksums = ['e9fa2e725ccbd69f4d996ab68bb65ff2'] patches = [ - 'GAMESS-US_rungms-slurm.patch', - 'GAMESS-US-20170420-R1_rungms_fix_PPN_not_initialized.patch', - 'GAMESS-US-20170420-R1_recent-gcc.patch', + 'GAMESS-US_rungms-slurm.patch', + 'GAMESS-US-20170420-R1_rungms_fix_PPN_not_initialized.patch', + 'GAMESS-US-20170420-R1_recent-gcc.patch', ] # increase these numbers if your system is bigger in terms of cores-per-node or number of nodes diff --git a/easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20170420-R1-intel-2016b-sockets.eb b/easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20170420-R1-intel-2016b-sockets.eb index 756354fcc7..f227f1556e 100644 --- a/easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20170420-R1-intel-2016b-sockets.eb +++ b/easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20170420-R1-intel-2016b-sockets.eb @@ -28,8 +28,8 @@ sources = ['gamess-%(version)s.tar.gz'] checksums = ['e9fa2e725ccbd69f4d996ab68bb65ff2'] patches = [ - 'GAMESS-US_rungms-slurm.patch', - 'GAMESS-US-20170420-R1_rungms_fix_PPN_not_initialized.patch', + 'GAMESS-US_rungms-slurm.patch', + 'GAMESS-US-20170420-R1_rungms_fix_PPN_not_initialized.patch', ] # increase these numbers if your system is bigger in terms of cores-per-node or number of nodes diff --git a/easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20170420-R1-intel-2016b.eb b/easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20170420-R1-intel-2016b.eb index 7a10fdb215..5a67a77274 100644 --- a/easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20170420-R1-intel-2016b.eb +++ b/easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20170420-R1-intel-2016b.eb @@ -26,8 +26,8 @@ sources = ['gamess-%(version)s.tar.gz'] checksums = ['e9fa2e725ccbd69f4d996ab68bb65ff2'] patches = [ - 'GAMESS-US_rungms-slurm.patch', - 'GAMESS-US-20170420-R1_rungms_fix_PPN_not_initialized.patch', + 'GAMESS-US_rungms-slurm.patch', + 'GAMESS-US-20170420-R1_rungms_fix_PPN_not_initialized.patch', ] # increase these numbers if your system is bigger in terms of cores-per-node or number of nodes -- GitLab From 94f225009eae9ac4471852c4e701ba93bb79b29e Mon Sep 17 00:00:00 2001 From: Pol Llovet Date: Thu, 20 Jul 2017 09:56:02 -0600 Subject: [PATCH 1215/1603] Updating deprecated PLINK urls --- easybuild/easyconfigs/p/PLINK/PLINK-1.07-foss-2015b.eb | 4 ++-- easybuild/easyconfigs/p/PLINK/PLINK-1.07-foss-2016a.eb | 4 ++-- easybuild/easyconfigs/p/PLINK/PLINK-1.07-foss-2016b.eb | 4 ++-- easybuild/easyconfigs/p/PLINK/PLINK-1.07-ictce-5.3.0.eb | 4 ++-- easybuild/easyconfigs/p/PLINK/PLINK-1.07-ictce-6.2.5.eb | 4 ++-- 5 files changed, 10 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/p/PLINK/PLINK-1.07-foss-2015b.eb b/easybuild/easyconfigs/p/PLINK/PLINK-1.07-foss-2015b.eb index 7d60edd787..f172624a26 100644 --- a/easybuild/easyconfigs/p/PLINK/PLINK-1.07-foss-2015b.eb +++ b/easybuild/easyconfigs/p/PLINK/PLINK-1.07-foss-2015b.eb @@ -10,7 +10,7 @@ easyblock = 'MakeCp' name = 'PLINK' version = '1.07' -homepage = 'http://pngu.mgh.harvard.edu/~purcell/plink/' +homepage = 'http://zzz.bwh.harvard.edu/plink/' description = """ PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. The focus of PLINK is purely on analysis of genotype/phenotype data, so there is no support for @@ -22,7 +22,7 @@ toolchain = {'name': 'foss', 'version': '2015b'} toolchainopts = {'openmp': True} sources = ['%(namelower)s-%(version)s-src.zip'] -source_urls = ['http://pngu.mgh.harvard.edu/~purcell/plink/dist/'] +source_urls = ['http://zzz.bwh.harvard.edu/plink/dist/'] patches = ['PLINK-1.07_redeclaration.patch'] diff --git a/easybuild/easyconfigs/p/PLINK/PLINK-1.07-foss-2016a.eb b/easybuild/easyconfigs/p/PLINK/PLINK-1.07-foss-2016a.eb index 5b4efc33f6..08a47b6d0e 100644 --- a/easybuild/easyconfigs/p/PLINK/PLINK-1.07-foss-2016a.eb +++ b/easybuild/easyconfigs/p/PLINK/PLINK-1.07-foss-2016a.eb @@ -10,7 +10,7 @@ easyblock = 'MakeCp' name = 'PLINK' version = '1.07' -homepage = 'http://pngu.mgh.harvard.edu/~purcell/plink/' +homepage = 'http://zzz.bwh.harvard.edu/plink/' description = """ PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. The focus of PLINK is purely on analysis of genotype/phenotype data, so there is no support for @@ -22,7 +22,7 @@ toolchain = {'name': 'foss', 'version': '2016a'} toolchainopts = {'openmp': True} sources = ['%(namelower)s-%(version)s-src.zip'] -source_urls = ['http://pngu.mgh.harvard.edu/~purcell/plink/dist/'] +source_urls = ['http://zzz.bwh.harvard.edu/plink/dist/'] patches = ['PLINK-1.07_redeclaration.patch'] diff --git a/easybuild/easyconfigs/p/PLINK/PLINK-1.07-foss-2016b.eb b/easybuild/easyconfigs/p/PLINK/PLINK-1.07-foss-2016b.eb index 26b293a777..9782f91b1d 100644 --- a/easybuild/easyconfigs/p/PLINK/PLINK-1.07-foss-2016b.eb +++ b/easybuild/easyconfigs/p/PLINK/PLINK-1.07-foss-2016b.eb @@ -10,7 +10,7 @@ easyblock = 'MakeCp' name = 'PLINK' version = '1.07' -homepage = 'http://pngu.mgh.harvard.edu/~purcell/plink/' +homepage = 'http://zzz.bwh.harvard.edu/plink/' description = """ PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. The focus of PLINK is purely on analysis of genotype/phenotype data, so there is no support for @@ -22,7 +22,7 @@ toolchain = {'name': 'foss', 'version': '2016b'} toolchainopts = {'openmp': True} sources = ['%(namelower)s-%(version)s-src.zip'] -source_urls = ['http://pngu.mgh.harvard.edu/~purcell/plink/dist/'] +source_urls = ['hhttp://zzz.bwh.harvard.edu/plink/dist/'] patches = ['PLINK-1.07_redeclaration.patch'] diff --git a/easybuild/easyconfigs/p/PLINK/PLINK-1.07-ictce-5.3.0.eb b/easybuild/easyconfigs/p/PLINK/PLINK-1.07-ictce-5.3.0.eb index 1c0a984949..5a77a49bf9 100644 --- a/easybuild/easyconfigs/p/PLINK/PLINK-1.07-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/p/PLINK/PLINK-1.07-ictce-5.3.0.eb @@ -11,14 +11,14 @@ easyblock = 'MakeCp' name = 'PLINK' version = '1.07' -homepage = 'http://pngu.mgh.harvard.edu/~purcell/plink/' +homepage = 'http://zzz.bwh.harvard.edu/plink/' description = "plink-1.07-src: Whole-genome association analysis toolset" toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'openmp': True} sources = ['%(namelower)s-%(version)s-src.zip'] -source_urls = ['http://pngu.mgh.harvard.edu/~purcell/plink/dist/'] +source_urls = ['http://zzz.bwh.harvard.edu/plink/dist/'] dependencies = [('zlib', '1.2.7')] diff --git a/easybuild/easyconfigs/p/PLINK/PLINK-1.07-ictce-6.2.5.eb b/easybuild/easyconfigs/p/PLINK/PLINK-1.07-ictce-6.2.5.eb index c6adbf0428..8f4e1d77e1 100644 --- a/easybuild/easyconfigs/p/PLINK/PLINK-1.07-ictce-6.2.5.eb +++ b/easybuild/easyconfigs/p/PLINK/PLINK-1.07-ictce-6.2.5.eb @@ -8,7 +8,7 @@ easyblock = 'MakeCp' name = 'PLINK' version = '1.07' -homepage = 'http://pngu.mgh.harvard.edu/~purcell/plink/' +homepage = 'http://zzz.bwh.harvard.edu/plink/' description = """ PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. The focus of PLINK is purely on analysis of genotype/phenotype data, so there is no support for @@ -20,7 +20,7 @@ toolchain = {'name': 'ictce', 'version': '6.2.5'} toolchainopts = {'openmp': True} sources = ['%(namelower)s-%(version)s-src.zip'] -source_urls = ['http://pngu.mgh.harvard.edu/~purcell/plink/dist/'] +source_urls = ['http://zzz.bwh.harvard.edu/plink/dist/'] dependencies = [('zlib', '1.2.8')] -- GitLab From a94e3ea95cd8798022c02c3f88fea0ac74275d16 Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Thu, 20 Jul 2017 15:30:42 -0500 Subject: [PATCH 1216/1603] style fix --- easybuild/easyconfigs/s/SQLite/SQLite-3.19.3-GCCcore-6.4.0.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.19.3-GCCcore-6.4.0.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.19.3-GCCcore-6.4.0.eb index 9d9a1ef2eb..e10115f361 100644 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.19.3-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.19.3-GCCcore-6.4.0.eb @@ -24,8 +24,7 @@ toolchainopts = {'pic': True} # eg. http://www.sqlite.org/2017/sqlite-autoconf-3190300.tar.gz source_urls = ['http://www.sqlite.org/2017/'] -version_str = '%%(version_major)s%s00' % ''.join('%02d' % - int(x) for x in version.split('.')[1:]) +version_str = '%%(version_major)s%s00' % ''.join('%02d' % int(x) for x in version.split('.')[1:]) sources = ['sqlite-autoconf-%s.tar.gz' % version_str] checksums = ['06129c03dced9f87733a8cba408871bd60673b8f93b920ba8d815efab0a06301'] -- GitLab From fe6a3c30c2ce1d89566f02131620809e80725053 Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Thu, 20 Jul 2017 16:34:22 -0500 Subject: [PATCH 1217/1603] Delete libsigsegv-2.11-GCC-6.4.0-2.28.eb going with GCCcore for now --- .../libsigsegv-2.11-GCC-6.4.0-2.28.eb | 24 ------------------- 1 file changed, 24 deletions(-) delete mode 100644 easybuild/easyconfigs/l/libsigsegv/libsigsegv-2.11-GCC-6.4.0-2.28.eb diff --git a/easybuild/easyconfigs/l/libsigsegv/libsigsegv-2.11-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/l/libsigsegv/libsigsegv-2.11-GCC-6.4.0-2.28.eb deleted file mode 100644 index 716653df4c..0000000000 --- a/easybuild/easyconfigs/l/libsigsegv/libsigsegv-2.11-GCC-6.4.0-2.28.eb +++ /dev/null @@ -1,24 +0,0 @@ -# Authors:: Jack Perdue - TAMU HPRC - http://hprc.tamu.edu - -easyblock = 'ConfigureMake' - -name = 'libsigsegv' -version = '2.11' - -homepage = 'https://www.gnu.org/software/libsigsegv/' - -description = """ - GNU libsigsegv is a library for handling page faults in user mode. -""" - -toolchain = {'name': 'GCC', 'version': '6.4.0-2.28'} - -source_urls = [GNU_SOURCE] -sources = [SOURCELOWER_TAR_GZ] - -sanity_check_paths = { - 'files': ['include/sigsegv.h', 'lib/libsigsegv.a', 'lib/libsigsegv.la'], - 'dirs': [], -} - -moduleclass = 'lib' -- GitLab From 5005f6ce03899b84b16a7cb0cd5c945548162ac2 Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Thu, 20 Jul 2017 16:51:50 -0500 Subject: [PATCH 1218/1603] cleanup and checksum --- .../l/libsigsegv/libsigsegv-2.11-GCCcore-6.4.0.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/l/libsigsegv/libsigsegv-2.11-GCCcore-6.4.0.eb b/easybuild/easyconfigs/l/libsigsegv/libsigsegv-2.11-GCCcore-6.4.0.eb index 519b35b032..d65a11de5b 100644 --- a/easybuild/easyconfigs/l/libsigsegv/libsigsegv-2.11-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/l/libsigsegv/libsigsegv-2.11-GCCcore-6.4.0.eb @@ -7,14 +7,14 @@ version = '2.11' homepage = 'https://www.gnu.org/software/libsigsegv/' -description = """ - GNU libsigsegv is a library for handling page faults in user mode. -""" +description = "GNU libsigsegv is a library for handling page faults in user mode." toolchain = {'name': 'GCCcore', 'version': '6.4.0'} +toolchainopts = {'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] +checksums = ['dd7c2eb2ef6c47189406d562c1dc0f96f2fc808036834d596075d58377e37a18'] builddependencies = [ ('binutils', '2.28'), -- GitLab From 77fbf8e39cf718bd3a2a3612812a8e64c9784911 Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Fri, 21 Jul 2017 06:58:25 -0500 Subject: [PATCH 1219/1603] adding easyconfigs: BEDTools-2.26.0-GCCcore-6.4.0.eb --- .../BEDTools/BEDTools-2.26.0-GCCcore-6.4.0.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/b/BEDTools/BEDTools-2.26.0-GCCcore-6.4.0.eb diff --git a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.26.0-GCCcore-6.4.0.eb b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.26.0-GCCcore-6.4.0.eb new file mode 100644 index 0000000000..13cda05cc9 --- /dev/null +++ b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.26.0-GCCcore-6.4.0.eb @@ -0,0 +1,39 @@ +# Author: Maxime Schmitt, University of Luxembourg +# Author: Adam Huffman, The Francis Crick Institute +# +# Based on the work of: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics (SIB) +# Biozentrum - University of Basel + +easyblock = 'MakeCp' + +name = 'BEDTools' +version = '2.26.0' + +homepage = "https://github.com/arq5x/bedtools2" + +description = """ + The BEDTools utilities allow one to address common genomics tasks such as + finding feature overlaps and computing coverage. The utilities are largely + based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM. +""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} + +source_urls = ['https://github.com/arq5x/bedtools2/releases/download/v%(version)s/'] +sources = ['bedtools-%(version)s.tar.gz'] +checksums = ['65f32f32cbf1b91ba42854b40c604aa6a16c7d3b3ec110d6acf438eb22df0a4a'] + +builddependencies = [ + ('binutils', '2.28'), +] + +files_to_copy = ["bin", "docs", "data", "genomes", "scripts", "test"] + +sanity_check_paths = { + 'dirs': files_to_copy, + 'files': ['bin/%s' % x for x in + ['bedtools', 'pairToBed', 'mergeBed', 'bedToBam', 'fastaFromBed']], +} + +moduleclass = 'bio' -- GitLab From 2556099b3b4383a2b3a701191be143366e8b40c5 Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Fri, 21 Jul 2017 07:11:26 -0500 Subject: [PATCH 1220/1603] adding easyconfigs: Blitz++-0.10-GCCcore-6.4.0.eb --- .../b/Blitz++/Blitz++-0.10-GCCcore-6.4.0.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/b/Blitz++/Blitz++-0.10-GCCcore-6.4.0.eb diff --git a/easybuild/easyconfigs/b/Blitz++/Blitz++-0.10-GCCcore-6.4.0.eb b/easybuild/easyconfigs/b/Blitz++/Blitz++-0.10-GCCcore-6.4.0.eb new file mode 100644 index 0000000000..7789563ca5 --- /dev/null +++ b/easybuild/easyconfigs/b/Blitz++/Blitz++-0.10-GCCcore-6.4.0.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'Blitz++' +version = '0.10' + +homepage = 'http://blitz.sourceforge.net/' + +description = """ + Blitz++ is a (LGPLv3+) licensed meta-template library for array manipulation + in C++ with a speed comparable to Fortran implementations, while preserving an + object-oriented interface +""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} +toolchainopts = {'pic': True} + +source_urls = [('https://sourceforge.net/projects/blitz/files/blitz/%(name)s %(version)s', 'download')] +sources = ['blitz-%(version)s.tar.gz'] +checksums = ['804ef0e6911d43642a2ea1894e47c6007e4c185c866a7d68bad1e4c8ac4e6f94'] + +builddependencies = [ + ('binutils', '2.28'), +] + +configopts = '--enable-shared' + +sanity_check_paths = { + 'files': ['lib/libblitz.a'], + 'dirs': ['include/blitz/array', 'include/blitz/gnu', 'include/blitz/meta', + 'include/random', 'lib/pkgconfig'], +} + +moduleclass = 'lib' -- GitLab From 73f4b1698f0ef494a8e7d4139408a42a4d9471eb Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Fri, 21 Jul 2017 07:55:53 -0500 Subject: [PATCH 1221/1603] adding easyconfigs: CLISP-2.49-GCCcore-6.4.0.eb --- .../c/CLISP/CLISP-2.49-GCCcore-6.4.0.eb | 51 +++++++++++++++++++ 1 file changed, 51 insertions(+) create mode 100644 easybuild/easyconfigs/c/CLISP/CLISP-2.49-GCCcore-6.4.0.eb diff --git a/easybuild/easyconfigs/c/CLISP/CLISP-2.49-GCCcore-6.4.0.eb b/easybuild/easyconfigs/c/CLISP/CLISP-2.49-GCCcore-6.4.0.eb new file mode 100644 index 0000000000..d9d3d1bf33 --- /dev/null +++ b/easybuild/easyconfigs/c/CLISP/CLISP-2.49-GCCcore-6.4.0.eb @@ -0,0 +1,51 @@ +# Authors:: Jack Perdue - TAMU HPRC - http://hprc.tamu.edu + +easyblock = 'ConfigureMake' + +name = 'CLISP' +version = '2.49' + +homepage = 'http://www.clisp.org/' + +description = """ + Common Lisp is a high-level, general-purpose, object-oriented, dynamic, + functional programming language. +""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['8132ff353afaa70e6b19367a25ae3d5a43627279c25647c220641fed00f8e890'] + +builddependencies = [ + ('binutils', '2.28'), +] + +dependencies = [ + ('DB', '6.2.32'), + ('libffcall', '1.13'), + ('libreadline', '7.0'), + ('libsigsegv', '2.11'), + ('PCRE', '8.41'), + ('zlib', '1.2.11'), +] + +prebuildopts = """ + sed -e 's/ac_cv_have_decl_rl_readline_state" = x""yes/ac_cv_have_decl_rl_readline_state" = x""JKP/'\ + -i.eb modules/readline/configure + cd src +""" + +preinstallopts = """ + cd src +""" + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/clisp', 'lib/%(namelower)s-%(version)s/base/lisp.a'], + 'dirs': ['share/aclocal', 'share/doc'], +} + +moduleclass = 'lang' -- GitLab From b59b726b6b27d71570aaecd9fe0acb822dbf219e Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Fri, 21 Jul 2017 08:25:41 -0500 Subject: [PATCH 1222/1603] adding easyconfigs: DBus-1.10.20-GCCcore-6.4.0.eb --- .../d/DBus/DBus-1.10.20-GCCcore-6.4.0.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/d/DBus/DBus-1.10.20-GCCcore-6.4.0.eb diff --git a/easybuild/easyconfigs/d/DBus/DBus-1.10.20-GCCcore-6.4.0.eb b/easybuild/easyconfigs/d/DBus/DBus-1.10.20-GCCcore-6.4.0.eb new file mode 100644 index 0000000000..99bd5ca7ab --- /dev/null +++ b/easybuild/easyconfigs/d/DBus/DBus-1.10.20-GCCcore-6.4.0.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'DBus' +version = '1.10.20' + +homepage = 'http://dbus.freedesktop.org/' + +description = """ + D-Bus is a message bus system, a simple way for applications to talk + to one another. In addition to interprocess communication, D-Bus helps + coordinate process lifecycle; it makes it simple and reliable to code + a "single instance" application or daemon, and to launch applications + and daemons on demand when their services are needed. +""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} +toolchainopts = {'pic': True} + +source_urls = ['http://dbus.freedesktop.org/releases/dbus'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['e574b9780b5425fde4d973bb596e7ea0f09e00fe2edd662da9016e976c460b48'] + +builddependencies = [ + ('binutils', '2.28'), +] + +dependencies = [ + ('expat', '2.2.1'), +] + +sanity_check_paths = { + 'files': ['bin/dbus-%s' % x for x in + ['cleanup-sockets', 'daemon', 'launch', 'monitor', + 'run-session', 'send', 'uuidgen']] + + ['lib/libdbus-1.%s' % x for x in ['a', SHLIB_EXT]], + 'dirs': ['include', 'share'], +} + +moduleclass = 'devel' -- GitLab From 3ee3c867b399e7ae583f18793ab106c792d2a449 Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Fri, 21 Jul 2017 08:36:06 -0500 Subject: [PATCH 1223/1603] adding easyconfigs: Eigen-3.3.4-GCCcore-6.4.0.eb --- .../e/Eigen/Eigen-3.3.4-GCCcore-6.4.0.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/e/Eigen/Eigen-3.3.4-GCCcore-6.4.0.eb diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.3.4-GCCcore-6.4.0.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.3.4-GCCcore-6.4.0.eb new file mode 100644 index 0000000000..7fd77a3b5e --- /dev/null +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.3.4-GCCcore-6.4.0.eb @@ -0,0 +1,33 @@ +name = 'Eigen' +version = '3.3.4' + +homepage = 'http://eigen.tuxfamily.org/index.php?title=Main_Page' + +description = """ + Eigen is a C++ template library for linear algebra: + matrices, vectors, numerical solvers, and related algorithms. +""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} + +source_urls = ['http://bitbucket.org/%(namelower)s/%(namelower)s/get'] +sources = ['%(version)s.tar.bz2'] +checksums = ['dd254beb0bafc695d0f62ae1a222ff85b52dbaa3a16f76e781dce22d0d20a4a6'] + +# both in Eigen 2.x an 3.x +include_files = ['Cholesky', 'Core', 'Dense', 'Eigen', 'Geometry', 'LU', + 'QR', 'QtAlignedMalloc', 'SVD', 'Sparse', 'StdVector'] + +# only 3.x +include_files.extend(['CholmodSupport', 'Eigenvalues', 'Householder', + 'IterativeLinearSolvers', 'Jacobi', 'OrderingMethods', + 'PaStiXSupport', 'PardisoSupport', 'SparseCholesky', + 'SparseCore', 'StdDeque', 'StdList', + 'SuperLUSupport', 'UmfPackSupport']) + +sanity_check_paths = { + 'files': ['include/Eigen/%s' % x for x in include_files], + 'dirs': ['include'], +} + +moduleclass = 'math' -- GitLab From 8a4309a6151f85c12881d7649541e4b79a066066 Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Fri, 21 Jul 2017 08:49:32 -0500 Subject: [PATCH 1224/1603] adding easyconfigs: gperf-3.1-GCCcore-6.4.0.eb --- .../g/gperf/gperf-3.1-GCCcore-6.4.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/g/gperf/gperf-3.1-GCCcore-6.4.0.eb diff --git a/easybuild/easyconfigs/g/gperf/gperf-3.1-GCCcore-6.4.0.eb b/easybuild/easyconfigs/g/gperf/gperf-3.1-GCCcore-6.4.0.eb new file mode 100644 index 0000000000..6dd680f7e4 --- /dev/null +++ b/easybuild/easyconfigs/g/gperf/gperf-3.1-GCCcore-6.4.0.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'gperf' +version = '3.1' + +homepage = 'http://www.gnu.org/software/gperf/' + +description = """ + GNU gperf is a perfect hash function generator. For a given list of strings, + it produces a hash function and hash table, in form of C or C++ code, for + looking up a value depending on the input string. The hash function is + perfect, which means that the hash table has no collisions, and the hash + table lookup needs a single string comparison only. +""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['588546b945bba4b70b6a3a616e80b4ab466e3f33024a352fc2198112cdbb3ae2'] + +builddependencies = [ + ('binutils', '2.28'), +] + +sanity_check_paths = { + 'files': ['bin/gperf'], + 'dirs': [] +} + +moduleclass = 'devel' -- GitLab From 7d8f23154e056e5585b1b43dd402b0d4fa9464b4 Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Fri, 21 Jul 2017 09:08:10 -0500 Subject: [PATCH 1225/1603] adding easyconfigs: libunistring-0.9.7-GCCcore-6.4.0.eb --- .../libunistring-0.9.7-GCCcore-6.4.0.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/l/libunistring/libunistring-0.9.7-GCCcore-6.4.0.eb diff --git a/easybuild/easyconfigs/l/libunistring/libunistring-0.9.7-GCCcore-6.4.0.eb b/easybuild/easyconfigs/l/libunistring/libunistring-0.9.7-GCCcore-6.4.0.eb new file mode 100644 index 0000000000..8d845c9877 --- /dev/null +++ b/easybuild/easyconfigs/l/libunistring/libunistring-0.9.7-GCCcore-6.4.0.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'libunistring' +version = '0.9.7' + +homepage = 'http://www.gnu.org/software/libunistring/' + +description = """ + This library provides functions for manipulating Unicode strings and for + manipulating C strings according to the Unicode standard. +""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_XZ] +source_urls = [GNU_SOURCE] +checksums = ['2e3764512aaf2ce598af5a38818c0ea23dedf1ff5460070d1b6cee5c3336e797'] + +builddependencies = [ + ('binutils', '2.28'), +] + +parallel = 1 + +sanity_check_paths = { + 'files': ['lib/libunistring.a', 'lib/libunistring.%s' % SHLIB_EXT] + + ['include/uni%s.h' % x for x in ['case', 'conv', 'ctype', 'lbrk', 'name', 'norm', + 'stdio', 'str', 'types', 'wbrk', 'width']], + 'dirs': ['include/unistring'], +} + +moduleclass = 'lib' -- GitLab From 5dc3a28322e7f90edfd1909590812913106be11b Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Fri, 21 Jul 2017 09:35:18 -0500 Subject: [PATCH 1226/1603] adding easyconfigs: Guile-2.2.2-GCCcore-6.4.0.eb --- .../g/Guile/Guile-2.2.2-GCCcore-6.4.0.eb | 43 +++++++++++++++++++ .../l/libffi/libffi-3.2.1-GCCcore-6.4.0.eb | 34 +++++++++++++++ .../libunistring-0.9.7-GCCcore-6.4.0.eb | 33 ++++++++++++++ 3 files changed, 110 insertions(+) create mode 100644 easybuild/easyconfigs/g/Guile/Guile-2.2.2-GCCcore-6.4.0.eb create mode 100644 easybuild/easyconfigs/l/libffi/libffi-3.2.1-GCCcore-6.4.0.eb create mode 100644 easybuild/easyconfigs/l/libunistring/libunistring-0.9.7-GCCcore-6.4.0.eb diff --git a/easybuild/easyconfigs/g/Guile/Guile-2.2.2-GCCcore-6.4.0.eb b/easybuild/easyconfigs/g/Guile/Guile-2.2.2-GCCcore-6.4.0.eb new file mode 100644 index 0000000000..395d150d5b --- /dev/null +++ b/easybuild/easyconfigs/g/Guile/Guile-2.2.2-GCCcore-6.4.0.eb @@ -0,0 +1,43 @@ +easyblock = 'ConfigureMake' + +name = 'Guile' +version = '2.2.2' + +homepage = 'https://www.gnu.org/software/guile/' + +description = """ + Guile is a programming language, designed to help programmers create flexible + applications that can be extended by users or other programmers with plug-ins, + modules, or scripts. +""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} +toolchainopts = {'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['3d9b94183b19f04dd4317da87beedafd1c947142f3d861ca1f0224e7a75127ee'] + +builddependencies = [ + ('Autotools', '20170619'), + ('binutils', '2.28'), +] + +dependencies = [ + ('gc', '7.6.0'), + ('GMP', '6.1.2'), + ('libffi', '3.2.1'), + ('libunistring', '0.9.7'), +] + +sanity_check_paths = { + 'files': ['bin/guild', 'bin/guile', 'bin/guile-config', + 'bin/guile-snarf', 'bin/guile-tools', + 'include/guile/%(version_major_minor)s/libguile.h', + 'lib/libguile-%(version_major_minor)s.a', + 'lib/libguile-%%(version_major_minor)s.%s' % SHLIB_EXT], + 'dirs': ['include/guile/%(version_major_minor)s/libguile', + 'lib/guile/%(version_major_minor)s/ccache'], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/l/libffi/libffi-3.2.1-GCCcore-6.4.0.eb b/easybuild/easyconfigs/l/libffi/libffi-3.2.1-GCCcore-6.4.0.eb new file mode 100644 index 0000000000..35fa02052a --- /dev/null +++ b/easybuild/easyconfigs/l/libffi/libffi-3.2.1-GCCcore-6.4.0.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'libffi' +version = '3.2.1' + +homepage = 'http://sourceware.org/libffi/' + +description = """ + The libffi library provides a portable, high level programming interface to + various calling conventions. This allows a programmer to call any function + specified by a call interface description at run-time. +""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} +toolchainopts = {'pic': True} + +source_urls = [ + 'ftp://sourceware.org/pub/libffi/', + 'http://www.mirrorservice.org/sites/sourceware.org/pub/libffi/', +] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['d06ebb8e1d9a22d19e38d63fdb83954253f39bedc5d46232a05645685722ca37'] + +builddependencies = [ + ('binutils', '2.28'), +] + +sanity_check_paths = { + 'files': [('lib/libffi.%s' % SHLIB_EXT, 'lib64/libffi.%s' % SHLIB_EXT), + ('lib/libffi.a', 'lib64/libffi.a')], + 'dirs': ['lib', 'lib64'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libunistring/libunistring-0.9.7-GCCcore-6.4.0.eb b/easybuild/easyconfigs/l/libunistring/libunistring-0.9.7-GCCcore-6.4.0.eb new file mode 100644 index 0000000000..8d845c9877 --- /dev/null +++ b/easybuild/easyconfigs/l/libunistring/libunistring-0.9.7-GCCcore-6.4.0.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'libunistring' +version = '0.9.7' + +homepage = 'http://www.gnu.org/software/libunistring/' + +description = """ + This library provides functions for manipulating Unicode strings and for + manipulating C strings according to the Unicode standard. +""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_XZ] +source_urls = [GNU_SOURCE] +checksums = ['2e3764512aaf2ce598af5a38818c0ea23dedf1ff5460070d1b6cee5c3336e797'] + +builddependencies = [ + ('binutils', '2.28'), +] + +parallel = 1 + +sanity_check_paths = { + 'files': ['lib/libunistring.a', 'lib/libunistring.%s' % SHLIB_EXT] + + ['include/uni%s.h' % x for x in ['case', 'conv', 'ctype', 'lbrk', 'name', 'norm', + 'stdio', 'str', 'types', 'wbrk', 'width']], + 'dirs': ['include/unistring'], +} + +moduleclass = 'lib' -- GitLab From 6ad085d0cb5eb1dd485902f1e4f5f5cd54cf6412 Mon Sep 17 00:00:00 2001 From: jrbosch Date: Fri, 21 Jul 2017 11:26:56 -0400 Subject: [PATCH 1227/1603] add GROMACS easyconfig with GPU enabled and foss 2016b toolchain --- ...ACS-2016.3-foss-2016b-GPU-enabled-build.eb | 45 +++++++++++++++++++ ...ACS-2016.3_amend_search_for_nvml_lib.patch | 2 +- 2 files changed, 46 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-2016.3-foss-2016b-GPU-enabled-build.eb diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.3-foss-2016b-GPU-enabled-build.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.3-foss-2016b-GPU-enabled-build.eb new file mode 100644 index 0000000000..7d8210d268 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.3-foss-2016b-GPU-enabled-build.eb @@ -0,0 +1,45 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2016 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, +# Ghent University / The Francis Crick Institute +# Authors:: +# * Wiktor Jurkowski +# * Fotis Georgatos +# * George Tsouloupas +# * Kenneth Hoste +# * Adam Huffman +# License:: MIT/GPL +## + +name = 'GROMACS' +version = '2016.3' +versionsuffix = '-GPU-enabled-build' + +homepage = 'http://www.gromacs.org' +description = """ +GROMACS is a versatile package to perform molecular dynamics, + i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. + +This is a GPU enabled build, containing both MPI and threadMPI builds. +""" + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = ['ftp://ftp.gromacs.org/pub/gromacs/'] +sources = [SOURCELOWER_TAR_GZ] + +patches = [ + 'GROMACS-%(version)s_amend_search_for_nvml_lib.patch', +] + +dependencies = [ + ('CUDA', '8.0.61_375.26'), +] + +builddependencies = [ + ('CMake', '3.7.2'), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.3_amend_search_for_nvml_lib.patch b/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.3_amend_search_for_nvml_lib.patch index 8ae9027f34..b30455aecc 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.3_amend_search_for_nvml_lib.patch +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.3_amend_search_for_nvml_lib.patch @@ -8,7 +8,7 @@ diff -ru gromacs-2016.orig/cmake/FindNVML.cmake gromacs-2016/cmake/FindNVML.cmak # passed to the installer, or the root where they later found the # kit to be installed. Below, we cater for both possibilities. - set( NVML_LIB_PATHS /usr/lib64 ) -+ set( NVML_LIB_PATHS /usr/lib64 /usr/lib/nvidia-367 /usr/lib/nvidia-375) ++ set( NVML_LIB_PATHS /usr/lib64 /usr/lib64/nvidia /usr/lib/nvidia-367 /usr/lib/nvidia-375) if(GPU_DEPLOYMENT_KIT_ROOT_DIR) list(APPEND NVML_LIB_PATHS "${GPU_DEPLOYMENT_KIT_ROOT_DIR}/src/gdk/nvml/lib" -- GitLab From d7d3f98ef76a5048ec1c04b5deecc17585f26b73 Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Fri, 21 Jul 2017 11:12:11 -0500 Subject: [PATCH 1228/1603] adding easyconfigs: pkg-config-0.29.2-GCCcore-6.4.0.eb --- .../pkg-config-0.29.2-GCCcore-6.4.0.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2-GCCcore-6.4.0.eb diff --git a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2-GCCcore-6.4.0.eb b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2-GCCcore-6.4.0.eb new file mode 100644 index 0000000000..c02bedf48d --- /dev/null +++ b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2-GCCcore-6.4.0.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'pkg-config' +version = '0.29.2' + +homepage = 'http://www.freedesktop.org/wiki/Software/pkg-config/' + +description = """ + pkg-config is a helper tool used when compiling applications and libraries. + It helps you insert the correct compiler options on the command line so an + application can use gcc -o test test.c `pkg-config --libs --cflags glib-2.0` + for instance, rather than hard-coding values on where to find glib (or other + libraries). +""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} + +source_urls = ['https://pkg-config.freedesktop.org/releases/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['6fc69c01688c9458a57eb9a1664c9aba372ccda420a02bf4429fe610e7e7d591'] + +builddependencies = [ + ('binutils', '2.28'), +] + +# don't use PAX, it might break. +tar_config_opts = True + +configopts = " --with-internal-glib" + +sanity_check_paths = { + 'files': ['bin/pkg-config'], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From 1491145f89ce6732bff600e8087173da71544eca Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Fri, 21 Jul 2017 11:13:04 -0500 Subject: [PATCH 1229/1603] adding easyconfigs: libcerf-1.5-GCCcore-6.4.0.eb --- .../l/libcerf/libcerf-1.5-GCCcore-6.4.0.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/l/libcerf/libcerf-1.5-GCCcore-6.4.0.eb diff --git a/easybuild/easyconfigs/l/libcerf/libcerf-1.5-GCCcore-6.4.0.eb b/easybuild/easyconfigs/l/libcerf/libcerf-1.5-GCCcore-6.4.0.eb new file mode 100644 index 0000000000..5489e38fa7 --- /dev/null +++ b/easybuild/easyconfigs/l/libcerf/libcerf-1.5-GCCcore-6.4.0.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'libcerf' +version = '1.5' + +homepage = 'http://apps.jcns.fz-juelich.de/doku/sc/libcerf' + +description = """ + libcerf is a self-contained numeric library that provides an efficient and + accurate implementation of complex error functions, along with Dawson, + Faddeeva, and Voigt functions. +""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} +toolchainopts = {'pic': True} + +source_urls = [ + 'http://apps.jcns.fz-juelich.de/src/libcerf/', + 'http://apps.jcns.fz-juelich.de/src/libcerf/old', +] +sources = [SOURCE_TGZ] +checksums = ['e36dc147e7fff81143074a21550c259b5aac1b99fc314fc0ae33294231ca5c86'] + +builddependencies = [ + ('Autotools', '20170619'), + ('binutils', '2.28'), + ('libtool', '2.4.6'), +] + +sanity_check_paths = { + 'files': ['lib/libcerf.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'math' -- GitLab From dd7f25269b3caf75267bbc72b1f8c422a1bff436 Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Fri, 21 Jul 2017 11:32:38 -0500 Subject: [PATCH 1230/1603] adding easyconfigs: libgd-2.2.4-GCCcore-6.4.0.eb --- .../l/libgd/libgd-2.2.4-GCCcore-6.4.0.eb | 33 +++++++++++++++ .../libjpeg-turbo-1.5.2-GCCcore-6.4.0.eb | 41 +++++++++++++++++++ 2 files changed, 74 insertions(+) create mode 100644 easybuild/easyconfigs/l/libgd/libgd-2.2.4-GCCcore-6.4.0.eb create mode 100644 easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.5.2-GCCcore-6.4.0.eb diff --git a/easybuild/easyconfigs/l/libgd/libgd-2.2.4-GCCcore-6.4.0.eb b/easybuild/easyconfigs/l/libgd/libgd-2.2.4-GCCcore-6.4.0.eb new file mode 100644 index 0000000000..463baf18d2 --- /dev/null +++ b/easybuild/easyconfigs/l/libgd/libgd-2.2.4-GCCcore-6.4.0.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'libgd' +version = '2.2.4' + +homepage = 'https://libgd.github.io/' + +description = "GD is an open source code library for the dynamic creation of images by programmers." + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/libgd/libgd/releases/download/gd-%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['487a650aa614217ed08ab1bd1aa5d282f9d379cfd95c756aed0b43406381be65'] + +builddependencies = [ + ('binutils', '2.28'), +] + +dependencies = [ + ('fontconfig', '2.12.1'), + ('libjpeg-turbo', '1.5.2'), + ('libpng', '1.6.30'), + ('zlib', '1.2.11'), +] + +sanity_check_paths = { + 'files': ["lib/libgd.a", "lib/libgd.%s" % SHLIB_EXT], + 'dirs': ["bin", "include"], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.5.2-GCCcore-6.4.0.eb b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.5.2-GCCcore-6.4.0.eb new file mode 100644 index 0000000000..8d3ce16df6 --- /dev/null +++ b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.5.2-GCCcore-6.4.0.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'libjpeg-turbo' +version = '1.5.2' + +homepage = 'http://sourceforge.net/projects/libjpeg-turbo/' + +description = """ + libjpeg-turbo is a fork of the original IJG libjpeg which uses SIMD to + accelerate baseline JPEG compression and decompression. libjpeg is a library + that implements JPEG image encoding, decoding and transcoding. +""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['9098943b270388727ae61de82adec73cf9f0dbb240b3bc8b172595ebf405b528'] + +builddependencies = [ + ('binutils', '2.28'), +] + +dependencies = [ + ('NASM', '2.13.01'), +] + +configopts = "--with-jpeg8" + +runtest = "test" + +sanity_check_paths = { + 'files': ['bin/cjpeg', 'bin/djpeg', 'bin/jpegtran', 'bin/rdjpgcom', + 'bin/tjbench', 'bin/wrjpgcom', 'lib/libjpeg.a', + 'lib/libjpeg.%s' % SHLIB_EXT, 'lib/libturbojpeg.a', + 'lib/libturbojpeg.%s' % SHLIB_EXT], + 'dirs': ['include', 'share'], +} + +moduleclass = 'lib' -- GitLab From adeb9bb2a9cd6918c1f206e42311825bf4a8a756 Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Fri, 21 Jul 2017 12:44:20 -0500 Subject: [PATCH 1231/1603] adding easyconfigs: OpenPGM-5.2.122-GCCcore-6.4.0.eb --- .../OpenPGM/OpenPGM-5.2.122-GCCcore-6.4.0.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-GCCcore-6.4.0.eb diff --git a/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-GCCcore-6.4.0.eb b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-GCCcore-6.4.0.eb new file mode 100644 index 0000000000..88a05b260e --- /dev/null +++ b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-GCCcore-6.4.0.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'OpenPGM' +version = '5.2.122' + +homepage = 'http://code.google.com/p/openpgm/' + +description = """ + OpenPGM is an open source implementation of the Pragmatic General Multicast + (PGM) specification in RFC 3208 available at www.ietf.org. PGM is a reliable + and scalable multicast protocol that enables receivers to detect loss, request + retransmission of lost data, or notify an application of unrecoverable loss. + PGM is a receiver-reliable protocol, which means the receiver is responsible + for ensuring all data is received, absolving the sender of reception + responsibility. +""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/openpgm/'] +sources = ['libpgm-%(version)s.tar.gz'] +checksums = ['6b895f550b95284dcde7189b01e04a9a1c1f94579af31b1eebd32c2207a1ba2c'] + +builddependencies = [ + ('binutils', '2.28'), +] + +start_dir = 'pgm' + +sanity_check_paths = { + 'files': ['lib/libpgm.%s' % SHLIB_EXT, 'lib/libpgm.a'], + 'dirs': ['include'], +} + +moduleclass = 'system' -- GitLab From 217f8e695bd496e581899383550b95d5585a4ec6 Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Fri, 21 Jul 2017 13:01:29 -0500 Subject: [PATCH 1232/1603] adding easyconfigs: util-linux-2.30-GCCcore-6.4.0.eb --- .../util-linux-2.30-GCCcore-6.4.0.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/u/util-linux/util-linux-2.30-GCCcore-6.4.0.eb diff --git a/easybuild/easyconfigs/u/util-linux/util-linux-2.30-GCCcore-6.4.0.eb b/easybuild/easyconfigs/u/util-linux/util-linux-2.30-GCCcore-6.4.0.eb new file mode 100644 index 0000000000..3556edda8d --- /dev/null +++ b/easybuild/easyconfigs/u/util-linux/util-linux-2.30-GCCcore-6.4.0.eb @@ -0,0 +1,42 @@ +easyblock = 'ConfigureMake' + +name = 'util-linux' +version = '2.30' + +homepage = 'http://www.kernel.org/pub/linux/utils/util-linux' + +description = "Set of Linux utilities" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} +toolchainopts = {'pic': True} + +source_urls = ['%s/v%%(version_major_minor)s' % homepage] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['e84cc32566abf28b84efb5ee326e1f3597c3d19b9916740f50c75bd57e498ce0'] + +# disable account related utilities (they need OS dependant pam-devel files) +# disable wall and friends (requires group changing permissions for install user) +# install systemd service files in install dir +# install bash completion files in install dir +configopts = "--disable-chfn-chsh --disable-login --disable-su " +configopts += "--disable-wall --disable-use-tty-group " +configopts += "--disable-makeinstall-chown --disable-makeinstall-setuid " +configopts += "--with-systemdsystemunitdir='${prefix}/systemd' " +configopts += "--with-bashcompletiondir='${prefix}/share/bash-completion/completions' " +# disable building Python bindings (since we don't include Python as a dep) +configopts += "--without-python " + +builddependencies = [ + ('binutils', '2.28'), +] + +dependencies = [ + ('ncurses', '6.0'), +] + +sanity_check_paths = { + 'files': ['lib/lib%s.a' % x for x in ['blkid', 'mount', 'uuid']], + 'dirs': ['include', 'bin', 'share', 'sbin'], +} + +moduleclass = 'tools' -- GitLab From 592668fa98063559f9089f1ef2a832a410bb0472 Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Sat, 22 Jul 2017 06:22:27 -0500 Subject: [PATCH 1233/1603] adding easyconfigs: x264-20170721-GCCcore-6.4.0.eb --- .../x/x264/x264-20170721-GCCcore-6.4.0.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/x/x264/x264-20170721-GCCcore-6.4.0.eb diff --git a/easybuild/easyconfigs/x/x264/x264-20170721-GCCcore-6.4.0.eb b/easybuild/easyconfigs/x/x264/x264-20170721-GCCcore-6.4.0.eb new file mode 100644 index 0000000000..073bcb840c --- /dev/null +++ b/easybuild/easyconfigs/x/x264/x264-20170721-GCCcore-6.4.0.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'x264' +version = '20170721' + +homepage = 'http://www.videolan.org/developers/x264.html' + +description = """ + x264 is a free software library and application for encoding video streams + into the H.264/MPEG-4 AVC compression format, and is released under the + terms of the GNU GPL. +""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} +toolchainopts = {'pic': True} + +source_urls = [ + 'https://download.videolan.org/pub/videolan/x264/snapshots/', + 'ftp://ftp.videolan.org/pub/videolan/x264/snapshots/', +] +sources = ['x264-snapshot-%(version)s-2245-stable.tar.bz2'] +checksums = ['1459f7b6683c90eafd9d7bf623a574968a94814cdf4b2fb57c0f73bf414d2c8d'] + +builddependencies = [ + ('binutils', '2.28'), +] + +dependencies = [ + ('Yasm', '1.3.0'), +] + +configopts = " --enable-shared --enable-static" + +sanity_check_paths = { + 'files': ['bin/x264', 'include/x264_config.h', 'include/x264.h', + 'lib/libx264.a', 'lib/libx264.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' -- GitLab From d8aa6264c758a46dbd3e383ac01a0746afcb70fb Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Sat, 22 Jul 2017 06:36:30 -0500 Subject: [PATCH 1234/1603] adding easyconfigs: Xerces-C++-3.1.4-GCCcore-6.4.0.eb --- .../Xerces-C++-3.1.4-GCCcore-6.4.0.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.1.4-GCCcore-6.4.0.eb diff --git a/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.1.4-GCCcore-6.4.0.eb b/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.1.4-GCCcore-6.4.0.eb new file mode 100644 index 0000000000..3832c17c46 --- /dev/null +++ b/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.1.4-GCCcore-6.4.0.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'Xerces-C++' +version = '3.1.4' + +homepage = 'http://xerces.apache.org/xerces-c/' + +description = """ + Xerces-C++ is a validating XML parser written in a portable subset of C++. + Xerces-C++ makes it easy to give your application the ability to read and + write XML data. A shared library is provided for parsing, generating, + manipulating, and validating XML documents using the DOM, SAX, and SAX2 + APIs. +""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} + +source_urls = ['http://archive.apache.org/dist/xerces/c/%(version_major)s/sources/'] +sources = ['xerces-c-%(version)s.tar.gz'] +checksums = ['c98eedac4cf8a73b09366ad349cb3ef30640e7a3089d360d40a3dde93f66ecf6'] + +builddependencies = [ + ('binutils', '2.28'), +] + +dependencies = [ + ('cURL', '7.54.1'), +] + +sanity_check_paths = { + 'files': ['bin/XInclude', 'lib/libxerces-c.%s' % SHLIB_EXT], + 'dirs': ['include/xercesc/xinclude'], +} + +moduleclass = 'lib' -- GitLab From fab9fae15011bfe8f957612c7a578ba9e8187e33 Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Sat, 22 Jul 2017 06:50:55 -0500 Subject: [PATCH 1235/1603] adding easyconfigs: StringTie-1.3.3-GCCcore-6.4.0.eb --- .../StringTie-1.3.3-GCCcore-6.4.0.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/s/StringTie/StringTie-1.3.3-GCCcore-6.4.0.eb diff --git a/easybuild/easyconfigs/s/StringTie/StringTie-1.3.3-GCCcore-6.4.0.eb b/easybuild/easyconfigs/s/StringTie/StringTie-1.3.3-GCCcore-6.4.0.eb new file mode 100644 index 0000000000..4af7c0ed99 --- /dev/null +++ b/easybuild/easyconfigs/s/StringTie/StringTie-1.3.3-GCCcore-6.4.0.eb @@ -0,0 +1,35 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'MakeCp' + +name = 'StringTie' +version = '1.3.3' + +homepage = 'http://ccb.jhu.edu/software/stringtie/' + +description = """ + StringTie is a fast and highly efficient assembler of RNA-Seq alignments + into potential transcripts. +""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} + +source_urls = ['http://ccb.jhu.edu/software/stringtie/dl/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['c01b16a681dc55f114dbfc2fcd725f615b2d9a79058ff8c110047cfa9cbe2976'] + +builddependencies = [ + ('binutils', '2.28'), +] + +files_to_copy = [(['stringtie'], 'bin'), 'README', 'LICENSE'] + +sanity_check_paths = { + 'files': ['bin/stringtie'], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From d337a8b2274e4c37032c27356e39ca02facdac7c Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Sat, 22 Jul 2017 07:17:27 -0500 Subject: [PATCH 1236/1603] adding easyconfigs: Qhull-2015.2-GCCcore-6.4.0.eb --- .../q/Qhull/Qhull-2015.2-GCCcore-6.4.0.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/q/Qhull/Qhull-2015.2-GCCcore-6.4.0.eb diff --git a/easybuild/easyconfigs/q/Qhull/Qhull-2015.2-GCCcore-6.4.0.eb b/easybuild/easyconfigs/q/Qhull/Qhull-2015.2-GCCcore-6.4.0.eb new file mode 100644 index 0000000000..9734e3543a --- /dev/null +++ b/easybuild/easyconfigs/q/Qhull/Qhull-2015.2-GCCcore-6.4.0.eb @@ -0,0 +1,45 @@ +easyblock = 'CMakeMake' + +name = 'Qhull' +version = '2015.2' + +homepage = 'http://www.qhull.org' + +description = """ + Qhull computes the convex hull, Delaunay triangulation, Voronoi diagram, + halfspace intersection about a point, furthest-site Delaunay triangulation, + and furthest-site Voronoi diagram. The source code runs in 2-d, 3-d, 4-d, and + higher dimensions. Qhull implements the Quickhull algorithm for computing the + convex hull. +""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.qhull.org/download/'] +sources = ['%(namelower)s-%(version_major)s-src-7.%(version_minor)s.0.tgz'] +checksums = ['78b010925c3b577adc3d58278787d7df08f7c8fb02c3490e375eab91bb58a436'] + +patches = [ + 'Qhull-%(version)s-intel-fix.patch', + 'Qhull_pkgconfig.patch', +] + +builddependencies = [ + ('binutils', '2.28'), + ('CMake', '3.8.2'), +] + +sanity_check_paths = { + 'files': ['bin/qhull', 'lib/libqhull.%s' % SHLIB_EXT, + 'lib/pkgconfig/qhull.pc'], + 'dirs': [], +} + +modextrapaths = { + 'CPATH': ['qhull/include'], +} + +parallel = 1 + +moduleclass = 'math' -- GitLab From 41a89ae9d2873dadfe5f3d680ec059255f2d1ce0 Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Sat, 22 Jul 2017 07:30:16 -0500 Subject: [PATCH 1237/1603] fix EB URL --- .../easyconfigs/s/StringTie/StringTie-1.3.3-GCCcore-6.4.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/StringTie/StringTie-1.3.3-GCCcore-6.4.0.eb b/easybuild/easyconfigs/s/StringTie/StringTie-1.3.3-GCCcore-6.4.0.eb index 4af7c0ed99..8347d427b4 100644 --- a/easybuild/easyconfigs/s/StringTie/StringTie-1.3.3-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/s/StringTie/StringTie-1.3.3-GCCcore-6.4.0.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders # Author: Pablo Escobar Lopez # sciCORE - University of Basel # SIB Swiss Institute of Bioinformatics -- GitLab From 11743dfa52e8fc92ad9d29abfe9b349976d1e6ad Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Sat, 22 Jul 2017 09:51:51 -0500 Subject: [PATCH 1238/1603] adding easyconfigs: numactl-2.0.11-GCCcore-6.4.0.eb --- .../n/numactl/numactl-2.0.11-GCCcore-6.4.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCCcore-6.4.0.eb diff --git a/easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCCcore-6.4.0.eb b/easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCCcore-6.4.0.eb new file mode 100644 index 0000000000..7ce46ec76c --- /dev/null +++ b/easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCCcore-6.4.0.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'numactl' +version = '2.0.11' + +homepage = 'http://oss.sgi.com/projects/libnuma/' + +description = """ + The numactl program allows you to run your application program on specific + cpu's and memory nodes. It does this by supplying a NUMA memory policy to + the operating system before running your program. The libnuma library provides + convenient ways for you to add NUMA memory policies into your own program. +""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} +toolchainopts = {'pic': True} + +source_urls = ['ftp://oss.sgi.com/www/projects/libnuma/download/'] +sources = [SOURCE_TAR_GZ] +checksums = ['450c091235f891ee874a8651b179c30f57a1391ca5c4673354740ba65e527861'] + +builddependencies = [ + ('binutils', '2.28'), +] + +sanity_check_paths = { + 'files': ['bin/numactl', 'bin/numastat', 'lib/libnuma.%s' % SHLIB_EXT, 'lib/libnuma.a'], + 'dirs': ['share/man', 'include'] +} + +moduleclass = 'tools' -- GitLab From cecf4e6330edc61b7c419df38a61bbb263e01148 Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Sun, 23 Jul 2017 12:58:02 -0500 Subject: [PATCH 1239/1603] adding easyconfigs: LittleCMS-2.8-GCCcore-6.4.0.eb --- .../LittleCMS/LittleCMS-2.8-GCCcore-6.4.0.eb | 35 ++++++++++++++++ .../libjpeg-turbo-1.5.2-GCCcore-6.4.0.eb | 41 +++++++++++++++++++ 2 files changed, 76 insertions(+) create mode 100644 easybuild/easyconfigs/l/LittleCMS/LittleCMS-2.8-GCCcore-6.4.0.eb create mode 100644 easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.5.2-GCCcore-6.4.0.eb diff --git a/easybuild/easyconfigs/l/LittleCMS/LittleCMS-2.8-GCCcore-6.4.0.eb b/easybuild/easyconfigs/l/LittleCMS/LittleCMS-2.8-GCCcore-6.4.0.eb new file mode 100644 index 0000000000..fda360d04d --- /dev/null +++ b/easybuild/easyconfigs/l/LittleCMS/LittleCMS-2.8-GCCcore-6.4.0.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'LittleCMS' +version = '2.8' + +homepage = 'http://www.littlecms.com/' + +description = """ + Little CMS intends to be an OPEN SOURCE small-footprint color management + engine, with special focus on accuracy and performance. +""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} +toolchainopts = {'pic': True} + +source_urls = ['http://sourceforge.net/projects/lcms/files/lcms/%(version)s/'] +sources = ['lcms2-%(version)s.tar.gz'] +checksums = ['66d02b229d2ea9474e62c2b6cd6720fde946155cd1d0d2bffdab829790a0fb22'] + +builddependencies = [ + ('binutils', '2.28'), +] + +dependencies = [ + ('libjpeg-turbo', '1.5.2'), +] + +sanity_check_paths = { + 'files': ['bin/jpgicc', 'bin/linkicc', 'bin/psicc', 'bin/transicc', + 'include/lcms2.h', 'include/lcms2_plugin.h', 'lib/liblcms2.a', + 'lib/liblcms2.%s' % SHLIB_EXT, 'lib/pkgconfig/lcms2.pc'], + 'dirs': ['share/man'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.5.2-GCCcore-6.4.0.eb b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.5.2-GCCcore-6.4.0.eb new file mode 100644 index 0000000000..8d3ce16df6 --- /dev/null +++ b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.5.2-GCCcore-6.4.0.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'libjpeg-turbo' +version = '1.5.2' + +homepage = 'http://sourceforge.net/projects/libjpeg-turbo/' + +description = """ + libjpeg-turbo is a fork of the original IJG libjpeg which uses SIMD to + accelerate baseline JPEG compression and decompression. libjpeg is a library + that implements JPEG image encoding, decoding and transcoding. +""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['9098943b270388727ae61de82adec73cf9f0dbb240b3bc8b172595ebf405b528'] + +builddependencies = [ + ('binutils', '2.28'), +] + +dependencies = [ + ('NASM', '2.13.01'), +] + +configopts = "--with-jpeg8" + +runtest = "test" + +sanity_check_paths = { + 'files': ['bin/cjpeg', 'bin/djpeg', 'bin/jpegtran', 'bin/rdjpgcom', + 'bin/tjbench', 'bin/wrjpgcom', 'lib/libjpeg.a', + 'lib/libjpeg.%s' % SHLIB_EXT, 'lib/libturbojpeg.a', + 'lib/libturbojpeg.%s' % SHLIB_EXT], + 'dirs': ['include', 'share'], +} + +moduleclass = 'lib' -- GitLab From 05782da44b5db1407fcd265e5ed26148f8973335 Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Sun, 23 Jul 2017 21:14:33 -0500 Subject: [PATCH 1240/1603] adding easyconfigs: nettle-3.3-GCCcore-6.4.0.eb --- .../n/nettle/nettle-3.3-GCCcore-6.4.0.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/n/nettle/nettle-3.3-GCCcore-6.4.0.eb diff --git a/easybuild/easyconfigs/n/nettle/nettle-3.3-GCCcore-6.4.0.eb b/easybuild/easyconfigs/n/nettle/nettle-3.3-GCCcore-6.4.0.eb new file mode 100644 index 0000000000..ec88285ad3 --- /dev/null +++ b/easybuild/easyconfigs/n/nettle/nettle-3.3-GCCcore-6.4.0.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'nettle' +version = '3.3' + +homepage = 'http://www.lysator.liu.se/~nisse/nettle/' + +description = """ + Nettle is a cryptographic library that is designed to fit easily in more or + less any context: In crypto toolkits for object-oriented languages (C++, + Python, Pike, ...), in applications like LSH or GNUPG, or even in + kernel space. +""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} +toolchainopts = {'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['46942627d5d0ca11720fec18d81fc38f7ef837ea4197c1f630e71ce0d470b11e'] + +builddependencies = [ + ('binutils', '2.28'), +] + +dependencies = [ + ('GMP', '6.1.2'), +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['nettle-hash', 'nettle-lfib-stream', + 'pkcs1-conv', 'sexp-conv']] + + ['lib64/libhogweed.a', 'lib64/libhogweed.%s' % SHLIB_EXT, + 'lib64/libnettle.a', 'lib64/libnettle.%s' % SHLIB_EXT], + 'dirs': ['include/nettle'], +} + +moduleclass = 'lib' -- GitLab From 20a3b73cc962b9526d078de85c8a002e95e300b3 Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Sun, 23 Jul 2017 21:46:01 -0500 Subject: [PATCH 1241/1603] adding easyconfigs: MPFR-3.1.5-GCCcore-6.4.0.eb --- .../m/MPFR/MPFR-3.1.5-GCCcore-6.4.0.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/m/MPFR/MPFR-3.1.5-GCCcore-6.4.0.eb diff --git a/easybuild/easyconfigs/m/MPFR/MPFR-3.1.5-GCCcore-6.4.0.eb b/easybuild/easyconfigs/m/MPFR/MPFR-3.1.5-GCCcore-6.4.0.eb new file mode 100644 index 0000000000..b3d040944b --- /dev/null +++ b/easybuild/easyconfigs/m/MPFR/MPFR-3.1.5-GCCcore-6.4.0.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'MPFR' +version = '3.1.5' + +homepage = 'http://www.mpfr.org' + +description = """ + The MPFR library is a C library for multiple-precision floating-point + computations with correct rounding. +""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} + +source_urls = ['http://www.mpfr.org/mpfr-%(version)s/'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['ca498c1c7a74dd37a576f353312d1e68d490978de4395fa28f1cbd46a364e658'] + +patches = ['MPFR_ictce_remove-deprecated-mp.patch'] + +builddependencies = [ + ('binutils', '2.28'), +] + +dependencies = [ + ('GMP', '6.1.2'), +] + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libmpfr.%s' % SHLIB_EXT, 'include/mpfr.h'], + 'dirs': [], +} + +moduleclass = 'math' -- GitLab From 86a06bdd617bfb5428ceb5224ecb94bfec00c7df Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Sun, 23 Jul 2017 22:19:49 -0500 Subject: [PATCH 1242/1603] adding easyconfigs: METIS-5.1.0-GCCcore-6.4.0.eb --- .../m/METIS/METIS-5.1.0-GCCcore-6.4.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/m/METIS/METIS-5.1.0-GCCcore-6.4.0.eb diff --git a/easybuild/easyconfigs/m/METIS/METIS-5.1.0-GCCcore-6.4.0.eb b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-GCCcore-6.4.0.eb new file mode 100644 index 0000000000..3845c5050b --- /dev/null +++ b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-GCCcore-6.4.0.eb @@ -0,0 +1,34 @@ +name = 'METIS' +version = '5.1.0' + +homepage = 'http://glaros.dtc.umn.edu/gkhome/metis/metis/overview' + +description = """ + METIS is a set of serial programs for partitioning graphs, partitioning + finite element meshes, and producing fill reducing orderings for sparse + matrices. The algorithms implemented in METIS are based on the multilevel + recursive-bisection, multilevel k-way, and multi-constraint partitioning + schemes. +""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} +toolchainopts = {'pic': True} + +source_urls = [ + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis', + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/OLD', +] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['76faebe03f6c963127dbb73c13eab58c9a3faeae48779f049066a21c087c5db2'] + +# We use 32bit for indices and 64bit for content +patches = ['METIS-5.1.0-use-doubles.patch'] + +builddependencies = [ + ('binutils', '2.28'), + ('CMake', '3.8.2'), +] + +configopts = ['', 'shared=1'] + +moduleclass = 'math' -- GitLab From 8c74f9fc39db31ab3c7780e50e5c732bbb57a93d Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Mon, 24 Jul 2017 10:29:55 +0200 Subject: [PATCH 1243/1603] fix moduleclass for Cookiecutter --- .../Cookiecutter-1.4.0-goolf-1.7.20-Python-2.7.11.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/Cookiecutter/Cookiecutter-1.4.0-goolf-1.7.20-Python-2.7.11.eb b/easybuild/easyconfigs/c/Cookiecutter/Cookiecutter-1.4.0-goolf-1.7.20-Python-2.7.11.eb index df729ad2ff..928a132412 100644 --- a/easybuild/easyconfigs/c/Cookiecutter/Cookiecutter-1.4.0-goolf-1.7.20-Python-2.7.11.eb +++ b/easybuild/easyconfigs/c/Cookiecutter/Cookiecutter-1.4.0-goolf-1.7.20-Python-2.7.11.eb @@ -78,4 +78,4 @@ sanity_check_paths = { modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} -moduleclass = 'bio' +moduleclass = 'tools' -- GitLab From 284d51c25c7736dfc250f3415454e6d0c4671c4f Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Mon, 24 Jul 2017 07:53:10 -0500 Subject: [PATCH 1244/1603] adding easyconfigs: Java-1.8.0_141.eb --- .../easyconfigs/j/Java/Java-1.8.0_141.eb | 20 +++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 easybuild/easyconfigs/j/Java/Java-1.8.0_141.eb diff --git a/easybuild/easyconfigs/j/Java/Java-1.8.0_141.eb b/easybuild/easyconfigs/j/Java/Java-1.8.0_141.eb new file mode 100644 index 0000000000..5ecb4ab81c --- /dev/null +++ b/easybuild/easyconfigs/j/Java/Java-1.8.0_141.eb @@ -0,0 +1,20 @@ +name = 'Java' +version = '1.8.0_141' + +homepage = 'http://java.com/' + +description = """ + Java Platform, Standard Edition (Java SE) lets you develop and deploy + Java applications on desktops and servers. +""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +# download the tar.gz directly from +# http://www.oracle.com/technetwork/java/javase/downloads/index.html +(vp, vs) = version.split('_') +altver = '%su%s' % (vp.split('.')[1], vs) +sources = ['jdk-%s-linux-x64.tar.gz' % altver] +checksums = ['041d5218fbea6cd7e81c8c15e51d0d32911573af2ed69e066787a8dc8a39ba4f'] + +moduleclass = 'lang' -- GitLab From ee0c897759c9410ea13ef0b611d07b5d47185da5 Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Mon, 24 Jul 2017 08:15:13 -0500 Subject: [PATCH 1245/1603] adding easyconfigs: ART-2016.06.05-GCCcore-6.4.0.eb --- .../a/ART/ART-2016.06.05-GCCcore-6.4.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/a/ART/ART-2016.06.05-GCCcore-6.4.0.eb diff --git a/easybuild/easyconfigs/a/ART/ART-2016.06.05-GCCcore-6.4.0.eb b/easybuild/easyconfigs/a/ART/ART-2016.06.05-GCCcore-6.4.0.eb new file mode 100644 index 0000000000..f15d1e1ba6 --- /dev/null +++ b/easybuild/easyconfigs/a/ART/ART-2016.06.05-GCCcore-6.4.0.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'ART' +version = '2016.06.05' + +homepage = 'http://www.niehs.nih.gov/research/resources/software/biostatistics/art/' + +description = """ + ART is a set of simulation tools to generate synthetic next-generation sequencing reads" +""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} + +source_urls = ['http://www.niehs.nih.gov/research/resources/assets/docs/'] +sources = ['artsrcmountrainier%slinuxtgz.tgz' % ''.join(version.split('.'))] +checksums = ['69aede60884eb848de043aae5294274b7ca6348b7384a8380f0ac5a4dfeff488'] + +builddependencies = [ + ('binutils', '2.28'), +] + +dependencies = [ + ('GSL', '2.4'), +] + +sanity_check_paths = { + 'files': ['bin/aln2bed.pl', 'bin/art_454', 'bin/art_illumina', + 'bin/art_profiler_454', 'bin/art_profiler_illumina', + 'bin/art_SOLiD', 'bin/combinedAvg.pl', 'bin/empDist.pl', + 'bin/fastqReadAvg.pl', 'bin/map2bed.pl', 'bin/summation.pl'], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From ce1dcd63f731e2750806bd2f2922a475e9f446ee Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Mon, 24 Jul 2017 08:40:57 -0500 Subject: [PATCH 1246/1603] adding easyconfigs: Blosc-1.12.1-GCCcore-6.4.0.eb --- .../b/Blosc/Blosc-1.12.1-GCCcore-6.4.0.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/b/Blosc/Blosc-1.12.1-GCCcore-6.4.0.eb diff --git a/easybuild/easyconfigs/b/Blosc/Blosc-1.12.1-GCCcore-6.4.0.eb b/easybuild/easyconfigs/b/Blosc/Blosc-1.12.1-GCCcore-6.4.0.eb new file mode 100644 index 0000000000..ca8add747d --- /dev/null +++ b/easybuild/easyconfigs/b/Blosc/Blosc-1.12.1-GCCcore-6.4.0.eb @@ -0,0 +1,27 @@ +easyblock = 'CMakeMake' + +name = 'Blosc' +version = '1.12.1' + +homepage = 'http://www.blosc.org/' + +description = "Blosc, an extremely fast, multi-threaded, meta-compressor library" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} + +source_urls = ['https://github.com/Blosc/c-blosc/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['e04535e816bb942bedc9a0ba209944d1eb34e26e2d9cca37f114e8ee292cb3c8'] + +builddependencies = [ + ('binutils', '2.28'), + ('CMake', '3.8.2'), +] + +sanity_check_paths = { + 'files': ['include/blosc-export.h', 'include/blosc.h', 'lib/libblosc.a', + 'lib/libblosc.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' -- GitLab From 68c9c7d7e9c1b4a80b4e208f690c7f353257c4a0 Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Mon, 24 Jul 2017 09:01:44 -0500 Subject: [PATCH 1247/1603] adding easyconfigs: BWA-0.7.15-GCCcore-6.4.0.eb --- .../b/BWA/BWA-0.7.15-GCCcore-6.4.0.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/b/BWA/BWA-0.7.15-GCCcore-6.4.0.eb diff --git a/easybuild/easyconfigs/b/BWA/BWA-0.7.15-GCCcore-6.4.0.eb b/easybuild/easyconfigs/b/BWA/BWA-0.7.15-GCCcore-6.4.0.eb new file mode 100644 index 0000000000..01ef5ad9dc --- /dev/null +++ b/easybuild/easyconfigs/b/BWA/BWA-0.7.15-GCCcore-6.4.0.eb @@ -0,0 +1,41 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Cyprus Institute / CaSToRC, Uni.Lu/LCSB, NTUA +# Authors:: George Tsouloupas , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +# +# Version >= 0.7.15 +# Author: Adam Huffman +# The Francis Crick Institute +# +# Note that upstream development is mainly at: https://github.com/lh3/bwa +## + +name = 'BWA' +version = '0.7.15' + +homepage = 'http://bio-bwa.sourceforge.net/' + +description = """ + Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively + short nucleotide sequences against a long reference sequence such as the human + genome. +""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['https://github.com/lh3/%(name)s/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['126d247e6ab8a8c215bec248f9174a15c6d960c193330e659a2b686f2964cfbd'] + +builddependencies = [ + ('binutils', '2.28'), +] + +moduleclass = 'bio' -- GitLab From 2a5855b03fe9099918fc63aa1842f80287d5d111 Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Mon, 24 Jul 2017 09:26:38 -0500 Subject: [PATCH 1248/1603] adding easyconfigs: CppUnit-1.12.1-GCCcore-6.4.0.eb --- .../c/CppUnit/CppUnit-1.12.1-GCCcore-6.4.0.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/c/CppUnit/CppUnit-1.12.1-GCCcore-6.4.0.eb diff --git a/easybuild/easyconfigs/c/CppUnit/CppUnit-1.12.1-GCCcore-6.4.0.eb b/easybuild/easyconfigs/c/CppUnit/CppUnit-1.12.1-GCCcore-6.4.0.eb new file mode 100644 index 0000000000..048b593ee0 --- /dev/null +++ b/easybuild/easyconfigs/c/CppUnit/CppUnit-1.12.1-GCCcore-6.4.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'CppUnit' +version = '1.12.1' + +homepage = 'http://sourceforge.net/projects/cppunit/' + +description = """ + CppUnit is the C++ port of the famous JUnit framework for unit testing. +""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['ac28a04c8e6c9217d910b0ae7122832d28d9917fa668bcc9e0b8b09acb4ea44a'] + +builddependencies = [ + ('binutils', '2.28'), +] + +sanity_check_paths = { + 'files': ['lib/libcppunit.a', 'lib/libcppunit.%s' % SHLIB_EXT, + 'lib/pkgconfig/cppunit.pc'], + 'dirs': ['bin', 'include/cppunit', 'share'], +} + +moduleclass = 'tools' -- GitLab From b54e0653afafe1a941826399fefb9f5e7186b7b3 Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Mon, 24 Jul 2017 09:50:56 -0500 Subject: [PATCH 1249/1603] adding easyconfigs: Doxygen-1.8.13-GCCcore-6.4.0.eb --- .../d/Doxygen/Doxygen-1.8.13-GCCcore-6.4.0.eb | 26 ++++++++++++++ .../pkg-config-0.29.2-GCCcore-6.4.0.eb | 36 +++++++++++++++++++ 2 files changed, 62 insertions(+) create mode 100644 easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.13-GCCcore-6.4.0.eb create mode 100644 easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2-GCCcore-6.4.0.eb diff --git a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.13-GCCcore-6.4.0.eb b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.13-GCCcore-6.4.0.eb new file mode 100644 index 0000000000..ed9c7f458e --- /dev/null +++ b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.13-GCCcore-6.4.0.eb @@ -0,0 +1,26 @@ +name = 'Doxygen' +version = '1.8.13' + +homepage = 'http://www.doxygen.org' + +description = """ + Doxygen is a documentation system for C++, C, Java, Objective-C, Python, + IDL (Corba and Microsoft flavors), Fortran, VHDL, PHP, C#, and to some + extent D. +""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} + +source_urls = ['http://ftp.stack.nl/pub/users/dimitri/'] +sources = ['%(namelower)s-%(version)s.src.tar.gz'] +checksums = ['af667887bd7a87dc0dbf9ac8d86c96b552dfb8ca9c790ed1cbffaa6131573f6b'] + +builddependencies = [ + ('binutils', '2.28'), + ('Bison', '3.0.4'), + ('CMake', '3.8.2'), + ('flex', '2.6.4'), + ('pkg-config', '0.29.2'), +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2-GCCcore-6.4.0.eb b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2-GCCcore-6.4.0.eb new file mode 100644 index 0000000000..c02bedf48d --- /dev/null +++ b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2-GCCcore-6.4.0.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'pkg-config' +version = '0.29.2' + +homepage = 'http://www.freedesktop.org/wiki/Software/pkg-config/' + +description = """ + pkg-config is a helper tool used when compiling applications and libraries. + It helps you insert the correct compiler options on the command line so an + application can use gcc -o test test.c `pkg-config --libs --cflags glib-2.0` + for instance, rather than hard-coding values on where to find glib (or other + libraries). +""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} + +source_urls = ['https://pkg-config.freedesktop.org/releases/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['6fc69c01688c9458a57eb9a1664c9aba372ccda420a02bf4429fe610e7e7d591'] + +builddependencies = [ + ('binutils', '2.28'), +] + +# don't use PAX, it might break. +tar_config_opts = True + +configopts = " --with-internal-glib" + +sanity_check_paths = { + 'files': ['bin/pkg-config'], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From 4ba5efbc6a22807c30d91e6dad0e80f686f4700b Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Mon, 24 Jul 2017 10:12:05 -0500 Subject: [PATCH 1250/1603] adding easyconfigs: eudev-3.2.2-GCCcore-6.4.0.eb --- .../e/eudev/eudev-3.2.2-GCCcore-6.4.0.eb | 40 +++++++++++++++++++ .../g/gperf/gperf-3.1-GCCcore-6.4.0.eb | 31 ++++++++++++++ 2 files changed, 71 insertions(+) create mode 100644 easybuild/easyconfigs/e/eudev/eudev-3.2.2-GCCcore-6.4.0.eb create mode 100644 easybuild/easyconfigs/g/gperf/gperf-3.1-GCCcore-6.4.0.eb diff --git a/easybuild/easyconfigs/e/eudev/eudev-3.2.2-GCCcore-6.4.0.eb b/easybuild/easyconfigs/e/eudev/eudev-3.2.2-GCCcore-6.4.0.eb new file mode 100644 index 0000000000..a6182b36f4 --- /dev/null +++ b/easybuild/easyconfigs/e/eudev/eudev-3.2.2-GCCcore-6.4.0.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'eudev' +version = '3.2.2' + +homepage = 'https://wiki.gentoo.org/wiki/Project:Eudev' + +description = """ + eudev is a fork of systemd-udev with the goal of obtaining better + compatibility with existing software such as OpenRC and Upstart, + older kernels, various toolchains and anything else required by + users and various distributions. +""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} + +source_urls = ['http://dev.gentoo.org/~blueness/%(name)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['3e4c56ec2fc1854afd0a31f3affa48f922c62d40ee12a0c1a4b4f152ef5b0f63'] + +patches = ['%(name)s-3.1.2_pre-2.6.34_kernel.patch'] + +builddependencies = [ + ('binutils', '2.28'), + ('gperf', '3.1'), +] + +osdependencies = [('kernel-headers', 'linux-libc-dev')] + +configopts = '--disable-blkid --disable-selinux --disable-manpages ' + +runtest = 'check' + +sanity_check_paths = { + 'files': ['bin/udevadm', 'include/libudev.h', 'include/udev.h', + 'lib/libudev.so.1'], + 'dirs': [], +} + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/g/gperf/gperf-3.1-GCCcore-6.4.0.eb b/easybuild/easyconfigs/g/gperf/gperf-3.1-GCCcore-6.4.0.eb new file mode 100644 index 0000000000..6dd680f7e4 --- /dev/null +++ b/easybuild/easyconfigs/g/gperf/gperf-3.1-GCCcore-6.4.0.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'gperf' +version = '3.1' + +homepage = 'http://www.gnu.org/software/gperf/' + +description = """ + GNU gperf is a perfect hash function generator. For a given list of strings, + it produces a hash function and hash table, in form of C or C++ code, for + looking up a value depending on the input string. The hash function is + perfect, which means that the hash table has no collisions, and the hash + table lookup needs a single string comparison only. +""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['588546b945bba4b70b6a3a616e80b4ab466e3f33024a352fc2198112cdbb3ae2'] + +builddependencies = [ + ('binutils', '2.28'), +] + +sanity_check_paths = { + 'files': ['bin/gperf'], + 'dirs': [] +} + +moduleclass = 'devel' -- GitLab From d4ef20f7ad04bc73be38c195d5621f1bff787e29 Mon Sep 17 00:00:00 2001 From: Robert Date: Wed, 26 Jul 2017 12:27:36 +0930 Subject: [PATCH 1251/1603] GRIDSS easyconfig added --- .../GRIDSS-1.4.1-foss-2016b-Java-1.8.0_121.eb | 47 +++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 easybuild/easyconfigs/g/GRIDSS/GRIDSS-1.4.1-foss-2016b-Java-1.8.0_121.eb diff --git a/easybuild/easyconfigs/g/GRIDSS/GRIDSS-1.4.1-foss-2016b-Java-1.8.0_121.eb b/easybuild/easyconfigs/g/GRIDSS/GRIDSS-1.4.1-foss-2016b-Java-1.8.0_121.eb new file mode 100644 index 0000000000..da8862ae04 --- /dev/null +++ b/easybuild/easyconfigs/g/GRIDSS/GRIDSS-1.4.1-foss-2016b-Java-1.8.0_121.eb @@ -0,0 +1,47 @@ +## +# This is a contribution from Phoenix HPC Service, The University of Adelaide, Australia +# Homepage: https://www.adelaide.edu.au/phoenix/ +# +# Copyright:: adelaide.edu.au/phoenix +# Authors:: Robert Qiao , Exe Escobedo +# License:: GPL-v3.0 +# +# Notes:: +## + +easyblock = 'Binary' + +name = 'GRIDSS' +version = '1.4.1' + +homepage = 'https://github.com/PapenfussLab/gridss' +description = """ GRIDSS a module software suite containing tools +useful for the detection genomic rearrangements. +GRIDSS includes a genome-wide break-end assembler, +as well as a structural variation caller for Illumina sequencing data. +GRIDSS calls variants based on alignment-guided positional de Bruijn graph +genome-wide break-end assembly, split read, and read pair evidence. +""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['https://github.com/PapenfussLab/gridss/releases/download/v%(version)s'] +sources = ['%(name)s-%(version)s-jar-with-dependencies.jar'] + +java = 'Java' +javaver = '1.8.0_121' +versionsuffix = '-%s-%s' % (java, javaver) + +dependencies = [ + (java, javaver, '', True), + ('R', '3.4.0'), +] + +sanity_check_paths = { + 'files': ['%(name)s-%(version)s-jar-with-dependencies.jar'], + 'dirs': [], +} + +modloadmsg = 'To execute GRIDSS run: java -jar $EBROOTGRIDSS/%(name)s-%(version)s-jar-with-dependencies.jar\n' + +moduleclass = 'bio' -- GitLab From da70e5076f4b1ee2cad32def558cd126b31713d0 Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Wed, 26 Jul 2017 08:33:56 -0500 Subject: [PATCH 1252/1603] adding easyconfigs: hwloc-1.11.7-GCCcore-6.4.0.eb --- .../h/hwloc/hwloc-1.11.7-GCCcore-6.4.0.eb | 41 +++++++++++++++++++ .../n/numactl/numactl-2.0.11-GCCcore-6.4.0.eb | 31 ++++++++++++++ 2 files changed, 72 insertions(+) create mode 100644 easybuild/easyconfigs/h/hwloc/hwloc-1.11.7-GCCcore-6.4.0.eb create mode 100644 easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCCcore-6.4.0.eb diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.7-GCCcore-6.4.0.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.7-GCCcore-6.4.0.eb new file mode 100644 index 0000000000..aed499874e --- /dev/null +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.7-GCCcore-6.4.0.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'hwloc' +version = '1.11.7' + +homepage = 'http://www.open-mpi.org/projects/hwloc/' + +description = """ + The Portable Hardware Locality (hwloc) software package provides a portable + abstraction (across OS, versions, architectures, ...) of the hierarchical + topology of modern architectures, including NUMA memory nodes, sockets, shared + caches, cores and simultaneous multithreading. It also gathers various system + attributes such as cache and memory information as well as the locality of I/O + devices such as network interfaces, InfiniBand HCAs or GPUs. It primarily + aims at helping applications with gathering information about modern computing + hardware so as to exploit it accordingly and efficiently. +""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} + +source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] +sources = [SOURCE_TAR_GZ] +checksums = ['ac16bed9cdd3c63bca1fe1ac3de522a1376b1487c4fc85b7b19592e28fd98e26'] + +builddependencies = [ + ('binutils', '2.28'), +] + +dependencies = [ + ('numactl', '2.0.11'), +] + +configopts = "--enable-libnuma=$EBROOTNUMACTL" + +sanity_check_paths = { + 'files': ['bin/lstopo', 'include/hwloc/linux.h', 'sbin/hwloc-dump-hwdata', + 'lib/libhwloc.%s' % SHLIB_EXT], + 'dirs': ['share/man/man3'], +} + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCCcore-6.4.0.eb b/easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCCcore-6.4.0.eb new file mode 100644 index 0000000000..7ce46ec76c --- /dev/null +++ b/easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCCcore-6.4.0.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'numactl' +version = '2.0.11' + +homepage = 'http://oss.sgi.com/projects/libnuma/' + +description = """ + The numactl program allows you to run your application program on specific + cpu's and memory nodes. It does this by supplying a NUMA memory policy to + the operating system before running your program. The libnuma library provides + convenient ways for you to add NUMA memory policies into your own program. +""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} +toolchainopts = {'pic': True} + +source_urls = ['ftp://oss.sgi.com/www/projects/libnuma/download/'] +sources = [SOURCE_TAR_GZ] +checksums = ['450c091235f891ee874a8651b179c30f57a1391ca5c4673354740ba65e527861'] + +builddependencies = [ + ('binutils', '2.28'), +] + +sanity_check_paths = { + 'files': ['bin/numactl', 'bin/numastat', 'lib/libnuma.%s' % SHLIB_EXT, 'lib/libnuma.a'], + 'dirs': ['share/man', 'include'] +} + +moduleclass = 'tools' -- GitLab From 3da7cf78fb7bb50b1edc37d9223477382a598ab3 Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Wed, 26 Jul 2017 09:30:17 -0500 Subject: [PATCH 1253/1603] adding easyconfigs: libevent-2.1.8-GCCcore-6.4.0.eb --- .../libevent/libevent-2.1.8-GCCcore-6.4.0.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/l/libevent/libevent-2.1.8-GCCcore-6.4.0.eb diff --git a/easybuild/easyconfigs/l/libevent/libevent-2.1.8-GCCcore-6.4.0.eb b/easybuild/easyconfigs/l/libevent/libevent-2.1.8-GCCcore-6.4.0.eb new file mode 100644 index 0000000000..2b1365f41e --- /dev/null +++ b/easybuild/easyconfigs/l/libevent/libevent-2.1.8-GCCcore-6.4.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'libevent' +version = '2.1.8' + +homepage = 'http://libevent.org/' + +description = """ + The libevent API provides a mechanism to execute a callback function when + a specific event occurs on a file descriptor or after a timeout has been + reached. Furthermore, libevent also support callbacks due to signals or + regular timeouts. +""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/%(name)s/%(name)s/releases/download/release-%(version)s-stable/'] +sources = ['%(name)s-%(version)s-stable.tar.gz'] +checksums = ['965cc5a8bb46ce4199a47e9b2c9e1cae3b137e8356ffdad6d94d3b9069b71dc2'] + +builddependencies = [ + ('binutils', '2.28'), +] + +sanity_check_paths = { + 'files': ['bin/event_rpcgen.py', 'include/event.h', 'include/event2/event.h', + 'lib/libevent_core.%s' % SHLIB_EXT, 'lib/pkgconfig/libevent.pc'], + 'dirs': [], +} + +moduleclass = 'lib' -- GitLab From a594817e166bac17c9d70276af611030be22379d Mon Sep 17 00:00:00 2001 From: Robert Date: Thu, 27 Jul 2017 10:34:11 +0930 Subject: [PATCH 1254/1603] GRIDSS removed --- .../GRIDSS-1.4.1-foss-2016b-Java-1.8.0_121.eb | 47 ------------------- 1 file changed, 47 deletions(-) delete mode 100644 easybuild/easyconfigs/g/GRIDSS/GRIDSS-1.4.1-foss-2016b-Java-1.8.0_121.eb diff --git a/easybuild/easyconfigs/g/GRIDSS/GRIDSS-1.4.1-foss-2016b-Java-1.8.0_121.eb b/easybuild/easyconfigs/g/GRIDSS/GRIDSS-1.4.1-foss-2016b-Java-1.8.0_121.eb deleted file mode 100644 index da8862ae04..0000000000 --- a/easybuild/easyconfigs/g/GRIDSS/GRIDSS-1.4.1-foss-2016b-Java-1.8.0_121.eb +++ /dev/null @@ -1,47 +0,0 @@ -## -# This is a contribution from Phoenix HPC Service, The University of Adelaide, Australia -# Homepage: https://www.adelaide.edu.au/phoenix/ -# -# Copyright:: adelaide.edu.au/phoenix -# Authors:: Robert Qiao , Exe Escobedo -# License:: GPL-v3.0 -# -# Notes:: -## - -easyblock = 'Binary' - -name = 'GRIDSS' -version = '1.4.1' - -homepage = 'https://github.com/PapenfussLab/gridss' -description = """ GRIDSS a module software suite containing tools -useful for the detection genomic rearrangements. -GRIDSS includes a genome-wide break-end assembler, -as well as a structural variation caller for Illumina sequencing data. -GRIDSS calls variants based on alignment-guided positional de Bruijn graph -genome-wide break-end assembly, split read, and read pair evidence. -""" - -toolchain = {'name': 'foss', 'version': '2016b'} - -source_urls = ['https://github.com/PapenfussLab/gridss/releases/download/v%(version)s'] -sources = ['%(name)s-%(version)s-jar-with-dependencies.jar'] - -java = 'Java' -javaver = '1.8.0_121' -versionsuffix = '-%s-%s' % (java, javaver) - -dependencies = [ - (java, javaver, '', True), - ('R', '3.4.0'), -] - -sanity_check_paths = { - 'files': ['%(name)s-%(version)s-jar-with-dependencies.jar'], - 'dirs': [], -} - -modloadmsg = 'To execute GRIDSS run: java -jar $EBROOTGRIDSS/%(name)s-%(version)s-jar-with-dependencies.jar\n' - -moduleclass = 'bio' -- GitLab From cf13ceae12d3bf04f635a240c8200c43e7867ea2 Mon Sep 17 00:00:00 2001 From: Robert Qiao Date: Thu, 27 Jul 2017 11:33:32 +0930 Subject: [PATCH 1255/1603] erratum --- easybuild/easyconfigs/b/BWA/BWA-0.7.15-foss-2016b.eb | 2 +- .../PyTables/PyTables-3.3.0-foss-2016b-Python-2.7.12.eb | 2 ++ .../p/Pysam/Pysam-0.10.0-foss-2016b-Python-2.7.12.eb | 9 ++++++--- 3 files changed, 9 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/b/BWA/BWA-0.7.15-foss-2016b.eb b/easybuild/easyconfigs/b/BWA/BWA-0.7.15-foss-2016b.eb index ceb6b4b6b3..b34d5dc185 100644 --- a/easybuild/easyconfigs/b/BWA/BWA-0.7.15-foss-2016b.eb +++ b/easybuild/easyconfigs/b/BWA/BWA-0.7.15-foss-2016b.eb @@ -18,7 +18,7 @@ description = """Burrows-Wheeler Aligner (BWA) is an efficient program that alig relatively short nucleotide sequences against a long reference sequence such as the human genome.""" toolchain = {'name': 'foss', 'version': '2016b'} -toolchainopts = {'optarch': True, 'pic': True, 'usempi': True} +toolchainopts = {'optarch': True, 'pic': True} sources = [SOURCELOWER_TAR_BZ2] source_urls = [('http://sourceforge.net/projects/bio-bwa/files/', 'download')] diff --git a/easybuild/easyconfigs/p/PyTables/PyTables-3.3.0-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/PyTables/PyTables-3.3.0-foss-2016b-Python-2.7.12.eb index 69afe0d8b8..17ca3dd82f 100644 --- a/easybuild/easyconfigs/p/PyTables/PyTables-3.3.0-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/p/PyTables/PyTables-3.3.0-foss-2016b-Python-2.7.12.eb @@ -34,6 +34,8 @@ dependencies = [ ('Python', '2.7.12'), ('numexpr', '2.6.1', versionsuffix), ('HDF5', '1.8.18'), + ('LZO', '2.10'), + ('Blosc', '1.12.1'), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/p/Pysam/Pysam-0.10.0-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/Pysam/Pysam-0.10.0-foss-2016b-Python-2.7.12.eb index 417ee652b8..3d9c40570f 100644 --- a/easybuild/easyconfigs/p/Pysam/Pysam-0.10.0-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/p/Pysam/Pysam-0.10.0-foss-2016b-Python-2.7.12.eb @@ -18,11 +18,11 @@ description = """Pysam is a python module for reading and manipulating Samfiles. toolchain = {'name': 'foss', 'version': '2016b'} -parallel = 1 +source_urls = ['https://github.com/pysam-developers/pysam/archive/'] +sources = ['v%(version)s.tar.gz'] dependencies = [ ('Python', '2.7.12'), - ('Cython', '0.25.2', versionsuffix), ('ncurses', '6.0'), ('zlib', '1.2.8'), ('cURL', '7.49.1'), @@ -33,6 +33,9 @@ exts_defaultclass = 'PythonPackage' exts_filter = ("python -c 'import %(ext_name)s'", '') exts_list = [ + ('Cython', '0.25.2', { + 'source_urls': ['https://pypi.python.org/packages/source/c/cython/'], + }), ('pysam', version, { 'source_tmpl': 'v%(version)s.tar.gz', 'source_urls': ['https://github.com/pysam-developers/pysam/archive/'], @@ -45,7 +48,7 @@ modextrapaths = { sanity_check_paths = { 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages/pysam-%(version)s-py%(pyshortver)s-linux-x86_64.egg'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], } moduleclass = 'bio' -- GitLab From 38e5a51f88ca9ec5022f79b2d01ea15ddf3b54e9 Mon Sep 17 00:00:00 2001 From: Robert Date: Thu, 27 Jul 2017 11:36:21 +0930 Subject: [PATCH 1256/1603] more deps added --- .../b/Blosc/Blosc-1.12.1-foss-2016b.eb | 32 +++++++++++++++++ .../easyconfigs/l/LZO/LZO-2.10-foss-2016b.eb | 34 +++++++++++++++++++ 2 files changed, 66 insertions(+) create mode 100644 easybuild/easyconfigs/b/Blosc/Blosc-1.12.1-foss-2016b.eb create mode 100644 easybuild/easyconfigs/l/LZO/LZO-2.10-foss-2016b.eb diff --git a/easybuild/easyconfigs/b/Blosc/Blosc-1.12.1-foss-2016b.eb b/easybuild/easyconfigs/b/Blosc/Blosc-1.12.1-foss-2016b.eb new file mode 100644 index 0000000000..e6c95a3b77 --- /dev/null +++ b/easybuild/easyconfigs/b/Blosc/Blosc-1.12.1-foss-2016b.eb @@ -0,0 +1,32 @@ +## +# This is a contribution from Phoenix HPC Service, The University of Adelaide, Australia +# Homepage: https://www.adelaide.edu.au/phoenix/ +# +# Copyright:: Copyright 2014-2017 adelaide.edu.au/phoenix +# Authors:: Robert Qiao , Exequiel Sepulveda +# License:: BSD +# +# Notes:: +## + +easyblock = 'CMakeMake' + +name = 'Blosc' +version = '1.12.1' + +homepage = 'http://www.blosc.org/' +description = "Blosc, an extremely fast, multi-threaded, meta-compressor library" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['https://github.com/Blosc/c-blosc/archive/'] +sources = ['v%(version)s.tar.gz'] + +builddependencies = [('CMake', '3.7.2')] + +sanity_check_paths = { + 'files': ['include/blosc-export.h', 'include/blosc.h', 'lib/libblosc.a', 'lib/libblosc.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/LZO/LZO-2.10-foss-2016b.eb b/easybuild/easyconfigs/l/LZO/LZO-2.10-foss-2016b.eb new file mode 100644 index 0000000000..3e18b6f723 --- /dev/null +++ b/easybuild/easyconfigs/l/LZO/LZO-2.10-foss-2016b.eb @@ -0,0 +1,34 @@ +## +# This is a contribution from Phoenix HPC Service, The University of Adelaide, Australia +# Homepage: https://www.adelaide.edu.au/phoenix/ +# +# Copyright:: Copyright 2014-2017 adelaide.edu.au/phoenix +# Authors:: Robert Qiao , Exequiel Sepulveda +# License:: MIT/GPL +# +# Notes:: Adopted from EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Fotis Georgatos +## + +easyblock = 'ConfigureMake' + +name = 'LZO' +version = '2.10' + +homepage = 'http://www.oberhumer.com/opensource/lzo/' +description = "Portable lossless data compression library" + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [homepage + 'download/'] + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'pic': True} + +runtest = 'test' + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib', 'include'] +} + +moduleclass = 'devel' -- GitLab From 43185b86cd36a25234b106afeba9810d7a349f16 Mon Sep 17 00:00:00 2001 From: Robert Qiao Date: Thu, 27 Jul 2017 11:51:14 +0930 Subject: [PATCH 1257/1603] erratum --- .../p/Pysam/Pysam-0.10.0-foss-2016b-Python-2.7.12.eb | 3 --- 1 file changed, 3 deletions(-) diff --git a/easybuild/easyconfigs/p/Pysam/Pysam-0.10.0-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/Pysam/Pysam-0.10.0-foss-2016b-Python-2.7.12.eb index 3d9c40570f..1883ed4c3a 100644 --- a/easybuild/easyconfigs/p/Pysam/Pysam-0.10.0-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/p/Pysam/Pysam-0.10.0-foss-2016b-Python-2.7.12.eb @@ -18,9 +18,6 @@ description = """Pysam is a python module for reading and manipulating Samfiles. toolchain = {'name': 'foss', 'version': '2016b'} -source_urls = ['https://github.com/pysam-developers/pysam/archive/'] -sources = ['v%(version)s.tar.gz'] - dependencies = [ ('Python', '2.7.12'), ('ncurses', '6.0'), -- GitLab From 319aab57534399ac9c28f73068fc9120e2e192a2 Mon Sep 17 00:00:00 2001 From: Robert Date: Thu, 27 Jul 2017 12:29:11 +0930 Subject: [PATCH 1258/1603] formatting error --- .../GroopM-0.3.4-foss-2016b-Python-2.7.12.eb | 2 +- .../libunistring-0.9.7-GCCcore-6.4.0.eb | 33 --------------- .../Pysam-0.10.0-foss-2016b-Python-2.7.12.eb | 4 +- .../util-linux-2.30-GCCcore-6.4.0.eb | 42 ------------------- 4 files changed, 3 insertions(+), 78 deletions(-) delete mode 100644 easybuild/easyconfigs/l/libunistring/libunistring-0.9.7-GCCcore-6.4.0.eb delete mode 100644 easybuild/easyconfigs/u/util-linux/util-linux-2.30-GCCcore-6.4.0.eb diff --git a/easybuild/easyconfigs/g/GroopM/GroopM-0.3.4-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/g/GroopM/GroopM-0.3.4-foss-2016b-Python-2.7.12.eb index 508fa6454b..c2df780ed6 100644 --- a/easybuild/easyconfigs/g/GroopM/GroopM-0.3.4-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/g/GroopM/GroopM-0.3.4-foss-2016b-Python-2.7.12.eb @@ -28,7 +28,7 @@ sources = [SOURCE_TAR_GZ] dependencies = [ ('Python', '2.7.12'), ('Cython', '0.25.2', versionsuffix), - ('matplotlib', '1.5.2', versionsuffix), + ('matplotlib', '1.5.2', versionsuffix), ('Pysam', '0.10.0', versionsuffix), ('PyTables', '3.3.0', versionsuffix), ('PIL', '1.1.7', versionsuffix), diff --git a/easybuild/easyconfigs/l/libunistring/libunistring-0.9.7-GCCcore-6.4.0.eb b/easybuild/easyconfigs/l/libunistring/libunistring-0.9.7-GCCcore-6.4.0.eb deleted file mode 100644 index 8d845c9877..0000000000 --- a/easybuild/easyconfigs/l/libunistring/libunistring-0.9.7-GCCcore-6.4.0.eb +++ /dev/null @@ -1,33 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'libunistring' -version = '0.9.7' - -homepage = 'http://www.gnu.org/software/libunistring/' - -description = """ - This library provides functions for manipulating Unicode strings and for - manipulating C strings according to the Unicode standard. -""" - -toolchain = {'name': 'GCCcore', 'version': '6.4.0'} -toolchainopts = {'pic': True} - -sources = [SOURCELOWER_TAR_XZ] -source_urls = [GNU_SOURCE] -checksums = ['2e3764512aaf2ce598af5a38818c0ea23dedf1ff5460070d1b6cee5c3336e797'] - -builddependencies = [ - ('binutils', '2.28'), -] - -parallel = 1 - -sanity_check_paths = { - 'files': ['lib/libunistring.a', 'lib/libunistring.%s' % SHLIB_EXT] + - ['include/uni%s.h' % x for x in ['case', 'conv', 'ctype', 'lbrk', 'name', 'norm', - 'stdio', 'str', 'types', 'wbrk', 'width']], - 'dirs': ['include/unistring'], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/Pysam/Pysam-0.10.0-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/Pysam/Pysam-0.10.0-foss-2016b-Python-2.7.12.eb index 1883ed4c3a..2b20d1cb81 100644 --- a/easybuild/easyconfigs/p/Pysam/Pysam-0.10.0-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/p/Pysam/Pysam-0.10.0-foss-2016b-Python-2.7.12.eb @@ -21,8 +21,8 @@ toolchain = {'name': 'foss', 'version': '2016b'} dependencies = [ ('Python', '2.7.12'), ('ncurses', '6.0'), - ('zlib', '1.2.8'), - ('cURL', '7.49.1'), + ('zlib', '1.2.8'), + ('cURL', '7.49.1'), ] # this is a bundle of Python packages diff --git a/easybuild/easyconfigs/u/util-linux/util-linux-2.30-GCCcore-6.4.0.eb b/easybuild/easyconfigs/u/util-linux/util-linux-2.30-GCCcore-6.4.0.eb deleted file mode 100644 index 3556edda8d..0000000000 --- a/easybuild/easyconfigs/u/util-linux/util-linux-2.30-GCCcore-6.4.0.eb +++ /dev/null @@ -1,42 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'util-linux' -version = '2.30' - -homepage = 'http://www.kernel.org/pub/linux/utils/util-linux' - -description = "Set of Linux utilities" - -toolchain = {'name': 'GCCcore', 'version': '6.4.0'} -toolchainopts = {'pic': True} - -source_urls = ['%s/v%%(version_major_minor)s' % homepage] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['e84cc32566abf28b84efb5ee326e1f3597c3d19b9916740f50c75bd57e498ce0'] - -# disable account related utilities (they need OS dependant pam-devel files) -# disable wall and friends (requires group changing permissions for install user) -# install systemd service files in install dir -# install bash completion files in install dir -configopts = "--disable-chfn-chsh --disable-login --disable-su " -configopts += "--disable-wall --disable-use-tty-group " -configopts += "--disable-makeinstall-chown --disable-makeinstall-setuid " -configopts += "--with-systemdsystemunitdir='${prefix}/systemd' " -configopts += "--with-bashcompletiondir='${prefix}/share/bash-completion/completions' " -# disable building Python bindings (since we don't include Python as a dep) -configopts += "--without-python " - -builddependencies = [ - ('binutils', '2.28'), -] - -dependencies = [ - ('ncurses', '6.0'), -] - -sanity_check_paths = { - 'files': ['lib/lib%s.a' % x for x in ['blkid', 'mount', 'uuid']], - 'dirs': ['include', 'bin', 'share', 'sbin'], -} - -moduleclass = 'tools' -- GitLab From 0ead13292dc089ed82d30720b162597a017b97a0 Mon Sep 17 00:00:00 2001 From: Robert Date: Thu, 27 Jul 2017 12:34:43 +0930 Subject: [PATCH 1259/1603] formatting error correction --- .../p/Pysam/Pysam-0.10.0-foss-2016b-Python-2.7.12.eb | 2 +- easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1-foss-2016b.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/Pysam/Pysam-0.10.0-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/Pysam/Pysam-0.10.0-foss-2016b-Python-2.7.12.eb index 2b20d1cb81..b341dbe1c1 100644 --- a/easybuild/easyconfigs/p/Pysam/Pysam-0.10.0-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/p/Pysam/Pysam-0.10.0-foss-2016b-Python-2.7.12.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # sciCORE - University of Basel # SIB Swiss Institute of Bioinformatics diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1-foss-2016b.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1-foss-2016b.eb index d688d2f69e..b99bb23bc1 100644 --- a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1-foss-2016b.eb +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1-foss-2016b.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA # Authors:: Robert Schmidt , Cedric Laczny , Fotis Georgatos -- GitLab From 9036bcfbbc5d32f247f48e568e96f4ab263277a8 Mon Sep 17 00:00:00 2001 From: Robert Date: Thu, 27 Jul 2017 12:41:35 +0930 Subject: [PATCH 1260/1603] format error correction --- easybuild/easyconfigs/b/BWA/BWA-0.7.15-foss-2016b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/BWA/BWA-0.7.15-foss-2016b.eb b/easybuild/easyconfigs/b/BWA/BWA-0.7.15-foss-2016b.eb index b34d5dc185..2e5a357fa6 100644 --- a/easybuild/easyconfigs/b/BWA/BWA-0.7.15-foss-2016b.eb +++ b/easybuild/easyconfigs/b/BWA/BWA-0.7.15-foss-2016b.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # # Copyright:: Copyright 2012-2014 Cyprus Institute / CaSToRC, Uni.Lu/LCSB, NTUA # Authors:: George Tsouloupas , Fotis Georgatos -- GitLab From cd0c8c5b5f0aef72e4b7e6d8d504031cfd77aa9d Mon Sep 17 00:00:00 2001 From: Robert Qiao Date: Thu, 27 Jul 2017 17:59:17 +0930 Subject: [PATCH 1261/1603] BAMM checksum --- easybuild/easyconfigs/b/BAMM/BAMM-2.5.0-foss-2016b.eb | 2 ++ .../g/GroopM/GroopM-0.3.4-foss-2016b-Python-2.7.12.eb | 1 + 2 files changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/b/BAMM/BAMM-2.5.0-foss-2016b.eb b/easybuild/easyconfigs/b/BAMM/BAMM-2.5.0-foss-2016b.eb index 67e73478f5..455fb6ff14 100644 --- a/easybuild/easyconfigs/b/BAMM/BAMM-2.5.0-foss-2016b.eb +++ b/easybuild/easyconfigs/b/BAMM/BAMM-2.5.0-foss-2016b.eb @@ -25,6 +25,8 @@ toolchainopts = {'usempi': True} source_urls = ['https://github.com/macroevolution/bamm/archive'] sources = ['v%(version)s.tar.gz'] +checksum = ['sha256':'8fb42c11aa636f74b14d780029e98558e5b2f1f0c18732deb957f598268061ee'] + builddependencies = [ ('CMake', '3.7.2'), ] diff --git a/easybuild/easyconfigs/g/GroopM/GroopM-0.3.4-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/g/GroopM/GroopM-0.3.4-foss-2016b-Python-2.7.12.eb index c2df780ed6..12f6cbd8f8 100644 --- a/easybuild/easyconfigs/g/GroopM/GroopM-0.3.4-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/g/GroopM/GroopM-0.3.4-foss-2016b-Python-2.7.12.eb @@ -20,6 +20,7 @@ description = """ GroopM is a metagenomic binning toolset. It leverages spatio-t dynamics (differential coverage) to accurately (and almost automatically) extract population genomes from multi-sample metagenomic datasets. """ + toolchain = {'name': 'foss', 'version': '2016b'} source_urls = [PYPI_SOURCE] -- GitLab From 4b397081891f476c2b4c9b299554c44275d5e543 Mon Sep 17 00:00:00 2001 From: Robert Date: Thu, 27 Jul 2017 18:29:34 +0930 Subject: [PATCH 1262/1603] checksum added --- easybuild/easyconfigs/b/BAMM/BAMM-2.5.0-foss-2016b.eb | 2 +- easybuild/easyconfigs/b/BWA/BWA-0.7.15-foss-2016b.eb | 2 ++ .../easyconfigs/b/BamM/BamM-1.7.3-foss-2016b-Python-2.7.12.eb | 2 ++ easybuild/easyconfigs/b/Blosc/Blosc-1.12.1-foss-2016b.eb | 1 + easybuild/easyconfigs/l/LZO/LZO-2.10-foss-2016b.eb | 2 ++ .../easyconfigs/p/PIL/PIL-1.1.7-foss-2016b-Python-2.7.12.eb | 2 ++ 6 files changed, 10 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/BAMM/BAMM-2.5.0-foss-2016b.eb b/easybuild/easyconfigs/b/BAMM/BAMM-2.5.0-foss-2016b.eb index 455fb6ff14..f3fb7d53c9 100644 --- a/easybuild/easyconfigs/b/BAMM/BAMM-2.5.0-foss-2016b.eb +++ b/easybuild/easyconfigs/b/BAMM/BAMM-2.5.0-foss-2016b.eb @@ -25,7 +25,7 @@ toolchainopts = {'usempi': True} source_urls = ['https://github.com/macroevolution/bamm/archive'] sources = ['v%(version)s.tar.gz'] -checksum = ['sha256':'8fb42c11aa636f74b14d780029e98558e5b2f1f0c18732deb957f598268061ee'] +checksums = ['526eef85ef011780ee21fe65cbc10ecc62efe54044102ae40bdef49c2985b4f4','sha256'] builddependencies = [ ('CMake', '3.7.2'), diff --git a/easybuild/easyconfigs/b/BWA/BWA-0.7.15-foss-2016b.eb b/easybuild/easyconfigs/b/BWA/BWA-0.7.15-foss-2016b.eb index 2e5a357fa6..50d340dd46 100644 --- a/easybuild/easyconfigs/b/BWA/BWA-0.7.15-foss-2016b.eb +++ b/easybuild/easyconfigs/b/BWA/BWA-0.7.15-foss-2016b.eb @@ -23,4 +23,6 @@ toolchainopts = {'optarch': True, 'pic': True} sources = [SOURCELOWER_TAR_BZ2] source_urls = [('http://sourceforge.net/projects/bio-bwa/files/', 'download')] +checksums = ['fcf470a46a1dbe2f96a1c5b87c530554', 'md5'] + moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BamM/BamM-1.7.3-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/b/BamM/BamM-1.7.3-foss-2016b-Python-2.7.12.eb index d0986b1904..127247b759 100644 --- a/easybuild/easyconfigs/b/BamM/BamM-1.7.3-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/b/BamM/BamM-1.7.3-foss-2016b-Python-2.7.12.eb @@ -24,6 +24,8 @@ toolchainopts = {'usempi': True} source_urls = ['https://github.com/Ecogenomics/BamM/archive'] sources = ['%(version)s.tar.gz'] +checksums = ['1a30a5014aa64aea23f12b82c8e474044af126c9e6ddb575530ab14b6ef765b8', 'sha256'] + dependencies = [ ('Python', '2.7.12'), ('SAMtools', '1.3.1'), diff --git a/easybuild/easyconfigs/b/Blosc/Blosc-1.12.1-foss-2016b.eb b/easybuild/easyconfigs/b/Blosc/Blosc-1.12.1-foss-2016b.eb index e6c95a3b77..27f46a5ff7 100644 --- a/easybuild/easyconfigs/b/Blosc/Blosc-1.12.1-foss-2016b.eb +++ b/easybuild/easyconfigs/b/Blosc/Blosc-1.12.1-foss-2016b.eb @@ -22,6 +22,7 @@ toolchain = {'name': 'foss', 'version': '2016b'} source_urls = ['https://github.com/Blosc/c-blosc/archive/'] sources = ['v%(version)s.tar.gz'] +checksums = ['e04535e816bb942bedc9a0ba209944d1eb34e26e2d9cca37f114e8ee292cb3c8', 'sha256'] builddependencies = [('CMake', '3.7.2')] sanity_check_paths = { diff --git a/easybuild/easyconfigs/l/LZO/LZO-2.10-foss-2016b.eb b/easybuild/easyconfigs/l/LZO/LZO-2.10-foss-2016b.eb index 3e18b6f723..c441b07fff 100644 --- a/easybuild/easyconfigs/l/LZO/LZO-2.10-foss-2016b.eb +++ b/easybuild/easyconfigs/l/LZO/LZO-2.10-foss-2016b.eb @@ -21,6 +21,8 @@ description = "Portable lossless data compression library" sources = [SOURCELOWER_TAR_GZ] source_urls = [homepage + 'download/'] +checksums = ['c0f892943208266f9b6543b3ae308fab6284c5c90e627931446fb49b4221a072', 'sha256'] + toolchain = {'name': 'foss', 'version': '2016b'} toolchainopts = {'pic': True} diff --git a/easybuild/easyconfigs/p/PIL/PIL-1.1.7-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/PIL/PIL-1.1.7-foss-2016b-Python-2.7.12.eb index 447ed8f4a5..c9faf5c376 100644 --- a/easybuild/easyconfigs/p/PIL/PIL-1.1.7-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/p/PIL/PIL-1.1.7-foss-2016b-Python-2.7.12.eb @@ -24,6 +24,8 @@ toolchain = {'name': 'foss', 'version': '2016b'} source_urls = ['http://effbot.org/downloads/'] sources = ['Imaging-%(version)s.tar.gz'] +checksums = ['895bc7c2498c8e1f9b99938f1a40dc86b3f149741f105cf7c7bd2e0725405211', 'sha256'] + patches = ['PIL-%(version)s-find-deps.patch'] dependencies = [ -- GitLab From 967c0760a1ec83a1dca0a36b39aed82249471556 Mon Sep 17 00:00:00 2001 From: Robert Date: Thu, 27 Jul 2017 18:51:05 +0930 Subject: [PATCH 1263/1603] formatting error --- easybuild/easyconfigs/b/BAMM/BAMM-2.5.0-foss-2016b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/BAMM/BAMM-2.5.0-foss-2016b.eb b/easybuild/easyconfigs/b/BAMM/BAMM-2.5.0-foss-2016b.eb index f3fb7d53c9..8121c45137 100644 --- a/easybuild/easyconfigs/b/BAMM/BAMM-2.5.0-foss-2016b.eb +++ b/easybuild/easyconfigs/b/BAMM/BAMM-2.5.0-foss-2016b.eb @@ -25,7 +25,7 @@ toolchainopts = {'usempi': True} source_urls = ['https://github.com/macroevolution/bamm/archive'] sources = ['v%(version)s.tar.gz'] -checksums = ['526eef85ef011780ee21fe65cbc10ecc62efe54044102ae40bdef49c2985b4f4','sha256'] +checksums = ['526eef85ef011780ee21fe65cbc10ecc62efe54044102ae40bdef49c2985b4f4', 'sha256'] builddependencies = [ ('CMake', '3.7.2'), -- GitLab From 1aa1485ec33bfa6a4859838ddd8377e552056d60 Mon Sep 17 00:00:00 2001 From: Robert Date: Fri, 28 Jul 2017 15:09:55 +0930 Subject: [PATCH 1264/1603] libtools included for BamM --- .../easyconfigs/b/BamM/BamM-1.7.3-foss-2016b-Python-2.7.12.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/b/BamM/BamM-1.7.3-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/b/BamM/BamM-1.7.3-foss-2016b-Python-2.7.12.eb index 127247b759..e984cb7d44 100644 --- a/easybuild/easyconfigs/b/BamM/BamM-1.7.3-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/b/BamM/BamM-1.7.3-foss-2016b-Python-2.7.12.eb @@ -26,6 +26,10 @@ sources = ['%(version)s.tar.gz'] checksums = ['1a30a5014aa64aea23f12b82c8e474044af126c9e6ddb575530ab14b6ef765b8', 'sha256'] +buildopts = [ + ('libtool', '2.4.6'), +] + dependencies = [ ('Python', '2.7.12'), ('SAMtools', '1.3.1'), -- GitLab From f698b4ee26696140fc041b2da53dbddaccc1eb80 Mon Sep 17 00:00:00 2001 From: Robert Date: Fri, 28 Jul 2017 15:29:11 +0930 Subject: [PATCH 1265/1603] PIL checksum updated --- .../easyconfigs/p/PIL/PIL-1.1.7-foss-2016b-Python-2.7.12.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PIL/PIL-1.1.7-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/PIL/PIL-1.1.7-foss-2016b-Python-2.7.12.eb index c9faf5c376..e3972be37c 100644 --- a/easybuild/easyconfigs/p/PIL/PIL-1.1.7-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/p/PIL/PIL-1.1.7-foss-2016b-Python-2.7.12.eb @@ -24,7 +24,7 @@ toolchain = {'name': 'foss', 'version': '2016b'} source_urls = ['http://effbot.org/downloads/'] sources = ['Imaging-%(version)s.tar.gz'] -checksums = ['895bc7c2498c8e1f9b99938f1a40dc86b3f149741f105cf7c7bd2e0725405211', 'sha256'] +checksums = ['895bc7c2498c8e1f9b99938f1a40dc86b3f149741f105cf7c7bd2e0725405211'] patches = ['PIL-%(version)s-find-deps.patch'] -- GitLab From 029e8f838f6a180415aa145bc626d2cfe576e919 Mon Sep 17 00:00:00 2001 From: Robert Date: Sat, 29 Jul 2017 00:03:17 +0930 Subject: [PATCH 1266/1603] BamM typo correction --- .../easyconfigs/b/BamM/BamM-1.7.3-foss-2016b-Python-2.7.12.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/BamM/BamM-1.7.3-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/b/BamM/BamM-1.7.3-foss-2016b-Python-2.7.12.eb index e984cb7d44..9fee9ab6a5 100644 --- a/easybuild/easyconfigs/b/BamM/BamM-1.7.3-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/b/BamM/BamM-1.7.3-foss-2016b-Python-2.7.12.eb @@ -26,7 +26,7 @@ sources = ['%(version)s.tar.gz'] checksums = ['1a30a5014aa64aea23f12b82c8e474044af126c9e6ddb575530ab14b6ef765b8', 'sha256'] -buildopts = [ +builddependencies = [ ('libtool', '2.4.6'), ] -- GitLab From 084936e3093f9797191baa6555b53f921f8ebf02 Mon Sep 17 00:00:00 2001 From: Robert Date: Sat, 29 Jul 2017 00:12:54 +0930 Subject: [PATCH 1267/1603] PyTable openmp enabled --- .../p/PyTables/PyTables-3.3.0-foss-2016b-Python-2.7.12.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PyTables/PyTables-3.3.0-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/PyTables/PyTables-3.3.0-foss-2016b-Python-2.7.12.eb index 17ca3dd82f..1c01866e0c 100644 --- a/easybuild/easyconfigs/p/PyTables/PyTables-3.3.0-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/p/PyTables/PyTables-3.3.0-foss-2016b-Python-2.7.12.eb @@ -25,7 +25,7 @@ description = """PyTables is a package for managing hierarchical datasets and de relational or object oriented databases.""" toolchain = {'name': 'foss', 'version': '2016b'} -toolchainopts = {'usempi': True} +toolchainopts = {'openmp': True, 'usempi': True} source_urls = ['https://github.com/PyTables/PyTables/archive/'] sources = ['v%(version)s.tar.gz'] -- GitLab From 28b767c0395f6cb5deb4bc65988ff3ff16b32bec Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Sat, 29 Jul 2017 07:30:50 -0500 Subject: [PATCH 1268/1603] maintain sanity? --- .../e/Eigen/Eigen-3.3.4-GCCcore-6.4.0.eb | 16 ---------------- 1 file changed, 16 deletions(-) diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.3.4-GCCcore-6.4.0.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.3.4-GCCcore-6.4.0.eb index 7fd77a3b5e..50d8127475 100644 --- a/easybuild/easyconfigs/e/Eigen/Eigen-3.3.4-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.3.4-GCCcore-6.4.0.eb @@ -14,20 +14,4 @@ source_urls = ['http://bitbucket.org/%(namelower)s/%(namelower)s/get'] sources = ['%(version)s.tar.bz2'] checksums = ['dd254beb0bafc695d0f62ae1a222ff85b52dbaa3a16f76e781dce22d0d20a4a6'] -# both in Eigen 2.x an 3.x -include_files = ['Cholesky', 'Core', 'Dense', 'Eigen', 'Geometry', 'LU', - 'QR', 'QtAlignedMalloc', 'SVD', 'Sparse', 'StdVector'] - -# only 3.x -include_files.extend(['CholmodSupport', 'Eigenvalues', 'Householder', - 'IterativeLinearSolvers', 'Jacobi', 'OrderingMethods', - 'PaStiXSupport', 'PardisoSupport', 'SparseCholesky', - 'SparseCore', 'StdDeque', 'StdList', - 'SuperLUSupport', 'UmfPackSupport']) - -sanity_check_paths = { - 'files': ['include/Eigen/%s' % x for x in include_files], - 'dirs': ['include'], -} - moduleclass = 'math' -- GitLab From fde9be252bf4ee9831e3f0e5f38767f398dd3f1c Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Sat, 29 Jul 2017 09:26:04 -0500 Subject: [PATCH 1269/1603] update source_urls --- easybuild/easyconfigs/c/CLISP/CLISP-2.49-GCCcore-6.4.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/c/CLISP/CLISP-2.49-GCCcore-6.4.0.eb b/easybuild/easyconfigs/c/CLISP/CLISP-2.49-GCCcore-6.4.0.eb index d9d3d1bf33..3c1b56f7a9 100644 --- a/easybuild/easyconfigs/c/CLISP/CLISP-2.49-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/c/CLISP/CLISP-2.49-GCCcore-6.4.0.eb @@ -14,7 +14,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '6.4.0'} -source_urls = [GNU_SOURCE] +source_urls = ['ftp://ftp.gnu.org/pub/gnu/%(namelower)s/release/%(version)s'] sources = [SOURCELOWER_TAR_BZ2] checksums = ['8132ff353afaa70e6b19367a25ae3d5a43627279c25647c220641fed00f8e890'] @@ -32,7 +32,7 @@ dependencies = [ ] prebuildopts = """ - sed -e 's/ac_cv_have_decl_rl_readline_state" = x""yes/ac_cv_have_decl_rl_readline_state" = x""JKP/'\ + sed -e 's/ac_cv_have_decl_rl_readline_state" = x""yes/ac_cv_have_decl_rl_readline_state" = x""FOOBAR/'\ -i.eb modules/readline/configure cd src """ -- GitLab From 3c45e078c04c75583e6a8d441b025c2c7abcb613 Mon Sep 17 00:00:00 2001 From: Robert Qiao Date: Mon, 31 Jul 2017 00:57:08 +0930 Subject: [PATCH 1270/1603] PyTable patch applied --- .../p/PyTables/PyTables-3.3.0-foss-2016b-Python-2.7.12.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/p/PyTables/PyTables-3.3.0-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/PyTables/PyTables-3.3.0-foss-2016b-Python-2.7.12.eb index 17ca3dd82f..feafbc59b9 100644 --- a/easybuild/easyconfigs/p/PyTables/PyTables-3.3.0-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/p/PyTables/PyTables-3.3.0-foss-2016b-Python-2.7.12.eb @@ -30,6 +30,8 @@ toolchainopts = {'usempi': True} source_urls = ['https://github.com/PyTables/PyTables/archive/'] sources = ['v%(version)s.tar.gz'] +patches = ['pyTables-3.2.2-fix-libs.patch'] + dependencies = [ ('Python', '2.7.12'), ('numexpr', '2.6.1', versionsuffix), -- GitLab From 23625fc62166e63234e92ce4efdceaddc5efc8aa Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Sun, 30 Jul 2017 11:13:54 -0500 Subject: [PATCH 1271/1603] adding easyconfigs: Python-2.7.13-GCCcore-6.4.0-bare.eb --- .../Python-2.7.13-GCCcore-6.4.0-bare.eb | 56 +++++++++++++++++++ 1 file changed, 56 insertions(+) create mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.13-GCCcore-6.4.0-bare.eb diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.13-GCCcore-6.4.0-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.13-GCCcore-6.4.0-bare.eb new file mode 100644 index 0000000000..0860032fc3 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.13-GCCcore-6.4.0-bare.eb @@ -0,0 +1,56 @@ +name = 'Python' +version = '2.7.13' +versionsuffix = '-bare' + +homepage = 'http://python.org/' + +description = """ + Python is a programming language that lets you work more quickly and + integrate your systems more effectively. + +Note: This module is meant to provide a builddependency for other Python + modules while using EasyBuild's --minimaltoolchain option. Modules + built with it will require the full Python later +""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] +checksums = ['a4f05a0720ce0fd92626f0278b6b433eee9a6173ddf2bced7957dfb599a5ece1'] + +builddependencies = [ + ('binutils', '2.28'), +] + +dependencies = [ + ('bzip2', '1.0.6'), + ('libreadline', '7.0'), + ('ncurses', '6.0'), + ('SQLite', '3.19.3'), + ('zlib', '1.2.11'), +] + +osdependencies = [ + # rely upon distribution for timely security updates + ('openssl-devel', 'libssl-dev', 'libopenssl-devel'), +] + +# We hide this by default since users should not use it in production, +# high-performance Python should be delivered at compiler level with +# a default extension set +# hidden = True + +# bare installation: only known module deps for GCCcore tools included +exts_list = [] + +# Until such time that EasyBuild accepts 'rpath' as a toolchainopt... +# add RPATH so this can be used as a builddependency for "bare" PythonPackages +preconfigopts = """ + sed -e\ + 's:$(LINKCC) $(LDFLAGS) $(LINKFORSHARED):$(LINKCC) $(LDFLAGS) $(LINKFORSHARED) -Wl,-rpath=%(installdir)s/lib:'\ + -i.eb Makefile.pre.in +""" + +moduleclass = 'lang' -- GitLab From a7ac403f432ad2c13e58f3acc796e63458b8b954 Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Sun, 30 Jul 2017 11:48:09 -0500 Subject: [PATCH 1272/1603] Delete libunistring-0.9.7-GCCcore-6.4.0.eb --- .../libunistring-0.9.7-GCCcore-6.4.0.eb | 33 ------------------- 1 file changed, 33 deletions(-) delete mode 100644 easybuild/easyconfigs/l/libunistring/libunistring-0.9.7-GCCcore-6.4.0.eb diff --git a/easybuild/easyconfigs/l/libunistring/libunistring-0.9.7-GCCcore-6.4.0.eb b/easybuild/easyconfigs/l/libunistring/libunistring-0.9.7-GCCcore-6.4.0.eb deleted file mode 100644 index 8d845c9877..0000000000 --- a/easybuild/easyconfigs/l/libunistring/libunistring-0.9.7-GCCcore-6.4.0.eb +++ /dev/null @@ -1,33 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'libunistring' -version = '0.9.7' - -homepage = 'http://www.gnu.org/software/libunistring/' - -description = """ - This library provides functions for manipulating Unicode strings and for - manipulating C strings according to the Unicode standard. -""" - -toolchain = {'name': 'GCCcore', 'version': '6.4.0'} -toolchainopts = {'pic': True} - -sources = [SOURCELOWER_TAR_XZ] -source_urls = [GNU_SOURCE] -checksums = ['2e3764512aaf2ce598af5a38818c0ea23dedf1ff5460070d1b6cee5c3336e797'] - -builddependencies = [ - ('binutils', '2.28'), -] - -parallel = 1 - -sanity_check_paths = { - 'files': ['lib/libunistring.a', 'lib/libunistring.%s' % SHLIB_EXT] + - ['include/uni%s.h' % x for x in ['case', 'conv', 'ctype', 'lbrk', 'name', 'norm', - 'stdio', 'str', 'types', 'wbrk', 'width']], - 'dirs': ['include/unistring'], -} - -moduleclass = 'lib' -- GitLab From 1c28386218cdc615b5771570f4049e33fc3a8a90 Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Sun, 30 Jul 2017 12:02:30 -0500 Subject: [PATCH 1273/1603] Delete libjpeg-turbo-1.5.2-GCCcore-6.4.0.eb --- .../libjpeg-turbo-1.5.2-GCCcore-6.4.0.eb | 41 ------------------- 1 file changed, 41 deletions(-) delete mode 100644 easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.5.2-GCCcore-6.4.0.eb diff --git a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.5.2-GCCcore-6.4.0.eb b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.5.2-GCCcore-6.4.0.eb deleted file mode 100644 index 8d3ce16df6..0000000000 --- a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.5.2-GCCcore-6.4.0.eb +++ /dev/null @@ -1,41 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'libjpeg-turbo' -version = '1.5.2' - -homepage = 'http://sourceforge.net/projects/libjpeg-turbo/' - -description = """ - libjpeg-turbo is a fork of the original IJG libjpeg which uses SIMD to - accelerate baseline JPEG compression and decompression. libjpeg is a library - that implements JPEG image encoding, decoding and transcoding. -""" - -toolchain = {'name': 'GCCcore', 'version': '6.4.0'} -toolchainopts = {'pic': True} - -source_urls = [SOURCEFORGE_SOURCE] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['9098943b270388727ae61de82adec73cf9f0dbb240b3bc8b172595ebf405b528'] - -builddependencies = [ - ('binutils', '2.28'), -] - -dependencies = [ - ('NASM', '2.13.01'), -] - -configopts = "--with-jpeg8" - -runtest = "test" - -sanity_check_paths = { - 'files': ['bin/cjpeg', 'bin/djpeg', 'bin/jpegtran', 'bin/rdjpgcom', - 'bin/tjbench', 'bin/wrjpgcom', 'lib/libjpeg.a', - 'lib/libjpeg.%s' % SHLIB_EXT, 'lib/libturbojpeg.a', - 'lib/libturbojpeg.%s' % SHLIB_EXT], - 'dirs': ['include', 'share'], -} - -moduleclass = 'lib' -- GitLab From a75dcbc044720f4a6b8f0c0ad624664849c070bf Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Sun, 30 Jul 2017 21:28:39 -0500 Subject: [PATCH 1274/1603] Delete Python-2.7.13-GCCcore-6.4.0-bare.eb --- .../Python-2.7.13-GCCcore-6.4.0-bare.eb | 53 ------------------- 1 file changed, 53 deletions(-) delete mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.13-GCCcore-6.4.0-bare.eb diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.13-GCCcore-6.4.0-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.13-GCCcore-6.4.0-bare.eb deleted file mode 100644 index 42f2730022..0000000000 --- a/easybuild/easyconfigs/p/Python/Python-2.7.13-GCCcore-6.4.0-bare.eb +++ /dev/null @@ -1,53 +0,0 @@ -name = 'Python' -version = '2.7.13' -versionsuffix = '-bare' - -homepage = 'http://python.org/' - -description = """ - Python is a programming language that lets you work more quickly and - integrate your systems more effectively. - -Note: This module is meant to provide a builddependency for other Python - modules while using EasyBuild's --minimaltoolchain option. Modules - built with it will require the full Python later -""" - -toolchain = {'name': 'GCCcore', 'version': '6.4.0'} -toolchainopts = {'pic': True} - -source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] -sources = [SOURCE_TGZ] - -builddependencies = [ - ('binutils', '2.28'), -] - -dependencies = [ - ('bzip2', '1.0.6'), - ('libreadline', '7.0'), - ('ncurses', '6.0'), - ('SQLite', '3.19.3'), - ('zlib', '1.2.11'), -] - -osdependencies = [ - # rely upon distribution for timely security updates - ('openssl-devel', 'libssl-dev', 'libopenssl-devel'), -] - -# We hide this by default since users should not use it in production, -# high-performance Python should be delivered at compiler level with -# a default extension set -#hidden = True - -# bare installation: only known module deps for GCCcore tools included -exts_list = [] - -# Until such time that EasyBuild accepts 'rpath' as a toolchainopt... -# add RPATH so this can be as a builddependency later -prebuildopts = """ - sed -e 's:Modules/python.o \\\\:-Wl,-rpath=%(installdir)s/lib Modules/python.o \\\\:' -i.eb Makefile -""" - -moduleclass = 'lang' -- GitLab From a3a406c2b7102dd2f0c9c482541b568f95b7e312 Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Sun, 30 Jul 2017 21:30:52 -0500 Subject: [PATCH 1275/1603] Delete SQLite-3.19.3-GCCcore-6.4.0.eb --- .../s/SQLite/SQLite-3.19.3-GCCcore-6.4.0.eb | 49 ------------------- 1 file changed, 49 deletions(-) delete mode 100644 easybuild/easyconfigs/s/SQLite/SQLite-3.19.3-GCCcore-6.4.0.eb diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.19.3-GCCcore-6.4.0.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.19.3-GCCcore-6.4.0.eb deleted file mode 100644 index 9d9a1ef2eb..0000000000 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.19.3-GCCcore-6.4.0.eb +++ /dev/null @@ -1,49 +0,0 @@ -## -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# -# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA -# Authors:: Fotis Georgatos -# License:: MIT/GPL -# $Id$ -# -# This work implements a part of the HPCBIOS project and is a component of the -# policy: http://hpcbios.readthedocs.org/en/latest/ -## - -easyblock = 'ConfigureMake' - -name = 'SQLite' -version = '3.19.3' - -homepage = 'http://www.sqlite.org/' - -description = 'SQLite: SQL Database Engine in a C Library' - -toolchain = {'name': 'GCCcore', 'version': '6.4.0'} -toolchainopts = {'pic': True} - -# eg. http://www.sqlite.org/2017/sqlite-autoconf-3190300.tar.gz -source_urls = ['http://www.sqlite.org/2017/'] -version_str = '%%(version_major)s%s00' % ''.join('%02d' % - int(x) for x in version.split('.')[1:]) -sources = ['sqlite-autoconf-%s.tar.gz' % version_str] -checksums = ['06129c03dced9f87733a8cba408871bd60673b8f93b920ba8d815efab0a06301'] - -builddependencies = [ - ('binutils', '2.28'), -] - -dependencies = [ - ('libreadline', '7.0'), - ('Tcl', '8.6.6'), -] - -parallel = 1 - -sanity_check_paths = { - 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', - 'lib/libsqlite3.a', 'lib/libsqlite3.%s' % SHLIB_EXT], - 'dirs': ['lib/pkgconfig'], -} - -moduleclass = 'devel' -- GitLab From 0c423acce71c630ac5c6cfad40118b75c405e9b6 Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Sun, 30 Jul 2017 21:32:47 -0500 Subject: [PATCH 1276/1603] Delete Tcl-8.6.6-GCCcore-6.4.0.eb --- .../t/Tcl/Tcl-8.6.6-GCCcore-6.4.0.eb | 42 ------------------- 1 file changed, 42 deletions(-) delete mode 100644 easybuild/easyconfigs/t/Tcl/Tcl-8.6.6-GCCcore-6.4.0.eb diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.6-GCCcore-6.4.0.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.6-GCCcore-6.4.0.eb deleted file mode 100644 index cffeed4270..0000000000 --- a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.6-GCCcore-6.4.0.eb +++ /dev/null @@ -1,42 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'Tcl' -version = '8.6.6' - -homepage = 'http://www.tcl.tk/' - -description = """ - Tcl (Tool Command Language) is a very powerful but easy to learn dynamic - programming language, suitable for a very wide range of uses, including web - and desktop applications, networking, administration, testing and many more. -""" - -toolchain = {'name': 'GCCcore', 'version': '6.4.0'} - -source_urls = ["http://prdownloads.sourceforge.net/tcl"] -sources = ['%(namelower)s%(version)s-src.tar.gz'] -checksums = ['a265409781e4b3edcc4ef822533071b34c3dc6790b893963809b9fe221befe07'] - -builddependencies = [ - ('binutils', '2.28'), -] - -dependencies = [ - ('zlib', '1.2.11'), -] - -configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' - -runtest = 'test' - -start_dir = 'unix' - -sanity_check_paths = { - 'files': ['bin/tclsh%(version_major)s.%(version_minor)s', 'include/tcl.h', - 'lib/libtcl%%(version_major)s.%%(version_minor)s.%s' % SHLIB_EXT, - 'lib/tclConfig.sh', 'man/man1/tclsh.1'], - 'dirs': ['share'], -} - - -moduleclass = 'lang' -- GitLab From 6c75575777ad354b2dd5a8b944c0136ab16d4e03 Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Sun, 30 Jul 2017 22:02:20 -0500 Subject: [PATCH 1277/1603] Delete Tcl-8.6.6-GCCcore-6.4.0.eb --- .../t/Tcl/Tcl-8.6.6-GCCcore-6.4.0.eb | 42 ------------------- 1 file changed, 42 deletions(-) delete mode 100644 easybuild/easyconfigs/t/Tcl/Tcl-8.6.6-GCCcore-6.4.0.eb diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.6-GCCcore-6.4.0.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.6-GCCcore-6.4.0.eb deleted file mode 100644 index cffeed4270..0000000000 --- a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.6-GCCcore-6.4.0.eb +++ /dev/null @@ -1,42 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'Tcl' -version = '8.6.6' - -homepage = 'http://www.tcl.tk/' - -description = """ - Tcl (Tool Command Language) is a very powerful but easy to learn dynamic - programming language, suitable for a very wide range of uses, including web - and desktop applications, networking, administration, testing and many more. -""" - -toolchain = {'name': 'GCCcore', 'version': '6.4.0'} - -source_urls = ["http://prdownloads.sourceforge.net/tcl"] -sources = ['%(namelower)s%(version)s-src.tar.gz'] -checksums = ['a265409781e4b3edcc4ef822533071b34c3dc6790b893963809b9fe221befe07'] - -builddependencies = [ - ('binutils', '2.28'), -] - -dependencies = [ - ('zlib', '1.2.11'), -] - -configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' - -runtest = 'test' - -start_dir = 'unix' - -sanity_check_paths = { - 'files': ['bin/tclsh%(version_major)s.%(version_minor)s', 'include/tcl.h', - 'lib/libtcl%%(version_major)s.%%(version_minor)s.%s' % SHLIB_EXT, - 'lib/tclConfig.sh', 'man/man1/tclsh.1'], - 'dirs': ['share'], -} - - -moduleclass = 'lang' -- GitLab From 50f5d5c089d44c209bca454a419f3176ab3d57f4 Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Sun, 30 Jul 2017 22:13:24 -0500 Subject: [PATCH 1278/1603] Delete SQLite-3.19.3-GCCcore-6.4.0.eb --- .../s/SQLite/SQLite-3.19.3-GCCcore-6.4.0.eb | 49 ------------------- 1 file changed, 49 deletions(-) delete mode 100644 easybuild/easyconfigs/s/SQLite/SQLite-3.19.3-GCCcore-6.4.0.eb diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.19.3-GCCcore-6.4.0.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.19.3-GCCcore-6.4.0.eb deleted file mode 100644 index 9d9a1ef2eb..0000000000 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.19.3-GCCcore-6.4.0.eb +++ /dev/null @@ -1,49 +0,0 @@ -## -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# -# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA -# Authors:: Fotis Georgatos -# License:: MIT/GPL -# $Id$ -# -# This work implements a part of the HPCBIOS project and is a component of the -# policy: http://hpcbios.readthedocs.org/en/latest/ -## - -easyblock = 'ConfigureMake' - -name = 'SQLite' -version = '3.19.3' - -homepage = 'http://www.sqlite.org/' - -description = 'SQLite: SQL Database Engine in a C Library' - -toolchain = {'name': 'GCCcore', 'version': '6.4.0'} -toolchainopts = {'pic': True} - -# eg. http://www.sqlite.org/2017/sqlite-autoconf-3190300.tar.gz -source_urls = ['http://www.sqlite.org/2017/'] -version_str = '%%(version_major)s%s00' % ''.join('%02d' % - int(x) for x in version.split('.')[1:]) -sources = ['sqlite-autoconf-%s.tar.gz' % version_str] -checksums = ['06129c03dced9f87733a8cba408871bd60673b8f93b920ba8d815efab0a06301'] - -builddependencies = [ - ('binutils', '2.28'), -] - -dependencies = [ - ('libreadline', '7.0'), - ('Tcl', '8.6.6'), -] - -parallel = 1 - -sanity_check_paths = { - 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', - 'lib/libsqlite3.a', 'lib/libsqlite3.%s' % SHLIB_EXT], - 'dirs': ['lib/pkgconfig'], -} - -moduleclass = 'devel' -- GitLab From 5c4acb95df7f7f96f5aafb834c283c326c32ff67 Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Sun, 30 Jul 2017 22:14:45 -0500 Subject: [PATCH 1279/1603] Delete Python-2.7.13-GCCcore-6.4.0-bare.eb --- .../Python-2.7.13-GCCcore-6.4.0-bare.eb | 53 ------------------- 1 file changed, 53 deletions(-) delete mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.13-GCCcore-6.4.0-bare.eb diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.13-GCCcore-6.4.0-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.13-GCCcore-6.4.0-bare.eb deleted file mode 100644 index 42f2730022..0000000000 --- a/easybuild/easyconfigs/p/Python/Python-2.7.13-GCCcore-6.4.0-bare.eb +++ /dev/null @@ -1,53 +0,0 @@ -name = 'Python' -version = '2.7.13' -versionsuffix = '-bare' - -homepage = 'http://python.org/' - -description = """ - Python is a programming language that lets you work more quickly and - integrate your systems more effectively. - -Note: This module is meant to provide a builddependency for other Python - modules while using EasyBuild's --minimaltoolchain option. Modules - built with it will require the full Python later -""" - -toolchain = {'name': 'GCCcore', 'version': '6.4.0'} -toolchainopts = {'pic': True} - -source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] -sources = [SOURCE_TGZ] - -builddependencies = [ - ('binutils', '2.28'), -] - -dependencies = [ - ('bzip2', '1.0.6'), - ('libreadline', '7.0'), - ('ncurses', '6.0'), - ('SQLite', '3.19.3'), - ('zlib', '1.2.11'), -] - -osdependencies = [ - # rely upon distribution for timely security updates - ('openssl-devel', 'libssl-dev', 'libopenssl-devel'), -] - -# We hide this by default since users should not use it in production, -# high-performance Python should be delivered at compiler level with -# a default extension set -#hidden = True - -# bare installation: only known module deps for GCCcore tools included -exts_list = [] - -# Until such time that EasyBuild accepts 'rpath' as a toolchainopt... -# add RPATH so this can be as a builddependency later -prebuildopts = """ - sed -e 's:Modules/python.o \\\\:-Wl,-rpath=%(installdir)s/lib Modules/python.o \\\\:' -i.eb Makefile -""" - -moduleclass = 'lang' -- GitLab From b7c4726f9a935ee6ab09e5533b08923f081beb45 Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Sun, 30 Jul 2017 22:44:00 -0500 Subject: [PATCH 1280/1603] Delete Python-2.7.13-GCCcore-6.4.0-bare.eb --- .../Python-2.7.13-GCCcore-6.4.0-bare.eb | 53 ------------------- 1 file changed, 53 deletions(-) delete mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.13-GCCcore-6.4.0-bare.eb diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.13-GCCcore-6.4.0-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.13-GCCcore-6.4.0-bare.eb deleted file mode 100644 index 42f2730022..0000000000 --- a/easybuild/easyconfigs/p/Python/Python-2.7.13-GCCcore-6.4.0-bare.eb +++ /dev/null @@ -1,53 +0,0 @@ -name = 'Python' -version = '2.7.13' -versionsuffix = '-bare' - -homepage = 'http://python.org/' - -description = """ - Python is a programming language that lets you work more quickly and - integrate your systems more effectively. - -Note: This module is meant to provide a builddependency for other Python - modules while using EasyBuild's --minimaltoolchain option. Modules - built with it will require the full Python later -""" - -toolchain = {'name': 'GCCcore', 'version': '6.4.0'} -toolchainopts = {'pic': True} - -source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] -sources = [SOURCE_TGZ] - -builddependencies = [ - ('binutils', '2.28'), -] - -dependencies = [ - ('bzip2', '1.0.6'), - ('libreadline', '7.0'), - ('ncurses', '6.0'), - ('SQLite', '3.19.3'), - ('zlib', '1.2.11'), -] - -osdependencies = [ - # rely upon distribution for timely security updates - ('openssl-devel', 'libssl-dev', 'libopenssl-devel'), -] - -# We hide this by default since users should not use it in production, -# high-performance Python should be delivered at compiler level with -# a default extension set -#hidden = True - -# bare installation: only known module deps for GCCcore tools included -exts_list = [] - -# Until such time that EasyBuild accepts 'rpath' as a toolchainopt... -# add RPATH so this can be as a builddependency later -prebuildopts = """ - sed -e 's:Modules/python.o \\\\:-Wl,-rpath=%(installdir)s/lib Modules/python.o \\\\:' -i.eb Makefile -""" - -moduleclass = 'lang' -- GitLab From 2882d52b16ed84921f8d81eb8c9c15e64e96abbf Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Sun, 30 Jul 2017 22:48:34 -0500 Subject: [PATCH 1281/1603] Delete Tcl-8.6.6-GCCcore-6.4.0.eb --- .../t/Tcl/Tcl-8.6.6-GCCcore-6.4.0.eb | 42 ------------------- 1 file changed, 42 deletions(-) delete mode 100644 easybuild/easyconfigs/t/Tcl/Tcl-8.6.6-GCCcore-6.4.0.eb diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.6-GCCcore-6.4.0.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.6-GCCcore-6.4.0.eb deleted file mode 100644 index cffeed4270..0000000000 --- a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.6-GCCcore-6.4.0.eb +++ /dev/null @@ -1,42 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'Tcl' -version = '8.6.6' - -homepage = 'http://www.tcl.tk/' - -description = """ - Tcl (Tool Command Language) is a very powerful but easy to learn dynamic - programming language, suitable for a very wide range of uses, including web - and desktop applications, networking, administration, testing and many more. -""" - -toolchain = {'name': 'GCCcore', 'version': '6.4.0'} - -source_urls = ["http://prdownloads.sourceforge.net/tcl"] -sources = ['%(namelower)s%(version)s-src.tar.gz'] -checksums = ['a265409781e4b3edcc4ef822533071b34c3dc6790b893963809b9fe221befe07'] - -builddependencies = [ - ('binutils', '2.28'), -] - -dependencies = [ - ('zlib', '1.2.11'), -] - -configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' - -runtest = 'test' - -start_dir = 'unix' - -sanity_check_paths = { - 'files': ['bin/tclsh%(version_major)s.%(version_minor)s', 'include/tcl.h', - 'lib/libtcl%%(version_major)s.%%(version_minor)s.%s' % SHLIB_EXT, - 'lib/tclConfig.sh', 'man/man1/tclsh.1'], - 'dirs': ['share'], -} - - -moduleclass = 'lang' -- GitLab From 510bbce052acacc75653f3a60428fbc57a802c43 Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Sun, 30 Jul 2017 22:49:37 -0500 Subject: [PATCH 1282/1603] Delete SQLite-3.19.3-GCCcore-6.4.0.eb --- .../s/SQLite/SQLite-3.19.3-GCCcore-6.4.0.eb | 49 ------------------- 1 file changed, 49 deletions(-) delete mode 100644 easybuild/easyconfigs/s/SQLite/SQLite-3.19.3-GCCcore-6.4.0.eb diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.19.3-GCCcore-6.4.0.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.19.3-GCCcore-6.4.0.eb deleted file mode 100644 index 9d9a1ef2eb..0000000000 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.19.3-GCCcore-6.4.0.eb +++ /dev/null @@ -1,49 +0,0 @@ -## -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# -# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA -# Authors:: Fotis Georgatos -# License:: MIT/GPL -# $Id$ -# -# This work implements a part of the HPCBIOS project and is a component of the -# policy: http://hpcbios.readthedocs.org/en/latest/ -## - -easyblock = 'ConfigureMake' - -name = 'SQLite' -version = '3.19.3' - -homepage = 'http://www.sqlite.org/' - -description = 'SQLite: SQL Database Engine in a C Library' - -toolchain = {'name': 'GCCcore', 'version': '6.4.0'} -toolchainopts = {'pic': True} - -# eg. http://www.sqlite.org/2017/sqlite-autoconf-3190300.tar.gz -source_urls = ['http://www.sqlite.org/2017/'] -version_str = '%%(version_major)s%s00' % ''.join('%02d' % - int(x) for x in version.split('.')[1:]) -sources = ['sqlite-autoconf-%s.tar.gz' % version_str] -checksums = ['06129c03dced9f87733a8cba408871bd60673b8f93b920ba8d815efab0a06301'] - -builddependencies = [ - ('binutils', '2.28'), -] - -dependencies = [ - ('libreadline', '7.0'), - ('Tcl', '8.6.6'), -] - -parallel = 1 - -sanity_check_paths = { - 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', - 'lib/libsqlite3.a', 'lib/libsqlite3.%s' % SHLIB_EXT], - 'dirs': ['lib/pkgconfig'], -} - -moduleclass = 'devel' -- GitLab From c3663ed7ff25ee37f67a6b84550ff964eacfe019 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Mon, 31 Jul 2017 07:18:00 +0200 Subject: [PATCH 1283/1603] Remove sanity check Already covered by EasyBlock --- .../easyconfigs/b/Bowtie2/Bowtie2-2.3.2-foss-2016b.eb | 9 --------- 1 file changed, 9 deletions(-) diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.3.2-foss-2016b.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.3.2-foss-2016b.eb index bea5f1dfd7..5fcd3f7ba0 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.3.2-foss-2016b.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.3.2-foss-2016b.eb @@ -29,15 +29,6 @@ checksums = ['ef0fe6d712eb3f9fbd784a5772547a28859a71eb6c455ef670b0f11a56cc73f7'] dependencies = [('tbb', '2017_U5')] -sanity_check_paths = { - 'files': ['bin/%s' % x for x in ['bowtie2', 'bowtie2-align-l', 'bowtie2-align-s', 'bowtie2-build', - 'bowtie2-build-l', 'bowtie2-build-s', 'bowtie2-inspect', 'bowtie2-inspect-l', - 'bowtie2-inspect-s']], - 'dirs': [] -} - -sanity_check_commands = [('bowtie2', '--version')] - # to add script folder to path just uncomment this line # modextrapaths = {'PATH': 'scripts'} -- GitLab From 1cb3ce7bcb03c19a0e8d952e30be2e2113e86534 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Mon, 31 Jul 2017 07:19:34 +0200 Subject: [PATCH 1284/1603] Remove sanity check Already covered by EasyBlock --- .../easyconfigs/b/Bowtie/Bowtie-1.2.1.1-foss-2016b.eb | 8 -------- 1 file changed, 8 deletions(-) diff --git a/easybuild/easyconfigs/b/Bowtie/Bowtie-1.2.1.1-foss-2016b.eb b/easybuild/easyconfigs/b/Bowtie/Bowtie-1.2.1.1-foss-2016b.eb index 28f4c0d027..8e5cbc7d40 100644 --- a/easybuild/easyconfigs/b/Bowtie/Bowtie-1.2.1.1-foss-2016b.eb +++ b/easybuild/easyconfigs/b/Bowtie/Bowtie-1.2.1.1-foss-2016b.eb @@ -17,12 +17,4 @@ checksums = ['71d708c957380e115ba420a96ac5f8456c6a61760a5f4dbe06305df6a42131d8'] dependencies = [('tbb', '2017_U5')] -sanity_check_paths = { - 'files': ['bin/%s' % x for x in ['bowtie', 'bowtie-align-l', 'bowtie-align-s', 'bowtie-build', 'bowtie-build-l', - 'bowtie-build-s', 'bowtie-inspect', 'bowtie-inspect-l', 'bowtie-inspect-s']], - 'dirs': [] -} - -sanity_check_commands = [('bowtie', '--version')] - moduleclass = 'bio' -- GitLab From 713a2c1ec1ffab2596f660925a5e5767bdcac529 Mon Sep 17 00:00:00 2001 From: Robert Qiao Date: Mon, 31 Jul 2017 22:09:24 +0930 Subject: [PATCH 1285/1603] BamM removed --- .../BamM-1.7.3-foss-2016b-Python-2.7.12.eb | 44 ------------------- 1 file changed, 44 deletions(-) delete mode 100644 easybuild/easyconfigs/b/BamM/BamM-1.7.3-foss-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/b/BamM/BamM-1.7.3-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/b/BamM/BamM-1.7.3-foss-2016b-Python-2.7.12.eb deleted file mode 100644 index 9fee9ab6a5..0000000000 --- a/easybuild/easyconfigs/b/BamM/BamM-1.7.3-foss-2016b-Python-2.7.12.eb +++ /dev/null @@ -1,44 +0,0 @@ -## -# This is a contribution from Phoenix HPC Service, The University of Adelaide, Australia -# Homepage: https://www.adelaide.edu.au/phoenix/ -# -# Copyright:: Copyright 2014-2017 adelaide.edu.au/phoenix -# Authors:: Robert Qiao , Exequiel Sepulveda -# License:: GPL-v3.0 -# -# Notes:: -## - -easyblock = 'PythonPackage' - -name = 'BamM' -version = '1.7.3' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'http://ecogenomics.github.io/BamM/' -description = """ BamM is a c library, wrapped in python, that parses BAM files """ - -toolchain = {'name': 'foss', 'version': '2016b'} -toolchainopts = {'usempi': True} - -source_urls = ['https://github.com/Ecogenomics/BamM/archive'] -sources = ['%(version)s.tar.gz'] - -checksums = ['1a30a5014aa64aea23f12b82c8e474044af126c9e6ddb575530ab14b6ef765b8', 'sha256'] - -builddependencies = [ - ('libtool', '2.4.6'), -] - -dependencies = [ - ('Python', '2.7.12'), - ('SAMtools', '1.3.1'), - ('BWA', '0.7.15'), -] - -sanity_check_paths = { - 'files': ['bin/bamm'], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -moduleclass = 'bio' -- GitLab From 8533fa5024fe9ab7aec8921a3a863eeb09a23e42 Mon Sep 17 00:00:00 2001 From: jrbosch Date: Mon, 31 Jul 2017 11:19:19 -0400 Subject: [PATCH 1286/1603] improving easyconfig file --- ...d-build.eb => GROMACS-2016.3-foss-2016b-GPU-enabled.eb} | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) rename easybuild/easyconfigs/g/GROMACS/{GROMACS-2016.3-foss-2016b-GPU-enabled-build.eb => GROMACS-2016.3-foss-2016b-GPU-enabled.eb} (89%) diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.3-foss-2016b-GPU-enabled-build.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.3-foss-2016b-GPU-enabled.eb similarity index 89% rename from easybuild/easyconfigs/g/GROMACS/GROMACS-2016.3-foss-2016b-GPU-enabled-build.eb rename to easybuild/easyconfigs/g/GROMACS/GROMACS-2016.3-foss-2016b-GPU-enabled.eb index 7d8210d268..6d8f8f3924 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.3-foss-2016b-GPU-enabled-build.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.3-foss-2016b-GPU-enabled.eb @@ -14,7 +14,7 @@ name = 'GROMACS' version = '2016.3' -versionsuffix = '-GPU-enabled-build' +versionsuffix = '-GPU-enabled' homepage = 'http://www.gromacs.org' description = """ @@ -30,6 +30,10 @@ toolchainopts = {'openmp': True, 'usempi': True} source_urls = ['ftp://ftp.gromacs.org/pub/gromacs/'] sources = [SOURCELOWER_TAR_GZ] +checksums = [ + '7bf00e74a9d38b7cef9356141d20e4ba9387289cbbfd4d11be479ef932d77d27', # gromacs-2016.3.tar.gz +] + patches = [ 'GROMACS-%(version)s_amend_search_for_nvml_lib.patch', ] @@ -43,3 +47,4 @@ builddependencies = [ ] moduleclass = 'bio' + -- GitLab From ddbb0927511b643674aba0c7287b75f7474ac1c5 Mon Sep 17 00:00:00 2001 From: Robert Date: Tue, 1 Aug 2017 00:52:54 +0930 Subject: [PATCH 1287/1603] reorganising --- .../BamM-1.7.3-foss-2016b-Python-2.7.12.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/b/BamM/BamM-1.7.3-foss-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/b/BamM/BamM-1.7.3-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/b/BamM/BamM-1.7.3-foss-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..0e28fe9620 --- /dev/null +++ b/easybuild/easyconfigs/b/BamM/BamM-1.7.3-foss-2016b-Python-2.7.12.eb @@ -0,0 +1,45 @@ +## +# This is a contribution from Phoenix HPC Service, The University of Adelaide, Australia +# Homepage: https://www.adelaide.edu.au/phoenix/ +# +# Copyright:: Copyright 2014-2017 adelaide.edu.au/phoenix +# Authors:: Robert Qiao , Exequiel Sepulveda +# License:: GPL-v3.0 +# +# Notes:: +## + +easyblock = 'PythonPackage' + +name = 'BamM' +version = '1.7.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://ecogenomics.github.io/BamM/' +description = """ BamM is a c library, wrapped in python, that parses BAM files """ + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/Ecogenomics/BamM/archive'] +sources = ['%(version)s.tar.gz'] + +checksums = ['1a30a5014aa64aea23f12b82c8e474044af126c9e6ddb575530ab14b6ef765b8', 'sha256'] + +builddependencies = [ + ('libtool', '2.4.6'), + ('Automake', '1.15'), +] + +dependencies = [ + ('Python', '2.7.13'), + ('SAMtools', '1.3.1'), + ('BWA', '0.7.15'), +] + +sanity_check_paths = { + 'files': ['bin/bamm'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'bio' -- GitLab From d3cfdf8e4a286ef29220276b24080694a8850c04 Mon Sep 17 00:00:00 2001 From: jrbosch Date: Mon, 31 Jul 2017 11:40:12 -0400 Subject: [PATCH 1288/1603] removing blank line at end of file --- .../g/GROMACS/GROMACS-2016.3-foss-2016b-GPU-enabled.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.3-foss-2016b-GPU-enabled.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.3-foss-2016b-GPU-enabled.eb index 6d8f8f3924..38bb91bb4e 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.3-foss-2016b-GPU-enabled.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.3-foss-2016b-GPU-enabled.eb @@ -47,4 +47,3 @@ builddependencies = [ ] moduleclass = 'bio' - -- GitLab From 536b36ca5afe18fc801b1cfc9411db0aa3ccb313 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Tue, 1 Aug 2017 11:46:43 +0100 Subject: [PATCH 1289/1603] adding easyconfigs: SAMtools-1.5-foss-2016b.eb --- .../s/SAMtools/SAMtools-1.5-foss-2016b.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100755 easybuild/easyconfigs/s/SAMtools/SAMtools-1.5-foss-2016b.eb diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.5-foss-2016b.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.5-foss-2016b.eb new file mode 100755 index 0000000000..30006e4f3c --- /dev/null +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.5-foss-2016b.eb @@ -0,0 +1,38 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Robert Schmidt , Cedric Laczny , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# Modified by: Adam Huffman +# The Francis Crick Institute +# +# Modified for version 1.4 by: Kurt Lust, UAntwerpen +# +## +name = 'SAMtools' +version = '1.5' + +homepage = 'http://www.htslib.org/' +description = """SAM Tools provide various utilities for manipulating alignments in the SAM format, + including sorting, merging, indexing and generating alignments in a per-position format.""" + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['8542da26832ee08c1978713f5f6188ff750635b50d8ab126a0c7bb2ac1ae2df6'] + +# The htslib component of SAMtools 1.4 uses zlib, bzip2 and lzma compression. +# The latter is currently provided by XZ. +dependencies = [ + ('ncurses', '6.0'), + ('zlib', '1.2.8'), + ('bzip2', '1.0.6'), + ('XZ', '5.2.2'), +] + +moduleclass = 'bio' -- GitLab From 12634789b1a3b8f8f7cf60e7cc40f4e4fa4603f5 Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Tue, 1 Aug 2017 06:53:03 -0500 Subject: [PATCH 1290/1603] adding easyconfigs: Cython-0.26-GCCcore-6.4.0-Python-2.7.13-bare.eb --- ...n-0.26-GCCcore-6.4.0-Python-2.7.13-bare.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/c/Cython/Cython-0.26-GCCcore-6.4.0-Python-2.7.13-bare.eb diff --git a/easybuild/easyconfigs/c/Cython/Cython-0.26-GCCcore-6.4.0-Python-2.7.13-bare.eb b/easybuild/easyconfigs/c/Cython/Cython-0.26-GCCcore-6.4.0-Python-2.7.13-bare.eb new file mode 100644 index 0000000000..9875d3b964 --- /dev/null +++ b/easybuild/easyconfigs/c/Cython/Cython-0.26-GCCcore-6.4.0-Python-2.7.13-bare.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonPackage' + +name = 'Cython' +version = '0.26' +pyver = '2.7.13' +pyshortver = '2.7' +pysubver = '-bare' +versionsuffix = '-Python-%s%s' % (pyver, pysubver) + +homepage = 'https://pypi.python.org/pypi/Cython/' + +description = """ + The Cython language makes writing C extensions for the Python language as easy + as Python itself. Cython is a source code translator based on the well-known + Pyrex, but supports more cutting edge functionality and optimizations. +""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['4c24e2c22ddaed624d35229dc5db25049e9e225c6f64f3364326836cad8f2c66'] + +builddependencies = [ + ('binutils', '2.28'), + ('Python', pyver, pysubver), +] + +sanity_check_paths = { + 'files': ['bin/cygdb', 'bin/%(namelower)s', + 'lib/python%s/site-packages/%%(namelower)s.py' % pyshortver], + 'dirs': ['lib/python%s/site-packages/%%(name)s' % pyshortver], +} + +moduleclass = 'lang' -- GitLab From 9157a389daf2d304b1a42a33202176c1cf975680 Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Tue, 1 Aug 2017 07:13:11 -0500 Subject: [PATCH 1291/1603] comment patch --- easybuild/easyconfigs/p/pigz/pigz-2.3.4-GCCcore-6.4.0.eb | 4 ++++ easybuild/easyconfigs/p/pigz/pigz-2.3.4_Makefile.patch | 3 +++ 2 files changed, 7 insertions(+) diff --git a/easybuild/easyconfigs/p/pigz/pigz-2.3.4-GCCcore-6.4.0.eb b/easybuild/easyconfigs/p/pigz/pigz-2.3.4-GCCcore-6.4.0.eb index 0042955a0b..f5201cbea5 100644 --- a/easybuild/easyconfigs/p/pigz/pigz-2.3.4-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/p/pigz/pigz-2.3.4-GCCcore-6.4.0.eb @@ -26,6 +26,10 @@ checksums = ['6f031fa40bc15b1d80d502ff91f83ba14f4b079e886bfb83221374f7bf5c8f9a'] # Patch Makefile so zlib provided by EasyBuild is picked up patches = ['%(name)s-%(version)s_Makefile.patch'] +builddependencies = [ + ('binutils', '2.28'), +] + dependencies = [ ('zlib', '1.2.11'), ] diff --git a/easybuild/easyconfigs/p/pigz/pigz-2.3.4_Makefile.patch b/easybuild/easyconfigs/p/pigz/pigz-2.3.4_Makefile.patch index 05008c1033..685a17d8ca 100644 --- a/easybuild/easyconfigs/p/pigz/pigz-2.3.4_Makefile.patch +++ b/easybuild/easyconfigs/p/pigz/pigz-2.3.4_Makefile.patch @@ -1,3 +1,6 @@ +# Patch Makefile so zlib provided by EasyBuild is picked up +# Authors:: Jack Perdue - TAMU HPRC - http://hprc.tamu.edu + --- Makefile.orig 2017-07-12 22:16:56.931252958 -0500 +++ Makefile 2017-07-12 22:25:34.472386094 -0500 @@ -1,12 +1,11 @@ -- GitLab From 7b99aa36388573e1f5fa6244c6f43d5894b91198 Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Tue, 1 Aug 2017 08:05:14 -0500 Subject: [PATCH 1292/1603] add upstream patch --- .../c/CLISP/CLISP-2.49-GCCcore-6.4.0.eb | 5 +++-- .../c/CLISP/patch-modules_readline_readline.lisp | 15 +++++++++++++++ 2 files changed, 18 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/c/CLISP/patch-modules_readline_readline.lisp diff --git a/easybuild/easyconfigs/c/CLISP/CLISP-2.49-GCCcore-6.4.0.eb b/easybuild/easyconfigs/c/CLISP/CLISP-2.49-GCCcore-6.4.0.eb index 3c1b56f7a9..1f086b8886 100644 --- a/easybuild/easyconfigs/c/CLISP/CLISP-2.49-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/c/CLISP/CLISP-2.49-GCCcore-6.4.0.eb @@ -18,6 +18,9 @@ source_urls = ['ftp://ftp.gnu.org/pub/gnu/%(namelower)s/release/%(version)s'] sources = [SOURCELOWER_TAR_BZ2] checksums = ['8132ff353afaa70e6b19367a25ae3d5a43627279c25647c220641fed00f8e890'] +# from: https://sourceforge.net/p/clisp/bugs/688/ +patches = ['patch-modules_readline_readline.lisp'] + builddependencies = [ ('binutils', '2.28'), ] @@ -32,8 +35,6 @@ dependencies = [ ] prebuildopts = """ - sed -e 's/ac_cv_have_decl_rl_readline_state" = x""yes/ac_cv_have_decl_rl_readline_state" = x""FOOBAR/'\ - -i.eb modules/readline/configure cd src """ diff --git a/easybuild/easyconfigs/c/CLISP/patch-modules_readline_readline.lisp b/easybuild/easyconfigs/c/CLISP/patch-modules_readline_readline.lisp new file mode 100644 index 0000000000..19c54f96d6 --- /dev/null +++ b/easybuild/easyconfigs/c/CLISP/patch-modules_readline_readline.lisp @@ -0,0 +1,15 @@ +$NetBSD: patch-modules_readline_readline.lisp,v 1.1 2016/09/20 14:10:25 wiz Exp $ + +rl_readline_state changed from int to unsigned long in readline-7.0. + +--- modules/readline/readline.lisp.orig 2010-01-06 22:18:03.000000000 +0000 ++++ modules/readline/readline.lisp +@@ -424,7 +424,7 @@ name in ~/.inputrc. This is preferred wa + "The version of this incarnation of the readline library, e.g., 0x0402.")) + (def-c-var gnu-readline-p (:name "rl_gnu_readline_p") (:type int) + (:documentation "True if this is real GNU readline.")) +-(def-c-var readline-state (:name "rl_readline_state") (:type int) ++(def-c-var readline-state (:name "rl_readline_state") (:type ulong) + (:documentation "Flags word encapsulating the current readline state.")) + (def-c-var editing-mode (:name "rl_editing_mode") (:type int) + (:documentation "Says which editing mode readline is currently using. -- GitLab From 549d46d3606c36ee0fe3678a50d12e0173e8018f Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Tue, 1 Aug 2017 15:23:56 +0100 Subject: [PATCH 1293/1603] adding easyconfigs: BWA-0.7.16a-foss-2016b.eb, BWA-0.7.16a-intel-2017a.eb --- .../b/BWA/BWA-0.7.16a-foss-2016b.eb | 34 +++++++++++++++++++ .../b/BWA/BWA-0.7.16a-intel-2017a.eb | 34 +++++++++++++++++++ 2 files changed, 68 insertions(+) create mode 100755 easybuild/easyconfigs/b/BWA/BWA-0.7.16a-foss-2016b.eb create mode 100755 easybuild/easyconfigs/b/BWA/BWA-0.7.16a-intel-2017a.eb diff --git a/easybuild/easyconfigs/b/BWA/BWA-0.7.16a-foss-2016b.eb b/easybuild/easyconfigs/b/BWA/BWA-0.7.16a-foss-2016b.eb new file mode 100755 index 0000000000..cfc64d5813 --- /dev/null +++ b/easybuild/easyconfigs/b/BWA/BWA-0.7.16a-foss-2016b.eb @@ -0,0 +1,34 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Cyprus Institute / CaSToRC, Uni.Lu/LCSB, NTUA +# Authors:: George Tsouloupas , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +# +# Version >= 0.7.15 +# Author: Adam Huffman +# The Francis Crick Institute +# +# Note that upstream development is mainly at: https://github.com/lh3/bwa +## + +name = 'BWA' +version = '0.7.16a' +subver = '0.7.16' + +homepage = 'http://bio-bwa.sourceforge.net/' +description = """Burrows-Wheeler Aligner (BWA) is an efficient program that aligns + relatively short nucleotide sequences against a long reference sequence such as the human genome.""" + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/lh3/bwa/releases/download/v%s/' % subver] +sources = ['%(namelower)s-%(version)s.tar.bz2'] +checksums = ['8fecdb5f88871351bbe050c18d6078121456c36ad75c5c78f33a926560ffc170'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BWA/BWA-0.7.16a-intel-2017a.eb b/easybuild/easyconfigs/b/BWA/BWA-0.7.16a-intel-2017a.eb new file mode 100755 index 0000000000..c1ee916e24 --- /dev/null +++ b/easybuild/easyconfigs/b/BWA/BWA-0.7.16a-intel-2017a.eb @@ -0,0 +1,34 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Cyprus Institute / CaSToRC, Uni.Lu/LCSB, NTUA +# Authors:: George Tsouloupas , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +# +# Version >= 0.7.15 +# Author: Adam Huffman +# The Francis Crick Institute +# +# Note that upstream development is mainly at: https://github.com/lh3/bwa +## + +name = 'BWA' +version = '0.7.16a' +subver = '0.7.16' + +homepage = 'http://bio-bwa.sourceforge.net/' +description = """Burrows-Wheeler Aligner (BWA) is an efficient program that aligns + relatively short nucleotide sequences against a long reference sequence such as the human genome.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/lh3/bwa/releases/download/v%s/' % subver] +sources = ['%(namelower)s-%(version)s.tar.bz2'] +checksums = ['8fecdb5f88871351bbe050c18d6078121456c36ad75c5c78f33a926560ffc170'] + +moduleclass = 'bio' -- GitLab From b5c5581f2145e580d19c85de9ddddd2e3b0d6be9 Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Tue, 1 Aug 2017 13:31:26 -0500 Subject: [PATCH 1294/1603] adding easyconfigs: Java-1.8.0_144.eb --- .../easyconfigs/j/Java/Java-1.8.0_144.eb | 20 +++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 easybuild/easyconfigs/j/Java/Java-1.8.0_144.eb diff --git a/easybuild/easyconfigs/j/Java/Java-1.8.0_144.eb b/easybuild/easyconfigs/j/Java/Java-1.8.0_144.eb new file mode 100644 index 0000000000..dc8a2bb0a1 --- /dev/null +++ b/easybuild/easyconfigs/j/Java/Java-1.8.0_144.eb @@ -0,0 +1,20 @@ +name = 'Java' +version = '1.8.0_144' + +homepage = 'http://java.com/' + +description = """ + Java Platform, Standard Edition (Java SE) lets you develop and deploy + Java applications on desktops and servers. +""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +# download the tar.gz directly from +# http://www.oracle.com/technetwork/java/javase/downloads/index.html +(vp, vs) = version.split('_') +altver = '%su%s' % (vp.split('.')[1], vs) +sources = ['jdk-%s-linux-x64.tar.gz' % altver] +checksums = ['e8a341ce566f32c3d06f6d0f0eeea9a0f434f538d22af949ae58bc86f2eeaae4'] + +moduleclass = 'lang' -- GitLab From 81a338c4cded59a94ad8d9fbb6020e6be37053c0 Mon Sep 17 00:00:00 2001 From: frenchwr Date: Wed, 2 Aug 2017 14:26:02 -0500 Subject: [PATCH 1295/1603] add updated version of singularity --- .../Singularity-2.3.1-GCC-5.4.0-2.26.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/s/Singularity/Singularity-2.3.1-GCC-5.4.0-2.26.eb diff --git a/easybuild/easyconfigs/s/Singularity/Singularity-2.3.1-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/s/Singularity/Singularity-2.3.1-GCC-5.4.0-2.26.eb new file mode 100644 index 0000000000..a71dd25439 --- /dev/null +++ b/easybuild/easyconfigs/s/Singularity/Singularity-2.3.1-GCC-5.4.0-2.26.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'Singularity' +version = '2.3.1' + +homepage = 'http://gmkurtzer.github.io/singularity' +description = """Singularity is a portable application stack packaging and runtime utility.""" + +toolchain = {'name': 'GCC', 'version': '5.4.0-2.26'} + +source_urls = ['https://github.com/gmkurtzer/singularity/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['d25be31b443969b12179fbdb6db38c24002f06234bf923424bda1d662ad34e71'] + +builddependencies = [('Autotools', '20150215')] + +preconfigopts = './autogen.sh && ' + +sanity_check_paths = { + 'files': ['bin/run-singularity', 'bin/singularity', 'etc/singularity/singularity.conf', + 'libexec/singularity/bin/action-suid'], + 'dirs': ['etc', 'libexec/singularity'], +} + +# next steps after instalations +# INSTALATION_PATH=your_instalation_path +# chown root:root $INSTALATION_PATH/Singularity/*/etc/singularity/singularity.conf +# chown root:root $INSTALATION_PATH/Singularity/*/libexec/singularity/bin/*-suid +# chown root:root $INSTALATION_PATH/Singularity/*/var/singularity/mnt/container +# chmod 4755 $INSTALATION_PATH/Singularity/*/libexec/singularity/bin/*-suid +# chmod +s $INSTALATION_PATH/Singularity/*/libexec/singularity/bin/*-suid + +moduleclass = 'tools' + -- GitLab From a1876330f2da4c05deb5ed983bfdf402806ed979 Mon Sep 17 00:00:00 2001 From: frenchwr Date: Wed, 2 Aug 2017 15:10:14 -0500 Subject: [PATCH 1296/1603] fix style --- .../s/Singularity/Singularity-2.3.1-GCC-5.4.0-2.26.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/Singularity/Singularity-2.3.1-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/s/Singularity/Singularity-2.3.1-GCC-5.4.0-2.26.eb index a71dd25439..3852a69875 100644 --- a/easybuild/easyconfigs/s/Singularity/Singularity-2.3.1-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/s/Singularity/Singularity-2.3.1-GCC-5.4.0-2.26.eb @@ -17,7 +17,7 @@ builddependencies = [('Autotools', '20150215')] preconfigopts = './autogen.sh && ' sanity_check_paths = { - 'files': ['bin/run-singularity', 'bin/singularity', 'etc/singularity/singularity.conf', + 'files': ['bin/run-singularity', 'bin/singularity', 'etc/singularity/singularity.conf', 'libexec/singularity/bin/action-suid'], 'dirs': ['etc', 'libexec/singularity'], } @@ -31,4 +31,3 @@ sanity_check_paths = { # chmod +s $INSTALATION_PATH/Singularity/*/libexec/singularity/bin/*-suid moduleclass = 'tools' - -- GitLab From 6768de1892c9b7c0d6a10732bdd8766d51334585 Mon Sep 17 00:00:00 2001 From: frenchwr Date: Thu, 3 Aug 2017 07:20:52 -0500 Subject: [PATCH 1297/1603] fix spelling of installation --- .../s/Singularity/Singularity-2.3.1-GCC-5.4.0-2.26.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/Singularity/Singularity-2.3.1-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/s/Singularity/Singularity-2.3.1-GCC-5.4.0-2.26.eb index 3852a69875..7e7221e7b3 100644 --- a/easybuild/easyconfigs/s/Singularity/Singularity-2.3.1-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/s/Singularity/Singularity-2.3.1-GCC-5.4.0-2.26.eb @@ -22,7 +22,7 @@ sanity_check_paths = { 'dirs': ['etc', 'libexec/singularity'], } -# next steps after instalations +# next steps after installation # INSTALATION_PATH=your_instalation_path # chown root:root $INSTALATION_PATH/Singularity/*/etc/singularity/singularity.conf # chown root:root $INSTALATION_PATH/Singularity/*/libexec/singularity/bin/*-suid -- GitLab From ddc316e4d204267c6bec0b5301460c6e3f43b32a Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Thu, 3 Aug 2017 16:04:55 +0200 Subject: [PATCH 1298/1603] {bio}[foss/2017a] Trinity 2.4.0 (REVIEW) --- .../b/Bowtie/Bowtie-1.1.2-GCCcore-6.3.0.eb | 18 + .../b/Bowtie2/Bowtie2-2.3.2-foss-2017a.eb | 32 + .../p/Perl/Perl-5.24.1-foss-2017a.eb | 907 ++++++++++++++++++ .../t/Trinity/Trinity-2.4.0-foss-2017a.eb | 34 + .../t/tbb/tbb-2017_U6-GCCcore-6.3.0.eb | 17 + 5 files changed, 1008 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2-GCCcore-6.3.0.eb create mode 100644 easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.3.2-foss-2017a.eb create mode 100644 easybuild/easyconfigs/p/Perl/Perl-5.24.1-foss-2017a.eb create mode 100644 easybuild/easyconfigs/t/Trinity/Trinity-2.4.0-foss-2017a.eb create mode 100644 easybuild/easyconfigs/t/tbb/tbb-2017_U6-GCCcore-6.3.0.eb diff --git a/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2-GCCcore-6.3.0.eb b/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..a46b5265d0 --- /dev/null +++ b/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2-GCCcore-6.3.0.eb @@ -0,0 +1,18 @@ +# Modified from existing version by: +# Robert Schmidt +# Ottawa Hospital Research Institute - Bioinformatics Team +name = 'Bowtie' +version = '1.1.2' + +homepage = 'http://bowtie-bio.sourceforge.net/index.shtml' +description = """Bowtie is an ultrafast, memory-efficient short read aligner. +It aligns short DNA sequences (reads) to the human genome. +""" + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} +toolchainopts = {'pic': True} + +sources = ['%(namelower)s-%(version)s-src.zip'] +source_urls = ['http://download.sourceforge.net/bowtie-bio/'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.3.2-foss-2017a.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.3.2-foss-2017a.eb new file mode 100644 index 0000000000..9d4236c5ff --- /dev/null +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.3.2-foss-2017a.eb @@ -0,0 +1,32 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# Modified by: Robert Schmidt +# Ottawa Hospital Research Institute - Bioinformatics Team +# Modified by: Adam Huffman +# The Francis Crick Institute +# Modified by: Kurt Lust, UAntwerp + +name = 'Bowtie2' +version = '2.3.2' + +homepage = 'http://bowtie-bio.sourceforge.net/bowtie2/index.shtml' +description = """ Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads + to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s + of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. + Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, + its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.""" + +toolchain = {'name': 'foss', 'version': '2017a'} +toolchainopts = {'pic': True, 'cstd': 'gnu++98'} + +sources = ['%(namelower)s-%(version)s-source.zip'] +source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')] + +dependencies = [('tbb', '2017_U6')] + +# to add script folder to path just uncomment this line +# modextrapaths = {'PATH': 'scripts'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.24.1-foss-2017a.eb b/easybuild/easyconfigs/p/Perl/Perl-5.24.1-foss-2017a.eb new file mode 100644 index 0000000000..c45b3b6b14 --- /dev/null +++ b/easybuild/easyconfigs/p/Perl/Perl-5.24.1-foss-2017a.eb @@ -0,0 +1,907 @@ +name = 'Perl' +version = '5.24.1' + +homepage = 'https://www.perl.org/' +description = """Larry Wall's Practical Extraction and Report Language""" + +toolchain = {'name': 'foss', 'version': '2017a'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.cpan.org/src/%(version_major)s.0'] +sources = [SOURCELOWER_TAR_GZ] + +# !! order of extensions is important !! +# extensions updated on April 4th 2017 +exts_list = [ + ('Config::General', '2.63', { + 'source_tmpl': 'Config-General-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TL/TLINDEN'], + }), + ('File::Listing', '6.04', { + 'source_tmpl': 'File-Listing-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('ExtUtils::InstallPaths', '0.011', { + 'source_tmpl': 'ExtUtils-InstallPaths-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('ExtUtils::Helpers', '0.026', { + 'source_tmpl': 'ExtUtils-Helpers-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('Test::Harness', '3.38', { + 'source_tmpl': 'Test-Harness-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('ExtUtils::Config', '0.008', { + 'source_tmpl': 'ExtUtils-Config-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('Module::Build::Tiny', '0.039', { + 'source_tmpl': 'Module-Build-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('aliased', '0.34', { + 'source_tmpl': 'aliased-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Text::Glob', '0.11', { + 'source_tmpl': 'Text-Glob-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RC/RCLAMP'], + }), + ('Regexp::Common', '2016060801', { + 'source_tmpl': 'Regexp-Common-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AB/ABIGAIL'], + }), + ('GO::Utils', '0.15', { + 'source_tmpl': 'go-perl-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CM/CMUNGALL'], + }), + ('Module::Pluggable', '5.2', { + 'source_tmpl': 'Module-Pluggable-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SI/SIMONW'], + }), + ('Test::Fatal', '0.014', { + 'source_tmpl': 'Test-Fatal-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Test::Warnings', '0.026', { + 'source_tmpl': 'Test-Warnings-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('File::ShareDir::Install', '0.11', { + 'source_tmpl': 'File-ShareDir-Install-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('DateTime::Locale', '1.16', { + 'source_tmpl': 'DateTime-Locale-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('DateTime::TimeZone', '2.11', { + 'source_tmpl': 'DateTime-TimeZone-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('Test::Requires', '0.10', { + 'source_tmpl': 'Test-Requires-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TOKUHIROM'], + }), + ('Module::Implementation', '0.09', { + 'source_tmpl': 'Module-Implementation-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('Module::Build', '0.4222', { + 'source_tmpl': 'Module-Build-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('Module::Runtime', '0.014', { + 'source_tmpl': 'Module-Runtime-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/Z/ZE/ZEFRAM'], + }), + ('Try::Tiny', '0.28', { + 'source_tmpl': 'Try-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Params::Validate', '1.26', { + 'source_tmpl': 'Params-Validate-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('List::MoreUtils', '0.418', { + 'source_tmpl': 'List-MoreUtils-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + }), + ('Exporter::Tiny', '0.044', { + 'source_tmpl': 'Exporter-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TOBYINK'], + }), + ('Class::Singleton', '1.5', { + 'source_tmpl': 'Class-Singleton-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHAY'], + }), + ('DateTime', '1.42', { + 'source_tmpl': 'DateTime-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('File::Find::Rule::Perl', '1.15', { + 'source_tmpl': 'File-Find-Rule-Perl-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Readonly', '2.05', { + 'source_tmpl': 'Readonly-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SA/SANKO'], + }), + ('Git', '0.41', { + 'source_tmpl': 'Git-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MS/MSOUTH'], + }), + ('Tree::DAG_Node', '1.29', { + 'source_tmpl': 'Tree-DAG_Node-%(version)s.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + }), + ('Template', '2.26', { + 'source_tmpl': 'Template-Toolkit-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AB/ABW'], + }), + ('FreezeThaw', '0.5001', { + 'source_tmpl': 'FreezeThaw-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IL/ILYAZ/modules'], + }), + ('DBI', '1.636', { + 'source_tmpl': 'DBI-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TI/TIMB'], + }), + ('DBD::SQLite', '1.54', { + 'source_tmpl': 'DBD-SQLite-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IS/ISHIGAKI'], + }), + ('Math::Bezier', '0.01', { + 'source_tmpl': 'Math-Bezier-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AB/ABW'], + }), + ('Archive::Extract', '0.80', { + 'source_tmpl': 'Archive-Extract-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + }), + ('DBIx::Simple', '1.35', { + 'source_tmpl': 'DBIx-Simple-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JU/JUERD'], + }), + ('Shell', '0.73', { + 'source_tmpl': 'Shell-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/F/FE/FERREIRA'], + }), + ('File::Spec', '3.62', { + 'source_tmpl': 'PathTools-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Test::Simple', '1.302078', { + 'source_tmpl': 'Test-Simple-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + }), + ('Set::Scalar', '1.29', { + 'source_tmpl': 'Set-Scalar-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAVIDO'], + }), + ('IO::Stringy', '2.111', { + 'source_tmpl': 'IO-stringy-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DS/DSKOLL'], + }), + ('Encode::Locale', '1.05', { + 'source_tmpl': 'Encode-Locale-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('XML::SAX::Base', '1.09', { + 'source_tmpl': 'XML-SAX-Base-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GR/GRANTM'], + }), + ('XML::NamespaceSupport', '1.12', { + 'source_tmpl': 'XML-NamespaceSupport-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PERIGRIN'], + }), + ('XML::SAX', '0.99', { + 'source_tmpl': 'XML-SAX-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GR/GRANTM'], + }), + ('Test::LeakTrace', '0.15', { + 'source_tmpl': 'Test-LeakTrace-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GF/GFUJI'], + }), + ('Test::Exception', '0.43', { + 'source_tmpl': 'Test-Exception-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + }), + ('Text::Table', '1.132', { + 'source_tmpl': 'Text-Table-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'], + }), + ('MIME::Types', '2.13', { + 'source_tmpl': 'MIME-Types-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARKOV'], + }), + ('Module::Build::XSUtil', '0.16', { + 'source_tmpl': 'Module-Build-XSUtil-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HI/HIDEAKIO'], + }), + ('Tie::Function', '0.02', { + 'source_tmpl': 'Tie-Function-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAVIDNICO/handy_tied_functions'], + }), + ('Template::Plugin::Number::Format', '1.06', { + 'source_tmpl': 'Template-Plugin-Number-Format-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DARREN'], + }), + ('HTML::Parser', '3.72', { + 'source_tmpl': 'HTML-Parser-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('Date::Handler', '1.2', { + 'source_tmpl': 'Date-Handler-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BB/BBEAUSEJ'], + }), + ('Params::Util', '1.07', { + 'source_tmpl': 'Params-Util-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + }), + ('IO::HTML', '1.001', { + 'source_tmpl': 'IO-HTML-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CJ/CJM'], + }), + ('Data::Grove', '0.08', { + 'source_tmpl': 'libxml-perl-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KM/KMACLEOD'], + }), + ('Class::ISA', '0.36', { + 'source_tmpl': 'Class-ISA-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SM/SMUELLER'], + }), + ('URI', '1.71', { + 'source_tmpl': 'URI-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Ima::DBI', '0.35', { + 'source_tmpl': 'Ima-DBI-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PERRIN'], + }), + ('Tie::IxHash', '1.23', { + 'source_tmpl': 'Tie-IxHash-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CH/CHORNY'], + }), + ('GO', '0.04', { + 'source_tmpl': 'go-db-perl-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SJ/SJCARBON'], + }), + ('Class::DBI::SQLite', '0.11', { + 'source_tmpl': 'Class-DBI-SQLite-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA'], + }), + ('Pod::POM', '2.01', { + 'source_tmpl': 'Pod-POM-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB'], + }), + ('Math::Round', '0.07', { + 'source_tmpl': 'Math-Round-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GR/GROMMEL'], + }), + ('Text::Diff', '1.44', { + 'source_tmpl': 'Text-Diff-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB'], + }), + ('Log::Message::Simple', '0.10', { + 'source_tmpl': 'Log-Message-Simple-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + }), + ('IO::Socket::SSL', '2.047', { + 'source_tmpl': 'IO-Socket-SSL-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SU/SULLR'], + }), + ('Fennec::Lite', '0.004', { + 'source_tmpl': 'Fennec-Lite-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + }), + ('Sub::Uplevel', '0.2800', { + 'source_tmpl': 'Sub-Uplevel-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + }), + ('Meta::Builder', '0.003', { + 'source_tmpl': 'Meta-Builder-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + }), + ('Exporter::Declare', '0.114', { + 'source_tmpl': 'Exporter-Declare-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + }), + ('Getopt::Long', '2.49.1', { + 'source_tmpl': 'Getopt-Long-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JV/JV'], + }), + ('Log::Message', '0.08', { + 'source_tmpl': 'Log-Message-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + }), + ('Mouse', 'v2.4.9', { + 'source_tmpl': 'Mouse-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SY/SYOHEX'], + }), + ('Test::Version', '2.05', { + 'source_tmpl': 'Test-Version-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE'], + }), + ('DBIx::Admin::TableInfo', '3.03', { + 'source_tmpl': 'DBIx-Admin-TableInfo-%(version)s.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + }), + ('Net::HTTP', '6.13', { + 'source_tmpl': 'Net-HTTP-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'], + }), + ('Test::Deep', '1.126', { + 'source_tmpl': 'Test-Deep-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Test::Warn', '0.32', { + 'source_tmpl': 'Test-Warn-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BIGJ'], + }), + ('MRO::Compat', '0.13', { + 'source_tmpl': 'MRO-Compat-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + }), + ('Moo', '2.003002', { + 'source_tmpl': 'Moo-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + }), + ('Hash::Merge', '0.200', { + 'source_tmpl': 'Hash-Merge-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + }), + ('SQL::Abstract', '1.84', { + 'source_tmpl': 'SQL-Abstract-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IL/ILMARI'], + }), + ('HTML::Form', '6.03', { + 'source_tmpl': 'HTML-Form-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('File::Copy::Recursive', '0.38', { + 'source_tmpl': 'File-Copy-Recursive-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DM/DMUEY'], + }), + ('Number::Compare', '0.03', { + 'source_tmpl': 'Number-Compare-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RC/RCLAMP'], + }), + ('IPC::Run', '0.94', { + 'source_tmpl': 'IPC-Run-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR'], + }), + ('HTML::Entities::Interpolate', '1.10', { + 'source_tmpl': 'HTML-Entities-Interpolate-%(version)s.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + }), + ('Test::ClassAPI', '1.06', { + 'source_tmpl': 'Test-ClassAPI-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + }), + ('Test::Most', '0.35', { + 'source_tmpl': 'Test-Most-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OV/OVID'], + }), + ('Class::Accessor', '0.34', { + 'source_tmpl': 'Class-Accessor-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KA/KASEI'], + }), + ('Test::Differences', '0.64', { + 'source_tmpl': 'Test-Differences-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DC/DCANTRELL'], + }), + ('HTTP::Tiny', '0.070', { + 'source_tmpl': 'HTTP-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + }), + ('Package::DeprecationManager', '0.17', { + 'source_tmpl': 'Package-DeprecationManager-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('Digest::SHA1', '2.13', { + 'source_tmpl': 'Digest-SHA1-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('Date::Language', '2.30', { + 'source_tmpl': 'TimeDate-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GB/GBARR'], + }), + ('version', '0.9917', { + 'source_tmpl': 'version-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JP/JPEACOCK'], + }), + ('Sub::Uplevel', '0.2800', { + 'source_tmpl': 'Sub-Uplevel-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + }), + ('XML::Bare', '0.53', { + 'source_tmpl': 'XML-Bare-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CO/CODECHILD'], + 'patches': ['XML-Bare-0.53_icc.patch'], + }), + ('Dist::CheckConflicts', '0.11', { + 'source_tmpl': 'Dist-CheckConflicts-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DO/DOY'], + }), + ('Sub::Name', '0.21', { + 'source_tmpl': 'Sub-Name-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Time::Piece', '1.31', { + 'source_tmpl': 'Time-Piece-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ES/ESAYM'], + }), + ('Digest::HMAC', '1.03', { + 'source_tmpl': 'Digest-HMAC-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('HTTP::Negotiate', '6.01', { + 'source_tmpl': 'HTTP-Negotiate-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('MIME::Lite', '3.030', { + 'source_tmpl': 'MIME-Lite-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Crypt::Rijndael', '1.13', { + 'source_tmpl': 'Crypt-Rijndael-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('B::Lint', '1.20', { + 'source_tmpl': 'B-Lint-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Canary::Stability', '2012', { + 'source_tmpl': 'Canary-Stability-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/ML/MLEHMANN'], + }), + ('AnyEvent', '7.13', { + 'source_tmpl': 'AnyEvent-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/ML/MLEHMANN'], + }), + ('Object::Accessor', '0.48', { + 'source_tmpl': 'Object-Accessor-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + }), + ('Data::UUID', '1.221', { + 'source_tmpl': 'Data-UUID-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Test::Pod', '1.51', { + 'source_tmpl': 'Test-Pod-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('AppConfig', '1.71', { + 'source_tmpl': 'AppConfig-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB'], + }), + ('Net::SMTP::SSL', '1.04', { + 'source_tmpl': 'Net-SMTP-SSL-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('XML::Tiny', '2.06', { + 'source_tmpl': 'XML-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DC/DCANTRELL'], + }), + ('HTML::Tagset', '3.20', { + 'source_tmpl': 'HTML-Tagset-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PETDANCE'], + }), + ('HTML::Tree', '5.03', { + 'source_tmpl': 'HTML-Tree-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CJ/CJM'], + }), + ('Devel::GlobalDestruction', '0.14', { + 'source_tmpl': 'Devel-GlobalDestruction-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + }), + ('WWW::RobotRules', '6.02', { + 'source_tmpl': 'WWW-RobotRules-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('Expect', '1.33', { + 'source_tmpl': 'Expect-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JA/JACOBY'], + }), + ('Term::UI', '0.46', { + 'source_tmpl': 'Term-UI-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + }), + ('Net::SNMP', 'v6.0.1', { + 'source_tmpl': 'Net-SNMP-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DT/DTOWN'], + }), + ('XML::SAX::Writer', '0.56', { + 'source_tmpl': 'XML-SAX-Writer-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PERIGRIN'], + }), + ('Statistics::Descriptive', '3.0612', { + 'source_tmpl': 'Statistics-Descriptive-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'], + }), + ('Class::Load', '0.23', { + 'source_tmpl': 'Class-Load-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('LWP::Simple', '6.25', { + 'source_tmpl': 'libwww-perl-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'], + }), + ('Time::Piece::MySQL', '0.06', { + 'source_tmpl': 'Time-Piece-MySQL-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KA/KASEI'], + }), + ('Package::Stash::XS', '0.28', { + 'source_tmpl': 'Package-Stash-XS-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DO/DOY'], + }), + ('GD::Graph', '1.54', { + 'source_tmpl': 'GDGraph-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RU/RUZ'], + }), + ('Set::Array', '0.30', { + 'source_tmpl': 'Set-Array-%(version)s.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + }), + ('boolean', '0.46', { + 'source_tmpl': 'boolean-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IN/INGY'], + }), + ('Number::Format', '1.75', { + 'source_tmpl': 'Number-Format-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/W/WR/WRW'], + }), + ('Data::Stag', '0.14', { + 'source_tmpl': 'Data-Stag-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CM/CMUNGALL'], + }), + ('Test::NoWarnings', '1.04', { + 'source_tmpl': 'Test-NoWarnings-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + }), + ('Crypt::DES', '2.07', { + 'source_tmpl': 'Crypt-DES-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DP/DPARIS'], + }), + ('Exporter', '5.72', { + 'source_tmpl': 'Exporter-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR'], + }), + ('Class::Inspector', '1.31', { + 'source_tmpl': 'Class-Inspector-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE'], + }), + ('Parse::RecDescent', '1.967014', { + 'source_tmpl': 'Parse-RecDescent-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JT/JTBRAUN'], + }), + ('Carp', '1.38', { + 'source_tmpl': 'Carp-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('XML::XPath', '1.40', { + 'source_tmpl': 'XML-XPath-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MANWAR'], + }), + ('Capture::Tiny', '0.46', { + 'source_tmpl': 'Capture-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + }), + ('JSON', '2.90', { + 'source_tmpl': 'JSON-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MAKAMAKA'], + }), + ('Sub::Exporter', '0.987', { + 'source_tmpl': 'Sub-Exporter-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Class::Load::XS', '0.09', { + 'source_tmpl': 'Class-Load-XS-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Set::IntSpan::Fast', '1.15', { + 'source_tmpl': 'Set-IntSpan-Fast-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AN/ANDYA'], + }), + ('Sub::Exporter::Progressive', '0.001013', { + 'source_tmpl': 'Sub-Exporter-Progressive-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/F/FR/FREW'], + }), + ('Data::Dumper::Concise', '2.022', { + 'source_tmpl': 'Data-Dumper-Concise-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/F/FR/FREW'], + }), + ('File::Slurp::Tiny', '0.004', { + 'source_tmpl': 'File-Slurp-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('Algorithm::Diff', '1.1903', { + 'source_tmpl': 'Algorithm-Diff-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TY/TYEMQ'], + }), + ('AnyData', '0.12', { + 'source_tmpl': 'AnyData-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + }), + ('Text::Iconv', '1.7', { + 'source_tmpl': 'Text-Iconv-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MP/MPIOTR'], + }), + ('Class::Data::Inheritable', '0.08', { + 'source_tmpl': 'Class-Data-Inheritable-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TM/TMTM'], + }), + ('Text::Balanced', '2.03', { + 'source_tmpl': 'Text-Balanced-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHAY'], + }), + ('strictures', '2.000003', { + 'source_tmpl': 'strictures-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + }), + ('Switch', '2.17', { + 'source_tmpl': 'Switch-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CH/CHORNY'], + }), + ('File::Which', '1.21', { + 'source_tmpl': 'File-Which-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE'], + }), + ('Email::Date::Format', '1.005', { + 'source_tmpl': 'Email-Date-Format-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Error', '0.17024', { + 'source_tmpl': 'Error-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'], + }), + ('Mock::Quick', '1.111', { + 'source_tmpl': 'Mock-Quick-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + }), + ('Text::CSV', '1.92', { + 'source_tmpl': 'Text-CSV-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IS/ISHIGAKI'], + }), + ('Test::Output', '1.031', { + 'source_tmpl': 'Test-Output-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BD/BDFOY'], + }), + ('Class::DBI', 'v3.0.17', { + 'source_tmpl': 'Class-DBI-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TM/TMTM'], + }), + ('List::AllUtils', '0.14', { + 'source_tmpl': 'List-AllUtils-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('UNIVERSAL::moniker', '0.08', { + 'source_tmpl': 'UNIVERSAL-moniker-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KA/KASEI'], + }), + ('Exception::Class', '1.42', { + 'source_tmpl': 'Exception-Class-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('File::CheckTree', '4.42', { + 'source_tmpl': 'File-CheckTree-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Math::VecStat', '0.08', { + 'source_tmpl': 'Math-VecStat-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AS/ASPINELLI'], + }), + ('Pod::LaTeX', '0.61', { + 'source_tmpl': 'Pod-LaTeX-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TJ/TJENNESS'], + }), + ('Eval::Closure', '0.14', { + 'source_tmpl': 'Eval-Closure-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DO/DOY'], + }), + ('HTTP::Request', '6.11', { + 'source_tmpl': 'HTTP-Message-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('XML::Twig', '3.52', { + 'source_tmpl': 'XML-Twig-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIROD'], + }), + ('IO::String', '1.08', { + 'source_tmpl': 'IO-String-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('XML::Simple', '2.22', { + 'source_tmpl': 'XML-Simple-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GR/GRANTM'], + }), + ('Sub::Install', '0.928', { + 'source_tmpl': 'Sub-Install-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('HTTP::Cookies', '6.03', { + 'source_tmpl': 'HTTP-Cookies-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'], + }), + ('Pod::Plainer', '1.04', { + 'source_tmpl': 'Pod-Plainer-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RM/RMBARKER'], + }), + ('Test::Exception::LessClever', '0.009', { + 'source_tmpl': 'Test-Exception-LessClever-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('LWP::MediaTypes', '6.02', { + 'source_tmpl': 'LWP-MediaTypes-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('Scalar::Util', '1.47', { + 'source_tmpl': 'Scalar-List-Utils-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PEVANS'], + }), + ('Data::Section::Simple', '0.07', { + 'source_tmpl': 'Data-Section-Simple-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA'], + }), + ('Class::Trigger', '0.14', { + 'source_tmpl': 'Class-Trigger-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA'], + }), + ('HTTP::Daemon', '6.01', { + 'source_tmpl': 'HTTP-Daemon-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('File::HomeDir', '1.00', { + 'source_tmpl': 'File-HomeDir-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + }), + ('HTTP::Date', '6.02', { + 'source_tmpl': 'HTTP-Date-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('Authen::SASL', '2.16', { + 'source_tmpl': 'Authen-SASL-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GB/GBARR'], + }), + ('Clone', '0.38', { + 'source_tmpl': 'Clone-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GARU'], + }), + ('Data::Types', '0.09', { + 'source_tmpl': 'Data-Types-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DW/DWHEELER'], + }), + ('Import::Into', '1.002005', { + 'source_tmpl': 'Import-Into-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + }), + ('DateTime::Tiny', '1.06', { + 'source_tmpl': 'DateTime-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + }), + ('DBD::AnyData', '0.110', { + 'source_tmpl': 'DBD-AnyData-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + }), + ('Text::Format', '0.60', { + 'source_tmpl': 'Text-Format-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'], + }), + ('Devel::CheckCompiler', '0.07', { + 'source_tmpl': 'Devel-CheckCompiler-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SY/SYOHEX'], + }), + ('Log::Handler', '0.88', { + 'source_tmpl': 'Log-Handler-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BL/BLOONIX'], + }), + ('DBIx::ContextualFetch', '1.03', { + 'source_tmpl': 'DBIx-ContextualFetch-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TM/TMTM'], + }), + ('Devel::StackTrace', '2.02', { + 'source_tmpl': 'Devel-StackTrace-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('Term::ReadKey', '2.14', { + 'source_tmpl': 'TermReadKey-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KJ/KJALB'], + }), + ('Set::IntSpan', '1.19', { + 'source_tmpl': 'Set-IntSpan-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SW/SWMCD'], + }), + ('Moose', '2.2004', { + 'source_tmpl': 'Moose-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Algorithm::Dependency', '1.110', { + 'source_tmpl': 'Algorithm-Dependency-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + }), + ('Font::TTF', '1.06', { + 'source_tmpl': 'Font-TTF-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BH/BHALLISSY'], + }), + ('IPC::Run3', '0.048', { + 'source_tmpl': 'IPC-Run3-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('File::Find::Rule', '0.34', { + 'source_tmpl': 'File-Find-Rule-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RC/RCLAMP'], + }), + ('SQL::Statement', '1.410', { + 'source_tmpl': 'SQL-Statement-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + }), + ('File::Slurp', '9999.19', { + 'source_tmpl': 'File-Slurp-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/U/UR/URI'], + }), + ('Package::Stash', '0.37', { + 'source_tmpl': 'Package-Stash-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DO/DOY'], + }), + ('Data::OptList', '0.110', { + 'source_tmpl': 'Data-OptList-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('CPANPLUS', '0.9164', { + 'source_tmpl': 'CPANPLUS-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + }), + ('IO::Tty', '1.12', { + 'source_tmpl': 'IO-Tty-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR'], + }), + ('Text::Soundex', '3.05', { + 'source_tmpl': 'Text-Soundex-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Lingua::EN::PluralToSingular', '0.19', { + 'source_tmpl': 'Lingua-EN-PluralToSingular-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BK/BKB'], + }), + ('Want', '0.29', { + 'source_tmpl': 'Want-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RO/ROBIN'], + }), + ('Cwd::Guard', '0.05', { + 'source_tmpl': 'Cwd-Guard-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KA/KAZEBURO'], + }), + ('Bundle::BioPerl', '2.1.9', { + 'source_tmpl': 'Bundle-BioPerl-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS'], + }), + ('Mail::Util', '2.18', { + 'source_tmpl': 'MailTools-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARKOV'], + }), + ('Text::Template', '1.47', { + 'source_tmpl': 'Text-Template-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MS/MSCHOUT'], + }), + ('PDF::API2', '2.031', { + 'source_tmpl': 'PDF-API2-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SS/SSIMMS'], + }), + ('Devel::CheckLib', '1.11', { + 'source_tmpl': 'Devel-CheckLib-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MATTN'], + }), + ('SVG', '2.77', { + 'source_tmpl': 'SVG-2.77.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/M/MA/MANWAR/'], + }), + ('Statistics::Basic', '1.6611', { + 'source_tmpl': 'Statistics-Basic-1.6611.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/J/JE/JETTERO/'], + }), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/t/Trinity/Trinity-2.4.0-foss-2017a.eb b/easybuild/easyconfigs/t/Trinity/Trinity-2.4.0-foss-2017a.eb new file mode 100644 index 0000000000..90175fa060 --- /dev/null +++ b/easybuild/easyconfigs/t/Trinity/Trinity-2.4.0-foss-2017a.eb @@ -0,0 +1,34 @@ +name = 'Trinity' +version = '2.4.0' +java = 'Java' +javaver = '1.8.0_121' + +homepage = 'http://trinityrnaseq.github.io' +description = """Trinity represents a novel method for the efficient and robust de novo reconstruction + of transcriptomes from RNA-Seq data. Trinity combines three independent software modules: Inchworm, + Chrysalis, and Butterfly, applied sequentially to process large volumes of RNA-Seq reads.""" +toolchain = {'name': 'foss', 'version': '2017a'} +toolchainopts = {'optarch': True} + +source_urls = ['https://github.com/trinityrnaseq/trinityrnaseq/archive/'] +sources = ['%(name)s-v%(version)s.tar.gz'] + +patches = [ + 'chrysalis_commandline_noconsts_2012-10-05.patch', +] + +builddependencies = [ + ('Autotools', '20150215', '', ('GCCcore', '6.3.0')), +] + +dependencies = [ + (java, javaver, '', True), + ('ant', '1.10.1', '-%s-%s' % (java, javaver), True), + ('Bowtie', '1.1.2'), + ('Bowtie2', '2.3.2'), + ('ncurses', '6.0'), + ('zlib', '1.2.11'), + ('Perl', '5.24.1'), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/tbb/tbb-2017_U6-GCCcore-6.3.0.eb b/easybuild/easyconfigs/t/tbb/tbb-2017_U6-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..34c5460e40 --- /dev/null +++ b/easybuild/easyconfigs/t/tbb/tbb-2017_U6-GCCcore-6.3.0.eb @@ -0,0 +1,17 @@ +name = 'tbb' +version = '2017_U6' + +homepage = 'https://01.org/tbb/' +description = """Intel(R) Threading Building Blocks (Intel(R) TBB) lets you easily write parallel C++ programs that + take full advantage of multicore performance, that are portable, composable and have future-proof scalability.""" + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} + +source_urls = ['https://github.com/01org/tbb/archive/'] +sources = ['%(version)s.tar.gz'] + +builddependencies = [ + ('binutils', '2.27') +] + +moduleclass = 'lib' -- GitLab From e15e7694acac56eb321dabd5de7158e4eff98f9a Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Thu, 3 Aug 2017 15:20:42 -0500 Subject: [PATCH 1299/1603] adding easyconfigs: sparsehash-2.0.3-GCCcore-6.4.0.eb --- .../sparsehash-2.0.3-GCCcore-6.4.0.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/s/sparsehash/sparsehash-2.0.3-GCCcore-6.4.0.eb diff --git a/easybuild/easyconfigs/s/sparsehash/sparsehash-2.0.3-GCCcore-6.4.0.eb b/easybuild/easyconfigs/s/sparsehash/sparsehash-2.0.3-GCCcore-6.4.0.eb new file mode 100644 index 0000000000..affa39b4de --- /dev/null +++ b/easybuild/easyconfigs/s/sparsehash/sparsehash-2.0.3-GCCcore-6.4.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'sparsehash' +version = '2.0.3' + +homepage = 'https://code.google.com/p/sparsehash/' + +description = """ + An extremely memory-efficient hash_map implementation. 2 bits/entry overhead! + The SparseHash library contains several hash-map implementations, including + implementations that optimize for space or speed. +""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/sparsehash/sparsehash/archive'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['05e986a5c7327796dad742182b2d10805a8d4f511ad090da0490f146c1ff7a8c'] + +builddependencies = [ + ('binutils', '2.28'), +] + +sanity_check_paths = { + 'files': ['include/google/type_traits.h'], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From 11119dba02d9b77580f4d19a75846fd06eb8d506 Mon Sep 17 00:00:00 2001 From: Robert Qiao Date: Fri, 4 Aug 2017 06:36:40 +0000 Subject: [PATCH 1300/1603] BamM erratum and deps --- .../a/Autoconf/Autoconf-2.62-foss-2016b.eb | 37 +++++++++++++++ .../a/Autoconf/Autoconf-2.68-foss-2016b.eb | 37 +++++++++++++++ .../a/Automake/Automake-1.11.3-foss-2016b.eb | 36 +++++++++++++++ .../a/Automake/Automake-1.11.6-foss-2016b.eb | 36 +++++++++++++++ .../b/BWA/BWA-0.7.12-foss-2016b.eb | 35 +++++++++++++++ .../BamM-1.7.3-foss-2016b-Python-2.7.12.eb | 14 +++--- .../s/SAMtools/SAMtools-1.2-foss-2016b.eb | 34 ++++++++++++++ .../t/texinfo/texinfo-6.4-GCCcore-5.4.0.eb | 45 +++++++++++++++++++ 8 files changed, 268 insertions(+), 6 deletions(-) create mode 100644 easybuild/easyconfigs/a/Autoconf/Autoconf-2.62-foss-2016b.eb create mode 100644 easybuild/easyconfigs/a/Autoconf/Autoconf-2.68-foss-2016b.eb create mode 100644 easybuild/easyconfigs/a/Automake/Automake-1.11.3-foss-2016b.eb create mode 100644 easybuild/easyconfigs/a/Automake/Automake-1.11.6-foss-2016b.eb create mode 100644 easybuild/easyconfigs/b/BWA/BWA-0.7.12-foss-2016b.eb create mode 100644 easybuild/easyconfigs/s/SAMtools/SAMtools-1.2-foss-2016b.eb create mode 100644 easybuild/easyconfigs/t/texinfo/texinfo-6.4-GCCcore-5.4.0.eb diff --git a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.62-foss-2016b.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.62-foss-2016b.eb new file mode 100644 index 0000000000..e9f3329ee6 --- /dev/null +++ b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.62-foss-2016b.eb @@ -0,0 +1,37 @@ +## +# This is a contribution from Phoenix HPC Service, The University of Adelaide, Australia +# Homepage: https://www.adelaide.edu.au/phoenix/ +# +# Copyright:: adelaide.edu.au/phoenix +# Authors:: Robert Qiao , Exe Escobedo +# License:: +# +# Notes:: +## + +easyblock = 'ConfigureMake' + +name = 'Autoconf' +version = '2.62' + +homepage = 'http://www.gnu.org/software/autoconf/' +description = """Autoconf is an extensible package of M4 macros that produce shell scripts + to automatically configure software source code packages. These scripts can adapt the + packages to many kinds of UNIX-like systems without manual user intervention. Autoconf + creates a configuration script for a package from a template file that lists the + operating system features that the package can use, in the form of M4 macro calls.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('M4', '1.4.17')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["autoconf", "autoheader", "autom4te", "autoreconf", "autoscan", + "autoupdate", "ifnames"]], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.68-foss-2016b.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.68-foss-2016b.eb new file mode 100644 index 0000000000..5e317e5ad2 --- /dev/null +++ b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.68-foss-2016b.eb @@ -0,0 +1,37 @@ +## +# This is a contribution from Phoenix HPC Service, The University of Adelaide, Australia +# Homepage: https://www.adelaide.edu.au/phoenix/ +# +# Copyright:: adelaide.edu.au/phoenix +# Authors:: Robert Qiao , Exe Escobedo +# License:: +# +# Notes:: +## + +easyblock = 'ConfigureMake' + +name = 'Autoconf' +version = '2.68' + +homepage = 'http://www.gnu.org/software/autoconf/' +description = """Autoconf is an extensible package of M4 macros that produce shell scripts + to automatically configure software source code packages. These scripts can adapt the + packages to many kinds of UNIX-like systems without manual user intervention. Autoconf + creates a configuration script for a package from a template file that lists the + operating system features that the package can use, in the form of M4 macro calls.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('M4', '1.4.17')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["autoconf", "autoheader", "autom4te", "autoreconf", "autoscan", + "autoupdate", "ifnames"]], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.11.3-foss-2016b.eb b/easybuild/easyconfigs/a/Automake/Automake-1.11.3-foss-2016b.eb new file mode 100644 index 0000000000..ce98c370d2 --- /dev/null +++ b/easybuild/easyconfigs/a/Automake/Automake-1.11.3-foss-2016b.eb @@ -0,0 +1,36 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +# +# Modified:: Robert Qiao +# @ adelaide.edu.au/phoenix +## + +easyblock = 'ConfigureMake' + +name = 'Automake' +version = "1.11.3" + +homepage = 'http://www.gnu.org/software/automake/automake.html' +description = "Automake: GNU Standards-compliant Makefile generator" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('Autoconf', '2.68')] + +sanity_check_paths = { + 'files': ['bin/automake', 'bin/aclocal'], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.11.6-foss-2016b.eb b/easybuild/easyconfigs/a/Automake/Automake-1.11.6-foss-2016b.eb new file mode 100644 index 0000000000..3ea4446d37 --- /dev/null +++ b/easybuild/easyconfigs/a/Automake/Automake-1.11.6-foss-2016b.eb @@ -0,0 +1,36 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +# +# Modified:: Robert Qiao +# @ adelaide.edu.au/phoenix +## + +easyblock = 'ConfigureMake' + +name = 'Automake' +version = "1.11.6" + +homepage = 'http://www.gnu.org/software/automake/automake.html' +description = "Automake: GNU Standards-compliant Makefile generator" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('Autoconf', '2.62')] + +sanity_check_paths = { + 'files': ['bin/automake', 'bin/aclocal'], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/BWA/BWA-0.7.12-foss-2016b.eb b/easybuild/easyconfigs/b/BWA/BWA-0.7.12-foss-2016b.eb new file mode 100644 index 0000000000..e4305c6932 --- /dev/null +++ b/easybuild/easyconfigs/b/BWA/BWA-0.7.12-foss-2016b.eb @@ -0,0 +1,35 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Cyprus Institute / CaSToRC, Uni.Lu/LCSB, NTUA +# Authors:: George Tsouloupas , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +# +# Version >= 0.7.13 +# Author: Adam Huffman +# The Francis Crick Institute +# +# Note that upstream development is mainly at: https://github.com/lh3/bwa +# +# Modified by: Robert Qiao +# @ adelaide.edu.au/phoenix +## + +name = 'BWA' +version = '0.7.12' + +homepage = 'http://bio-bwa.sourceforge.net/' +description = """Burrows-Wheeler Aligner (BWA) is an efficient program that aligns + relatively short nucleotide sequences against a long reference sequence such as the human genome.""" + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['https://github.com/lh3/%(name)s/archive/'] +sources = ['%(version)s.tar.gz'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BamM/BamM-1.7.3-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/b/BamM/BamM-1.7.3-foss-2016b-Python-2.7.12.eb index 0e28fe9620..1badadd105 100644 --- a/easybuild/easyconfigs/b/BamM/BamM-1.7.3-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/b/BamM/BamM-1.7.3-foss-2016b-Python-2.7.12.eb @@ -24,17 +24,19 @@ toolchainopts = {'usempi': True} source_urls = ['https://github.com/Ecogenomics/BamM/archive'] sources = ['%(version)s.tar.gz'] -checksums = ['1a30a5014aa64aea23f12b82c8e474044af126c9e6ddb575530ab14b6ef765b8', 'sha256'] +checksums = [ + '1a30a5014aa64aea23f12b82c8e474044af126c9e6ddb575530ab14b6ef765b8', +] builddependencies = [ - ('libtool', '2.4.6'), - ('Automake', '1.15'), + ('Automake', '1.11.3'), + ('texinfo', '6.4', '', ('GCCcore','5.4.0')), ] dependencies = [ - ('Python', '2.7.13'), - ('SAMtools', '1.3.1'), - ('BWA', '0.7.15'), + ('Python', '2.7.12'), + ('SAMtools', '1.2'), + ('BWA', '0.7.12'), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.2-foss-2016b.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.2-foss-2016b.eb new file mode 100644 index 0000000000..56960c20c6 --- /dev/null +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.2-foss-2016b.eb @@ -0,0 +1,34 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Robert Schmidt , Cedric Laczny , Fotis Georgatos +# License:: MIT/GPL +# +# Modified:: Robert Qiao +# @ adelaide.edu.au/phoenix +## + +name = 'SAMtools' +version = '1.2' + +homepage = 'http://www.htslib.org/' +description = """SAM Tools provide various utilities for manipulating alignments in the SAM format, + including sorting, merging, indexing and generating alignments in a per-position format.""" + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s'] + +patches = ['SAMtools-1.1_Makefile.patch'] + +dependencies = [ + ('ncurses', '6.0'), + ('zlib', '1.2.8'), +] + +parallel = 1 + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/texinfo/texinfo-6.4-GCCcore-5.4.0.eb b/easybuild/easyconfigs/t/texinfo/texinfo-6.4-GCCcore-5.4.0.eb new file mode 100644 index 0000000000..35739f65d5 --- /dev/null +++ b/easybuild/easyconfigs/t/texinfo/texinfo-6.4-GCCcore-5.4.0.eb @@ -0,0 +1,45 @@ +## +# This is a contribution from Phoenix HPC Service, The University of Adelaide, Australia +# Homepage: https://www.adelaide.edu.au/phoenix/ +# +# Copyright:: adelaide.edu.au/phoenix +# Authors:: Robert Qiao , Exe Escobedo +# License:: +# +# Notes:: +## + +easyblock = 'ConfigureMake' + +name = 'texinfo' +version = '6.4' + +homepage = 'https://www.gnu.org/software/texinfo/' +description = """Texinfo is the official documentation format of the GNU project.""" + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_XZ] + +toolchain = {'name': 'GCCcore', 'version': '5.4.0'} + +osdependencies = ['texlive'] + +preinstallopts = "make TEXMF=%(installdir)s/texmf install-tex && " + +# This will overwrite a users $TEXMFHOME so this module is best used as a build dependency +modextravars = {'TEXMFHOME': '%(installdir)s/texmf'} +modloadmsg = "\n\nWARNING: This texinfo module has (re)defined the value for the environment variable $TEXMFHOME.\n" +modloadmsg += "If you use a custom texmf directory (such as ~/texmf) you should copy files found in the\n" +modloadmsg += "new $TEXMFHOME to your custom directory and reset the value of $TEXMFHOME to point to that space:\n" +modloadmsg += "\tcp -r $TEXMFHOME/* /path/to/your/texmf\n" +modloadmsg += "\texport TEXMFHOME=/path/to/your/texmf\n\n" + +sanity_check_paths = { + 'files': [ + 'texmf/tex/texinfo/texinfo.tex', + 'bin/install-info', 'bin/makeinfo', 'bin/pdftexi2dvi', 'bin/pod2texi', 'bin/texi2pdf' + ], + 'dirs': ['bin', 'share', 'texmf'], +} + +moduleclass = 'devel' -- GitLab From 39bfe187e40a12b1d5d2f6cb14c616c512c411ab Mon Sep 17 00:00:00 2001 From: Robert Qiao Date: Fri, 4 Aug 2017 08:16:57 +0000 Subject: [PATCH 1301/1603] libunistring-0.9.7-GCCcore-6.4.0.eb restored --- .../libunistring-0.9.7-GCCcore-6.4.0.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/l/libunistring/libunistring-0.9.7-GCCcore-6.4.0.eb diff --git a/easybuild/easyconfigs/l/libunistring/libunistring-0.9.7-GCCcore-6.4.0.eb b/easybuild/easyconfigs/l/libunistring/libunistring-0.9.7-GCCcore-6.4.0.eb new file mode 100644 index 0000000000..8d845c9877 --- /dev/null +++ b/easybuild/easyconfigs/l/libunistring/libunistring-0.9.7-GCCcore-6.4.0.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'libunistring' +version = '0.9.7' + +homepage = 'http://www.gnu.org/software/libunistring/' + +description = """ + This library provides functions for manipulating Unicode strings and for + manipulating C strings according to the Unicode standard. +""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_XZ] +source_urls = [GNU_SOURCE] +checksums = ['2e3764512aaf2ce598af5a38818c0ea23dedf1ff5460070d1b6cee5c3336e797'] + +builddependencies = [ + ('binutils', '2.28'), +] + +parallel = 1 + +sanity_check_paths = { + 'files': ['lib/libunistring.a', 'lib/libunistring.%s' % SHLIB_EXT] + + ['include/uni%s.h' % x for x in ['case', 'conv', 'ctype', 'lbrk', 'name', 'norm', + 'stdio', 'str', 'types', 'wbrk', 'width']], + 'dirs': ['include/unistring'], +} + +moduleclass = 'lib' -- GitLab From 8df4310bfe0eb6b811c0b194f31da99ff52a8252 Mon Sep 17 00:00:00 2001 From: Robert Qiao Date: Fri, 4 Aug 2017 08:19:31 +0000 Subject: [PATCH 1302/1603] util-linux-2.30-GCCcore-6.4.0.eb restored --- .../util-linux-2.30-GCCcore-6.4.0.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/u/util-linux/util-linux-2.30-GCCcore-6.4.0.eb diff --git a/easybuild/easyconfigs/u/util-linux/util-linux-2.30-GCCcore-6.4.0.eb b/easybuild/easyconfigs/u/util-linux/util-linux-2.30-GCCcore-6.4.0.eb new file mode 100644 index 0000000000..3556edda8d --- /dev/null +++ b/easybuild/easyconfigs/u/util-linux/util-linux-2.30-GCCcore-6.4.0.eb @@ -0,0 +1,42 @@ +easyblock = 'ConfigureMake' + +name = 'util-linux' +version = '2.30' + +homepage = 'http://www.kernel.org/pub/linux/utils/util-linux' + +description = "Set of Linux utilities" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} +toolchainopts = {'pic': True} + +source_urls = ['%s/v%%(version_major_minor)s' % homepage] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['e84cc32566abf28b84efb5ee326e1f3597c3d19b9916740f50c75bd57e498ce0'] + +# disable account related utilities (they need OS dependant pam-devel files) +# disable wall and friends (requires group changing permissions for install user) +# install systemd service files in install dir +# install bash completion files in install dir +configopts = "--disable-chfn-chsh --disable-login --disable-su " +configopts += "--disable-wall --disable-use-tty-group " +configopts += "--disable-makeinstall-chown --disable-makeinstall-setuid " +configopts += "--with-systemdsystemunitdir='${prefix}/systemd' " +configopts += "--with-bashcompletiondir='${prefix}/share/bash-completion/completions' " +# disable building Python bindings (since we don't include Python as a dep) +configopts += "--without-python " + +builddependencies = [ + ('binutils', '2.28'), +] + +dependencies = [ + ('ncurses', '6.0'), +] + +sanity_check_paths = { + 'files': ['lib/lib%s.a' % x for x in ['blkid', 'mount', 'uuid']], + 'dirs': ['include', 'bin', 'share', 'sbin'], +} + +moduleclass = 'tools' -- GitLab From 063c7e7cbe169a93b54864cceca377342416bca1 Mon Sep 17 00:00:00 2001 From: Robert Qiao Date: Fri, 4 Aug 2017 08:29:21 +0000 Subject: [PATCH 1303/1603] BamM style erratum --- .../easyconfigs/b/BamM/BamM-1.7.3-foss-2016b-Python-2.7.12.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/BamM/BamM-1.7.3-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/b/BamM/BamM-1.7.3-foss-2016b-Python-2.7.12.eb index 1badadd105..f16e116a9d 100644 --- a/easybuild/easyconfigs/b/BamM/BamM-1.7.3-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/b/BamM/BamM-1.7.3-foss-2016b-Python-2.7.12.eb @@ -30,7 +30,7 @@ checksums = [ builddependencies = [ ('Automake', '1.11.3'), - ('texinfo', '6.4', '', ('GCCcore','5.4.0')), + ('texinfo', '6.4', '', ('GCCcore', '5.4.0')), ] dependencies = [ -- GitLab From fd668ccbdfb333024df931f65aa141c832a501b8 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Fri, 4 Aug 2017 11:46:38 +0200 Subject: [PATCH 1304/1603] Checksums added --- .../b/Bowtie/Bowtie-1.1.2-GCCcore-6.3.0.eb | 1 + .../b/Bowtie2/Bowtie2-2.3.2-foss-2017a.eb | 1 + .../p/Perl/Perl-5.24.1-foss-2017a.eb | 223 ++++++++++++++++++ .../t/Trinity/Trinity-2.4.0-foss-2017a.eb | 1 + .../t/tbb/tbb-2017_U6-GCCcore-6.3.0.eb | 1 + 5 files changed, 227 insertions(+) diff --git a/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2-GCCcore-6.3.0.eb b/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2-GCCcore-6.3.0.eb index a46b5265d0..ffaca077d2 100644 --- a/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2-GCCcore-6.3.0.eb @@ -14,5 +14,6 @@ toolchainopts = {'pic': True} sources = ['%(namelower)s-%(version)s-src.zip'] source_urls = ['http://download.sourceforge.net/bowtie-bio/'] +checksums = ['b1e9ccc825207efd1893d9e33244c681bcb89b9b2b811eb95a9f5a92eab637ae'] moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.3.2-foss-2017a.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.3.2-foss-2017a.eb index 9d4236c5ff..0222eced42 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.3.2-foss-2017a.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.3.2-foss-2017a.eb @@ -23,6 +23,7 @@ toolchainopts = {'pic': True, 'cstd': 'gnu++98'} sources = ['%(namelower)s-%(version)s-source.zip'] source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')] +checksums = ['ef0fe6d712eb3f9fbd784a5772547a28859a71eb6c455ef670b0f11a56cc73f7'] dependencies = [('tbb', '2017_U6')] diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.24.1-foss-2017a.eb b/easybuild/easyconfigs/p/Perl/Perl-5.24.1-foss-2017a.eb index c45b3b6b14..82a8efae48 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.24.1-foss-2017a.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.24.1-foss-2017a.eb @@ -9,6 +9,7 @@ toolchainopts = {'pic': True} source_urls = ['http://www.cpan.org/src/%(version_major)s.0'] sources = [SOURCELOWER_TAR_GZ] +checksums = ['e6c185c9b09bdb3f1b13f678999050c639859a7ef39c8cad418448075f5918af'] # !! order of extensions is important !! # extensions updated on April 4th 2017 @@ -16,891 +17,1113 @@ exts_list = [ ('Config::General', '2.63', { 'source_tmpl': 'Config-General-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TL/TLINDEN'], + 'checksums': ['0a9bf977b8aabe76343e88095d2296c8a422410fd2a05a1901f2b20e2e1f6fad'], }), ('File::Listing', '6.04', { 'source_tmpl': 'File-Listing-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + 'checksums': ['1e0050fcd6789a2179ec0db282bf1e90fb92be35d1171588bd9c47d52d959cf5'], }), ('ExtUtils::InstallPaths', '0.011', { 'source_tmpl': 'ExtUtils-InstallPaths-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['7609fa048cdcf1451cad5b1d7d494f30e3d5bad0672d15404f1ea60e1df0067c'], }), ('ExtUtils::Helpers', '0.026', { 'source_tmpl': 'ExtUtils-Helpers-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['de901b6790a4557cf4ec908149e035783b125bf115eb9640feb1bc1c24c33416'], }), ('Test::Harness', '3.38', { 'source_tmpl': 'Test-Harness-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['af906dd279217a6db5064a058658f2b1d5aa1d307ed6f142d96ac4d339754c01'], }), ('ExtUtils::Config', '0.008', { 'source_tmpl': 'ExtUtils-Config-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['ae5104f634650dce8a79b7ed13fb59d67a39c213a6776cfdaa3ee749e62f1a8c'], }), ('Module::Build::Tiny', '0.039', { 'source_tmpl': 'Module-Build-Tiny-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['7d580ff6ace0cbe555bf36b86dc8ea232581530cbeaaea09bccb57b55797f11c'], }), ('aliased', '0.34', { 'source_tmpl': 'aliased-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['c350524507cd827fab864e5d4c2cc350b1babaa12fa95aec0ca00843fcc7deeb'], }), ('Text::Glob', '0.11', { 'source_tmpl': 'Text-Glob-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RC/RCLAMP'], + 'checksums': ['069ccd49d3f0a2dedb115f4bdc9fbac07a83592840953d1fcdfc39eb9d305287'], }), ('Regexp::Common', '2016060801', { 'source_tmpl': 'Regexp-Common-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AB/ABIGAIL'], + 'checksums': ['fc2fc178facf0292974d6511bad677dd038fe60d7ac118e3b83a1ca9e98a8403'], }), ('GO::Utils', '0.15', { 'source_tmpl': 'go-perl-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CM/CMUNGALL'], + 'checksums': ['423d26155ee85ca51ab2270cee59f4e85b193e57ac3a29aff827298c0a396b12'], }), ('Module::Pluggable', '5.2', { 'source_tmpl': 'Module-Pluggable-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SI/SIMONW'], + 'checksums': ['b3f2ad45e4fd10b3fb90d912d78d8b795ab295480db56dc64e86b9fa75c5a6df'], }), ('Test::Fatal', '0.014', { 'source_tmpl': 'Test-Fatal-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['bcdcef5c7b2790a187ebca810b0a08221a63256062cfab3c3b98685d91d1cbb0'], }), ('Test::Warnings', '0.026', { 'source_tmpl': 'Test-Warnings-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['ae2b68b1b5616704598ce07f5118efe42dc4605834453b7b2be14e26f9cc9a08'], }), ('File::ShareDir::Install', '0.11', { 'source_tmpl': 'File-ShareDir-Install-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['32bf8772e9fea60866074b27ff31ab5bc3f88972d61915e84cbbb98455e00cc8'], }), ('DateTime::Locale', '1.16', { 'source_tmpl': 'DateTime-Locale-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + 'checksums': ['dfaf4c42149c0622e80721773b8d7229d7785280503585895c9fe9f51e076cfe'], }), ('DateTime::TimeZone', '2.11', { 'source_tmpl': 'DateTime-TimeZone-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + 'checksums': ['a7c0b2581d2bf6d5cc535364099a67678a9f6ee608e5042dff9ef9c4c577ea6b'], }), ('Test::Requires', '0.10', { 'source_tmpl': 'Test-Requires-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TOKUHIROM'], + 'checksums': ['2768a391d50ab94b95cefe540b9232d7046c13ee86d01859e04c044903222eb5'], }), ('Module::Implementation', '0.09', { 'source_tmpl': 'Module-Implementation-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + 'checksums': ['c15f1a12f0c2130c9efff3c2e1afe5887b08ccd033bd132186d1e7d5087fd66d'], }), ('Module::Build', '0.4222', { 'source_tmpl': 'Module-Build-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['e74b45d9a74736472b74830599cec0d1123f992760f9cd97104f94bee800b160'], }), ('Module::Runtime', '0.014', { 'source_tmpl': 'Module-Runtime-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/Z/ZE/ZEFRAM'], + 'checksums': ['4c44fe0ea255a9fd00741ee545063f6692d2a28e7ef2fbaad1b24a92803362a4'], }), ('Try::Tiny', '0.28', { 'source_tmpl': 'Try-Tiny-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['f1d166be8aa19942c4504c9111dade7aacb981bc5b3a2a5c5f6019646db8c146'], }), ('Params::Validate', '1.26', { 'source_tmpl': 'Params-Validate-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + 'checksums': ['821ac3cfa9715b94f60926faf316b9ff722785594b37036202371ad2303a72ed'], }), ('List::MoreUtils', '0.418', { 'source_tmpl': 'List-MoreUtils-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + 'checksums': ['365651edea4e0c806576e4dcfc3dfb98bb4cbb343bc5c3e04cdc7b5b71ed4988'], }), ('Exporter::Tiny', '0.044', { 'source_tmpl': 'Exporter-Tiny-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TOBYINK'], + 'checksums': ['eda868cc2da094b685ceace4245b83de11f439feb98e0ec8246cfbb9109c88ab'], }), ('Class::Singleton', '1.5', { 'source_tmpl': 'Class-Singleton-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHAY'], + 'checksums': ['38220d04f02e3a803193c2575a1644cce0b95ad4b95c19eb932b94e2647ef678'], }), ('DateTime', '1.42', { 'source_tmpl': 'DateTime-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + 'checksums': ['efa4badf07365d1b03ee5527fc79baaf7d8b449bf7baad13599f04177232416e'], }), ('File::Find::Rule::Perl', '1.15', { 'source_tmpl': 'File-Find-Rule-Perl-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['9a48433f86e08ce18e03526e2982de52162eb909d19735460f07eefcaf463ea6'], }), ('Readonly', '2.05', { 'source_tmpl': 'Readonly-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SA/SANKO'], + 'checksums': ['4b23542491af010d44a5c7c861244738acc74ababae6b8838d354dfb19462b5e'], }), ('Git', '0.41', { 'source_tmpl': 'Git-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MS/MSOUTH'], + 'checksums': ['9d4de21612253a1d3252ff7657d7e832dcf3cc2a748a8c84f73de618a3a38239'], }), ('Tree::DAG_Node', '1.29', { 'source_tmpl': 'Tree-DAG_Node-%(version)s.tgz', 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + 'checksums': ['2d04eb011aa06cee633c367d1f322b8d937020fde5d5393fad6a26c93725c4a8'], }), ('Template', '2.26', { 'source_tmpl': 'Template-Toolkit-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AB/ABW'], + 'checksums': 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'source_tmpl': 'Math-VecStat-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AS/ASPINELLI'], + 'checksums': ['409a8e0e4b1025c8e80f628f65a9778aa77ab285161406ca4a6c097b13656d0d'], }), ('Pod::LaTeX', '0.61', { 'source_tmpl': 'Pod-LaTeX-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TJ/TJENNESS'], + 'checksums': ['15a840ea1c8a76cd3c865fbbf2fec33b03615c0daa50f9c800c54e0cf0659d46'], }), ('Eval::Closure', '0.14', { 'source_tmpl': 'Eval-Closure-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DO/DOY'], + 'checksums': ['ea0944f2f5ec98d895bef6d503e6e4a376fea6383a6bc64c7670d46ff2218cad'], }), ('HTTP::Request', '6.11', { 'source_tmpl': 'HTTP-Message-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['e7b368077ae6a188d99920411d8f52a8e5acfb39574d4f5c24f46fd22533d81b'], }), ('XML::Twig', '3.52', { 'source_tmpl': 'XML-Twig-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIROD'], + 'checksums': ['fef75826c24f2b877d0a0d2645212fc4fb9756ed4d2711614ac15c497e8680ad'], }), ('IO::String', '1.08', { 'source_tmpl': 'IO-String-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + 'checksums': ['2a3f4ad8442d9070780e58ef43722d19d1ee21a803bf7c8206877a10482de5a0'], }), ('XML::Simple', '2.22', { 'source_tmpl': 'XML-Simple-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GR/GRANTM'], + 'checksums': ['b9450ef22ea9644ae5d6ada086dc4300fa105be050a2030ebd4efd28c198eb49'], }), ('Sub::Install', '0.928', { 'source_tmpl': 'Sub-Install-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['61e567a7679588887b7b86d427bc476ea6d77fffe7e0d17d640f89007d98ef0f'], }), ('HTTP::Cookies', '6.03', { 'source_tmpl': 'HTTP-Cookies-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'], + 'checksums': ['05051f2761832317554b0be4b74012c35fd278f6af2c9d218f055e0de891457c'], }), ('Pod::Plainer', '1.04', { 'source_tmpl': 'Pod-Plainer-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RM/RMBARKER'], + 'checksums': ['1bbfbf7d1d4871e5a83bab2137e22d089078206815190eb1d5c1260a3499456f'], }), ('Test::Exception::LessClever', '0.009', { 'source_tmpl': 'Test-Exception-LessClever-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['3b2731a44956a11f74b46b3ecf0734fab651e1c0bcf120f8b407aa1b4d43ac34'], }), ('LWP::MediaTypes', '6.02', { 'source_tmpl': 'LWP-MediaTypes-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + 'checksums': ['18790b0cc5f0a51468495c3847b16738f785a2d460403595001e0b932e5db676'], }), ('Scalar::Util', '1.47', { 'source_tmpl': 'Scalar-List-Utils-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PEVANS'], + 'checksums': ['c483347372a96972d61fd186522a9dafc2da899ef2951964513b7e8efb37efe1'], }), ('Data::Section::Simple', '0.07', { 'source_tmpl': 'Data-Section-Simple-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA'], + 'checksums': ['0b3035ffdb909aa1f7ded6b608fa9d894421c82c097d51e7171170d67579a9cb'], }), ('Class::Trigger', '0.14', { 'source_tmpl': 'Class-Trigger-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA'], + 'checksums': ['6b1e45acc561e0708e00a2fcf16e157cad8b8963d1bf73726f77dd809b8aebc4'], }), ('HTTP::Daemon', '6.01', { 'source_tmpl': 'HTTP-Daemon-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + 'checksums': ['43fd867742701a3f9fcc7bd59838ab72c6490c0ebaf66901068ec6997514adc2'], }), ('File::HomeDir', '1.00', { 'source_tmpl': 'File-HomeDir-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + 'checksums': ['85b94f3513093ec0a25b91f9f2571918519ae6f2b7a1e8546f8f78d09a877143'], }), ('HTTP::Date', '6.02', { 'source_tmpl': 'HTTP-Date-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + 'checksums': ['e8b9941da0f9f0c9c01068401a5e81341f0e3707d1c754f8e11f42a7e629e333'], }), ('Authen::SASL', '2.16', { 'source_tmpl': 'Authen-SASL-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GB/GBARR'], + 'checksums': ['6614fa7518f094f853741b63c73f3627168c5d3aca89b1d02b1016dc32854e09'], }), ('Clone', '0.38', { 'source_tmpl': 'Clone-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GARU'], + 'checksums': ['9fb0534bb7ef6ca1f6cc1dc3f29750d6d424394d14c40efdc77832fad3cebde8'], }), ('Data::Types', '0.09', { 'source_tmpl': 'Data-Types-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DW/DWHEELER'], + 'checksums': ['b2296fdcf9addc8e8fc39e15eb2c3d81145f6355258438bc783b12b02c41cb81'], }), ('Import::Into', '1.002005', { 'source_tmpl': 'Import-Into-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + 'checksums': ['bd9e77a3fb662b40b43b18d3280cd352edf9fad8d94283e518181cc1ce9f0567'], }), ('DateTime::Tiny', '1.06', { 'source_tmpl': 'DateTime-Tiny-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + 'checksums': ['bd725df481d7223ee787e154c116098b08a129f55e0763194b07ebea3dda33ec'], }), ('DBD::AnyData', '0.110', { 'source_tmpl': 'DBD-AnyData-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + 'checksums': ['247f0d88e55076fd3f6c7bf3fd527989d62fcc1ef9bde9bf2ee11c280adcaeab'], }), ('Text::Format', '0.60', { 'source_tmpl': 'Text-Format-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'], + 'checksums': ['664f313570604624ff9e1fc9b26b6d04e06897b3e4eac83089fc0905a692a2b8'], }), ('Devel::CheckCompiler', '0.07', { 'source_tmpl': 'Devel-CheckCompiler-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SY/SYOHEX'], + 'checksums': ['768b7697b4b8d4d372c7507b65e9dd26aa4223f7100183bbb4d3af46d43869b5'], }), ('Log::Handler', '0.88', { 'source_tmpl': 'Log-Handler-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BL/BLOONIX'], + 'checksums': ['45bf540ab2138ed3ff93afc205b0516dc75755b86acdcc5e75c41347833c293d'], }), ('DBIx::ContextualFetch', '1.03', { 'source_tmpl': 'DBIx-ContextualFetch-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TM/TMTM'], + 'checksums': ['85e2f805bfc81cd738c294316b27a515397036f397a0ff1c6c8d754c38530306'], }), ('Devel::StackTrace', '2.02', { 'source_tmpl': 'Devel-StackTrace-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + 'checksums': ['cbbd96db0ecf194ed140198090eaea0e327d9a378a4aa15f9a34b3138a91931f'], }), ('Term::ReadKey', '2.14', { 'source_tmpl': 'TermReadKey-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KJ/KJALB'], + 'checksums': ['6009158cd9889f8c00da78af99847ace5052f1ca04fa30eb3411fdc26d54c9a8'], }), ('Set::IntSpan', '1.19', { 'source_tmpl': 'Set-IntSpan-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SW/SWMCD'], + 'checksums': ['11b7549b13ec5d87cc695dd4c777cd02983dd5fe9866012877fb530f48b3dfd0'], }), ('Moose', '2.2004', { 'source_tmpl': 'Moose-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['e4c881bf8d8fd5821aea8a8c7c57ed850c2373d4800949798a55c06ca9e8d2b0'], }), ('Algorithm::Dependency', '1.110', { 'source_tmpl': 'Algorithm-Dependency-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + 'checksums': ['f27733e8d89cf2ab621284c2584da90ab0cb743ba2295ee739fe51bf92561e37'], }), ('Font::TTF', '1.06', { 'source_tmpl': 'Font-TTF-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BH/BHALLISSY'], + 'checksums': ['4b697d444259759ea02d2c442c9bffe5ffe14c9214084a01f743693a944cc293'], }), ('IPC::Run3', '0.048', { 'source_tmpl': 'IPC-Run3-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['3d81c3cc1b5cff69cca9361e2c6e38df0352251ae7b41e2ff3febc850e463565'], }), ('File::Find::Rule', '0.34', { 'source_tmpl': 'File-Find-Rule-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RC/RCLAMP'], + 'checksums': ['7e6f16cc33eb1f29ff25bee51d513f4b8a84947bbfa18edb2d3cc40a2d64cafe'], }), ('SQL::Statement', '1.410', { 'source_tmpl': 'SQL-Statement-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + 'checksums': ['7367fcda896367c96d98416cad423c9f98adb7e04b793c5c7deb3052a1213182'], }), ('File::Slurp', '9999.19', { 'source_tmpl': 'File-Slurp-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/U/UR/URI'], + 'checksums': ['ce29ebe995097ebd6e9bc03284714cdfa0c46dc94f6b14a56980747ea3253643'], }), ('Package::Stash', '0.37', { 'source_tmpl': 'Package-Stash-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DO/DOY'], + 'checksums': ['06ab05388f9130cd377c0e1d3e3bafeed6ef6a1e22104571a9e1d7bfac787b2c'], }), ('Data::OptList', '0.110', { 'source_tmpl': 'Data-OptList-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['366117cb2966473f2559f2f4575ff6ae69e84c69a0f30a0773e1b51a457ef5c3'], }), ('CPANPLUS', '0.9164', { 'source_tmpl': 'CPANPLUS-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + 'checksums': ['3fcd8c7bb1973df484236fc3d59ed17c8a35057f56546ba44bfc780b97fec0a8'], }), ('IO::Tty', '1.12', { 'source_tmpl': 'IO-Tty-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR'], + 'checksums': ['a2ef8770d3309178203f8c8ac25e623e63cf76e97830fd3be280ade1a555290d'], }), ('Text::Soundex', '3.05', { 'source_tmpl': 'Text-Soundex-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['f6dd55b4280b25dea978221839864382560074e1d6933395faee2510c2db60ed'], }), ('Lingua::EN::PluralToSingular', '0.19', { 'source_tmpl': 'Lingua-EN-PluralToSingular-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BK/BKB'], + 'checksums': ['c71b6c1aec01aae9c42aef0d9f147a437e91a7cc5cea6e4abbc35440638f299e'], }), ('Want', '0.29', { 'source_tmpl': 'Want-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RO/ROBIN'], + 'checksums': ['b4e4740b8d4cb783591273c636bd68304892e28d89e88abf9273b1de17f552f7'], }), ('Cwd::Guard', '0.05', { 'source_tmpl': 'Cwd-Guard-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KA/KAZEBURO'], + 'checksums': ['7afc7ca2b9502e440241938ad97a3e7ebd550180ebd6142e1db394186b268e77'], }), ('Bundle::BioPerl', '2.1.9', { 'source_tmpl': 'Bundle-BioPerl-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS'], + 'checksums': ['c343ba97f49d86e7fb14aef4cfe3124992e2a5c3168e53a54606dd611d73e5c7'], }), ('Mail::Util', '2.18', { 'source_tmpl': 'MailTools-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARKOV'], + 'checksums': ['dfee9e770257371112f20d978e637759e81bc4f19e97b083585c71ecab37b527'], }), ('Text::Template', '1.47', { 'source_tmpl': 'Text-Template-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MS/MSCHOUT'], + 'checksums': ['50d742c74482478aa01008d468290fcfbc0b9a1219cfe1284076f1f31f0be8fc'], }), ('PDF::API2', '2.031', { 'source_tmpl': 'PDF-API2-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SS/SSIMMS'], + 'checksums': ['6ea5d38f99dfb1e8acf57c9c7579659b3eee84944295a135f90e607e0a3f43e9'], }), ('Devel::CheckLib', '1.11', { 'source_tmpl': 'Devel-CheckLib-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MATTN'], + 'checksums': ['bd6d1c187e80be6de1f0d37add441ba8f14950c7bc1f54e764770ed484b232c1'], }), ('SVG', '2.77', { 'source_tmpl': 'SVG-2.77.tar.gz', 'source_urls': ['http://search.cpan.org/CPAN/authors/id/M/MA/MANWAR/'], + 'checksums': ['1f01cf2dc666a2ba3bf5219ec9e2290143e5e569747431412c8423916a9846c5'], }), ('Statistics::Basic', '1.6611', { 'source_tmpl': 'Statistics-Basic-1.6611.tar.gz', 'source_urls': ['http://search.cpan.org/CPAN/authors/id/J/JE/JETTERO/'], + 'checksums': ['6855ce5615fd3e1af4cfc451a9bf44ff29a3140b4e7130034f1f0af2511a94fb'], }), ] diff --git a/easybuild/easyconfigs/t/Trinity/Trinity-2.4.0-foss-2017a.eb b/easybuild/easyconfigs/t/Trinity/Trinity-2.4.0-foss-2017a.eb index 90175fa060..167f098cd2 100644 --- a/easybuild/easyconfigs/t/Trinity/Trinity-2.4.0-foss-2017a.eb +++ b/easybuild/easyconfigs/t/Trinity/Trinity-2.4.0-foss-2017a.eb @@ -12,6 +12,7 @@ toolchainopts = {'optarch': True} source_urls = ['https://github.com/trinityrnaseq/trinityrnaseq/archive/'] sources = ['%(name)s-v%(version)s.tar.gz'] +checksums = ['2e91ed242923205b060164398aa325e5fe824040732d86c74ece4f98d7a6f220'] patches = [ 'chrysalis_commandline_noconsts_2012-10-05.patch', diff --git a/easybuild/easyconfigs/t/tbb/tbb-2017_U6-GCCcore-6.3.0.eb b/easybuild/easyconfigs/t/tbb/tbb-2017_U6-GCCcore-6.3.0.eb index 34c5460e40..1b8ceddb15 100644 --- a/easybuild/easyconfigs/t/tbb/tbb-2017_U6-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/t/tbb/tbb-2017_U6-GCCcore-6.3.0.eb @@ -9,6 +9,7 @@ toolchain = {'name': 'GCCcore', 'version': '6.3.0'} source_urls = ['https://github.com/01org/tbb/archive/'] sources = ['%(version)s.tar.gz'] +checksums = ['1f7df7af6045179a45eba9b5dfde74d185ee7f573328f103c137696f81e4ae5a'] builddependencies = [ ('binutils', '2.27') -- GitLab From 22350337eb4eb73d2bafce5d2abd9108507f8305 Mon Sep 17 00:00:00 2001 From: frenchwr Date: Fri, 4 Aug 2017 09:19:44 -0500 Subject: [PATCH 1305/1603] fix additional typos in comments --- .../Singularity/Singularity-2.3.1-GCC-5.4.0-2.26.eb | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/s/Singularity/Singularity-2.3.1-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/s/Singularity/Singularity-2.3.1-GCC-5.4.0-2.26.eb index 7e7221e7b3..b3cde73978 100644 --- a/easybuild/easyconfigs/s/Singularity/Singularity-2.3.1-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/s/Singularity/Singularity-2.3.1-GCC-5.4.0-2.26.eb @@ -23,11 +23,11 @@ sanity_check_paths = { } # next steps after installation -# INSTALATION_PATH=your_instalation_path -# chown root:root $INSTALATION_PATH/Singularity/*/etc/singularity/singularity.conf -# chown root:root $INSTALATION_PATH/Singularity/*/libexec/singularity/bin/*-suid -# chown root:root $INSTALATION_PATH/Singularity/*/var/singularity/mnt/container -# chmod 4755 $INSTALATION_PATH/Singularity/*/libexec/singularity/bin/*-suid -# chmod +s $INSTALATION_PATH/Singularity/*/libexec/singularity/bin/*-suid +# INSTALLATION_PATH=your_installation_path +# chown root:root $INSTALLATION_PATH/Singularity/*/etc/singularity/singularity.conf +# chown root:root $INSTALLATION_PATH/Singularity/*/libexec/singularity/bin/*-suid +# chown root:root $INSTALLATION_PATH/Singularity/*/var/singularity/mnt/container +# chmod 4755 $INSTALLATION_PATH/Singularity/*/libexec/singularity/bin/*-suid +# chmod +s $INSTALLATION_PATH/Singularity/*/libexec/singularity/bin/*-suid moduleclass = 'tools' -- GitLab From 90b9071e2d237db34221573e104e8847b8029bac Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Sat, 5 Aug 2017 06:24:11 -0500 Subject: [PATCH 1306/1603] adding easyconfigs: htop-2.0.1.eb --- easybuild/easyconfigs/h/htop/htop-2.0.1.eb | 29 ++++++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/h/htop/htop-2.0.1.eb diff --git a/easybuild/easyconfigs/h/htop/htop-2.0.1.eb b/easybuild/easyconfigs/h/htop/htop-2.0.1.eb new file mode 100644 index 0000000000..c7e830f3a7 --- /dev/null +++ b/easybuild/easyconfigs/h/htop/htop-2.0.1.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'htop' +version = "2.0.1" + +homepage = 'http://hisham.hm/htop/' + +description = """An interactive process viewer for Unix""" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = ['http://hisham.hm/htop/releases/%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['f410626dfaf6b70fdf73cd7bb33cae768869707028d847fed94a978e974f5666'] + +dependencies = [ + ('ncurses', '6.0'), +] + +prebuildopts = """ + sed -e 's/^LIBS = -lncursesw -lm/LIBS = -lncursesw -lm -ltinfo/' -i.eb Makefile +""" + +sanity_check_paths = { + 'files': ['bin/htop'], + 'dirs': ['share'], +} + +moduleclass = 'tools' -- GitLab From 1c5255de37fc32764fdc3747f3fefcaf52d6692f Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Sun, 6 Aug 2017 08:07:00 +0100 Subject: [PATCH 1307/1603] Fix inline functions --- .../b/BFAST/BFAST-0.7.0a-foss-2016b.eb | 42 +++++++++++++++++++ .../b/BFAST/BFAST-0.7.0a-inline.patch | 28 +++++++++++++ 2 files changed, 70 insertions(+) create mode 100755 easybuild/easyconfigs/b/BFAST/BFAST-0.7.0a-foss-2016b.eb create mode 100755 easybuild/easyconfigs/b/BFAST/BFAST-0.7.0a-inline.patch diff --git a/easybuild/easyconfigs/b/BFAST/BFAST-0.7.0a-foss-2016b.eb b/easybuild/easyconfigs/b/BFAST/BFAST-0.7.0a-foss-2016b.eb new file mode 100755 index 0000000000..2126725d43 --- /dev/null +++ b/easybuild/easyconfigs/b/BFAST/BFAST-0.7.0a-foss-2016b.eb @@ -0,0 +1,42 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## +# Modified for foss/2016b by Adam Huffman, Francis Crick Institute + +easyblock = 'ConfigureMake' + +name = 'BFAST' +version = '0.7.0a' + +homepage = 'http://bfast.sourceforge.net/' +description = """BFAST facilitates the fast and accurate mapping of short reads to reference sequences. + Some advantages of BFAST include: + 1) Speed: enables billions of short reads to be mapped quickly. + 2) Accuracy: A priori probabilities for mapping reads with defined set of variants. + 3) An easy way to measurably tune accuracy at the expense of speed.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +verdir = ''.join(char for char in version if not char.isalpha()) +source_urls = ['http://sourceforge.net/projects/bfast/files/bfast/%s/' % verdir, 'download'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['ed8de49693165a87d5dbef352207c424b1bf6f670a83acf49a4f4f188444995e'] + +dependencies = [('bzip2', '1.0.6')] + +patches = ['BFAST-0.7.0a-inline.patch'] + +sanity_check_paths = { + 'files': ["bin/bfast"], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BFAST/BFAST-0.7.0a-inline.patch b/easybuild/easyconfigs/b/BFAST/BFAST-0.7.0a-inline.patch new file mode 100755 index 0000000000..c936129c8c --- /dev/null +++ b/easybuild/easyconfigs/b/BFAST/BFAST-0.7.0a-inline.patch @@ -0,0 +1,28 @@ +# mismatch in function declaration, taken from +# http://www.vcru.wisc.edu/simonlab/bioinformatics/programs/install/bfast.htm +diff -ur bfast-0.7.0a/bfast/BLib.h bfast-0.7.0a.new/bfast/BLib.h +--- bfast-0.7.0a/bfast/BLib.h 2011-09-03 19:44:58.000000000 +0100 ++++ bfast-0.7.0a.new/bfast/BLib.h 2017-08-06 07:56:35.943546000 +0100 +@@ -16,7 +16,7 @@ + int ParseFastaHeaderLine(char*); + char ToLower(char); + void ToLowerRead(char*, int); +-inline char ToUpper(char); ++char ToUpper(char); + void ToUpperRead(char*, int); + void ReverseRead(char*, char*, int); + void ReverseReadFourBit(int8_t*, int8_t*, int); +diff -ur bfast-0.7.0a/bfast/ScoringMatrix.h bfast-0.7.0a.new/bfast/ScoringMatrix.h +--- bfast-0.7.0a/bfast/ScoringMatrix.h 2011-09-03 19:44:59.000000000 +0100 ++++ bfast-0.7.0a.new/bfast/ScoringMatrix.h 2017-08-06 07:56:49.351357000 +0100 +@@ -3,8 +3,8 @@ + + #include "BLibDefinitions.h" + +-inline int32_t ScoringMatrixGetNTScore(char, char, ScoringMatrix*); +-inline int32_t ScoringMatrixGetColorScore(char, char, ScoringMatrix*); ++int32_t ScoringMatrixGetNTScore(char, char, ScoringMatrix*); ++int32_t ScoringMatrixGetColorScore(char, char, ScoringMatrix*); + + int ScoringMatrixRead(char*, ScoringMatrix*, int); + void ScoringMatrixInitialize(ScoringMatrix*); -- GitLab From de2861a5f8a80113e9d6156936b200178d347c72 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 6 Aug 2017 15:09:55 +0200 Subject: [PATCH 1308/1603] add checksum for Seurat sources --- .../easyconfigs/s/Seurat/Seurat-1.4.0.16-intel-2017a-R-3.4.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/s/Seurat/Seurat-1.4.0.16-intel-2017a-R-3.4.0.eb b/easybuild/easyconfigs/s/Seurat/Seurat-1.4.0.16-intel-2017a-R-3.4.0.eb index 47751ee440..60c2927733 100644 --- a/easybuild/easyconfigs/s/Seurat/Seurat-1.4.0.16-intel-2017a-R-3.4.0.eb +++ b/easybuild/easyconfigs/s/Seurat/Seurat-1.4.0.16-intel-2017a-R-3.4.0.eb @@ -14,6 +14,7 @@ sources = [{ 'filename': SOURCE_TAR_GZ, 'download_filename': '3bd092a.tar.gz', }] +checksums = ['2079b09698aadc1f3fdd3de5ac708add7196f4713d9f6a01b85d05b3a6ba2ec5'] dependencies = [('R', '3.4.0', '-X11-20170314')] -- GitLab From f8a8ee43919df30083788376ccebbd1a2c1ebd77 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 7 Aug 2017 10:44:20 +0200 Subject: [PATCH 1309/1603] adding easyconfigs: XGBoost-0.6a2-intel-2017a-Python-3.6.1.eb --- .../XGBoost-0.6a2-intel-2017a-Python-3.6.1.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/x/XGBoost/XGBoost-0.6a2-intel-2017a-Python-3.6.1.eb diff --git a/easybuild/easyconfigs/x/XGBoost/XGBoost-0.6a2-intel-2017a-Python-3.6.1.eb b/easybuild/easyconfigs/x/XGBoost/XGBoost-0.6a2-intel-2017a-Python-3.6.1.eb new file mode 100644 index 0000000000..c34999e2b6 --- /dev/null +++ b/easybuild/easyconfigs/x/XGBoost/XGBoost-0.6a2-intel-2017a-Python-3.6.1.eb @@ -0,0 +1,23 @@ +easyblock = 'PythonPackage' + +name = 'XGBoost' +version = '0.6a2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/dmlc/xgboost' +description = """XGBoost is an optimized distributed gradient boosting library designed to be highly efficient, + flexible and portable.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('Python', '3.6.1')] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'lib' -- GitLab From 78a47cf1ddc2c495c683f1121785f0b316feb269 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 7 Aug 2017 11:02:03 +0200 Subject: [PATCH 1310/1603] add SHA256 checksum in XGBoost easyconfigs --- .../x/XGBoost/XGBoost-0.6a2-intel-2016b-Python-2.7.12.eb | 1 + .../x/XGBoost/XGBoost-0.6a2-intel-2016b-Python-3.5.2.eb | 1 + .../x/XGBoost/XGBoost-0.6a2-intel-2017a-Python-3.6.1.eb | 1 + 3 files changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/x/XGBoost/XGBoost-0.6a2-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/x/XGBoost/XGBoost-0.6a2-intel-2016b-Python-2.7.12.eb index 4359ea417d..da4a0e2bda 100644 --- a/easybuild/easyconfigs/x/XGBoost/XGBoost-0.6a2-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/x/XGBoost/XGBoost-0.6a2-intel-2016b-Python-2.7.12.eb @@ -12,6 +12,7 @@ toolchain = {'name': 'intel', 'version': '2016b'} source_urls = [PYPI_SOURCE] sources = [SOURCELOWER_TAR_GZ] +checksums = ['ebc4e2bf8c8266212e342ff8ec4f6ae469e8c41a05d099b6778de8424ce32563'] dependencies = [('Python', '2.7.12')] diff --git a/easybuild/easyconfigs/x/XGBoost/XGBoost-0.6a2-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/x/XGBoost/XGBoost-0.6a2-intel-2016b-Python-3.5.2.eb index f4be4224b1..a979a43a6f 100644 --- a/easybuild/easyconfigs/x/XGBoost/XGBoost-0.6a2-intel-2016b-Python-3.5.2.eb +++ b/easybuild/easyconfigs/x/XGBoost/XGBoost-0.6a2-intel-2016b-Python-3.5.2.eb @@ -12,6 +12,7 @@ toolchain = {'name': 'intel', 'version': '2016b'} source_urls = [PYPI_SOURCE] sources = [SOURCELOWER_TAR_GZ] +checksums = ['ebc4e2bf8c8266212e342ff8ec4f6ae469e8c41a05d099b6778de8424ce32563'] dependencies = [('Python', '3.5.2')] diff --git a/easybuild/easyconfigs/x/XGBoost/XGBoost-0.6a2-intel-2017a-Python-3.6.1.eb b/easybuild/easyconfigs/x/XGBoost/XGBoost-0.6a2-intel-2017a-Python-3.6.1.eb index c34999e2b6..6269db2cd4 100644 --- a/easybuild/easyconfigs/x/XGBoost/XGBoost-0.6a2-intel-2017a-Python-3.6.1.eb +++ b/easybuild/easyconfigs/x/XGBoost/XGBoost-0.6a2-intel-2017a-Python-3.6.1.eb @@ -12,6 +12,7 @@ toolchain = {'name': 'intel', 'version': '2017a'} source_urls = [PYPI_SOURCE] sources = [SOURCELOWER_TAR_GZ] +checksums = ['ebc4e2bf8c8266212e342ff8ec4f6ae469e8c41a05d099b6778de8424ce32563'] dependencies = [('Python', '3.6.1')] -- GitLab From 2f5e440be70dcbe0a3b3e075ef349e36a0da7397 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 7 Aug 2017 11:39:44 +0200 Subject: [PATCH 1311/1603] adding easyconfigs: I-TASSER-5.1.eb --- .../easyconfigs/i/I-TASSER/I-TASSER-5.1.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/i/I-TASSER/I-TASSER-5.1.eb diff --git a/easybuild/easyconfigs/i/I-TASSER/I-TASSER-5.1.eb b/easybuild/easyconfigs/i/I-TASSER/I-TASSER-5.1.eb new file mode 100644 index 0000000000..f505003e03 --- /dev/null +++ b/easybuild/easyconfigs/i/I-TASSER/I-TASSER-5.1.eb @@ -0,0 +1,31 @@ +easyblock = 'PackedBinary' + +name = 'I-TASSER' +version = '5.1' + +homepage = 'http://zhanglab.ccmb.med.umich.edu/I-TASSER/' +description = """I-TASSER is a set of pre-compiled binaries and scripts for protein structure and function +modelling and comparison.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +# Can't download from the web site automatically as registration is required. +# The source code may be downloaded manually from http://zhanglab.ccmb.med.umich.edu. +sources = ['%(name)s%(version)s.tar.bz2'] +checksums = ['c127f4932c11bb3f8940ad8510a3429b8e7dc14595cfee230af7cc52196a5396'] + +dependencies = [ + ('BLAST', '2.2.26', '-Linux_x86_64'), + ('Java', '1.7.0_80'), +] + +sanity_check_paths = { + 'files': ['I-TASSERmod/runI-TASSER.pl'], + 'dirs': ['bin', 'blast', 'COACH', 'COFACTOR', 'I-TASSERmod', 'PSSpred'], +} + +# You may find it desirable to put this variable in the module file. +# The command to do so has been put here (commented out) as a convenience. +# modextravars = {'IMINTASSERDB': '/path/to/databases/I-TASSER/%(version)s'} + +moduleclass = 'bio' -- GitLab From 46a05e3b80361c673890e5162088885e514c2223 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 7 Aug 2017 12:08:55 +0200 Subject: [PATCH 1312/1603] adding easyconfigs: rjags-4-6-intel-2017a-R-3.4.0.eb, JAGS-4.2.0-intel-2017a.eb --- .../j/JAGS/JAGS-4.2.0-intel-2017a.eb | 32 +++++++++++++++++++ .../r/rjags/rjags-4-6-intel-2017a-R-3.4.0.eb | 28 ++++++++++++++++ 2 files changed, 60 insertions(+) create mode 100644 easybuild/easyconfigs/j/JAGS/JAGS-4.2.0-intel-2017a.eb create mode 100644 easybuild/easyconfigs/r/rjags/rjags-4-6-intel-2017a-R-3.4.0.eb diff --git a/easybuild/easyconfigs/j/JAGS/JAGS-4.2.0-intel-2017a.eb b/easybuild/easyconfigs/j/JAGS/JAGS-4.2.0-intel-2017a.eb new file mode 100644 index 0000000000..6b1311fff0 --- /dev/null +++ b/easybuild/easyconfigs/j/JAGS/JAGS-4.2.0-intel-2017a.eb @@ -0,0 +1,32 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = 'ConfigureMake' + +name = 'JAGS' +version = '4.2.0' + +homepage = 'http://mcmc-jags.sourceforge.net/' +description = """JAGS is Just Another Gibbs Sampler. It is a program for analysis + of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation """ + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [('http://sourceforge.net/projects/mcmc-jags/files/JAGS/%(version_major)s.x/Source/', 'download')] +sources = [SOURCE_TAR_GZ] + +configopts = ' --with-blas="-lmkl" --with-lapack="-lmkl" ' + +sanity_check_paths = { + 'files': ["bin/jags", "libexec/jags-terminal", "lib/libjags.%s" % SHLIB_EXT], + 'dirs': [] +} + +modextrapaths = { + 'JAGS_INCLUDE': 'include/JAGS', + 'JAGS_LIB': 'lib', +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/r/rjags/rjags-4-6-intel-2017a-R-3.4.0.eb b/easybuild/easyconfigs/r/rjags/rjags-4-6-intel-2017a-R-3.4.0.eb new file mode 100644 index 0000000000..7a91a922a5 --- /dev/null +++ b/easybuild/easyconfigs/r/rjags/rjags-4-6-intel-2017a-R-3.4.0.eb @@ -0,0 +1,28 @@ +easyblock = 'RPackage' + +name = 'rjags' +version = '4-6' +versionsuffix = '-R-%(rver)s' + +homepage = 'http://cran.r-project.org/web/packages/rjags' +description = """The rjags package is an interface to the JAGS library.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [ + 'http://cran.r-project.org/src/contrib/', + 'http://cran.r-project.org/src/contrib/Archive/rjags/', +] +sources = ['%(name)s_%(version)s.tar.gz'] + +dependencies = [ + ('R', '3.4.0', '-X11-20170314'), + ('JAGS', '4.2.0'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['rjags'], +} + +moduleclass = 'math' -- GitLab From 725d2ded96d5dbd5e3314c2b0f4d897691c16b89 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 7 Aug 2017 13:19:48 +0200 Subject: [PATCH 1313/1603] adding easyconfigs: Biopython-1.70-intel-2017a-Python-3.6.1.eb --- ...Biopython-1.70-intel-2017a-Python-3.6.1.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/b/Biopython/Biopython-1.70-intel-2017a-Python-3.6.1.eb diff --git a/easybuild/easyconfigs/b/Biopython/Biopython-1.70-intel-2017a-Python-3.6.1.eb b/easybuild/easyconfigs/b/Biopython/Biopython-1.70-intel-2017a-Python-3.6.1.eb new file mode 100644 index 0000000000..a9ed1da426 --- /dev/null +++ b/easybuild/easyconfigs/b/Biopython/Biopython-1.70-intel-2017a-Python-3.6.1.eb @@ -0,0 +1,38 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2013 The Cyprus Institute +# Authors:: Andreas Panteli , Thekla Loizou , +# George Tsouloupas +# License:: MIT/GPL +# +## +easyblock = 'PythonPackage' + +name = 'Biopython' +version = '1.70' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.biopython.org' +description = """Biopython is a set of freely available tools for biological computation written +in Python by an international team of developers. It is a distributed collaborative effort to +develop Python libraries and applications which address the needs of current and future work in +bioinformatics. """ + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['http://biopython.org/DIST'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('Python', '3.6.1') +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/Bio', 'lib/python%(pyshortver)s/site-packages/BioSQL'] +} + +options = {'modulename': 'Bio'} + +moduleclass = 'bio' -- GitLab From 0adb0dc158fc71ae4a5be0f8c95b8be8751ef494 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 7 Aug 2017 15:18:40 +0200 Subject: [PATCH 1314/1603] rename CLISP patch + add upstream ref + minor style cleanups in easyconfig --- .../c/CLISP/CLISP-2.49-GCCcore-6.4.0.eb | 14 ++++---------- ...readline.lisp => CLISP-2.49_fix-readline.patch} | 2 ++ 2 files changed, 6 insertions(+), 10 deletions(-) rename easybuild/easyconfigs/c/CLISP/{patch-modules_readline_readline.lisp => CLISP-2.49_fix-readline.patch} (93%) diff --git a/easybuild/easyconfigs/c/CLISP/CLISP-2.49-GCCcore-6.4.0.eb b/easybuild/easyconfigs/c/CLISP/CLISP-2.49-GCCcore-6.4.0.eb index 1f086b8886..b37bd540bf 100644 --- a/easybuild/easyconfigs/c/CLISP/CLISP-2.49-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/c/CLISP/CLISP-2.49-GCCcore-6.4.0.eb @@ -14,12 +14,11 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '6.4.0'} -source_urls = ['ftp://ftp.gnu.org/pub/gnu/%(namelower)s/release/%(version)s'] +source_urls = [GNU_SOURCE + '/release/%(version)s'] sources = [SOURCELOWER_TAR_BZ2] checksums = ['8132ff353afaa70e6b19367a25ae3d5a43627279c25647c220641fed00f8e890'] -# from: https://sourceforge.net/p/clisp/bugs/688/ -patches = ['patch-modules_readline_readline.lisp'] +patches = ['CLISP-%(version)s_fix-readline.patch'] builddependencies = [ ('binutils', '2.28'), @@ -34,13 +33,8 @@ dependencies = [ ('zlib', '1.2.11'), ] -prebuildopts = """ - cd src -""" - -preinstallopts = """ - cd src -""" +prebuildopts = "cd src && " +preinstallopts = prebuildopts parallel = 1 diff --git a/easybuild/easyconfigs/c/CLISP/patch-modules_readline_readline.lisp b/easybuild/easyconfigs/c/CLISP/CLISP-2.49_fix-readline.patch similarity index 93% rename from easybuild/easyconfigs/c/CLISP/patch-modules_readline_readline.lisp rename to easybuild/easyconfigs/c/CLISP/CLISP-2.49_fix-readline.patch index 19c54f96d6..44e4e73952 100644 --- a/easybuild/easyconfigs/c/CLISP/patch-modules_readline_readline.lisp +++ b/easybuild/easyconfigs/c/CLISP/CLISP-2.49_fix-readline.patch @@ -1,3 +1,5 @@ +obtained from https://sourceforge.net/p/clisp/bugs/688/ + $NetBSD: patch-modules_readline_readline.lisp,v 1.1 2016/09/20 14:10:25 wiz Exp $ rl_readline_state changed from int to unsigned long in readline-7.0. -- GitLab From a3450c32904c16b0483628fdb0b531bb8ab8b638 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 7 Aug 2017 15:57:22 +0200 Subject: [PATCH 1315/1603] adding easyconfigs: FDS-6.5.3-intel-2017a.eb --- .../f/FDS/FDS-6.5.3-intel-2017a.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/f/FDS/FDS-6.5.3-intel-2017a.eb diff --git a/easybuild/easyconfigs/f/FDS/FDS-6.5.3-intel-2017a.eb b/easybuild/easyconfigs/f/FDS/FDS-6.5.3-intel-2017a.eb new file mode 100644 index 0000000000..00c8e74036 --- /dev/null +++ b/easybuild/easyconfigs/f/FDS/FDS-6.5.3-intel-2017a.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'FDS' +version = '6.5.3' + +homepage = 'https://pages.nist.gov/fds-smv/' +description = """Fire Dynamics Simulator (FDS) is a large-eddy simulation (LES) code for low-speed flows, + with an emphasis on smoke and heat transport from fires.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://github.com/firemodels/fds/archive/'] +sources = ['FDS%(version)s.tar.gz'] +checksums = ['e15173651512575967e3769f6730425e616a3deb0291475564db729cf526be13'] + +unpack_options = '--strip-components=1' + +start_dir = 'Build' + +# just run make in the install dir +skipsteps = ['configure', 'install'] +buildininstalldir = True + +target = 'impi_intel_linux_64' +buildopts = '%s FFLAGS="$FFLAGS -fpp" FCOMPL="$FC" obj=fds' % target + +modextrapaths = {'PATH': 'Build'} + +sanity_check_paths = { + 'files': ['Build/fds'], + 'dirs': [], +} + +sanity_check_commands = [("fds 2>&1 | grep 'MPI Enabled;'", '')] + +moduleclass = 'phys' -- GitLab From da954e9fe1afedcf9ed07401e7dae80de69d9bf8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 7 Aug 2017 16:24:39 +0200 Subject: [PATCH 1316/1603] adding easyconfigs: Mathematica-11.1.1.eb --- .../m/Mathematica/Mathematica-11.1.1.eb | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) create mode 100644 easybuild/easyconfigs/m/Mathematica/Mathematica-11.1.1.eb diff --git a/easybuild/easyconfigs/m/Mathematica/Mathematica-11.1.1.eb b/easybuild/easyconfigs/m/Mathematica/Mathematica-11.1.1.eb new file mode 100644 index 0000000000..6bf4ec7171 --- /dev/null +++ b/easybuild/easyconfigs/m/Mathematica/Mathematica-11.1.1.eb @@ -0,0 +1,17 @@ +name = 'Mathematica' +version = '11.1.1' + +homepage = 'http://www.wolfram.com/mathematica' +description = """Mathematica is a computational software program used in many scientific, engineering, mathematical +and computing fields.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['Mathematica_%(version)s_LINUX.sh'] +checksums = ['80cb3a25337d809bf865e5405cf5975dccf1dcaa20874ee301c98d41011281ce'] + +license_server = 'license.example.com' + +sanity_check_commands = [('mathematica', '--version')] + +moduleclass = 'math' -- GitLab From 6de68f8401aca249aecb08b9676746e5a5bdca70 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 7 Aug 2017 17:13:48 +0200 Subject: [PATCH 1317/1603] add checksum for Biopython 1.70 --- .../b/Biopython/Biopython-1.70-intel-2017a-Python-3.6.1.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/b/Biopython/Biopython-1.70-intel-2017a-Python-3.6.1.eb b/easybuild/easyconfigs/b/Biopython/Biopython-1.70-intel-2017a-Python-3.6.1.eb index a9ed1da426..e9f9d1c3f3 100644 --- a/easybuild/easyconfigs/b/Biopython/Biopython-1.70-intel-2017a-Python-3.6.1.eb +++ b/easybuild/easyconfigs/b/Biopython/Biopython-1.70-intel-2017a-Python-3.6.1.eb @@ -23,6 +23,7 @@ toolchain = {'name': 'intel', 'version': '2017a'} source_urls = ['http://biopython.org/DIST'] sources = [SOURCELOWER_TAR_GZ] +checksums = ['4a7c5298f03d1a45523f32bae1fffcff323ea9dce007fb1241af092f5ab2e45b'] dependencies = [ ('Python', '3.6.1') -- GitLab From c82c602516a11e9bd356b4f2e7b05ac36352961d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 7 Aug 2017 17:38:00 +0200 Subject: [PATCH 1318/1603] add checksum for CLISP patch --- easybuild/easyconfigs/c/CLISP/CLISP-2.49-GCCcore-6.4.0.eb | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CLISP/CLISP-2.49-GCCcore-6.4.0.eb b/easybuild/easyconfigs/c/CLISP/CLISP-2.49-GCCcore-6.4.0.eb index b37bd540bf..e8a86bb97c 100644 --- a/easybuild/easyconfigs/c/CLISP/CLISP-2.49-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/c/CLISP/CLISP-2.49-GCCcore-6.4.0.eb @@ -16,10 +16,15 @@ toolchain = {'name': 'GCCcore', 'version': '6.4.0'} source_urls = [GNU_SOURCE + '/release/%(version)s'] sources = [SOURCELOWER_TAR_BZ2] -checksums = ['8132ff353afaa70e6b19367a25ae3d5a43627279c25647c220641fed00f8e890'] patches = ['CLISP-%(version)s_fix-readline.patch'] +checksums = [ + '8132ff353afaa70e6b19367a25ae3d5a43627279c25647c220641fed00f8e890', # clisp-2.49.tar.bz2 + '903ca7367721e5bfe216fd8151659c4d127739311fac61f812e0031faec100ea', # CLISP-2.49_fix-readline.patch +] + + builddependencies = [ ('binutils', '2.28'), ] -- GitLab From b01e6bd9091dbe6e941189b25346812e488c0a8c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 7 Aug 2017 17:42:19 +0200 Subject: [PATCH 1319/1603] add checksums for rjags and JAGS --- easybuild/easyconfigs/j/JAGS/JAGS-4.2.0-intel-2017a.eb | 1 + easybuild/easyconfigs/r/rjags/rjags-4-6-intel-2017a-R-3.4.0.eb | 1 + 2 files changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/j/JAGS/JAGS-4.2.0-intel-2017a.eb b/easybuild/easyconfigs/j/JAGS/JAGS-4.2.0-intel-2017a.eb index 6b1311fff0..946cc65fab 100644 --- a/easybuild/easyconfigs/j/JAGS/JAGS-4.2.0-intel-2017a.eb +++ b/easybuild/easyconfigs/j/JAGS/JAGS-4.2.0-intel-2017a.eb @@ -16,6 +16,7 @@ toolchain = {'name': 'intel', 'version': '2017a'} source_urls = [('http://sourceforge.net/projects/mcmc-jags/files/JAGS/%(version_major)s.x/Source/', 'download')] sources = [SOURCE_TAR_GZ] +checksums = ['af3e9d2896d3e712f99e2a0c81091c6b08f096650af6aa9d0c631c0790409cf7'] configopts = ' --with-blas="-lmkl" --with-lapack="-lmkl" ' diff --git a/easybuild/easyconfigs/r/rjags/rjags-4-6-intel-2017a-R-3.4.0.eb b/easybuild/easyconfigs/r/rjags/rjags-4-6-intel-2017a-R-3.4.0.eb index 7a91a922a5..2809740b9c 100644 --- a/easybuild/easyconfigs/r/rjags/rjags-4-6-intel-2017a-R-3.4.0.eb +++ b/easybuild/easyconfigs/r/rjags/rjags-4-6-intel-2017a-R-3.4.0.eb @@ -14,6 +14,7 @@ source_urls = [ 'http://cran.r-project.org/src/contrib/Archive/rjags/', ] sources = ['%(name)s_%(version)s.tar.gz'] +checksums = ['cf24bb1e7c8445bafb49097089ad33e5bd5d8efbccf16fc7e32ad230f05f89ad'] dependencies = [ ('R', '3.4.0', '-X11-20170314'), -- GitLab From 354930bb6c724d6d8c42f8c51259d2e252c1d8f8 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 7 Aug 2017 23:07:23 +0100 Subject: [PATCH 1320/1603] Use slice for variable rather than hardcoding --- easybuild/easyconfigs/b/BWA/BWA-0.7.16a-foss-2016b.eb | 2 +- easybuild/easyconfigs/b/BWA/BWA-0.7.16a-intel-2017a.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/b/BWA/BWA-0.7.16a-foss-2016b.eb b/easybuild/easyconfigs/b/BWA/BWA-0.7.16a-foss-2016b.eb index cfc64d5813..e2a6be01fd 100755 --- a/easybuild/easyconfigs/b/BWA/BWA-0.7.16a-foss-2016b.eb +++ b/easybuild/easyconfigs/b/BWA/BWA-0.7.16a-foss-2016b.eb @@ -18,7 +18,7 @@ name = 'BWA' version = '0.7.16a' -subver = '0.7.16' +subver = version[:-1] homepage = 'http://bio-bwa.sourceforge.net/' description = """Burrows-Wheeler Aligner (BWA) is an efficient program that aligns diff --git a/easybuild/easyconfigs/b/BWA/BWA-0.7.16a-intel-2017a.eb b/easybuild/easyconfigs/b/BWA/BWA-0.7.16a-intel-2017a.eb index c1ee916e24..742b3bab04 100755 --- a/easybuild/easyconfigs/b/BWA/BWA-0.7.16a-intel-2017a.eb +++ b/easybuild/easyconfigs/b/BWA/BWA-0.7.16a-intel-2017a.eb @@ -18,7 +18,7 @@ name = 'BWA' version = '0.7.16a' -subver = '0.7.16' +subver = version[:-1] homepage = 'http://bio-bwa.sourceforge.net/' description = """Burrows-Wheeler Aligner (BWA) is an efficient program that aligns -- GitLab From cdec53fa0ba852cfb0fd6cd14fe4a5a01d7940df Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 8 Aug 2017 09:43:00 +0200 Subject: [PATCH 1321/1603] Javaver fixed --- easybuild/easyconfigs/t/Trinity/Trinity-2.4.0-foss-2017a.eb | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/t/Trinity/Trinity-2.4.0-foss-2017a.eb b/easybuild/easyconfigs/t/Trinity/Trinity-2.4.0-foss-2017a.eb index 167f098cd2..3b41093451 100644 --- a/easybuild/easyconfigs/t/Trinity/Trinity-2.4.0-foss-2017a.eb +++ b/easybuild/easyconfigs/t/Trinity/Trinity-2.4.0-foss-2017a.eb @@ -1,7 +1,5 @@ name = 'Trinity' version = '2.4.0' -java = 'Java' -javaver = '1.8.0_121' homepage = 'http://trinityrnaseq.github.io' description = """Trinity represents a novel method for the efficient and robust de novo reconstruction @@ -24,7 +22,7 @@ builddependencies = [ dependencies = [ (java, javaver, '', True), - ('ant', '1.10.1', '-%s-%s' % (java, javaver), True), + ('ant', '1.10.1', '-Java-%(javaver)s', True), ('Bowtie', '1.1.2'), ('Bowtie2', '2.3.2'), ('ncurses', '6.0'), -- GitLab From f1587543e394dabd680f276d384039a23f147ac0 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 8 Aug 2017 09:53:18 +0200 Subject: [PATCH 1322/1603] Javaver fixed --- easybuild/easyconfigs/t/Trinity/Trinity-2.4.0-foss-2017a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/Trinity/Trinity-2.4.0-foss-2017a.eb b/easybuild/easyconfigs/t/Trinity/Trinity-2.4.0-foss-2017a.eb index 3b41093451..4bcd727913 100644 --- a/easybuild/easyconfigs/t/Trinity/Trinity-2.4.0-foss-2017a.eb +++ b/easybuild/easyconfigs/t/Trinity/Trinity-2.4.0-foss-2017a.eb @@ -21,7 +21,7 @@ builddependencies = [ ] dependencies = [ - (java, javaver, '', True), + (java, '1.8.0_121', '', True), ('ant', '1.10.1', '-Java-%(javaver)s', True), ('Bowtie', '1.1.2'), ('Bowtie2', '2.3.2'), -- GitLab From adf461f774c30062f14e2c396aa88091e1312354 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 8 Aug 2017 10:38:38 +0200 Subject: [PATCH 1323/1603] Java --- easybuild/easyconfigs/t/Trinity/Trinity-2.4.0-foss-2017a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/Trinity/Trinity-2.4.0-foss-2017a.eb b/easybuild/easyconfigs/t/Trinity/Trinity-2.4.0-foss-2017a.eb index 4bcd727913..c700a10e06 100644 --- a/easybuild/easyconfigs/t/Trinity/Trinity-2.4.0-foss-2017a.eb +++ b/easybuild/easyconfigs/t/Trinity/Trinity-2.4.0-foss-2017a.eb @@ -21,7 +21,7 @@ builddependencies = [ ] dependencies = [ - (java, '1.8.0_121', '', True), + ('Java', '1.8.0_121', '', True), ('ant', '1.10.1', '-Java-%(javaver)s', True), ('Bowtie', '1.1.2'), ('Bowtie2', '2.3.2'), -- GitLab From 89f8a5dce9f556ac693ca4d71e57e161d380e1d9 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 8 Aug 2017 14:00:52 +0200 Subject: [PATCH 1324/1603] {chem}[dummy] ORCA 4.0.1 (REVIEW) --- .../o/ORCA/ORCA-4.0.1-OpenMPI-2.0.2.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/o/ORCA/ORCA-4.0.1-OpenMPI-2.0.2.eb diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-4.0.1-OpenMPI-2.0.2.eb b/easybuild/easyconfigs/o/ORCA/ORCA-4.0.1-OpenMPI-2.0.2.eb new file mode 100644 index 0000000000..1ad67b2230 --- /dev/null +++ b/easybuild/easyconfigs/o/ORCA/ORCA-4.0.1-OpenMPI-2.0.2.eb @@ -0,0 +1,37 @@ +easyblock = "PackedBinary" + +name = "ORCA" +version = '4.0.1' + +ompi_ver = '2.0.2' +versionsuffix = '-OpenMPI-%s' % ompi_ver + +homepage = 'http://cec.mpg.de/forum/' +description = """ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum chemistry + with specific emphasis on spectroscopic properties of open-shell molecules. + It features a wide variety of standard quantum chemical methods ranging from semiempirical methods to DFT to single- + and multireference correlated ab initio methods. + It can also treat environmental and relativistic effects.""" + +toolchain = {'name': 'dummy', 'version': ''} + +# Download from https://cec.mpg.de/orcadownload/index.php +sources = ['%%(namelower)s_%s_linux_x86-64_openmpi%s.tar.xz' % (version.replace('.', '_'), ompi_ver.replace('.', ''))] + +checksums = ['49f4e155a5425d9be2b1e90bf2fa7b61'] + +dependencies = [('OpenMPI', ompi_ver, '-GCC-6.3.0-2.27')] + +sanity_check_paths = { + 'files': ['orca_%s%s' % (x, y) for x in ['anoint', 'casscf', 'cis', 'cleanup', 'cpscf', + 'eprnmr', 'gtoint', 'mdci', 'mp2', 'mrci', 'pc', + 'rocis', 'scf', 'scfgrad', 'soc'] for y in ['', '_mpi']] + + ['orca_%s' % x for x in ['2mkl', 'asa', 'chelpg', 'ciprep', 'eca', 'ecplib', + 'euler', 'fci', 'fitpes', 'gstep', 'loc', 'mapspc', + 'md', 'mergefrag', 'ndoint', 'numfreq', 'plot', + 'pltvib', 'pop', 'rel', 'vib', 'vpot']] + + ['orca'], + 'dirs': [], +} + +moduleclass = 'chem' -- GitLab From 069e22ec09388be69e935942db08781fe8114c53 Mon Sep 17 00:00:00 2001 From: Robert Qiao Date: Tue, 8 Aug 2017 12:38:43 +0000 Subject: [PATCH 1325/1603] checksum style fixed --- easybuild/easyconfigs/b/BAMM/BAMM-2.5.0-foss-2016b.eb | 2 +- easybuild/easyconfigs/b/BWA/BWA-0.7.15-foss-2016b.eb | 2 +- easybuild/easyconfigs/b/Blosc/Blosc-1.12.1-foss-2016b.eb | 2 +- easybuild/easyconfigs/l/LZO/LZO-2.10-foss-2016b.eb | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/b/BAMM/BAMM-2.5.0-foss-2016b.eb b/easybuild/easyconfigs/b/BAMM/BAMM-2.5.0-foss-2016b.eb index 8121c45137..3dedc086be 100644 --- a/easybuild/easyconfigs/b/BAMM/BAMM-2.5.0-foss-2016b.eb +++ b/easybuild/easyconfigs/b/BAMM/BAMM-2.5.0-foss-2016b.eb @@ -25,7 +25,7 @@ toolchainopts = {'usempi': True} source_urls = ['https://github.com/macroevolution/bamm/archive'] sources = ['v%(version)s.tar.gz'] -checksums = ['526eef85ef011780ee21fe65cbc10ecc62efe54044102ae40bdef49c2985b4f4', 'sha256'] +checksums = ['526eef85ef011780ee21fe65cbc10ecc62efe54044102ae40bdef49c2985b4f4'] builddependencies = [ ('CMake', '3.7.2'), diff --git a/easybuild/easyconfigs/b/BWA/BWA-0.7.15-foss-2016b.eb b/easybuild/easyconfigs/b/BWA/BWA-0.7.15-foss-2016b.eb index 50d340dd46..6f791c6734 100644 --- a/easybuild/easyconfigs/b/BWA/BWA-0.7.15-foss-2016b.eb +++ b/easybuild/easyconfigs/b/BWA/BWA-0.7.15-foss-2016b.eb @@ -23,6 +23,6 @@ toolchainopts = {'optarch': True, 'pic': True} sources = [SOURCELOWER_TAR_BZ2] source_urls = [('http://sourceforge.net/projects/bio-bwa/files/', 'download')] -checksums = ['fcf470a46a1dbe2f96a1c5b87c530554', 'md5'] +checksums = ['2f56afefa49acc9bf45f12edb58e412565086cc20be098b8bf15ec07de8c0515'] moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/Blosc/Blosc-1.12.1-foss-2016b.eb b/easybuild/easyconfigs/b/Blosc/Blosc-1.12.1-foss-2016b.eb index 27f46a5ff7..50a94f1293 100644 --- a/easybuild/easyconfigs/b/Blosc/Blosc-1.12.1-foss-2016b.eb +++ b/easybuild/easyconfigs/b/Blosc/Blosc-1.12.1-foss-2016b.eb @@ -22,7 +22,7 @@ toolchain = {'name': 'foss', 'version': '2016b'} source_urls = ['https://github.com/Blosc/c-blosc/archive/'] sources = ['v%(version)s.tar.gz'] -checksums = ['e04535e816bb942bedc9a0ba209944d1eb34e26e2d9cca37f114e8ee292cb3c8', 'sha256'] +checksums = ['e04535e816bb942bedc9a0ba209944d1eb34e26e2d9cca37f114e8ee292cb3c8'] builddependencies = [('CMake', '3.7.2')] sanity_check_paths = { diff --git a/easybuild/easyconfigs/l/LZO/LZO-2.10-foss-2016b.eb b/easybuild/easyconfigs/l/LZO/LZO-2.10-foss-2016b.eb index c441b07fff..1490555ba3 100644 --- a/easybuild/easyconfigs/l/LZO/LZO-2.10-foss-2016b.eb +++ b/easybuild/easyconfigs/l/LZO/LZO-2.10-foss-2016b.eb @@ -21,7 +21,7 @@ description = "Portable lossless data compression library" sources = [SOURCELOWER_TAR_GZ] source_urls = [homepage + 'download/'] -checksums = ['c0f892943208266f9b6543b3ae308fab6284c5c90e627931446fb49b4221a072', 'sha256'] +checksums = ['c0f892943208266f9b6543b3ae308fab6284c5c90e627931446fb49b4221a072'] toolchain = {'name': 'foss', 'version': '2016b'} toolchainopts = {'pic': True} -- GitLab From c02f91fc622ef3a89ecf46bd628390ced2ee74d6 Mon Sep 17 00:00:00 2001 From: Robert Qiao Date: Tue, 8 Aug 2017 12:44:18 +0000 Subject: [PATCH 1326/1603] Autoconf/Automake version cleanup --- .../a/Autoconf/Autoconf-2.62-foss-2016b.eb | 37 ------------------- .../a/Automake/Automake-1.11.6-foss-2016b.eb | 36 ------------------ 2 files changed, 73 deletions(-) delete mode 100644 easybuild/easyconfigs/a/Autoconf/Autoconf-2.62-foss-2016b.eb delete mode 100644 easybuild/easyconfigs/a/Automake/Automake-1.11.6-foss-2016b.eb diff --git a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.62-foss-2016b.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.62-foss-2016b.eb deleted file mode 100644 index e9f3329ee6..0000000000 --- a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.62-foss-2016b.eb +++ /dev/null @@ -1,37 +0,0 @@ -## -# This is a contribution from Phoenix HPC Service, The University of Adelaide, Australia -# Homepage: https://www.adelaide.edu.au/phoenix/ -# -# Copyright:: adelaide.edu.au/phoenix -# Authors:: Robert Qiao , Exe Escobedo -# License:: -# -# Notes:: -## - -easyblock = 'ConfigureMake' - -name = 'Autoconf' -version = '2.62' - -homepage = 'http://www.gnu.org/software/autoconf/' -description = """Autoconf is an extensible package of M4 macros that produce shell scripts - to automatically configure software source code packages. These scripts can adapt the - packages to many kinds of UNIX-like systems without manual user intervention. Autoconf - creates a configuration script for a package from a template file that lists the - operating system features that the package can use, in the form of M4 macro calls.""" - -toolchain = {'name': 'foss', 'version': '2016b'} - -source_urls = [GNU_SOURCE] -sources = [SOURCELOWER_TAR_GZ] - -dependencies = [('M4', '1.4.17')] - -sanity_check_paths = { - 'files': ["bin/%s" % x for x in ["autoconf", "autoheader", "autom4te", "autoreconf", "autoscan", - "autoupdate", "ifnames"]], - 'dirs': [], -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.11.6-foss-2016b.eb b/easybuild/easyconfigs/a/Automake/Automake-1.11.6-foss-2016b.eb deleted file mode 100644 index 3ea4446d37..0000000000 --- a/easybuild/easyconfigs/a/Automake/Automake-1.11.6-foss-2016b.eb +++ /dev/null @@ -1,36 +0,0 @@ -## -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# -# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA -# Authors:: Fotis Georgatos -# License:: MIT/GPL -# $Id$ -# -# This work implements a part of the HPCBIOS project and is a component of the policy: -# http://hpcbios.readthedocs.org/en/latest/ -# -# Modified:: Robert Qiao -# @ adelaide.edu.au/phoenix -## - -easyblock = 'ConfigureMake' - -name = 'Automake' -version = "1.11.6" - -homepage = 'http://www.gnu.org/software/automake/automake.html' -description = "Automake: GNU Standards-compliant Makefile generator" - -toolchain = {'name': 'foss', 'version': '2016b'} - -source_urls = [GNU_SOURCE] -sources = [SOURCELOWER_TAR_GZ] - -dependencies = [('Autoconf', '2.62')] - -sanity_check_paths = { - 'files': ['bin/automake', 'bin/aclocal'], - 'dirs': [] -} - -moduleclass = 'devel' -- GitLab From a93ff0b4ad83d46f404a81522d02762f99e38f44 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 8 Aug 2017 18:17:17 +0200 Subject: [PATCH 1327/1603] adding easyconfigs: HDF5-1.10.1-foss-2017a.eb --- .../h/HDF5/HDF5-1.10.1-foss-2017a.eb | 20 +++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.10.1-foss-2017a.eb diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.10.1-foss-2017a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.1-foss-2017a.eb new file mode 100644 index 0000000000..6701351463 --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.1-foss-2017a.eb @@ -0,0 +1,20 @@ +name = 'HDF5' +version = '1.10.1' + +homepage = 'https://support.hdfgroup.org/HDF5/' +description = """HDF5 is a unique technology suite that makes possible the management of + extremely large and complex data collections.""" + +toolchain = {'name': 'foss', 'version': '2017a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['43a2f9466702fb1db31df98ae6677f15'] + +dependencies = [ + ('zlib', '1.2.11'), + ('Szip', '2.1'), +] + +moduleclass = 'data' -- GitLab From 97df9bca46a1e6ea25f9b6871dd8b250a374ca59 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Tue, 8 Aug 2017 17:45:30 +0100 Subject: [PATCH 1328/1603] adding easyconfigs: minimap2-2.0rc1-foss-2016b.eb --- .../m/minimap2/minimap2-2.0rc1-foss-2016b.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100755 easybuild/easyconfigs/m/minimap2/minimap2-2.0rc1-foss-2016b.eb diff --git a/easybuild/easyconfigs/m/minimap2/minimap2-2.0rc1-foss-2016b.eb b/easybuild/easyconfigs/m/minimap2/minimap2-2.0rc1-foss-2016b.eb new file mode 100755 index 0000000000..446f7da053 --- /dev/null +++ b/easybuild/easyconfigs/m/minimap2/minimap2-2.0rc1-foss-2016b.eb @@ -0,0 +1,34 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Adam Huffman +# The Francis Crick Institute +# adam.huffman@crick.ac.uk + +easyblock = 'MakeCp' + +name = 'minimap2' +version = '2.0rc1' + +homepage = 'https://github.com/lh3/minimap2' +description = """Minimap2 is a fast sequence mapping and alignment program that can find overlaps between + long noisy reads, or map long reads or their assemblies to a reference genome optionally with detailed + alignment (i.e. CIGAR). At present, it works efficiently with query sequences from a few kilobases to + ~100 megabases in length at an error rate ~15%. Minimap2 outputs in the PAF or the SAM format. On limited + test data sets, minimap2 is over 20 times faster than most other long-read aligners. It will replace + BWA-MEM for long reads and contig alignment.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +sources = ['%(name)s-%(version)s.tar.bz2'] +source_urls = ['https://github.com/lh3/%(name)s/releases/download/v%(version)s/'] +checksums = ['452a13d7e944da941b6f1996392890dbe4b7f4256954dd06c99ea69939446a5b'] + +files_to_copy = [(['%(name)s'], 'bin'), 'LICENSE.txt', 'NEWS.md', 'README.md', '%(name)s.1'] + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': [] +} + +modextrapaths = {'MANPATH': ''} + +moduleclass = 'bio' -- GitLab From a1d8e577eecf7df5e448e2661b030bdb370f4227 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 8 Aug 2017 19:05:55 +0200 Subject: [PATCH 1329/1603] also add checksums to Perl 5.24.1 easyconfig using intel/2017a --- .../p/Perl/Perl-5.24.1-intel-2017a.eb | 223 ++++++++++++++++++ 1 file changed, 223 insertions(+) diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.24.1-intel-2017a.eb b/easybuild/easyconfigs/p/Perl/Perl-5.24.1-intel-2017a.eb index 4dc5dd9a5c..e827a0f69a 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.24.1-intel-2017a.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.24.1-intel-2017a.eb @@ -9,6 +9,7 @@ toolchainopts = {'pic': True} source_urls = ['http://www.cpan.org/src/%(version_major)s.0'] sources = [SOURCELOWER_TAR_GZ] +checksums = ['e6c185c9b09bdb3f1b13f678999050c639859a7ef39c8cad418448075f5918af'] # !! order of extensions is important !! # extensions updated on April 4th 2017 @@ -16,891 +17,1113 @@ exts_list = [ ('Config::General', '2.63', { 'source_tmpl': 'Config-General-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TL/TLINDEN'], + 'checksums': ['0a9bf977b8aabe76343e88095d2296c8a422410fd2a05a1901f2b20e2e1f6fad'], }), ('File::Listing', '6.04', { 'source_tmpl': 'File-Listing-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + 'checksums': ['1e0050fcd6789a2179ec0db282bf1e90fb92be35d1171588bd9c47d52d959cf5'], }), ('ExtUtils::InstallPaths', '0.011', { 'source_tmpl': 'ExtUtils-InstallPaths-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['7609fa048cdcf1451cad5b1d7d494f30e3d5bad0672d15404f1ea60e1df0067c'], }), ('ExtUtils::Helpers', '0.026', { 'source_tmpl': 'ExtUtils-Helpers-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['de901b6790a4557cf4ec908149e035783b125bf115eb9640feb1bc1c24c33416'], }), ('Test::Harness', '3.38', { 'source_tmpl': 'Test-Harness-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['af906dd279217a6db5064a058658f2b1d5aa1d307ed6f142d96ac4d339754c01'], }), ('ExtUtils::Config', '0.008', { 'source_tmpl': 'ExtUtils-Config-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['ae5104f634650dce8a79b7ed13fb59d67a39c213a6776cfdaa3ee749e62f1a8c'], }), ('Module::Build::Tiny', '0.039', { 'source_tmpl': 'Module-Build-Tiny-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['7d580ff6ace0cbe555bf36b86dc8ea232581530cbeaaea09bccb57b55797f11c'], }), ('aliased', '0.34', { 'source_tmpl': 'aliased-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['c350524507cd827fab864e5d4c2cc350b1babaa12fa95aec0ca00843fcc7deeb'], }), ('Text::Glob', '0.11', { 'source_tmpl': 'Text-Glob-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RC/RCLAMP'], + 'checksums': ['069ccd49d3f0a2dedb115f4bdc9fbac07a83592840953d1fcdfc39eb9d305287'], }), ('Regexp::Common', '2016060801', { 'source_tmpl': 'Regexp-Common-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AB/ABIGAIL'], + 'checksums': ['fc2fc178facf0292974d6511bad677dd038fe60d7ac118e3b83a1ca9e98a8403'], }), ('GO::Utils', '0.15', { 'source_tmpl': 'go-perl-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CM/CMUNGALL'], + 'checksums': ['423d26155ee85ca51ab2270cee59f4e85b193e57ac3a29aff827298c0a396b12'], }), ('Module::Pluggable', '5.2', { 'source_tmpl': 'Module-Pluggable-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SI/SIMONW'], + 'checksums': ['b3f2ad45e4fd10b3fb90d912d78d8b795ab295480db56dc64e86b9fa75c5a6df'], }), ('Test::Fatal', '0.014', { 'source_tmpl': 'Test-Fatal-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['bcdcef5c7b2790a187ebca810b0a08221a63256062cfab3c3b98685d91d1cbb0'], }), ('Test::Warnings', '0.026', { 'source_tmpl': 'Test-Warnings-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['ae2b68b1b5616704598ce07f5118efe42dc4605834453b7b2be14e26f9cc9a08'], }), ('File::ShareDir::Install', '0.11', { 'source_tmpl': 'File-ShareDir-Install-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['32bf8772e9fea60866074b27ff31ab5bc3f88972d61915e84cbbb98455e00cc8'], }), ('DateTime::Locale', '1.16', { 'source_tmpl': 'DateTime-Locale-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + 'checksums': ['dfaf4c42149c0622e80721773b8d7229d7785280503585895c9fe9f51e076cfe'], }), ('DateTime::TimeZone', '2.11', { 'source_tmpl': 'DateTime-TimeZone-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + 'checksums': ['a7c0b2581d2bf6d5cc535364099a67678a9f6ee608e5042dff9ef9c4c577ea6b'], }), ('Test::Requires', '0.10', { 'source_tmpl': 'Test-Requires-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TOKUHIROM'], + 'checksums': ['2768a391d50ab94b95cefe540b9232d7046c13ee86d01859e04c044903222eb5'], }), ('Module::Implementation', '0.09', { 'source_tmpl': 'Module-Implementation-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + 'checksums': ['c15f1a12f0c2130c9efff3c2e1afe5887b08ccd033bd132186d1e7d5087fd66d'], }), ('Module::Build', '0.4222', { 'source_tmpl': 'Module-Build-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['e74b45d9a74736472b74830599cec0d1123f992760f9cd97104f94bee800b160'], }), ('Module::Runtime', '0.014', { 'source_tmpl': 'Module-Runtime-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/Z/ZE/ZEFRAM'], + 'checksums': ['4c44fe0ea255a9fd00741ee545063f6692d2a28e7ef2fbaad1b24a92803362a4'], }), ('Try::Tiny', '0.28', { 'source_tmpl': 'Try-Tiny-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': 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['06ab05388f9130cd377c0e1d3e3bafeed6ef6a1e22104571a9e1d7bfac787b2c'], }), ('Data::OptList', '0.110', { 'source_tmpl': 'Data-OptList-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['366117cb2966473f2559f2f4575ff6ae69e84c69a0f30a0773e1b51a457ef5c3'], }), ('CPANPLUS', '0.9164', { 'source_tmpl': 'CPANPLUS-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + 'checksums': ['3fcd8c7bb1973df484236fc3d59ed17c8a35057f56546ba44bfc780b97fec0a8'], }), ('IO::Tty', '1.12', { 'source_tmpl': 'IO-Tty-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR'], + 'checksums': ['a2ef8770d3309178203f8c8ac25e623e63cf76e97830fd3be280ade1a555290d'], }), ('Text::Soundex', '3.05', { 'source_tmpl': 'Text-Soundex-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['f6dd55b4280b25dea978221839864382560074e1d6933395faee2510c2db60ed'], }), ('Lingua::EN::PluralToSingular', '0.19', { 'source_tmpl': 'Lingua-EN-PluralToSingular-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BK/BKB'], + 'checksums': ['c71b6c1aec01aae9c42aef0d9f147a437e91a7cc5cea6e4abbc35440638f299e'], }), ('Want', '0.29', { 'source_tmpl': 'Want-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RO/ROBIN'], + 'checksums': ['b4e4740b8d4cb783591273c636bd68304892e28d89e88abf9273b1de17f552f7'], }), ('Cwd::Guard', '0.05', { 'source_tmpl': 'Cwd-Guard-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KA/KAZEBURO'], + 'checksums': ['7afc7ca2b9502e440241938ad97a3e7ebd550180ebd6142e1db394186b268e77'], }), ('Bundle::BioPerl', '2.1.9', { 'source_tmpl': 'Bundle-BioPerl-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS'], + 'checksums': ['c343ba97f49d86e7fb14aef4cfe3124992e2a5c3168e53a54606dd611d73e5c7'], }), ('Mail::Util', '2.18', { 'source_tmpl': 'MailTools-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARKOV'], + 'checksums': ['dfee9e770257371112f20d978e637759e81bc4f19e97b083585c71ecab37b527'], }), ('Text::Template', '1.47', { 'source_tmpl': 'Text-Template-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MS/MSCHOUT'], + 'checksums': ['50d742c74482478aa01008d468290fcfbc0b9a1219cfe1284076f1f31f0be8fc'], }), ('PDF::API2', '2.031', { 'source_tmpl': 'PDF-API2-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SS/SSIMMS'], + 'checksums': ['6ea5d38f99dfb1e8acf57c9c7579659b3eee84944295a135f90e607e0a3f43e9'], }), ('Devel::CheckLib', '1.11', { 'source_tmpl': 'Devel-CheckLib-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MATTN'], + 'checksums': ['bd6d1c187e80be6de1f0d37add441ba8f14950c7bc1f54e764770ed484b232c1'], }), ('SVG', '2.77', { 'source_tmpl': 'SVG-2.77.tar.gz', 'source_urls': ['http://search.cpan.org/CPAN/authors/id/M/MA/MANWAR/'], + 'checksums': ['1f01cf2dc666a2ba3bf5219ec9e2290143e5e569747431412c8423916a9846c5'], }), ('Statistics::Basic', '1.6611', { 'source_tmpl': 'Statistics-Basic-1.6611.tar.gz', 'source_urls': ['http://search.cpan.org/CPAN/authors/id/J/JE/JETTERO/'], + 'checksums': ['6855ce5615fd3e1af4cfc451a9bf44ff29a3140b4e7130034f1f0af2511a94fb'], }), ] -- GitLab From f5563b9e1225aee2a01c31a3ff508ee9556ecb63 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 9 Aug 2017 09:18:20 +0200 Subject: [PATCH 1330/1603] remove easyconfig for hwloc 1.11.7 with GCC-6.4.0-2.28 toolchain, GCCcore 6.4.0 suffices --- .../h/hwloc/hwloc-1.11.7-GCC-6.4.0-2.28.eb | 24 ------------------- 1 file changed, 24 deletions(-) delete mode 100644 easybuild/easyconfigs/h/hwloc/hwloc-1.11.7-GCC-6.4.0-2.28.eb diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.7-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.7-GCC-6.4.0-2.28.eb deleted file mode 100644 index b5be4b59bc..0000000000 --- a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.7-GCC-6.4.0-2.28.eb +++ /dev/null @@ -1,24 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'hwloc' -version = '1.11.7' - -homepage = 'http://www.open-mpi.org/projects/hwloc/' -description = """The Portable Hardware Locality (hwloc) software package provides a portable abstraction -(across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including -NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various -system attributes such as cache and memory information as well as the locality of I/O devices such as -network interfaces, InfiniBand HCAs or GPUs. It primarily aims at helping applications with gathering -information about modern computing hardware so as to exploit it accordingly and efficiently.""" - -toolchain = {'name': 'GCC', 'version': '6.4.0-2.28'} - -source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] -sources = [SOURCE_TAR_GZ] -checksums = ['ac16bed9cdd3c63bca1fe1ac3de522a1376b1487c4fc85b7b19592e28fd98e26'] - -dependencies = [('numactl', '2.0.11')] - -configopts = "--enable-libnuma=$EBROOTNUMACTL" - -moduleclass = 'system' -- GitLab From 55a2995bcebdc6e08ed8d42fd5aece88bc5c7994 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 9 Aug 2017 09:18:36 +0200 Subject: [PATCH 1331/1603] fix @verdurin's remarks --- easybuild/easyconfigs/f/foss/foss-2017b.eb | 3 +-- .../easyconfigs/o/OpenMPI/OpenMPI-2.1.1-GCC-6.4.0-2.28.eb | 3 +++ 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/f/foss/foss-2017b.eb b/easybuild/easyconfigs/f/foss/foss-2017b.eb index 5ce20b722f..a0cf18555c 100644 --- a/easybuild/easyconfigs/f/foss/foss-2017b.eb +++ b/easybuild/easyconfigs/f/foss/foss-2017b.eb @@ -20,9 +20,8 @@ blassuff = '-LAPACK-3.7.0' comp_mpi_tc_name = 'gompi' comp_mpi_tc = (comp_mpi_tc_name, version) -# compiler toolchain depencies # we need GCC and OpenMPI as explicit dependencies instead of gompi toolchain -# because of toolchain preperation functions +# because of toolchain preparation functions # For binutils, stick to http://wiki.osdev.org/Cross-Compiler_Successful_Builds dependencies = [ ('GCC', gccver), diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.1-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.1-GCC-6.4.0-2.28.eb index c55bade938..bef1256a37 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.1-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.1-GCC-6.4.0-2.28.eb @@ -20,6 +20,9 @@ configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading +# to enable SLURM integration (site-specific) +# configopts += '--with-slurm --with-pmi=/usr/include/slurm --with-pmi-libdir=/usr' + # needed for --with-verbs osdependencies = [('libibverbs-dev', 'libibverbs-devel')] -- GitLab From e64985bc522c497005df71667ff3648f08f42a4b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 9 Aug 2017 12:00:46 +0200 Subject: [PATCH 1332/1603] adding easyconfigs: xarray-0.9.6-intel-2017a-Python-2.7.13.eb --- .../xarray-0.9.6-intel-2017a-Python-2.7.13.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/x/xarray/xarray-0.9.6-intel-2017a-Python-2.7.13.eb diff --git a/easybuild/easyconfigs/x/xarray/xarray-0.9.6-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/x/xarray/xarray-0.9.6-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..d49636fa5c --- /dev/null +++ b/easybuild/easyconfigs/x/xarray/xarray-0.9.6-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'xarray' +version = '0.9.6' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/pydata/xarray' +description = """xarray (formerly xray) is an open source project and Python package that aims to bring + the labeled data power of pandas to the physical sciences, by providing N-dimensional variants of the + core pandas data structures.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['f649a41d43b5a6c64bdcbd57e994932656b689f9593a86dd0be95778a2b47494'] + +dependencies = [('Python', '2.7.13')] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'data' -- GitLab From f669fbe3b50e4a1de9b7610c5913b49ed79204ae Mon Sep 17 00:00:00 2001 From: Maxime Boissonneault Date: Wed, 9 Aug 2017 13:03:43 +0000 Subject: [PATCH 1333/1603] added checksum --- .../a/Armadillo/Armadillo-7.950.1-intel-2016b-Python-2.7.12.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/a/Armadillo/Armadillo-7.950.1-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/a/Armadillo/Armadillo-7.950.1-intel-2016b-Python-2.7.12.eb index ca56813122..ee8b4d3fb7 100644 --- a/easybuild/easyconfigs/a/Armadillo/Armadillo-7.950.1-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/a/Armadillo/Armadillo-7.950.1-intel-2016b-Python-2.7.12.eb @@ -11,6 +11,7 @@ toolchain = {'name': 'intel', 'version': '2016b'} sources = [SOURCELOWER_TAR_XZ] source_urls = ['http://sourceforge.net/projects/arma/files'] +checksums = ['a32da32a0ea420b8397a53e4b40ed279c1a5fc791dd492a2ced81ffb14ad0d1b'] dependencies = [ ('Boost', '1.63.0', versionsuffix), -- GitLab From 911cb575b323af0fb1e3df4402ccbe7e69075250 Mon Sep 17 00:00:00 2001 From: Fokke Dijkstra Date: Wed, 9 Aug 2017 15:23:32 +0200 Subject: [PATCH 1334/1603] HTSlib 1.4.1 for foss 2016a --- .../h/HTSlib/HTSlib-1.4.1-foss-2016a.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/h/HTSlib/HTSlib-1.4.1-foss-2016a.eb diff --git a/easybuild/easyconfigs/h/HTSlib/HTSlib-1.4.1-foss-2016a.eb b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.4.1-foss-2016a.eb new file mode 100644 index 0000000000..187d2f6581 --- /dev/null +++ b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.4.1-foss-2016a.eb @@ -0,0 +1,36 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# 1.4 modified by: +# Adam Huffman +# The Francis Crick Institute + +easyblock = 'ConfigureMake' + +name = 'HTSlib' +version = '1.4.1' + +homepage = "http://www.htslib.org/" +description = """A C library for reading/writing high-throughput sequencing data. + This package includes the utilities bgzip and tabix""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s/'] +sources = [SOURCELOWER_TAR_BZ2] + +# cURL added for S3 support +dependencies = [ + ('zlib', '1.2.8'), + ('bzip2', '1.0.6'), + ('XZ', '5.2.2'), + ('cURL', '7.49.1'), +] + +sanity_check_paths = { + 'files': ["bin/bgzip", "bin/tabix", "lib/libhts.%s" % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From e3b33c0fc35d2eb3b1c189bfecd1a32ded1c9921 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 9 Aug 2017 15:50:13 +0200 Subject: [PATCH 1335/1603] adding easyconfigs: UNAFold-3.8-intel-2017a-Perl-5.24.1.eb --- .../UNAFold-3.8-intel-2017a-Perl-5.24.1.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/u/UNAFold/UNAFold-3.8-intel-2017a-Perl-5.24.1.eb diff --git a/easybuild/easyconfigs/u/UNAFold/UNAFold-3.8-intel-2017a-Perl-5.24.1.eb b/easybuild/easyconfigs/u/UNAFold/UNAFold-3.8-intel-2017a-Perl-5.24.1.eb new file mode 100644 index 0000000000..1cc07a9de0 --- /dev/null +++ b/easybuild/easyconfigs/u/UNAFold/UNAFold-3.8-intel-2017a-Perl-5.24.1.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'UNAFold' +version = '3.8' +versionsuffix = '-Perl-%(perlver)s' + +homepage='http://mfold.rna.albany.edu/?q=DINAMelt/software' +description = """The UNAFold package contains several programs for performing energy minimization and partition + function calculations on nucleic acid sequences.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +sources = [SOURCELOWER_TAR_GZ] +#patches = ["ictce_inf.patch"] +checksums = ['f9392621762a74b02eb026caceb69568ea65b0cf0891ba25a805da721a90a275'] + +dependencies = [ + ('gnuplot', '5.0.6'), + ('Perl', '5.24.1'), +] + +sanity_check_paths = { + 'files': ['bin/concentration', 'bin/ct-energy', 'bin/hybrid', 'bin/hybrid2-min.pl', 'bin/sbs'], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From dd03b8c02555b7ec6542fc96944b3bd7e5e69767 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 9 Aug 2017 15:52:10 +0200 Subject: [PATCH 1336/1603] md5->sha256 --- easybuild/easyconfigs/o/ORCA/ORCA-4.0.1-OpenMPI-2.0.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-4.0.1-OpenMPI-2.0.2.eb b/easybuild/easyconfigs/o/ORCA/ORCA-4.0.1-OpenMPI-2.0.2.eb index 1ad67b2230..b28cb7f1c0 100644 --- a/easybuild/easyconfigs/o/ORCA/ORCA-4.0.1-OpenMPI-2.0.2.eb +++ b/easybuild/easyconfigs/o/ORCA/ORCA-4.0.1-OpenMPI-2.0.2.eb @@ -18,7 +18,7 @@ toolchain = {'name': 'dummy', 'version': ''} # Download from https://cec.mpg.de/orcadownload/index.php sources = ['%%(namelower)s_%s_linux_x86-64_openmpi%s.tar.xz' % (version.replace('.', '_'), ompi_ver.replace('.', ''))] -checksums = ['49f4e155a5425d9be2b1e90bf2fa7b61'] +checksums = ['6644b95fdb16e117b870fd9e5cea8b4f829f1547d5df4e87d52ef08e3f1ee310'] dependencies = [('OpenMPI', ompi_ver, '-GCC-6.3.0-2.27')] -- GitLab From 21ed5c9c1b985d640ea548781d2fd222e2f23043 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 9 Aug 2017 17:00:56 +0200 Subject: [PATCH 1337/1603] fix style issues --- .../u/UNAFold/UNAFold-3.8-intel-2017a-Perl-5.24.1.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/u/UNAFold/UNAFold-3.8-intel-2017a-Perl-5.24.1.eb b/easybuild/easyconfigs/u/UNAFold/UNAFold-3.8-intel-2017a-Perl-5.24.1.eb index 1cc07a9de0..91df69c67f 100644 --- a/easybuild/easyconfigs/u/UNAFold/UNAFold-3.8-intel-2017a-Perl-5.24.1.eb +++ b/easybuild/easyconfigs/u/UNAFold/UNAFold-3.8-intel-2017a-Perl-5.24.1.eb @@ -4,14 +4,13 @@ name = 'UNAFold' version = '3.8' versionsuffix = '-Perl-%(perlver)s' -homepage='http://mfold.rna.albany.edu/?q=DINAMelt/software' +homepage = 'http://mfold.rna.albany.edu/?q=DINAMelt/software' description = """The UNAFold package contains several programs for performing energy minimization and partition function calculations on nucleic acid sequences.""" toolchain = {'name': 'intel', 'version': '2017a'} sources = [SOURCELOWER_TAR_GZ] -#patches = ["ictce_inf.patch"] checksums = ['f9392621762a74b02eb026caceb69568ea65b0cf0891ba25a805da721a90a275'] dependencies = [ -- GitLab From 0539726cd946ac65d4e9bf3c37f6fe381d362c5e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 9 Aug 2017 20:17:59 +0200 Subject: [PATCH 1338/1603] add SHA256 checksums for foss/2017b components --- easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-gompi-2017b.eb | 2 +- easybuild/easyconfigs/h/HPL/HPL-2.2-foss-2017b.eb | 1 + .../easyconfigs/n/numactl/numactl-2.0.11-GCC-6.4.0-2.28.eb | 3 +-- .../easyconfigs/o/OpenMPI/OpenMPI-2.1.1-GCC-6.4.0-2.28.eb | 1 - ...ScaLAPACK-2.0.2-gompi-2017b-OpenBLAS-0.2.19-LAPACK-3.7.0.eb | 1 + 5 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-gompi-2017b.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-gompi-2017b.eb index eee27ec554..a21d63724d 100644 --- a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-gompi-2017b.eb +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-gompi-2017b.eb @@ -10,7 +10,7 @@ toolchainopts = {'pic': True} source_urls = [homepage] sources = ['fftw-%(version)s-pl2.tar.gz'] -checksums = ['927e481edbb32575397eb3d62535a856'] +checksums = ['a5de35c5c824a78a058ca54278c706cdf3d4abba1c56b63531c2cb05f5d57da2'] runtest = 'check' diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.2-foss-2017b.eb b/easybuild/easyconfigs/h/HPL/HPL-2.2-foss-2017b.eb index 7ff64c1745..45cfc68647 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.2-foss-2017b.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.2-foss-2017b.eb @@ -11,6 +11,7 @@ toolchainopts = {'usempi': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] +checksums = ['ac7534163a09e21a5fa763e4e16dfc119bc84043f6e6a807aba666518f8df440'] # fix Make dependencies, so parallel build also works patches = ['HPL_parallel-make.patch'] diff --git a/easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCC-6.4.0-2.28.eb index 521df8ded9..775fb405c3 100644 --- a/easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCC-6.4.0-2.28.eb @@ -12,8 +12,7 @@ toolchain = {'name': 'GCC', 'version': '6.4.0-2.28'} source_urls = ['ftp://oss.sgi.com/www/projects/libnuma/download/'] sources = [SOURCE_TAR_GZ] - -checksums = ['d3bc88b7ddb9f06d60898f4816ae9127'] +checksums = ['450c091235f891ee874a8651b179c30f57a1391ca5c4673354740ba65e527861'] sanity_check_paths = { 'files': ['bin/numactl', 'bin/numastat', 'lib/libnuma.%s' % SHLIB_EXT, 'lib/libnuma.a'], diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.1-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.1-GCC-6.4.0-2.28.eb index bef1256a37..c10c8f486d 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.1-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.1-GCC-6.4.0-2.28.eb @@ -10,7 +10,6 @@ toolchain = {'name': 'GCC', 'version': '6.4.0-2.28'} source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] - checksums = ['afe4bef3c4378bc76eea96c623d5aa4c1c98b9e057d281c646e68869292a77dc'] dependencies = [('hwloc', '1.11.7')] diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-2017b-OpenBLAS-0.2.19-LAPACK-3.7.0.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-2017b-OpenBLAS-0.2.19-LAPACK-3.7.0.eb index 84d34e0f8a..e698beb591 100644 --- a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-2017b-OpenBLAS-0.2.19-LAPACK-3.7.0.eb +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-2017b-OpenBLAS-0.2.19-LAPACK-3.7.0.eb @@ -10,6 +10,7 @@ toolchainopts = {'pic': True} source_urls = [homepage] sources = [SOURCELOWER_TGZ] +checksums = ['0c74aeae690fe5ee4db7926f49c5d0bb69ce09eea75beb915e00bba07530395c'] blaslib = 'OpenBLAS' blasver = '0.2.19' -- GitLab From 9df0f5a2642c08b44ce6cbf62202fc285e927df2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 9 Aug 2017 21:01:01 +0200 Subject: [PATCH 1339/1603] add zlib as depedency to recent util-linux easyconfigs --- .../easyconfigs/u/util-linux/util-linux-2.29-foss-2016b.eb | 5 ++++- .../easyconfigs/u/util-linux/util-linux-2.29-intel-2016b.eb | 5 ++++- .../u/util-linux/util-linux-2.30-GCCcore-6.4.0.eb | 1 + 3 files changed, 9 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/u/util-linux/util-linux-2.29-foss-2016b.eb b/easybuild/easyconfigs/u/util-linux/util-linux-2.29-foss-2016b.eb index 27b08c5298..246ed0de3f 100644 --- a/easybuild/easyconfigs/u/util-linux/util-linux-2.29-foss-2016b.eb +++ b/easybuild/easyconfigs/u/util-linux/util-linux-2.29-foss-2016b.eb @@ -23,7 +23,10 @@ configopts += "--with-bashcompletiondir='${prefix}/share/bash-completion/complet # disable building Python bindings (since we don't include Python as a dep) configopts += "--without-python " -dependencies = [('ncurses', '6.0')] +dependencies = [ + ('ncurses', '6.0'), + ('zlib', '1.2.8'), +] sanity_check_paths = { 'files': ['lib/lib%s.a' % x for x in ['blkid', 'mount', 'uuid']], diff --git a/easybuild/easyconfigs/u/util-linux/util-linux-2.29-intel-2016b.eb b/easybuild/easyconfigs/u/util-linux/util-linux-2.29-intel-2016b.eb index b5ac58a535..c4419d6080 100644 --- a/easybuild/easyconfigs/u/util-linux/util-linux-2.29-intel-2016b.eb +++ b/easybuild/easyconfigs/u/util-linux/util-linux-2.29-intel-2016b.eb @@ -23,7 +23,10 @@ configopts += "--with-bashcompletiondir='${prefix}/share/bash-completion/complet # disable building Python bindings (since we don't include Python as a dep) configopts += "--without-python " -dependencies = [('ncurses', '6.0')] +dependencies = [ + ('ncurses', '6.0'), + ('zlib', '1.2.8'), +] sanity_check_paths = { 'files': ['lib/lib%s.a' % x for x in ['blkid', 'mount', 'uuid']], diff --git a/easybuild/easyconfigs/u/util-linux/util-linux-2.30-GCCcore-6.4.0.eb b/easybuild/easyconfigs/u/util-linux/util-linux-2.30-GCCcore-6.4.0.eb index 3556edda8d..64826e9aa5 100644 --- a/easybuild/easyconfigs/u/util-linux/util-linux-2.30-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/u/util-linux/util-linux-2.30-GCCcore-6.4.0.eb @@ -32,6 +32,7 @@ builddependencies = [ dependencies = [ ('ncurses', '6.0'), + ('zlib', '1.2.11'), ] sanity_check_paths = { -- GitLab From a9d45090544d26746dd5e5a7f459d19dbd401906 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Thu, 10 Aug 2017 06:11:12 +0100 Subject: [PATCH 1340/1603] Fix manpage placement --- .../easyconfigs/m/minimap2/minimap2-2.0rc1-foss-2016b.eb | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/m/minimap2/minimap2-2.0rc1-foss-2016b.eb b/easybuild/easyconfigs/m/minimap2/minimap2-2.0rc1-foss-2016b.eb index 446f7da053..0e029fec25 100755 --- a/easybuild/easyconfigs/m/minimap2/minimap2-2.0rc1-foss-2016b.eb +++ b/easybuild/easyconfigs/m/minimap2/minimap2-2.0rc1-foss-2016b.eb @@ -22,13 +22,11 @@ sources = ['%(name)s-%(version)s.tar.bz2'] source_urls = ['https://github.com/lh3/%(name)s/releases/download/v%(version)s/'] checksums = ['452a13d7e944da941b6f1996392890dbe4b7f4256954dd06c99ea69939446a5b'] -files_to_copy = [(['%(name)s'], 'bin'), 'LICENSE.txt', 'NEWS.md', 'README.md', '%(name)s.1'] +files_to_copy = [(['%(name)s'], 'bin'), 'LICENSE.txt', 'NEWS.md', 'README.md', (['%(name)s.1'], 'share/man/man1')] sanity_check_paths = { 'files': ['bin/%(name)s'], 'dirs': [] } -modextrapaths = {'MANPATH': ''} - moduleclass = 'bio' -- GitLab From 37398674ade437e0a7add592eeb9cb1c15ab1900 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Thu, 10 Aug 2017 06:20:28 +0100 Subject: [PATCH 1341/1603] Fix hardcoded version for patch --- easybuild/easyconfigs/b/BFAST/BFAST-0.7.0a-foss-2016b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/BFAST/BFAST-0.7.0a-foss-2016b.eb b/easybuild/easyconfigs/b/BFAST/BFAST-0.7.0a-foss-2016b.eb index 2126725d43..aecff4c2cf 100755 --- a/easybuild/easyconfigs/b/BFAST/BFAST-0.7.0a-foss-2016b.eb +++ b/easybuild/easyconfigs/b/BFAST/BFAST-0.7.0a-foss-2016b.eb @@ -32,7 +32,7 @@ checksums = ['ed8de49693165a87d5dbef352207c424b1bf6f670a83acf49a4f4f188444995e'] dependencies = [('bzip2', '1.0.6')] -patches = ['BFAST-0.7.0a-inline.patch'] +patches = ['BFAST-%(version)s-inline.patch'] sanity_check_paths = { 'files': ["bin/bfast"], -- GitLab From 21354990e4e6b4ca169b93d563091db4c6b2693e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 10 Aug 2017 13:20:12 +0200 Subject: [PATCH 1342/1603] adding easyconfigs: netcdf4-python-1.2.9-intel-2017a-Python-2.7.13.eb, netCDF-4.4.1.1-intel-2017a-HDF5-1.10.1.eb --- .../netCDF-4.4.1.1-intel-2017a-HDF5-1.10.1.eb | 35 +++++++++++++++++++ ...-python-1.2.9-intel-2017a-Python-2.7.13.eb | 23 ++++++++++++ 2 files changed, 58 insertions(+) create mode 100644 easybuild/easyconfigs/n/netCDF/netCDF-4.4.1.1-intel-2017a-HDF5-1.10.1.eb create mode 100644 easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.2.9-intel-2017a-Python-2.7.13.eb diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.4.1.1-intel-2017a-HDF5-1.10.1.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.4.1.1-intel-2017a-HDF5-1.10.1.eb new file mode 100644 index 0000000000..713953985c --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.4.1.1-intel-2017a-HDF5-1.10.1.eb @@ -0,0 +1,35 @@ +name = 'netCDF' +version = '4.4.1.1' +hdf5_ver = '1.10.1' +versionsuffix = '-HDF5-%s' % hdf5_ver + +homepage = 'http://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://github.com/Unidata/netcdf-c/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['7f040a0542ed3f6d27f3002b074e509614e18d6c515b2005d1537fec01b24909'] + +dependencies = [ + ('HDF5', hdf5_ver), + ('cURL', '7.54.0'), + ('Szip', '2.1'), +] + +builddependencies = [ + ('CMake', '3.8.2'), + ('Doxygen', '1.8.13'), +] + +# make sure both static and shared libs are built +configopts = [ + "-DBUILD_SHARED_LIBS=OFF ", + "-DBUILD_SHARED_LIBS=ON ", +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.2.9-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.2.9-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..4f52ebe137 --- /dev/null +++ b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.2.9-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,23 @@ +name = 'netcdf4-python' +version = '1.2.9' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://unidata.github.io/netcdf4-python/' +description = """Python/numpy interface to netCDF.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/Unidata/netcdf4-python/archive/'] +sources = ['v%(version)srel.tar.gz'] +checksums = ['bbb6d40d33f5fe8fbf211b5706ff4af9484a91a5ab50d9f6607858bd34c1d10c'] + +patches = ['netcdf4-python-1.1.8-avoid-diskless-test.patch'] + +dependencies = [ + ('Python', '2.7.13'), + ('netCDF', '4.4.1.1', '-HDF5-1.10.1'), + ('cURL', '7.54.0'), +] + +moduleclass = 'data' -- GitLab From 5453a56c6d90a1a4c156518f456915812d0b4b33 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 10 Aug 2017 13:30:14 +0200 Subject: [PATCH 1343/1603] adding easyconfigs: HDF5-1.8.19-intel-2017a.eb --- .../h/HDF5/HDF5-1.8.19-intel-2017a.eb | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.8.19-intel-2017a.eb diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.19-intel-2017a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.19-intel-2017a.eb new file mode 100644 index 0000000000..a3a8e59731 --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.19-intel-2017a.eb @@ -0,0 +1,21 @@ +name = 'HDF5' +version = '1.8.19' + +homepage = 'https://support.hdfgroup.org/HDF5/' +description = """HDF5 is a unique technology suite that makes possible the management of + extremely large and complex data collections.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['a4335849f19fae88c264fd0df046bc321a78c536b2548fc508627a790564dc38'] + +dependencies = [ + ('zlib', '1.2.11'), + ('Szip', '2.1'), +] + +moduleclass = 'data' -- GitLab From 04bd562e08f6a7330a2d959010258bb85a2dd54c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 10 Aug 2017 13:47:57 +0200 Subject: [PATCH 1344/1603] adding easyconfigs: Pysam-0.8.4-intel-2016b-Python-2.7.12.eb --- .../Pysam-0.8.4-intel-2016b-Python-2.7.12.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/p/Pysam/Pysam-0.8.4-intel-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/p/Pysam/Pysam-0.8.4-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/Pysam/Pysam-0.8.4-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..76d42a604f --- /dev/null +++ b/easybuild/easyconfigs/p/Pysam/Pysam-0.8.4-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,37 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# 0.9.1.4: +# Modified by: Adam Huffman +# The Francis Crick Institute + +easyblock = 'PythonPackage' + +name = 'Pysam' +version = '0.8.4' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/pysam-developers/pysam' +description = """Pysam is a python module for reading and manipulating Samfiles. + It's a lightweight wrapper of the samtools C-API. Pysam also includes an interface for tabix.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['https://github.com/pysam-developers/pysam/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['4acbfe4b15b1db2417094ea64836d416a66e368e6c0e3031b597509f21e8c021'] + +dependencies = [ + ('Python', '2.7.12'), + ('ncurses', '6.0'), + ('zlib', '1.2.8'), + ('cURL', '7.52.1'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'bio' -- GitLab From 1d000e9562d0b02e7d8a045ae63870054a6892b9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 10 Aug 2017 17:52:55 +0200 Subject: [PATCH 1345/1603] also fix URLs in PLINK-1.07-x86_64.eb --- easybuild/easyconfigs/p/PLINK/PLINK-1.07-x86_64.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/PLINK/PLINK-1.07-x86_64.eb b/easybuild/easyconfigs/p/PLINK/PLINK-1.07-x86_64.eb index 7f7c8b29a2..f2b5d4628b 100644 --- a/easybuild/easyconfigs/p/PLINK/PLINK-1.07-x86_64.eb +++ b/easybuild/easyconfigs/p/PLINK/PLINK-1.07-x86_64.eb @@ -3,13 +3,13 @@ easyblock = 'PackedBinary' name = 'PLINK' version = '1.07-x86_64' -homepage = 'http://pngu.mgh.harvard.edu/~purcell/plink/' +homepage = 'http://zzz.bwh.harvard.edu/plink/dist' description = 'plink-1.07-src: Whole-genome association analysis toolset' toolchain = {'name': 'dummy', 'version': 'dummy'} sources = ['%(namelower)s-%(version)s.zip'] -source_urls = ['http://pngu.mgh.harvard.edu/~purcell/plink/dist/'] +source_urls = ['http://zzz.bwh.harvard.edu/plink/dist'] checksums = ['fd0bafeda42151b20534e4f97b0d97df'] -- GitLab From 063ff68e3f102c4615441176dcd1edf058882a2b Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Thu, 10 Aug 2017 13:29:44 -0500 Subject: [PATCH 1346/1603] cleanup --- easybuild/easyconfigs/h/htop/htop-2.0.1.eb | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/h/htop/htop-2.0.1.eb b/easybuild/easyconfigs/h/htop/htop-2.0.1.eb index c7e830f3a7..8c6054d0f4 100644 --- a/easybuild/easyconfigs/h/htop/htop-2.0.1.eb +++ b/easybuild/easyconfigs/h/htop/htop-2.0.1.eb @@ -17,9 +17,7 @@ dependencies = [ ('ncurses', '6.0'), ] -prebuildopts = """ - sed -e 's/^LIBS = -lncursesw -lm/LIBS = -lncursesw -lm -ltinfo/' -i.eb Makefile -""" +preconfigopts = 'LIBS="$LIBS -ltinfo"' sanity_check_paths = { 'files': ['bin/htop'], -- GitLab From a37a797d1ed63a7aa476594905721ff09741053f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 10 Aug 2017 22:49:19 +0200 Subject: [PATCH 1347/1603] add additional extensions for R 3.4.0 and Bioconductor 3.5 bundle --- .../R-bundle-Bioconductor-3.5-intel-2017a-R-3.4.0.eb | 2 ++ .../easyconfigs/r/R/R-3.4.0-intel-2017a-X11-20170314.eb | 9 +++++++++ 2 files changed, 11 insertions(+) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.5-intel-2017a-R-3.4.0.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.5-intel-2017a-R-3.4.0.eb index 9125415482..07b8eb5010 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.5-intel-2017a-R-3.4.0.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.5-intel-2017a-R-3.4.0.eb @@ -157,6 +157,8 @@ exts_list = [ ('RcppParallel', '4.3.20', ext_options), ('dada2', '1.4.0', bioconductor_options), ('LEA', '1.8.1', bioconductor_options), + ('scran', '1.4.5', bioconductor_options), + ('scater', '1.4.0', bioconductor_options), ] modextrapaths = {'R_LIBS': ''} diff --git a/easybuild/easyconfigs/r/R/R-3.4.0-intel-2017a-X11-20170314.eb b/easybuild/easyconfigs/r/R/R-3.4.0-intel-2017a-X11-20170314.eb index 10a1470cb3..70f5a7c2e7 100644 --- a/easybuild/easyconfigs/r/R/R-3.4.0-intel-2017a-X11-20170314.eb +++ b/easybuild/easyconfigs/r/R/R-3.4.0-intel-2017a-X11-20170314.eb @@ -535,6 +535,15 @@ exts_list = [ ('sn', '1.5-0', ext_options), ('tclust', '1.2-7', ext_options), ('ranger', '0.8.0', ext_options), + ('hexbin', '1.27.1', ext_options), + ('crosstalk', '1.0.0', ext_options), + ('pryr', '0.1.2', ext_options), + ('moments', '0.14', ext_options), + ('forcats', '0.2.0', ext_options), + ('laeken', '0.4.6', ext_options), + ('VIM', '4.7.0', ext_options), + ('proxy', '0.4-17', ext_options), + ('smoother', '1.1', ext_options), ] moduleclass = 'lang' -- GitLab From 7b7b1cade8d5be8a93f3129e67a2130bef171f15 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 10 Aug 2017 22:51:46 +0200 Subject: [PATCH 1348/1603] adding easyconfigs: SCnorm-0.99.7-intel-2017a-R-3.4.0.eb --- .../SCnorm-0.99.7-intel-2017a-R-3.4.0.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/s/SCnorm/SCnorm-0.99.7-intel-2017a-R-3.4.0.eb diff --git a/easybuild/easyconfigs/s/SCnorm/SCnorm-0.99.7-intel-2017a-R-3.4.0.eb b/easybuild/easyconfigs/s/SCnorm/SCnorm-0.99.7-intel-2017a-R-3.4.0.eb new file mode 100644 index 0000000000..b7ba7c4828 --- /dev/null +++ b/easybuild/easyconfigs/s/SCnorm/SCnorm-0.99.7-intel-2017a-R-3.4.0.eb @@ -0,0 +1,28 @@ +easyblock = 'RPackage' + +name = 'SCnorm' +version = '0.99.7' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://bioconductor.org/packages/SCnorm' +description = "This package implements SCnorm — a method to normalize single-cell RNA-seq data." + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [ + 'http://bioconductor.org/packages/release/bioc/src/contrib/', + 'https://bioconductor.org/packages/devel/bioc/src/contrib/', +] +sources = ['%(name)s_%(version)s.tar.gz'] + +dependencies = [ + ('R', '3.4.0', '-X11-20170314'), + ('R-bundle-Bioconductor', '3.5', versionsuffix), +] + +sanity_check_paths = { + 'files': [], + 'dirs': [name], +} + +moduleclass = 'data' -- GitLab From 8e46bc68bfe866049dd2214cb1c44a8635fc26aa Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 10 Aug 2017 22:53:44 +0200 Subject: [PATCH 1349/1603] adding easyconfigs: destiny-2.5.6-intel-2017a-R-3.4.0.eb --- .../destiny-2.5.6-intel-2017a-R-3.4.0.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/d/destiny/destiny-2.5.6-intel-2017a-R-3.4.0.eb diff --git a/easybuild/easyconfigs/d/destiny/destiny-2.5.6-intel-2017a-R-3.4.0.eb b/easybuild/easyconfigs/d/destiny/destiny-2.5.6-intel-2017a-R-3.4.0.eb new file mode 100644 index 0000000000..6dc1fa57a7 --- /dev/null +++ b/easybuild/easyconfigs/d/destiny/destiny-2.5.6-intel-2017a-R-3.4.0.eb @@ -0,0 +1,28 @@ +easyblock = 'RPackage' + +name = 'destiny' +version = '2.5.6' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://bioconductor.org/packages/destiny' +description = "R packages to create and plot diffusion maps." + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [ + 'http://bioconductor.org/packages/release/bioc/src/contrib/', + 'https://bioconductor.org/packages/devel/bioc/src/contrib/', +] +sources = ['%(name)s_%(version)s.tar.gz'] + +dependencies = [ + ('R', '3.4.0', '-X11-20170314'), + ('R-bundle-Bioconductor', '3.5', versionsuffix), +] + +sanity_check_paths = { + 'files': [], + 'dirs': [name], +} + +moduleclass = 'data' -- GitLab From a38c44f0e2a456b2eb06f29407dc748ba106f658 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 10 Aug 2017 22:54:10 +0200 Subject: [PATCH 1350/1603] adding easyconfigs: plotly-4.7.1-intel-2017a-R-3.4.0.eb --- .../plotly-4.7.1-intel-2017a-R-3.4.0.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/p/plotly/plotly-4.7.1-intel-2017a-R-3.4.0.eb diff --git a/easybuild/easyconfigs/p/plotly/plotly-4.7.1-intel-2017a-R-3.4.0.eb b/easybuild/easyconfigs/p/plotly/plotly-4.7.1-intel-2017a-R-3.4.0.eb new file mode 100644 index 0000000000..c2e0909198 --- /dev/null +++ b/easybuild/easyconfigs/p/plotly/plotly-4.7.1-intel-2017a-R-3.4.0.eb @@ -0,0 +1,38 @@ +easyblock = 'Bundle' + +name = 'plotly' +version = '4.7.1' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://cran.r-project.org/web/packages/plotly' +description = """Easily translate 'ggplot2' graphs to an interactive web-based version and/or + create custom web-based visualizations directly from R.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +dependencies = [('R', '3.4.0', '-X11-20170314')] + +exts_defaultclass = 'RPackage' +exts_list = [ + ('htmlwidgets', '0.9', { + 'source_urls': [ + 'http://cran.r-project.org/src/contrib/Archive/%(name)s', + 'http://cran.r-project.org/src/contrib/', + ], + 'source_tmpl': '%(name)s_%(version)s.tar.gz', + }), + (name, version, { + 'source_urls': [ + 'http://cran.r-project.org/src/contrib/Archive/%(name)s', + 'http://cran.r-project.org/src/contrib/', + ], + 'source_tmpl': '%(name)s_%(version)s.tar.gz', + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': [name], +} + +moduleclass = 'vis' -- GitLab From 568217f792d953a8833fe22941faa8700938b69c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 11 Aug 2017 10:46:06 +0200 Subject: [PATCH 1351/1603] add additional extensions for R 3.4.0 and Bioconductor 3.5 --- .../R-bundle-Bioconductor-3.5-intel-2017a-R-3.4.0.eb | 3 ++- .../easyconfigs/r/R/R-3.4.0-intel-2017a-X11-20170314.eb | 6 ++++++ 2 files changed, 8 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.5-intel-2017a-R-3.4.0.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.5-intel-2017a-R-3.4.0.eb index 07b8eb5010..b8dbe2076f 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.5-intel-2017a-R-3.4.0.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.5-intel-2017a-R-3.4.0.eb @@ -157,8 +157,9 @@ exts_list = [ ('RcppParallel', '4.3.20', ext_options), ('dada2', '1.4.0', bioconductor_options), ('LEA', '1.8.1', bioconductor_options), - ('scran', '1.4.5', bioconductor_options), + ('tximport', '1.4.0', bioconductor_options), ('scater', '1.4.0', bioconductor_options), + ('scran', '1.4.5', bioconductor_options), ] modextrapaths = {'R_LIBS': ''} diff --git a/easybuild/easyconfigs/r/R/R-3.4.0-intel-2017a-X11-20170314.eb b/easybuild/easyconfigs/r/R/R-3.4.0-intel-2017a-X11-20170314.eb index 70f5a7c2e7..920853bd95 100644 --- a/easybuild/easyconfigs/r/R/R-3.4.0-intel-2017a-X11-20170314.eb +++ b/easybuild/easyconfigs/r/R/R-3.4.0-intel-2017a-X11-20170314.eb @@ -544,6 +544,12 @@ exts_list = [ ('VIM', '4.7.0', ext_options), ('proxy', '0.4-17', ext_options), ('smoother', '1.1', ext_options), + ('dynamicTreeCut', '1.63-1', ext_options), + ('DT', '0.2', ext_options), + ('beeswarm', '0.2.3', ext_options), + ('vipor', '0.4.5', ext_options), + ('ggbeeswarm', '0.6.0', ext_options), + ('shinydashboard', '0.6.1', ext_options), ] moduleclass = 'lang' -- GitLab From 8c5dcfc0c83ac997c9f551de2363e74b68fae460 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 11 Aug 2017 11:13:20 +0200 Subject: [PATCH 1352/1603] fix moduleclass for SCnorm --- .../easyconfigs/s/SCnorm/SCnorm-0.99.7-intel-2017a-R-3.4.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SCnorm/SCnorm-0.99.7-intel-2017a-R-3.4.0.eb b/easybuild/easyconfigs/s/SCnorm/SCnorm-0.99.7-intel-2017a-R-3.4.0.eb index b7ba7c4828..4f521d3b57 100644 --- a/easybuild/easyconfigs/s/SCnorm/SCnorm-0.99.7-intel-2017a-R-3.4.0.eb +++ b/easybuild/easyconfigs/s/SCnorm/SCnorm-0.99.7-intel-2017a-R-3.4.0.eb @@ -25,4 +25,4 @@ sanity_check_paths = { 'dirs': [name], } -moduleclass = 'data' +moduleclass = 'bio' -- GitLab From f24db278a0010dc402c794bd3579b0ee166c8a0b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 11 Aug 2017 11:19:03 +0200 Subject: [PATCH 1353/1603] add SHA256 checksum for SCnorm --- .../easyconfigs/s/SCnorm/SCnorm-0.99.7-intel-2017a-R-3.4.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/s/SCnorm/SCnorm-0.99.7-intel-2017a-R-3.4.0.eb b/easybuild/easyconfigs/s/SCnorm/SCnorm-0.99.7-intel-2017a-R-3.4.0.eb index 4f521d3b57..9f1e6bee57 100644 --- a/easybuild/easyconfigs/s/SCnorm/SCnorm-0.99.7-intel-2017a-R-3.4.0.eb +++ b/easybuild/easyconfigs/s/SCnorm/SCnorm-0.99.7-intel-2017a-R-3.4.0.eb @@ -14,6 +14,7 @@ source_urls = [ 'https://bioconductor.org/packages/devel/bioc/src/contrib/', ] sources = ['%(name)s_%(version)s.tar.gz'] +checksums = ['f7f6b63aade398ab8f7860ca895914c7bd8161bf2387f2727fe44a897124ae02'] dependencies = [ ('R', '3.4.0', '-X11-20170314'), -- GitLab From a4bf421e4dd983aedbc04c259a2e1c252312e741 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 11 Aug 2017 11:19:47 +0200 Subject: [PATCH 1354/1603] add SHA256 checksum for destiny --- .../easyconfigs/d/destiny/destiny-2.5.6-intel-2017a-R-3.4.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/d/destiny/destiny-2.5.6-intel-2017a-R-3.4.0.eb b/easybuild/easyconfigs/d/destiny/destiny-2.5.6-intel-2017a-R-3.4.0.eb index 6dc1fa57a7..9e4e09b90c 100644 --- a/easybuild/easyconfigs/d/destiny/destiny-2.5.6-intel-2017a-R-3.4.0.eb +++ b/easybuild/easyconfigs/d/destiny/destiny-2.5.6-intel-2017a-R-3.4.0.eb @@ -14,6 +14,7 @@ source_urls = [ 'https://bioconductor.org/packages/devel/bioc/src/contrib/', ] sources = ['%(name)s_%(version)s.tar.gz'] +checksums = ['134210f9b8d6d58309a1f886065175c723e2612b4be819beb9e9fe5707b0f2ac'] dependencies = [ ('R', '3.4.0', '-X11-20170314'), -- GitLab From 30fc3680fb66269fbf1955204e82c8ea89161e75 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 11 Aug 2017 11:21:33 +0200 Subject: [PATCH 1355/1603] add SHA256 checksums for plotly --- .../easyconfigs/p/plotly/plotly-4.7.1-intel-2017a-R-3.4.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/p/plotly/plotly-4.7.1-intel-2017a-R-3.4.0.eb b/easybuild/easyconfigs/p/plotly/plotly-4.7.1-intel-2017a-R-3.4.0.eb index c2e0909198..ba3ed319ce 100644 --- a/easybuild/easyconfigs/p/plotly/plotly-4.7.1-intel-2017a-R-3.4.0.eb +++ b/easybuild/easyconfigs/p/plotly/plotly-4.7.1-intel-2017a-R-3.4.0.eb @@ -20,6 +20,7 @@ exts_list = [ 'http://cran.r-project.org/src/contrib/', ], 'source_tmpl': '%(name)s_%(version)s.tar.gz', + 'checksums': ['1154b541ccd868e41d3cf0d7f188f7275ec99f61fe2c7de21c8a05edb19b985e'], }), (name, version, { 'source_urls': [ @@ -27,6 +28,7 @@ exts_list = [ 'http://cran.r-project.org/src/contrib/', ], 'source_tmpl': '%(name)s_%(version)s.tar.gz', + 'checksums': ['7cd4b040f9bfd9356a8a2aba59ccf318cae6b5d94ded7463e2e823c10fa74972'], }), ] -- GitLab From baa269209e82059dceeafea96fcd07a260ad2681 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 11 Aug 2017 12:25:41 +0200 Subject: [PATCH 1356/1603] adding easyconfigs: Spark-2.2.0-Hadoop-2.6.eb --- .../s/Spark/Spark-2.2.0-Hadoop-2.6.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/s/Spark/Spark-2.2.0-Hadoop-2.6.eb diff --git a/easybuild/easyconfigs/s/Spark/Spark-2.2.0-Hadoop-2.6.eb b/easybuild/easyconfigs/s/Spark/Spark-2.2.0-Hadoop-2.6.eb new file mode 100644 index 0000000000..df2b02e0e1 --- /dev/null +++ b/easybuild/easyconfigs/s/Spark/Spark-2.2.0-Hadoop-2.6.eb @@ -0,0 +1,29 @@ +easyblock = 'Tarball' + +name = 'Spark' +version = '2.2.0' +versionsuffix = '-Hadoop-2.6' + +homepage = 'http://spark.apache.org' +description = """Spark is Hadoop MapReduce done in memory""" + +toolchain = {'name': 'dummy', 'version': ''} + +sources = ['%(namelower)s-%(version)s-bin-hadoop2.6.tgz'] +source_urls = [ + 'http://apache.belnet.be/%(namelower)s/%(namelower)s-%(version)s/', + 'http://www.eu.apache.org/dist/%(namelower)s/%(namelower)s-%(version)s/', + 'http://www.us.apache.org/dist/%(namelower)s/%(namelower)s-%(version)s/', +] +checksums = ['86f33f6f4fe545cb848600004144f09b6e8413af47ce02c1203c3ecda075288d'] + +dependencies = [('Java', '1.8.0_144')] + +sanity_check_paths = { + 'files': ['bin/spark-shell'], + 'dirs': ['python'] +} + +modextrapaths = {'PYTHONPATH': 'python'} + +moduleclass = 'devel' -- GitLab From 209ff80de20a266bbd365799cba52394f82c31dd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 11 Aug 2017 12:27:31 +0200 Subject: [PATCH 1357/1603] adding easyconfigs: CMake-3.9.1.eb, CMake-3.9.1-GCCcore-6.4.0.eb --- .../c/CMake/CMake-3.9.1-GCCcore-6.4.0.eb | 41 +++++++++++++++++++ easybuild/easyconfigs/c/CMake/CMake-3.9.1.eb | 29 +++++++++++++ 2 files changed, 70 insertions(+) create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.9.1-GCCcore-6.4.0.eb create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.9.1.eb diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.9.1-GCCcore-6.4.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.9.1-GCCcore-6.4.0.eb new file mode 100644 index 0000000000..3fbbcb5eaa --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.9.1-GCCcore-6.4.0.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.9.1' + +homepage = 'http://www.cmake.org' + +description = """ + CMake, the cross-platform, open-source build system. CMake is a family of + tools designed to build, test and package software. +""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['d768ee83d217f91bb597b3ca2ac663da7a8603c97e1f1a5184bc01e0ad2b12bb'] + +configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' + +builddependencies = [ + ('binutils', '2.28'), +] + +dependencies = [ + ('ncurses', '6.0'), + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.1.0c'), +] + +osdependencies = [ + ('openssl-devel', 'libssl-dev', 'libopenssl-devel'), +] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.9.1.eb b/easybuild/easyconfigs/c/CMake/CMake-3.9.1.eb new file mode 100644 index 0000000000..38fdb83b5d --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.9.1.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.9.1' + +homepage = 'http://www.cmake.org' +description = """CMake, the cross-platform, open-source build system. + CMake is a family of tools designed to build, test and package software.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['d768ee83d217f91bb597b3ca2ac663da7a8603c97e1f1a5184bc01e0ad2b12bb'] + +dependencies = [('ncurses', '6.0')] + +configopts = '-- -DCMAKE_USE_OPENSSL=1' + +# Use OS dependencies in order to ensure that CMake can build software that +# depends on them +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel'), 'ncurses-devel'] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From 67baf477eb6391664761b4ef2c3ebe212d016dd1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 11 Aug 2017 12:28:38 +0200 Subject: [PATCH 1358/1603] adding easyconfigs: Maven-3.5.0.eb --- easybuild/easyconfigs/m/Maven/Maven-3.5.0.eb | 23 ++++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/m/Maven/Maven-3.5.0.eb diff --git a/easybuild/easyconfigs/m/Maven/Maven-3.5.0.eb b/easybuild/easyconfigs/m/Maven/Maven-3.5.0.eb new file mode 100644 index 0000000000..cae59a3997 --- /dev/null +++ b/easybuild/easyconfigs/m/Maven/Maven-3.5.0.eb @@ -0,0 +1,23 @@ +easyblock = 'PackedBinary' + +name = 'Maven' +version = '3.5.0' + +homepage = 'http://maven.apache.org/index.html' +description = """Binary maven install, Apache Maven is a software project management and comprehension tool. Based on +the concept of a project object model (POM), Maven can manage a project's build, reporting and documentation from a +central piece of information. +""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['apache-maven-%(version)s-bin.tar.gz'] +source_urls = ['http://apache.org/dist/maven/maven-%(version_major)s/%(version)s/binaries/'] +checksums = ['beb91419245395bd69a4a6edad5ca3ec1a8b64e41457672dc687c173a495f034'] + +sanity_check_paths = { + 'files': ['bin/mvn'], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From ce235fddf743baf427ae5597f72375f0baa7fd6c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 11 Aug 2017 12:33:01 +0200 Subject: [PATCH 1359/1603] remove ncurses dep in dummy easyconfig for CMake 3.9.1 --- easybuild/easyconfigs/c/CMake/CMake-3.9.1.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.9.1.eb b/easybuild/easyconfigs/c/CMake/CMake-3.9.1.eb index 38fdb83b5d..deece4acb7 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.9.1.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.9.1.eb @@ -13,8 +13,6 @@ source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] checksums = ['d768ee83d217f91bb597b3ca2ac663da7a8603c97e1f1a5184bc01e0ad2b12bb'] -dependencies = [('ncurses', '6.0')] - configopts = '-- -DCMAKE_USE_OPENSSL=1' # Use OS dependencies in order to ensure that CMake can build software that -- GitLab From f76ab46a110c33923437d6b292d8671552b27051 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 11 Aug 2017 13:34:44 +0200 Subject: [PATCH 1360/1603] add Java version to versionsuffix for Spark 2.2.0 --- ...0-Hadoop-2.6.eb => Spark-2.2.0-Hadoop-2.6-Java-1.8.0_144.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/s/Spark/{Spark-2.2.0-Hadoop-2.6.eb => Spark-2.2.0-Hadoop-2.6-Java-1.8.0_144.eb} (94%) diff --git a/easybuild/easyconfigs/s/Spark/Spark-2.2.0-Hadoop-2.6.eb b/easybuild/easyconfigs/s/Spark/Spark-2.2.0-Hadoop-2.6-Java-1.8.0_144.eb similarity index 94% rename from easybuild/easyconfigs/s/Spark/Spark-2.2.0-Hadoop-2.6.eb rename to easybuild/easyconfigs/s/Spark/Spark-2.2.0-Hadoop-2.6-Java-1.8.0_144.eb index df2b02e0e1..8b3d26f8e7 100644 --- a/easybuild/easyconfigs/s/Spark/Spark-2.2.0-Hadoop-2.6.eb +++ b/easybuild/easyconfigs/s/Spark/Spark-2.2.0-Hadoop-2.6-Java-1.8.0_144.eb @@ -2,7 +2,7 @@ easyblock = 'Tarball' name = 'Spark' version = '2.2.0' -versionsuffix = '-Hadoop-2.6' +versionsuffix = '-Hadoop-2.6-Java-%(javaver)s' homepage = 'http://spark.apache.org' description = """Spark is Hadoop MapReduce done in memory""" -- GitLab From eb9e418eaaaa0cc6345d782158bcc71a22af1735 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 11 Aug 2017 13:35:52 +0200 Subject: [PATCH 1361/1603] change moduleclass to bio for destiny --- .../easyconfigs/d/destiny/destiny-2.5.6-intel-2017a-R-3.4.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/destiny/destiny-2.5.6-intel-2017a-R-3.4.0.eb b/easybuild/easyconfigs/d/destiny/destiny-2.5.6-intel-2017a-R-3.4.0.eb index 9e4e09b90c..7aaefec7f2 100644 --- a/easybuild/easyconfigs/d/destiny/destiny-2.5.6-intel-2017a-R-3.4.0.eb +++ b/easybuild/easyconfigs/d/destiny/destiny-2.5.6-intel-2017a-R-3.4.0.eb @@ -26,4 +26,4 @@ sanity_check_paths = { 'dirs': [name], } -moduleclass = 'data' +moduleclass = 'bio' -- GitLab From 7f20ae1797f55f023a4941774458b1c124de61a9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 11 Aug 2017 15:58:35 +0200 Subject: [PATCH 1362/1603] add checksum in easyconfig for HPL 2.2 w/ intel/2017b --- easybuild/easyconfigs/h/HPL/HPL-2.2-intel-2017b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.2-intel-2017b.eb b/easybuild/easyconfigs/h/HPL/HPL-2.2-intel-2017b.eb index 32a513858c..6fb2407196 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.2-intel-2017b.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.2-intel-2017b.eb @@ -11,6 +11,7 @@ toolchainopts = {'usempi': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] +checksums = ['ac7534163a09e21a5fa763e4e16dfc119bc84043f6e6a807aba666518f8df440'] # fix Make dependencies, so parallel build also works patches = ['HPL_parallel-make.patch'] -- GitLab From dee655242e772a456f7d7d1eb926a2b76d0cbeb9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 11 Aug 2017 15:58:52 +0200 Subject: [PATCH 1363/1603] fix URL for EasyBuild website (hpcugent -> easybuilders) --- easybuild/easyconfigs/i/icc/icc-2017.4.196-GCC-6.4.0-2.28.eb | 2 +- .../i/iccifort/iccifort-2017.4.196-GCC-6.4.0-2.28.eb | 2 +- .../easyconfigs/i/ifort/ifort-2017.4.196-GCC-6.4.0-2.28.eb | 2 +- easybuild/easyconfigs/i/iimpi/iimpi-2017b.eb | 2 +- easybuild/easyconfigs/i/imkl/imkl-2017.3.196-iimpi-2017b.eb | 2 +- .../impi/impi-2017.3.196-iccifort-2017.4.196-GCC-6.4.0-2.28.eb | 2 +- 6 files changed, 6 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/i/icc/icc-2017.4.196-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/i/icc/icc-2017.4.196-GCC-6.4.0-2.28.eb index 05acc34697..8bae3f29f2 100644 --- a/easybuild/easyconfigs/i/icc/icc-2017.4.196-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/i/icc/icc-2017.4.196-GCC-6.4.0-2.28.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild name = 'icc' version = '2017.4.196' diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2017.4.196-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2017.4.196-GCC-6.4.0-2.28.eb index a3c7d6585e..35f4cd4d02 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2017.4.196-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2017.4.196-GCC-6.4.0-2.28.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild easyblock = 'Toolchain' name = 'iccifort' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2017.4.196-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/i/ifort/ifort-2017.4.196-GCC-6.4.0-2.28.eb index b3b151820c..d3692d8024 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2017.4.196-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2017.4.196-GCC-6.4.0-2.28.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild name = 'ifort' version = '2017.4.196' diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-2017b.eb b/easybuild/easyconfigs/i/iimpi/iimpi-2017b.eb index 53c7c29886..76e9e5a6d7 100644 --- a/easybuild/easyconfigs/i/iimpi/iimpi-2017b.eb +++ b/easybuild/easyconfigs/i/iimpi/iimpi-2017b.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild easyblock = "Toolchain" name = 'iimpi' diff --git a/easybuild/easyconfigs/i/imkl/imkl-2017.3.196-iimpi-2017b.eb b/easybuild/easyconfigs/i/imkl/imkl-2017.3.196-iimpi-2017b.eb index 4d773b67ad..092481da75 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2017.3.196-iimpi-2017b.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2017.3.196-iimpi-2017b.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild name = 'imkl' version = '2017.3.196' diff --git a/easybuild/easyconfigs/i/impi/impi-2017.3.196-iccifort-2017.4.196-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/i/impi/impi-2017.3.196-iccifort-2017.4.196-GCC-6.4.0-2.28.eb index 2e46f8a579..827bd87f06 100644 --- a/easybuild/easyconfigs/i/impi/impi-2017.3.196-iccifort-2017.4.196-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/i/impi/impi-2017.3.196-iccifort-2017.4.196-GCC-6.4.0-2.28.eb @@ -1,4 +1,4 @@ -# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild name = 'impi' version = '2017.3.196' -- GitLab From efad9cdc6952a22eeed650e8f0e3767217c77abb Mon Sep 17 00:00:00 2001 From: Joachim Hein Date: Fri, 11 Aug 2017 18:06:08 +0200 Subject: [PATCH 1364/1603] matplotlib for python 2.7.1 in foss 2017a --- ...tplotlib-2.0.2-foss-2017a-Python-2.7.13.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.2-foss-2017a-Python-2.7.13.eb diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.2-foss-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.2-foss-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..1af6c380d6 --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.2-foss-2017a-Python-2.7.13.eb @@ -0,0 +1,44 @@ +easyblock = 'Bundle' + +name = 'matplotlib' +version = '2.0.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://matplotlib.org' +description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of + hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python + and ipython shell, web application servers, and six graphical user interface toolkits.""" + +toolchain = {'name': 'foss', 'version': '2017a'} + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' + +dependencies = [ + ('Python', '2.7.13'), + ('freetype', '2.7.1'), + ('libpng', '1.6.29'), +] + +exts_list = [ + ('Cycler', '0.10.0', { + 'modulename': 'cycler', + 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], + 'source_tmpl': 'cycler-%(version)s.tar.gz', + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], + }), +] + +# specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module +full_sanity_check = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +moduleclass = 'vis' -- GitLab From 1e3e3df517b23c481c5476da00783132f5133c02 Mon Sep 17 00:00:00 2001 From: Joachim Hein Date: Fri, 11 Aug 2017 18:30:19 +0200 Subject: [PATCH 1365/1603] checksum MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Added checksum as of boegel’s request (cut-n-paste from his email) --- .../m/matplotlib/matplotlib-2.0.2-foss-2017a-Python-2.7.13.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.2-foss-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.2-foss-2017a-Python-2.7.13.eb index 1af6c380d6..aa55e74d47 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.2-foss-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.2-foss-2017a-Python-2.7.13.eb @@ -25,9 +25,11 @@ exts_list = [ 'modulename': 'cycler', 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], 'source_tmpl': 'cycler-%(version)s.tar.gz', + 'checksums': ['cd7b2d1018258d7247a71425e9f26463dfb444d411c39569972f4ce586b0c9d8'], }), (name, version, { 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], + 'checksums': ['0ffbc44faa34a8b1704bc108c451ecf87988f900ef7ce757b8e2e84383121ff1'], }), ] -- GitLab From 4adbd650b01e08315db0e2adb2e3c1a077c4c4bf Mon Sep 17 00:00:00 2001 From: Joachim Hein Date: Fri, 11 Aug 2017 18:44:58 +0200 Subject: [PATCH 1366/1603] libpng version conflict resolution Working on different png versions in png and freetype dependency in matplotlib --- .../matplotlib/matplotlib-2.0.2-foss-2017a-Python-2.7.13.eb | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.2-foss-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.2-foss-2017a-Python-2.7.13.eb index aa55e74d47..bc892ebed0 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.2-foss-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.2-foss-2017a-Python-2.7.13.eb @@ -4,6 +4,8 @@ name = 'matplotlib' version = '2.0.2' versionsuffix = '-Python-%(pyver)s' +libpng_ver = '1.6.29' + homepage = 'http://matplotlib.org' description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python @@ -16,8 +18,8 @@ exts_defaultclass = 'PythonPackage' dependencies = [ ('Python', '2.7.13'), - ('freetype', '2.7.1'), - ('libpng', '1.6.29'), + ('libpng', libpng_ver), + ('freetype', '2.7.1', '-libpng'%s' % libpng_ver), ] exts_list = [ -- GitLab From d6a712a4961e52b2580b1da6b4b413ce63ea8d39 Mon Sep 17 00:00:00 2001 From: Joachim Hein Date: Fri, 11 Aug 2017 18:49:18 +0200 Subject: [PATCH 1367/1603] typo corrected --- .../m/matplotlib/matplotlib-2.0.2-foss-2017a-Python-2.7.13.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.2-foss-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.2-foss-2017a-Python-2.7.13.eb index bc892ebed0..11e7af5189 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.2-foss-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.2-foss-2017a-Python-2.7.13.eb @@ -19,7 +19,7 @@ exts_defaultclass = 'PythonPackage' dependencies = [ ('Python', '2.7.13'), ('libpng', libpng_ver), - ('freetype', '2.7.1', '-libpng'%s' % libpng_ver), + ('freetype', '2.7.1', '-libpng' % libpng_ver), ] exts_list = [ -- GitLab From 56deaf7a03420ed541d937aa1afdc4b9b1014ed3 Mon Sep 17 00:00:00 2001 From: Joachim Hein Date: Fri, 11 Aug 2017 18:53:02 +0200 Subject: [PATCH 1368/1603] another typo fix --- .../m/matplotlib/matplotlib-2.0.2-foss-2017a-Python-2.7.13.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.2-foss-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.2-foss-2017a-Python-2.7.13.eb index 11e7af5189..b374975f21 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.2-foss-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.2-foss-2017a-Python-2.7.13.eb @@ -19,7 +19,7 @@ exts_defaultclass = 'PythonPackage' dependencies = [ ('Python', '2.7.13'), ('libpng', libpng_ver), - ('freetype', '2.7.1', '-libpng' % libpng_ver), + ('freetype', '2.7.1', '-libpng-%s' % libpng_ver), ] exts_list = [ -- GitLab From e9a7d31877e88bfee688d3fd8bb0a23a2fe920c8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 12 Aug 2017 10:59:20 +0200 Subject: [PATCH 1369/1603] consistently add SHA256 checksums for easyconfigs added in PR #4650 --- .../easyconfigs/a/Autoconf/Autoconf-2.68-foss-2016b.eb | 1 + .../easyconfigs/a/Automake/Automake-1.11.3-foss-2016b.eb | 1 + easybuild/easyconfigs/b/BAMM/BAMM-2.5.0-foss-2016b.eb | 1 - easybuild/easyconfigs/b/BWA/BWA-0.7.12-foss-2016b.eb | 1 + easybuild/easyconfigs/b/BWA/BWA-0.7.15-foss-2016b.eb | 1 - .../b/BamM/BamM-1.7.3-foss-2016b-Python-2.7.12.eb | 5 +---- easybuild/easyconfigs/b/Blosc/Blosc-1.12.1-foss-2016b.eb | 2 +- .../c/Cython/Cython-0.25.2-foss-2016b-Python-2.7.12.eb | 1 + .../g/GroopM/GroopM-0.3.4-foss-2016b-Python-2.7.12.eb | 1 + easybuild/easyconfigs/l/LZO/LZO-2.10-foss-2016b.eb | 1 - .../p/PIL/PIL-1.1.7-foss-2016b-Python-2.7.12.eb | 7 ++++--- .../p/PyTables/PyTables-3.3.0-foss-2016b-Python-2.7.12.eb | 5 ++++- .../p/Pysam/Pysam-0.10.0-foss-2016b-Python-2.7.12.eb | 2 ++ .../easyconfigs/s/SAMtools/SAMtools-1.2-foss-2016b.eb | 5 ++++- .../easyconfigs/s/SAMtools/SAMtools-1.3.1-foss-2016b.eb | 5 ++++- .../easyconfigs/t/texinfo/texinfo-6.4-GCCcore-5.4.0.eb | 5 +++-- 16 files changed, 28 insertions(+), 16 deletions(-) diff --git a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.68-foss-2016b.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.68-foss-2016b.eb index 5e317e5ad2..4eb88ea428 100644 --- a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.68-foss-2016b.eb +++ b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.68-foss-2016b.eb @@ -25,6 +25,7 @@ toolchain = {'name': 'foss', 'version': '2016b'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] +checksums = ['eff70a2916f2e2b3ed7fe8a2d7e63d72cf3a23684b56456b319c3ebce0705d99'] dependencies = [('M4', '1.4.17')] diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.11.3-foss-2016b.eb b/easybuild/easyconfigs/a/Automake/Automake-1.11.3-foss-2016b.eb index ce98c370d2..14c71f2afe 100644 --- a/easybuild/easyconfigs/a/Automake/Automake-1.11.3-foss-2016b.eb +++ b/easybuild/easyconfigs/a/Automake/Automake-1.11.3-foss-2016b.eb @@ -25,6 +25,7 @@ toolchain = {'name': 'foss', 'version': '2016b'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] +checksums = ['921b5188057e57bdd9c0ba06e21d0b0ea7dafa61a9bd08a2b041215bcff12f55'] dependencies = [('Autoconf', '2.68')] diff --git a/easybuild/easyconfigs/b/BAMM/BAMM-2.5.0-foss-2016b.eb b/easybuild/easyconfigs/b/BAMM/BAMM-2.5.0-foss-2016b.eb index 3dedc086be..7594f00931 100644 --- a/easybuild/easyconfigs/b/BAMM/BAMM-2.5.0-foss-2016b.eb +++ b/easybuild/easyconfigs/b/BAMM/BAMM-2.5.0-foss-2016b.eb @@ -24,7 +24,6 @@ toolchainopts = {'usempi': True} source_urls = ['https://github.com/macroevolution/bamm/archive'] sources = ['v%(version)s.tar.gz'] - checksums = ['526eef85ef011780ee21fe65cbc10ecc62efe54044102ae40bdef49c2985b4f4'] builddependencies = [ diff --git a/easybuild/easyconfigs/b/BWA/BWA-0.7.12-foss-2016b.eb b/easybuild/easyconfigs/b/BWA/BWA-0.7.12-foss-2016b.eb index e4305c6932..b0a3f2b64e 100644 --- a/easybuild/easyconfigs/b/BWA/BWA-0.7.12-foss-2016b.eb +++ b/easybuild/easyconfigs/b/BWA/BWA-0.7.12-foss-2016b.eb @@ -31,5 +31,6 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = ['https://github.com/lh3/%(name)s/archive/'] sources = ['%(version)s.tar.gz'] +checksums = ['285f55b7fa1f9e873eda9a9b06752378a799ecdecbc886bbd9ba238045bf62e0'] moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BWA/BWA-0.7.15-foss-2016b.eb b/easybuild/easyconfigs/b/BWA/BWA-0.7.15-foss-2016b.eb index 6f791c6734..0b550e42bf 100644 --- a/easybuild/easyconfigs/b/BWA/BWA-0.7.15-foss-2016b.eb +++ b/easybuild/easyconfigs/b/BWA/BWA-0.7.15-foss-2016b.eb @@ -22,7 +22,6 @@ toolchainopts = {'optarch': True, 'pic': True} sources = [SOURCELOWER_TAR_BZ2] source_urls = [('http://sourceforge.net/projects/bio-bwa/files/', 'download')] - checksums = ['2f56afefa49acc9bf45f12edb58e412565086cc20be098b8bf15ec07de8c0515'] moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BamM/BamM-1.7.3-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/b/BamM/BamM-1.7.3-foss-2016b-Python-2.7.12.eb index f16e116a9d..8ce237eb4a 100644 --- a/easybuild/easyconfigs/b/BamM/BamM-1.7.3-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/b/BamM/BamM-1.7.3-foss-2016b-Python-2.7.12.eb @@ -23,10 +23,7 @@ toolchainopts = {'usempi': True} source_urls = ['https://github.com/Ecogenomics/BamM/archive'] sources = ['%(version)s.tar.gz'] - -checksums = [ - '1a30a5014aa64aea23f12b82c8e474044af126c9e6ddb575530ab14b6ef765b8', -] +checksums = ['1a30a5014aa64aea23f12b82c8e474044af126c9e6ddb575530ab14b6ef765b8'] builddependencies = [ ('Automake', '1.11.3'), diff --git a/easybuild/easyconfigs/b/Blosc/Blosc-1.12.1-foss-2016b.eb b/easybuild/easyconfigs/b/Blosc/Blosc-1.12.1-foss-2016b.eb index 50a94f1293..1e6167de54 100644 --- a/easybuild/easyconfigs/b/Blosc/Blosc-1.12.1-foss-2016b.eb +++ b/easybuild/easyconfigs/b/Blosc/Blosc-1.12.1-foss-2016b.eb @@ -21,8 +21,8 @@ toolchain = {'name': 'foss', 'version': '2016b'} source_urls = ['https://github.com/Blosc/c-blosc/archive/'] sources = ['v%(version)s.tar.gz'] - checksums = ['e04535e816bb942bedc9a0ba209944d1eb34e26e2d9cca37f114e8ee292cb3c8'] + builddependencies = [('CMake', '3.7.2')] sanity_check_paths = { diff --git a/easybuild/easyconfigs/c/Cython/Cython-0.25.2-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/c/Cython/Cython-0.25.2-foss-2016b-Python-2.7.12.eb index a99c8efcb6..9257f52f81 100644 --- a/easybuild/easyconfigs/c/Cython/Cython-0.25.2-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/c/Cython/Cython-0.25.2-foss-2016b-Python-2.7.12.eb @@ -24,6 +24,7 @@ toolchain = {'name': 'foss', 'version': '2016b'} source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] +checksums = ['f141d1f9c27a07b5a93f7dc5339472067e2d7140d1c5a9e20112a5665ca60306'] dependencies = [('Python', '2.7.12')] diff --git a/easybuild/easyconfigs/g/GroopM/GroopM-0.3.4-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/g/GroopM/GroopM-0.3.4-foss-2016b-Python-2.7.12.eb index 12f6cbd8f8..03b1e223bf 100644 --- a/easybuild/easyconfigs/g/GroopM/GroopM-0.3.4-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/g/GroopM/GroopM-0.3.4-foss-2016b-Python-2.7.12.eb @@ -25,6 +25,7 @@ toolchain = {'name': 'foss', 'version': '2016b'} source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] +checksums = ['48bdaeb9010e7d81785697a55edc394ef36c2646b310d625a24bec740f1b6080'] dependencies = [ ('Python', '2.7.12'), diff --git a/easybuild/easyconfigs/l/LZO/LZO-2.10-foss-2016b.eb b/easybuild/easyconfigs/l/LZO/LZO-2.10-foss-2016b.eb index 1490555ba3..4343f1f671 100644 --- a/easybuild/easyconfigs/l/LZO/LZO-2.10-foss-2016b.eb +++ b/easybuild/easyconfigs/l/LZO/LZO-2.10-foss-2016b.eb @@ -20,7 +20,6 @@ description = "Portable lossless data compression library" sources = [SOURCELOWER_TAR_GZ] source_urls = [homepage + 'download/'] - checksums = ['c0f892943208266f9b6543b3ae308fab6284c5c90e627931446fb49b4221a072'] toolchain = {'name': 'foss', 'version': '2016b'} diff --git a/easybuild/easyconfigs/p/PIL/PIL-1.1.7-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/PIL/PIL-1.1.7-foss-2016b-Python-2.7.12.eb index e3972be37c..d183ed8acb 100644 --- a/easybuild/easyconfigs/p/PIL/PIL-1.1.7-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/p/PIL/PIL-1.1.7-foss-2016b-Python-2.7.12.eb @@ -23,10 +23,11 @@ toolchain = {'name': 'foss', 'version': '2016b'} source_urls = ['http://effbot.org/downloads/'] sources = ['Imaging-%(version)s.tar.gz'] - -checksums = ['895bc7c2498c8e1f9b99938f1a40dc86b3f149741f105cf7c7bd2e0725405211'] - patches = ['PIL-%(version)s-find-deps.patch'] +checksums = [ + '895bc7c2498c8e1f9b99938f1a40dc86b3f149741f105cf7c7bd2e0725405211', # Imaging-1.1.7.tar.gz + '4a37bc66b7683e9eab2b762d6ee58b203e1ba34724782cbd53adbae77905899e', # PIL-1.1.7-find-deps.patch +] dependencies = [ ('zlib', '1.2.8'), diff --git a/easybuild/easyconfigs/p/PyTables/PyTables-3.3.0-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/PyTables/PyTables-3.3.0-foss-2016b-Python-2.7.12.eb index 1b47f5f820..39245661ae 100644 --- a/easybuild/easyconfigs/p/PyTables/PyTables-3.3.0-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/p/PyTables/PyTables-3.3.0-foss-2016b-Python-2.7.12.eb @@ -29,8 +29,11 @@ toolchainopts = {'openmp': True, 'usempi': True} source_urls = ['https://github.com/PyTables/PyTables/archive/'] sources = ['v%(version)s.tar.gz'] - patches = ['pyTables-3.2.2-fix-libs.patch'] +checksums = [ + 'dceb15fef556a2775121bcc695561df4ff0e09248e0ce3a2d58f5244a9f61421', # v3.3.0.tar.gz + '3a5695613215dca13a2e8e771762f1d541390884e438bc73263120d8bf377f43', # pyTables-3.2.2-fix-libs.patch +] dependencies = [ ('Python', '2.7.12'), diff --git a/easybuild/easyconfigs/p/Pysam/Pysam-0.10.0-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/Pysam/Pysam-0.10.0-foss-2016b-Python-2.7.12.eb index b341dbe1c1..d8682d26e1 100644 --- a/easybuild/easyconfigs/p/Pysam/Pysam-0.10.0-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/p/Pysam/Pysam-0.10.0-foss-2016b-Python-2.7.12.eb @@ -32,10 +32,12 @@ exts_filter = ("python -c 'import %(ext_name)s'", '') exts_list = [ ('Cython', '0.25.2', { 'source_urls': ['https://pypi.python.org/packages/source/c/cython/'], + 'checksums': ['f141d1f9c27a07b5a93f7dc5339472067e2d7140d1c5a9e20112a5665ca60306'], }), ('pysam', version, { 'source_tmpl': 'v%(version)s.tar.gz', 'source_urls': ['https://github.com/pysam-developers/pysam/archive/'], + 'checksums': ['c83b88df7e47fe2ac24996fb6ec5a304cd1301ee4688f3f94443e4a742b2bbd6'], }), ] diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.2-foss-2016b.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.2-foss-2016b.eb index 56960c20c6..af14010ad9 100644 --- a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.2-foss-2016b.eb +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.2-foss-2016b.eb @@ -21,8 +21,11 @@ toolchainopts = {'optarch': True, 'pic': True} sources = [SOURCELOWER_TAR_BZ2] source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s'] - patches = ['SAMtools-1.1_Makefile.patch'] +checksums = [ + '420e7a4a107fe37619b9d300b6379452eb8eb04a4a9b65c3ec69de82ccc26daa', # samtools-1.2.tar.bz2 + 'd0d6796db7edb9ceb0c410001c3b00b521d97bcf908650c8f7528a4438f765e1', # SAMtools-1.1_Makefile.patch +] dependencies = [ ('ncurses', '6.0'), diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1-foss-2016b.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1-foss-2016b.eb index b99bb23bc1..4e46414370 100644 --- a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1-foss-2016b.eb +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1-foss-2016b.eb @@ -22,9 +22,12 @@ toolchainopts = {'pic': True} source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s'] sources = [SOURCELOWER_TAR_BZ2] - # Patch Makefile to link against zlib provided by EB patches = ['SAMtools-%(version)s_Makefile.patch'] +checksums = [ + '6c3d74355e9cf2d9b2e1460273285d154107659efa36a155704b1e4358b7d67e', # samtools-1.3.1.tar.bz2 + '3760243ab6275ad111079794cc63a2f258b16cab39d94acc21eb774d029d245b', # SAMtools-1.3.1_Makefile.patch +] dependencies = [ ('ncurses', '6.0'), diff --git a/easybuild/easyconfigs/t/texinfo/texinfo-6.4-GCCcore-5.4.0.eb b/easybuild/easyconfigs/t/texinfo/texinfo-6.4-GCCcore-5.4.0.eb index 35739f65d5..5ff7e5d7fd 100644 --- a/easybuild/easyconfigs/t/texinfo/texinfo-6.4-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/t/texinfo/texinfo-6.4-GCCcore-5.4.0.eb @@ -17,10 +17,11 @@ version = '6.4' homepage = 'https://www.gnu.org/software/texinfo/' description = """Texinfo is the official documentation format of the GNU project.""" +toolchain = {'name': 'GCCcore', 'version': '5.4.0'} + source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_XZ] - -toolchain = {'name': 'GCCcore', 'version': '5.4.0'} +checksums = ['6ae2e61d87c6310f9af7c6f2426bd0470f251d1a6deb61fba83a3b3baff32c3a'] osdependencies = ['texlive'] -- GitLab From 9002b495652c0cce390214a046e56cc1b622d940 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 14 Aug 2017 12:12:59 +0200 Subject: [PATCH 1370/1603] kallisto/0.43.1 for intel/2017a --- .../k/kallisto/kallisto-0.43.1-intel-2017a.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/k/kallisto/kallisto-0.43.1-intel-2017a.eb diff --git a/easybuild/easyconfigs/k/kallisto/kallisto-0.43.1-intel-2017a.eb b/easybuild/easyconfigs/k/kallisto/kallisto-0.43.1-intel-2017a.eb new file mode 100644 index 0000000000..99b00b6213 --- /dev/null +++ b/easybuild/easyconfigs/k/kallisto/kallisto-0.43.1-intel-2017a.eb @@ -0,0 +1,31 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'CMakeMake' + +name = 'kallisto' +version = '0.43.1' + +homepage = 'http://pachterlab.github.io/kallisto/' +description = """kallisto is a program for quantifying abundances of transcripts from RNA-Seq data, or more generally + of target sequences using high-throughput sequencing reads.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://github.com/pachterlab/kallisto/archive/'] +sources = ['v%(version)s.tar.gz'] + +checksums = ['7baef1b3b67bcf81dc7c604db2ef30f5520b48d532bf28ec26331cb60ce69400'] + +builddependencies = [('CMake', '3.9.1')] + +dependencies = [('HDF5', '1.8.19')] + +separate_build_dir = True + +sanity_check_paths = { + 'files': ['bin/kallisto'], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From 12fefbd86a76953935091218305a3f36f1fa0bcb Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 14 Aug 2017 12:37:38 +0200 Subject: [PATCH 1371/1603] Add Rcorrector/1.0.2 for intel/2017a --- .../Jellyfish/Jellyfish-2.2.6-intel-2017a.eb | 32 +++++++++++++++++++ .../Rcorrector-1.0.2-intel-2017a.eb | 25 +++++++++++++++ .../r/Rcorrector/fix-makefile-1.0.2.patch | 12 +++++++ 3 files changed, 69 insertions(+) create mode 100644 easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.2.6-intel-2017a.eb create mode 100644 easybuild/easyconfigs/r/Rcorrector/Rcorrector-1.0.2-intel-2017a.eb create mode 100644 easybuild/easyconfigs/r/Rcorrector/fix-makefile-1.0.2.patch diff --git a/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.2.6-intel-2017a.eb b/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.2.6-intel-2017a.eb new file mode 100644 index 0000000000..96345d490a --- /dev/null +++ b/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.2.6-intel-2017a.eb @@ -0,0 +1,32 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'ConfigureMake' + +name = 'Jellyfish' +version = '2.2.6' + +homepage = 'http://www.genome.umd.edu/jellyfish.html' +description = """ Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['https://github.com/gmarcais/Jellyfish/releases/download/v%(version)s'] +sources = [SOURCELOWER_TAR_GZ] + +checksums = ['4532fb003a0494f6473bb97d52467904f631b94f7f9afb0d45b398f6c413692e'] + +parallel = 1 + +# The tests for the Bloom filter are statistical tests and can randomly fail, they actually don't make a lot of sense +runtest = "check GTEST_FILTER=-'*Bloom*'" + +postinstallcmds = ["cp config.h %(installdir)s/include/%(namelower)s-%(version)s/%(namelower)s/"] + +sanity_check_paths = { + 'files': ['bin/jellyfish'], + 'dirs': [] +} + +modextrapaths = {'CPATH': 'include/%(namelower)s-%(version)s'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/Rcorrector/Rcorrector-1.0.2-intel-2017a.eb b/easybuild/easyconfigs/r/Rcorrector/Rcorrector-1.0.2-intel-2017a.eb new file mode 100644 index 0000000000..5333492c70 --- /dev/null +++ b/easybuild/easyconfigs/r/Rcorrector/Rcorrector-1.0.2-intel-2017a.eb @@ -0,0 +1,25 @@ +easyblock = 'MakeCp' + +name = 'Rcorrector' +version = '1.0.2' + +homepage = 'https://github.com/mourisl/Rcorrector' +description = """Rcorrector(RNA-seq error CORRECTOR) is a kmer-based error correction method for RNA-seq data.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'cstd': 'c++11'} + +sources = ['v%(version)s.tar.gz'] +source_urls = ['https://github.com/mourisl/Rcorrector/archive'] + +patches = ['fix-makefile-%(version)s.patch'] + +dependencies = [('Jellyfish', '2.2.6')] + +files_to_copy = [('rcorrector', 'bin'), 'README.md', 'LICENSE', 'Sample'] + +sanity_check_paths = { + 'files': ['bin/rcorrector'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/Rcorrector/fix-makefile-1.0.2.patch b/easybuild/easyconfigs/r/Rcorrector/fix-makefile-1.0.2.patch new file mode 100644 index 0000000000..1e6d35c369 --- /dev/null +++ b/easybuild/easyconfigs/r/Rcorrector/fix-makefile-1.0.2.patch @@ -0,0 +1,12 @@ +--- Makefile.orig 2017-08-14 12:33:11.280163633 +0200 ++++ Makefile 2017-08-14 12:36:46.085730155 +0200 +@@ -1,6 +1,6 @@ +-CXX = g++ +-CXXFLAGS= -Wall -O3 -std=c++0x +-LINKFLAGS = -I . -lpthread -lz ++CXX := $(CXX) ++CXXFLAGS := $(CXXFLAGS) ++LINKFLAGS := -I. $(LDFLAGS) + DEBUG= + jellyfishPath = `which jellyfish` + jellyfishVersion = `jellyfish --version | cut -f2 -d' ' | cut -f1 -d'.'` -- GitLab From 4fce62f38778e3b39deac4cbb78a928f4d83cde9 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 14 Aug 2017 12:38:13 +0200 Subject: [PATCH 1372/1603] Trim_Galore/0.4.4 for intel/2017a --- ...cutadapt-1.14-intel-2017a-Python-2.7.14.eb | 32 ++++++++++++++++++ .../Trim_Galore-0.4.4-intel-2017a.eb | 33 +++++++++++++++++++ 2 files changed, 65 insertions(+) create mode 100644 easybuild/easyconfigs/c/cutadapt/cutadapt-1.14-intel-2017a-Python-2.7.14.eb create mode 100755 easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.4.4-intel-2017a.eb diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.14-intel-2017a-Python-2.7.14.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.14-intel-2017a-Python-2.7.14.eb new file mode 100644 index 0000000000..9397e22d2b --- /dev/null +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.14-intel-2017a-Python-2.7.14.eb @@ -0,0 +1,32 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics (SIB) +# Biozentrum - University of Basel +# Modified by: Adam Huffman +# The Francis Crick Institute + +easyblock = "PythonPackage" + +name = 'cutadapt' +version = '1.9.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://opensource.scilifelab.se/projects/cutadapt/' +description = """ Cutadapt finds and removes adapter sequences, primers, poly-A tails and + other types of unwanted sequence from your high-throughput sequencing reads. """ + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('Python', '2.7.12'), +] + +sanity_check_paths = { + 'files': ['bin/cutadapt'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/cutadapt/'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.4.4-intel-2017a.eb b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.4.4-intel-2017a.eb new file mode 100755 index 0000000000..40247e6a53 --- /dev/null +++ b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.4.4-intel-2017a.eb @@ -0,0 +1,33 @@ +# 0.4.2 modified by: +# Adam Huffman +# The Francis Crick Institute +# TODO: deal with the hardcoding of /usr/bin/perl + +easyblock = "PackedBinary" + +name = 'Trim_Galore' +version = '0.4.4' + +homepage = 'http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/' +description = """A wrapper tool around Cutadapt and FastQC to consistently apply + quality and adapter trimming to FastQ files, with some extra functionality for + MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +sources = ['%(namelower)s_v%(version)s.zip'] +source_urls = ['http://www.bioinformatics.babraham.ac.uk/projects/%(namelower)s'] + +install_cmd = "cp -a * %(installdir)s && chmod +x %(installdir)s/%(namelower)s" + +dependencies = [ + ('FastQC', '0.11.5', '-Java-1.8.0_74', True), + ('cutadapt', '1.14', '-Python-2.7.13'), +] + +sanity_check_paths = { + 'files': ["trim_galore"], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From ffc9f10ce1059662215fe6c5aa631224a69db5f8 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 14 Aug 2017 12:45:54 +0200 Subject: [PATCH 1373/1603] Fix small errors --- ...2.7.14.eb => cutadapt-1.14-intel-2017a-Python-2.7.13.eb} | 6 +++--- .../easyconfigs/k/kallisto/kallisto-0.43.1-intel-2017a.eb | 2 +- 2 files changed, 4 insertions(+), 4 deletions(-) rename easybuild/easyconfigs/c/cutadapt/{cutadapt-1.14-intel-2017a-Python-2.7.14.eb => cutadapt-1.14-intel-2017a-Python-2.7.13.eb} (89%) diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.14-intel-2017a-Python-2.7.14.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.14-intel-2017a-Python-2.7.13.eb similarity index 89% rename from easybuild/easyconfigs/c/cutadapt/cutadapt-1.14-intel-2017a-Python-2.7.14.eb rename to easybuild/easyconfigs/c/cutadapt/cutadapt-1.14-intel-2017a-Python-2.7.13.eb index 9397e22d2b..9443c3e602 100644 --- a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.14-intel-2017a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.14-intel-2017a-Python-2.7.13.eb @@ -8,20 +8,20 @@ easyblock = "PythonPackage" name = 'cutadapt' -version = '1.9.1' +version = '1.14' versionsuffix = '-Python-%(pyver)s' homepage = 'http://opensource.scilifelab.se/projects/cutadapt/' description = """ Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads. """ -toolchain = {'name': 'foss', 'version': '2016b'} +toolchain = {'name': 'intel', 'version': '2017a'} source_urls = [PYPI_SOURCE] sources = [SOURCELOWER_TAR_GZ] dependencies = [ - ('Python', '2.7.12'), + ('Python', '2.7.13'), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/k/kallisto/kallisto-0.43.1-intel-2017a.eb b/easybuild/easyconfigs/k/kallisto/kallisto-0.43.1-intel-2017a.eb index 99b00b6213..fd30492064 100644 --- a/easybuild/easyconfigs/k/kallisto/kallisto-0.43.1-intel-2017a.eb +++ b/easybuild/easyconfigs/k/kallisto/kallisto-0.43.1-intel-2017a.eb @@ -17,7 +17,7 @@ sources = ['v%(version)s.tar.gz'] checksums = ['7baef1b3b67bcf81dc7c604db2ef30f5520b48d532bf28ec26331cb60ce69400'] -builddependencies = [('CMake', '3.9.1')] +builddependencies = [('CMake', '3.8.2')] dependencies = [('HDF5', '1.8.19')] -- GitLab From 414c49627a27d835ff84b1bf897e2df96ac06fda Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 14 Aug 2017 13:53:54 +0200 Subject: [PATCH 1374/1603] Fix Rcorrector --- .../r/Rcorrector/Rcorrector-1.0.2-intel-2017a.eb | 8 ++++++-- .../easyconfigs/r/Rcorrector/fix-makefile-1.0.2.patch | 2 +- 2 files changed, 7 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/r/Rcorrector/Rcorrector-1.0.2-intel-2017a.eb b/easybuild/easyconfigs/r/Rcorrector/Rcorrector-1.0.2-intel-2017a.eb index 5333492c70..67947aaafa 100644 --- a/easybuild/easyconfigs/r/Rcorrector/Rcorrector-1.0.2-intel-2017a.eb +++ b/easybuild/easyconfigs/r/Rcorrector/Rcorrector-1.0.2-intel-2017a.eb @@ -14,12 +14,16 @@ source_urls = ['https://github.com/mourisl/Rcorrector/archive'] patches = ['fix-makefile-%(version)s.patch'] -dependencies = [('Jellyfish', '2.2.6')] +dependencies = [ + ('zlib', '1.2.11'), + ('Jellyfish', '2.2.6'), +] -files_to_copy = [('rcorrector', 'bin'), 'README.md', 'LICENSE', 'Sample'] +files_to_copy = [(['rcorrector'], 'bin'), 'README.md', 'LICENSE', 'Sample'] sanity_check_paths = { 'files': ['bin/rcorrector'], + 'dirs': [], } moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/Rcorrector/fix-makefile-1.0.2.patch b/easybuild/easyconfigs/r/Rcorrector/fix-makefile-1.0.2.patch index 1e6d35c369..7dab68cd0c 100644 --- a/easybuild/easyconfigs/r/Rcorrector/fix-makefile-1.0.2.patch +++ b/easybuild/easyconfigs/r/Rcorrector/fix-makefile-1.0.2.patch @@ -6,7 +6,7 @@ -LINKFLAGS = -I . -lpthread -lz +CXX := $(CXX) +CXXFLAGS := $(CXXFLAGS) -+LINKFLAGS := -I. $(LDFLAGS) ++LINKFLAGS := -I. $(LDFLAGS) $(LIBS) -lz DEBUG= jellyfishPath = `which jellyfish` jellyfishVersion = `jellyfish --version | cut -f2 -d' ' | cut -f1 -d'.'` -- GitLab From 09d0b2df0e35f2beead543d7644840f05d2dbf89 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 14 Aug 2017 14:27:15 +0200 Subject: [PATCH 1375/1603] Fix kallisto Upstream seems to have changed the tarball of 0.43.1 so the checksum is different... --- .../easyconfigs/k/kallisto/kallisto-0.43.1-intel-2017a.eb | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/k/kallisto/kallisto-0.43.1-intel-2017a.eb b/easybuild/easyconfigs/k/kallisto/kallisto-0.43.1-intel-2017a.eb index fd30492064..843003952a 100644 --- a/easybuild/easyconfigs/k/kallisto/kallisto-0.43.1-intel-2017a.eb +++ b/easybuild/easyconfigs/k/kallisto/kallisto-0.43.1-intel-2017a.eb @@ -15,11 +15,14 @@ toolchainopts = {'pic': True, 'usempi': True} source_urls = ['https://github.com/pachterlab/kallisto/archive/'] sources = ['v%(version)s.tar.gz'] -checksums = ['7baef1b3b67bcf81dc7c604db2ef30f5520b48d532bf28ec26331cb60ce69400'] +checksums = ['2164938c2c61c04e338c4c132cf749f56d39e6f0b4c517121bca1fbc218e430e'] builddependencies = [('CMake', '3.8.2')] -dependencies = [('HDF5', '1.8.19')] +dependencies = [ + ('zlib', '1.2.11'), + ('HDF5', '1.8.19'), +] separate_build_dir = True -- GitLab From 27e6b15d4c46583c5fa2e9e447073a936e91b3df Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 14 Aug 2017 14:47:52 +0200 Subject: [PATCH 1376/1603] Fix cutadapt sanity check --- .../c/cutadapt/cutadapt-1.14-intel-2017a-Python-2.7.13.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.14-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.14-intel-2017a-Python-2.7.13.eb index 9443c3e602..0bcc6df002 100644 --- a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.14-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.14-intel-2017a-Python-2.7.13.eb @@ -26,7 +26,7 @@ dependencies = [ sanity_check_paths = { 'files': ['bin/cutadapt'], - 'dirs': ['lib/python%(pyshortver)s/site-packages/cutadapt/'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], } moduleclass = 'bio' -- GitLab From 72eb37e0763cb87c69cd330e254687d2b6b2c679 Mon Sep 17 00:00:00 2001 From: Joachim Hein Date: Mon, 14 Aug 2017 15:16:13 +0200 Subject: [PATCH 1377/1603] Fixed indentation --- .../m/matplotlib/matplotlib-2.0.2-foss-2017a-Python-2.7.13.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.2-foss-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.2-foss-2017a-Python-2.7.13.eb index b374975f21..402493847b 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.2-foss-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.2-foss-2017a-Python-2.7.13.eb @@ -27,11 +27,11 @@ exts_list = [ 'modulename': 'cycler', 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], 'source_tmpl': 'cycler-%(version)s.tar.gz', - 'checksums': ['cd7b2d1018258d7247a71425e9f26463dfb444d411c39569972f4ce586b0c9d8'], + 'checksums': ['cd7b2d1018258d7247a71425e9f26463dfb444d411c39569972f4ce586b0c9d8'], }), (name, version, { 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], - 'checksums': ['0ffbc44faa34a8b1704bc108c451ecf87988f900ef7ce757b8e2e84383121ff1'], + 'checksums': ['0ffbc44faa34a8b1704bc108c451ecf87988f900ef7ce757b8e2e84383121ff1'], }), ] -- GitLab From b045d9af0df1b430c9f2b9ae52283ecffd1fc359 Mon Sep 17 00:00:00 2001 From: Joachim Hein Date: Tue, 15 Aug 2017 13:37:21 +0200 Subject: [PATCH 1378/1603] File set to install pyzmq in foss 2017a --- .../libsodium/libsodium-1.0.13-foss-2017a.eb | 22 ++++++++++++ .../o/OpenPGM/OpenPGM-5.2.122-foss-2017a.eb | 30 ++++++++++++++++ ...MQ-16.0.2-foss-2017a-Python-2.7.13-zmq4.eb | 30 ++++++++++++++++ .../util-linux-2.30.1-foss-2017a.eb | 34 ++++++++++++++++++ .../z/ZeroMQ/ZeroMQ-4.2.2-foss-2017a.eb | 36 +++++++++++++++++++ 5 files changed, 152 insertions(+) create mode 100644 easybuild/easyconfigs/l/libsodium/libsodium-1.0.13-foss-2017a.eb create mode 100644 easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-foss-2017a.eb create mode 100644 easybuild/easyconfigs/p/PyZMQ/PyZMQ-16.0.2-foss-2017a-Python-2.7.13-zmq4.eb create mode 100644 easybuild/easyconfigs/u/util-linux/util-linux-2.30.1-foss-2017a.eb create mode 100644 easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.2.2-foss-2017a.eb diff --git a/easybuild/easyconfigs/l/libsodium/libsodium-1.0.13-foss-2017a.eb b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.13-foss-2017a.eb new file mode 100644 index 0000000000..8853e15fa5 --- /dev/null +++ b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.13-foss-2017a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'libsodium' +version = '1.0.13' + +homepage = 'http://doc.libsodium.org/' +description = """Sodium is a modern, easy-to-use software library for encryption, decryption, signatures, + password hashing and more.""" + +toolchain = {'name': 'foss', 'version': '2017a'} + +source_urls = ['https://download.libsodium.org/libsodium/releases/'] +sources = [SOURCE_TAR_GZ] + +checksums = ['f38aac160a4bd05f06f743863e54e499'] + +sanity_check_paths = { + 'files': ['include/sodium.h', 'lib/libsodium.%s' % SHLIB_EXT, 'lib/libsodium.a'], + 'dirs': ['include/sodium', 'lib/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-foss-2017a.eb b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-foss-2017a.eb new file mode 100644 index 0000000000..93a030d6ea --- /dev/null +++ b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-foss-2017a.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'OpenPGM' +version = '5.2.122' + +homepage = 'http://code.google.com/p/openpgm/' +description = """OpenPGM is an open source implementation of the Pragmatic General Multicast (PGM) + specification in RFC 3208 available at www.ietf.org. PGM is a reliable and scalable multicast protocol + that enables receivers to detect loss, request retransmission of lost data, or notify an application + of unrecoverable loss. PGM is a receiver-reliable protocol, which means the receiver is responsible + for ensuring all data is received, absolving the sender of reception responsibility.""" + +toolchain = {'name': 'foss', 'version': '2017a'} +toolchainopts = {'pic': True} + +source_urls = ['https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/openpgm/'] +sources = ['libpgm-%(version)s.tar.gz'] + +checksums = ['d7673e9ff6cc33cf42fe9fb9a7bfbffa'] + +configopts = '--with-pic' + +start_dir = 'pgm' + +sanity_check_paths = { + 'files': ['lib/libpgm.%s' % SHLIB_EXT, 'lib/libpgm.a'], + 'dirs': ['include'], +} + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/p/PyZMQ/PyZMQ-16.0.2-foss-2017a-Python-2.7.13-zmq4.eb b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-16.0.2-foss-2017a-Python-2.7.13-zmq4.eb new file mode 100644 index 0000000000..ecb43ca881 --- /dev/null +++ b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-16.0.2-foss-2017a-Python-2.7.13-zmq4.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'PyZMQ' +version = '16.0.2' +zmqversion = '4.2.2' +versionsuffix = '-Python-%%(pyver)s-zmq%s' % zmqversion.split('.')[0] + +homepage = 'http://www.zeromq.org/bindings:python' +description = """Python bindings for ZeroMQ""" + +toolchain = {'name': 'foss', 'version': '2017a'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +checksums = ['9a8768b00a566a400d70318f8c359cfe'] + +dependencies = [ + ('Python', '2.7.13'), + ('ZeroMQ', zmqversion), +] + +options = {'modulename': 'zmq'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/zmq'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/u/util-linux/util-linux-2.30.1-foss-2017a.eb b/easybuild/easyconfigs/u/util-linux/util-linux-2.30.1-foss-2017a.eb new file mode 100644 index 0000000000..dabbcbd2d4 --- /dev/null +++ b/easybuild/easyconfigs/u/util-linux/util-linux-2.30.1-foss-2017a.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'util-linux' +version = '2.30.1' + +homepage = 'http://www.kernel.org/pub/linux/utils/util-linux' +description = """Set of Linux utilities""" + +toolchain = {'name': 'foss', 'version': '2017a'} + +source_urls = ['%s/v%%(version_major_minor)s' % homepage] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['22a860a2d98367e73e414a09dfaf3866'] + +# disable account related utilities (they need OS dependant pam-devel files) +# disable wall and friends (requires group changing permissions for install user) +# install systemd service files in install dir +# install bash completion files in install dir +configopts = "--disable-chfn-chsh --disable-login --disable-su " +configopts += "--disable-wall --disable-use-tty-group " +configopts += "--disable-makeinstall-chown --disable-makeinstall-setuid " +configopts += "--with-systemdsystemunitdir='${prefix}/systemd' " +configopts += "--with-bashcompletiondir='${prefix}/share/bash-completion/completions' " +# disable building Python bindings (since we don't include Python as a dep) +configopts += "--without-python " + +dependencies = [('ncurses', '6.0')] + +sanity_check_paths = { + 'files': ['lib/lib%s.a' % x for x in ['blkid', 'mount', 'uuid']], + 'dirs': ['include', 'bin', 'share', 'sbin'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.2.2-foss-2017a.eb b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.2.2-foss-2017a.eb new file mode 100644 index 0000000000..d690b704a1 --- /dev/null +++ b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.2.2-foss-2017a.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'ZeroMQ' +version = '4.2.2' + +homepage = 'http://www.zeromq.org/' +description = """ZeroMQ looks like an embeddable networking library but acts like a concurrency framework. + It gives you sockets that carry atomic messages across various transports like in-process, + inter-process, TCP, and multicast. You can connect sockets N-to-N with patterns like fanout, + pub-sub, task distribution, and request-reply. It's fast enough to be the fabric for clustered + products. Its asynchronous I/O model gives you scalable multicore applications, built as asynchronous + message-processing tasks. It has a score of language APIs and runs on most operating systems.""" + +toolchain = {'name': 'foss', 'version': '2017a'} + +source_urls = ['https://github.com/zeromq/libzmq/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['52499909b29604c1e47a86f1cb6a9115'] + +# --with-pgm will use shipped OpenPGM (in foreign subdir) +configopts = '--with-pic --with-system-pgm ' +configopts += 'OpenPGM_CFLAGS="-I$EBROOTOPENPGM/include/pgm-${EBVERSIONOPENPGM%.*}" ' +configopts += 'OpenPGM_LIBS="-L$EBROOTOPENPGM/lib -lpgm -lrt -lpthread -lm" ' + +dependencies = [ + ('OpenPGM', '5.2.122'), + ('util-linux', '2.30.1'), + ('libsodium', '1.0.13'), +] + +sanity_check_paths = { + 'files': ['lib/libzmq.so', 'lib/libzmq.a'], + 'dirs': ['include', 'lib'], +} + +moduleclass = 'devel' -- GitLab From 35bd7d2a41377eb818658fdeeb7b7c576dfcdf14 Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Tue, 15 Aug 2017 19:53:04 +0100 Subject: [PATCH 1379/1603] Update Tesla-Deployment-Kit-5.319.43.eb --- .../t/Tesla-Deployment-Kit/Tesla-Deployment-Kit-5.319.43.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/t/Tesla-Deployment-Kit/Tesla-Deployment-Kit-5.319.43.eb b/easybuild/easyconfigs/t/Tesla-Deployment-Kit/Tesla-Deployment-Kit-5.319.43.eb index e759c8ef98..4ec1dc753b 100644 --- a/easybuild/easyconfigs/t/Tesla-Deployment-Kit/Tesla-Deployment-Kit-5.319.43.eb +++ b/easybuild/easyconfigs/t/Tesla-Deployment-Kit/Tesla-Deployment-Kit-5.319.43.eb @@ -32,7 +32,9 @@ sanity_check_paths = { modextrapaths = { 'PATH': ['nvidia-healthmon'], 'CPATH': ['nvml/include'], + 'INCLUDEPATH': ['nvml/include'], 'MANPATH': ['nvml/doc/man'], + 'LIBRARY_PATH': ['nvml/lib', 'nvml/lib64'], 'LD_LIBRARY_PATH': ['nvml/lib', 'nvml/lib64'], } -- GitLab From 96bc1f02e26f442838b850d3414575798f34c300 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Wed, 16 Aug 2017 09:25:59 +0200 Subject: [PATCH 1380/1603] Add HTSeq with dependency --- .../HTSeq-0.9.1-foss-2016b-Python-2.7.12.eb | 35 +++++++++++++++++++ .../numpy-1.10.1-foss-2016b-Python-2.7.12.eb | 25 +++++++++++++ 2 files changed, 60 insertions(+) create mode 100644 easybuild/easyconfigs/h/HTSeq/HTSeq-0.9.1-foss-2016b-Python-2.7.12.eb create mode 100644 easybuild/easyconfigs/n/numpy/numpy-1.10.1-foss-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/h/HTSeq/HTSeq-0.9.1-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.9.1-foss-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..8c17ecee2f --- /dev/null +++ b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.9.1-foss-2016b-Python-2.7.12.eb @@ -0,0 +1,35 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = "PythonPackage" + +name = 'HTSeq' +version = '0.9.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www-huber.embl.de/users/anders/HTSeq/' +description = """A framework to process and analyze data from high-throughput sequencing (HTS) assays""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +checksums = ['af5bba775e3fb45ed4cde64c691ebef36b0bf7a86efd35c884ad0734c27ad485'] + +dependencies = [ + ('numpy', '1.10.1', versionsuffix), + ('Pysam', '0.9.1.4', versionsuffix), + ('Python', '2.7.12'), + ('matplotlib', '1.5.3', versionsuffix), +] + +sanity_check_paths = { + 'files': ["bin/htseq-count", "bin/htseq-qa"], + 'dirs': ["lib/python%(pyshortver)s/site-packages/%(name)s-%(version)s-py%(pyshortver)s-linux-x86_64.egg"], +} + +sanity_check_commands = [('htseq-count', '--help')] + +options = {'modulename': '%(name)s'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/n/numpy/numpy-1.10.1-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/n/numpy/numpy-1.10.1-foss-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..dfcb878733 --- /dev/null +++ b/easybuild/easyconfigs/n/numpy/numpy-1.10.1-foss-2016b-Python-2.7.12.eb @@ -0,0 +1,25 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +name = 'numpy' +version = '1.10.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.numpy.org' +description = """NumPy is the fundamental package for scientific computing with Python. It contains among other things: + a powerful N-dimensional array object, sophisticated (broadcasting) functions, tools for integrating C/C++ and Fortran + code, useful linear algebra, Fourier transform, and random number capabilities. Besides its obvious scientific uses, + NumPy can also be used as an efficient multi-dimensional container of generic data. Arbitrary data-types can be + defined. This allows NumPy to seamlessly and speedily integrate with a wide variety of databases.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_GZ] + +checksums = ['8b9f453f29ce96a14e625100d3dcf8926301d36c5f622623bf8820e748510858'] + +dependencies = [ + ('Python', '2.7.12'), +] + +moduleclass = 'math' -- GitLab From 8d824394660913f330c4ce59949d7ed33746b84a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Wed, 16 Aug 2017 12:12:29 +0200 Subject: [PATCH 1381/1603] Remove numpy numpy 1.11.1 is already included in the Python EasyConfig --- .../HTSeq-0.9.1-foss-2016b-Python-2.7.12.eb | 1 - .../numpy-1.10.1-foss-2016b-Python-2.7.12.eb | 25 ------------------- 2 files changed, 26 deletions(-) delete mode 100644 easybuild/easyconfigs/n/numpy/numpy-1.10.1-foss-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/h/HTSeq/HTSeq-0.9.1-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.9.1-foss-2016b-Python-2.7.12.eb index 8c17ecee2f..e34fbfe1e2 100644 --- a/easybuild/easyconfigs/h/HTSeq/HTSeq-0.9.1-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.9.1-foss-2016b-Python-2.7.12.eb @@ -17,7 +17,6 @@ sources = [SOURCE_TAR_GZ] checksums = ['af5bba775e3fb45ed4cde64c691ebef36b0bf7a86efd35c884ad0734c27ad485'] dependencies = [ - ('numpy', '1.10.1', versionsuffix), ('Pysam', '0.9.1.4', versionsuffix), ('Python', '2.7.12'), ('matplotlib', '1.5.3', versionsuffix), diff --git a/easybuild/easyconfigs/n/numpy/numpy-1.10.1-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/n/numpy/numpy-1.10.1-foss-2016b-Python-2.7.12.eb deleted file mode 100644 index dfcb878733..0000000000 --- a/easybuild/easyconfigs/n/numpy/numpy-1.10.1-foss-2016b-Python-2.7.12.eb +++ /dev/null @@ -1,25 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild - -name = 'numpy' -version = '1.10.1' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'http://www.numpy.org' -description = """NumPy is the fundamental package for scientific computing with Python. It contains among other things: - a powerful N-dimensional array object, sophisticated (broadcasting) functions, tools for integrating C/C++ and Fortran - code, useful linear algebra, Fourier transform, and random number capabilities. Besides its obvious scientific uses, - NumPy can also be used as an efficient multi-dimensional container of generic data. Arbitrary data-types can be - defined. This allows NumPy to seamlessly and speedily integrate with a wide variety of databases.""" - -toolchain = {'name': 'foss', 'version': '2016b'} - -source_urls = [SOURCEFORGE_SOURCE] -sources = [SOURCE_TAR_GZ] - -checksums = ['8b9f453f29ce96a14e625100d3dcf8926301d36c5f622623bf8820e748510858'] - -dependencies = [ - ('Python', '2.7.12'), -] - -moduleclass = 'math' -- GitLab From 3e9ac7675b08f99890c000748bbad72a3f5d847a Mon Sep 17 00:00:00 2001 From: Joachim Hein Date: Wed, 16 Aug 2017 12:15:18 +0200 Subject: [PATCH 1382/1603] h5py for Python 2.7 in foss 2017a (based on HDF5 1.8 and 1.10) This commit contains the full file set required to build h5py based on HDF5 1.8.19 and 1.10.1 in foss 2016a. This contains all pre-requisites required in EB 3.3.1. Also updated all h5py 2.7.0 configurations to do md5 checksum tests. --- .../h/HDF5/HDF5-1.10.1-foss-2017a.eb | 21 +++++++++++ .../h/HDF5/HDF5-1.8.19-foss-2017a.eb | 21 +++++++++++ ....0-foss-2017a-Python-2.7.13-HDF5-1.10.1.eb | 35 +++++++++++++++++++ ....0-foss-2017a-Python-2.7.13-HDF5-1.8.19.eb | 35 +++++++++++++++++++ .../h5py-2.7.0-intel-2016b-Python-2.7.12.eb | 1 + .../h5py-2.7.0-intel-2017a-Python-2.7.13.eb | 1 + ...l-2017a-Python-3.6.1-HDF5-1.10.0-patch1.eb | 1 + .../h5py-2.7.0-intel-2017a-Python-3.6.1.eb | 1 + ...kgconfig-1.2.2-foss-2017a-Python-2.7.13.eb | 26 ++++++++++++++ .../s/Szip/Szip-2.1.1-foss-2017a.eb | 25 +++++++++++++ 10 files changed, 167 insertions(+) create mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.10.1-foss-2017a.eb create mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.8.19-foss-2017a.eb create mode 100644 easybuild/easyconfigs/h/h5py/h5py-2.7.0-foss-2017a-Python-2.7.13-HDF5-1.10.1.eb create mode 100644 easybuild/easyconfigs/h/h5py/h5py-2.7.0-foss-2017a-Python-2.7.13-HDF5-1.8.19.eb create mode 100644 easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.2.2-foss-2017a-Python-2.7.13.eb create mode 100644 easybuild/easyconfigs/s/Szip/Szip-2.1.1-foss-2017a.eb diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.10.1-foss-2017a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.1-foss-2017a.eb new file mode 100644 index 0000000000..1735fdaa3c --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.1-foss-2017a.eb @@ -0,0 +1,21 @@ +name = 'HDF5' +version = '1.10.1' + +homepage = 'https://support.hdfgroup.org/HDF5/' +description = """HDF5 is a unique technology suite that makes possible the management of + extremely large and complex data collections.""" + +toolchain = {'name': 'foss', 'version': '2017a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['43a2f9466702fb1db31df98ae6677f15'] + +dependencies = [ + ('zlib', '1.2.11'), + ('Szip', '2.1.1'), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.19-foss-2017a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.19-foss-2017a.eb new file mode 100644 index 0000000000..ee3d1c9446 --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.19-foss-2017a.eb @@ -0,0 +1,21 @@ +name = 'HDF5' +version = '1.8.19' + +homepage = 'https://support.hdfgroup.org/HDF5/' +description = """HDF5 is a unique technology suite that makes possible the management of + extremely large and complex data collections.""" + +toolchain = {'name': 'foss', 'version': '2017a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['7f568e2464d4ab0a74d16b23956d900b'] + +dependencies = [ + ('zlib', '1.2.11'), + ('Szip', '2.1.1'), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.7.0-foss-2017a-Python-2.7.13-HDF5-1.10.1.eb b/easybuild/easyconfigs/h/h5py/h5py-2.7.0-foss-2017a-Python-2.7.13-HDF5-1.10.1.eb new file mode 100644 index 0000000000..3af541c153 --- /dev/null +++ b/easybuild/easyconfigs/h/h5py/h5py-2.7.0-foss-2017a-Python-2.7.13-HDF5-1.10.1.eb @@ -0,0 +1,35 @@ +easyblock = "PythonPackage" + +name = 'h5py' +version = '2.7.0' + +homepage = 'http://www.h5py.org/' +description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, + version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous + amounts of data.""" + +toolchain = {'name': 'foss', 'version': '2017a'} +toolchainopts = {'usempi': True} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['f62937f40f68d3b128b3941be239dd93'] + +hdf5ver = '1.10.1' +versionsuffix = '-Python-%%(pyver)s-HDF5-%s' % hdf5ver + +# to really use mpi enabled hdf5 we now seem to need a configure step +prebuildopts = ' python setup.py configure --mpi --hdf5=$EBROOTHDF5 && ' + +dependencies = [ + ('Python', '2.7.13'), + ('HDF5', hdf5ver), + ('pkgconfig', '1.2.2', '-Python-%(pyver)s'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.7.0-foss-2017a-Python-2.7.13-HDF5-1.8.19.eb b/easybuild/easyconfigs/h/h5py/h5py-2.7.0-foss-2017a-Python-2.7.13-HDF5-1.8.19.eb new file mode 100644 index 0000000000..eb3b1702ae --- /dev/null +++ b/easybuild/easyconfigs/h/h5py/h5py-2.7.0-foss-2017a-Python-2.7.13-HDF5-1.8.19.eb @@ -0,0 +1,35 @@ +easyblock = "PythonPackage" + +name = 'h5py' +version = '2.7.0' + +homepage = 'http://www.h5py.org/' +description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, + version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous + amounts of data.""" + +toolchain = {'name': 'foss', 'version': '2017a'} +toolchainopts = {'usempi': True} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['f62937f40f68d3b128b3941be239dd93'] + +hdf5ver = '1.8.19' +versionsuffix = '-Python-%%(pyver)s-HDF5-%s' % hdf5ver + +# to really use mpi enabled hdf5 we now seem to need a configure step +prebuildopts = ' python setup.py configure --mpi --hdf5=$EBROOTHDF5 && ' + +dependencies = [ + ('Python', '2.7.13'), + ('HDF5', hdf5ver), + ('pkgconfig', '1.2.2', '-Python-%(pyver)s'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.7.0-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/h/h5py/h5py-2.7.0-intel-2016b-Python-2.7.12.eb index adc15ffb81..404bad2e73 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.7.0-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.7.0-intel-2016b-Python-2.7.12.eb @@ -14,6 +14,7 @@ toolchainopts = {'usempi': True} source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] +checksums = ['f62937f40f68d3b128b3941be239dd93'] # to really use mpi enabled hdf5 we now seem to need a configure step prebuildopts = ' python setup.py configure --mpi --hdf5=$EBROOTHDF5 && ' diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.7.0-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/h/h5py/h5py-2.7.0-intel-2017a-Python-2.7.13.eb index 300f1e3d6e..e54f796b4d 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.7.0-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.7.0-intel-2017a-Python-2.7.13.eb @@ -14,6 +14,7 @@ toolchainopts = {'usempi': True} source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] +checksums = ['f62937f40f68d3b128b3941be239dd93'] # to really use mpi enabled hdf5 we now seem to need a configure step prebuildopts = ' python setup.py configure --mpi --hdf5=$EBROOTHDF5 && ' diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.7.0-intel-2017a-Python-3.6.1-HDF5-1.10.0-patch1.eb b/easybuild/easyconfigs/h/h5py/h5py-2.7.0-intel-2017a-Python-3.6.1-HDF5-1.10.0-patch1.eb index 22fe0fbf91..6a8d852d7a 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.7.0-intel-2017a-Python-3.6.1-HDF5-1.10.0-patch1.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.7.0-intel-2017a-Python-3.6.1-HDF5-1.10.0-patch1.eb @@ -15,6 +15,7 @@ toolchainopts = {'usempi': True} source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] +checksums = ['f62937f40f68d3b128b3941be239dd93'] # to really use mpi enabled hdf5 we now seem to need a configure step prebuildopts = ' python setup.py configure --mpi --hdf5=$EBROOTHDF5 && ' diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.7.0-intel-2017a-Python-3.6.1.eb b/easybuild/easyconfigs/h/h5py/h5py-2.7.0-intel-2017a-Python-3.6.1.eb index b00f2d835b..b93f4ba7bc 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.7.0-intel-2017a-Python-3.6.1.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.7.0-intel-2017a-Python-3.6.1.eb @@ -14,6 +14,7 @@ toolchainopts = {'usempi': True} source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] +checksums = ['f62937f40f68d3b128b3941be239dd93'] # to really use mpi enabled hdf5 we now seem to need a configure step prebuildopts = ' python setup.py configure --mpi --hdf5=$EBROOTHDF5 && ' diff --git a/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.2.2-foss-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.2.2-foss-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..da605c6661 --- /dev/null +++ b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.2.2-foss-2017a-Python-2.7.13.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'pkgconfig' +version = '1.2.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://github.com/matze/pkgconfig' +description = """pkgconfig is a Python module to interface with the pkg-config command line tool""" + +toolchain = {'name': 'foss', 'version': '2017a'} +toolchainopts = {'usempi': True} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.13'), + ('pkg-config', '0.29.2'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-foss-2017a.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-foss-2017a.eb new file mode 100644 index 0000000000..19df3f68d9 --- /dev/null +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-foss-2017a.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'Szip' +version = '2.1.1' + +homepage = 'http://www.hdfgroup.org/doc_resource/SZIP/' +description = "Szip compression software, providing lossless compression of scientific data" + +toolchain = {'name': 'foss', 'version': '2017a'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['dd579cf0f26d44afd10a0ad7291fc282'] + + +configopts = "--with-pic" + +sanity_check_paths = { + 'files': ["lib/libsz.a", "lib/libsz.%s" % SHLIB_EXT] + + ["include/%s" % x for x in ["ricehdf.h", "szip_adpt.h", "szlib.h"]], + 'dirs': [], +} + +moduleclass = 'tools' -- GitLab From c5fb6783026bc8347fc0a19ffce0c1e9d4c45bf1 Mon Sep 17 00:00:00 2001 From: Joachim Hein Date: Wed, 16 Aug 2017 12:24:02 +0200 Subject: [PATCH 1383/1603] removed some whitespace to resolve a conflict --- easybuild/easyconfigs/h/HDF5/HDF5-1.10.1-foss-2017a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.10.1-foss-2017a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.1-foss-2017a.eb index 1735fdaa3c..9b47efe44f 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.10.1-foss-2017a.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.1-foss-2017a.eb @@ -9,7 +9,6 @@ toolchain = {'name': 'foss', 'version': '2017a'} toolchainopts = {'pic': True, 'usempi': True} source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] - sources = [SOURCELOWER_TAR_GZ] checksums = ['43a2f9466702fb1db31df98ae6677f15'] -- GitLab From 86e86853cdb7a3f156a9ceb107040a71923ea63e Mon Sep 17 00:00:00 2001 From: Maarten Bosmans Date: Wed, 16 Aug 2017 12:31:43 +0200 Subject: [PATCH 1384/1603] iompi: OpenMPI dependency must come after icc/ifort --- easybuild/easyconfigs/i/iompi/iompi-2016.09-GCC-4.9.3-2.25.eb | 2 +- easybuild/easyconfigs/i/iompi/iompi-2016.09-GCC-5.4.0-2.26.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/i/iompi/iompi-2016.09-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/iompi/iompi-2016.09-GCC-4.9.3-2.25.eb index 9580ff5296..f69ecfb47a 100644 --- a/easybuild/easyconfigs/i/iompi/iompi-2016.09-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/iompi/iompi-2016.09-GCC-4.9.3-2.25.eb @@ -11,9 +11,9 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} compver = '2016.3.210-GCC-4.9.3-2.25' dependencies = [ - ('OpenMPI', '1.10.4', '', ('iccifort', compver)), ('icc', compver), ('ifort', compver), + ('OpenMPI', '1.10.4', '', ('iccifort', compver)), ] moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/iompi/iompi-2016.09-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/iompi/iompi-2016.09-GCC-5.4.0-2.26.eb index db8c7fb2af..7a279c30c6 100644 --- a/easybuild/easyconfigs/i/iompi/iompi-2016.09-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/iompi/iompi-2016.09-GCC-5.4.0-2.26.eb @@ -11,9 +11,9 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} compver = '2016.3.210-GCC-5.4.0-2.26' dependencies = [ - ('OpenMPI', '1.10.3', '', ('iccifort', compver)), ('icc', compver), ('ifort', compver), + ('OpenMPI', '1.10.3', '', ('iccifort', compver)), ] moduleclass = 'toolchain' -- GitLab From 2d5ea35387a3cab4c11619e00a0c4d7ac346a164 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Wed, 16 Aug 2017 12:57:28 +0200 Subject: [PATCH 1385/1603] Correct sanity_check_commands format --- .../easyconfigs/h/HTSeq/HTSeq-0.9.1-foss-2016b-Python-2.7.12.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/h/HTSeq/HTSeq-0.9.1-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.9.1-foss-2016b-Python-2.7.12.eb index e34fbfe1e2..0e056b9e6c 100644 --- a/easybuild/easyconfigs/h/HTSeq/HTSeq-0.9.1-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.9.1-foss-2016b-Python-2.7.12.eb @@ -27,7 +27,7 @@ sanity_check_paths = { 'dirs': ["lib/python%(pyshortver)s/site-packages/%(name)s-%(version)s-py%(pyshortver)s-linux-x86_64.egg"], } -sanity_check_commands = [('htseq-count', '--help')] +sanity_check_commands = [('htseq-count --help')] options = {'modulename': '%(name)s'} -- GitLab From 8f20796ee9e8fa3222d39f036cd01f18d2a1f5d7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 16 Aug 2017 13:27:11 +0200 Subject: [PATCH 1386/1603] adding easyconfigs: Qt-4.8.7-foss-2017a.eb, GLib-2.52.0-foss-2017a.eb, libGLU-9.0.0-foss-2017a.eb, Mesa-17.0.2-foss-2017a.eb, PCRE-8.40-foss-2017a.eb, util-linux-2.29.2-foss-2017a.eb, nettle-3.3-foss-2017a.eb, libdrm-2.4.76-foss-2017a.eb, Mako-1.0.6-foss-2017a-Python-2.7.13.eb, libxml2-2.9.4-foss-2017a-Python-2.7.13.eb --- .../g/GLib/GLib-2.52.0-foss-2017a.eb | 35 ++++++++++ .../l/libGLU/libGLU-9.0.0-foss-2017a.eb | 24 +++++++ .../l/libdrm/libdrm-2.4.76-foss-2017a.eb | 24 +++++++ .../libxml2-2.9.4-foss-2017a-Python-2.7.13.eb | 24 +++++++ .../Mako-1.0.6-foss-2017a-Python-2.7.13.eb | 22 +++++++ .../m/Mesa/Mesa-17.0.2-foss-2017a.eb | 66 +++++++++++++++++++ .../n/nettle/nettle-3.3-foss-2017a.eb | 30 +++++++++ .../p/PCRE/PCRE-8.40-foss-2017a.eb | 18 +++++ .../easyconfigs/q/Qt/Qt-4.8.7-foss-2017a.eb | 29 ++++++++ .../util-linux-2.29.2-foss-2017a.eb | 36 ++++++++++ 10 files changed, 308 insertions(+) create mode 100644 easybuild/easyconfigs/g/GLib/GLib-2.52.0-foss-2017a.eb create mode 100644 easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-foss-2017a.eb create mode 100644 easybuild/easyconfigs/l/libdrm/libdrm-2.4.76-foss-2017a.eb create mode 100644 easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-foss-2017a-Python-2.7.13.eb create mode 100644 easybuild/easyconfigs/m/Mako/Mako-1.0.6-foss-2017a-Python-2.7.13.eb create mode 100644 easybuild/easyconfigs/m/Mesa/Mesa-17.0.2-foss-2017a.eb create mode 100644 easybuild/easyconfigs/n/nettle/nettle-3.3-foss-2017a.eb create mode 100644 easybuild/easyconfigs/p/PCRE/PCRE-8.40-foss-2017a.eb create mode 100644 easybuild/easyconfigs/q/Qt/Qt-4.8.7-foss-2017a.eb create mode 100644 easybuild/easyconfigs/u/util-linux/util-linux-2.29.2-foss-2017a.eb diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.52.0-foss-2017a.eb b/easybuild/easyconfigs/g/GLib/GLib-2.52.0-foss-2017a.eb new file mode 100644 index 0000000000..46fb65d7e5 --- /dev/null +++ b/easybuild/easyconfigs/g/GLib/GLib-2.52.0-foss-2017a.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'GLib' +version = '2.52.0' + +homepage = 'http://www.gtk.org/' +description = """GLib is one of the base libraries of the GTK+ project""" + +toolchain = {'name': 'foss', 'version': '2017a'} +toolchainopts = {'pic': True} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('libffi', '3.2.1'), + ('gettext', '0.19.8.1'), + ('libxml2', '2.9.4'), + ('PCRE', '8.40'), + ('util-linux', '2.29.2'), +] + +builddependencies = [('Python', '2.7.13')] + +configopts = "--disable-maintainer-mode --disable-silent-rules --disable-libelf --disable-systemtap " +configopts += "--enable-static --enable-shared" + +postinstallcmds = ["sed -i -e 's|#!.*python|#!/usr/bin/env python|' %(installdir)s/bin/*"] + +sanity_check_paths = { + 'files': ['lib/libglib-%(version_major)s.0.a', 'lib/libglib-%%(version_major)s.0.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-foss-2017a.eb b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-foss-2017a.eb new file mode 100644 index 0000000000..ece6ffd732 --- /dev/null +++ b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-foss-2017a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'libGLU' +version = '9.0.0' + +homepage = 'ftp://ftp.freedesktop.org/pub/mesa/glu/' +description = """The OpenGL Utility Library (GLU) is a computer graphics library for OpenGL. """ + +toolchain = {'name': 'foss', 'version': '2017a'} +toolchainopts = {'pic': True} + +source_urls = ['ftp://ftp.freedesktop.org/pub/mesa/glu/'] +sources = ['glu-%(version)s.tar.bz2'] + +dependencies = [ + ('Mesa', '17.0.2'), +] + +sanity_check_paths = { + 'files': ['lib/libGLU.so.1'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.76-foss-2017a.eb b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.76-foss-2017a.eb new file mode 100644 index 0000000000..854d135004 --- /dev/null +++ b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.76-foss-2017a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'libdrm' +version = '2.4.76' + +homepage = 'http://dri.freedesktop.org' +description = """Direct Rendering Manager runtime library.""" + +source_urls = ['http://dri.freedesktop.org/libdrm/'] +sources = [SOURCELOWER_TAR_GZ] + +toolchain = {'name': 'foss', 'version': '2017a'} + +dependencies = [ + ('X11', '20170314'), +] + +sanity_check_paths = { + 'files': ['include/xf86drm.h', 'include/xf86drmMode.h', 'lib/libdrm_intel.%s' % SHLIB_EXT, + 'lib/libdrm_radeon.%s' % SHLIB_EXT, 'lib/libdrm.%s' % SHLIB_EXT, 'lib/libkms.%s' % SHLIB_EXT], + 'dirs': ['include/libdrm', 'include/libkms', 'lib/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-foss-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-foss-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..78ada08ea7 --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-foss-2017a-Python-2.7.13.eb @@ -0,0 +1,24 @@ +name = 'libxml2' +version = '2.9.4' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://xmlsoft.org/' +description = """Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable + outside of the Gnome platform).""" + +toolchain = {'name': 'foss', 'version': '2017a'} +toolchainopts = {'pic': True} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('zlib', '1.2.11'), + ('XZ', '5.2.3'), + ('Python', '2.7.13'), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/Mako/Mako-1.0.6-foss-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/m/Mako/Mako-1.0.6-foss-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..c503189159 --- /dev/null +++ b/easybuild/easyconfigs/m/Mako/Mako-1.0.6-foss-2017a-Python-2.7.13.eb @@ -0,0 +1,22 @@ +easyblock = 'PythonPackage' + +name = 'Mako' +version = '1.0.6' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.makotemplates.org' +description = """A super-fast templating language that borrows the best ideas from the existing templating languages""" + +toolchain = {'name': 'foss', 'version': '2017a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [('Python', '2.7.13')] + +sanity_check_paths = { + 'files': ['bin/mako-render'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s-%(version)s-py%(pyshortver)s.egg'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-17.0.2-foss-2017a.eb b/easybuild/easyconfigs/m/Mesa/Mesa-17.0.2-foss-2017a.eb new file mode 100644 index 0000000000..c658de768c --- /dev/null +++ b/easybuild/easyconfigs/m/Mesa/Mesa-17.0.2-foss-2017a.eb @@ -0,0 +1,66 @@ +# the purpose of the easyconfig is to build a Mesa for software rendering, +# not hardware rendering. This means you want at least SSE4.2. We build: +# - llvmpipe: the high-performance Gallium LLVM driver +# - swr: Intel's OpenSWR +# it will try to use the llvmpipe by default. It you want swr, do: +# GALLIUM_DRIVER=swr + +easyblock = 'ConfigureMake' + +name = 'Mesa' +version = '17.0.2' + +homepage = 'http://www.mesa3d.org/' +description = """Mesa is an open-source implementation of the OpenGL specification - + a system for rendering interactive 3D graphics.""" + +toolchain = {'name': 'foss', 'version': '2017a'} +# swr detects and builds parts specific for AVX and AVX2. If we use +# -xHost, this always gets overwritten and will fail. +toolchainopts = {'optarch': False} + +sources = [SOURCELOWER_TAR_XZ] +source_urls = [ + 'https://mesa.freedesktop.org/archive/', + 'https://mesa.freedesktop.org/archive/%(version)s', + 'ftp://ftp.freedesktop.org/pub/mesa/%(version)s', + 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x/%(version)s', +] +patches = ['Mesa-%(version)s_fix-strip-llvm-flags.patch'] + +builddependencies = [ + ('flex', '2.6.3'), + ('Bison', '3.0.4'), + ('Autotools', '20150215'), + ('pkg-config', '0.29.1'), + ('Mako', '1.0.6', '-Python-2.7.13'), + ('libxml2', '2.9.4', '-Python-2.7.13'), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('nettle', '3.3'), + ('libdrm', '2.4.76'), + ('LLVM', '4.0.0'), + ('X11', '20170314'), +] + +# GLU is not part anymore of Mesa package! +configopts = " --disable-osmesa --enable-gallium-osmesa --enable-gallium-llvm --enable-glx --disable-dri" +configopts += " --disable-gbm --disable-driglx-direct --with-gallium-drivers='swrast,swr' --disable-egl" +configopts += " --with-osmesa-bits=32 --enable-texture-float --enable-llvm-shared-libs " + +buildopts = 'V=1' + +sanity_check_paths = { + 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libOSMesa.%s' % SHLIB_EXT, + 'lib/libGLESv1_CM.%s' % SHLIB_EXT, 'lib/libGLESv2.%s' % SHLIB_EXT, + 'include/GL/glext.h', 'include/GL/gl_mangle.h', + 'include/GL/glx.h', 'include/GL/osmesa.h', + 'include/GL/gl.h', 'include/GL/glxext.h', + 'include/GL/glx_mangle.h', 'include/GLES/gl.h', + 'include/GLES2/gl2.h', 'include/GLES3/gl3.h'], + 'dirs': [] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/n/nettle/nettle-3.3-foss-2017a.eb b/easybuild/easyconfigs/n/nettle/nettle-3.3-foss-2017a.eb new file mode 100644 index 0000000000..f720881211 --- /dev/null +++ b/easybuild/easyconfigs/n/nettle/nettle-3.3-foss-2017a.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'nettle' +version = '3.3' + +homepage = 'http://www.lysator.liu.se/~nisse/nettle/' +description = """Nettle is a cryptographic library that is designed to fit easily + in more or less any context: In crypto toolkits for object-oriented + languages (C++, Python, Pike, ...), in applications like LSH or GNUPG, + or even in kernel space.""" + +toolchain = {'name': 'foss', 'version': '2017a'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('GMP', '6.1.2'), +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['nettle-hash', 'nettle-lfib-stream', 'pkcs1-conv', 'sexp-conv']] + + [('lib/libhogweed.a', 'lib64/libhogweed.a'), + ('lib/libhogweed.%s' % SHLIB_EXT, 'lib64/libhogweed.%s' % SHLIB_EXT), + ('lib/libnettle.a', 'lib64/libnettle.a'), + ('lib/libnettle.%s' % SHLIB_EXT, 'lib64/libnettle.%s' % SHLIB_EXT)], + 'dirs': ['include/nettle'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PCRE/PCRE-8.40-foss-2017a.eb b/easybuild/easyconfigs/p/PCRE/PCRE-8.40-foss-2017a.eb new file mode 100644 index 0000000000..cdea33d837 --- /dev/null +++ b/easybuild/easyconfigs/p/PCRE/PCRE-8.40-foss-2017a.eb @@ -0,0 +1,18 @@ +easyblock = 'ConfigureMake' + +name = 'PCRE' +version = '8.40' + +homepage = 'http://www.pcre.org/' +description = """The PCRE library is a set of functions that implement regular expression pattern matching using + the same syntax and semantics as Perl 5.""" + +toolchain = {'name': 'foss', 'version': '2017a'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +configopts = "--with-pic --disable-cpp --enable-utf --enable-unicode-properties" + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.7-foss-2017a.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.7-foss-2017a.eb new file mode 100644 index 0000000000..0c8d002a4f --- /dev/null +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.7-foss-2017a.eb @@ -0,0 +1,29 @@ +name = 'Qt' +version = '4.8.7' + +homepage = 'http://qt.io/' +description = "Qt is a comprehensive cross-platform C++ application framework." + +toolchain = {'name': 'foss', 'version': '2017a'} +toolchainopts = {'cstd': 'gnu++98'} + +source_urls = [ + 'http://download.qt.io/official_releases/qt/%(version_major_minor)s/%(version)s/', + 'http://download.qt.io/archive/qt/%(version_major_minor)s/%(version)s/' +] +sources = ['%(namelower)s-everywhere-opensource-src-%(version)s.tar.gz'] + +patches = ['Qt-%(version)s_phonon-export.patch'] + +builddependencies = [ + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('GLib', '2.52.0'), + ('libpng', '1.6.29'), + ('X11', '20170314'), + ('libGLU', '9.0.0'), +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/u/util-linux/util-linux-2.29.2-foss-2017a.eb b/easybuild/easyconfigs/u/util-linux/util-linux-2.29.2-foss-2017a.eb new file mode 100644 index 0000000000..2f535a4c3c --- /dev/null +++ b/easybuild/easyconfigs/u/util-linux/util-linux-2.29.2-foss-2017a.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'util-linux' +version = '2.29.2' + +homepage = 'http://www.kernel.org/pub/linux/utils/util-linux' +description = """Set of Linux utilities""" + +toolchain = {'name': 'foss', 'version': '2017a'} + +source_urls = ['%s/v%%(version_major_minor)s' % homepage] +sources = [SOURCELOWER_TAR_GZ] + +# disable account related utilities (they need OS dependant pam-devel files) +# disable wall and friends (requires group changing permissions for install user) +# install systemd service files in install dir +# install bash completion files in install dir +configopts = "--disable-chfn-chsh --disable-login --disable-su " +configopts += "--disable-wall --disable-use-tty-group " +configopts += "--disable-makeinstall-chown --disable-makeinstall-setuid " +configopts += "--with-systemdsystemunitdir='${prefix}/systemd' " +configopts += "--with-bashcompletiondir='${prefix}/share/bash-completion/completions' " +# disable building Python bindings (since we don't include Python as a dep) +configopts += "--without-python " + +dependencies = [ + ('ncurses', '6.0'), + ('zlib', '1.2.11'), +] + +sanity_check_paths = { + 'files': ['lib/lib%s.a' % x for x in ['blkid', 'mount', 'uuid']], + 'dirs': ['include', 'bin', 'share', 'sbin'], +} + +moduleclass = 'tools' -- GitLab From 45f126c30f716df0bb12f4e3b5685dcc095239f0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 16 Aug 2017 14:10:51 +0200 Subject: [PATCH 1387/1603] adding easyconfigs: Eigen-3.3.4.eb --- easybuild/easyconfigs/e/Eigen/Eigen-3.3.4.eb | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) create mode 100644 easybuild/easyconfigs/e/Eigen/Eigen-3.3.4.eb diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.3.4.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.3.4.eb new file mode 100644 index 0000000000..cb9b1ad328 --- /dev/null +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.3.4.eb @@ -0,0 +1,17 @@ +name = 'Eigen' +version = '3.3.4' + +homepage = 'http://eigen.tuxfamily.org/index.php?title=Main_Page' + +description = """ + Eigen is a C++ template library for linear algebra: + matrices, vectors, numerical solvers, and related algorithms. +""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['http://bitbucket.org/%(namelower)s/%(namelower)s/get'] +sources = ['%(version)s.tar.bz2'] +checksums = ['dd254beb0bafc695d0f62ae1a222ff85b52dbaa3a16f76e781dce22d0d20a4a6'] + +moduleclass = 'math' -- GitLab From 8afe68f7786e32cc9e033dcda6a54165d661479f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 16 Aug 2017 14:12:16 +0200 Subject: [PATCH 1388/1603] adding easyconfigs: MRtrix-3.0_RC2-foss-2017a-Python-2.7.13.eb --- ...MRtrix-3.0_RC2-foss-2017a-Python-2.7.13.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/m/MRtrix/MRtrix-3.0_RC2-foss-2017a-Python-2.7.13.eb diff --git a/easybuild/easyconfigs/m/MRtrix/MRtrix-3.0_RC2-foss-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/m/MRtrix/MRtrix-3.0_RC2-foss-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..aa0e747a56 --- /dev/null +++ b/easybuild/easyconfigs/m/MRtrix/MRtrix-3.0_RC2-foss-2017a-Python-2.7.13.eb @@ -0,0 +1,26 @@ +name = 'MRtrix' +version = '3.0_RC2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.brain.org.au/software/index.html#mrtrix' +description = """MRtrix provides a set of tools to perform diffusion-weighted MR white-matter tractography in a manner + robust to crossing fibres, using constrained spherical deconvolution (CSD) and probabilistic streamlines.""" + +toolchain = {'name': 'foss', 'version': '2017a'} +toolchainopts = {'cstd': 'c++11'} + +source_urls = ['https://github.com/MRtrix3/mrtrix3/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['88187f3498f4ee215b2a51d16acb7f2e6c33217e72403a7d48c2ec5da6e2218b'] + +builddependencies = [ + ('Eigen', '3.3.4', '', True), +] +dependencies = [ + ('zlib', '1.2.11'), + ('Python', '2.7.13'), + ('Mesa', '17.0.2'), + ('Qt', '4.8.7'), +] + +moduleclass = 'bio' -- GitLab From 25bfdc0abccfcc6042e694ff198ae8fff567669e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 16 Aug 2017 14:23:02 +0200 Subject: [PATCH 1389/1603] stick to GCCcore toolchain for libxml2 dep for Mesa --- .../libxml2-2.9.4-foss-2017a-Python-2.7.13.eb | 24 ------------------- .../m/Mesa/Mesa-17.0.2-foss-2017a.eb | 2 +- .../m/Mesa/Mesa-17.0.2-intel-2017a.eb | 2 +- 3 files changed, 2 insertions(+), 26 deletions(-) delete mode 100644 easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-foss-2017a-Python-2.7.13.eb diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-foss-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-foss-2017a-Python-2.7.13.eb deleted file mode 100644 index 78ada08ea7..0000000000 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-foss-2017a-Python-2.7.13.eb +++ /dev/null @@ -1,24 +0,0 @@ -name = 'libxml2' -version = '2.9.4' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'http://xmlsoft.org/' -description = """Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable - outside of the Gnome platform).""" - -toolchain = {'name': 'foss', 'version': '2017a'} -toolchainopts = {'pic': True} - -source_urls = [ - 'http://xmlsoft.org/sources/', - 'http://xmlsoft.org/sources/old/' -] -sources = [SOURCELOWER_TAR_GZ] - -dependencies = [ - ('zlib', '1.2.11'), - ('XZ', '5.2.3'), - ('Python', '2.7.13'), -] - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-17.0.2-foss-2017a.eb b/easybuild/easyconfigs/m/Mesa/Mesa-17.0.2-foss-2017a.eb index c658de768c..57eb46100f 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-17.0.2-foss-2017a.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-17.0.2-foss-2017a.eb @@ -34,7 +34,7 @@ builddependencies = [ ('Autotools', '20150215'), ('pkg-config', '0.29.1'), ('Mako', '1.0.6', '-Python-2.7.13'), - ('libxml2', '2.9.4', '-Python-2.7.13'), + ('libxml2', '2.9.4'), ] dependencies = [ diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-17.0.2-intel-2017a.eb b/easybuild/easyconfigs/m/Mesa/Mesa-17.0.2-intel-2017a.eb index 8bb12d31a3..89dd517431 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-17.0.2-intel-2017a.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-17.0.2-intel-2017a.eb @@ -34,7 +34,7 @@ builddependencies = [ ('Autotools', '20150215'), ('pkg-config', '0.29.1'), ('Mako', '1.0.6', '-Python-2.7.13'), - ('libxml2', '2.9.4', '-Python-2.7.13'), + ('libxml2', '2.9.4'), ] dependencies = [ -- GitLab From 8c10f8aff23bfb741fbcb82ffff2f721e50a8bfe Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 16 Aug 2017 15:22:09 +0200 Subject: [PATCH 1390/1603] stick to GCCcore toolchain for libdrm, nettle, PCRE, util-linux + add SHA256 checksums in touched easyconfigs --- .../g/GLib/GLib-2.52.0-foss-2017a.eb | 3 +++ .../l/libGLU/libGLU-9.0.0-foss-2017a.eb | 3 +++ ...017a.eb => libdrm-2.4.76-GCCcore-6.3.0.eb} | 11 +++++++++-- .../Mako-1.0.6-foss-2017a-Python-2.7.13.eb | 3 +++ .../m/Mesa/Mesa-17.0.2-foss-2017a.eb | 6 +++++- .../m/Mesa/Mesa-17.0.2-intel-2017a.eb | 6 +++++- ...s-2017a.eb => nettle-3.3-GCCcore-6.3.0.eb} | 10 +++++++++- ...ss-2017a.eb => PCRE-8.40-GCCcore-6.3.0.eb} | 10 +++++++++- .../easyconfigs/q/Qt/Qt-4.8.7-foss-2017a.eb | 4 ++++ ....eb => util-linux-2.29.2-GCCcore-6.3.0.eb} | 19 +++++++++++++------ 10 files changed, 63 insertions(+), 12 deletions(-) rename easybuild/easyconfigs/l/libdrm/{libdrm-2.4.76-foss-2017a.eb => libdrm-2.4.76-GCCcore-6.3.0.eb} (67%) rename easybuild/easyconfigs/n/nettle/{nettle-3.3-foss-2017a.eb => nettle-3.3-GCCcore-6.3.0.eb} (75%) rename easybuild/easyconfigs/p/PCRE/{PCRE-8.40-foss-2017a.eb => PCRE-8.40-GCCcore-6.3.0.eb} (60%) rename easybuild/easyconfigs/u/util-linux/{util-linux-2.29.2-foss-2017a.eb => util-linux-2.29.2-GCCcore-6.3.0.eb} (84%) diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.52.0-foss-2017a.eb b/easybuild/easyconfigs/g/GLib/GLib-2.52.0-foss-2017a.eb index 46fb65d7e5..52fb7942b9 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.52.0-foss-2017a.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.52.0-foss-2017a.eb @@ -11,6 +11,9 @@ toolchainopts = {'pic': True} source_urls = [FTPGNOME_SOURCE] sources = [SOURCELOWER_TAR_XZ] +checksums = [ + '4578e3e077b1b978cafeec8d28b676c680aba0c0475923874c4c993403df311a', # glib-2.52.0.tar.xz +] dependencies = [ ('libffi', '3.2.1'), diff --git a/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-foss-2017a.eb b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-foss-2017a.eb index ece6ffd732..9619bd114d 100644 --- a/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-foss-2017a.eb +++ b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-foss-2017a.eb @@ -11,6 +11,9 @@ toolchainopts = {'pic': True} source_urls = ['ftp://ftp.freedesktop.org/pub/mesa/glu/'] sources = ['glu-%(version)s.tar.bz2'] +checksums = [ + '1f7ad0d379a722fcbd303aa5650c6d7d5544fde83196b42a73d1193568a4df12', # glu-9.0.0.tar.bz2 +] dependencies = [ ('Mesa', '17.0.2'), diff --git a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.76-foss-2017a.eb b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.76-GCCcore-6.3.0.eb similarity index 67% rename from easybuild/easyconfigs/l/libdrm/libdrm-2.4.76-foss-2017a.eb rename to easybuild/easyconfigs/l/libdrm/libdrm-2.4.76-GCCcore-6.3.0.eb index 854d135004..d6e3c7e9a1 100644 --- a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.76-foss-2017a.eb +++ b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.76-GCCcore-6.3.0.eb @@ -6,14 +6,21 @@ version = '2.4.76' homepage = 'http://dri.freedesktop.org' description = """Direct Rendering Manager runtime library.""" +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} + source_urls = ['http://dri.freedesktop.org/libdrm/'] sources = [SOURCELOWER_TAR_GZ] - -toolchain = {'name': 'foss', 'version': '2017a'} +checksums = [ + '6e3fb50d7500acf06f7eed44d5b1d33cda26aef7f5ae6667ddcc626b435c2531', # libdrm-2.4.76.tar.gz +] dependencies = [ ('X11', '20170314'), ] +builddependencies = [ + # use same binutils version that was used when building GCCcore toolchain + ('binutils', '2.27', '', True), +] sanity_check_paths = { 'files': ['include/xf86drm.h', 'include/xf86drmMode.h', 'lib/libdrm_intel.%s' % SHLIB_EXT, diff --git a/easybuild/easyconfigs/m/Mako/Mako-1.0.6-foss-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/m/Mako/Mako-1.0.6-foss-2017a-Python-2.7.13.eb index c503189159..0f724f7b47 100644 --- a/easybuild/easyconfigs/m/Mako/Mako-1.0.6-foss-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/m/Mako/Mako-1.0.6-foss-2017a-Python-2.7.13.eb @@ -11,6 +11,9 @@ toolchain = {'name': 'foss', 'version': '2017a'} source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] +checksums = [ + '48559ebd872a8e77f92005884b3d88ffae552812cdf17db6768e5c3be5ebbe0d', # Mako-1.0.6.tar.gz +] dependencies = [('Python', '2.7.13')] diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-17.0.2-foss-2017a.eb b/easybuild/easyconfigs/m/Mesa/Mesa-17.0.2-foss-2017a.eb index 57eb46100f..bf4cca33d3 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-17.0.2-foss-2017a.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-17.0.2-foss-2017a.eb @@ -19,14 +19,18 @@ toolchain = {'name': 'foss', 'version': '2017a'} # -xHost, this always gets overwritten and will fail. toolchainopts = {'optarch': False} -sources = [SOURCELOWER_TAR_XZ] source_urls = [ 'https://mesa.freedesktop.org/archive/', 'https://mesa.freedesktop.org/archive/%(version)s', 'ftp://ftp.freedesktop.org/pub/mesa/%(version)s', 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x/%(version)s', ] +sources = [SOURCELOWER_TAR_XZ] patches = ['Mesa-%(version)s_fix-strip-llvm-flags.patch'] +checksums = [ + 'f8f191f909e01e65de38d5bdea5fb057f21649a3aed20948be02348e77a689d4', # mesa-17.0.2.tar.xz + '3edd64bc2a42b9065cfb86e872ba7e8a7c74144f7a867c2b5ec62d16078afb36', # Mesa-17.0.2_fix-strip-llvm-flags.patch +] builddependencies = [ ('flex', '2.6.3'), diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-17.0.2-intel-2017a.eb b/easybuild/easyconfigs/m/Mesa/Mesa-17.0.2-intel-2017a.eb index 89dd517431..fb11d4be67 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-17.0.2-intel-2017a.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-17.0.2-intel-2017a.eb @@ -19,14 +19,18 @@ toolchain = {'name': 'intel', 'version': '2017a'} # -xHost, this always gets overwritten and will fail. toolchainopts = {'optarch': False} -sources = [SOURCELOWER_TAR_XZ] source_urls = [ 'https://mesa.freedesktop.org/archive/', 'https://mesa.freedesktop.org/archive/%(version)s', 'ftp://ftp.freedesktop.org/pub/mesa/%(version)s', 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x/%(version)s', ] +sources = [SOURCELOWER_TAR_XZ] patches = ['Mesa-%(version)s_fix-strip-llvm-flags.patch'] +checksums = [ + 'f8f191f909e01e65de38d5bdea5fb057f21649a3aed20948be02348e77a689d4', # mesa-17.0.2.tar.xz + '3edd64bc2a42b9065cfb86e872ba7e8a7c74144f7a867c2b5ec62d16078afb36', # Mesa-17.0.2_fix-strip-llvm-flags.patch +] builddependencies = [ ('flex', '2.6.3'), diff --git a/easybuild/easyconfigs/n/nettle/nettle-3.3-foss-2017a.eb b/easybuild/easyconfigs/n/nettle/nettle-3.3-GCCcore-6.3.0.eb similarity index 75% rename from easybuild/easyconfigs/n/nettle/nettle-3.3-foss-2017a.eb rename to easybuild/easyconfigs/n/nettle/nettle-3.3-GCCcore-6.3.0.eb index f720881211..29bb670c94 100644 --- a/easybuild/easyconfigs/n/nettle/nettle-3.3-foss-2017a.eb +++ b/easybuild/easyconfigs/n/nettle/nettle-3.3-GCCcore-6.3.0.eb @@ -9,10 +9,18 @@ description = """Nettle is a cryptographic library that is designed to fit easil languages (C++, Python, Pike, ...), in applications like LSH or GNUPG, or even in kernel space.""" -toolchain = {'name': 'foss', 'version': '2017a'} +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +checksums = [ + '46942627d5d0ca11720fec18d81fc38f7ef837ea4197c1f630e71ce0d470b11e', # nettle-3.3.tar.gz +] + +builddependencies = [ + # use same binutils version that was used when building GCCcore toolchain + ('binutils', '2.27', '', True), +] dependencies = [ ('GMP', '6.1.2'), diff --git a/easybuild/easyconfigs/p/PCRE/PCRE-8.40-foss-2017a.eb b/easybuild/easyconfigs/p/PCRE/PCRE-8.40-GCCcore-6.3.0.eb similarity index 60% rename from easybuild/easyconfigs/p/PCRE/PCRE-8.40-foss-2017a.eb rename to easybuild/easyconfigs/p/PCRE/PCRE-8.40-GCCcore-6.3.0.eb index cdea33d837..9dc9830554 100644 --- a/easybuild/easyconfigs/p/PCRE/PCRE-8.40-foss-2017a.eb +++ b/easybuild/easyconfigs/p/PCRE/PCRE-8.40-GCCcore-6.3.0.eb @@ -7,11 +7,19 @@ homepage = 'http://www.pcre.org/' description = """The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax and semantics as Perl 5.""" -toolchain = {'name': 'foss', 'version': '2017a'} +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} toolchainopts = {'pic': True} source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCELOWER_TAR_GZ] +checksums = [ + '1d75ce90ea3f81ee080cdc04e68c9c25a9fb984861a0618be7bbf676b18eda3e', # pcre-8.40.tar.gz +] + +builddependencies = [ + # use same binutils version that was used when building GCCcore toolchain + ('binutils', '2.27', '', True), +] configopts = "--with-pic --disable-cpp --enable-utf --enable-unicode-properties" diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.7-foss-2017a.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.7-foss-2017a.eb index 0c8d002a4f..71fe074ee9 100644 --- a/easybuild/easyconfigs/q/Qt/Qt-4.8.7-foss-2017a.eb +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.7-foss-2017a.eb @@ -12,6 +12,10 @@ source_urls = [ 'http://download.qt.io/archive/qt/%(version_major_minor)s/%(version)s/' ] sources = ['%(namelower)s-everywhere-opensource-src-%(version)s.tar.gz'] +checksums = [ + 'e2882295097e47fe089f8ac741a95fef47e0a73a3f3cdf21b56990638f626ea0', # qt-everywhere-opensource-src-4.8.7.tar.gz + '3853c87c33695bfa57e207ffb0d94cb2565aa462eccdf44d2b2804fd44ecbad6', # Qt-4.8.7_phonon-export.patch +] patches = ['Qt-%(version)s_phonon-export.patch'] diff --git a/easybuild/easyconfigs/u/util-linux/util-linux-2.29.2-foss-2017a.eb b/easybuild/easyconfigs/u/util-linux/util-linux-2.29.2-GCCcore-6.3.0.eb similarity index 84% rename from easybuild/easyconfigs/u/util-linux/util-linux-2.29.2-foss-2017a.eb rename to easybuild/easyconfigs/u/util-linux/util-linux-2.29.2-GCCcore-6.3.0.eb index 2f535a4c3c..5bf5c2a724 100644 --- a/easybuild/easyconfigs/u/util-linux/util-linux-2.29.2-foss-2017a.eb +++ b/easybuild/easyconfigs/u/util-linux/util-linux-2.29.2-GCCcore-6.3.0.eb @@ -6,10 +6,22 @@ version = '2.29.2' homepage = 'http://www.kernel.org/pub/linux/utils/util-linux' description = """Set of Linux utilities""" -toolchain = {'name': 'foss', 'version': '2017a'} +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} source_urls = ['%s/v%%(version_major_minor)s' % homepage] sources = [SOURCELOWER_TAR_GZ] +checksums = [ + '29ccdf91d2c3245dc705f0ad3bf729ac41d8adcdbeff914e797c552ecb04a4c7', # util-linux-2.29.2.tar.gz +] + +builddependencies = [ + ('binutils', '2.27'), +] + +dependencies = [ + ('ncurses', '6.0'), + ('zlib', '1.2.11'), +] # disable account related utilities (they need OS dependant pam-devel files) # disable wall and friends (requires group changing permissions for install user) @@ -23,11 +35,6 @@ configopts += "--with-bashcompletiondir='${prefix}/share/bash-completion/complet # disable building Python bindings (since we don't include Python as a dep) configopts += "--without-python " -dependencies = [ - ('ncurses', '6.0'), - ('zlib', '1.2.11'), -] - sanity_check_paths = { 'files': ['lib/lib%s.a' % x for x in ['blkid', 'mount', 'uuid']], 'dirs': ['include', 'bin', 'share', 'sbin'], -- GitLab From b4c154bb6ff61b86d0a1737fd06f4c9a40998fe0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 16 Aug 2017 16:54:26 +0200 Subject: [PATCH 1391/1603] add comment on use of non-dummy toolchain for Eigen --- easybuild/easyconfigs/e/Eigen/Eigen-3.3.4.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.3.4.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.3.4.eb index cb9b1ad328..b82e85a0ae 100644 --- a/easybuild/easyconfigs/e/Eigen/Eigen-3.3.4.eb +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.3.4.eb @@ -8,6 +8,7 @@ description = """ matrices, vectors, numerical solvers, and related algorithms. """ +# only includes header files, so no need for a non-dummy toolchain toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = ['http://bitbucket.org/%(namelower)s/%(namelower)s/get'] -- GitLab From ba4309288352b822b4ea059a7819634a90401e8f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 16 Aug 2017 19:01:41 +0200 Subject: [PATCH 1392/1603] adding easyconfigs: GCC-7.2.0-2.29.eb --- .../b/Bison/Bison-3.0.4-GCCcore-7.2.0.eb | 28 ++++++++++ .../b/binutils/binutils-2.29-GCCcore-7.2.0.eb | 22 ++++++++ .../easyconfigs/b/binutils/binutils-2.29.eb | 21 ++++++++ .../f/flex/flex-2.6.4-GCCcore-7.2.0.eb | 30 +++++++++++ easybuild/easyconfigs/g/GCC/GCC-7.2.0-2.29.eb | 25 +++++++++ .../easyconfigs/g/GCCcore/GCCcore-7.2.0.eb | 53 +++++++++++++++++++ .../help2man/help2man-1.47.4-GCCcore-7.2.0.eb | 25 +++++++++ .../m/M4/M4-1.4.18-GCCcore-7.2.0.eb | 29 ++++++++++ .../z/zlib/zlib-1.2.11-GCCcore-7.2.0.eb | 26 +++++++++ 9 files changed, 259 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-7.2.0.eb create mode 100644 easybuild/easyconfigs/b/binutils/binutils-2.29-GCCcore-7.2.0.eb create mode 100644 easybuild/easyconfigs/b/binutils/binutils-2.29.eb create mode 100644 easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-7.2.0.eb create mode 100644 easybuild/easyconfigs/g/GCC/GCC-7.2.0-2.29.eb create mode 100644 easybuild/easyconfigs/g/GCCcore/GCCcore-7.2.0.eb create mode 100644 easybuild/easyconfigs/h/help2man/help2man-1.47.4-GCCcore-7.2.0.eb create mode 100644 easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.2.0.eb create mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-7.2.0.eb diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-7.2.0.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-7.2.0.eb new file mode 100644 index 0000000000..0b2a1818c2 --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-7.2.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'Bison' +version = '3.0.4' + +homepage = 'http://www.gnu.org/software/bison' +description = """Bison is a general-purpose parser generator that converts an annotated context-free grammar + into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.""" + +toolchain = {'name': 'GCCcore', 'version': '7.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['b67fd2daae7a64b5ba862c66c07c1addb9e6b1b05c5f2049392cfd8a2172952e'] + +builddependencies = [ + ('M4', '1.4.18'), + # use same binutils version that was used when building GCCcore toolchain + ('binutils', '2.29', '', True), +] + + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["bison", "yacc"]] + ["lib/liby.a"], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.29-GCCcore-7.2.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.29-GCCcore-7.2.0.eb new file mode 100644 index 0000000000..2e11b1cadf --- /dev/null +++ b/easybuild/easyconfigs/b/binutils/binutils-2.29-GCCcore-7.2.0.eb @@ -0,0 +1,22 @@ +name = 'binutils' +version = '2.29' + +homepage = 'http://directory.fsf.org/project/binutils/' +description = "binutils: GNU binary utilities" + +toolchain = {'name': 'GCCcore', 'version': '7.2.0'} + +sources = [SOURCE_TAR_GZ] +source_urls = [GNU_SOURCE] +checksums = ['172e8c89472cf52712fd23a9f14e9bca6182727fb45b0f8f482652a83d5a11b4'] + +builddependencies = [ + ('flex', '2.6.4'), + ('Bison', '3.0.4'), + # zlib required, but being linked in statically, so not a runtime dep + ('zlib', '1.2.11'), + # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils + ('binutils', version, '', True) +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.29.eb b/easybuild/easyconfigs/b/binutils/binutils-2.29.eb new file mode 100644 index 0000000000..6efb559b8a --- /dev/null +++ b/easybuild/easyconfigs/b/binutils/binutils-2.29.eb @@ -0,0 +1,21 @@ +name = 'binutils' +version = '2.29' + +homepage = 'http://directory.fsf.org/project/binutils/' + +description = "binutils: GNU binary utilities" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['172e8c89472cf52712fd23a9f14e9bca6182727fb45b0f8f482652a83d5a11b4'] + +builddependencies = [ + ('flex', '2.6.4'), + ('Bison', '3.0.4'), + # zlib required, but being linked in statically, so not a runtime dep + ('zlib', '1.2.11'), +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-7.2.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-7.2.0.eb new file mode 100644 index 0000000000..9df6e33418 --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-7.2.0.eb @@ -0,0 +1,30 @@ +name = 'flex' +version = '2.6.4' + +homepage = 'http://flex.sourceforge.net/' + +description = """ + Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, + sometimes called a tokenizer, is a program which recognizes lexical patterns + in text. +""" + +toolchain = {'name': 'GCCcore', 'version': '7.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/westes/flex/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['e87aae032bf07c26f85ac0ed3250998c37621d95f8bd748b31f15b33c45ee995'] + +builddependencies = [ + ('Bison', '3.0.4'), + ('help2man', '1.47.4'), + # use same binutils version that was used when building GCC toolchain + ('binutils', '2.29', '', True), +] + +dependencies = [ + ('M4', '1.4.18'), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/g/GCC/GCC-7.2.0-2.29.eb b/easybuild/easyconfigs/g/GCC/GCC-7.2.0-2.29.eb new file mode 100644 index 0000000000..8e1f8bd616 --- /dev/null +++ b/easybuild/easyconfigs/g/GCC/GCC-7.2.0-2.29.eb @@ -0,0 +1,25 @@ +easyblock = 'Bundle' + +name = 'GCC' +version = '7.2.0' + +binutilsver = '2.29' +versionsuffix = '-%s' % binutilsver + +homepage = 'http://gcc.gnu.org/' +description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, + as well as libraries for these languages (libstdc++, libgcj,...).""" + +toolchain = {'name': 'dummy', 'version': ''} + +dependencies = [ + ('GCCcore', version), + # binutils built on top of GCCcore, which was built on top of (dummy-built) binutils + ('binutils', binutilsver, '', ('GCCcore', version)), +] + +altroot = 'GCCcore' +altversion = 'GCCcore' + +# this bundle serves as a compiler-only toolchain, so it should be marked as compiler (important for HMNS) +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-7.2.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-7.2.0.eb new file mode 100644 index 0000000000..f12a1c7b74 --- /dev/null +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-7.2.0.eb @@ -0,0 +1,53 @@ +easyblock = 'EB_GCC' + +name = 'GCCcore' +version = '7.2.0' + +homepage = 'http://gcc.gnu.org/' +description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, + as well as libraries for these languages (libstdc++, libgcj,...).""" + +toolchain = {'name': 'dummy', 'version': ''} + +mpfr_version = '3.1.5' + +source_urls = [ + 'http://ftpmirror.gnu.org/gnu/gcc/gcc-%(version)s', # GCC auto-resolving HTTP mirror + 'http://ftpmirror.gnu.org/gnu/gmp', # idem for GMP + 'http://ftpmirror.gnu.org/gnu/mpfr', # idem for MPFR + 'http://www.multiprecision.org/mpc/download', # MPC official + 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies + 'http://gcc.cybermirror.org/infrastructure/', # HTTP mirror for GCC dependencies + 'http://isl.gforge.inria.fr/', # original HTTP source for ISL +] +sources = [ + 'gcc-%(version)s.tar.gz', + 'gmp-6.1.2.tar.bz2', + 'mpfr-%s.tar.bz2' % mpfr_version, + 'mpc-1.0.3.tar.gz', + 'isl-0.16.1.tar.bz2', +] +patches = [ + ('mpfr-%s-allpatches-20170801.patch' % mpfr_version, '../mpfr-%s' % mpfr_version), + 'GCCcore-6.2.0-fix-find-isl.patch', +] +checksums = [ + '0153a003d3b433459336a91610cca2995ee0fb3d71131bd72555f2231a6efcfc', # gcc-7.2.0.tar.gz + '5275bb04f4863a13516b2f39392ac5e272f5e1bb8057b18aec1c9b79d73d8fb2', # gmp-6.1.2.tar.bz2 + 'ca498c1c7a74dd37a576f353312d1e68d490978de4395fa28f1cbd46a364e658', # mpfr-3.1.5.tar.bz2 + '617decc6ea09889fb08ede330917a00b16809b8db88c29c31bfbb49cbf88ecc3', # mpc-1.0.3.tar.gz + '412538bb65c799ac98e17e8cfcdacbb257a57362acfaaff254b0fcae970126d2', # isl-0.16.1.tar.bz2 + '62f11d5750a3a2c76f6b33ad581b15c75a0292a575107cabdd8d1f0ccb4e20a1', # mpfr-3.1.5-allpatches-20170801.patch + '5ad909606d17d851c6ad629b4fddb6c1621844218b8d139fed18c502a7696c68', # GCCcore-6.2.0-fix-find-isl.patch +] + +builddependencies = [ + ('M4', '1.4.18'), + ('binutils', '2.29'), +] + +languages = ['c', 'c++', 'fortran'] + +withisl = True + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/h/help2man/help2man-1.47.4-GCCcore-7.2.0.eb b/easybuild/easyconfigs/h/help2man/help2man-1.47.4-GCCcore-7.2.0.eb new file mode 100644 index 0000000000..63e4b751a1 --- /dev/null +++ b/easybuild/easyconfigs/h/help2man/help2man-1.47.4-GCCcore-7.2.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'help2man' +version = '1.47.4' + +homepage = 'https://www.gnu.org/software/help2man/' +description = """help2man produces simple manual pages from the '--help' and '--version' output of other commands.""" + +toolchain = {'name': 'GCCcore', 'version': '7.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_XZ] +checksums = ['d4ecf697d13f14dd1a78c5995f06459bff706fd1ce593d1c02d81667c0207753'] + +builddependencies = [ + # use same binutils version that was used when building GCC toolchain + ('binutils', '2.29', '', True), +] + +sanity_check_paths = { + 'files': ['bin/help2man'], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.2.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.2.0.eb new file mode 100644 index 0000000000..4605723e36 --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.2.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'M4' +version = '1.4.18' + +homepage = 'http://www.gnu.org/software/m4/m4.html' +description = """GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible + although it has some extensions (for example, handling more than 9 positional parameters to macros). + GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc.""" + +toolchain = {'name': 'GCCcore', 'version': '7.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['ab2633921a5cd38e48797bf5521ad259bdc4b979078034a3b790d7fec5493fab'] + +# use same binutils version that was used when building GCC toolchain +builddependencies = [('binutils', '2.29', '', True)] + +# '-fgnu89-inline' is required to avoid linking errors with older glibc's, +# see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 +configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" + +sanity_check_paths = { + 'files': ['bin/m4'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-7.2.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-7.2.0.eb new file mode 100644 index 0000000000..016a24fff2 --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-7.2.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'zlib' +version = '1.2.11' + +homepage = 'http://www.zlib.net/' +description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is, + not covered by any patents -- lossless data-compression library for use on virtually any + computer hardware and operating system.""" + +toolchain = {'name': 'GCCcore', 'version': '7.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['http://zlib.net/fossils'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['c3e5e9fdd5004dcb542feda5ee4f0ff0744628baf8ed2dd5d66f8ca1197cb1a1'] + +# use same binutils version that was used when building GCC toolchain +builddependencies = [('binutils', '2.29', '', True)] + +sanity_check_paths = { + 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' -- GitLab From c2cbcf3e1644b9573cef726da3d1b387225cc6aa Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 16 Aug 2017 19:08:01 +0200 Subject: [PATCH 1393/1603] add missing patch file required by GCCcore-7.2.0.eb --- .../mpfr-3.1.5-allpatches-20170801.patch | 785 ++++++++++++++++++ 1 file changed, 785 insertions(+) create mode 100644 easybuild/easyconfigs/g/GCCcore/mpfr-3.1.5-allpatches-20170801.patch diff --git a/easybuild/easyconfigs/g/GCCcore/mpfr-3.1.5-allpatches-20170801.patch b/easybuild/easyconfigs/g/GCCcore/mpfr-3.1.5-allpatches-20170801.patch new file mode 100644 index 0000000000..fe26596b10 --- /dev/null +++ b/easybuild/easyconfigs/g/GCCcore/mpfr-3.1.5-allpatches-20170801.patch @@ -0,0 +1,785 @@ +# MPFR v3.1.5 patch dated 2017-06-06 +# downloaded via https://gforge.inria.fr/frs/?group_id=136 +diff -Naurd mpfr-3.1.5-a/PATCHES mpfr-3.1.5-b/PATCHES +--- mpfr-3.1.5-a/PATCHES 2016-12-15 08:35:46.476430238 +0000 ++++ mpfr-3.1.5-b/PATCHES 2016-12-15 08:35:46.544430346 +0000 +@@ -0,0 +1 @@ ++vasprintf +diff -Naurd mpfr-3.1.5-a/VERSION mpfr-3.1.5-b/VERSION +--- mpfr-3.1.5-a/VERSION 2016-09-27 07:58:14.000000000 +0000 ++++ mpfr-3.1.5-b/VERSION 2016-12-15 08:35:46.544430346 +0000 +@@ -1 +1 @@ +-3.1.5 ++3.1.5-p1 +diff -Naurd mpfr-3.1.5-a/src/mpfr.h mpfr-3.1.5-b/src/mpfr.h +--- mpfr-3.1.5-a/src/mpfr.h 2016-09-27 07:58:15.000000000 +0000 ++++ mpfr-3.1.5-b/src/mpfr.h 2016-12-15 08:35:46.540430340 +0000 +@@ -27,7 +27,7 @@ + #define MPFR_VERSION_MAJOR 3 + #define MPFR_VERSION_MINOR 1 + #define MPFR_VERSION_PATCHLEVEL 5 +-#define MPFR_VERSION_STRING "3.1.5" ++#define MPFR_VERSION_STRING "3.1.5-p1" + + /* Macros dealing with MPFR VERSION */ + #define MPFR_VERSION_NUM(a,b,c) (((a) << 16L) | ((b) << 8) | (c)) +diff -Naurd mpfr-3.1.5-a/src/vasprintf.c mpfr-3.1.5-b/src/vasprintf.c +--- mpfr-3.1.5-a/src/vasprintf.c 2016-09-27 07:58:15.000000000 +0000 ++++ mpfr-3.1.5-b/src/vasprintf.c 2016-12-15 08:35:46.520430308 +0000 +@@ -1593,7 +1593,7 @@ + } + else if (spec.spec == 'f' || spec.spec == 'F') + { +- if (spec.prec == -1) ++ if (spec.prec < 0) + spec.prec = 6; + if (regular_fg (np, p, spec, NULL) == -1) + goto error; +diff -Naurd mpfr-3.1.5-a/src/version.c mpfr-3.1.5-b/src/version.c +--- mpfr-3.1.5-a/src/version.c 2016-09-27 07:58:15.000000000 +0000 ++++ mpfr-3.1.5-b/src/version.c 2016-12-15 08:35:46.544430346 +0000 +@@ -25,5 +25,5 @@ + const char * + mpfr_get_version (void) + { +- return "3.1.5"; ++ return "3.1.5-p1"; + } +diff -Naurd mpfr-3.1.5-a/tests/tsprintf.c mpfr-3.1.5-b/tests/tsprintf.c +--- mpfr-3.1.5-a/tests/tsprintf.c 2016-09-27 07:58:14.000000000 +0000 ++++ mpfr-3.1.5-b/tests/tsprintf.c 2016-12-15 08:35:46.520430308 +0000 +@@ -1251,6 +1251,25 @@ + check_emin_aux (MPFR_EMIN_MIN); + } + ++static void ++test20161214 (void) ++{ ++ mpfr_t x; ++ char buf[32]; ++ const char s[] = "0x0.fffffffffffff8p+1024"; ++ int r; ++ ++ mpfr_init2 (x, 64); ++ mpfr_set_str (x, s, 16, MPFR_RNDN); ++ r = mpfr_snprintf (buf, 32, "%.*RDf", -2, x); ++ MPFR_ASSERTN(r == 316); ++ r = mpfr_snprintf (buf, 32, "%.*RDf", INT_MIN + 1, x); ++ MPFR_ASSERTN(r == 316); ++ r = mpfr_snprintf (buf, 32, "%.*RDf", INT_MIN, x); ++ MPFR_ASSERTN(r == 316); ++ mpfr_clear (x); ++} ++ + int + main (int argc, char **argv) + { +@@ -1271,6 +1290,7 @@ + mixed (); + check_emax (); + check_emin (); ++ test20161214 (); + + #if defined(HAVE_LOCALE_H) && defined(HAVE_SETLOCALE) + #if MPFR_LCONV_DPTS +diff -Naurd mpfr-3.1.5-a/PATCHES mpfr-3.1.5-b/PATCHES +--- mpfr-3.1.5-a/PATCHES 2016-12-19 22:11:17.022676737 +0000 ++++ mpfr-3.1.5-b/PATCHES 2016-12-19 22:11:17.094676820 +0000 +@@ -0,0 +1 @@ ++strtofr +diff -Naurd mpfr-3.1.5-a/VERSION mpfr-3.1.5-b/VERSION +--- mpfr-3.1.5-a/VERSION 2016-12-15 08:35:46.544430346 +0000 ++++ mpfr-3.1.5-b/VERSION 2016-12-19 22:11:17.094676820 +0000 +@@ -1 +1 @@ +-3.1.5-p1 ++3.1.5-p2 +diff -Naurd mpfr-3.1.5-a/src/mpfr.h mpfr-3.1.5-b/src/mpfr.h +--- mpfr-3.1.5-a/src/mpfr.h 2016-12-15 08:35:46.540430340 +0000 ++++ mpfr-3.1.5-b/src/mpfr.h 2016-12-19 22:11:17.090676815 +0000 +@@ -27,7 +27,7 @@ + #define MPFR_VERSION_MAJOR 3 + #define MPFR_VERSION_MINOR 1 + #define MPFR_VERSION_PATCHLEVEL 5 +-#define MPFR_VERSION_STRING "3.1.5-p1" ++#define MPFR_VERSION_STRING "3.1.5-p2" + + /* Macros dealing with MPFR VERSION */ + #define MPFR_VERSION_NUM(a,b,c) (((a) << 16L) | ((b) << 8) | (c)) +diff -Naurd mpfr-3.1.5-a/src/strtofr.c mpfr-3.1.5-b/src/strtofr.c +--- mpfr-3.1.5-a/src/strtofr.c 2016-09-27 07:58:15.000000000 +0000 ++++ mpfr-3.1.5-b/src/strtofr.c 2016-12-19 22:11:17.066676788 +0000 +@@ -743,11 +743,14 @@ + of the pstr_size most significant digits of pstr->mant, with + equality in case exact is non-zero. */ + +- /* test if rounding is possible, and if so exit the loop */ +- if (exact || mpfr_can_round_raw (result, ysize, +- (pstr->negative) ? -1 : 1, +- ysize_bits - err - 1, +- MPFR_RNDN, rnd, MPFR_PREC(x))) ++ /* test if rounding is possible, and if so exit the loop. ++ Note: we also need to be able to determine the correct ternary value, ++ thus we use the MPFR_PREC(x) + (rnd == MPFR_RNDN) trick. ++ For example if result = xxx...xxx111...111 and rnd = RNDN, ++ then we know the correct rounding is xxx...xx(x+1), but we cannot know ++ the correct ternary value. */ ++ if (exact || mpfr_round_p (result, ysize, ysize_bits - err - 1, ++ MPFR_PREC(x) + (rnd == MPFR_RNDN))) + break; + + next_loop: +diff -Naurd mpfr-3.1.5-a/src/version.c mpfr-3.1.5-b/src/version.c +--- mpfr-3.1.5-a/src/version.c 2016-12-15 08:35:46.544430346 +0000 ++++ mpfr-3.1.5-b/src/version.c 2016-12-19 22:11:17.094676820 +0000 +@@ -25,5 +25,5 @@ + const char * + mpfr_get_version (void) + { +- return "3.1.5-p1"; ++ return "3.1.5-p2"; + } +diff -Naurd mpfr-3.1.5-a/tests/tstrtofr.c mpfr-3.1.5-b/tests/tstrtofr.c +--- mpfr-3.1.5-a/tests/tstrtofr.c 2016-09-27 07:58:14.000000000 +0000 ++++ mpfr-3.1.5-b/tests/tstrtofr.c 2016-12-19 22:11:17.066676788 +0000 +@@ -1191,6 +1191,24 @@ + mpfr_clears (e, x1, x2, (mpfr_ptr) 0); + } + ++/* Note: the number is 5^47/2^9. */ ++static void ++bug20161217 (void) ++{ ++ mpfr_t fp, z; ++ static const char * num = "0.1387778780781445675529539585113525390625e31"; ++ int inex; ++ ++ mpfr_init2 (fp, 110); ++ mpfr_init2 (z, 110); ++ inex = mpfr_strtofr (fp, num, NULL, 10, MPFR_RNDN); ++ MPFR_ASSERTN(inex == 0); ++ mpfr_set_str_binary (z, "10001100001000010011110110011101101001010000001011011110010001010100010100100110111101000010001011001100001101E-9"); ++ MPFR_ASSERTN(mpfr_equal_p (fp, z)); ++ mpfr_clear (fp); ++ mpfr_clear (z); ++} ++ + int + main (int argc, char *argv[]) + { +@@ -1205,6 +1223,7 @@ + test20100310 (); + bug20120814 (); + bug20120829 (); ++ bug20161217 (); + + tests_end_mpfr (); + return 0; +diff -Naurd mpfr-3.1.5-a/PATCHES mpfr-3.1.5-b/PATCHES +--- mpfr-3.1.5-a/PATCHES 2017-06-06 19:21:17.580843571 +0000 ++++ mpfr-3.1.5-b/PATCHES 2017-06-06 19:21:17.604843293 +0000 +@@ -0,0 +1 @@ ++ret-macro +diff -Naurd mpfr-3.1.5-a/VERSION mpfr-3.1.5-b/VERSION +--- mpfr-3.1.5-a/VERSION 2016-12-19 22:11:17.094676820 +0000 ++++ mpfr-3.1.5-b/VERSION 2017-06-06 19:21:17.604843293 +0000 +@@ -1 +1 @@ +-3.1.5-p2 ++3.1.5-p3 +diff -Naurd mpfr-3.1.5-a/src/mpfr-impl.h mpfr-3.1.5-b/src/mpfr-impl.h +--- mpfr-3.1.5-a/src/mpfr-impl.h 2016-09-27 07:58:15.000000000 +0000 ++++ mpfr-3.1.5-b/src/mpfr-impl.h 2017-06-06 19:21:17.592843433 +0000 +@@ -873,7 +873,7 @@ + following two macros, unless the flag comes from another function + returning the ternary inexact value */ + #define MPFR_RET(I) return \ +- (I) ? ((__gmpfr_flags |= MPFR_FLAGS_INEXACT), (I)) : 0 ++ (I) != 0 ? ((__gmpfr_flags |= MPFR_FLAGS_INEXACT), (I)) : 0 + #define MPFR_RET_NAN return (__gmpfr_flags |= MPFR_FLAGS_NAN), 0 + + #define MPFR_SET_ERANGE() (__gmpfr_flags |= MPFR_FLAGS_ERANGE) +diff -Naurd mpfr-3.1.5-a/src/mpfr.h mpfr-3.1.5-b/src/mpfr.h +--- mpfr-3.1.5-a/src/mpfr.h 2016-12-19 22:11:17.090676815 +0000 ++++ mpfr-3.1.5-b/src/mpfr.h 2017-06-06 19:21:17.600843340 +0000 +@@ -27,7 +27,7 @@ + #define MPFR_VERSION_MAJOR 3 + #define MPFR_VERSION_MINOR 1 + #define MPFR_VERSION_PATCHLEVEL 5 +-#define MPFR_VERSION_STRING "3.1.5-p2" ++#define MPFR_VERSION_STRING "3.1.5-p3" + + /* Macros dealing with MPFR VERSION */ + #define MPFR_VERSION_NUM(a,b,c) (((a) << 16L) | ((b) << 8) | (c)) +diff -Naurd mpfr-3.1.5-a/src/version.c mpfr-3.1.5-b/src/version.c +--- mpfr-3.1.5-a/src/version.c 2016-12-19 22:11:17.094676820 +0000 ++++ mpfr-3.1.5-b/src/version.c 2017-06-06 19:21:17.604843293 +0000 +@@ -25,5 +25,5 @@ + const char * + mpfr_get_version (void) + { +- return "3.1.5-p2"; ++ return "3.1.5-p3"; + } +diff -Naurd mpfr-3.1.5-a/PATCHES mpfr-3.1.5-b/PATCHES +--- mpfr-3.1.5-a/PATCHES 2017-06-06 19:50:30.708438500 +0000 ++++ mpfr-3.1.5-b/PATCHES 2017-06-06 19:50:30.736438175 +0000 +@@ -0,0 +1 @@ ++tests-buffer-size +diff -Naurd mpfr-3.1.5-a/VERSION mpfr-3.1.5-b/VERSION +--- mpfr-3.1.5-a/VERSION 2017-06-06 19:21:17.604843293 +0000 ++++ mpfr-3.1.5-b/VERSION 2017-06-06 19:50:30.736438175 +0000 +@@ -1 +1 @@ +-3.1.5-p3 ++3.1.5-p4 +diff -Naurd mpfr-3.1.5-a/src/mpfr.h mpfr-3.1.5-b/src/mpfr.h +--- mpfr-3.1.5-a/src/mpfr.h 2017-06-06 19:21:17.600843340 +0000 ++++ mpfr-3.1.5-b/src/mpfr.h 2017-06-06 19:50:30.732438221 +0000 +@@ -27,7 +27,7 @@ + #define MPFR_VERSION_MAJOR 3 + #define MPFR_VERSION_MINOR 1 + #define MPFR_VERSION_PATCHLEVEL 5 +-#define MPFR_VERSION_STRING "3.1.5-p3" ++#define MPFR_VERSION_STRING "3.1.5-p4" + + /* Macros dealing with MPFR VERSION */ + #define MPFR_VERSION_NUM(a,b,c) (((a) << 16L) | ((b) << 8) | (c)) +diff -Naurd mpfr-3.1.5-a/src/version.c mpfr-3.1.5-b/src/version.c +--- mpfr-3.1.5-a/src/version.c 2017-06-06 19:21:17.604843293 +0000 ++++ mpfr-3.1.5-b/src/version.c 2017-06-06 19:50:30.736438175 +0000 +@@ -25,5 +25,5 @@ + const char * + mpfr_get_version (void) + { +- return "3.1.5-p3"; ++ return "3.1.5-p4"; + } +diff -Naurd mpfr-3.1.5-a/tests/tl2b.c mpfr-3.1.5-b/tests/tl2b.c +--- mpfr-3.1.5-a/tests/tl2b.c 2016-09-27 07:58:14.000000000 +0000 ++++ mpfr-3.1.5-b/tests/tl2b.c 2017-06-06 19:50:30.724438314 +0000 +@@ -83,7 +83,7 @@ + mpfr_srcptr t; + int beta, i; + int error = 0; +- char buffer[30]; ++ char buffer[256]; /* larger than needed, for maintainability */ + + for (beta = 2; beta <= BASE_MAX; beta++) + { +diff -Naurd mpfr-3.1.5-a/tests/tpow_all.c mpfr-3.1.5-b/tests/tpow_all.c +--- mpfr-3.1.5-a/tests/tpow_all.c 2016-09-27 07:58:14.000000000 +0000 ++++ mpfr-3.1.5-b/tests/tpow_all.c 2017-06-06 19:50:30.724438314 +0000 +@@ -498,7 +498,7 @@ + for (i = 0; i <= 12; i++) + { + unsigned int flags = 0; +- char sy[16]; ++ char sy[256]; /* larger than needed, for maintainability */ + + /* Test 2^(emin - i/4). + * --> Underflow iff i > 4. +diff -Naurd mpfr-3.1.5-a/PATCHES mpfr-3.1.5-b/PATCHES +--- mpfr-3.1.5-a/PATCHES 2017-06-06 19:57:01.947910247 +0000 ++++ mpfr-3.1.5-b/PATCHES 2017-06-06 19:57:01.971909970 +0000 +@@ -0,0 +1 @@ ++vasprintf-overflow-check +diff -Naurd mpfr-3.1.5-a/VERSION mpfr-3.1.5-b/VERSION +--- mpfr-3.1.5-a/VERSION 2017-06-06 19:50:30.736438175 +0000 ++++ mpfr-3.1.5-b/VERSION 2017-06-06 19:57:01.971909970 +0000 +@@ -1 +1 @@ +-3.1.5-p4 ++3.1.5-p5 +diff -Naurd mpfr-3.1.5-a/src/mpfr.h mpfr-3.1.5-b/src/mpfr.h +--- mpfr-3.1.5-a/src/mpfr.h 2017-06-06 19:50:30.732438221 +0000 ++++ mpfr-3.1.5-b/src/mpfr.h 2017-06-06 19:57:01.971909970 +0000 +@@ -27,7 +27,7 @@ + #define MPFR_VERSION_MAJOR 3 + #define MPFR_VERSION_MINOR 1 + #define MPFR_VERSION_PATCHLEVEL 5 +-#define MPFR_VERSION_STRING "3.1.5-p4" ++#define MPFR_VERSION_STRING "3.1.5-p5" + + /* Macros dealing with MPFR VERSION */ + #define MPFR_VERSION_NUM(a,b,c) (((a) << 16L) | ((b) << 8) | (c)) +diff -Naurd mpfr-3.1.5-a/src/vasprintf.c mpfr-3.1.5-b/src/vasprintf.c +--- mpfr-3.1.5-a/src/vasprintf.c 2016-12-15 08:35:46.520430308 +0000 ++++ mpfr-3.1.5-b/src/vasprintf.c 2017-06-06 19:57:01.963910062 +0000 +@@ -1452,7 +1452,7 @@ + struct printf_spec spec) + { + char *str; +- long total; ++ unsigned int total; /* can hold the sum of two non-negative int's + 1 */ + int uppercase; + + /* WARNING: left justification means right space padding */ +@@ -1645,43 +1645,43 @@ + + /* compute the number of characters to be written verifying it is not too + much */ ++ ++#define INCR_TOTAL(v) \ ++ do { \ ++ MPFR_ASSERTD ((v) >= 0); \ ++ if (MPFR_UNLIKELY ((v) > INT_MAX)) \ ++ goto error; \ ++ total += (v); \ ++ if (MPFR_UNLIKELY (total > INT_MAX)) \ ++ goto error; \ ++ } while (0) ++ + total = np->sign ? 1 : 0; +- total += np->prefix_size; +- total += np->ip_size; +- if (MPFR_UNLIKELY (total < 0 || total > INT_MAX)) +- goto error; +- total += np->ip_trailing_zeros; +- if (MPFR_UNLIKELY (total < 0 || total > INT_MAX)) +- goto error; ++ INCR_TOTAL (np->prefix_size); ++ INCR_TOTAL (np->ip_size); ++ INCR_TOTAL (np->ip_trailing_zeros); ++ MPFR_ASSERTD (np->ip_size + np->ip_trailing_zeros >= 1); + if (np->thousands_sep) + /* ' flag, style f and the thousands separator in current locale is not + reduced to the null character */ +- total += (np->ip_size + np->ip_trailing_zeros) / 3; +- if (MPFR_UNLIKELY (total < 0 || total > INT_MAX)) +- goto error; ++ INCR_TOTAL ((np->ip_size + np->ip_trailing_zeros - 1) / 3); + if (np->point) + ++total; +- total += np->fp_leading_zeros; +- if (MPFR_UNLIKELY (total < 0 || total > INT_MAX)) +- goto error; +- total += np->fp_size; +- if (MPFR_UNLIKELY (total < 0 || total > INT_MAX)) +- goto error; +- total += np->fp_trailing_zeros; +- if (MPFR_UNLIKELY (total < 0 || total > INT_MAX)) +- goto error; +- total += np->exp_size; +- if (MPFR_UNLIKELY (total < 0 || total > INT_MAX)) +- goto error; ++ INCR_TOTAL (np->fp_leading_zeros); ++ INCR_TOTAL (np->fp_size); ++ INCR_TOTAL (np->fp_trailing_zeros); ++ INCR_TOTAL (np->exp_size); + + if (spec.width > total) + /* pad with spaces or zeros depending on np->pad_type */ + { + np->pad_size = spec.width - total; + total += np->pad_size; /* here total == spec.width, +- so 0 < total < INT_MAX */ ++ so 0 < total <= INT_MAX */ ++ MPFR_ASSERTD (total == spec.width); + } + ++ MPFR_ASSERTD (total > 0 && total <= INT_MAX); + return total; + + error: +diff -Naurd mpfr-3.1.5-a/src/version.c mpfr-3.1.5-b/src/version.c +--- mpfr-3.1.5-a/src/version.c 2017-06-06 19:50:30.736438175 +0000 ++++ mpfr-3.1.5-b/src/version.c 2017-06-06 19:57:01.971909970 +0000 +@@ -25,5 +25,5 @@ + const char * + mpfr_get_version (void) + { +- return "3.1.5-p4"; ++ return "3.1.5-p5"; + } +diff -Naurd mpfr-3.1.5-a/PATCHES mpfr-3.1.5-b/PATCHES +--- mpfr-3.1.5-a/PATCHES 2017-06-06 20:17:02.489704106 +0000 ++++ mpfr-3.1.5-b/PATCHES 2017-06-06 20:17:02.513703814 +0000 +@@ -0,0 +1 @@ ++printf-errno +diff -Naurd mpfr-3.1.5-a/VERSION mpfr-3.1.5-b/VERSION +--- mpfr-3.1.5-a/VERSION 2017-06-06 19:57:01.971909970 +0000 ++++ mpfr-3.1.5-b/VERSION 2017-06-06 20:17:02.513703814 +0000 +@@ -1 +1 @@ +-3.1.5-p5 ++3.1.5-p6 +diff -Naurd mpfr-3.1.5-a/src/mpfr.h mpfr-3.1.5-b/src/mpfr.h +--- mpfr-3.1.5-a/src/mpfr.h 2017-06-06 19:57:01.971909970 +0000 ++++ mpfr-3.1.5-b/src/mpfr.h 2017-06-06 20:17:02.513703814 +0000 +@@ -27,7 +27,7 @@ + #define MPFR_VERSION_MAJOR 3 + #define MPFR_VERSION_MINOR 1 + #define MPFR_VERSION_PATCHLEVEL 5 +-#define MPFR_VERSION_STRING "3.1.5-p5" ++#define MPFR_VERSION_STRING "3.1.5-p6" + + /* Macros dealing with MPFR VERSION */ + #define MPFR_VERSION_NUM(a,b,c) (((a) << 16L) | ((b) << 8) | (c)) +diff -Naurd mpfr-3.1.5-a/src/printf.c mpfr-3.1.5-b/src/printf.c +--- mpfr-3.1.5-a/src/printf.c 2016-09-27 07:58:15.000000000 +0000 ++++ mpfr-3.1.5-b/src/printf.c 2017-06-06 20:17:02.501703960 +0000 +@@ -40,7 +40,6 @@ + # endif /* HAVE___VA_COPY */ + #endif /* HAVE_VA_COPY */ + +-#include + #include "mpfr-impl.h" + + #ifdef _MPFR_H_HAVE_FILE +diff -Naurd mpfr-3.1.5-a/src/vasprintf.c mpfr-3.1.5-b/src/vasprintf.c +--- mpfr-3.1.5-a/src/vasprintf.c 2017-06-06 19:57:01.963910062 +0000 ++++ mpfr-3.1.5-b/src/vasprintf.c 2017-06-06 20:17:02.501703960 +0000 +@@ -52,6 +52,8 @@ + #include /* for ptrdiff_t */ + #endif + ++#include ++ + #define MPFR_NEED_LONGLONG_H + #include "mpfr-intmax.h" + #include "mpfr-impl.h" +diff -Naurd mpfr-3.1.5-a/src/version.c mpfr-3.1.5-b/src/version.c +--- mpfr-3.1.5-a/src/version.c 2017-06-06 19:57:01.971909970 +0000 ++++ mpfr-3.1.5-b/src/version.c 2017-06-06 20:17:02.513703814 +0000 +@@ -25,5 +25,5 @@ + const char * + mpfr_get_version (void) + { +- return "3.1.5-p5"; ++ return "3.1.5-p6"; + } +diff -Naurd mpfr-3.1.5-a/tests/tprintf.c mpfr-3.1.5-b/tests/tprintf.c +--- mpfr-3.1.5-a/tests/tprintf.c 2016-09-27 07:58:14.000000000 +0000 ++++ mpfr-3.1.5-b/tests/tprintf.c 2017-06-06 20:17:02.501703960 +0000 +@@ -26,6 +26,7 @@ + #include + #include + #include ++#include + + #include "mpfr-intmax.h" + #include "mpfr-test.h" +@@ -109,6 +110,33 @@ + } + + static void ++check_vprintf_overflow (const char *fmt, ...) ++{ ++ va_list ap; ++ int r, e; ++ ++ va_start (ap, fmt); ++ errno = 0; ++ r = mpfr_vprintf (fmt, ap); ++ e = errno; ++ va_end (ap); ++ ++ if (r != -1 ++#ifdef EOVERFLOW ++ || e != EOVERFLOW ++#endif ++ ) ++ { ++ putchar ('\n'); ++ fprintf (stderr, "Error in mpfr_vprintf(\"%s\", ...)\n" ++ "Got r = %d, errno = %d\n", fmt, r, e); ++ exit (1); ++ } ++ ++ putchar ('\n'); ++} ++ ++static void + check_invalid_format (void) + { + int i = 0; +@@ -167,8 +195,8 @@ + mpfr_set_ui (x, 1, MPFR_RNDN); + mpfr_nextabove (x); + +- check_vprintf_failure ("%Rb", x); +- check_vprintf_failure ("%RA %RA %Ra %Ra", x, x, x, x); ++ check_vprintf_overflow ("%Rb", x); ++ check_vprintf_overflow ("%RA %RA %Ra %Ra", x, x, x, x); + + mpfr_clear (x); + } +diff -Naurd mpfr-3.1.5-a/PATCHES mpfr-3.1.5-b/PATCHES +--- mpfr-3.1.5-a/PATCHES 2017-06-06 20:24:00.580702002 +0000 ++++ mpfr-3.1.5-b/PATCHES 2017-06-06 20:24:00.604701719 +0000 +@@ -0,0 +1 @@ ++tsprintf-setlocale +diff -Naurd mpfr-3.1.5-a/VERSION mpfr-3.1.5-b/VERSION +--- mpfr-3.1.5-a/VERSION 2017-06-06 20:17:02.513703814 +0000 ++++ mpfr-3.1.5-b/VERSION 2017-06-06 20:24:00.604701719 +0000 +@@ -1 +1 @@ +-3.1.5-p6 ++3.1.5-p7 +diff -Naurd mpfr-3.1.5-a/src/mpfr.h mpfr-3.1.5-b/src/mpfr.h +--- mpfr-3.1.5-a/src/mpfr.h 2017-06-06 20:17:02.513703814 +0000 ++++ mpfr-3.1.5-b/src/mpfr.h 2017-06-06 20:24:00.604701719 +0000 +@@ -27,7 +27,7 @@ + #define MPFR_VERSION_MAJOR 3 + #define MPFR_VERSION_MINOR 1 + #define MPFR_VERSION_PATCHLEVEL 5 +-#define MPFR_VERSION_STRING "3.1.5-p6" ++#define MPFR_VERSION_STRING "3.1.5-p7" + + /* Macros dealing with MPFR VERSION */ + #define MPFR_VERSION_NUM(a,b,c) (((a) << 16L) | ((b) << 8) | (c)) +diff -Naurd mpfr-3.1.5-a/src/version.c mpfr-3.1.5-b/src/version.c +--- mpfr-3.1.5-a/src/version.c 2017-06-06 20:17:02.513703814 +0000 ++++ mpfr-3.1.5-b/src/version.c 2017-06-06 20:24:00.604701719 +0000 +@@ -25,5 +25,5 @@ + const char * + mpfr_get_version (void) + { +- return "3.1.5-p6"; ++ return "3.1.5-p7"; + } +diff -Naurd mpfr-3.1.5-a/tests/tsprintf.c mpfr-3.1.5-b/tests/tsprintf.c +--- mpfr-3.1.5-a/tests/tsprintf.c 2016-12-15 08:35:46.520430308 +0000 ++++ mpfr-3.1.5-b/tests/tsprintf.c 2017-06-06 20:24:00.596701813 +0000 +@@ -1273,13 +1273,12 @@ + int + main (int argc, char **argv) + { +- char *locale; + + tests_start_mpfr (); + + #if defined(HAVE_LOCALE_H) && defined(HAVE_SETLOCALE) + /* currently, we just check with 'C' locale */ +- locale = setlocale (LC_ALL, "C"); ++ setlocale (LC_ALL, "C"); + #endif + + bug20111102 (); +@@ -1297,7 +1296,7 @@ + locale_da_DK (); + /* Avoid a warning by doing the setlocale outside of this #if */ + #endif +- setlocale (LC_ALL, locale); ++ setlocale (LC_ALL, "C"); + #endif + + if (getenv ("MPFR_CHECK_LIBC_PRINTF")) +diff -Naurd mpfr-3.1.5-a/PATCHES mpfr-3.1.5-b/PATCHES +--- mpfr-3.1.5-a/PATCHES 2017-06-06 20:31:35.919341495 +0000 ++++ mpfr-3.1.5-b/PATCHES 2017-06-06 20:31:35.943341213 +0000 +@@ -0,0 +1 @@ ++mpf-compat-signed +diff -Naurd mpfr-3.1.5-a/VERSION mpfr-3.1.5-b/VERSION +--- mpfr-3.1.5-a/VERSION 2017-06-06 20:24:00.604701719 +0000 ++++ mpfr-3.1.5-b/VERSION 2017-06-06 20:31:35.943341213 +0000 +@@ -1 +1 @@ +-3.1.5-p7 ++3.1.5-p8 +diff -Naurd mpfr-3.1.5-a/src/mpf2mpfr.h mpfr-3.1.5-b/src/mpf2mpfr.h +--- mpfr-3.1.5-a/src/mpf2mpfr.h 2016-09-27 07:58:15.000000000 +0000 ++++ mpfr-3.1.5-b/src/mpf2mpfr.h 2017-06-06 20:31:35.931341353 +0000 +@@ -93,15 +93,15 @@ + #undef mpf_div_2exp + #define mpf_div_2exp(x,y,z) mpfr_div_2exp(x,y,z,MPFR_DEFAULT_RND) + #undef mpf_fits_slong_p +-#define mpf_fits_slong_p(x) mpfr_fits_ulong_p(x,MPFR_DEFAULT_RND) ++#define mpf_fits_slong_p(x) mpfr_fits_slong_p(x,MPFR_DEFAULT_RND) + #undef mpf_fits_ulong_p + #define mpf_fits_ulong_p(x) mpfr_fits_ulong_p(x,MPFR_DEFAULT_RND) + #undef mpf_fits_sint_p +-#define mpf_fits_sint_p(x) mpfr_fits_uint_p(x,MPFR_DEFAULT_RND) ++#define mpf_fits_sint_p(x) mpfr_fits_sint_p(x,MPFR_DEFAULT_RND) + #undef mpf_fits_uint_p + #define mpf_fits_uint_p(x) mpfr_fits_uint_p(x,MPFR_DEFAULT_RND) + #undef mpf_fits_sshort_p +-#define mpf_fits_sshort_p(x) mpfr_fits_ushort_p(x,MPFR_DEFAULT_RND) ++#define mpf_fits_sshort_p(x) mpfr_fits_sshort_p(x,MPFR_DEFAULT_RND) + #undef mpf_fits_ushort_p + #define mpf_fits_ushort_p(x) mpfr_fits_ushort_p(x,MPFR_DEFAULT_RND) + #undef mpf_get_str +@@ -113,7 +113,7 @@ + #undef mpf_get_ui + #define mpf_get_ui(x) mpfr_get_ui(x,MPFR_DEFAULT_RND) + #undef mpf_get_si +-#define mpf_get_si(x) mpfr_get_ui(x,MPFR_DEFAULT_RND) ++#define mpf_get_si(x) mpfr_get_si(x,MPFR_DEFAULT_RND) + #undef mpf_inp_str + #define mpf_inp_str(x,y,z) mpfr_inp_str(x,y,z,MPFR_DEFAULT_RND) + #undef mpf_set_str +diff -Naurd mpfr-3.1.5-a/src/mpfr-impl.h mpfr-3.1.5-b/src/mpfr-impl.h +--- mpfr-3.1.5-a/src/mpfr-impl.h 2017-06-06 19:21:17.592843433 +0000 ++++ mpfr-3.1.5-b/src/mpfr-impl.h 2017-06-06 20:31:35.931341353 +0000 +@@ -342,11 +342,15 @@ + #define MPFR_FLAGS_DIVBY0 32 + #define MPFR_FLAGS_ALL 63 + +-/* Replace some common functions for direct access to the global vars */ +-#define mpfr_get_emin() (__gmpfr_emin + 0) +-#define mpfr_get_emax() (__gmpfr_emax + 0) +-#define mpfr_get_default_rounding_mode() (__gmpfr_default_rounding_mode + 0) +-#define mpfr_get_default_prec() (__gmpfr_default_fp_bit_precision + 0) ++/* Replace some common functions for direct access to the global vars. ++ The casts prevent these macros from being used as a lvalue (and this ++ method makes sure that the expressions have the correct type). */ ++#define mpfr_get_emin() ((mpfr_exp_t) __gmpfr_emin) ++#define mpfr_get_emax() ((mpfr_exp_t) __gmpfr_emax) ++#define mpfr_get_default_rounding_mode() \ ++ ((mpfr_rnd_t) __gmpfr_default_rounding_mode) ++#define mpfr_get_default_prec() \ ++ ((mpfr_prec_t) __gmpfr_default_fp_bit_precision) + + #define mpfr_clear_flags() \ + ((void) (__gmpfr_flags = 0)) +diff -Naurd mpfr-3.1.5-a/src/mpfr.h mpfr-3.1.5-b/src/mpfr.h +--- mpfr-3.1.5-a/src/mpfr.h 2017-06-06 20:24:00.604701719 +0000 ++++ mpfr-3.1.5-b/src/mpfr.h 2017-06-06 20:31:35.939341259 +0000 +@@ -27,7 +27,7 @@ + #define MPFR_VERSION_MAJOR 3 + #define MPFR_VERSION_MINOR 1 + #define MPFR_VERSION_PATCHLEVEL 5 +-#define MPFR_VERSION_STRING "3.1.5-p7" ++#define MPFR_VERSION_STRING "3.1.5-p8" + + /* Macros dealing with MPFR VERSION */ + #define MPFR_VERSION_NUM(a,b,c) (((a) << 16L) | ((b) << 8) | (c)) +diff -Naurd mpfr-3.1.5-a/src/version.c mpfr-3.1.5-b/src/version.c +--- mpfr-3.1.5-a/src/version.c 2017-06-06 20:24:00.604701719 +0000 ++++ mpfr-3.1.5-b/src/version.c 2017-06-06 20:31:35.943341213 +0000 +@@ -25,5 +25,5 @@ + const char * + mpfr_get_version (void) + { +- return "3.1.5-p7"; ++ return "3.1.5-p8"; + } +diff -Naurd mpfr-3.1.5-a/tests/mpf_compat.h mpfr-3.1.5-b/tests/mpf_compat.h +--- mpfr-3.1.5-a/tests/mpf_compat.h 2016-09-27 07:58:14.000000000 +0000 ++++ mpfr-3.1.5-b/tests/mpf_compat.h 2017-06-06 20:31:35.931341353 +0000 +@@ -20,16 +20,10 @@ + http://www.gnu.org/licenses/ or write to the Free Software Foundation, Inc., + 51 Franklin St, Fifth Floor, Boston, MA 02110-1301, USA. */ + +-#if defined (__cplusplus) +-#include +-#else +-#include +-#endif + #include +-#include + +-#include "gmp.h" +-#include "mpfr.h" ++#include "mpfr-impl.h" ++ + #ifdef MPFR + #include "mpf2mpfr.h" + #endif +@@ -228,6 +222,16 @@ + exit (1); + } + ++ /* non-regression tests for bugs fixed in revision 11565 */ ++ mpf_set_si (x, -1); ++ MPFR_ASSERTN(mpf_fits_ulong_p (x) == 0); ++ MPFR_ASSERTN(mpf_fits_slong_p (x) != 0); ++ MPFR_ASSERTN(mpf_fits_uint_p (x) == 0); ++ MPFR_ASSERTN(mpf_fits_sint_p (x) != 0); ++ MPFR_ASSERTN(mpf_fits_ushort_p (x) == 0); ++ MPFR_ASSERTN(mpf_fits_sshort_p (x) != 0); ++ MPFR_ASSERTN(mpf_get_si (x) == -1); ++ + /* clear all variables */ + mpf_clear (y); + mpf_clear (x); +diff -Naurd mpfr-3.1.5-a/PATCHES mpfr-3.1.5-b/PATCHES +--- mpfr-3.1.5-a/PATCHES 2017-07-21 09:17:42.675157685 +0000 ++++ mpfr-3.1.5-b/PATCHES 2017-07-21 09:17:42.699157421 +0000 +@@ -0,0 +1 @@ ++sincos-overflow +diff -Naurd mpfr-3.1.5-a/VERSION mpfr-3.1.5-b/VERSION +--- mpfr-3.1.5-a/VERSION 2017-06-06 20:31:35.943341213 +0000 ++++ mpfr-3.1.5-b/VERSION 2017-07-21 09:17:42.699157421 +0000 +@@ -1 +1 @@ +-3.1.5-p8 ++3.1.5-p9 +diff -Naurd mpfr-3.1.5-a/src/mpfr.h mpfr-3.1.5-b/src/mpfr.h +--- mpfr-3.1.5-a/src/mpfr.h 2017-06-06 20:31:35.939341259 +0000 ++++ mpfr-3.1.5-b/src/mpfr.h 2017-07-21 09:17:42.699157421 +0000 +@@ -27,7 +27,7 @@ + #define MPFR_VERSION_MAJOR 3 + #define MPFR_VERSION_MINOR 1 + #define MPFR_VERSION_PATCHLEVEL 5 +-#define MPFR_VERSION_STRING "3.1.5-p8" ++#define MPFR_VERSION_STRING "3.1.5-p9" + + /* Macros dealing with MPFR VERSION */ + #define MPFR_VERSION_NUM(a,b,c) (((a) << 16L) | ((b) << 8) | (c)) +diff -Naurd mpfr-3.1.5-a/src/sin_cos.c mpfr-3.1.5-b/src/sin_cos.c +--- mpfr-3.1.5-a/src/sin_cos.c 2016-09-27 07:58:15.000000000 +0000 ++++ mpfr-3.1.5-b/src/sin_cos.c 2017-07-21 09:17:42.691157510 +0000 +@@ -350,10 +350,12 @@ + which reduces to T[k] = (2*i+2)*(2*i+3)*2^r-pp, + Q[k] = (2*i)*(2*i+1)*(2*i+2)*(2*i+3). */ + log2_nb_terms[k] = 1; +- mpz_set_ui (Q[k], (2 * i + 2) * (2 * i + 3)); ++ mpz_set_ui (Q[k], 2 * i + 2); ++ mpz_mul_ui (Q[k], Q[k], 2 * i + 3); + mpz_mul_2exp (T[k], Q[k], r); + mpz_sub (T[k], T[k], pp); +- mpz_mul_ui (Q[k], Q[k], (2 * i) * (2 * i + 1)); ++ mpz_mul_ui (Q[k], Q[k], 2 * i); ++ mpz_mul_ui (Q[k], Q[k], 2 * i + 1); + /* the next term of the series is divided by Q[k] and multiplied + by pp^2/2^(2r), thus the mult. factor < 1/2^mult[k] */ + mult[k] = mpz_sizeinbase (Q[k], 2) + 2 * r - size_ptoj[1] - 1; +diff -Naurd mpfr-3.1.5-a/src/version.c mpfr-3.1.5-b/src/version.c +--- mpfr-3.1.5-a/src/version.c 2017-06-06 20:31:35.943341213 +0000 ++++ mpfr-3.1.5-b/src/version.c 2017-07-21 09:17:42.699157421 +0000 +@@ -25,5 +25,5 @@ + const char * + mpfr_get_version (void) + { +- return "3.1.5-p8"; ++ return "3.1.5-p9"; + } +diff -Naurd mpfr-3.1.5-a/PATCHES mpfr-3.1.5-b/PATCHES +--- mpfr-3.1.5-a/PATCHES 2017-08-01 11:59:56.775365596 +0000 ++++ mpfr-3.1.5-b/PATCHES 2017-08-01 11:59:56.803365172 +0000 +@@ -0,0 +1 @@ ++mpf-compat-header +diff -Naurd mpfr-3.1.5-a/VERSION mpfr-3.1.5-b/VERSION +--- mpfr-3.1.5-a/VERSION 2017-07-21 09:17:42.699157421 +0000 ++++ mpfr-3.1.5-b/VERSION 2017-08-01 11:59:56.803365172 +0000 +@@ -1 +1 @@ +-3.1.5-p9 ++3.1.5-p10 +diff -Naurd mpfr-3.1.5-a/src/mpfr.h mpfr-3.1.5-b/src/mpfr.h +--- mpfr-3.1.5-a/src/mpfr.h 2017-07-21 09:17:42.699157421 +0000 ++++ mpfr-3.1.5-b/src/mpfr.h 2017-08-01 11:59:56.799365233 +0000 +@@ -27,7 +27,7 @@ + #define MPFR_VERSION_MAJOR 3 + #define MPFR_VERSION_MINOR 1 + #define MPFR_VERSION_PATCHLEVEL 5 +-#define MPFR_VERSION_STRING "3.1.5-p9" ++#define MPFR_VERSION_STRING "3.1.5-p10" + + /* Macros dealing with MPFR VERSION */ + #define MPFR_VERSION_NUM(a,b,c) (((a) << 16L) | ((b) << 8) | (c)) +diff -Naurd mpfr-3.1.5-a/src/version.c mpfr-3.1.5-b/src/version.c +--- mpfr-3.1.5-a/src/version.c 2017-07-21 09:17:42.699157421 +0000 ++++ mpfr-3.1.5-b/src/version.c 2017-08-01 11:59:56.803365172 +0000 +@@ -25,5 +25,5 @@ + const char * + mpfr_get_version (void) + { +- return "3.1.5-p9"; ++ return "3.1.5-p10"; + } +diff -Naurd mpfr-3.1.5-a/tests/mpf_compat.h mpfr-3.1.5-b/tests/mpf_compat.h +--- mpfr-3.1.5-a/tests/mpf_compat.h 2017-06-06 20:31:35.931341353 +0000 ++++ mpfr-3.1.5-b/tests/mpf_compat.h 2017-08-01 11:59:56.791365354 +0000 +@@ -22,7 +22,7 @@ + + #include + +-#include "mpfr-impl.h" ++#include "mpfr-test.h" + + #ifdef MPFR + #include "mpf2mpfr.h" -- GitLab From 8d8fca9a350521b543216f8709fe7cb481238b75 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 17 Aug 2017 10:19:27 +0200 Subject: [PATCH 1394/1603] add SC3 extension into bundle for Bioconductor 3.5 (+ dep extesions in R easyconfig) --- .../R-bundle-Bioconductor-3.5-intel-2017a-R-3.4.0.eb | 1 + easybuild/easyconfigs/r/R/R-3.4.0-intel-2017a-X11-20170314.eb | 2 ++ 2 files changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.5-intel-2017a-R-3.4.0.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.5-intel-2017a-R-3.4.0.eb index b8dbe2076f..43f571de80 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.5-intel-2017a-R-3.4.0.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.5-intel-2017a-R-3.4.0.eb @@ -160,6 +160,7 @@ exts_list = [ ('tximport', '1.4.0', bioconductor_options), ('scater', '1.4.0', bioconductor_options), ('scran', '1.4.5', bioconductor_options), + ('SC3', '1.4.2', bioconductor_options), ] modextrapaths = {'R_LIBS': ''} diff --git a/easybuild/easyconfigs/r/R/R-3.4.0-intel-2017a-X11-20170314.eb b/easybuild/easyconfigs/r/R/R-3.4.0-intel-2017a-X11-20170314.eb index 920853bd95..1f364643eb 100644 --- a/easybuild/easyconfigs/r/R/R-3.4.0-intel-2017a-X11-20170314.eb +++ b/easybuild/easyconfigs/r/R/R-3.4.0-intel-2017a-X11-20170314.eb @@ -550,6 +550,8 @@ exts_list = [ ('vipor', '0.4.5', ext_options), ('ggbeeswarm', '0.6.0', ext_options), ('shinydashboard', '0.6.1', ext_options), + ('rrcov', '1.4-3', ext_options), + ('WriteXLS', '4.0.0', ext_options), ] moduleclass = 'lang' -- GitLab From 17e5f9a308fb6b2031070219eb235e18dec0454c Mon Sep 17 00:00:00 2001 From: Joachim Hein Date: Thu, 17 Aug 2017 11:19:50 +0200 Subject: [PATCH 1395/1603] Addressing review comments: sha256sum, szip in GCCcore --- .../easyconfigs/h/HDF5/HDF5-1.10.1-foss-2017a.eb | 2 +- .../easyconfigs/h/HDF5/HDF5-1.10.1-intel-2017a.eb | 2 +- .../easyconfigs/h/HDF5/HDF5-1.8.19-foss-2017a.eb | 2 +- .../easyconfigs/h/HDF5/HDF5-1.8.19-intel-2017a.eb | 2 +- ...y-2.7.0-foss-2017a-Python-2.7.13-HDF5-1.10.1.eb | 2 +- ...y-2.7.0-foss-2017a-Python-2.7.13-HDF5-1.8.19.eb | 2 +- .../h/h5py/h5py-2.7.0-intel-2016b-Python-2.7.12.eb | 2 +- .../h/h5py/h5py-2.7.0-intel-2017a-Python-2.7.13.eb | 2 +- ...-intel-2017a-Python-3.6.1-HDF5-1.10.0-patch1.eb | 2 +- .../h/h5py/h5py-2.7.0-intel-2017a-Python-3.6.1.eb | 2 +- .../pkgconfig-1.2.2-foss-2017a-Python-2.7.13.eb | 1 + .../pkgconfig-1.2.2-intel-2017a-Python-2.7.13.eb | 1 + .../pkgconfig-1.2.2-intel-2017a-Python-3.6.1.eb | 1 + ...1-foss-2017a.eb => Szip-2.1.1-GCCcore-6.3.0.eb} | 14 +++++++++----- 14 files changed, 22 insertions(+), 15 deletions(-) rename easybuild/easyconfigs/s/Szip/{Szip-2.1.1-foss-2017a.eb => Szip-2.1.1-GCCcore-6.3.0.eb} (62%) diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.10.1-foss-2017a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.1-foss-2017a.eb index 9b47efe44f..3602950bf6 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.10.1-foss-2017a.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.1-foss-2017a.eb @@ -10,7 +10,7 @@ toolchainopts = {'pic': True, 'usempi': True} source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] -checksums = ['43a2f9466702fb1db31df98ae6677f15'] +checksums = ['048a9d149fb99aaa1680a712963f5a78e9c43b588d0e79d55e06760ec377c172'] dependencies = [ ('zlib', '1.2.11'), diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.10.1-intel-2017a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.1-intel-2017a.eb index 711b3163cb..5dce1430bd 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.10.1-intel-2017a.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.1-intel-2017a.eb @@ -10,7 +10,7 @@ toolchainopts = {'pic': True, 'usempi': True} source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] -checksums = ['43a2f9466702fb1db31df98ae6677f15'] +checksums = ['048a9d149fb99aaa1680a712963f5a78e9c43b588d0e79d55e06760ec377c172'] dependencies = [ ('zlib', '1.2.11'), diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.19-foss-2017a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.19-foss-2017a.eb index ee3d1c9446..9901d7d4d0 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.19-foss-2017a.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.19-foss-2017a.eb @@ -11,7 +11,7 @@ toolchainopts = {'pic': True, 'usempi': True} source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] -checksums = ['7f568e2464d4ab0a74d16b23956d900b'] +checksums = ['a4335849f19fae88c264fd0df046bc321a78c536b2548fc508627a790564dc38'] dependencies = [ ('zlib', '1.2.11'), diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.19-intel-2017a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.19-intel-2017a.eb index a3a8e59731..dd4bf512ac 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.19-intel-2017a.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.19-intel-2017a.eb @@ -15,7 +15,7 @@ checksums = ['a4335849f19fae88c264fd0df046bc321a78c536b2548fc508627a790564dc38'] dependencies = [ ('zlib', '1.2.11'), - ('Szip', '2.1'), + ('Szip', '2.1.1'), ] moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.7.0-foss-2017a-Python-2.7.13-HDF5-1.10.1.eb b/easybuild/easyconfigs/h/h5py/h5py-2.7.0-foss-2017a-Python-2.7.13-HDF5-1.10.1.eb index 3af541c153..8c68989177 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.7.0-foss-2017a-Python-2.7.13-HDF5-1.10.1.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.7.0-foss-2017a-Python-2.7.13-HDF5-1.10.1.eb @@ -13,7 +13,7 @@ toolchainopts = {'usempi': True} source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] -checksums = ['f62937f40f68d3b128b3941be239dd93'] +checksums = ['79254312df2e6154c4928f5e3b22f7a2847b6e5ffb05ddc33e37b16e76d36310'] hdf5ver = '1.10.1' versionsuffix = '-Python-%%(pyver)s-HDF5-%s' % hdf5ver diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.7.0-foss-2017a-Python-2.7.13-HDF5-1.8.19.eb b/easybuild/easyconfigs/h/h5py/h5py-2.7.0-foss-2017a-Python-2.7.13-HDF5-1.8.19.eb index eb3b1702ae..161594e20a 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.7.0-foss-2017a-Python-2.7.13-HDF5-1.8.19.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.7.0-foss-2017a-Python-2.7.13-HDF5-1.8.19.eb @@ -13,7 +13,7 @@ toolchainopts = {'usempi': True} source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] -checksums = ['f62937f40f68d3b128b3941be239dd93'] +checksums = ['79254312df2e6154c4928f5e3b22f7a2847b6e5ffb05ddc33e37b16e76d36310'] hdf5ver = '1.8.19' versionsuffix = '-Python-%%(pyver)s-HDF5-%s' % hdf5ver diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.7.0-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/h/h5py/h5py-2.7.0-intel-2016b-Python-2.7.12.eb index 404bad2e73..804ee87fa7 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.7.0-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.7.0-intel-2016b-Python-2.7.12.eb @@ -14,7 +14,7 @@ toolchainopts = {'usempi': True} source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] -checksums = ['f62937f40f68d3b128b3941be239dd93'] +checksums = ['79254312df2e6154c4928f5e3b22f7a2847b6e5ffb05ddc33e37b16e76d36310'] # to really use mpi enabled hdf5 we now seem to need a configure step prebuildopts = ' python setup.py configure --mpi --hdf5=$EBROOTHDF5 && ' diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.7.0-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/h/h5py/h5py-2.7.0-intel-2017a-Python-2.7.13.eb index e54f796b4d..d45cef772e 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.7.0-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.7.0-intel-2017a-Python-2.7.13.eb @@ -14,7 +14,7 @@ toolchainopts = {'usempi': True} source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] -checksums = ['f62937f40f68d3b128b3941be239dd93'] +checksums = ['79254312df2e6154c4928f5e3b22f7a2847b6e5ffb05ddc33e37b16e76d36310'] # to really use mpi enabled hdf5 we now seem to need a configure step prebuildopts = ' python setup.py configure --mpi --hdf5=$EBROOTHDF5 && ' diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.7.0-intel-2017a-Python-3.6.1-HDF5-1.10.0-patch1.eb b/easybuild/easyconfigs/h/h5py/h5py-2.7.0-intel-2017a-Python-3.6.1-HDF5-1.10.0-patch1.eb index 6a8d852d7a..cc8c2a68ed 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.7.0-intel-2017a-Python-3.6.1-HDF5-1.10.0-patch1.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.7.0-intel-2017a-Python-3.6.1-HDF5-1.10.0-patch1.eb @@ -15,7 +15,7 @@ toolchainopts = {'usempi': True} source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] -checksums = ['f62937f40f68d3b128b3941be239dd93'] +checksums = ['79254312df2e6154c4928f5e3b22f7a2847b6e5ffb05ddc33e37b16e76d36310'] # to really use mpi enabled hdf5 we now seem to need a configure step prebuildopts = ' python setup.py configure --mpi --hdf5=$EBROOTHDF5 && ' diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.7.0-intel-2017a-Python-3.6.1.eb b/easybuild/easyconfigs/h/h5py/h5py-2.7.0-intel-2017a-Python-3.6.1.eb index b93f4ba7bc..f4dfcfc6f1 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.7.0-intel-2017a-Python-3.6.1.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.7.0-intel-2017a-Python-3.6.1.eb @@ -14,7 +14,7 @@ toolchainopts = {'usempi': True} source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] -checksums = ['f62937f40f68d3b128b3941be239dd93'] +checksums = ['79254312df2e6154c4928f5e3b22f7a2847b6e5ffb05ddc33e37b16e76d36310'] # to really use mpi enabled hdf5 we now seem to need a configure step prebuildopts = ' python setup.py configure --mpi --hdf5=$EBROOTHDF5 && ' diff --git a/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.2.2-foss-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.2.2-foss-2017a-Python-2.7.13.eb index da605c6661..e54de3e92a 100644 --- a/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.2.2-foss-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.2.2-foss-2017a-Python-2.7.13.eb @@ -12,6 +12,7 @@ toolchainopts = {'usempi': True} source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] +checksums = ['3685ba02a9b72654a764b728b559f327e1dbd7dc6ebc310a1bd429666ee202aa'] dependencies = [ ('Python', '2.7.13'), diff --git a/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.2.2-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.2.2-intel-2017a-Python-2.7.13.eb index 0df86ffc84..ff106d3134 100644 --- a/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.2.2-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.2.2-intel-2017a-Python-2.7.13.eb @@ -12,6 +12,7 @@ toolchainopts = {'usempi': True} source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] +checksums = ['3685ba02a9b72654a764b728b559f327e1dbd7dc6ebc310a1bd429666ee202aa'] dependencies = [ ('Python', '2.7.13'), diff --git a/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.2.2-intel-2017a-Python-3.6.1.eb b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.2.2-intel-2017a-Python-3.6.1.eb index 5b31de03c1..a39cb8174c 100644 --- a/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.2.2-intel-2017a-Python-3.6.1.eb +++ b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.2.2-intel-2017a-Python-3.6.1.eb @@ -12,6 +12,7 @@ toolchainopts = {'usempi': True} source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] +checksums = ['3685ba02a9b72654a764b728b559f327e1dbd7dc6ebc310a1bd429666ee202aa'] dependencies = [ ('Python', '3.6.1'), diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-foss-2017a.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-6.3.0.eb similarity index 62% rename from easybuild/easyconfigs/s/Szip/Szip-2.1.1-foss-2017a.eb rename to easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-6.3.0.eb index 19df3f68d9..16ddff6e90 100644 --- a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-foss-2017a.eb +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-6.3.0.eb @@ -4,17 +4,21 @@ name = 'Szip' version = '2.1.1' homepage = 'http://www.hdfgroup.org/doc_resource/SZIP/' -description = "Szip compression software, providing lossless compression of scientific data" -toolchain = {'name': 'foss', 'version': '2017a'} +description = """ + Szip compression software, providing lossless compression of scientific data +""" + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} toolchainopts = {'pic': True} source_urls = ['http://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] -checksums = ['dd579cf0f26d44afd10a0ad7291fc282'] - +checksums = ['897dda94e1d4bf88c91adeaad88c07b468b18eaf2d6125c47acac57e540904a9'] -configopts = "--with-pic" +builddependencies = [ + ('binutils', '2.28'), +] sanity_check_paths = { 'files': ["lib/libsz.a", "lib/libsz.%s" % SHLIB_EXT] + -- GitLab From 0d0d6d0b469c15c92504ba22fe2faa998da13659 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 17 Aug 2017 13:49:13 +0200 Subject: [PATCH 1396/1603] add mpath as extension for R 3.4.0 --- easybuild/easyconfigs/r/R/R-3.4.0-intel-2017a-X11-20170314.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/r/R/R-3.4.0-intel-2017a-X11-20170314.eb b/easybuild/easyconfigs/r/R/R-3.4.0-intel-2017a-X11-20170314.eb index 1f364643eb..8ec992e75a 100644 --- a/easybuild/easyconfigs/r/R/R-3.4.0-intel-2017a-X11-20170314.eb +++ b/easybuild/easyconfigs/r/R/R-3.4.0-intel-2017a-X11-20170314.eb @@ -552,6 +552,7 @@ exts_list = [ ('shinydashboard', '0.6.1', ext_options), ('rrcov', '1.4-3', ext_options), ('WriteXLS', '4.0.0', ext_options), + ('mpath', '0.2-4', ext_options), ] moduleclass = 'lang' -- GitLab From 8849bb384b10a8a0592898404f99cd9f26fba263 Mon Sep 17 00:00:00 2001 From: Joachim Hein Date: Thu, 17 Aug 2017 15:14:16 +0200 Subject: [PATCH 1397/1603] Update to sha256 and proper sanity check on shared object --- .../easyconfigs/l/libsodium/libsodium-1.0.13-foss-2017a.eb | 2 +- easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-foss-2015a.eb | 2 +- easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-foss-2016a.eb | 2 +- easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-foss-2016b.eb | 2 +- easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-foss-2017a.eb | 2 +- .../easyconfigs/o/OpenPGM/OpenPGM-5.2.122-goolf-1.4.10.eb | 2 +- .../easyconfigs/o/OpenPGM/OpenPGM-5.2.122-goolf-1.7.20.eb | 2 +- .../easyconfigs/o/OpenPGM/OpenPGM-5.2.122-ictce-5.3.0.eb | 2 +- .../easyconfigs/o/OpenPGM/OpenPGM-5.2.122-ictce-5.5.0.eb | 2 +- .../easyconfigs/o/OpenPGM/OpenPGM-5.2.122-intel-2015a.eb | 2 +- .../easyconfigs/o/OpenPGM/OpenPGM-5.2.122-intel-2015b.eb | 2 +- .../easyconfigs/o/OpenPGM/OpenPGM-5.2.122-intel-2016a.eb | 2 ++ .../easyconfigs/o/OpenPGM/OpenPGM-5.2.122-intel-2016b.eb | 2 +- .../easyconfigs/o/OpenPGM/OpenPGM-5.2.122-intel-2017a.eb | 2 +- .../p/PyZMQ/PyZMQ-16.0.2-foss-2016b-Python-2.7.12-zmq4.eb | 2 +- .../p/PyZMQ/PyZMQ-16.0.2-foss-2016b-Python-3.5.2-zmq4.eb | 2 +- .../p/PyZMQ/PyZMQ-16.0.2-foss-2017a-Python-2.7.13-zmq4.eb | 2 +- .../p/PyZMQ/PyZMQ-16.0.2-intel-2016b-Python-2.7.12-zmq4.eb | 2 +- .../p/PyZMQ/PyZMQ-16.0.2-intel-2016b-Python-3.5.2-zmq4.eb | 2 +- .../p/PyZMQ/PyZMQ-16.0.2-intel-2017a-Python-2.7.13-zmq4.eb | 2 +- .../easyconfigs/u/util-linux/util-linux-2.30.1-foss-2017a.eb | 2 +- easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.2.2-foss-2017a.eb | 4 ++-- easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.2.2-intel-2017a.eb | 2 +- 23 files changed, 25 insertions(+), 23 deletions(-) diff --git a/easybuild/easyconfigs/l/libsodium/libsodium-1.0.13-foss-2017a.eb b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.13-foss-2017a.eb index 8853e15fa5..567630149b 100644 --- a/easybuild/easyconfigs/l/libsodium/libsodium-1.0.13-foss-2017a.eb +++ b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.13-foss-2017a.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'foss', 'version': '2017a'} source_urls = ['https://download.libsodium.org/libsodium/releases/'] sources = [SOURCE_TAR_GZ] -checksums = ['f38aac160a4bd05f06f743863e54e499'] +checksums = ['9c13accb1a9e59ab3affde0e60ef9a2149ed4d6e8f99c93c7a5b97499ee323fd'] sanity_check_paths = { 'files': ['include/sodium.h', 'lib/libsodium.%s' % SHLIB_EXT, 'lib/libsodium.a'], diff --git a/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-foss-2015a.eb b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-foss-2015a.eb index 2ae64198e6..8c9749f6d7 100644 --- a/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-foss-2015a.eb +++ b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-foss-2015a.eb @@ -15,7 +15,7 @@ toolchain = {'name': 'foss', 'version': '2015a'} source_urls = ['https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/openpgm/'] sources = ['libpgm-%(version)s.tar.gz'] -checksums = ['d7673e9ff6cc33cf42fe9fb9a7bfbffa'] +checksums = ['6b895f550b95284dcde7189b01e04a9a1c1f94579af31b1eebd32c2207a1ba2c'] configopts = '--with-pic' diff --git a/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-foss-2016a.eb b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-foss-2016a.eb index a3d2763924..1e572118ec 100644 --- a/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-foss-2016a.eb +++ b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-foss-2016a.eb @@ -15,7 +15,7 @@ toolchain = {'name': 'foss', 'version': '2016a'} source_urls = ['https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/openpgm/'] sources = ['libpgm-%(version)s.tar.gz'] -checksums = ['d7673e9ff6cc33cf42fe9fb9a7bfbffa'] +checksums = ['6b895f550b95284dcde7189b01e04a9a1c1f94579af31b1eebd32c2207a1ba2c'] configopts = '--with-pic' diff --git a/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-foss-2016b.eb b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-foss-2016b.eb index 3584a3c705..a79da5bcde 100644 --- a/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-foss-2016b.eb +++ b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-foss-2016b.eb @@ -16,7 +16,7 @@ toolchainopts = {'pic': True} source_urls = ['https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/openpgm/'] sources = ['libpgm-%(version)s.tar.gz'] -checksums = ['d7673e9ff6cc33cf42fe9fb9a7bfbffa'] +checksums = ['6b895f550b95284dcde7189b01e04a9a1c1f94579af31b1eebd32c2207a1ba2c'] configopts = '--with-pic' diff --git a/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-foss-2017a.eb b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-foss-2017a.eb index 93a030d6ea..52f0a98f0e 100644 --- a/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-foss-2017a.eb +++ b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-foss-2017a.eb @@ -16,7 +16,7 @@ toolchainopts = {'pic': True} source_urls = ['https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/openpgm/'] sources = ['libpgm-%(version)s.tar.gz'] -checksums = ['d7673e9ff6cc33cf42fe9fb9a7bfbffa'] +checksums = ['6b895f550b95284dcde7189b01e04a9a1c1f94579af31b1eebd32c2207a1ba2c'] configopts = '--with-pic' diff --git a/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-goolf-1.4.10.eb b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-goolf-1.4.10.eb index ba0d346657..c72f7c67ea 100644 --- a/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-goolf-1.4.10.eb @@ -15,7 +15,7 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} source_urls = ['https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/openpgm/'] sources = ['%s-%s.tar.gz' % ('libpgm', version)] -checksums = ['d7673e9ff6cc33cf42fe9fb9a7bfbffa'] +checksums = ['6b895f550b95284dcde7189b01e04a9a1c1f94579af31b1eebd32c2207a1ba2c'] configopts = '--with-pic' diff --git a/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-goolf-1.7.20.eb b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-goolf-1.7.20.eb index 34fa9dd22f..5e32b43ba4 100644 --- a/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-goolf-1.7.20.eb @@ -15,7 +15,7 @@ toolchain = {'name': 'goolf', 'version': '1.7.20'} source_urls = ['https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/openpgm/'] sources = ['libpgm-%(version)s.tar.gz'] -checksums = ['d7673e9ff6cc33cf42fe9fb9a7bfbffa'] +checksums = ['6b895f550b95284dcde7189b01e04a9a1c1f94579af31b1eebd32c2207a1ba2c'] configopts = '--with-pic' diff --git a/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-ictce-5.3.0.eb b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-ictce-5.3.0.eb index 5c73a02ebe..c1cc929d31 100644 --- a/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-ictce-5.3.0.eb @@ -16,7 +16,7 @@ toolchain = {'name': 'ictce', 'version': '5.3.0'} source_urls = ['https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/openpgm/'] sources = ['%s-%s.tar.gz' % ('libpgm', version)] -checksums = ['d7673e9ff6cc33cf42fe9fb9a7bfbffa'] +checksums = ['6b895f550b95284dcde7189b01e04a9a1c1f94579af31b1eebd32c2207a1ba2c'] configopts = '--with-pic' diff --git a/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-ictce-5.5.0.eb b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-ictce-5.5.0.eb index d10ebd9897..1adecf3498 100644 --- a/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-ictce-5.5.0.eb @@ -15,7 +15,7 @@ toolchain = {'name': 'ictce', 'version': '5.5.0'} source_urls = ['https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/openpgm/'] sources = ['%s-%s.tar.gz' % ('libpgm', version)] -checksums = ['d7673e9ff6cc33cf42fe9fb9a7bfbffa'] +checksums = ['6b895f550b95284dcde7189b01e04a9a1c1f94579af31b1eebd32c2207a1ba2c'] configopts = '--with-pic' diff --git a/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-intel-2015a.eb b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-intel-2015a.eb index b7949218e2..58b6d631b5 100644 --- a/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-intel-2015a.eb +++ b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-intel-2015a.eb @@ -15,7 +15,7 @@ toolchain = {'name': 'intel', 'version': '2015a'} source_urls = ['https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/openpgm/'] sources = ['libpgm-%(version)s.tar.gz'] -checksums = ['d7673e9ff6cc33cf42fe9fb9a7bfbffa'] +checksums = ['6b895f550b95284dcde7189b01e04a9a1c1f94579af31b1eebd32c2207a1ba2c'] configopts = '--with-pic' diff --git a/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-intel-2015b.eb b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-intel-2015b.eb index abec09000c..07b7e0f6ed 100644 --- a/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-intel-2015b.eb +++ b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-intel-2015b.eb @@ -16,7 +16,7 @@ toolchainopts = {'pic': True} source_urls = ['https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/openpgm/'] sources = ['libpgm-%(version)s.tar.gz'] -checksums = ['d7673e9ff6cc33cf42fe9fb9a7bfbffa'] +checksums = ['6b895f550b95284dcde7189b01e04a9a1c1f94579af31b1eebd32c2207a1ba2c'] configopts = '--with-pic' diff --git a/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-intel-2016a.eb b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-intel-2016a.eb index 803b19d70e..682da56278 100644 --- a/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-intel-2016a.eb +++ b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-intel-2016a.eb @@ -16,6 +16,8 @@ toolchainopts = {'pic': True} source_urls = ['https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/openpgm/'] sources = ['libpgm-%(version)s.tar.gz'] +checksums = ['6b895f550b95284dcde7189b01e04a9a1c1f94579af31b1eebd32c2207a1ba2c'] + configopts = '--with-pic' start_dir = 'pgm' diff --git a/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-intel-2016b.eb b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-intel-2016b.eb index f8d13d0834..d3070d3fff 100644 --- a/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-intel-2016b.eb +++ b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-intel-2016b.eb @@ -16,7 +16,7 @@ toolchainopts = {'pic': True} source_urls = ['https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/openpgm/'] sources = ['libpgm-%(version)s.tar.gz'] -checksums = ['d7673e9ff6cc33cf42fe9fb9a7bfbffa'] +checksums = ['6b895f550b95284dcde7189b01e04a9a1c1f94579af31b1eebd32c2207a1ba2c'] configopts = '--with-pic' diff --git a/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-intel-2017a.eb b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-intel-2017a.eb index d604042523..3a38432402 100644 --- a/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-intel-2017a.eb +++ b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-intel-2017a.eb @@ -16,7 +16,7 @@ toolchainopts = {'pic': True} source_urls = ['https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/openpgm/'] sources = ['libpgm-%(version)s.tar.gz'] -checksums = ['d7673e9ff6cc33cf42fe9fb9a7bfbffa'] +checksums = ['6b895f550b95284dcde7189b01e04a9a1c1f94579af31b1eebd32c2207a1ba2c'] configopts = '--with-pic' diff --git a/easybuild/easyconfigs/p/PyZMQ/PyZMQ-16.0.2-foss-2016b-Python-2.7.12-zmq4.eb b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-16.0.2-foss-2016b-Python-2.7.12-zmq4.eb index 2ae02cf975..d3c80e646a 100644 --- a/easybuild/easyconfigs/p/PyZMQ/PyZMQ-16.0.2-foss-2016b-Python-2.7.12-zmq4.eb +++ b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-16.0.2-foss-2016b-Python-2.7.12-zmq4.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'foss', 'version': '2016b'} source_urls = [PYPI_LOWER_SOURCE] sources = [SOURCELOWER_TAR_GZ] -checksums = ['9a8768b00a566a400d70318f8c359cfe'] +checksums = ['0322543fff5ab6f87d11a8a099c4c07dd8a1719040084b6ce9162bcdf5c45c9d'] dependencies = [ ('Python', '2.7.12'), diff --git a/easybuild/easyconfigs/p/PyZMQ/PyZMQ-16.0.2-foss-2016b-Python-3.5.2-zmq4.eb b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-16.0.2-foss-2016b-Python-3.5.2-zmq4.eb index a6d0276b23..6cf529a2fe 100644 --- a/easybuild/easyconfigs/p/PyZMQ/PyZMQ-16.0.2-foss-2016b-Python-3.5.2-zmq4.eb +++ b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-16.0.2-foss-2016b-Python-3.5.2-zmq4.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'foss', 'version': '2016b'} source_urls = [PYPI_LOWER_SOURCE] sources = [SOURCELOWER_TAR_GZ] -checksums = ['9a8768b00a566a400d70318f8c359cfe'] +checksums = ['0322543fff5ab6f87d11a8a099c4c07dd8a1719040084b6ce9162bcdf5c45c9d'] dependencies = [ ('Python', '3.5.2'), diff --git a/easybuild/easyconfigs/p/PyZMQ/PyZMQ-16.0.2-foss-2017a-Python-2.7.13-zmq4.eb b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-16.0.2-foss-2017a-Python-2.7.13-zmq4.eb index ecb43ca881..02249f164c 100644 --- a/easybuild/easyconfigs/p/PyZMQ/PyZMQ-16.0.2-foss-2017a-Python-2.7.13-zmq4.eb +++ b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-16.0.2-foss-2017a-Python-2.7.13-zmq4.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'foss', 'version': '2017a'} source_urls = [PYPI_LOWER_SOURCE] sources = [SOURCELOWER_TAR_GZ] -checksums = ['9a8768b00a566a400d70318f8c359cfe'] +checksums = ['0322543fff5ab6f87d11a8a099c4c07dd8a1719040084b6ce9162bcdf5c45c9d'] dependencies = [ ('Python', '2.7.13'), diff --git a/easybuild/easyconfigs/p/PyZMQ/PyZMQ-16.0.2-intel-2016b-Python-2.7.12-zmq4.eb b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-16.0.2-intel-2016b-Python-2.7.12-zmq4.eb index 83db644170..a00c9bd4c1 100644 --- a/easybuild/easyconfigs/p/PyZMQ/PyZMQ-16.0.2-intel-2016b-Python-2.7.12-zmq4.eb +++ b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-16.0.2-intel-2016b-Python-2.7.12-zmq4.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'intel', 'version': '2016b'} source_urls = [PYPI_LOWER_SOURCE] sources = [SOURCELOWER_TAR_GZ] -checksums = ['9a8768b00a566a400d70318f8c359cfe'] +checksums = ['0322543fff5ab6f87d11a8a099c4c07dd8a1719040084b6ce9162bcdf5c45c9d'] dependencies = [ ('Python', '2.7.12'), diff --git a/easybuild/easyconfigs/p/PyZMQ/PyZMQ-16.0.2-intel-2016b-Python-3.5.2-zmq4.eb b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-16.0.2-intel-2016b-Python-3.5.2-zmq4.eb index 0d5d945f58..fb1bfb907f 100644 --- a/easybuild/easyconfigs/p/PyZMQ/PyZMQ-16.0.2-intel-2016b-Python-3.5.2-zmq4.eb +++ b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-16.0.2-intel-2016b-Python-3.5.2-zmq4.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'intel', 'version': '2016b'} source_urls = [PYPI_LOWER_SOURCE] sources = [SOURCELOWER_TAR_GZ] -checksums = ['9a8768b00a566a400d70318f8c359cfe'] +checksums = ['0322543fff5ab6f87d11a8a099c4c07dd8a1719040084b6ce9162bcdf5c45c9d'] dependencies = [ ('Python', '3.5.2'), diff --git a/easybuild/easyconfigs/p/PyZMQ/PyZMQ-16.0.2-intel-2017a-Python-2.7.13-zmq4.eb b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-16.0.2-intel-2017a-Python-2.7.13-zmq4.eb index 3ee565a8d9..e68bb9c4ba 100644 --- a/easybuild/easyconfigs/p/PyZMQ/PyZMQ-16.0.2-intel-2017a-Python-2.7.13-zmq4.eb +++ b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-16.0.2-intel-2017a-Python-2.7.13-zmq4.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'intel', 'version': '2017a'} source_urls = [PYPI_LOWER_SOURCE] sources = [SOURCELOWER_TAR_GZ] -checksums = ['9a8768b00a566a400d70318f8c359cfe'] +checksums = ['0322543fff5ab6f87d11a8a099c4c07dd8a1719040084b6ce9162bcdf5c45c9d'] dependencies = [ ('Python', '2.7.13'), diff --git a/easybuild/easyconfigs/u/util-linux/util-linux-2.30.1-foss-2017a.eb b/easybuild/easyconfigs/u/util-linux/util-linux-2.30.1-foss-2017a.eb index dabbcbd2d4..2a3a18b7cb 100644 --- a/easybuild/easyconfigs/u/util-linux/util-linux-2.30.1-foss-2017a.eb +++ b/easybuild/easyconfigs/u/util-linux/util-linux-2.30.1-foss-2017a.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'foss', 'version': '2017a'} source_urls = ['%s/v%%(version_major_minor)s' % homepage] sources = [SOURCELOWER_TAR_GZ] -checksums = ['22a860a2d98367e73e414a09dfaf3866'] +checksums = ['88bb1d08f0d67fb1b548c3e2160f7f40fb552cdf6b771a5dd1b94e1e04fc1d9a'] # disable account related utilities (they need OS dependant pam-devel files) # disable wall and friends (requires group changing permissions for install user) diff --git a/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.2.2-foss-2017a.eb b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.2.2-foss-2017a.eb index d690b704a1..d71e55139a 100644 --- a/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.2.2-foss-2017a.eb +++ b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.2.2-foss-2017a.eb @@ -15,7 +15,7 @@ toolchain = {'name': 'foss', 'version': '2017a'} source_urls = ['https://github.com/zeromq/libzmq/releases/download/v%(version)s/'] sources = [SOURCELOWER_TAR_GZ] -checksums = ['52499909b29604c1e47a86f1cb6a9115'] +checksums = ['5b23f4ca9ef545d5bd3af55d305765e3ee06b986263b31967435d285a3e6df6b'] # --with-pgm will use shipped OpenPGM (in foreign subdir) configopts = '--with-pic --with-system-pgm ' @@ -29,7 +29,7 @@ dependencies = [ ] sanity_check_paths = { - 'files': ['lib/libzmq.so', 'lib/libzmq.a'], + 'files': ['lib/libzmq.%s' % SHLIB_EXT, 'lib/libzmq.a'], 'dirs': ['include', 'lib'], } diff --git a/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.2.2-intel-2017a.eb b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.2.2-intel-2017a.eb index 165ba15944..20cd4f5b63 100644 --- a/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.2.2-intel-2017a.eb +++ b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.2.2-intel-2017a.eb @@ -15,7 +15,7 @@ toolchain = {'name': 'intel', 'version': '2017a'} source_urls = ['https://github.com/zeromq/libzmq/releases/download/v%(version)s/'] sources = [SOURCELOWER_TAR_GZ] -checksums = ['52499909b29604c1e47a86f1cb6a9115'] +checksums = ['5b23f4ca9ef545d5bd3af55d305765e3ee06b986263b31967435d285a3e6df6b'] # --with-pgm will use shipped OpenPGM (in foreign subdir) configopts = '--with-pic --with-system-pgm ' -- GitLab From 7bce5dbda57fa1608fefc8065593494bf26f9b10 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 17 Aug 2017 18:02:17 +0200 Subject: [PATCH 1398/1603] adding easyconfigs: Hadoop-2.6.0-cdh5.12.0-native.eb, snappy-1.1.6.eb --- .../h/Hadoop/Hadoop-2.6.0-cdh5.12.0-native.eb | 31 +++++++++++++++++++ .../easyconfigs/s/snappy/snappy-1.1.6.eb | 24 ++++++++++++++ 2 files changed, 55 insertions(+) create mode 100644 easybuild/easyconfigs/h/Hadoop/Hadoop-2.6.0-cdh5.12.0-native.eb create mode 100644 easybuild/easyconfigs/s/snappy/snappy-1.1.6.eb diff --git a/easybuild/easyconfigs/h/Hadoop/Hadoop-2.6.0-cdh5.12.0-native.eb b/easybuild/easyconfigs/h/Hadoop/Hadoop-2.6.0-cdh5.12.0-native.eb new file mode 100644 index 0000000000..bc2f4774b0 --- /dev/null +++ b/easybuild/easyconfigs/h/Hadoop/Hadoop-2.6.0-cdh5.12.0-native.eb @@ -0,0 +1,31 @@ +name = 'Hadoop' +version = '2.6.0-cdh5.12.0' +versionsuffix = '-native' + +homepage = 'http://archive.cloudera.com/cdh5/cdh/5/' +description = """Hadoop MapReduce by Cloudera""" + +toolchain = {'name': 'dummy', 'version': ''} + +sources = ['%(namelower)s-%(version)s-src.tar.gz'] +source_urls = ['http://archive.cloudera.com/cdh5/cdh/5/'] +checksums = ['6eb2ff649ae1c5d1271732ca766b4e03728190ac4274ab00748ef8c44aa6e8d5'] + +patches = ['Hadoop-TeraSort-on-local-filesystem.patch'] + +builddependencies = [ + ('Maven', '3.5.0'), + ('protobuf', '2.5.0'), # *must* be this version + ('CMake', '3.9.1'), + ('snappy', '1.1.6'), +] + +dependencies = [('Java', '1.7.0_80')] + +build_native_libs = True + +extra_native_libs = [('snappy', 'lib/libsnappy.so*')] + +parallel = 1 + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/snappy/snappy-1.1.6.eb b/easybuild/easyconfigs/s/snappy/snappy-1.1.6.eb new file mode 100644 index 0000000000..7a976b306d --- /dev/null +++ b/easybuild/easyconfigs/s/snappy/snappy-1.1.6.eb @@ -0,0 +1,24 @@ +easyblock = 'CMakeMake' + +name = 'snappy' +version = '1.1.6' + +homepage = 'https://github.com/google/snappy' +description = """Snappy is a compression/decompression library. It does not aim +for maximum compression, or compatibility with any other compression library; +instead, it aims for very high speeds and reasonable compression.""" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = ['https://github.com/google/snappy/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['6fa92cde5b2caefd0d9a60336991ba42e5a7ddc3bdc36c5610451373751d0495'] + +builddependencies = [('CMake', '3.9.1')] + +sanity_check_paths = { + 'files': ['lib/libsnappy.%s' % SHLIB_EXT], + 'dirs': ['include'] +} + +moduleclass = 'lib' -- GitLab From 03e0bd232f702b9af03b74695867e0beee07fa31 Mon Sep 17 00:00:00 2001 From: Joachim Hein Date: Fri, 18 Aug 2017 12:30:33 +0200 Subject: [PATCH 1399/1603] Python 3.6.1 in foss 2016 with matplot lib and h5py bindings Python 3.6.1 in foss 2016 with matplot lib and h5py bindings Also sha256 checksum for Python 3.6.1 in intel 2017a --- ...7.0-foss-2017a-Python-3.6.1-HDF5-1.10.1.eb | 35 +++++ ...7.0-foss-2017a-Python-3.6.1-HDF5-1.8.19.eb | 35 +++++ ...atplotlib-2.0.2-foss-2017a-Python-3.6.1.eb | 48 +++++++ .../p/Python/Python-3.6.1-foss-2017a.eb | 134 ++++++++++++++++++ .../p/Python/Python-3.6.1-intel-2017a.eb | 1 + ...pkgconfig-1.2.2-foss-2017a-Python-3.6.1.eb | 27 ++++ 6 files changed, 280 insertions(+) create mode 100644 easybuild/easyconfigs/h/h5py/h5py-2.7.0-foss-2017a-Python-3.6.1-HDF5-1.10.1.eb create mode 100644 easybuild/easyconfigs/h/h5py/h5py-2.7.0-foss-2017a-Python-3.6.1-HDF5-1.8.19.eb create mode 100644 easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.2-foss-2017a-Python-3.6.1.eb create mode 100644 easybuild/easyconfigs/p/Python/Python-3.6.1-foss-2017a.eb create mode 100644 easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.2.2-foss-2017a-Python-3.6.1.eb diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.7.0-foss-2017a-Python-3.6.1-HDF5-1.10.1.eb b/easybuild/easyconfigs/h/h5py/h5py-2.7.0-foss-2017a-Python-3.6.1-HDF5-1.10.1.eb new file mode 100644 index 0000000000..3ed36781b7 --- /dev/null +++ b/easybuild/easyconfigs/h/h5py/h5py-2.7.0-foss-2017a-Python-3.6.1-HDF5-1.10.1.eb @@ -0,0 +1,35 @@ +easyblock = "PythonPackage" + +name = 'h5py' +version = '2.7.0' + +homepage = 'http://www.h5py.org/' +description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, + version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous + amounts of data.""" + +toolchain = {'name': 'foss', 'version': '2017a'} +toolchainopts = {'usempi': True} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['79254312df2e6154c4928f5e3b22f7a2847b6e5ffb05ddc33e37b16e76d36310'] + +hdf5ver = '1.10.1' +versionsuffix = '-Python-%%(pyver)s-HDF5-%s' % hdf5ver + +# to really use mpi enabled hdf5 we now seem to need a configure step +prebuildopts = ' python setup.py configure --mpi --hdf5=$EBROOTHDF5 && ' + +dependencies = [ + ('Python', '3.6.1'), + ('HDF5', hdf5ver), + ('pkgconfig', '1.2.2', '-Python-%(pyver)s'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.7.0-foss-2017a-Python-3.6.1-HDF5-1.8.19.eb b/easybuild/easyconfigs/h/h5py/h5py-2.7.0-foss-2017a-Python-3.6.1-HDF5-1.8.19.eb new file mode 100644 index 0000000000..458d5d85f9 --- /dev/null +++ b/easybuild/easyconfigs/h/h5py/h5py-2.7.0-foss-2017a-Python-3.6.1-HDF5-1.8.19.eb @@ -0,0 +1,35 @@ +easyblock = "PythonPackage" + +name = 'h5py' +version = '2.7.0' + +homepage = 'http://www.h5py.org/' +description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, + version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous + amounts of data.""" + +toolchain = {'name': 'foss', 'version': '2017a'} +toolchainopts = {'usempi': True} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['79254312df2e6154c4928f5e3b22f7a2847b6e5ffb05ddc33e37b16e76d36310'] + +hdf5ver = '1.8.19' +versionsuffix = '-Python-%%(pyver)s-HDF5-%s' % hdf5ver + +# to really use mpi enabled hdf5 we now seem to need a configure step +prebuildopts = ' python setup.py configure --mpi --hdf5=$EBROOTHDF5 && ' + +dependencies = [ + ('Python', '3.6.1'), + ('HDF5', hdf5ver), + ('pkgconfig', '1.2.2', '-Python-%(pyver)s'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.2-foss-2017a-Python-3.6.1.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.2-foss-2017a-Python-3.6.1.eb new file mode 100644 index 0000000000..4d2040eef8 --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.0.2-foss-2017a-Python-3.6.1.eb @@ -0,0 +1,48 @@ +easyblock = 'Bundle' + +name = 'matplotlib' +version = '2.0.2' +versionsuffix = '-Python-%(pyver)s' + +libpng_ver = '1.6.29' + +homepage = 'http://matplotlib.org' +description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of + hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python + and ipython shell, web application servers, and six graphical user interface toolkits.""" + +toolchain = {'name': 'foss', 'version': '2017a'} + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' + +dependencies = [ + ('Python', '3.6.1'), + ('libpng', libpng_ver), + ('freetype', '2.7.1', '-libpng-%s' % libpng_ver), +] + +exts_list = [ + ('Cycler', '0.10.0', { + 'modulename': 'cycler', + 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], + 'source_tmpl': 'cycler-%(version)s.tar.gz', + 'checksums': ['cd7b2d1018258d7247a71425e9f26463dfb444d411c39569972f4ce586b0c9d8'], + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], + 'checksums': ['0ffbc44faa34a8b1704bc108c451ecf87988f900ef7ce757b8e2e84383121ff1'], + }), +] + +# specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module +full_sanity_check = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/Python/Python-3.6.1-foss-2017a.eb b/easybuild/easyconfigs/p/Python/Python-3.6.1-foss-2017a.eb new file mode 100644 index 0000000000..6f2470bf49 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-3.6.1-foss-2017a.eb @@ -0,0 +1,134 @@ +name = 'Python' +version = '3.6.1' + +homepage = 'http://python.org/' +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" + +toolchain = {'name': 'foss', 'version': '2017a'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] +checksums = ['aa50b0143df7c89ce91be020fe41382613a817354b33acdc6641b44f8ced3828'] + +# python needs bzip2 to build the bz2 package +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.11'), + ('libreadline', '7.0'), + ('ncurses', '6.0'), + ('SQLite', '3.17.0'), + ('GMP', '6.1.2'), + ('XZ', '5.2.3'), + ('libffi', '3.2.1'), + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.2k'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# order is important! +# package versions updated May 28th 2015 +exts_list = [ + # note: more recent versions of setuptools (v34.x) can not be installed from source anymore, + # see https://github.com/pypa/setuptools/issues/980 + ('setuptools', '33.1.1', { + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], + 'source_tmpl': '%(name)s-%(version)s.zip', + }), + ('pip', '9.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], + }), + ('nose', '1.3.7', { + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], + }), + ('numpy', '1.12.1', { + 'source_urls': ['https://pypi.python.org/packages/source/n/numpy'], + 'source_tmpl': '%(name)s-%(version)s.zip', + 'patches': ['numpy-1.12.0-mkl.patch'], + }), + ('scipy', '0.19.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/scipy'], + 'source_tmpl': '%(name)s-%(version)s.zip', + }), + ('blist', '1.3.6', { + 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], + }), + ('mpi4py', '2.0.0', { + 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + }), + ('paycheck', '1.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], + 'patches': [ + 'paycheck-1.0.2_setup-open-README-utf8.patch', + ], + }), + ('pbr', '2.0.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], + }), + ('lockfile', '0.12.2', { + 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], + }), + ('Cython', '0.25.2', { + 'source_urls': ['https://pypi.python.org/packages/source/c/cython/'], + }), + ('six', '1.10.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), + ('dateutil', '2.6.0', { + 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], + }), + ('deap', '1.0.2', { + 'source_tmpl': '%(name)s-%(version)s.post2.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], + 'patches': [ + 'deap-1.0.2_setup-open-README-utf8.patch', + ], + }), + ('decorator', '4.0.11', { + 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], + }), + ('arff', '2.1.0', { + 'source_tmpl': 'liac-%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], + }), + ('pycrypto', '2.6.1', { + 'modulename': 'Crypto', + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], + }), + ('ecdsa', '0.13', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), + ('cryptography', '1.8.1', { + 'source_urls': ['https://pypi.python.org/packages/source/c/cryptography/'], + }), + ('paramiko', '2.1.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], + }), + ('pyparsing', '2.2.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], + }), + ('netifaces', '0.10.5', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], + }), + ('netaddr', '0.7.19', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], + }), + ('pandas', '0.19.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], + }), + ('virtualenv', '15.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/v/virtualenv'], + }), + ('docopt', '0.6.2', { + 'source_urls': ['https://pypi.python.org/packages/source/d/docopt'], + }), + ('joblib', '0.11', { + 'source_urls': ['https://pypi.python.org/packages/source/j/joblib'], + }), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-3.6.1-intel-2017a.eb b/easybuild/easyconfigs/p/Python/Python-3.6.1-intel-2017a.eb index 9157c902c6..d4d83a1db6 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.6.1-intel-2017a.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.6.1-intel-2017a.eb @@ -10,6 +10,7 @@ toolchainopts = {'pic': True} source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] sources = [SOURCE_TGZ] +checksums = ['aa50b0143df7c89ce91be020fe41382613a817354b33acdc6641b44f8ced3828'] # python needs bzip2 to build the bz2 package dependencies = [ diff --git a/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.2.2-foss-2017a-Python-3.6.1.eb b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.2.2-foss-2017a-Python-3.6.1.eb new file mode 100644 index 0000000000..c13a3834cc --- /dev/null +++ b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.2.2-foss-2017a-Python-3.6.1.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'pkgconfig' +version = '1.2.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://github.com/matze/pkgconfig' +description = """pkgconfig is a Python module to interface with the pkg-config command line tool""" + +toolchain = {'name': 'foss', 'version': '2017a'} +toolchainopts = {'usempi': True} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['3685ba02a9b72654a764b728b559f327e1dbd7dc6ebc310a1bd429666ee202aa'] + +dependencies = [ + ('Python', '3.6.1'), + ('pkg-config', '0.29.2'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +moduleclass = 'data' -- GitLab From b6884d899b3f8d30be801205d27e6a70080bf4e9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 18 Aug 2017 21:53:54 +0200 Subject: [PATCH 1400/1603] adding easyconfigs: LLVM-4.0.1-intel-2017a.eb, CMake-3.9.1-GCCcore-6.3.0.eb --- .../c/CMake/CMake-3.9.1-GCCcore-6.3.0.eb | 37 ++++++++++++++++ .../l/LLVM/LLVM-4.0.1-intel-2017a.eb | 43 +++++++++++++++++++ 2 files changed, 80 insertions(+) create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.9.1-GCCcore-6.3.0.eb create mode 100644 easybuild/easyconfigs/l/LLVM/LLVM-4.0.1-intel-2017a.eb diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.9.1-GCCcore-6.3.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.9.1-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..9984bec310 --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.9.1-GCCcore-6.3.0.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.9.1' + +homepage = 'http://www.cmake.org' +description = """CMake, the cross-platform, open-source build system. + CMake is a family of tools designed to build, test and package software.""" + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['d768ee83d217f91bb597b3ca2ac663da7a8603c97e1f1a5184bc01e0ad2b12bb'] + +configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' + +builddependencies = [ + ('binutils', '2.27'), +] + + +dependencies = [ + ('ncurses', '6.0'), + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.1.0c'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/LLVM/LLVM-4.0.1-intel-2017a.eb b/easybuild/easyconfigs/l/LLVM/LLVM-4.0.1-intel-2017a.eb new file mode 100644 index 0000000000..6b4e290032 --- /dev/null +++ b/easybuild/easyconfigs/l/LLVM/LLVM-4.0.1-intel-2017a.eb @@ -0,0 +1,43 @@ +easyblock = 'CMakeMake' + +name = 'LLVM' +version = '4.0.1' + +homepage = "http://llvm.org/" +description = """The LLVM Core libraries provide a modern source- and target-independent + optimizer, along with code generation support for many popular CPUs + (as well as some less common ones!) These libraries are built around a well + specified code representation known as the LLVM intermediate representation + ("LLVM IR"). The LLVM Core libraries are well documented, and it is + particularly easy to invent your own language (or port an existing compiler) + to use LLVM as an optimizer and code generator.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'cstd': 'gnu++11'} + +source_urls = ["http://llvm.org/releases/%(version)s"] +sources = ["llvm-%(version)s.src.tar.xz"] +checksums = ['da783db1f82d516791179fe103c71706046561f7972b18f0049242dee6712b51'] + +builddependencies = [ + ('CMake', '3.9.1'), + ('Python', '2.7.13'), +] + +dependencies = [ + ('ncurses', '6.0'), + ('zlib', '1.2.11'), +] + +configopts = '-DBUILD_SHARED_LIBS=ON -DCMAKE_EXE_LINKER_FLAGS="$LDFLAGS -shared-intel" ' +# required to install extra tools in bin/ +configopts += "-DLLVM_INSTALL_UTILS=ON -DLLVM_TARGETS_TO_BUILD=X86 -DLLVM_ENABLE_ZLIB=ON" + +sanity_check_paths = { + 'files': ['bin/llvm-ar', 'bin/FileCheck'], + 'dirs': ['include/llvm', 'include/llvm-c'], +} + +separate_build_dir = True + +moduleclass = 'compiler' -- GitLab From cffa66404ab06849f6819cb2695a2ce5c6076c69 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 18 Aug 2017 22:20:56 +0200 Subject: [PATCH 1401/1603] fix style issue in CMake easyconfig w.r.t. order of parameters --- easybuild/easyconfigs/c/CMake/CMake-3.9.1-GCCcore-6.3.0.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.9.1-GCCcore-6.3.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.9.1-GCCcore-6.3.0.eb index 9984bec310..4b9208d088 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.9.1-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.9.1-GCCcore-6.3.0.eb @@ -13,12 +13,11 @@ source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] checksums = ['d768ee83d217f91bb597b3ca2ac663da7a8603c97e1f1a5184bc01e0ad2b12bb'] -configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' - builddependencies = [ ('binutils', '2.27'), ] +configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' dependencies = [ ('ncurses', '6.0'), -- GitLab From 75f2082004bdb82ed55cd2a91c041e2c3b489e19 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 18 Aug 2017 23:42:01 +0200 Subject: [PATCH 1402/1603] adding easyconfigs: Python-2.7.13-GCCcore-6.3.0-bare.eb --- .../Python-2.7.13-GCCcore-6.3.0-bare.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.13-GCCcore-6.3.0-bare.eb diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.13-GCCcore-6.3.0-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.13-GCCcore-6.3.0-bare.eb new file mode 100644 index 0000000000..7fc2c97ae9 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.13-GCCcore-6.3.0-bare.eb @@ -0,0 +1,39 @@ +name = 'Python' +version = '2.7.13' +versionsuffix = '-bare' + +homepage = 'http://python.org/' + +description = """ + Python is a programming language that lets you work more quickly and + integrate your systems more effectively. +""" + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] +checksums = ['a4f05a0720ce0fd92626f0278b6b433eee9a6173ddf2bced7957dfb599a5ece1'] + +builddependencies = [ + ('binutils', '2.27'), +] + +dependencies = [ + ('bzip2', '1.0.6'), + ('libreadline', '7.0'), + ('ncurses', '6.0'), + ('SQLite', '3.17.0'), + ('zlib', '1.2.11'), +] + +osdependencies = [ + # rely upon distribution for timely security updates + ('openssl-devel', 'libssl-dev', 'libopenssl-devel'), +] + +# bare installation: no extensions +exts_list = [] + +moduleclass = 'lang' -- GitLab From a4f03b8db7da6aaa5640f97c11f3a19380754981 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 18 Aug 2017 23:43:55 +0200 Subject: [PATCH 1403/1603] adding easyconfigs: GLib-2.53.5-GCCcore-6.3.0.eb, PCRE-8.41-GCCcore-6.3.0.eb, util-linux-2.30.1-GCCcore-6.3.0.eb --- .../g/GLib/GLib-2.53.5-GCCcore-6.3.0.eb | 41 ++++++++++++++++++ .../p/PCRE/PCRE-8.41-GCCcore-6.3.0.eb | 42 ++++++++++++++++++ .../util-linux-2.30.1-GCCcore-6.3.0.eb | 43 +++++++++++++++++++ 3 files changed, 126 insertions(+) create mode 100644 easybuild/easyconfigs/g/GLib/GLib-2.53.5-GCCcore-6.3.0.eb create mode 100644 easybuild/easyconfigs/p/PCRE/PCRE-8.41-GCCcore-6.3.0.eb create mode 100644 easybuild/easyconfigs/u/util-linux/util-linux-2.30.1-GCCcore-6.3.0.eb diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.53.5-GCCcore-6.3.0.eb b/easybuild/easyconfigs/g/GLib/GLib-2.53.5-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..2efa0e3d05 --- /dev/null +++ b/easybuild/easyconfigs/g/GLib/GLib-2.53.5-GCCcore-6.3.0.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'GLib' +version = '2.53.5' + +homepage = 'http://www.gtk.org/' +description = """GLib is one of the base libraries of the GTK+ project""" + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} +toolchainopts = {'pic': True} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['991421f41a4ed4cc1637e5f9db0d03fd236d2cbd19f3c5b097a343bec5126602'] + +builddependencies = [ + ('binutils', '2.27'), + ('Python', '2.7.13', '-bare'), +] +dependencies = [ + ('libffi', '3.2.1'), + ('gettext', '0.19.8.1'), + ('libxml2', '2.9.4'), + ('PCRE', '8.41'), + ('util-linux', '2.30.1'), +] + +# avoid using hardcoded path to Python binary in build step +preconfigopts = "export PYTHON=python && " + +configopts = "--disable-maintainer-mode --disable-silent-rules --disable-libelf --disable-systemtap " +configopts += "--enable-static --enable-shared" + +postinstallcmds = ["sed -i -e 's|#!.*python|#!/usr/bin/env python|' %(installdir)s/bin/*"] + +sanity_check_paths = { + 'files': ['lib/libglib-%(version_major)s.0.a', 'lib/libglib-%%(version_major)s.0.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/PCRE/PCRE-8.41-GCCcore-6.3.0.eb b/easybuild/easyconfigs/p/PCRE/PCRE-8.41-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..02188b2e07 --- /dev/null +++ b/easybuild/easyconfigs/p/PCRE/PCRE-8.41-GCCcore-6.3.0.eb @@ -0,0 +1,42 @@ +easyblock = 'ConfigureMake' + +name = 'PCRE' +version = '8.41' + +homepage = 'http://www.pcre.org/' + +description = """ + The PCRE library is a set of functions that implement regular expression + pattern matching using the same syntax and semantics as Perl 5. +""" + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['244838e1f1d14f7e2fa7681b857b3a8566b74215f28133f14a8f5e59241b682c'] + +builddependencies = [ + ('binutils', '2.27'), +] + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.11'), +] + +configopts = """\ + --enable-utf\ + --enable-unicode-properties\ + --enable-pcre16\ + --enable-pcre32\ +""" + +sanity_check_paths = { + 'files': ['bin/pcre-config', 'include/pcre.h', + 'share/man/man3/pcre.3', 'lib/libpcre32.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig', 'share/doc/pcre/html', 'share/man/man1'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/u/util-linux/util-linux-2.30.1-GCCcore-6.3.0.eb b/easybuild/easyconfigs/u/util-linux/util-linux-2.30.1-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..621bc7fecc --- /dev/null +++ b/easybuild/easyconfigs/u/util-linux/util-linux-2.30.1-GCCcore-6.3.0.eb @@ -0,0 +1,43 @@ +easyblock = 'ConfigureMake' + +name = 'util-linux' +version = '2.30.1' + +homepage = 'http://www.kernel.org/pub/linux/utils/util-linux' + +description = "Set of Linux utilities" + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['%s/v%%(version_major_minor)s' % homepage] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['88bb1d08f0d67fb1b548c3e2160f7f40fb552cdf6b771a5dd1b94e1e04fc1d9a'] + +# disable account related utilities (they need OS dependant pam-devel files) +# disable wall and friends (requires group changing permissions for install user) +# install systemd service files in install dir +# install bash completion files in install dir +configopts = "--disable-chfn-chsh --disable-login --disable-su " +configopts += "--disable-wall --disable-use-tty-group " +configopts += "--disable-makeinstall-chown --disable-makeinstall-setuid " +configopts += "--with-systemdsystemunitdir='${prefix}/systemd' " +configopts += "--with-bashcompletiondir='${prefix}/share/bash-completion/completions' " +# disable building Python bindings (since we don't include Python as a dep) +configopts += "--without-python " + +builddependencies = [ + ('binutils', '2.27'), +] + +dependencies = [ + ('ncurses', '6.0'), + ('zlib', '1.2.11'), +] + +sanity_check_paths = { + 'files': ['lib/lib%s.a' % x for x in ['blkid', 'mount', 'uuid']], + 'dirs': ['include', 'bin', 'share', 'sbin'], +} + +moduleclass = 'tools' -- GitLab From 2f1d84ea6cc11b024b8898ebbe5b94ce2649faf6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 18 Aug 2017 23:53:08 +0200 Subject: [PATCH 1404/1603] adding easyconfigs: cairo-1.14.10-GCCcore-6.3.0.eb --- .../c/cairo/cairo-1.14.10-GCCcore-6.3.0.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/c/cairo/cairo-1.14.10-GCCcore-6.3.0.eb diff --git a/easybuild/easyconfigs/c/cairo/cairo-1.14.10-GCCcore-6.3.0.eb b/easybuild/easyconfigs/c/cairo/cairo-1.14.10-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..db1409df81 --- /dev/null +++ b/easybuild/easyconfigs/c/cairo/cairo-1.14.10-GCCcore-6.3.0.eb @@ -0,0 +1,43 @@ +easyblock = 'ConfigureMake' + +name = 'cairo' +version = '1.14.10' + +homepage = 'http://cairographics.org' +description = """Cairo is a 2D graphics library with support for multiple output devices. + Currently supported output targets include the X Window System (via both Xlib and XCB), Quartz, Win32, image buffers, + PostScript, PDF, and SVG file output. Experimental backends include OpenGL, BeOS, OS/2, and DirectFB""" + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} + +source_urls = ['http://cairographics.org/releases/'] +sources = [SOURCE_TAR_XZ] +checksums = ['7e87878658f2c9951a14fc64114d4958c0e65ac47530b8ac3078b2ce41b66a09'] + +builddependencies = [ + ('binutils', '2.27'), +] +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.11'), + ('freetype', '2.7.1', '-libpng-1.6.29'), + ('pixman', '0.34.0'), + ('expat', '2.2.0'), + ('GLib', '2.53.5'), + ('X11', '20170314'), +] + +# disable symbol lookup, which requires -lbfd, to avoid link issues with (non-PIC) libiberty.a provided by GCC +configopts = "--enable-symbol-lookup=no --enable-gobject=yes --enable-svg=yes --enable-tee=yes --enable-xlib-xcb " + +sanity_check_paths = { + 'files': ['bin/cairo-trace', 'lib/cairo/libcairo-trace.so', 'lib/cairo/libcairo-trace.a', + 'lib/libcairo.a', 'lib/libcairo-gobject.a', 'lib/libcairo-script-interpreter.a', + 'lib/libcairo-gobject.so', 'lib/libcairo-script-interpreter.so', 'lib/libcairo.so'] + + ['include/cairo/cairo%s.h' % x for x in ['', '-deprecated', '-features', '-ft', '-gobject', '-pdf', '-ps', + '-script', '-script-interpreter', '-svg', '-version', '-xcb', + '-xlib', '-xlib-xrender']], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'vis' -- GitLab From 583177017704639c3c5808dbb9362d37fb763fea Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 19 Aug 2017 00:00:14 +0200 Subject: [PATCH 1405/1603] adding easyconfigs: GObject-Introspection-1.53.5-intel-2017a.eb, GObject-Introspection-1.53.5-intel-2017a-Python-3.6.1.eb --- ...pection-1.53.5-intel-2017a-Python-3.6.1.eb | 49 +++++++++++++++++++ ...Object-Introspection-1.53.5-intel-2017a.eb | 48 ++++++++++++++++++ 2 files changed, 97 insertions(+) create mode 100644 easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.53.5-intel-2017a-Python-3.6.1.eb create mode 100644 easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.53.5-intel-2017a.eb diff --git a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.53.5-intel-2017a-Python-3.6.1.eb b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.53.5-intel-2017a-Python-3.6.1.eb new file mode 100644 index 0000000000..38b0f0bd4c --- /dev/null +++ b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.53.5-intel-2017a-Python-3.6.1.eb @@ -0,0 +1,49 @@ +easyblock = 'ConfigureMake' + +name = 'GObject-Introspection' +version = '1.53.5' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://wiki.gnome.org/GObjectIntrospection/' +description = """GObject introspection is a middleware layer between C libraries + (using GObject) and language bindings. The C library can be scanned at + compile time and generate a metadata file, in addition to the actual + native C library. Then at runtime, language bindings can read this + metadata and automatically provide bindings to call into the C library.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['b8271d3e3e3044289d06e824605a53b2518593bc2b071db6c90485c837ff437d'] + +dependencies = [ + ('GLib', '2.53.5'), + ('libffi', '3.2.1'), + ('Python', '3.6.1'), +] + +builddependencies = [ + ('Autotools', '20150215'), + ('flex', '2.6.4'), + ('Bison', '3.0.4'), + ('cairo', '1.14.10'), +] + +preconfigopts = "env GI_SCANNER_DISABLE_CACHE=true PYTHON=python3" + +# avoid using hard-coded path to 'python' in shebang of scripts +buildopts = "PYTHON=python3" + +modextrapaths = { + 'GI_TYPELIB_PATH': 'share', + 'XDG_DATA_DIRS': 'share', +} + +sanity_check_paths = { + 'files': ['bin/g-ir-%s' % x for x in ['annotation-tool', 'compiler', 'generate', 'scanner']] + + ['lib/libgirepository-1.0.%s' % x for x in ['so', 'a']], + 'dirs': ['include', 'share'] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.53.5-intel-2017a.eb b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.53.5-intel-2017a.eb new file mode 100644 index 0000000000..aece01777b --- /dev/null +++ b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.53.5-intel-2017a.eb @@ -0,0 +1,48 @@ +easyblock = 'ConfigureMake' + +name = 'GObject-Introspection' +version = '1.53.5' + +homepage = 'https://wiki.gnome.org/GObjectIntrospection/' +description = """GObject introspection is a middleware layer between C libraries + (using GObject) and language bindings. The C library can be scanned at + compile time and generate a metadata file, in addition to the actual + native C library. Then at runtime, language bindings can read this + metadata and automatically provide bindings to call into the C library.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['b8271d3e3e3044289d06e824605a53b2518593bc2b071db6c90485c837ff437d'] + +dependencies = [ + ('GLib', '2.53.5'), + ('libffi', '3.2.1'), + ('Python', '2.7.13'), +] + +builddependencies = [ + ('Autotools', '20150215'), + ('flex', '2.6.4'), + ('Bison', '3.0.4'), + ('cairo', '1.14.10'), +] + +preconfigopts = "env GI_SCANNER_DISABLE_CACHE=true " + +# avoid using hard-coded path to 'python' in shebang of scripts +buildopts = "PYTHON=python" + +modextrapaths = { + 'GI_TYPELIB_PATH': 'share', + 'XDG_DATA_DIRS': 'share', +} + +sanity_check_paths = { + 'files': ['bin/g-ir-%s' % x for x in ['annotation-tool', 'compiler', 'generate', 'scanner']] + + ['lib/libgirepository-1.0.%s' % x for x in ['so', 'a']], + 'dirs': ['include', 'share'] +} + +moduleclass = 'devel' -- GitLab From 7c5faa79b9008b00594982c1a5d42eeb88e2a768 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 19 Aug 2017 00:06:10 +0200 Subject: [PATCH 1406/1603] adding easyconfigs: Gdk-Pixbuf-2.36.8-intel-2017a.eb, libjpeg-turbo-1.5.2-GCCcore-6.3.0.eb, NASM-2.13.01-GCCcore-6.3.0.eb --- .../Gdk-Pixbuf-2.36.8-intel-2017a.eb | 37 +++++++++++++++++ .../libjpeg-turbo-1.5.2-GCCcore-6.3.0.eb | 41 +++++++++++++++++++ .../n/NASM/NASM-2.13.01-GCCcore-6.3.0.eb | 37 +++++++++++++++++ 3 files changed, 115 insertions(+) create mode 100644 easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.36.8-intel-2017a.eb create mode 100644 easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.5.2-GCCcore-6.3.0.eb create mode 100644 easybuild/easyconfigs/n/NASM/NASM-2.13.01-GCCcore-6.3.0.eb diff --git a/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.36.8-intel-2017a.eb b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.36.8-intel-2017a.eb new file mode 100644 index 0000000000..ab5bc95377 --- /dev/null +++ b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.36.8-intel-2017a.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'Gdk-Pixbuf' +version = '2.36.8' + +homepage = 'https://developer.gnome.org/gdk-pixbuf/stable/' +description = """ + The Gdk Pixbuf is a toolkit for image loading and pixel buffer manipulation. + It is used by GTK+ 2 and GTK+ 3 to load and manipulate images. In the past it + was distributed as part of GTK+ 2 but it was split off into a separate package + in preparation for the change to GTK+ 3. +""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['5d68e5283cdc0bf9bda99c3e6a1d52ad07a03364fa186b6c26cfc86fcd396a19'] + +builddependencies = [ + ('GObject-Introspection', '1.53.5', '-Python-2.7.13') +] +dependencies = [ + ('GLib', '2.53.5'), + ('libjpeg-turbo', '1.5.2'), + ('libpng', '1.6.29'), + ('LibTIFF', '4.0.8'), +] + +configopts = "--disable-maintainer-mode --enable-debug=no --enable-introspection=yes " +configopts += "--disable-Bsymbolic --without-gdiplus --enable-shared --enable-static" + +modextrapaths = { + 'XDG_DATA_DIRS': 'share', +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.5.2-GCCcore-6.3.0.eb b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.5.2-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..95e20db02a --- /dev/null +++ b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.5.2-GCCcore-6.3.0.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'libjpeg-turbo' +version = '1.5.2' + +homepage = 'http://sourceforge.net/projects/libjpeg-turbo/' + +description = """ + libjpeg-turbo is a fork of the original IJG libjpeg which uses SIMD to + accelerate baseline JPEG compression and decompression. libjpeg is a library + that implements JPEG image encoding, decoding and transcoding. +""" + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['9098943b270388727ae61de82adec73cf9f0dbb240b3bc8b172595ebf405b528'] + +builddependencies = [ + ('binutils', '2.27'), +] + +dependencies = [ + ('NASM', '2.13.01'), +] + +configopts = "--with-jpeg8" + +runtest = "test" + +sanity_check_paths = { + 'files': ['bin/cjpeg', 'bin/djpeg', 'bin/jpegtran', 'bin/rdjpgcom', + 'bin/tjbench', 'bin/wrjpgcom', 'lib/libjpeg.a', + 'lib/libjpeg.%s' % SHLIB_EXT, 'lib/libturbojpeg.a', + 'lib/libturbojpeg.%s' % SHLIB_EXT], + 'dirs': ['include', 'share'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/NASM/NASM-2.13.01-GCCcore-6.3.0.eb b/easybuild/easyconfigs/n/NASM/NASM-2.13.01-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..a720e4ab7d --- /dev/null +++ b/easybuild/easyconfigs/n/NASM/NASM-2.13.01-GCCcore-6.3.0.eb @@ -0,0 +1,37 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-90.html +## + +easyblock = 'ConfigureMake' + +name = 'NASM' +version = '2.13.01' + +homepage = 'http://www.nasm.us/' + +description = """NASM: General-purpose x86 assembler""" + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} + +source_urls = ['http://www.nasm.us/pub/nasm/releasebuilds/%(version)s'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['08f97baf0a7f892128c6413cfa93b69dc5825fbbd06c70928aea028835d198fa'] + +builddependencies = [ + ('binutils', '2.27'), +] + +sanity_check_paths = { + 'files': ['bin/nasm'], + 'dirs': [], +} + +moduleclass = 'lang' -- GitLab From 609d68f0d568834a5deabe24fc7e00dc75e2c088 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 19 Aug 2017 00:23:13 +0200 Subject: [PATCH 1407/1603] add missing versionsuffix in GObject-Introspection 1.53.5 easyconfig --- ...=> GObject-Introspection-1.53.5-intel-2017a-Python-2.7.13.eb} | 1 + 1 file changed, 1 insertion(+) rename easybuild/easyconfigs/g/GObject-Introspection/{GObject-Introspection-1.53.5-intel-2017a.eb => GObject-Introspection-1.53.5-intel-2017a-Python-2.7.13.eb} (97%) diff --git a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.53.5-intel-2017a.eb b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.53.5-intel-2017a-Python-2.7.13.eb similarity index 97% rename from easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.53.5-intel-2017a.eb rename to easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.53.5-intel-2017a-Python-2.7.13.eb index aece01777b..f1ccf8567b 100644 --- a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.53.5-intel-2017a.eb +++ b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.53.5-intel-2017a-Python-2.7.13.eb @@ -2,6 +2,7 @@ easyblock = 'ConfigureMake' name = 'GObject-Introspection' version = '1.53.5' +versionsuffix = '-Python-%(pyver)s' homepage = 'https://wiki.gnome.org/GObjectIntrospection/' description = """GObject introspection is a middleware layer between C libraries -- GitLab From a218966c483974a203b30fd23c7326e726a2c1d7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 21 Aug 2017 11:00:32 +0200 Subject: [PATCH 1408/1603] fix typo in comment in util-linux easyconfig --- .../easyconfigs/u/util-linux/util-linux-2.30.1-GCCcore-6.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/u/util-linux/util-linux-2.30.1-GCCcore-6.3.0.eb b/easybuild/easyconfigs/u/util-linux/util-linux-2.30.1-GCCcore-6.3.0.eb index 621bc7fecc..b471d8db48 100644 --- a/easybuild/easyconfigs/u/util-linux/util-linux-2.30.1-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/u/util-linux/util-linux-2.30.1-GCCcore-6.3.0.eb @@ -14,7 +14,7 @@ source_urls = ['%s/v%%(version_major_minor)s' % homepage] sources = [SOURCELOWER_TAR_GZ] checksums = ['88bb1d08f0d67fb1b548c3e2160f7f40fb552cdf6b771a5dd1b94e1e04fc1d9a'] -# disable account related utilities (they need OS dependant pam-devel files) +# disable account related utilities (they need OS dependent pam-devel files) # disable wall and friends (requires group changing permissions for install user) # install systemd service files in install dir # install bash completion files in install dir -- GitLab From 31e9d567f6ccb26a9c3b409be527fefb8b3ba48c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 21 Aug 2017 11:01:31 +0200 Subject: [PATCH 1409/1603] fix typo in comment in util-linux easyconfigs: dependant -> dependent --- .../easyconfigs/u/util-linux/util-linux-2.22.2-goolf-1.4.10.eb | 2 +- .../easyconfigs/u/util-linux/util-linux-2.22.2-ictce-5.3.0.eb | 2 +- .../easyconfigs/u/util-linux/util-linux-2.22.2-ictce-5.5.0.eb | 2 +- .../easyconfigs/u/util-linux/util-linux-2.22.2-intel-2014b.eb | 2 +- .../easyconfigs/u/util-linux/util-linux-2.24-ictce-5.5.0.eb | 2 +- .../easyconfigs/u/util-linux/util-linux-2.24.1-ictce-5.5.0.eb | 2 +- .../easyconfigs/u/util-linux/util-linux-2.26.1-foss-2015a.eb | 2 +- .../easyconfigs/u/util-linux/util-linux-2.26.1-goolf-1.4.10.eb | 2 +- .../easyconfigs/u/util-linux/util-linux-2.26.1-intel-2015a.eb | 2 +- .../easyconfigs/u/util-linux/util-linux-2.26.2-intel-2015a.eb | 2 +- .../easyconfigs/u/util-linux/util-linux-2.27.1-foss-2015a.eb | 2 +- .../easyconfigs/u/util-linux/util-linux-2.27.1-foss-2016a.eb | 2 +- .../easyconfigs/u/util-linux/util-linux-2.27.1-goolf-1.7.20.eb | 2 +- .../easyconfigs/u/util-linux/util-linux-2.27.1-intel-2015b.eb | 2 +- .../easyconfigs/u/util-linux/util-linux-2.27.1-intel-2016a.eb | 2 +- .../easyconfigs/u/util-linux/util-linux-2.28-foss-2016a.eb | 2 +- .../easyconfigs/u/util-linux/util-linux-2.28-intel-2016a.eb | 2 +- .../easyconfigs/u/util-linux/util-linux-2.28.1-intel-2016b.eb | 2 +- .../easyconfigs/u/util-linux/util-linux-2.29-foss-2016b.eb | 2 +- .../easyconfigs/u/util-linux/util-linux-2.29-intel-2016b.eb | 2 +- .../easyconfigs/u/util-linux/util-linux-2.29.2-GCCcore-6.3.0.eb | 2 +- .../easyconfigs/u/util-linux/util-linux-2.29.2-intel-2017a.eb | 2 +- .../easyconfigs/u/util-linux/util-linux-2.30-GCCcore-6.4.0.eb | 2 +- 23 files changed, 23 insertions(+), 23 deletions(-) diff --git a/easybuild/easyconfigs/u/util-linux/util-linux-2.22.2-goolf-1.4.10.eb b/easybuild/easyconfigs/u/util-linux/util-linux-2.22.2-goolf-1.4.10.eb index 75238f2124..81903c5057 100644 --- a/easybuild/easyconfigs/u/util-linux/util-linux-2.22.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/u/util-linux/util-linux-2.22.2-goolf-1.4.10.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} source_urls = ['%s/v%%(version_major_minor)s' % homepage] sources = [SOURCELOWER_TAR_GZ] -# disable account related utilities (they need OS dependant pam-devel files) +# disable account related utilities (they need OS dependent pam-devel files) # disable wall and friends (requires group changing permissions for install user) # install systemd service files in install dir configopts = '--disable-chfn-chsh --disable-login --disable-su ' diff --git a/easybuild/easyconfigs/u/util-linux/util-linux-2.22.2-ictce-5.3.0.eb b/easybuild/easyconfigs/u/util-linux/util-linux-2.22.2-ictce-5.3.0.eb index ed49a78c1e..bd42d229bf 100644 --- a/easybuild/easyconfigs/u/util-linux/util-linux-2.22.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/u/util-linux/util-linux-2.22.2-ictce-5.3.0.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'ictce', 'version': '5.3.0'} source_urls = ['%s/v%%(version_major_minor)s' % homepage] sources = [SOURCELOWER_TAR_GZ] -# disable account related utilities (they need OS dependant pam-devel files) +# disable account related utilities (they need OS dependent pam-devel files) # disable wall and friends (requires group changing permissions for install user) # install systemd service files in install dir configopts = '--disable-chfn-chsh --disable-login --disable-su ' diff --git a/easybuild/easyconfigs/u/util-linux/util-linux-2.22.2-ictce-5.5.0.eb b/easybuild/easyconfigs/u/util-linux/util-linux-2.22.2-ictce-5.5.0.eb index 43d67f412c..422eb3286d 100644 --- a/easybuild/easyconfigs/u/util-linux/util-linux-2.22.2-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/u/util-linux/util-linux-2.22.2-ictce-5.5.0.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'ictce', 'version': '5.5.0'} source_urls = ['%s/v%%(version_major_minor)s' % homepage] sources = [SOURCELOWER_TAR_GZ] -# disable account related utilities (they need OS dependant pam-devel files) +# disable account related utilities (they need OS dependent pam-devel files) # disable wall and friends (requires group changing permissions for install user) # install systemd service files in install dir configopts = '--disable-chfn-chsh --disable-login --disable-su ' diff --git a/easybuild/easyconfigs/u/util-linux/util-linux-2.22.2-intel-2014b.eb b/easybuild/easyconfigs/u/util-linux/util-linux-2.22.2-intel-2014b.eb index df0a957cf2..ca73870581 100644 --- a/easybuild/easyconfigs/u/util-linux/util-linux-2.22.2-intel-2014b.eb +++ b/easybuild/easyconfigs/u/util-linux/util-linux-2.22.2-intel-2014b.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'intel', 'version': '2014b'} source_urls = ['%s/v%s' % (homepage, '.'.join(version.split('.')[0:2]))] sources = [SOURCELOWER_TAR_GZ] -# disable account related utilities (they need OS dependant pam-devel files) +# disable account related utilities (they need OS dependent pam-devel files) # disable wall and friends (requires group changing permissions for install user) # install systemd service files in install dir configopts = '--disable-chfn-chsh --disable-login --disable-su ' diff --git a/easybuild/easyconfigs/u/util-linux/util-linux-2.24-ictce-5.5.0.eb b/easybuild/easyconfigs/u/util-linux/util-linux-2.24-ictce-5.5.0.eb index be21e2d15b..6191146acc 100644 --- a/easybuild/easyconfigs/u/util-linux/util-linux-2.24-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/u/util-linux/util-linux-2.24-ictce-5.5.0.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'ictce', 'version': '5.5.0'} source_urls = ['%s/v%%(version_major_minor)s' % homepage] sources = [SOURCELOWER_TAR_GZ] -# disable account related utilities (they need OS dependant pam-devel files) +# disable account related utilities (they need OS dependent pam-devel files) # disable wall and friends (requires group changing permissions for install user) # install systemd service files in install dir configopts = '--disable-chfn-chsh --disable-login --disable-su ' diff --git a/easybuild/easyconfigs/u/util-linux/util-linux-2.24.1-ictce-5.5.0.eb b/easybuild/easyconfigs/u/util-linux/util-linux-2.24.1-ictce-5.5.0.eb index f71360b39b..1e0d6678bb 100644 --- a/easybuild/easyconfigs/u/util-linux/util-linux-2.24.1-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/u/util-linux/util-linux-2.24.1-ictce-5.5.0.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'ictce', 'version': '5.5.0'} source_urls = ['%s/v%%(version_major_minor)s' % homepage] sources = [SOURCELOWER_TAR_GZ] -# disable account related utilities (they need OS dependant pam-devel files) +# disable account related utilities (they need OS dependent pam-devel files) # disable wall and friends (requires group changing permissions for install user) # install systemd service files in install dir # install bash completion files in install dir diff --git a/easybuild/easyconfigs/u/util-linux/util-linux-2.26.1-foss-2015a.eb b/easybuild/easyconfigs/u/util-linux/util-linux-2.26.1-foss-2015a.eb index 61d17ba4f2..14dd7f74c2 100644 --- a/easybuild/easyconfigs/u/util-linux/util-linux-2.26.1-foss-2015a.eb +++ b/easybuild/easyconfigs/u/util-linux/util-linux-2.26.1-foss-2015a.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'foss', 'version': '2015a'} source_urls = ['%s/v%%(version_major_minor)s' % homepage] sources = [SOURCELOWER_TAR_GZ] -# disable account related utilities (they need OS dependant pam-devel files) +# disable account related utilities (they need OS dependent pam-devel files) # disable wall and friends (requires group changing permissions for install user) # install systemd service files in install dir # install bash completion files in install dir diff --git a/easybuild/easyconfigs/u/util-linux/util-linux-2.26.1-goolf-1.4.10.eb b/easybuild/easyconfigs/u/util-linux/util-linux-2.26.1-goolf-1.4.10.eb index 395c68df0e..e65c62be4d 100644 --- a/easybuild/easyconfigs/u/util-linux/util-linux-2.26.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/u/util-linux/util-linux-2.26.1-goolf-1.4.10.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} source_urls = ['%s/v%%(version_major_minor)s' % homepage] sources = [SOURCELOWER_TAR_GZ] -# disable account related utilities (they need OS dependant pam-devel files) +# disable account related utilities (they need OS dependent pam-devel files) # disable wall and friends (requires group changing permissions for install user) # install systemd service files in install dir # install bash completion files in install dir diff --git a/easybuild/easyconfigs/u/util-linux/util-linux-2.26.1-intel-2015a.eb b/easybuild/easyconfigs/u/util-linux/util-linux-2.26.1-intel-2015a.eb index c339492021..780e638954 100644 --- a/easybuild/easyconfigs/u/util-linux/util-linux-2.26.1-intel-2015a.eb +++ b/easybuild/easyconfigs/u/util-linux/util-linux-2.26.1-intel-2015a.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'intel', 'version': '2015a'} source_urls = ['%s/v%%(version_major_minor)s' % homepage] sources = [SOURCELOWER_TAR_GZ] -# disable account related utilities (they need OS dependant pam-devel files) +# disable account related utilities (they need OS dependent pam-devel files) # disable wall and friends (requires group changing permissions for install user) # install systemd service files in install dir # install bash completion files in install dir diff --git a/easybuild/easyconfigs/u/util-linux/util-linux-2.26.2-intel-2015a.eb b/easybuild/easyconfigs/u/util-linux/util-linux-2.26.2-intel-2015a.eb index dae5a4f297..49b97f0469 100644 --- a/easybuild/easyconfigs/u/util-linux/util-linux-2.26.2-intel-2015a.eb +++ b/easybuild/easyconfigs/u/util-linux/util-linux-2.26.2-intel-2015a.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'intel', 'version': '2015a'} source_urls = ['%s/v%%(version_major_minor)s' % homepage] sources = [SOURCELOWER_TAR_GZ] -# disable account related utilities (they need OS dependant pam-devel files) +# disable account related utilities (they need OS dependent pam-devel files) # disable wall and friends (requires group changing permissions for install user) # install systemd service files in install dir # install bash completion files in install dir diff --git a/easybuild/easyconfigs/u/util-linux/util-linux-2.27.1-foss-2015a.eb b/easybuild/easyconfigs/u/util-linux/util-linux-2.27.1-foss-2015a.eb index 50b1fff058..308354e936 100644 --- a/easybuild/easyconfigs/u/util-linux/util-linux-2.27.1-foss-2015a.eb +++ b/easybuild/easyconfigs/u/util-linux/util-linux-2.27.1-foss-2015a.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'foss', 'version': '2015a'} source_urls = ['%s/v%%(version_major_minor)s' % homepage] sources = [SOURCELOWER_TAR_GZ] -# disable account related utilities (they need OS dependant pam-devel files) +# disable account related utilities (they need OS dependent pam-devel files) # disable wall and friends (requires group changing permissions for install user) # install systemd service files in install dir # install bash completion files in install dir diff --git a/easybuild/easyconfigs/u/util-linux/util-linux-2.27.1-foss-2016a.eb b/easybuild/easyconfigs/u/util-linux/util-linux-2.27.1-foss-2016a.eb index 6e398ddd1e..d83f975613 100644 --- a/easybuild/easyconfigs/u/util-linux/util-linux-2.27.1-foss-2016a.eb +++ b/easybuild/easyconfigs/u/util-linux/util-linux-2.27.1-foss-2016a.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'foss', 'version': '2016a'} source_urls = ['%s/v%%(version_major_minor)s' % homepage] sources = [SOURCELOWER_TAR_GZ] -# disable account related utilities (they need OS dependant pam-devel files) +# disable account related utilities (they need OS dependent pam-devel files) # disable wall and friends (requires group changing permissions for install user) # install systemd service files in install dir # install bash completion files in install dir diff --git a/easybuild/easyconfigs/u/util-linux/util-linux-2.27.1-goolf-1.7.20.eb b/easybuild/easyconfigs/u/util-linux/util-linux-2.27.1-goolf-1.7.20.eb index 1e98256d45..39cfa2cf22 100644 --- a/easybuild/easyconfigs/u/util-linux/util-linux-2.27.1-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/u/util-linux/util-linux-2.27.1-goolf-1.7.20.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'goolf', 'version': '1.7.20'} source_urls = ['%s/v%%(version_major_minor)s' % homepage] sources = [SOURCELOWER_TAR_GZ] -# disable account related utilities (they need OS dependant pam-devel files) +# disable account related utilities (they need OS dependent pam-devel files) # disable wall and friends (requires group changing permissions for install user) # install systemd service files in install dir # install bash completion files in install dir diff --git a/easybuild/easyconfigs/u/util-linux/util-linux-2.27.1-intel-2015b.eb b/easybuild/easyconfigs/u/util-linux/util-linux-2.27.1-intel-2015b.eb index 98645a6d82..3e60a2861b 100644 --- a/easybuild/easyconfigs/u/util-linux/util-linux-2.27.1-intel-2015b.eb +++ b/easybuild/easyconfigs/u/util-linux/util-linux-2.27.1-intel-2015b.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'intel', 'version': '2015b'} source_urls = ['%s/v%%(version_major_minor)s' % homepage] sources = [SOURCELOWER_TAR_GZ] -# disable account related utilities (they need OS dependant pam-devel files) +# disable account related utilities (they need OS dependent pam-devel files) # disable wall and friends (requires group changing permissions for install user) # install systemd service files in install dir # install bash completion files in install dir diff --git a/easybuild/easyconfigs/u/util-linux/util-linux-2.27.1-intel-2016a.eb b/easybuild/easyconfigs/u/util-linux/util-linux-2.27.1-intel-2016a.eb index fa18d8bb1d..15641da974 100644 --- a/easybuild/easyconfigs/u/util-linux/util-linux-2.27.1-intel-2016a.eb +++ b/easybuild/easyconfigs/u/util-linux/util-linux-2.27.1-intel-2016a.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'intel', 'version': '2016a'} source_urls = ['%s/v%%(version_major_minor)s' % homepage] sources = [SOURCELOWER_TAR_GZ] -# disable account related utilities (they need OS dependant pam-devel files) +# disable account related utilities (they need OS dependent pam-devel files) # disable wall and friends (requires group changing permissions for install user) # install systemd service files in install dir # install bash completion files in install dir diff --git a/easybuild/easyconfigs/u/util-linux/util-linux-2.28-foss-2016a.eb b/easybuild/easyconfigs/u/util-linux/util-linux-2.28-foss-2016a.eb index 8c21c443e7..abee4fd267 100644 --- a/easybuild/easyconfigs/u/util-linux/util-linux-2.28-foss-2016a.eb +++ b/easybuild/easyconfigs/u/util-linux/util-linux-2.28-foss-2016a.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'foss', 'version': '2016a'} source_urls = ['%s/v%%(version_major_minor)s' % homepage] sources = [SOURCELOWER_TAR_GZ] -# disable account related utilities (they need OS dependant pam-devel files) +# disable account related utilities (they need OS dependent pam-devel files) # disable wall and friends (requires group changing permissions for install user) # install systemd service files in install dir # install bash completion files in install dir diff --git a/easybuild/easyconfigs/u/util-linux/util-linux-2.28-intel-2016a.eb b/easybuild/easyconfigs/u/util-linux/util-linux-2.28-intel-2016a.eb index d86cc6a029..eabf986da0 100644 --- a/easybuild/easyconfigs/u/util-linux/util-linux-2.28-intel-2016a.eb +++ b/easybuild/easyconfigs/u/util-linux/util-linux-2.28-intel-2016a.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'intel', 'version': '2016a'} source_urls = ['%s/v%%(version_major_minor)s' % homepage] sources = [SOURCELOWER_TAR_GZ] -# disable account related utilities (they need OS dependant pam-devel files) +# disable account related utilities (they need OS dependent pam-devel files) # disable wall and friends (requires group changing permissions for install user) # install systemd service files in install dir # install bash completion files in install dir diff --git a/easybuild/easyconfigs/u/util-linux/util-linux-2.28.1-intel-2016b.eb b/easybuild/easyconfigs/u/util-linux/util-linux-2.28.1-intel-2016b.eb index d02d397e23..fc43956ffe 100644 --- a/easybuild/easyconfigs/u/util-linux/util-linux-2.28.1-intel-2016b.eb +++ b/easybuild/easyconfigs/u/util-linux/util-linux-2.28.1-intel-2016b.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'intel', 'version': '2016b'} source_urls = ['%s/v%%(version_major_minor)s' % homepage] sources = [SOURCELOWER_TAR_GZ] -# disable account related utilities (they need OS dependant pam-devel files) +# disable account related utilities (they need OS dependent pam-devel files) # disable wall and friends (requires group changing permissions for install user) # install systemd service files in install dir # install bash completion files in install dir diff --git a/easybuild/easyconfigs/u/util-linux/util-linux-2.29-foss-2016b.eb b/easybuild/easyconfigs/u/util-linux/util-linux-2.29-foss-2016b.eb index 246ed0de3f..0cc9df6b12 100644 --- a/easybuild/easyconfigs/u/util-linux/util-linux-2.29-foss-2016b.eb +++ b/easybuild/easyconfigs/u/util-linux/util-linux-2.29-foss-2016b.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'foss', 'version': '2016b'} source_urls = ['%s/v%%(version_major_minor)s' % homepage] sources = [SOURCELOWER_TAR_GZ] -# disable account related utilities (they need OS dependant pam-devel files) +# disable account related utilities (they need OS dependent pam-devel files) # disable wall and friends (requires group changing permissions for install user) # install systemd service files in install dir # install bash completion files in install dir diff --git a/easybuild/easyconfigs/u/util-linux/util-linux-2.29-intel-2016b.eb b/easybuild/easyconfigs/u/util-linux/util-linux-2.29-intel-2016b.eb index c4419d6080..d57a1808da 100644 --- a/easybuild/easyconfigs/u/util-linux/util-linux-2.29-intel-2016b.eb +++ b/easybuild/easyconfigs/u/util-linux/util-linux-2.29-intel-2016b.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'intel', 'version': '2016b'} source_urls = ['%s/v%%(version_major_minor)s' % homepage] sources = [SOURCELOWER_TAR_GZ] -# disable account related utilities (they need OS dependant pam-devel files) +# disable account related utilities (they need OS dependent pam-devel files) # disable wall and friends (requires group changing permissions for install user) # install systemd service files in install dir # install bash completion files in install dir diff --git a/easybuild/easyconfigs/u/util-linux/util-linux-2.29.2-GCCcore-6.3.0.eb b/easybuild/easyconfigs/u/util-linux/util-linux-2.29.2-GCCcore-6.3.0.eb index 5bf5c2a724..3820461aa7 100644 --- a/easybuild/easyconfigs/u/util-linux/util-linux-2.29.2-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/u/util-linux/util-linux-2.29.2-GCCcore-6.3.0.eb @@ -23,7 +23,7 @@ dependencies = [ ('zlib', '1.2.11'), ] -# disable account related utilities (they need OS dependant pam-devel files) +# disable account related utilities (they need OS dependent pam-devel files) # disable wall and friends (requires group changing permissions for install user) # install systemd service files in install dir # install bash completion files in install dir diff --git a/easybuild/easyconfigs/u/util-linux/util-linux-2.29.2-intel-2017a.eb b/easybuild/easyconfigs/u/util-linux/util-linux-2.29.2-intel-2017a.eb index b794436556..5307a135b9 100644 --- a/easybuild/easyconfigs/u/util-linux/util-linux-2.29.2-intel-2017a.eb +++ b/easybuild/easyconfigs/u/util-linux/util-linux-2.29.2-intel-2017a.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'intel', 'version': '2017a'} source_urls = ['%s/v%%(version_major_minor)s' % homepage] sources = [SOURCELOWER_TAR_GZ] -# disable account related utilities (they need OS dependant pam-devel files) +# disable account related utilities (they need OS dependent pam-devel files) # disable wall and friends (requires group changing permissions for install user) # install systemd service files in install dir # install bash completion files in install dir diff --git a/easybuild/easyconfigs/u/util-linux/util-linux-2.30-GCCcore-6.4.0.eb b/easybuild/easyconfigs/u/util-linux/util-linux-2.30-GCCcore-6.4.0.eb index 64826e9aa5..6d30be4b89 100644 --- a/easybuild/easyconfigs/u/util-linux/util-linux-2.30-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/u/util-linux/util-linux-2.30-GCCcore-6.4.0.eb @@ -14,7 +14,7 @@ source_urls = ['%s/v%%(version_major_minor)s' % homepage] sources = [SOURCELOWER_TAR_GZ] checksums = ['e84cc32566abf28b84efb5ee326e1f3597c3d19b9916740f50c75bd57e498ce0'] -# disable account related utilities (they need OS dependant pam-devel files) +# disable account related utilities (they need OS dependent pam-devel files) # disable wall and friends (requires group changing permissions for install user) # install systemd service files in install dir # install bash completion files in install dir -- GitLab From 849f45794f799c94a4dbae33c0825c32bfcac6e0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 21 Aug 2017 11:57:23 +0200 Subject: [PATCH 1410/1603] add SHA256 checksums in util-linux easyconfigs --- .../u/util-linux/util-linux-2.22.2-goolf-1.4.10.eb | 1 + .../easyconfigs/u/util-linux/util-linux-2.22.2-ictce-5.3.0.eb | 1 + .../easyconfigs/u/util-linux/util-linux-2.22.2-ictce-5.5.0.eb | 1 + .../easyconfigs/u/util-linux/util-linux-2.22.2-intel-2014b.eb | 1 + .../easyconfigs/u/util-linux/util-linux-2.24-ictce-5.5.0.eb | 1 + .../easyconfigs/u/util-linux/util-linux-2.24.1-ictce-5.5.0.eb | 1 + .../easyconfigs/u/util-linux/util-linux-2.26.1-foss-2015a.eb | 1 + .../u/util-linux/util-linux-2.26.1-goolf-1.4.10.eb | 1 + .../easyconfigs/u/util-linux/util-linux-2.26.1-intel-2015a.eb | 1 + .../easyconfigs/u/util-linux/util-linux-2.26.2-intel-2015a.eb | 1 + .../easyconfigs/u/util-linux/util-linux-2.27.1-foss-2015a.eb | 1 + .../easyconfigs/u/util-linux/util-linux-2.27.1-foss-2016a.eb | 1 + .../u/util-linux/util-linux-2.27.1-goolf-1.7.20.eb | 1 + .../easyconfigs/u/util-linux/util-linux-2.27.1-intel-2015b.eb | 1 + .../easyconfigs/u/util-linux/util-linux-2.27.1-intel-2016a.eb | 1 + .../easyconfigs/u/util-linux/util-linux-2.28-foss-2016a.eb | 1 + .../easyconfigs/u/util-linux/util-linux-2.28-intel-2016a.eb | 1 + .../easyconfigs/u/util-linux/util-linux-2.28.1-intel-2016b.eb | 1 + .../easyconfigs/u/util-linux/util-linux-2.29-foss-2016b.eb | 1 + .../easyconfigs/u/util-linux/util-linux-2.29-intel-2016b.eb | 1 + .../u/util-linux/util-linux-2.29.2-GCCcore-6.3.0.eb | 4 +--- .../easyconfigs/u/util-linux/util-linux-2.29.2-intel-2017a.eb | 1 + 22 files changed, 22 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/u/util-linux/util-linux-2.22.2-goolf-1.4.10.eb b/easybuild/easyconfigs/u/util-linux/util-linux-2.22.2-goolf-1.4.10.eb index 81903c5057..ba27f710e3 100644 --- a/easybuild/easyconfigs/u/util-linux/util-linux-2.22.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/u/util-linux/util-linux-2.22.2-goolf-1.4.10.eb @@ -10,6 +10,7 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} source_urls = ['%s/v%%(version_major_minor)s' % homepage] sources = [SOURCELOWER_TAR_GZ] +checksums = ['79d5a1ac095b1a4cc1bd13e43f8f65bfaa5b9793c61a559b5de137ce316170bd'] # disable account related utilities (they need OS dependent pam-devel files) # disable wall and friends (requires group changing permissions for install user) diff --git a/easybuild/easyconfigs/u/util-linux/util-linux-2.22.2-ictce-5.3.0.eb b/easybuild/easyconfigs/u/util-linux/util-linux-2.22.2-ictce-5.3.0.eb index bd42d229bf..27588804c6 100644 --- a/easybuild/easyconfigs/u/util-linux/util-linux-2.22.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/u/util-linux/util-linux-2.22.2-ictce-5.3.0.eb @@ -10,6 +10,7 @@ toolchain = {'name': 'ictce', 'version': '5.3.0'} source_urls = ['%s/v%%(version_major_minor)s' % homepage] sources = [SOURCELOWER_TAR_GZ] +checksums = ['79d5a1ac095b1a4cc1bd13e43f8f65bfaa5b9793c61a559b5de137ce316170bd'] # disable account related utilities (they need OS dependent pam-devel files) # disable wall and friends (requires group changing permissions for install user) diff --git a/easybuild/easyconfigs/u/util-linux/util-linux-2.22.2-ictce-5.5.0.eb b/easybuild/easyconfigs/u/util-linux/util-linux-2.22.2-ictce-5.5.0.eb index 422eb3286d..807046abfc 100644 --- a/easybuild/easyconfigs/u/util-linux/util-linux-2.22.2-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/u/util-linux/util-linux-2.22.2-ictce-5.5.0.eb @@ -10,6 +10,7 @@ toolchain = {'name': 'ictce', 'version': '5.5.0'} source_urls = ['%s/v%%(version_major_minor)s' % homepage] sources = [SOURCELOWER_TAR_GZ] +checksums = ['79d5a1ac095b1a4cc1bd13e43f8f65bfaa5b9793c61a559b5de137ce316170bd'] # disable account related utilities (they need OS dependent pam-devel files) # disable wall and friends (requires group changing permissions for install user) diff --git a/easybuild/easyconfigs/u/util-linux/util-linux-2.22.2-intel-2014b.eb b/easybuild/easyconfigs/u/util-linux/util-linux-2.22.2-intel-2014b.eb index ca73870581..ead6224d8a 100644 --- a/easybuild/easyconfigs/u/util-linux/util-linux-2.22.2-intel-2014b.eb +++ b/easybuild/easyconfigs/u/util-linux/util-linux-2.22.2-intel-2014b.eb @@ -10,6 +10,7 @@ toolchain = {'name': 'intel', 'version': '2014b'} source_urls = ['%s/v%s' % (homepage, '.'.join(version.split('.')[0:2]))] sources = [SOURCELOWER_TAR_GZ] +checksums = ['79d5a1ac095b1a4cc1bd13e43f8f65bfaa5b9793c61a559b5de137ce316170bd'] # disable account related utilities (they need OS dependent pam-devel files) # disable wall and friends (requires group changing permissions for install user) diff --git a/easybuild/easyconfigs/u/util-linux/util-linux-2.24-ictce-5.5.0.eb b/easybuild/easyconfigs/u/util-linux/util-linux-2.24-ictce-5.5.0.eb index 6191146acc..c3b23acffb 100644 --- a/easybuild/easyconfigs/u/util-linux/util-linux-2.24-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/u/util-linux/util-linux-2.24-ictce-5.5.0.eb @@ -10,6 +10,7 @@ toolchain = {'name': 'ictce', 'version': '5.5.0'} source_urls = ['%s/v%%(version_major_minor)s' % homepage] sources = [SOURCELOWER_TAR_GZ] +checksums = ['b9b51673b21b99e296b9c1de31d81a1f0cd36b28afec5c6b1b3f273319c2f3b7'] # disable account related utilities (they need OS dependent pam-devel files) # disable wall and friends (requires group changing permissions for install user) diff --git a/easybuild/easyconfigs/u/util-linux/util-linux-2.24.1-ictce-5.5.0.eb b/easybuild/easyconfigs/u/util-linux/util-linux-2.24.1-ictce-5.5.0.eb index 1e0d6678bb..f4f54bd198 100644 --- a/easybuild/easyconfigs/u/util-linux/util-linux-2.24.1-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/u/util-linux/util-linux-2.24.1-ictce-5.5.0.eb @@ -10,6 +10,7 @@ toolchain = {'name': 'ictce', 'version': '5.5.0'} source_urls = ['%s/v%%(version_major_minor)s' % homepage] sources = [SOURCELOWER_TAR_GZ] +checksums = ['d50003cba43a910475b25456057e715f63c69cf5d26d7d1e085bf678ebe6ac0e'] # disable account related utilities (they need OS dependent pam-devel files) # disable wall and friends (requires group changing permissions for install user) diff --git a/easybuild/easyconfigs/u/util-linux/util-linux-2.26.1-foss-2015a.eb b/easybuild/easyconfigs/u/util-linux/util-linux-2.26.1-foss-2015a.eb index 14dd7f74c2..abb4bbb8f0 100644 --- a/easybuild/easyconfigs/u/util-linux/util-linux-2.26.1-foss-2015a.eb +++ b/easybuild/easyconfigs/u/util-linux/util-linux-2.26.1-foss-2015a.eb @@ -10,6 +10,7 @@ toolchain = {'name': 'foss', 'version': '2015a'} source_urls = ['%s/v%%(version_major_minor)s' % homepage] sources = [SOURCELOWER_TAR_GZ] +checksums = ['cf80b7e3d9011600d888cf19cfc0d124960e490ba87faa62705e62acbaac0b8c'] # disable account related utilities (they need OS dependent pam-devel files) # disable wall and friends (requires group changing permissions for install user) diff --git a/easybuild/easyconfigs/u/util-linux/util-linux-2.26.1-goolf-1.4.10.eb b/easybuild/easyconfigs/u/util-linux/util-linux-2.26.1-goolf-1.4.10.eb index e65c62be4d..b39cc377a2 100644 --- a/easybuild/easyconfigs/u/util-linux/util-linux-2.26.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/u/util-linux/util-linux-2.26.1-goolf-1.4.10.eb @@ -10,6 +10,7 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} source_urls = ['%s/v%%(version_major_minor)s' % homepage] sources = [SOURCELOWER_TAR_GZ] +checksums = ['cf80b7e3d9011600d888cf19cfc0d124960e490ba87faa62705e62acbaac0b8c'] # disable account related utilities (they need OS dependent pam-devel files) # disable wall and friends (requires group changing permissions for install user) diff --git a/easybuild/easyconfigs/u/util-linux/util-linux-2.26.1-intel-2015a.eb b/easybuild/easyconfigs/u/util-linux/util-linux-2.26.1-intel-2015a.eb index 780e638954..406aa59e1e 100644 --- a/easybuild/easyconfigs/u/util-linux/util-linux-2.26.1-intel-2015a.eb +++ b/easybuild/easyconfigs/u/util-linux/util-linux-2.26.1-intel-2015a.eb @@ -10,6 +10,7 @@ toolchain = {'name': 'intel', 'version': '2015a'} source_urls = ['%s/v%%(version_major_minor)s' % homepage] sources = [SOURCELOWER_TAR_GZ] +checksums = ['cf80b7e3d9011600d888cf19cfc0d124960e490ba87faa62705e62acbaac0b8c'] # disable account related utilities (they need OS dependent pam-devel files) # disable wall and friends (requires group changing permissions for install user) diff --git a/easybuild/easyconfigs/u/util-linux/util-linux-2.26.2-intel-2015a.eb b/easybuild/easyconfigs/u/util-linux/util-linux-2.26.2-intel-2015a.eb index 49b97f0469..1c833e1478 100644 --- a/easybuild/easyconfigs/u/util-linux/util-linux-2.26.2-intel-2015a.eb +++ b/easybuild/easyconfigs/u/util-linux/util-linux-2.26.2-intel-2015a.eb @@ -10,6 +10,7 @@ toolchain = {'name': 'intel', 'version': '2015a'} source_urls = ['%s/v%%(version_major_minor)s' % homepage] sources = [SOURCELOWER_TAR_GZ] +checksums = ['f38979533ce43905a111580d17b1cf57169e5e04a54b5d00f18069b2271967ca'] # disable account related utilities (they need OS dependent pam-devel files) # disable wall and friends (requires group changing permissions for install user) diff --git a/easybuild/easyconfigs/u/util-linux/util-linux-2.27.1-foss-2015a.eb b/easybuild/easyconfigs/u/util-linux/util-linux-2.27.1-foss-2015a.eb index 308354e936..0277934af6 100644 --- a/easybuild/easyconfigs/u/util-linux/util-linux-2.27.1-foss-2015a.eb +++ b/easybuild/easyconfigs/u/util-linux/util-linux-2.27.1-foss-2015a.eb @@ -10,6 +10,7 @@ toolchain = {'name': 'foss', 'version': '2015a'} source_urls = ['%s/v%%(version_major_minor)s' % homepage] sources = [SOURCELOWER_TAR_GZ] +checksums = ['133c14f625d40e90e73e9d200faf3f2ce87937b99f923c84e5504ac0badc71d6'] # disable account related utilities (they need OS dependent pam-devel files) # disable wall and friends (requires group changing permissions for install user) diff --git a/easybuild/easyconfigs/u/util-linux/util-linux-2.27.1-foss-2016a.eb b/easybuild/easyconfigs/u/util-linux/util-linux-2.27.1-foss-2016a.eb index d83f975613..52f6553426 100644 --- a/easybuild/easyconfigs/u/util-linux/util-linux-2.27.1-foss-2016a.eb +++ b/easybuild/easyconfigs/u/util-linux/util-linux-2.27.1-foss-2016a.eb @@ -10,6 +10,7 @@ toolchain = {'name': 'foss', 'version': '2016a'} source_urls = ['%s/v%%(version_major_minor)s' % homepage] sources = [SOURCELOWER_TAR_GZ] +checksums = ['133c14f625d40e90e73e9d200faf3f2ce87937b99f923c84e5504ac0badc71d6'] # disable account related utilities (they need OS dependent pam-devel files) # disable wall and friends (requires group changing permissions for install user) diff --git a/easybuild/easyconfigs/u/util-linux/util-linux-2.27.1-goolf-1.7.20.eb b/easybuild/easyconfigs/u/util-linux/util-linux-2.27.1-goolf-1.7.20.eb index 39cfa2cf22..7457b234c7 100644 --- a/easybuild/easyconfigs/u/util-linux/util-linux-2.27.1-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/u/util-linux/util-linux-2.27.1-goolf-1.7.20.eb @@ -10,6 +10,7 @@ toolchain = {'name': 'goolf', 'version': '1.7.20'} source_urls = ['%s/v%%(version_major_minor)s' % homepage] sources = [SOURCELOWER_TAR_GZ] +checksums = ['133c14f625d40e90e73e9d200faf3f2ce87937b99f923c84e5504ac0badc71d6'] # disable account related utilities (they need OS dependent pam-devel files) # disable wall and friends (requires group changing permissions for install user) diff --git a/easybuild/easyconfigs/u/util-linux/util-linux-2.27.1-intel-2015b.eb b/easybuild/easyconfigs/u/util-linux/util-linux-2.27.1-intel-2015b.eb index 3e60a2861b..f7a17a0f74 100644 --- a/easybuild/easyconfigs/u/util-linux/util-linux-2.27.1-intel-2015b.eb +++ b/easybuild/easyconfigs/u/util-linux/util-linux-2.27.1-intel-2015b.eb @@ -10,6 +10,7 @@ toolchain = {'name': 'intel', 'version': '2015b'} source_urls = ['%s/v%%(version_major_minor)s' % homepage] sources = [SOURCELOWER_TAR_GZ] +checksums = ['133c14f625d40e90e73e9d200faf3f2ce87937b99f923c84e5504ac0badc71d6'] # disable account related utilities (they need OS dependent pam-devel files) # disable wall and friends (requires group changing permissions for install user) diff --git a/easybuild/easyconfigs/u/util-linux/util-linux-2.27.1-intel-2016a.eb b/easybuild/easyconfigs/u/util-linux/util-linux-2.27.1-intel-2016a.eb index 15641da974..6b117e4b69 100644 --- a/easybuild/easyconfigs/u/util-linux/util-linux-2.27.1-intel-2016a.eb +++ b/easybuild/easyconfigs/u/util-linux/util-linux-2.27.1-intel-2016a.eb @@ -10,6 +10,7 @@ toolchain = {'name': 'intel', 'version': '2016a'} source_urls = ['%s/v%%(version_major_minor)s' % homepage] sources = [SOURCELOWER_TAR_GZ] +checksums = ['133c14f625d40e90e73e9d200faf3f2ce87937b99f923c84e5504ac0badc71d6'] # disable account related utilities (they need OS dependent pam-devel files) # disable wall and friends (requires group changing permissions for install user) diff --git a/easybuild/easyconfigs/u/util-linux/util-linux-2.28-foss-2016a.eb b/easybuild/easyconfigs/u/util-linux/util-linux-2.28-foss-2016a.eb index abee4fd267..4c43415043 100644 --- a/easybuild/easyconfigs/u/util-linux/util-linux-2.28-foss-2016a.eb +++ b/easybuild/easyconfigs/u/util-linux/util-linux-2.28-foss-2016a.eb @@ -10,6 +10,7 @@ toolchain = {'name': 'foss', 'version': '2016a'} source_urls = ['%s/v%%(version_major_minor)s' % homepage] sources = [SOURCELOWER_TAR_GZ] +checksums = ['b79901455901d0e8cd5aa58671dcc9118fa333cce805a26904155e80a621f595'] # disable account related utilities (they need OS dependent pam-devel files) # disable wall and friends (requires group changing permissions for install user) diff --git a/easybuild/easyconfigs/u/util-linux/util-linux-2.28-intel-2016a.eb b/easybuild/easyconfigs/u/util-linux/util-linux-2.28-intel-2016a.eb index eabf986da0..b1143ef21e 100644 --- a/easybuild/easyconfigs/u/util-linux/util-linux-2.28-intel-2016a.eb +++ b/easybuild/easyconfigs/u/util-linux/util-linux-2.28-intel-2016a.eb @@ -10,6 +10,7 @@ toolchain = {'name': 'intel', 'version': '2016a'} source_urls = ['%s/v%%(version_major_minor)s' % homepage] sources = [SOURCELOWER_TAR_GZ] +checksums = ['b79901455901d0e8cd5aa58671dcc9118fa333cce805a26904155e80a621f595'] # disable account related utilities (they need OS dependent pam-devel files) # disable wall and friends (requires group changing permissions for install user) diff --git a/easybuild/easyconfigs/u/util-linux/util-linux-2.28.1-intel-2016b.eb b/easybuild/easyconfigs/u/util-linux/util-linux-2.28.1-intel-2016b.eb index fc43956ffe..042a50a556 100644 --- a/easybuild/easyconfigs/u/util-linux/util-linux-2.28.1-intel-2016b.eb +++ b/easybuild/easyconfigs/u/util-linux/util-linux-2.28.1-intel-2016b.eb @@ -10,6 +10,7 @@ toolchain = {'name': 'intel', 'version': '2016b'} source_urls = ['%s/v%%(version_major_minor)s' % homepage] sources = [SOURCELOWER_TAR_GZ] +checksums = ['2e16882f018161dc55f36435f09dc29c15072c86630226a7552aeb43789e1644'] # disable account related utilities (they need OS dependent pam-devel files) # disable wall and friends (requires group changing permissions for install user) diff --git a/easybuild/easyconfigs/u/util-linux/util-linux-2.29-foss-2016b.eb b/easybuild/easyconfigs/u/util-linux/util-linux-2.29-foss-2016b.eb index 0cc9df6b12..0f580869d3 100644 --- a/easybuild/easyconfigs/u/util-linux/util-linux-2.29-foss-2016b.eb +++ b/easybuild/easyconfigs/u/util-linux/util-linux-2.29-foss-2016b.eb @@ -10,6 +10,7 @@ toolchain = {'name': 'foss', 'version': '2016b'} source_urls = ['%s/v%%(version_major_minor)s' % homepage] sources = [SOURCELOWER_TAR_GZ] +checksums = ['36d2fe6fcc962b6b4354ecd427ad766bc4ad29581f83afe67c3eadbdc5245a1f'] # disable account related utilities (they need OS dependent pam-devel files) # disable wall and friends (requires group changing permissions for install user) diff --git a/easybuild/easyconfigs/u/util-linux/util-linux-2.29-intel-2016b.eb b/easybuild/easyconfigs/u/util-linux/util-linux-2.29-intel-2016b.eb index d57a1808da..b575865c16 100644 --- a/easybuild/easyconfigs/u/util-linux/util-linux-2.29-intel-2016b.eb +++ b/easybuild/easyconfigs/u/util-linux/util-linux-2.29-intel-2016b.eb @@ -10,6 +10,7 @@ toolchain = {'name': 'intel', 'version': '2016b'} source_urls = ['%s/v%%(version_major_minor)s' % homepage] sources = [SOURCELOWER_TAR_GZ] +checksums = ['36d2fe6fcc962b6b4354ecd427ad766bc4ad29581f83afe67c3eadbdc5245a1f'] # disable account related utilities (they need OS dependent pam-devel files) # disable wall and friends (requires group changing permissions for install user) diff --git a/easybuild/easyconfigs/u/util-linux/util-linux-2.29.2-GCCcore-6.3.0.eb b/easybuild/easyconfigs/u/util-linux/util-linux-2.29.2-GCCcore-6.3.0.eb index 3820461aa7..f0e822bdd1 100644 --- a/easybuild/easyconfigs/u/util-linux/util-linux-2.29.2-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/u/util-linux/util-linux-2.29.2-GCCcore-6.3.0.eb @@ -10,9 +10,7 @@ toolchain = {'name': 'GCCcore', 'version': '6.3.0'} source_urls = ['%s/v%%(version_major_minor)s' % homepage] sources = [SOURCELOWER_TAR_GZ] -checksums = [ - '29ccdf91d2c3245dc705f0ad3bf729ac41d8adcdbeff914e797c552ecb04a4c7', # util-linux-2.29.2.tar.gz -] +checksums = ['29ccdf91d2c3245dc705f0ad3bf729ac41d8adcdbeff914e797c552ecb04a4c7'] builddependencies = [ ('binutils', '2.27'), diff --git a/easybuild/easyconfigs/u/util-linux/util-linux-2.29.2-intel-2017a.eb b/easybuild/easyconfigs/u/util-linux/util-linux-2.29.2-intel-2017a.eb index 5307a135b9..2a57603e7b 100644 --- a/easybuild/easyconfigs/u/util-linux/util-linux-2.29.2-intel-2017a.eb +++ b/easybuild/easyconfigs/u/util-linux/util-linux-2.29.2-intel-2017a.eb @@ -10,6 +10,7 @@ toolchain = {'name': 'intel', 'version': '2017a'} source_urls = ['%s/v%%(version_major_minor)s' % homepage] sources = [SOURCELOWER_TAR_GZ] +checksums = ['29ccdf91d2c3245dc705f0ad3bf729ac41d8adcdbeff914e797c552ecb04a4c7'] # disable account related utilities (they need OS dependent pam-devel files) # disable wall and friends (requires group changing permissions for install user) -- GitLab From 9fb094133d0925fbf9787a25a111a052ab6b4975 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 21 Aug 2017 12:24:18 +0200 Subject: [PATCH 1411/1603] remove superfluous $CPATH update in GLib 2.44.0 easyconfig --- easybuild/easyconfigs/g/GLib/GLib-2.44.0-GCC-4.9.2.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.44.0-GCC-4.9.2.eb b/easybuild/easyconfigs/g/GLib/GLib-2.44.0-GCC-4.9.2.eb index 94d03a2c3d..1129e629db 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.44.0-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.44.0-GCC-4.9.2.eb @@ -19,6 +19,4 @@ dependencies = [ ] builddependencies = [('Python', '2.7.9', '-bare')] -modextrapaths = {'CPATH': ['include/glib-2.0', 'lib/glib-2.0/include']} - moduleclass = 'vis' -- GitLab From 4cc0417c184912b1831340c640f0d09b2404e390 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 21 Aug 2017 23:18:50 +0200 Subject: [PATCH 1412/1603] use SHLIB_EXT in cairo easyconfig rather than hardcoding .so --- easybuild/easyconfigs/c/cairo/cairo-1.14.10-GCCcore-6.3.0.eb | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/c/cairo/cairo-1.14.10-GCCcore-6.3.0.eb b/easybuild/easyconfigs/c/cairo/cairo-1.14.10-GCCcore-6.3.0.eb index db1409df81..0decbb331e 100644 --- a/easybuild/easyconfigs/c/cairo/cairo-1.14.10-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/c/cairo/cairo-1.14.10-GCCcore-6.3.0.eb @@ -31,9 +31,10 @@ dependencies = [ configopts = "--enable-symbol-lookup=no --enable-gobject=yes --enable-svg=yes --enable-tee=yes --enable-xlib-xcb " sanity_check_paths = { - 'files': ['bin/cairo-trace', 'lib/cairo/libcairo-trace.so', 'lib/cairo/libcairo-trace.a', + 'files': ['bin/cairo-trace', 'lib/cairo/libcairo-trace.%s' % SHLIB_EXT, 'lib/cairo/libcairo-trace.a', 'lib/libcairo.a', 'lib/libcairo-gobject.a', 'lib/libcairo-script-interpreter.a', - 'lib/libcairo-gobject.so', 'lib/libcairo-script-interpreter.so', 'lib/libcairo.so'] + + 'lib/libcairo-gobject.%s' % SHLIB_EXT, 'lib/libcairo-script-interpreter.%s' % SHLIB_EXT, + 'lib/libcairo.%s' % SHLIB_EXT] + ['include/cairo/cairo%s.h' % x for x in ['', '-deprecated', '-features', '-ft', '-gobject', '-pdf', '-ps', '-script', '-script-interpreter', '-svg', '-version', '-xcb', '-xlib', '-xlib-xrender']], -- GitLab From 105827f6a3b9104064f58c268bb1d4beb50f3dcf Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 22 Aug 2017 08:16:20 +0200 Subject: [PATCH 1413/1603] .so -> SHLIB_EXT in GObject-Introspection 1.53.5 easyconfigs --- .../GObject-Introspection-1.53.5-intel-2017a-Python-2.7.13.eb | 2 +- .../GObject-Introspection-1.53.5-intel-2017a-Python-3.6.1.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.53.5-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.53.5-intel-2017a-Python-2.7.13.eb index f1ccf8567b..85392bca63 100644 --- a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.53.5-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.53.5-intel-2017a-Python-2.7.13.eb @@ -42,7 +42,7 @@ modextrapaths = { sanity_check_paths = { 'files': ['bin/g-ir-%s' % x for x in ['annotation-tool', 'compiler', 'generate', 'scanner']] + - ['lib/libgirepository-1.0.%s' % x for x in ['so', 'a']], + ['lib/libgirepository-1.0.%s' % x for x in [SHLIB_EXT, 'a']], 'dirs': ['include', 'share'] } diff --git a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.53.5-intel-2017a-Python-3.6.1.eb b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.53.5-intel-2017a-Python-3.6.1.eb index 38b0f0bd4c..82eb56eec7 100644 --- a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.53.5-intel-2017a-Python-3.6.1.eb +++ b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.53.5-intel-2017a-Python-3.6.1.eb @@ -42,7 +42,7 @@ modextrapaths = { sanity_check_paths = { 'files': ['bin/g-ir-%s' % x for x in ['annotation-tool', 'compiler', 'generate', 'scanner']] + - ['lib/libgirepository-1.0.%s' % x for x in ['so', 'a']], + ['lib/libgirepository-1.0.%s' % x for x in [SHLIB_EXT, 'a']], 'dirs': ['include', 'share'] } -- GitLab From 8cad7d4f825a22c85bd9dcc9854fe282ecff1787 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 23 Aug 2017 13:30:21 +0200 Subject: [PATCH 1414/1603] adding easyconfigs: mdtest-1.9.3-intel-2017a.eb --- .../m/mdtest/mdtest-1.9.3-intel-2017a.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/m/mdtest/mdtest-1.9.3-intel-2017a.eb diff --git a/easybuild/easyconfigs/m/mdtest/mdtest-1.9.3-intel-2017a.eb b/easybuild/easyconfigs/m/mdtest/mdtest-1.9.3-intel-2017a.eb new file mode 100644 index 0000000000..f78dcbfde9 --- /dev/null +++ b/easybuild/easyconfigs/m/mdtest/mdtest-1.9.3-intel-2017a.eb @@ -0,0 +1,41 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = 'MakeCp' + +name = 'mdtest' +version = '1.9.3' + +homepage = 'http://sourceforge.net/projects/mdtest/' +description = """ mdtest is an MPI-coordinated metadata benchmark test that performs + open/stat/close operations on files and directories and then reports the performance.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'usempi': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TGZ] +checksums = ['b7e76252031232cf0bba91475f48d0c77dd2e0a56a2e871f1d48e6f247109d8a'] + +dependencies = [('zlib', '1.2.11')] + +parallel = 1 + +buildopts = ' CC="$CC"' + +files_to_copy = [ + (['mdtest'], 'bin'), + (['mdtest.1'], 'man/man1'), + "README", + "RELEASE_LOG", + "scripts" +] + +sanity_check_paths = { + 'files': ['bin/mdtest'], + 'dirs': [], +} + +moduleclass = 'tools' -- GitLab From 0ba16d9c403e61de257ef8ae39d1c20fdd97320f Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 23 Aug 2017 14:45:02 +0200 Subject: [PATCH 1415/1603] Add SOAPdenovo-Trans/1.04 for intel/2017a --- .../SOAPdenovo-Trans-1.04-intel-2017a.eb | 32 +++++++++++++++++++ .../SOAPdenovo-Trans/fix-makefiles-1.04.patch | 30 +++++++++++++++++ 2 files changed, 62 insertions(+) create mode 100644 easybuild/easyconfigs/s/SOAPdenovo-Trans/SOAPdenovo-Trans-1.04-intel-2017a.eb create mode 100644 easybuild/easyconfigs/s/SOAPdenovo-Trans/fix-makefiles-1.04.patch diff --git a/easybuild/easyconfigs/s/SOAPdenovo-Trans/SOAPdenovo-Trans-1.04-intel-2017a.eb b/easybuild/easyconfigs/s/SOAPdenovo-Trans/SOAPdenovo-Trans-1.04-intel-2017a.eb new file mode 100644 index 0000000000..339fff4b72 --- /dev/null +++ b/easybuild/easyconfigs/s/SOAPdenovo-Trans/SOAPdenovo-Trans-1.04-intel-2017a.eb @@ -0,0 +1,32 @@ +easyblock = 'MakeCp' + +name = 'SOAPdenovo-Trans' +version = '1.04' + +homepage = 'http://soap.genomics.org.cn/SOAPdenovo-Trans.html' +description = """SOAPdenovo-Trans is a de novo transcriptome assembler basing on the SOAPdenovo framework, +adapt to alternative splicing and different expression level among transcripts. +""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +sources = ['4e25da665b38172.tar.gz'] # no releases tagged on github +source_urls = ['https://github.com/aquaskyline/SOAPdenovo-Trans/archive/'] + +patches = ['fix-makefiles-%(version)s.patch'] + +dependencies = [('zlib', '1.2.11')] + +start_dir = 'src' + +buildopts = ' && make 127mer=1' + +files_to_copy = [(['../SOAPdenovo-Trans-127mer', '../SOAPdenovo-Trans-31mer'], 'bin'), '../LICENSE', + '../README.md', '../VERSION'] + +sanity_check_paths = { + 'files': ['bin/SOAPdenovo-Trans-127mer', 'bin/SOAPdenovo-Trans-31mer'], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SOAPdenovo-Trans/fix-makefiles-1.04.patch b/easybuild/easyconfigs/s/SOAPdenovo-Trans/fix-makefiles-1.04.patch new file mode 100644 index 0000000000..edb305d008 --- /dev/null +++ b/easybuild/easyconfigs/s/SOAPdenovo-Trans/fix-makefiles-1.04.patch @@ -0,0 +1,30 @@ +# Fix makefile to use EB values +# Ward Poelmans +--- SOAPdenovo-Trans-src-v1.04.orig/src/Makefile 2014-04-15 04:37:16.000000000 +0200 ++++ SOAPdenovo-Trans-src-v1.04/src/Makefile 2017-08-23 07:54:58.108664416 +0200 +@@ -1,5 +1,5 @@ +-CC= gcc +-CFLAGS= -O3 -fomit-frame-pointer -static ++CC := $(CC) ++CFLAGS := -fomit-frame-pointer $(CFLAGS) + #CFLAGS= -O3 -g -D_DEBUG + DFLAGS= + +@@ -32,7 +32,7 @@ + INCLUDES= -Iinc + SUBDIRS= . + LIBPATH= +-LIBS= -pthread -lm -lrt -lbam -lz -L./inc ++LIBS := $(LIBS) -lrt -lbam -lz -L./inc + EXTRA_FLAGS= + + BIT_ERR = 0 +@@ -73,7 +73,7 @@ + @test $(BIT_ERR) != 1 || sh -c 'echo "Fatal: 64bit CPU and Operating System required!";false;' + + SOAPdenovo: envTest $(OBJS) +- @$(CC) $(CFLAGS) -o $(PROG) $(OBJS) $(LIBPATH) $(LIBS) $(ENTRAFLAGS) ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $(PROG) $(OBJS) $(LIBPATH) $(LIBS) $(ENTRAFLAGS) + @printf "Linking...\r" + @printf "$(PROG) compilation done.\n"; + -- GitLab From a94900d75d6e1c3c05299927f67a920f66381c1f Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 23 Aug 2017 14:45:39 +0200 Subject: [PATCH 1416/1603] Add SPAdes/3.10.1 for foss/2017a --- .../s/SPAdes/SPAdes-3.10.1-foss-2017a.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/s/SPAdes/SPAdes-3.10.1-foss-2017a.eb diff --git a/easybuild/easyconfigs/s/SPAdes/SPAdes-3.10.1-foss-2017a.eb b/easybuild/easyconfigs/s/SPAdes/SPAdes-3.10.1-foss-2017a.eb new file mode 100644 index 0000000000..7c013e44e4 --- /dev/null +++ b/easybuild/easyconfigs/s/SPAdes/SPAdes-3.10.1-foss-2017a.eb @@ -0,0 +1,45 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# 3.9.0: +# Modified by: +# Adam Huffman +# The Francis Crick Institute + +easyblock = "CMakeMake" + +name = 'SPAdes' +version = '3.10.1' + +homepage = 'http://cab.spbu.ru/software/spades/' +description = """Genome assembler for single-cell and isolates data sets""" + +toolchain = {'name': 'foss', 'version': '2017a'} + +source_urls = ['http://cab.spbu.ru/files/release%(version)s'] +sources = [SOURCE_TAR_GZ] + +builddependencies = [('CMake', '3.8.2')] + +dependencies = [ + ('zlib', '1.2.11'), + ('bzip2', '1.0.6'), + ('libreadline', '7.0'), +] + +start_dir = 'src' + +separate_build_dir = True + +configopts = ' -DBoost_NO_BOOST_CMAKE=ON' + +sanity_check_commands = [('spades.py', '--test')] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['bwa-spades', 'dipspades', 'dipspades.py', + 'hammer', 'ionhammer', 'spades', 'spades.py']], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From a10eead80ac4f54bf38cfa9a7ebd54217eb9d3ee Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 23 Aug 2017 16:08:46 +0200 Subject: [PATCH 1417/1603] bump OpenBLAS to 0.2.20 in foss/2017b, with inclusion of two important patches --- easybuild/easyconfigs/f/foss/foss-2017b.eb | 7 +- ...BLAS-0.2.19-GCC-6.4.0-2.28-LAPACK-3.7.0.eb | 56 ------ .../OpenBLAS-0.2.19_LAPACK-3.7.0-fixes.patch | 35 ---- .../OpenBLAS-0.2.20-GCC-6.4.0-2.28.eb | 50 +++++ ...20_fix-Intel-L1-cache-size-detection.patch | 188 ++++++++++++++++++ .../OpenBLAS-0.2.20_revert-honor-cpuset.patch | 135 +++++++++++++ ...PACK-2.0.2-gompi-2017b-OpenBLAS-0.2.20.eb} | 7 +- 7 files changed, 379 insertions(+), 99 deletions(-) delete mode 100644 easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-GCC-6.4.0-2.28-LAPACK-3.7.0.eb delete mode 100644 easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19_LAPACK-3.7.0-fixes.patch create mode 100644 easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.20-GCC-6.4.0-2.28.eb create mode 100644 easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.20_fix-Intel-L1-cache-size-detection.patch create mode 100644 easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.20_revert-honor-cpuset.patch rename easybuild/easyconfigs/s/ScaLAPACK/{ScaLAPACK-2.0.2-gompi-2017b-OpenBLAS-0.2.19-LAPACK-3.7.0.eb => ScaLAPACK-2.0.2-gompi-2017b-OpenBLAS-0.2.20.eb} (76%) diff --git a/easybuild/easyconfigs/f/foss/foss-2017b.eb b/easybuild/easyconfigs/f/foss/foss-2017b.eb index a0cf18555c..d217118e86 100644 --- a/easybuild/easyconfigs/f/foss/foss-2017b.eb +++ b/easybuild/easyconfigs/f/foss/foss-2017b.eb @@ -12,9 +12,8 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} gccver = '6.4.0-2.28' blaslib = 'OpenBLAS' -blasver = '0.2.19' +blasver = '0.2.20' blas = '%s-%s' % (blaslib, blasver) -blassuff = '-LAPACK-3.7.0' # toolchain used to build foss dependencies comp_mpi_tc_name = 'gompi' @@ -26,9 +25,9 @@ comp_mpi_tc = (comp_mpi_tc_name, version) dependencies = [ ('GCC', gccver), ('OpenMPI', '2.1.1', '', ('GCC', gccver)), - (blaslib, blasver, blassuff, ('GCC', gccver)), + (blaslib, blasver, '', ('GCC', gccver)), ('FFTW', '3.3.6', '', comp_mpi_tc), - ('ScaLAPACK', '2.0.2', '-%s%s' % (blas, blassuff), comp_mpi_tc), + ('ScaLAPACK', '2.0.2', '-%s' % blas, comp_mpi_tc), ] moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-GCC-6.4.0-2.28-LAPACK-3.7.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-GCC-6.4.0-2.28-LAPACK-3.7.0.eb deleted file mode 100644 index 21faaaf7ab..0000000000 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-GCC-6.4.0-2.28-LAPACK-3.7.0.eb +++ /dev/null @@ -1,56 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'OpenBLAS' -version = '0.2.19' - -lapackver = '3.7.0' -versionsuffix = '-LAPACK-%s' % lapackver - -homepage = 'http://xianyi.github.com/OpenBLAS/' -description = """OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version.""" - -toolchain = {'name': 'GCC', 'version': '6.4.0-2.28'} - -lapack_src = 'lapack-%s.tgz' % lapackver -large_src = 'large.tgz' -timing_src = 'timing.tgz' - -lapack_unpack_cmd = 'cd %(name)s-%(version)s; rm -rf lapack-netlib;' -lapack_unpack_cmd += 'mkdir lapack-netlib;' -lapack_unpack_cmd += 'tar -C lapack-netlib --strip-components=1 -zxf %s; cd -' - -sources = [ - 'v%(version)s.tar.gz', - (lapack_src, lapack_unpack_cmd), - large_src, - timing_src, -] -source_urls = [ - # order matters, trying to download the LAPACK tarball from GitHub causes trouble - "http://www.netlib.org/lapack/", - "http://www.netlib.org/lapack/timing/", - "https://github.com/xianyi/OpenBLAS/archive/", -] - -patches = [ - (large_src, '.'), - (timing_src, '.'), - 'OpenBLAS-%(version)s_LAPACK-3.7.0-fixes.patch', -] - -skipsteps = ['configure'] - -buildopts = 'BINARY=64 USE_THREAD=1 CC="$CC" FC="$F77" NO_AFFINITY=1' -installopts = "USE_THREAD=1 PREFIX=%(installdir)s" - -# extensive testing can be enabled by uncommenting the line below -# runtest = 'PATH=.:$PATH lapack-timing' - -sanity_check_paths = { - 'files': ['include/cblas.h', 'include/f77blas.h', 'include/lapacke_config.h', 'include/lapacke.h', - 'include/lapacke_mangling.h', 'include/lapacke_utils.h', 'include/openblas_config.h', - 'lib/libopenblas.a', 'lib/libopenblas.%s' % SHLIB_EXT], - 'dirs': [], -} - -moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19_LAPACK-3.7.0-fixes.patch b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19_LAPACK-3.7.0-fixes.patch deleted file mode 100644 index 54c1b5525d..0000000000 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19_LAPACK-3.7.0-fixes.patch +++ /dev/null @@ -1,35 +0,0 @@ -fixes to combine OpenBLAS 0.2.19 with LAPACK 3.7.0 -* upstream bugfix in Makefile for LAPACK 3.7.0, cfr. https://github.com/Reference-LAPACK/lapack/commit/c5788233f95fed2c7f008ea079e8257a85348287 -* fix copying of lapacke_mangling.h, since it was renamed in LAPACK 3.7.0 -author: Kenneth Hoste (HPC-UGent) ---- OpenBLAS-0.2.19/Makefile.install.orig 2017-01-04 15:51:12.483541471 +0100 -+++ OpenBLAS-0.2.19/Makefile.install 2017-01-04 15:51:27.583647000 +0100 -@@ -50,7 +50,7 @@ - @echo Copying LAPACKE header files to $(DESTDIR)$(OPENBLAS_INCLUDE_DIR) - @-install -pm644 $(NETLIB_LAPACK_DIR)/LAPACKE/include/lapacke.h "$(DESTDIR)$(OPENBLAS_INCLUDE_DIR)/lapacke.h" - @-install -pm644 $(NETLIB_LAPACK_DIR)/LAPACKE/include/lapacke_config.h "$(DESTDIR)$(OPENBLAS_INCLUDE_DIR)/lapacke_config.h" -- @-install -pm644 $(NETLIB_LAPACK_DIR)/LAPACKE/include/lapacke_mangling_with_flags.h "$(DESTDIR)$(OPENBLAS_INCLUDE_DIR)/lapacke_mangling.h" -+ @-install -pm644 $(NETLIB_LAPACK_DIR)/LAPACKE/include/lapacke_mangling.h "$(DESTDIR)$(OPENBLAS_INCLUDE_DIR)/lapacke_mangling.h" - @-install -pm644 $(NETLIB_LAPACK_DIR)/LAPACKE/include/lapacke_utils.h "$(DESTDIR)$(OPENBLAS_INCLUDE_DIR)/lapacke_utils.h" - endif - ---- OpenBLAS-0.2.19/lapack-netlib/SRC/CMakeLists.txt.orig -+++ OpenBLAS-0.2.19/lapack-netlib/SRC/CMakeLists.txt -@@ -454,7 +454,6 @@ set(ZLASRC - zgelqt.f zgelqt3.f zgemlqt.f - zgetsls.f zgeqr.f zlatsqr.f zlamtsqr.f zgemqr.f - zgelq.f zlaswlq.f zlamswlq.f zgemlq.f -- ztplqt.f ztplqt2.f ztpmlqt.f - zhetrd_2stage.f zhetrd_he2hb.f zhetrd_hb2st.F zhb2st_kernels.f - zheevd_2stage.f zheev_2stage.f zheevx_2stage.f zheevr_2stage.f - zhbev_2stage.f zhbevx_2stage.f zhbevd_2stage.f zhegv_2stage.f) ---- OpenBLAS-0.2.19/lapack-netlib/SRC/Makefile.orig -+++ OpenBLAS-0.2.19/lapack-netlib/SRC/Makefile -@@ -464,7 +464,6 @@ ZLASRC = \ - zgelqt.o zgelqt3.o zgemlqt.o \ - zgetsls.o zgeqr.o zlatsqr.o zlamtsqr.o zgemqr.o \ - zgelq.o zlaswlq.o zlamswlq.o zgemlq.o \ -- ztplqt.o ztplqt2.o ztpmlqt.o \ - zhetrd_2stage.o zhetrd_he2hb.o zhetrd_hb2st.o zhb2st_kernels.o \ - zheevd_2stage.o zheev_2stage.o zheevx_2stage.o zheevr_2stage.o \ - zhbev_2stage.o zhbevx_2stage.o zhbevd_2stage.o zhegv_2stage.o diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.20-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.20-GCC-6.4.0-2.28.eb new file mode 100644 index 0000000000..1b9ef9d2f9 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.20-GCC-6.4.0-2.28.eb @@ -0,0 +1,50 @@ +easyblock = 'ConfigureMake' + +name = 'OpenBLAS' +version = '0.2.20' + +homepage = 'http://xianyi.github.com/OpenBLAS/' +description = "OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version." + +toolchain = {'name': 'GCC', 'version': '6.4.0-2.28'} + +large_src = 'large.tgz' +timing_src = 'timing.tgz' + +source_urls = [ + # order matters, trying to download the large.tgz/timing.tgz LAPACK tarballs from GitHub causes trouble + 'http://www.netlib.org/lapack/timing/', + 'https://github.com/xianyi/OpenBLAS/archive/', +] +sources = ['v%(version)s.tar.gz'] +checksums = [ + '5ef38b15d9c652985774869efd548b8e3e972e1e99475c673b25537ed7bcf394', # v0.2.20.tar.gz (OpenBLAS) + 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz + '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz + '1d043e4838ec1f90b2b49318b780e3ab13b46133cb72a8d83eb0e3b1b056c4d6', # OpenBLAS-0.2.20_fix-Intel-L1-cache-size-detection.patch + '1e6a046ab658c6e0b351de901d2812db28c2042f9f141416144c2faaf71fbb37', # OpenBLAS-0.2.20_revert-honor-cpuset.patch +] + +patches = [ + (large_src, '.'), + (timing_src, '.'), + 'OpenBLAS-%(version)s_fix-Intel-L1-cache-size-detection.patch', + 'OpenBLAS-%(version)s_revert-honor-cpuset.patch', +] + +skipsteps = ['configure'] + +buildopts = 'BINARY=64 USE_THREAD=1 CC="$CC" FC="$F77" NO_AFFINITY=1' +installopts = "USE_THREAD=1 PREFIX=%(installdir)s" + +# extensive testing can be enabled by uncommenting the line below +# runtest = 'PATH=.:$PATH lapack-timing' + +sanity_check_paths = { + 'files': ['include/cblas.h', 'include/f77blas.h', 'include/lapacke_config.h', 'include/lapacke.h', + 'include/lapacke_mangling.h', 'include/lapacke_utils.h', 'include/openblas_config.h', + 'lib/libopenblas.a', 'lib/libopenblas.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.20_fix-Intel-L1-cache-size-detection.patch b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.20_fix-Intel-L1-cache-size-detection.patch new file mode 100644 index 0000000000..f974460dc6 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.20_fix-Intel-L1-cache-size-detection.patch @@ -0,0 +1,188 @@ +fixes detection of L1 cache size on Intel processors, incl. Intel Haswell) +see https://github.com/xianyi/OpenBLAS/pull/1236 && https://github.com/xianyi/OpenBLAS/issues/1232 +--- a/cpuid_x86.c ++++ b/cpuid_x86.c +@@ -71,12 +71,23 @@ void cpuid(int op, int *eax, int *ebx, int *ecx, int *edx) + *edx = cpuInfo[3]; + } + ++void cpuid_count(int op, int count, int *eax, int *ebx, int *ecx, int *edx) ++{ ++ int cpuInfo[4] = {-1}; ++ __cpuidex(cpuInfo, op, count); ++ *eax = cpuInfo[0]; ++ *ebx = cpuInfo[1]; ++ *ecx = cpuInfo[2]; ++ *edx = cpuInfo[3]; ++} ++ + #else + + #ifndef CPUIDEMU + + #if defined(__APPLE__) && defined(__i386__) + void cpuid(int op, int *eax, int *ebx, int *ecx, int *edx); ++void cpuid_count(int op, int count, int *eax, int *ebx, int *ecx, int *edx); + #else + static C_INLINE void cpuid(int op, int *eax, int *ebx, int *ecx, int *edx){ + #if defined(__i386__) && defined(__PIC__) +@@ -90,6 +101,19 @@ static C_INLINE void cpuid(int op, int *eax, int *ebx, int *ecx, int *edx){ + ("cpuid": "=a" (*eax), "=b" (*ebx), "=c" (*ecx), "=d" (*edx) : "a" (op) : "cc"); + #endif + } ++ ++static C_INLINE void cpuid_count(int op, int count ,int *eax, int *ebx, int *ecx, int *edx){ ++#if defined(__i386__) && defined(__PIC__) ++ __asm__ __volatile__ ++ ("mov %%ebx, %%edi;" ++ "cpuid;" ++ "xchgl %%ebx, %%edi;" ++ : "=a" (*eax), "=D" (*ebx), "=c" (*ecx), "=d" (*edx) : "0" (op), "2" (count) : "cc"); ++#else ++ __asm__ __volatile__ ++ ("cpuid": "=a" (*eax), "=b" (*ebx), "=c" (*ecx), "=d" (*edx) : "0" (op), "2" (count) : "cc"); ++#endif ++} + #endif + + #else +@@ -157,6 +157,10 @@ void cpuid(unsigned int op, unsigned int *eax, unsigned int *ebx, unsigned int * + *edx = idlist[current].d; + } + ++void cpuid_count (unsigned int op, unsigned int count, unsigned int *eax, unsigned int *ebx, unsigned int *ecx, unsigned int *edx) { ++ return cpuid (op, eax, ebx, ecx, edx); ++} ++ + #endif + + #endif // _MSC_VER +@@ -312,9 +336,9 @@ int get_cacheinfo(int type, cache_info_t *cacheinfo){ + cpuid(0, &cpuid_level, &ebx, &ecx, &edx); + + if (cpuid_level > 1) { +- ++ int numcalls =0 ; + cpuid(2, &eax, &ebx, &ecx, &edx); +- ++ numcalls = BITMASK(eax, 0, 0xff); //FIXME some systems may require repeated calls to read all entries + info[ 0] = BITMASK(eax, 8, 0xff); + info[ 1] = BITMASK(eax, 16, 0xff); + info[ 2] = BITMASK(eax, 24, 0xff); +@@ -335,7 +359,6 @@ int get_cacheinfo(int type, cache_info_t *cacheinfo){ + info[14] = BITMASK(edx, 24, 0xff); + + for (i = 0; i < 15; i++){ +- + switch (info[i]){ + + /* This table is from http://www.sandpile.org/ia32/cpuid.htm */ +@@ -637,12 +660,13 @@ int get_cacheinfo(int type, cache_info_t *cacheinfo){ + LD1.linesize = 64; + break; + case 0x63 : +- DTB.size = 2048; +- DTB.associative = 4; +- DTB.linesize = 32; +- LDTB.size = 4096; +- LDTB.associative= 4; +- LDTB.linesize = 32; ++ DTB.size = 2048; ++ DTB.associative = 4; ++ DTB.linesize = 32; ++ LDTB.size = 4096; ++ LDTB.associative= 4; ++ LDTB.linesize = 32; ++ break; + case 0x66 : + LD1.size = 8; + LD1.associative = 4; +@@ -675,12 +699,13 @@ int get_cacheinfo(int type, cache_info_t *cacheinfo){ + LC1.associative = 8; + break; + case 0x76 : +- ITB.size = 2048; +- ITB.associative = 0; +- ITB.linesize = 8; +- LITB.size = 4096; +- LITB.associative= 0; +- LITB.linesize = 8; ++ ITB.size = 2048; ++ ITB.associative = 0; ++ ITB.linesize = 8; ++ LITB.size = 4096; ++ LITB.associative= 0; ++ LITB.linesize = 8; ++ break; + case 0x77 : + LC1.size = 16; + LC1.associative = 4; +@@ -891,6 +916,68 @@ int get_cacheinfo(int type, cache_info_t *cacheinfo){ + } + + if (get_vendor() == VENDOR_INTEL) { ++ if(LD1.size<=0 || LC1.size<=0){ ++ //If we didn't detect L1 correctly before, ++ int count; ++ for (count=0;count <4;count++) { ++ cpuid_count(4, count, &eax, &ebx, &ecx, &edx); ++ switch (eax &0x1f) { ++ case 0: ++ continue; ++ case 1: ++ case 3: ++ { ++ switch ((eax >>5) &0x07) ++ { ++ case 1: ++ { ++// fprintf(stderr,"L1 data cache...\n"); ++ int sets = ecx+1; ++ int lines = (ebx & 0x0fff) +1; ++ ebx>>=12; ++ int part = (ebx&0x03ff)+1; ++ ebx >>=10; ++ int assoc = (ebx&0x03ff)+1; ++ LD1.size = (assoc*part*lines*sets)/1024; ++ LD1.associative = assoc; ++ LD1.linesize= lines; ++ break; ++ } ++ default: ++ break; ++ } ++ break; ++ } ++ case 2: ++ { ++ switch ((eax >>5) &0x07) ++ { ++ case 1: ++ { ++// fprintf(stderr,"L1 instruction cache...\n"); ++ int sets = ecx+1; ++ int lines = (ebx & 0x0fff) +1; ++ ebx>>=12; ++ int part = (ebx&0x03ff)+1; ++ ebx >>=10; ++ int assoc = (ebx&0x03ff)+1; ++ LC1.size = (assoc*part*lines*sets)/1024; ++ LC1.associative = assoc; ++ LC1.linesize= lines; ++ break; ++ } ++ default: ++ break; ++ } ++ break; ++ ++ } ++ default: ++ break; ++ } ++ } ++ } ++ + cpuid(0x80000000, &cpuid_level, &ebx, &ecx, &edx); + if (cpuid_level >= 0x80000006) { + if(L2.size<=0){ diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.20_revert-honor-cpuset.patch b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.20_revert-honor-cpuset.patch new file mode 100644 index 0000000000..240b757a97 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.20_revert-honor-cpuset.patch @@ -0,0 +1,135 @@ +revert changes to honor cgroup/cpuset limits that was merged prematurely in OpenBLAS 0.2.20 +see https://github.com/xianyi/OpenBLAS/pull/1247 +diff --git a/driver/others/init.c b/driver/others/init.c +index 4c75d72e4..3e6176967 100644 +--- a/driver/others/init.c ++++ b/driver/others/init.c +@@ -778,11 +778,11 @@ static int initialized = 0; + void gotoblas_affinity_init(void) { + + int cpu, num_avail; +-#ifndef USE_OPENMP ++#ifndef USE_OPENMP + cpu_set_t cpu_mask; + #endif + int i; +- ++ + if (initialized) return; + + initialized = 1; +@@ -826,54 +826,15 @@ void gotoblas_affinity_init(void) { + common -> shmid = pshmid; + + if (common -> magic != SH_MAGIC) { +- cpu_set_t *cpusetp; +- int nums; +- int ret; +- + #ifdef DEBUG + fprintf(stderr, "Shared Memory Initialization.\n"); + #endif + + //returns the number of processors which are currently online +- +- nums = sysconf(_SC_NPROCESSORS_CONF); +- +-#if !defined(__GLIBC_PREREQ) || !__GLIBC_PREREQ(2, 3) +- common->num_procs = nums; +-#elif __GLIBC_PREREQ(2, 7) +- cpusetp = CPU_ALLOC(nums); +- if (cpusetp == NULL) { +- common->num_procs = nums; +- } else { +- size_t size; +- size = CPU_ALLOC_SIZE(nums); +- ret = sched_getaffinity(0,size,cpusetp); +- if (ret!=0) +- common->num_procs = nums; +- else +- common->num_procs = CPU_COUNT_S(size,cpusetp); +- } +- CPU_FREE(cpusetp); +-#else +- ret = sched_getaffinity(0,sizeof(cpu_set_t), cpusetp); +- if (ret!=0) { +- common->num_procs = nums; +- } else { +-#if !__GLIBC_PREREQ(2, 6) +- int i; +- int n = 0; +- for (i=0;inum_procs = n; +- } +-#else +- common->num_procs = CPU_COUNT(sizeof(cpu_set_t),cpusetp); +-#endif +- +-#endif ++ common -> num_procs = sysconf(_SC_NPROCESSORS_CONF);; + + if(common -> num_procs > MAX_CPUS) { +- fprintf(stderr, "\nOpenBLAS Warning : The number of CPU/Cores(%d) is beyond the limit(%d). Terminated.\n", common->num_procs, MAX_CPUS); ++ fprintf(stderr, "\nOpenBLAS Warining : The number of CPU/Cores(%d) is beyond the limit(%d). Terminated.\n", common->num_procs, MAX_CPUS); + exit(1); + } + +@@ -886,7 +847,7 @@ void gotoblas_affinity_init(void) { + if (common -> num_nodes > 1) numa_mapping(); + + common -> final_num_procs = 0; +- for(i = 0; i < common -> avail_count; i++) common -> final_num_procs += rcount(common -> avail[i]) + 1; //Make the max cpu number. ++ for(i = 0; i < common -> avail_count; i++) common -> final_num_procs += rcount(common -> avail[i]) + 1; //Make the max cpu number. + + for (cpu = 0; cpu < common -> final_num_procs; cpu ++) common -> cpu_use[cpu] = 0; + +diff --git a/driver/others/memory.c b/driver/others/memory.c +index 38d063715..916950315 100644 +--- a/driver/others/memory.c ++++ b/driver/others/memory.c +@@ -175,44 +175,7 @@ int get_num_procs(void); + #else + int get_num_procs(void) { + static int nums = 0; +-cpu_set_t *cpusetp; +-size_t size; +-int ret; +-int i,n; +- + if (!nums) nums = sysconf(_SC_NPROCESSORS_CONF); +-#if !defined(OS_LINUX) +- return nums; +-#endif +- +-#if !defined(__GLIBC_PREREQ) +- return nums; +-#endif +-#if !__GLIBC_PREREQ(2, 3) +- return nums; +-#endif +- +-#if !__GLIBC_PREREQ(2, 7) +- ret = sched_getaffinity(0,sizeof(cpu_set_t), cpusetp); +- if (ret!=0) return nums; +- n=0; +-#if !__GLIBC_PREREQ(2, 6) +- for (i=0;i Date: Wed, 23 Aug 2017 16:13:17 +0200 Subject: [PATCH 1418/1603] don't specify NO_AFFINITY=1, also specify USE_OPENMP=1 for OpenBLAS 0.2.20 (cfr. #4524) --- .../easyconfigs/o/OpenBLAS/OpenBLAS-0.2.20-GCC-6.4.0-2.28.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.20-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.20-GCC-6.4.0-2.28.eb index 1b9ef9d2f9..756eeba375 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.20-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.20-GCC-6.4.0-2.28.eb @@ -34,8 +34,8 @@ patches = [ skipsteps = ['configure'] -buildopts = 'BINARY=64 USE_THREAD=1 CC="$CC" FC="$F77" NO_AFFINITY=1' -installopts = "USE_THREAD=1 PREFIX=%(installdir)s" +buildopts = 'BINARY=64 USE_THREAD=1 USE_OPENMP=1 CC="$CC" FC="$F77"' +installopts = "USE_THREAD=1 USE_OPENMP=1 PREFIX=%(installdir)s" # extensive testing can be enabled by uncommenting the line below # runtest = 'PATH=.:$PATH lapack-timing' -- GitLab From cb502ba11a8014b593d6633182a7438e3abe36a9 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 23 Aug 2017 16:15:52 +0200 Subject: [PATCH 1419/1603] Use github tagged tarball --- .../s/SOAPdenovo-Trans/SOAPdenovo-Trans-1.04-intel-2017a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SOAPdenovo-Trans/SOAPdenovo-Trans-1.04-intel-2017a.eb b/easybuild/easyconfigs/s/SOAPdenovo-Trans/SOAPdenovo-Trans-1.04-intel-2017a.eb index 339fff4b72..23f71d7d40 100644 --- a/easybuild/easyconfigs/s/SOAPdenovo-Trans/SOAPdenovo-Trans-1.04-intel-2017a.eb +++ b/easybuild/easyconfigs/s/SOAPdenovo-Trans/SOAPdenovo-Trans-1.04-intel-2017a.eb @@ -10,7 +10,7 @@ adapt to alternative splicing and different expression level among transcripts. toolchain = {'name': 'intel', 'version': '2017a'} -sources = ['4e25da665b38172.tar.gz'] # no releases tagged on github +sources = ['%(version)s.tar.gz'] source_urls = ['https://github.com/aquaskyline/SOAPdenovo-Trans/archive/'] patches = ['fix-makefiles-%(version)s.patch'] -- GitLab From cd4fa66e00de701eeef52eecc6960d2301180985 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 23 Aug 2017 16:29:58 +0200 Subject: [PATCH 1420/1603] remove undeeded numactl-2.0.11-GCC-6.4.0-2.28.eb, existing numactl-2.0.11-GCCcore-6.4.0.eb suffices --- .../numactl/numactl-2.0.11-GCC-6.4.0-2.28.eb | 22 ------------------- 1 file changed, 22 deletions(-) delete mode 100644 easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCC-6.4.0-2.28.eb diff --git a/easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCC-6.4.0-2.28.eb deleted file mode 100644 index 775fb405c3..0000000000 --- a/easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCC-6.4.0-2.28.eb +++ /dev/null @@ -1,22 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'numactl' -version = '2.0.11' - -homepage = 'http://oss.sgi.com/projects/libnuma/' -description = """The numactl program allows you to run your application program on specific cpu's and memory nodes. -It does this by supplying a NUMA memory policy to the operating system before running your program. -The libnuma library provides convenient ways for you to add NUMA memory policies into your own program.""" - -toolchain = {'name': 'GCC', 'version': '6.4.0-2.28'} - -source_urls = ['ftp://oss.sgi.com/www/projects/libnuma/download/'] -sources = [SOURCE_TAR_GZ] -checksums = ['450c091235f891ee874a8651b179c30f57a1391ca5c4673354740ba65e527861'] - -sanity_check_paths = { - 'files': ['bin/numactl', 'bin/numastat', 'lib/libnuma.%s' % SHLIB_EXT, 'lib/libnuma.a'], - 'dirs': ['share/man', 'include'] -} - -moduleclass = 'tools' -- GitLab From 719d650d2f0800633f46817cd5929ff833909a49 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 23 Aug 2017 16:38:58 +0200 Subject: [PATCH 1421/1603] add back accidentally removed OpenBLAS-0.2.19_LAPACK-3.7.0-fixes.patch --- .../OpenBLAS-0.2.19_LAPACK-3.7.0-fixes.patch | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19_LAPACK-3.7.0-fixes.patch diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19_LAPACK-3.7.0-fixes.patch b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19_LAPACK-3.7.0-fixes.patch new file mode 100644 index 0000000000..54c1b5525d --- /dev/null +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19_LAPACK-3.7.0-fixes.patch @@ -0,0 +1,35 @@ +fixes to combine OpenBLAS 0.2.19 with LAPACK 3.7.0 +* upstream bugfix in Makefile for LAPACK 3.7.0, cfr. https://github.com/Reference-LAPACK/lapack/commit/c5788233f95fed2c7f008ea079e8257a85348287 +* fix copying of lapacke_mangling.h, since it was renamed in LAPACK 3.7.0 +author: Kenneth Hoste (HPC-UGent) +--- OpenBLAS-0.2.19/Makefile.install.orig 2017-01-04 15:51:12.483541471 +0100 ++++ OpenBLAS-0.2.19/Makefile.install 2017-01-04 15:51:27.583647000 +0100 +@@ -50,7 +50,7 @@ + @echo Copying LAPACKE header files to $(DESTDIR)$(OPENBLAS_INCLUDE_DIR) + @-install -pm644 $(NETLIB_LAPACK_DIR)/LAPACKE/include/lapacke.h "$(DESTDIR)$(OPENBLAS_INCLUDE_DIR)/lapacke.h" + @-install -pm644 $(NETLIB_LAPACK_DIR)/LAPACKE/include/lapacke_config.h "$(DESTDIR)$(OPENBLAS_INCLUDE_DIR)/lapacke_config.h" +- @-install -pm644 $(NETLIB_LAPACK_DIR)/LAPACKE/include/lapacke_mangling_with_flags.h "$(DESTDIR)$(OPENBLAS_INCLUDE_DIR)/lapacke_mangling.h" ++ @-install -pm644 $(NETLIB_LAPACK_DIR)/LAPACKE/include/lapacke_mangling.h "$(DESTDIR)$(OPENBLAS_INCLUDE_DIR)/lapacke_mangling.h" + @-install -pm644 $(NETLIB_LAPACK_DIR)/LAPACKE/include/lapacke_utils.h "$(DESTDIR)$(OPENBLAS_INCLUDE_DIR)/lapacke_utils.h" + endif + +--- OpenBLAS-0.2.19/lapack-netlib/SRC/CMakeLists.txt.orig ++++ OpenBLAS-0.2.19/lapack-netlib/SRC/CMakeLists.txt +@@ -454,7 +454,6 @@ set(ZLASRC + zgelqt.f zgelqt3.f zgemlqt.f + zgetsls.f zgeqr.f zlatsqr.f zlamtsqr.f zgemqr.f + zgelq.f zlaswlq.f zlamswlq.f zgemlq.f +- ztplqt.f ztplqt2.f ztpmlqt.f + zhetrd_2stage.f zhetrd_he2hb.f zhetrd_hb2st.F zhb2st_kernels.f + zheevd_2stage.f zheev_2stage.f zheevx_2stage.f zheevr_2stage.f + zhbev_2stage.f zhbevx_2stage.f zhbevd_2stage.f zhegv_2stage.f) +--- OpenBLAS-0.2.19/lapack-netlib/SRC/Makefile.orig ++++ OpenBLAS-0.2.19/lapack-netlib/SRC/Makefile +@@ -464,7 +464,6 @@ ZLASRC = \ + zgelqt.o zgelqt3.o zgemlqt.o \ + zgetsls.o zgeqr.o zlatsqr.o zlamtsqr.o zgemqr.o \ + zgelq.o zlaswlq.o zlamswlq.o zgemlq.o \ +- ztplqt.o ztplqt2.o ztpmlqt.o \ + zhetrd_2stage.o zhetrd_he2hb.o zhetrd_hb2st.o zhb2st_kernels.o \ + zheevd_2stage.o zheev_2stage.o zheevx_2stage.o zheevr_2stage.o \ + zhbev_2stage.o zhbevx_2stage.o zhbevd_2stage.o zhegv_2stage.o -- GitLab From 4050d91e64ff5df26be246f647645798ef6a0ff4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 23 Aug 2017 17:16:15 +0200 Subject: [PATCH 1422/1603] fix too long line in OpenBLAS 0.2.20 easyconfig --- .../easyconfigs/o/OpenBLAS/OpenBLAS-0.2.20-GCC-6.4.0-2.28.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.20-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.20-GCC-6.4.0-2.28.eb index 756eeba375..5b7ec851fc 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.20-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.20-GCC-6.4.0-2.28.eb @@ -21,7 +21,8 @@ checksums = [ '5ef38b15d9c652985774869efd548b8e3e972e1e99475c673b25537ed7bcf394', # v0.2.20.tar.gz (OpenBLAS) 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz - '1d043e4838ec1f90b2b49318b780e3ab13b46133cb72a8d83eb0e3b1b056c4d6', # OpenBLAS-0.2.20_fix-Intel-L1-cache-size-detection.patch + # OpenBLAS-0.2.20_fix-Intel-L1-cache-size-detection.patch + '1d043e4838ec1f90b2b49318b780e3ab13b46133cb72a8d83eb0e3b1b056c4d6', '1e6a046ab658c6e0b351de901d2812db28c2042f9f141416144c2faaf71fbb37', # OpenBLAS-0.2.20_revert-honor-cpuset.patch ] -- GitLab From b38703d0ff80c1dbec4975a3666888b1c0feba0d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 23 Aug 2017 19:39:38 +0200 Subject: [PATCH 1423/1603] add sanity check to Gdk-Pixbuf 2.36.8 easyconfig --- .../g/Gdk-Pixbuf/Gdk-Pixbuf-2.36.8-intel-2017a.eb | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.36.8-intel-2017a.eb b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.36.8-intel-2017a.eb index ab5bc95377..b403b98025 100644 --- a/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.36.8-intel-2017a.eb +++ b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.36.8-intel-2017a.eb @@ -30,6 +30,11 @@ dependencies = [ configopts = "--disable-maintainer-mode --enable-debug=no --enable-introspection=yes " configopts += "--disable-Bsymbolic --without-gdiplus --enable-shared --enable-static" +sanity_check_paths = { + 'files': ['lib/libgdk_pixbuf-%(version_major)s.0.a', 'lib/libgdk_pixbuf-%%(version_major)s.0.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include/gdk-pixbuf-%(version_major)s.0', 'lib/gdk-pixbuf-%(version_major)s.0', 'share'], +} + modextrapaths = { 'XDG_DATA_DIRS': 'share', } -- GitLab From f98a697ef596b916fb8849b5185e890118272cf7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 24 Aug 2017 15:16:52 +0200 Subject: [PATCH 1424/1603] adding easyconfigs: MERCKX-20170330-intel-2017a-Python-2.7.13.eb --- ...RCKX-20170330-intel-2017a-Python-2.7.13.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/m/MERCKX/MERCKX-20170330-intel-2017a-Python-2.7.13.eb diff --git a/easybuild/easyconfigs/m/MERCKX/MERCKX-20170330-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/m/MERCKX/MERCKX-20170330-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..50c7e7e7b5 --- /dev/null +++ b/easybuild/easyconfigs/m/MERCKX/MERCKX-20170330-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,34 @@ +easyblock = 'Tarball' + +name = 'MERCKX' +version = '20170330' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/madewild/MERCKX' +description = "Multilingual Entity/Resource Combiner & Knowledge eXtractor" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['https://github.com/madewild/MERCKX/archive/'] +sources = [{'filename': SOURCE_TAR_GZ, 'download_filename': '03b88e8.tar.gz'}] +checksums = ['f27480585c8bafac51d348c5a3916c18ed453592bc799903f2bb84dbc4134171'] + +dependencies = [ + ('Python', '2.7.13'), + ('NLTK', '3.2.4', versionsuffix), +] + +postinstallcmds = [ + "chmod a+x %(installdir)s/merckx*.py", + "sed -i 's/python merckx-init.py/merckx-init.py/' %(installdir)s/merckx-init.sh", +] + +sanity_check_paths = { + 'files': ['merckx.py', 'merckx-init.py', 'merckx-init.sh'], + 'dirs': [], +} +sanity_check_commands = ['merckx.py --help'] + +modextrapaths = {'PATH': ''} + +moduleclass = 'tools' -- GitLab From 817d98cb670a3d680cf2ab3aa27613c38db82421 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 24 Aug 2017 15:34:36 +0200 Subject: [PATCH 1425/1603] adding easyconfigs: CD-HIT-4.6.8-intel-2017a.eb --- .../c/CD-HIT/CD-HIT-4.6.8-intel-2017a.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.6.8-intel-2017a.eb diff --git a/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.6.8-intel-2017a.eb b/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.6.8-intel-2017a.eb new file mode 100644 index 0000000000..4985a93e26 --- /dev/null +++ b/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.6.8-intel-2017a.eb @@ -0,0 +1,35 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'MakeCp' + +name = 'CD-HIT' +version = '4.6.8' + +homepage = 'http://weizhong-lab.ucsd.edu/cd-hit/' +description = """ CD-HIT is a very widely used program for clustering and + comparing protein or nucleotide sequences.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'openmp': True} + +source_urls = ['https://github.com/weizhongli/cdhit/archive/'] +sources = ['V%(version)s.tar.gz'] +checksums = ['37d685e4aa849314401805fe4d4db707e1d06070368475e313d6f3cb8fb65949'] + +# make sure compilation flags are passed down (e.g. to enable OpenMP) +buildopts = ' CC="$CXX" CCFLAGS="$CPPFLAGS $CXXFLAGS"' + +# put here the list of generated executables when compiling +list_of_executables = ['cd-hit', 'cd-hit-est', 'cd-hit-2d', 'cd-hit-est-2d', 'cd-hit-div', 'cd-hit-454'] + +# this is the real EasyBuild line to copy all the executables and perl scripts to "bin" +files_to_copy = [(list_of_executables, 'bin'), (['*.pl'], 'bin'), 'README', 'doc', 'license.txt'] + +postinstallcmds = ["sed -i 's@#!/usr/bin/perl@/usr/bin/env perl@' %(installdir)s/bin/*.pl"] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in list_of_executables], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From 6a89b1d3350f37aa2cd3fe286326a0560c095a57 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 24 Aug 2017 15:38:26 +0200 Subject: [PATCH 1426/1603] add easyconfig for NLTK 3.2.4 as dep for MERCKX --- .../NLTK-3.2.4-intel-2017a-Python-2.7.13.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/n/NLTK/NLTK-3.2.4-intel-2017a-Python-2.7.13.eb diff --git a/easybuild/easyconfigs/n/NLTK/NLTK-3.2.4-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/n/NLTK/NLTK-3.2.4-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..d48fd45a34 --- /dev/null +++ b/easybuild/easyconfigs/n/NLTK/NLTK-3.2.4-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,23 @@ +easyblock = 'PythonPackage' + +name = 'NLTK' +version = '3.2.4' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.nltk.org/' +description = "NLTK is a leading platform for building Python programs to work with human language data." + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['8682ae52f5de4f2ba7b77bd78222a38575ad01ef29946214b254dfdf93a3a0eb'] + +dependencies = [('Python', '2.7.13')] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'data' -- GitLab From aed638c12fb80dac99c5c249282cd4b330d70534 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 24 Aug 2017 16:00:35 +0200 Subject: [PATCH 1427/1603] adding easyconfigs: OpenRefine-2.7-Java-1.8.0_121.eb --- .../OpenRefine-2.7-Java-1.8.0_121.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenRefine/OpenRefine-2.7-Java-1.8.0_121.eb diff --git a/easybuild/easyconfigs/o/OpenRefine/OpenRefine-2.7-Java-1.8.0_121.eb b/easybuild/easyconfigs/o/OpenRefine/OpenRefine-2.7-Java-1.8.0_121.eb new file mode 100644 index 0000000000..393c2fdcb0 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenRefine/OpenRefine-2.7-Java-1.8.0_121.eb @@ -0,0 +1,33 @@ +easyblock = 'PackedBinary' + +name = 'OpenRefine' +version = '2.7' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'https://github.com/OpenRefine/OpenRefine' +description = """OpenRefine is a power tool that allows you to load data, understand it, clean it up, reconcile it, + and augment it with data coming from the web.""" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = ['https://github.com/OpenRefine/OpenRefine/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['16f8c86db061d1c24f1fc64897eb23742e73415a019dd8ea3f39782de833146b'] + +builddependencies = [ + ('ant', '1.10.1', '-Java-%(javaver)s', True), +] +dependencies = [ + ('Java', '1.8.0_121'), +] + +install_cmd = "cp -a OpenRefine-%(version)s/* %(installdir)s && cd %(installdir)s && ./refine build" + +sanity_check_paths = { + 'files': ['refine'], + 'dirs': ['server/classes'], +} + +modextrapaths = {'PATH': 'refine'} + +moduleclass = 'tools' -- GitLab From 66050db403caa2dae56b01515e55a9f4e3c6e12b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 24 Aug 2017 17:12:51 +0200 Subject: [PATCH 1428/1603] bump Java dep in OpenRefine to 1.8.0_144 --- .../a/ant/ant-1.10.1-Java-1.8.0_144.eb | 27 +++++++++++++++ .../j/JUnit/JUnit-4.12-Java-1.8.0_144.eb | 23 +++++++++++++ .../OpenRefine-2.7-Java-1.8.0_144.eb | 33 +++++++++++++++++++ 3 files changed, 83 insertions(+) create mode 100644 easybuild/easyconfigs/a/ant/ant-1.10.1-Java-1.8.0_144.eb create mode 100644 easybuild/easyconfigs/j/JUnit/JUnit-4.12-Java-1.8.0_144.eb create mode 100644 easybuild/easyconfigs/o/OpenRefine/OpenRefine-2.7-Java-1.8.0_144.eb diff --git a/easybuild/easyconfigs/a/ant/ant-1.10.1-Java-1.8.0_144.eb b/easybuild/easyconfigs/a/ant/ant-1.10.1-Java-1.8.0_144.eb new file mode 100644 index 0000000000..77159ab0f1 --- /dev/null +++ b/easybuild/easyconfigs/a/ant/ant-1.10.1-Java-1.8.0_144.eb @@ -0,0 +1,27 @@ +name = 'ant' +version = '1.10.1' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'http://ant.apache.org/' +description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in + build files as targets and extension points dependent upon each other. The main known usage of Ant is the build of + Java applications.""" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = ['http://archive.apache.org/dist/%(name)s/source/'] +sources = ['apache-%(name)s-%(version)s-src.tar.gz'] +checksums = ['68f7ced0aa15d1f9f672f23d67c86deaf728e9576936313cfbff4f7a0e6ce382'] + +dependencies = [('Java', '1.8.0_144')] + +builddependencies = [('JUnit', '4.12', versionsuffix)] + +sanity_check_paths = { + 'files': ['bin/ant', 'lib/ant.jar', 'lib/ant.jar'], + 'dirs': [], +} + +modextravars = {'ANT_HOME': '%(installdir)s'} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/j/JUnit/JUnit-4.12-Java-1.8.0_144.eb b/easybuild/easyconfigs/j/JUnit/JUnit-4.12-Java-1.8.0_144.eb new file mode 100644 index 0000000000..4d57c600d0 --- /dev/null +++ b/easybuild/easyconfigs/j/JUnit/JUnit-4.12-Java-1.8.0_144.eb @@ -0,0 +1,23 @@ +easyblock = 'JAR' + +name = 'JUnit' +version = '4.12' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'http://sourceforge.net/projects/junit' +description = """A programmer-oriented testing framework for Java.""" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = ['http://search.maven.org/remotecontent?filepath=junit/junit/%(version)s/'] +sources = ['%(namelower)s-%(version)s.jar'] +checksums = ['59721f0805e223d84b90677887d9ff567dc534d7c502ca903c0c2b17f05c116a'] + +dependencies = [('Java', '1.8.0_144')] + +sanity_check_paths = { + 'files': sources, + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/o/OpenRefine/OpenRefine-2.7-Java-1.8.0_144.eb b/easybuild/easyconfigs/o/OpenRefine/OpenRefine-2.7-Java-1.8.0_144.eb new file mode 100644 index 0000000000..43fc8d1f70 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenRefine/OpenRefine-2.7-Java-1.8.0_144.eb @@ -0,0 +1,33 @@ +easyblock = 'PackedBinary' + +name = 'OpenRefine' +version = '2.7' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'https://github.com/OpenRefine/OpenRefine' +description = """OpenRefine is a power tool that allows you to load data, understand it, clean it up, reconcile it, + and augment it with data coming from the web.""" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = ['https://github.com/OpenRefine/OpenRefine/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['16f8c86db061d1c24f1fc64897eb23742e73415a019dd8ea3f39782de833146b'] + +builddependencies = [ + ('ant', '1.10.1', '-Java-%(javaver)s', True), +] +dependencies = [ + ('Java', '1.8.0_144'), +] + +install_cmd = "cp -a OpenRefine-%(version)s/* %(installdir)s && cd %(installdir)s && ./refine build" + +sanity_check_paths = { + 'files': ['refine'], + 'dirs': ['server/classes'], +} + +modextrapaths = {'PATH': 'refine'} + +moduleclass = 'tools' -- GitLab From 18c4cc19ec5c3c48d2b3d4f100351f0af0f5a861 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 24 Aug 2017 17:16:25 +0200 Subject: [PATCH 1429/1603] remove OpenRefine easyconfig with old Java dep --- .../OpenRefine-2.7-Java-1.8.0_121.eb | 33 ------------------- 1 file changed, 33 deletions(-) delete mode 100644 easybuild/easyconfigs/o/OpenRefine/OpenRefine-2.7-Java-1.8.0_121.eb diff --git a/easybuild/easyconfigs/o/OpenRefine/OpenRefine-2.7-Java-1.8.0_121.eb b/easybuild/easyconfigs/o/OpenRefine/OpenRefine-2.7-Java-1.8.0_121.eb deleted file mode 100644 index 393c2fdcb0..0000000000 --- a/easybuild/easyconfigs/o/OpenRefine/OpenRefine-2.7-Java-1.8.0_121.eb +++ /dev/null @@ -1,33 +0,0 @@ -easyblock = 'PackedBinary' - -name = 'OpenRefine' -version = '2.7' -versionsuffix = '-Java-%(javaver)s' - -homepage = 'https://github.com/OpenRefine/OpenRefine' -description = """OpenRefine is a power tool that allows you to load data, understand it, clean it up, reconcile it, - and augment it with data coming from the web.""" - -toolchain = {'name': 'dummy', 'version': ''} - -source_urls = ['https://github.com/OpenRefine/OpenRefine/archive/'] -sources = ['%(version)s.tar.gz'] -checksums = ['16f8c86db061d1c24f1fc64897eb23742e73415a019dd8ea3f39782de833146b'] - -builddependencies = [ - ('ant', '1.10.1', '-Java-%(javaver)s', True), -] -dependencies = [ - ('Java', '1.8.0_121'), -] - -install_cmd = "cp -a OpenRefine-%(version)s/* %(installdir)s && cd %(installdir)s && ./refine build" - -sanity_check_paths = { - 'files': ['refine'], - 'dirs': ['server/classes'], -} - -modextrapaths = {'PATH': 'refine'} - -moduleclass = 'tools' -- GitLab From 1852cc2ce64030d518f4d15a821dbfc567495bc1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 24 Aug 2017 18:12:39 +0200 Subject: [PATCH 1430/1603] adding easyconfigs: OpenNLP-1.8.1.eb --- .../easyconfigs/o/OpenNLP/OpenNLP-1.8.1.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenNLP/OpenNLP-1.8.1.eb diff --git a/easybuild/easyconfigs/o/OpenNLP/OpenNLP-1.8.1.eb b/easybuild/easyconfigs/o/OpenNLP/OpenNLP-1.8.1.eb new file mode 100644 index 0000000000..e5c7079e52 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenNLP/OpenNLP-1.8.1.eb @@ -0,0 +1,33 @@ +easyblock = 'PackedBinary' + +name = 'OpenNLP' +version = '1.8.1' + +homepage = 'https://opennlp.apache.org/' +description = """The Apache OpenNLP library is a machine learning based toolkit for the processing of + natural language text.""" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = [APACHE_SOURCE + '/%(namelower)s-%(version)s'] +sources = ['apache-opennlp-%(version)s-src.tar.gz'] +checksums = ['f0a09a499503dae318df28b4c78ea9eb6f9c3d47fbaa4cc019bb647af3d0567e'] + +dependencies = [ + ('Java', '1.8.0_144'), + ('Maven', '3.5.0'), # both build & runtime dep +] + +install_cmd = "cd apache-opennlp-%(version)s-src && mvn install -B && " +install_cmd += "tar xfvz opennlp-distr/target/apache-opennlp-1.8.1-bin.tar.gz && " +install_cmd += "cp -a apache-opennlp-%(version)s/* %(installdir)s" + +sanity_check_paths = { + 'files': ['bin/opennlp'], + 'dirs': ['lib'], +} +sanity_check_commands = ['opennlp'] + +modextravars = {'OPENNLP_HOME': '%(installdir)s'} + +moduleclass = 'lib' -- GitLab From 40e376a158eda204d1683840bac15d5e584ccc68 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 24 Aug 2017 18:27:24 +0200 Subject: [PATCH 1431/1603] Maven is only a build dep for OpenNLP --- easybuild/easyconfigs/o/OpenNLP/OpenNLP-1.8.1.eb | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenNLP/OpenNLP-1.8.1.eb b/easybuild/easyconfigs/o/OpenNLP/OpenNLP-1.8.1.eb index e5c7079e52..00bf00b919 100644 --- a/easybuild/easyconfigs/o/OpenNLP/OpenNLP-1.8.1.eb +++ b/easybuild/easyconfigs/o/OpenNLP/OpenNLP-1.8.1.eb @@ -13,10 +13,8 @@ source_urls = [APACHE_SOURCE + '/%(namelower)s-%(version)s'] sources = ['apache-opennlp-%(version)s-src.tar.gz'] checksums = ['f0a09a499503dae318df28b4c78ea9eb6f9c3d47fbaa4cc019bb647af3d0567e'] -dependencies = [ - ('Java', '1.8.0_144'), - ('Maven', '3.5.0'), # both build & runtime dep -] +builddependencies = [('Maven', '3.5.0')] +dependencies = [('Java', '1.8.0_144')] install_cmd = "cd apache-opennlp-%(version)s-src && mvn install -B && " install_cmd += "tar xfvz opennlp-distr/target/apache-opennlp-1.8.1-bin.tar.gz && " -- GitLab From 3037f86b525fbe146307106ecd8084ae2807886a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 25 Aug 2017 12:00:34 +0200 Subject: [PATCH 1432/1603] avoid that /Users/kehoste/.m2 is abused by Maven when installing OpenNLP --- easybuild/easyconfigs/o/OpenNLP/OpenNLP-1.8.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OpenNLP/OpenNLP-1.8.1.eb b/easybuild/easyconfigs/o/OpenNLP/OpenNLP-1.8.1.eb index 00bf00b919..19f1ce98bb 100644 --- a/easybuild/easyconfigs/o/OpenNLP/OpenNLP-1.8.1.eb +++ b/easybuild/easyconfigs/o/OpenNLP/OpenNLP-1.8.1.eb @@ -16,7 +16,7 @@ checksums = ['f0a09a499503dae318df28b4c78ea9eb6f9c3d47fbaa4cc019bb647af3d0567e'] builddependencies = [('Maven', '3.5.0')] dependencies = [('Java', '1.8.0_144')] -install_cmd = "cd apache-opennlp-%(version)s-src && mvn install -B && " +install_cmd = "cd apache-opennlp-%(version)s-src && mvn install -Dmaven.repo.local=%(builddir)s/m2 -B && " install_cmd += "tar xfvz opennlp-distr/target/apache-opennlp-1.8.1-bin.tar.gz && " install_cmd += "cp -a apache-opennlp-%(version)s/* %(installdir)s" -- GitLab From 4ab1282e9a4acb12b4525030f4d27f44cbd7a51e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 25 Aug 2017 12:13:48 +0200 Subject: [PATCH 1433/1603] include timereg as extension in R 3.4.0 easyconfig --- easybuild/easyconfigs/r/R/R-3.4.0-intel-2017a-X11-20170314.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/r/R/R-3.4.0-intel-2017a-X11-20170314.eb b/easybuild/easyconfigs/r/R/R-3.4.0-intel-2017a-X11-20170314.eb index 8ec992e75a..5ba7780140 100644 --- a/easybuild/easyconfigs/r/R/R-3.4.0-intel-2017a-X11-20170314.eb +++ b/easybuild/easyconfigs/r/R/R-3.4.0-intel-2017a-X11-20170314.eb @@ -553,6 +553,7 @@ exts_list = [ ('rrcov', '1.4-3', ext_options), ('WriteXLS', '4.0.0', ext_options), ('mpath', '0.2-4', ext_options), + ('timereg', '1.9.1', ext_options), ] moduleclass = 'lang' -- GitLab From 0b749943cf9fd8ab527e22bbeb1b994aaa03f9cf Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 25 Aug 2017 13:13:52 +0200 Subject: [PATCH 1434/1603] adding easyconfigs: Tika-1.16.eb --- easybuild/easyconfigs/t/Tika/Tika-1.16.eb | 28 +++++++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/t/Tika/Tika-1.16.eb diff --git a/easybuild/easyconfigs/t/Tika/Tika-1.16.eb b/easybuild/easyconfigs/t/Tika/Tika-1.16.eb new file mode 100644 index 0000000000..d0d0317869 --- /dev/null +++ b/easybuild/easyconfigs/t/Tika/Tika-1.16.eb @@ -0,0 +1,28 @@ +easyblock = 'PackedBinary' + +name = 'Tika' +version = '1.16' + +homepage = 'https://tika.apache.org/' +description = """The Apache Tika toolkit detects and extracts metadata and text from over a thousand different + file types (such as PPT, XLS, and PDF).""" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = [APACHE_SOURCE] +sources = ['tika-%(version)s-src.zip'] +checksums = ['7da47d09c48b2cd1b9acf4eea89d7f4a24d43388a867e4126cf35ee44336a260'] + +builddependencies = [('Maven', '3.5.0')] +dependencies = [('Java', '1.8.0_144')] + +install_cmd = "cd tika-%(version)s && mvn install -Dmaven.repo.local=%(builddir)s/m2 -DskipTests -B && " +install_cmd += "cp -a tika-app/target/tika-app-%(version)s.jar %(installdir)s && " +install_cmd += "cp -a tika-server/target/tika-server-%(version)s.jar %(installdir)s" + +sanity_check_paths = { + 'files': ['tika-app-%(version)s.jar', 'tika-server-%(version)s.jar'], + 'dirs': [], +} + +moduleclass = 'lib' -- GitLab From 7e0fbf00bda90b6d5e807340bc33a3fe87cce7c6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 25 Aug 2017 13:17:41 +0200 Subject: [PATCH 1435/1603] adding easyconfigs: Lucene-Geo-Gazetteer-20170718.eb --- .../Lucene-Geo-Gazetteer-20170718.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/l/Lucene-Geo-Gazetteer/Lucene-Geo-Gazetteer-20170718.eb diff --git a/easybuild/easyconfigs/l/Lucene-Geo-Gazetteer/Lucene-Geo-Gazetteer-20170718.eb b/easybuild/easyconfigs/l/Lucene-Geo-Gazetteer/Lucene-Geo-Gazetteer-20170718.eb new file mode 100644 index 0000000000..5d3e6d1cda --- /dev/null +++ b/easybuild/easyconfigs/l/Lucene-Geo-Gazetteer/Lucene-Geo-Gazetteer-20170718.eb @@ -0,0 +1,38 @@ +easyblock = 'PackedBinary' + +name = 'Lucene-Geo-Gazetteer' +version = '20170718' + +homepage = 'https://github.com/chrismattmann/lucene-geo-gazetteer' +description = """A command line gazetteer built around the Geonames.org dataset, that uses the Apache Lucene library + to create a searchable gazetter.""" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = ['https://github.com/chrismattmann/lucene-geo-gazetteer/archive/'] +sources = [{'filename': SOURCE_TAR_GZ, 'download_filename': '6c38272.tar.gz'}] +checksums = ['2ed355bfdcf865d815df9dc52ee747eeb8a15d065ef159ebf933ad36e1555ad4'] + +builddependencies = [('Maven', '3.5.0')] +dependencies = [('Java', '')] + +unpack_options = '--strip-components=1' + +install_cmd = "cp -a * %(installdir)s && cd %(installdir)s && " +install_cmd += "mvn install -Dmaven.repo.local=%(builddir)s/m2 -B assembly:assembly" + +# strip out hardcoded value for -i option, since user can not write to install directory +postinstallcmds = [ + "sed -i.bk 's/-i \$DIR_PATH[^ ]*//g' %(installdir)s/src/main/bin/lucene-geo-gazetteer", + "rm %(installdir)s/src/main/bin/lucene-geo-gazetteer.bk", +] + +sanity_check_paths = { + 'files': ['src/main/bin/lucene-geo-gazetteer'], + 'dirs': [], +} +sanity_check_commands = ["lucene-geo-gazetteer --help | grep 'usage: lucene-geo-gazetteer'"] + +modextrapaths = {'PATH': 'src/main/bin'} + +moduleclass = 'tools' -- GitLab From 89ca2019a6c973181827641b5186b181d17da65e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 25 Aug 2017 14:00:37 +0200 Subject: [PATCH 1436/1603] fix Java version + type in description for Lucene-Geo-Gazetteer --- .../l/Lucene-Geo-Gazetteer/Lucene-Geo-Gazetteer-20170718.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/Lucene-Geo-Gazetteer/Lucene-Geo-Gazetteer-20170718.eb b/easybuild/easyconfigs/l/Lucene-Geo-Gazetteer/Lucene-Geo-Gazetteer-20170718.eb index 5d3e6d1cda..27896fdb17 100644 --- a/easybuild/easyconfigs/l/Lucene-Geo-Gazetteer/Lucene-Geo-Gazetteer-20170718.eb +++ b/easybuild/easyconfigs/l/Lucene-Geo-Gazetteer/Lucene-Geo-Gazetteer-20170718.eb @@ -5,7 +5,7 @@ version = '20170718' homepage = 'https://github.com/chrismattmann/lucene-geo-gazetteer' description = """A command line gazetteer built around the Geonames.org dataset, that uses the Apache Lucene library - to create a searchable gazetter.""" + to create a searchable gazetteer.""" toolchain = {'name': 'dummy', 'version': ''} @@ -14,7 +14,7 @@ sources = [{'filename': SOURCE_TAR_GZ, 'download_filename': '6c38272.tar.gz'}] checksums = ['2ed355bfdcf865d815df9dc52ee747eeb8a15d065ef159ebf933ad36e1555ad4'] builddependencies = [('Maven', '3.5.0')] -dependencies = [('Java', '')] +dependencies = [('Java', '1.8.0_144')] unpack_options = '--strip-components=1' -- GitLab From e5816d394c6b90bb20d8bcbaca5a4c966462ca13 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 25 Aug 2017 15:01:09 +0200 Subject: [PATCH 1437/1603] remove trailing whitespace --- .../l/Lucene-Geo-Gazetteer/Lucene-Geo-Gazetteer-20170718.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/Lucene-Geo-Gazetteer/Lucene-Geo-Gazetteer-20170718.eb b/easybuild/easyconfigs/l/Lucene-Geo-Gazetteer/Lucene-Geo-Gazetteer-20170718.eb index 27896fdb17..c21c6baf85 100644 --- a/easybuild/easyconfigs/l/Lucene-Geo-Gazetteer/Lucene-Geo-Gazetteer-20170718.eb +++ b/easybuild/easyconfigs/l/Lucene-Geo-Gazetteer/Lucene-Geo-Gazetteer-20170718.eb @@ -1,7 +1,7 @@ easyblock = 'PackedBinary' name = 'Lucene-Geo-Gazetteer' -version = '20170718' +version = '20170718' homepage = 'https://github.com/chrismattmann/lucene-geo-gazetteer' description = """A command line gazetteer built around the Geonames.org dataset, that uses the Apache Lucene library -- GitLab From 01eaf0a4725f0c8afc02cbc04b26a0c35805d7b5 Mon Sep 17 00:00:00 2001 From: Alan O'Cais Date: Mon, 28 Aug 2017 15:10:15 +0200 Subject: [PATCH 1438/1603] Update ncurses to not build a separate libtinfo but provide a soft link instead. Force linking to ncurses in libreadline --- easybuild/easyconfigs/l/libreadline/libreadline-6.3.eb | 2 +- easybuild/easyconfigs/n/ncurses/ncurses-6.0.eb | 10 ++++++---- 2 files changed, 7 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3.eb index 36625b1717..501aa1480f 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3.eb @@ -20,7 +20,7 @@ patches = ['libreadline-%(version)s-bugfix.patch'] dependencies = [('ncurses', '6.0')] # for the termcap symbols, use EB ncurses -preconfigopts = "env LDFLAGS='-lncurses'" +buildopts = "SHLIB_LIBS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.0.eb index ce06be716d..70d6035d01 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-6.0.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.0.eb @@ -18,13 +18,15 @@ patches = ['ncurses-%(version)s_gcc-5.patch'] configopts = [ # default build - '--with-shared --enable-overwrite --with-termlib', + '--with-shared --enable-overwrite', # the UTF-8 enabled version (ncursesw) - '--with-shared --enable-overwrite --with-termlib ' + - '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] -libs = ["form", "menu", "ncurses", "panel", "tinfo"] +# Symlink to ncurses for libtinfo (since it can handle the API) so it doesn't get picked up from the OS +postinstallcmds = ["ln -s %(installdir)s/lib/libncurses.so %(installdir)s/lib/libtinfo.so"] + +libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses%(version_major)s-config", "reset", "tabs", "tic", "toe", "tput", "tset"]] + -- GitLab From af14f209a3566b26fe7b7f9e58d268a80c5bc222 Mon Sep 17 00:00:00 2001 From: ocaisa Date: Mon, 28 Aug 2017 15:29:44 +0200 Subject: [PATCH 1439/1603] For pic code, need to set CFLAGS when using dummy --- easybuild/easyconfigs/l/libreadline/libreadline-6.3.eb | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3.eb index 501aa1480f..a447c94536 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3.eb @@ -10,7 +10,6 @@ description = """The GNU Readline library provides a set of functions for use by to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands.""" toolchain = {'name': 'dummy', 'version': ''} -toolchainopts = {'pic': True} sources = ['readline-%(version)s.tar.gz'] source_urls = ['http://ftp.gnu.org/gnu/readline'] @@ -19,8 +18,11 @@ patches = ['libreadline-%(version)s-bugfix.patch'] dependencies = [('ncurses', '6.0')] +# need to take care of $CFLAGS ourselves with dummy toolchain +# we need to add -fPIC, but should also include -O* option to avoid compiling with -O0 (default for GCC) +buildopts = 'CFLAGS="-O2 -fPIC" ' # for the termcap symbols, use EB ncurses -buildopts = "SHLIB_LIBS='-lncurses'" +buildopts += "SHLIB_LIBS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + -- GitLab From 6c903cdfb3bbe9f25ea02e34b29252e0242525db Mon Sep 17 00:00:00 2001 From: ocaisa Date: Mon, 28 Aug 2017 15:31:28 +0200 Subject: [PATCH 1440/1603] For pic code need to set CFLAGS ourselves... when using dummy --- easybuild/easyconfigs/n/ncurses/ncurses-6.0.eb | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.0.eb index 70d6035d01..ffa0fa14ff 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-6.0.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.0.eb @@ -8,7 +8,7 @@ description = """The Ncurses (new curses) library is a free software emulation o and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] @@ -23,6 +23,10 @@ configopts = [ '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] +# need to take care of $CFLAGS ourselves with dummy toolchain +# we need to add -fPIC, but should also include -O* option to avoid compiling with -O0 (default for GCC) +buildopts = ['CFLAGS="-O2 -fPIC"', 'CFLAGS="-O2 -fPIC"'] + # Symlink to ncurses for libtinfo (since it can handle the API) so it doesn't get picked up from the OS postinstallcmds = ["ln -s %(installdir)s/lib/libncurses.so %(installdir)s/lib/libtinfo.so"] -- GitLab From 3057402c95193819855022c708f32bc181d51acf Mon Sep 17 00:00:00 2001 From: ocaisa Date: Mon, 28 Aug 2017 15:31:47 +0200 Subject: [PATCH 1441/1603] Update ncurses-6.0.eb --- easybuild/easyconfigs/n/ncurses/ncurses-6.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.0.eb index ffa0fa14ff..39eefbffc6 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-6.0.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.0.eb @@ -9,7 +9,6 @@ description = """The Ncurses (new curses) library is a free software emulation o function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.""" toolchain = {'name': 'dummy', 'version': ''} -toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -- GitLab From 4eb6374295c7e1dbf1639ec9e88bd2df42807e2c Mon Sep 17 00:00:00 2001 From: ocaisa Date: Mon, 28 Aug 2017 16:03:42 +0200 Subject: [PATCH 1442/1603] Keep buildopts syntax consistent --- easybuild/easyconfigs/l/libreadline/libreadline-6.3.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3.eb index a447c94536..141b4c010a 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3.eb @@ -20,7 +20,7 @@ dependencies = [('ncurses', '6.0')] # need to take care of $CFLAGS ourselves with dummy toolchain # we need to add -fPIC, but should also include -O* option to avoid compiling with -O0 (default for GCC) -buildopts = 'CFLAGS="-O2 -fPIC" ' +buildopts = "CFLAGS='-O2 -fPIC' " # for the termcap symbols, use EB ncurses buildopts += "SHLIB_LIBS='-lncurses'" -- GitLab From ab0d6033d41b349c574498be777e5cba51f8da41 Mon Sep 17 00:00:00 2001 From: ocaisa Date: Mon, 28 Aug 2017 17:31:38 +0200 Subject: [PATCH 1443/1603] Do the symlinking for both .a and .so --- easybuild/easyconfigs/n/ncurses/ncurses-6.0.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.0.eb index 39eefbffc6..65bcee84f5 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-6.0.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.0.eb @@ -27,7 +27,10 @@ configopts = [ buildopts = ['CFLAGS="-O2 -fPIC"', 'CFLAGS="-O2 -fPIC"'] # Symlink to ncurses for libtinfo (since it can handle the API) so it doesn't get picked up from the OS -postinstallcmds = ["ln -s %(installdir)s/lib/libncurses.so %(installdir)s/lib/libtinfo.so"] +postinstallcmds = [ + "ln -s %(installdir)s/lib/libncurses.so %(installdir)s/lib/libtinfo.so", + "ln -s %(installdir)s/lib/libncurses.so %(installdir)s/lib/libtinfo.a" +] libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { -- GitLab From 14e42a18b4942379b38bb3ea66ea67f09bc2251e Mon Sep 17 00:00:00 2001 From: ocaisa Date: Mon, 28 Aug 2017 17:34:26 +0200 Subject: [PATCH 1444/1603] Update ncurses-6.0.eb --- easybuild/easyconfigs/n/ncurses/ncurses-6.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.0.eb index 65bcee84f5..6f86928521 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-6.0.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.0.eb @@ -29,7 +29,7 @@ buildopts = ['CFLAGS="-O2 -fPIC"', 'CFLAGS="-O2 -fPIC"'] # Symlink to ncurses for libtinfo (since it can handle the API) so it doesn't get picked up from the OS postinstallcmds = [ "ln -s %(installdir)s/lib/libncurses.so %(installdir)s/lib/libtinfo.so", - "ln -s %(installdir)s/lib/libncurses.so %(installdir)s/lib/libtinfo.a" + "ln -s %(installdir)s/lib/libncurses.a %(installdir)s/lib/libtinfo.a" ] libs = ["form", "menu", "ncurses", "panel"] -- GitLab From b979bc9f2a2bb279c45a3488a14334d5a2a745d9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 29 Aug 2017 15:36:41 +0200 Subject: [PATCH 1445/1603] less promotional descriptions for Intel compilers, MPI & MKL --- .../easyconfigs/i/icc/icc-2017.4.196-GCC-6.4.0-2.28.eb | 2 +- .../i/iccifort/iccifort-2017.4.196-GCC-6.4.0-2.28.eb | 3 +-- .../easyconfigs/i/ifort/ifort-2017.4.196-GCC-6.4.0-2.28.eb | 2 +- easybuild/easyconfigs/i/imkl/imkl-2017.3.196-iimpi-2017b.eb | 6 ++---- .../impi-2017.3.196-iccifort-2017.4.196-GCC-6.4.0-2.28.eb | 4 +--- easybuild/easyconfigs/i/intel/intel-2017b.eb | 3 +-- 6 files changed, 7 insertions(+), 13 deletions(-) diff --git a/easybuild/easyconfigs/i/icc/icc-2017.4.196-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/i/icc/icc-2017.4.196-GCC-6.4.0-2.28.eb index 8bae3f29f2..718eae9dd7 100644 --- a/easybuild/easyconfigs/i/icc/icc-2017.4.196-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/i/icc/icc-2017.4.196-GCC-6.4.0-2.28.eb @@ -4,7 +4,7 @@ name = 'icc' version = '2017.4.196' homepage = 'http://software.intel.com/en-us/intel-compilers/' -description = "C and C++ compiler from Intel" +description = "Intel C and C++ compilers" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2017.4.196-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2017.4.196-GCC-6.4.0-2.28.eb index 35f4cd4d02..a34c1351e0 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2017.4.196-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2017.4.196-GCC-6.4.0-2.28.eb @@ -6,8 +6,7 @@ version = '2017.4.196' versionsuffix = '-GCC-6.4.0-2.28' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' -description = """Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and - Intel MKL""" +description = "Intel C, C++ & Fortran compilers" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/ifort/ifort-2017.4.196-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/i/ifort/ifort-2017.4.196-GCC-6.4.0-2.28.eb index d3692d8024..9fc6419c66 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2017.4.196-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2017.4.196-GCC-6.4.0-2.28.eb @@ -4,7 +4,7 @@ name = 'ifort' version = '2017.4.196' homepage = 'http://software.intel.com/en-us/intel-compilers/' -description = "Fortran compiler from Intel" +description = "Intel Fortran compiler" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/imkl/imkl-2017.3.196-iimpi-2017b.eb b/easybuild/easyconfigs/i/imkl/imkl-2017.3.196-iimpi-2017b.eb index 092481da75..9199c8b2b8 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2017.3.196-iimpi-2017b.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2017.3.196-iimpi-2017b.eb @@ -4,10 +4,8 @@ name = 'imkl' version = '2017.3.196' homepage = 'http://software.intel.com/en-us/intel-mkl/' -description = """Intel Math Kernel Library is a library of highly optimized, - extensively threaded math routines for science, engineering, and financial - applications that require maximum performance. Core math functions include - BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.""" +description = """Intel Math Kernel Library (MKL), a library of highly optimized, + extensively threaded math functions, including BLAS, (Sca)LAPACK, Fast Fourier Transforms (FFT), etc.""" toolchain = {'name': 'iimpi', 'version': '2017b'} diff --git a/easybuild/easyconfigs/i/impi/impi-2017.3.196-iccifort-2017.4.196-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/i/impi/impi-2017.3.196-iccifort-2017.4.196-GCC-6.4.0-2.28.eb index 827bd87f06..bd671dc906 100644 --- a/easybuild/easyconfigs/i/impi/impi-2017.3.196-iccifort-2017.4.196-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/i/impi/impi-2017.3.196-iccifort-2017.4.196-GCC-6.4.0-2.28.eb @@ -4,9 +4,7 @@ name = 'impi' version = '2017.3.196' homepage = 'http://software.intel.com/en-us/intel-mpi-library/' -description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric message - passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for - Linux OS implements the Message Passing Interface, version 2 (MPI-2) specification.""" +description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'iccifort', 'version': '2017.4.196-GCC-6.4.0-2.28'} diff --git a/easybuild/easyconfigs/i/intel/intel-2017b.eb b/easybuild/easyconfigs/i/intel/intel-2017b.eb index 79c32a59cd..06ebd20c1f 100644 --- a/easybuild/easyconfigs/i/intel/intel-2017b.eb +++ b/easybuild/easyconfigs/i/intel/intel-2017b.eb @@ -4,8 +4,7 @@ name = 'intel' version = '2017b' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' -description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & - Intel MKL.""" +description = "Compiler toolchain including Intel compilers, Intel MPI and Intel Math Kernel Library (MKL)." toolchain = {'name': 'dummy', 'version': 'dummy'} -- GitLab From ae78af31c6048b06e12acc2a141abefe636e80ff Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 29 Aug 2017 17:45:53 +0200 Subject: [PATCH 1446/1603] adding easyconfigs: NWChem-6.6.revision27746-intel-2017a-2015-10-20-Python-2.7.13.eb --- ...46-intel-2017a-2015-10-20-Python-2.7.13.eb | 85 +++++++++++++++++++ 1 file changed, 85 insertions(+) create mode 100644 easybuild/easyconfigs/n/NWChem/NWChem-6.6.revision27746-intel-2017a-2015-10-20-Python-2.7.13.eb diff --git a/easybuild/easyconfigs/n/NWChem/NWChem-6.6.revision27746-intel-2017a-2015-10-20-Python-2.7.13.eb b/easybuild/easyconfigs/n/NWChem/NWChem-6.6.revision27746-intel-2017a-2015-10-20-Python-2.7.13.eb new file mode 100644 index 0000000000..d229dc70b0 --- /dev/null +++ b/easybuild/easyconfigs/n/NWChem/NWChem-6.6.revision27746-intel-2017a-2015-10-20-Python-2.7.13.eb @@ -0,0 +1,85 @@ +name = 'NWChem' +version = '6.6.revision27746' +verdate = '2015-10-20' +versionsuffix = '-%s-Python-%%(pyver)s' % verdate + +homepage = 'http://www.nwchem-sw.org' +description = """NWChem aims to provide its users with computational chemistry tools that are scalable both in + their ability to treat large scientific computational chemistry problems efficiently, and in their use of available + parallel computing resources from high-performance parallel supercomputers to conventional workstation clusters. + NWChem software can handle: biomolecules, nanostructures, and solid-state; from quantum to classical, and all + combinations; Gaussian basis functions or plane-waves; scaling from one to thousands of processors; properties + and relativity.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'i8': True} + +source_urls = ['http://www.nwchem-sw.org/download.php?f='] +sources = ['Nwchem-%%(version)s-src.%s.tar.bz2' % verdate] +patches = [ + 'NWChem_fix-date.patch', + 'NWChem-%(version)s-parallelbuild.patch', + # patches for NWChem 6.6 (27746 revision) available on Aug 29th 2017 + 'Tddft_mxvec20.patch.gz', + 'Tools_lib64.patch.gz', + 'Config_libs66.patch.gz', + 'Cosmo_meminit.patch.gz', + 'Sym_abelian.patch.gz', + 'Xccvs98.patch.gz', + 'Dplot_tolrho.patch.gz', + 'Driver_smalleig.patch.gz', + 'Ga_argv.patch.gz', + 'Raman_displ.patch.gz', + 'Ga_defs.patch.gz', + 'Zgesvd.patch.gz', + 'Cosmo_dftprint.patch.gz', + 'Txs_gcc6.patch.gz', + 'Gcc6_optfix.patch.gz', + 'Util_gnumakefile.patch.gz', + 'Util_getppn.patch.gz', + 'Gcc6_macs_optfix.patch.gz', + 'Notdir_fc.patch.gz', + 'Xatom_vdw.patch.gz', + 'Hfmke.patch.gz', + 'Cdfti2nw66.patch.gz', +] +checksums = [ + '7b9b324883500c412476420d3591c283c1a68068b2ab6ce185d869d82497f798', # Nwchem-6.6.revision27746-src.2015-10-20.tar.bz2 + '215ec54f6132f2c9306bd636456722a36f0f1d98a67a0c8cbd10c5d1eed68feb', # NWChem_fix-date.patch + '454f3dc53058b0b0d23c94522b88bc1107904a1d696ca536e2991db3447de7a5', # NWChem-6.6.revision27746-parallelbuild.patch + 'cdfa8a5ae7d6ee09999407573b171beb91e37e1558a3bfb2d651982a85f0bc8f', # Tddft_mxvec20.patch.gz + '76b8d3e1b77829b683234c8307fde55bc9249b87410914b605a76586c8f32dae', # Tools_lib64.patch.gz + 'aa17f03cbb22ad7d883e799e0fddad1b5957f5f30b09f14a1a2caeeb9663cc07', # Config_libs66.patch.gz + '569c5ee528f3922ee60ca831eb20ec6591633a36f80efa76cbbe41cabeb9b624', # Cosmo_meminit.patch.gz + 'aa693e645a98dbafbb990e26145d65b100d6075254933f36326cf00bac3c29e0', # Sym_abelian.patch.gz + '1c0b0f1293e3b9b05e9e51e7d5b99977ccf1edb4b072872c8316452f6cea6f13', # Xccvs98.patch.gz + '2ebb1a5575c44eef4139da91f0e1e60057b2eccdba7f57a8fb577e840c326cbb', # Dplot_tolrho.patch.gz + 'dd65bfbae6b472b94c8ee81d74f6c3ece37c8fc8766ff7a3551d8005d44815b8', # Driver_smalleig.patch.gz + '8a78cb2af14314b92be9d241b801e9b9fed5527b9cb47a083134c7becdfa7cf1', # Ga_argv.patch.gz + '6a16f0f589a5cbb8d316f68bd2e6a0d46cd47f1c699a4b256a3973130061f6c3', # Raman_displ.patch.gz + 'c6f1a48338d196e1db22bcfc6087e2b2e6eea50a34d3a2b2d3e90cccf43742a9', # Ga_defs.patch.gz + '4af592c047dc3e0bc4962376ae2c6ca868eb7a0b40a347ed9b88e887016ad9ed', # Zgesvd.patch.gz + 'd3b73431a68d6733eb7b669d471e18a83e03fa8e40c48e536fe8edecd99250ff', # Cosmo_dftprint.patch.gz + '139692215718cd7414896470c0cc8b7817a73ece1e4ca93bf752cf1081a195af', # Txs_gcc6.patch.gz + '15cff43ab0509e0b0e83c49890032a848d6b7116bd6c8e5678e6c933f2d051ab', # Gcc6_optfix.patch.gz + '5dd82b9bd55583152295c999a0e4d72dd9d5c6ab7aa91117c2aae57a95a14ba1', # Util_gnumakefile.patch.gz + '8be418e1f8750778a31056f1fdf2a693fa4a12ea86a531f1ddf6f3620421027e', # Util_getppn.patch.gz + 'fade16098a1f54983040cdeb807e4e310425d7f66358807554e08392685a7164', # Gcc6_macs_optfix.patch.gz + 'a6a233951eb254d8aff5b243ca648def21fa491807a66c442f59c437f040ee69', # Notdir_fc.patch.gz + '7f4851ed15ecd86845e93530430eae11ed5b94695db70b0cc465c2aadcfabc1b', # Xatom_vdw.patch.gz + '3b33600d6a50155aff25926ecf778dbae046ecc20c9b61fbf554bb7f364f4518', # Hfmke.patch.gz + 'aea45f439a80d374ae84988d8cf95b78b7bb1047e3665265ee8fc55c0c5b176b', # Cdfti2nw66.patch.gz +] + +dependencies = [('Python', '2.7.13')] + +# This easyconfig is using the default for armci_network (OPENIB) and +# thus needs infiniband libraries. +osdependencies = [ + ('libibverbs-dev', 'libibverbs-devel'), + ('libibumad-dev', 'libibumad-devel'), +] + +modules = 'all python' + +moduleclass = 'chem' -- GitLab From 2283c3481033ab14f37ec7f77878bb515f21ed88 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 29 Aug 2017 20:19:14 +0200 Subject: [PATCH 1447/1603] indicate inclusion of patches in versionsuffix for NWChem 6.6 with intel/2017a --- ...ntel-2017a-2015-10-20-patches-20170814-Python-2.7.13.eb} | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/n/NWChem/{NWChem-6.6.revision27746-intel-2017a-2015-10-20-Python-2.7.13.eb => NWChem-6.6.revision27746-intel-2017a-2015-10-20-patches-20170814-Python-2.7.13.eb} (93%) diff --git a/easybuild/easyconfigs/n/NWChem/NWChem-6.6.revision27746-intel-2017a-2015-10-20-Python-2.7.13.eb b/easybuild/easyconfigs/n/NWChem/NWChem-6.6.revision27746-intel-2017a-2015-10-20-patches-20170814-Python-2.7.13.eb similarity index 93% rename from easybuild/easyconfigs/n/NWChem/NWChem-6.6.revision27746-intel-2017a-2015-10-20-Python-2.7.13.eb rename to easybuild/easyconfigs/n/NWChem/NWChem-6.6.revision27746-intel-2017a-2015-10-20-patches-20170814-Python-2.7.13.eb index d229dc70b0..5e0724e042 100644 --- a/easybuild/easyconfigs/n/NWChem/NWChem-6.6.revision27746-intel-2017a-2015-10-20-Python-2.7.13.eb +++ b/easybuild/easyconfigs/n/NWChem/NWChem-6.6.revision27746-intel-2017a-2015-10-20-patches-20170814-Python-2.7.13.eb @@ -1,7 +1,7 @@ name = 'NWChem' version = '6.6.revision27746' verdate = '2015-10-20' -versionsuffix = '-%s-Python-%%(pyver)s' % verdate +versionsuffix = '-%s-patches-20170814-Python-%%(pyver)s' % verdate homepage = 'http://www.nwchem-sw.org' description = """NWChem aims to provide its users with computational chemistry tools that are scalable both in @@ -19,7 +19,9 @@ sources = ['Nwchem-%%(version)s-src.%s.tar.bz2' % verdate] patches = [ 'NWChem_fix-date.patch', 'NWChem-%(version)s-parallelbuild.patch', - # patches for NWChem 6.6 (27746 revision) available on Aug 29th 2017 + # available patches for NWChem 6.6 (27746 revision), + # cfr. http://www.nwchem-sw.org/index.php/Download#Patches_for_the_27746_revision_of_NWChem_6.6 + # most recent: Cdfti2nw66.patch.gz (Aug 14th 2017) 'Tddft_mxvec20.patch.gz', 'Tools_lib64.patch.gz', 'Config_libs66.patch.gz', -- GitLab From 04195f093ebda49e12387879d3999755688f23ea Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 29 Aug 2017 20:19:56 +0200 Subject: [PATCH 1448/1603] fix long line in NWChem easyconfig --- ...46-intel-2017a-2015-10-20-patches-20170814-Python-2.7.13.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/NWChem/NWChem-6.6.revision27746-intel-2017a-2015-10-20-patches-20170814-Python-2.7.13.eb b/easybuild/easyconfigs/n/NWChem/NWChem-6.6.revision27746-intel-2017a-2015-10-20-patches-20170814-Python-2.7.13.eb index 5e0724e042..2387d265fb 100644 --- a/easybuild/easyconfigs/n/NWChem/NWChem-6.6.revision27746-intel-2017a-2015-10-20-patches-20170814-Python-2.7.13.eb +++ b/easybuild/easyconfigs/n/NWChem/NWChem-6.6.revision27746-intel-2017a-2015-10-20-patches-20170814-Python-2.7.13.eb @@ -46,7 +46,8 @@ patches = [ 'Cdfti2nw66.patch.gz', ] checksums = [ - '7b9b324883500c412476420d3591c283c1a68068b2ab6ce185d869d82497f798', # Nwchem-6.6.revision27746-src.2015-10-20.tar.bz2 + # Nwchem-6.6.revision27746-src.2015-10-20.tar.bz2 + '7b9b324883500c412476420d3591c283c1a68068b2ab6ce185d869d82497f798', '215ec54f6132f2c9306bd636456722a36f0f1d98a67a0c8cbd10c5d1eed68feb', # NWChem_fix-date.patch '454f3dc53058b0b0d23c94522b88bc1107904a1d696ca536e2991db3447de7a5', # NWChem-6.6.revision27746-parallelbuild.patch 'cdfa8a5ae7d6ee09999407573b171beb91e37e1558a3bfb2d651982a85f0bc8f', # Tddft_mxvec20.patch.gz -- GitLab From 262f0837b10ad0ca304f4fcd4e9d2fb60c661f57 Mon Sep 17 00:00:00 2001 From: ocaisa Date: Wed, 30 Aug 2017 09:34:15 +0200 Subject: [PATCH 1449/1603] Address comments --- easybuild/easyconfigs/n/ncurses/ncurses-6.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.0.eb index 6f86928521..de7f258d00 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-6.0.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.0.eb @@ -24,9 +24,9 @@ configopts = [ # need to take care of $CFLAGS ourselves with dummy toolchain # we need to add -fPIC, but should also include -O* option to avoid compiling with -O0 (default for GCC) -buildopts = ['CFLAGS="-O2 -fPIC"', 'CFLAGS="-O2 -fPIC"'] +buildopts = 'CFLAGS="-O2 -fPIC"' -# Symlink to ncurses for libtinfo (since it can handle the API) so it doesn't get picked up from the OS +# Symlink libtinfo to libncurses (since it can handle the API) so it doesn't get picked up from the OS postinstallcmds = [ "ln -s %(installdir)s/lib/libncurses.so %(installdir)s/lib/libtinfo.so", "ln -s %(installdir)s/lib/libncurses.a %(installdir)s/lib/libtinfo.a" -- GitLab From 88af660a5875ac371cb234e3e4c307cd42d748ee Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 30 Aug 2017 09:54:04 +0200 Subject: [PATCH 1450/1603] include Autotools as build dep for netCDF --- easybuild/easyconfigs/n/netCDF/netCDF-4.3.3.1-foss-2015a.eb | 1 + easybuild/easyconfigs/n/netCDF/netCDF-4.3.3.1-foss-2015b.eb | 1 + easybuild/easyconfigs/n/netCDF/netCDF-4.3.3.1-foss-2016a.eb | 1 + easybuild/easyconfigs/n/netCDF/netCDF-4.3.3.1-intel-2015a.eb | 1 + easybuild/easyconfigs/n/netCDF/netCDF-4.3.3.1-intel-2015b.eb | 1 + .../easyconfigs/n/netCDF/netCDF-4.3.3.1-intel-2016.02-GCC-4.9.eb | 1 + easybuild/easyconfigs/n/netCDF/netCDF-4.3.3.1-intel-2016a.eb | 1 + easybuild/easyconfigs/n/netCDF/netCDF-4.4.0-foss-2016a.eb | 1 + easybuild/easyconfigs/n/netCDF/netCDF-4.4.0-intel-2016a.eb | 1 + easybuild/easyconfigs/n/netCDF/netCDF-4.4.0-iomkl-2016.07.eb | 1 + .../n/netCDF/netCDF-4.4.0-iomkl-2016.09-GCC-4.9.3-2.25.eb | 1 + easybuild/easyconfigs/n/netCDF/netCDF-4.4.1-foss-2016a.eb | 1 + easybuild/easyconfigs/n/netCDF/netCDF-4.4.1-foss-2016b.eb | 1 + easybuild/easyconfigs/n/netCDF/netCDF-4.4.1-intel-2016a.eb | 1 + easybuild/easyconfigs/n/netCDF/netCDF-4.4.1-intel-2016b.eb | 1 + easybuild/easyconfigs/n/netCDF/netCDF-4.4.1.1-foss-2016b.eb | 1 + easybuild/easyconfigs/n/netCDF/netCDF-4.4.1.1-intel-2016b.eb | 1 + .../n/netCDF/netCDF-4.4.1.1-intel-2017a-HDF5-1.10.1.eb | 1 + .../n/netCDF/netCDF-4.4.1.1-intel-2017a-HDF5-1.8.18.eb | 1 + easybuild/easyconfigs/n/netCDF/netCDF-4.4.1.1-intel-2017a.eb | 1 + 20 files changed, 20 insertions(+) diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.3.3.1-foss-2015a.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.3.1-foss-2015a.eb index 67ec8a7992..cb332e5b48 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.3.3.1-foss-2015a.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.3.1-foss-2015a.eb @@ -21,6 +21,7 @@ dependencies = [ ] builddependencies = [ + ('Autotools', '20150215'), ('CMake', '3.4.1'), ('Doxygen', '1.8.11'), ] diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.3.3.1-foss-2015b.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.3.1-foss-2015b.eb index d5f3ba2170..86c8418dd5 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.3.3.1-foss-2015b.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.3.1-foss-2015b.eb @@ -21,6 +21,7 @@ dependencies = [ ] builddependencies = [ + ('Autotools', '20150215'), ('CMake', '3.4.1'), ('Doxygen', '1.8.10'), ] diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.3.3.1-foss-2016a.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.3.1-foss-2016a.eb index 921f90805c..3a0cebe701 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.3.3.1-foss-2016a.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.3.1-foss-2016a.eb @@ -21,6 +21,7 @@ dependencies = [ ] builddependencies = [ + ('Autotools', '20150215'), ('CMake', '3.4.1'), ('Doxygen', '1.8.11'), ] diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.3.3.1-intel-2015a.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.3.1-intel-2015a.eb index ee5055dfe4..85cc8383ce 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.3.3.1-intel-2015a.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.3.1-intel-2015a.eb @@ -21,6 +21,7 @@ dependencies = [ ] builddependencies = [ + ('Autotools', '20150215'), ('CMake', '3.2.2'), ('Doxygen', '1.8.9.1', '', ('GCC', '4.9.2')), ] diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.3.3.1-intel-2015b.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.3.1-intel-2015b.eb index 3722efdeb2..90402a2b11 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.3.3.1-intel-2015b.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.3.1-intel-2015b.eb @@ -21,6 +21,7 @@ dependencies = [ ] builddependencies = [ + ('Autotools', '20150215'), ('CMake', '3.4.1'), ('Doxygen', '1.8.10'), ] diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.3.3.1-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.3.1-intel-2016.02-GCC-4.9.eb index cff46757ad..bc9bd0ed7a 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.3.3.1-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.3.1-intel-2016.02-GCC-4.9.eb @@ -21,6 +21,7 @@ dependencies = [ ] builddependencies = [ + ('Autotools', '20150215'), ('CMake', '3.4.1'), ('Doxygen', '1.8.10'), ] diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.3.3.1-intel-2016a.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.3.1-intel-2016a.eb index 40796ae26b..960e78bc12 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.3.3.1-intel-2016a.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.3.1-intel-2016a.eb @@ -21,6 +21,7 @@ dependencies = [ ] builddependencies = [ + ('Autotools', '20150215'), ('CMake', '3.4.1'), ('Doxygen', '1.8.11'), ] diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.4.0-foss-2016a.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.4.0-foss-2016a.eb index 39406d6275..3ecf42980e 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.4.0-foss-2016a.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.4.0-foss-2016a.eb @@ -21,6 +21,7 @@ dependencies = [ ] builddependencies = [ + ('Autotools', '20150215'), ('CMake', '3.4.3'), ('Doxygen', '1.8.11'), ] diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.4.0-intel-2016a.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.4.0-intel-2016a.eb index 719c330b9d..3e1a5c0408 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.4.0-intel-2016a.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.4.0-intel-2016a.eb @@ -21,6 +21,7 @@ dependencies = [ ] builddependencies = [ + ('Autotools', '20150215'), ('CMake', '3.4.3'), ('Doxygen', '1.8.11'), ] diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.4.0-iomkl-2016.07.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.4.0-iomkl-2016.07.eb index a0a822a673..be8771fd7d 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.4.0-iomkl-2016.07.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.4.0-iomkl-2016.07.eb @@ -20,6 +20,7 @@ dependencies = [ ] builddependencies = [ + ('Autotools', '20150215'), ('CMake', '3.4.1'), ('Doxygen', '1.8.11'), ('Szip', '2.1'), diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.4.0-iomkl-2016.09-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.4.0-iomkl-2016.09-GCC-4.9.3-2.25.eb index eec48bea4a..253b8cea83 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.4.0-iomkl-2016.09-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.4.0-iomkl-2016.09-GCC-4.9.3-2.25.eb @@ -18,6 +18,7 @@ dependencies = [ ] builddependencies = [ + ('Autotools', '20150215'), ('CMake', '3.4.1'), ('Doxygen', '1.8.11'), ('Szip', '2.1'), diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.4.1-foss-2016a.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.4.1-foss-2016a.eb index 8e1936bec6..45da7a6542 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.4.1-foss-2016a.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.4.1-foss-2016a.eb @@ -21,6 +21,7 @@ dependencies = [ ] builddependencies = [ + ('Autotools', '20150215'), ('CMake', '3.5.2'), ('Doxygen', '1.8.11'), ] diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.4.1-foss-2016b.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.4.1-foss-2016b.eb index f688f2156e..9a8b44243a 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.4.1-foss-2016b.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.4.1-foss-2016b.eb @@ -21,6 +21,7 @@ dependencies = [ ] builddependencies = [ + ('Autotools', '20150215'), ('CMake', '3.5.2'), ('Doxygen', '1.8.11'), ] diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.4.1-intel-2016a.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.4.1-intel-2016a.eb index e66c2bd0e4..43f0af3fe2 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.4.1-intel-2016a.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.4.1-intel-2016a.eb @@ -21,6 +21,7 @@ dependencies = [ ] builddependencies = [ + ('Autotools', '20150215'), ('CMake', '3.5.2'), ('Doxygen', '1.8.11'), ] diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.4.1-intel-2016b.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.4.1-intel-2016b.eb index 9835133043..d526314012 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.4.1-intel-2016b.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.4.1-intel-2016b.eb @@ -21,6 +21,7 @@ dependencies = [ ] builddependencies = [ + ('Autotools', '20150215'), ('CMake', '3.5.2'), ('Doxygen', '1.8.11'), ] diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.4.1.1-foss-2016b.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.4.1.1-foss-2016b.eb index 5da2b108a0..77eec6d4cf 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.4.1.1-foss-2016b.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.4.1.1-foss-2016b.eb @@ -21,6 +21,7 @@ dependencies = [ ] builddependencies = [ + ('Autotools', '20150215'), ('CMake', '3.5.2'), ('Doxygen', '1.8.11'), ] diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.4.1.1-intel-2016b.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.4.1.1-intel-2016b.eb index 24dee36e77..1ae7e5f216 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.4.1.1-intel-2016b.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.4.1.1-intel-2016b.eb @@ -21,6 +21,7 @@ dependencies = [ ] builddependencies = [ + ('Autotools', '20150215'), ('CMake', '3.5.2'), ('Doxygen', '1.8.11'), ] diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.4.1.1-intel-2017a-HDF5-1.10.1.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.4.1.1-intel-2017a-HDF5-1.10.1.eb index 713953985c..02029aff9f 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.4.1.1-intel-2017a-HDF5-1.10.1.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.4.1.1-intel-2017a-HDF5-1.10.1.eb @@ -22,6 +22,7 @@ dependencies = [ ] builddependencies = [ + ('Autotools', '20150215'), ('CMake', '3.8.2'), ('Doxygen', '1.8.13'), ] diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.4.1.1-intel-2017a-HDF5-1.8.18.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.4.1.1-intel-2017a-HDF5-1.8.18.eb index 8bc6d56640..7a31742b3a 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.4.1.1-intel-2017a-HDF5-1.8.18.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.4.1.1-intel-2017a-HDF5-1.8.18.eb @@ -23,6 +23,7 @@ dependencies = [ ] builddependencies = [ + ('Autotools', '20150215'), ('CMake', '3.7.2'), ('Doxygen', '1.8.13'), ] diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.4.1.1-intel-2017a.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.4.1.1-intel-2017a.eb index d30a65ec63..da116afc70 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.4.1.1-intel-2017a.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.4.1.1-intel-2017a.eb @@ -21,6 +21,7 @@ dependencies = [ ] builddependencies = [ + ('Autotools', '20150215'), ('CMake', '3.7.2'), ('Doxygen', '1.8.13'), ] -- GitLab From c3a074f711cbc8980fd79876a7d9c918cc54afce Mon Sep 17 00:00:00 2001 From: Martin Rosgaard Date: Wed, 30 Aug 2017 11:35:39 +0200 Subject: [PATCH 1451/1603] adding easyconfigs: PnetCDF-1.8.1-intel-2017a.eb, ParallelIO-2.2.2a-intel-2017a.eb --- .../ParallelIO-2.2.2a-intel-2017a.eb | 39 +++++++++++++++++++ .../p/PnetCDF/PnetCDF-1.8.1-intel-2017a.eb | 23 +++++++++++ 2 files changed, 62 insertions(+) create mode 100644 easybuild/easyconfigs/p/ParallelIO/ParallelIO-2.2.2a-intel-2017a.eb create mode 100644 easybuild/easyconfigs/p/PnetCDF/PnetCDF-1.8.1-intel-2017a.eb diff --git a/easybuild/easyconfigs/p/ParallelIO/ParallelIO-2.2.2a-intel-2017a.eb b/easybuild/easyconfigs/p/ParallelIO/ParallelIO-2.2.2a-intel-2017a.eb new file mode 100644 index 0000000000..78c03677c6 --- /dev/null +++ b/easybuild/easyconfigs/p/ParallelIO/ParallelIO-2.2.2a-intel-2017a.eb @@ -0,0 +1,39 @@ +easyblock = 'CMakeMake' + +name = 'ParallelIO' +version = '2.2.2a' + +homepage = 'https://github.com/NCAR/ParallelIO' +description = """A high-level Parallel I/O Library for structured grid applications""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'usempi': True} + +## underscore = "${version//./_}" something like this ?? +## sources = ['pio%(underscore)s.tar.gz'] bash sub in easyconf ?? +sources = ['pio2_2_2a.tar.gz'] +source_urls = ['https://github.com/NCAR/ParallelIO/archive/'] + +separate_build_dir = True + +dependencies = [ + ('PnetCDF', '1.8.1', '', ('intel', '2017a')), + ('netCDF-Fortran', '4.4.4', '', ('intel', '2017a')) +] + +builddependencies = [ + ('CMake', '3.8.2', '', ('intel', '2017a')), +] + +configopts = "-DPIO_ENABLE_TIMING=OFF " + +sanity_check_paths = { + 'files': [], + 'dirs': [('include','lib')] +} + +modextravars = { + 'PIO': '%(installdir)s', +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/p/PnetCDF/PnetCDF-1.8.1-intel-2017a.eb b/easybuild/easyconfigs/p/PnetCDF/PnetCDF-1.8.1-intel-2017a.eb new file mode 100644 index 0000000000..77ad478ab0 --- /dev/null +++ b/easybuild/easyconfigs/p/PnetCDF/PnetCDF-1.8.1-intel-2017a.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'PnetCDF' +version = '1.8.1' + +homepage = 'https://trac.mcs.anl.gov/projects/parallel-netcdf' +description = """Parallel netCDF: A Parallel I/O Library for NetCDF File Access""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +sources = ['parallel-netcdf-%(version)s.tar.gz'] +source_urls = ['http://cucis.ece.northwestern.edu/projects/PnetCDF/Release/'] + +sanity_check_paths = { + 'files': ['bin/pnetcdf_version'], + 'dirs': [] +} + +modextravars = { + 'PNETCDF': '%(installdir)s', +} + +moduleclass = 'data' -- GitLab From c9a331b5d5de4d0a3b6b950e3059302215388379 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 30 Aug 2017 12:22:54 +0200 Subject: [PATCH 1452/1603] bump version for expat, fontconfig and libpng easyconfigs that use GCCcore/6.4.0 --- easybuild/easyconfigs/d/DBus/DBus-1.10.20-GCCcore-6.4.0.eb | 2 +- ...-2.2.1-GCCcore-6.4.0.eb => expat-2.2.4-GCCcore-6.4.0.eb} | 4 ++-- ...-GCCcore-6.4.0.eb => fontconfig-2.12.4-GCCcore-6.4.0.eb} | 6 +++--- .../easyconfigs/f/freetype/freetype-2.8-GCCcore-6.4.0.eb | 2 +- easybuild/easyconfigs/l/libgd/libgd-2.2.4-GCCcore-6.4.0.eb | 4 ++-- ...6.30-GCCcore-6.4.0.eb => libpng-1.6.32-GCCcore-6.4.0.eb} | 3 ++- 6 files changed, 11 insertions(+), 10 deletions(-) rename easybuild/easyconfigs/e/expat/{expat-2.2.1-GCCcore-6.4.0.eb => expat-2.2.4-GCCcore-6.4.0.eb} (84%) rename easybuild/easyconfigs/f/fontconfig/{fontconfig-2.12.1-GCCcore-6.4.0.eb => fontconfig-2.12.4-GCCcore-6.4.0.eb} (82%) rename easybuild/easyconfigs/l/libpng/{libpng-1.6.30-GCCcore-6.4.0.eb => libpng-1.6.32-GCCcore-6.4.0.eb} (88%) diff --git a/easybuild/easyconfigs/d/DBus/DBus-1.10.20-GCCcore-6.4.0.eb b/easybuild/easyconfigs/d/DBus/DBus-1.10.20-GCCcore-6.4.0.eb index 99bd5ca7ab..b514618917 100644 --- a/easybuild/easyconfigs/d/DBus/DBus-1.10.20-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/d/DBus/DBus-1.10.20-GCCcore-6.4.0.eb @@ -25,7 +25,7 @@ builddependencies = [ ] dependencies = [ - ('expat', '2.2.1'), + ('expat', '2.2.4'), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/e/expat/expat-2.2.1-GCCcore-6.4.0.eb b/easybuild/easyconfigs/e/expat/expat-2.2.4-GCCcore-6.4.0.eb similarity index 84% rename from easybuild/easyconfigs/e/expat/expat-2.2.1-GCCcore-6.4.0.eb rename to easybuild/easyconfigs/e/expat/expat-2.2.4-GCCcore-6.4.0.eb index 87f8150c28..0b3c3b3cc3 100644 --- a/easybuild/easyconfigs/e/expat/expat-2.2.1-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/e/expat/expat-2.2.4-GCCcore-6.4.0.eb @@ -1,7 +1,7 @@ easyblock = 'ConfigureMake' name = 'expat' -version = '2.2.1' +version = '2.2.4' homepage = 'http://expat.sourceforge.net/' @@ -16,7 +16,7 @@ toolchainopts = {'pic': True} source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCELOWER_TAR_BZ2] -checksums = ['1868cadae4c82a018e361e2b2091de103cd820aaacb0d6cfa49bd2cd83978885'] +checksums = ['03ad85db965f8ab2d27328abcf0bc5571af6ec0a414874b2066ee3fdd372019e'] builddependencies = [ ('binutils', '2.28'), diff --git a/easybuild/easyconfigs/f/fontconfig/fontconfig-2.12.1-GCCcore-6.4.0.eb b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.12.4-GCCcore-6.4.0.eb similarity index 82% rename from easybuild/easyconfigs/f/fontconfig/fontconfig-2.12.1-GCCcore-6.4.0.eb rename to easybuild/easyconfigs/f/fontconfig/fontconfig-2.12.4-GCCcore-6.4.0.eb index 985994992e..74e751cff6 100644 --- a/easybuild/easyconfigs/f/fontconfig/fontconfig-2.12.1-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.12.4-GCCcore-6.4.0.eb @@ -1,7 +1,7 @@ easyblock = 'ConfigureMake' name = 'fontconfig' -version = '2.12.1' +version = '2.12.4' homepage = 'http://www.freedesktop.org/software/fontconfig' @@ -15,14 +15,14 @@ toolchainopts = {'pic': True} source_urls = ['http://www.freedesktop.org/software/fontconfig/release/'] sources = [SOURCE_TAR_GZ] -checksums = ['a9f42d03949f948a3a4f762287dbc16e53a927c91a07ee64207ebd90a9e5e292'] +checksums = ['fd5a6a663f4c4a00e196523902626654dd0c4a78686cbc6e472f338e50fdf806'] builddependencies = [ ('binutils', '2.28'), ] dependencies = [ - ('expat', '2.2.1'), + ('expat', '2.2.4'), ('freetype', '2.8'), ] diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.8-GCCcore-6.4.0.eb b/easybuild/easyconfigs/f/freetype/freetype-2.8-GCCcore-6.4.0.eb index 683ea59e3d..69e87c2fdd 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.8-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.8-GCCcore-6.4.0.eb @@ -24,7 +24,7 @@ builddependencies = [ dependencies = [ ('bzip2', '1.0.6'), - ('libpng', '1.6.30'), + ('libpng', '1.6.32'), ('zlib', '1.2.11'), ] diff --git a/easybuild/easyconfigs/l/libgd/libgd-2.2.4-GCCcore-6.4.0.eb b/easybuild/easyconfigs/l/libgd/libgd-2.2.4-GCCcore-6.4.0.eb index 463baf18d2..fb6d920952 100644 --- a/easybuild/easyconfigs/l/libgd/libgd-2.2.4-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/l/libgd/libgd-2.2.4-GCCcore-6.4.0.eb @@ -19,9 +19,9 @@ builddependencies = [ ] dependencies = [ - ('fontconfig', '2.12.1'), + ('fontconfig', '2.12.4'), ('libjpeg-turbo', '1.5.2'), - ('libpng', '1.6.30'), + ('libpng', '1.6.32'), ('zlib', '1.2.11'), ] diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.30-GCCcore-6.4.0.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.32-GCCcore-6.4.0.eb similarity index 88% rename from easybuild/easyconfigs/l/libpng/libpng-1.6.30-GCCcore-6.4.0.eb rename to easybuild/easyconfigs/l/libpng/libpng-1.6.32-GCCcore-6.4.0.eb index 6dc219faec..88d9dd7aec 100644 --- a/easybuild/easyconfigs/l/libpng/libpng-1.6.30-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.32-GCCcore-6.4.0.eb @@ -1,7 +1,7 @@ easyblock = 'ConfigureMake' name = 'libpng' -version = '1.6.30' +version = '1.6.32' homepage = 'http://www.libpng.org/pub/png/libpng.html' @@ -12,6 +12,7 @@ toolchainopts = {'pic': True} source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCELOWER_TAR_GZ] +checksums = ['1a8ae5c8eafad895cc3fce78fbcb6fdef663b8eb8375f04616e6496360093abb'] builddependencies = [ ('binutils', '2.28'), -- GitLab From abcc333217866da07e932589eed57c79200de49e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 30 Aug 2017 13:20:41 +0200 Subject: [PATCH 1453/1603] stick to CMake 3.9.1 with GCCcore 6.4.0 toolchain --- .../b/Blosc/Blosc-1.12.1-GCCcore-6.4.0.eb | 2 +- .../c/CMake/CMake-3.8.2-GCCcore-6.4.0.eb | 41 ------------------- .../f/FreeXL/FreeXL-1.0.2-GCCcore-6.4.0.eb | 2 +- .../j/JasPer/JasPer-2.0.12-GCCcore-6.4.0.eb | 2 +- .../q/Qhull/Qhull-2015.2-GCCcore-6.4.0.eb | 2 +- 5 files changed, 4 insertions(+), 45 deletions(-) delete mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.8.2-GCCcore-6.4.0.eb diff --git a/easybuild/easyconfigs/b/Blosc/Blosc-1.12.1-GCCcore-6.4.0.eb b/easybuild/easyconfigs/b/Blosc/Blosc-1.12.1-GCCcore-6.4.0.eb index ca8add747d..e03707ac2e 100644 --- a/easybuild/easyconfigs/b/Blosc/Blosc-1.12.1-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/b/Blosc/Blosc-1.12.1-GCCcore-6.4.0.eb @@ -15,7 +15,7 @@ checksums = ['e04535e816bb942bedc9a0ba209944d1eb34e26e2d9cca37f114e8ee292cb3c8'] builddependencies = [ ('binutils', '2.28'), - ('CMake', '3.8.2'), + ('CMake', '3.9.1'), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.8.2-GCCcore-6.4.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.8.2-GCCcore-6.4.0.eb deleted file mode 100644 index 80d38b2735..0000000000 --- a/easybuild/easyconfigs/c/CMake/CMake-3.8.2-GCCcore-6.4.0.eb +++ /dev/null @@ -1,41 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'CMake' -version = '3.8.2' - -homepage = 'http://www.cmake.org' - -description = """ - CMake, the cross-platform, open-source build system. CMake is a family of - tools designed to build, test and package software. -""" - -toolchain = {'name': 'GCCcore', 'version': '6.4.0'} - -source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['da3072794eb4c09f2d782fcee043847b99bb4cf8d4573978d9b2024214d6e92d'] - -configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' - -builddependencies = [ - ('binutils', '2.28'), -] - -dependencies = [ - ('ncurses', '6.0'), - # OS dependency should be preferred if the os version is more recent then this version, - # it's nice to have an up to date openssl for security reasons - # ('OpenSSL', '1.1.0c'), -] - -osdependencies = [ - ('openssl-devel', 'libssl-dev', 'libopenssl-devel'), -] - -sanity_check_paths = { - 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], - 'dirs': [], -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.2-GCCcore-6.4.0.eb b/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.2-GCCcore-6.4.0.eb index f0015556cc..fffed92426 100644 --- a/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.2-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.2-GCCcore-6.4.0.eb @@ -19,7 +19,7 @@ checksums = ['b39a4814a0f53f5e09a9192c41e3e51bd658843f770399023a963eb064f6409d'] builddependencies = [ ('binutils', '2.28'), - ('CMake', '3.8.2'), + ('CMake', '3.9.1'), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/j/JasPer/JasPer-2.0.12-GCCcore-6.4.0.eb b/easybuild/easyconfigs/j/JasPer/JasPer-2.0.12-GCCcore-6.4.0.eb index b2d812f323..3714a84e8e 100644 --- a/easybuild/easyconfigs/j/JasPer/JasPer-2.0.12-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/j/JasPer/JasPer-2.0.12-GCCcore-6.4.0.eb @@ -20,7 +20,7 @@ checksums = ['5b24faf5ed38670d6286e45ab7516b26458d05e7929b435afe569176765f4dda'] builddependencies = [ ('binutils', '2.28'), - ('CMake', '3.8.2'), + ('CMake', '3.9.1'), ] separate_build_dir = True diff --git a/easybuild/easyconfigs/q/Qhull/Qhull-2015.2-GCCcore-6.4.0.eb b/easybuild/easyconfigs/q/Qhull/Qhull-2015.2-GCCcore-6.4.0.eb index 9734e3543a..c077c6a6ba 100644 --- a/easybuild/easyconfigs/q/Qhull/Qhull-2015.2-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/q/Qhull/Qhull-2015.2-GCCcore-6.4.0.eb @@ -27,7 +27,7 @@ patches = [ builddependencies = [ ('binutils', '2.28'), - ('CMake', '3.8.2'), + ('CMake', '3.9.1'), ] sanity_check_paths = { -- GitLab From ebdc24e6f2754b06f9f37b9f1e5eeda2faf2c5e9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 30 Aug 2017 13:32:14 +0200 Subject: [PATCH 1454/1603] bump version for cURL, libsodium and FreeXL easyconfigs that use GCCcore/6.4.0, remove non-dummy Eigen easyconfig (headers only) --- ...re-6.4.0.eb => cURL-7.55.1-GCCcore-6.4.0.eb} | 15 ++++++++------- .../e/Eigen/Eigen-3.3.4-GCCcore-6.4.0.eb | 17 ----------------- ...e-6.4.0.eb => FreeXL-1.0.3-GCCcore-6.4.0.eb} | 4 ++-- ...4.0.eb => libsodium-1.0.13-GCCcore-6.4.0.eb} | 4 ++-- .../Xerces-C++-3.1.4-GCCcore-6.4.0.eb | 2 +- 5 files changed, 13 insertions(+), 29 deletions(-) rename easybuild/easyconfigs/c/cURL/{cURL-7.54.1-GCCcore-6.4.0.eb => cURL-7.55.1-GCCcore-6.4.0.eb} (91%) delete mode 100644 easybuild/easyconfigs/e/Eigen/Eigen-3.3.4-GCCcore-6.4.0.eb rename easybuild/easyconfigs/f/FreeXL/{FreeXL-1.0.2-GCCcore-6.4.0.eb => FreeXL-1.0.3-GCCcore-6.4.0.eb} (85%) rename easybuild/easyconfigs/l/libsodium/{libsodium-1.0.12-GCCcore-6.4.0.eb => libsodium-1.0.13-GCCcore-6.4.0.eb} (86%) diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.54.1-GCCcore-6.4.0.eb b/easybuild/easyconfigs/c/cURL/cURL-7.55.1-GCCcore-6.4.0.eb similarity index 91% rename from easybuild/easyconfigs/c/cURL/cURL-7.54.1-GCCcore-6.4.0.eb rename to easybuild/easyconfigs/c/cURL/cURL-7.55.1-GCCcore-6.4.0.eb index 852ba24f5c..8c4d2ecaf0 100644 --- a/easybuild/easyconfigs/c/cURL/cURL-7.54.1-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/c/cURL/cURL-7.55.1-GCCcore-6.4.0.eb @@ -1,7 +1,7 @@ easyblock = 'ConfigureMake' name = 'cURL' -version = '7.54.1' +version = '7.55.1' homepage = 'http://curl.haxx.se' @@ -19,20 +19,21 @@ toolchain = {'name': 'GCCcore', 'version': '6.4.0'} source_urls = ['http://curl.haxx.se/download/'] sources = [SOURCELOWER_TAR_GZ] - -osdependencies = [ - ('openssl-devel', 'libssl-dev', 'libopenssl-devel'), -] +checksums = ['09576ea5e66672648d83dce3af16d0cb294d4cba2b5d166ade39655c495f4a20'] builddependencies = [ ('binutils', '2.28'), ] dependencies = [ + ('zlib', '1.2.11'), # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons - # ('OpenSSL', '1.1.0e') - ('zlib', '1.2.11'), + # ('OpenSSL', '1.1.0f') +] + +osdependencies = [ + ('openssl-devel', 'libssl-dev', 'libopenssl-devel'), ] configopts = '--with-zlib' diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.3.4-GCCcore-6.4.0.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.3.4-GCCcore-6.4.0.eb deleted file mode 100644 index 50d8127475..0000000000 --- a/easybuild/easyconfigs/e/Eigen/Eigen-3.3.4-GCCcore-6.4.0.eb +++ /dev/null @@ -1,17 +0,0 @@ -name = 'Eigen' -version = '3.3.4' - -homepage = 'http://eigen.tuxfamily.org/index.php?title=Main_Page' - -description = """ - Eigen is a C++ template library for linear algebra: - matrices, vectors, numerical solvers, and related algorithms. -""" - -toolchain = {'name': 'GCCcore', 'version': '6.4.0'} - -source_urls = ['http://bitbucket.org/%(namelower)s/%(namelower)s/get'] -sources = ['%(version)s.tar.bz2'] -checksums = ['dd254beb0bafc695d0f62ae1a222ff85b52dbaa3a16f76e781dce22d0d20a4a6'] - -moduleclass = 'math' diff --git a/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.2-GCCcore-6.4.0.eb b/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.3-GCCcore-6.4.0.eb similarity index 85% rename from easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.2-GCCcore-6.4.0.eb rename to easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.3-GCCcore-6.4.0.eb index fffed92426..5f74ada210 100644 --- a/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.2-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.3-GCCcore-6.4.0.eb @@ -1,7 +1,7 @@ easyblock = 'ConfigureMake' name = 'FreeXL' -version = '1.0.2' +version = '1.0.3' homepage = 'https://www.gaia-gis.it/fossil/freexl/index' @@ -15,7 +15,7 @@ toolchainopts = {'pic': True} source_urls = ['http://www.gaia-gis.it/gaia-sins/freexl-sources/'] sources = [SOURCELOWER_TAR_GZ] -checksums = ['b39a4814a0f53f5e09a9192c41e3e51bd658843f770399023a963eb064f6409d'] +checksums = ['f8ed29e03a6155454e538fce621e53991a270fcee31120ded339cff2523650a8'] builddependencies = [ ('binutils', '2.28'), diff --git a/easybuild/easyconfigs/l/libsodium/libsodium-1.0.12-GCCcore-6.4.0.eb b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.13-GCCcore-6.4.0.eb similarity index 86% rename from easybuild/easyconfigs/l/libsodium/libsodium-1.0.12-GCCcore-6.4.0.eb rename to easybuild/easyconfigs/l/libsodium/libsodium-1.0.13-GCCcore-6.4.0.eb index 927f15bb68..247097915a 100644 --- a/easybuild/easyconfigs/l/libsodium/libsodium-1.0.12-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.13-GCCcore-6.4.0.eb @@ -1,7 +1,7 @@ easyblock = 'ConfigureMake' name = 'libsodium' -version = '1.0.12' +version = '1.0.13' homepage = 'http://doc.libsodium.org/' @@ -15,7 +15,7 @@ toolchainopts = {'pic': True} source_urls = ['https://download.libsodium.org/libsodium/releases/'] sources = [SOURCE_TAR_GZ] -checksums = ['b8648f1bb3a54b0251cf4ffa4f0d76ded13977d4fa7517d988f4c902dd8e2f95'] +checksums = ['9c13accb1a9e59ab3affde0e60ef9a2149ed4d6e8f99c93c7a5b97499ee323fd'] builddependencies = [ ('binutils', '2.28'), diff --git a/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.1.4-GCCcore-6.4.0.eb b/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.1.4-GCCcore-6.4.0.eb index 3832c17c46..1d9545e9d9 100644 --- a/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.1.4-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.1.4-GCCcore-6.4.0.eb @@ -24,7 +24,7 @@ builddependencies = [ ] dependencies = [ - ('cURL', '7.54.1'), + ('cURL', '7.55.1'), ] sanity_check_paths = { -- GitLab From 12de95ddb5d6c14762d9dcdba1d037327b263d87 Mon Sep 17 00:00:00 2001 From: Martin Rosgaard Date: Wed, 30 Aug 2017 14:57:55 +0200 Subject: [PATCH 1455/1603] CMake GCCcore as ParallelIO dep and add checksums for this config and PnetCDF --- .../p/ParallelIO/ParallelIO-2.2.2a-intel-2017a.eb | 7 ++++--- .../easyconfigs/p/PnetCDF/PnetCDF-1.8.1-intel-2017a.eb | 1 + 2 files changed, 5 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/p/ParallelIO/ParallelIO-2.2.2a-intel-2017a.eb b/easybuild/easyconfigs/p/ParallelIO/ParallelIO-2.2.2a-intel-2017a.eb index 78c03677c6..60f276c3f1 100644 --- a/easybuild/easyconfigs/p/ParallelIO/ParallelIO-2.2.2a-intel-2017a.eb +++ b/easybuild/easyconfigs/p/ParallelIO/ParallelIO-2.2.2a-intel-2017a.eb @@ -9,10 +9,11 @@ description = """A high-level Parallel I/O Library for structured grid applicati toolchain = {'name': 'intel', 'version': '2017a'} toolchainopts = {'usempi': True} -## underscore = "${version//./_}" something like this ?? -## sources = ['pio%(underscore)s.tar.gz'] bash sub in easyconf ?? +# underscore = "${version//./_}" bash substition like this +# sources = ['pio%(underscore)s.tar.gz'] in an easyconfig file ? sources = ['pio2_2_2a.tar.gz'] source_urls = ['https://github.com/NCAR/ParallelIO/archive/'] +checksums = ['052a03e8e3b5ac244dc53b397a9920af3066efffa216ea7f8e5e4ac73a8b8033'] separate_build_dir = True @@ -22,7 +23,7 @@ dependencies = [ ] builddependencies = [ - ('CMake', '3.8.2', '', ('intel', '2017a')), + ('CMake', '3.8.2', '', ('GCCcore', '6.3.0')), ] configopts = "-DPIO_ENABLE_TIMING=OFF " diff --git a/easybuild/easyconfigs/p/PnetCDF/PnetCDF-1.8.1-intel-2017a.eb b/easybuild/easyconfigs/p/PnetCDF/PnetCDF-1.8.1-intel-2017a.eb index 77ad478ab0..170ae98a1f 100644 --- a/easybuild/easyconfigs/p/PnetCDF/PnetCDF-1.8.1-intel-2017a.eb +++ b/easybuild/easyconfigs/p/PnetCDF/PnetCDF-1.8.1-intel-2017a.eb @@ -10,6 +10,7 @@ toolchain = {'name': 'intel', 'version': '2017a'} sources = ['parallel-netcdf-%(version)s.tar.gz'] source_urls = ['http://cucis.ece.northwestern.edu/projects/PnetCDF/Release/'] +checksums = ['8d7d4c9c7b39bb1cbbcf087e0d726551c50f0cc30d44aed3df63daf3772c9043'] sanity_check_paths = { 'files': ['bin/pnetcdf_version'], -- GitLab From 2f848cea61598ee8ff1693a2bc3d1d9be9520ea6 Mon Sep 17 00:00:00 2001 From: ocaisa Date: Wed, 30 Aug 2017 16:50:23 +0200 Subject: [PATCH 1456/1603] Linking to ncurses was not done correctly... Use `buildopts` instead, see http://www.linuxfromscratch.org/lfs/view/8.0/chapter06/readline.html --- .../easyconfigs/l/libreadline/libreadline-7.0-GCCcore-6.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-7.0-GCCcore-6.3.0.eb b/easybuild/easyconfigs/l/libreadline/libreadline-7.0-GCCcore-6.3.0.eb index 66d703c987..8a2b1e4f5f 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-7.0-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-7.0-GCCcore-6.3.0.eb @@ -19,7 +19,7 @@ builddependencies = [('binutils', '2.27')] dependencies = [('ncurses', '6.0')] # for the termcap symbols, use EB ncurses -preconfigopts = "env LDFLAGS='-lncurses'" +buildopts += "SHLIB_LIBS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + -- GitLab From e91377c50aa92f4e112c533dfc3550e8830a50cd Mon Sep 17 00:00:00 2001 From: ocaisa Date: Wed, 30 Aug 2017 17:43:16 +0200 Subject: [PATCH 1457/1603] Remove stray + --- .../easyconfigs/l/libreadline/libreadline-7.0-GCCcore-6.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-7.0-GCCcore-6.3.0.eb b/easybuild/easyconfigs/l/libreadline/libreadline-7.0-GCCcore-6.3.0.eb index 8a2b1e4f5f..b77f11d21b 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-7.0-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-7.0-GCCcore-6.3.0.eb @@ -19,7 +19,7 @@ builddependencies = [('binutils', '2.27')] dependencies = [('ncurses', '6.0')] # for the termcap symbols, use EB ncurses -buildopts += "SHLIB_LIBS='-lncurses'" +buildopts = "SHLIB_LIBS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + -- GitLab From d92fd4cc6a4a8e5d0bcd4259527cb66e1bd6d80b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 30 Aug 2017 21:03:36 +0200 Subject: [PATCH 1458/1603] remove bare Python easyconfig using GCCcore/6.4.0 toolchain + easyconfigs that require it --- ...n-0.26-GCCcore-6.4.0-Python-2.7.13-bare.eb | 35 ------------ ...L-3.12-GCCcore-6.4.0-Python-2.7.13-bare.eb | 38 ------------- .../Python-2.7.13-GCCcore-6.4.0-bare.eb | 56 ------------------- ...36.2.0-GCCcore-6.4.0-Python-2.7.13-bare.eb | 33 ----------- ...1.10.0-GCCcore-6.4.0-Python-2.7.13-bare.eb | 31 ---------- 5 files changed, 193 deletions(-) delete mode 100644 easybuild/easyconfigs/c/Cython/Cython-0.26-GCCcore-6.4.0-Python-2.7.13-bare.eb delete mode 100644 easybuild/easyconfigs/p/PyYAML/PyYAML-3.12-GCCcore-6.4.0-Python-2.7.13-bare.eb delete mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.13-GCCcore-6.4.0-bare.eb delete mode 100644 easybuild/easyconfigs/s/setuptools/setuptools-36.2.0-GCCcore-6.4.0-Python-2.7.13-bare.eb delete mode 100644 easybuild/easyconfigs/s/six/six-1.10.0-GCCcore-6.4.0-Python-2.7.13-bare.eb diff --git a/easybuild/easyconfigs/c/Cython/Cython-0.26-GCCcore-6.4.0-Python-2.7.13-bare.eb b/easybuild/easyconfigs/c/Cython/Cython-0.26-GCCcore-6.4.0-Python-2.7.13-bare.eb deleted file mode 100644 index 9875d3b964..0000000000 --- a/easybuild/easyconfigs/c/Cython/Cython-0.26-GCCcore-6.4.0-Python-2.7.13-bare.eb +++ /dev/null @@ -1,35 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'Cython' -version = '0.26' -pyver = '2.7.13' -pyshortver = '2.7' -pysubver = '-bare' -versionsuffix = '-Python-%s%s' % (pyver, pysubver) - -homepage = 'https://pypi.python.org/pypi/Cython/' - -description = """ - The Cython language makes writing C extensions for the Python language as easy - as Python itself. Cython is a source code translator based on the well-known - Pyrex, but supports more cutting edge functionality and optimizations. -""" - -toolchain = {'name': 'GCCcore', 'version': '6.4.0'} - -source_urls = [PYPI_SOURCE] -sources = [SOURCE_TAR_GZ] -checksums = ['4c24e2c22ddaed624d35229dc5db25049e9e225c6f64f3364326836cad8f2c66'] - -builddependencies = [ - ('binutils', '2.28'), - ('Python', pyver, pysubver), -] - -sanity_check_paths = { - 'files': ['bin/cygdb', 'bin/%(namelower)s', - 'lib/python%s/site-packages/%%(namelower)s.py' % pyshortver], - 'dirs': ['lib/python%s/site-packages/%%(name)s' % pyshortver], -} - -moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12-GCCcore-6.4.0-Python-2.7.13-bare.eb b/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12-GCCcore-6.4.0-Python-2.7.13-bare.eb deleted file mode 100644 index eb4c534d26..0000000000 --- a/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12-GCCcore-6.4.0-Python-2.7.13-bare.eb +++ /dev/null @@ -1,38 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'PyYAML' -version = '3.12' -pyver = '2.7.13' -pyshortver = '2.7' -pysubver = '-bare' -versionsuffix = '-Python-%s%s' % (pyver, pysubver) - -homepage = 'https://pypi.python.org/pypi/PyYAML/' - -description = """ - PyYAML is a YAML parser and emitter for the Python programming language. -""" - -toolchain = {'name': 'GCCcore', 'version': '6.4.0'} - -source_urls = [PYPI_SOURCE] -sources = [SOURCE_TAR_GZ] -checksums = ['592766c6303207a20efc445587778322d7f73b161bd994f227adaa341ba212ab'] - -builddependencies = [ - ('binutils', '2.28'), - ('Python', pyver, pysubver), -] - -dependencies = [ - ('libyaml', '0.1.6'), -] - -options = {'modulename': 'yaml'} - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%s/site-packages' % pyshortver], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.13-GCCcore-6.4.0-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.13-GCCcore-6.4.0-bare.eb deleted file mode 100644 index 0860032fc3..0000000000 --- a/easybuild/easyconfigs/p/Python/Python-2.7.13-GCCcore-6.4.0-bare.eb +++ /dev/null @@ -1,56 +0,0 @@ -name = 'Python' -version = '2.7.13' -versionsuffix = '-bare' - -homepage = 'http://python.org/' - -description = """ - Python is a programming language that lets you work more quickly and - integrate your systems more effectively. - -Note: This module is meant to provide a builddependency for other Python - modules while using EasyBuild's --minimaltoolchain option. Modules - built with it will require the full Python later -""" - -toolchain = {'name': 'GCCcore', 'version': '6.4.0'} -toolchainopts = {'pic': True} - -source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] -sources = [SOURCE_TGZ] -checksums = ['a4f05a0720ce0fd92626f0278b6b433eee9a6173ddf2bced7957dfb599a5ece1'] - -builddependencies = [ - ('binutils', '2.28'), -] - -dependencies = [ - ('bzip2', '1.0.6'), - ('libreadline', '7.0'), - ('ncurses', '6.0'), - ('SQLite', '3.19.3'), - ('zlib', '1.2.11'), -] - -osdependencies = [ - # rely upon distribution for timely security updates - ('openssl-devel', 'libssl-dev', 'libopenssl-devel'), -] - -# We hide this by default since users should not use it in production, -# high-performance Python should be delivered at compiler level with -# a default extension set -# hidden = True - -# bare installation: only known module deps for GCCcore tools included -exts_list = [] - -# Until such time that EasyBuild accepts 'rpath' as a toolchainopt... -# add RPATH so this can be used as a builddependency for "bare" PythonPackages -preconfigopts = """ - sed -e\ - 's:$(LINKCC) $(LDFLAGS) $(LINKFORSHARED):$(LINKCC) $(LDFLAGS) $(LINKFORSHARED) -Wl,-rpath=%(installdir)s/lib:'\ - -i.eb Makefile.pre.in -""" - -moduleclass = 'lang' diff --git a/easybuild/easyconfigs/s/setuptools/setuptools-36.2.0-GCCcore-6.4.0-Python-2.7.13-bare.eb b/easybuild/easyconfigs/s/setuptools/setuptools-36.2.0-GCCcore-6.4.0-Python-2.7.13-bare.eb deleted file mode 100644 index 9b5a4054e1..0000000000 --- a/easybuild/easyconfigs/s/setuptools/setuptools-36.2.0-GCCcore-6.4.0-Python-2.7.13-bare.eb +++ /dev/null @@ -1,33 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'setuptools' -version = '36.2.0' -pyver = '2.7.13' -pyshortver = '2.7' -pysubver = '-bare' -versionsuffix = '-Python-%s%s' % (pyver, pysubver) - -homepage = 'http://pypi.python.org/pypi/setuptools/' - -description = """ - Download, build, install, upgrade, and uninstall Python packages -- easily! -""" - -toolchain = {'name': 'GCCcore', 'version': '6.4.0'} - -source_urls = [PYPI_SOURCE] -sources = [SOURCE_ZIP] -checksums = ['4c2bda3829c9dbbe9c2b33d89c4b1cb6d45813615ab8e248ad352e3697a96d81'] - -builddependencies = [ - ('Python', pyver, pysubver), -] - -pylibdir = "lib/python%s/site-packages/%s" % (pyshortver, name) -sanity_check_paths = { - 'files': ["bin/easy_install", "%s-%s-py%s.egg" % - (pylibdir, version, pyshortver)], - 'dirs': [] -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/six/six-1.10.0-GCCcore-6.4.0-Python-2.7.13-bare.eb b/easybuild/easyconfigs/s/six/six-1.10.0-GCCcore-6.4.0-Python-2.7.13-bare.eb deleted file mode 100644 index f5345426c3..0000000000 --- a/easybuild/easyconfigs/s/six/six-1.10.0-GCCcore-6.4.0-Python-2.7.13-bare.eb +++ /dev/null @@ -1,31 +0,0 @@ -# Author:: Jack Perdue - TAMU HPRC - http://sc.tamu.edu - -easyblock = 'PythonPackage' - -name = 'six' -version = '1.10.0' -pyver = '2.7.13' -pyshortver = '2.7' -pysubver = '-bare' -versionsuffix = '-Python-%s%s' % (pyver, pysubver) - -homepage = 'https://pypi.python.org/pypi/six/1.10.0' - -description = "Python 2 and 3 compatibility utilities" - -toolchain = {'name': 'GCCcore', 'version': '6.4.0'} - -sources = [SOURCE_TAR_GZ] -source_urls = [PYPI_LOWER_SOURCE] -checksums = ['105f8d68616f8248e24bf0e9372ef04d3cc10104f1980f54d57b2ce73a5ad56a'] - -builddependencies = [ - ('Python', pyver, pysubver), -] - -sanity_check_paths = { - 'files': ['lib/python%s/site-packages/%%(name)s.py' % pyshortver], - 'dirs': [], -} - -moduleclass = 'devel' -- GitLab From a0c8ece7bb26403b943259027ed7143fd90b6deb Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 30 Aug 2017 21:28:53 +0200 Subject: [PATCH 1459/1603] bump version for libyaml, SQLite & Tcl easyconfigs that use GCCcore/6.4.0 --- ....1.6-GCCcore-6.4.0.eb => libyaml-0.1.7-GCCcore-6.4.0.eb} | 4 ++-- ...19.3-GCCcore-6.4.0.eb => SQLite-3.20.1-GCCcore-6.4.0.eb} | 6 +++--- ...cl-8.6.6-GCCcore-6.4.0.eb => Tcl-8.6.7-GCCcore-6.4.0.eb} | 4 ++-- 3 files changed, 7 insertions(+), 7 deletions(-) rename easybuild/easyconfigs/l/libyaml/{libyaml-0.1.6-GCCcore-6.4.0.eb => libyaml-0.1.7-GCCcore-6.4.0.eb} (88%) rename easybuild/easyconfigs/s/SQLite/{SQLite-3.19.3-GCCcore-6.4.0.eb => SQLite-3.20.1-GCCcore-6.4.0.eb} (90%) rename easybuild/easyconfigs/t/Tcl/{Tcl-8.6.6-GCCcore-6.4.0.eb => Tcl-8.6.7-GCCcore-6.4.0.eb} (90%) diff --git a/easybuild/easyconfigs/l/libyaml/libyaml-0.1.6-GCCcore-6.4.0.eb b/easybuild/easyconfigs/l/libyaml/libyaml-0.1.7-GCCcore-6.4.0.eb similarity index 88% rename from easybuild/easyconfigs/l/libyaml/libyaml-0.1.6-GCCcore-6.4.0.eb rename to easybuild/easyconfigs/l/libyaml/libyaml-0.1.7-GCCcore-6.4.0.eb index 156fcf6ef5..975e8ba0b5 100644 --- a/easybuild/easyconfigs/l/libyaml/libyaml-0.1.6-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/l/libyaml/libyaml-0.1.7-GCCcore-6.4.0.eb @@ -10,7 +10,7 @@ easyblock = 'ConfigureMake' name = 'libyaml' -version = '0.1.6' +version = '0.1.7' homepage = 'http://pyyaml.org/wiki/LibYAML' @@ -20,7 +20,7 @@ toolchain = {'name': 'GCCcore', 'version': '6.4.0'} source_urls = ['http://pyyaml.org/download/libyaml/'] sources = ['yaml-%(version)s.tar.gz'] -checksums = ['7da6971b4bd08a986dd2a61353bc422362bd0edcc67d7ebaac68c95f74182749'] +checksums = ['8088e457264a98ba451a90b8661fcb4f9d6f478f7265d48322a196cec2480729'] builddependencies = [ ('binutils', '2.28'), diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.19.3-GCCcore-6.4.0.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.20.1-GCCcore-6.4.0.eb similarity index 90% rename from easybuild/easyconfigs/s/SQLite/SQLite-3.19.3-GCCcore-6.4.0.eb rename to easybuild/easyconfigs/s/SQLite/SQLite-3.20.1-GCCcore-6.4.0.eb index e10115f361..7d34b6b0e7 100644 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.19.3-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.20.1-GCCcore-6.4.0.eb @@ -13,7 +13,7 @@ easyblock = 'ConfigureMake' name = 'SQLite' -version = '3.19.3' +version = '3.20.1' homepage = 'http://www.sqlite.org/' @@ -26,7 +26,7 @@ toolchainopts = {'pic': True} source_urls = ['http://www.sqlite.org/2017/'] version_str = '%%(version_major)s%s00' % ''.join('%02d' % int(x) for x in version.split('.')[1:]) sources = ['sqlite-autoconf-%s.tar.gz' % version_str] -checksums = ['06129c03dced9f87733a8cba408871bd60673b8f93b920ba8d815efab0a06301'] +checksums = ['ec66595b29bc0798b023a5122021ea646ab4fa9e2f735937c5426feeba950742'] builddependencies = [ ('binutils', '2.28'), @@ -34,7 +34,7 @@ builddependencies = [ dependencies = [ ('libreadline', '7.0'), - ('Tcl', '8.6.6'), + ('Tcl', '8.6.7'), ] parallel = 1 diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.6-GCCcore-6.4.0.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.7-GCCcore-6.4.0.eb similarity index 90% rename from easybuild/easyconfigs/t/Tcl/Tcl-8.6.6-GCCcore-6.4.0.eb rename to easybuild/easyconfigs/t/Tcl/Tcl-8.6.7-GCCcore-6.4.0.eb index cffeed4270..08a9084d56 100644 --- a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.6-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.7-GCCcore-6.4.0.eb @@ -1,7 +1,7 @@ easyblock = 'ConfigureMake' name = 'Tcl' -version = '8.6.6' +version = '8.6.7' homepage = 'http://www.tcl.tk/' @@ -15,7 +15,7 @@ toolchain = {'name': 'GCCcore', 'version': '6.4.0'} source_urls = ["http://prdownloads.sourceforge.net/tcl"] sources = ['%(namelower)s%(version)s-src.tar.gz'] -checksums = ['a265409781e4b3edcc4ef822533071b34c3dc6790b893963809b9fe221befe07'] +checksums = ['7c6b8f84e37332423cfe5bae503440d88450da8cc1243496249faa5268026ba5'] builddependencies = [ ('binutils', '2.28'), -- GitLab From 16ba2457acd12c7bf6aa43da2ea3931999615c8e Mon Sep 17 00:00:00 2001 From: Martin Rosgaard Date: Thu, 31 Aug 2017 09:58:53 +0200 Subject: [PATCH 1460/1603] ParallelIO-intel-2017a: source string _ substitution and rm tc from deps --- .../p/ParallelIO/ParallelIO-2.2.2a-intel-2017a.eb | 8 +++----- 1 file changed, 3 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/p/ParallelIO/ParallelIO-2.2.2a-intel-2017a.eb b/easybuild/easyconfigs/p/ParallelIO/ParallelIO-2.2.2a-intel-2017a.eb index 60f276c3f1..0fb02af4a6 100644 --- a/easybuild/easyconfigs/p/ParallelIO/ParallelIO-2.2.2a-intel-2017a.eb +++ b/easybuild/easyconfigs/p/ParallelIO/ParallelIO-2.2.2a-intel-2017a.eb @@ -9,17 +9,15 @@ description = """A high-level Parallel I/O Library for structured grid applicati toolchain = {'name': 'intel', 'version': '2017a'} toolchainopts = {'usempi': True} -# underscore = "${version//./_}" bash substition like this -# sources = ['pio%(underscore)s.tar.gz'] in an easyconfig file ? -sources = ['pio2_2_2a.tar.gz'] +sources = ['pio%s.tar.gz' % '_'.join(version.split('.'))] source_urls = ['https://github.com/NCAR/ParallelIO/archive/'] checksums = ['052a03e8e3b5ac244dc53b397a9920af3066efffa216ea7f8e5e4ac73a8b8033'] separate_build_dir = True dependencies = [ - ('PnetCDF', '1.8.1', '', ('intel', '2017a')), - ('netCDF-Fortran', '4.4.4', '', ('intel', '2017a')) + ('PnetCDF', '1.8.1'), + ('netCDF-Fortran', '4.4.4') ] builddependencies = [ -- GitLab From 45218e57029dcf9c5573ca7afe290a53b8a9ef43 Mon Sep 17 00:00:00 2001 From: Martin Rosgaard Date: Thu, 31 Aug 2017 11:24:06 +0200 Subject: [PATCH 1461/1603] ParallelIO and PnetCDF 4space indent and 1space after , --- .../p/ParallelIO/ParallelIO-2.2.2a-intel-2017a.eb | 10 +++++----- .../easyconfigs/p/PnetCDF/PnetCDF-1.8.1-intel-2017a.eb | 4 ++-- 2 files changed, 7 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/p/ParallelIO/ParallelIO-2.2.2a-intel-2017a.eb b/easybuild/easyconfigs/p/ParallelIO/ParallelIO-2.2.2a-intel-2017a.eb index 0fb02af4a6..5cf34e7172 100644 --- a/easybuild/easyconfigs/p/ParallelIO/ParallelIO-2.2.2a-intel-2017a.eb +++ b/easybuild/easyconfigs/p/ParallelIO/ParallelIO-2.2.2a-intel-2017a.eb @@ -16,23 +16,23 @@ checksums = ['052a03e8e3b5ac244dc53b397a9920af3066efffa216ea7f8e5e4ac73a8b8033'] separate_build_dir = True dependencies = [ - ('PnetCDF', '1.8.1'), - ('netCDF-Fortran', '4.4.4') + ('PnetCDF', '1.8.1'), + ('netCDF-Fortran', '4.4.4') ] builddependencies = [ - ('CMake', '3.8.2', '', ('GCCcore', '6.3.0')), + ('CMake', '3.8.2', '', ('GCCcore', '6.3.0')) ] configopts = "-DPIO_ENABLE_TIMING=OFF " sanity_check_paths = { - 'files': [], + 'files': [], 'dirs': [('include','lib')] } modextravars = { - 'PIO': '%(installdir)s', + 'PIO': '%(installdir)s' } moduleclass = 'data' diff --git a/easybuild/easyconfigs/p/PnetCDF/PnetCDF-1.8.1-intel-2017a.eb b/easybuild/easyconfigs/p/PnetCDF/PnetCDF-1.8.1-intel-2017a.eb index 170ae98a1f..605ea27a21 100644 --- a/easybuild/easyconfigs/p/PnetCDF/PnetCDF-1.8.1-intel-2017a.eb +++ b/easybuild/easyconfigs/p/PnetCDF/PnetCDF-1.8.1-intel-2017a.eb @@ -13,12 +13,12 @@ source_urls = ['http://cucis.ece.northwestern.edu/projects/PnetCDF/Release/'] checksums = ['8d7d4c9c7b39bb1cbbcf087e0d726551c50f0cc30d44aed3df63daf3772c9043'] sanity_check_paths = { - 'files': ['bin/pnetcdf_version'], + 'files': ['bin/pnetcdf_version'], 'dirs': [] } modextravars = { - 'PNETCDF': '%(installdir)s', + 'PNETCDF': '%(installdir)s', } moduleclass = 'data' -- GitLab From 16fdb68b3ccbdead67e638f34d2c3f46b78ad340 Mon Sep 17 00:00:00 2001 From: iotaka Date: Thu, 31 Aug 2017 12:17:43 +0200 Subject: [PATCH 1462/1603] CGNS 3.3.1 --- .../c/CGNS/CGNS-3.3.1-foss-2016b.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/c/CGNS/CGNS-3.3.1-foss-2016b.eb diff --git a/easybuild/easyconfigs/c/CGNS/CGNS-3.3.1-foss-2016b.eb b/easybuild/easyconfigs/c/CGNS/CGNS-3.3.1-foss-2016b.eb new file mode 100644 index 0000000000..ca48818de4 --- /dev/null +++ b/easybuild/easyconfigs/c/CGNS/CGNS-3.3.1-foss-2016b.eb @@ -0,0 +1,24 @@ +name = 'CGNS' +version = '3.3.1' + +homepage = 'https://cgns.github.io/' +description = """The CGNS system is designed to facilitate the exchange of data between sites and applications, and to help stabilize the archiving of aerodynamic data.""" + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://github.com/CGNS/CGNS/archive/v%(version)s.tar.gz'] +sources = [SOURCE_TAR_GZ] +checksums = ['65c55998270c3e125e28ec5c3742e15d'] + +easyblock = 'CMakeMake' + +dependencies = [ + ('HDF5', '1.10.0-patch1'), +] + +builddependencies = [ + ('CMake', '3.6.1'), +] + +moduleclass = 'cae' -- GitLab From 525856e7a399a5610fb3ad93e999a1fb9048ca8a Mon Sep 17 00:00:00 2001 From: iotaka Date: Thu, 31 Aug 2017 12:27:04 +0200 Subject: [PATCH 1463/1603] fix @pescobar suggestions --- easybuild/easyconfigs/c/CGNS/CGNS-3.3.1-foss-2016b.eb | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/c/CGNS/CGNS-3.3.1-foss-2016b.eb b/easybuild/easyconfigs/c/CGNS/CGNS-3.3.1-foss-2016b.eb index ca48818de4..d48a53b4ed 100644 --- a/easybuild/easyconfigs/c/CGNS/CGNS-3.3.1-foss-2016b.eb +++ b/easybuild/easyconfigs/c/CGNS/CGNS-3.3.1-foss-2016b.eb @@ -1,8 +1,11 @@ +easyblock = 'CMakeMake' + name = 'CGNS' version = '3.3.1' homepage = 'https://cgns.github.io/' -description = """The CGNS system is designed to facilitate the exchange of data between sites and applications, and to help stabilize the archiving of aerodynamic data.""" +description = """The CGNS system is designed to facilitate the exchange of data between sites and applications, + and to help stabilize the archiving of aerodynamic data.""" toolchain = {'name': 'foss', 'version': '2016b'} toolchainopts = {'pic': True, 'usempi': True} @@ -11,8 +14,6 @@ source_urls = ['https://github.com/CGNS/CGNS/archive/v%(version)s.tar.gz'] sources = [SOURCE_TAR_GZ] checksums = ['65c55998270c3e125e28ec5c3742e15d'] -easyblock = 'CMakeMake' - dependencies = [ ('HDF5', '1.10.0-patch1'), ] -- GitLab From caad843d538a7c838d25747ebee7a006c1d8b6b3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 31 Aug 2017 13:39:06 +0200 Subject: [PATCH 1464/1603] fix linking to ncurses in libreadline 7.0 easyconfig using GCCcore/6.4.0 --- .../easyconfigs/l/libreadline/libreadline-7.0-GCCcore-6.4.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-7.0-GCCcore-6.4.0.eb b/easybuild/easyconfigs/l/libreadline/libreadline-7.0-GCCcore-6.4.0.eb index b26a32205d..6f3826b4d5 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-7.0-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-7.0-GCCcore-6.4.0.eb @@ -30,7 +30,7 @@ dependencies = [ ] # for the termcap symbols, use EB ncurses -preconfigopts = "env LDFLAGS='-lncurses'" +buildopts = "SHLIB_LIBS='-lncurses'" sanity_check_paths = { 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + -- GitLab From c2f52fe768c9dcaaedc6c81b81050517beb8289f Mon Sep 17 00:00:00 2001 From: Martin Rosgaard Date: Thu, 31 Aug 2017 13:42:06 +0200 Subject: [PATCH 1465/1603] addressing travis style complaints --- .../p/ParallelIO/ParallelIO-2.2.2a-intel-2017a.eb | 8 ++++---- .../easyconfigs/p/PnetCDF/PnetCDF-1.8.1-intel-2017a.eb | 2 +- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/p/ParallelIO/ParallelIO-2.2.2a-intel-2017a.eb b/easybuild/easyconfigs/p/ParallelIO/ParallelIO-2.2.2a-intel-2017a.eb index 5cf34e7172..e7c22a9446 100644 --- a/easybuild/easyconfigs/p/ParallelIO/ParallelIO-2.2.2a-intel-2017a.eb +++ b/easybuild/easyconfigs/p/ParallelIO/ParallelIO-2.2.2a-intel-2017a.eb @@ -17,18 +17,18 @@ separate_build_dir = True dependencies = [ ('PnetCDF', '1.8.1'), - ('netCDF-Fortran', '4.4.4') + ('netCDF-Fortran', '4.4.4'), ] builddependencies = [ - ('CMake', '3.8.2', '', ('GCCcore', '6.3.0')) + ('CMake', '3.8.2', '', ('GCCcore', '6.3.0')), ] configopts = "-DPIO_ENABLE_TIMING=OFF " sanity_check_paths = { - 'files': [], - 'dirs': [('include','lib')] + 'files': ['lib/piof.a'], + 'dirs': [('include','lib')], } modextravars = { diff --git a/easybuild/easyconfigs/p/PnetCDF/PnetCDF-1.8.1-intel-2017a.eb b/easybuild/easyconfigs/p/PnetCDF/PnetCDF-1.8.1-intel-2017a.eb index 605ea27a21..6c3b0f7759 100644 --- a/easybuild/easyconfigs/p/PnetCDF/PnetCDF-1.8.1-intel-2017a.eb +++ b/easybuild/easyconfigs/p/PnetCDF/PnetCDF-1.8.1-intel-2017a.eb @@ -14,7 +14,7 @@ checksums = ['8d7d4c9c7b39bb1cbbcf087e0d726551c50f0cc30d44aed3df63daf3772c9043'] sanity_check_paths = { 'files': ['bin/pnetcdf_version'], - 'dirs': [] + 'dirs': [('include','lib','bin')], } modextravars = { -- GitLab From d82d768bfb7f5fb98630442a2a7118ccd3a9805c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 31 Aug 2017 13:53:35 +0200 Subject: [PATCH 1466/1603] add peperr extension for R 3.4.0 --- easybuild/easyconfigs/r/R/R-3.4.0-intel-2017a-X11-20170314.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/r/R/R-3.4.0-intel-2017a-X11-20170314.eb b/easybuild/easyconfigs/r/R/R-3.4.0-intel-2017a-X11-20170314.eb index 5ba7780140..bebb932536 100644 --- a/easybuild/easyconfigs/r/R/R-3.4.0-intel-2017a-X11-20170314.eb +++ b/easybuild/easyconfigs/r/R/R-3.4.0-intel-2017a-X11-20170314.eb @@ -554,6 +554,7 @@ exts_list = [ ('WriteXLS', '4.0.0', ext_options), ('mpath', '0.2-4', ext_options), ('timereg', '1.9.1', ext_options), + ('peperr' , '1.1-7', ext_options), ] moduleclass = 'lang' -- GitLab From d92eba74cb48ba32969f80867a8c6221feb9e7ed Mon Sep 17 00:00:00 2001 From: iotaka Date: Thu, 31 Aug 2017 14:41:05 +0200 Subject: [PATCH 1467/1603] Update CGNS-3.3.1-foss-2016b.eb changed source_urls and sources --- easybuild/easyconfigs/c/CGNS/CGNS-3.3.1-foss-2016b.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/c/CGNS/CGNS-3.3.1-foss-2016b.eb b/easybuild/easyconfigs/c/CGNS/CGNS-3.3.1-foss-2016b.eb index d48a53b4ed..6dc23c93a4 100644 --- a/easybuild/easyconfigs/c/CGNS/CGNS-3.3.1-foss-2016b.eb +++ b/easybuild/easyconfigs/c/CGNS/CGNS-3.3.1-foss-2016b.eb @@ -10,8 +10,8 @@ description = """The CGNS system is designed to facilitate the exchange of data toolchain = {'name': 'foss', 'version': '2016b'} toolchainopts = {'pic': True, 'usempi': True} -source_urls = ['https://github.com/CGNS/CGNS/archive/v%(version)s.tar.gz'] -sources = [SOURCE_TAR_GZ] +source_urls = ['https://github.com/CGNS/CGNS/archive/'] +sources = ['v%(version)s.tar.gz'] checksums = ['65c55998270c3e125e28ec5c3742e15d'] dependencies = [ -- GitLab From ccb49d5ece60f7258a2d4577d543f76b86a281cb Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 31 Aug 2017 14:56:54 +0200 Subject: [PATCH 1468/1603] fix minor style issue --- easybuild/easyconfigs/r/R/R-3.4.0-intel-2017a-X11-20170314.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R/R-3.4.0-intel-2017a-X11-20170314.eb b/easybuild/easyconfigs/r/R/R-3.4.0-intel-2017a-X11-20170314.eb index bebb932536..194e3eb272 100644 --- a/easybuild/easyconfigs/r/R/R-3.4.0-intel-2017a-X11-20170314.eb +++ b/easybuild/easyconfigs/r/R/R-3.4.0-intel-2017a-X11-20170314.eb @@ -554,7 +554,7 @@ exts_list = [ ('WriteXLS', '4.0.0', ext_options), ('mpath', '0.2-4', ext_options), ('timereg', '1.9.1', ext_options), - ('peperr' , '1.1-7', ext_options), + ('peperr', '1.1-7', ext_options), ] moduleclass = 'lang' -- GitLab From f31e9ac7d54c4fec58f0e2dad265f2d8b0cd719e Mon Sep 17 00:00:00 2001 From: iotaka Date: Thu, 31 Aug 2017 16:20:48 +0200 Subject: [PATCH 1469/1603] Update CGNS-3.3.1-foss-2016b.eb added @pescobar --- easybuild/easyconfigs/c/CGNS/CGNS-3.3.1-foss-2016b.eb | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/c/CGNS/CGNS-3.3.1-foss-2016b.eb b/easybuild/easyconfigs/c/CGNS/CGNS-3.3.1-foss-2016b.eb index 6dc23c93a4..5e9f2fac97 100644 --- a/easybuild/easyconfigs/c/CGNS/CGNS-3.3.1-foss-2016b.eb +++ b/easybuild/easyconfigs/c/CGNS/CGNS-3.3.1-foss-2016b.eb @@ -23,3 +23,9 @@ builddependencies = [ ] moduleclass = 'cae' + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["cgnscheck", "cgnscompress", "cgnsconvert", "cgnsdiff", + "cgnslist, "cgnsnames", "cgnsupdate"], "lib/libcgns.so", "include/cgnslib.h" ], + 'dirs': [], +} -- GitLab From 0769bf707e8b4b7042e673cb92460fd68ad7ab9d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 31 Aug 2017 18:21:53 +0200 Subject: [PATCH 1470/1603] adding easyconfigs: MATLAB-2013b.eb --- easybuild/easyconfigs/m/MATLAB/MATLAB-2013b.eb | 15 +++++++++++++++ 1 file changed, 15 insertions(+) create mode 100644 easybuild/easyconfigs/m/MATLAB/MATLAB-2013b.eb diff --git a/easybuild/easyconfigs/m/MATLAB/MATLAB-2013b.eb b/easybuild/easyconfigs/m/MATLAB/MATLAB-2013b.eb new file mode 100644 index 0000000000..a43a1a8b75 --- /dev/null +++ b/easybuild/easyconfigs/m/MATLAB/MATLAB-2013b.eb @@ -0,0 +1,15 @@ +name = 'MATLAB' +version = '2013b' + +homepage = 'http://www.mathworks.com/products/matlab' +description = """MATLAB is a high-level language and interactive environment + that enables you to perform computationally intensive tasks faster than with + traditional programming languages such as C, C++, and Fortran.""" + +toolchain = {'name': 'dummy', 'version': ''} + +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('Java', '1.7.0_80')] + +moduleclass = 'math' -- GitLab From 0e5842de187544a47ca08f739c0bf013ce415ac5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 31 Aug 2017 19:42:01 +0200 Subject: [PATCH 1471/1603] adding easyconfigs: ROOT-6.06.02-intel-2017a-Python-2.7.13.eb, CFITSIO-3.41-GCCcore-6.3.0.eb --- .../c/CFITSIO/CFITSIO-3.41-GCCcore-6.3.0.eb | 24 ++++++++ .../ROOT-6.06.02-intel-2017a-Python-2.7.13.eb | 59 +++++++++++++++++++ 2 files changed, 83 insertions(+) create mode 100644 easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.41-GCCcore-6.3.0.eb create mode 100644 easybuild/easyconfigs/r/ROOT/ROOT-6.06.02-intel-2017a-Python-2.7.13.eb diff --git a/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.41-GCCcore-6.3.0.eb b/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.41-GCCcore-6.3.0.eb new file mode 100644 index 0000000000..b66d494bcc --- /dev/null +++ b/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.41-GCCcore-6.3.0.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'CFITSIO' +version = '3.41' + +homepage = 'http://heasarc.gsfc.nasa.gov/fitsio/' +description = """CFITSIO is a library of C and Fortran subroutines for reading and writing data files in +FITS (Flexible Image Transport System) data format.""" + +toolchain = {'name': 'GCCcore', 'version': '6.3.0'} +toolchainopts = {'pic': True} + +srcversion = '%s0' % version.replace('.', '') +source_urls = ['http://heasarc.gsfc.nasa.gov/FTP/software/fitsio/c/'] +sources = ['%%(namelower)s%s.tar.gz' % srcversion] + +builddependencies = [('binutils', '2.27')] + +sanity_check_paths = { + 'files': ['lib/libcfitsio.a'], + 'dirs': ['include'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-6.06.02-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/r/ROOT/ROOT-6.06.02-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..b1f9dab124 --- /dev/null +++ b/easybuild/easyconfigs/r/ROOT/ROOT-6.06.02-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,59 @@ +name = 'ROOT' +version = '6.06.02' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://root.cern.ch/drupal/' +description = """The ROOT system provides a set of OO frameworks with all the functionality + needed to handle and analyze large amounts of data in a very efficient way.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True} + +sources = ['%(namelower)s_v%(version)s.source.tar.gz'] +source_urls = ['ftp://root.cern.ch/root/'] +patches = [ + 'configure_FftwFromMkl_28.patch', + 'ROOT-v5_recent-ifort.patch', + 'ROOT-v5.34.26_libX.patch', +] + +dependencies = [ + ('GSL', '2.3'), + ('libxml2', '2.9.4'), + ('PCRE', '8.41'), + ('CFITSIO', '3.41'), + ('freetype', '2.7.1', '-libpng-1.6.29'), + ('Python', '2.7.13'), + ('zlib', '1.2.11'), + ('X11', '20170314'), + ('Mesa', '17.0.2'), + ('libGLU', '9.0.0'), + ('GL2PS', '1.4.0'), +] + +# use external ZLIB +preconfigopts = 'env ZLIB=$EBROOTZLIB ' + +# architecture +arch = 'linuxx8664icc' + +# disable features +configopts = ' --disable-xrootd --disable-mysql --disable-krb5 --disable-odbc ' +configopts += ' --disable-oracle --disable-pgsql --disable-qt --disable-sqlite' +# enable features +configopts += ' --enable-unuran --enable-table --enable-explicitlink --enable-minuit2 --enable-roofit' +configopts += ' --with-gsl-incdir=$EBROOTGSL/include/gsl --with-gsl-libdir=$EBROOTGSL/lib' +configopts += ' --with-fftw3-incdir=$MKLROOT/mkl/include/fftw --with-fftw3-libdir=$MKLROOT/mkl/lib/intel64' +configopts += ' --with-xml-incdir=$EBROOTLIBXML2/include/libxml2/libxml --with-xml-libdir=$EBROOTLIBXML2/lib' +configopts += ' --with-python-libdir=$EBROOTPYTHON/lib' +configopts += ' --with-cfitsio-incdir=$EBROOTCFITSIO/include --with-cfitsio-libdir=$EBROOTCFITSIO/lib' +configopts += ' --with-opengl-incdir=$EBROOTMESA/include --with-opengl-libdir=$EBROOTMESA/lib' +configopts += ' --with-x11-libdir=$EBROOTX11/lib --with-xext-libdir=$EBROOTLIBX11/lib' +configopts += ' --with-xft-libdir=$EBROOTX11/lib' +configopts += ' --with-xpm-incdir=$EBROOTX11/include --with-xpm-libdir=$EBROOTX11/lib' + +sanity_check_commands = ["python -c 'import ROOT'"] + +modextrapaths = {'PYTHONPATH': 'lib/'} + +moduleclass = 'data' -- GitLab From 72c0ababdb931d680214893c690afe85f849223b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 31 Aug 2017 19:43:35 +0200 Subject: [PATCH 1472/1603] adding easyconfigs: XZ-5.2.3-GCCcore-6.4.0.eb, gettext-0.19.8.1-GCCcore-6.4.0.eb, libxml2-2.9.4-GCCcore-6.4.0.eb --- .../gettext/gettext-0.19.8.1-GCCcore-6.4.0.eb | 26 ++++++++++++++++ .../l/libxml2/libxml2-2.9.4-GCCcore-6.4.0.eb | 26 ++++++++++++++++ .../x/XZ/XZ-5.2.3-GCCcore-6.4.0.eb | 31 +++++++++++++++++++ 3 files changed, 83 insertions(+) create mode 100644 easybuild/easyconfigs/g/gettext/gettext-0.19.8.1-GCCcore-6.4.0.eb create mode 100644 easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-GCCcore-6.4.0.eb create mode 100644 easybuild/easyconfigs/x/XZ/XZ-5.2.3-GCCcore-6.4.0.eb diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.8.1-GCCcore-6.4.0.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.8.1-GCCcore-6.4.0.eb new file mode 100644 index 0000000000..3c9be38c7f --- /dev/null +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.8.1-GCCcore-6.4.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'gettext' +version = '0.19.8.1' + +homepage = 'http://www.gnu.org/software/gettext/' +description = """GNU 'gettext' is an important step for the GNU Translation Project, as it is an asset on which we may +build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools +and documentation""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} + +sources = [SOURCE_TAR_GZ] +source_urls = [GNU_SOURCE] + +dependencies = [ + ('libxml2', '2.9.4'), + ('ncurses', '6.0'), +] + +# use same binutils version that was used when building GCCcore toolchain +builddependencies = [('binutils', '2.28')] + +configopts = '--without-emacs --with-libxml2-prefix=$EBROOTLIBXML2' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-GCCcore-6.4.0.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-GCCcore-6.4.0.eb new file mode 100644 index 0000000000..3672386817 --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-GCCcore-6.4.0.eb @@ -0,0 +1,26 @@ +name = 'libxml2' +version = '2.9.4' + +homepage = 'http://xmlsoft.org/' +description = """Libxml2 is the XML C parser and +toolchain developed for the Gnome project + (but usable outside of the Gnome platform).""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} +toolchainopts = {'pic': True} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('zlib', '1.2.11'), + ('XZ', '5.2.3'), +] + +# use same binutils version that was used when building GCCcore toolchain +builddependencies = [('binutils', '2.28')] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.3-GCCcore-6.4.0.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.3-GCCcore-6.4.0.eb new file mode 100644 index 0000000000..276a5fb2d6 --- /dev/null +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.3-GCCcore-6.4.0.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'XZ' +version = '5.2.3' + +homepage = 'http://tukaani.org/xz/' +description = "xz: XZ utilities" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://tukaani.org/xz/'] + +patches = ['XZ-5.2.2_compat-libs.patch'] + +builddependencies = [ + # use gettext built with dummy as build dep to avoid cyclic dependency (XZ -> gettext -> libxml2 -> XZ) + ('gettext', '0.19.8.1', '', True), + # use same binutils version that was used when building GCCcore toolchain + ('binutils', '2.28'), +] + +# may become useful in non-x86 archs +# configopts = ' --disable-assembler ' + +sanity_check_paths = { + 'files': ["bin/xz", "bin/lzmainfo"], + 'dirs': [] +} + +moduleclass = 'tools' -- GitLab From 0fd6c42dce8717516d2e48984ee0797e13131cdd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 31 Aug 2017 19:51:14 +0200 Subject: [PATCH 1473/1603] adding easyconfigs: PYTHIA-8.226-intel-2017a-Python-2.7.13.eb --- .../PYTHIA-8.226-intel-2017a-Python-2.7.13.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/p/PYTHIA/PYTHIA-8.226-intel-2017a-Python-2.7.13.eb diff --git a/easybuild/easyconfigs/p/PYTHIA/PYTHIA-8.226-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/p/PYTHIA/PYTHIA-8.226-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..945a05625b --- /dev/null +++ b/easybuild/easyconfigs/p/PYTHIA/PYTHIA-8.226-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'PYTHIA' +version = '8.226' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://home.thep.lu.se/~torbjorn/Pythia.html' +description = """PYTHIA is a standard tool for the generation of events in high-energy collisions, + comprising a coherent set of physics models for the evolution from a few-body hard + process to a complex multiparticle final state.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True} + +source_urls = ['http://home.thep.lu.se/~torbjorn/pythia8/'] +sources = ['pythia%(version_major)s%(version_minor)s.tgz'] +checksums = ['8ff4281bce9d22b17f1ec88e9e9353e8172512d5ef96296ace9486860e9ed2c9'] + +dependencies = [ + ('zlib', '1.2.11'), + ('Python', '2.7.13'), + ('ROOT', '6.06.02', versionsuffix), +] + +configopts = '--cxx="$CXX" --cxx-common="$CXXFLAGS" ' +configopts += '--with-gzip --with-python --with-python-include=$EBROOTPYTHON/include/python*/ --with-root' + +sanity_check_paths = { + 'files': ['bin/pythia%(version_major)s-config', 'lib/libpythia%(version_major)s.a', + 'lib/libpythia%%(version_major)s.%s' % SHLIB_EXT, 'lib/pythia8.py', 'lib/_pythia8.%s' % SHLIB_EXT], + 'dirs': ['include/Pythia%(version_major)s', 'include/Pythia%(version_major)sPlugins', 'share'], +} +sanity_check_commands = ["python -c 'import pythia%(version_major)s'"] + +modextrapaths = {'PYTHONPATH': 'lib'} + +moduleclass = 'phys' -- GitLab From 0c03dc497dc7747fc01e44ac13692a45b3870b5c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 31 Aug 2017 21:34:10 +0200 Subject: [PATCH 1474/1603] add check to see whether binutils is included as build dep when GCCore toolchain is used --- .../easyconfigs/b/BWA/BWA-0.7.15-GCCcore-5.4.0.eb | 2 ++ .../b/Bowtie/Bowtie-1.1.2-GCCcore-5.4.0.eb | 2 ++ .../b/Bowtie/Bowtie-1.1.2-GCCcore-6.3.0.eb | 2 ++ .../d/Doxygen/Doxygen-1.8.11-GCCcore-5.4.0.eb | 1 + .../easyconfigs/g/gSOAP/gSOAP-2.8.48-GCCcore-6.3.0.eb | 1 + .../easyconfigs/g/gzip/gzip-1.8-GCCcore-6.4.0.eb | 2 ++ .../easyconfigs/p/Perl/Perl-5.24.0-GCCcore-4.9.3.eb | 2 +- test/easyconfigs/easyconfigs.py | 11 +++++++++++ 8 files changed, 22 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/BWA/BWA-0.7.15-GCCcore-5.4.0.eb b/easybuild/easyconfigs/b/BWA/BWA-0.7.15-GCCcore-5.4.0.eb index 726ee69664..3436d2092a 100644 --- a/easybuild/easyconfigs/b/BWA/BWA-0.7.15-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/b/BWA/BWA-0.7.15-GCCcore-5.4.0.eb @@ -23,4 +23,6 @@ toolchainopts = {'pic': True} sources = ['v%(version)s.tar.gz'] source_urls = ['https://github.com/lh3/%(name)s/archive/'] +builddependencies = [('binutils', '2.26')] + moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2-GCCcore-5.4.0.eb b/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2-GCCcore-5.4.0.eb index f12c5655a0..75231c322f 100644 --- a/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2-GCCcore-5.4.0.eb @@ -15,4 +15,6 @@ toolchainopts = {'pic': True} sources = ['%(namelower)s-%(version)s-src.zip'] source_urls = ['http://download.sourceforge.net/bowtie-bio/'] +builddependencies = [('binutils', '2.26')] + moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2-GCCcore-6.3.0.eb b/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2-GCCcore-6.3.0.eb index ffaca077d2..feb579d4dc 100644 --- a/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2-GCCcore-6.3.0.eb @@ -16,4 +16,6 @@ sources = ['%(namelower)s-%(version)s-src.zip'] source_urls = ['http://download.sourceforge.net/bowtie-bio/'] checksums = ['b1e9ccc825207efd1893d9e33244c681bcb89b9b2b811eb95a9f5a92eab637ae'] +builddependencies = [('binutils', '2.27')] + moduleclass = 'bio' diff --git a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-GCCcore-5.4.0.eb b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-GCCcore-5.4.0.eb index f55dbe8583..7bf2a381a2 100644 --- a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-GCCcore-5.4.0.eb @@ -11,6 +11,7 @@ sources = ['%(namelower)s-%(version)s.src.tar.gz'] source_urls = ['http://ftp.stack.nl/pub/users/dimitri/'] builddependencies = [ + ('binutils', '2.26'), ('CMake', '3.7.1'), ('flex', '2.6.0'), ('Bison', '3.0.4'), diff --git a/easybuild/easyconfigs/g/gSOAP/gSOAP-2.8.48-GCCcore-6.3.0.eb b/easybuild/easyconfigs/g/gSOAP/gSOAP-2.8.48-GCCcore-6.3.0.eb index 1d8dbc1f53..4e022733f1 100644 --- a/easybuild/easyconfigs/g/gSOAP/gSOAP-2.8.48-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/g/gSOAP/gSOAP-2.8.48-GCCcore-6.3.0.eb @@ -19,6 +19,7 @@ sources = ['%(namelower)s_%(version)s.zip'] source_urls = ['https://downloads.sourceforge.net/project/gsoap%(version_major)s/gsoap-%(version_major_minor)s/'] builddependencies = [ + ('binutils', '2.27'), ('Bison', '3.0.4'), ('flex', '2.6.3'), ] diff --git a/easybuild/easyconfigs/g/gzip/gzip-1.8-GCCcore-6.4.0.eb b/easybuild/easyconfigs/g/gzip/gzip-1.8-GCCcore-6.4.0.eb index fcd38e2364..c58749ad07 100644 --- a/easybuild/easyconfigs/g/gzip/gzip-1.8-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/g/gzip/gzip-1.8-GCCcore-6.4.0.eb @@ -16,6 +16,8 @@ source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['1ff7aedb3d66a0d73f442f6261e4b3860df6fd6c94025c2cb31a202c9c60fe0e'] +builddependencies = [('binutils', '2.28')] + sanity_check_paths = { 'files': ["bin/gunzip", "bin/gzip", "bin/uncompress"], 'dirs': [], diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.24.0-GCCcore-4.9.3.eb b/easybuild/easyconfigs/p/Perl/Perl-5.24.0-GCCcore-4.9.3.eb index 62d5ecc186..e6b26a5332 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.24.0-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.24.0-GCCcore-4.9.3.eb @@ -10,7 +10,7 @@ toolchainopts = {'pic': True} source_urls = ['http://www.cpan.org/src/%(version_major)s.0'] sources = [SOURCELOWER_TAR_GZ] -dependencies = [('binutils', '2.25')] +builddependencies = [('binutils', '2.25')] exts_list = [ ('Config::General', '2.61', { diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 2dac08069f..7b45707a18 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -249,6 +249,17 @@ def template_easyconfig_test(self, spec): for old_url in old_urls: self.assertFalse(old_url in ec.rawtxt, "Old URL '%s' not found in %s" % (old_url, spec)) + # make sure binutils is included as a build dep if toolchain is GCCcore + if ec['toolchain']['name'] == 'GCCcore': + # with 'Tarball' easyblock: only unpacking, no building; Eigen is also just a tarball + requires_binutils = ec['easyblock'] not in ['Tarball'] and ec['name'] not in ['Eigen'] + # if no sources/extensions/components are specified, it's just a bundle (nothing is being compiled) + requires_binutils &= bool(ec['sources'] or ec['exts_list'] or ec.get('components')) + + if requires_binutils: + dep_names = [d['name'] for d in ec['builddependencies']] + self.assertTrue('binutils' in dep_names, "binutils is a build dep in %s: %s" % (spec, dep_names)) + # make sure all patch files are available specdir = os.path.dirname(spec) specfn = os.path.basename(spec) -- GitLab From 4c4e7e1e5e7b28d4bd6224fc017d4db1744503b9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 31 Aug 2017 21:44:27 +0200 Subject: [PATCH 1475/1603] bump version & fix source URL for ROOT, add checksums for ROOT & CFITSIO --- .../c/CFITSIO/CFITSIO-3.41-GCCcore-6.3.0.eb | 1 + ...13.eb => ROOT-6.10.04-intel-2017a-Python-2.7.13.eb} | 10 ++++++++-- 2 files changed, 9 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/r/ROOT/{ROOT-6.06.02-intel-2017a-Python-2.7.13.eb => ROOT-6.10.04-intel-2017a-Python-2.7.13.eb} (81%) diff --git a/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.41-GCCcore-6.3.0.eb b/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.41-GCCcore-6.3.0.eb index b66d494bcc..76eae3e43e 100644 --- a/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.41-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.41-GCCcore-6.3.0.eb @@ -13,6 +13,7 @@ toolchainopts = {'pic': True} srcversion = '%s0' % version.replace('.', '') source_urls = ['http://heasarc.gsfc.nasa.gov/FTP/software/fitsio/c/'] sources = ['%%(namelower)s%s.tar.gz' % srcversion] +checksums = ['a556ac7ea1965545dcb4d41cfef8e4915eeb8c0faa1b52f7ff70870f8bb5734c'] builddependencies = [('binutils', '2.27')] diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-6.06.02-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/r/ROOT/ROOT-6.10.04-intel-2017a-Python-2.7.13.eb similarity index 81% rename from easybuild/easyconfigs/r/ROOT/ROOT-6.06.02-intel-2017a-Python-2.7.13.eb rename to easybuild/easyconfigs/r/ROOT/ROOT-6.10.04-intel-2017a-Python-2.7.13.eb index b1f9dab124..6294637101 100644 --- a/easybuild/easyconfigs/r/ROOT/ROOT-6.06.02-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/r/ROOT/ROOT-6.10.04-intel-2017a-Python-2.7.13.eb @@ -1,5 +1,5 @@ name = 'ROOT' -version = '6.06.02' +version = '6.10.04' versionsuffix = '-Python-%(pyver)s' homepage = 'http://root.cern.ch/drupal/' @@ -9,13 +9,19 @@ description = """The ROOT system provides a set of OO frameworks with all the fu toolchain = {'name': 'intel', 'version': '2017a'} toolchainopts = {'pic': True} +source_urls = ['https://root.cern.ch/download/'] sources = ['%(namelower)s_v%(version)s.source.tar.gz'] -source_urls = ['ftp://root.cern.ch/root/'] patches = [ 'configure_FftwFromMkl_28.patch', 'ROOT-v5_recent-ifort.patch', 'ROOT-v5.34.26_libX.patch', ] +checksums = [ + '461bde21d78608422310f04c599e84ce8dfbdd91caf12c2a54db6c01f8228f5b', # root_v6.10.04.source.tar.gz + '064eeb2a39dc8c96ba707f2a2bfd591c892f64e47e54df2d7d57f5f87a998a48', # configure_FftwFromMkl_28.patch + '54477336c6453e46ba18b465a61c181107943c47816b0744626ba147ad5df1c2', # ROOT-v5_recent-ifort.patch + 'f97179b55bf862d884aba037eef12eed00829fb13f303c464d974331801cc2df', # ROOT-v5.34.26_libX.patch +] dependencies = [ ('GSL', '2.3'), -- GitLab From 47e8084c8214aa3e0fcd9028b7833d499be43f0b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 31 Aug 2017 21:46:38 +0200 Subject: [PATCH 1476/1603] add missing checksums --- .../g/gettext/gettext-0.19.8.1-GCCcore-6.4.0.eb | 3 ++- .../easyconfigs/l/libxml2/libxml2-2.9.4-GCCcore-6.4.0.eb | 1 + easybuild/easyconfigs/x/XZ/XZ-5.2.3-GCCcore-6.4.0.eb | 7 +++++-- 3 files changed, 8 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.8.1-GCCcore-6.4.0.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.8.1-GCCcore-6.4.0.eb index 3c9be38c7f..33c63f6e34 100644 --- a/easybuild/easyconfigs/g/gettext/gettext-0.19.8.1-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.8.1-GCCcore-6.4.0.eb @@ -10,8 +10,9 @@ and documentation""" toolchain = {'name': 'GCCcore', 'version': '6.4.0'} -sources = [SOURCE_TAR_GZ] source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['ff942af0e438ced4a8b0ea4b0b6e0d6d657157c5e2364de57baa279c1c125c43'] dependencies = [ ('libxml2', '2.9.4'), diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-GCCcore-6.4.0.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-GCCcore-6.4.0.eb index 3672386817..da9c497548 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-GCCcore-6.4.0.eb @@ -14,6 +14,7 @@ source_urls = [ 'http://xmlsoft.org/sources/old/' ] sources = [SOURCELOWER_TAR_GZ] +checksums = ['ffb911191e509b966deb55de705387f14156e1a56b21824357cdf0053233633c'] dependencies = [ ('zlib', '1.2.11'), diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.3-GCCcore-6.4.0.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.3-GCCcore-6.4.0.eb index 276a5fb2d6..c02558f16a 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.3-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.3-GCCcore-6.4.0.eb @@ -8,10 +8,13 @@ description = "xz: XZ utilities" toolchain = {'name': 'GCCcore', 'version': '6.4.0'} -sources = [SOURCELOWER_TAR_BZ2] source_urls = ['http://tukaani.org/xz/'] - +sources = [SOURCELOWER_TAR_BZ2] patches = ['XZ-5.2.2_compat-libs.patch'] +checksums = [ + 'fd9ca16de1052aac899ad3495ad20dfa906c27b4a5070102a2ec35ca3a4740c1', # xz-5.2.3.tar.bz2 + '578da3ea2ddb551972891a60fe31478b16a516d6ea8b6aa3af89e1d558adb703', # XZ-5.2.2_compat-libs.patch +] builddependencies = [ # use gettext built with dummy as build dep to avoid cyclic dependency (XZ -> gettext -> libxml2 -> XZ) -- GitLab From 7ae484f03ca743bf96b245ba30f8a98ee659d91f Mon Sep 17 00:00:00 2001 From: iotaka Date: Fri, 1 Sep 2017 09:15:54 +0200 Subject: [PATCH 1477/1603] Update CGNS-3.3.1-foss-2016b.eb --- easybuild/easyconfigs/c/CGNS/CGNS-3.3.1-foss-2016b.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/c/CGNS/CGNS-3.3.1-foss-2016b.eb b/easybuild/easyconfigs/c/CGNS/CGNS-3.3.1-foss-2016b.eb index 5e9f2fac97..9ee315a082 100644 --- a/easybuild/easyconfigs/c/CGNS/CGNS-3.3.1-foss-2016b.eb +++ b/easybuild/easyconfigs/c/CGNS/CGNS-3.3.1-foss-2016b.eb @@ -25,7 +25,7 @@ builddependencies = [ moduleclass = 'cae' sanity_check_paths = { - 'files': ["bin/%s" % x for x in ["cgnscheck", "cgnscompress", "cgnsconvert", "cgnsdiff", - "cgnslist, "cgnsnames", "cgnsupdate"], "lib/libcgns.so", "include/cgnslib.h" ], + 'files': ["bin/%s" % x for x in ["cgnscheck", "cgnscompress", "cgnsconvert", "cgnsdiff", + "cgnslist", "cgnsnames", "cgnsupdate"]], 'dirs': [], } -- GitLab From 34d414f80843b0f68b5d2c75dd0c559c312c4caf Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 1 Sep 2017 10:19:19 +0200 Subject: [PATCH 1478/1603] adding easyconfigs: Perl-5.26.0-intel-2017a.eb --- .../p/Perl/Perl-5.26.0-intel-2017a.eb | 1596 +++++++++++++++++ 1 file changed, 1596 insertions(+) create mode 100644 easybuild/easyconfigs/p/Perl/Perl-5.26.0-intel-2017a.eb diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.26.0-intel-2017a.eb b/easybuild/easyconfigs/p/Perl/Perl-5.26.0-intel-2017a.eb new file mode 100644 index 0000000000..51fdb404df --- /dev/null +++ b/easybuild/easyconfigs/p/Perl/Perl-5.26.0-intel-2017a.eb @@ -0,0 +1,1596 @@ +name = 'Perl' +version = '5.26.0' + +homepage = 'https://www.perl.org/' +description = """Larry Wall's Practical Extraction and Report Language""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.cpan.org/src/%(version_major)s.0'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['ebe7c66906d4fb55449380ab1b7e004eeef52c38d3443fa301f8e17a1a4cb67f'] + +# !! order of extensions is important !! +# extensions updated on August 29th 2017 +exts_list = [ + ('Config::General', '2.63', { + 'source_tmpl': 'Config-General-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TL/TLINDEN'], + 'checksums': [ + '0a9bf977b8aabe76343e88095d2296c8a422410fd2a05a1901f2b20e2e1f6fad', # Config-General-2.63.tar.gz + ], + }), + ('File::Listing', '6.04', { + 'source_tmpl': 'File-Listing-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + 'checksums': [ + '1e0050fcd6789a2179ec0db282bf1e90fb92be35d1171588bd9c47d52d959cf5', # File-Listing-6.04.tar.gz + ], + }), + ('ExtUtils::InstallPaths', '0.011', { + 'source_tmpl': 'ExtUtils-InstallPaths-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': [ + '7609fa048cdcf1451cad5b1d7d494f30e3d5bad0672d15404f1ea60e1df0067c', # ExtUtils-InstallPaths-0.011.tar.gz + ], + }), + ('ExtUtils::Helpers', '0.026', { + 'source_tmpl': 'ExtUtils-Helpers-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': [ + 'de901b6790a4557cf4ec908149e035783b125bf115eb9640feb1bc1c24c33416', # ExtUtils-Helpers-0.026.tar.gz + ], + }), + ('Test::Harness', '3.39', { + 'source_tmpl': 'Test-Harness-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': [ + '69bd44c81c6e1d2db18e298ecf631852608893ddfddb332a7d55285bbfc51132', # Test-Harness-3.39.tar.gz + ], + }), + ('ExtUtils::Config', '0.008', { + 'source_tmpl': 'ExtUtils-Config-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': [ + 'ae5104f634650dce8a79b7ed13fb59d67a39c213a6776cfdaa3ee749e62f1a8c', # ExtUtils-Config-0.008.tar.gz + ], + }), + ('Module::Build::Tiny', '0.039', { + 'source_tmpl': 'Module-Build-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': [ + '7d580ff6ace0cbe555bf36b86dc8ea232581530cbeaaea09bccb57b55797f11c', # Module-Build-Tiny-0.039.tar.gz + ], + }), + ('aliased', '0.34', { + 'source_tmpl': 'aliased-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': [ + 'c350524507cd827fab864e5d4c2cc350b1babaa12fa95aec0ca00843fcc7deeb', # aliased-0.34.tar.gz + ], + }), + ('Text::Glob', '0.11', { + 'source_tmpl': 'Text-Glob-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RC/RCLAMP'], + 'checksums': [ + '069ccd49d3f0a2dedb115f4bdc9fbac07a83592840953d1fcdfc39eb9d305287', # Text-Glob-0.11.tar.gz + ], + }), + ('Regexp::Common', '2017060201', { + 'source_tmpl': 'Regexp-Common-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AB/ABIGAIL'], + 'checksums': [ + 'ee07853aee06f310e040b6bf1a0199a18d81896d3219b9b35c9630d0eb69089b', # Regexp-Common-2017060201.tar.gz + ], + }), + ('GO::Utils', '0.15', { + 'source_tmpl': 'go-perl-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CM/CMUNGALL'], + 'checksums': [ + '423d26155ee85ca51ab2270cee59f4e85b193e57ac3a29aff827298c0a396b12', # go-perl-0.15.tar.gz + ], + }), + ('Module::Pluggable', '5.2', { + 'source_tmpl': 'Module-Pluggable-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SI/SIMONW'], + 'checksums': [ + 'b3f2ad45e4fd10b3fb90d912d78d8b795ab295480db56dc64e86b9fa75c5a6df', # Module-Pluggable-5.2.tar.gz + ], + }), + ('Test::Fatal', '0.014', { + 'source_tmpl': 'Test-Fatal-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': [ + 'bcdcef5c7b2790a187ebca810b0a08221a63256062cfab3c3b98685d91d1cbb0', # Test-Fatal-0.014.tar.gz + ], + }), + ('Test::Warnings', '0.026', { + 'source_tmpl': 'Test-Warnings-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': [ + 'ae2b68b1b5616704598ce07f5118efe42dc4605834453b7b2be14e26f9cc9a08', # Test-Warnings-0.026.tar.gz + ], + }), + ('File::ShareDir::Install', '0.11', { + 'source_tmpl': 'File-ShareDir-Install-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': [ + '32bf8772e9fea60866074b27ff31ab5bc3f88972d61915e84cbbb98455e00cc8', # File-ShareDir-Install-0.11.tar.gz + ], + }), + ('DateTime::Locale', '1.16', { + 'source_tmpl': 'DateTime-Locale-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + 'checksums': [ + 'dfaf4c42149c0622e80721773b8d7229d7785280503585895c9fe9f51e076cfe', # DateTime-Locale-1.16.tar.gz + ], + }), + ('DateTime::TimeZone', '2.13', { + 'source_tmpl': 'DateTime-TimeZone-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + 'checksums': [ + '333d39ccd6b883460409b9113bec43be256c3e763beedfb97b9eb274c9d4e18c', # DateTime-TimeZone-2.13.tar.gz + ], + }), + ('Test::Requires', '0.10', { + 'source_tmpl': 'Test-Requires-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TOKUHIROM'], + 'checksums': [ + '2768a391d50ab94b95cefe540b9232d7046c13ee86d01859e04c044903222eb5', # Test-Requires-0.10.tar.gz + ], + }), + ('Module::Implementation', '0.09', { + 'source_tmpl': 'Module-Implementation-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + 'checksums': [ + 'c15f1a12f0c2130c9efff3c2e1afe5887b08ccd033bd132186d1e7d5087fd66d', # Module-Implementation-0.09.tar.gz + ], + }), + ('Module::Build', '0.4224', { + 'source_tmpl': 'Module-Build-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': [ + 'a6ca15d78244a7b50fdbf27f85c85f4035aa799ce7dd018a0d98b358ef7bc782', # Module-Build-0.4224.tar.gz + ], + }), + ('Module::Runtime', '0.015', { + 'source_tmpl': 'Module-Runtime-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/Z/ZE/ZEFRAM'], + 'checksums': [ + '67fcfaf4e33072924975675da9004bacc43fff9f61396135b93627cbe38e43c0', # Module-Runtime-0.015.tar.gz + ], + }), + ('Try::Tiny', '0.28', { + 'source_tmpl': 'Try-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': [ + 'f1d166be8aa19942c4504c9111dade7aacb981bc5b3a2a5c5f6019646db8c146', # Try-Tiny-0.28.tar.gz + ], + }), + ('Params::Validate', '1.29', { + 'source_tmpl': 'Params-Validate-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + 'checksums': [ + '49a68dfb430bea028042479111d19068e08095e5a467e320b7ab7bde3d729733', # Params-Validate-1.29.tar.gz + ], + }), + ('List::MoreUtils', '0.423', { + 'source_tmpl': 'List-MoreUtils-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + 'checksums': [ + 'b4d90b24809b399fda3772a45b1af9e29d89becf8ba4a4f78fa36234e4ed5396', # List-MoreUtils-0.423.tar.gz + ], + }), + ('Exporter::Tiny', '1.000000', { + 'source_tmpl': 'Exporter-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TOBYINK'], + 'checksums': [ + 'ffdd77d57de099e8f64dd942ef12a00a3f4313c2531f342339eeed2d366ad078', # Exporter-Tiny-1.000000.tar.gz + ], + }), + ('Class::Singleton', '1.5', { + 'source_tmpl': 'Class-Singleton-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHAY'], + 'checksums': [ + '38220d04f02e3a803193c2575a1644cce0b95ad4b95c19eb932b94e2647ef678', # Class-Singleton-1.5.tar.gz + ], + }), + ('DateTime', '1.44', { + 'source_tmpl': 'DateTime-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + 'checksums': [ + 'a7165a9b1bcef735e76ea44c184ea741840249dd1862b8465f3777cd8f0bd701', # DateTime-1.44.tar.gz + ], + }), + ('File::Find::Rule::Perl', '1.15', { + 'source_tmpl': 'File-Find-Rule-Perl-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': [ + '9a48433f86e08ce18e03526e2982de52162eb909d19735460f07eefcaf463ea6', # File-Find-Rule-Perl-1.15.tar.gz + ], + }), + ('Readonly', '2.05', { + 'source_tmpl': 'Readonly-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SA/SANKO'], + 'checksums': [ + '4b23542491af010d44a5c7c861244738acc74ababae6b8838d354dfb19462b5e', # Readonly-2.05.tar.gz + ], + }), + ('Git', '0.41', { + 'source_tmpl': 'Git-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MS/MSOUTH'], + 'checksums': [ + '9d4de21612253a1d3252ff7657d7e832dcf3cc2a748a8c84f73de618a3a38239', # Git-0.41.tar.gz + ], + }), + ('Tree::DAG_Node', '1.29', { + 'source_tmpl': 'Tree-DAG_Node-%(version)s.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + 'checksums': [ + '2d04eb011aa06cee633c367d1f322b8d937020fde5d5393fad6a26c93725c4a8', # Tree-DAG_Node-1.29.tgz + ], + }), + ('Template', '2.27', { + 'source_tmpl': 'Template-Toolkit-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AB/ABW'], + 'checksums': [ + '1311a403264d0134c585af0309ff2a9d5074b8ece23ece5660d31ec96bf2c6dc', # Template-Toolkit-2.27.tar.gz + ], + }), + ('FreezeThaw', '0.5001', { + 'source_tmpl': 'FreezeThaw-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IL/ILYAZ/modules'], + 'checksums': [ + '3c5e08329106f9cee3ab444b81331c5935f83084a151d88505e7a465da540f41', # FreezeThaw-0.5001.tar.gz + ], + }), + ('DBI', '1.637', { + 'source_tmpl': 'DBI-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TI/TIMB'], + 'checksums': [ + '2557712593e80142c3b50877e00369b6ce78fa26d44edc42156d81a5cdd26bc6', # DBI-1.637.tar.gz + ], + }), + ('DBD::SQLite', '1.54', { + 'source_tmpl': 'DBD-SQLite-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IS/ISHIGAKI'], + 'checksums': [ + '3929a6dbd8d71630f0cb57f85dcef9588cd7ac4c9fa12db79df77b9d3a4d7269', # DBD-SQLite-1.54.tar.gz + ], + }), + ('Math::Bezier', '0.01', { + 'source_tmpl': 'Math-Bezier-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AB/ABW'], + 'checksums': [ + '11a815fc45fdf0efabb1822ab77faad8b9eea162572c5f0940c8ed7d56e6b8b8', # Math-Bezier-0.01.tar.gz + ], + }), + ('Archive::Extract', '0.80', { + 'source_tmpl': 'Archive-Extract-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + 'checksums': [ + '25cbc2d5626c14d39a0b5e4fe8383941e085c9a7e0aa873d86e81b6e709025f4', # Archive-Extract-0.80.tar.gz + ], + }), + ('DBIx::Simple', '1.35', { + 'source_tmpl': 'DBIx-Simple-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JU/JUERD'], + 'checksums': [ + '445535b3dfab88140c7a0d2776b1e78f254dc7e9c81072d5a01afc95a5db499a', # DBIx-Simple-1.35.tar.gz + ], + }), + ('Shell', '0.73', { + 'source_tmpl': 'Shell-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/F/FE/FERREIRA'], + 'checksums': [ + 'f7dbebf65261ed0e5abd0f57052b64d665a1a830bab4c8bbc220f235bd39caf5', # Shell-0.73.tar.gz + ], + }), + ('File::Spec', '3.62', { + 'source_tmpl': 'PathTools-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': [ + '36350e12f58871437ba03391f80a506e447e3c6630cc37d0625bc25ff1c7b4d2', # PathTools-3.62.tar.gz + ], + }), + ('Test::Simple', '1.302086', { + 'source_tmpl': 'Test-Simple-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + 'checksums': [ + '21e4c93c52529a10ef970afcf2cdb5719bcfef5f71af09cad3675fcf021995b1', # Test-Simple-1.302086.tar.gz + ], + }), + ('Set::Scalar', '1.29', { + 'source_tmpl': 'Set-Scalar-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAVIDO'], + 'checksums': [ + 'a3dc1526f3dde72d3c64ea00007b86ce608cdcd93567cf6e6e42dc10fdc4511d', # Set-Scalar-1.29.tar.gz + ], + }), + ('IO::Stringy', '2.111', { + 'source_tmpl': 'IO-stringy-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DS/DSKOLL'], + 'checksums': [ + '8c67fd6608c3c4e74f7324f1404a856c331dbf48d9deda6aaa8296ea41bf199d', # IO-stringy-2.111.tar.gz + ], + }), + ('Encode::Locale', '1.05', { + 'source_tmpl': 'Encode-Locale-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + 'checksums': [ + '176fa02771f542a4efb1dbc2a4c928e8f4391bf4078473bd6040d8f11adb0ec1', # Encode-Locale-1.05.tar.gz + ], + }), + ('XML::SAX::Base', '1.09', { + 'source_tmpl': 'XML-SAX-Base-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GR/GRANTM'], + 'checksums': [ + '66cb355ba4ef47c10ca738bd35999723644386ac853abbeb5132841f5e8a2ad0', # XML-SAX-Base-1.09.tar.gz + ], + }), + ('XML::NamespaceSupport', '1.12', { + 'source_tmpl': 'XML-NamespaceSupport-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PERIGRIN'], + 'checksums': [ + '47e995859f8dd0413aa3f22d350c4a62da652e854267aa0586ae544ae2bae5ef', # XML-NamespaceSupport-1.12.tar.gz + ], + }), + ('XML::SAX', '0.99', { + 'source_tmpl': 'XML-SAX-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GR/GRANTM'], + 'checksums': [ + '32b04b8e36b6cc4cfc486de2d859d87af5386dd930f2383c49347050d6f5ad84', # XML-SAX-0.99.tar.gz + ], + }), + ('Test::LeakTrace', '0.16', { + 'source_tmpl': 'Test-LeakTrace-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEEJO'], + 'checksums': [ + '5f089eed915f1ec8c743f6d2777c3ecd0ca01df2f7b9e10038d316952583e403', # Test-LeakTrace-0.16.tar.gz + ], + }), + ('Test::Exception', '0.43', { + 'source_tmpl': 'Test-Exception-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + 'checksums': [ + '156b13f07764f766d8b45a43728f2439af81a3512625438deab783b7883eb533', # Test-Exception-0.43.tar.gz + ], + }), + ('Text::Table', '1.133', { + 'source_tmpl': 'Text-Table-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'], + 'checksums': [ + 'cd9ee04860d09a19a9d6bd2254a4bf3144ac14a63c08f15a1e28601b4b2f7012', # Text-Table-1.133.tar.gz + ], + }), + ('MIME::Types', '2.13', { + 'source_tmpl': 'MIME-Types-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARKOV'], + 'checksums': [ + '99c3376357bbe22cc8b6c78f560aa18d81621287695cd629008a6c4e66b77bf8', # MIME-Types-2.13.tar.gz + ], + }), + ('Module::Build::XSUtil', '0.16', { + 'source_tmpl': 'Module-Build-XSUtil-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HI/HIDEAKIO'], + 'checksums': [ + '15762fa4e43b41302cff261c7ad75aacdc874f416981f206d783f20acd023adb', # Module-Build-XSUtil-0.16.tar.gz + ], + }), + ('Tie::Function', '0.02', { + 'source_tmpl': 'Tie-Function-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAVIDNICO/handy_tied_functions'], + 'checksums': [ + '0b1617af218dfab911ba0fbd72210529a246efe140332da77fe3e03d11000117', # Tie-Function-0.02.tar.gz + ], + }), + ('Template::Plugin::Number::Format', '1.06', { + 'source_tmpl': 'Template-Plugin-Number-Format-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DARREN'], + 'checksums': [ + '0865836a1bcbc34d4a0ee34b5ccc14d7b511f1fd300bf390f002dac349539843', # Template-Plugin-Number-Format-1.06.tar.gz + ], + }), + ('HTML::Parser', '3.72', { + 'source_tmpl': 'HTML-Parser-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + 'checksums': [ + 'ec28c7e1d9e67c45eca197077f7cdc41ead1bb4c538c7f02a3296a4bb92f608b', # HTML-Parser-3.72.tar.gz + ], + }), + ('Date::Handler', '1.2', { + 'source_tmpl': 'Date-Handler-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BB/BBEAUSEJ'], + 'checksums': [ + 'c36fd2b68d48c2e17417bf2873c78820f3ae02460fdf5976b8eeab887d59e16c', # Date-Handler-1.2.tar.gz + ], + }), + ('Params::Util', '1.07', { + 'source_tmpl': 'Params-Util-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + 'checksums': [ + '30f1ec3f2cf9ff66ae96f973333f23c5f558915bb6266881eac7423f52d7c76c', # Params-Util-1.07.tar.gz + ], + }), + ('IO::HTML', '1.001', { + 'source_tmpl': 'IO-HTML-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CJ/CJM'], + 'checksums': [ + 'ea78d2d743794adc028bc9589538eb867174b4e165d7d8b5f63486e6b828e7e0', # IO-HTML-1.001.tar.gz + ], + }), + ('Data::Grove', '0.08', { + 'source_tmpl': 'libxml-perl-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KM/KMACLEOD'], + 'checksums': [ + '4571059b7b5d48b7ce52b01389e95d798bf5cf2020523c153ff27b498153c9cb', # libxml-perl-0.08.tar.gz + ], + }), + ('Class::ISA', '0.36', { + 'source_tmpl': 'Class-ISA-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SM/SMUELLER'], + 'checksums': [ + '8816f34e9a38e849a10df756030dccf9fe061a196c11ac3faafd7113c929b964', # Class-ISA-0.36.tar.gz + ], + }), + ('URI', '1.72', { + 'source_tmpl': 'URI-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': [ + '35f14431d4b300de4be1163b0b5332de2d7fbda4f05ff1ed198a8e9330d40a32', # URI-1.72.tar.gz + ], + }), + ('Ima::DBI', '0.35', { + 'source_tmpl': 'Ima-DBI-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PERRIN'], + 'checksums': [ + '8b481ceedbf0ae4a83effb80581550008bfdd3885ef01145e3733c7097c00a08', # Ima-DBI-0.35.tar.gz + ], + }), + ('Tie::IxHash', '1.23', { + 'source_tmpl': 'Tie-IxHash-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CH/CHORNY'], + 'checksums': [ + 'fabb0b8c97e67c9b34b6cc18ed66f6c5e01c55b257dcf007555e0b027d4caf56', # Tie-IxHash-1.23.tar.gz + ], + }), + ('GO', '0.04', { + 'source_tmpl': 'go-db-perl-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SJ/SJCARBON'], + 'checksums': [ + '8eb73d591ad767e7cf26def40cffd84833875f1ad51e456960b9ed73dc23641b', # go-db-perl-0.04.tar.gz + ], + }), + ('Class::DBI::SQLite', '0.11', { + 'source_tmpl': 'Class-DBI-SQLite-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA'], + 'checksums': [ + 'c4661b00afb7e53c97ac36e13f34dde43c1a93540a2f4ff97e6182b0c731e4e7', # Class-DBI-SQLite-0.11.tar.gz + ], + }), + ('Pod::POM', '2.01', { + 'source_tmpl': 'Pod-POM-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB'], + 'checksums': [ + '1b50fba9bbdde3ead192beeba0eaddd0c614e3afb1743fa6fff805f57c56f7f4', # Pod-POM-2.01.tar.gz + ], + }), + ('Math::Round', '0.07', { + 'source_tmpl': 'Math-Round-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GR/GROMMEL'], + 'checksums': [ + '73a7329a86e54a5c29a440382e5803095b58f33129e61a1df0093b4824de9327', # Math-Round-0.07.tar.gz + ], + }), + ('Text::Diff', '1.45', { + 'source_tmpl': 'Text-Diff-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB'], + 'checksums': [ + 'e8baa07b1b3f53e00af3636898bbf73aec9a0ff38f94536ede1dbe96ef086f04', # Text-Diff-1.45.tar.gz + ], + }), + ('Log::Message::Simple', '0.10', { + 'source_tmpl': 'Log-Message-Simple-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + 'checksums': [ + 'aa12d1a4c0ac260b94d448fa01feba242a8a85cb6cbfdc66432e3b5b468add96', # Log-Message-Simple-0.10.tar.gz + ], + }), + ('IO::Socket::SSL', '2.050', { + 'source_tmpl': 'IO-Socket-SSL-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SU/SULLR'], + 'checksums': [ + '54e6716e40df8b1c168d8f54a0b8f215313739bd99dda17adb7c00fe94656692', # IO-Socket-SSL-2.050.tar.gz + ], + }), + ('Fennec::Lite', '0.004', { + 'source_tmpl': 'Fennec-Lite-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + 'checksums': [ + 'dce28e3932762c2ff92aa52d90405c06e898e81cb7b164ccae8966ae77f1dcab', # Fennec-Lite-0.004.tar.gz + ], + }), + ('Sub::Uplevel', '0.2800', { + 'source_tmpl': 'Sub-Uplevel-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + 'checksums': [ + 'b4f3f63b80f680a421332d8851ddbe5a8e72fcaa74d5d1d98f3c8cc4a3ece293', # Sub-Uplevel-0.2800.tar.gz + ], + }), + ('Meta::Builder', '0.003', { + 'source_tmpl': 'Meta-Builder-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + 'checksums': [ + 'e7ac289b88d1662e87708d716877ac66a1a8414660996fe58c1db96d834a5375', # Meta-Builder-0.003.tar.gz + ], + }), + ('Exporter::Declare', '0.114', { + 'source_tmpl': 'Exporter-Declare-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + 'checksums': [ + '4bd70d6ca76f6f6ba7e4c618d4ac93b8593a58f1233ccbe18b10f5f204f1d4e4', # Exporter-Declare-0.114.tar.gz + ], + }), + ('Getopt::Long', '2.50', { + 'source_tmpl': 'Getopt-Long-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JV/JV'], + 'checksums': [ + '20881adb2b73e83825f9a0a3b141db11b3a555e1d3775b13d81d0481623e4b67', # Getopt-Long-2.50.tar.gz + ], + }), + ('Log::Message', '0.08', { + 'source_tmpl': 'Log-Message-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + 'checksums': [ + 'bd697dd62aaf26d118e9f0a0813429deb1c544e4501559879b61fcbdfe99fe46', # Log-Message-0.08.tar.gz + ], + }), + ('Mouse', 'v2.4.10', { + 'source_tmpl': 'Mouse-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GF/GFUJI'], + 'checksums': [ + 'b995dda1918fcebecff34458b6abd16c06b6a7844572c7293d72a24d18126d14', # Mouse-v2.4.10.tar.gz + ], + }), + ('Test::Version', '2.05', { + 'source_tmpl': 'Test-Version-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE'], + 'checksums': [ + '39c0ec02663da0e56962bdafaef6790cf83d12b4d90e8a4cdc971d57d869d63f', # Test-Version-2.05.tar.gz + ], + }), + ('DBIx::Admin::TableInfo', '3.03', { + 'source_tmpl': 'DBIx-Admin-TableInfo-%(version)s.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + 'checksums': [ + 'a852530f95957a43aa794f2edf5f3fe4ecec35bd20150c38136d4c23d85328b6', # DBIx-Admin-TableInfo-3.03.tgz + ], + }), + ('Net::HTTP', '6.16', { + 'source_tmpl': 'Net-HTTP-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'], + 'checksums': [ + '70c45b6aaf3e9fb1ce30a1fc3cf828cfaee45c5c0bd147b2f617efade1765e78', # Net-HTTP-6.16.tar.gz + ], + }), + ('Test::Deep', '1.127', { + 'source_tmpl': 'Test-Deep-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': [ + 'b78cfc59c41ba91f47281e2c1d2bfc4b3b1b42bfb76b4378bc88cc37b7af7268', # Test-Deep-1.127.tar.gz + ], + }), + ('Test::Warn', '0.32', { + 'source_tmpl': 'Test-Warn-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BIGJ'], + 'checksums': [ + '2fc516e71f9ef453be22a4619d91eb3f78df414a57dfa0fd745d3bff50bf73d2', # Test-Warn-0.32.tar.gz + ], + }), + ('MRO::Compat', '0.13', { + 'source_tmpl': 'MRO-Compat-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + 'checksums': [ + '8a2c3b6ccc19328d5579d02a7d91285e2afd85d801f49d423a8eb16f323da4f8', # MRO-Compat-0.13.tar.gz + ], + }), + ('Moo', '2.003002', { + 'source_tmpl': 'Moo-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + 'checksums': [ + 'f3e9741e79baa63e89f5a08706cd80d18c0a5a37e3d898847e002310e06582f1', # Moo-2.003002.tar.gz + ], + }), + ('Hash::Merge', '0.200', { + 'source_tmpl': 'Hash-Merge-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + 'checksums': [ + '47f9f03330b7595c94e73bdd17dc6682ba59d1cc89e63f4e319617f4bb122a64', # Hash-Merge-0.200.tar.gz + ], + }), + ('SQL::Abstract', '1.84', { + 'source_tmpl': 'SQL-Abstract-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IL/ILMARI'], + 'checksums': [ + '655f4aa3d4ea7ca0a7bafb2beff84010d5c77f0ee4413baa0c86456bf6db5e75', # SQL-Abstract-1.84.tar.gz + ], + }), + ('HTML::Form', '6.03', { + 'source_tmpl': 'HTML-Form-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + 'checksums': [ + '68c01d94f005d5ca9c4d55ad2a1bf3a8d034a5fc6db187d91a4c42f3fdc9fc36', # HTML-Form-6.03.tar.gz + ], + }), + ('File::Copy::Recursive', '0.38', { + 'source_tmpl': 'File-Copy-Recursive-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DM/DMUEY'], + 'checksums': [ + '84ccbddf3894a88a2c2b6be68ff6ef8960037803bb36aa228b31944cfdf6deeb', # File-Copy-Recursive-0.38.tar.gz + ], + }), + ('Number::Compare', '0.03', { + 'source_tmpl': 'Number-Compare-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RC/RCLAMP'], + 'checksums': [ + '83293737e803b43112830443fb5208ec5208a2e6ea512ed54ef8e4dd2b880827', # Number-Compare-0.03.tar.gz + ], + }), + ('IPC::Run', '0.96', { + 'source_tmpl': 'IPC-Run-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR'], + 'checksums': [ + 'bbd24ff027e1c232b3dc027562c9f4386da72b76991d30f9f3d4119e87cf4640', # IPC-Run-0.96.tar.gz + ], + }), + ('HTML::Entities::Interpolate', '1.10', { + 'source_tmpl': 'HTML-Entities-Interpolate-%(version)s.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + 'checksums': [ + 'f15a9df92c282419f7010964aca1ada844ddfae7afc735cd2ba1bb20883e955c', # HTML-Entities-Interpolate-1.10.tgz + ], + }), + ('File::Remove', '1.57', { + 'source_tmpl': 'File-Remove-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'], + 'checksums': [ + 'b3becd60165c38786d18285f770b8b06ebffe91797d8c00cc4730614382501ad', # File-Remove-1.57.tar.gz + ], + }), + ('YAML::Tiny', '1.70', { + 'source_tmpl': 'YAML-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': [ + 'bbce4b52b5eafdb04e3043975a08dbf394d00b7d2c958adb9d03d9f7e9291255', # YAML-Tiny-1.70.tar.gz + ], + }), + ('Module::Install', '1.18', { + 'source_tmpl': 'Module-Install-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': [ + '29068ac33502cec959844c206516c09cc4a847cb57327d41015f605153ca645e', # Module-Install-1.18.tar.gz + ], + }), + ('Test::ClassAPI', '1.06', { + 'source_tmpl': 'Test-ClassAPI-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + 'checksums': [ + '06f82d076501701d78b8dc40b7688507bcc6c58b1beafd559e05bb0644df00a2', # Test-ClassAPI-1.06.tar.gz + ], + }), + ('Test::Most', '0.35', { + 'source_tmpl': 'Test-Most-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OV/OVID'], + 'checksums': [ + '9897a6f4d751598d2ed1047e01c1554b01d0f8c96c45e7e845229782bf6f657f', # Test-Most-0.35.tar.gz + ], + }), + ('Class::Accessor', '0.34', { + 'source_tmpl': 'Class-Accessor-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KA/KASEI'], + 'checksums': [ + 'cdb1e0cdf8380fb9b63b44c33ce5afc1068736d55ac5904bf0eaa1efc1c3cefc', # Class-Accessor-0.34.tar.gz + ], + }), + ('Test::Differences', '0.64', { + 'source_tmpl': 'Test-Differences-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DC/DCANTRELL'], + 'checksums': [ + '9f459dd9c2302a0a73e2f5528a0ce7d09d6766f073187ae2c69e603adf2eb276', # Test-Differences-0.64.tar.gz + ], + }), + ('HTTP::Tiny', '0.070', { + 'source_tmpl': 'HTTP-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + 'checksums': [ + '74f385d1e96de887a4df5a222d93afdc7d81ea9ad721a56ff3d8449bb12f7733', # HTTP-Tiny-0.070.tar.gz + ], + }), + ('Package::DeprecationManager', '0.17', { + 'source_tmpl': 'Package-DeprecationManager-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + 'checksums': [ + '1d743ada482b5c9871d894966e87d4c20edc96931bb949fb2638b000ddd6684b', # Package-DeprecationManager-0.17.tar.gz + ], + }), + ('Digest::SHA1', '2.13', { + 'source_tmpl': 'Digest-SHA1-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + 'checksums': [ + '68c1dac2187421f0eb7abf71452a06f190181b8fc4b28ededf5b90296fb943cc', # Digest-SHA1-2.13.tar.gz + ], + }), + ('Date::Language', '2.30', { + 'source_tmpl': 'TimeDate-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GB/GBARR'], + 'checksums': [ + '75bd254871cb5853a6aa0403ac0be270cdd75c9d1b6639f18ecba63c15298e86', # TimeDate-2.30.tar.gz + ], + }), + ('version', '0.9918', { + 'source_tmpl': 'version-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JP/JPEACOCK'], + 'checksums': [ + '54175c7ead4e2259c2fb2b83440b821e4287842067227e48fb899b5cae52237b', # version-0.9918.tar.gz + ], + }), + ('Sub::Uplevel', '0.2800', { + 'source_tmpl': 'Sub-Uplevel-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + 'checksums': [ + 'b4f3f63b80f680a421332d8851ddbe5a8e72fcaa74d5d1d98f3c8cc4a3ece293', # Sub-Uplevel-0.2800.tar.gz + ], + }), + ('XML::Bare', '0.53', { + 'source_tmpl': 'XML-Bare-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CO/CODECHILD'], + 'patches': ['XML-Bare-0.53_icc.patch'], + 'checksums': [ + '865e198e98d904be1683ef5a53a4948f02dabdacde59fc554a082ffbcc5baefd', # XML-Bare-0.53.tar.gz + '7d005e44222a0ce130b8ba4912a869675c0aa9ce4d1b95caba06b683b69f2b20', # XML-Bare-0.53_icc.patch + ], + }), + ('Dist::CheckConflicts', '0.11', { + 'source_tmpl': 'Dist-CheckConflicts-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DO/DOY'], + 'checksums': [ + 'ea844b9686c94d666d9d444321d764490b2cde2f985c4165b4c2c77665caedc4', # Dist-CheckConflicts-0.11.tar.gz + ], + }), + ('Sub::Name', '0.21', { + 'source_tmpl': 'Sub-Name-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': [ + 'bd32e9dee07047c10ae474c9f17d458b6e9885a6db69474c7a494ccc34c27117', # Sub-Name-0.21.tar.gz + ], + }), + ('Time::Piece', '1.3201', { + 'source_tmpl': 'Time-Piece-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ES/ESAYM'], + 'checksums': [ + '81dbe694474a13d9683c392edd54bd77b6bd6d20b41433358487b51eb71e31bd', # Time-Piece-1.3201.tar.gz + ], + }), + ('Digest::HMAC', '1.03', { + 'source_tmpl': 'Digest-HMAC-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + 'checksums': [ + '3bc72c6d3ff144d73aefb90e9a78d33612d58cf1cd1631ecfb8985ba96da4a59', # Digest-HMAC-1.03.tar.gz + ], + }), + ('HTTP::Negotiate', '6.01', { + 'source_tmpl': 'HTTP-Negotiate-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + 'checksums': [ + '1c729c1ea63100e878405cda7d66f9adfd3ed4f1d6cacaca0ee9152df728e016', # HTTP-Negotiate-6.01.tar.gz + ], + }), + ('MIME::Lite', '3.030', { + 'source_tmpl': 'MIME-Lite-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': [ + '8f39901bc580bc3dce69e10415305e4435ff90264c63d29f707b4566460be962', # MIME-Lite-3.030.tar.gz + ], + }), + ('Crypt::Rijndael', '1.13', { + 'source_tmpl': 'Crypt-Rijndael-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': [ + 'cd7209a6dfe0a3dc8caffe1aa2233b0e6effec7572d76a7a93feefffe636214e', # Crypt-Rijndael-1.13.tar.gz + ], + }), + ('B::Lint', '1.20', { + 'source_tmpl': 'B-Lint-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': [ + 'dc49408964fd8b7963859c92e013f0b9f92f74be5a7c2a78e3996279827c10b3', # B-Lint-1.20.tar.gz + ], + }), + ('Canary::Stability', '2012', { + 'source_tmpl': 'Canary-Stability-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/ML/MLEHMANN'], + 'checksums': [ + 'fd240b111d834dbae9630c59b42fae2145ca35addc1965ea311edf0d07817107', # Canary-Stability-2012.tar.gz + ], + }), + ('AnyEvent', '7.14', { + 'source_tmpl': 'AnyEvent-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/ML/MLEHMANN'], + 'checksums': [ + '539358d225bad34b4a64f5217f8c2a707b15e3a28c74120c9dd2270c7cca7d2a', # AnyEvent-7.14.tar.gz + ], + }), + ('Object::Accessor', '0.48', { + 'source_tmpl': 'Object-Accessor-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + 'checksums': [ + '76cb824a27b6b4e560409fcf6fd5b3bfbbd38b72f1f3d37ed0b54bd9c0baeade', # Object-Accessor-0.48.tar.gz + ], + }), + ('Data::UUID', '1.221', { + 'source_tmpl': 'Data-UUID-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': [ + '3cc7b2a3a7b74b45a059e013f7fd878078500ea4b7269036f84556b022078667', # Data-UUID-1.221.tar.gz + ], + }), + ('Test::Pod', '1.51', { + 'source_tmpl': 'Test-Pod-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': [ + 'c1a1d3cedf4a579e3aad89c36f9878a8542b6656dbe71f1581420f49582d7efb', # Test-Pod-1.51.tar.gz + ], + }), + ('AppConfig', '1.71', { + 'source_tmpl': 'AppConfig-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB'], + 'checksums': [ + '1177027025ecb09ee64d9f9f255615c04db5e14f7536c344af632032eb887b0f', # AppConfig-1.71.tar.gz + ], + }), + ('Net::SMTP::SSL', '1.04', { + 'source_tmpl': 'Net-SMTP-SSL-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': [ + '7b29c45add19d3d5084b751f7ba89a8e40479a446ce21cfd9cc741e558332a00', # Net-SMTP-SSL-1.04.tar.gz + ], + }), + ('XML::Tiny', '2.07', { + 'source_tmpl': 'XML-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DC/DCANTRELL'], + 'checksums': [ + 'ce39fcb53e0fe9f1cbcd86ddf152e1db48566266b70ec0769ef364eeabdd8941', # XML-Tiny-2.07.tar.gz + ], + }), + ('HTML::Tagset', '3.20', { + 'source_tmpl': 'HTML-Tagset-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PETDANCE'], + 'checksums': [ + 'adb17dac9e36cd011f5243881c9739417fd102fce760f8de4e9be4c7131108e2', # HTML-Tagset-3.20.tar.gz + ], + }), + ('HTML::Tree', '5.06', { + 'source_tmpl': 'HTML-Tree-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KE/KENTNL'], + 'checksums': [ + '9c36eb19cbdf9a5906c858948ca51c35bd7561f52cc18c43281acbe57327536e', # HTML-Tree-5.06.tar.gz + ], + }), + ('Devel::GlobalDestruction', '0.14', { + 'source_tmpl': 'Devel-GlobalDestruction-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + 'checksums': [ + '34b8a5f29991311468fe6913cadaba75fd5d2b0b3ee3bb41fe5b53efab9154ab', # Devel-GlobalDestruction-0.14.tar.gz + ], + }), + ('WWW::RobotRules', '6.02', { + 'source_tmpl': 'WWW-RobotRules-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + 'checksums': [ + '46b502e7a288d559429891eeb5d979461dd3ecc6a5c491ead85d165b6e03a51e', # WWW-RobotRules-6.02.tar.gz + ], + }), + ('Expect', '1.35', { + 'source_tmpl': 'Expect-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JA/JACOBY'], + 'checksums': [ + '09d92761421decd495853103379165a99efbf452c720f30277602cf23679fd06', # Expect-1.35.tar.gz + ], + }), + ('Term::UI', '0.46', { + 'source_tmpl': 'Term-UI-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + 'checksums': [ + '91946c80d7f4aab0ca4bfedc3bbe0a75b37cab1a29bd7bca3b3b7456d417e9a6', # Term-UI-0.46.tar.gz + ], + }), + ('Net::SNMP', 'v6.0.1', { + 'source_tmpl': 'Net-SNMP-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DT/DTOWN'], + 'checksums': [ + '14c37bc1cbb3f3cdc7d6c13e0f27a859f14cdcfd5ea54a0467a88bc259b0b741', # Net-SNMP-v6.0.1.tar.gz + ], + }), + ('XML::SAX::Writer', '0.57', { + 'source_tmpl': 'XML-SAX-Writer-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PERIGRIN'], + 'checksums': [ + '3d61d07ef43b0126f5b4de4f415a256fa859fa88dc4fdabaad70b7be7c682cf0', # XML-SAX-Writer-0.57.tar.gz + ], + }), + ('Statistics::Descriptive', '3.0612', { + 'source_tmpl': 'Statistics-Descriptive-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'], + 'checksums': [ + '772413148e5e00efb32f277c4254aa78b9112490a896208dcd0025813afdbf7a', # Statistics-Descriptive-3.0612.tar.gz + ], + }), + ('Class::Load', '0.24', { + 'source_tmpl': 'Class-Load-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': [ + '0bb983da46c146534fc77a556d6e40d925142f2eb43103534025ee545265ca36', # Class-Load-0.24.tar.gz + ], + }), + ('LWP::Simple', '6.26', { + 'source_tmpl': 'libwww-perl-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'], + 'checksums': [ + 'd0c5435275f8638ff36fff8f655ad2ccad1156e66cc47bfacfb9e44fc585b24f', # libwww-perl-6.26.tar.gz + ], + }), + ('Time::Piece::MySQL', '0.06', { + 'source_tmpl': 'Time-Piece-MySQL-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KA/KASEI'], + 'checksums': [ + '319601feec17fae344988a5ee91cfc6a0bcfe742af77dba254724c3268b2a60f', # Time-Piece-MySQL-0.06.tar.gz + ], + }), + ('Package::Stash::XS', '0.28', { + 'source_tmpl': 'Package-Stash-XS-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DO/DOY'], + 'checksums': [ + '23d8c5c25768ef1dc0ce53b975796762df0d6e244445d06e48d794886c32d486', # Package-Stash-XS-0.28.tar.gz + ], + }), + ('GD::Graph', '1.54', { + 'source_tmpl': 'GDGraph-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RU/RUZ'], + 'checksums': [ + 'b96f5c10b656c17d16ab65a1777c908297b028d3b6815f6d54b2337f006bfa4f', # GDGraph-1.54.tar.gz + ], + }), + ('Set::Array', '0.30', { + 'source_tmpl': 'Set-Array-%(version)s.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + 'checksums': [ + 'd9f024c8e3637feccdebcf6479b6754b6c92f1209f567feaf0c23818af31ee3c', # Set-Array-0.30.tgz + ], + }), + ('boolean', '0.46', { + 'source_tmpl': 'boolean-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IN/INGY'], + 'checksums': [ + '95c088085c3e83bf680fe6ce16d8264ec26310490f7d1680e416ea7a118f156a', # boolean-0.46.tar.gz + ], + }), + ('Number::Format', '1.75', { + 'source_tmpl': 'Number-Format-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/W/WR/WRW'], + 'checksums': [ + '82d659cb16461764fd44d11a9ce9e6a4f5e8767dc1069eb03467c6e55de257f3', # Number-Format-1.75.tar.gz + ], + }), + ('Data::Stag', '0.14', { + 'source_tmpl': 'Data-Stag-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CM/CMUNGALL'], + 'checksums': [ + '4ab122508d2fb86d171a15f4006e5cf896d5facfa65219c0b243a89906258e59', # Data-Stag-0.14.tar.gz + ], + }), + ('Test::NoWarnings', '1.04', { + 'source_tmpl': 'Test-NoWarnings-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + 'checksums': [ + '638a57658cb119af1fe5b15e73d47c2544dcfef84af0c6b1b2e97f08202b686c', # Test-NoWarnings-1.04.tar.gz + ], + }), + ('Crypt::DES', '2.07', { + 'source_tmpl': 'Crypt-DES-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DP/DPARIS'], + 'checksums': [ + '2db1ebb5837b4cb20051c0ee5b733b4453e3137df0a92306034c867621edd7e7', # Crypt-DES-2.07.tar.gz + ], + }), + ('Exporter', '5.72', { + 'source_tmpl': 'Exporter-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR'], + 'checksums': [ + 'cd13b7a0e91e8505a0ce4b25f40fab2c92bb28a99ef0d03da1001d95a32f0291', # Exporter-5.72.tar.gz + ], + }), + ('Class::Inspector', '1.32', { + 'source_tmpl': 'Class-Inspector-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE'], + 'checksums': [ + 'cefadc8b5338e43e570bc43f583e7c98d535c17b196bcf9084bb41d561cc0535', # Class-Inspector-1.32.tar.gz + ], + }), + ('Parse::RecDescent', '1.967015', { + 'source_tmpl': 'Parse-RecDescent-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JT/JTBRAUN'], + 'checksums': [ + '1943336a4cb54f1788a733f0827c0c55db4310d5eae15e542639c9dd85656e37', # Parse-RecDescent-1.967015.tar.gz + ], + }), + ('Carp', '1.38', { + 'source_tmpl': 'Carp-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': [ + 'a5a9ce3cbb959dfefa8c2dd16552567199b286d39b0e55053ca247c038977101', # Carp-1.38.tar.gz + ], + }), + ('XML::XPath', '1.42', { + 'source_tmpl': 'XML-XPath-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MANWAR'], + 'checksums': [ + '9e6ac67c2cead5f918a060b8b9ccdbdcaa6d610be8517bba42a96cd56748b512', # XML-XPath-1.42.tar.gz + ], + }), + ('Capture::Tiny', '0.46', { + 'source_tmpl': 'Capture-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + 'checksums': [ + '5d7a6a830cf7f2b2960bf8b8afaac16a537ede64f3023827acea5bd24ca77015', # Capture-Tiny-0.46.tar.gz + ], + }), + ('JSON', '2.94', { + 'source_tmpl': 'JSON-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IS/ISHIGAKI'], + 'checksums': [ + '12271b5cee49943bbdde430eef58f1fe64ba6561980b22c69585e08fc977dc6d', # JSON-2.94.tar.gz + ], + }), + ('Sub::Exporter', '0.987', { + 'source_tmpl': 'Sub-Exporter-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': [ + '543cb2e803ab913d44272c7da6a70bb62c19e467f3b12aaac4c9523259b083d6', # Sub-Exporter-0.987.tar.gz + ], + }), + ('Class::Load::XS', '0.10', { + 'source_tmpl': 'Class-Load-XS-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': [ + '5bc22cf536ebfd2564c5bdaf42f0d8a4cee3d1930fc8b44b7d4a42038622add1', # Class-Load-XS-0.10.tar.gz + ], + }), + ('Set::IntSpan::Fast', '1.15', { + 'source_tmpl': 'Set-IntSpan-Fast-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AN/ANDYA'], + 'checksums': [ + 'cfb1768c24f55208e87405b17f537f0f303fa141891d0b22d509a941aa57e24e', # Set-IntSpan-Fast-1.15.tar.gz + ], + }), + ('Sub::Exporter::Progressive', '0.001013', { + 'source_tmpl': 'Sub-Exporter-Progressive-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/F/FR/FREW'], + 'checksums': [ + 'd535b7954d64da1ac1305b1fadf98202769e3599376854b2ced90c382beac056', # Sub-Exporter-Progressive-0.001013.tar.gz + ], + }), + ('Data::Dumper::Concise', '2.023', { + 'source_tmpl': 'Data-Dumper-Concise-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': [ + 'a6c22f113caf31137590def1b7028a7e718eface3228272d0672c25e035d5853', # Data-Dumper-Concise-2.023.tar.gz + ], + }), + ('File::Slurp::Tiny', '0.004', { + 'source_tmpl': 'File-Slurp-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': [ + '452995beeabf0e923e65fdc627a725dbb12c9e10c00d8018c16d10ba62757f1e', # File-Slurp-Tiny-0.004.tar.gz + ], + }), + ('Algorithm::Diff', '1.1903', { + 'source_tmpl': 'Algorithm-Diff-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TY/TYEMQ'], + 'checksums': [ + '30e84ac4b31d40b66293f7b1221331c5a50561a39d580d85004d9c1fff991751', # Algorithm-Diff-1.1903.tar.gz + ], + }), + ('AnyData', '0.12', { + 'source_tmpl': 'AnyData-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + 'checksums': [ + 'be6a957f04a2feba9b305536b132deceba1f455db295b221a63e75567fadbcfc', # AnyData-0.12.tar.gz + ], + }), + ('Text::Iconv', '1.7', { + 'source_tmpl': 'Text-Iconv-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MP/MPIOTR'], + 'checksums': [ + '5b80b7d5e709d34393bcba88971864a17b44a5bf0f9e4bcee383d029e7d2d5c3', # Text-Iconv-1.7.tar.gz + ], + }), + ('Class::Data::Inheritable', '0.08', { + 'source_tmpl': 'Class-Data-Inheritable-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TM/TMTM'], + 'checksums': [ + '9967feceea15227e442ec818723163eb6d73b8947e31f16ab806f6e2391af14a', # Class-Data-Inheritable-0.08.tar.gz + ], + }), + ('Text::Balanced', '2.03', { + 'source_tmpl': 'Text-Balanced-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHAY'], + 'checksums': [ + '057753f8f0568b53921f66a60a89c30092b73329bcc61a2c43339ab70c9792c8', # Text-Balanced-2.03.tar.gz + ], + }), + ('strictures', '2.000003', { + 'source_tmpl': 'strictures-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + 'checksums': [ + '27f8ea096a521e9754d36ea32889c2cda28346d04e3e399e7ea118d182dbaf22', # strictures-2.000003.tar.gz + ], + }), + ('Switch', '2.17', { + 'source_tmpl': 'Switch-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CH/CHORNY'], + 'checksums': [ + '31354975140fe6235ac130a109496491ad33dd42f9c62189e23f49f75f936d75', # Switch-2.17.tar.gz + ], + }), + ('File::Which', '1.21', { + 'source_tmpl': 'File-Which-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE'], + 'checksums': [ + '9def5f10316bfd944e56b7f8a2501be1d44c288325309462aa9345e340854bcc', # File-Which-1.21.tar.gz + ], + }), + ('Email::Date::Format', '1.005', { + 'source_tmpl': 'Email-Date-Format-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': [ + '579c617e303b9d874411c7b61b46b59d36f815718625074ae6832e7bb9db5104', # Email-Date-Format-1.005.tar.gz + ], + }), + ('Error', '0.17025', { + 'source_tmpl': 'Error-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'], + 'checksums': [ + '6c9f474ad3d4fe0cabff6b6be532cb1dd348245986d4a6b600ad921d5cfdefaf', # Error-0.17025.tar.gz + ], + }), + ('Mock::Quick', '1.111', { + 'source_tmpl': 'Mock-Quick-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + 'checksums': [ + 'ff786008bf8c022064ececd3b7ed89c76b35e8d1eac6cf472a9f51771c1c9f2c', # Mock-Quick-1.111.tar.gz + ], + }), + ('Text::CSV', '1.95', { + 'source_tmpl': 'Text-CSV-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IS/ISHIGAKI'], + 'checksums': [ + '7e0a11d9c1129a55b68a26aa4b37c894279df255aa63ec8341d514ab848dbf61', # Text-CSV-1.95.tar.gz + ], + }), + ('Test::Output', '1.031', { + 'source_tmpl': 'Test-Output-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BD/BDFOY'], + 'checksums': [ + 'f8b8f37185717872727d06f6c078fa77db794410faf2f6da4d37b0b7650f7ea4', # Test-Output-1.031.tar.gz + ], + }), + ('Class::DBI', 'v3.0.17', { + 'source_tmpl': 'Class-DBI-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TM/TMTM'], + 'checksums': [ + '541354fe361c56850cb11261f6ca089a14573fa764792447444ff736ae626206', # Class-DBI-v3.0.17.tar.gz + ], + }), + ('List::AllUtils', '0.14', { + 'source_tmpl': 'List-AllUtils-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + 'checksums': [ + 'e45aa65927ae1975a000cc2fed14274627fa5e2bd09bab826a5f2c41d17ef6cd', # List-AllUtils-0.14.tar.gz + ], + }), + ('UNIVERSAL::moniker', '0.08', { + 'source_tmpl': 'UNIVERSAL-moniker-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KA/KASEI'], + 'checksums': [ + '94ce27a546cd57cb52e080a8f2533a7cc2350028388582485bd1039a37871f9c', # UNIVERSAL-moniker-0.08.tar.gz + ], + }), + ('Exception::Class', '1.43', { + 'source_tmpl': 'Exception-Class-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + 'checksums': [ + 'ff3b4b3f706e84aaa87ab0dee5cec6bd7a8fc9f72cf76d115212541fa0a13760', # Exception-Class-1.43.tar.gz + ], + }), + ('File::CheckTree', '4.42', { + 'source_tmpl': 'File-CheckTree-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': [ + '66fb417f8ff8a5e5b7ea25606156e70e204861c59fa8c3831925b4dd3f155f8a', # File-CheckTree-4.42.tar.gz + ], + }), + ('Math::VecStat', '0.08', { + 'source_tmpl': 'Math-VecStat-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AS/ASPINELLI'], + 'checksums': [ + '409a8e0e4b1025c8e80f628f65a9778aa77ab285161406ca4a6c097b13656d0d', # Math-VecStat-0.08.tar.gz + ], + }), + ('Pod::LaTeX', '0.61', { + 'source_tmpl': 'Pod-LaTeX-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TJ/TJENNESS'], + 'checksums': [ + '15a840ea1c8a76cd3c865fbbf2fec33b03615c0daa50f9c800c54e0cf0659d46', # Pod-LaTeX-0.61.tar.gz + ], + }), + ('Eval::Closure', '0.14', { + 'source_tmpl': 'Eval-Closure-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DO/DOY'], + 'checksums': [ + 'ea0944f2f5ec98d895bef6d503e6e4a376fea6383a6bc64c7670d46ff2218cad', # Eval-Closure-0.14.tar.gz + ], + }), + ('HTTP::Request', '6.13', { + 'source_tmpl': 'HTTP-Message-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'], + 'checksums': [ + 'f25f38428de851e5661e72f124476494852eb30812358b07f1c3a289f6f5eded', # HTTP-Message-6.13.tar.gz + ], + }), + ('XML::Twig', '3.52', { + 'source_tmpl': 'XML-Twig-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIROD'], + 'checksums': [ + 'fef75826c24f2b877d0a0d2645212fc4fb9756ed4d2711614ac15c497e8680ad', # XML-Twig-3.52.tar.gz + ], + }), + ('IO::String', '1.08', { + 'source_tmpl': 'IO-String-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + 'checksums': [ + '2a3f4ad8442d9070780e58ef43722d19d1ee21a803bf7c8206877a10482de5a0', # IO-String-1.08.tar.gz + ], + }), + ('XML::Simple', '2.24', { + 'source_tmpl': 'XML-Simple-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GR/GRANTM'], + 'checksums': [ + '9a14819fd17c75fbb90adcec0446ceab356cab0ccaff870f2e1659205dc2424f', # XML-Simple-2.24.tar.gz + ], + }), + ('Sub::Install', '0.928', { + 'source_tmpl': 'Sub-Install-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': [ + '61e567a7679588887b7b86d427bc476ea6d77fffe7e0d17d640f89007d98ef0f', # Sub-Install-0.928.tar.gz + ], + }), + ('HTTP::Cookies', '6.04', { + 'source_tmpl': 'HTTP-Cookies-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'], + 'checksums': [ + '0cc7f079079dcad8293fea36875ef58dd1bfd75ce1a6c244cd73ed9523eb13d4', # HTTP-Cookies-6.04.tar.gz + ], + }), + ('Pod::Plainer', '1.04', { + 'source_tmpl': 'Pod-Plainer-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RM/RMBARKER'], + 'checksums': [ + '1bbfbf7d1d4871e5a83bab2137e22d089078206815190eb1d5c1260a3499456f', # Pod-Plainer-1.04.tar.gz + ], + }), + ('Test::Exception::LessClever', '0.009', { + 'source_tmpl': 'Test-Exception-LessClever-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': [ + '3b2731a44956a11f74b46b3ecf0734fab651e1c0bcf120f8b407aa1b4d43ac34', # Test-Exception-LessClever-0.009.tar.gz + ], + }), + ('LWP::MediaTypes', '6.02', { + 'source_tmpl': 'LWP-MediaTypes-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + 'checksums': [ + '18790b0cc5f0a51468495c3847b16738f785a2d460403595001e0b932e5db676', # LWP-MediaTypes-6.02.tar.gz + ], + }), + ('Scalar::Util', '1.48', { + 'source_tmpl': 'Scalar-List-Utils-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PEVANS'], + 'checksums': [ + '0e5318308789ba3625e053001da0a6c5218dc73e561a207d1b91131d06c0d09f', # Scalar-List-Utils-1.48.tar.gz + ], + }), + ('Data::Section::Simple', '0.07', { + 'source_tmpl': 'Data-Section-Simple-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA'], + 'checksums': [ + '0b3035ffdb909aa1f7ded6b608fa9d894421c82c097d51e7171170d67579a9cb', # Data-Section-Simple-0.07.tar.gz + ], + }), + ('Class::Trigger', '0.14', { + 'source_tmpl': 'Class-Trigger-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA'], + 'checksums': [ + '6b1e45acc561e0708e00a2fcf16e157cad8b8963d1bf73726f77dd809b8aebc4', # Class-Trigger-0.14.tar.gz + ], + }), + ('HTTP::Daemon', '6.01', { + 'source_tmpl': 'HTTP-Daemon-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + 'checksums': [ + '43fd867742701a3f9fcc7bd59838ab72c6490c0ebaf66901068ec6997514adc2', # HTTP-Daemon-6.01.tar.gz + ], + }), + ('File::HomeDir', '1.002', { + 'source_tmpl': 'File-HomeDir-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + 'checksums': [ + 'eb4c0c85775138460cd4013d8117232f08e88381c95c6a93b3d11e969185c274', # File-HomeDir-1.002.tar.gz + ], + }), + ('HTTP::Date', '6.02', { + 'source_tmpl': 'HTTP-Date-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + 'checksums': [ + 'e8b9941da0f9f0c9c01068401a5e81341f0e3707d1c754f8e11f42a7e629e333', # HTTP-Date-6.02.tar.gz + ], + }), + ('Authen::SASL', '2.16', { + 'source_tmpl': 'Authen-SASL-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GB/GBARR'], + 'checksums': [ + '6614fa7518f094f853741b63c73f3627168c5d3aca89b1d02b1016dc32854e09', # Authen-SASL-2.16.tar.gz + ], + }), + ('Clone', '0.39', { + 'source_tmpl': 'Clone-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GARU'], + 'checksums': [ + 'acb046683e49d650b113634ecf57df000816a49e611b0fff70bf3f93568bfa2d', # Clone-0.39.tar.gz + ], + }), + ('Data::Types', '0.09', { + 'source_tmpl': 'Data-Types-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DW/DWHEELER'], + 'checksums': [ + 'b2296fdcf9addc8e8fc39e15eb2c3d81145f6355258438bc783b12b02c41cb81', # Data-Types-0.09.tar.gz + ], + }), + ('Import::Into', '1.002005', { + 'source_tmpl': 'Import-Into-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + 'checksums': [ + 'bd9e77a3fb662b40b43b18d3280cd352edf9fad8d94283e518181cc1ce9f0567', # Import-Into-1.002005.tar.gz + ], + }), + ('DateTime::Tiny', '1.06', { + 'source_tmpl': 'DateTime-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + 'checksums': [ + 'bd725df481d7223ee787e154c116098b08a129f55e0763194b07ebea3dda33ec', # DateTime-Tiny-1.06.tar.gz + ], + }), + ('DBD::AnyData', '0.110', { + 'source_tmpl': 'DBD-AnyData-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + 'checksums': [ + '247f0d88e55076fd3f6c7bf3fd527989d62fcc1ef9bde9bf2ee11c280adcaeab', # DBD-AnyData-0.110.tar.gz + ], + }), + ('Text::Format', '0.60', { + 'source_tmpl': 'Text-Format-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'], + 'checksums': [ + '664f313570604624ff9e1fc9b26b6d04e06897b3e4eac83089fc0905a692a2b8', # Text-Format-0.60.tar.gz + ], + }), + ('Devel::CheckCompiler', '0.07', { + 'source_tmpl': 'Devel-CheckCompiler-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SY/SYOHEX'], + 'checksums': [ + '768b7697b4b8d4d372c7507b65e9dd26aa4223f7100183bbb4d3af46d43869b5', # Devel-CheckCompiler-0.07.tar.gz + ], + }), + ('Log::Handler', '0.88', { + 'source_tmpl': 'Log-Handler-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BL/BLOONIX'], + 'checksums': [ + '45bf540ab2138ed3ff93afc205b0516dc75755b86acdcc5e75c41347833c293d', # Log-Handler-0.88.tar.gz + ], + }), + ('DBIx::ContextualFetch', '1.03', { + 'source_tmpl': 'DBIx-ContextualFetch-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TM/TMTM'], + 'checksums': [ + '85e2f805bfc81cd738c294316b27a515397036f397a0ff1c6c8d754c38530306', # DBIx-ContextualFetch-1.03.tar.gz + ], + }), + ('Devel::StackTrace', '2.02', { + 'source_tmpl': 'Devel-StackTrace-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + 'checksums': [ + 'cbbd96db0ecf194ed140198090eaea0e327d9a378a4aa15f9a34b3138a91931f', # Devel-StackTrace-2.02.tar.gz + ], + }), + ('Term::ReadKey', '2.37', { + 'source_tmpl': 'TermReadKey-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JS/JSTOWE'], + 'checksums': [ + '4a9383cf2e0e0194668fe2bd546e894ffad41d556b41d2f2f577c8db682db241', # TermReadKey-2.37.tar.gz + ], + }), + ('Set::IntSpan', '1.19', { + 'source_tmpl': 'Set-IntSpan-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SW/SWMCD'], + 'checksums': [ + '11b7549b13ec5d87cc695dd4c777cd02983dd5fe9866012877fb530f48b3dfd0', # Set-IntSpan-1.19.tar.gz + ], + }), + ('Moose', '2.2006', { + 'source_tmpl': 'Moose-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': [ + 'a4e00ab25cc41bebc5e7a11d71375fb5e64b56d5f91159afee225d698e06392b', # Moose-2.2006.tar.gz + ], + }), + ('Algorithm::Dependency', '1.110', { + 'source_tmpl': 'Algorithm-Dependency-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + 'checksums': [ + 'f27733e8d89cf2ab621284c2584da90ab0cb743ba2295ee739fe51bf92561e37', # Algorithm-Dependency-1.110.tar.gz + ], + }), + ('Font::TTF', '1.06', { + 'source_tmpl': 'Font-TTF-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BH/BHALLISSY'], + 'checksums': [ + '4b697d444259759ea02d2c442c9bffe5ffe14c9214084a01f743693a944cc293', # Font-TTF-1.06.tar.gz + ], + }), + ('IPC::Run3', '0.048', { + 'source_tmpl': 'IPC-Run3-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': [ + '3d81c3cc1b5cff69cca9361e2c6e38df0352251ae7b41e2ff3febc850e463565', # IPC-Run3-0.048.tar.gz + ], + }), + ('File::Find::Rule', '0.34', { + 'source_tmpl': 'File-Find-Rule-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RC/RCLAMP'], + 'checksums': [ + '7e6f16cc33eb1f29ff25bee51d513f4b8a84947bbfa18edb2d3cc40a2d64cafe', # File-Find-Rule-0.34.tar.gz + ], + }), + ('SQL::Statement', '1.412', { + 'source_tmpl': 'SQL-Statement-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + 'checksums': [ + '65c870883379c11b53f19ead10aaac241ccc86a90bbab77f6376fe750720e5c8', # SQL-Statement-1.412.tar.gz + ], + }), + ('File::Slurp', '9999.19', { + 'source_tmpl': 'File-Slurp-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/U/UR/URI'], + 'checksums': [ + 'ce29ebe995097ebd6e9bc03284714cdfa0c46dc94f6b14a56980747ea3253643', # File-Slurp-9999.19.tar.gz + ], + }), + ('Package::Stash', '0.37', { + 'source_tmpl': 'Package-Stash-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DO/DOY'], + 'checksums': [ + '06ab05388f9130cd377c0e1d3e3bafeed6ef6a1e22104571a9e1d7bfac787b2c', # Package-Stash-0.37.tar.gz + ], + }), + ('Data::OptList', '0.110', { + 'source_tmpl': 'Data-OptList-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': [ + '366117cb2966473f2559f2f4575ff6ae69e84c69a0f30a0773e1b51a457ef5c3', # Data-OptList-0.110.tar.gz + ], + }), + ('CPANPLUS', '0.9168', { + 'source_tmpl': 'CPANPLUS-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + 'checksums': [ + 'ea7b3278a688721729244de4d8efc57536be833458d93172c412bdc7c3c1ed02', # CPANPLUS-0.9168.tar.gz + ], + }), + ('IO::Tty', '1.12', { + 'source_tmpl': 'IO-Tty-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR'], + 'checksums': [ + 'a2ef8770d3309178203f8c8ac25e623e63cf76e97830fd3be280ade1a555290d', # IO-Tty-1.12.tar.gz + ], + }), + ('Text::Soundex', '3.05', { + 'source_tmpl': 'Text-Soundex-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': [ + 'f6dd55b4280b25dea978221839864382560074e1d6933395faee2510c2db60ed', # Text-Soundex-3.05.tar.gz + ], + }), + ('Lingua::EN::PluralToSingular', '0.19', { + 'source_tmpl': 'Lingua-EN-PluralToSingular-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BK/BKB'], + 'checksums': [ + 'c71b6c1aec01aae9c42aef0d9f147a437e91a7cc5cea6e4abbc35440638f299e', # Lingua-EN-PluralToSingular-0.19.tar.gz + ], + }), + ('Want', '0.29', { + 'source_tmpl': 'Want-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RO/ROBIN'], + 'checksums': [ + 'b4e4740b8d4cb783591273c636bd68304892e28d89e88abf9273b1de17f552f7', # Want-0.29.tar.gz + ], + }), + ('Cwd::Guard', '0.05', { + 'source_tmpl': 'Cwd-Guard-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KA/KAZEBURO'], + 'checksums': [ + '7afc7ca2b9502e440241938ad97a3e7ebd550180ebd6142e1db394186b268e77', # Cwd-Guard-0.05.tar.gz + ], + }), + ('Bundle::BioPerl', '2.1.9', { + 'source_tmpl': 'Bundle-BioPerl-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS'], + 'checksums': [ + 'c343ba97f49d86e7fb14aef4cfe3124992e2a5c3168e53a54606dd611d73e5c7', # Bundle-BioPerl-2.1.9.tar.gz + ], + }), + ('Mail::Util', '2.19', { + 'source_tmpl': 'MailTools-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARKOV'], + 'checksums': [ + 'c17ed702efea8eab56fe92961c07cd4980cee26ca6f13aff2688dc8af69c5e1a', # MailTools-2.19.tar.gz + ], + }), + ('Text::Template', '1.47', { + 'source_tmpl': 'Text-Template-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MS/MSCHOUT'], + 'checksums': [ + '50d742c74482478aa01008d468290fcfbc0b9a1219cfe1284076f1f31f0be8fc', # Text-Template-1.47.tar.gz + ], + }), + ('PDF::API2', '2.033', { + 'source_tmpl': 'PDF-API2-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SS/SSIMMS'], + 'checksums': [ + '9c0866ec1a3053f73afaca5f5cdbe6925903b4ce606f4bf4ac317731a69d27a0', # PDF-API2-2.033.tar.gz + ], + }), + ('Devel::CheckLib', '1.11', { + 'source_tmpl': 'Devel-CheckLib-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MATTN'], + 'checksums': [ + 'bd6d1c187e80be6de1f0d37add441ba8f14950c7bc1f54e764770ed484b232c1', # Devel-CheckLib-1.11.tar.gz + ], + }), + ('SVG', '2.78', { + 'source_tmpl': 'SVG-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MANWAR'], + 'checksums': [ + 'a665c1f18c0529f3da0f4b631976eb47e0f71f6d6784ef3f44d32fd76643d6bb', # SVG-2.78.tar.gz + ], + }), + ('Statistics::Basic', '1.6611', { + 'source_tmpl': 'Statistics-Basic-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JE/JETTERO'], + 'checksums': [ + '6855ce5615fd3e1af4cfc451a9bf44ff29a3140b4e7130034f1f0af2511a94fb', # Statistics-Basic-1.6611.tar.gz + ], + }), +] + +moduleclass = 'lang' -- GitLab From 1b6f4a55373362feba5c01927f3a29535911c4b5 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Lopez Date: Fri, 1 Sep 2017 10:48:45 +0200 Subject: [PATCH 1479/1603] moving moduleclass to bottom of the easyconfig --- easybuild/easyconfigs/c/CGNS/CGNS-3.3.1-foss-2016b.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/c/CGNS/CGNS-3.3.1-foss-2016b.eb b/easybuild/easyconfigs/c/CGNS/CGNS-3.3.1-foss-2016b.eb index 9ee315a082..d1ef0ef3c7 100644 --- a/easybuild/easyconfigs/c/CGNS/CGNS-3.3.1-foss-2016b.eb +++ b/easybuild/easyconfigs/c/CGNS/CGNS-3.3.1-foss-2016b.eb @@ -22,10 +22,10 @@ builddependencies = [ ('CMake', '3.6.1'), ] -moduleclass = 'cae' - sanity_check_paths = { 'files': ["bin/%s" % x for x in ["cgnscheck", "cgnscompress", "cgnsconvert", "cgnsdiff", "cgnslist", "cgnsnames", "cgnsupdate"]], 'dirs': [], } + +moduleclass = 'cae' -- GitLab From 263b45c1b3f02cbddd55c301e383a292138e79bd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 1 Sep 2017 11:19:48 +0200 Subject: [PATCH 1480/1603] add CMake + pkg-config as build deps, clean up configopts & co handled by updated ROOT easyblock --- .../ROOT-6.10.04-intel-2017a-Python-2.7.13.eb | 34 ++++++------------- 1 file changed, 11 insertions(+), 23 deletions(-) diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-6.10.04-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/r/ROOT/ROOT-6.10.04-intel-2017a-Python-2.7.13.eb index 6294637101..a5fbff5994 100644 --- a/easybuild/easyconfigs/r/ROOT/ROOT-6.10.04-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/r/ROOT/ROOT-6.10.04-intel-2017a-Python-2.7.13.eb @@ -23,6 +23,10 @@ checksums = [ 'f97179b55bf862d884aba037eef12eed00829fb13f303c464d974331801cc2df', # ROOT-v5.34.26_libX.patch ] +builddependencies = [ + ('CMake', '3.8.2'), + ('pkg-config', '0.29.2'), +] dependencies = [ ('GSL', '2.3'), ('libxml2', '2.9.4'), @@ -35,31 +39,15 @@ dependencies = [ ('Mesa', '17.0.2'), ('libGLU', '9.0.0'), ('GL2PS', '1.4.0'), + ('FFTW', '3.3.6'), + ('SQLite', '3.17.0'), + ('XZ', '5.2.3'), ] -# use external ZLIB -preconfigopts = 'env ZLIB=$EBROOTZLIB ' - -# architecture -arch = 'linuxx8664icc' - -# disable features -configopts = ' --disable-xrootd --disable-mysql --disable-krb5 --disable-odbc ' -configopts += ' --disable-oracle --disable-pgsql --disable-qt --disable-sqlite' -# enable features -configopts += ' --enable-unuran --enable-table --enable-explicitlink --enable-minuit2 --enable-roofit' -configopts += ' --with-gsl-incdir=$EBROOTGSL/include/gsl --with-gsl-libdir=$EBROOTGSL/lib' -configopts += ' --with-fftw3-incdir=$MKLROOT/mkl/include/fftw --with-fftw3-libdir=$MKLROOT/mkl/lib/intel64' -configopts += ' --with-xml-incdir=$EBROOTLIBXML2/include/libxml2/libxml --with-xml-libdir=$EBROOTLIBXML2/lib' -configopts += ' --with-python-libdir=$EBROOTPYTHON/lib' -configopts += ' --with-cfitsio-incdir=$EBROOTCFITSIO/include --with-cfitsio-libdir=$EBROOTCFITSIO/lib' -configopts += ' --with-opengl-incdir=$EBROOTMESA/include --with-opengl-libdir=$EBROOTMESA/lib' -configopts += ' --with-x11-libdir=$EBROOTX11/lib --with-xext-libdir=$EBROOTLIBX11/lib' -configopts += ' --with-xft-libdir=$EBROOTX11/lib' -configopts += ' --with-xpm-incdir=$EBROOTX11/include --with-xpm-libdir=$EBROOTX11/lib' - -sanity_check_commands = ["python -c 'import ROOT'"] +# disable some components +configopts = "-Dxrootd=OFF -Dmysql=OFF -Dkrb5=OFF -Dodbc=OFF -Doracle=OFF -Dpgsql=OFF -Dqt=OFF " -modextrapaths = {'PYTHONPATH': 'lib/'} +# make sure some components are enabled +configopts += "-Dunuran=ON -Dtable=ON -Dexplicitlink=ON -Dminuit2=ON -Droofit=ON " moduleclass = 'data' -- GitLab From 716c441a7d08d238d48612b9477eb8709f24488b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 1 Sep 2017 11:32:13 +0200 Subject: [PATCH 1481/1603] fix toolchain version in Perl 5.26.0 easyconfig, should be intel/2017b --- .../{Perl-5.26.0-intel-2017a.eb => Perl-5.26.0-intel-2017b.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/p/Perl/{Perl-5.26.0-intel-2017a.eb => Perl-5.26.0-intel-2017b.eb} (99%) diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.26.0-intel-2017a.eb b/easybuild/easyconfigs/p/Perl/Perl-5.26.0-intel-2017b.eb similarity index 99% rename from easybuild/easyconfigs/p/Perl/Perl-5.26.0-intel-2017a.eb rename to easybuild/easyconfigs/p/Perl/Perl-5.26.0-intel-2017b.eb index 51fdb404df..9d460cc82d 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.26.0-intel-2017a.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.26.0-intel-2017b.eb @@ -4,7 +4,7 @@ version = '5.26.0' homepage = 'https://www.perl.org/' description = """Larry Wall's Practical Extraction and Report Language""" -toolchain = {'name': 'intel', 'version': '2017a'} +toolchain = {'name': 'intel', 'version': '2017b'} toolchainopts = {'pic': True} source_urls = ['http://www.cpan.org/src/%(version_major)s.0'] -- GitLab From 65e03a503196a7288745f55e68a8f19dd4f0cf3a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 1 Sep 2017 11:33:46 +0200 Subject: [PATCH 1482/1603] fix long lines --- .../easyconfigs/p/Perl/Perl-5.26.0-intel-2017b.eb | 15 ++++++++++----- 1 file changed, 10 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.26.0-intel-2017b.eb b/easybuild/easyconfigs/p/Perl/Perl-5.26.0-intel-2017b.eb index 9d460cc82d..750a9f9177 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.26.0-intel-2017b.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.26.0-intel-2017b.eb @@ -389,7 +389,8 @@ exts_list = [ 'source_tmpl': 'Template-Plugin-Number-Format-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DARREN'], 'checksums': [ - '0865836a1bcbc34d4a0ee34b5ccc14d7b511f1fd300bf390f002dac349539843', # Template-Plugin-Number-Format-1.06.tar.gz + # Template-Plugin-Number-Format-1.06.tar.gz + '0865836a1bcbc34d4a0ee34b5ccc14d7b511f1fd300bf390f002dac349539843', ], }), ('HTML::Parser', '3.72', { @@ -711,7 +712,8 @@ exts_list = [ 'source_tmpl': 'Package-DeprecationManager-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], 'checksums': [ - '1d743ada482b5c9871d894966e87d4c20edc96931bb949fb2638b000ddd6684b', # Package-DeprecationManager-0.17.tar.gz + # Package-DeprecationManager-0.17.tar.gz + '1d743ada482b5c9871d894966e87d4c20edc96931bb949fb2638b000ddd6684b', ], }), ('Digest::SHA1', '2.13', { @@ -1077,7 +1079,8 @@ exts_list = [ 'source_tmpl': 'Sub-Exporter-Progressive-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/F/FR/FREW'], 'checksums': [ - 'd535b7954d64da1ac1305b1fadf98202769e3599376854b2ced90c382beac056', # Sub-Exporter-Progressive-0.001013.tar.gz + # Sub-Exporter-Progressive-0.001013.tar.gz + 'd535b7954d64da1ac1305b1fadf98202769e3599376854b2ced90c382beac056', ], }), ('Data::Dumper::Concise', '2.023', { @@ -1294,7 +1297,8 @@ exts_list = [ 'source_tmpl': 'Test-Exception-LessClever-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], 'checksums': [ - '3b2731a44956a11f74b46b3ecf0734fab651e1c0bcf120f8b407aa1b4d43ac34', # Test-Exception-LessClever-0.009.tar.gz + # Test-Exception-LessClever-0.009.tar.gz + '3b2731a44956a11f74b46b3ecf0734fab651e1c0bcf120f8b407aa1b4d43ac34', ], }), ('LWP::MediaTypes', '6.02', { @@ -1525,7 +1529,8 @@ exts_list = [ 'source_tmpl': 'Lingua-EN-PluralToSingular-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BK/BKB'], 'checksums': [ - 'c71b6c1aec01aae9c42aef0d9f147a437e91a7cc5cea6e4abbc35440638f299e', # Lingua-EN-PluralToSingular-0.19.tar.gz + # Lingua-EN-PluralToSingular-0.19.tar.gz + 'c71b6c1aec01aae9c42aef0d9f147a437e91a7cc5cea6e4abbc35440638f299e', ], }), ('Want', '0.29', { -- GitLab From 4c3220d5666d97cfe1cbb75129a6e5bf6a6003e5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 1 Sep 2017 11:34:20 +0200 Subject: [PATCH 1483/1603] also add easyconfig for Perl 5.26.0 with foss/2017b --- .../p/Perl/Perl-5.26.0-foss-2017b.eb | 1601 +++++++++++++++++ 1 file changed, 1601 insertions(+) create mode 100644 easybuild/easyconfigs/p/Perl/Perl-5.26.0-foss-2017b.eb diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.26.0-foss-2017b.eb b/easybuild/easyconfigs/p/Perl/Perl-5.26.0-foss-2017b.eb new file mode 100644 index 0000000000..1b7202c060 --- /dev/null +++ b/easybuild/easyconfigs/p/Perl/Perl-5.26.0-foss-2017b.eb @@ -0,0 +1,1601 @@ +name = 'Perl' +version = '5.26.0' + +homepage = 'https://www.perl.org/' +description = """Larry Wall's Practical Extraction and Report Language""" + +toolchain = {'name': 'foss', 'version': '2017b'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.cpan.org/src/%(version_major)s.0'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['ebe7c66906d4fb55449380ab1b7e004eeef52c38d3443fa301f8e17a1a4cb67f'] + +# !! order of extensions is important !! +# extensions updated on August 29th 2017 +exts_list = [ + ('Config::General', '2.63', { + 'source_tmpl': 'Config-General-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TL/TLINDEN'], + 'checksums': [ + '0a9bf977b8aabe76343e88095d2296c8a422410fd2a05a1901f2b20e2e1f6fad', # Config-General-2.63.tar.gz + ], + }), + ('File::Listing', '6.04', { + 'source_tmpl': 'File-Listing-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + 'checksums': [ + '1e0050fcd6789a2179ec0db282bf1e90fb92be35d1171588bd9c47d52d959cf5', # File-Listing-6.04.tar.gz + ], + }), + ('ExtUtils::InstallPaths', '0.011', { + 'source_tmpl': 'ExtUtils-InstallPaths-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': [ + '7609fa048cdcf1451cad5b1d7d494f30e3d5bad0672d15404f1ea60e1df0067c', # ExtUtils-InstallPaths-0.011.tar.gz + ], + }), + ('ExtUtils::Helpers', '0.026', { + 'source_tmpl': 'ExtUtils-Helpers-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': [ + 'de901b6790a4557cf4ec908149e035783b125bf115eb9640feb1bc1c24c33416', # ExtUtils-Helpers-0.026.tar.gz + ], + }), + ('Test::Harness', '3.39', { + 'source_tmpl': 'Test-Harness-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': [ + '69bd44c81c6e1d2db18e298ecf631852608893ddfddb332a7d55285bbfc51132', # Test-Harness-3.39.tar.gz + ], + }), + ('ExtUtils::Config', '0.008', { + 'source_tmpl': 'ExtUtils-Config-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': [ + 'ae5104f634650dce8a79b7ed13fb59d67a39c213a6776cfdaa3ee749e62f1a8c', # ExtUtils-Config-0.008.tar.gz + ], + }), + ('Module::Build::Tiny', '0.039', { + 'source_tmpl': 'Module-Build-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': [ + '7d580ff6ace0cbe555bf36b86dc8ea232581530cbeaaea09bccb57b55797f11c', # Module-Build-Tiny-0.039.tar.gz + ], + }), + ('aliased', '0.34', { + 'source_tmpl': 'aliased-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': [ + 'c350524507cd827fab864e5d4c2cc350b1babaa12fa95aec0ca00843fcc7deeb', # aliased-0.34.tar.gz + ], + }), + ('Text::Glob', '0.11', { + 'source_tmpl': 'Text-Glob-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RC/RCLAMP'], + 'checksums': [ + '069ccd49d3f0a2dedb115f4bdc9fbac07a83592840953d1fcdfc39eb9d305287', # Text-Glob-0.11.tar.gz + ], + }), + ('Regexp::Common', '2017060201', { + 'source_tmpl': 'Regexp-Common-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AB/ABIGAIL'], + 'checksums': [ + 'ee07853aee06f310e040b6bf1a0199a18d81896d3219b9b35c9630d0eb69089b', # Regexp-Common-2017060201.tar.gz + ], + }), + ('GO::Utils', '0.15', { + 'source_tmpl': 'go-perl-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CM/CMUNGALL'], + 'checksums': [ + '423d26155ee85ca51ab2270cee59f4e85b193e57ac3a29aff827298c0a396b12', # go-perl-0.15.tar.gz + ], + }), + ('Module::Pluggable', '5.2', { + 'source_tmpl': 'Module-Pluggable-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SI/SIMONW'], + 'checksums': [ + 'b3f2ad45e4fd10b3fb90d912d78d8b795ab295480db56dc64e86b9fa75c5a6df', # Module-Pluggable-5.2.tar.gz + ], + }), + ('Test::Fatal', '0.014', { + 'source_tmpl': 'Test-Fatal-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': [ + 'bcdcef5c7b2790a187ebca810b0a08221a63256062cfab3c3b98685d91d1cbb0', # Test-Fatal-0.014.tar.gz + ], + }), + ('Test::Warnings', '0.026', { + 'source_tmpl': 'Test-Warnings-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': [ + 'ae2b68b1b5616704598ce07f5118efe42dc4605834453b7b2be14e26f9cc9a08', # Test-Warnings-0.026.tar.gz + ], + }), + ('File::ShareDir::Install', '0.11', { + 'source_tmpl': 'File-ShareDir-Install-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': [ + '32bf8772e9fea60866074b27ff31ab5bc3f88972d61915e84cbbb98455e00cc8', # File-ShareDir-Install-0.11.tar.gz + ], + }), + ('DateTime::Locale', '1.16', { + 'source_tmpl': 'DateTime-Locale-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + 'checksums': [ + 'dfaf4c42149c0622e80721773b8d7229d7785280503585895c9fe9f51e076cfe', # DateTime-Locale-1.16.tar.gz + ], + }), + ('DateTime::TimeZone', '2.13', { + 'source_tmpl': 'DateTime-TimeZone-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + 'checksums': [ + '333d39ccd6b883460409b9113bec43be256c3e763beedfb97b9eb274c9d4e18c', # DateTime-TimeZone-2.13.tar.gz + ], + }), + ('Test::Requires', '0.10', { + 'source_tmpl': 'Test-Requires-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TOKUHIROM'], + 'checksums': [ + '2768a391d50ab94b95cefe540b9232d7046c13ee86d01859e04c044903222eb5', # Test-Requires-0.10.tar.gz + ], + }), + ('Module::Implementation', '0.09', { + 'source_tmpl': 'Module-Implementation-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + 'checksums': [ + 'c15f1a12f0c2130c9efff3c2e1afe5887b08ccd033bd132186d1e7d5087fd66d', # Module-Implementation-0.09.tar.gz + ], + }), + ('Module::Build', '0.4224', { + 'source_tmpl': 'Module-Build-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': [ + 'a6ca15d78244a7b50fdbf27f85c85f4035aa799ce7dd018a0d98b358ef7bc782', # Module-Build-0.4224.tar.gz + ], + }), + ('Module::Runtime', '0.015', { + 'source_tmpl': 'Module-Runtime-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/Z/ZE/ZEFRAM'], + 'checksums': [ + '67fcfaf4e33072924975675da9004bacc43fff9f61396135b93627cbe38e43c0', # Module-Runtime-0.015.tar.gz + ], + }), + ('Try::Tiny', '0.28', { + 'source_tmpl': 'Try-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': [ + 'f1d166be8aa19942c4504c9111dade7aacb981bc5b3a2a5c5f6019646db8c146', # Try-Tiny-0.28.tar.gz + ], + }), + ('Params::Validate', '1.29', { + 'source_tmpl': 'Params-Validate-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + 'checksums': [ + '49a68dfb430bea028042479111d19068e08095e5a467e320b7ab7bde3d729733', # Params-Validate-1.29.tar.gz + ], + }), + ('List::MoreUtils', '0.423', { + 'source_tmpl': 'List-MoreUtils-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + 'checksums': [ + 'b4d90b24809b399fda3772a45b1af9e29d89becf8ba4a4f78fa36234e4ed5396', # List-MoreUtils-0.423.tar.gz + ], + }), + ('Exporter::Tiny', '1.000000', { + 'source_tmpl': 'Exporter-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TOBYINK'], + 'checksums': [ + 'ffdd77d57de099e8f64dd942ef12a00a3f4313c2531f342339eeed2d366ad078', # Exporter-Tiny-1.000000.tar.gz + ], + }), + ('Class::Singleton', '1.5', { + 'source_tmpl': 'Class-Singleton-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHAY'], + 'checksums': [ + '38220d04f02e3a803193c2575a1644cce0b95ad4b95c19eb932b94e2647ef678', # Class-Singleton-1.5.tar.gz + ], + }), + ('DateTime', '1.44', { + 'source_tmpl': 'DateTime-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + 'checksums': [ + 'a7165a9b1bcef735e76ea44c184ea741840249dd1862b8465f3777cd8f0bd701', # DateTime-1.44.tar.gz + ], + }), + ('File::Find::Rule::Perl', '1.15', { + 'source_tmpl': 'File-Find-Rule-Perl-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': [ + '9a48433f86e08ce18e03526e2982de52162eb909d19735460f07eefcaf463ea6', # File-Find-Rule-Perl-1.15.tar.gz + ], + }), + ('Readonly', '2.05', { + 'source_tmpl': 'Readonly-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SA/SANKO'], + 'checksums': [ + '4b23542491af010d44a5c7c861244738acc74ababae6b8838d354dfb19462b5e', # Readonly-2.05.tar.gz + ], + }), + ('Git', '0.41', { + 'source_tmpl': 'Git-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MS/MSOUTH'], + 'checksums': [ + '9d4de21612253a1d3252ff7657d7e832dcf3cc2a748a8c84f73de618a3a38239', # Git-0.41.tar.gz + ], + }), + ('Tree::DAG_Node', '1.29', { + 'source_tmpl': 'Tree-DAG_Node-%(version)s.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + 'checksums': [ + '2d04eb011aa06cee633c367d1f322b8d937020fde5d5393fad6a26c93725c4a8', # Tree-DAG_Node-1.29.tgz + ], + }), + ('Template', '2.27', { + 'source_tmpl': 'Template-Toolkit-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AB/ABW'], + 'checksums': [ + '1311a403264d0134c585af0309ff2a9d5074b8ece23ece5660d31ec96bf2c6dc', # Template-Toolkit-2.27.tar.gz + ], + }), + ('FreezeThaw', '0.5001', { + 'source_tmpl': 'FreezeThaw-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IL/ILYAZ/modules'], + 'checksums': [ + '3c5e08329106f9cee3ab444b81331c5935f83084a151d88505e7a465da540f41', # FreezeThaw-0.5001.tar.gz + ], + }), + ('DBI', '1.637', { + 'source_tmpl': 'DBI-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TI/TIMB'], + 'checksums': [ + '2557712593e80142c3b50877e00369b6ce78fa26d44edc42156d81a5cdd26bc6', # DBI-1.637.tar.gz + ], + }), + ('DBD::SQLite', '1.54', { + 'source_tmpl': 'DBD-SQLite-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IS/ISHIGAKI'], + 'checksums': [ + '3929a6dbd8d71630f0cb57f85dcef9588cd7ac4c9fa12db79df77b9d3a4d7269', # DBD-SQLite-1.54.tar.gz + ], + }), + ('Math::Bezier', '0.01', { + 'source_tmpl': 'Math-Bezier-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AB/ABW'], + 'checksums': [ + '11a815fc45fdf0efabb1822ab77faad8b9eea162572c5f0940c8ed7d56e6b8b8', # Math-Bezier-0.01.tar.gz + ], + }), + ('Archive::Extract', '0.80', { + 'source_tmpl': 'Archive-Extract-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + 'checksums': [ + '25cbc2d5626c14d39a0b5e4fe8383941e085c9a7e0aa873d86e81b6e709025f4', # Archive-Extract-0.80.tar.gz + ], + }), + ('DBIx::Simple', '1.35', { + 'source_tmpl': 'DBIx-Simple-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JU/JUERD'], + 'checksums': [ + '445535b3dfab88140c7a0d2776b1e78f254dc7e9c81072d5a01afc95a5db499a', # DBIx-Simple-1.35.tar.gz + ], + }), + ('Shell', '0.73', { + 'source_tmpl': 'Shell-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/F/FE/FERREIRA'], + 'checksums': [ + 'f7dbebf65261ed0e5abd0f57052b64d665a1a830bab4c8bbc220f235bd39caf5', # Shell-0.73.tar.gz + ], + }), + ('File::Spec', '3.62', { + 'source_tmpl': 'PathTools-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': [ + '36350e12f58871437ba03391f80a506e447e3c6630cc37d0625bc25ff1c7b4d2', # PathTools-3.62.tar.gz + ], + }), + ('Test::Simple', '1.302086', { + 'source_tmpl': 'Test-Simple-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + 'checksums': [ + '21e4c93c52529a10ef970afcf2cdb5719bcfef5f71af09cad3675fcf021995b1', # Test-Simple-1.302086.tar.gz + ], + }), + ('Set::Scalar', '1.29', { + 'source_tmpl': 'Set-Scalar-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAVIDO'], + 'checksums': [ + 'a3dc1526f3dde72d3c64ea00007b86ce608cdcd93567cf6e6e42dc10fdc4511d', # Set-Scalar-1.29.tar.gz + ], + }), + ('IO::Stringy', '2.111', { + 'source_tmpl': 'IO-stringy-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DS/DSKOLL'], + 'checksums': [ + '8c67fd6608c3c4e74f7324f1404a856c331dbf48d9deda6aaa8296ea41bf199d', # IO-stringy-2.111.tar.gz + ], + }), + ('Encode::Locale', '1.05', { + 'source_tmpl': 'Encode-Locale-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + 'checksums': [ + '176fa02771f542a4efb1dbc2a4c928e8f4391bf4078473bd6040d8f11adb0ec1', # Encode-Locale-1.05.tar.gz + ], + }), + ('XML::SAX::Base', '1.09', { + 'source_tmpl': 'XML-SAX-Base-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GR/GRANTM'], + 'checksums': [ + '66cb355ba4ef47c10ca738bd35999723644386ac853abbeb5132841f5e8a2ad0', # XML-SAX-Base-1.09.tar.gz + ], + }), + ('XML::NamespaceSupport', '1.12', { + 'source_tmpl': 'XML-NamespaceSupport-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PERIGRIN'], + 'checksums': [ + '47e995859f8dd0413aa3f22d350c4a62da652e854267aa0586ae544ae2bae5ef', # XML-NamespaceSupport-1.12.tar.gz + ], + }), + ('XML::SAX', '0.99', { + 'source_tmpl': 'XML-SAX-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GR/GRANTM'], + 'checksums': [ + '32b04b8e36b6cc4cfc486de2d859d87af5386dd930f2383c49347050d6f5ad84', # XML-SAX-0.99.tar.gz + ], + }), + ('Test::LeakTrace', '0.16', { + 'source_tmpl': 'Test-LeakTrace-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEEJO'], + 'checksums': [ + '5f089eed915f1ec8c743f6d2777c3ecd0ca01df2f7b9e10038d316952583e403', # Test-LeakTrace-0.16.tar.gz + ], + }), + ('Test::Exception', '0.43', { + 'source_tmpl': 'Test-Exception-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + 'checksums': [ + '156b13f07764f766d8b45a43728f2439af81a3512625438deab783b7883eb533', # Test-Exception-0.43.tar.gz + ], + }), + ('Text::Table', '1.133', { + 'source_tmpl': 'Text-Table-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'], + 'checksums': [ + 'cd9ee04860d09a19a9d6bd2254a4bf3144ac14a63c08f15a1e28601b4b2f7012', # Text-Table-1.133.tar.gz + ], + }), + ('MIME::Types', '2.13', { + 'source_tmpl': 'MIME-Types-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARKOV'], + 'checksums': [ + '99c3376357bbe22cc8b6c78f560aa18d81621287695cd629008a6c4e66b77bf8', # MIME-Types-2.13.tar.gz + ], + }), + ('Module::Build::XSUtil', '0.16', { + 'source_tmpl': 'Module-Build-XSUtil-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HI/HIDEAKIO'], + 'checksums': [ + '15762fa4e43b41302cff261c7ad75aacdc874f416981f206d783f20acd023adb', # Module-Build-XSUtil-0.16.tar.gz + ], + }), + ('Tie::Function', '0.02', { + 'source_tmpl': 'Tie-Function-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAVIDNICO/handy_tied_functions'], + 'checksums': [ + '0b1617af218dfab911ba0fbd72210529a246efe140332da77fe3e03d11000117', # Tie-Function-0.02.tar.gz + ], + }), + ('Template::Plugin::Number::Format', '1.06', { + 'source_tmpl': 'Template-Plugin-Number-Format-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DARREN'], + 'checksums': [ + # Template-Plugin-Number-Format-1.06.tar.gz + '0865836a1bcbc34d4a0ee34b5ccc14d7b511f1fd300bf390f002dac349539843', + ], + }), + ('HTML::Parser', '3.72', { + 'source_tmpl': 'HTML-Parser-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + 'checksums': [ + 'ec28c7e1d9e67c45eca197077f7cdc41ead1bb4c538c7f02a3296a4bb92f608b', # HTML-Parser-3.72.tar.gz + ], + }), + ('Date::Handler', '1.2', { + 'source_tmpl': 'Date-Handler-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BB/BBEAUSEJ'], + 'checksums': [ + 'c36fd2b68d48c2e17417bf2873c78820f3ae02460fdf5976b8eeab887d59e16c', # Date-Handler-1.2.tar.gz + ], + }), + ('Params::Util', '1.07', { + 'source_tmpl': 'Params-Util-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + 'checksums': [ + '30f1ec3f2cf9ff66ae96f973333f23c5f558915bb6266881eac7423f52d7c76c', # Params-Util-1.07.tar.gz + ], + }), + ('IO::HTML', '1.001', { + 'source_tmpl': 'IO-HTML-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CJ/CJM'], + 'checksums': [ + 'ea78d2d743794adc028bc9589538eb867174b4e165d7d8b5f63486e6b828e7e0', # IO-HTML-1.001.tar.gz + ], + }), + ('Data::Grove', '0.08', { + 'source_tmpl': 'libxml-perl-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KM/KMACLEOD'], + 'checksums': [ + '4571059b7b5d48b7ce52b01389e95d798bf5cf2020523c153ff27b498153c9cb', # libxml-perl-0.08.tar.gz + ], + }), + ('Class::ISA', '0.36', { + 'source_tmpl': 'Class-ISA-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SM/SMUELLER'], + 'checksums': [ + '8816f34e9a38e849a10df756030dccf9fe061a196c11ac3faafd7113c929b964', # Class-ISA-0.36.tar.gz + ], + }), + ('URI', '1.72', { + 'source_tmpl': 'URI-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': [ + '35f14431d4b300de4be1163b0b5332de2d7fbda4f05ff1ed198a8e9330d40a32', # URI-1.72.tar.gz + ], + }), + ('Ima::DBI', '0.35', { + 'source_tmpl': 'Ima-DBI-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PERRIN'], + 'checksums': [ + '8b481ceedbf0ae4a83effb80581550008bfdd3885ef01145e3733c7097c00a08', # Ima-DBI-0.35.tar.gz + ], + }), + ('Tie::IxHash', '1.23', { + 'source_tmpl': 'Tie-IxHash-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CH/CHORNY'], + 'checksums': [ + 'fabb0b8c97e67c9b34b6cc18ed66f6c5e01c55b257dcf007555e0b027d4caf56', # Tie-IxHash-1.23.tar.gz + ], + }), + ('GO', '0.04', { + 'source_tmpl': 'go-db-perl-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SJ/SJCARBON'], + 'checksums': [ + '8eb73d591ad767e7cf26def40cffd84833875f1ad51e456960b9ed73dc23641b', # go-db-perl-0.04.tar.gz + ], + }), + ('Class::DBI::SQLite', '0.11', { + 'source_tmpl': 'Class-DBI-SQLite-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA'], + 'checksums': [ + 'c4661b00afb7e53c97ac36e13f34dde43c1a93540a2f4ff97e6182b0c731e4e7', # Class-DBI-SQLite-0.11.tar.gz + ], + }), + ('Pod::POM', '2.01', { + 'source_tmpl': 'Pod-POM-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB'], + 'checksums': [ + '1b50fba9bbdde3ead192beeba0eaddd0c614e3afb1743fa6fff805f57c56f7f4', # Pod-POM-2.01.tar.gz + ], + }), + ('Math::Round', '0.07', { + 'source_tmpl': 'Math-Round-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GR/GROMMEL'], + 'checksums': [ + '73a7329a86e54a5c29a440382e5803095b58f33129e61a1df0093b4824de9327', # Math-Round-0.07.tar.gz + ], + }), + ('Text::Diff', '1.45', { + 'source_tmpl': 'Text-Diff-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB'], + 'checksums': [ + 'e8baa07b1b3f53e00af3636898bbf73aec9a0ff38f94536ede1dbe96ef086f04', # Text-Diff-1.45.tar.gz + ], + }), + ('Log::Message::Simple', '0.10', { + 'source_tmpl': 'Log-Message-Simple-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + 'checksums': [ + 'aa12d1a4c0ac260b94d448fa01feba242a8a85cb6cbfdc66432e3b5b468add96', # Log-Message-Simple-0.10.tar.gz + ], + }), + ('IO::Socket::SSL', '2.050', { + 'source_tmpl': 'IO-Socket-SSL-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SU/SULLR'], + 'checksums': [ + '54e6716e40df8b1c168d8f54a0b8f215313739bd99dda17adb7c00fe94656692', # IO-Socket-SSL-2.050.tar.gz + ], + }), + ('Fennec::Lite', '0.004', { + 'source_tmpl': 'Fennec-Lite-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + 'checksums': [ + 'dce28e3932762c2ff92aa52d90405c06e898e81cb7b164ccae8966ae77f1dcab', # Fennec-Lite-0.004.tar.gz + ], + }), + ('Sub::Uplevel', '0.2800', { + 'source_tmpl': 'Sub-Uplevel-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + 'checksums': [ + 'b4f3f63b80f680a421332d8851ddbe5a8e72fcaa74d5d1d98f3c8cc4a3ece293', # Sub-Uplevel-0.2800.tar.gz + ], + }), + ('Meta::Builder', '0.003', { + 'source_tmpl': 'Meta-Builder-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + 'checksums': [ + 'e7ac289b88d1662e87708d716877ac66a1a8414660996fe58c1db96d834a5375', # Meta-Builder-0.003.tar.gz + ], + }), + ('Exporter::Declare', '0.114', { + 'source_tmpl': 'Exporter-Declare-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + 'checksums': [ + '4bd70d6ca76f6f6ba7e4c618d4ac93b8593a58f1233ccbe18b10f5f204f1d4e4', # Exporter-Declare-0.114.tar.gz + ], + }), + ('Getopt::Long', '2.50', { + 'source_tmpl': 'Getopt-Long-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JV/JV'], + 'checksums': [ + '20881adb2b73e83825f9a0a3b141db11b3a555e1d3775b13d81d0481623e4b67', # Getopt-Long-2.50.tar.gz + ], + }), + ('Log::Message', '0.08', { + 'source_tmpl': 'Log-Message-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + 'checksums': [ + 'bd697dd62aaf26d118e9f0a0813429deb1c544e4501559879b61fcbdfe99fe46', # Log-Message-0.08.tar.gz + ], + }), + ('Mouse', 'v2.4.10', { + 'source_tmpl': 'Mouse-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GF/GFUJI'], + 'checksums': [ + 'b995dda1918fcebecff34458b6abd16c06b6a7844572c7293d72a24d18126d14', # Mouse-v2.4.10.tar.gz + ], + }), + ('Test::Version', '2.05', { + 'source_tmpl': 'Test-Version-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE'], + 'checksums': [ + '39c0ec02663da0e56962bdafaef6790cf83d12b4d90e8a4cdc971d57d869d63f', # Test-Version-2.05.tar.gz + ], + }), + ('DBIx::Admin::TableInfo', '3.03', { + 'source_tmpl': 'DBIx-Admin-TableInfo-%(version)s.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + 'checksums': [ + 'a852530f95957a43aa794f2edf5f3fe4ecec35bd20150c38136d4c23d85328b6', # DBIx-Admin-TableInfo-3.03.tgz + ], + }), + ('Net::HTTP', '6.16', { + 'source_tmpl': 'Net-HTTP-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'], + 'checksums': [ + '70c45b6aaf3e9fb1ce30a1fc3cf828cfaee45c5c0bd147b2f617efade1765e78', # Net-HTTP-6.16.tar.gz + ], + }), + ('Test::Deep', '1.127', { + 'source_tmpl': 'Test-Deep-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': [ + 'b78cfc59c41ba91f47281e2c1d2bfc4b3b1b42bfb76b4378bc88cc37b7af7268', # Test-Deep-1.127.tar.gz + ], + }), + ('Test::Warn', '0.32', { + 'source_tmpl': 'Test-Warn-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BIGJ'], + 'checksums': [ + '2fc516e71f9ef453be22a4619d91eb3f78df414a57dfa0fd745d3bff50bf73d2', # Test-Warn-0.32.tar.gz + ], + }), + ('MRO::Compat', '0.13', { + 'source_tmpl': 'MRO-Compat-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + 'checksums': [ + '8a2c3b6ccc19328d5579d02a7d91285e2afd85d801f49d423a8eb16f323da4f8', # MRO-Compat-0.13.tar.gz + ], + }), + ('Moo', '2.003002', { + 'source_tmpl': 'Moo-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + 'checksums': [ + 'f3e9741e79baa63e89f5a08706cd80d18c0a5a37e3d898847e002310e06582f1', # Moo-2.003002.tar.gz + ], + }), + ('Hash::Merge', '0.200', { + 'source_tmpl': 'Hash-Merge-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + 'checksums': [ + '47f9f03330b7595c94e73bdd17dc6682ba59d1cc89e63f4e319617f4bb122a64', # Hash-Merge-0.200.tar.gz + ], + }), + ('SQL::Abstract', '1.84', { + 'source_tmpl': 'SQL-Abstract-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IL/ILMARI'], + 'checksums': [ + '655f4aa3d4ea7ca0a7bafb2beff84010d5c77f0ee4413baa0c86456bf6db5e75', # SQL-Abstract-1.84.tar.gz + ], + }), + ('HTML::Form', '6.03', { + 'source_tmpl': 'HTML-Form-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + 'checksums': [ + '68c01d94f005d5ca9c4d55ad2a1bf3a8d034a5fc6db187d91a4c42f3fdc9fc36', # HTML-Form-6.03.tar.gz + ], + }), + ('File::Copy::Recursive', '0.38', { + 'source_tmpl': 'File-Copy-Recursive-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DM/DMUEY'], + 'checksums': [ + '84ccbddf3894a88a2c2b6be68ff6ef8960037803bb36aa228b31944cfdf6deeb', # File-Copy-Recursive-0.38.tar.gz + ], + }), + ('Number::Compare', '0.03', { + 'source_tmpl': 'Number-Compare-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RC/RCLAMP'], + 'checksums': [ + '83293737e803b43112830443fb5208ec5208a2e6ea512ed54ef8e4dd2b880827', # Number-Compare-0.03.tar.gz + ], + }), + ('IPC::Run', '0.96', { + 'source_tmpl': 'IPC-Run-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR'], + 'checksums': [ + 'bbd24ff027e1c232b3dc027562c9f4386da72b76991d30f9f3d4119e87cf4640', # IPC-Run-0.96.tar.gz + ], + }), + ('HTML::Entities::Interpolate', '1.10', { + 'source_tmpl': 'HTML-Entities-Interpolate-%(version)s.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + 'checksums': [ + 'f15a9df92c282419f7010964aca1ada844ddfae7afc735cd2ba1bb20883e955c', # HTML-Entities-Interpolate-1.10.tgz + ], + }), + ('File::Remove', '1.57', { + 'source_tmpl': 'File-Remove-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'], + 'checksums': [ + 'b3becd60165c38786d18285f770b8b06ebffe91797d8c00cc4730614382501ad', # File-Remove-1.57.tar.gz + ], + }), + ('YAML::Tiny', '1.70', { + 'source_tmpl': 'YAML-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': [ + 'bbce4b52b5eafdb04e3043975a08dbf394d00b7d2c958adb9d03d9f7e9291255', # YAML-Tiny-1.70.tar.gz + ], + }), + ('Module::Install', '1.18', { + 'source_tmpl': 'Module-Install-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': [ + '29068ac33502cec959844c206516c09cc4a847cb57327d41015f605153ca645e', # Module-Install-1.18.tar.gz + ], + }), + ('Test::ClassAPI', '1.06', { + 'source_tmpl': 'Test-ClassAPI-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + 'checksums': [ + '06f82d076501701d78b8dc40b7688507bcc6c58b1beafd559e05bb0644df00a2', # Test-ClassAPI-1.06.tar.gz + ], + }), + ('Test::Most', '0.35', { + 'source_tmpl': 'Test-Most-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OV/OVID'], + 'checksums': [ + '9897a6f4d751598d2ed1047e01c1554b01d0f8c96c45e7e845229782bf6f657f', # Test-Most-0.35.tar.gz + ], + }), + ('Class::Accessor', '0.34', { + 'source_tmpl': 'Class-Accessor-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KA/KASEI'], + 'checksums': [ + 'cdb1e0cdf8380fb9b63b44c33ce5afc1068736d55ac5904bf0eaa1efc1c3cefc', # Class-Accessor-0.34.tar.gz + ], + }), + ('Test::Differences', '0.64', { + 'source_tmpl': 'Test-Differences-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DC/DCANTRELL'], + 'checksums': [ + '9f459dd9c2302a0a73e2f5528a0ce7d09d6766f073187ae2c69e603adf2eb276', # Test-Differences-0.64.tar.gz + ], + }), + ('HTTP::Tiny', '0.070', { + 'source_tmpl': 'HTTP-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + 'checksums': [ + '74f385d1e96de887a4df5a222d93afdc7d81ea9ad721a56ff3d8449bb12f7733', # HTTP-Tiny-0.070.tar.gz + ], + }), + ('Package::DeprecationManager', '0.17', { + 'source_tmpl': 'Package-DeprecationManager-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + 'checksums': [ + # Package-DeprecationManager-0.17.tar.gz + '1d743ada482b5c9871d894966e87d4c20edc96931bb949fb2638b000ddd6684b', + ], + }), + ('Digest::SHA1', '2.13', { + 'source_tmpl': 'Digest-SHA1-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + 'checksums': [ + '68c1dac2187421f0eb7abf71452a06f190181b8fc4b28ededf5b90296fb943cc', # Digest-SHA1-2.13.tar.gz + ], + }), + ('Date::Language', '2.30', { + 'source_tmpl': 'TimeDate-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GB/GBARR'], + 'checksums': [ + '75bd254871cb5853a6aa0403ac0be270cdd75c9d1b6639f18ecba63c15298e86', # TimeDate-2.30.tar.gz + ], + }), + ('version', '0.9918', { + 'source_tmpl': 'version-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JP/JPEACOCK'], + 'checksums': [ + '54175c7ead4e2259c2fb2b83440b821e4287842067227e48fb899b5cae52237b', # version-0.9918.tar.gz + ], + }), + ('Sub::Uplevel', '0.2800', { + 'source_tmpl': 'Sub-Uplevel-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + 'checksums': [ + 'b4f3f63b80f680a421332d8851ddbe5a8e72fcaa74d5d1d98f3c8cc4a3ece293', # Sub-Uplevel-0.2800.tar.gz + ], + }), + ('XML::Bare', '0.53', { + 'source_tmpl': 'XML-Bare-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CO/CODECHILD'], + 'patches': ['XML-Bare-0.53_icc.patch'], + 'checksums': [ + '865e198e98d904be1683ef5a53a4948f02dabdacde59fc554a082ffbcc5baefd', # XML-Bare-0.53.tar.gz + '7d005e44222a0ce130b8ba4912a869675c0aa9ce4d1b95caba06b683b69f2b20', # XML-Bare-0.53_icc.patch + ], + }), + ('Dist::CheckConflicts', '0.11', { + 'source_tmpl': 'Dist-CheckConflicts-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DO/DOY'], + 'checksums': [ + 'ea844b9686c94d666d9d444321d764490b2cde2f985c4165b4c2c77665caedc4', # Dist-CheckConflicts-0.11.tar.gz + ], + }), + ('Sub::Name', '0.21', { + 'source_tmpl': 'Sub-Name-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': [ + 'bd32e9dee07047c10ae474c9f17d458b6e9885a6db69474c7a494ccc34c27117', # Sub-Name-0.21.tar.gz + ], + }), + ('Time::Piece', '1.3201', { + 'source_tmpl': 'Time-Piece-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ES/ESAYM'], + 'checksums': [ + '81dbe694474a13d9683c392edd54bd77b6bd6d20b41433358487b51eb71e31bd', # Time-Piece-1.3201.tar.gz + ], + }), + ('Digest::HMAC', '1.03', { + 'source_tmpl': 'Digest-HMAC-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + 'checksums': [ + '3bc72c6d3ff144d73aefb90e9a78d33612d58cf1cd1631ecfb8985ba96da4a59', # Digest-HMAC-1.03.tar.gz + ], + }), + ('HTTP::Negotiate', '6.01', { + 'source_tmpl': 'HTTP-Negotiate-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + 'checksums': [ + '1c729c1ea63100e878405cda7d66f9adfd3ed4f1d6cacaca0ee9152df728e016', # HTTP-Negotiate-6.01.tar.gz + ], + }), + ('MIME::Lite', '3.030', { + 'source_tmpl': 'MIME-Lite-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': [ + '8f39901bc580bc3dce69e10415305e4435ff90264c63d29f707b4566460be962', # MIME-Lite-3.030.tar.gz + ], + }), + ('Crypt::Rijndael', '1.13', { + 'source_tmpl': 'Crypt-Rijndael-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': [ + 'cd7209a6dfe0a3dc8caffe1aa2233b0e6effec7572d76a7a93feefffe636214e', # Crypt-Rijndael-1.13.tar.gz + ], + }), + ('B::Lint', '1.20', { + 'source_tmpl': 'B-Lint-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': [ + 'dc49408964fd8b7963859c92e013f0b9f92f74be5a7c2a78e3996279827c10b3', # B-Lint-1.20.tar.gz + ], + }), + ('Canary::Stability', '2012', { + 'source_tmpl': 'Canary-Stability-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/ML/MLEHMANN'], + 'checksums': [ + 'fd240b111d834dbae9630c59b42fae2145ca35addc1965ea311edf0d07817107', # Canary-Stability-2012.tar.gz + ], + }), + ('AnyEvent', '7.14', { + 'source_tmpl': 'AnyEvent-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/ML/MLEHMANN'], + 'checksums': [ + '539358d225bad34b4a64f5217f8c2a707b15e3a28c74120c9dd2270c7cca7d2a', # AnyEvent-7.14.tar.gz + ], + }), + ('Object::Accessor', '0.48', { + 'source_tmpl': 'Object-Accessor-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + 'checksums': [ + '76cb824a27b6b4e560409fcf6fd5b3bfbbd38b72f1f3d37ed0b54bd9c0baeade', # Object-Accessor-0.48.tar.gz + ], + }), + ('Data::UUID', '1.221', { + 'source_tmpl': 'Data-UUID-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': [ + '3cc7b2a3a7b74b45a059e013f7fd878078500ea4b7269036f84556b022078667', # Data-UUID-1.221.tar.gz + ], + }), + ('Test::Pod', '1.51', { + 'source_tmpl': 'Test-Pod-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': [ + 'c1a1d3cedf4a579e3aad89c36f9878a8542b6656dbe71f1581420f49582d7efb', # Test-Pod-1.51.tar.gz + ], + }), + ('AppConfig', '1.71', { + 'source_tmpl': 'AppConfig-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB'], + 'checksums': [ + '1177027025ecb09ee64d9f9f255615c04db5e14f7536c344af632032eb887b0f', # AppConfig-1.71.tar.gz + ], + }), + ('Net::SMTP::SSL', '1.04', { + 'source_tmpl': 'Net-SMTP-SSL-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': [ + '7b29c45add19d3d5084b751f7ba89a8e40479a446ce21cfd9cc741e558332a00', # Net-SMTP-SSL-1.04.tar.gz + ], + }), + ('XML::Tiny', '2.07', { + 'source_tmpl': 'XML-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DC/DCANTRELL'], + 'checksums': [ + 'ce39fcb53e0fe9f1cbcd86ddf152e1db48566266b70ec0769ef364eeabdd8941', # XML-Tiny-2.07.tar.gz + ], + }), + ('HTML::Tagset', '3.20', { + 'source_tmpl': 'HTML-Tagset-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PETDANCE'], + 'checksums': [ + 'adb17dac9e36cd011f5243881c9739417fd102fce760f8de4e9be4c7131108e2', # HTML-Tagset-3.20.tar.gz + ], + }), + ('HTML::Tree', '5.06', { + 'source_tmpl': 'HTML-Tree-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KE/KENTNL'], + 'checksums': [ + '9c36eb19cbdf9a5906c858948ca51c35bd7561f52cc18c43281acbe57327536e', # HTML-Tree-5.06.tar.gz + ], + }), + ('Devel::GlobalDestruction', '0.14', { + 'source_tmpl': 'Devel-GlobalDestruction-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + 'checksums': [ + '34b8a5f29991311468fe6913cadaba75fd5d2b0b3ee3bb41fe5b53efab9154ab', # Devel-GlobalDestruction-0.14.tar.gz + ], + }), + ('WWW::RobotRules', '6.02', { + 'source_tmpl': 'WWW-RobotRules-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + 'checksums': [ + '46b502e7a288d559429891eeb5d979461dd3ecc6a5c491ead85d165b6e03a51e', # WWW-RobotRules-6.02.tar.gz + ], + }), + ('Expect', '1.35', { + 'source_tmpl': 'Expect-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JA/JACOBY'], + 'checksums': [ + '09d92761421decd495853103379165a99efbf452c720f30277602cf23679fd06', # Expect-1.35.tar.gz + ], + }), + ('Term::UI', '0.46', { + 'source_tmpl': 'Term-UI-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + 'checksums': [ + '91946c80d7f4aab0ca4bfedc3bbe0a75b37cab1a29bd7bca3b3b7456d417e9a6', # Term-UI-0.46.tar.gz + ], + }), + ('Net::SNMP', 'v6.0.1', { + 'source_tmpl': 'Net-SNMP-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DT/DTOWN'], + 'checksums': [ + '14c37bc1cbb3f3cdc7d6c13e0f27a859f14cdcfd5ea54a0467a88bc259b0b741', # Net-SNMP-v6.0.1.tar.gz + ], + }), + ('XML::SAX::Writer', '0.57', { + 'source_tmpl': 'XML-SAX-Writer-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PERIGRIN'], + 'checksums': [ + '3d61d07ef43b0126f5b4de4f415a256fa859fa88dc4fdabaad70b7be7c682cf0', # XML-SAX-Writer-0.57.tar.gz + ], + }), + ('Statistics::Descriptive', '3.0612', { + 'source_tmpl': 'Statistics-Descriptive-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'], + 'checksums': [ + '772413148e5e00efb32f277c4254aa78b9112490a896208dcd0025813afdbf7a', # Statistics-Descriptive-3.0612.tar.gz + ], + }), + ('Class::Load', '0.24', { + 'source_tmpl': 'Class-Load-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': [ + '0bb983da46c146534fc77a556d6e40d925142f2eb43103534025ee545265ca36', # Class-Load-0.24.tar.gz + ], + }), + ('LWP::Simple', '6.26', { + 'source_tmpl': 'libwww-perl-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'], + 'checksums': [ + 'd0c5435275f8638ff36fff8f655ad2ccad1156e66cc47bfacfb9e44fc585b24f', # libwww-perl-6.26.tar.gz + ], + }), + ('Time::Piece::MySQL', '0.06', { + 'source_tmpl': 'Time-Piece-MySQL-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KA/KASEI'], + 'checksums': [ + '319601feec17fae344988a5ee91cfc6a0bcfe742af77dba254724c3268b2a60f', # Time-Piece-MySQL-0.06.tar.gz + ], + }), + ('Package::Stash::XS', '0.28', { + 'source_tmpl': 'Package-Stash-XS-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DO/DOY'], + 'checksums': [ + '23d8c5c25768ef1dc0ce53b975796762df0d6e244445d06e48d794886c32d486', # Package-Stash-XS-0.28.tar.gz + ], + }), + ('GD::Graph', '1.54', { + 'source_tmpl': 'GDGraph-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RU/RUZ'], + 'checksums': [ + 'b96f5c10b656c17d16ab65a1777c908297b028d3b6815f6d54b2337f006bfa4f', # GDGraph-1.54.tar.gz + ], + }), + ('Set::Array', '0.30', { + 'source_tmpl': 'Set-Array-%(version)s.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + 'checksums': [ + 'd9f024c8e3637feccdebcf6479b6754b6c92f1209f567feaf0c23818af31ee3c', # Set-Array-0.30.tgz + ], + }), + ('boolean', '0.46', { + 'source_tmpl': 'boolean-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IN/INGY'], + 'checksums': [ + '95c088085c3e83bf680fe6ce16d8264ec26310490f7d1680e416ea7a118f156a', # boolean-0.46.tar.gz + ], + }), + ('Number::Format', '1.75', { + 'source_tmpl': 'Number-Format-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/W/WR/WRW'], + 'checksums': [ + '82d659cb16461764fd44d11a9ce9e6a4f5e8767dc1069eb03467c6e55de257f3', # Number-Format-1.75.tar.gz + ], + }), + ('Data::Stag', '0.14', { + 'source_tmpl': 'Data-Stag-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CM/CMUNGALL'], + 'checksums': [ + '4ab122508d2fb86d171a15f4006e5cf896d5facfa65219c0b243a89906258e59', # Data-Stag-0.14.tar.gz + ], + }), + ('Test::NoWarnings', '1.04', { + 'source_tmpl': 'Test-NoWarnings-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + 'checksums': [ + '638a57658cb119af1fe5b15e73d47c2544dcfef84af0c6b1b2e97f08202b686c', # Test-NoWarnings-1.04.tar.gz + ], + }), + ('Crypt::DES', '2.07', { + 'source_tmpl': 'Crypt-DES-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DP/DPARIS'], + 'checksums': [ + '2db1ebb5837b4cb20051c0ee5b733b4453e3137df0a92306034c867621edd7e7', # Crypt-DES-2.07.tar.gz + ], + }), + ('Exporter', '5.72', { + 'source_tmpl': 'Exporter-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR'], + 'checksums': [ + 'cd13b7a0e91e8505a0ce4b25f40fab2c92bb28a99ef0d03da1001d95a32f0291', # Exporter-5.72.tar.gz + ], + }), + ('Class::Inspector', '1.32', { + 'source_tmpl': 'Class-Inspector-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE'], + 'checksums': [ + 'cefadc8b5338e43e570bc43f583e7c98d535c17b196bcf9084bb41d561cc0535', # Class-Inspector-1.32.tar.gz + ], + }), + ('Parse::RecDescent', '1.967015', { + 'source_tmpl': 'Parse-RecDescent-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JT/JTBRAUN'], + 'checksums': [ + '1943336a4cb54f1788a733f0827c0c55db4310d5eae15e542639c9dd85656e37', # Parse-RecDescent-1.967015.tar.gz + ], + }), + ('Carp', '1.38', { + 'source_tmpl': 'Carp-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': [ + 'a5a9ce3cbb959dfefa8c2dd16552567199b286d39b0e55053ca247c038977101', # Carp-1.38.tar.gz + ], + }), + ('XML::XPath', '1.42', { + 'source_tmpl': 'XML-XPath-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MANWAR'], + 'checksums': [ + '9e6ac67c2cead5f918a060b8b9ccdbdcaa6d610be8517bba42a96cd56748b512', # XML-XPath-1.42.tar.gz + ], + }), + ('Capture::Tiny', '0.46', { + 'source_tmpl': 'Capture-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + 'checksums': [ + '5d7a6a830cf7f2b2960bf8b8afaac16a537ede64f3023827acea5bd24ca77015', # Capture-Tiny-0.46.tar.gz + ], + }), + ('JSON', '2.94', { + 'source_tmpl': 'JSON-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IS/ISHIGAKI'], + 'checksums': [ + '12271b5cee49943bbdde430eef58f1fe64ba6561980b22c69585e08fc977dc6d', # JSON-2.94.tar.gz + ], + }), + ('Sub::Exporter', '0.987', { + 'source_tmpl': 'Sub-Exporter-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': [ + '543cb2e803ab913d44272c7da6a70bb62c19e467f3b12aaac4c9523259b083d6', # Sub-Exporter-0.987.tar.gz + ], + }), + ('Class::Load::XS', '0.10', { + 'source_tmpl': 'Class-Load-XS-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': [ + '5bc22cf536ebfd2564c5bdaf42f0d8a4cee3d1930fc8b44b7d4a42038622add1', # Class-Load-XS-0.10.tar.gz + ], + }), + ('Set::IntSpan::Fast', '1.15', { + 'source_tmpl': 'Set-IntSpan-Fast-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AN/ANDYA'], + 'checksums': [ + 'cfb1768c24f55208e87405b17f537f0f303fa141891d0b22d509a941aa57e24e', # Set-IntSpan-Fast-1.15.tar.gz + ], + }), + ('Sub::Exporter::Progressive', '0.001013', { + 'source_tmpl': 'Sub-Exporter-Progressive-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/F/FR/FREW'], + 'checksums': [ + # Sub-Exporter-Progressive-0.001013.tar.gz + 'd535b7954d64da1ac1305b1fadf98202769e3599376854b2ced90c382beac056', + ], + }), + ('Data::Dumper::Concise', '2.023', { + 'source_tmpl': 'Data-Dumper-Concise-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': [ + 'a6c22f113caf31137590def1b7028a7e718eface3228272d0672c25e035d5853', # Data-Dumper-Concise-2.023.tar.gz + ], + }), + ('File::Slurp::Tiny', '0.004', { + 'source_tmpl': 'File-Slurp-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': [ + '452995beeabf0e923e65fdc627a725dbb12c9e10c00d8018c16d10ba62757f1e', # File-Slurp-Tiny-0.004.tar.gz + ], + }), + ('Algorithm::Diff', '1.1903', { + 'source_tmpl': 'Algorithm-Diff-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TY/TYEMQ'], + 'checksums': [ + '30e84ac4b31d40b66293f7b1221331c5a50561a39d580d85004d9c1fff991751', # Algorithm-Diff-1.1903.tar.gz + ], + }), + ('AnyData', '0.12', { + 'source_tmpl': 'AnyData-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + 'checksums': [ + 'be6a957f04a2feba9b305536b132deceba1f455db295b221a63e75567fadbcfc', # AnyData-0.12.tar.gz + ], + }), + ('Text::Iconv', '1.7', { + 'source_tmpl': 'Text-Iconv-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MP/MPIOTR'], + 'checksums': [ + '5b80b7d5e709d34393bcba88971864a17b44a5bf0f9e4bcee383d029e7d2d5c3', # Text-Iconv-1.7.tar.gz + ], + }), + ('Class::Data::Inheritable', '0.08', { + 'source_tmpl': 'Class-Data-Inheritable-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TM/TMTM'], + 'checksums': [ + '9967feceea15227e442ec818723163eb6d73b8947e31f16ab806f6e2391af14a', # Class-Data-Inheritable-0.08.tar.gz + ], + }), + ('Text::Balanced', '2.03', { + 'source_tmpl': 'Text-Balanced-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHAY'], + 'checksums': [ + '057753f8f0568b53921f66a60a89c30092b73329bcc61a2c43339ab70c9792c8', # Text-Balanced-2.03.tar.gz + ], + }), + ('strictures', '2.000003', { + 'source_tmpl': 'strictures-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + 'checksums': [ + '27f8ea096a521e9754d36ea32889c2cda28346d04e3e399e7ea118d182dbaf22', # strictures-2.000003.tar.gz + ], + }), + ('Switch', '2.17', { + 'source_tmpl': 'Switch-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CH/CHORNY'], + 'checksums': [ + '31354975140fe6235ac130a109496491ad33dd42f9c62189e23f49f75f936d75', # Switch-2.17.tar.gz + ], + }), + ('File::Which', '1.21', { + 'source_tmpl': 'File-Which-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE'], + 'checksums': [ + '9def5f10316bfd944e56b7f8a2501be1d44c288325309462aa9345e340854bcc', # File-Which-1.21.tar.gz + ], + }), + ('Email::Date::Format', '1.005', { + 'source_tmpl': 'Email-Date-Format-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': [ + '579c617e303b9d874411c7b61b46b59d36f815718625074ae6832e7bb9db5104', # Email-Date-Format-1.005.tar.gz + ], + }), + ('Error', '0.17025', { + 'source_tmpl': 'Error-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'], + 'checksums': [ + '6c9f474ad3d4fe0cabff6b6be532cb1dd348245986d4a6b600ad921d5cfdefaf', # Error-0.17025.tar.gz + ], + }), + ('Mock::Quick', '1.111', { + 'source_tmpl': 'Mock-Quick-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + 'checksums': [ + 'ff786008bf8c022064ececd3b7ed89c76b35e8d1eac6cf472a9f51771c1c9f2c', # Mock-Quick-1.111.tar.gz + ], + }), + ('Text::CSV', '1.95', { + 'source_tmpl': 'Text-CSV-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IS/ISHIGAKI'], + 'checksums': [ + '7e0a11d9c1129a55b68a26aa4b37c894279df255aa63ec8341d514ab848dbf61', # Text-CSV-1.95.tar.gz + ], + }), + ('Test::Output', '1.031', { + 'source_tmpl': 'Test-Output-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BD/BDFOY'], + 'checksums': [ + 'f8b8f37185717872727d06f6c078fa77db794410faf2f6da4d37b0b7650f7ea4', # Test-Output-1.031.tar.gz + ], + }), + ('Class::DBI', 'v3.0.17', { + 'source_tmpl': 'Class-DBI-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TM/TMTM'], + 'checksums': [ + '541354fe361c56850cb11261f6ca089a14573fa764792447444ff736ae626206', # Class-DBI-v3.0.17.tar.gz + ], + }), + ('List::AllUtils', '0.14', { + 'source_tmpl': 'List-AllUtils-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + 'checksums': [ + 'e45aa65927ae1975a000cc2fed14274627fa5e2bd09bab826a5f2c41d17ef6cd', # List-AllUtils-0.14.tar.gz + ], + }), + ('UNIVERSAL::moniker', '0.08', { + 'source_tmpl': 'UNIVERSAL-moniker-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KA/KASEI'], + 'checksums': [ + '94ce27a546cd57cb52e080a8f2533a7cc2350028388582485bd1039a37871f9c', # UNIVERSAL-moniker-0.08.tar.gz + ], + }), + ('Exception::Class', '1.43', { + 'source_tmpl': 'Exception-Class-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + 'checksums': [ + 'ff3b4b3f706e84aaa87ab0dee5cec6bd7a8fc9f72cf76d115212541fa0a13760', # Exception-Class-1.43.tar.gz + ], + }), + ('File::CheckTree', '4.42', { + 'source_tmpl': 'File-CheckTree-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': [ + '66fb417f8ff8a5e5b7ea25606156e70e204861c59fa8c3831925b4dd3f155f8a', # File-CheckTree-4.42.tar.gz + ], + }), + ('Math::VecStat', '0.08', { + 'source_tmpl': 'Math-VecStat-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AS/ASPINELLI'], + 'checksums': [ + '409a8e0e4b1025c8e80f628f65a9778aa77ab285161406ca4a6c097b13656d0d', # Math-VecStat-0.08.tar.gz + ], + }), + ('Pod::LaTeX', '0.61', { + 'source_tmpl': 'Pod-LaTeX-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TJ/TJENNESS'], + 'checksums': [ + '15a840ea1c8a76cd3c865fbbf2fec33b03615c0daa50f9c800c54e0cf0659d46', # Pod-LaTeX-0.61.tar.gz + ], + }), + ('Eval::Closure', '0.14', { + 'source_tmpl': 'Eval-Closure-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DO/DOY'], + 'checksums': [ + 'ea0944f2f5ec98d895bef6d503e6e4a376fea6383a6bc64c7670d46ff2218cad', # Eval-Closure-0.14.tar.gz + ], + }), + ('HTTP::Request', '6.13', { + 'source_tmpl': 'HTTP-Message-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'], + 'checksums': [ + 'f25f38428de851e5661e72f124476494852eb30812358b07f1c3a289f6f5eded', # HTTP-Message-6.13.tar.gz + ], + }), + ('XML::Twig', '3.52', { + 'source_tmpl': 'XML-Twig-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIROD'], + 'checksums': [ + 'fef75826c24f2b877d0a0d2645212fc4fb9756ed4d2711614ac15c497e8680ad', # XML-Twig-3.52.tar.gz + ], + }), + ('IO::String', '1.08', { + 'source_tmpl': 'IO-String-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + 'checksums': [ + '2a3f4ad8442d9070780e58ef43722d19d1ee21a803bf7c8206877a10482de5a0', # IO-String-1.08.tar.gz + ], + }), + ('XML::Simple', '2.24', { + 'source_tmpl': 'XML-Simple-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GR/GRANTM'], + 'checksums': [ + '9a14819fd17c75fbb90adcec0446ceab356cab0ccaff870f2e1659205dc2424f', # XML-Simple-2.24.tar.gz + ], + }), + ('Sub::Install', '0.928', { + 'source_tmpl': 'Sub-Install-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': [ + '61e567a7679588887b7b86d427bc476ea6d77fffe7e0d17d640f89007d98ef0f', # Sub-Install-0.928.tar.gz + ], + }), + ('HTTP::Cookies', '6.04', { + 'source_tmpl': 'HTTP-Cookies-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'], + 'checksums': [ + '0cc7f079079dcad8293fea36875ef58dd1bfd75ce1a6c244cd73ed9523eb13d4', # HTTP-Cookies-6.04.tar.gz + ], + }), + ('Pod::Plainer', '1.04', { + 'source_tmpl': 'Pod-Plainer-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RM/RMBARKER'], + 'checksums': [ + '1bbfbf7d1d4871e5a83bab2137e22d089078206815190eb1d5c1260a3499456f', # Pod-Plainer-1.04.tar.gz + ], + }), + ('Test::Exception::LessClever', '0.009', { + 'source_tmpl': 'Test-Exception-LessClever-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': [ + # Test-Exception-LessClever-0.009.tar.gz + '3b2731a44956a11f74b46b3ecf0734fab651e1c0bcf120f8b407aa1b4d43ac34', + ], + }), + ('LWP::MediaTypes', '6.02', { + 'source_tmpl': 'LWP-MediaTypes-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + 'checksums': [ + '18790b0cc5f0a51468495c3847b16738f785a2d460403595001e0b932e5db676', # LWP-MediaTypes-6.02.tar.gz + ], + }), + ('Scalar::Util', '1.48', { + 'source_tmpl': 'Scalar-List-Utils-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PEVANS'], + 'checksums': [ + '0e5318308789ba3625e053001da0a6c5218dc73e561a207d1b91131d06c0d09f', # Scalar-List-Utils-1.48.tar.gz + ], + }), + ('Data::Section::Simple', '0.07', { + 'source_tmpl': 'Data-Section-Simple-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA'], + 'checksums': [ + '0b3035ffdb909aa1f7ded6b608fa9d894421c82c097d51e7171170d67579a9cb', # Data-Section-Simple-0.07.tar.gz + ], + }), + ('Class::Trigger', '0.14', { + 'source_tmpl': 'Class-Trigger-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA'], + 'checksums': [ + '6b1e45acc561e0708e00a2fcf16e157cad8b8963d1bf73726f77dd809b8aebc4', # Class-Trigger-0.14.tar.gz + ], + }), + ('HTTP::Daemon', '6.01', { + 'source_tmpl': 'HTTP-Daemon-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + 'checksums': [ + '43fd867742701a3f9fcc7bd59838ab72c6490c0ebaf66901068ec6997514adc2', # HTTP-Daemon-6.01.tar.gz + ], + }), + ('File::HomeDir', '1.002', { + 'source_tmpl': 'File-HomeDir-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + 'checksums': [ + 'eb4c0c85775138460cd4013d8117232f08e88381c95c6a93b3d11e969185c274', # File-HomeDir-1.002.tar.gz + ], + }), + ('HTTP::Date', '6.02', { + 'source_tmpl': 'HTTP-Date-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + 'checksums': [ + 'e8b9941da0f9f0c9c01068401a5e81341f0e3707d1c754f8e11f42a7e629e333', # HTTP-Date-6.02.tar.gz + ], + }), + ('Authen::SASL', '2.16', { + 'source_tmpl': 'Authen-SASL-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GB/GBARR'], + 'checksums': [ + '6614fa7518f094f853741b63c73f3627168c5d3aca89b1d02b1016dc32854e09', # Authen-SASL-2.16.tar.gz + ], + }), + ('Clone', '0.39', { + 'source_tmpl': 'Clone-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GARU'], + 'checksums': [ + 'acb046683e49d650b113634ecf57df000816a49e611b0fff70bf3f93568bfa2d', # Clone-0.39.tar.gz + ], + }), + ('Data::Types', '0.09', { + 'source_tmpl': 'Data-Types-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DW/DWHEELER'], + 'checksums': [ + 'b2296fdcf9addc8e8fc39e15eb2c3d81145f6355258438bc783b12b02c41cb81', # Data-Types-0.09.tar.gz + ], + }), + ('Import::Into', '1.002005', { + 'source_tmpl': 'Import-Into-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + 'checksums': [ + 'bd9e77a3fb662b40b43b18d3280cd352edf9fad8d94283e518181cc1ce9f0567', # Import-Into-1.002005.tar.gz + ], + }), + ('DateTime::Tiny', '1.06', { + 'source_tmpl': 'DateTime-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + 'checksums': [ + 'bd725df481d7223ee787e154c116098b08a129f55e0763194b07ebea3dda33ec', # DateTime-Tiny-1.06.tar.gz + ], + }), + ('DBD::AnyData', '0.110', { + 'source_tmpl': 'DBD-AnyData-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + 'checksums': [ + '247f0d88e55076fd3f6c7bf3fd527989d62fcc1ef9bde9bf2ee11c280adcaeab', # DBD-AnyData-0.110.tar.gz + ], + }), + ('Text::Format', '0.60', { + 'source_tmpl': 'Text-Format-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'], + 'checksums': [ + '664f313570604624ff9e1fc9b26b6d04e06897b3e4eac83089fc0905a692a2b8', # Text-Format-0.60.tar.gz + ], + }), + ('Devel::CheckCompiler', '0.07', { + 'source_tmpl': 'Devel-CheckCompiler-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SY/SYOHEX'], + 'checksums': [ + '768b7697b4b8d4d372c7507b65e9dd26aa4223f7100183bbb4d3af46d43869b5', # Devel-CheckCompiler-0.07.tar.gz + ], + }), + ('Log::Handler', '0.88', { + 'source_tmpl': 'Log-Handler-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BL/BLOONIX'], + 'checksums': [ + '45bf540ab2138ed3ff93afc205b0516dc75755b86acdcc5e75c41347833c293d', # Log-Handler-0.88.tar.gz + ], + }), + ('DBIx::ContextualFetch', '1.03', { + 'source_tmpl': 'DBIx-ContextualFetch-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TM/TMTM'], + 'checksums': [ + '85e2f805bfc81cd738c294316b27a515397036f397a0ff1c6c8d754c38530306', # DBIx-ContextualFetch-1.03.tar.gz + ], + }), + ('Devel::StackTrace', '2.02', { + 'source_tmpl': 'Devel-StackTrace-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + 'checksums': [ + 'cbbd96db0ecf194ed140198090eaea0e327d9a378a4aa15f9a34b3138a91931f', # Devel-StackTrace-2.02.tar.gz + ], + }), + ('Term::ReadKey', '2.37', { + 'source_tmpl': 'TermReadKey-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JS/JSTOWE'], + 'checksums': [ + '4a9383cf2e0e0194668fe2bd546e894ffad41d556b41d2f2f577c8db682db241', # TermReadKey-2.37.tar.gz + ], + }), + ('Set::IntSpan', '1.19', { + 'source_tmpl': 'Set-IntSpan-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SW/SWMCD'], + 'checksums': [ + '11b7549b13ec5d87cc695dd4c777cd02983dd5fe9866012877fb530f48b3dfd0', # Set-IntSpan-1.19.tar.gz + ], + }), + ('Moose', '2.2006', { + 'source_tmpl': 'Moose-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': [ + 'a4e00ab25cc41bebc5e7a11d71375fb5e64b56d5f91159afee225d698e06392b', # Moose-2.2006.tar.gz + ], + }), + ('Algorithm::Dependency', '1.110', { + 'source_tmpl': 'Algorithm-Dependency-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + 'checksums': [ + 'f27733e8d89cf2ab621284c2584da90ab0cb743ba2295ee739fe51bf92561e37', # Algorithm-Dependency-1.110.tar.gz + ], + }), + ('Font::TTF', '1.06', { + 'source_tmpl': 'Font-TTF-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BH/BHALLISSY'], + 'checksums': [ + '4b697d444259759ea02d2c442c9bffe5ffe14c9214084a01f743693a944cc293', # Font-TTF-1.06.tar.gz + ], + }), + ('IPC::Run3', '0.048', { + 'source_tmpl': 'IPC-Run3-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': [ + '3d81c3cc1b5cff69cca9361e2c6e38df0352251ae7b41e2ff3febc850e463565', # IPC-Run3-0.048.tar.gz + ], + }), + ('File::Find::Rule', '0.34', { + 'source_tmpl': 'File-Find-Rule-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RC/RCLAMP'], + 'checksums': [ + '7e6f16cc33eb1f29ff25bee51d513f4b8a84947bbfa18edb2d3cc40a2d64cafe', # File-Find-Rule-0.34.tar.gz + ], + }), + ('SQL::Statement', '1.412', { + 'source_tmpl': 'SQL-Statement-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + 'checksums': [ + '65c870883379c11b53f19ead10aaac241ccc86a90bbab77f6376fe750720e5c8', # SQL-Statement-1.412.tar.gz + ], + }), + ('File::Slurp', '9999.19', { + 'source_tmpl': 'File-Slurp-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/U/UR/URI'], + 'checksums': [ + 'ce29ebe995097ebd6e9bc03284714cdfa0c46dc94f6b14a56980747ea3253643', # File-Slurp-9999.19.tar.gz + ], + }), + ('Package::Stash', '0.37', { + 'source_tmpl': 'Package-Stash-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DO/DOY'], + 'checksums': [ + '06ab05388f9130cd377c0e1d3e3bafeed6ef6a1e22104571a9e1d7bfac787b2c', # Package-Stash-0.37.tar.gz + ], + }), + ('Data::OptList', '0.110', { + 'source_tmpl': 'Data-OptList-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': [ + '366117cb2966473f2559f2f4575ff6ae69e84c69a0f30a0773e1b51a457ef5c3', # Data-OptList-0.110.tar.gz + ], + }), + ('CPANPLUS', '0.9168', { + 'source_tmpl': 'CPANPLUS-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + 'checksums': [ + 'ea7b3278a688721729244de4d8efc57536be833458d93172c412bdc7c3c1ed02', # CPANPLUS-0.9168.tar.gz + ], + }), + ('IO::Tty', '1.12', { + 'source_tmpl': 'IO-Tty-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR'], + 'checksums': [ + 'a2ef8770d3309178203f8c8ac25e623e63cf76e97830fd3be280ade1a555290d', # IO-Tty-1.12.tar.gz + ], + }), + ('Text::Soundex', '3.05', { + 'source_tmpl': 'Text-Soundex-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': [ + 'f6dd55b4280b25dea978221839864382560074e1d6933395faee2510c2db60ed', # Text-Soundex-3.05.tar.gz + ], + }), + ('Lingua::EN::PluralToSingular', '0.19', { + 'source_tmpl': 'Lingua-EN-PluralToSingular-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BK/BKB'], + 'checksums': [ + # Lingua-EN-PluralToSingular-0.19.tar.gz + 'c71b6c1aec01aae9c42aef0d9f147a437e91a7cc5cea6e4abbc35440638f299e', + ], + }), + ('Want', '0.29', { + 'source_tmpl': 'Want-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RO/ROBIN'], + 'checksums': [ + 'b4e4740b8d4cb783591273c636bd68304892e28d89e88abf9273b1de17f552f7', # Want-0.29.tar.gz + ], + }), + ('Cwd::Guard', '0.05', { + 'source_tmpl': 'Cwd-Guard-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KA/KAZEBURO'], + 'checksums': [ + '7afc7ca2b9502e440241938ad97a3e7ebd550180ebd6142e1db394186b268e77', # Cwd-Guard-0.05.tar.gz + ], + }), + ('Bundle::BioPerl', '2.1.9', { + 'source_tmpl': 'Bundle-BioPerl-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS'], + 'checksums': [ + 'c343ba97f49d86e7fb14aef4cfe3124992e2a5c3168e53a54606dd611d73e5c7', # Bundle-BioPerl-2.1.9.tar.gz + ], + }), + ('Mail::Util', '2.19', { + 'source_tmpl': 'MailTools-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARKOV'], + 'checksums': [ + 'c17ed702efea8eab56fe92961c07cd4980cee26ca6f13aff2688dc8af69c5e1a', # MailTools-2.19.tar.gz + ], + }), + ('Text::Template', '1.47', { + 'source_tmpl': 'Text-Template-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MS/MSCHOUT'], + 'checksums': [ + '50d742c74482478aa01008d468290fcfbc0b9a1219cfe1284076f1f31f0be8fc', # Text-Template-1.47.tar.gz + ], + }), + ('PDF::API2', '2.033', { + 'source_tmpl': 'PDF-API2-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SS/SSIMMS'], + 'checksums': [ + '9c0866ec1a3053f73afaca5f5cdbe6925903b4ce606f4bf4ac317731a69d27a0', # PDF-API2-2.033.tar.gz + ], + }), + ('Devel::CheckLib', '1.11', { + 'source_tmpl': 'Devel-CheckLib-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MATTN'], + 'checksums': [ + 'bd6d1c187e80be6de1f0d37add441ba8f14950c7bc1f54e764770ed484b232c1', # Devel-CheckLib-1.11.tar.gz + ], + }), + ('SVG', '2.78', { + 'source_tmpl': 'SVG-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MANWAR'], + 'checksums': [ + 'a665c1f18c0529f3da0f4b631976eb47e0f71f6d6784ef3f44d32fd76643d6bb', # SVG-2.78.tar.gz + ], + }), + ('Statistics::Basic', '1.6611', { + 'source_tmpl': 'Statistics-Basic-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JE/JETTERO'], + 'checksums': [ + '6855ce5615fd3e1af4cfc451a9bf44ff29a3140b4e7130034f1f0af2511a94fb', # Statistics-Basic-1.6611.tar.gz + ], + }), +] + +moduleclass = 'lang' -- GitLab From ecf7c6174eeb4d61e7ad4b2dfbbbe20b914e9678 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 1 Sep 2017 11:44:42 +0200 Subject: [PATCH 1484/1603] bump version of ROOT dependency --- .../p/PYTHIA/PYTHIA-8.226-intel-2017a-Python-2.7.13.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PYTHIA/PYTHIA-8.226-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/p/PYTHIA/PYTHIA-8.226-intel-2017a-Python-2.7.13.eb index 945a05625b..2e3a670906 100644 --- a/easybuild/easyconfigs/p/PYTHIA/PYTHIA-8.226-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/p/PYTHIA/PYTHIA-8.226-intel-2017a-Python-2.7.13.eb @@ -19,7 +19,7 @@ checksums = ['8ff4281bce9d22b17f1ec88e9e9353e8172512d5ef96296ace9486860e9ed2c9'] dependencies = [ ('zlib', '1.2.11'), ('Python', '2.7.13'), - ('ROOT', '6.06.02', versionsuffix), + ('ROOT', '6.10.04', versionsuffix), ] configopts = '--cxx="$CXX" --cxx-common="$CXXFLAGS" ' -- GitLab From d952c96699388745ae6c54fb60eb12ebdae4607a Mon Sep 17 00:00:00 2001 From: iotaka Date: Fri, 1 Sep 2017 12:04:44 +0200 Subject: [PATCH 1485/1603] Update CGNS-3.3.1-foss-2016b.eb --- easybuild/easyconfigs/c/CGNS/CGNS-3.3.1-foss-2016b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CGNS/CGNS-3.3.1-foss-2016b.eb b/easybuild/easyconfigs/c/CGNS/CGNS-3.3.1-foss-2016b.eb index d1ef0ef3c7..3c201e828b 100644 --- a/easybuild/easyconfigs/c/CGNS/CGNS-3.3.1-foss-2016b.eb +++ b/easybuild/easyconfigs/c/CGNS/CGNS-3.3.1-foss-2016b.eb @@ -12,7 +12,7 @@ toolchainopts = {'pic': True, 'usempi': True} source_urls = ['https://github.com/CGNS/CGNS/archive/'] sources = ['v%(version)s.tar.gz'] -checksums = ['65c55998270c3e125e28ec5c3742e15d'] +checksums = ['81093693b2e21a99c5640b82b267a495625b663d7b8125d5f1e9e7aaa1f8d469'] dependencies = [ ('HDF5', '1.10.0-patch1'), -- GitLab From 0fcce8882180470c9cb6374b462acadba494bf49 Mon Sep 17 00:00:00 2001 From: Martin Rosgaard Date: Fri, 1 Sep 2017 13:09:01 +0200 Subject: [PATCH 1486/1603] replace sanchk dirs with files in ParallelIO, space after all commas in PnetCDF and ParallelIO --- .../p/ParallelIO/ParallelIO-2.2.2a-intel-2017a.eb | 6 +++--- .../easyconfigs/p/PnetCDF/PnetCDF-1.8.1-intel-2017a.eb | 2 +- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/p/ParallelIO/ParallelIO-2.2.2a-intel-2017a.eb b/easybuild/easyconfigs/p/ParallelIO/ParallelIO-2.2.2a-intel-2017a.eb index e7c22a9446..692c33dd47 100644 --- a/easybuild/easyconfigs/p/ParallelIO/ParallelIO-2.2.2a-intel-2017a.eb +++ b/easybuild/easyconfigs/p/ParallelIO/ParallelIO-2.2.2a-intel-2017a.eb @@ -21,14 +21,14 @@ dependencies = [ ] builddependencies = [ - ('CMake', '3.8.2', '', ('GCCcore', '6.3.0')), + ('CMake', '3.8.2'), ] configopts = "-DPIO_ENABLE_TIMING=OFF " sanity_check_paths = { - 'files': ['lib/piof.a'], - 'dirs': [('include','lib')], + 'files': ['lib/libpiof.a', 'include/pio.mod'], + 'dirs': [], } modextravars = { diff --git a/easybuild/easyconfigs/p/PnetCDF/PnetCDF-1.8.1-intel-2017a.eb b/easybuild/easyconfigs/p/PnetCDF/PnetCDF-1.8.1-intel-2017a.eb index 6c3b0f7759..9badb348f2 100644 --- a/easybuild/easyconfigs/p/PnetCDF/PnetCDF-1.8.1-intel-2017a.eb +++ b/easybuild/easyconfigs/p/PnetCDF/PnetCDF-1.8.1-intel-2017a.eb @@ -14,7 +14,7 @@ checksums = ['8d7d4c9c7b39bb1cbbcf087e0d726551c50f0cc30d44aed3df63daf3772c9043'] sanity_check_paths = { 'files': ['bin/pnetcdf_version'], - 'dirs': [('include','lib','bin')], + 'dirs': ['include', 'lib'], } modextravars = { -- GitLab From 53bb24a3fa3b64db8b2e78009d4977bacb2dadf0 Mon Sep 17 00:00:00 2001 From: Martin Rosgaard Date: Fri, 1 Sep 2017 13:33:06 +0200 Subject: [PATCH 1487/1603] rm trailing whitespace in PnetCDF and ParallelIO --- .../p/ParallelIO/ParallelIO-2.2.2a-intel-2017a.eb | 10 +++++----- .../easyconfigs/p/PnetCDF/PnetCDF-1.8.1-intel-2017a.eb | 6 +++--- 2 files changed, 8 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/p/ParallelIO/ParallelIO-2.2.2a-intel-2017a.eb b/easybuild/easyconfigs/p/ParallelIO/ParallelIO-2.2.2a-intel-2017a.eb index 692c33dd47..fe293af317 100644 --- a/easybuild/easyconfigs/p/ParallelIO/ParallelIO-2.2.2a-intel-2017a.eb +++ b/easybuild/easyconfigs/p/ParallelIO/ParallelIO-2.2.2a-intel-2017a.eb @@ -16,19 +16,19 @@ checksums = ['052a03e8e3b5ac244dc53b397a9920af3066efffa216ea7f8e5e4ac73a8b8033'] separate_build_dir = True dependencies = [ - ('PnetCDF', '1.8.1'), - ('netCDF-Fortran', '4.4.4'), + ('PnetCDF', '1.8.1'), + ('netCDF-Fortran', '4.4.4'), ] builddependencies = [ - ('CMake', '3.8.2'), + ('CMake', '3.8.2'), ] configopts = "-DPIO_ENABLE_TIMING=OFF " sanity_check_paths = { - 'files': ['lib/libpiof.a', 'include/pio.mod'], - 'dirs': [], + 'files': ['lib/libpiof.a', 'include/pio.mod'], + 'dirs': [], } modextravars = { diff --git a/easybuild/easyconfigs/p/PnetCDF/PnetCDF-1.8.1-intel-2017a.eb b/easybuild/easyconfigs/p/PnetCDF/PnetCDF-1.8.1-intel-2017a.eb index 9badb348f2..fcfc6e3551 100644 --- a/easybuild/easyconfigs/p/PnetCDF/PnetCDF-1.8.1-intel-2017a.eb +++ b/easybuild/easyconfigs/p/PnetCDF/PnetCDF-1.8.1-intel-2017a.eb @@ -13,12 +13,12 @@ source_urls = ['http://cucis.ece.northwestern.edu/projects/PnetCDF/Release/'] checksums = ['8d7d4c9c7b39bb1cbbcf087e0d726551c50f0cc30d44aed3df63daf3772c9043'] sanity_check_paths = { - 'files': ['bin/pnetcdf_version'], - 'dirs': ['include', 'lib'], + 'files': ['bin/pnetcdf_version'], + 'dirs': ['include', 'lib'], } modextravars = { - 'PNETCDF': '%(installdir)s', + 'PNETCDF': '%(installdir)s', } moduleclass = 'data' -- GitLab From e43f8a3d8d90fa3413af2cdf04932280c7a1610c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 1 Sep 2017 17:18:11 +0200 Subject: [PATCH 1488/1603] rename sratoolkit 2.5.7 to SRA-Toolkit to match already existing easyconfigs --- .../SRA-Toolkit-2.5.7-centos_linux64.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/s/{sratoolkit/sratoolkit-2.5.7.eb => SRA-Toolkit/SRA-Toolkit-2.5.7-centos_linux64.eb} (97%) diff --git a/easybuild/easyconfigs/s/sratoolkit/sratoolkit-2.5.7.eb b/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-2.5.7-centos_linux64.eb similarity index 97% rename from easybuild/easyconfigs/s/sratoolkit/sratoolkit-2.5.7.eb rename to easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-2.5.7-centos_linux64.eb index adcf73dd1b..acdc89643a 100644 --- a/easybuild/easyconfigs/s/sratoolkit/sratoolkit-2.5.7.eb +++ b/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-2.5.7-centos_linux64.eb @@ -7,7 +7,7 @@ easyblock = 'PackedBinary' -name = 'sratoolkit' +name = 'SRA-Toolkit' version = '2.5.7' homepage = 'http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software' -- GitLab From b01436fc06ce4054695fa2d45f30d90710c16830 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 1 Sep 2017 17:23:14 +0200 Subject: [PATCH 1489/1603] {bio}[dummy] SRA-Toolkit 2.8.2-1 --- .../SRA-Toolkit-2.8.2-1-centos_linux64.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-2.8.2-1-centos_linux64.eb diff --git a/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-2.8.2-1-centos_linux64.eb b/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-2.8.2-1-centos_linux64.eb new file mode 100644 index 0000000000..066acd56e7 --- /dev/null +++ b/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-2.8.2-1-centos_linux64.eb @@ -0,0 +1,29 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Author: Adam Huffman +# adam.huffman@crick.ac.uk +# The Francis Crick Institute +# Based on work by npklein + +easyblock = 'PackedBinary' + +name = 'SRA-Toolkit' +version = '2.8.2-1' + +homepage = 'http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software' +description = """The SRA Toolkit, and the source-code SRA System Development + Kit (SDK), will allow you to programmatically access data housed within SRA + and convert it from the SRA format""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['http://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/%(version)s/'] +sources = ['sratoolkit.%(version)s-centos_linux64.tar.gz'] +checksums = ['b053061aae7c6d00162fe0f514be4128a60365b4b2b5b36e7f4798b348b55cf5'] + +sanity_check_paths = { + 'files': ['bin/abi-load', 'bin/fastq-dump', 'bin/sff-load', 'bin/vdb-dump'], + 'dirs': [] +} + +moduleclass = 'bio' -- GitLab From 28d19f80f3ca372a9e4d3b13bb1acbd3a399778f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 1 Sep 2017 18:16:50 +0200 Subject: [PATCH 1490/1603] add missing versionsuffix & use it in sources spec --- .../s/SRA-Toolkit/SRA-Toolkit-2.5.7-centos_linux64.eb | 3 ++- .../s/SRA-Toolkit/SRA-Toolkit-2.8.2-1-centos_linux64.eb | 3 ++- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-2.5.7-centos_linux64.eb b/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-2.5.7-centos_linux64.eb index acdc89643a..4a6fa7558e 100644 --- a/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-2.5.7-centos_linux64.eb +++ b/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-2.5.7-centos_linux64.eb @@ -9,6 +9,7 @@ easyblock = 'PackedBinary' name = 'SRA-Toolkit' version = '2.5.7' +versionsuffix = '-centos_linux64' homepage = 'http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software' description = """The SRA Toolkit, and the source-code SRA System Development @@ -18,7 +19,7 @@ description = """The SRA Toolkit, and the source-code SRA System Development toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = ['http://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/%(version)s/'] -sources = ['sratoolkit.%(version)s-centos_linux64.tar.gz'] +sources = ['sratoolkit.%(version)s%(versionsuffix)s.tar.gz'] sanity_check_paths = { 'files': ['bin/abi-load', 'bin/fastq-dump', 'bin/sff-load', 'bin/vdb-dump'], diff --git a/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-2.8.2-1-centos_linux64.eb b/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-2.8.2-1-centos_linux64.eb index 066acd56e7..07eca4b967 100644 --- a/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-2.8.2-1-centos_linux64.eb +++ b/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-2.8.2-1-centos_linux64.eb @@ -9,6 +9,7 @@ easyblock = 'PackedBinary' name = 'SRA-Toolkit' version = '2.8.2-1' +versionsuffix = '-centos_linux64' homepage = 'http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software' description = """The SRA Toolkit, and the source-code SRA System Development @@ -18,7 +19,7 @@ description = """The SRA Toolkit, and the source-code SRA System Development toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = ['http://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/%(version)s/'] -sources = ['sratoolkit.%(version)s-centos_linux64.tar.gz'] +sources = ['sratoolkit.%(version)s%(versionsuffix)s.tar.gz'] checksums = ['b053061aae7c6d00162fe0f514be4128a60365b4b2b5b36e7f4798b348b55cf5'] sanity_check_paths = { -- GitLab From 9df8c5cdaf58c095de59d2d1e6a6b3a453724cb7 Mon Sep 17 00:00:00 2001 From: Martin Rosgaard Date: Mon, 4 Sep 2017 13:33:53 +0200 Subject: [PATCH 1491/1603] trying preconfig opts for ParallelIO --- .../easyconfigs/p/ParallelIO/ParallelIO-2.2.2a-intel-2017a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/p/ParallelIO/ParallelIO-2.2.2a-intel-2017a.eb b/easybuild/easyconfigs/p/ParallelIO/ParallelIO-2.2.2a-intel-2017a.eb index fe293af317..b20a236c79 100644 --- a/easybuild/easyconfigs/p/ParallelIO/ParallelIO-2.2.2a-intel-2017a.eb +++ b/easybuild/easyconfigs/p/ParallelIO/ParallelIO-2.2.2a-intel-2017a.eb @@ -24,6 +24,7 @@ builddependencies = [ ('CMake', '3.8.2'), ] +preconfigopts = "NETCDF_C=$EBROOTNETCDF NETCDF_F=$EBROOTNETCDFMINFORTRAN " configopts = "-DPIO_ENABLE_TIMING=OFF " sanity_check_paths = { -- GitLab From 0ad69a6abfd40e36d3877f1f7d84333523ed6c25 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 4 Sep 2017 18:24:41 +0200 Subject: [PATCH 1492/1603] adding easyconfigs: GATK-3.8-0-Java-1.8.0_144.eb --- .../g/GATK/GATK-3.8-0-Java-1.8.0_144.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/g/GATK/GATK-3.8-0-Java-1.8.0_144.eb diff --git a/easybuild/easyconfigs/g/GATK/GATK-3.8-0-Java-1.8.0_144.eb b/easybuild/easyconfigs/g/GATK/GATK-3.8-0-Java-1.8.0_144.eb new file mode 100644 index 0000000000..443c272e9d --- /dev/null +++ b/easybuild/easyconfigs/g/GATK/GATK-3.8-0-Java-1.8.0_144.eb @@ -0,0 +1,44 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2013 Cyprus Institute / CaSToRC, University of Luxembourg / LCSB +# Authors:: George Tsouloupas , Fotis Georgatos , +# Kenneth Hoste (UGent) +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +# Modified by: Adam Huffman +# The Francis Crick Institute +## + +easyblock = 'Tarball' + +name = 'GATK' +version = '3.8-0' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'http://www.broadinstitute.org/gatk/' +description = """The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute + to analyse next-generation resequencing data. The toolkit offers a wide variety of tools, + with a primary focus on variant discovery and genotyping as well as strong emphasis on + data quality assurance. Its robust architecture, powerful processing engine and + high-performance computing features make it capable of taking on projects of any size.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +# download manually from http://www.broadinstitute.org/gatk/download +sources = ['GenomeAnalysisTK-%(version)s.tar.bz2'] +checksums = ['d1017b851f0cc6442b75ac88dd438e58203fa3ef1d1c38eb280071ae3803b9f1'] + +dependencies = [('Java', '1.8.0_144')] + +modloadmsg = "To execute GATK run: java -jar $EBROOTGATK/GenomeAnalysisTK.jar\n" + +sanity_check_paths = { + 'files': ["GenomeAnalysisTK.jar"], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From d1fec54c9fec6c5289348095cb213712d06eca0b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 5 Sep 2017 09:12:36 +0200 Subject: [PATCH 1493/1603] adding easyconfigs: parallel-20170822-intel-2017a.eb --- .../parallel/parallel-20170822-intel-2017a.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/p/parallel/parallel-20170822-intel-2017a.eb diff --git a/easybuild/easyconfigs/p/parallel/parallel-20170822-intel-2017a.eb b/easybuild/easyconfigs/p/parallel/parallel-20170822-intel-2017a.eb new file mode 100644 index 0000000000..35d523f42b --- /dev/null +++ b/easybuild/easyconfigs/p/parallel/parallel-20170822-intel-2017a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'parallel' +version = '20170822' + +homepage = 'http://savannah.gnu.org/projects/parallel/' +description = """parallel: Build and execute shell commands in parallel""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['8949bfa3057e194119a85a8cba2c8e0bdd46b5f5851eda583d2386b95c039148'] + +dependencies = [ + ('Perl', '5.24.1'), +] + +sanity_check_paths = { + 'files': ['bin/parallel'], + 'dirs': [] +} + +moduleclass = 'tools' -- GitLab From 60bf55591313aa5d6aae4317ac167aa3d9d02707 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Tue, 5 Sep 2017 13:53:45 +0200 Subject: [PATCH 1494/1603] Quorum/1.1.1 for intel/2017a --- .../q/Quorum/Quorum-1.1.1-intel-2017a.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/q/Quorum/Quorum-1.1.1-intel-2017a.eb diff --git a/easybuild/easyconfigs/q/Quorum/Quorum-1.1.1-intel-2017a.eb b/easybuild/easyconfigs/q/Quorum/Quorum-1.1.1-intel-2017a.eb new file mode 100644 index 0000000000..6842eb5e85 --- /dev/null +++ b/easybuild/easyconfigs/q/Quorum/Quorum-1.1.1-intel-2017a.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'Quorum' +version = '1.1.1' + +homepage = 'http://www.genome.umd.edu/quorum.html' +description = """QuorUM is an error corrector for Illumina reads""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['https://github.com/gmarcais/Quorum/releases/download/v%(version)s'] +checksums = ['45d099835eaad43cf915e118e9cb6423411d68c7f35a8145bc725dca366c82b5'] + +dependencies = [('Jellyfish', '2.2.6')] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['merge_mate_pairs', 'quorum', 'quorum_create_database', + 'quorum_error_correct_reads', 'split_mate_pairs']], + 'dirs': [] +} + +moduleclass = 'bio' -- GitLab From 2ac11ddd7dcdad2ac5c3b56ae6ebad1f0b36bd3c Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Tue, 5 Sep 2017 13:56:29 +0200 Subject: [PATCH 1495/1603] Added CVXOPT/1.1.9 --- .../c/CVXOPT/CVXOPT-1.1.9-fix-setup-py.patch | 130 ++++++++++++++++++ .../CVXOPT-1.1.9-intel-2017a-Python-2.7.13.eb | 38 +++++ 2 files changed, 168 insertions(+) create mode 100644 easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.1.9-fix-setup-py.patch create mode 100644 easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.1.9-intel-2017a-Python-2.7.13.eb diff --git a/easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.1.9-fix-setup-py.patch b/easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.1.9-fix-setup-py.patch new file mode 100644 index 0000000000..5a36e6e338 --- /dev/null +++ b/easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.1.9-fix-setup-py.patch @@ -0,0 +1,130 @@ +# Patches the setup.py to use EB settings for BLAS/LAPACK, FFTW, etc +# wpoely86@gmail.com +diff -ur cvxopt-1.1.9.orig/setup.py cvxopt-1.1.9/setup.py +--- cvxopt-1.1.9.orig/setup.py 2016-11-30 08:35:21.000000000 +0100 ++++ cvxopt-1.1.9/setup.py 2017-09-04 15:11:41.855020186 +0200 +@@ -80,10 +80,12 @@ + LAPACK_LIB = os.environ.get("CVXOPT_LAPACK_LIB",LAPACK_LIB) + BLAS_LIB_DIR = os.environ.get("CVXOPT_BLAS_LIB_DIR",BLAS_LIB_DIR) + BLAS_EXTRA_LINK_ARGS = os.environ.get("CVXOPT_BLAS_EXTRA_LINK_ARGS",BLAS_EXTRA_LINK_ARGS) ++FFTW_EXTRA_LINK_ARGS = os.environ.get("CVXOPT_FFTW_EXTRA_LINK_ARGS","") + DATA_FILES = os.environ.get("CVXOPT_DATA_FILES",[]) + if type(BLAS_LIB) is str: BLAS_LIB = BLAS_LIB.strip().split(';') + if type(LAPACK_LIB) is str: LAPACK_LIB = LAPACK_LIB.strip().split(';') +-if type(BLAS_EXTRA_LINK_ARGS) is str: BLAS_EXTRA_LINK_ARGS = BLAS_EXTRA_LINK_ARGS.strip().split(';') ++if type(BLAS_EXTRA_LINK_ARGS) is str: BLAS_EXTRA_LINK_ARGS = BLAS_EXTRA_LINK_ARGS.strip().split(' ') ++if type(FFTW_EXTRA_LINK_ARGS) is str: FFTW_EXTRA_LINK_ARGS = FFTW_EXTRA_LINK_ARGS.strip().split(' ') + if type(DATA_FILES) is str: DATA_FILES = DATA_FILES.strip().split(';') + BUILD_GSL = int(os.environ.get("CVXOPT_BUILD_GSL",BUILD_GSL)) + GSL_LIB_DIR = os.environ.get("CVXOPT_GSL_LIB_DIR",GSL_LIB_DIR) +@@ -112,7 +114,7 @@ + # optional modules + + if BUILD_GSL: +- gsl = Extension('gsl', libraries = ['m', 'gsl'] + BLAS_LIB, ++ gsl = Extension('gsl', libraries = ['m', 'gsl'], + include_dirs = [ GSL_INC_DIR ], + library_dirs = [ GSL_LIB_DIR, BLAS_LIB_DIR ], + extra_link_args = BLAS_EXTRA_LINK_ARGS, +@@ -120,10 +122,10 @@ + extmods += [gsl]; + + if BUILD_FFTW: +- fftw = Extension('fftw', libraries = ['fftw3'] + BLAS_LIB, ++ fftw = Extension('fftw', + include_dirs = [ FFTW_INC_DIR ], + library_dirs = [ FFTW_LIB_DIR, BLAS_LIB_DIR ], +- extra_link_args = BLAS_EXTRA_LINK_ARGS, ++ extra_link_args = BLAS_EXTRA_LINK_ARGS + FFTW_EXTRA_LINK_ARGS, + sources = ['src/C/fftw.c'] ) + extmods += [fftw]; + +@@ -135,7 +137,7 @@ + extmods += [glpk]; + + if BUILD_DSDP: +- dsdp = Extension('dsdp', libraries = ['dsdp'] + LAPACK_LIB + BLAS_LIB, ++ dsdp = Extension('dsdp', libraries = ['dsdp'], + include_dirs = [ DSDP_INC_DIR ], + library_dirs = [ DSDP_LIB_DIR, BLAS_LIB_DIR ], + extra_link_args = BLAS_EXTRA_LINK_ARGS, +@@ -144,19 +146,19 @@ + + # Required modules + +-base = Extension('base', libraries = ['m'] + LAPACK_LIB + BLAS_LIB, ++base = Extension('base', libraries = ['m'], + library_dirs = [ BLAS_LIB_DIR ], + define_macros = MACROS, + extra_link_args = BLAS_EXTRA_LINK_ARGS, + sources = ['src/C/base.c','src/C/dense.c','src/C/sparse.c']) + +-blas = Extension('blas', libraries = BLAS_LIB, ++blas = Extension('blas', + library_dirs = [ BLAS_LIB_DIR ], + define_macros = MACROS, + extra_link_args = BLAS_EXTRA_LINK_ARGS, + sources = ['src/C/blas.c'] ) + +-lapack = Extension('lapack', libraries = LAPACK_LIB + BLAS_LIB, ++lapack = Extension('lapack', + library_dirs = [ BLAS_LIB_DIR ], + define_macros = MACROS, + extra_link_args = BLAS_EXTRA_LINK_ARGS, +@@ -164,9 +166,10 @@ + + if not SUITESPARSE_SRC_DIR: + umfpack = Extension('umfpack', +- libraries = ['umfpack','cholmod','amd','colamd','suitesparseconfig'] + LAPACK_LIB + BLAS_LIB + RT_LIB, ++ libraries = ['umfpack','cholmod','amd','colamd','suitesparseconfig'] + RT_LIB, + include_dirs = [SUITESPARSE_INC_DIR], + library_dirs = [SUITESPARSE_LIB_DIR, BLAS_LIB_DIR], ++ extra_link_args = BLAS_EXTRA_LINK_ARGS, + sources = ['src/C/umfpack.c']) + else: + umfpack = Extension('umfpack', +@@ -177,7 +180,6 @@ + SUITESPARSE_SRC_DIR + '/SuiteSparse_config' ], + library_dirs = [ BLAS_LIB_DIR ], + define_macros = MACROS + [('NTIMER', '1'), ('NCHOLMOD', '1')], +- libraries = LAPACK_LIB + BLAS_LIB, + extra_compile_args = ['-Wno-unknown-pragmas'], + extra_link_args = BLAS_EXTRA_LINK_ARGS, + sources = [ 'src/C/umfpack.c', +@@ -190,14 +192,14 @@ + + if not SUITESPARSE_SRC_DIR: + cholmod = Extension('cholmod', +- libraries = ['cholmod','colamd','amd','suitesparseconfig'] + LAPACK_LIB + BLAS_LIB + RT_LIB, ++ libraries = ['cholmod','colamd','amd','suitesparseconfig'] + RT_LIB, + include_dirs = [SUITESPARSE_INC_DIR], + library_dirs = [SUITESPARSE_LIB_DIR, BLAS_LIB_DIR], ++ extra_link_args = BLAS_EXTRA_LINK_ARGS, + sources = [ 'src/C/cholmod.c' ]) + else: + cholmod = Extension('cholmod', + library_dirs = [ BLAS_LIB_DIR ], +- libraries = LAPACK_LIB + BLAS_LIB, + include_dirs = [ SUITESPARSE_SRC_DIR + '/CHOLMOD/Include', + SUITESPARSE_SRC_DIR + '/COLAMD', + SUITESPARSE_SRC_DIR + '/AMD/Include', +@@ -219,17 +221,18 @@ + libraries = ['amd','suitesparseconfig'] + RT_LIB, + include_dirs = [SUITESPARSE_INC_DIR], + library_dirs = [SUITESPARSE_LIB_DIR], ++ extra_link_args = BLAS_EXTRA_LINK_ARGS, + sources = ['src/C/amd.c']) + else: + amd = Extension('amd', + include_dirs = [SUITESPARSE_SRC_DIR + '/AMD/Include', + SUITESPARSE_SRC_DIR + '/SuiteSparse_config' ], + define_macros = MACROS + [('NTIMER', '1')], ++ extra_link_args = BLAS_EXTRA_LINK_ARGS, + sources = [ 'src/C/amd.c', SUITESPARSE_SRC_DIR + '/SuiteSparse_config/SuiteSparse_config.c'] + + glob(SUITESPARSE_SRC_DIR + '/AMD/Source/*.c') ) + + misc_solvers = Extension('misc_solvers', +- libraries = LAPACK_LIB + BLAS_LIB, + library_dirs = [ BLAS_LIB_DIR ], + define_macros = MACROS, + extra_link_args = BLAS_EXTRA_LINK_ARGS, diff --git a/easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.1.9-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.1.9-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..673c7c6791 --- /dev/null +++ b/easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.1.9-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,38 @@ +easyblock = "PythonPackage" + +name = 'CVXOPT' +version = '1.1.9' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://cvxopt.org' +description = """CVXOPT is a free software package for convex optimization based on the Python programming language. + Its main purpose is to make the development of software for convex optimization applications straightforward by + building on Python's extensive standard library and on the strengths of Python as a high-level programming language. +""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/cvxopt/cvxopt/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['09997fec809179c9bb9fe8cdd202ad6ecb675f890658219022f492e0797122ee'] + +patches = ['%(name)s-%(version)s-fix-setup-py.patch'] + +dependencies = [ + ('Python', '2.7.13'), + ('SuiteSparse', '4.5.5', '-METIS-5.1.0'), + ('GSL', '2.3'), +] + +prebuildopts = 'CVXOPT_BUILD_FFTW=1 CVXOPT_BUILD_GSL=1 CVXOPT_BLAS_EXTRA_LINK_ARGS="$LIBLAPACK" ' +prebuildopts += 'CVXOPT_FFTW_EXTRA_LINK_ARGS="$LIBFFT" CVXOPT_SUITESPARSE_SRC_DIR=$EBROOTSUITESPARSE' + +installopts = ' && nosetests' + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'math' -- GitLab From 74717e269d6faf0bcea66712897bd1f6576b7b1e Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Tue, 5 Sep 2017 14:19:17 +0200 Subject: [PATCH 1496/1603] Added Shannon for intel/2017a --- .../s/Shannon/Shannon-30a861-intel-2017a.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/s/Shannon/Shannon-30a861-intel-2017a.eb diff --git a/easybuild/easyconfigs/s/Shannon/Shannon-30a861-intel-2017a.eb b/easybuild/easyconfigs/s/Shannon/Shannon-30a861-intel-2017a.eb new file mode 100644 index 0000000000..a1587a74b6 --- /dev/null +++ b/easybuild/easyconfigs/s/Shannon/Shannon-30a861-intel-2017a.eb @@ -0,0 +1,31 @@ +easyblock = 'Tarball' + +name = 'Shannon' +version = '30a861' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://sreeramkannan.github.io/Shannon/' +description = """Shannon is a program for assembling transcripts from RNA-Seq data""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +sources = ['%(version)s.tar.gz'] +source_urls = ['https://github.com/sreeramkannan/Shannon/archive/'] + +dependencies = [ + ('Python', '2.7.13'), + ('CVXOPT', '1.1.9', versionsuffix), + ('Jellyfish', '2.2.6'), + ('Quorum', '1.1.1'), +] + +postinstallcmds = ["sed -i '1 i#!/usr/bin/env python' %(installdir)s/*.py", "chmod +x %(installdir)s/*.py"] + +modextrapaths = {'PATH': ['']} + +sanity_check_paths = { + 'files': [], + 'dirs': ["."] +} + +moduleclass = 'bio' -- GitLab From 30031781a08d750e5cc8dc34ae9d27bd8f0cce67 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Tue, 5 Sep 2017 15:35:19 +0200 Subject: [PATCH 1497/1603] Fix errors --- easybuild/easyconfigs/q/Quorum/Quorum-1.1.1-intel-2017a.eb | 2 +- ...tel-2017a.eb => Shannon-30a861-intel-2017a-Python-2.7.13.eb} | 0 2 files changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/s/Shannon/{Shannon-30a861-intel-2017a.eb => Shannon-30a861-intel-2017a-Python-2.7.13.eb} (100%) diff --git a/easybuild/easyconfigs/q/Quorum/Quorum-1.1.1-intel-2017a.eb b/easybuild/easyconfigs/q/Quorum/Quorum-1.1.1-intel-2017a.eb index 6842eb5e85..0382266af3 100644 --- a/easybuild/easyconfigs/q/Quorum/Quorum-1.1.1-intel-2017a.eb +++ b/easybuild/easyconfigs/q/Quorum/Quorum-1.1.1-intel-2017a.eb @@ -16,7 +16,7 @@ dependencies = [('Jellyfish', '2.2.6')] sanity_check_paths = { 'files': ['bin/%s' % x for x in ['merge_mate_pairs', 'quorum', 'quorum_create_database', - 'quorum_error_correct_reads', 'split_mate_pairs']], + 'quorum_error_correct_reads', 'split_mate_pairs']], 'dirs': [] } diff --git a/easybuild/easyconfigs/s/Shannon/Shannon-30a861-intel-2017a.eb b/easybuild/easyconfigs/s/Shannon/Shannon-30a861-intel-2017a-Python-2.7.13.eb similarity index 100% rename from easybuild/easyconfigs/s/Shannon/Shannon-30a861-intel-2017a.eb rename to easybuild/easyconfigs/s/Shannon/Shannon-30a861-intel-2017a-Python-2.7.13.eb -- GitLab From fc16b0d70eda5c8c9681a7677381ace962506106 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Tue, 5 Sep 2017 16:40:55 +0200 Subject: [PATCH 1498/1603] Renamed to be consistent with github tagging --- ...04-intel-2017a.eb => SOAPdenovo-Trans-1.0.4-intel-2017a.eb} | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) rename easybuild/easyconfigs/s/SOAPdenovo-Trans/{SOAPdenovo-Trans-1.04-intel-2017a.eb => SOAPdenovo-Trans-1.0.4-intel-2017a.eb} (89%) diff --git a/easybuild/easyconfigs/s/SOAPdenovo-Trans/SOAPdenovo-Trans-1.04-intel-2017a.eb b/easybuild/easyconfigs/s/SOAPdenovo-Trans/SOAPdenovo-Trans-1.0.4-intel-2017a.eb similarity index 89% rename from easybuild/easyconfigs/s/SOAPdenovo-Trans/SOAPdenovo-Trans-1.04-intel-2017a.eb rename to easybuild/easyconfigs/s/SOAPdenovo-Trans/SOAPdenovo-Trans-1.0.4-intel-2017a.eb index 23f71d7d40..e2e16d74fd 100644 --- a/easybuild/easyconfigs/s/SOAPdenovo-Trans/SOAPdenovo-Trans-1.04-intel-2017a.eb +++ b/easybuild/easyconfigs/s/SOAPdenovo-Trans/SOAPdenovo-Trans-1.0.4-intel-2017a.eb @@ -1,7 +1,7 @@ easyblock = 'MakeCp' name = 'SOAPdenovo-Trans' -version = '1.04' +version = '1.0.4' homepage = 'http://soap.genomics.org.cn/SOAPdenovo-Trans.html' description = """SOAPdenovo-Trans is a de novo transcriptome assembler basing on the SOAPdenovo framework, @@ -12,6 +12,7 @@ toolchain = {'name': 'intel', 'version': '2017a'} sources = ['%(version)s.tar.gz'] source_urls = ['https://github.com/aquaskyline/SOAPdenovo-Trans/archive/'] +checksums = ['378a54cde0ebe240fb515ba67197c053cf95393645c1ae1399b3a611be2a9795'] patches = ['fix-makefiles-%(version)s.patch'] -- GitLab From 9cf6849fa55a93304b046bdfb64424681126f3f4 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Tue, 5 Sep 2017 17:05:29 +0200 Subject: [PATCH 1499/1603] Rename patch too --- .../{fix-makefiles-1.04.patch => fix-makefiles-1.0.4.patch} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/s/SOAPdenovo-Trans/{fix-makefiles-1.04.patch => fix-makefiles-1.0.4.patch} (100%) diff --git a/easybuild/easyconfigs/s/SOAPdenovo-Trans/fix-makefiles-1.04.patch b/easybuild/easyconfigs/s/SOAPdenovo-Trans/fix-makefiles-1.0.4.patch similarity index 100% rename from easybuild/easyconfigs/s/SOAPdenovo-Trans/fix-makefiles-1.04.patch rename to easybuild/easyconfigs/s/SOAPdenovo-Trans/fix-makefiles-1.0.4.patch -- GitLab From 93a83bf8c9e7fdc029f6ba1dc6a6d7cff4f60d89 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 5 Sep 2017 21:49:52 +0200 Subject: [PATCH 1500/1603] adding easyconfigs: PHAST-1.4-intel-2017a.eb, CLAPACK-3.2.1-intel-2017a.eb --- .../c/CLAPACK/CLAPACK-3.2.1-intel-2017a.eb | 29 ++++++++++++++++ .../p/PHAST/PHAST-1.4-intel-2017a.eb | 34 +++++++++++++++++++ 2 files changed, 63 insertions(+) create mode 100644 easybuild/easyconfigs/c/CLAPACK/CLAPACK-3.2.1-intel-2017a.eb create mode 100644 easybuild/easyconfigs/p/PHAST/PHAST-1.4-intel-2017a.eb diff --git a/easybuild/easyconfigs/c/CLAPACK/CLAPACK-3.2.1-intel-2017a.eb b/easybuild/easyconfigs/c/CLAPACK/CLAPACK-3.2.1-intel-2017a.eb new file mode 100644 index 0000000000..a52bcdd9d4 --- /dev/null +++ b/easybuild/easyconfigs/c/CLAPACK/CLAPACK-3.2.1-intel-2017a.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'CLAPACK' +version = '3.2.1' + +homepage = 'http://www.netlib.org/clapack' +description = "C version of LAPACK" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['http://www.netlib.org/clapack/'] +sources = [SOURCELOWER_TGZ] +checksums = ['6dc4c382164beec8aaed8fd2acc36ad24232c406eda6db462bd4c41d5e455fac'] + +unpack_options = '--strip-components=1' +buildininstalldir = True +skipsteps = ['configure', 'install'] + +prebuildopts = 'cp make.inc.example make.inc && ' +buildopts = 'CC="$CC" LOADER="$CC" ' + +parallel = 1 + +sanity_check_paths = { + 'files': ['lapack_LINUX.a', 'tmglib_LINUX.a'], + 'dirs': [], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/PHAST/PHAST-1.4-intel-2017a.eb b/easybuild/easyconfigs/p/PHAST/PHAST-1.4-intel-2017a.eb new file mode 100644 index 0000000000..85d3553135 --- /dev/null +++ b/easybuild/easyconfigs/p/PHAST/PHAST-1.4-intel-2017a.eb @@ -0,0 +1,34 @@ +easyblock = 'MakeCp' + +name = 'PHAST' +version = '1.4' + +homepage = 'http://compgen.cshl.edu/phast/' +description = "PHAST is a freely available software package for comparative and evolutionary genomics." + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['https://github.com/CshlSiepelLab/phast/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['287c77599c51256a3adbd62ed217cb6d6a547fcec2c29262e9d61fa32ed92b99'] + +dependencies = [ + ('CLAPACK', '3.2.1'), + ('PCRE', '8.41'), +] + +skipsteps = ['configure'] + +start_dir = 'src' + +prebuildopts = 'CPATH=$EBROOTCLAPACK/F2CLIBS/libf2c:$EBROOTCLAPACK/INCLUDE:$CPATH ' +buildopts = 'CC="$CC" CLAPACKPATH=$EBROOTCLAPACK' + +files_to_copy = ['bin', 'data', (['doc/man/*'], 'share/man/man1')] + +sanity_check_paths = { + 'files': ['bin/phast'], + 'dirs': ['data', 'share/man/man1'], +} + +moduleclass = 'bio' -- GitLab From 1086110079c7752a9559b94f4f22a31865ea1160 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 6 Sep 2017 11:02:49 +0200 Subject: [PATCH 1501/1603] Fix remarks --- .../CVXOPT-1.1.9-intel-2017a-Python-2.7.13.eb | 4 ++- ...cutadapt-1.14-intel-2017a-Python-2.7.13.eb | 1 + .../f/FastQC/FastQC-0.11.5-Java-1.8.0_144.eb | 34 +++++++++++++++++++ .../Jellyfish/Jellyfish-2.2.6-intel-2017a.eb | 1 - .../k/kallisto/kallisto-0.43.1-intel-2017a.eb | 5 ++- .../q/Quorum/Quorum-1.1.1-intel-2017a.eb | 2 +- ...h => Rcorrector-1.0.2-fix-makefiles.patch} | 2 ++ .../Rcorrector-1.0.2-intel-2017a.eb | 7 ++-- ...OAPdenovo-Trans-1.0.4-fix-makefiles.patch} | 0 .../SOAPdenovo-Trans-1.0.4-intel-2017a.eb | 8 ++--- .../s/SPAdes/SPAdes-3.10.1-foss-2017a.eb | 3 +- ...hannon-30a861-intel-2017a-Python-2.7.13.eb | 16 ++++++--- .../Trim_Galore-0.4.4-intel-2017a.eb | 8 +++-- 13 files changed, 69 insertions(+), 22 deletions(-) create mode 100644 easybuild/easyconfigs/f/FastQC/FastQC-0.11.5-Java-1.8.0_144.eb rename easybuild/easyconfigs/r/Rcorrector/{fix-makefile-1.0.2.patch => Rcorrector-1.0.2-fix-makefiles.patch} (87%) rename easybuild/easyconfigs/s/SOAPdenovo-Trans/{fix-makefiles-1.0.4.patch => SOAPdenovo-Trans-1.0.4-fix-makefiles.patch} (100%) diff --git a/easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.1.9-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.1.9-intel-2017a-Python-2.7.13.eb index 673c7c6791..76a6d8895c 100644 --- a/easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.1.9-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.1.9-intel-2017a-Python-2.7.13.eb @@ -15,10 +15,12 @@ toolchainopts = {'pic': True} source_urls = ['https://github.com/cvxopt/cvxopt/archive/'] sources = ['%(version)s.tar.gz'] -checksums = ['09997fec809179c9bb9fe8cdd202ad6ecb675f890658219022f492e0797122ee'] patches = ['%(name)s-%(version)s-fix-setup-py.patch'] +checksums = ['09997fec809179c9bb9fe8cdd202ad6ecb675f890658219022f492e0797122ee', + '89058d53c55dcdc94a9b7a6ea8c6a6e78a693210d1d27a4178f68926ae5099e3'] + dependencies = [ ('Python', '2.7.13'), ('SuiteSparse', '4.5.5', '-METIS-5.1.0'), diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.14-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.14-intel-2017a-Python-2.7.13.eb index 0bcc6df002..72895a6781 100644 --- a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.14-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.14-intel-2017a-Python-2.7.13.eb @@ -19,6 +19,7 @@ toolchain = {'name': 'intel', 'version': '2017a'} source_urls = [PYPI_SOURCE] sources = [SOURCELOWER_TAR_GZ] +checksums = ['f32990a8b2f8b53f8f4c723ada3d256a8e8476febdd296506764cc8e83397d3d'] dependencies = [ ('Python', '2.7.13'), diff --git a/easybuild/easyconfigs/f/FastQC/FastQC-0.11.5-Java-1.8.0_144.eb b/easybuild/easyconfigs/f/FastQC/FastQC-0.11.5-Java-1.8.0_144.eb new file mode 100644 index 0000000000..95a61408bf --- /dev/null +++ b/easybuild/easyconfigs/f/FastQC/FastQC-0.11.5-Java-1.8.0_144.eb @@ -0,0 +1,34 @@ +easyblock = 'PackedBinary' + +name = 'FastQC' +version = '0.11.5' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'http://www.bioinformatics.babraham.ac.uk/projects/fastqc/' +description = """FastQC is a quality control application for high throughput sequence data. + It reads in sequence data in a variety of formats and can either provide an interactive + application to review the results of several different QC checks, or create an HTML based + report which can be integrated into a pipeline.""" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = ['http://www.bioinformatics.babraham.ac.uk/projects/%(namelower)s'] +sources = ['%(namelower)s_v%(version)s.zip'] +checksums = ['dd7a5ad80ceed2588cf6d6ffe35e0f161c0d9977ed08355f5e4d9473282cbd66', + '684701634440864750c9a0b99d81e122a1def78672d436daf5497bff61d9a356'] + +patches = ['FastQC_shebang.patch'] + +dependencies = [('Java', '1.8.0_144')] + +postinstallcmds = ["chmod +x %(installdir)s/fastqc"] + +sanity_check_paths = { + 'files': ['fastqc', 'fastqc_icon.ico', 'INSTALL.txt', 'jbzip2-0.9.jar', 'LICENSE.txt', 'LICENSE_JHDF5.txt', + 'README.txt', 'RELEASE_NOTES.txt', 'run_fastqc.bat', 'sam-1.103.jar', 'cisd-jhdf5.jar'], + 'dirs': ['Configuration', 'Help', 'Templates', 'uk', 'net', 'org'], +} + +sanity_check_commands = [('fastqc', '-v')] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.2.6-intel-2017a.eb b/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.2.6-intel-2017a.eb index 96345d490a..183ced70a6 100644 --- a/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.2.6-intel-2017a.eb +++ b/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.2.6-intel-2017a.eb @@ -12,7 +12,6 @@ toolchain = {'name': 'intel', 'version': '2017a'} source_urls = ['https://github.com/gmarcais/Jellyfish/releases/download/v%(version)s'] sources = [SOURCELOWER_TAR_GZ] - checksums = ['4532fb003a0494f6473bb97d52467904f631b94f7f9afb0d45b398f6c413692e'] parallel = 1 diff --git a/easybuild/easyconfigs/k/kallisto/kallisto-0.43.1-intel-2017a.eb b/easybuild/easyconfigs/k/kallisto/kallisto-0.43.1-intel-2017a.eb index 843003952a..68095961ff 100644 --- a/easybuild/easyconfigs/k/kallisto/kallisto-0.43.1-intel-2017a.eb +++ b/easybuild/easyconfigs/k/kallisto/kallisto-0.43.1-intel-2017a.eb @@ -14,14 +14,13 @@ toolchainopts = {'pic': True, 'usempi': True} source_urls = ['https://github.com/pachterlab/kallisto/archive/'] sources = ['v%(version)s.tar.gz'] - checksums = ['2164938c2c61c04e338c4c132cf749f56d39e6f0b4c517121bca1fbc218e430e'] -builddependencies = [('CMake', '3.8.2')] +builddependencies = [('CMake', '3.9.1')] dependencies = [ ('zlib', '1.2.11'), - ('HDF5', '1.8.19'), + ('HDF5', '1.10.1'), ] separate_build_dir = True diff --git a/easybuild/easyconfigs/q/Quorum/Quorum-1.1.1-intel-2017a.eb b/easybuild/easyconfigs/q/Quorum/Quorum-1.1.1-intel-2017a.eb index 0382266af3..494be9237d 100644 --- a/easybuild/easyconfigs/q/Quorum/Quorum-1.1.1-intel-2017a.eb +++ b/easybuild/easyconfigs/q/Quorum/Quorum-1.1.1-intel-2017a.eb @@ -8,8 +8,8 @@ description = """QuorUM is an error corrector for Illumina reads""" toolchain = {'name': 'intel', 'version': '2017a'} -sources = [SOURCELOWER_TAR_GZ] source_urls = ['https://github.com/gmarcais/Quorum/releases/download/v%(version)s'] +sources = [SOURCELOWER_TAR_GZ] checksums = ['45d099835eaad43cf915e118e9cb6423411d68c7f35a8145bc725dca366c82b5'] dependencies = [('Jellyfish', '2.2.6')] diff --git a/easybuild/easyconfigs/r/Rcorrector/fix-makefile-1.0.2.patch b/easybuild/easyconfigs/r/Rcorrector/Rcorrector-1.0.2-fix-makefiles.patch similarity index 87% rename from easybuild/easyconfigs/r/Rcorrector/fix-makefile-1.0.2.patch rename to easybuild/easyconfigs/r/Rcorrector/Rcorrector-1.0.2-fix-makefiles.patch index 7dab68cd0c..b70fb17e7f 100644 --- a/easybuild/easyconfigs/r/Rcorrector/fix-makefile-1.0.2.patch +++ b/easybuild/easyconfigs/r/Rcorrector/Rcorrector-1.0.2-fix-makefiles.patch @@ -1,3 +1,5 @@ +# Patch makefile to use EB values +# wpoely86@gmail.com --- Makefile.orig 2017-08-14 12:33:11.280163633 +0200 +++ Makefile 2017-08-14 12:36:46.085730155 +0200 @@ -1,6 +1,6 @@ diff --git a/easybuild/easyconfigs/r/Rcorrector/Rcorrector-1.0.2-intel-2017a.eb b/easybuild/easyconfigs/r/Rcorrector/Rcorrector-1.0.2-intel-2017a.eb index 67947aaafa..8a86e3f1cf 100644 --- a/easybuild/easyconfigs/r/Rcorrector/Rcorrector-1.0.2-intel-2017a.eb +++ b/easybuild/easyconfigs/r/Rcorrector/Rcorrector-1.0.2-intel-2017a.eb @@ -9,10 +9,11 @@ description = """Rcorrector(RNA-seq error CORRECTOR) is a kmer-based error corre toolchain = {'name': 'intel', 'version': '2017a'} toolchainopts = {'cstd': 'c++11'} -sources = ['v%(version)s.tar.gz'] source_urls = ['https://github.com/mourisl/Rcorrector/archive'] - -patches = ['fix-makefile-%(version)s.patch'] +sources = ['v%(version)s.tar.gz'] +patches = ['%(name)s-%(version)s-fix-makefile.patch'] +checksums = ['426c7ab5fbb968536dbb4daf6913599f99b50eaabbea8013930da77f1235d9c6', + '157f7edca282499444aeddb22114a262a9ffef7311ea534b8e83509f6f7bf6b4'] dependencies = [ ('zlib', '1.2.11'), diff --git a/easybuild/easyconfigs/s/SOAPdenovo-Trans/fix-makefiles-1.0.4.patch b/easybuild/easyconfigs/s/SOAPdenovo-Trans/SOAPdenovo-Trans-1.0.4-fix-makefiles.patch similarity index 100% rename from easybuild/easyconfigs/s/SOAPdenovo-Trans/fix-makefiles-1.0.4.patch rename to easybuild/easyconfigs/s/SOAPdenovo-Trans/SOAPdenovo-Trans-1.0.4-fix-makefiles.patch diff --git a/easybuild/easyconfigs/s/SOAPdenovo-Trans/SOAPdenovo-Trans-1.0.4-intel-2017a.eb b/easybuild/easyconfigs/s/SOAPdenovo-Trans/SOAPdenovo-Trans-1.0.4-intel-2017a.eb index e2e16d74fd..9b78a12c9c 100644 --- a/easybuild/easyconfigs/s/SOAPdenovo-Trans/SOAPdenovo-Trans-1.0.4-intel-2017a.eb +++ b/easybuild/easyconfigs/s/SOAPdenovo-Trans/SOAPdenovo-Trans-1.0.4-intel-2017a.eb @@ -10,11 +10,11 @@ adapt to alternative splicing and different expression level among transcripts. toolchain = {'name': 'intel', 'version': '2017a'} -sources = ['%(version)s.tar.gz'] source_urls = ['https://github.com/aquaskyline/SOAPdenovo-Trans/archive/'] -checksums = ['378a54cde0ebe240fb515ba67197c053cf95393645c1ae1399b3a611be2a9795'] - -patches = ['fix-makefiles-%(version)s.patch'] +sources = ['%(version)s.tar.gz'] +patches = ['%(name)s-%(version)s-fix-makefiles.patch'] +checksums = ['378a54cde0ebe240fb515ba67197c053cf95393645c1ae1399b3a611be2a9795', + '15c420a5e2c2a5a5837dbb1223a6b02b78f059b162e82952c7ceee83fdfdcffb'] dependencies = [('zlib', '1.2.11')] diff --git a/easybuild/easyconfigs/s/SPAdes/SPAdes-3.10.1-foss-2017a.eb b/easybuild/easyconfigs/s/SPAdes/SPAdes-3.10.1-foss-2017a.eb index 7c013e44e4..7327cf5610 100644 --- a/easybuild/easyconfigs/s/SPAdes/SPAdes-3.10.1-foss-2017a.eb +++ b/easybuild/easyconfigs/s/SPAdes/SPAdes-3.10.1-foss-2017a.eb @@ -19,8 +19,9 @@ toolchain = {'name': 'foss', 'version': '2017a'} source_urls = ['http://cab.spbu.ru/files/release%(version)s'] sources = [SOURCE_TAR_GZ] +checksums = ['d49dd9eb947767a14a9896072a1bce107fb8bf39ed64133a9e2f24fb1f240d96'] -builddependencies = [('CMake', '3.8.2')] +builddependencies = [('CMake', '3.9.1')] dependencies = [ ('zlib', '1.2.11'), diff --git a/easybuild/easyconfigs/s/Shannon/Shannon-30a861-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/s/Shannon/Shannon-30a861-intel-2017a-Python-2.7.13.eb index a1587a74b6..5e33a04643 100644 --- a/easybuild/easyconfigs/s/Shannon/Shannon-30a861-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/s/Shannon/Shannon-30a861-intel-2017a-Python-2.7.13.eb @@ -1,7 +1,8 @@ easyblock = 'Tarball' name = 'Shannon' -version = '30a861' +version = '20170511' +commit = '30a8619' versionsuffix = '-Python-%(pyver)s' homepage = 'https://sreeramkannan.github.io/Shannon/' @@ -9,8 +10,12 @@ description = """Shannon is a program for assembling transcripts from RNA-Seq da toolchain = {'name': 'intel', 'version': '2017a'} -sources = ['%(version)s.tar.gz'] +sources = [{ + 'filename': '%s.tar.gz' % commit, + 'download_filename': '%(name)s-%(version)s.tar.gz', +}] source_urls = ['https://github.com/sreeramkannan/Shannon/archive/'] +checksums = ['436a5ec9723a13314cd18f95b89e18d4da94f3710545291d4b18162447f28ab3'] dependencies = [ ('Python', '2.7.13'), @@ -19,13 +24,14 @@ dependencies = [ ('Quorum', '1.1.1'), ] -postinstallcmds = ["sed -i '1 i#!/usr/bin/env python' %(installdir)s/*.py", "chmod +x %(installdir)s/*.py"] +postinstallcmds = ["sed -i '1 i#!/usr/bin/env python' %(installdir)s/*.py", + "chmod +x %(installdir)s/*.py"] modextrapaths = {'PATH': ['']} sanity_check_paths = { - 'files': [], - 'dirs': ["."] + 'files': ['shannon.py', 'run_quorum.py'], + 'dirs': [] } moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.4.4-intel-2017a.eb b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.4.4-intel-2017a.eb index 40247e6a53..d1bbd95d59 100755 --- a/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.4.4-intel-2017a.eb +++ b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.4.4-intel-2017a.eb @@ -1,7 +1,6 @@ # 0.4.2 modified by: # Adam Huffman # The Francis Crick Institute -# TODO: deal with the hardcoding of /usr/bin/perl easyblock = "PackedBinary" @@ -15,13 +14,16 @@ description = """A wrapper tool around Cutadapt and FastQC to consistently apply toolchain = {'name': 'intel', 'version': '2017a'} -sources = ['%(namelower)s_v%(version)s.zip'] source_urls = ['http://www.bioinformatics.babraham.ac.uk/projects/%(namelower)s'] +sources = ['%(namelower)s_v%(version)s.zip'] +checksums = ['ccd7eecc73327da29230f3e7c7311a4e21b2cfe7282be18fa059ba900fc33116'] install_cmd = "cp -a * %(installdir)s && chmod +x %(installdir)s/%(namelower)s" +postinstallcmds = ["sed -i '1 i#!/usr/bin/env perl' %(installdir)s/%(namelower)s"] + dependencies = [ - ('FastQC', '0.11.5', '-Java-1.8.0_74', True), + ('FastQC', '0.11.5', '-Java-1.8.0_144', True), ('cutadapt', '1.14', '-Python-2.7.13'), ] -- GitLab From 4ee3d5b7f70078f03a8feced8741ed175d5b1261 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 6 Sep 2017 11:24:45 +0200 Subject: [PATCH 1502/1603] Fix typos --- ....2-fix-makefiles.patch => Rcorrector-1.0.2-fix-makefile.patch} | 0 ...on-2.7.13.eb => Shannon-20170511-intel-2017a-Python-2.7.13.eb} | 0 2 files changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/r/Rcorrector/{Rcorrector-1.0.2-fix-makefiles.patch => Rcorrector-1.0.2-fix-makefile.patch} (100%) rename easybuild/easyconfigs/s/Shannon/{Shannon-30a861-intel-2017a-Python-2.7.13.eb => Shannon-20170511-intel-2017a-Python-2.7.13.eb} (100%) diff --git a/easybuild/easyconfigs/r/Rcorrector/Rcorrector-1.0.2-fix-makefiles.patch b/easybuild/easyconfigs/r/Rcorrector/Rcorrector-1.0.2-fix-makefile.patch similarity index 100% rename from easybuild/easyconfigs/r/Rcorrector/Rcorrector-1.0.2-fix-makefiles.patch rename to easybuild/easyconfigs/r/Rcorrector/Rcorrector-1.0.2-fix-makefile.patch diff --git a/easybuild/easyconfigs/s/Shannon/Shannon-30a861-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/s/Shannon/Shannon-20170511-intel-2017a-Python-2.7.13.eb similarity index 100% rename from easybuild/easyconfigs/s/Shannon/Shannon-30a861-intel-2017a-Python-2.7.13.eb rename to easybuild/easyconfigs/s/Shannon/Shannon-20170511-intel-2017a-Python-2.7.13.eb -- GitLab From 486da9c113a9e1ca66afd021e7d77e6ad4687465 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 6 Sep 2017 11:42:01 +0200 Subject: [PATCH 1503/1603] Wrong keys for download in Shannon --- .../s/Shannon/Shannon-20170511-intel-2017a-Python-2.7.13.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/Shannon/Shannon-20170511-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/s/Shannon/Shannon-20170511-intel-2017a-Python-2.7.13.eb index 5e33a04643..329a6b0178 100644 --- a/easybuild/easyconfigs/s/Shannon/Shannon-20170511-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/s/Shannon/Shannon-20170511-intel-2017a-Python-2.7.13.eb @@ -11,8 +11,8 @@ description = """Shannon is a program for assembling transcripts from RNA-Seq da toolchain = {'name': 'intel', 'version': '2017a'} sources = [{ - 'filename': '%s.tar.gz' % commit, - 'download_filename': '%(name)s-%(version)s.tar.gz', + 'filename': '%(name)s-%(version)s.tar.gz', + 'download_filename': '%s.tar.gz' % commit, }] source_urls = ['https://github.com/sreeramkannan/Shannon/archive/'] checksums = ['436a5ec9723a13314cd18f95b89e18d4da94f3710545291d4b18162447f28ab3'] -- GitLab From 727e538a24c7f008c8e08a9d46ac92469110a94e Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 6 Sep 2017 12:09:33 +0200 Subject: [PATCH 1504/1603] Fix wrong checksum --- .../easyconfigs/r/Rcorrector/Rcorrector-1.0.2-intel-2017a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/Rcorrector/Rcorrector-1.0.2-intel-2017a.eb b/easybuild/easyconfigs/r/Rcorrector/Rcorrector-1.0.2-intel-2017a.eb index 8a86e3f1cf..d7e2978510 100644 --- a/easybuild/easyconfigs/r/Rcorrector/Rcorrector-1.0.2-intel-2017a.eb +++ b/easybuild/easyconfigs/r/Rcorrector/Rcorrector-1.0.2-intel-2017a.eb @@ -13,7 +13,7 @@ source_urls = ['https://github.com/mourisl/Rcorrector/archive'] sources = ['v%(version)s.tar.gz'] patches = ['%(name)s-%(version)s-fix-makefile.patch'] checksums = ['426c7ab5fbb968536dbb4daf6913599f99b50eaabbea8013930da77f1235d9c6', - '157f7edca282499444aeddb22114a262a9ffef7311ea534b8e83509f6f7bf6b4'] + '785a24b8af0b075d813ee4cd83f7480dd35365d9a0a2b81d80b6eb210bcf0bd0'] dependencies = [ ('zlib', '1.2.11'), -- GitLab From bcdc00c45775fea8acb89965799e071356f82648 Mon Sep 17 00:00:00 2001 From: Joachim Hein Date: Wed, 6 Sep 2017 16:04:21 +0200 Subject: [PATCH 1505/1603] Fileset for an iomkl toolchain build ontop of the intel/foss 2017b components --- .../h/HPL/HPL-2.2-iomkl-2017.09.eb | 19 ++++++++++ .../i/imkl/imkl-2017.3.196-iompi-2017.09.eb | 38 +++++++++++++++++++ .../easyconfigs/i/iomkl/iomkl-2017.09.eb | 22 +++++++++++ .../easyconfigs/i/iompi/iompi-2017.09.eb | 21 ++++++++++ ....1.1-iccifort-2017.4.196-GCC-6.4.0-2.28.eb | 35 +++++++++++++++++ 5 files changed, 135 insertions(+) create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.2-iomkl-2017.09.eb create mode 100644 easybuild/easyconfigs/i/imkl/imkl-2017.3.196-iompi-2017.09.eb create mode 100644 easybuild/easyconfigs/i/iomkl/iomkl-2017.09.eb create mode 100644 easybuild/easyconfigs/i/iompi/iompi-2017.09.eb create mode 100644 easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.1-iccifort-2017.4.196-GCC-6.4.0-2.28.eb diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.2-iomkl-2017.09.eb b/easybuild/easyconfigs/h/HPL/HPL-2.2-iomkl-2017.09.eb new file mode 100644 index 0000000000..c308491cd1 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.2-iomkl-2017.09.eb @@ -0,0 +1,19 @@ +name = 'HPL' +version = '2.2' + +homepage = 'http://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'iomkl', 'version': '2017.09'} +toolchainopts = {'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] +checksums = ['ac7534163a09e21a5fa763e4e16dfc119bc84043f6e6a807aba666518f8df440'] + +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/i/imkl/imkl-2017.3.196-iompi-2017.09.eb b/easybuild/easyconfigs/i/imkl/imkl-2017.3.196-iompi-2017.09.eb new file mode 100644 index 0000000000..45797675e0 --- /dev/null +++ b/easybuild/easyconfigs/i/imkl/imkl-2017.3.196-iompi-2017.09.eb @@ -0,0 +1,38 @@ +# This is an easyconfig file for EasyBuild, see https://easybuilders.github.io/easybuild/ + +name = 'imkl' +version = '2017.3.196' + +homepage = 'http://software.intel.com/en-us/intel-mkl/' +description = """Intel Math Kernel Library is a library of highly optimized, + extensively threaded math routines for science, engineering, and financial + applications that require maximum performance. Core math functions include + BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.""" + +toolchain = {'name': 'iompi', 'version': '2017.09'} + +sources = ['l_mkl_%(version)s.tgz'] +checksums = ['fd7295870fa164d6138c9818304f25f2bb263c814a6c6539c9fe4e104055f1ca'] + +dontcreateinstalldir = 'True' + +license_file = HOME + '/licenses/intel/license.lic' + +interfaces = True + +postinstallcmds = [ + # extract the examples + 'tar xvzf %(installdir)s/mkl/examples/examples_cluster_c.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_cluster_f.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_core_c.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_core_f.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_f95.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_mic_c.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_mic_f.tgz -C %(installdir)s/mkl/examples/' +] + +modextravars = { + 'MKL_EXAMPLES': '%(installdir)s/mkl/examples/', +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/iomkl/iomkl-2017.09.eb b/easybuild/easyconfigs/i/iomkl/iomkl-2017.09.eb new file mode 100644 index 0000000000..15adfb064c --- /dev/null +++ b/easybuild/easyconfigs/i/iomkl/iomkl-2017.09.eb @@ -0,0 +1,22 @@ +easyblock = "Toolchain" + +name = 'iomkl' +version = '2017.09' + +homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' +description = """Intel Cluster Toolchain Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MKL & + OpenMPI.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +compver = '2017.4.196' +gccsuff = '-GCC-6.4.0-2.28' + +dependencies = [ + ('icc', compver, gccsuff), + ('ifort', compver, gccsuff), + ('OpenMPI', '2.1.1', '', ('iccifort', '%s%s' % (compver, gccsuff))), + ('imkl', '2017.3.196', '', ('iompi', version)), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/iompi/iompi-2017.09.eb b/easybuild/easyconfigs/i/iompi/iompi-2017.09.eb new file mode 100644 index 0000000000..50586799ed --- /dev/null +++ b/easybuild/easyconfigs/i/iompi/iompi-2017.09.eb @@ -0,0 +1,21 @@ +# This is an easyconfig file for EasyBuild, see https://easybuilders.github.io/easybuild/ +easyblock = "Toolchain" + +name = 'iompi' +version = '2017.09' + +homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' +description = """Intel C/C++ and Fortran compilers, alongside Open MPI.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +compver = '2017.4.196' +compversuff = '-GCC-6.4.0-2.28' + +dependencies = [ + ('icc', compver, compversuff), + ('ifort', compver, compversuff), + ('OpenMPI', '2.1.1', '', ('iccifort', '%s%s' % (compver, compversuff))), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.1-iccifort-2017.4.196-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.1-iccifort-2017.4.196-GCC-6.4.0-2.28.eb new file mode 100644 index 0000000000..92aa7215fa --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.1-iccifort-2017.4.196-GCC-6.4.0-2.28.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'OpenMPI' +version = '2.1.1' + +homepage = 'http://www.open-mpi.org/' +description = """The Open MPI Project is an open source MPI-2 implementation.""" + +toolchain = {'name': 'iccifort', 'version': '2017.4.196-GCC-6.4.0-2.28'} + +sources = [SOURCELOWER_TAR_GZ] + +source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['afe4bef3c4378bc76eea96c623d5aa4c1c98b9e057d281c646e68869292a77dc'] + +dependencies = [('hwloc', '1.11.7')] + +configopts = '--enable-shared --enable-mpi-thread-multiple --with-verbs ' +configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path +configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support +configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading + +# needed for --with-verbs +osdependencies = [('libibverbs-dev', 'libibverbs-devel')] + +libs = ["mpi_mpifh", "mpi", "ompitrace", "open-pal", "open-rte"] +sanity_check_paths = { + 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] + + ["include/%s.h" % x for x in ["mpi-ext", "mpif-config", "mpif", "mpi", "mpi_portable_platform"]], + 'dirs': [], +} + +moduleclass = 'mpi' -- GitLab From c6fb74940ea92a890a771ec704070cc4a5ed28e0 Mon Sep 17 00:00:00 2001 From: Joachim Hein Date: Wed, 6 Sep 2017 20:52:26 +0200 Subject: [PATCH 1506/1603] changed toolchain version from 2017.09 to 2017b --- .../h/HPL/{HPL-2.2-iomkl-2017.09.eb => HPL-2.2-iomkl-2017b.eb} | 2 +- ...17.3.196-iompi-2017.09.eb => imkl-2017.3.196-iompi-2017b.eb} | 2 +- .../easyconfigs/i/iomkl/{iomkl-2017.09.eb => iomkl-2017b.eb} | 2 +- .../easyconfigs/i/iompi/{iompi-2017.09.eb => iompi-2017b.eb} | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) rename easybuild/easyconfigs/h/HPL/{HPL-2.2-iomkl-2017.09.eb => HPL-2.2-iomkl-2017b.eb} (93%) rename easybuild/easyconfigs/i/imkl/{imkl-2017.3.196-iompi-2017.09.eb => imkl-2017.3.196-iompi-2017b.eb} (96%) rename easybuild/easyconfigs/i/iomkl/{iomkl-2017.09.eb => iomkl-2017b.eb} (96%) rename easybuild/easyconfigs/i/iompi/{iompi-2017.09.eb => iompi-2017b.eb} (96%) diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.2-iomkl-2017.09.eb b/easybuild/easyconfigs/h/HPL/HPL-2.2-iomkl-2017b.eb similarity index 93% rename from easybuild/easyconfigs/h/HPL/HPL-2.2-iomkl-2017.09.eb rename to easybuild/easyconfigs/h/HPL/HPL-2.2-iomkl-2017b.eb index c308491cd1..18faf1a6a7 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.2-iomkl-2017.09.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.2-iomkl-2017b.eb @@ -6,7 +6,7 @@ description = """HPL is a software package that solves a (random) dense linear s arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the High Performance Computing Linpack Benchmark.""" -toolchain = {'name': 'iomkl', 'version': '2017.09'} +toolchain = {'name': 'iomkl', 'version': '2017b'} toolchainopts = {'usempi': True} sources = [SOURCELOWER_TAR_GZ] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2017.3.196-iompi-2017.09.eb b/easybuild/easyconfigs/i/imkl/imkl-2017.3.196-iompi-2017b.eb similarity index 96% rename from easybuild/easyconfigs/i/imkl/imkl-2017.3.196-iompi-2017.09.eb rename to easybuild/easyconfigs/i/imkl/imkl-2017.3.196-iompi-2017b.eb index 45797675e0..74a22643af 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2017.3.196-iompi-2017.09.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2017.3.196-iompi-2017b.eb @@ -9,7 +9,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, applications that require maximum performance. Core math functions include BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.""" -toolchain = {'name': 'iompi', 'version': '2017.09'} +toolchain = {'name': 'iompi', 'version': '2017b'} sources = ['l_mkl_%(version)s.tgz'] checksums = ['fd7295870fa164d6138c9818304f25f2bb263c814a6c6539c9fe4e104055f1ca'] diff --git a/easybuild/easyconfigs/i/iomkl/iomkl-2017.09.eb b/easybuild/easyconfigs/i/iomkl/iomkl-2017b.eb similarity index 96% rename from easybuild/easyconfigs/i/iomkl/iomkl-2017.09.eb rename to easybuild/easyconfigs/i/iomkl/iomkl-2017b.eb index 15adfb064c..3a41c0a1b3 100644 --- a/easybuild/easyconfigs/i/iomkl/iomkl-2017.09.eb +++ b/easybuild/easyconfigs/i/iomkl/iomkl-2017b.eb @@ -1,7 +1,7 @@ easyblock = "Toolchain" name = 'iomkl' -version = '2017.09' +version = '2017b' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = """Intel Cluster Toolchain Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MKL & diff --git a/easybuild/easyconfigs/i/iompi/iompi-2017.09.eb b/easybuild/easyconfigs/i/iompi/iompi-2017b.eb similarity index 96% rename from easybuild/easyconfigs/i/iompi/iompi-2017.09.eb rename to easybuild/easyconfigs/i/iompi/iompi-2017b.eb index 50586799ed..218aa8ffd0 100644 --- a/easybuild/easyconfigs/i/iompi/iompi-2017.09.eb +++ b/easybuild/easyconfigs/i/iompi/iompi-2017b.eb @@ -2,7 +2,7 @@ easyblock = "Toolchain" name = 'iompi' -version = '2017.09' +version = '2017b' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = """Intel C/C++ and Fortran compilers, alongside Open MPI.""" -- GitLab From 620e8cfbf64a24f08e8a0e071bb54e51f93c5067 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 7 Sep 2017 07:06:40 +0200 Subject: [PATCH 1507/1603] add missing binutils build dep for texinfo --- easybuild/easyconfigs/t/texinfo/texinfo-6.4-GCCcore-5.4.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/t/texinfo/texinfo-6.4-GCCcore-5.4.0.eb b/easybuild/easyconfigs/t/texinfo/texinfo-6.4-GCCcore-5.4.0.eb index 5ff7e5d7fd..26d55908b2 100644 --- a/easybuild/easyconfigs/t/texinfo/texinfo-6.4-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/t/texinfo/texinfo-6.4-GCCcore-5.4.0.eb @@ -23,6 +23,8 @@ source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_XZ] checksums = ['6ae2e61d87c6310f9af7c6f2426bd0470f251d1a6deb61fba83a3b3baff32c3a'] +builddependencies = [('binutils', '2.26')] + osdependencies = ['texlive'] preinstallopts = "make TEXMF=%(installdir)s/texmf install-tex && " -- GitLab From 7d4ed56161b13407b73730e0a4969bc58216913b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 7 Sep 2017 11:07:08 +0200 Subject: [PATCH 1508/1603] adding easyconfigs: Boost-1.65.0-intel-2017a-Python-2.7.13.eb --- .../Boost-1.65.0-intel-2017a-Python-2.7.13.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.65.0-intel-2017a-Python-2.7.13.eb diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.65.0-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/b/Boost/Boost-1.65.0-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..29bd589891 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.65.0-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,24 @@ +name = 'Boost' +version = '1.65.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.boost.org/' +description = "Boost provides free peer-reviewed portable C++ source libraries." + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'usempi': True, 'pic': True} + +source_urls = ['https://sourceforge.net/projects/%(namelower)s/files/%(namelower)s/%(version)s'] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] +checksums = ['8a142d33ab4b4ed0de3abea3280ae3b2ce91c48c09478518c73e5dd2ba8f20aa'] + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.11'), + ('Python', '2.7.13'), +] + +# also build boost_mpi +boost_mpi = True + +moduleclass = 'devel' -- GitLab From 4ec7d7c41f69cfea03b67c86a82af25d1a2fcbcd Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 7 Sep 2017 13:53:43 +0200 Subject: [PATCH 1509/1603] Added QML/0.2.10 for intel/2017a --- .../q/QML/QML-0.2.10-fix-setup.py.patch | 32 +++++++++++++++++++ .../QML-0.2.10-intel-2017a-Python-2.7.13.eb | 31 ++++++++++++++++++ 2 files changed, 63 insertions(+) create mode 100644 easybuild/easyconfigs/q/QML/QML-0.2.10-fix-setup.py.patch create mode 100644 easybuild/easyconfigs/q/QML/QML-0.2.10-intel-2017a-Python-2.7.13.eb diff --git a/easybuild/easyconfigs/q/QML/QML-0.2.10-fix-setup.py.patch b/easybuild/easyconfigs/q/QML/QML-0.2.10-fix-setup.py.patch new file mode 100644 index 0000000000..91d7f04e61 --- /dev/null +++ b/easybuild/easyconfigs/q/QML/QML-0.2.10-fix-setup.py.patch @@ -0,0 +1,32 @@ +# patch setup.py to use EB values for building +# wpoely86@gmail.com +diff -ur qml-0.2.10.orig/setup.py qml-0.2.10/setup.py +--- qml-0.2.10.orig/setup.py 2017-06-02 18:14:17.000000000 +0200 ++++ qml-0.2.10/setup.py 2017-09-07 13:44:12.648192634 +0200 +@@ -1,3 +1,4 @@ ++import os + import sys + from numpy.distutils.core import Extension, setup + +@@ -16,10 +17,17 @@ + FORTRAN = "f90" + + # GNU (default) +-COMPILER_FLAGS = ["-O3", "-fopenmp", "-m64", "-march=native", "-fPIC", +- "-Wno-maybe-uninitialized", "-Wno-unused-function", "-Wno-cpp"] +-LINKER_FLAGS = ["-lgomp"] +-MATH_LINKER_FLAGS = ["-lblas", "-llapack"] ++COMPILER_FLAGS = os.environ.get("CFLAGS", '').split(' ') ++if not COMPILER_FLAGS: ++ COMPILER_FLAGS = ["-O3", "-fopenmp", "-m64", "-march=native", "-fPIC", "-Wno-maybe-uninitialized", "-Wno-unused-function", "-Wno-cpp"] ++ ++LINKER_FLAGS = os.environ.get("LDFLAGS", '').split(' ') ++if not LINKER_FLAGS: ++ LINKER_FLAGS = ["-lgomp"] ++ ++MATH_LINKER_FLAGS = os.environ.get("LIBLAPACK", '').split(' ') ++if not MATH_LINKER_FLAGS: ++ MATH_LINKER_FLAGS = ["-lblas", "-llapack"] + + # For clang without OpenMP: (i.e. most Apple/mac system) + if sys.platform == "darwin" and all(["gnu" not in arg for arg in sys.argv]): diff --git a/easybuild/easyconfigs/q/QML/QML-0.2.10-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/q/QML/QML-0.2.10-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..19b0dc9a7d --- /dev/null +++ b/easybuild/easyconfigs/q/QML/QML-0.2.10-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,31 @@ +easyblock = "PythonPackage" + +name = "QML" +version = "0.2.10" +versionsuffix = "-Python-%(pyver)s" + +homepage = "http://www.qmlcode.org" +description = """QML is a Python2/3-compatible toolkit for representation learning of properties + of molecules and solids.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True} + +source_urls = [PYPI_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +patches = ['%(name)s-%(version)s-fix-setup.py.patch'] +checksums = [ + '48e0b6b03b28a981e75358a890bfb7e47048562eec62a4d60190c499b8805685', # qml-0.2.10.tar.gz + 'cc820f0aa800150aa08a5de95869fd0aa39bcc8e2c6eb1ba6918ecef21873535', # QML-0.2.10-fix-setup.py.patch +] + +dependencies = [ + ('Python', '2.7.13'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'chem' -- GitLab From ef2cf845b6473e1f080ec0bb79239da54c971347 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 7 Sep 2017 13:59:33 +0200 Subject: [PATCH 1510/1603] Fix checksums --- .../c/CVXOPT/CVXOPT-1.1.9-intel-2017a-Python-2.7.13.eb | 6 ++++-- .../easyconfigs/f/FastQC/FastQC-0.11.5-Java-1.8.0_144.eb | 6 ++++-- .../r/Rcorrector/Rcorrector-1.0.2-intel-2017a.eb | 6 ++++-- .../SOAPdenovo-Trans/SOAPdenovo-Trans-1.0.4-intel-2017a.eb | 6 ++++-- 4 files changed, 16 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.1.9-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.1.9-intel-2017a-Python-2.7.13.eb index 76a6d8895c..e991d56311 100644 --- a/easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.1.9-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.1.9-intel-2017a-Python-2.7.13.eb @@ -18,8 +18,10 @@ sources = ['%(version)s.tar.gz'] patches = ['%(name)s-%(version)s-fix-setup-py.patch'] -checksums = ['09997fec809179c9bb9fe8cdd202ad6ecb675f890658219022f492e0797122ee', - '89058d53c55dcdc94a9b7a6ea8c6a6e78a693210d1d27a4178f68926ae5099e3'] +checksums = [ + '09997fec809179c9bb9fe8cdd202ad6ecb675f890658219022f492e0797122ee', # 1.1.9.tar.gz + '89058d53c55dcdc94a9b7a6ea8c6a6e78a693210d1d27a4178f68926ae5099e3', # CVXOPT-1.1.9-fix-setup-py.patch +] dependencies = [ ('Python', '2.7.13'), diff --git a/easybuild/easyconfigs/f/FastQC/FastQC-0.11.5-Java-1.8.0_144.eb b/easybuild/easyconfigs/f/FastQC/FastQC-0.11.5-Java-1.8.0_144.eb index 95a61408bf..46332ee18a 100644 --- a/easybuild/easyconfigs/f/FastQC/FastQC-0.11.5-Java-1.8.0_144.eb +++ b/easybuild/easyconfigs/f/FastQC/FastQC-0.11.5-Java-1.8.0_144.eb @@ -14,8 +14,10 @@ toolchain = {'name': 'dummy', 'version': ''} source_urls = ['http://www.bioinformatics.babraham.ac.uk/projects/%(namelower)s'] sources = ['%(namelower)s_v%(version)s.zip'] -checksums = ['dd7a5ad80ceed2588cf6d6ffe35e0f161c0d9977ed08355f5e4d9473282cbd66', - '684701634440864750c9a0b99d81e122a1def78672d436daf5497bff61d9a356'] +checksums = [ + 'dd7a5ad80ceed2588cf6d6ffe35e0f161c0d9977ed08355f5e4d9473282cbd66', # fastqc_v0.11.5.zip + '684701634440864750c9a0b99d81e122a1def78672d436daf5497bff61d9a356', # FastQC_shebang.patch +] patches = ['FastQC_shebang.patch'] diff --git a/easybuild/easyconfigs/r/Rcorrector/Rcorrector-1.0.2-intel-2017a.eb b/easybuild/easyconfigs/r/Rcorrector/Rcorrector-1.0.2-intel-2017a.eb index d7e2978510..9a2677bbd0 100644 --- a/easybuild/easyconfigs/r/Rcorrector/Rcorrector-1.0.2-intel-2017a.eb +++ b/easybuild/easyconfigs/r/Rcorrector/Rcorrector-1.0.2-intel-2017a.eb @@ -12,8 +12,10 @@ toolchainopts = {'cstd': 'c++11'} source_urls = ['https://github.com/mourisl/Rcorrector/archive'] sources = ['v%(version)s.tar.gz'] patches = ['%(name)s-%(version)s-fix-makefile.patch'] -checksums = ['426c7ab5fbb968536dbb4daf6913599f99b50eaabbea8013930da77f1235d9c6', - '785a24b8af0b075d813ee4cd83f7480dd35365d9a0a2b81d80b6eb210bcf0bd0'] +checksums = [ + '426c7ab5fbb968536dbb4daf6913599f99b50eaabbea8013930da77f1235d9c6', # v1.0.2.tar.gz + '785a24b8af0b075d813ee4cd83f7480dd35365d9a0a2b81d80b6eb210bcf0bd0', # Rcorrector-1.0.2-fix-makefile.patch +] dependencies = [ ('zlib', '1.2.11'), diff --git a/easybuild/easyconfigs/s/SOAPdenovo-Trans/SOAPdenovo-Trans-1.0.4-intel-2017a.eb b/easybuild/easyconfigs/s/SOAPdenovo-Trans/SOAPdenovo-Trans-1.0.4-intel-2017a.eb index 9b78a12c9c..75f99d4008 100644 --- a/easybuild/easyconfigs/s/SOAPdenovo-Trans/SOAPdenovo-Trans-1.0.4-intel-2017a.eb +++ b/easybuild/easyconfigs/s/SOAPdenovo-Trans/SOAPdenovo-Trans-1.0.4-intel-2017a.eb @@ -13,8 +13,10 @@ toolchain = {'name': 'intel', 'version': '2017a'} source_urls = ['https://github.com/aquaskyline/SOAPdenovo-Trans/archive/'] sources = ['%(version)s.tar.gz'] patches = ['%(name)s-%(version)s-fix-makefiles.patch'] -checksums = ['378a54cde0ebe240fb515ba67197c053cf95393645c1ae1399b3a611be2a9795', - '15c420a5e2c2a5a5837dbb1223a6b02b78f059b162e82952c7ceee83fdfdcffb'] +checksums = [ + '378a54cde0ebe240fb515ba67197c053cf95393645c1ae1399b3a611be2a9795', # 1.0.4.tar.gz + '15c420a5e2c2a5a5837dbb1223a6b02b78f059b162e82952c7ceee83fdfdcffb', # SOAPdenovo-Trans-1.0.4-fix-makefiles.patch +] dependencies = [('zlib', '1.2.11')] -- GitLab From 68f3c0b441de8d0596c316fe8d2cd1fae141a1e6 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 7 Sep 2017 14:04:22 +0200 Subject: [PATCH 1511/1603] Make @boegel happy --- .../s/Shannon/Shannon-20170511-intel-2017a-Python-2.7.13.eb | 6 ++++-- .../t/Trim_Galore/Trim_Galore-0.4.4-intel-2017a.eb | 5 ++--- 2 files changed, 6 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/s/Shannon/Shannon-20170511-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/s/Shannon/Shannon-20170511-intel-2017a-Python-2.7.13.eb index 329a6b0178..f0f143ee06 100644 --- a/easybuild/easyconfigs/s/Shannon/Shannon-20170511-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/s/Shannon/Shannon-20170511-intel-2017a-Python-2.7.13.eb @@ -24,8 +24,10 @@ dependencies = [ ('Quorum', '1.1.1'), ] -postinstallcmds = ["sed -i '1 i#!/usr/bin/env python' %(installdir)s/*.py", - "chmod +x %(installdir)s/*.py"] +postinstallcmds = [ + "sed -i '1 i#!/usr/bin/env python' %(installdir)s/*.py", + "chmod +x %(installdir)s/*.py", +] modextrapaths = {'PATH': ['']} diff --git a/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.4.4-intel-2017a.eb b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.4.4-intel-2017a.eb index d1bbd95d59..934d2bd412 100755 --- a/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.4.4-intel-2017a.eb +++ b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.4.4-intel-2017a.eb @@ -18,9 +18,8 @@ source_urls = ['http://www.bioinformatics.babraham.ac.uk/projects/%(namelower)s' sources = ['%(namelower)s_v%(version)s.zip'] checksums = ['ccd7eecc73327da29230f3e7c7311a4e21b2cfe7282be18fa059ba900fc33116'] -install_cmd = "cp -a * %(installdir)s && chmod +x %(installdir)s/%(namelower)s" - -postinstallcmds = ["sed -i '1 i#!/usr/bin/env perl' %(installdir)s/%(namelower)s"] +install_cmd = "cp -a * %(installdir)s && chmod +x %(installdir)s/%(namelower)s && " +install_cmd += "sed -i '1 i#!/usr/bin/env perl' %(installdir)s/%(namelower)s" dependencies = [ ('FastQC', '0.11.5', '-Java-1.8.0_144', True), -- GitLab From 7ad310a3dc0c681b2f6c64b324a75a513e620e7e Mon Sep 17 00:00:00 2001 From: Oliver Stueker Date: Thu, 7 Sep 2017 11:29:21 -0230 Subject: [PATCH 1512/1603] address reviewer's comments of PR easybuilders/easybuild-easyconfigs#4912 --- .../g/GAMESS-US/GAMESS-US-20170420-R1-foss-2016b.eb | 2 +- .../GAMESS-US/GAMESS-US-20170420-R1-intel-2016b-sockets.eb | 6 ++++-- .../g/GAMESS-US/GAMESS-US-20170420-R1-intel-2016b.eb | 2 +- .../g/GAMESS-US/GAMESS-US-20170420-R1_recent-gcc.patch | 4 ++++ ...MESS-US-20170420-R1_rungms_fix_PPN_not_initialized.patch | 5 +++++ 5 files changed, 15 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20170420-R1-foss-2016b.eb b/easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20170420-R1-foss-2016b.eb index 3d445caa7f..f5b143f23b 100644 --- a/easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20170420-R1-foss-2016b.eb +++ b/easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20170420-R1-foss-2016b.eb @@ -23,7 +23,7 @@ toolchainopts = {'usempi': True} # manually download via http://www.msg.chem.iastate.edu/gamess/download.html (requires registration) # rename gamess-current.tar.gz by changing 'current' to the proper version sources = ['gamess-%(version)s.tar.gz'] -checksums = ['e9fa2e725ccbd69f4d996ab68bb65ff2'] +checksums = ['6a6747e147293d7d5a47ec472d095abfb3a22bd86887297d68fbab2e5be18da7'] patches = [ 'GAMESS-US_rungms-slurm.patch', diff --git a/easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20170420-R1-intel-2016b-sockets.eb b/easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20170420-R1-intel-2016b-sockets.eb index f227f1556e..fe674c939c 100644 --- a/easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20170420-R1-intel-2016b-sockets.eb +++ b/easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20170420-R1-intel-2016b-sockets.eb @@ -20,12 +20,11 @@ description = """ The General Atomic and Molecular Electronic Structure System ( toolchain = {'name': 'intel', 'version': '2016b'} toolchainopts = {'usempi': False} -ddi_comm = 'sockets' # manually download via http://www.msg.chem.iastate.edu/gamess/download.html (requires registration) # rename gamess-current.tar.gz by changing 'current' to the proper version sources = ['gamess-%(version)s.tar.gz'] -checksums = ['e9fa2e725ccbd69f4d996ab68bb65ff2'] +checksums = ['6a6747e147293d7d5a47ec472d095abfb3a22bd86887297d68fbab2e5be18da7'] patches = [ 'GAMESS-US_rungms-slurm.patch', @@ -37,4 +36,7 @@ patches = [ maxcpus = '1000' maxnodes = '100000' +# Build GAMESS for using TCP/IP sockets instead of MPI: +ddi_comm = 'sockets' + moduleclass = 'chem' diff --git a/easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20170420-R1-intel-2016b.eb b/easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20170420-R1-intel-2016b.eb index 5a67a77274..1ce230b90e 100644 --- a/easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20170420-R1-intel-2016b.eb +++ b/easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20170420-R1-intel-2016b.eb @@ -23,7 +23,7 @@ toolchainopts = {'usempi': True} # manually download via http://www.msg.chem.iastate.edu/gamess/download.html (requires registration) # rename gamess-current.tar.gz by changing 'current' to the proper version sources = ['gamess-%(version)s.tar.gz'] -checksums = ['e9fa2e725ccbd69f4d996ab68bb65ff2'] +checksums = ['6a6747e147293d7d5a47ec472d095abfb3a22bd86887297d68fbab2e5be18da7'] patches = [ 'GAMESS-US_rungms-slurm.patch', diff --git a/easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20170420-R1_recent-gcc.patch b/easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20170420-R1_recent-gcc.patch index 3287498882..9f23726852 100644 --- a/easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20170420-R1_recent-gcc.patch +++ b/easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20170420-R1_recent-gcc.patch @@ -1,3 +1,7 @@ +This patch adds support for GCC 5.4 to the GAMESS-US build scripts. + +Written by Oliver Stueker, ACENET/Compute Canada +Memorial University of Newfoundland, St. John's, Canada --- config.orig 2017-07-18 19:34:32.056678893 +0000 +++ config 2017-07-18 19:48:37.701737302 +0000 @@ -410,6 +410,7 @@ diff --git a/easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20170420-R1_rungms_fix_PPN_not_initialized.patch b/easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20170420-R1_rungms_fix_PPN_not_initialized.patch index 0e6126bbf3..61c75f484d 100644 --- a/easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20170420-R1_rungms_fix_PPN_not_initialized.patch +++ b/easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20170420-R1_rungms_fix_PPN_not_initialized.patch @@ -1,3 +1,8 @@ +This patch avoids rungms from failing in cases where PPN (processors per node) +is not defined. + +Written by Oliver Stueker, ACENET/Compute Canada +Memorial University of Newfoundland, St. John's, Canada --- rungms.orig 2017-07-19 16:53:29.325530604 +0000 +++ rungms 2017-07-19 16:55:39.627358245 +0000 @@ -538,6 +538,7 @@ -- GitLab From 16305e4860e5f7d5bf38b785f469fb46e8a16a28 Mon Sep 17 00:00:00 2001 From: Oliver Stueker Date: Thu, 7 Sep 2017 12:13:36 -0230 Subject: [PATCH 1513/1603] support for recent GCC versions in config and comp scripts --- .../GAMESS-US-20170420-R1_recent-gcc.patch | 54 +++++++++++++++---- 1 file changed, 45 insertions(+), 9 deletions(-) diff --git a/easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20170420-R1_recent-gcc.patch b/easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20170420-R1_recent-gcc.patch index 9f23726852..5c179eb2e6 100644 --- a/easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20170420-R1_recent-gcc.patch +++ b/easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20170420-R1_recent-gcc.patch @@ -1,56 +1,92 @@ -This patch adds support for GCC 5.4 to the GAMESS-US build scripts. +Include support for recent GCC versions in config and comp scripts. Written by Oliver Stueker, ACENET/Compute Canada Memorial University of Newfoundland, St. John's, Canada --- config.orig 2017-07-18 19:34:32.056678893 +0000 -+++ config 2017-07-18 19:48:37.701737302 +0000 -@@ -410,6 +410,7 @@ ++++ config 2017-09-07 12:06:45.507029663 +0000 +@@ -410,6 +410,13 @@ case 5.1: case 5.2: case 5.3: + case 5.4: ++ case 6.1: ++ case 6.2: ++ case 6.3: ++ case 6.4: ++ case 7.1: ++ case 7.2: echo " Good, the newest gfortrans can compile REAL*16 data type." breaksw default: -@@ -810,6 +811,7 @@ +@@ -810,6 +817,13 @@ case 5.1: case 5.2: case 5.3: + case 5.4: ++ case 6.1: ++ case 6.2: ++ case 6.3: ++ case 6.4: ++ case 7.1: ++ case 7.2: echo " Good, the newest gfortrans can compile REAL*16 data type." breaksw default: --- comp.orig 2017-07-19 11:55:05.490262037 +0000 -+++ comp 2017-07-19 11:52:47.986565565 +0000 -@@ -1593,6 +1593,7 @@ ++++ comp 2017-09-07 12:06:45.507029663 +0000 +@@ -1593,6 +1593,13 @@ case 5.1: case 5.2: case 5.3: + case 5.4: ++ case 6.1: ++ case 6.2: ++ case 6.3: ++ case 6.4: ++ case 7.1: ++ case 7.2: if ($MODULE == cosmo) set OPT='-O0' if ($MODULE == dcscf) set OPT='-O0' if ($MODULE == tddgrd) set OPT='-O0' -@@ -1823,6 +1824,7 @@ +@@ -1823,6 +1830,13 @@ case 5.1: case 5.2: case 5.3: + case 5.4: ++ case 6.1: ++ case 6.2: ++ case 6.3: ++ case 6.4: ++ case 7.1: ++ case 7.2: if ($MODULE == cosmo) set OPT='-O0' # same issue as seen in 4.6 if ($MODULE == dcscf) set OPT='-O0' # exam44, continues from 4.7 if ($MODULE == tddgrd) set OPT='-O0' # exam41, continues from 4.6 -@@ -2074,6 +2076,7 @@ +@@ -2074,6 +2088,13 @@ case 5.1: case 5.2: case 5.3: + case 5.4: ++ case 6.1: ++ case 6.2: ++ case 6.3: ++ case 6.4: ++ case 7.1: ++ case 7.2: if ($MODULE == cosmo) set OPT='-O0' if ($MODULE == dcscf) set OPT='-O0' if ($MODULE == tddgrd) set OPT='-O0' -@@ -2191,6 +2194,7 @@ +@@ -2191,6 +2212,13 @@ case 5.1: case 5.2: case 5.3: + case 5.4: ++ case 6.1: ++ case 6.2: ++ case 6.3: ++ case 6.4: ++ case 7.1: ++ case 7.2: if ($MODULE == cosmo) set OPT='-O0' if ($MODULE == dcscf) set OPT='-O0' if ($MODULE == tddgrd) set OPT='-O0' -- GitLab From 8d7e0d76a36d9f6829ed618af07e85af169f2bbd Mon Sep 17 00:00:00 2001 From: Oliver Stueker Date: Thu, 7 Sep 2017 15:04:31 -0230 Subject: [PATCH 1514/1603] GAMESS-US: removing easyconfig for FOSS toolchain It makes problems as discussed at: https://github.com/easybuilders/easybuild-easyconfigs/pull/4912#issuecomment-327832302 --- .../GAMESS-US-20170420-R1-foss-2016b.eb | 39 ------------------- 1 file changed, 39 deletions(-) delete mode 100644 easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20170420-R1-foss-2016b.eb diff --git a/easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20170420-R1-foss-2016b.eb b/easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20170420-R1-foss-2016b.eb deleted file mode 100644 index f5b143f23b..0000000000 --- a/easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20170420-R1-foss-2016b.eb +++ /dev/null @@ -1,39 +0,0 @@ -## -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# -# Copyright:: Copyright 2012-2017 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, -# Ghent University / The Francis Crick Institute -# -# Authors:: -# * Kenneth Hoste -# * Ward Poelmans -# * Oliver Stueker -# License:: MIT/GPL -## -name = 'GAMESS-US' -version = '20170420-R1' - -homepage = 'http://www.msg.chem.iastate.edu/gamess/index.html' -description = """ The General Atomic and Molecular Electronic Structure System (GAMESS) - is a general ab initio quantum chemistry package. """ - -toolchain = {'name': 'foss', 'version': '2016b'} -toolchainopts = {'usempi': True} - -# manually download via http://www.msg.chem.iastate.edu/gamess/download.html (requires registration) -# rename gamess-current.tar.gz by changing 'current' to the proper version -sources = ['gamess-%(version)s.tar.gz'] -checksums = ['6a6747e147293d7d5a47ec472d095abfb3a22bd86887297d68fbab2e5be18da7'] - -patches = [ - 'GAMESS-US_rungms-slurm.patch', - 'GAMESS-US-20170420-R1_rungms_fix_PPN_not_initialized.patch', - 'GAMESS-US-20170420-R1_recent-gcc.patch', -] - -# increase these numbers if your system is bigger in terms of cores-per-node or number of nodes -# it's OK if these values are larger than what your system provides -maxcpus = '1000' -maxnodes = '100000' - -moduleclass = 'chem' -- GitLab From 097208970272fbca3b4d01277c16c6c4f82709df Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Thu, 7 Sep 2017 20:16:48 -0500 Subject: [PATCH 1515/1603] CMakeversion/patchname/patchchecksum --- .../c/CMake/CMake-3.9.1-GCCcore-6.4.0.eb | 41 +++++++++++++++++++ .../m/METIS/METIS-5.1.0-GCCcore-6.4.0.eb | 10 +++-- 2 files changed, 48 insertions(+), 3 deletions(-) create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.9.1-GCCcore-6.4.0.eb diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.9.1-GCCcore-6.4.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.9.1-GCCcore-6.4.0.eb new file mode 100644 index 0000000000..3fbbcb5eaa --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.9.1-GCCcore-6.4.0.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.9.1' + +homepage = 'http://www.cmake.org' + +description = """ + CMake, the cross-platform, open-source build system. CMake is a family of + tools designed to build, test and package software. +""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['d768ee83d217f91bb597b3ca2ac663da7a8603c97e1f1a5184bc01e0ad2b12bb'] + +configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' + +builddependencies = [ + ('binutils', '2.28'), +] + +dependencies = [ + ('ncurses', '6.0'), + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.1.0c'), +] + +osdependencies = [ + ('openssl-devel', 'libssl-dev', 'libopenssl-devel'), +] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/m/METIS/METIS-5.1.0-GCCcore-6.4.0.eb b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-GCCcore-6.4.0.eb index 3845c5050b..7ee8221276 100644 --- a/easybuild/easyconfigs/m/METIS/METIS-5.1.0-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-GCCcore-6.4.0.eb @@ -19,14 +19,18 @@ source_urls = [ 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/OLD', ] sources = [SOURCELOWER_TAR_GZ] -checksums = ['76faebe03f6c963127dbb73c13eab58c9a3faeae48779f049066a21c087c5db2'] # We use 32bit for indices and 64bit for content -patches = ['METIS-5.1.0-use-doubles.patch'] +patches = ['%(name)s-%(version)s-use-doubles.patch'] + +checksums = [ + '76faebe03f6c963127dbb73c13eab58c9a3faeae48779f049066a21c087c5db2', # source + '7e38a3ec8f2b8e3d189239bade5b28c0dd1c564485050109164fa71a6a767c67', # patch +] builddependencies = [ ('binutils', '2.28'), - ('CMake', '3.8.2'), + ('CMake', '3.9.1'), ] configopts = ['', 'shared=1'] -- GitLab From 08776789eb88f71bd189a25c4e62879583db9a82 Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Thu, 7 Sep 2017 20:27:33 -0500 Subject: [PATCH 1516/1603] update CMake ver --- .../c/CMake/CMake-3.9.1-GCCcore-6.4.0.eb | 41 +++++++++++++++++++ .../d/Doxygen/Doxygen-1.8.13-GCCcore-6.4.0.eb | 2 +- 2 files changed, 42 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.9.1-GCCcore-6.4.0.eb diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.9.1-GCCcore-6.4.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.9.1-GCCcore-6.4.0.eb new file mode 100644 index 0000000000..3fbbcb5eaa --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.9.1-GCCcore-6.4.0.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.9.1' + +homepage = 'http://www.cmake.org' + +description = """ + CMake, the cross-platform, open-source build system. CMake is a family of + tools designed to build, test and package software. +""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['d768ee83d217f91bb597b3ca2ac663da7a8603c97e1f1a5184bc01e0ad2b12bb'] + +configopts = '-- -DCMAKE_USE_OPENSSL=1 -DCMAKE_PREFIX_PATH=$EBROOTNCURSES' + +builddependencies = [ + ('binutils', '2.28'), +] + +dependencies = [ + ('ncurses', '6.0'), + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.1.0c'), +] + +osdependencies = [ + ('openssl-devel', 'libssl-dev', 'libopenssl-devel'), +] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.13-GCCcore-6.4.0.eb b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.13-GCCcore-6.4.0.eb index ed9c7f458e..0209b2249c 100644 --- a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.13-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.13-GCCcore-6.4.0.eb @@ -18,7 +18,7 @@ checksums = ['af667887bd7a87dc0dbf9ac8d86c96b552dfb8ca9c790ed1cbffaa6131573f6b'] builddependencies = [ ('binutils', '2.28'), ('Bison', '3.0.4'), - ('CMake', '3.8.2'), + ('CMake', '3.9.1'), ('flex', '2.6.4'), ('pkg-config', '0.29.2'), ] -- GitLab From 81be4f4e503de5246b4bc76a74025e5eb0182aa2 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Fri, 8 Sep 2017 16:26:37 +0800 Subject: [PATCH 1517/1603] prepare release notes for eb340 --- RELEASE_NOTES | 43 +++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 43 insertions(+) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index e766c8da3c..c52846e489 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -6,6 +6,49 @@ These release notes can also be consulted at http://easybuild.readthedocs.org/en The latest version of easybuild-easyconfig provides 7,313 easyconfig files, for 1,262 different software packages, 25 different (compiler) toolchains, 13 software bundles and 1 meta-package. +v3.4.0 (September 8th 2017) +--------------------------- + +feature release +- added easyconfigs for foss/2017b and intel/2017b common toolchains (#4768), (#4618) +- added example easyconfig files for 31 new software packages: + - BAMM (#4650), BamM (#4650), bcl2fastq2 (#4902), CGNS (#5078), CLAPACK (#5096), CLISP (#4926), cadaver (#4873), destiny (#5009), GroopM (#4650), Lucene-Geo-Gazetteer (#5064), libffcall (#4850), libsigsegv (#4840), MERCKX (#5056), minimap2 (#4991), ncompress (#4852), OpenNLP (#5059), OpenRefine (#5058), PHAST (#5096), PYTHIA (#5083), ParallelIO (#5071), PnetCDF (#5071), plotly (#5010), QML (#5101), Quorum (#5095), Rcorrector (#5095), SCnorm (#5008), sratoolkit (#2715), Shannon (#5095), Tika (#5063), UNAFold (#4997), VERSE (#4843) +- added additional easyconfigs for various supported software packages, including: + - ART 2016.06.05, Armadillo 7.950.1, Autoconf 2.68, Autoconf 2.69, Automake 1.11.3, Automake 1.15.1, Autotools 20170619, ant 1.10.1, BAMM 2.5.0, BEDTools 2.26.0, BFAST 0.7.0a, BLAST+ 2.6.0, BWA 0.7.12, BWA 0.7.15, BWA 0.7.15, BWA 0.7.16a, BWA 0.7.16a, BamM 1.7.3, Biopython 1.70, Bison 3.0.4, Blitz++ 0.10, Blosc 1.12.1, Blosc 1.12.1, Boost 1.65.0, Bowtie 1.1.2, Bowtie 1.2.1.1, Bowtie2 2.3.2, Bowtie2 2.3.2, bcl2fastq2 2.19.1, binutils 2.29, binutils 2.29.eb, byacc 20170709, bzip2 1.0.6, CD HIT, CFITSIO 3.41, CGNS 3.3.1, CLAPACK 3.2.1, CLISP 2.49, CMake 3.9.1, CMake 3.9.1, CMake 3.9.1.eb, CVXOPT 1.1.9, CppUnit 1.12.1, Cython 0.25.2, cURL 7.55.1, cadaver 0.23.3, cairo 1.14.10, cutadapt 1.14, DB 6.2.32, DBus 1.10.20, destiny 2.5.6, EasyBuild 3.3.1.eb, Eigen 3.3.4.eb, eudev 3.2.2, expat 2.2.4, FDS 6.5.3, FFTW 3.3.6, FastQC 0.11.5, FreeXL 1.0.3, flex 2.6.4, fontconfig 2.12.4, foss 2017b.eb, freetype 2.8, GAMESS US, GAMESS US, GATK 3.8, GCC 7.2.0, GCCcore 7.2.0.eb, GLib 2.52.0, GLib 2.53.5, GMP 6.1.2, GObject Introspection, GObject Introspection, GROMACS 2016.3, GSL 2.4, Gdk Pixbuf, GroopM 0.3.4, Guile 2.2.2, gc 7.6.0, gettext 0.19.8.1, gompi 2017b.eb, gperf 3.1, gzip 1.8, HDF 4.2.13, HDF5 1.10.1, HDF5 1.8.19, HDF5 1.8.19, HPL 2.2, HPL 2.2, HPL 2.2, HTSeq 0.9.1, Hadoop 2.6.0, h5py 2.7.0, h5py 2.7.0, h5py 2.7.0, h5py 2.7.0, help2man 1.47.4, htop 2.0.1.eb, hwloc 1.11.7, I TASSER, icc 2017.4.196, iccifort 2017.4.196, ifort 2017.4.196, iimpi 2017b.eb, imkl 2017.3.196, imkl 2017.3.196, impi 2017.3.196, intel 2017b.eb, iomkl 2017b.eb, iompi 2017b.eb, JAGS 4.2.0, JUnit 4.12, JasPer 2.0.12, Java 1.8.0_141.eb, Java 1.8.0_144.eb, Jellyfish 2.2.6, kallisto 0.43.1, LLVM 4.0.1, LZO 2.10, LibUUID 1.0.3, LittleCMS 2.8, Lucene Geo, libGLU 9.0.0, libcerf 1.5, libdrm 2.4.76, libevent 2.1.8, libffcall 1.13, libffi 3.2.1, libgd 2.2.4, libjpeg turbo, libjpeg turbo, libpng 1.6.32, libpthread stubs, libreadline 7.0, libsigsegv 2.11, libsodium 1.0.13, libsodium 1.0.13, libspatialindex 1.8.5, libtool 2.4.6, libunistring 0.9.7, libxml2 2.9.4, libyaml 0.1.7, M4 1.4.18, MATLAB 2013b.eb, MERCKX 20170330, MPFR 3.1.5, MRtrix 3.0_RC2, Mako 1.0.6, Mathematica 11.1.1.eb, Maven 3.5.0.eb, Mesa 17.0.2, Mesquite 2.3.0, matplotlib 2.0.2, matplotlib 2.0.2, mdtest 1.9.3, minimap2 2.0rc1, muParser 2.2.5, NASM 2.13.01, NASM 2.13.01, NLTK 3.2.4, NWChem 6.6.revision27746, ncompress 4.2.4.4, ncurses 6.0, netCDF 4.4.1.1, netcdf4 python, nettle 3.3, nettle 3.3, numactl 2.0.11, ORCA 4.0.1, OpenBLAS 0.2.20, OpenMPI 2.1.1, OpenMPI 2.1.1, OpenNLP 1.8.1.eb, OpenPGM 5.2.122, OpenPGM 5.2.122, OpenRefine 2.7, PAPI 5.5.1, PCRE 8.40, PCRE 8.41, PCRE 8.41, PHAST 1.4, PIL 1.1.7, PYTHIA 8.226, ParallelIO 2.2.2a, Perl 5.24.1, Perl 5.26.0, Perl 5.26.0, PnetCDF 1.8.1, PyTables 3.3.0, PyZMQ 16.0.2, Pysam 0.10.0, Pysam 0.8.4, Python 2.7.13, Python 3.6.1, parallel 20170822, picard 2.10.1, picard 2.6.0, pigz 2.3.4, pixman 0.34.0, pkg config, pkgconfig 1.2.2, pkgconfig 1.2.2, plotly 4.7.1, QML 0.2.10, Qhull 2015.2, Qt 4.8.7, Quorum 1.1.1, ROOT 6.10.04, Rcorrector 1.0.2, rjags 4, SAMtools 1.2, SAMtools 1.3.1, SAMtools 1.5, SCnorm 0.99.7, SOAPdenovo Trans, SPAdes 3.10.1, SQLite 3.20.1, SRA Toolkit, SRA Toolkit, ScaLAPACK 2.0.2, Seurat 1.4.0.16, Shannon 20170511, Siesta 4.0.1, Siesta 4.1, Singularity 2.3.1, Spark 2.2.0, StringTie 1.3.3, Szip 2.1.1, Szip 2.1.1, snappy 1.1.6.eb, Tcl 8.6.7, Tika 1.16.eb, Trim_Galore 0.4.4, Trinity 2.4.0, tbb 2017_U6, texinfo 6.4, UNAFold 3.8, util linux, util linux, util linux, util linux, VERSE 0.1.5, Voro++ 0.4.6, vsc mympirun, XGBoost 0.6a2, XZ 5.2.3, Xerces C++, x264 20170721, xarray 0.9.6, Yasm 1.3.0, ZeroMQ 4.2.2, zlib 1.2.11 +- minor enhancements, including: + - added Rmpi patch file for R built with intel toolchains incl. impi 5.x) (#4623) + - use single-line description in setup.py (#4881) + - Updating deprecated PLINK urls (#4920) + - rename CLISP patch + add upstream ref + minor style cleanups in easyconfig (#4986) + - add required zlib dependency for util-linux 2.29.2 (#4900) + - also add checksums to Perl 5.24.1 easyconfig using intel/2017a (#4992) + - add zlib as depedency to recent util-linux easyconfigs (#4998) + - add additional extensions for R 3.4.0 and Bioconductor 3.5 bundle (#5007) + - add SC3 extension into bundle for Bioconductor 3.5 (+ dep extesions in R easyconfig) (#5028) + - add mpath as extension for R 3.4.0 (#5029) + - remove superfluous $CPATH update in GLib 2.44.0 easyconfig (#5053) + - include timereg as extension in R 3.4.0 easyconfig (#5062) + - update ncurses to not build a separate libtinfo but provide a soft link instead. Force linking to ncurses in libreadline (#5067) + - bump version for various easyconfigs that use GCCcore/6.4.0 (#5073) + - remove bare Python easyconfig using GCCcore/6.4.0 toolchain + easyconfigs that require it (#5075) + - bump version for libyaml, SQLite & Tcl easyconfigs that use GCCcore/6.4.0 (#5076) + - add peperr extension for R 3.4.0 (#5079) + - include Autotools as build dep for netCDF (#5077) + - add check to see whether binutils is included as build dep when GCCore toolchain is used (#5084) + - update Tesla-Deployment-Kit-5.319.43.eb (#5018) +- various bug fixes, including: + - fix version and source for Seurat, add extensions required by Seurat in R 3.4.0 easyconfig (#4889) + - use modextrapaths instead of modextravars in OpenMM easyconfig (#4903) + - fix moduleclass for Cookiecutter (#4947) + - also fix URLs in PLINK-1.07-x86_64.eb (#5006) + - iompi: OpenMPI dependency must come after icc/ifort (#5024) + - fix typo in comment in util-linux easyconfigs & add SHA256 checksums (#5052) + - avoid that /Users/kehoste/.m2 is abused by Maven when installing OpenNLP (#5061) + - linking to ncurses was not done correctly (#5074) + - iomkl toolchain matching on intel/foss 2017b (#5097) + - add missing binutils build dep for texinfo (#5099) + + v3.3.1 (July 12th 2017) ----------------------- -- GitLab From 7bc3456672572650859ec00cbb6eb6bcb84d5c8d Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Fri, 8 Sep 2017 06:11:02 -0500 Subject: [PATCH 1518/1603] fix homepage --- .../easyconfigs/s/sparsehash/sparsehash-2.0.3-GCCcore-6.4.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/sparsehash/sparsehash-2.0.3-GCCcore-6.4.0.eb b/easybuild/easyconfigs/s/sparsehash/sparsehash-2.0.3-GCCcore-6.4.0.eb index affa39b4de..1c99ca060b 100644 --- a/easybuild/easyconfigs/s/sparsehash/sparsehash-2.0.3-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/s/sparsehash/sparsehash-2.0.3-GCCcore-6.4.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'sparsehash' version = '2.0.3' -homepage = 'https://code.google.com/p/sparsehash/' +homepage = 'https://github.com/sparsehash/sparsehash' description = """ An extremely memory-efficient hash_map implementation. 2 bits/entry overhead! -- GitLab From 41ba14f7a063d960807336283bbaca77d0f141e4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 8 Sep 2017 21:36:18 +0200 Subject: [PATCH 1519/1603] bump version to 3.4.0 + minor edits in release notes --- RELEASE_NOTES | 57 +++++++++++++++++++++++---------------------------- setup.py | 2 +- 2 files changed, 27 insertions(+), 32 deletions(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index c52846e489..898568a4e3 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -3,49 +3,44 @@ For more detailed information, please see the git log. These release notes can also be consulted at http://easybuild.readthedocs.org/en/latest/Release_notes.html. -The latest version of easybuild-easyconfig provides 7,313 easyconfig files, for 1,262 different software packages, +The latest version of easybuild-easyconfig provides 7,566 easyconfig files, for 1,293 different software packages, 25 different (compiler) toolchains, 13 software bundles and 1 meta-package. -v3.4.0 (September 8th 2017) ---------------------------- +v3.4.0 (September 10th 2017) +---------------------------- feature release - added easyconfigs for foss/2017b and intel/2017b common toolchains (#4768), (#4618) +- added new easyconfigs for existing toolchains: + - iomkl/2017b (#5097) - added example easyconfig files for 31 new software packages: - - BAMM (#4650), BamM (#4650), bcl2fastq2 (#4902), CGNS (#5078), CLAPACK (#5096), CLISP (#4926), cadaver (#4873), destiny (#5009), GroopM (#4650), Lucene-Geo-Gazetteer (#5064), libffcall (#4850), libsigsegv (#4840), MERCKX (#5056), minimap2 (#4991), ncompress (#4852), OpenNLP (#5059), OpenRefine (#5058), PHAST (#5096), PYTHIA (#5083), ParallelIO (#5071), PnetCDF (#5071), plotly (#5010), QML (#5101), Quorum (#5095), Rcorrector (#5095), SCnorm (#5008), sratoolkit (#2715), Shannon (#5095), Tika (#5063), UNAFold (#4997), VERSE (#4843) + - BAMM (#4650), BamM (#4650), bcl2fastq2 (#4902), CGNS (#5078), CLAPACK (#5096), CLISP (#4926, #4986), + cadaver (#4873), destiny (#5009), GroopM (#4650), Lucene-Geo-Gazetteer (#5064), libffcall (#4850), + libsigsegv (#4840), MERCKX (#5056), minimap2 (#4991), ncompress (#4852), OpenNLP (#5059, #5061), + OpenRefine (#5058), PHAST (#5096), PYTHIA (#5083), ParallelIO (#5071), PnetCDF (#5071), plotly (#5010), + QML (#5101), Quorum (#5095), Rcorrector (#5095), SCnorm (#5008), SOAPdenovo-Trans (#5095), Shannon (#5095), + Tika (#5063), UNAFold (#4997), VERSE (#4843) - added additional easyconfigs for various supported software packages, including: - - ART 2016.06.05, Armadillo 7.950.1, Autoconf 2.68, Autoconf 2.69, Automake 1.11.3, Automake 1.15.1, Autotools 20170619, ant 1.10.1, BAMM 2.5.0, BEDTools 2.26.0, BFAST 0.7.0a, BLAST+ 2.6.0, BWA 0.7.12, BWA 0.7.15, BWA 0.7.15, BWA 0.7.16a, BWA 0.7.16a, BamM 1.7.3, Biopython 1.70, Bison 3.0.4, Blitz++ 0.10, Blosc 1.12.1, Blosc 1.12.1, Boost 1.65.0, Bowtie 1.1.2, Bowtie 1.2.1.1, Bowtie2 2.3.2, Bowtie2 2.3.2, bcl2fastq2 2.19.1, binutils 2.29, binutils 2.29.eb, byacc 20170709, bzip2 1.0.6, CD HIT, CFITSIO 3.41, CGNS 3.3.1, CLAPACK 3.2.1, CLISP 2.49, CMake 3.9.1, CMake 3.9.1, CMake 3.9.1.eb, CVXOPT 1.1.9, CppUnit 1.12.1, Cython 0.25.2, cURL 7.55.1, cadaver 0.23.3, cairo 1.14.10, cutadapt 1.14, DB 6.2.32, DBus 1.10.20, destiny 2.5.6, EasyBuild 3.3.1.eb, Eigen 3.3.4.eb, eudev 3.2.2, expat 2.2.4, FDS 6.5.3, FFTW 3.3.6, FastQC 0.11.5, FreeXL 1.0.3, flex 2.6.4, fontconfig 2.12.4, foss 2017b.eb, freetype 2.8, GAMESS US, GAMESS US, GATK 3.8, GCC 7.2.0, GCCcore 7.2.0.eb, GLib 2.52.0, GLib 2.53.5, GMP 6.1.2, GObject Introspection, GObject Introspection, GROMACS 2016.3, GSL 2.4, Gdk Pixbuf, GroopM 0.3.4, Guile 2.2.2, gc 7.6.0, gettext 0.19.8.1, gompi 2017b.eb, gperf 3.1, gzip 1.8, HDF 4.2.13, HDF5 1.10.1, HDF5 1.8.19, HDF5 1.8.19, HPL 2.2, HPL 2.2, HPL 2.2, HTSeq 0.9.1, Hadoop 2.6.0, h5py 2.7.0, h5py 2.7.0, h5py 2.7.0, h5py 2.7.0, help2man 1.47.4, htop 2.0.1.eb, hwloc 1.11.7, I TASSER, icc 2017.4.196, iccifort 2017.4.196, ifort 2017.4.196, iimpi 2017b.eb, imkl 2017.3.196, imkl 2017.3.196, impi 2017.3.196, intel 2017b.eb, iomkl 2017b.eb, iompi 2017b.eb, JAGS 4.2.0, JUnit 4.12, JasPer 2.0.12, Java 1.8.0_141.eb, Java 1.8.0_144.eb, Jellyfish 2.2.6, kallisto 0.43.1, LLVM 4.0.1, LZO 2.10, LibUUID 1.0.3, LittleCMS 2.8, Lucene Geo, libGLU 9.0.0, libcerf 1.5, libdrm 2.4.76, libevent 2.1.8, libffcall 1.13, libffi 3.2.1, libgd 2.2.4, libjpeg turbo, libjpeg turbo, libpng 1.6.32, libpthread stubs, libreadline 7.0, libsigsegv 2.11, libsodium 1.0.13, libsodium 1.0.13, libspatialindex 1.8.5, libtool 2.4.6, libunistring 0.9.7, libxml2 2.9.4, libyaml 0.1.7, M4 1.4.18, MATLAB 2013b.eb, MERCKX 20170330, MPFR 3.1.5, MRtrix 3.0_RC2, Mako 1.0.6, Mathematica 11.1.1.eb, Maven 3.5.0.eb, Mesa 17.0.2, Mesquite 2.3.0, matplotlib 2.0.2, matplotlib 2.0.2, mdtest 1.9.3, minimap2 2.0rc1, muParser 2.2.5, NASM 2.13.01, NASM 2.13.01, NLTK 3.2.4, NWChem 6.6.revision27746, ncompress 4.2.4.4, ncurses 6.0, netCDF 4.4.1.1, netcdf4 python, nettle 3.3, nettle 3.3, numactl 2.0.11, ORCA 4.0.1, OpenBLAS 0.2.20, OpenMPI 2.1.1, OpenMPI 2.1.1, OpenNLP 1.8.1.eb, OpenPGM 5.2.122, OpenPGM 5.2.122, OpenRefine 2.7, PAPI 5.5.1, PCRE 8.40, PCRE 8.41, PCRE 8.41, PHAST 1.4, PIL 1.1.7, PYTHIA 8.226, ParallelIO 2.2.2a, Perl 5.24.1, Perl 5.26.0, Perl 5.26.0, PnetCDF 1.8.1, PyTables 3.3.0, PyZMQ 16.0.2, Pysam 0.10.0, Pysam 0.8.4, Python 2.7.13, Python 3.6.1, parallel 20170822, picard 2.10.1, picard 2.6.0, pigz 2.3.4, pixman 0.34.0, pkg config, pkgconfig 1.2.2, pkgconfig 1.2.2, plotly 4.7.1, QML 0.2.10, Qhull 2015.2, Qt 4.8.7, Quorum 1.1.1, ROOT 6.10.04, Rcorrector 1.0.2, rjags 4, SAMtools 1.2, SAMtools 1.3.1, SAMtools 1.5, SCnorm 0.99.7, SOAPdenovo Trans, SPAdes 3.10.1, SQLite 3.20.1, SRA Toolkit, SRA Toolkit, ScaLAPACK 2.0.2, Seurat 1.4.0.16, Shannon 20170511, Siesta 4.0.1, Siesta 4.1, Singularity 2.3.1, Spark 2.2.0, StringTie 1.3.3, Szip 2.1.1, Szip 2.1.1, snappy 1.1.6.eb, Tcl 8.6.7, Tika 1.16.eb, Trim_Galore 0.4.4, Trinity 2.4.0, tbb 2017_U6, texinfo 6.4, UNAFold 3.8, util linux, util linux, util linux, util linux, VERSE 0.1.5, Voro++ 0.4.6, vsc mympirun, XGBoost 0.6a2, XZ 5.2.3, Xerces C++, x264 20170721, xarray 0.9.6, Yasm 1.3.0, ZeroMQ 4.2.2, zlib 1.2.11 + - Boost 1.65.0, binutils 2.29, GAMESS-US 20170420-R1, GCC(core) 7.2.0, gzip 1.8, HDF5 1.8.19, LLVM 4.0.1, + MRtrix 3.0_RC2, Perl 5.26.0, ROOT 6.10.04, Spark 2.2.0 - minor enhancements, including: - - added Rmpi patch file for R built with intel toolchains incl. impi 5.x) (#4623) - - use single-line description in setup.py (#4881) - - Updating deprecated PLINK urls (#4920) - - rename CLISP patch + add upstream ref + minor style cleanups in easyconfig (#4986) - - add required zlib dependency for util-linux 2.29.2 (#4900) - - also add checksums to Perl 5.24.1 easyconfig using intel/2017a (#4992) - - add zlib as depedency to recent util-linux easyconfigs (#4998) - - add additional extensions for R 3.4.0 and Bioconductor 3.5 bundle (#5007) - - add SC3 extension into bundle for Bioconductor 3.5 (+ dep extesions in R easyconfig) (#5028) - - add mpath as extension for R 3.4.0 (#5029) - - remove superfluous $CPATH update in GLib 2.44.0 easyconfig (#5053) - - include timereg as extension in R 3.4.0 easyconfig (#5062) - - update ncurses to not build a separate libtinfo but provide a soft link instead. Force linking to ncurses in libreadline (#5067) - - bump version for various easyconfigs that use GCCcore/6.4.0 (#5073) - - remove bare Python easyconfig using GCCcore/6.4.0 toolchain + easyconfigs that require it (#5075) - - bump version for libyaml, SQLite & Tcl easyconfigs that use GCCcore/6.4.0 (#5076) - - add peperr extension for R 3.4.0 (#5079) - - include Autotools as build dep for netCDF (#5077) - - add check to see whether binutils is included as build dep when GCCore toolchain is used (#5084) - - update Tesla-Deployment-Kit-5.319.43.eb (#5018) + - add checksums to Perl 5.24.1 easyconfigs (#4973, #4992) + - add additional extensions for R 3.4.0 and Bioconductor 3.5 bundle (#5007, #5028, #5029, #5062, #5079) + - also define $INCLUDEPATH and $LIBRARY_PATH in Tesla-Deployment-Kit easyconfig (#5018) + - add check to see whether binutils is included as build dep when GCCcore toolchain is used (#5084) - various bug fixes, including: - - fix version and source for Seurat, add extensions required by Seurat in R 3.4.0 easyconfig (#4889) + - added Rmpi patch file for R built with intel toolchains incl. impi 5.x (#4623) + - use single-line description in setup.py (#4881) + - fix version and source for Seurat + add extensions required by Seurat in R 3.4.0 easyconfig (#4889) + - add zlib as dependency to util-linux easyconfigs (#4900, #4998) - use modextrapaths instead of modextravars in OpenMM easyconfig (#4903) + - update deprecated PLINK urls (#4920, #5006) - fix moduleclass for Cookiecutter (#4947) - - also fix URLs in PLINK-1.07-x86_64.eb (#5006) - - iompi: OpenMPI dependency must come after icc/ifort (#5024) + - fix order of OpenMPI dependency in iomkl easyconfig, must come after icc/ifort (#5024) - fix typo in comment in util-linux easyconfigs & add SHA256 checksums (#5052) - - avoid that /Users/kehoste/.m2 is abused by Maven when installing OpenNLP (#5061) - - linking to ncurses was not done correctly (#5074) - - iomkl toolchain matching on intel/foss 2017b (#5097) + - remove superfluous $CPATH update in GLib 2.44.0 easyconfig (#5053) + - update ncurses to not build a separate libtinfo but provide a soft link instead + force linking to ncurses in libreadline (#5067, #5074) + - include Autotools as build dep for netCDF (#5077) - add missing binutils build dep for texinfo (#5099) diff --git a/setup.py b/setup.py index 49f7189df7..a34f7bed38 100644 --- a/setup.py +++ b/setup.py @@ -47,7 +47,7 @@ from distutils import log # recent setuptools versions will *TRANSFORM* something like 'X.Y.Zdev' into 'X.Y.Z.dev0', with a warning like # UserWarning: Normalizing '2.4.0dev' to '2.4.0.dev0' # This causes problems further up the dependency chain... -VERSION = '3.4.0.dev0' +VERSION = '3.4.0' API_VERSION = VERSION.split('.')[0] EB_VERSION = '.'.join(VERSION.split('.')[0:2]) -- GitLab From 7c4a16187971e955d427f7a7f6c3b5504b500368 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 10 Sep 2017 23:18:15 +0200 Subject: [PATCH 1520/1603] bump version to v3.4.0 --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index a34f7bed38..df6b66c143 100644 --- a/setup.py +++ b/setup.py @@ -47,7 +47,7 @@ from distutils import log # recent setuptools versions will *TRANSFORM* something like 'X.Y.Zdev' into 'X.Y.Z.dev0', with a warning like # UserWarning: Normalizing '2.4.0dev' to '2.4.0.dev0' # This causes problems further up the dependency chain... -VERSION = '3.4.0' +VERSION = '3.5.0.dev0' API_VERSION = VERSION.split('.')[0] EB_VERSION = '.'.join(VERSION.split('.')[0:2]) -- GitLab From 0bfc05fea47cefb8b7a68e580614c2a3b7143763 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 10 Sep 2017 23:25:38 +0200 Subject: [PATCH 1521/1603] adding easyconfigs: EasyBuild-3.4.0.eb --- .../e/EasyBuild/EasyBuild-3.4.0.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.4.0.eb diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.4.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.4.0.eb new file mode 100644 index 0000000000..581ed37dc0 --- /dev/null +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.4.0.eb @@ -0,0 +1,45 @@ +easyblock = 'EB_EasyBuildMeta' + +name = 'EasyBuild' +version = '3.4.0' + +homepage = 'https://easybuilders.github.io/easybuild' +description = """EasyBuild is a software build and installation framework + written in Python that allows you to install software in a structured, + repeatable and robust way.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = [ + # vsc-install + 'https://pypi.python.org/packages/82/ec/19d85d2bb91b562195d00db9ac82d7529904e7eabc0597720966bf74714f/', + # vsc-base + 'https://pypi.python.org/packages/f7/66/1ff7ecc4a93ba37e063f5bfbe395e95a547b1dec73b017c2724f4475a958/', + # easybuild-framework + 'https://pypi.python.org/packages/6a/56/70e72d757112c7ee8f7fceb033f150d423d168b08eeb3f4adaeb02114d70', + # easybuild-easyblocks + 'https://pypi.python.org/packages/47/f2/60674a7bdf4be589ea55c684227bc50a987b64249aedfc725ad85bd9e5d7', + # easybuild-easyconfigs + 'https://pypi.python.org/packages/a2/46/ef2a9d4a89394402d74ef281ffdb2c423bde1131fdc8bf2425513538fbe4', +] +# order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) +sources = [ + 'vsc-install-0.10.26.tar.gz', + 'vsc-base-2.5.8.tar.gz', + 'easybuild-framework-%(version)s.tar.gz', + 'easybuild-easyblocks-%(version)s.tar.gz', + 'easybuild-easyconfigs-%(version)s.tar.gz', +] +checksums = [ + 'f97b5ca8b171964c12347e5b814ae5266698f5ea134056f04ff752a1eb562f30', # vsc-install-0.10.26.tar.gz + '7fcd300f842edf4baade7d0b7a3b462ca7dfb2a411a7532694a90127c6646ee2', # vsc-base-2.5.8.tar.gz + '74b952d612c390acd87d367adc813307c35baa49669effd7cd593392922d5b0d', # easybuild-framework-3.4.0.tar.gz + 'd6b1459fbe5b8d8fd66a36e49606959508ec18e23eed281972e1180fccad52ac', # easybuild-easyblocks-3.4.0.tar.gz + 'e9ebe7fb70ddb4fa00ce41ddb92119c3e7ee99ff1422f5f299f958d7da99294e', # easybuild-easyconfigs-3.4.0.tar.gz +] + +# EasyBuild is a (set of) Python packages, so it depends on Python +# usually, we want to use the system Python, so no actual Python dependency is listed +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +moduleclass = 'tools' -- GitLab From 5a06831c96c83aabe8824833acdad8bf079a0222 Mon Sep 17 00:00:00 2001 From: Fokke Dijkstra Date: Tue, 12 Sep 2017 14:37:38 +0200 Subject: [PATCH 1522/1603] Fixed github url and added checksum. --- easybuild/easyconfigs/h/HTSlib/HTSlib-1.4.1-foss-2016a.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/h/HTSlib/HTSlib-1.4.1-foss-2016a.eb b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.4.1-foss-2016a.eb index 187d2f6581..a04c1df219 100644 --- a/easybuild/easyconfigs/h/HTSlib/HTSlib-1.4.1-foss-2016a.eb +++ b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.4.1-foss-2016a.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel @@ -20,6 +20,8 @@ toolchain = {'name': 'foss', 'version': '2016a'} source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s/'] sources = [SOURCELOWER_TAR_BZ2] +checksums = ['e549fee04d95c1cf8f46347e9e9bbd93'] + # cURL added for S3 support dependencies = [ ('zlib', '1.2.8'), -- GitLab From df9e602133f24366b456a5db2360f14351dab09a Mon Sep 17 00:00:00 2001 From: John Donners Date: Wed, 13 Sep 2017 22:20:17 +0200 Subject: [PATCH 1523/1603] adding easyconfigs: NEST-2.12.0-foss-2015b.eb --- .../n/NEST/NEST-2.12.0-foss-2015b.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/n/NEST/NEST-2.12.0-foss-2015b.eb diff --git a/easybuild/easyconfigs/n/NEST/NEST-2.12.0-foss-2015b.eb b/easybuild/easyconfigs/n/NEST/NEST-2.12.0-foss-2015b.eb new file mode 100644 index 0000000000..700407b571 --- /dev/null +++ b/easybuild/easyconfigs/n/NEST/NEST-2.12.0-foss-2015b.eb @@ -0,0 +1,35 @@ +easyblock = 'CMakeMake' + +name = 'NEST' +version = '2.12.0' + +homepage = 'http://www.nest-simulator.org/' +description = """NEST is a simulator for spiking neural network models + that focuses on the dynamics, size and structure of neural systems rather + than on the exact morphology of individual neurons.""" + +toolchain = {'name': 'foss', 'version': '2015b'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = ['nest-%(version)s.tar.gz'] +source_urls = ['https://github.com/nest/nest-simulator/releases/download/v%(version)s/'] + +dependencies = [ + ('Python', '2.7.9'), + ('libreadline', '6.3'), + ('GSL', '2.1'), + ('libtool', '2.4.6', '-GNU-4.9.3-2.25', True), +] + +configopts = '-DREADLINE_ROOT_DIR=$EBROOTLIBREADLINE' + +builddependencies = [ + ('CMake', '3.4.1'), + ('Doxygen', '1.8.10'), +] + +modextrapaths = { + 'PYTHONPATH': ['lib/python2.7/site-packages'], +} + +moduleclass = 'math' -- GitLab From da24af89d0e5a40bd235899ecddb1e1709d6aacb Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Fri, 15 Sep 2017 09:25:26 +0200 Subject: [PATCH 1524/1603] {bio}[intel/2017a] AUGUSTUS 3.2.3 source_urls corrected (REVIEW) --- .../a/AUGUSTUS/AUGUSTUS-3.2.3-intel-2017a-Python-2.7.13.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.2.3-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.2.3-intel-2017a-Python-2.7.13.eb index e754db2e6d..7f1484baf5 100644 --- a/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.2.3-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.2.3-intel-2017a-Python-2.7.13.eb @@ -9,7 +9,10 @@ description = "AUGUSTUS is a program that predicts genes in eukaryotic genomic s toolchain = {'name': 'intel', 'version': '2017a'} -source_urls = ['http://bioinf.uni-greifswald.de/augustus/binaries/'] +source_urls = [ + 'http://bioinf.uni-greifswald.de/augustus/binaries/', + 'http://bioinf.uni-greifswald.de/augustus/binaries/old/', +] sources = [SOURCELOWER_TAR_GZ] patches = ['AUGUSTUS-%(version)s_fix-hardcoding.patch'] -- GitLab From e161671b19ea8fa7fe1e581eac29fb48ef4da16f Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Fri, 15 Sep 2017 09:28:47 +0200 Subject: [PATCH 1525/1603] {bio}[intel/2017a] BUSCO 1.22 (REVIEW) --- .../BUSCO-1.22-intel-2017a-Python-2.7.13.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/b/BUSCO/BUSCO-1.22-intel-2017a-Python-2.7.13.eb diff --git a/easybuild/easyconfigs/b/BUSCO/BUSCO-1.22-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/b/BUSCO/BUSCO-1.22-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..dc39f4fd13 --- /dev/null +++ b/easybuild/easyconfigs/b/BUSCO/BUSCO-1.22-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,35 @@ +easyblock = 'Tarball' + +name = 'BUSCO' +version = '1.22' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://busco.ezlab.org/' +description = "BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs" + +toolchain = {'name': 'intel', 'version': '2017a'} + + +source_urls = ['http://busco.ezlab.org/v1/files/'] +sources = ['%(name)s_v%(version)s.tar.gz'] + +checksums = ['86088bbd2128ea04ad9e1b2ebd18201f4c79a48a161ba2593feb12abb8a2d0e2'] + +dependencies = [ + ('Python', '2.7.13'), + ('BLAST+', '2.6.0', versionsuffix), + ('HMMER', '3.1b2'), + ('AUGUSTUS', '3.2.3', versionsuffix), + ('EMBOSS', '6.6.0', '-X11-20170314'), +] + +postinstallcmds = ['chmod +x %(installdir)s/*.py'] + +sanity_check_paths = { + 'files': ['BUSCO_v1.22.py'], + 'dirs': ['sample_data'], +} + +modextrapaths = {'PATH': '.'} + +moduleclass = 'bio' -- GitLab From 17c6b3d457f11c509391b52106959d71550e6d28 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Fri, 15 Sep 2017 09:32:41 +0200 Subject: [PATCH 1526/1603] {bio}[intel/2017a] EMBOSS 6.6.0 w/ X11-20170314 (REVIEW) --- .../EMBOSS-6.6.0-intel-2017a-X11-20170314.eb | 52 +++++++++++++++++++ 1 file changed, 52 insertions(+) create mode 100644 easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-intel-2017a-X11-20170314.eb diff --git a/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-intel-2017a-X11-20170314.eb b/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-intel-2017a-X11-20170314.eb new file mode 100644 index 0000000000..ce07a55a67 --- /dev/null +++ b/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-intel-2017a-X11-20170314.eb @@ -0,0 +1,52 @@ +# authors: Kenneth Hoste (Ghent University), George Tsouloupas , Fotis Georgatos +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +# foss-2016b modified by: +# Adam Huffman +# The Francis Crick Institute + +easyblock = 'ConfigureMake' + +name = 'EMBOSS' +version = '6.6.0' +x11ver = '20170314' +versionsuffix = '-X11-%s' % x11ver + +homepage = 'http://emboss.sourceforge.net/' +description = """EMBOSS is 'The European Molecular Biology Open Software Suite'. + EMBOSS is a free Open Source software analysis package specially developed for + the needs of the molecular biology (e.g. EMBnet) user community.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [ + 'ftp://emboss.open-bio.org/pub/EMBOSS/', + 'ftp://emboss.open-bio.org/pub/EMBOSS/old/%(version_major_minor)s.0', +] + +sources = [SOURCE_TAR_GZ] + +patches = ['EMBOSS_disable-embossupdate.patch'] + +dependencies = [ + ('X11', x11ver), + ('libgd', '2.2.4'), + ('libharu', '2.3.0'), + ('Java', '1.8.0_121', '', True), +] + +configopts = " --with-hpdf=$EBROOTLIBHARU " + +# jemboss.jar does not build in a parallel build +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['seqret', 'aligncopy', 'profit', 'prophet']] + + ['lib/lib%s.a' % x for x in ['acd', 'ajax', 'ajaxdb', 'ajaxg', 'eexpat', 'ensembl', + 'epcre', 'eplplot', 'ezlib', 'nucleus']] + + ['share/EMBOSS/jemboss/lib/jemboss.jar'], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From 7eafd9a85ccadff6b812e91deba1a2adc0d62088 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Fri, 15 Sep 2017 09:35:29 +0200 Subject: [PATCH 1527/1603] {bio}[intel/2017a] Infernal 1.1.2 (REVIEW) --- .../i/Infernal/Infernal-1.1.2-intel-2017a.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/i/Infernal/Infernal-1.1.2-intel-2017a.eb diff --git a/easybuild/easyconfigs/i/Infernal/Infernal-1.1.2-intel-2017a.eb b/easybuild/easyconfigs/i/Infernal/Infernal-1.1.2-intel-2017a.eb new file mode 100644 index 0000000000..735863a602 --- /dev/null +++ b/easybuild/easyconfigs/i/Infernal/Infernal-1.1.2-intel-2017a.eb @@ -0,0 +1,36 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Cedric Laczny , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + +easyblock = 'ConfigureMake' + +name = 'Infernal' +version = "1.1.2" + +homepage = 'http://eddylab.org/infernal/' +description = """Infernal ("INFERence of RNA ALignment") is for searching DNA sequence databases + for RNA structure and sequence similarities.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://eddylab.org/%(namelower)s'] + +checksums = ['ac8c24f484205cfb7124c38d6dc638a28f2b9035b9433efec5dc753c7e84226b'] + +sanity_check_paths = { + 'files': ['bin/cm%s' % x for x in ['align', 'build', 'calibrate', 'convert', 'emit', + 'fetch', 'press', 'scan', 'search', 'stat']], + 'dirs': [] +} + +moduleclass = 'bio' -- GitLab From e141d2b282488f7c8b8c2014b63f34919a2e4d12 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Fri, 15 Sep 2017 09:38:42 +0200 Subject: [PATCH 1528/1603] {bio}[intel/2017a] khmer 2.1.1 /w Python-2.7.13 (REVIEW) --- .../khmer-2.1.1-intel-2017a-Python-2.7.13.eb | 51 +++++++++++++++++++ 1 file changed, 51 insertions(+) create mode 100644 easybuild/easyconfigs/k/khmer/khmer-2.1.1-intel-2017a-Python-2.7.13.eb diff --git a/easybuild/easyconfigs/k/khmer/khmer-2.1.1-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/k/khmer/khmer-2.1.1-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..e834dfed99 --- /dev/null +++ b/easybuild/easyconfigs/k/khmer/khmer-2.1.1-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,51 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# 1.4.1 modified by: +# Adam Huffman +# The Francis Crick Institute + +easyblock = "Bundle" + +name = 'khmer' +version = '2.1.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/ged-lab/khmer/' +description = """ In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more """ + +toolchain = {'name': 'intel', 'version': '2017a'} + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' + +dependencies = [ + ('Python', '2.7.13'), +] + +exts_list = [ + ('bz2file', '0.98', { + 'source_urls': ['https://pypi.python.org/packages/source/b/bz2file'], + 'checksums': ['64c1f811e31556ba9931953c8ec7b397488726c63e09a4c67004f43bdd28da88'], + }), + ('screed', '1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/screed'], + 'checksums': ['5db69f8c413a984ade62eb8344a6eb2be26555d74be86d38512673c1cf621b91'], + }), + ('khmer', '2.1.1', { + 'source_urls': ['https://github.com/ged-lab/khmer/archive/'], + 'source_tmpl': 'v%(version)s.tar.gz', + 'checksums': ['39981730c2e08ee183c5ce6ce80cfe2bd6d813cfa37b9ae1f7be0dd1a01dae85'], + }), +] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["count-median.py", "extract-long-sequences.py", "filter-abund.py", + "load-into-counting.py", "sample-reads-randomly.py"]], + 'dirs': ["lib/python%(pyshortver)s/site-packages/khmer-%(version)s-py%(pyshortver)s-linux-x86_64.egg"], +} + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +moduleclass = 'bio' -- GitLab From a5dd3efd9382bf07a51b940b38667e7bfef84145 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Fri, 15 Sep 2017 11:22:00 +0200 Subject: [PATCH 1529/1603] Down with PEP8\! --- .../k/khmer/khmer-2.1.1-intel-2017a-Python-2.7.13.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/k/khmer/khmer-2.1.1-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/k/khmer/khmer-2.1.1-intel-2017a-Python-2.7.13.eb index e834dfed99..92bba843cd 100644 --- a/easybuild/easyconfigs/k/khmer/khmer-2.1.1-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/k/khmer/khmer-2.1.1-intel-2017a-Python-2.7.13.eb @@ -28,16 +28,16 @@ exts_list = [ ('bz2file', '0.98', { 'source_urls': ['https://pypi.python.org/packages/source/b/bz2file'], 'checksums': ['64c1f811e31556ba9931953c8ec7b397488726c63e09a4c67004f43bdd28da88'], - }), + }), ('screed', '1.0', { 'source_urls': ['https://pypi.python.org/packages/source/s/screed'], 'checksums': ['5db69f8c413a984ade62eb8344a6eb2be26555d74be86d38512673c1cf621b91'], - }), + }), ('khmer', '2.1.1', { 'source_urls': ['https://github.com/ged-lab/khmer/archive/'], 'source_tmpl': 'v%(version)s.tar.gz', 'checksums': ['39981730c2e08ee183c5ce6ce80cfe2bd6d813cfa37b9ae1f7be0dd1a01dae85'], - }), + }), ] sanity_check_paths = { -- GitLab From 76add53eee7fc90cabc54d84214736603eb7d7e2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 15 Sep 2017 14:18:17 +0200 Subject: [PATCH 1530/1603] adding easyconfigs: Perl-5.26.0-GCCcore-6.4.0.eb --- .../p/Perl/Perl-5.26.0-GCCcore-6.4.0.eb | 1603 +++++++++++++++++ 1 file changed, 1603 insertions(+) create mode 100644 easybuild/easyconfigs/p/Perl/Perl-5.26.0-GCCcore-6.4.0.eb diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.26.0-GCCcore-6.4.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.26.0-GCCcore-6.4.0.eb new file mode 100644 index 0000000000..1024af2eb5 --- /dev/null +++ b/easybuild/easyconfigs/p/Perl/Perl-5.26.0-GCCcore-6.4.0.eb @@ -0,0 +1,1603 @@ +name = 'Perl' +version = '5.26.0' + +homepage = 'https://www.perl.org/' +description = """Larry Wall's Practical Extraction and Report Language""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.cpan.org/src/%(version_major)s.0'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['ebe7c66906d4fb55449380ab1b7e004eeef52c38d3443fa301f8e17a1a4cb67f'] + +builddependencies = [('binutils', '2.28')] + +# !! order of extensions is important !! +# extensions updated on August 29th 2017 +exts_list = [ + ('Config::General', '2.63', { + 'source_tmpl': 'Config-General-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TL/TLINDEN'], + 'checksums': [ + '0a9bf977b8aabe76343e88095d2296c8a422410fd2a05a1901f2b20e2e1f6fad', # Config-General-2.63.tar.gz + ], + }), + ('File::Listing', '6.04', { + 'source_tmpl': 'File-Listing-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + 'checksums': [ + '1e0050fcd6789a2179ec0db282bf1e90fb92be35d1171588bd9c47d52d959cf5', # File-Listing-6.04.tar.gz + ], + }), + ('ExtUtils::InstallPaths', '0.011', { + 'source_tmpl': 'ExtUtils-InstallPaths-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': [ + '7609fa048cdcf1451cad5b1d7d494f30e3d5bad0672d15404f1ea60e1df0067c', # ExtUtils-InstallPaths-0.011.tar.gz + ], + }), + ('ExtUtils::Helpers', '0.026', { + 'source_tmpl': 'ExtUtils-Helpers-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': [ + 'de901b6790a4557cf4ec908149e035783b125bf115eb9640feb1bc1c24c33416', # ExtUtils-Helpers-0.026.tar.gz + ], + }), + ('Test::Harness', '3.39', { + 'source_tmpl': 'Test-Harness-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': [ + '69bd44c81c6e1d2db18e298ecf631852608893ddfddb332a7d55285bbfc51132', # Test-Harness-3.39.tar.gz + ], + }), + ('ExtUtils::Config', '0.008', { + 'source_tmpl': 'ExtUtils-Config-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': [ + 'ae5104f634650dce8a79b7ed13fb59d67a39c213a6776cfdaa3ee749e62f1a8c', # ExtUtils-Config-0.008.tar.gz + ], + }), + ('Module::Build::Tiny', '0.039', { + 'source_tmpl': 'Module-Build-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': [ + '7d580ff6ace0cbe555bf36b86dc8ea232581530cbeaaea09bccb57b55797f11c', # Module-Build-Tiny-0.039.tar.gz + ], + }), + ('aliased', '0.34', { + 'source_tmpl': 'aliased-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': [ + 'c350524507cd827fab864e5d4c2cc350b1babaa12fa95aec0ca00843fcc7deeb', # aliased-0.34.tar.gz + ], + }), + ('Text::Glob', '0.11', { + 'source_tmpl': 'Text-Glob-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RC/RCLAMP'], + 'checksums': [ + '069ccd49d3f0a2dedb115f4bdc9fbac07a83592840953d1fcdfc39eb9d305287', # Text-Glob-0.11.tar.gz + ], + }), + ('Regexp::Common', '2017060201', { + 'source_tmpl': 'Regexp-Common-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AB/ABIGAIL'], + 'checksums': [ + 'ee07853aee06f310e040b6bf1a0199a18d81896d3219b9b35c9630d0eb69089b', # Regexp-Common-2017060201.tar.gz + ], + }), + ('GO::Utils', '0.15', { + 'source_tmpl': 'go-perl-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CM/CMUNGALL'], + 'checksums': [ + '423d26155ee85ca51ab2270cee59f4e85b193e57ac3a29aff827298c0a396b12', # go-perl-0.15.tar.gz + ], + }), + ('Module::Pluggable', '5.2', { + 'source_tmpl': 'Module-Pluggable-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SI/SIMONW'], + 'checksums': [ + 'b3f2ad45e4fd10b3fb90d912d78d8b795ab295480db56dc64e86b9fa75c5a6df', # Module-Pluggable-5.2.tar.gz + ], + }), + ('Test::Fatal', '0.014', { + 'source_tmpl': 'Test-Fatal-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': [ + 'bcdcef5c7b2790a187ebca810b0a08221a63256062cfab3c3b98685d91d1cbb0', # Test-Fatal-0.014.tar.gz + ], + }), + ('Test::Warnings', '0.026', { + 'source_tmpl': 'Test-Warnings-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': [ + 'ae2b68b1b5616704598ce07f5118efe42dc4605834453b7b2be14e26f9cc9a08', # Test-Warnings-0.026.tar.gz + ], + }), + ('File::ShareDir::Install', '0.11', { + 'source_tmpl': 'File-ShareDir-Install-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': [ + '32bf8772e9fea60866074b27ff31ab5bc3f88972d61915e84cbbb98455e00cc8', # File-ShareDir-Install-0.11.tar.gz + ], + }), + ('DateTime::Locale', '1.16', { + 'source_tmpl': 'DateTime-Locale-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + 'checksums': [ + 'dfaf4c42149c0622e80721773b8d7229d7785280503585895c9fe9f51e076cfe', # DateTime-Locale-1.16.tar.gz + ], + }), + ('DateTime::TimeZone', '2.13', { + 'source_tmpl': 'DateTime-TimeZone-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + 'checksums': [ + '333d39ccd6b883460409b9113bec43be256c3e763beedfb97b9eb274c9d4e18c', # DateTime-TimeZone-2.13.tar.gz + ], + }), + ('Test::Requires', '0.10', { + 'source_tmpl': 'Test-Requires-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TOKUHIROM'], + 'checksums': [ + '2768a391d50ab94b95cefe540b9232d7046c13ee86d01859e04c044903222eb5', # Test-Requires-0.10.tar.gz + ], + }), + ('Module::Implementation', '0.09', { + 'source_tmpl': 'Module-Implementation-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + 'checksums': [ + 'c15f1a12f0c2130c9efff3c2e1afe5887b08ccd033bd132186d1e7d5087fd66d', # Module-Implementation-0.09.tar.gz + ], + }), + ('Module::Build', '0.4224', { + 'source_tmpl': 'Module-Build-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': [ + 'a6ca15d78244a7b50fdbf27f85c85f4035aa799ce7dd018a0d98b358ef7bc782', # Module-Build-0.4224.tar.gz + ], + }), + ('Module::Runtime', '0.015', { + 'source_tmpl': 'Module-Runtime-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/Z/ZE/ZEFRAM'], + 'checksums': [ + '67fcfaf4e33072924975675da9004bacc43fff9f61396135b93627cbe38e43c0', # Module-Runtime-0.015.tar.gz + ], + }), + ('Try::Tiny', '0.28', { + 'source_tmpl': 'Try-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': [ + 'f1d166be8aa19942c4504c9111dade7aacb981bc5b3a2a5c5f6019646db8c146', # Try-Tiny-0.28.tar.gz + ], + }), + ('Params::Validate', '1.29', { + 'source_tmpl': 'Params-Validate-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + 'checksums': [ + '49a68dfb430bea028042479111d19068e08095e5a467e320b7ab7bde3d729733', # Params-Validate-1.29.tar.gz + ], + }), + ('List::MoreUtils', '0.423', { + 'source_tmpl': 'List-MoreUtils-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + 'checksums': [ + 'b4d90b24809b399fda3772a45b1af9e29d89becf8ba4a4f78fa36234e4ed5396', # List-MoreUtils-0.423.tar.gz + ], + }), + ('Exporter::Tiny', '1.000000', { + 'source_tmpl': 'Exporter-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TOBYINK'], + 'checksums': [ + 'ffdd77d57de099e8f64dd942ef12a00a3f4313c2531f342339eeed2d366ad078', # Exporter-Tiny-1.000000.tar.gz + ], + }), + ('Class::Singleton', '1.5', { + 'source_tmpl': 'Class-Singleton-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHAY'], + 'checksums': [ + '38220d04f02e3a803193c2575a1644cce0b95ad4b95c19eb932b94e2647ef678', # Class-Singleton-1.5.tar.gz + ], + }), + ('DateTime', '1.44', { + 'source_tmpl': 'DateTime-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + 'checksums': [ + 'a7165a9b1bcef735e76ea44c184ea741840249dd1862b8465f3777cd8f0bd701', # DateTime-1.44.tar.gz + ], + }), + ('File::Find::Rule::Perl', '1.15', { + 'source_tmpl': 'File-Find-Rule-Perl-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': [ + '9a48433f86e08ce18e03526e2982de52162eb909d19735460f07eefcaf463ea6', # File-Find-Rule-Perl-1.15.tar.gz + ], + }), + ('Readonly', '2.05', { + 'source_tmpl': 'Readonly-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SA/SANKO'], + 'checksums': [ + '4b23542491af010d44a5c7c861244738acc74ababae6b8838d354dfb19462b5e', # Readonly-2.05.tar.gz + ], + }), + ('Git', '0.41', { + 'source_tmpl': 'Git-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MS/MSOUTH'], + 'checksums': [ + '9d4de21612253a1d3252ff7657d7e832dcf3cc2a748a8c84f73de618a3a38239', # Git-0.41.tar.gz + ], + }), + ('Tree::DAG_Node', '1.29', { + 'source_tmpl': 'Tree-DAG_Node-%(version)s.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + 'checksums': [ + '2d04eb011aa06cee633c367d1f322b8d937020fde5d5393fad6a26c93725c4a8', # Tree-DAG_Node-1.29.tgz + ], + }), + ('Template', '2.27', { + 'source_tmpl': 'Template-Toolkit-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AB/ABW'], + 'checksums': [ + '1311a403264d0134c585af0309ff2a9d5074b8ece23ece5660d31ec96bf2c6dc', # Template-Toolkit-2.27.tar.gz + ], + }), + ('FreezeThaw', '0.5001', { + 'source_tmpl': 'FreezeThaw-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IL/ILYAZ/modules'], + 'checksums': [ + '3c5e08329106f9cee3ab444b81331c5935f83084a151d88505e7a465da540f41', # FreezeThaw-0.5001.tar.gz + ], + }), + ('DBI', '1.637', { + 'source_tmpl': 'DBI-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TI/TIMB'], + 'checksums': [ + '2557712593e80142c3b50877e00369b6ce78fa26d44edc42156d81a5cdd26bc6', # DBI-1.637.tar.gz + ], + }), + ('DBD::SQLite', '1.54', { + 'source_tmpl': 'DBD-SQLite-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IS/ISHIGAKI'], + 'checksums': [ + '3929a6dbd8d71630f0cb57f85dcef9588cd7ac4c9fa12db79df77b9d3a4d7269', # DBD-SQLite-1.54.tar.gz + ], + }), + ('Math::Bezier', '0.01', { + 'source_tmpl': 'Math-Bezier-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AB/ABW'], + 'checksums': [ + '11a815fc45fdf0efabb1822ab77faad8b9eea162572c5f0940c8ed7d56e6b8b8', # Math-Bezier-0.01.tar.gz + ], + }), + ('Archive::Extract', '0.80', { + 'source_tmpl': 'Archive-Extract-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + 'checksums': [ + '25cbc2d5626c14d39a0b5e4fe8383941e085c9a7e0aa873d86e81b6e709025f4', # Archive-Extract-0.80.tar.gz + ], + }), + ('DBIx::Simple', '1.35', { + 'source_tmpl': 'DBIx-Simple-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JU/JUERD'], + 'checksums': [ + '445535b3dfab88140c7a0d2776b1e78f254dc7e9c81072d5a01afc95a5db499a', # DBIx-Simple-1.35.tar.gz + ], + }), + ('Shell', '0.73', { + 'source_tmpl': 'Shell-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/F/FE/FERREIRA'], + 'checksums': [ + 'f7dbebf65261ed0e5abd0f57052b64d665a1a830bab4c8bbc220f235bd39caf5', # Shell-0.73.tar.gz + ], + }), + ('File::Spec', '3.62', { + 'source_tmpl': 'PathTools-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': [ + '36350e12f58871437ba03391f80a506e447e3c6630cc37d0625bc25ff1c7b4d2', # PathTools-3.62.tar.gz + ], + }), + ('Test::Simple', '1.302086', { + 'source_tmpl': 'Test-Simple-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + 'checksums': [ + '21e4c93c52529a10ef970afcf2cdb5719bcfef5f71af09cad3675fcf021995b1', # Test-Simple-1.302086.tar.gz + ], + }), + ('Set::Scalar', '1.29', { + 'source_tmpl': 'Set-Scalar-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAVIDO'], + 'checksums': [ + 'a3dc1526f3dde72d3c64ea00007b86ce608cdcd93567cf6e6e42dc10fdc4511d', # Set-Scalar-1.29.tar.gz + ], + }), + ('IO::Stringy', '2.111', { + 'source_tmpl': 'IO-stringy-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DS/DSKOLL'], + 'checksums': [ + '8c67fd6608c3c4e74f7324f1404a856c331dbf48d9deda6aaa8296ea41bf199d', # IO-stringy-2.111.tar.gz + ], + }), + ('Encode::Locale', '1.05', { + 'source_tmpl': 'Encode-Locale-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + 'checksums': [ + '176fa02771f542a4efb1dbc2a4c928e8f4391bf4078473bd6040d8f11adb0ec1', # Encode-Locale-1.05.tar.gz + ], + }), + ('XML::SAX::Base', '1.09', { + 'source_tmpl': 'XML-SAX-Base-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GR/GRANTM'], + 'checksums': [ + '66cb355ba4ef47c10ca738bd35999723644386ac853abbeb5132841f5e8a2ad0', # XML-SAX-Base-1.09.tar.gz + ], + }), + ('XML::NamespaceSupport', '1.12', { + 'source_tmpl': 'XML-NamespaceSupport-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PERIGRIN'], + 'checksums': [ + '47e995859f8dd0413aa3f22d350c4a62da652e854267aa0586ae544ae2bae5ef', # XML-NamespaceSupport-1.12.tar.gz + ], + }), + ('XML::SAX', '0.99', { + 'source_tmpl': 'XML-SAX-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GR/GRANTM'], + 'checksums': [ + '32b04b8e36b6cc4cfc486de2d859d87af5386dd930f2383c49347050d6f5ad84', # XML-SAX-0.99.tar.gz + ], + }), + ('Test::LeakTrace', '0.16', { + 'source_tmpl': 'Test-LeakTrace-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEEJO'], + 'checksums': [ + '5f089eed915f1ec8c743f6d2777c3ecd0ca01df2f7b9e10038d316952583e403', # Test-LeakTrace-0.16.tar.gz + ], + }), + ('Test::Exception', '0.43', { + 'source_tmpl': 'Test-Exception-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + 'checksums': [ + '156b13f07764f766d8b45a43728f2439af81a3512625438deab783b7883eb533', # Test-Exception-0.43.tar.gz + ], + }), + ('Text::Table', '1.133', { + 'source_tmpl': 'Text-Table-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'], + 'checksums': [ + 'cd9ee04860d09a19a9d6bd2254a4bf3144ac14a63c08f15a1e28601b4b2f7012', # Text-Table-1.133.tar.gz + ], + }), + ('MIME::Types', '2.13', { + 'source_tmpl': 'MIME-Types-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARKOV'], + 'checksums': [ + '99c3376357bbe22cc8b6c78f560aa18d81621287695cd629008a6c4e66b77bf8', # MIME-Types-2.13.tar.gz + ], + }), + ('Module::Build::XSUtil', '0.16', { + 'source_tmpl': 'Module-Build-XSUtil-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HI/HIDEAKIO'], + 'checksums': [ + '15762fa4e43b41302cff261c7ad75aacdc874f416981f206d783f20acd023adb', # Module-Build-XSUtil-0.16.tar.gz + ], + }), + ('Tie::Function', '0.02', { + 'source_tmpl': 'Tie-Function-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAVIDNICO/handy_tied_functions'], + 'checksums': [ + '0b1617af218dfab911ba0fbd72210529a246efe140332da77fe3e03d11000117', # Tie-Function-0.02.tar.gz + ], + }), + ('Template::Plugin::Number::Format', '1.06', { + 'source_tmpl': 'Template-Plugin-Number-Format-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DARREN'], + 'checksums': [ + # Template-Plugin-Number-Format-1.06.tar.gz + '0865836a1bcbc34d4a0ee34b5ccc14d7b511f1fd300bf390f002dac349539843', + ], + }), + ('HTML::Parser', '3.72', { + 'source_tmpl': 'HTML-Parser-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + 'checksums': [ + 'ec28c7e1d9e67c45eca197077f7cdc41ead1bb4c538c7f02a3296a4bb92f608b', # HTML-Parser-3.72.tar.gz + ], + }), + ('Date::Handler', '1.2', { + 'source_tmpl': 'Date-Handler-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BB/BBEAUSEJ'], + 'checksums': [ + 'c36fd2b68d48c2e17417bf2873c78820f3ae02460fdf5976b8eeab887d59e16c', # Date-Handler-1.2.tar.gz + ], + }), + ('Params::Util', '1.07', { + 'source_tmpl': 'Params-Util-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + 'checksums': [ + '30f1ec3f2cf9ff66ae96f973333f23c5f558915bb6266881eac7423f52d7c76c', # Params-Util-1.07.tar.gz + ], + }), + ('IO::HTML', '1.001', { + 'source_tmpl': 'IO-HTML-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CJ/CJM'], + 'checksums': [ + 'ea78d2d743794adc028bc9589538eb867174b4e165d7d8b5f63486e6b828e7e0', # IO-HTML-1.001.tar.gz + ], + }), + ('Data::Grove', '0.08', { + 'source_tmpl': 'libxml-perl-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KM/KMACLEOD'], + 'checksums': [ + '4571059b7b5d48b7ce52b01389e95d798bf5cf2020523c153ff27b498153c9cb', # libxml-perl-0.08.tar.gz + ], + }), + ('Class::ISA', '0.36', { + 'source_tmpl': 'Class-ISA-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SM/SMUELLER'], + 'checksums': [ + '8816f34e9a38e849a10df756030dccf9fe061a196c11ac3faafd7113c929b964', # Class-ISA-0.36.tar.gz + ], + }), + ('URI', '1.72', { + 'source_tmpl': 'URI-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': [ + '35f14431d4b300de4be1163b0b5332de2d7fbda4f05ff1ed198a8e9330d40a32', # URI-1.72.tar.gz + ], + }), + ('Ima::DBI', '0.35', { + 'source_tmpl': 'Ima-DBI-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PERRIN'], + 'checksums': [ + '8b481ceedbf0ae4a83effb80581550008bfdd3885ef01145e3733c7097c00a08', # Ima-DBI-0.35.tar.gz + ], + }), + ('Tie::IxHash', '1.23', { + 'source_tmpl': 'Tie-IxHash-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CH/CHORNY'], + 'checksums': [ + 'fabb0b8c97e67c9b34b6cc18ed66f6c5e01c55b257dcf007555e0b027d4caf56', # Tie-IxHash-1.23.tar.gz + ], + }), + ('GO', '0.04', { + 'source_tmpl': 'go-db-perl-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SJ/SJCARBON'], + 'checksums': [ + '8eb73d591ad767e7cf26def40cffd84833875f1ad51e456960b9ed73dc23641b', # go-db-perl-0.04.tar.gz + ], + }), + ('Class::DBI::SQLite', '0.11', { + 'source_tmpl': 'Class-DBI-SQLite-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA'], + 'checksums': [ + 'c4661b00afb7e53c97ac36e13f34dde43c1a93540a2f4ff97e6182b0c731e4e7', # Class-DBI-SQLite-0.11.tar.gz + ], + }), + ('Pod::POM', '2.01', { + 'source_tmpl': 'Pod-POM-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB'], + 'checksums': [ + '1b50fba9bbdde3ead192beeba0eaddd0c614e3afb1743fa6fff805f57c56f7f4', # Pod-POM-2.01.tar.gz + ], + }), + ('Math::Round', '0.07', { + 'source_tmpl': 'Math-Round-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GR/GROMMEL'], + 'checksums': [ + '73a7329a86e54a5c29a440382e5803095b58f33129e61a1df0093b4824de9327', # Math-Round-0.07.tar.gz + ], + }), + ('Text::Diff', '1.45', { + 'source_tmpl': 'Text-Diff-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB'], + 'checksums': [ + 'e8baa07b1b3f53e00af3636898bbf73aec9a0ff38f94536ede1dbe96ef086f04', # Text-Diff-1.45.tar.gz + ], + }), + ('Log::Message::Simple', '0.10', { + 'source_tmpl': 'Log-Message-Simple-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + 'checksums': [ + 'aa12d1a4c0ac260b94d448fa01feba242a8a85cb6cbfdc66432e3b5b468add96', # Log-Message-Simple-0.10.tar.gz + ], + }), + ('IO::Socket::SSL', '2.050', { + 'source_tmpl': 'IO-Socket-SSL-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SU/SULLR'], + 'checksums': [ + '54e6716e40df8b1c168d8f54a0b8f215313739bd99dda17adb7c00fe94656692', # IO-Socket-SSL-2.050.tar.gz + ], + }), + ('Fennec::Lite', '0.004', { + 'source_tmpl': 'Fennec-Lite-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + 'checksums': [ + 'dce28e3932762c2ff92aa52d90405c06e898e81cb7b164ccae8966ae77f1dcab', # Fennec-Lite-0.004.tar.gz + ], + }), + ('Sub::Uplevel', '0.2800', { + 'source_tmpl': 'Sub-Uplevel-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + 'checksums': [ + 'b4f3f63b80f680a421332d8851ddbe5a8e72fcaa74d5d1d98f3c8cc4a3ece293', # Sub-Uplevel-0.2800.tar.gz + ], + }), + ('Meta::Builder', '0.003', { + 'source_tmpl': 'Meta-Builder-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + 'checksums': [ + 'e7ac289b88d1662e87708d716877ac66a1a8414660996fe58c1db96d834a5375', # Meta-Builder-0.003.tar.gz + ], + }), + ('Exporter::Declare', '0.114', { + 'source_tmpl': 'Exporter-Declare-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + 'checksums': [ + '4bd70d6ca76f6f6ba7e4c618d4ac93b8593a58f1233ccbe18b10f5f204f1d4e4', # Exporter-Declare-0.114.tar.gz + ], + }), + ('Getopt::Long', '2.50', { + 'source_tmpl': 'Getopt-Long-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JV/JV'], + 'checksums': [ + '20881adb2b73e83825f9a0a3b141db11b3a555e1d3775b13d81d0481623e4b67', # Getopt-Long-2.50.tar.gz + ], + }), + ('Log::Message', '0.08', { + 'source_tmpl': 'Log-Message-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + 'checksums': [ + 'bd697dd62aaf26d118e9f0a0813429deb1c544e4501559879b61fcbdfe99fe46', # Log-Message-0.08.tar.gz + ], + }), + ('Mouse', 'v2.4.10', { + 'source_tmpl': 'Mouse-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GF/GFUJI'], + 'checksums': [ + 'b995dda1918fcebecff34458b6abd16c06b6a7844572c7293d72a24d18126d14', # Mouse-v2.4.10.tar.gz + ], + }), + ('Test::Version', '2.05', { + 'source_tmpl': 'Test-Version-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE'], + 'checksums': [ + '39c0ec02663da0e56962bdafaef6790cf83d12b4d90e8a4cdc971d57d869d63f', # Test-Version-2.05.tar.gz + ], + }), + ('DBIx::Admin::TableInfo', '3.03', { + 'source_tmpl': 'DBIx-Admin-TableInfo-%(version)s.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + 'checksums': [ + 'a852530f95957a43aa794f2edf5f3fe4ecec35bd20150c38136d4c23d85328b6', # DBIx-Admin-TableInfo-3.03.tgz + ], + }), + ('Net::HTTP', '6.16', { + 'source_tmpl': 'Net-HTTP-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'], + 'checksums': [ + '70c45b6aaf3e9fb1ce30a1fc3cf828cfaee45c5c0bd147b2f617efade1765e78', # Net-HTTP-6.16.tar.gz + ], + }), + ('Test::Deep', '1.127', { + 'source_tmpl': 'Test-Deep-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': [ + 'b78cfc59c41ba91f47281e2c1d2bfc4b3b1b42bfb76b4378bc88cc37b7af7268', # Test-Deep-1.127.tar.gz + ], + }), + ('Test::Warn', '0.32', { + 'source_tmpl': 'Test-Warn-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BIGJ'], + 'checksums': [ + '2fc516e71f9ef453be22a4619d91eb3f78df414a57dfa0fd745d3bff50bf73d2', # Test-Warn-0.32.tar.gz + ], + }), + ('MRO::Compat', '0.13', { + 'source_tmpl': 'MRO-Compat-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + 'checksums': [ + '8a2c3b6ccc19328d5579d02a7d91285e2afd85d801f49d423a8eb16f323da4f8', # MRO-Compat-0.13.tar.gz + ], + }), + ('Moo', '2.003002', { + 'source_tmpl': 'Moo-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + 'checksums': [ + 'f3e9741e79baa63e89f5a08706cd80d18c0a5a37e3d898847e002310e06582f1', # Moo-2.003002.tar.gz + ], + }), + ('Hash::Merge', '0.200', { + 'source_tmpl': 'Hash-Merge-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + 'checksums': [ + '47f9f03330b7595c94e73bdd17dc6682ba59d1cc89e63f4e319617f4bb122a64', # Hash-Merge-0.200.tar.gz + ], + }), + ('SQL::Abstract', '1.84', { + 'source_tmpl': 'SQL-Abstract-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IL/ILMARI'], + 'checksums': [ + '655f4aa3d4ea7ca0a7bafb2beff84010d5c77f0ee4413baa0c86456bf6db5e75', # SQL-Abstract-1.84.tar.gz + ], + }), + ('HTML::Form', '6.03', { + 'source_tmpl': 'HTML-Form-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + 'checksums': [ + '68c01d94f005d5ca9c4d55ad2a1bf3a8d034a5fc6db187d91a4c42f3fdc9fc36', # HTML-Form-6.03.tar.gz + ], + }), + ('File::Copy::Recursive', '0.38', { + 'source_tmpl': 'File-Copy-Recursive-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DM/DMUEY'], + 'checksums': [ + '84ccbddf3894a88a2c2b6be68ff6ef8960037803bb36aa228b31944cfdf6deeb', # File-Copy-Recursive-0.38.tar.gz + ], + }), + ('Number::Compare', '0.03', { + 'source_tmpl': 'Number-Compare-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RC/RCLAMP'], + 'checksums': [ + '83293737e803b43112830443fb5208ec5208a2e6ea512ed54ef8e4dd2b880827', # Number-Compare-0.03.tar.gz + ], + }), + ('IPC::Run', '0.96', { + 'source_tmpl': 'IPC-Run-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR'], + 'checksums': [ + 'bbd24ff027e1c232b3dc027562c9f4386da72b76991d30f9f3d4119e87cf4640', # IPC-Run-0.96.tar.gz + ], + }), + ('HTML::Entities::Interpolate', '1.10', { + 'source_tmpl': 'HTML-Entities-Interpolate-%(version)s.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + 'checksums': [ + 'f15a9df92c282419f7010964aca1ada844ddfae7afc735cd2ba1bb20883e955c', # HTML-Entities-Interpolate-1.10.tgz + ], + }), + ('File::Remove', '1.57', { + 'source_tmpl': 'File-Remove-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'], + 'checksums': [ + 'b3becd60165c38786d18285f770b8b06ebffe91797d8c00cc4730614382501ad', # File-Remove-1.57.tar.gz + ], + }), + ('YAML::Tiny', '1.70', { + 'source_tmpl': 'YAML-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': [ + 'bbce4b52b5eafdb04e3043975a08dbf394d00b7d2c958adb9d03d9f7e9291255', # YAML-Tiny-1.70.tar.gz + ], + }), + ('Module::Install', '1.18', { + 'source_tmpl': 'Module-Install-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': [ + '29068ac33502cec959844c206516c09cc4a847cb57327d41015f605153ca645e', # Module-Install-1.18.tar.gz + ], + }), + ('Test::ClassAPI', '1.06', { + 'source_tmpl': 'Test-ClassAPI-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + 'checksums': [ + '06f82d076501701d78b8dc40b7688507bcc6c58b1beafd559e05bb0644df00a2', # Test-ClassAPI-1.06.tar.gz + ], + }), + ('Test::Most', '0.35', { + 'source_tmpl': 'Test-Most-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OV/OVID'], + 'checksums': [ + '9897a6f4d751598d2ed1047e01c1554b01d0f8c96c45e7e845229782bf6f657f', # Test-Most-0.35.tar.gz + ], + }), + ('Class::Accessor', '0.34', { + 'source_tmpl': 'Class-Accessor-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KA/KASEI'], + 'checksums': [ + 'cdb1e0cdf8380fb9b63b44c33ce5afc1068736d55ac5904bf0eaa1efc1c3cefc', # Class-Accessor-0.34.tar.gz + ], + }), + ('Test::Differences', '0.64', { + 'source_tmpl': 'Test-Differences-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DC/DCANTRELL'], + 'checksums': [ + '9f459dd9c2302a0a73e2f5528a0ce7d09d6766f073187ae2c69e603adf2eb276', # Test-Differences-0.64.tar.gz + ], + }), + ('HTTP::Tiny', '0.070', { + 'source_tmpl': 'HTTP-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + 'checksums': [ + '74f385d1e96de887a4df5a222d93afdc7d81ea9ad721a56ff3d8449bb12f7733', # HTTP-Tiny-0.070.tar.gz + ], + }), + ('Package::DeprecationManager', '0.17', { + 'source_tmpl': 'Package-DeprecationManager-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + 'checksums': [ + # Package-DeprecationManager-0.17.tar.gz + '1d743ada482b5c9871d894966e87d4c20edc96931bb949fb2638b000ddd6684b', + ], + }), + ('Digest::SHA1', '2.13', { + 'source_tmpl': 'Digest-SHA1-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + 'checksums': [ + '68c1dac2187421f0eb7abf71452a06f190181b8fc4b28ededf5b90296fb943cc', # Digest-SHA1-2.13.tar.gz + ], + }), + ('Date::Language', '2.30', { + 'source_tmpl': 'TimeDate-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GB/GBARR'], + 'checksums': [ + '75bd254871cb5853a6aa0403ac0be270cdd75c9d1b6639f18ecba63c15298e86', # TimeDate-2.30.tar.gz + ], + }), + ('version', '0.9918', { + 'source_tmpl': 'version-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JP/JPEACOCK'], + 'checksums': [ + '54175c7ead4e2259c2fb2b83440b821e4287842067227e48fb899b5cae52237b', # version-0.9918.tar.gz + ], + }), + ('Sub::Uplevel', '0.2800', { + 'source_tmpl': 'Sub-Uplevel-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + 'checksums': [ + 'b4f3f63b80f680a421332d8851ddbe5a8e72fcaa74d5d1d98f3c8cc4a3ece293', # Sub-Uplevel-0.2800.tar.gz + ], + }), + ('XML::Bare', '0.53', { + 'source_tmpl': 'XML-Bare-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CO/CODECHILD'], + 'patches': ['XML-Bare-0.53_icc.patch'], + 'checksums': [ + '865e198e98d904be1683ef5a53a4948f02dabdacde59fc554a082ffbcc5baefd', # XML-Bare-0.53.tar.gz + '7d005e44222a0ce130b8ba4912a869675c0aa9ce4d1b95caba06b683b69f2b20', # XML-Bare-0.53_icc.patch + ], + }), + ('Dist::CheckConflicts', '0.11', { + 'source_tmpl': 'Dist-CheckConflicts-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DO/DOY'], + 'checksums': [ + 'ea844b9686c94d666d9d444321d764490b2cde2f985c4165b4c2c77665caedc4', # Dist-CheckConflicts-0.11.tar.gz + ], + }), + ('Sub::Name', '0.21', { + 'source_tmpl': 'Sub-Name-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': [ + 'bd32e9dee07047c10ae474c9f17d458b6e9885a6db69474c7a494ccc34c27117', # Sub-Name-0.21.tar.gz + ], + }), + ('Time::Piece', '1.3201', { + 'source_tmpl': 'Time-Piece-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ES/ESAYM'], + 'checksums': [ + '81dbe694474a13d9683c392edd54bd77b6bd6d20b41433358487b51eb71e31bd', # Time-Piece-1.3201.tar.gz + ], + }), + ('Digest::HMAC', '1.03', { + 'source_tmpl': 'Digest-HMAC-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + 'checksums': [ + '3bc72c6d3ff144d73aefb90e9a78d33612d58cf1cd1631ecfb8985ba96da4a59', # Digest-HMAC-1.03.tar.gz + ], + }), + ('HTTP::Negotiate', '6.01', { + 'source_tmpl': 'HTTP-Negotiate-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + 'checksums': [ + '1c729c1ea63100e878405cda7d66f9adfd3ed4f1d6cacaca0ee9152df728e016', # HTTP-Negotiate-6.01.tar.gz + ], + }), + ('MIME::Lite', '3.030', { + 'source_tmpl': 'MIME-Lite-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': [ + '8f39901bc580bc3dce69e10415305e4435ff90264c63d29f707b4566460be962', # MIME-Lite-3.030.tar.gz + ], + }), + ('Crypt::Rijndael', '1.13', { + 'source_tmpl': 'Crypt-Rijndael-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': [ + 'cd7209a6dfe0a3dc8caffe1aa2233b0e6effec7572d76a7a93feefffe636214e', # Crypt-Rijndael-1.13.tar.gz + ], + }), + ('B::Lint', '1.20', { + 'source_tmpl': 'B-Lint-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': [ + 'dc49408964fd8b7963859c92e013f0b9f92f74be5a7c2a78e3996279827c10b3', # B-Lint-1.20.tar.gz + ], + }), + ('Canary::Stability', '2012', { + 'source_tmpl': 'Canary-Stability-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/ML/MLEHMANN'], + 'checksums': [ + 'fd240b111d834dbae9630c59b42fae2145ca35addc1965ea311edf0d07817107', # Canary-Stability-2012.tar.gz + ], + }), + ('AnyEvent', '7.14', { + 'source_tmpl': 'AnyEvent-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/ML/MLEHMANN'], + 'checksums': [ + '539358d225bad34b4a64f5217f8c2a707b15e3a28c74120c9dd2270c7cca7d2a', # AnyEvent-7.14.tar.gz + ], + }), + ('Object::Accessor', '0.48', { + 'source_tmpl': 'Object-Accessor-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + 'checksums': [ + '76cb824a27b6b4e560409fcf6fd5b3bfbbd38b72f1f3d37ed0b54bd9c0baeade', # Object-Accessor-0.48.tar.gz + ], + }), + ('Data::UUID', '1.221', { + 'source_tmpl': 'Data-UUID-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': [ + '3cc7b2a3a7b74b45a059e013f7fd878078500ea4b7269036f84556b022078667', # Data-UUID-1.221.tar.gz + ], + }), + ('Test::Pod', '1.51', { + 'source_tmpl': 'Test-Pod-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': [ + 'c1a1d3cedf4a579e3aad89c36f9878a8542b6656dbe71f1581420f49582d7efb', # Test-Pod-1.51.tar.gz + ], + }), + ('AppConfig', '1.71', { + 'source_tmpl': 'AppConfig-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB'], + 'checksums': [ + '1177027025ecb09ee64d9f9f255615c04db5e14f7536c344af632032eb887b0f', # AppConfig-1.71.tar.gz + ], + }), + ('Net::SMTP::SSL', '1.04', { + 'source_tmpl': 'Net-SMTP-SSL-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': [ + '7b29c45add19d3d5084b751f7ba89a8e40479a446ce21cfd9cc741e558332a00', # Net-SMTP-SSL-1.04.tar.gz + ], + }), + ('XML::Tiny', '2.07', { + 'source_tmpl': 'XML-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DC/DCANTRELL'], + 'checksums': [ + 'ce39fcb53e0fe9f1cbcd86ddf152e1db48566266b70ec0769ef364eeabdd8941', # XML-Tiny-2.07.tar.gz + ], + }), + ('HTML::Tagset', '3.20', { + 'source_tmpl': 'HTML-Tagset-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PETDANCE'], + 'checksums': [ + 'adb17dac9e36cd011f5243881c9739417fd102fce760f8de4e9be4c7131108e2', # HTML-Tagset-3.20.tar.gz + ], + }), + ('HTML::Tree', '5.06', { + 'source_tmpl': 'HTML-Tree-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KE/KENTNL'], + 'checksums': [ + '9c36eb19cbdf9a5906c858948ca51c35bd7561f52cc18c43281acbe57327536e', # HTML-Tree-5.06.tar.gz + ], + }), + ('Devel::GlobalDestruction', '0.14', { + 'source_tmpl': 'Devel-GlobalDestruction-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + 'checksums': [ + '34b8a5f29991311468fe6913cadaba75fd5d2b0b3ee3bb41fe5b53efab9154ab', # Devel-GlobalDestruction-0.14.tar.gz + ], + }), + ('WWW::RobotRules', '6.02', { + 'source_tmpl': 'WWW-RobotRules-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + 'checksums': [ + '46b502e7a288d559429891eeb5d979461dd3ecc6a5c491ead85d165b6e03a51e', # WWW-RobotRules-6.02.tar.gz + ], + }), + ('Expect', '1.35', { + 'source_tmpl': 'Expect-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JA/JACOBY'], + 'checksums': [ + '09d92761421decd495853103379165a99efbf452c720f30277602cf23679fd06', # Expect-1.35.tar.gz + ], + }), + ('Term::UI', '0.46', { + 'source_tmpl': 'Term-UI-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + 'checksums': [ + '91946c80d7f4aab0ca4bfedc3bbe0a75b37cab1a29bd7bca3b3b7456d417e9a6', # Term-UI-0.46.tar.gz + ], + }), + ('Net::SNMP', 'v6.0.1', { + 'source_tmpl': 'Net-SNMP-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DT/DTOWN'], + 'checksums': [ + '14c37bc1cbb3f3cdc7d6c13e0f27a859f14cdcfd5ea54a0467a88bc259b0b741', # Net-SNMP-v6.0.1.tar.gz + ], + }), + ('XML::SAX::Writer', '0.57', { + 'source_tmpl': 'XML-SAX-Writer-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PERIGRIN'], + 'checksums': [ + '3d61d07ef43b0126f5b4de4f415a256fa859fa88dc4fdabaad70b7be7c682cf0', # XML-SAX-Writer-0.57.tar.gz + ], + }), + ('Statistics::Descriptive', '3.0612', { + 'source_tmpl': 'Statistics-Descriptive-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'], + 'checksums': [ + '772413148e5e00efb32f277c4254aa78b9112490a896208dcd0025813afdbf7a', # Statistics-Descriptive-3.0612.tar.gz + ], + }), + ('Class::Load', '0.24', { + 'source_tmpl': 'Class-Load-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': [ + '0bb983da46c146534fc77a556d6e40d925142f2eb43103534025ee545265ca36', # Class-Load-0.24.tar.gz + ], + }), + ('LWP::Simple', '6.26', { + 'source_tmpl': 'libwww-perl-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'], + 'checksums': [ + 'd0c5435275f8638ff36fff8f655ad2ccad1156e66cc47bfacfb9e44fc585b24f', # libwww-perl-6.26.tar.gz + ], + }), + ('Time::Piece::MySQL', '0.06', { + 'source_tmpl': 'Time-Piece-MySQL-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KA/KASEI'], + 'checksums': [ + '319601feec17fae344988a5ee91cfc6a0bcfe742af77dba254724c3268b2a60f', # Time-Piece-MySQL-0.06.tar.gz + ], + }), + ('Package::Stash::XS', '0.28', { + 'source_tmpl': 'Package-Stash-XS-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DO/DOY'], + 'checksums': [ + '23d8c5c25768ef1dc0ce53b975796762df0d6e244445d06e48d794886c32d486', # Package-Stash-XS-0.28.tar.gz + ], + }), + ('GD::Graph', '1.54', { + 'source_tmpl': 'GDGraph-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RU/RUZ'], + 'checksums': [ + 'b96f5c10b656c17d16ab65a1777c908297b028d3b6815f6d54b2337f006bfa4f', # GDGraph-1.54.tar.gz + ], + }), + ('Set::Array', '0.30', { + 'source_tmpl': 'Set-Array-%(version)s.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + 'checksums': [ + 'd9f024c8e3637feccdebcf6479b6754b6c92f1209f567feaf0c23818af31ee3c', # Set-Array-0.30.tgz + ], + }), + ('boolean', '0.46', { + 'source_tmpl': 'boolean-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IN/INGY'], + 'checksums': [ + '95c088085c3e83bf680fe6ce16d8264ec26310490f7d1680e416ea7a118f156a', # boolean-0.46.tar.gz + ], + }), + ('Number::Format', '1.75', { + 'source_tmpl': 'Number-Format-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/W/WR/WRW'], + 'checksums': [ + '82d659cb16461764fd44d11a9ce9e6a4f5e8767dc1069eb03467c6e55de257f3', # Number-Format-1.75.tar.gz + ], + }), + ('Data::Stag', '0.14', { + 'source_tmpl': 'Data-Stag-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CM/CMUNGALL'], + 'checksums': [ + '4ab122508d2fb86d171a15f4006e5cf896d5facfa65219c0b243a89906258e59', # Data-Stag-0.14.tar.gz + ], + }), + ('Test::NoWarnings', '1.04', { + 'source_tmpl': 'Test-NoWarnings-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + 'checksums': [ + '638a57658cb119af1fe5b15e73d47c2544dcfef84af0c6b1b2e97f08202b686c', # Test-NoWarnings-1.04.tar.gz + ], + }), + ('Crypt::DES', '2.07', { + 'source_tmpl': 'Crypt-DES-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DP/DPARIS'], + 'checksums': [ + '2db1ebb5837b4cb20051c0ee5b733b4453e3137df0a92306034c867621edd7e7', # Crypt-DES-2.07.tar.gz + ], + }), + ('Exporter', '5.72', { + 'source_tmpl': 'Exporter-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR'], + 'checksums': [ + 'cd13b7a0e91e8505a0ce4b25f40fab2c92bb28a99ef0d03da1001d95a32f0291', # Exporter-5.72.tar.gz + ], + }), + ('Class::Inspector', '1.32', { + 'source_tmpl': 'Class-Inspector-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE'], + 'checksums': [ + 'cefadc8b5338e43e570bc43f583e7c98d535c17b196bcf9084bb41d561cc0535', # Class-Inspector-1.32.tar.gz + ], + }), + ('Parse::RecDescent', '1.967015', { + 'source_tmpl': 'Parse-RecDescent-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JT/JTBRAUN'], + 'checksums': [ + '1943336a4cb54f1788a733f0827c0c55db4310d5eae15e542639c9dd85656e37', # Parse-RecDescent-1.967015.tar.gz + ], + }), + ('Carp', '1.38', { + 'source_tmpl': 'Carp-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': [ + 'a5a9ce3cbb959dfefa8c2dd16552567199b286d39b0e55053ca247c038977101', # Carp-1.38.tar.gz + ], + }), + ('XML::XPath', '1.42', { + 'source_tmpl': 'XML-XPath-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MANWAR'], + 'checksums': [ + '9e6ac67c2cead5f918a060b8b9ccdbdcaa6d610be8517bba42a96cd56748b512', # XML-XPath-1.42.tar.gz + ], + }), + ('Capture::Tiny', '0.46', { + 'source_tmpl': 'Capture-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + 'checksums': [ + '5d7a6a830cf7f2b2960bf8b8afaac16a537ede64f3023827acea5bd24ca77015', # Capture-Tiny-0.46.tar.gz + ], + }), + ('JSON', '2.94', { + 'source_tmpl': 'JSON-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IS/ISHIGAKI'], + 'checksums': [ + '12271b5cee49943bbdde430eef58f1fe64ba6561980b22c69585e08fc977dc6d', # JSON-2.94.tar.gz + ], + }), + ('Sub::Exporter', '0.987', { + 'source_tmpl': 'Sub-Exporter-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': [ + '543cb2e803ab913d44272c7da6a70bb62c19e467f3b12aaac4c9523259b083d6', # Sub-Exporter-0.987.tar.gz + ], + }), + ('Class::Load::XS', '0.10', { + 'source_tmpl': 'Class-Load-XS-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': [ + '5bc22cf536ebfd2564c5bdaf42f0d8a4cee3d1930fc8b44b7d4a42038622add1', # Class-Load-XS-0.10.tar.gz + ], + }), + ('Set::IntSpan::Fast', '1.15', { + 'source_tmpl': 'Set-IntSpan-Fast-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AN/ANDYA'], + 'checksums': [ + 'cfb1768c24f55208e87405b17f537f0f303fa141891d0b22d509a941aa57e24e', # Set-IntSpan-Fast-1.15.tar.gz + ], + }), + ('Sub::Exporter::Progressive', '0.001013', { + 'source_tmpl': 'Sub-Exporter-Progressive-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/F/FR/FREW'], + 'checksums': [ + # Sub-Exporter-Progressive-0.001013.tar.gz + 'd535b7954d64da1ac1305b1fadf98202769e3599376854b2ced90c382beac056', + ], + }), + ('Data::Dumper::Concise', '2.023', { + 'source_tmpl': 'Data-Dumper-Concise-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': [ + 'a6c22f113caf31137590def1b7028a7e718eface3228272d0672c25e035d5853', # Data-Dumper-Concise-2.023.tar.gz + ], + }), + ('File::Slurp::Tiny', '0.004', { + 'source_tmpl': 'File-Slurp-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': [ + '452995beeabf0e923e65fdc627a725dbb12c9e10c00d8018c16d10ba62757f1e', # File-Slurp-Tiny-0.004.tar.gz + ], + }), + ('Algorithm::Diff', '1.1903', { + 'source_tmpl': 'Algorithm-Diff-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TY/TYEMQ'], + 'checksums': [ + '30e84ac4b31d40b66293f7b1221331c5a50561a39d580d85004d9c1fff991751', # Algorithm-Diff-1.1903.tar.gz + ], + }), + ('AnyData', '0.12', { + 'source_tmpl': 'AnyData-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + 'checksums': [ + 'be6a957f04a2feba9b305536b132deceba1f455db295b221a63e75567fadbcfc', # AnyData-0.12.tar.gz + ], + }), + ('Text::Iconv', '1.7', { + 'source_tmpl': 'Text-Iconv-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MP/MPIOTR'], + 'checksums': [ + '5b80b7d5e709d34393bcba88971864a17b44a5bf0f9e4bcee383d029e7d2d5c3', # Text-Iconv-1.7.tar.gz + ], + }), + ('Class::Data::Inheritable', '0.08', { + 'source_tmpl': 'Class-Data-Inheritable-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TM/TMTM'], + 'checksums': [ + '9967feceea15227e442ec818723163eb6d73b8947e31f16ab806f6e2391af14a', # Class-Data-Inheritable-0.08.tar.gz + ], + }), + ('Text::Balanced', '2.03', { + 'source_tmpl': 'Text-Balanced-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHAY'], + 'checksums': [ + '057753f8f0568b53921f66a60a89c30092b73329bcc61a2c43339ab70c9792c8', # Text-Balanced-2.03.tar.gz + ], + }), + ('strictures', '2.000003', { + 'source_tmpl': 'strictures-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + 'checksums': [ + '27f8ea096a521e9754d36ea32889c2cda28346d04e3e399e7ea118d182dbaf22', # strictures-2.000003.tar.gz + ], + }), + ('Switch', '2.17', { + 'source_tmpl': 'Switch-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CH/CHORNY'], + 'checksums': [ + '31354975140fe6235ac130a109496491ad33dd42f9c62189e23f49f75f936d75', # Switch-2.17.tar.gz + ], + }), + ('File::Which', '1.21', { + 'source_tmpl': 'File-Which-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE'], + 'checksums': [ + '9def5f10316bfd944e56b7f8a2501be1d44c288325309462aa9345e340854bcc', # File-Which-1.21.tar.gz + ], + }), + ('Email::Date::Format', '1.005', { + 'source_tmpl': 'Email-Date-Format-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': [ + '579c617e303b9d874411c7b61b46b59d36f815718625074ae6832e7bb9db5104', # Email-Date-Format-1.005.tar.gz + ], + }), + ('Error', '0.17025', { + 'source_tmpl': 'Error-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'], + 'checksums': [ + '6c9f474ad3d4fe0cabff6b6be532cb1dd348245986d4a6b600ad921d5cfdefaf', # Error-0.17025.tar.gz + ], + }), + ('Mock::Quick', '1.111', { + 'source_tmpl': 'Mock-Quick-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + 'checksums': [ + 'ff786008bf8c022064ececd3b7ed89c76b35e8d1eac6cf472a9f51771c1c9f2c', # Mock-Quick-1.111.tar.gz + ], + }), + ('Text::CSV', '1.95', { + 'source_tmpl': 'Text-CSV-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IS/ISHIGAKI'], + 'checksums': [ + '7e0a11d9c1129a55b68a26aa4b37c894279df255aa63ec8341d514ab848dbf61', # Text-CSV-1.95.tar.gz + ], + }), + ('Test::Output', '1.031', { + 'source_tmpl': 'Test-Output-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BD/BDFOY'], + 'checksums': [ + 'f8b8f37185717872727d06f6c078fa77db794410faf2f6da4d37b0b7650f7ea4', # Test-Output-1.031.tar.gz + ], + }), + ('Class::DBI', 'v3.0.17', { + 'source_tmpl': 'Class-DBI-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TM/TMTM'], + 'checksums': [ + '541354fe361c56850cb11261f6ca089a14573fa764792447444ff736ae626206', # Class-DBI-v3.0.17.tar.gz + ], + }), + ('List::AllUtils', '0.14', { + 'source_tmpl': 'List-AllUtils-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + 'checksums': [ + 'e45aa65927ae1975a000cc2fed14274627fa5e2bd09bab826a5f2c41d17ef6cd', # List-AllUtils-0.14.tar.gz + ], + }), + ('UNIVERSAL::moniker', '0.08', { + 'source_tmpl': 'UNIVERSAL-moniker-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KA/KASEI'], + 'checksums': [ + '94ce27a546cd57cb52e080a8f2533a7cc2350028388582485bd1039a37871f9c', # UNIVERSAL-moniker-0.08.tar.gz + ], + }), + ('Exception::Class', '1.43', { + 'source_tmpl': 'Exception-Class-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + 'checksums': [ + 'ff3b4b3f706e84aaa87ab0dee5cec6bd7a8fc9f72cf76d115212541fa0a13760', # Exception-Class-1.43.tar.gz + ], + }), + ('File::CheckTree', '4.42', { + 'source_tmpl': 'File-CheckTree-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': [ + '66fb417f8ff8a5e5b7ea25606156e70e204861c59fa8c3831925b4dd3f155f8a', # File-CheckTree-4.42.tar.gz + ], + }), + ('Math::VecStat', '0.08', { + 'source_tmpl': 'Math-VecStat-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AS/ASPINELLI'], + 'checksums': [ + '409a8e0e4b1025c8e80f628f65a9778aa77ab285161406ca4a6c097b13656d0d', # Math-VecStat-0.08.tar.gz + ], + }), + ('Pod::LaTeX', '0.61', { + 'source_tmpl': 'Pod-LaTeX-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TJ/TJENNESS'], + 'checksums': [ + '15a840ea1c8a76cd3c865fbbf2fec33b03615c0daa50f9c800c54e0cf0659d46', # Pod-LaTeX-0.61.tar.gz + ], + }), + ('Eval::Closure', '0.14', { + 'source_tmpl': 'Eval-Closure-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DO/DOY'], + 'checksums': [ + 'ea0944f2f5ec98d895bef6d503e6e4a376fea6383a6bc64c7670d46ff2218cad', # Eval-Closure-0.14.tar.gz + ], + }), + ('HTTP::Request', '6.13', { + 'source_tmpl': 'HTTP-Message-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'], + 'checksums': [ + 'f25f38428de851e5661e72f124476494852eb30812358b07f1c3a289f6f5eded', # HTTP-Message-6.13.tar.gz + ], + }), + ('XML::Twig', '3.52', { + 'source_tmpl': 'XML-Twig-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIROD'], + 'checksums': [ + 'fef75826c24f2b877d0a0d2645212fc4fb9756ed4d2711614ac15c497e8680ad', # XML-Twig-3.52.tar.gz + ], + }), + ('IO::String', '1.08', { + 'source_tmpl': 'IO-String-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + 'checksums': [ + '2a3f4ad8442d9070780e58ef43722d19d1ee21a803bf7c8206877a10482de5a0', # IO-String-1.08.tar.gz + ], + }), + ('XML::Simple', '2.24', { + 'source_tmpl': 'XML-Simple-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GR/GRANTM'], + 'checksums': [ + '9a14819fd17c75fbb90adcec0446ceab356cab0ccaff870f2e1659205dc2424f', # XML-Simple-2.24.tar.gz + ], + }), + ('Sub::Install', '0.928', { + 'source_tmpl': 'Sub-Install-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': [ + '61e567a7679588887b7b86d427bc476ea6d77fffe7e0d17d640f89007d98ef0f', # Sub-Install-0.928.tar.gz + ], + }), + ('HTTP::Cookies', '6.04', { + 'source_tmpl': 'HTTP-Cookies-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'], + 'checksums': [ + '0cc7f079079dcad8293fea36875ef58dd1bfd75ce1a6c244cd73ed9523eb13d4', # HTTP-Cookies-6.04.tar.gz + ], + }), + ('Pod::Plainer', '1.04', { + 'source_tmpl': 'Pod-Plainer-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RM/RMBARKER'], + 'checksums': [ + '1bbfbf7d1d4871e5a83bab2137e22d089078206815190eb1d5c1260a3499456f', # Pod-Plainer-1.04.tar.gz + ], + }), + ('Test::Exception::LessClever', '0.009', { + 'source_tmpl': 'Test-Exception-LessClever-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': [ + # Test-Exception-LessClever-0.009.tar.gz + '3b2731a44956a11f74b46b3ecf0734fab651e1c0bcf120f8b407aa1b4d43ac34', + ], + }), + ('LWP::MediaTypes', '6.02', { + 'source_tmpl': 'LWP-MediaTypes-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + 'checksums': [ + '18790b0cc5f0a51468495c3847b16738f785a2d460403595001e0b932e5db676', # LWP-MediaTypes-6.02.tar.gz + ], + }), + ('Scalar::Util', '1.48', { + 'source_tmpl': 'Scalar-List-Utils-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PEVANS'], + 'checksums': [ + '0e5318308789ba3625e053001da0a6c5218dc73e561a207d1b91131d06c0d09f', # Scalar-List-Utils-1.48.tar.gz + ], + }), + ('Data::Section::Simple', '0.07', { + 'source_tmpl': 'Data-Section-Simple-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA'], + 'checksums': [ + '0b3035ffdb909aa1f7ded6b608fa9d894421c82c097d51e7171170d67579a9cb', # Data-Section-Simple-0.07.tar.gz + ], + }), + ('Class::Trigger', '0.14', { + 'source_tmpl': 'Class-Trigger-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA'], + 'checksums': [ + '6b1e45acc561e0708e00a2fcf16e157cad8b8963d1bf73726f77dd809b8aebc4', # Class-Trigger-0.14.tar.gz + ], + }), + ('HTTP::Daemon', '6.01', { + 'source_tmpl': 'HTTP-Daemon-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + 'checksums': [ + '43fd867742701a3f9fcc7bd59838ab72c6490c0ebaf66901068ec6997514adc2', # HTTP-Daemon-6.01.tar.gz + ], + }), + ('File::HomeDir', '1.002', { + 'source_tmpl': 'File-HomeDir-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + 'checksums': [ + 'eb4c0c85775138460cd4013d8117232f08e88381c95c6a93b3d11e969185c274', # File-HomeDir-1.002.tar.gz + ], + }), + ('HTTP::Date', '6.02', { + 'source_tmpl': 'HTTP-Date-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + 'checksums': [ + 'e8b9941da0f9f0c9c01068401a5e81341f0e3707d1c754f8e11f42a7e629e333', # HTTP-Date-6.02.tar.gz + ], + }), + ('Authen::SASL', '2.16', { + 'source_tmpl': 'Authen-SASL-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GB/GBARR'], + 'checksums': [ + '6614fa7518f094f853741b63c73f3627168c5d3aca89b1d02b1016dc32854e09', # Authen-SASL-2.16.tar.gz + ], + }), + ('Clone', '0.39', { + 'source_tmpl': 'Clone-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GARU'], + 'checksums': [ + 'acb046683e49d650b113634ecf57df000816a49e611b0fff70bf3f93568bfa2d', # Clone-0.39.tar.gz + ], + }), + ('Data::Types', '0.09', { + 'source_tmpl': 'Data-Types-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DW/DWHEELER'], + 'checksums': [ + 'b2296fdcf9addc8e8fc39e15eb2c3d81145f6355258438bc783b12b02c41cb81', # Data-Types-0.09.tar.gz + ], + }), + ('Import::Into', '1.002005', { + 'source_tmpl': 'Import-Into-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + 'checksums': [ + 'bd9e77a3fb662b40b43b18d3280cd352edf9fad8d94283e518181cc1ce9f0567', # Import-Into-1.002005.tar.gz + ], + }), + ('DateTime::Tiny', '1.06', { + 'source_tmpl': 'DateTime-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + 'checksums': [ + 'bd725df481d7223ee787e154c116098b08a129f55e0763194b07ebea3dda33ec', # DateTime-Tiny-1.06.tar.gz + ], + }), + ('DBD::AnyData', '0.110', { + 'source_tmpl': 'DBD-AnyData-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + 'checksums': [ + '247f0d88e55076fd3f6c7bf3fd527989d62fcc1ef9bde9bf2ee11c280adcaeab', # DBD-AnyData-0.110.tar.gz + ], + }), + ('Text::Format', '0.60', { + 'source_tmpl': 'Text-Format-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'], + 'checksums': [ + '664f313570604624ff9e1fc9b26b6d04e06897b3e4eac83089fc0905a692a2b8', # Text-Format-0.60.tar.gz + ], + }), + ('Devel::CheckCompiler', '0.07', { + 'source_tmpl': 'Devel-CheckCompiler-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SY/SYOHEX'], + 'checksums': [ + '768b7697b4b8d4d372c7507b65e9dd26aa4223f7100183bbb4d3af46d43869b5', # Devel-CheckCompiler-0.07.tar.gz + ], + }), + ('Log::Handler', '0.88', { + 'source_tmpl': 'Log-Handler-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BL/BLOONIX'], + 'checksums': [ + '45bf540ab2138ed3ff93afc205b0516dc75755b86acdcc5e75c41347833c293d', # Log-Handler-0.88.tar.gz + ], + }), + ('DBIx::ContextualFetch', '1.03', { + 'source_tmpl': 'DBIx-ContextualFetch-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TM/TMTM'], + 'checksums': [ + '85e2f805bfc81cd738c294316b27a515397036f397a0ff1c6c8d754c38530306', # DBIx-ContextualFetch-1.03.tar.gz + ], + }), + ('Devel::StackTrace', '2.02', { + 'source_tmpl': 'Devel-StackTrace-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + 'checksums': [ + 'cbbd96db0ecf194ed140198090eaea0e327d9a378a4aa15f9a34b3138a91931f', # Devel-StackTrace-2.02.tar.gz + ], + }), + ('Term::ReadKey', '2.37', { + 'source_tmpl': 'TermReadKey-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JS/JSTOWE'], + 'checksums': [ + '4a9383cf2e0e0194668fe2bd546e894ffad41d556b41d2f2f577c8db682db241', # TermReadKey-2.37.tar.gz + ], + }), + ('Set::IntSpan', '1.19', { + 'source_tmpl': 'Set-IntSpan-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SW/SWMCD'], + 'checksums': [ + '11b7549b13ec5d87cc695dd4c777cd02983dd5fe9866012877fb530f48b3dfd0', # Set-IntSpan-1.19.tar.gz + ], + }), + ('Moose', '2.2006', { + 'source_tmpl': 'Moose-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': [ + 'a4e00ab25cc41bebc5e7a11d71375fb5e64b56d5f91159afee225d698e06392b', # Moose-2.2006.tar.gz + ], + }), + ('Algorithm::Dependency', '1.110', { + 'source_tmpl': 'Algorithm-Dependency-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + 'checksums': [ + 'f27733e8d89cf2ab621284c2584da90ab0cb743ba2295ee739fe51bf92561e37', # Algorithm-Dependency-1.110.tar.gz + ], + }), + ('Font::TTF', '1.06', { + 'source_tmpl': 'Font-TTF-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BH/BHALLISSY'], + 'checksums': [ + '4b697d444259759ea02d2c442c9bffe5ffe14c9214084a01f743693a944cc293', # Font-TTF-1.06.tar.gz + ], + }), + ('IPC::Run3', '0.048', { + 'source_tmpl': 'IPC-Run3-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': [ + '3d81c3cc1b5cff69cca9361e2c6e38df0352251ae7b41e2ff3febc850e463565', # IPC-Run3-0.048.tar.gz + ], + }), + ('File::Find::Rule', '0.34', { + 'source_tmpl': 'File-Find-Rule-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RC/RCLAMP'], + 'checksums': [ + '7e6f16cc33eb1f29ff25bee51d513f4b8a84947bbfa18edb2d3cc40a2d64cafe', # File-Find-Rule-0.34.tar.gz + ], + }), + ('SQL::Statement', '1.412', { + 'source_tmpl': 'SQL-Statement-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + 'checksums': [ + '65c870883379c11b53f19ead10aaac241ccc86a90bbab77f6376fe750720e5c8', # SQL-Statement-1.412.tar.gz + ], + }), + ('File::Slurp', '9999.19', { + 'source_tmpl': 'File-Slurp-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/U/UR/URI'], + 'checksums': [ + 'ce29ebe995097ebd6e9bc03284714cdfa0c46dc94f6b14a56980747ea3253643', # File-Slurp-9999.19.tar.gz + ], + }), + ('Package::Stash', '0.37', { + 'source_tmpl': 'Package-Stash-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DO/DOY'], + 'checksums': [ + '06ab05388f9130cd377c0e1d3e3bafeed6ef6a1e22104571a9e1d7bfac787b2c', # Package-Stash-0.37.tar.gz + ], + }), + ('Data::OptList', '0.110', { + 'source_tmpl': 'Data-OptList-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': [ + '366117cb2966473f2559f2f4575ff6ae69e84c69a0f30a0773e1b51a457ef5c3', # Data-OptList-0.110.tar.gz + ], + }), + ('CPANPLUS', '0.9168', { + 'source_tmpl': 'CPANPLUS-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + 'checksums': [ + 'ea7b3278a688721729244de4d8efc57536be833458d93172c412bdc7c3c1ed02', # CPANPLUS-0.9168.tar.gz + ], + }), + ('IO::Tty', '1.12', { + 'source_tmpl': 'IO-Tty-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR'], + 'checksums': [ + 'a2ef8770d3309178203f8c8ac25e623e63cf76e97830fd3be280ade1a555290d', # IO-Tty-1.12.tar.gz + ], + }), + ('Text::Soundex', '3.05', { + 'source_tmpl': 'Text-Soundex-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': [ + 'f6dd55b4280b25dea978221839864382560074e1d6933395faee2510c2db60ed', # Text-Soundex-3.05.tar.gz + ], + }), + ('Lingua::EN::PluralToSingular', '0.19', { + 'source_tmpl': 'Lingua-EN-PluralToSingular-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BK/BKB'], + 'checksums': [ + # Lingua-EN-PluralToSingular-0.19.tar.gz + 'c71b6c1aec01aae9c42aef0d9f147a437e91a7cc5cea6e4abbc35440638f299e', + ], + }), + ('Want', '0.29', { + 'source_tmpl': 'Want-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RO/ROBIN'], + 'checksums': [ + 'b4e4740b8d4cb783591273c636bd68304892e28d89e88abf9273b1de17f552f7', # Want-0.29.tar.gz + ], + }), + ('Cwd::Guard', '0.05', { + 'source_tmpl': 'Cwd-Guard-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KA/KAZEBURO'], + 'checksums': [ + '7afc7ca2b9502e440241938ad97a3e7ebd550180ebd6142e1db394186b268e77', # Cwd-Guard-0.05.tar.gz + ], + }), + ('Bundle::BioPerl', '2.1.9', { + 'source_tmpl': 'Bundle-BioPerl-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS'], + 'checksums': [ + 'c343ba97f49d86e7fb14aef4cfe3124992e2a5c3168e53a54606dd611d73e5c7', # Bundle-BioPerl-2.1.9.tar.gz + ], + }), + ('Mail::Util', '2.19', { + 'source_tmpl': 'MailTools-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARKOV'], + 'checksums': [ + 'c17ed702efea8eab56fe92961c07cd4980cee26ca6f13aff2688dc8af69c5e1a', # MailTools-2.19.tar.gz + ], + }), + ('Text::Template', '1.47', { + 'source_tmpl': 'Text-Template-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MS/MSCHOUT'], + 'checksums': [ + '50d742c74482478aa01008d468290fcfbc0b9a1219cfe1284076f1f31f0be8fc', # Text-Template-1.47.tar.gz + ], + }), + ('PDF::API2', '2.033', { + 'source_tmpl': 'PDF-API2-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SS/SSIMMS'], + 'checksums': [ + '9c0866ec1a3053f73afaca5f5cdbe6925903b4ce606f4bf4ac317731a69d27a0', # PDF-API2-2.033.tar.gz + ], + }), + ('Devel::CheckLib', '1.11', { + 'source_tmpl': 'Devel-CheckLib-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MATTN'], + 'checksums': [ + 'bd6d1c187e80be6de1f0d37add441ba8f14950c7bc1f54e764770ed484b232c1', # Devel-CheckLib-1.11.tar.gz + ], + }), + ('SVG', '2.78', { + 'source_tmpl': 'SVG-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MANWAR'], + 'checksums': [ + 'a665c1f18c0529f3da0f4b631976eb47e0f71f6d6784ef3f44d32fd76643d6bb', # SVG-2.78.tar.gz + ], + }), + ('Statistics::Basic', '1.6611', { + 'source_tmpl': 'Statistics-Basic-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JE/JETTERO'], + 'checksums': [ + '6855ce5615fd3e1af4cfc451a9bf44ff29a3140b4e7130034f1f0af2511a94fb', # Statistics-Basic-1.6611.tar.gz + ], + }), +] + +moduleclass = 'lang' -- GitLab From 2edc2e161715a617a6ac3def4347cc5d9e742535 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 15 Sep 2017 15:06:01 +0200 Subject: [PATCH 1531/1603] adding easyconfigs: FFmpeg-3.3.4-intel-2017a.eb, x264-20170913-intel-2017a.eb --- .../f/FFmpeg/FFmpeg-3.3.4-intel-2017a.eb | 33 +++++++++++++++++ .../x/x264/x264-20170913-intel-2017a.eb | 36 +++++++++++++++++++ 2 files changed, 69 insertions(+) create mode 100644 easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.3.4-intel-2017a.eb create mode 100644 easybuild/easyconfigs/x/x264/x264-20170913-intel-2017a.eb diff --git a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.3.4-intel-2017a.eb b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.3.4-intel-2017a.eb new file mode 100644 index 0000000000..cd11763563 --- /dev/null +++ b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.3.4-intel-2017a.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'FFmpeg' +version = '3.3.4' + +homepage = 'https://www.ffmpeg.org/' +description = """A complete, cross-platform solution to record, convert and stream audio and video.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['http://ffmpeg.org/releases/'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['5ef5e9276c311c74ab2e9d301c2d7ee10e1f2cbd758c6f13d6cb9514dffbac7e'] + +dependencies = [ + ('NASM', '2.12.02'), + ('zlib', '1.2.11'), + ('bzip2', '1.0.6'), + ('x264', '20170913'), + ('X11', '20170314'), +] + +configopts = '--enable-pic --enable-shared --enable-gpl --enable-version3 --enable-nonfree --cc="$CC" --cxx="$CXX" ' +configopts += '--enable-libx264' + +sanity_check_paths = { + 'files': ['bin/ff%s' % x for x in ['mpeg', 'probe', 'server']] + + ['lib/lib%s.%s' % (x, y) for x in ['avdevice', 'avfilter', 'avformat', 'avcodec', 'postproc', + 'swresample', 'swscale', 'avutil'] for y in [SHLIB_EXT, 'a']], + 'dirs': ['include'] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/x/x264/x264-20170913-intel-2017a.eb b/easybuild/easyconfigs/x/x264/x264-20170913-intel-2017a.eb new file mode 100644 index 0000000000..e83a97dff0 --- /dev/null +++ b/easybuild/easyconfigs/x/x264/x264-20170913-intel-2017a.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'x264' +version = '20170913' + +homepage = 'http://www.videolan.org/developers/x264.html' + +description = """ + x264 is a free software library and application for encoding video streams + into the H.264/MPEG-4 AVC compression format, and is released under the + terms of the GNU GPL. +""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True} + +source_urls = [ + 'https://download.videolan.org/pub/videolan/x264/snapshots/', + 'ftp://ftp.videolan.org/pub/videolan/x264/snapshots/', +] +sources = ['x264-snapshot-%(version)s-2245-stable.tar.bz2'] +checksums = ['7d6764556065f5625cc99e2bdb811f9cce980adc98a2ddf87466fdf32f0f71c1'] + +dependencies = [ + ('Yasm', '1.3.0'), +] + +configopts = " --enable-shared --enable-static" + +sanity_check_paths = { + 'files': ['bin/x264', 'include/x264_config.h', 'include/x264.h', + 'lib/libx264.a', 'lib/libx264.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' -- GitLab From b3c0c8a6b79eef130fe534810859939db1276230 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 15 Sep 2017 22:34:43 +0200 Subject: [PATCH 1532/1603] fix building Bison 2.5 on systems with recent glibc --- easybuild/easyconfigs/b/Bison/Bison-2.5-GCC-4.6.3.eb | 3 ++- .../easyconfigs/b/Bison/Bison-2.5-goolf-1.4.10.eb | 3 ++- .../easyconfigs/b/Bison/Bison-2.5-ictce-5.3.0.eb | 3 ++- .../easyconfigs/b/Bison/Bison-2.5-ictce-5.4.0.eb | 3 ++- .../easyconfigs/b/Bison/Bison-2.5-ictce-5.5.0.eb | 3 ++- .../easyconfigs/b/Bison/Bison-2.5-intel-2014b.eb | 3 ++- .../easyconfigs/b/Bison/Bison-2.5_fix-gets.patch | 12 ++++++++++++ 7 files changed, 24 insertions(+), 6 deletions(-) create mode 100644 easybuild/easyconfigs/b/Bison/Bison-2.5_fix-gets.patch diff --git a/easybuild/easyconfigs/b/Bison/Bison-2.5-GCC-4.6.3.eb b/easybuild/easyconfigs/b/Bison/Bison-2.5-GCC-4.6.3.eb index ad34232c28..42ca390125 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-2.5-GCC-4.6.3.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-2.5-GCC-4.6.3.eb @@ -9,8 +9,9 @@ into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser toolchain = {'name': 'GCC', 'version': '4.6.3'} -sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +patches = ['Bison-%(version)s_fix-gets.patch'] builddependencies = [('M4', '1.4.16')] diff --git a/easybuild/easyconfigs/b/Bison/Bison-2.5-goolf-1.4.10.eb b/easybuild/easyconfigs/b/Bison/Bison-2.5-goolf-1.4.10.eb index 5c91aa97e5..d8c2bec8aa 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-2.5-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-2.5-goolf-1.4.10.eb @@ -9,8 +9,9 @@ into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser toolchain = {'name': 'goolf', 'version': '1.4.10'} -sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +patches = ['Bison-%(version)s_fix-gets.patch'] builddependencies = [('M4', '1.4.16')] diff --git a/easybuild/easyconfigs/b/Bison/Bison-2.5-ictce-5.3.0.eb b/easybuild/easyconfigs/b/Bison/Bison-2.5-ictce-5.3.0.eb index 3257ed4046..ae581fd5f3 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-2.5-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-2.5-ictce-5.3.0.eb @@ -10,8 +10,9 @@ description = """Bison is a general-purpose parser generator that converts an an toolchain = {'name': 'ictce', 'version': '5.3.0'} -sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +patches = ['Bison-%(version)s_fix-gets.patch'] builddependencies = [('M4', '1.4.16')] diff --git a/easybuild/easyconfigs/b/Bison/Bison-2.5-ictce-5.4.0.eb b/easybuild/easyconfigs/b/Bison/Bison-2.5-ictce-5.4.0.eb index 18dbc65289..80311e8c5d 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-2.5-ictce-5.4.0.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-2.5-ictce-5.4.0.eb @@ -10,8 +10,9 @@ description = """Bison is a general-purpose parser generator that converts an an toolchain = {'name': 'ictce', 'version': '5.4.0'} -sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +patches = ['Bison-%(version)s_fix-gets.patch'] builddependencies = [('M4', '1.4.16')] diff --git a/easybuild/easyconfigs/b/Bison/Bison-2.5-ictce-5.5.0.eb b/easybuild/easyconfigs/b/Bison/Bison-2.5-ictce-5.5.0.eb index 37e75810f2..de950cdbac 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-2.5-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-2.5-ictce-5.5.0.eb @@ -9,8 +9,9 @@ description = """Bison is a general-purpose parser generator that converts an an toolchain = {'name': 'ictce', 'version': '5.5.0'} -sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +patches = ['Bison-%(version)s_fix-gets.patch'] builddependencies = [('M4', '1.4.16')] diff --git a/easybuild/easyconfigs/b/Bison/Bison-2.5-intel-2014b.eb b/easybuild/easyconfigs/b/Bison/Bison-2.5-intel-2014b.eb index 5f58f02694..d7728a98f9 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-2.5-intel-2014b.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-2.5-intel-2014b.eb @@ -9,8 +9,9 @@ description = """Bison is a general-purpose parser generator that converts an an toolchain = {'name': 'intel', 'version': '2014b'} -sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +patches = ['Bison-%(version)s_fix-gets.patch'] builddependencies = [('M4', '1.4.16')] diff --git a/easybuild/easyconfigs/b/Bison/Bison-2.5_fix-gets.patch b/easybuild/easyconfigs/b/Bison/Bison-2.5_fix-gets.patch new file mode 100644 index 0000000000..d3b646825b --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-2.5_fix-gets.patch @@ -0,0 +1,12 @@ +fix for "'gets' undeclared here" error with recent glibc +see also https://bugs.gentoo.org/424978 +--- bison-2.5/lib/stdio.in.h.orig 2017-09-15 22:19:26.014249360 +0200 ++++ bison-2.5/lib/stdio.in.h 2017-09-15 22:19:47.694669181 +0200 +@@ -181,7 +181,6 @@ + so any use of gets warrants an unconditional warning. Assume it is + always declared, since it is required by C89. */ + #undef gets +-_GL_WARN_ON_USE (gets, "gets is a security hole - use fgets instead"); + + #if @GNULIB_FOPEN@ + # if @REPLACE_FOPEN@ -- GitLab From 763369422903dd08e401c2117bf51b2dc8ebdeed Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 15 Sep 2017 22:37:02 +0200 Subject: [PATCH 1533/1603] add SHA256 checksums in Bison 2.5 easyconfigs --- easybuild/easyconfigs/b/Bison/Bison-2.5-GCC-4.6.3.eb | 4 ++++ easybuild/easyconfigs/b/Bison/Bison-2.5-goolf-1.4.10.eb | 4 ++++ easybuild/easyconfigs/b/Bison/Bison-2.5-ictce-5.3.0.eb | 4 ++++ easybuild/easyconfigs/b/Bison/Bison-2.5-ictce-5.4.0.eb | 4 ++++ easybuild/easyconfigs/b/Bison/Bison-2.5-ictce-5.5.0.eb | 4 ++++ easybuild/easyconfigs/b/Bison/Bison-2.5-intel-2014b.eb | 4 ++++ 6 files changed, 24 insertions(+) diff --git a/easybuild/easyconfigs/b/Bison/Bison-2.5-GCC-4.6.3.eb b/easybuild/easyconfigs/b/Bison/Bison-2.5-GCC-4.6.3.eb index 42ca390125..3222d06042 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-2.5-GCC-4.6.3.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-2.5-GCC-4.6.3.eb @@ -12,6 +12,10 @@ toolchain = {'name': 'GCC', 'version': '4.6.3'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] patches = ['Bison-%(version)s_fix-gets.patch'] +checksums = [ + '722def46e4a19a5b7a579ef30db1965f86c37c1a20a5f0113743a2e4399f7c99', # bison-2.5.tar.gz + 'a048873fe6491e7c97bb380e9df5e6869089719166a4d73424edd00628b830b2', # Bison-2.5_fix-gets.patch +] builddependencies = [('M4', '1.4.16')] diff --git a/easybuild/easyconfigs/b/Bison/Bison-2.5-goolf-1.4.10.eb b/easybuild/easyconfigs/b/Bison/Bison-2.5-goolf-1.4.10.eb index d8c2bec8aa..527ccebc43 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-2.5-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-2.5-goolf-1.4.10.eb @@ -12,6 +12,10 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] patches = ['Bison-%(version)s_fix-gets.patch'] +checksums = [ + '722def46e4a19a5b7a579ef30db1965f86c37c1a20a5f0113743a2e4399f7c99', # bison-2.5.tar.gz + 'a048873fe6491e7c97bb380e9df5e6869089719166a4d73424edd00628b830b2', # Bison-2.5_fix-gets.patch +] builddependencies = [('M4', '1.4.16')] diff --git a/easybuild/easyconfigs/b/Bison/Bison-2.5-ictce-5.3.0.eb b/easybuild/easyconfigs/b/Bison/Bison-2.5-ictce-5.3.0.eb index ae581fd5f3..37ee888ca6 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-2.5-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-2.5-ictce-5.3.0.eb @@ -13,6 +13,10 @@ toolchain = {'name': 'ictce', 'version': '5.3.0'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] patches = ['Bison-%(version)s_fix-gets.patch'] +checksums = [ + '722def46e4a19a5b7a579ef30db1965f86c37c1a20a5f0113743a2e4399f7c99', # bison-2.5.tar.gz + 'a048873fe6491e7c97bb380e9df5e6869089719166a4d73424edd00628b830b2', # Bison-2.5_fix-gets.patch +] builddependencies = [('M4', '1.4.16')] diff --git a/easybuild/easyconfigs/b/Bison/Bison-2.5-ictce-5.4.0.eb b/easybuild/easyconfigs/b/Bison/Bison-2.5-ictce-5.4.0.eb index 80311e8c5d..ddb9da74fd 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-2.5-ictce-5.4.0.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-2.5-ictce-5.4.0.eb @@ -13,6 +13,10 @@ toolchain = {'name': 'ictce', 'version': '5.4.0'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] patches = ['Bison-%(version)s_fix-gets.patch'] +checksums = [ + '722def46e4a19a5b7a579ef30db1965f86c37c1a20a5f0113743a2e4399f7c99', # bison-2.5.tar.gz + 'a048873fe6491e7c97bb380e9df5e6869089719166a4d73424edd00628b830b2', # Bison-2.5_fix-gets.patch +] builddependencies = [('M4', '1.4.16')] diff --git a/easybuild/easyconfigs/b/Bison/Bison-2.5-ictce-5.5.0.eb b/easybuild/easyconfigs/b/Bison/Bison-2.5-ictce-5.5.0.eb index de950cdbac..e22ac277b1 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-2.5-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-2.5-ictce-5.5.0.eb @@ -12,6 +12,10 @@ toolchain = {'name': 'ictce', 'version': '5.5.0'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] patches = ['Bison-%(version)s_fix-gets.patch'] +checksums = [ + '722def46e4a19a5b7a579ef30db1965f86c37c1a20a5f0113743a2e4399f7c99', # bison-2.5.tar.gz + 'a048873fe6491e7c97bb380e9df5e6869089719166a4d73424edd00628b830b2', # Bison-2.5_fix-gets.patch +] builddependencies = [('M4', '1.4.16')] diff --git a/easybuild/easyconfigs/b/Bison/Bison-2.5-intel-2014b.eb b/easybuild/easyconfigs/b/Bison/Bison-2.5-intel-2014b.eb index d7728a98f9..d06627a083 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-2.5-intel-2014b.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-2.5-intel-2014b.eb @@ -12,6 +12,10 @@ toolchain = {'name': 'intel', 'version': '2014b'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] patches = ['Bison-%(version)s_fix-gets.patch'] +checksums = [ + '722def46e4a19a5b7a579ef30db1965f86c37c1a20a5f0113743a2e4399f7c99', # bison-2.5.tar.gz + 'a048873fe6491e7c97bb380e9df5e6869089719166a4d73424edd00628b830b2', # Bison-2.5_fix-gets.patch +] builddependencies = [('M4', '1.4.16')] -- GitLab From 930924b7fa1b57ebabf5b3e2337eb6ca18a4957b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 15 Sep 2017 22:38:20 +0200 Subject: [PATCH 1534/1603] clean up use of wcleanAll in OpenFOAM-Extend easyconfigs, now handled by OpenFOAM easyblock --- .../OpenFOAM-Extend-3.0-goolf-1.4.10-20140227.eb | 2 -- .../o/OpenFOAM-Extend/OpenFOAM-Extend-3.1-gimkl-2.11.5.eb | 2 -- .../o/OpenFOAM-Extend/OpenFOAM-Extend-3.1-goolf-1.4.10.eb | 2 -- .../o/OpenFOAM-Extend/OpenFOAM-Extend-3.2-gimkl-2.11.5.eb | 2 -- .../o/OpenFOAM-Extend/OpenFOAM-Extend-3.2-intel-2016a.eb | 2 -- 5 files changed, 10 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenFOAM-Extend/OpenFOAM-Extend-3.0-goolf-1.4.10-20140227.eb b/easybuild/easyconfigs/o/OpenFOAM-Extend/OpenFOAM-Extend-3.0-goolf-1.4.10-20140227.eb index 2a3beb3683..4e58dd99b5 100644 --- a/easybuild/easyconfigs/o/OpenFOAM-Extend/OpenFOAM-Extend-3.0-goolf-1.4.10-20140227.eb +++ b/easybuild/easyconfigs/o/OpenFOAM-Extend/OpenFOAM-Extend-3.0-goolf-1.4.10-20140227.eb @@ -38,8 +38,6 @@ builddependencies = [ ('CMake', '2.8.12'), ] -prebuildopts = "(wcleanAll || echo 'all is fine') && " # clean up everything first (and ignore any errors) - # too many builds in parallel actually slows down the build maxparallel = 4 diff --git a/easybuild/easyconfigs/o/OpenFOAM-Extend/OpenFOAM-Extend-3.1-gimkl-2.11.5.eb b/easybuild/easyconfigs/o/OpenFOAM-Extend/OpenFOAM-Extend-3.1-gimkl-2.11.5.eb index 06755b2786..d6646f84d0 100644 --- a/easybuild/easyconfigs/o/OpenFOAM-Extend/OpenFOAM-Extend-3.1-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/o/OpenFOAM-Extend/OpenFOAM-Extend-3.1-gimkl-2.11.5.eb @@ -40,8 +40,6 @@ builddependencies = [ ] -prebuildopts = "(wcleanAll || echo 'all is fine') && " # clean up everything first (and ignore any errors) - # too many builds in parallel actually slows down the build maxparallel = 4 diff --git a/easybuild/easyconfigs/o/OpenFOAM-Extend/OpenFOAM-Extend-3.1-goolf-1.4.10.eb b/easybuild/easyconfigs/o/OpenFOAM-Extend/OpenFOAM-Extend-3.1-goolf-1.4.10.eb index bebef71955..1ae1e9fb7d 100644 --- a/easybuild/easyconfigs/o/OpenFOAM-Extend/OpenFOAM-Extend-3.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/o/OpenFOAM-Extend/OpenFOAM-Extend-3.1-goolf-1.4.10.eb @@ -38,8 +38,6 @@ builddependencies = [ ('CMake', '2.8.12'), ] -prebuildopts = "(wcleanAll || echo 'all is fine') && " # clean up everything first (and ignore any errors) - # too many builds in parallel actually slows down the build maxparallel = 4 diff --git a/easybuild/easyconfigs/o/OpenFOAM-Extend/OpenFOAM-Extend-3.2-gimkl-2.11.5.eb b/easybuild/easyconfigs/o/OpenFOAM-Extend/OpenFOAM-Extend-3.2-gimkl-2.11.5.eb index 4ddd37d882..a65e02dfc0 100644 --- a/easybuild/easyconfigs/o/OpenFOAM-Extend/OpenFOAM-Extend-3.2-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/o/OpenFOAM-Extend/OpenFOAM-Extend-3.2-gimkl-2.11.5.eb @@ -40,8 +40,6 @@ builddependencies = [ ('CMake', '3.3.2'), ] -prebuildopts = "(wcleanAll || echo 'all is fine') && " # clean up everything first (and ignore any errors) - # too many builds in parallel actually slows down the build maxparallel = 4 diff --git a/easybuild/easyconfigs/o/OpenFOAM-Extend/OpenFOAM-Extend-3.2-intel-2016a.eb b/easybuild/easyconfigs/o/OpenFOAM-Extend/OpenFOAM-Extend-3.2-intel-2016a.eb index 00e9eaf007..e10830c3f9 100644 --- a/easybuild/easyconfigs/o/OpenFOAM-Extend/OpenFOAM-Extend-3.2-intel-2016a.eb +++ b/easybuild/easyconfigs/o/OpenFOAM-Extend/OpenFOAM-Extend-3.2-intel-2016a.eb @@ -40,8 +40,6 @@ builddependencies = [ ('CMake', '3.5.2'), ] -prebuildopts = "(wcleanAll || echo 'all is fine') && " # clean up everything first (and ignore any errors) - # too many builds in parallel actually slows down the build maxparallel = 4 -- GitLab From 89f832ad300308211023364a6c75beb4984f9432 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 15 Sep 2017 22:47:10 +0200 Subject: [PATCH 1535/1603] also consider rdma-core-devel as alternative to libibverbs-devel OS dependency --- .../g/GlobalArrays/GlobalArrays-5.3-intel-2015a-openib.eb | 2 +- .../g/GlobalArrays/GlobalArrays-5.4b-foss-2015a-openib.eb | 2 +- ...746-intel-2017a-2015-10-20-patches-20170814-Python-2.7.13.eb | 2 +- ...em-6.6.revision27746-iomkl-2017a-2015-10-20-Python-2.7.12.eb | 2 +- .../easyconfigs/o/OpenMPI/OpenMPI-1.10.1-GCC-4.9.3-2.25.eb | 2 +- .../easyconfigs/o/OpenMPI/OpenMPI-1.10.2-GCC-4.9.3-2.25.eb | 2 +- .../easyconfigs/o/OpenMPI/OpenMPI-1.10.2-GCC-5.3.0-2.26.eb | 2 +- .../easyconfigs/o/OpenMPI/OpenMPI-1.10.2-GCC-6.1.0-2.27.eb | 2 +- .../o/OpenMPI/OpenMPI-1.10.2-PGI-16.3-GCC-4.9.3-2.25.eb | 2 +- .../o/OpenMPI/OpenMPI-1.10.2-PGI-16.4-GCC-5.3.0-2.26.eb | 2 +- .../easyconfigs/o/OpenMPI/OpenMPI-1.10.3-GCC-5.4.0-2.26.eb | 2 +- .../easyconfigs/o/OpenMPI/OpenMPI-1.10.3-GCC-6.1.0-2.27.eb | 2 +- .../easyconfigs/o/OpenMPI/OpenMPI-1.10.3-gcccuda-2016.08.eb | 2 +- .../OpenMPI-1.10.3-iccifort-2016.3.210-GCC-5.4.0-2.26.eb | 2 +- .../o/OpenMPI/OpenMPI-1.10.4-PGI-16.7-GCC-5.4.0-2.26.eb | 2 +- .../OpenMPI-1.10.4-iccifort-2016.3.210-GCC-4.9.3-2.25.eb | 2 +- easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-GCC-4.6.3.eb | 2 +- easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-ictce-5.5.0.eb | 2 +- easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.6.4.eb | 2 +- easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2.eb | 2 +- easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.2.eb | 2 +- easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1.eb | 2 +- easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2.eb | 2 +- easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.3.eb | 2 +- .../o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.2.144.eb | 2 +- .../o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211.eb | 2 +- easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.7.3-GCC-4.8.2.eb | 2 +- easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.1-GCC-4.8.3.eb | 2 +- easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-GCC-4.9.2.eb | 2 +- .../o/OpenMPI/OpenMPI-1.8.3-iccifort-2013_sp1.4.211.eb | 2 +- easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GCC-4.8.4.eb | 2 +- easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GCC-4.9.2.eb | 2 +- .../o/OpenMPI/OpenMPI-1.8.4-iccifort-2015.1.133-GCC-4.9.2.eb | 2 +- .../o/OpenMPI/OpenMPI-1.8.4-iccifort-2015.2.164-GCC-4.9.2.eb | 2 +- easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.5-GNU-4.9.2-2.25.eb | 2 +- easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.6-GNU-4.9.3-2.25.eb | 2 +- easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.8-GNU-4.9.3-2.25.eb | 2 +- .../OpenMPI/OpenMPI-1.8.8-iccifort-2015.3.187-GNU-4.9.3-2.25.eb | 2 +- easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.0-GCC-5.2.0.eb | 2 +- easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.1-GCC-6.2.0-2.27.eb | 2 +- .../easyconfigs/o/OpenMPI/OpenMPI-2.0.1-gcccuda-2016.10.eb | 2 +- .../OpenMPI/OpenMPI-2.0.1-iccifort-2017.1.132-GCC-5.4.0-2.26.eb | 2 +- easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.2-GCC-6.3.0-2.27.eb | 2 +- .../easyconfigs/o/OpenMPI/OpenMPI-2.0.2-gcccuda-2017.01.eb | 2 +- .../OpenMPI/OpenMPI-2.0.2-iccifort-2017.1.132-GCC-6.3.0-2.27.eb | 2 +- easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.0-GCC-6.3.0-2.28.eb | 2 +- easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.1-GCC-6.4.0-2.28.eb | 2 +- .../OpenMPI/OpenMPI-2.1.1-iccifort-2017.4.196-GCC-6.4.0-2.28.eb | 2 +- 48 files changed, 48 insertions(+), 48 deletions(-) diff --git a/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.3-intel-2015a-openib.eb b/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.3-intel-2015a-openib.eb index 160dbeb127..f9d09c3724 100644 --- a/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.3-intel-2015a-openib.eb +++ b/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.3-intel-2015a-openib.eb @@ -13,7 +13,7 @@ toolchainopts = {'usempi': True} source_urls = ['http://hpc.pnl.gov/globalarrays/download/'] sources = ['ga-%(version_major)s-%(version_minor)s.tgz'] -osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +osdependencies = [('libibverbs-dev', 'libibverbs-devel', 'rdma-core-devel')] configopts = '--with-openib' configopts += ' --with-blas8="-L$BLAS_LIB_DIR $LIBBLAS" --with-lapack="-L$LAPACK_LIB_DIR $LIBLAPACK"' diff --git a/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.4b-foss-2015a-openib.eb b/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.4b-foss-2015a-openib.eb index 0acd5d9070..285f667fcb 100644 --- a/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.4b-foss-2015a-openib.eb +++ b/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.4b-foss-2015a-openib.eb @@ -13,7 +13,7 @@ toolchainopts = {'usempi': True} source_urls = ['http://hpc.pnl.gov/globalarrays/download/'] sources = ['ga-%s.tgz' % version.replace(".", "-")] -osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +osdependencies = [('libibverbs-dev', 'libibverbs-devel', 'rdma-core-devel')] configopts = '--with-openib' configopts += ' --with-blas8="-L$BLAS_LIB_DIR $LIBBLAS" --with-lapack="-L$LAPACK_LIB_DIR $LIBLAPACK"' diff --git a/easybuild/easyconfigs/n/NWChem/NWChem-6.6.revision27746-intel-2017a-2015-10-20-patches-20170814-Python-2.7.13.eb b/easybuild/easyconfigs/n/NWChem/NWChem-6.6.revision27746-intel-2017a-2015-10-20-patches-20170814-Python-2.7.13.eb index 2387d265fb..d7189c7794 100644 --- a/easybuild/easyconfigs/n/NWChem/NWChem-6.6.revision27746-intel-2017a-2015-10-20-patches-20170814-Python-2.7.13.eb +++ b/easybuild/easyconfigs/n/NWChem/NWChem-6.6.revision27746-intel-2017a-2015-10-20-patches-20170814-Python-2.7.13.eb @@ -79,7 +79,7 @@ dependencies = [('Python', '2.7.13')] # This easyconfig is using the default for armci_network (OPENIB) and # thus needs infiniband libraries. osdependencies = [ - ('libibverbs-dev', 'libibverbs-devel'), + ('libibverbs-dev', 'libibverbs-devel', 'rdma-core-devel'), ('libibumad-dev', 'libibumad-devel'), ] diff --git a/easybuild/easyconfigs/n/NWChem/NWChem-6.6.revision27746-iomkl-2017a-2015-10-20-Python-2.7.12.eb b/easybuild/easyconfigs/n/NWChem/NWChem-6.6.revision27746-iomkl-2017a-2015-10-20-Python-2.7.12.eb index 27d258eaee..f85393e44f 100644 --- a/easybuild/easyconfigs/n/NWChem/NWChem-6.6.revision27746-iomkl-2017a-2015-10-20-Python-2.7.12.eb +++ b/easybuild/easyconfigs/n/NWChem/NWChem-6.6.revision27746-iomkl-2017a-2015-10-20-Python-2.7.12.eb @@ -27,7 +27,7 @@ dependencies = [('Python', '2.7.12')] # This easyconfig is using the default for armci_network (OPENIB) and # thus needs infiniband libraries. osdependencies = [ - ('libibverbs-dev', 'libibverbs-devel'), + ('libibverbs-dev', 'libibverbs-devel', 'rdma-core-devel'), ('libibumad-dev', 'libibumad-devel'), ] diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.1-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.1-GCC-4.9.3-2.25.eb index c91ebdd221..dfafbdd293 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.1-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.1-GCC-4.9.3-2.25.eb @@ -19,7 +19,7 @@ configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading # needed for --with-verbs -osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +osdependencies = [('libibverbs-dev', 'libibverbs-devel', 'rdma-core-devel')] libs = ["mpi_cxx", "mpi_mpifh", "mpi", "ompitrace", "open-pal", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-GCC-4.9.3-2.25.eb index 6afba2f292..9fba34d7ad 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-GCC-4.9.3-2.25.eb @@ -19,7 +19,7 @@ configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading # needed for --with-verbs -osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +osdependencies = [('libibverbs-dev', 'libibverbs-devel', 'rdma-core-devel')] libs = ["mpi_cxx", "mpi_mpifh", "mpi", "ompitrace", "open-pal", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-GCC-5.3.0-2.26.eb index 4502f5c9f4..d464f30b2f 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-GCC-5.3.0-2.26.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-GCC-5.3.0-2.26.eb @@ -19,7 +19,7 @@ configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading # needed for --with-verbs -osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +osdependencies = [('libibverbs-dev', 'libibverbs-devel', 'rdma-core-devel')] libs = ["mpi_cxx", "mpi_mpifh", "mpi", "ompitrace", "open-pal", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-GCC-6.1.0-2.27.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-GCC-6.1.0-2.27.eb index 422607a28b..8b0c5ebd22 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-GCC-6.1.0-2.27.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-GCC-6.1.0-2.27.eb @@ -20,7 +20,7 @@ configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading # needed for --with-verbs -osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +osdependencies = [('libibverbs-dev', 'libibverbs-devel', 'rdma-core-devel')] libs = ["mpi_cxx", "mpi_mpifh", "mpi", "ompitrace", "open-pal", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-PGI-16.3-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-PGI-16.3-GCC-4.9.3-2.25.eb index 26ff9690ec..6cea8ce3bc 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-PGI-16.3-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-PGI-16.3-GCC-4.9.3-2.25.eb @@ -20,7 +20,7 @@ configopts += '--with-cxxrtlib="-lgcc_s -lstdc++"' # for vt-mpi-unify dependencies = [('hwloc', '1.11.3')] # needed for --with-verbs -osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +osdependencies = [('libibverbs-dev', 'libibverbs-devel', 'rdma-core-devel')] libs = ["mpi_cxx", "mpi_mpifh", "mpi", "ompitrace", "open-pal", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-PGI-16.4-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-PGI-16.4-GCC-5.3.0-2.26.eb index 64e4eca3c7..a3e3a91273 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-PGI-16.4-GCC-5.3.0-2.26.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-PGI-16.4-GCC-5.3.0-2.26.eb @@ -20,7 +20,7 @@ configopts += '--with-cxxrtlib="-lgcc_s -lstdc++"' # for vt-mpi-unify dependencies = [('hwloc', '1.11.3')] # needed for --with-verbs -osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +osdependencies = [('libibverbs-dev', 'libibverbs-devel', 'rdma-core-devel')] libs = ["mpi_cxx", "mpi_mpifh", "mpi", "ompitrace", "open-pal", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.3-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.3-GCC-5.4.0-2.26.eb index 1f3b3eb045..d4e8e40907 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.3-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.3-GCC-5.4.0-2.26.eb @@ -19,7 +19,7 @@ configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading # needed for --with-verbs -osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +osdependencies = [('libibverbs-dev', 'libibverbs-devel', 'rdma-core-devel')] libs = ["mpi_cxx", "mpi_mpifh", "mpi", "ompitrace", "open-pal", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.3-GCC-6.1.0-2.27.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.3-GCC-6.1.0-2.27.eb index ded2f408ed..8d96ce4344 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.3-GCC-6.1.0-2.27.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.3-GCC-6.1.0-2.27.eb @@ -20,7 +20,7 @@ configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading # needed for --with-verbs -osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +osdependencies = [('libibverbs-dev', 'libibverbs-devel', 'rdma-core-devel')] libs = ["mpi_cxx", "mpi_mpifh", "mpi", "ompitrace", "open-pal", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.3-gcccuda-2016.08.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.3-gcccuda-2016.08.eb index 917b152207..bac6321f61 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.3-gcccuda-2016.08.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.3-gcccuda-2016.08.eb @@ -19,7 +19,7 @@ configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support configopts += '--with-cuda=$CUDA_HOME ' # CUDA-aware build; N.B. --disable-dlopen is incompatible # needed for --with-verbs -osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +osdependencies = [('libibverbs-dev', 'libibverbs-devel', 'rdma-core-devel')] libs = ["mpi_cxx", "mpi_mpifh", "mpi", "ompitrace", "open-pal", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.3-iccifort-2016.3.210-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.3-iccifort-2016.3.210-GCC-5.4.0-2.26.eb index ed7694b56f..6d1e297ce3 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.3-iccifort-2016.3.210-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.3-iccifort-2016.3.210-GCC-5.4.0-2.26.eb @@ -20,7 +20,7 @@ configopts += '--disable-dlopen ' # statically link component, don't do dynamic dependencies = [('hwloc', '1.11.3')] # needed for --with-verbs -osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +osdependencies = [('libibverbs-dev', 'libibverbs-devel', 'rdma-core-devel')] libs = ["mpi_cxx", "mpi_mpifh", "mpi", "ompitrace", "open-pal", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.4-PGI-16.7-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.4-PGI-16.7-GCC-5.4.0-2.26.eb index f7b06dcb04..fa72c729f1 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.4-PGI-16.7-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.4-PGI-16.7-GCC-5.4.0-2.26.eb @@ -22,7 +22,7 @@ configopts += '--with-cxxrtlib="-lgcc_s -lstdc++"' # for vt-mpi-unify dependencies = [('hwloc', '1.11.4')] # needed for --with-verbs -osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +osdependencies = [('libibverbs-dev', 'libibverbs-devel', 'rdma-core-devel')] libs = ["mpi_cxx", "mpi_mpifh", "mpi", "ompitrace", "open-pal", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.4-iccifort-2016.3.210-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.4-iccifort-2016.3.210-GCC-4.9.3-2.25.eb index c16d7bf245..03bd80d81c 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.4-iccifort-2016.3.210-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.4-iccifort-2016.3.210-GCC-4.9.3-2.25.eb @@ -20,7 +20,7 @@ configopts += '--disable-dlopen ' # statically link component, don't do dynamic dependencies = [('hwloc', '1.11.3')] # needed for --with-verbs -osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +osdependencies = [('libibverbs-dev', 'libibverbs-devel', 'rdma-core-devel')] libs = ["mpi_cxx", "mpi_mpifh", "mpi", "ompitrace", "open-pal", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-GCC-4.6.3.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-GCC-4.6.3.eb index af837e0815..71d41c1e0f 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-GCC-4.6.3.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-GCC-4.6.3.eb @@ -15,7 +15,7 @@ configopts = '--with-threads=posix --enable-shared --enable-mpi-threads --with-o configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path # needed for --with-openib -osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +osdependencies = [('libibverbs-dev', 'libibverbs-devel', 'rdma-core-devel')] libs = ["mca_common_sm", "mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "open-pal", "open-rte"] sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-ictce-5.5.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-ictce-5.5.0.eb index 70d3c85032..18c61b4abf 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-ictce-5.5.0.eb @@ -24,7 +24,7 @@ configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading # needed for --with-openib -osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +osdependencies = [('libibverbs-dev', 'libibverbs-devel', 'rdma-core-devel')] libs = ["mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "open-pal", "open-rte"] sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.6.4.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.6.4.eb index fc479108fe..e0fdbd9b1d 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.6.4.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.6.4.eb @@ -19,7 +19,7 @@ configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading # needed for --with-openib -osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +osdependencies = [('libibverbs-dev', 'libibverbs-devel', 'rdma-core-devel')] libs = ["mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "open-pal", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2.eb index 168f6f9d23..46d2a4a233 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2.eb @@ -19,7 +19,7 @@ configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading # needed for --with-openib -osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +osdependencies = [('libibverbs-dev', 'libibverbs-devel', 'rdma-core-devel')] libs = ["mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "open-pal", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.2.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.2.eb index 933369e32b..1af8bec01f 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.2.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.2.eb @@ -22,7 +22,7 @@ configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading # needed for --with-openib -osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +osdependencies = [('libibverbs-dev', 'libibverbs-devel', 'rdma-core-devel')] libs = ["mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "open-pal", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1.eb index 231057cda1..9c74aa620d 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1.eb @@ -20,7 +20,7 @@ configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading # needed for --with-openib -osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +osdependencies = [('libibverbs-dev', 'libibverbs-devel', 'rdma-core-devel')] libs = ["mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "open-pal", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2.eb index 8b4682c1db..8985983b3f 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2.eb @@ -23,7 +23,7 @@ configopts += '--with-hwloc=$EBROOTHWLOC ' dependencies = [('hwloc', '1.8.1')] # needed for --with-openib -osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +osdependencies = [('libibverbs-dev', 'libibverbs-devel', 'rdma-core-devel')] libs = ["mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "open-pal", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.3.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.3.eb index 90ce3018de..65455ee083 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.3.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.3.eb @@ -23,7 +23,7 @@ configopts += '--with-hwloc=$EBROOTHWLOC ' dependencies = [('hwloc', '1.8.1')] # needed for --with-openib -osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +osdependencies = [('libibverbs-dev', 'libibverbs-devel', 'rdma-core-devel')] libs = ["mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "open-pal", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.2.144.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.2.144.eb index 069c5ad3b9..678e7e1afb 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.2.144.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.2.144.eb @@ -18,7 +18,7 @@ configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support dependencies = [('hwloc', '1.8.1')] # needed for --with-openib -osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +osdependencies = [('libibverbs-dev', 'libibverbs-devel', 'rdma-core-devel')] libs = ["mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "open-pal", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211.eb index 7ee3a0b737..dc145861ff 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211.eb @@ -18,7 +18,7 @@ configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support dependencies = [('hwloc', '1.9')] # needed for --with-openib -osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +osdependencies = [('libibverbs-dev', 'libibverbs-devel', 'rdma-core-devel')] libs = ["mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "open-pal", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.7.3-GCC-4.8.2.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.7.3-GCC-4.8.2.eb index 6687a0ffa0..81d45b5e89 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.7.3-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.7.3-GCC-4.8.2.eb @@ -21,7 +21,7 @@ configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading # needed for --with-verbs -osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +osdependencies = [('libibverbs-dev', 'libibverbs-devel', 'rdma-core-devel')] libs = ["mpi_cxx", "mpi_mpifh", "mpi", "ompitrace", "open-pal", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.1-GCC-4.8.3.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.1-GCC-4.8.3.eb index eeb7c2fe82..5503a3e1f6 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.1-GCC-4.8.3.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.1-GCC-4.8.3.eb @@ -19,7 +19,7 @@ configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading # needed for --with-verbs -osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +osdependencies = [('libibverbs-dev', 'libibverbs-devel', 'rdma-core-devel')] libs = ["mpi_cxx", "mpi_mpifh", "mpi", "ompitrace", "open-pal", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-GCC-4.9.2.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-GCC-4.9.2.eb index a47fa4f0f1..8e54eb0f67 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-GCC-4.9.2.eb @@ -19,7 +19,7 @@ configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading # needed for --with-verbs -osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +osdependencies = [('libibverbs-dev', 'libibverbs-devel', 'rdma-core-devel')] libs = ["mpi_cxx", "mpi_mpifh", "mpi", "ompitrace", "open-pal", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-iccifort-2013_sp1.4.211.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-iccifort-2013_sp1.4.211.eb index 19949c397c..f0ceedd49e 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-iccifort-2013_sp1.4.211.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-iccifort-2013_sp1.4.211.eb @@ -19,7 +19,7 @@ configopts += '--disable-dlopen ' # statically link component, don't do dynamic dependencies = [('hwloc', '1.9')] # needed for --with-verbs -osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +osdependencies = [('libibverbs-dev', 'libibverbs-devel', 'rdma-core-devel')] libs = ["mpi_cxx", "mpi_mpifh", "mpi", "ompitrace", "open-pal", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GCC-4.8.4.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GCC-4.8.4.eb index 2eb439ac34..e841ac6255 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GCC-4.8.4.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GCC-4.8.4.eb @@ -19,7 +19,7 @@ configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading # needed for --with-verbs -osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +osdependencies = [('libibverbs-dev', 'libibverbs-devel', 'rdma-core-devel')] libs = ["mpi_cxx", "mpi_mpifh", "mpi", "ompitrace", "open-pal", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GCC-4.9.2.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GCC-4.9.2.eb index e009a63259..825a80feb7 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GCC-4.9.2.eb @@ -19,7 +19,7 @@ configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading # needed for --with-verbs -osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +osdependencies = [('libibverbs-dev', 'libibverbs-devel', 'rdma-core-devel')] libs = ["mpi_cxx", "mpi_mpifh", "mpi", "ompitrace", "open-pal", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-iccifort-2015.1.133-GCC-4.9.2.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-iccifort-2015.1.133-GCC-4.9.2.eb index d39ca71b30..6731564586 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-iccifort-2015.1.133-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-iccifort-2015.1.133-GCC-4.9.2.eb @@ -20,7 +20,7 @@ configopts += '--disable-dlopen ' # statically link component, don't do dynamic dependencies = [('hwloc', '1.10.0')] # needed for --with-verbs -osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +osdependencies = [('libibverbs-dev', 'libibverbs-devel', 'rdma-core-devel')] libs = ["mpi_cxx", "mpi_mpifh", "mpi", "ompitrace", "open-pal", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-iccifort-2015.2.164-GCC-4.9.2.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-iccifort-2015.2.164-GCC-4.9.2.eb index 86eed73b49..d46d33479e 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-iccifort-2015.2.164-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-iccifort-2015.2.164-GCC-4.9.2.eb @@ -20,7 +20,7 @@ configopts += '--disable-dlopen ' # statically link component, don't do dynamic dependencies = [('hwloc', '1.10.0')] # needed for --with-verbs -osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +osdependencies = [('libibverbs-dev', 'libibverbs-devel', 'rdma-core-devel')] libs = ["mpi_cxx", "mpi_mpifh", "mpi", "ompitrace", "open-pal", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.5-GNU-4.9.2-2.25.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.5-GNU-4.9.2-2.25.eb index 095d22d991..089abe6b34 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.5-GNU-4.9.2-2.25.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.5-GNU-4.9.2-2.25.eb @@ -19,7 +19,7 @@ configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading # needed for --with-verbs -osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +osdependencies = [('libibverbs-dev', 'libibverbs-devel', 'rdma-core-devel')] libs = ["mpi_cxx", "mpi_mpifh", "mpi", "ompitrace", "open-pal", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.6-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.6-GNU-4.9.3-2.25.eb index 3e69e3901f..b77284839a 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.6-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.6-GNU-4.9.3-2.25.eb @@ -19,7 +19,7 @@ configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading # needed for --with-verbs -osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +osdependencies = [('libibverbs-dev', 'libibverbs-devel', 'rdma-core-devel')] libs = ["mpi_cxx", "mpi_mpifh", "mpi", "ompitrace", "open-pal", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.8-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.8-GNU-4.9.3-2.25.eb index 5206425bdf..d15e963eea 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.8-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.8-GNU-4.9.3-2.25.eb @@ -19,7 +19,7 @@ configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading # needed for --with-verbs -osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +osdependencies = [('libibverbs-dev', 'libibverbs-devel', 'rdma-core-devel')] libs = ["mpi_cxx", "mpi_mpifh", "mpi", "ompitrace", "open-pal", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.8-iccifort-2015.3.187-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.8-iccifort-2015.3.187-GNU-4.9.3-2.25.eb index 34da0e5297..a2ec79195b 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.8-iccifort-2015.3.187-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.8-iccifort-2015.3.187-GNU-4.9.3-2.25.eb @@ -20,7 +20,7 @@ configopts += '--disable-dlopen ' # statically link component, don't do dynamic dependencies = [('hwloc', '1.11.1')] # needed for --with-verbs -osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +osdependencies = [('libibverbs-dev', 'libibverbs-devel', 'rdma-core-devel')] libs = ["mpi_cxx", "mpi_mpifh", "mpi", "ompitrace", "open-pal", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.0-GCC-5.2.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.0-GCC-5.2.0.eb index ced6423707..2d2f70b198 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.0-GCC-5.2.0.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.0-GCC-5.2.0.eb @@ -20,7 +20,7 @@ configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading # needed for --with-verbs -osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +osdependencies = [('libibverbs-dev', 'libibverbs-devel', 'rdma-core-devel')] # VampirTrace is no longer used : https://www.open-mpi.org/community/lists/announce/2016/07/0085.php libs = ["mpi_mpifh", "mpi", "ompitrace", "open-pal", "open-rte"] diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.1-GCC-6.2.0-2.27.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.1-GCC-6.2.0-2.27.eb index dccf9a16b7..e14a09912c 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.1-GCC-6.2.0-2.27.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.1-GCC-6.2.0-2.27.eb @@ -20,7 +20,7 @@ configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading # needed for --with-verbs -osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +osdependencies = [('libibverbs-dev', 'libibverbs-devel', 'rdma-core-devel')] libs = ["mpi_mpifh", "mpi", "ompitrace", "open-pal", "open-rte"] sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.1-gcccuda-2016.10.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.1-gcccuda-2016.10.eb index bc5a7af11f..472ec78a20 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.1-gcccuda-2016.10.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.1-gcccuda-2016.10.eb @@ -20,7 +20,7 @@ configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support configopts += '--with-cuda=$CUDA_HOME ' # CUDA-aware build; N.B. --disable-dlopen is incompatible # needed for --with-verbs -osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +osdependencies = [('libibverbs-dev', 'libibverbs-devel', 'rdma-core-devel')] libs = ["mpi_mpifh", "mpi", "ompitrace", "open-pal", "open-rte"] sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.1-iccifort-2017.1.132-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.1-iccifort-2017.1.132-GCC-5.4.0-2.26.eb index 79bff619c0..c1cae1b060 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.1-iccifort-2017.1.132-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.1-iccifort-2017.1.132-GCC-5.4.0-2.26.eb @@ -20,7 +20,7 @@ configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading # needed for --with-verbs -osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +osdependencies = [('libibverbs-dev', 'libibverbs-devel', 'rdma-core-devel')] libs = ["mpi_mpifh", "mpi", "ompitrace", "open-pal", "open-rte"] sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.2-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.2-GCC-6.3.0-2.27.eb index 3e05777f37..1dad8c8a27 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.2-GCC-6.3.0-2.27.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.2-GCC-6.3.0-2.27.eb @@ -21,7 +21,7 @@ configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading # needed for --with-verbs -osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +osdependencies = [('libibverbs-dev', 'libibverbs-devel', 'rdma-core-devel')] libs = ["mpi_mpifh", "mpi", "ompitrace", "open-pal", "open-rte"] sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.2-gcccuda-2017.01.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.2-gcccuda-2017.01.eb index f4abe2cc5c..b815f736b5 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.2-gcccuda-2017.01.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.2-gcccuda-2017.01.eb @@ -21,7 +21,7 @@ configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support configopts += '--with-cuda=$CUDA_HOME ' # CUDA-aware build; N.B. --disable-dlopen is incompatible # needed for --with-verbs -osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +osdependencies = [('libibverbs-dev', 'libibverbs-devel', 'rdma-core-devel')] libs = ["mpi_mpifh", "mpi", "ompitrace", "open-pal", "open-rte"] sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.2-iccifort-2017.1.132-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.2-iccifort-2017.1.132-GCC-6.3.0-2.27.eb index b2aa187ae0..a843f506c3 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.2-iccifort-2017.1.132-GCC-6.3.0-2.27.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.2-iccifort-2017.1.132-GCC-6.3.0-2.27.eb @@ -20,7 +20,7 @@ configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading # needed for --with-verbs -osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +osdependencies = [('libibverbs-dev', 'libibverbs-devel', 'rdma-core-devel')] libs = ["mpi_mpifh", "mpi", "ompitrace", "open-pal", "open-rte"] sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.0-GCC-6.3.0-2.28.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.0-GCC-6.3.0-2.28.eb index f0864ac518..765dbf2d89 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.0-GCC-6.3.0-2.28.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.0-GCC-6.3.0-2.28.eb @@ -21,7 +21,7 @@ configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading # needed for --with-verbs -osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +osdependencies = [('libibverbs-dev', 'libibverbs-devel', 'rdma-core-devel')] libs = ["mpi_mpifh", "mpi", "ompitrace", "open-pal", "open-rte"] sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.1-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.1-GCC-6.4.0-2.28.eb index c10c8f486d..addd1e04b1 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.1-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.1-GCC-6.4.0-2.28.eb @@ -23,7 +23,7 @@ configopts += '--disable-dlopen ' # statically link component, don't do dynamic # configopts += '--with-slurm --with-pmi=/usr/include/slurm --with-pmi-libdir=/usr' # needed for --with-verbs -osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +osdependencies = [('libibverbs-dev', 'libibverbs-devel', 'rdma-core-devel')] libs = ["mpi_mpifh", "mpi", "ompitrace", "open-pal", "open-rte"] sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.1-iccifort-2017.4.196-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.1-iccifort-2017.4.196-GCC-6.4.0-2.28.eb index 92aa7215fa..06480a4783 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.1-iccifort-2017.4.196-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.1-iccifort-2017.4.196-GCC-6.4.0-2.28.eb @@ -22,7 +22,7 @@ configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading # needed for --with-verbs -osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +osdependencies = [('libibverbs-dev', 'libibverbs-devel', 'rdma-core-devel')] libs = ["mpi_mpifh", "mpi", "ompitrace", "open-pal", "open-rte"] sanity_check_paths = { -- GitLab From 2eea6449998755fda289bec417af663f4c12707a Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Sun, 17 Sep 2017 21:03:32 +0200 Subject: [PATCH 1536/1603] Style corrected --- .../b/BUSCO/BUSCO-1.22-intel-2017a-Python-2.7.13.eb | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/b/BUSCO/BUSCO-1.22-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/b/BUSCO/BUSCO-1.22-intel-2017a-Python-2.7.13.eb index dc39f4fd13..b3b4e14eaf 100644 --- a/easybuild/easyconfigs/b/BUSCO/BUSCO-1.22-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/b/BUSCO/BUSCO-1.22-intel-2017a-Python-2.7.13.eb @@ -9,7 +9,6 @@ description = "BUSCO: assessing genome assembly and annotation completeness with toolchain = {'name': 'intel', 'version': '2017a'} - source_urls = ['http://busco.ezlab.org/v1/files/'] sources = ['%(name)s_v%(version)s.tar.gz'] @@ -26,10 +25,10 @@ dependencies = [ postinstallcmds = ['chmod +x %(installdir)s/*.py'] sanity_check_paths = { - 'files': ['BUSCO_v1.22.py'], + 'files': ['BUSCO_v%(version)s.py'], 'dirs': ['sample_data'], } -modextrapaths = {'PATH': '.'} +modextrapaths = {'PATH': ''} moduleclass = 'bio' -- GitLab From 39570f1f1ff749fd45a485de937641f75b43ba17 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Sun, 17 Sep 2017 21:08:27 +0200 Subject: [PATCH 1537/1603] Checksum + Java bump --- .../e/EMBOSS/EMBOSS-6.6.0-intel-2017a-X11-20170314.eb | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-intel-2017a-X11-20170314.eb b/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-intel-2017a-X11-20170314.eb index ce07a55a67..7eac56a2c1 100644 --- a/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-intel-2017a-X11-20170314.eb +++ b/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-intel-2017a-X11-20170314.eb @@ -24,16 +24,18 @@ source_urls = [ 'ftp://emboss.open-bio.org/pub/EMBOSS/', 'ftp://emboss.open-bio.org/pub/EMBOSS/old/%(version_major_minor)s.0', ] - sources = [SOURCE_TAR_GZ] - patches = ['EMBOSS_disable-embossupdate.patch'] +checksums = [ + '7184a763d39ad96bb598bfd531628a34aa53e474db9e7cac4416c2a40ab10c6e', # EMBOSS-6.6.0.tar.gz + '3e5e0fbbcb78d62dbfb4586cc9c69d7e602c661f12414d193b2be46024377fd6', # EMBOSS_disable-embossupdate.patch +] dependencies = [ ('X11', x11ver), ('libgd', '2.2.4'), ('libharu', '2.3.0'), - ('Java', '1.8.0_121', '', True), + ('Java', '1.8.0_144', '', True), ] configopts = " --with-hpdf=$EBROOTLIBHARU " -- GitLab From bb9232e07fb72fe3864de97e2d0b07c996d7b2dc Mon Sep 17 00:00:00 2001 From: John Donners Date: Mon, 18 Sep 2017 08:28:00 +0200 Subject: [PATCH 1538/1603] Updated mostly as suggested. --- .../NEST-2.12.0-foss-2015b-Python-2.7.9.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/n/NEST/NEST-2.12.0-foss-2015b-Python-2.7.9.eb diff --git a/easybuild/easyconfigs/n/NEST/NEST-2.12.0-foss-2015b-Python-2.7.9.eb b/easybuild/easyconfigs/n/NEST/NEST-2.12.0-foss-2015b-Python-2.7.9.eb new file mode 100644 index 0000000000..f549b80fd7 --- /dev/null +++ b/easybuild/easyconfigs/n/NEST/NEST-2.12.0-foss-2015b-Python-2.7.9.eb @@ -0,0 +1,40 @@ +easyblock = 'CMakeMake' + +name = 'NEST' +version = '2.12.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.nest-simulator.org/' +description = """NEST is a simulator for spiking neural network models + that focuses on the dynamics, size and structure of neural systems rather + than on the exact morphology of individual neurons.""" + +toolchain = {'name': 'foss', 'version': '2015b'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/nest/nest-simulator/releases/download/v%(version)s/'] +sources = ['nest-%(version)s.tar.gz'] +checksums = ['bac578f38bb0621618ee9d5f2f1febfee60cddc000ff32e51a5f5470bb3df40d'] + +dependencies = [ + ('Python', '2.7.9'), + ('libreadline', '6.3'), + ('GSL', '2.1'), + ('libtool', '2.4.6'), + ('ncurses', '5.9'), +] + + +configopts = '-DREADLINE_ROOT_DIR=$EBROOTLIBREADLINE -Dwith-mpi=OFF' + +builddependencies = [ + ('CMake', '3.4.1'), + ('Doxygen', '1.8.10'), + ('pkg-config','0.27.1'), +] + +modextrapaths = { + 'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'math' -- GitLab From cd102d72ec7303c57285691ffe4cd63d55c69d05 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 18 Sep 2017 09:08:54 +0200 Subject: [PATCH 1539/1603] consistently use empty toolchain version in icc easyconfigs to ensure that GCC(core) dep is loaded during installation --- easybuild/easyconfigs/i/icc/icc-11.1.073-32bit.eb | 2 +- easybuild/easyconfigs/i/icc/icc-11.1.073.eb | 2 +- easybuild/easyconfigs/i/icc/icc-11.1.075.eb | 2 +- easybuild/easyconfigs/i/icc/icc-2011.10.319.eb | 2 +- easybuild/easyconfigs/i/icc/icc-2011.13.367.eb | 2 +- easybuild/easyconfigs/i/icc/icc-2011.3.174.eb | 2 +- easybuild/easyconfigs/i/icc/icc-2011.6.233.eb | 2 +- easybuild/easyconfigs/i/icc/icc-2013.1.117.eb | 2 +- easybuild/easyconfigs/i/icc/icc-2013.2.146.eb | 2 +- easybuild/easyconfigs/i/icc/icc-2013.3.163.eb | 2 +- easybuild/easyconfigs/i/icc/icc-2013.4.183.eb | 2 +- easybuild/easyconfigs/i/icc/icc-2013.5.192.eb | 2 +- easybuild/easyconfigs/i/icc/icc-2013_sp1.0.080.eb | 2 +- easybuild/easyconfigs/i/icc/icc-2013_sp1.1.106.eb | 2 +- easybuild/easyconfigs/i/icc/icc-2013_sp1.2.144.eb | 2 +- easybuild/easyconfigs/i/icc/icc-2013_sp1.3.174.eb | 2 +- easybuild/easyconfigs/i/icc/icc-2013_sp1.4.211.eb | 2 +- easybuild/easyconfigs/i/icc/icc-2015.0.090.eb | 2 +- easybuild/easyconfigs/i/icc/icc-2015.1.133.eb | 2 +- easybuild/easyconfigs/i/icc/icc-2015.3.187.eb | 2 +- easybuild/easyconfigs/i/icc/icc-2016.0.109.eb | 2 +- easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-4.9.3-2.25.eb | 2 +- easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-5.3.0-2.26.eb | 2 +- easybuild/easyconfigs/i/icc/icc-2016.3.210-GCC-4.9.3-2.25.eb | 2 +- easybuild/easyconfigs/i/icc/icc-2016.3.210-GCC-5.3.0-2.26.eb | 2 +- easybuild/easyconfigs/i/icc/icc-2016.3.210-GCC-5.4.0-2.26.eb | 2 +- easybuild/easyconfigs/i/icc/icc-2017.0.098-GCC-5.4.0-2.26.eb | 2 +- easybuild/easyconfigs/i/icc/icc-2017.1.132-GCC-5.4.0-2.26.eb | 2 +- easybuild/easyconfigs/i/icc/icc-2017.1.132-GCC-6.3.0-2.27.eb | 2 +- easybuild/easyconfigs/i/icc/icc-2017.2.174-GCC-6.3.0-2.27.eb | 2 +- easybuild/easyconfigs/i/icc/icc-2017.4.196-GCC-6.4.0-2.28.eb | 2 +- 31 files changed, 31 insertions(+), 31 deletions(-) diff --git a/easybuild/easyconfigs/i/icc/icc-11.1.073-32bit.eb b/easybuild/easyconfigs/i/icc/icc-11.1.073-32bit.eb index 6db65c8a2e..f7e00fc1b4 100644 --- a/easybuild/easyconfigs/i/icc/icc-11.1.073-32bit.eb +++ b/easybuild/easyconfigs/i/icc/icc-11.1.073-32bit.eb @@ -5,7 +5,7 @@ versionsuffix = '-32bit' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "C and C++ compiler from Intel" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['l_cproc_p_%s.tgz' % version] diff --git a/easybuild/easyconfigs/i/icc/icc-11.1.073.eb b/easybuild/easyconfigs/i/icc/icc-11.1.073.eb index 426c8d4726..46c63ad80a 100644 --- a/easybuild/easyconfigs/i/icc/icc-11.1.073.eb +++ b/easybuild/easyconfigs/i/icc/icc-11.1.073.eb @@ -4,7 +4,7 @@ version = '11.1.073' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "C and C++ compiler from Intel" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['l_cproc_p_%s.tgz' % version] diff --git a/easybuild/easyconfigs/i/icc/icc-11.1.075.eb b/easybuild/easyconfigs/i/icc/icc-11.1.075.eb index 367d02cc42..1de1f4271c 100644 --- a/easybuild/easyconfigs/i/icc/icc-11.1.075.eb +++ b/easybuild/easyconfigs/i/icc/icc-11.1.075.eb @@ -4,7 +4,7 @@ version = '11.1.075' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "C and C++ compiler from Intel" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['l_cproc_p_%s_intel64.tgz' % version] diff --git a/easybuild/easyconfigs/i/icc/icc-2011.10.319.eb b/easybuild/easyconfigs/i/icc/icc-2011.10.319.eb index df976c997d..6d6f6e5414 100644 --- a/easybuild/easyconfigs/i/icc/icc-2011.10.319.eb +++ b/easybuild/easyconfigs/i/icc/icc-2011.10.319.eb @@ -4,7 +4,7 @@ version = '2011.10.319' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "C and C++ compiler from Intel" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['l_ccompxe_intel64_%s.tgz' % version] diff --git a/easybuild/easyconfigs/i/icc/icc-2011.13.367.eb b/easybuild/easyconfigs/i/icc/icc-2011.13.367.eb index 0e9f729010..c7bc79ecf5 100644 --- a/easybuild/easyconfigs/i/icc/icc-2011.13.367.eb +++ b/easybuild/easyconfigs/i/icc/icc-2011.13.367.eb @@ -4,7 +4,7 @@ version = '2011.13.367' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "C and C++ compiler from Intel" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['l_ccompxe_%s.tgz' % version] diff --git a/easybuild/easyconfigs/i/icc/icc-2011.3.174.eb b/easybuild/easyconfigs/i/icc/icc-2011.3.174.eb index 69a166ec56..6079fd63e8 100644 --- a/easybuild/easyconfigs/i/icc/icc-2011.3.174.eb +++ b/easybuild/easyconfigs/i/icc/icc-2011.3.174.eb @@ -4,7 +4,7 @@ version = '2011.3.174' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "C and C++ compiler from Intel" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['l_ccompxe_intel64_%s.tgz' % version] diff --git a/easybuild/easyconfigs/i/icc/icc-2011.6.233.eb b/easybuild/easyconfigs/i/icc/icc-2011.6.233.eb index 5c240e5c11..d2d824632a 100644 --- a/easybuild/easyconfigs/i/icc/icc-2011.6.233.eb +++ b/easybuild/easyconfigs/i/icc/icc-2011.6.233.eb @@ -4,7 +4,7 @@ version = '2011.6.233' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "C and C++ compiler from Intel" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['l_ccompxe_intel64_%s.tgz' % version] diff --git a/easybuild/easyconfigs/i/icc/icc-2013.1.117.eb b/easybuild/easyconfigs/i/icc/icc-2013.1.117.eb index f259138a7e..f5c33e155b 100644 --- a/easybuild/easyconfigs/i/icc/icc-2013.1.117.eb +++ b/easybuild/easyconfigs/i/icc/icc-2013.1.117.eb @@ -4,7 +4,7 @@ version = '2013.1.117' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "C and C++ compiler from Intel" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['l_ccompxe_%s.tgz' % version] diff --git a/easybuild/easyconfigs/i/icc/icc-2013.2.146.eb b/easybuild/easyconfigs/i/icc/icc-2013.2.146.eb index c135115579..61bd49e43c 100644 --- a/easybuild/easyconfigs/i/icc/icc-2013.2.146.eb +++ b/easybuild/easyconfigs/i/icc/icc-2013.2.146.eb @@ -4,7 +4,7 @@ version = '2013.2.146' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "C and C++ compiler from Intel" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['l_ccompxe_%s.tgz' % version] diff --git a/easybuild/easyconfigs/i/icc/icc-2013.3.163.eb b/easybuild/easyconfigs/i/icc/icc-2013.3.163.eb index b9b8d9d6de..470e9a2fb4 100644 --- a/easybuild/easyconfigs/i/icc/icc-2013.3.163.eb +++ b/easybuild/easyconfigs/i/icc/icc-2013.3.163.eb @@ -4,7 +4,7 @@ version = '2013.3.163' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "C and C++ compiler from Intel" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['l_ccompxe_%s.tgz' % version] diff --git a/easybuild/easyconfigs/i/icc/icc-2013.4.183.eb b/easybuild/easyconfigs/i/icc/icc-2013.4.183.eb index db58351c1b..09f67d57b8 100644 --- a/easybuild/easyconfigs/i/icc/icc-2013.4.183.eb +++ b/easybuild/easyconfigs/i/icc/icc-2013.4.183.eb @@ -4,7 +4,7 @@ version = '2013.4.183' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "C and C++ compiler from Intel" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['l_ccompxe_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/icc/icc-2013.5.192.eb b/easybuild/easyconfigs/i/icc/icc-2013.5.192.eb index e42dd9678e..faabee9053 100644 --- a/easybuild/easyconfigs/i/icc/icc-2013.5.192.eb +++ b/easybuild/easyconfigs/i/icc/icc-2013.5.192.eb @@ -4,7 +4,7 @@ version = '2013.5.192' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "C and C++ compiler from Intel" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['l_ccompxe_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/icc/icc-2013_sp1.0.080.eb b/easybuild/easyconfigs/i/icc/icc-2013_sp1.0.080.eb index ace7d02238..9a52f9485c 100644 --- a/easybuild/easyconfigs/i/icc/icc-2013_sp1.0.080.eb +++ b/easybuild/easyconfigs/i/icc/icc-2013_sp1.0.080.eb @@ -4,7 +4,7 @@ version = '2013_sp1.0.080' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "C and C++ compiler from Intel" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['l_ccompxe_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/icc/icc-2013_sp1.1.106.eb b/easybuild/easyconfigs/i/icc/icc-2013_sp1.1.106.eb index b62448cecd..8632a6cdd6 100644 --- a/easybuild/easyconfigs/i/icc/icc-2013_sp1.1.106.eb +++ b/easybuild/easyconfigs/i/icc/icc-2013_sp1.1.106.eb @@ -4,7 +4,7 @@ version = '2013_sp1.1.106' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "C and C++ compiler from Intel" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['l_ccompxe_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/icc/icc-2013_sp1.2.144.eb b/easybuild/easyconfigs/i/icc/icc-2013_sp1.2.144.eb index 939c072363..e4a65fd62a 100644 --- a/easybuild/easyconfigs/i/icc/icc-2013_sp1.2.144.eb +++ b/easybuild/easyconfigs/i/icc/icc-2013_sp1.2.144.eb @@ -4,7 +4,7 @@ version = '2013_sp1.2.144' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "C and C++ compiler from Intel" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['l_ccompxe_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/icc/icc-2013_sp1.3.174.eb b/easybuild/easyconfigs/i/icc/icc-2013_sp1.3.174.eb index 3ebed03a03..a30b07ef34 100644 --- a/easybuild/easyconfigs/i/icc/icc-2013_sp1.3.174.eb +++ b/easybuild/easyconfigs/i/icc/icc-2013_sp1.3.174.eb @@ -4,7 +4,7 @@ version = '2013_sp1.3.174' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "C and C++ compiler from Intel" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['l_ccompxe_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/icc/icc-2013_sp1.4.211.eb b/easybuild/easyconfigs/i/icc/icc-2013_sp1.4.211.eb index 26892de20b..c8fe08d4d1 100644 --- a/easybuild/easyconfigs/i/icc/icc-2013_sp1.4.211.eb +++ b/easybuild/easyconfigs/i/icc/icc-2013_sp1.4.211.eb @@ -5,7 +5,7 @@ version = '2013_sp1.4.211' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "C and C++ compiler from Intel" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['l_ccompxe_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/icc/icc-2015.0.090.eb b/easybuild/easyconfigs/i/icc/icc-2015.0.090.eb index 352973960c..0844c56bf1 100644 --- a/easybuild/easyconfigs/i/icc/icc-2015.0.090.eb +++ b/easybuild/easyconfigs/i/icc/icc-2015.0.090.eb @@ -4,7 +4,7 @@ version = '2015.0.090' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "C and C++ compiler from Intel" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['l_ccompxe_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/icc/icc-2015.1.133.eb b/easybuild/easyconfigs/i/icc/icc-2015.1.133.eb index 326875c307..08fdab1423 100644 --- a/easybuild/easyconfigs/i/icc/icc-2015.1.133.eb +++ b/easybuild/easyconfigs/i/icc/icc-2015.1.133.eb @@ -4,7 +4,7 @@ version = '2015.1.133' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "C and C++ compiler from Intel" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['l_ccompxe_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/icc/icc-2015.3.187.eb b/easybuild/easyconfigs/i/icc/icc-2015.3.187.eb index 833da3c0c7..f435774709 100644 --- a/easybuild/easyconfigs/i/icc/icc-2015.3.187.eb +++ b/easybuild/easyconfigs/i/icc/icc-2015.3.187.eb @@ -4,7 +4,7 @@ version = '2015.3.187' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "C and C++ compiler from Intel" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['l_ccompxe_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/icc/icc-2016.0.109.eb b/easybuild/easyconfigs/i/icc/icc-2016.0.109.eb index 5ca90df672..ac3b139eff 100644 --- a/easybuild/easyconfigs/i/icc/icc-2016.0.109.eb +++ b/easybuild/easyconfigs/i/icc/icc-2016.0.109.eb @@ -6,7 +6,7 @@ version = '2016.0.109' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "C and C++ compiler from Intel" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_cpp.tgz'] diff --git a/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-4.9.3-2.25.eb index c51aeed69f..ddae823dc3 100644 --- a/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-4.9.3-2.25.eb @@ -6,7 +6,7 @@ version = '2016.2.181' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "C and C++ compiler from Intel" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_cpp_update%(version_minor)s.tgz'] diff --git a/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-5.3.0-2.26.eb index 9efd4f304a..d03f2d3cb5 100644 --- a/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-5.3.0-2.26.eb +++ b/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-5.3.0-2.26.eb @@ -6,7 +6,7 @@ version = '2016.2.181' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "C and C++ compiler from Intel" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_cpp_update%(version_minor)s.tgz'] diff --git a/easybuild/easyconfigs/i/icc/icc-2016.3.210-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/icc/icc-2016.3.210-GCC-4.9.3-2.25.eb index c834d93024..bbe90dab4f 100644 --- a/easybuild/easyconfigs/i/icc/icc-2016.3.210-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/icc/icc-2016.3.210-GCC-4.9.3-2.25.eb @@ -6,7 +6,7 @@ version = '2016.3.210' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "C and C++ compiler from Intel" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_cpp_update%(version_minor)s.tgz'] diff --git a/easybuild/easyconfigs/i/icc/icc-2016.3.210-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/icc/icc-2016.3.210-GCC-5.3.0-2.26.eb index 100faf7343..19f9a279fc 100644 --- a/easybuild/easyconfigs/i/icc/icc-2016.3.210-GCC-5.3.0-2.26.eb +++ b/easybuild/easyconfigs/i/icc/icc-2016.3.210-GCC-5.3.0-2.26.eb @@ -6,7 +6,7 @@ version = '2016.3.210' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "C and C++ compiler from Intel" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_cpp_update%(version_minor)s.tgz'] diff --git a/easybuild/easyconfigs/i/icc/icc-2016.3.210-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/icc/icc-2016.3.210-GCC-5.4.0-2.26.eb index 0e2464f373..9e624b5c3f 100644 --- a/easybuild/easyconfigs/i/icc/icc-2016.3.210-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/icc/icc-2016.3.210-GCC-5.4.0-2.26.eb @@ -6,7 +6,7 @@ version = '2016.3.210' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "C and C++ compiler from Intel" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_cpp_update%(version_minor)s.tgz'] diff --git a/easybuild/easyconfigs/i/icc/icc-2017.0.098-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/icc/icc-2017.0.098-GCC-5.4.0-2.26.eb index 41ed689a72..e554131ea4 100644 --- a/easybuild/easyconfigs/i/icc/icc-2017.0.098-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/icc/icc-2017.0.098-GCC-5.4.0-2.26.eb @@ -6,7 +6,7 @@ version = '2017.0.098' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "C and C++ compiler from Intel" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_cpp.tgz'] diff --git a/easybuild/easyconfigs/i/icc/icc-2017.1.132-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/icc/icc-2017.1.132-GCC-5.4.0-2.26.eb index 77118ae45d..9f1524cfe8 100644 --- a/easybuild/easyconfigs/i/icc/icc-2017.1.132-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/icc/icc-2017.1.132-GCC-5.4.0-2.26.eb @@ -6,7 +6,7 @@ version = '2017.1.132' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "C and C++ compiler from Intel" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition_for_cpp.tgz'] diff --git a/easybuild/easyconfigs/i/icc/icc-2017.1.132-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/i/icc/icc-2017.1.132-GCC-6.3.0-2.27.eb index 362d477441..1b9a91bff7 100644 --- a/easybuild/easyconfigs/i/icc/icc-2017.1.132-GCC-6.3.0-2.27.eb +++ b/easybuild/easyconfigs/i/icc/icc-2017.1.132-GCC-6.3.0-2.27.eb @@ -6,7 +6,7 @@ version = '2017.1.132' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "C and C++ compiler from Intel" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition_for_cpp.tgz'] diff --git a/easybuild/easyconfigs/i/icc/icc-2017.2.174-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/i/icc/icc-2017.2.174-GCC-6.3.0-2.27.eb index 55411b8971..9f323aeae8 100644 --- a/easybuild/easyconfigs/i/icc/icc-2017.2.174-GCC-6.3.0-2.27.eb +++ b/easybuild/easyconfigs/i/icc/icc-2017.2.174-GCC-6.3.0-2.27.eb @@ -6,7 +6,7 @@ version = '2017.2.174' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "C and C++ compiler from Intel" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition_for_cpp.tgz'] diff --git a/easybuild/easyconfigs/i/icc/icc-2017.4.196-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/i/icc/icc-2017.4.196-GCC-6.4.0-2.28.eb index 718eae9dd7..a0716886c4 100644 --- a/easybuild/easyconfigs/i/icc/icc-2017.4.196-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/i/icc/icc-2017.4.196-GCC-6.4.0-2.28.eb @@ -6,7 +6,7 @@ version = '2017.4.196' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "Intel C and C++ compilers" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition_for_cpp.tgz'] -- GitLab From 1915d0e5ec1cb0a10833fdca657a72927e888fca Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 18 Sep 2017 09:12:14 +0200 Subject: [PATCH 1540/1603] consistently use empty toolchain version in ifort easyconfigs to ensure that GCC(core) dep is loaded during installation --- easybuild/easyconfigs/i/ifort/ifort-11.1.073-32bit.eb | 2 +- easybuild/easyconfigs/i/ifort/ifort-11.1.073.eb | 2 +- easybuild/easyconfigs/i/ifort/ifort-11.1.075.eb | 2 +- easybuild/easyconfigs/i/ifort/ifort-2011.10.319.eb | 2 +- easybuild/easyconfigs/i/ifort/ifort-2011.13.367.eb | 2 +- easybuild/easyconfigs/i/ifort/ifort-2011.3.174.eb | 2 +- easybuild/easyconfigs/i/ifort/ifort-2011.6.233.eb | 2 +- easybuild/easyconfigs/i/ifort/ifort-2013.1.117.eb | 2 +- easybuild/easyconfigs/i/ifort/ifort-2013.2.146.eb | 2 +- easybuild/easyconfigs/i/ifort/ifort-2013.3.163.eb | 2 +- easybuild/easyconfigs/i/ifort/ifort-2013.4.183.eb | 2 +- easybuild/easyconfigs/i/ifort/ifort-2013.5.192.eb | 2 +- easybuild/easyconfigs/i/ifort/ifort-2013_sp1.0.080.eb | 2 +- easybuild/easyconfigs/i/ifort/ifort-2013_sp1.1.106.eb | 2 +- easybuild/easyconfigs/i/ifort/ifort-2013_sp1.2.144.eb | 2 +- easybuild/easyconfigs/i/ifort/ifort-2013_sp1.3.174.eb | 2 +- easybuild/easyconfigs/i/ifort/ifort-2013_sp1.4.211.eb | 2 +- easybuild/easyconfigs/i/ifort/ifort-2015.0.090.eb | 2 +- easybuild/easyconfigs/i/ifort/ifort-2015.1.133.eb | 2 +- easybuild/easyconfigs/i/ifort/ifort-2015.3.187.eb | 2 +- easybuild/easyconfigs/i/ifort/ifort-2016.0.109.eb | 2 +- .../easyconfigs/i/ifort/ifort-2016.2.181-GCC-4.9.3-2.25.eb | 2 +- .../easyconfigs/i/ifort/ifort-2016.2.181-GCC-5.3.0-2.26.eb | 2 +- .../easyconfigs/i/ifort/ifort-2016.3.210-GCC-4.9.3-2.25.eb | 2 +- .../easyconfigs/i/ifort/ifort-2016.3.210-GCC-5.3.0-2.26.eb | 2 +- .../easyconfigs/i/ifort/ifort-2016.3.210-GCC-5.4.0-2.26.eb | 2 +- .../easyconfigs/i/ifort/ifort-2017.0.098-GCC-5.4.0-2.26.eb | 2 +- .../easyconfigs/i/ifort/ifort-2017.1.132-GCC-5.4.0-2.26.eb | 2 +- .../easyconfigs/i/ifort/ifort-2017.1.132-GCC-6.3.0-2.27.eb | 2 +- .../easyconfigs/i/ifort/ifort-2017.2.174-GCC-6.3.0-2.27.eb | 2 +- .../easyconfigs/i/ifort/ifort-2017.4.196-GCC-6.4.0-2.28.eb | 2 +- 31 files changed, 31 insertions(+), 31 deletions(-) diff --git a/easybuild/easyconfigs/i/ifort/ifort-11.1.073-32bit.eb b/easybuild/easyconfigs/i/ifort/ifort-11.1.073-32bit.eb index 640705e6d0..fc74e58925 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-11.1.073-32bit.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-11.1.073-32bit.eb @@ -5,7 +5,7 @@ versionsuffix = '-32bit' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "Fortran compiler from Intel" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['l_cprof_p_%s.tgz' % version] diff --git a/easybuild/easyconfigs/i/ifort/ifort-11.1.073.eb b/easybuild/easyconfigs/i/ifort/ifort-11.1.073.eb index ee69dc8e33..ba9c113010 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-11.1.073.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-11.1.073.eb @@ -4,7 +4,7 @@ version = '11.1.073' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "Fortran compiler from Intel" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['l_cprof_p_%s.tgz' % version] diff --git a/easybuild/easyconfigs/i/ifort/ifort-11.1.075.eb b/easybuild/easyconfigs/i/ifort/ifort-11.1.075.eb index 1372125c7c..daf3938aa9 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-11.1.075.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-11.1.075.eb @@ -4,7 +4,7 @@ version = '11.1.075' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "Fortran compiler from Intel" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['l_cprof_p_%s_intel64.tgz' % version] diff --git a/easybuild/easyconfigs/i/ifort/ifort-2011.10.319.eb b/easybuild/easyconfigs/i/ifort/ifort-2011.10.319.eb index 222eeaca4e..1188123d79 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2011.10.319.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2011.10.319.eb @@ -4,7 +4,7 @@ version = '2011.10.319' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "Fortran compiler from Intel" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['l_fcompxe_intel64_%s.tgz' % version] diff --git a/easybuild/easyconfigs/i/ifort/ifort-2011.13.367.eb b/easybuild/easyconfigs/i/ifort/ifort-2011.13.367.eb index ef3f60866f..f68f6572f8 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2011.13.367.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2011.13.367.eb @@ -4,7 +4,7 @@ version = '2011.13.367' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "Fortran compiler from Intel" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['l_fcompxe_%s.tgz' % version] diff --git a/easybuild/easyconfigs/i/ifort/ifort-2011.3.174.eb b/easybuild/easyconfigs/i/ifort/ifort-2011.3.174.eb index 5b08216822..1e7388c150 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2011.3.174.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2011.3.174.eb @@ -4,7 +4,7 @@ version = '2011.3.174' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "Fortran compiler from Intel" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['l_fcompxe_intel64_%s.tgz' % version] diff --git a/easybuild/easyconfigs/i/ifort/ifort-2011.6.233.eb b/easybuild/easyconfigs/i/ifort/ifort-2011.6.233.eb index ad4923d074..1b72efc8cb 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2011.6.233.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2011.6.233.eb @@ -4,7 +4,7 @@ version = '2011.6.233' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "Fortran compiler from Intel" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['l_fcompxe_intel64_%s.tgz' % version] diff --git a/easybuild/easyconfigs/i/ifort/ifort-2013.1.117.eb b/easybuild/easyconfigs/i/ifort/ifort-2013.1.117.eb index 43b7969dc4..248cf71e35 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2013.1.117.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2013.1.117.eb @@ -4,7 +4,7 @@ version = '2013.1.117' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "Fortran compiler from Intel" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['l_fcompxe_%s.tgz' % version] diff --git a/easybuild/easyconfigs/i/ifort/ifort-2013.2.146.eb b/easybuild/easyconfigs/i/ifort/ifort-2013.2.146.eb index 018ac9b87d..f05bd2bc41 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2013.2.146.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2013.2.146.eb @@ -4,7 +4,7 @@ version = '2013.2.146' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "Fortran compiler from Intel" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['l_fcompxe_%s.tgz' % version] diff --git a/easybuild/easyconfigs/i/ifort/ifort-2013.3.163.eb b/easybuild/easyconfigs/i/ifort/ifort-2013.3.163.eb index d84bb054d0..019cf97f80 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2013.3.163.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2013.3.163.eb @@ -4,7 +4,7 @@ version = '2013.3.163' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "Fortran compiler from Intel" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['l_fcompxe_%s.tgz' % version] diff --git a/easybuild/easyconfigs/i/ifort/ifort-2013.4.183.eb b/easybuild/easyconfigs/i/ifort/ifort-2013.4.183.eb index e1ae8632f1..e163dff16b 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2013.4.183.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2013.4.183.eb @@ -4,7 +4,7 @@ version = '2013.4.183' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "Fortran compiler from Intel" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['l_fcompxe_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/ifort/ifort-2013.5.192.eb b/easybuild/easyconfigs/i/ifort/ifort-2013.5.192.eb index 7b9de4dea5..a8b58b1f42 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2013.5.192.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2013.5.192.eb @@ -4,7 +4,7 @@ version = '2013.5.192' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "Fortran compiler from Intel" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['l_fcompxe_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/ifort/ifort-2013_sp1.0.080.eb b/easybuild/easyconfigs/i/ifort/ifort-2013_sp1.0.080.eb index 6402e2f9ac..f72b543550 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2013_sp1.0.080.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2013_sp1.0.080.eb @@ -4,7 +4,7 @@ version = '2013_sp1.0.080' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "Fortran compiler from Intel" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['l_fcompxe_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/ifort/ifort-2013_sp1.1.106.eb b/easybuild/easyconfigs/i/ifort/ifort-2013_sp1.1.106.eb index c762cdb26a..67537c71be 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2013_sp1.1.106.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2013_sp1.1.106.eb @@ -4,7 +4,7 @@ version = '2013_sp1.1.106' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "Fortran compiler from Intel" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['l_fcompxe_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/ifort/ifort-2013_sp1.2.144.eb b/easybuild/easyconfigs/i/ifort/ifort-2013_sp1.2.144.eb index f987a0ac44..9e2cea7b90 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2013_sp1.2.144.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2013_sp1.2.144.eb @@ -4,7 +4,7 @@ version = '2013_sp1.2.144' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "Fortran compiler from Intel" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['l_fcompxe_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/ifort/ifort-2013_sp1.3.174.eb b/easybuild/easyconfigs/i/ifort/ifort-2013_sp1.3.174.eb index a605451b28..50877f89fb 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2013_sp1.3.174.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2013_sp1.3.174.eb @@ -4,7 +4,7 @@ version = '2013_sp1.3.174' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "Fortran compiler from Intel" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['l_fcompxe_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/ifort/ifort-2013_sp1.4.211.eb b/easybuild/easyconfigs/i/ifort/ifort-2013_sp1.4.211.eb index 104d8f2770..da926f7b5f 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2013_sp1.4.211.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2013_sp1.4.211.eb @@ -5,7 +5,7 @@ version = '2013_sp1.4.211' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "Fortran compiler from Intel" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['l_fcompxe_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/ifort/ifort-2015.0.090.eb b/easybuild/easyconfigs/i/ifort/ifort-2015.0.090.eb index b312c804d8..311ec00de4 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2015.0.090.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2015.0.090.eb @@ -4,7 +4,7 @@ version = '2015.0.090' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "Fortran compiler from Intel" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['l_fcompxe_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/ifort/ifort-2015.1.133.eb b/easybuild/easyconfigs/i/ifort/ifort-2015.1.133.eb index c2c4c3e7d1..bc7e3e7415 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2015.1.133.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2015.1.133.eb @@ -4,7 +4,7 @@ version = '2015.1.133' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "Fortran compiler from Intel" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['l_fcompxe_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/ifort/ifort-2015.3.187.eb b/easybuild/easyconfigs/i/ifort/ifort-2015.3.187.eb index 6e0324f9b5..881bbb96d2 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2015.3.187.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2015.3.187.eb @@ -4,7 +4,7 @@ version = '2015.3.187' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "Fortran compiler from Intel" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['l_fcompxe_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/ifort/ifort-2016.0.109.eb b/easybuild/easyconfigs/i/ifort/ifort-2016.0.109.eb index d138aad0c3..7579c77a3d 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2016.0.109.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2016.0.109.eb @@ -6,7 +6,7 @@ version = '2016.0.109' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "Fortran compiler from Intel" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_fortran.tgz'] diff --git a/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-4.9.3-2.25.eb index ece99a7387..3ee959b67b 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-4.9.3-2.25.eb @@ -6,7 +6,7 @@ version = '2016.2.181' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "Fortran compiler from Intel" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_fortran_update%(version_minor)s.tgz'] diff --git a/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-5.3.0-2.26.eb index 5bba923e8f..f0b7f28bbb 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-5.3.0-2.26.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-5.3.0-2.26.eb @@ -6,7 +6,7 @@ version = '2016.2.181' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "Fortran compiler from Intel" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_fortran_update%(version_minor)s.tgz'] diff --git a/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-4.9.3-2.25.eb index 856da5d488..3b0e1e5deb 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-4.9.3-2.25.eb @@ -6,7 +6,7 @@ version = '2016.3.210' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "Fortran compiler from Intel" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_fortran_update%(version_minor)s.tgz'] diff --git a/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-5.3.0-2.26.eb index 1204efb964..a3e1cae6fd 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-5.3.0-2.26.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-5.3.0-2.26.eb @@ -6,7 +6,7 @@ version = '2016.3.210' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "Fortran compiler from Intel" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_fortran_update%(version_minor)s.tgz'] diff --git a/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-5.4.0-2.26.eb index 52c45d2af4..b9a9fa4899 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-5.4.0-2.26.eb @@ -6,7 +6,7 @@ version = '2016.3.210' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "Fortran compiler from Intel" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_fortran_update%(version_minor)s.tgz'] diff --git a/easybuild/easyconfigs/i/ifort/ifort-2017.0.098-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/ifort/ifort-2017.0.098-GCC-5.4.0-2.26.eb index b49a02c89a..7354161167 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2017.0.098-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2017.0.098-GCC-5.4.0-2.26.eb @@ -6,7 +6,7 @@ version = '2017.0.098' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "Fortran compiler from Intel" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_fortran.tgz'] diff --git a/easybuild/easyconfigs/i/ifort/ifort-2017.1.132-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/ifort/ifort-2017.1.132-GCC-5.4.0-2.26.eb index 8f58c81952..2f49c69f89 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2017.1.132-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2017.1.132-GCC-5.4.0-2.26.eb @@ -6,7 +6,7 @@ version = '2017.1.132' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "Fortran compiler from Intel" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition_for_fortran.tgz'] diff --git a/easybuild/easyconfigs/i/ifort/ifort-2017.1.132-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/i/ifort/ifort-2017.1.132-GCC-6.3.0-2.27.eb index 215324831e..fba2517442 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2017.1.132-GCC-6.3.0-2.27.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2017.1.132-GCC-6.3.0-2.27.eb @@ -6,7 +6,7 @@ version = '2017.1.132' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "Fortran compiler from Intel" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition_for_fortran.tgz'] diff --git a/easybuild/easyconfigs/i/ifort/ifort-2017.2.174-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/i/ifort/ifort-2017.2.174-GCC-6.3.0-2.27.eb index 1d5cac3fad..aa15e0062d 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2017.2.174-GCC-6.3.0-2.27.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2017.2.174-GCC-6.3.0-2.27.eb @@ -6,7 +6,7 @@ version = '2017.2.174' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "Fortran compiler from Intel" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition_for_fortran.tgz'] diff --git a/easybuild/easyconfigs/i/ifort/ifort-2017.4.196-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/i/ifort/ifort-2017.4.196-GCC-6.4.0-2.28.eb index 9fc6419c66..26e9eb1393 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2017.4.196-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2017.4.196-GCC-6.4.0-2.28.eb @@ -6,7 +6,7 @@ version = '2017.4.196' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "Intel Fortran compiler" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition_for_fortran.tgz'] -- GitLab From 441ea91b432f477523690ed822bc8acf5162472d Mon Sep 17 00:00:00 2001 From: John Donners Date: Mon, 18 Sep 2017 10:20:08 +0200 Subject: [PATCH 1541/1603] Fixed style --- .../easyconfigs/n/NEST/NEST-2.12.0-foss-2015b-Python-2.7.9.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/NEST/NEST-2.12.0-foss-2015b-Python-2.7.9.eb b/easybuild/easyconfigs/n/NEST/NEST-2.12.0-foss-2015b-Python-2.7.9.eb index f549b80fd7..badbb5845d 100644 --- a/easybuild/easyconfigs/n/NEST/NEST-2.12.0-foss-2015b-Python-2.7.9.eb +++ b/easybuild/easyconfigs/n/NEST/NEST-2.12.0-foss-2015b-Python-2.7.9.eb @@ -30,7 +30,7 @@ configopts = '-DREADLINE_ROOT_DIR=$EBROOTLIBREADLINE -Dwith-mpi=OFF' builddependencies = [ ('CMake', '3.4.1'), ('Doxygen', '1.8.10'), - ('pkg-config','0.27.1'), + ('pkg-config', '0.27.1'), ] modextrapaths = { -- GitLab From d3eb5d0f7c299e046773b57429a990782ce45030 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 18 Sep 2017 11:31:47 +0200 Subject: [PATCH 1542/1603] include LAME/x265 dependencies to FFmpeg 3.3.4 easyconfig --- .../f/FFmpeg/FFmpeg-3.3.4-intel-2017a.eb | 4 ++- .../l/LAME/LAME-3.99.5-intel-2017a.eb | 31 +++++++++++++++++++ .../x/x265/x265-2.5-intel-2017a.eb | 30 ++++++++++++++++++ 3 files changed, 64 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/l/LAME/LAME-3.99.5-intel-2017a.eb create mode 100644 easybuild/easyconfigs/x/x265/x265-2.5-intel-2017a.eb diff --git a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.3.4-intel-2017a.eb b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.3.4-intel-2017a.eb index cd11763563..c5e0304ea7 100644 --- a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.3.4-intel-2017a.eb +++ b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.3.4-intel-2017a.eb @@ -17,11 +17,13 @@ dependencies = [ ('zlib', '1.2.11'), ('bzip2', '1.0.6'), ('x264', '20170913'), + ('LAME', '3.99.5'), + ('x265', '2.5'), ('X11', '20170314'), ] configopts = '--enable-pic --enable-shared --enable-gpl --enable-version3 --enable-nonfree --cc="$CC" --cxx="$CXX" ' -configopts += '--enable-libx264' +configopts += '--enable-libx264 --enable-libx265 --enable-libmp3lame' sanity_check_paths = { 'files': ['bin/ff%s' % x for x in ['mpeg', 'probe', 'server']] + diff --git a/easybuild/easyconfigs/l/LAME/LAME-3.99.5-intel-2017a.eb b/easybuild/easyconfigs/l/LAME/LAME-3.99.5-intel-2017a.eb new file mode 100644 index 0000000000..7c59b9ecd3 --- /dev/null +++ b/easybuild/easyconfigs/l/LAME/LAME-3.99.5-intel-2017a.eb @@ -0,0 +1,31 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Author: Stephane Thiell +### + +easyblock = 'ConfigureMake' + +name = 'LAME' +version = '3.99.5' + +homepage = 'http://lame.sourceforge.net/' +description = """LAME is a high quality MPEG Audio Layer III (MP3) encoder licensed under the LGPL.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['https://sourceforge.net/projects/lame/files/lame/%(version_major_minor)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['24346b4158e4af3bd9f2e194bb23eb473c75fb7377011523353196b19b9a23ff'] + +dependencies = [('ncurses', '6.0')] + +# configure is broken: add workaround to find libncurses... +configure_cmd_prefix = "FRONTEND_LDADD='-L${EBROOTNCURSES}/lib' " + +sanity_check_paths = { + 'files': ['bin/lame', 'include/lame/lame.h', 'lib/libmp3lame.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/x/x265/x265-2.5-intel-2017a.eb b/easybuild/easyconfigs/x/x265/x265-2.5-intel-2017a.eb new file mode 100644 index 0000000000..2d4c17170e --- /dev/null +++ b/easybuild/easyconfigs/x/x265/x265-2.5-intel-2017a.eb @@ -0,0 +1,30 @@ +easyblock = 'CMakeMake' + +name = 'x265' +version = '2.5' + +homepage = 'http://x265.org/' +description = """x265 is a free software library and application for encoding video streams into the H.265 + AVC compression format, and is released under the terms of the GNU GPL.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [ + 'http://ftp.videolan.org/pub/videolan/x265/', + 'http://download.videolan.org/pub/videolan/x265/', +] +sources = ['%(name)s_%(version)s.tar.gz'] +checksums = ['2e53259b504a7edb9b21b9800163b1ff4c90e60c74e23e7001d423c69c5d3d17'] + +dependencies = [('Yasm', '1.3.0')] + +builddependencies = [('CMake', '3.9.1')] + +start_dir = 'source' + +sanity_check_paths = { + 'files': ['bin/x265', 'include/x265_config.h', 'include/x265.h', 'lib/libx265.a', 'lib/libx265.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' -- GitLab From d39e02ccaca9ed22168274f2b6e55db00a4a1e20 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 18 Sep 2017 12:01:17 +0200 Subject: [PATCH 1543/1603] bump NASM version in FFmpeg 3.3.4 easyconfig --- easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.3.4-intel-2017a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.3.4-intel-2017a.eb b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.3.4-intel-2017a.eb index c5e0304ea7..4be73253c5 100644 --- a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.3.4-intel-2017a.eb +++ b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.3.4-intel-2017a.eb @@ -13,7 +13,7 @@ sources = [SOURCELOWER_TAR_BZ2] checksums = ['5ef5e9276c311c74ab2e9d301c2d7ee10e1f2cbd758c6f13d6cb9514dffbac7e'] dependencies = [ - ('NASM', '2.12.02'), + ('NASM', '2.13.01'), ('zlib', '1.2.11'), ('bzip2', '1.0.6'), ('x264', '20170913'), -- GitLab From 5f749445a1027ec7d3757d49ae2e342fcdb4837e Mon Sep 17 00:00:00 2001 From: John Donners Date: Mon, 18 Sep 2017 12:59:42 +0200 Subject: [PATCH 1544/1603] Fixed style & added sanity check --- .../NEST-2.12.0-foss-2015b-Python-2.7.9.eb | 10 ++++-- .../n/NEST/NEST-2.12.0-foss-2015b.eb | 35 ------------------- 2 files changed, 7 insertions(+), 38 deletions(-) delete mode 100644 easybuild/easyconfigs/n/NEST/NEST-2.12.0-foss-2015b.eb diff --git a/easybuild/easyconfigs/n/NEST/NEST-2.12.0-foss-2015b-Python-2.7.9.eb b/easybuild/easyconfigs/n/NEST/NEST-2.12.0-foss-2015b-Python-2.7.9.eb index badbb5845d..69a7a9c332 100644 --- a/easybuild/easyconfigs/n/NEST/NEST-2.12.0-foss-2015b-Python-2.7.9.eb +++ b/easybuild/easyconfigs/n/NEST/NEST-2.12.0-foss-2015b-Python-2.7.9.eb @@ -16,6 +16,8 @@ source_urls = ['https://github.com/nest/nest-simulator/releases/download/v%(vers sources = ['nest-%(version)s.tar.gz'] checksums = ['bac578f38bb0621618ee9d5f2f1febfee60cddc000ff32e51a5f5470bb3df40d'] +configopts = '-DREADLINE_ROOT_DIR=$EBROOTLIBREADLINE -Dwith-mpi=OFF' + dependencies = [ ('Python', '2.7.9'), ('libreadline', '6.3'), @@ -24,9 +26,6 @@ dependencies = [ ('ncurses', '5.9'), ] - -configopts = '-DREADLINE_ROOT_DIR=$EBROOTLIBREADLINE -Dwith-mpi=OFF' - builddependencies = [ ('CMake', '3.4.1'), ('Doxygen', '1.8.10'), @@ -37,4 +36,9 @@ modextrapaths = { 'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages'], } +sanity_check_paths = { + 'files': ['bin/nest','lib/libnest.so','lib/libmodels.so'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + moduleclass = 'math' diff --git a/easybuild/easyconfigs/n/NEST/NEST-2.12.0-foss-2015b.eb b/easybuild/easyconfigs/n/NEST/NEST-2.12.0-foss-2015b.eb deleted file mode 100644 index 700407b571..0000000000 --- a/easybuild/easyconfigs/n/NEST/NEST-2.12.0-foss-2015b.eb +++ /dev/null @@ -1,35 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'NEST' -version = '2.12.0' - -homepage = 'http://www.nest-simulator.org/' -description = """NEST is a simulator for spiking neural network models - that focuses on the dynamics, size and structure of neural systems rather - than on the exact morphology of individual neurons.""" - -toolchain = {'name': 'foss', 'version': '2015b'} -toolchainopts = {'optarch': True, 'pic': True} - -sources = ['nest-%(version)s.tar.gz'] -source_urls = ['https://github.com/nest/nest-simulator/releases/download/v%(version)s/'] - -dependencies = [ - ('Python', '2.7.9'), - ('libreadline', '6.3'), - ('GSL', '2.1'), - ('libtool', '2.4.6', '-GNU-4.9.3-2.25', True), -] - -configopts = '-DREADLINE_ROOT_DIR=$EBROOTLIBREADLINE' - -builddependencies = [ - ('CMake', '3.4.1'), - ('Doxygen', '1.8.10'), -] - -modextrapaths = { - 'PYTHONPATH': ['lib/python2.7/site-packages'], -} - -moduleclass = 'math' -- GitLab From 33208697e2f31e2da2c0d5bc04b5febb90ccfa62 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 18 Sep 2017 13:35:58 +0200 Subject: [PATCH 1545/1603] Add extra install file to Rcorrector User gave feedback that this files is also required. --- .../easyconfigs/r/Rcorrector/Rcorrector-1.0.2-intel-2017a.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/Rcorrector/Rcorrector-1.0.2-intel-2017a.eb b/easybuild/easyconfigs/r/Rcorrector/Rcorrector-1.0.2-intel-2017a.eb index 9a2677bbd0..abc3fb35ad 100644 --- a/easybuild/easyconfigs/r/Rcorrector/Rcorrector-1.0.2-intel-2017a.eb +++ b/easybuild/easyconfigs/r/Rcorrector/Rcorrector-1.0.2-intel-2017a.eb @@ -19,10 +19,13 @@ checksums = [ dependencies = [ ('zlib', '1.2.11'), + ('Perl', '5.24.1'), ('Jellyfish', '2.2.6'), ] -files_to_copy = [(['rcorrector'], 'bin'), 'README.md', 'LICENSE', 'Sample'] +files_to_copy = [(['rcorrector', 'run_rcorrector.pl'], 'bin'), 'README.md', 'LICENSE', 'Sample'] + +postinstallcmds = ["chmod +x %(installdir)s/bin/run_rcorrector.pl"] sanity_check_paths = { 'files': ['bin/rcorrector'], -- GitLab From c3cf16889e302d480254f460a3b80f9fe3eec929 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 18 Sep 2017 17:49:35 +0200 Subject: [PATCH 1546/1603] adding easyconfigs: Tensorflow-1.3.0-intel-2017a-Python-2.7.13.eb, protobuf-python-3.4.0-intel-2017a-Python-2.7.13.eb, protobuf-3.4.0-intel-2017a.eb --- ...-python-3.4.0-intel-2017a-Python-2.7.13.eb | 30 ++++++++++++ .../p/protobuf/protobuf-3.4.0-intel-2017a.eb | 24 +++++++++ ...sorflow-1.3.0-intel-2017a-Python-2.7.13.eb | 49 +++++++++++++++++++ 3 files changed, 103 insertions(+) create mode 100644 easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.4.0-intel-2017a-Python-2.7.13.eb create mode 100644 easybuild/easyconfigs/p/protobuf/protobuf-3.4.0-intel-2017a.eb create mode 100755 easybuild/easyconfigs/t/Tensorflow/Tensorflow-1.3.0-intel-2017a-Python-2.7.13.eb diff --git a/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.4.0-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.4.0-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..84dd7d4ec1 --- /dev/null +++ b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.4.0-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'protobuf-python' +version = '3.4.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/google/protobuf/' +description = """Python Protocol Buffers runtime library.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['https://github.com/google/protobuf/archive/v%(version)s'] +sources = [SOURCE_TAR_GZ] +checksums = ['f6600abeee3babfa18591961a0ff21e7db6a6d9ef82418a261ec4fee44ee6d44'] + +dependencies = [ + ('Python', '2.7.13'), + ('protobuf', version) +] + +start_dir = 'python' + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +options = {'modulename': 'google.protobuf'} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/protobuf/protobuf-3.4.0-intel-2017a.eb b/easybuild/easyconfigs/p/protobuf/protobuf-3.4.0-intel-2017a.eb new file mode 100644 index 0000000000..4f15d746b8 --- /dev/null +++ b/easybuild/easyconfigs/p/protobuf/protobuf-3.4.0-intel-2017a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'protobuf' +version = '3.4.0' + +homepage = 'https://github.com/google/protobuf/' +description = """Google Protocol Buffers""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['https://github.com/google/protobuf/archive/v%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['f6600abeee3babfa18591961a0ff21e7db6a6d9ef82418a261ec4fee44ee6d44'] + +builddependencies = [('Autotools', '20150215')] + +preconfigopts = "./autogen.sh && " + +sanity_check_paths = { + 'files': ['bin/protoc', 'lib/libprotobuf.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/t/Tensorflow/Tensorflow-1.3.0-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/t/Tensorflow/Tensorflow-1.3.0-intel-2017a-Python-2.7.13.eb new file mode 100755 index 0000000000..c6295ee512 --- /dev/null +++ b/easybuild/easyconfigs/t/Tensorflow/Tensorflow-1.3.0-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,49 @@ +easyblock = 'Bundle' + +name = 'Tensorflow' +version = '1.3.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://www.tensorflow.org/' +description = "An open-source software library for Machine Intelligence" + +toolchain = {'name': 'intel', 'version': '2017a'} + +pymaj = '2' +pymin = '7' +pymajmin = pymaj + pymin + +dependencies = [ + ('Python', '%s.%s.13' % (pymaj, pymin)), + ('protobuf-python', '3.4.0', versionsuffix), +] + +exts_defaultclass = 'PythonPackage' +exts_filter = ("python -c 'import %(ext_name)s'", '') + +exts_list = [ + ('backports.weakref', '1.0.post1', { + 'modulename': 'backports.weakref', + 'source_urls': ['https://pypi.python.org/packages/source/b/backports.weakref'], + 'checksums': ['bc4170a29915f8b22c9e7c4939701859650f2eb84184aee80da329ac0b9825c2'], + }), + ('Tensorflow', '1.3.0', { + 'source_tmpl': 'tensorflow-%(version)s-cp27-cp27mu-manylinux1_x86_64.whl', + 'source_urls': ['https://pypi.python.org/packages/source/t/Tensorflow'], + 'unpack_sources': False, + 'use_pip': True, + 'checksums': ['0bf3866115184d97993d702f2f47cd557fa5a26b6661aa94aa16c05e4a545cfb'], + }), +] + +# specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module +full_sanity_check = True + +sanity_check_paths = { + 'files': ['bin/tensorboard'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +moduleclass = 'lib' -- GitLab From 54138d2c717c9e7157c655d4154a4b3a5e9e89e1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 18 Sep 2017 17:58:25 +0200 Subject: [PATCH 1547/1603] adding easyconfigs: GTK+-2.24.31-intel-2017a.eb, ATK-2.26.0-intel-2017a.eb, Gdk-Pixbuf-2.36.10-intel-2017a.eb, Pango-1.40.12-intel-2017a.eb, HarfBuzz-1.5.1-intel-2017a.eb --- .../a/ATK/ATK-2.26.0-intel-2017a.eb | 35 ++++++++++++++ .../g/GTK+/GTK+-2.24.31-intel-2017a.eb | 26 +++++++++++ .../Gdk-Pixbuf-2.36.10-intel-2017a.eb | 46 +++++++++++++++++++ .../h/HarfBuzz/HarfBuzz-1.5.1-intel-2017a.eb | 35 ++++++++++++++ .../p/Pango/Pango-1.40.12-intel-2017a.eb | 32 +++++++++++++ 5 files changed, 174 insertions(+) create mode 100644 easybuild/easyconfigs/a/ATK/ATK-2.26.0-intel-2017a.eb create mode 100644 easybuild/easyconfigs/g/GTK+/GTK+-2.24.31-intel-2017a.eb create mode 100644 easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.36.10-intel-2017a.eb create mode 100644 easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.5.1-intel-2017a.eb create mode 100644 easybuild/easyconfigs/p/Pango/Pango-1.40.12-intel-2017a.eb diff --git a/easybuild/easyconfigs/a/ATK/ATK-2.26.0-intel-2017a.eb b/easybuild/easyconfigs/a/ATK/ATK-2.26.0-intel-2017a.eb new file mode 100644 index 0000000000..b57356af82 --- /dev/null +++ b/easybuild/easyconfigs/a/ATK/ATK-2.26.0-intel-2017a.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'ATK' +version = '2.26.0' + +homepage = 'https://developer.gnome.org/ATK/stable/' +description = """ + ATK provides the set of accessibility interfaces that are implemented by other + toolkits and applications. Using the ATK interfaces, accessibility tools have + full access to view and control running applications. +""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['eafe49d5c4546cb723ec98053290d7e0b8d85b3fdb123938213acb7bb4178827'] + +dependencies = [ + ('GLib', '2.53.5'), + ('GObject-Introspection', '1.53.5', '-Python-2.7.13'), +] + +configopts = "--enable-introspection=yes" + +modextrapaths = { + 'XDG_DATA_DIRS': 'share', +} + +sanity_check_paths = { + 'files': ['lib/libatk-1.0.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GTK+/GTK+-2.24.31-intel-2017a.eb b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.31-intel-2017a.eb new file mode 100644 index 0000000000..bf67ec5ff0 --- /dev/null +++ b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.31-intel-2017a.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'GTK+' +version = '2.24.31' + +homepage = 'https://developer.gnome.org/gtk+/stable/' +description = """ + The GTK+ 2 package contains libraries used for creating graphical user interfaces for applications. +""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['68c1922732c7efc08df4656a5366dcc3afdc8791513400dac276009b40954658'] + +dependencies = [ + ('ATK', '2.26.0'), + ('Gdk-Pixbuf', '2.36.10'), + ('Pango', '1.40.12'), + ('GObject-Introspection', '1.53.5', '-Python-2.7.13'), +] + +configopts = "--disable-silent-rules --disable-glibtest --enable-introspection=yes --disable-visibility " + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.36.10-intel-2017a.eb b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.36.10-intel-2017a.eb new file mode 100644 index 0000000000..864e90432a --- /dev/null +++ b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.36.10-intel-2017a.eb @@ -0,0 +1,46 @@ +easyblock = 'ConfigureMake' + +name = 'Gdk-Pixbuf' +version = '2.36.10' + +homepage = 'https://developer.gnome.org/gdk-pixbuf/stable/' +description = """ + The Gdk Pixbuf is a toolkit for image loading and pixel buffer manipulation. + It is used by GTK+ 2 and GTK+ 3 to load and manipulate images. In the past it + was distributed as part of GTK+ 2 but it was split off into a separate package + in preparation for the change to GTK+ 3. +""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +patches = ['Gdk-Pixbuf-%(version)s-disable-gio-sniffing.patch'] +checksums = [ + 'f8f6fa896b89475c73b6e9e8d2a2b062fc359c4b4ccb8e96470d6ab5da949ace', # gdk-pixbuf-2.36.10.tar.xz + '840231db69ccc2a1335c4f29c305cdd0ba570254e779c2a274611aaff968878e', # Gdk-Pixbuf-2.36.10-disable-gio-sniffing.patch +] + +builddependencies = [ + ('GObject-Introspection', '1.53.5', '-Python-2.7.13') +] +dependencies = [ + ('GLib', '2.53.5'), + ('libjpeg-turbo', '1.5.2'), + ('libpng', '1.6.29'), + ('LibTIFF', '4.0.8'), +] + +configopts = "--disable-maintainer-mode --enable-debug=no --enable-introspection=yes " +configopts += "--disable-Bsymbolic --without-gdiplus --enable-shared --enable-static" + +sanity_check_paths = { + 'files': ['lib/libgdk_pixbuf-%(version_major)s.0.a', 'lib/libgdk_pixbuf-%%(version_major)s.0.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include/gdk-pixbuf-%(version_major)s.0', 'lib/gdk-pixbuf-%(version_major)s.0', 'share'], +} + +modextrapaths = { + 'XDG_DATA_DIRS': 'share', +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.5.1-intel-2017a.eb b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.5.1-intel-2017a.eb new file mode 100644 index 0000000000..c315e68dd6 --- /dev/null +++ b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.5.1-intel-2017a.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'HarfBuzz' +version = '1.5.1' + +homepage = 'http://www.freedesktop.org/wiki/Software/HarfBuzz' +description = """HarfBuzz is an OpenType text shaping engine.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['http://www.freedesktop.org/software/harfbuzz/release/'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['56838dfdad2729b8866763c82d623354d138a4d99d9ffb710c7d377b5cfc7c51'] + +dependencies = [ + ('GLib', '2.53.5'), + ('cairo', '1.14.10'), + ('freetype', '2.7.1', '-libpng-1.6.29'), +] + +builddependencies = [('GObject-Introspection', '1.53.5', '-Python-2.7.13')] + +configopts = "--enable-introspection=yes --with-gobject=yes --enable-static --enable-shared --with-cairo " + +modextrapaths = { + 'GI_TYPELIB_PATH': 'share', + 'XDG_DATA_DIRS': 'share', +} + +sanity_check_paths = { + 'files': ['lib/libharfbuzz.%s' % SHLIB_EXT, 'bin/hb-view'], + 'dirs': [] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.40.12-intel-2017a.eb b/easybuild/easyconfigs/p/Pango/Pango-1.40.12-intel-2017a.eb new file mode 100644 index 0000000000..10766b3c74 --- /dev/null +++ b/easybuild/easyconfigs/p/Pango/Pango-1.40.12-intel-2017a.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'Pango' +version = '1.40.12' + +homepage = 'http://www.pango.org/' +description = """Pango is a library for laying out and rendering of text, with an emphasis on internationalization. +Pango can be used anywhere that text layout is needed, though most of the work on Pango so far has been done in the +context of the GTK+ widget toolkit. Pango forms the core of text and font handling for GTK+-2.x.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['75f1a9a8e4e2b28cbc078b50c1fa927ee4ded994d1ade97c5603e2d1f3161cfc'] + +dependencies = [ + ('X11', '20170314'), + ('GLib', '2.53.5'), + ('cairo', '1.14.10'), + ('HarfBuzz', '1.5.1'), +] + +builddependencies = [('GObject-Introspection', '1.53.5', '-Python-2.7.13')] + +configopts = "--disable-silent-rules --enable-introspection=yes --enable-static --enable-shared " + +modextrapaths = { + 'XDG_DATA_DIRS': 'share', +} + +moduleclass = 'vis' -- GitLab From b011fd143b43294eba6af37624f546761a49e1a6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 18 Sep 2017 17:59:44 +0200 Subject: [PATCH 1548/1603] adding easyconfigs: OpenCV-3.3.0-intel-2017a.eb --- .../o/OpenCV/OpenCV-3.3.0-intel-2017a.eb | 89 +++++++++++++++++++ 1 file changed, 89 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenCV/OpenCV-3.3.0-intel-2017a.eb diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.3.0-intel-2017a.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.3.0-intel-2017a.eb new file mode 100644 index 0000000000..ede04d5755 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.3.0-intel-2017a.eb @@ -0,0 +1,89 @@ +easyblock = 'CMakeMake' + +name = 'OpenCV' +version = '3.3.0' + +homepage = 'http://opencv.org/' +description = """OpenCV (Open Source Computer Vision Library) is an open source computer vision + and machine learning software library. OpenCV was built to provide + a common infrastructure for computer vision applications and to accelerate + the use of machine perception in the commercial products.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [ + 'https://github.com/Itseez/opencv/archive/', + # The Hash is version dependent! see 3rdparty/ippicv/downloader.cmake + 'https://raw.githubusercontent.com/Itseez/opencv_3rdparty/81a676001ca8075ada498583e4166079e5744668/ippicv', +] +sources = [ + '%(version)s.zip', + {'filename': 'ippicv_linux_20151201.tgz', 'extract_cmd': "cp %s %(builddir)s"}, +] +checksums = [ + '3546c3837f88177c898e4172942da7a3ca6c4e8e98a33d0cbccb2b499167c5ba', # 3.3.0.zip + '4333833e40afaa22c804169e44f9a63e357e21476b765a5683bcb3760107f0da', # ippicv_linux_20151201.tgz +] + +#patches = ['OpenCV-3.1.0_with_IPP.patch'] + +builddependencies = [ + ('CMake', '3.9.1'), +] + +dependencies = [ + ('Python', '2.7.13'), + ('zlib', '1.2.11'), + ('FFmpeg', '3.3.4'), + ('libjpeg-turbo', '1.5.2'), + ('libpng', '1.6.29'), + ('LibTIFF', '4.0.8'), + ('JasPer', '2.0.12'), + ('Java', '1.8.0_144', '', True), + ('ant', '1.10.1', '-Java-%(javaver)s', True), + ('GLib', '2.53.5'), + ('GTK+', '2.24.31'), +] + +separate_build_dir = True + +preconfigopts = 'export IPPROOT=$EBROOTICC/ipp && ' + +# The destination directory is "linux-" see 3rdparty/ippicv/downloader.cmake +ippicv_dir = '3rdparty/ippicv/downloads/linux-808b791a6eac9ed78d32a7666804320e/' +preconfigopts = "mkdir -p %s && cp -a ../*.tgz %s && " % (ippicv_dir, ippicv_dir) + +configopts = '-DCMAKE_BUILD_TYPE=RELEASE ' +configopts += '-DBUILD_PYTHON_SUPPORT=ON ' +configopts += '-DPYTHON_PACKAGES_PATH=%(installdir)s/lib/python%(pyshortver)s/site-packages ' +configopts += '-DBUILD_NEW_PYTHON_SUPPORT=ON ' +configopts += '-DZLIB_LIBRARY=$EBROOTZLIB/lib/libz.%s ' % SHLIB_EXT +configopts += '-DZLIB_INCLUDE_DIR=$EBROOTZLIB/include ' +configopts += '-DTIFF_LIBRARY=$EBROOTLIBTIFF/lib/libtiff.%s ' % SHLIB_EXT +configopts += '-DTIFF_INCLUDE_DIR=$EBROOTLIBTIFF/include ' +configopts += '-DPNG_LIBRARY=$EBROOTLIBPNG/lib/libpng.%s ' % SHLIB_EXT +configopts += '-DPNG_INCLUDE_DIR=$EBROOTLIBPNG/include ' +configopts += '-DJPEG_LIBRARY=$EBROOTLIBJPEGMINTURBO/lib/libjpeg.%s ' % SHLIB_EXT +configopts += '-DJPEG_INCLUDE_DIR=$EBROOTLIBJPEGMINTURBO/include ' +configopts += '-DJASPER_LIBRARY=$EBROOTJASPER/lib/libjasper.a ' +configopts += '-DJASPER_INCLUDE_DIR=$EBROOTJASPER/include ' +configopts += '-DWITH_IPP=ON ' +configopts += '-DENABLE_SSE=ON -DENABLE_SSE2=ON -DENABLE_SSE3=ON ' +configopts += '-DWITH_CUDA=OFF ' + +postinstallcmds = ["cp 3rdparty/ippicv/ippicv_lnx/lib/intel64/libippicv.* %(installdir)s/lib"] + +sanity_check_paths = { + 'files': ['lib/libopencv_core.%s' % SHLIB_EXT] + + ['lib/python%%(pyshortver)s/site-packages/cv2.%s' % SHLIB_EXT] + + ['lib/libippicv.a'] + + ['bin/opencv_%s' % x for x in ['annotation', 'createsamples', 'traincascade']], + 'dirs': ['include'] +} + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', + 'CLASSPATH': 'share/OpenCV/java', +} + +moduleclass = 'vis' -- GitLab From 019c3377a79f27a1cecadd06e9345ae3f208f182 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 18 Sep 2017 18:07:40 +0200 Subject: [PATCH 1549/1603] add missing patch file for Gdk-Pixbuf --- .../Gdk-Pixbuf-2.36.10-disable-gio-sniffing.patch | 15 +++++++++++++++ 1 file changed, 15 insertions(+) create mode 100644 easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.36.10-disable-gio-sniffing.patch diff --git a/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.36.10-disable-gio-sniffing.patch b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.36.10-disable-gio-sniffing.patch new file mode 100644 index 0000000000..3d5360847f --- /dev/null +++ b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.36.10-disable-gio-sniffing.patch @@ -0,0 +1,15 @@ +hard disable GIO sniffing to avoid relying on shared-mime-info, +and use fallback mechanism to use built-in sniffing based on magic numbers +author: Kenneth Hoste (HPC-UGent) +--- gdk-pixbuf-2.36.10.orig/configure 2017-09-11 13:00:43.000000000 +0200 ++++ gdk-pixbuf-2.36.10/configure 2017-09-18 16:44:23.341170372 +0200 +@@ -19316,6 +19316,9 @@ + fi + + ++# hard disable sniffing, which requires shared-mime-info ++gio_can_sniff=no ++ + if test x$gio_can_sniff = x; then + # Will not run on win32, so require shared-mime-info + -- GitLab From 9c800bab72af59a9d93de54a6da13ede895d6c75 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 18 Sep 2017 18:12:12 +0200 Subject: [PATCH 1550/1603] also add easyconfig for Tensorflow 1.3.0 with Python 3.6.1 --- ...f-python-3.4.0-intel-2017a-Python-3.6.1.eb | 30 ++++++++++++ ...sorflow-1.3.0-intel-2017a-Python-2.7.13.eb | 2 +- ...nsorflow-1.3.0-intel-2017a-Python-3.6.1.eb | 49 +++++++++++++++++++ 3 files changed, 80 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.4.0-intel-2017a-Python-3.6.1.eb create mode 100755 easybuild/easyconfigs/t/Tensorflow/Tensorflow-1.3.0-intel-2017a-Python-3.6.1.eb diff --git a/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.4.0-intel-2017a-Python-3.6.1.eb b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.4.0-intel-2017a-Python-3.6.1.eb new file mode 100644 index 0000000000..bffc1e1ae8 --- /dev/null +++ b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.4.0-intel-2017a-Python-3.6.1.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'protobuf-python' +version = '3.4.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/google/protobuf/' +description = """Python Protocol Buffers runtime library.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['https://github.com/google/protobuf/archive/v%(version)s'] +sources = [SOURCE_TAR_GZ] +checksums = ['f6600abeee3babfa18591961a0ff21e7db6a6d9ef82418a261ec4fee44ee6d44'] + +dependencies = [ + ('Python', '3.6.1'), + ('protobuf', version) +] + +start_dir = 'python' + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +options = {'modulename': 'google.protobuf'} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/t/Tensorflow/Tensorflow-1.3.0-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/t/Tensorflow/Tensorflow-1.3.0-intel-2017a-Python-2.7.13.eb index c6295ee512..129b16a4e4 100755 --- a/easybuild/easyconfigs/t/Tensorflow/Tensorflow-1.3.0-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/t/Tensorflow/Tensorflow-1.3.0-intel-2017a-Python-2.7.13.eb @@ -28,7 +28,7 @@ exts_list = [ 'checksums': ['bc4170a29915f8b22c9e7c4939701859650f2eb84184aee80da329ac0b9825c2'], }), ('Tensorflow', '1.3.0', { - 'source_tmpl': 'tensorflow-%(version)s-cp27-cp27mu-manylinux1_x86_64.whl', + 'source_tmpl': 'tensorflow-%%(version)s-cp%(py)s-cp%(py)smu-manylinux1_x86_64.whl' % {'py': pymajmin}, 'source_urls': ['https://pypi.python.org/packages/source/t/Tensorflow'], 'unpack_sources': False, 'use_pip': True, diff --git a/easybuild/easyconfigs/t/Tensorflow/Tensorflow-1.3.0-intel-2017a-Python-3.6.1.eb b/easybuild/easyconfigs/t/Tensorflow/Tensorflow-1.3.0-intel-2017a-Python-3.6.1.eb new file mode 100755 index 0000000000..5fd396a68b --- /dev/null +++ b/easybuild/easyconfigs/t/Tensorflow/Tensorflow-1.3.0-intel-2017a-Python-3.6.1.eb @@ -0,0 +1,49 @@ +easyblock = 'Bundle' + +name = 'Tensorflow' +version = '1.3.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://www.tensorflow.org/' +description = "An open-source software library for Machine Intelligence" + +toolchain = {'name': 'intel', 'version': '2017a'} + +pymaj = '3' +pymin = '6' +pymajmin = pymaj + pymin + +dependencies = [ + ('Python', '%s.%s.1' % (pymaj, pymin)), + ('protobuf-python', '3.4.0', versionsuffix), +] + +exts_defaultclass = 'PythonPackage' +exts_filter = ("python -c 'import %(ext_name)s'", '') + +exts_list = [ + ('backports.weakref', '1.0.post1', { + 'modulename': 'backports.weakref', + 'source_urls': ['https://pypi.python.org/packages/source/b/backports.weakref'], + 'checksums': ['bc4170a29915f8b22c9e7c4939701859650f2eb84184aee80da329ac0b9825c2'], + }), + ('Tensorflow', '1.3.0', { + 'source_tmpl': 'tensorflow-%%(version)s-cp%(py)s-cp%(py)sm-manylinux1_x86_64.whl' % {'py': pymajmin}, + 'source_urls': ['https://pypi.python.org/packages/source/t/Tensorflow'], + 'unpack_sources': False, + 'use_pip': True, + 'checksums': ['a535a4a32aaaf5c59dc582ed472f321a86bf1786d17931c017c0ec7c8f1a1c02'], + }), +] + +# specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module +full_sanity_check = True + +sanity_check_paths = { + 'files': ['bin/tensorboard'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +moduleclass = 'lib' -- GitLab From 10626dfc9c7bd529ce461daef2db2fbc550162a7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 18 Sep 2017 20:25:08 +0200 Subject: [PATCH 1551/1603] GObject-Introspection is just a build dep for ATK & GTK+ --- easybuild/easyconfigs/a/ATK/ATK-2.26.0-intel-2017a.eb | 4 +++- easybuild/easyconfigs/g/GTK+/GTK+-2.24.31-intel-2017a.eb | 4 +++- 2 files changed, 6 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/a/ATK/ATK-2.26.0-intel-2017a.eb b/easybuild/easyconfigs/a/ATK/ATK-2.26.0-intel-2017a.eb index b57356af82..842e810c1e 100644 --- a/easybuild/easyconfigs/a/ATK/ATK-2.26.0-intel-2017a.eb +++ b/easybuild/easyconfigs/a/ATK/ATK-2.26.0-intel-2017a.eb @@ -16,9 +16,11 @@ source_urls = [FTPGNOME_SOURCE] sources = [SOURCELOWER_TAR_XZ] checksums = ['eafe49d5c4546cb723ec98053290d7e0b8d85b3fdb123938213acb7bb4178827'] +builddependencies = [ + ('GObject-Introspection', '1.53.5', '-Python-2.7.13'), +] dependencies = [ ('GLib', '2.53.5'), - ('GObject-Introspection', '1.53.5', '-Python-2.7.13'), ] configopts = "--enable-introspection=yes" diff --git a/easybuild/easyconfigs/g/GTK+/GTK+-2.24.31-intel-2017a.eb b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.31-intel-2017a.eb index bf67ec5ff0..e9ae2112ba 100644 --- a/easybuild/easyconfigs/g/GTK+/GTK+-2.24.31-intel-2017a.eb +++ b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.31-intel-2017a.eb @@ -14,11 +14,13 @@ source_urls = [FTPGNOME_SOURCE] sources = [SOURCELOWER_TAR_XZ] checksums = ['68c1922732c7efc08df4656a5366dcc3afdc8791513400dac276009b40954658'] +builddependencies = [ + ('GObject-Introspection', '1.53.5', '-Python-2.7.13'), +] dependencies = [ ('ATK', '2.26.0'), ('Gdk-Pixbuf', '2.36.10'), ('Pango', '1.40.12'), - ('GObject-Introspection', '1.53.5', '-Python-2.7.13'), ] configopts = "--disable-silent-rules --disable-glibtest --enable-introspection=yes --disable-visibility " -- GitLab From c9ccabdffa24aa23759255dbc1274dc943763923 Mon Sep 17 00:00:00 2001 From: John Donners Date: Mon, 18 Sep 2017 20:31:52 +0200 Subject: [PATCH 1552/1603] Fixed style & sanity check. Added CMAKE_INSTALL_LIBDIR=lib --- .../easyconfigs/n/NEST/NEST-2.12.0-foss-2015b-Python-2.7.9.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/n/NEST/NEST-2.12.0-foss-2015b-Python-2.7.9.eb b/easybuild/easyconfigs/n/NEST/NEST-2.12.0-foss-2015b-Python-2.7.9.eb index 69a7a9c332..cc85bcdf97 100644 --- a/easybuild/easyconfigs/n/NEST/NEST-2.12.0-foss-2015b-Python-2.7.9.eb +++ b/easybuild/easyconfigs/n/NEST/NEST-2.12.0-foss-2015b-Python-2.7.9.eb @@ -16,7 +16,7 @@ source_urls = ['https://github.com/nest/nest-simulator/releases/download/v%(vers sources = ['nest-%(version)s.tar.gz'] checksums = ['bac578f38bb0621618ee9d5f2f1febfee60cddc000ff32e51a5f5470bb3df40d'] -configopts = '-DREADLINE_ROOT_DIR=$EBROOTLIBREADLINE -Dwith-mpi=OFF' +configopts = '-DREADLINE_ROOT_DIR=$EBROOTLIBREADLINE -DCMAKE_INSTALL_LIBDIR=lib -Dwith-mpi=OFF' dependencies = [ ('Python', '2.7.9'), @@ -37,7 +37,7 @@ modextrapaths = { } sanity_check_paths = { - 'files': ['bin/nest','lib/libnest.so','lib/libmodels.so'], + 'files': ['bin/nest', 'lib/libnest.so', 'lib/libmodels.so'], 'dirs': ['lib/python%(pyshortver)s/site-packages'], } -- GitLab From 2640cc2e8ded903c6892965e2ab2fc58c7d0b0e8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 19 Sep 2017 13:14:56 +0200 Subject: [PATCH 1553/1603] adding easyconfigs: vsc-mympirun-4.0.2.eb --- .../v/vsc-mympirun/vsc-mympirun-4.0.2.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100755 easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-4.0.2.eb diff --git a/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-4.0.2.eb b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-4.0.2.eb new file mode 100755 index 0000000000..09d422daec --- /dev/null +++ b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-4.0.2.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'vsc-mympirun' +version = '4.0.2' + +homepage = 'https://github.com/hpcugent/vsc-mympirun' +description = """VSC-tools is a set of Python libraries and scripts that are commonly used within HPC-UGent.""" + +# we build this to work with every python version +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['a6ef244a80e29ddb1197c1d1bfac6f7b9a0092abb44c4cff789db42e27a3e1ad'] + +builddependencies = [('vsc-install', '0.10.26')] +dependencies = [('vsc-base', '2.5.8')] + +osdependencies = ['python-setuptools'] + +# we ship something in bin/fake +modextrapaths = {'PATH': 'bin/fake'} + +# don't check for import of vsc.mympirun, since that may fail if vsc-base is picked up from the OS +options = {'modulename': 'vsc'} + +pyshortver = '.'.join(SYS_PYTHON_VERSION.split('.')[:2]) +sanity_check_paths = { + 'files': ['bin/mympirun', 'bin/mympisanity'], + 'dirs': ['bin/fake', 'lib/python%s/site-packages' % pyshortver], +} +sanity_check_commands = ["mympirun --help"] + +moduleclass = 'tools' -- GitLab From 778b8d9e5b617231021d920252ca00e605267b3d Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 19 Sep 2017 13:34:18 +0200 Subject: [PATCH 1554/1603] adding easyconfigs: HPL-2.2-giolf-2017b.eb --- .../f/FFTW/FFTW-3.3.6-gimpi-2017b.eb | 18 ++++++++++ easybuild/easyconfigs/g/gimpi/gimpi-2017b.eb | 18 ++++++++++ easybuild/easyconfigs/g/giolf/giolf-2017b.eb | 33 +++++++++++++++++++ .../easyconfigs/h/HPL/HPL-2.2-giolf-2017b.eb | 19 +++++++++++ .../i/impi/impi-2017.3.196-GCC-6.4.0-2.28.eb | 31 +++++++++++++++++ ...APACK-2.0.2-gimpi-2017b-OpenBLAS-0.2.20.eb | 25 ++++++++++++++ 6 files changed, 144 insertions(+) create mode 100644 easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-gimpi-2017b.eb create mode 100644 easybuild/easyconfigs/g/gimpi/gimpi-2017b.eb create mode 100644 easybuild/easyconfigs/g/giolf/giolf-2017b.eb create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.2-giolf-2017b.eb create mode 100644 easybuild/easyconfigs/i/impi/impi-2017.3.196-GCC-6.4.0-2.28.eb create mode 100644 easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gimpi-2017b-OpenBLAS-0.2.20.eb diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-gimpi-2017b.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-gimpi-2017b.eb new file mode 100644 index 0000000000..d94bac964a --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-gimpi-2017b.eb @@ -0,0 +1,18 @@ +name = 'FFTW' +version = '3.3.6' + +homepage = 'http://www.fftw.org' +description = """FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) + in one or more dimensions, of arbitrary input size, and of both real and complex data.""" + +toolchain = {'name': 'gimpi', 'version': '2017b'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = ['fftw-%(version)s-pl2.tar.gz'] +checksums = ['a5de35c5c824a78a058ca54278c706cdf3d4abba1c56b63531c2cb05f5d57da2'] + +skipsteps = ['test'] +#runtest = 'check' + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/g/gimpi/gimpi-2017b.eb b/easybuild/easyconfigs/g/gimpi/gimpi-2017b.eb new file mode 100644 index 0000000000..5d1bb3c4be --- /dev/null +++ b/easybuild/easyconfigs/g/gimpi/gimpi-2017b.eb @@ -0,0 +1,18 @@ +easyblock = "Toolchain" + +name = 'gimpi' +version = '2017b' + +homepage = '(none)' +description = """GNU Compiler Collection (GCC) based compiler toolchain with Intel MPI.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +comp = ('GCC', '6.4.0-2.28') + +dependencies = [ + comp, + ('impi', '2017.3.196', '', comp), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/g/giolf/giolf-2017b.eb b/easybuild/easyconfigs/g/giolf/giolf-2017b.eb new file mode 100644 index 0000000000..baba7c3841 --- /dev/null +++ b/easybuild/easyconfigs/g/giolf/giolf-2017b.eb @@ -0,0 +1,33 @@ +easyblock = 'Toolchain' + +name = 'giolf' +version = '2017b' + +homepage = '(none)' +description = """GNU Compiler Collection (GCC) based compiler toolchain, including + IntelMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +gccver = '6.4.0-2.28' + +blaslib = 'OpenBLAS' +blasver = '0.2.20' +blas = '%s-%s' % (blaslib, blasver) + +# toolchain used to build foss dependencies +comp_mpi_tc_name = 'gimpi' +comp_mpi_tc = (comp_mpi_tc_name, version) + +# we need GCC and OpenMPI as explicit dependencies instead of gompi toolchain +# because of toolchain preparation functions +# For binutils, stick to http://wiki.osdev.org/Cross-Compiler_Successful_Builds +dependencies = [ + ('GCC', gccver), + ('impi', '2017.3.196', '', ('GCC', gccver)), + (blaslib, blasver, '', ('GCC', gccver)), + ('FFTW', '3.3.6', '', comp_mpi_tc), + ('ScaLAPACK', '2.0.2', '-%s' % blas, comp_mpi_tc), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.2-giolf-2017b.eb b/easybuild/easyconfigs/h/HPL/HPL-2.2-giolf-2017b.eb new file mode 100644 index 0000000000..8f4e07e348 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.2-giolf-2017b.eb @@ -0,0 +1,19 @@ +name = 'HPL' +version = '2.2' + +homepage = 'http://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'giolf', 'version': '2017b'} +toolchainopts = {'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] +checksums = ['ac7534163a09e21a5fa763e4e16dfc119bc84043f6e6a807aba666518f8df440'] + +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/i/impi/impi-2017.3.196-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/i/impi/impi-2017.3.196-GCC-6.4.0-2.28.eb new file mode 100644 index 0000000000..6f72d5d7da --- /dev/null +++ b/easybuild/easyconfigs/i/impi/impi-2017.3.196-GCC-6.4.0-2.28.eb @@ -0,0 +1,31 @@ +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild + +name = 'impi' +version = '2017.3.196' + +homepage = 'http://software.intel.com/en-us/intel-mpi-library/' +description = "Intel MPI Library, compatible with MPICH ABI" + +toolchain = {'name': 'GCC', 'version': '6.4.0-2.28'} + +sources = ['l_mpi_%(version)s.tgz'] + +checksums = ['dad9efbc5bbd3fd27cce7e1e2507ad77f342d5ecc929747ae141c890e7fb87f0'] + +dontcreateinstalldir = 'True' + +components = ['intel-mpi', 'intel-psxe', 'intel-imb'] + +# set up all the mpi commands to default to intel compilers +# set_mpi_wrappers_all = 'True' + +postinstallcmds = [ + 'ln -s %(installdir)s/lib64/libmpi.so %(installdir)s/lib64/libmpich.so', + 'ln -s %(installdir)s/lib64/libmpigc4.so %(installdir)s/lib64/libmpichcxx.so', + 'ln -s %(installdir)s/lib64/libmpigf.so %(installdir)s/lib64/libfmpich.so', + 'ln -s %(installdir)s/lib64/libmpigf.so %(installdir)s/lib64/libmpichf90.so', + 'ln -s %(installdir)s/lib64/libmpi.so %(installdir)s/lib64/libmpl.so', + 'ln -s %(installdir)s/lib64/libmpi.so %(installdir)s/lib64/libopa.so' +] + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gimpi-2017b-OpenBLAS-0.2.20.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gimpi-2017b-OpenBLAS-0.2.20.eb new file mode 100644 index 0000000000..7a2fe0f9ae --- /dev/null +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gimpi-2017b-OpenBLAS-0.2.20.eb @@ -0,0 +1,25 @@ +name = 'ScaLAPACK' +version = '2.0.2' + +homepage = 'http://www.netlib.org/scalapack/' +description = """The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines + redesigned for distributed memory MIMD parallel computers.""" + +toolchain = {'name': 'gimpi', 'version': '2017b'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = [SOURCELOWER_TGZ] +checksums = ['0c74aeae690fe5ee4db7926f49c5d0bb69ce09eea75beb915e00bba07530395c'] + +blaslib = 'OpenBLAS' +blasver = '0.2.20' + +versionsuffix = "-%s-%s" % (blaslib, blasver) + +dependencies = [(blaslib, blasver, '', ('GCC', '6.4.0-2.28'))] + +# parallel build tends to fail, so disabling it +parallel = 1 + +moduleclass = 'numlib' -- GitLab From eb7d8c538def3307b7f92defeda8320b24b51f4d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 19 Sep 2017 14:56:15 +0200 Subject: [PATCH 1555/1603] adding easyconfigs: ncview-2.1.7-intel-2017a.eb --- .../n/ncview/ncview-2.1.7-intel-2017a.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/n/ncview/ncview-2.1.7-intel-2017a.eb diff --git a/easybuild/easyconfigs/n/ncview/ncview-2.1.7-intel-2017a.eb b/easybuild/easyconfigs/n/ncview/ncview-2.1.7-intel-2017a.eb new file mode 100644 index 0000000000..14f46ddbc2 --- /dev/null +++ b/easybuild/easyconfigs/n/ncview/ncview-2.1.7-intel-2017a.eb @@ -0,0 +1,45 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2014 The Cyprus Institute +# Authors:: Thekla Loizou +# License:: MIT/GPL +# +## +easyblock = 'ConfigureMake' + +name = 'ncview' +version = '2.1.7' + +homepage = 'http://meteora.ucsd.edu/~pierce/ncview_home_page.html' +description = """Ncview is a visual browser for netCDF format files. +Typically you would use ncview to get a quick and easy, push-button +look at your netCDF files. You can view simple movies of the data, +view along various dimensions, take a look at the actual data values, +change color maps, invert the data, etc.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'usempi': True, 'pic': True} + +source_urls = ['ftp://cirrus.ucsd.edu/pub/ncview/'] +sources = [SOURCE_TAR_GZ] +checksums = ['a14c2dddac0fc78dad9e4e7e35e2119562589738f4ded55ff6e0eca04d682c82'] + +# specified compiler is hard checked against (full path to) compiler used for netCDF... +preconfigopts = "CC=$(which $CC) " +configopts = "--with-udunits2_incdir=$EBROOTUDUNITS/include --with-udunits2_libdir=$EBROOTUDUNITS/lib " +configopts += "--with-nc-config=$EBROOTNETCDF/bin/nc-config" + +dependencies = [ + ('netCDF', '4.4.1.1'), + ('netCDF-Fortran', '4.4.4'), + ('UDUNITS', '2.2.24'), + ('X11', '20170314'), +] + +sanity_check_paths = { + 'files': ['bin/ncview'], + 'dirs': [], +} + +moduleclass = 'vis' -- GitLab From 50e67ada89c2e07c3e9b03a264473ba74d325ee5 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 19 Sep 2017 15:04:58 +0200 Subject: [PATCH 1556/1603] Re-enable checks for FFTW --- easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-gimpi-2017b.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-gimpi-2017b.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-gimpi-2017b.eb index d94bac964a..1b29288e0d 100644 --- a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-gimpi-2017b.eb +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-gimpi-2017b.eb @@ -12,7 +12,6 @@ source_urls = [homepage] sources = ['fftw-%(version)s-pl2.tar.gz'] checksums = ['a5de35c5c824a78a058ca54278c706cdf3d4abba1c56b63531c2cb05f5d57da2'] -skipsteps = ['test'] -#runtest = 'check' +runtest = 'check' moduleclass = 'numlib' -- GitLab From 4f4b5128af6e40ace609d2148b850a4a2ef4deb4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 19 Sep 2017 18:12:05 +0200 Subject: [PATCH 1557/1603] fix compatibility of ncview with NCL/NCO by using netCDF* on top of HDF5 1.8.18 --- easybuild/easyconfigs/n/ncview/ncview-2.1.7-intel-2017a.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/n/ncview/ncview-2.1.7-intel-2017a.eb b/easybuild/easyconfigs/n/ncview/ncview-2.1.7-intel-2017a.eb index 14f46ddbc2..7579a24f85 100644 --- a/easybuild/easyconfigs/n/ncview/ncview-2.1.7-intel-2017a.eb +++ b/easybuild/easyconfigs/n/ncview/ncview-2.1.7-intel-2017a.eb @@ -31,8 +31,8 @@ configopts = "--with-udunits2_incdir=$EBROOTUDUNITS/include --with-udunits2_libd configopts += "--with-nc-config=$EBROOTNETCDF/bin/nc-config" dependencies = [ - ('netCDF', '4.4.1.1'), - ('netCDF-Fortran', '4.4.4'), + ('netCDF', '4.4.1.1', '-HDF5-1.8.18'), + ('netCDF-Fortran', '4.4.4', '-HDF5-1.8.18'), ('UDUNITS', '2.2.24'), ('X11', '20170314'), ] -- GitLab From e5170cdda29dad58b51c889353aef7c69d6c14d2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 20 Sep 2017 08:51:55 +0200 Subject: [PATCH 1558/1603] adding easyconfigs: scikit-learn-0.19.0-intel-2017a-Python-3.6.1.eb --- ...t-learn-0.19.0-intel-2017a-Python-3.6.1.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100755 easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.19.0-intel-2017a-Python-3.6.1.eb diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.19.0-intel-2017a-Python-3.6.1.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.19.0-intel-2017a-Python-3.6.1.eb new file mode 100755 index 0000000000..327753864d --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.19.0-intel-2017a-Python-3.6.1.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonPackage' + +name = 'scikit-learn' +version = '0.19.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://scikit-learn.org/stable/index.html' +description = """Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, +building upon numpy, scipy, and matplotlib. As a machine-learning module, +it provides versatile tools for data mining and analysis in any field of science and engineering. +It strives to be simple and efficient, accessible to everybody, and reusable in various contexts.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['24f5cb67559e0df27827b1804b197431c08880d2ec9285724fac90906830021f'] + +dependencies = [ + ('Python', '3.6.1'), + ('matplotlib', '2.0.2', versionsuffix + '-libpng-1.6.29'), +] + +options = {'modulename': 'sklearn'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/sklearn'], +} + +moduleclass = 'data' -- GitLab From 20f7795bfee318b0af26a235fb981e60911f25bd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 20 Sep 2017 08:52:19 +0200 Subject: [PATCH 1559/1603] adding easyconfigs: scikit-image-0.13.0-intel-2017a-Python-3.6.1.eb, Pillow-4.2.1-intel-2017a-Python-3.6.1.eb --- .../Pillow-4.2.1-intel-2017a-Python-3.6.1.eb | 28 ++++++++++ ...t-image-0.13.0-intel-2017a-Python-3.6.1.eb | 51 +++++++++++++++++++ 2 files changed, 79 insertions(+) create mode 100644 easybuild/easyconfigs/p/Pillow/Pillow-4.2.1-intel-2017a-Python-3.6.1.eb create mode 100644 easybuild/easyconfigs/s/scikit-image/scikit-image-0.13.0-intel-2017a-Python-3.6.1.eb diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-4.2.1-intel-2017a-Python-3.6.1.eb b/easybuild/easyconfigs/p/Pillow/Pillow-4.2.1-intel-2017a-Python-3.6.1.eb new file mode 100644 index 0000000000..0b05e830a7 --- /dev/null +++ b/easybuild/easyconfigs/p/Pillow/Pillow-4.2.1-intel-2017a-Python-3.6.1.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'Pillow' +version = '4.2.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://pillow.readthedocs.org/' +description = """Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. + PIL is the Python Imaging Library by Fredrik Lundh and Contributors.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['c724f65870e545316f9e82e4c6d608ab5aa9dd82d5185e5b2e72119378740073'] + +dependencies = [ + ('Python', '3.6.1'), + ('libjpeg-turbo', '1.5.2'), + ('libpng', '1.6.29'), + ('zlib', '1.2.11'), + ('LibTIFF', '4.0.8'), + ('freetype', '2.7.1', '-libpng-1.6.29'), +] + +options = {'modulename': 'PIL'} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/s/scikit-image/scikit-image-0.13.0-intel-2017a-Python-3.6.1.eb b/easybuild/easyconfigs/s/scikit-image/scikit-image-0.13.0-intel-2017a-Python-3.6.1.eb new file mode 100644 index 0000000000..071a57a08c --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-image/scikit-image-0.13.0-intel-2017a-Python-3.6.1.eb @@ -0,0 +1,51 @@ +easyblock = 'Bundle' + +name = 'scikit-image' +version = '0.13.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://scikit-learn.org/stable/index.html' +description = """Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, +building upon numpy, scipy, and matplotlib. As a machine-learning module, +it provides versatile tools for data mining and analysis in any field of science and engineering. +It strives to be simple and efficient, accessible to everybody, and reusable in various contexts.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' + +dependencies = [ + ('Python', '3.6.1'), + ('Qhull', '2015.2'), + ('matplotlib', '2.0.2', versionsuffix + '-libpng-1.6.29'), + ('Pillow', '4.2.1', versionsuffix), +] + +exts_list = [ + ('networkx', '1.11', { + 'source_urls': ['https://pypi.python.org/packages/source/n/networkx'], + 'checksums': [ + '0d0e70e10dfb47601cbb3425a00e03e2a2e97477be6f80638fef91d54dd1e4b8', # networkx-1.11.tar.gz + ], + }), + ('scikit-image', '0.13.0', { + 'modulename': 'skimage', + 'source_urls': ['https://pypi.python.org/packages/source/s/scikit-image'], + 'checksums': [ + '77a636bdc08c7668a15951894548c527f0c8c5c2abc86cb850de17551af51e3e', # scikit-image-0.13.0.tar.gz + ], + }), +] + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +# specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module +full_sanity_check = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +moduleclass = 'vis' -- GitLab From 26916de04fdc1671570e6f8c1abfbbd125e465f2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 20 Sep 2017 08:52:45 +0200 Subject: [PATCH 1560/1603] adding easyconfigs: Keras-2.0.8-intel-2017a-Python-3.6.1.eb, h5py-2.7.1-intel-2017a-Python-3.6.1.eb --- .../h5py-2.7.1-intel-2017a-Python-3.6.1.eb | 33 +++++++++++++++++++ .../Keras-2.0.8-intel-2017a-Python-3.6.1.eb | 32 ++++++++++++++++++ 2 files changed, 65 insertions(+) create mode 100644 easybuild/easyconfigs/h/h5py/h5py-2.7.1-intel-2017a-Python-3.6.1.eb create mode 100644 easybuild/easyconfigs/k/Keras/Keras-2.0.8-intel-2017a-Python-3.6.1.eb diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.7.1-intel-2017a-Python-3.6.1.eb b/easybuild/easyconfigs/h/h5py/h5py-2.7.1-intel-2017a-Python-3.6.1.eb new file mode 100644 index 0000000000..356f080aeb --- /dev/null +++ b/easybuild/easyconfigs/h/h5py/h5py-2.7.1-intel-2017a-Python-3.6.1.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonPackage' + +name = 'h5py' +version = '2.7.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.h5py.org/' +description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, + version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous + amounts of data.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'usempi': True} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['180a688311e826ff6ae6d3bda9b5c292b90b28787525ddfcb10a29d5ddcae2cc'] + +# to really use mpi enabled hdf5 we now seem to need a configure step +prebuildopts = ' python setup.py configure --mpi --hdf5=$EBROOTHDF5 && ' + +dependencies = [ + ('Python', '3.6.1'), + ('HDF5', '1.10.1'), + ('pkgconfig', '1.2.2', '-Python-%(pyver)s'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/k/Keras/Keras-2.0.8-intel-2017a-Python-3.6.1.eb b/easybuild/easyconfigs/k/Keras/Keras-2.0.8-intel-2017a-Python-3.6.1.eb new file mode 100644 index 0000000000..94353499b7 --- /dev/null +++ b/easybuild/easyconfigs/k/Keras/Keras-2.0.8-intel-2017a-Python-3.6.1.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonPackage' + +name = 'Keras' +version = '2.0.8' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://keras.io/' +description = """Keras is a minimalist, highly modular neural networks library, written in Python and +capable of running on top of either TensorFlow or Theano.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['899dc6aaed366f20100b9f80cf1093ea5b43eecc74afd1dc63a4e48dfa776ab9'] + +dependencies = [ + ('Python', '3.6.1'), + ('Theano', '0.9.0', versionsuffix), + ('h5py', '2.7.1', versionsuffix), + ('PyYAML', '3.12', versionsuffix), +] + +# it defaults to Tensorflow +modextravars = {'KERAS_BACKEND': 'theano'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'math' -- GitLab From b47c9f026f622ebbc896483b88b2f793c1a935d7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 20 Sep 2017 15:32:09 +0200 Subject: [PATCH 1561/1603] include easyconfigs for OpenCV 3.3.0 on top of both Python 2.7.13 & Python 3.6.1 --- ...OpenCV-3.3.0-intel-2017a-Python-2.7.13.eb} | 1 + .../OpenCV-3.3.0-intel-2017a-Python-3.6.1.eb | 90 +++++++++++++++++++ 2 files changed, 91 insertions(+) rename easybuild/easyconfigs/o/OpenCV/{OpenCV-3.3.0-intel-2017a.eb => OpenCV-3.3.0-intel-2017a-Python-2.7.13.eb} (98%) create mode 100644 easybuild/easyconfigs/o/OpenCV/OpenCV-3.3.0-intel-2017a-Python-3.6.1.eb diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.3.0-intel-2017a.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.3.0-intel-2017a-Python-2.7.13.eb similarity index 98% rename from easybuild/easyconfigs/o/OpenCV/OpenCV-3.3.0-intel-2017a.eb rename to easybuild/easyconfigs/o/OpenCV/OpenCV-3.3.0-intel-2017a-Python-2.7.13.eb index ede04d5755..28f5a61bf4 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.3.0-intel-2017a.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.3.0-intel-2017a-Python-2.7.13.eb @@ -2,6 +2,7 @@ easyblock = 'CMakeMake' name = 'OpenCV' version = '3.3.0' +versionsuffix = '-Python-%(pyver)s' homepage = 'http://opencv.org/' description = """OpenCV (Open Source Computer Vision Library) is an open source computer vision diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.3.0-intel-2017a-Python-3.6.1.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.3.0-intel-2017a-Python-3.6.1.eb new file mode 100644 index 0000000000..8b3e08f063 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.3.0-intel-2017a-Python-3.6.1.eb @@ -0,0 +1,90 @@ +easyblock = 'CMakeMake' + +name = 'OpenCV' +version = '3.3.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://opencv.org/' +description = """OpenCV (Open Source Computer Vision Library) is an open source computer vision + and machine learning software library. OpenCV was built to provide + a common infrastructure for computer vision applications and to accelerate + the use of machine perception in the commercial products.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [ + 'https://github.com/Itseez/opencv/archive/', + # The Hash is version dependent! see 3rdparty/ippicv/downloader.cmake + 'https://raw.githubusercontent.com/Itseez/opencv_3rdparty/81a676001ca8075ada498583e4166079e5744668/ippicv', +] +sources = [ + '%(version)s.zip', + {'filename': 'ippicv_linux_20151201.tgz', 'extract_cmd': "cp %s %(builddir)s"}, +] +checksums = [ + '3546c3837f88177c898e4172942da7a3ca6c4e8e98a33d0cbccb2b499167c5ba', # 3.3.0.zip + '4333833e40afaa22c804169e44f9a63e357e21476b765a5683bcb3760107f0da', # ippicv_linux_20151201.tgz +] + +#patches = ['OpenCV-3.1.0_with_IPP.patch'] + +builddependencies = [ + ('CMake', '3.9.1'), +] + +dependencies = [ + ('Python', '3.6.1'), + ('zlib', '1.2.11'), + ('FFmpeg', '3.3.4'), + ('libjpeg-turbo', '1.5.2'), + ('libpng', '1.6.29'), + ('LibTIFF', '4.0.8'), + ('JasPer', '2.0.12'), + ('Java', '1.8.0_144', '', True), + ('ant', '1.10.1', '-Java-%(javaver)s', True), + ('GLib', '2.53.5'), + ('GTK+', '2.24.31'), +] + +separate_build_dir = True + +preconfigopts = 'export IPPROOT=$EBROOTICC/ipp && ' + +# The destination directory is "linux-" see 3rdparty/ippicv/downloader.cmake +ippicv_dir = '3rdparty/ippicv/downloads/linux-808b791a6eac9ed78d32a7666804320e/' +preconfigopts = "mkdir -p %s && cp -a ../*.tgz %s && " % (ippicv_dir, ippicv_dir) + +configopts = '-DCMAKE_BUILD_TYPE=RELEASE ' +configopts += '-DBUILD_PYTHON_SUPPORT=ON ' +configopts += '-DPYTHON_PACKAGES_PATH=%(installdir)s/lib/python%(pyshortver)s/site-packages ' +configopts += '-DBUILD_NEW_PYTHON_SUPPORT=ON ' +configopts += '-DZLIB_LIBRARY=$EBROOTZLIB/lib/libz.%s ' % SHLIB_EXT +configopts += '-DZLIB_INCLUDE_DIR=$EBROOTZLIB/include ' +configopts += '-DTIFF_LIBRARY=$EBROOTLIBTIFF/lib/libtiff.%s ' % SHLIB_EXT +configopts += '-DTIFF_INCLUDE_DIR=$EBROOTLIBTIFF/include ' +configopts += '-DPNG_LIBRARY=$EBROOTLIBPNG/lib/libpng.%s ' % SHLIB_EXT +configopts += '-DPNG_INCLUDE_DIR=$EBROOTLIBPNG/include ' +configopts += '-DJPEG_LIBRARY=$EBROOTLIBJPEGMINTURBO/lib/libjpeg.%s ' % SHLIB_EXT +configopts += '-DJPEG_INCLUDE_DIR=$EBROOTLIBJPEGMINTURBO/include ' +configopts += '-DJASPER_LIBRARY=$EBROOTJASPER/lib/libjasper.a ' +configopts += '-DJASPER_INCLUDE_DIR=$EBROOTJASPER/include ' +configopts += '-DWITH_IPP=ON ' +configopts += '-DENABLE_SSE=ON -DENABLE_SSE2=ON -DENABLE_SSE3=ON ' +configopts += '-DWITH_CUDA=OFF ' + +postinstallcmds = ["cp 3rdparty/ippicv/ippicv_lnx/lib/intel64/libippicv.* %(installdir)s/lib"] + +sanity_check_paths = { + 'files': ['lib/libopencv_core.%s' % SHLIB_EXT] + + ['lib/python%%(pyshortver)s/site-packages/cv2.%s' % SHLIB_EXT] + + ['lib/libippicv.a'] + + ['bin/opencv_%s' % x for x in ['annotation', 'createsamples', 'traincascade']], + 'dirs': ['include'] +} + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', + 'CLASSPATH': 'share/OpenCV/java', +} + +moduleclass = 'vis' -- GitLab From 6cd28e26d9a315b32d71d0ae3fbe58f540f7f5b8 Mon Sep 17 00:00:00 2001 From: Fokke Dijkstra Date: Wed, 20 Sep 2017 15:56:13 +0200 Subject: [PATCH 1562/1603] Boost 1.61.0 for foss 2016a and Python 3.5.1 --- .../Boost-1.61.0-foss-2016a-Python-3.5.1.eb | 27 +++++++++++++++++++ .../b/Boost/Boost-1.61.0_python3.patch | 24 +++++++++++++++++ 2 files changed, 51 insertions(+) create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.61.0-foss-2016a-Python-3.5.1.eb create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.61.0_python3.patch diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.61.0-foss-2016a-Python-3.5.1.eb b/easybuild/easyconfigs/b/Boost/Boost-1.61.0-foss-2016a-Python-3.5.1.eb new file mode 100644 index 0000000000..059817b2f2 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.61.0-foss-2016a-Python-3.5.1.eb @@ -0,0 +1,27 @@ +name = 'Boost' +version = '1.61.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] + +patches = [ + 'Boost-%(version)s_python3.patch', +] + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('Python', '3.5.1'), +] + +# also build boost_mpi +boost_mpi = True + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.61.0_python3.patch b/easybuild/easyconfigs/b/Boost/Boost-1.61.0_python3.patch new file mode 100644 index 0000000000..279cbfb666 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.61.0_python3.patch @@ -0,0 +1,24 @@ +#Boost checks Python include in $(prefix)/include/python$(version) +#some cases it is in $(prefix)/include/python$(version)m +#see more: https://svn.boost.org/trac/boost/ticket/11120 +# Aug 27th 2016 by B. Hajgato (Free Univeristy Brussels - VUB) +--- boost_1_60_0/tools/build/src/tools/python.jam.org 2015-10-16 20:55:36.000000000 +0200 ++++ boost_1_60_0/tools/build/src/tools/python.jam 2016-07-27 16:20:52.549560154 +0200 +@@ -539,7 +539,16 @@ + } + else + { +- includes ?= $(prefix)/include/python$(version) ; ++ if not($(prefix)/include/python$(version)m) ++ { ++ debug-message "Used include path: $(prefix)/include/python$(version)m" ; ++ includes ?= $(prefix)/include/python$(version)m ; ++ } ++ else ++ { ++ debug-message "Used include path: $(prefix)/include/python$(version)" ; ++ includes ?= $(prefix)/include/python$(version) ; ++ } + + local lib = $(exec-prefix)/lib ; + libraries ?= $(lib)/python$(version)/config $(lib) ; -- GitLab From a1ab0934daff713ca57a6cf36bb4f2da70066a65 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 20 Sep 2017 16:03:46 +0200 Subject: [PATCH 1563/1603] check OpenCV Python bindings using 'import cv2' --- .../o/OpenCV/OpenCV-3.3.0-intel-2017a-Python-2.7.13.eb | 7 +++---- .../o/OpenCV/OpenCV-3.3.0-intel-2017a-Python-3.6.1.eb | 7 +++---- 2 files changed, 6 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.3.0-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.3.0-intel-2017a-Python-2.7.13.eb index 28f5a61bf4..86d85fc759 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.3.0-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.3.0-intel-2017a-Python-2.7.13.eb @@ -75,12 +75,11 @@ configopts += '-DWITH_CUDA=OFF ' postinstallcmds = ["cp 3rdparty/ippicv/ippicv_lnx/lib/intel64/libippicv.* %(installdir)s/lib"] sanity_check_paths = { - 'files': ['lib/libopencv_core.%s' % SHLIB_EXT] + - ['lib/python%%(pyshortver)s/site-packages/cv2.%s' % SHLIB_EXT] + - ['lib/libippicv.a'] + + 'files': ['lib/libopencv_core.%s' % SHLIB_EXT, 'lib/libippicv.a'] + ['bin/opencv_%s' % x for x in ['annotation', 'createsamples', 'traincascade']], - 'dirs': ['include'] + 'dirs': ['include', 'lib/python%(pyshortver)s/site-packages'] } +sanity_check_commands = ["python -c 'import cv2'"] modextrapaths = { 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.3.0-intel-2017a-Python-3.6.1.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.3.0-intel-2017a-Python-3.6.1.eb index 8b3e08f063..c55533839f 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.3.0-intel-2017a-Python-3.6.1.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.3.0-intel-2017a-Python-3.6.1.eb @@ -75,12 +75,11 @@ configopts += '-DWITH_CUDA=OFF ' postinstallcmds = ["cp 3rdparty/ippicv/ippicv_lnx/lib/intel64/libippicv.* %(installdir)s/lib"] sanity_check_paths = { - 'files': ['lib/libopencv_core.%s' % SHLIB_EXT] + - ['lib/python%%(pyshortver)s/site-packages/cv2.%s' % SHLIB_EXT] + - ['lib/libippicv.a'] + + 'files': ['lib/libopencv_core.%s' % SHLIB_EXT, 'lib/libippicv.a'] + ['bin/opencv_%s' % x for x in ['annotation', 'createsamples', 'traincascade']], - 'dirs': ['include'] + 'dirs': ['include', 'lib/python%(pyshortver)s/site-packages'] } +sanity_check_commands = ["python -c 'import cv2'"] modextrapaths = { 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', -- GitLab From 9a71a96c80719476e0eac20a98edda597bb26859 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Wed, 20 Sep 2017 16:08:48 +0200 Subject: [PATCH 1564/1603] use lower version of intel toolchain for compatibility with CUDA/8.0.61 --- ...CUDA-2016.1.2-intel-2016b-Python-2.7.12.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyCUDA/PyCUDA-2016.1.2-intel-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2016.1.2-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2016.1.2-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000..ca33a5b257 --- /dev/null +++ b/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2016.1.2-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonPackage' + +name = 'PyCUDA' +version = '2016.1.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://mathema.tician.de/software/pycuda' +description = """PyCUDA lets you access Nvidia’s CUDA parallel computation API from Python.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('Python', '2.7.12'), + ('CUDA', '8.0.61', '', True), + ('Boost', '1.61.0', versionsuffix), +] + +prebuildopts = "./configure.py --cuda-root=$EBROOTCUDA --boost-inc-dir=$EBROOTBOOST/include/boost/ " +prebuildopts += "--boost-lib-dir=$EBROOTBOOST/lib/ --no-use-shipped-boost --boost-python-libname=boost_python && " + +options = {'modulename': '%(namelower)s'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'lang' -- GitLab From 5772038807d4f1c891c0afafdb89673b879627a8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 20 Sep 2017 16:49:32 +0200 Subject: [PATCH 1565/1603] drop commented out 'patches' line --- .../o/OpenCV/OpenCV-3.3.0-intel-2017a-Python-2.7.13.eb | 2 -- .../o/OpenCV/OpenCV-3.3.0-intel-2017a-Python-3.6.1.eb | 2 -- 2 files changed, 4 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.3.0-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.3.0-intel-2017a-Python-2.7.13.eb index 86d85fc759..9fa6eb12d3 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.3.0-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.3.0-intel-2017a-Python-2.7.13.eb @@ -26,8 +26,6 @@ checksums = [ '4333833e40afaa22c804169e44f9a63e357e21476b765a5683bcb3760107f0da', # ippicv_linux_20151201.tgz ] -#patches = ['OpenCV-3.1.0_with_IPP.patch'] - builddependencies = [ ('CMake', '3.9.1'), ] diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.3.0-intel-2017a-Python-3.6.1.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.3.0-intel-2017a-Python-3.6.1.eb index c55533839f..5df44827ab 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.3.0-intel-2017a-Python-3.6.1.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.3.0-intel-2017a-Python-3.6.1.eb @@ -26,8 +26,6 @@ checksums = [ '4333833e40afaa22c804169e44f9a63e357e21476b765a5683bcb3760107f0da', # ippicv_linux_20151201.tgz ] -#patches = ['OpenCV-3.1.0_with_IPP.patch'] - builddependencies = [ ('CMake', '3.9.1'), ] -- GitLab From f334238fc57624d8ccadf452e3ed173a89e49270 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 20 Sep 2017 17:16:24 +0200 Subject: [PATCH 1566/1603] add patch for Boost 1.64.0 to fix missing include --- .../easyconfigs/b/Boost/Boost-1.64.0-intel-2017a.eb | 5 +++++ .../Boost-1.64.0_fix-include-array_wrapper.patch | 13 +++++++++++++ 2 files changed, 18 insertions(+) create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.64.0_fix-include-array_wrapper.patch diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.64.0-intel-2017a.eb b/easybuild/easyconfigs/b/Boost/Boost-1.64.0-intel-2017a.eb index 981136de99..446a15ecf7 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.64.0-intel-2017a.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.64.0-intel-2017a.eb @@ -9,6 +9,11 @@ toolchainopts = {'pic': True, 'usempi': True} source_urls = [SOURCEFORGE_SOURCE] sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] +patches = ['Boost-%(version)s_fix-include-array_wrapper.patch'] +checksums = [ + '0445c22a5ef3bd69f5dfb48354978421a85ab395254a26b1ffb0aa1bfd63a108', # boost_1_64_0.tar.gz + 'aaf0657246d9cde4857954b6d1b9f9454370896b2077294461357d47951ca891', # Boost-1.64.0_fix-include-array_wrapper.patch +] dependencies = [ ('bzip2', '1.0.6'), diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.64.0_fix-include-array_wrapper.patch b/easybuild/easyconfigs/b/Boost/Boost-1.64.0_fix-include-array_wrapper.patch new file mode 100644 index 0000000000..dd7ab54a9e --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.64.0_fix-include-array_wrapper.patch @@ -0,0 +1,13 @@ +see also https://svn.boost.org/trac10/ticket/12516 +and https://github.com/boostorg/serialization/commit/1d86261581230e2dc5d617a9b16287d326f3e229 +--- a/include/boost/serialization/array.hpp ++++ b/include/boost/serialization/array.hpp +@@ -23,6 +23,8 @@ namespace std{ + } // namespace std + #endif + ++#include ++ + #ifndef BOOST_NO_CXX11_HDR_ARRAY + + #include -- GitLab From 024d5e7bd9f18d5a0dae0abd946cadc484444448 Mon Sep 17 00:00:00 2001 From: Fokke Dijkstra Date: Wed, 20 Sep 2017 17:32:52 +0200 Subject: [PATCH 1567/1603] Changed checksum to sha256. --- easybuild/easyconfigs/h/HTSlib/HTSlib-1.4.1-foss-2016a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/h/HTSlib/HTSlib-1.4.1-foss-2016a.eb b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.4.1-foss-2016a.eb index a04c1df219..c2312d38ff 100644 --- a/easybuild/easyconfigs/h/HTSlib/HTSlib-1.4.1-foss-2016a.eb +++ b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.4.1-foss-2016a.eb @@ -20,7 +20,7 @@ toolchain = {'name': 'foss', 'version': '2016a'} source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s/'] sources = [SOURCELOWER_TAR_BZ2] -checksums = ['e549fee04d95c1cf8f46347e9e9bbd93'] +checksums = ['85d2dd59ffa614a307d64e9f74a9f999f0912661a8b802ebcc95f537d39933b3'] # cURL added for S3 support dependencies = [ -- GitLab From 6818d3b6298d775625bde8aebd5cb46115226b0a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 20 Sep 2017 20:35:06 +0200 Subject: [PATCH 1568/1603] adding easyconfigs: nanonet-2.0.0-intel-2017a-Python-2.7.13.eb, h5py-2.7.1-intel-2017a-Python-2.7.13.eb --- .../h5py-2.7.1-intel-2017a-Python-2.7.13.eb | 33 +++++++++++ ...nanonet-2.0.0-intel-2017a-Python-2.7.13.eb | 56 +++++++++++++++++++ 2 files changed, 89 insertions(+) create mode 100644 easybuild/easyconfigs/h/h5py/h5py-2.7.1-intel-2017a-Python-2.7.13.eb create mode 100644 easybuild/easyconfigs/n/nanonet/nanonet-2.0.0-intel-2017a-Python-2.7.13.eb diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.7.1-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/h/h5py/h5py-2.7.1-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..a34bfde78b --- /dev/null +++ b/easybuild/easyconfigs/h/h5py/h5py-2.7.1-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonPackage' + +name = 'h5py' +version = '2.7.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.h5py.org/' +description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, + version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous + amounts of data.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'usempi': True} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['180a688311e826ff6ae6d3bda9b5c292b90b28787525ddfcb10a29d5ddcae2cc'] + +# to really use mpi enabled hdf5 we now seem to need a configure step +prebuildopts = ' python setup.py configure --mpi --hdf5=$EBROOTHDF5 && ' + +dependencies = [ + ('Python', '2.7.13'), + ('HDF5', '1.10.1'), + ('pkgconfig', '1.2.2', '-Python-%(pyver)s'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/nanonet/nanonet-2.0.0-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/n/nanonet/nanonet-2.0.0-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..2408eb945f --- /dev/null +++ b/easybuild/easyconfigs/n/nanonet/nanonet-2.0.0-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,56 @@ +easyblock = 'Bundle' + +name = 'nanonet' +version = '2.0.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/nanoporetech/nanonet' +description = "Nanonet provides recurrent neural network basecalling for Oxford Nanopore MinION data." + +toolchain = {'name': 'intel', 'version': '2017a'} + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' + +dependencies = [ + ('Python', '2.7.13'), + ('h5py', '2.7.1', versionsuffix), + ('netcdf4-python', '1.2.9', versionsuffix), +] + +exts_list = [ + ('myriad', '0.1.4', { + 'source_tmpl': 'myriad-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/m/myriad'], + 'checksums': [ + 'ae1d836f0e9c37b90b94c185555e485e2c7e36458a4709e39e4aefc3945fdfd5', # myriad-0.1.4.zip + ], + }), + ('watchdog', '0.8.3', { + 'source_urls': ['https://pypi.python.org/packages/source/w/watchdog'], + 'checksums': [ + '7e65882adb7746039b6f3876ee174952f8eaaa34491ba34333ddf1fe35de4162', # watchdog-0.8.3.tar.gz + ], + }), + ('nanonet', '2.0.0', { + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/nanoporetech/nanonet/archive'], + 'installopts': 'with2d', + 'checksums': [ + '9896fa8ecf012505a7cc5610afd54323271ec6b966ce0a0ac9fb7be4149da9d9', # v2.0.0.tar.gz + ], + }), +] + +# specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module +full_sanity_check = True + +sanity_check_paths = { + 'files': ['bin/nanonet2d', 'bin/nanonetcall', 'bin/nanonettrain'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} +sanity_check_commands = ["nanonet2d --help"] + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +moduleclass = 'bio' -- GitLab From 341de8497d53f7b3844ec9ec30770fbfcc6029a7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 20 Sep 2017 20:51:01 +0200 Subject: [PATCH 1569/1603] adding easyconfigs: Boost-1.65.1-intel-2017a-Python-2.7.13.eb --- .../Boost-1.65.1-intel-2017a-Python-2.7.13.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.65.1-intel-2017a-Python-2.7.13.eb diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.65.1-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/b/Boost/Boost-1.65.1-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..fbc1037c7d --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.65.1-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,24 @@ +name = 'Boost' +version = '1.65.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.boost.org/' +description = "Boost provides free peer-reviewed portable C++ source libraries." + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'usempi': True, 'pic': True} + +source_urls = ['https://sourceforge.net/projects/%(namelower)s/files/%(namelower)s/%(version)s'] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] +checksums = ['a13de2c8fbad635e6ba9c8f8714a0e6b4264b60a29b964b940a22554705b6b60'] + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.11'), + ('Python', '2.7.13'), +] + +# also build boost_mpi +boost_mpi = True + +moduleclass = 'devel' -- GitLab From 9e5cc648d976a5545b7ea14118f0f416d1a63216 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 20 Sep 2017 21:21:32 +0200 Subject: [PATCH 1570/1603] add missing Boost & PyYAML dependencies for nanonet + dep pkgs for watchdog --- .../nanonet-2.0.0-intel-2017a-Python-2.7.13.eb | 16 +++++++++++++++- 1 file changed, 15 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/nanonet/nanonet-2.0.0-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/n/nanonet/nanonet-2.0.0-intel-2017a-Python-2.7.13.eb index 2408eb945f..29924d9a58 100644 --- a/easybuild/easyconfigs/n/nanonet/nanonet-2.0.0-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/n/nanonet/nanonet-2.0.0-intel-2017a-Python-2.7.13.eb @@ -16,6 +16,8 @@ dependencies = [ ('Python', '2.7.13'), ('h5py', '2.7.1', versionsuffix), ('netcdf4-python', '1.2.9', versionsuffix), + ('PyYAML', '3.12', versionsuffix), + ('Boost', '1.64.0', versionsuffix), # must stick to 1.64.0, using 1.65.x leads to build failures ] exts_list = [ @@ -26,6 +28,18 @@ exts_list = [ 'ae1d836f0e9c37b90b94c185555e485e2c7e36458a4709e39e4aefc3945fdfd5', # myriad-0.1.4.zip ], }), + ('pathtools', '0.1.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pathtools'], + 'checksums': [ + '7c35c5421a39bb82e58018febd90e3b6e5db34c5443aaaf742b3f33d4655f1c0', # pathtools-0.1.2.tar.gz + ], + }), + ('argh', '0.26.2', { + 'source_urls': ['https://pypi.python.org/packages/source/a/argh'], + 'checksums': [ + 'e9535b8c84dc9571a48999094fda7f33e63c3f1b74f3e5f3ac0105a58405bb65', # argh-0.26.2.tar.gz + ], + }), ('watchdog', '0.8.3', { 'source_urls': ['https://pypi.python.org/packages/source/w/watchdog'], 'checksums': [ @@ -33,9 +47,9 @@ exts_list = [ ], }), ('nanonet', '2.0.0', { + 'installopts': 'with2d', 'source_tmpl': 'v%(version)s.tar.gz', 'source_urls': ['https://github.com/nanoporetech/nanonet/archive'], - 'installopts': 'with2d', 'checksums': [ '9896fa8ecf012505a7cc5610afd54323271ec6b966ce0a0ac9fb7be4149da9d9', # v2.0.0.tar.gz ], -- GitLab From 8ebf4b78a81a21bd86ff6c9d912d22b1b290366b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 20 Sep 2017 21:26:21 +0200 Subject: [PATCH 1571/1603] add easyconfig for Boost dep of nanonet --- .../Boost-1.64.0-intel-2017a-Python-2.7.13.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.64.0-intel-2017a-Python-2.7.13.eb diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.64.0-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/b/Boost/Boost-1.64.0-intel-2017a-Python-2.7.13.eb new file mode 100644 index 0000000000..4d835046ac --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.64.0-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,24 @@ +name = 'Boost' +version = '1.64.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.boost.org/' +description = "Boost provides free peer-reviewed portable C++ source libraries." + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'usempi': True, 'pic': True} + +source_urls = ['https://sourceforge.net/projects/%(namelower)s/files/%(namelower)s/%(version)s'] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] +checksums = ['0445c22a5ef3bd69f5dfb48354978421a85ab395254a26b1ffb0aa1bfd63a108'] + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.11'), + ('Python', '2.7.13'), +] + +# also build boost_mpi +boost_mpi = True + +moduleclass = 'devel' -- GitLab From 5f8a1212b6faefef5ab436258891459814dc8f9c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 21 Sep 2017 11:51:41 +0200 Subject: [PATCH 1572/1603] adding easyconfigs: Albacore-2.0.2-intel-2017a-Python-3.6.1.eb, numpy-1.13.1-intel-2017a-Python-3.6.1.eb --- ...Albacore-2.0.2-intel-2017a-Python-3.6.1.eb | 55 +++++++++++++++++++ .../numpy-1.13.1-intel-2017a-Python-3.6.1.eb | 26 +++++++++ 2 files changed, 81 insertions(+) create mode 100644 easybuild/easyconfigs/a/Albacore/Albacore-2.0.2-intel-2017a-Python-3.6.1.eb create mode 100644 easybuild/easyconfigs/n/numpy/numpy-1.13.1-intel-2017a-Python-3.6.1.eb diff --git a/easybuild/easyconfigs/a/Albacore/Albacore-2.0.2-intel-2017a-Python-3.6.1.eb b/easybuild/easyconfigs/a/Albacore/Albacore-2.0.2-intel-2017a-Python-3.6.1.eb new file mode 100644 index 0000000000..b4bf5a35ab --- /dev/null +++ b/easybuild/easyconfigs/a/Albacore/Albacore-2.0.2-intel-2017a-Python-3.6.1.eb @@ -0,0 +1,55 @@ +easyblock = 'Bundle' + +name = 'Albacore' +version = '2.0.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://community.nanoporetech.com/protocols/albacore-offline-basecalli' +description = """Albacore is a software project that provides an entry point to the Oxford Nanopore basecalling + algorithms.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' + +pyver = '3.6.1' +pymajmin = ''.join(pyver.split('.')[:2]) +dependencies = [ + ('Python', pyver), + ('numpy' ,'1.13.1', versionsuffix), + ('h5py', '2.7.1', versionsuffix), +] + +exts_list = [ + ('ont-fast5-api', '0.4.1', { + 'source_urls': ['https://pypi.python.org/packages/source/o/ont-fast5-api'], + 'checksums': ['9c738b592613f5013c4cd3001c4448b5378454ce92e63ff795d134a4eca30fd0'], + 'modulename': 'ont_fast5_api', + }), + ('progressbar33', '2.4', { + 'source_urls': ['https://pypi.python.org/packages/source/p/progressbar33'], + 'checksums': ['51fe0d9b3b4023db2f983eeccdfc8c9846b84db8443b9bee002c7f58f4376eff'], + 'modulename': 'progressbar', + }), + (name, version, { + 'source_tmpl': 'ont_albacore-%%(version)s-cp%(pyv)s-cp%(pyv)sm-manylinux1_x86_64.whl' % {'pyv': pymajmin}, + 'source_urls': ['https://mirror.oxfordnanoportal.com/software/analysis/'], + 'checksums': ['5473d3cdededf592cff73d8130fa1e483d51e789d46403eec7b5ff3b478db5e2'], + 'unpack_sources': False, + 'use_pip': True, + }), +] + +# specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module +full_sanity_check = True + +sanity_check_paths = { + 'files': ['bin/full_1dsq_basecaller.py', 'bin/paired_read_basecaller.py', 'bin/read_fast5_basecaller.py'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} +sanity_check_commands = ["read_fast5_basecaller.py --help"] + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/n/numpy/numpy-1.13.1-intel-2017a-Python-3.6.1.eb b/easybuild/easyconfigs/n/numpy/numpy-1.13.1-intel-2017a-Python-3.6.1.eb new file mode 100644 index 0000000000..f74e6368fc --- /dev/null +++ b/easybuild/easyconfigs/n/numpy/numpy-1.13.1-intel-2017a-Python-3.6.1.eb @@ -0,0 +1,26 @@ +name = 'numpy' +version = '1.13.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.numpy.org' +description = """NumPy is the fundamental package for scientific computing with Python. It contains among other things: + a powerful N-dimensional array object, sophisticated (broadcasting) functions, tools for integrating C/C++ and Fortran + code, useful linear algebra, Fourier transform, and random number capabilities. Besides its obvious scientific uses, + NumPy can also be used as an efficient multi-dimensional container of generic data. Arbitrary data-types can be + defined. This allows NumPy to seamlessly and speedily integrate with a wide variety of databases.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_ZIP] +patches = ['numpy-1.12.0-mkl.patch'] +checksums = [ + 'c9b0283776085cb2804efff73e9955ca279ba4edafd58d3ead70b61d209c4fbb', # numpy-1.13.1.zip + 'f212296ed289eb1b4e3f703997499dee8a2cdd0af78b55e017477487b6377ca4', # numpy-1.12.0-mkl.patch +] + +dependencies = [ + ('Python', '3.6.1'), +] + +moduleclass = 'math' -- GitLab From f65829d7c03bc7fd0dd385b26e5cbf485f20c42f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 21 Sep 2017 12:03:10 +0200 Subject: [PATCH 1573/1603] fix Albacore homepage --- .../a/Albacore/Albacore-2.0.2-intel-2017a-Python-3.6.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/Albacore/Albacore-2.0.2-intel-2017a-Python-3.6.1.eb b/easybuild/easyconfigs/a/Albacore/Albacore-2.0.2-intel-2017a-Python-3.6.1.eb index b4bf5a35ab..d897059032 100644 --- a/easybuild/easyconfigs/a/Albacore/Albacore-2.0.2-intel-2017a-Python-3.6.1.eb +++ b/easybuild/easyconfigs/a/Albacore/Albacore-2.0.2-intel-2017a-Python-3.6.1.eb @@ -4,7 +4,7 @@ name = 'Albacore' version = '2.0.2' versionsuffix = '-Python-%(pyver)s' -homepage = 'https://community.nanoporetech.com/protocols/albacore-offline-basecalli' +homepage = 'https://community.nanoporetech.com/protocols/albacore-offline-basecalli/v/abec_2003_v1_revz_29nov2016' description = """Albacore is a software project that provides an entry point to the Oxford Nanopore basecalling algorithms.""" -- GitLab From 68e357cbb6f1b40ad034ff30b34c809b660fe413 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Thu, 21 Sep 2017 12:07:19 +0200 Subject: [PATCH 1574/1603] add sha256 checksum --- .../p/PyCUDA/PyCUDA-2016.1.2-intel-2016b-Python-2.7.12.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2016.1.2-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2016.1.2-intel-2016b-Python-2.7.12.eb index ca33a5b257..2899a206f1 100644 --- a/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2016.1.2-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2016.1.2-intel-2016b-Python-2.7.12.eb @@ -11,6 +11,7 @@ toolchain = {'name': 'intel', 'version': '2016b'} source_urls = [PYPI_LOWER_SOURCE] sources = [SOURCELOWER_TAR_GZ] +checksums = ['a7dbdac7e2f0c0d2ad98f5f281d5a9d29d6673b3c20210e261b96e9a2d0b6e37'] dependencies = [ ('Python', '2.7.12'), -- GitLab From f6dbde53b3a938046a8de4d7a7304b88eb6d6fc5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 21 Sep 2017 12:26:42 +0200 Subject: [PATCH 1575/1603] fix style issue --- .../a/Albacore/Albacore-2.0.2-intel-2017a-Python-3.6.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/Albacore/Albacore-2.0.2-intel-2017a-Python-3.6.1.eb b/easybuild/easyconfigs/a/Albacore/Albacore-2.0.2-intel-2017a-Python-3.6.1.eb index d897059032..ca51a6691f 100644 --- a/easybuild/easyconfigs/a/Albacore/Albacore-2.0.2-intel-2017a-Python-3.6.1.eb +++ b/easybuild/easyconfigs/a/Albacore/Albacore-2.0.2-intel-2017a-Python-3.6.1.eb @@ -17,7 +17,7 @@ pyver = '3.6.1' pymajmin = ''.join(pyver.split('.')[:2]) dependencies = [ ('Python', pyver), - ('numpy' ,'1.13.1', versionsuffix), + ('numpy', '1.13.1', versionsuffix), ('h5py', '2.7.1', versionsuffix), ] -- GitLab From 1bf6d1e082b1b10787db61f48c4a1bcefbe2c02a Mon Sep 17 00:00:00 2001 From: Xavier Besseron Date: Thu, 21 Sep 2017 12:37:28 +0200 Subject: [PATCH 1576/1603] Disable optarch --- .../easyconfigs/v/Valgrind/Valgrind-3.11.0-intel-2016a.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/v/Valgrind/Valgrind-3.11.0-intel-2016a.eb b/easybuild/easyconfigs/v/Valgrind/Valgrind-3.11.0-intel-2016a.eb index ec140b0ac3..a30c0a1433 100644 --- a/easybuild/easyconfigs/v/Valgrind/Valgrind-3.11.0-intel-2016a.eb +++ b/easybuild/easyconfigs/v/Valgrind/Valgrind-3.11.0-intel-2016a.eb @@ -10,6 +10,7 @@ sources = [SOURCELOWER_TAR_BZ2] source_urls = ['http://valgrind.org/downloads/'] toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'optarch': False} configopts = ' --with-mpicc="$MPICC"' @@ -19,8 +20,7 @@ binaries = [ ] sanity_check_paths = { - 'files': ['bin/%s' % x for x in binaries] - + ['lib/valgrind/libmpiwrap-amd64-linux.%s' % SHLIB_EXT], + 'files': ['bin/%s' % x for x in binaries] + ['lib/valgrind/libmpiwrap-amd64-linux.so'], 'dirs': [] } -- GitLab From be547d2f4cbb97dd67988df3e02564620b5421e0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 21 Sep 2017 12:39:33 +0200 Subject: [PATCH 1577/1603] adding easyconfigs: Valgrind-3.13.0-intel-2017a.eb --- .../v/Valgrind/Valgrind-3.13.0-intel-2017a.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/v/Valgrind/Valgrind-3.13.0-intel-2017a.eb diff --git a/easybuild/easyconfigs/v/Valgrind/Valgrind-3.13.0-intel-2017a.eb b/easybuild/easyconfigs/v/Valgrind/Valgrind-3.13.0-intel-2017a.eb new file mode 100644 index 0000000000..e0b621f67d --- /dev/null +++ b/easybuild/easyconfigs/v/Valgrind/Valgrind-3.13.0-intel-2017a.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'Valgrind' +version = '3.13.0' + +homepage = 'http://valgrind.org/downloads/' +description = "Valgrind: Debugging and profiling tools" + +source_urls = [ + 'ftp://sourceware.org/pub/valgrind/', + 'http://www.mirrorservice.org/sites/sourceware.org/pub/valgrind/', +] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['d76680ef03f00cd5e970bbdcd4e57fb1f6df7d2e2c071635ef2be74790190c3b'] + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'optarch': False} + +configopts = ' --with-mpicc="$MPICC"' + +binaries = [ + 'callgrind_annotate', 'callgrind_control', 'cg_annotate', 'cg_diff', + 'cg_merge', 'ms_print', 'valgrind', 'valgrind-listener', 'vgdb' +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in binaries] + + ['lib/valgrind/libmpiwrap-amd64-linux.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'debugger' -- GitLab From c592a12aa9384645940864f921573e97fb1a8dde Mon Sep 17 00:00:00 2001 From: Xavier Besseron Date: Thu, 21 Sep 2017 12:44:35 +0200 Subject: [PATCH 1578/1603] Use SHLIB_EXT for shared lib name --- .../easyconfigs/v/Valgrind/Valgrind-3.11.0-intel-2016a.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/v/Valgrind/Valgrind-3.11.0-intel-2016a.eb b/easybuild/easyconfigs/v/Valgrind/Valgrind-3.11.0-intel-2016a.eb index a30c0a1433..52fd021d39 100644 --- a/easybuild/easyconfigs/v/Valgrind/Valgrind-3.11.0-intel-2016a.eb +++ b/easybuild/easyconfigs/v/Valgrind/Valgrind-3.11.0-intel-2016a.eb @@ -20,7 +20,8 @@ binaries = [ ] sanity_check_paths = { - 'files': ['bin/%s' % x for x in binaries] + ['lib/valgrind/libmpiwrap-amd64-linux.so'], + 'files': ['bin/%s' % x for x in binaries] + + ['lib/valgrind/libmpiwrap-amd64-linux.%s' % SHLIB_EXT], 'dirs': [] } -- GitLab From 2af19de7810fa536d6d991d2561242d19bd1f378 Mon Sep 17 00:00:00 2001 From: Xavier Besseron Date: Thu, 21 Sep 2017 12:45:28 +0200 Subject: [PATCH 1579/1603] Add bonus easyconfig Valgrind-3.11.0-intel-2017a.eb --- .../v/Valgrind/Valgrind-3.11.0-intel-2017a.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/v/Valgrind/Valgrind-3.11.0-intel-2017a.eb diff --git a/easybuild/easyconfigs/v/Valgrind/Valgrind-3.11.0-intel-2017a.eb b/easybuild/easyconfigs/v/Valgrind/Valgrind-3.11.0-intel-2017a.eb new file mode 100644 index 0000000000..f4ee1bb95d --- /dev/null +++ b/easybuild/easyconfigs/v/Valgrind/Valgrind-3.11.0-intel-2017a.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'Valgrind' +version = '3.11.0' + +homepage = 'http://valgrind.org/downloads/' +description = "Valgrind: Debugging and profiling tools" + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://valgrind.org/downloads/'] + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'optarch': False} + +configopts = ' --with-mpicc="$MPICC"' + +binaries = [ + 'callgrind_annotate', 'callgrind_control', 'cg_annotate', 'cg_diff', + 'cg_merge', 'ms_print', 'valgrind', 'valgrind-listener', 'vgdb' +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in binaries] + + ['lib/valgrind/libmpiwrap-amd64-linux.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'debugger' -- GitLab From 16b0b69c7ec34be7c7779cd9a3e580647ab92184 Mon Sep 17 00:00:00 2001 From: Fokke Dijkstra Date: Thu, 21 Sep 2017 12:48:41 +0200 Subject: [PATCH 1580/1603] Added checksums and moved patch into a single line. --- .../b/Boost/Boost-1.61.0-foss-2016a-Python-3.5.1.eb | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.61.0-foss-2016a-Python-3.5.1.eb b/easybuild/easyconfigs/b/Boost/Boost-1.61.0-foss-2016a-Python-3.5.1.eb index 059817b2f2..59134e3929 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.61.0-foss-2016a-Python-3.5.1.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.61.0-foss-2016a-Python-3.5.1.eb @@ -10,9 +10,11 @@ toolchainopts = {'pic': True, 'usempi': True} source_urls = [SOURCEFORGE_SOURCE] sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] +patches = ['Boost-%(version)s_python3.patch'] -patches = [ - 'Boost-%(version)s_python3.patch', +checksums = [ + 'a77c7cc660ec02704c6884fbb20c552d52d60a18f26573c9cee0788bf00ed7e6', # boost_1_61_0.tar.gz + 'c5a19baf309f63c28cf46d6cf1b9f7b9a78a525902a24c5919091d6075926985', # Boost-1.61.0_python3.patch ] dependencies = [ -- GitLab From 28f2063493399254d7665d487181e5d4f1c84d90 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 21 Sep 2017 12:59:02 +0200 Subject: [PATCH 1581/1603] remove PyCUDA easyconfig for intel/2017a, doesn't work due to incompatibility between GCC 6.3.0 & CUDA 8 --- ...CUDA-2016.1.2-intel-2017a-Python-2.7.13.eb | 31 ------------------- 1 file changed, 31 deletions(-) delete mode 100644 easybuild/easyconfigs/p/PyCUDA/PyCUDA-2016.1.2-intel-2017a-Python-2.7.13.eb diff --git a/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2016.1.2-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2016.1.2-intel-2017a-Python-2.7.13.eb deleted file mode 100644 index fd93f89fda..0000000000 --- a/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2016.1.2-intel-2017a-Python-2.7.13.eb +++ /dev/null @@ -1,31 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'PyCUDA' -version = '2016.1.2' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'http://mathema.tician.de/software/pycuda' -description = """PyCUDA lets you access Nvidia’s CUDA parallel computation API from Python.""" - -toolchain = {'name': 'intel', 'version': '2017a'} - -source_urls = [PYPI_LOWER_SOURCE] -sources = [SOURCELOWER_TAR_GZ] - -dependencies = [ - ('Python', '2.7.13'), - ('CUDA', '8.0.61', '', True), - ('Boost', '1.63.0', versionsuffix), -] - -prebuildopts = "./configure.py --cuda-root=$EBROOTCUDA --boost-inc-dir=$EBROOTBOOST/include/boost/ " -prebuildopts += "--boost-lib-dir=$EBROOTBOOST/lib/ --no-use-shipped-boost --boost-python-libname=boost_python && " - -options = {'modulename': '%(namelower)s'} - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -moduleclass = 'lang' -- GitLab From 0c2105b7a892a0176253a527ab6e36ef854c859f Mon Sep 17 00:00:00 2001 From: Xavier Besseron Date: Thu, 21 Sep 2017 13:01:23 +0200 Subject: [PATCH 1582/1603] Delete Valgrind-3.11.0-intel-2017a.eb --- .../v/Valgrind/Valgrind-3.11.0-intel-2017a.eb | 28 ------------------- 1 file changed, 28 deletions(-) delete mode 100644 easybuild/easyconfigs/v/Valgrind/Valgrind-3.11.0-intel-2017a.eb diff --git a/easybuild/easyconfigs/v/Valgrind/Valgrind-3.11.0-intel-2017a.eb b/easybuild/easyconfigs/v/Valgrind/Valgrind-3.11.0-intel-2017a.eb deleted file mode 100644 index f4ee1bb95d..0000000000 --- a/easybuild/easyconfigs/v/Valgrind/Valgrind-3.11.0-intel-2017a.eb +++ /dev/null @@ -1,28 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'Valgrind' -version = '3.11.0' - -homepage = 'http://valgrind.org/downloads/' -description = "Valgrind: Debugging and profiling tools" - -sources = [SOURCELOWER_TAR_BZ2] -source_urls = ['http://valgrind.org/downloads/'] - -toolchain = {'name': 'intel', 'version': '2017a'} -toolchainopts = {'optarch': False} - -configopts = ' --with-mpicc="$MPICC"' - -binaries = [ - 'callgrind_annotate', 'callgrind_control', 'cg_annotate', 'cg_diff', - 'cg_merge', 'ms_print', 'valgrind', 'valgrind-listener', 'vgdb' -] - -sanity_check_paths = { - 'files': ['bin/%s' % x for x in binaries] - + ['lib/valgrind/libmpiwrap-amd64-linux.%s' % SHLIB_EXT], - 'dirs': [] -} - -moduleclass = 'debugger' -- GitLab From f23f51e89d729b585d557b25fd2a0b2d8563cc43 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 21 Sep 2017 13:20:23 +0200 Subject: [PATCH 1583/1603] move up 'toolchain' spec in Valgrind easyconfig --- .../easyconfigs/v/Valgrind/Valgrind-3.13.0-intel-2017a.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/v/Valgrind/Valgrind-3.13.0-intel-2017a.eb b/easybuild/easyconfigs/v/Valgrind/Valgrind-3.13.0-intel-2017a.eb index e0b621f67d..3dd5dbb5a0 100644 --- a/easybuild/easyconfigs/v/Valgrind/Valgrind-3.13.0-intel-2017a.eb +++ b/easybuild/easyconfigs/v/Valgrind/Valgrind-3.13.0-intel-2017a.eb @@ -6,6 +6,9 @@ version = '3.13.0' homepage = 'http://valgrind.org/downloads/' description = "Valgrind: Debugging and profiling tools" +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'optarch': False} + source_urls = [ 'ftp://sourceware.org/pub/valgrind/', 'http://www.mirrorservice.org/sites/sourceware.org/pub/valgrind/', @@ -13,9 +16,6 @@ source_urls = [ sources = [SOURCELOWER_TAR_BZ2] checksums = ['d76680ef03f00cd5e970bbdcd4e57fb1f6df7d2e2c071635ef2be74790190c3b'] -toolchain = {'name': 'intel', 'version': '2017a'} -toolchainopts = {'optarch': False} - configopts = ' --with-mpicc="$MPICC"' binaries = [ -- GitLab From 7b2a1dd14f298af7fb66170116d80f07c9894cc1 Mon Sep 17 00:00:00 2001 From: Xavier Besseron Date: Thu, 21 Sep 2017 13:49:25 +0200 Subject: [PATCH 1584/1603] Cosmetic changes --- .../v/Valgrind/Valgrind-3.11.0-intel-2016a.eb | 15 ++++++++------- 1 file changed, 8 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/v/Valgrind/Valgrind-3.11.0-intel-2016a.eb b/easybuild/easyconfigs/v/Valgrind/Valgrind-3.11.0-intel-2016a.eb index 52fd021d39..24b8c53bc5 100644 --- a/easybuild/easyconfigs/v/Valgrind/Valgrind-3.11.0-intel-2016a.eb +++ b/easybuild/easyconfigs/v/Valgrind/Valgrind-3.11.0-intel-2016a.eb @@ -3,15 +3,16 @@ easyblock = 'ConfigureMake' name = 'Valgrind' version = '3.11.0' -homepage = 'http://valgrind.org/downloads/' +homepage = 'http://valgrind.org/' description = "Valgrind: Debugging and profiling tools" -sources = [SOURCELOWER_TAR_BZ2] -source_urls = ['http://valgrind.org/downloads/'] - toolchain = {'name': 'intel', 'version': '2016a'} toolchainopts = {'optarch': False} +source_urls = ['http://valgrind.org/downloads/'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['6c396271a8c1ddd5a6fb9abe714ea1e8a86fce85b30ab26b4266aeb4c2413b42'] + configopts = ' --with-mpicc="$MPICC"' binaries = [ @@ -20,9 +21,9 @@ binaries = [ ] sanity_check_paths = { - 'files': ['bin/%s' % x for x in binaries] - + ['lib/valgrind/libmpiwrap-amd64-linux.%s' % SHLIB_EXT], + 'files': ['bin/%s' % x for x in binaries] + + ['lib/valgrind/libmpiwrap-amd64-linux.%s' % SHLIB_EXT], 'dirs': [] -} +} moduleclass = 'debugger' -- GitLab From 38cf4e71a682966a40976afdae6f96c21cf4ca19 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 21 Sep 2017 13:51:58 +0200 Subject: [PATCH 1585/1603] fix homepage in Valgrind easyconfig --- easybuild/easyconfigs/v/Valgrind/Valgrind-3.13.0-intel-2017a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/v/Valgrind/Valgrind-3.13.0-intel-2017a.eb b/easybuild/easyconfigs/v/Valgrind/Valgrind-3.13.0-intel-2017a.eb index 3dd5dbb5a0..ab0e7d94ae 100644 --- a/easybuild/easyconfigs/v/Valgrind/Valgrind-3.13.0-intel-2017a.eb +++ b/easybuild/easyconfigs/v/Valgrind/Valgrind-3.13.0-intel-2017a.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'Valgrind' version = '3.13.0' -homepage = 'http://valgrind.org/downloads/' +homepage = 'http://valgrind.org' description = "Valgrind: Debugging and profiling tools" toolchain = {'name': 'intel', 'version': '2017a'} -- GitLab From a36eddd94704b0c828598be653ba2b25fb202450 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Thu, 21 Sep 2017 16:28:15 +0200 Subject: [PATCH 1586/1603] add Template.pm perl module to the extensions list --- .../w/worker/worker-1.6.7-intel-2016b.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) diff --git a/easybuild/easyconfigs/w/worker/worker-1.6.7-intel-2016b.eb b/easybuild/easyconfigs/w/worker/worker-1.6.7-intel-2016b.eb index 3ba6c18a9a..c5f4024ac2 100644 --- a/easybuild/easyconfigs/w/worker/worker-1.6.7-intel-2016b.eb +++ b/easybuild/easyconfigs/w/worker/worker-1.6.7-intel-2016b.eb @@ -45,6 +45,13 @@ exts_list = [ 'source_tmpl': 'TimeDate-2.30.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GB/GBARR'], }), + ('Template', '2.27', { + 'source_tmpl': 'Template-Toolkit-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AB/ABW'], + 'checksums': [ + '1311a403264d0134c585af0309ff2a9d5074b8ece23ece5660d31ec96bf2c6dc', # Template-Toolkit-2.27.tar.gz + ], + }), ] modextrapaths = { @@ -62,4 +69,23 @@ postinstallcmds = [ 'sed -i "s@ module_path = .*@ module_path = %(installdir)s/../../../modules/all@g" %(installdir)s/conf/worker.conf', ] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in [ + 'dbilogstrip', + 'dbiprof', + 'dbiproxy', + 'tpage', + 'ttree', + 'wcat', + 'wconvert', + 'wload', + 'worker', + 'wreduce', + 'wresume', + 'wsub', + 'wsummarize', + ]], + 'dirs': ['lib/perl', 'lib/tt', 'lib64/perl5'], +} + moduleclass = 'tools' -- GitLab From cfb3f83611bab91f65b2ebb896e70a7d945efcdd Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Thu, 21 Sep 2017 16:29:54 +0200 Subject: [PATCH 1587/1603] add sha256 checksums --- .../w/worker/worker-1.6.7-intel-2016b.eb | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) diff --git a/easybuild/easyconfigs/w/worker/worker-1.6.7-intel-2016b.eb b/easybuild/easyconfigs/w/worker/worker-1.6.7-intel-2016b.eb index c5f4024ac2..c2b7efd3e7 100644 --- a/easybuild/easyconfigs/w/worker/worker-1.6.7-intel-2016b.eb +++ b/easybuild/easyconfigs/w/worker/worker-1.6.7-intel-2016b.eb @@ -12,6 +12,7 @@ toolchain = {'name': 'dummy', 'version': ''} source_urls = ['https://github.com/gjbex/worker/archive/'] sources = ['%(version)s.tar.gz'] +checksums = ['350ffa36c792c5733ae202e76cc266648fca1311a835e9d73c98ed4f13a6835f'] tcname = 'intel' tcver = '2016b' @@ -24,26 +25,44 @@ exts_list = [ ('Config::General', '2.61', { 'source_tmpl': 'Config-General-2.61.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TL/TLINDEN'], + 'checksums': [ + '379a160ddac33c02045d2b7e20b37ca9b155722ce20374f9f245e519f7d7a6ca', # Config-General-2.61.tar.gz + ], }), ('IO::Stringy', '2.111', { 'source_tmpl': 'IO-stringy-2.111.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DS/DSKOLL'], + 'checksums': [ + '8c67fd6608c3c4e74f7324f1404a856c331dbf48d9deda6aaa8296ea41bf199d', # IO-stringy-2.111.tar.gz + ], }), ('Text::CSV', '1.33', { 'source_tmpl': 'Text-CSV-1.33.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MAKAMAKA'], + 'checksums': [ + '9c5b8fb9baffd58f02ed2b3f0b6d9a6454198f18a80e7f3a049680ddbdb24115', # Text-CSV-1.33.tar.gz + ], }), ('DBI', '1.636', { 'source_tmpl': 'DBI-1.636.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TI/TIMB'], + 'checksums': [ + '8f7ddce97c04b4b7a000e65e5d05f679c964d62c8b02c94c1a7d815bb2dd676c', # DBI-1.636.tar.gz + ], }), ('DBD::SQLite', '1.50', { 'source_tmpl': 'DBD-SQLite-1.50.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IS/ISHIGAKI'], + 'checksums': [ + '3ac513ab73944fd7d4b672e1fe885dc522b6369d38f46a68e67e0045bf159ce1', # DBD-SQLite-1.50.tar.gz + ], }), ('Date::Language', '2.30', { 'source_tmpl': 'TimeDate-2.30.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GB/GBARR'], + 'checksums': [ + '75bd254871cb5853a6aa0403ac0be270cdd75c9d1b6639f18ecba63c15298e86', # TimeDate-2.30.tar.gz + ], }), ('Template', '2.27', { 'source_tmpl': 'Template-Toolkit-%(version)s.tar.gz', -- GitLab From 978c7f3786d0bafe93a21c8b7c632c5d0ee363b3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 21 Sep 2017 16:35:15 +0200 Subject: [PATCH 1588/1603] {cae}[intel/2017a] OpenFOAM-Extend v4.0 --- .../h/hwloc/hwloc-1.11.8-intel-2017a.eb | 37 +++++++++++++++ .../m/Mesquite/Mesquite-2.3.0-intel-2017a.eb | 15 ++++++ .../OpenFOAM-Extend-4.0-intel-2017a.eb | 46 +++++++++++++++++++ .../ParMGridGen-1.0-intel-2017a.eb | 27 +++++++++++ 4 files changed, 125 insertions(+) create mode 100644 easybuild/easyconfigs/h/hwloc/hwloc-1.11.8-intel-2017a.eb create mode 100644 easybuild/easyconfigs/m/Mesquite/Mesquite-2.3.0-intel-2017a.eb create mode 100644 easybuild/easyconfigs/o/OpenFOAM-Extend/OpenFOAM-Extend-4.0-intel-2017a.eb create mode 100644 easybuild/easyconfigs/p/ParMGridGen/ParMGridGen-1.0-intel-2017a.eb diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.8-intel-2017a.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.8-intel-2017a.eb new file mode 100644 index 0000000000..619573b44d --- /dev/null +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.8-intel-2017a.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'hwloc' +version = '1.11.8' + +homepage = 'http://www.open-mpi.org/projects/hwloc/' + +description = """ + The Portable Hardware Locality (hwloc) software package provides a portable + abstraction (across OS, versions, architectures, ...) of the hierarchical + topology of modern architectures, including NUMA memory nodes, sockets, shared + caches, cores and simultaneous multithreading. It also gathers various system + attributes such as cache and memory information as well as the locality of I/O + devices such as network interfaces, InfiniBand HCAs or GPUs. It primarily + aims at helping applications with gathering information about modern computing + hardware so as to exploit it accordingly and efficiently. +""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] +sources = [SOURCE_TAR_GZ] +checksums = ['8af89b1164a330e36d18210360ea9bb305e19f9773d1c882855d261a13054ea8'] + +dependencies = [ + ('numactl', '2.0.11'), +] + +configopts = "--enable-libnuma=$EBROOTNUMACTL" + +sanity_check_paths = { + 'files': ['bin/lstopo', 'include/hwloc/linux.h', 'sbin/hwloc-dump-hwdata', + 'lib/libhwloc.%s' % SHLIB_EXT], + 'dirs': ['share/man/man3'], +} + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/m/Mesquite/Mesquite-2.3.0-intel-2017a.eb b/easybuild/easyconfigs/m/Mesquite/Mesquite-2.3.0-intel-2017a.eb new file mode 100644 index 0000000000..dc505ca541 --- /dev/null +++ b/easybuild/easyconfigs/m/Mesquite/Mesquite-2.3.0-intel-2017a.eb @@ -0,0 +1,15 @@ +easyblock = 'ConfigureMake' + +name = 'Mesquite' +version = '2.3.0' + +homepage = 'https://software.sandia.gov/mesquite/' +description = """Mesh-Quality Improvement Library""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True} + +source_urls = ['https://software.sandia.gov/mesquite/'] +sources = [SOURCELOWER_TAR_GZ] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/o/OpenFOAM-Extend/OpenFOAM-Extend-4.0-intel-2017a.eb b/easybuild/easyconfigs/o/OpenFOAM-Extend/OpenFOAM-Extend-4.0-intel-2017a.eb new file mode 100644 index 0000000000..b2fc23dde1 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM-Extend/OpenFOAM-Extend-4.0-intel-2017a.eb @@ -0,0 +1,46 @@ +easyblock = 'EB_OpenFOAM' + +name = 'OpenFOAM-Extend' +version = '4.0' + +homepage = 'http://www.extend-project.de/' +description = """OpenFOAM is a free, open source CFD software package. +OpenFOAM has an extensive range of features to solve anything from complex fluid flows +involving chemical reactions, turbulence and heat transfer, +to solid dynamics and electromagnetics.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/Unofficial-Extend-Project-Mirror/foam-extend-foam-extend-%(version)s/archive'] +sources = ['v%(version)s.tar.gz'] + +patches = [ + 'OpenFOAM-Extend-3.2-ParMGridGen.patch', + 'OpenFOAM-Extend-3.1_build-qa.patch', + 'OpenFOAM-Extend-3.1_comp-mpi.patch', + 'OpenFOAM-Extend-3.1_skip-ThirdParty-OpenMPI.patch', +] + +dependencies = [ + ('hwloc', '1.11.8'), + ('ParMETIS', '4.0.3'), + ('METIS', '5.1.0'), # order matters, METIS need to be listed after ParMETIS to get $CPATH right + ('SCOTCH', '6.0.4'), + ('Mesquite', '2.3.0'), + ('ParMGridGen', '1.0'), + ('Python', '2.7.13'), + # Libccmio v2.6.1, zoltan v3.5 +] + +builddependencies = [ + ('flex', '2.6.4'), + ('Bison', '3.0.4'), + ('M4', '1.4.18'), + ('CMake', '3.9.1'), +] + +# too many builds in parallel actually slows down the build +maxparallel = 4 + +moduleclass = 'cae' diff --git a/easybuild/easyconfigs/p/ParMGridGen/ParMGridGen-1.0-intel-2017a.eb b/easybuild/easyconfigs/p/ParMGridGen/ParMGridGen-1.0-intel-2017a.eb new file mode 100644 index 0000000000..2254b7c913 --- /dev/null +++ b/easybuild/easyconfigs/p/ParMGridGen/ParMGridGen-1.0-intel-2017a.eb @@ -0,0 +1,27 @@ +easyblock = 'MakeCp' + +name = 'ParMGridGen' +version = '1.0' + +homepage = 'http://www-users.cs.umn.edu/~moulitsa/software.html' +description = """ParMGridGen is an MPI-based parallel library that is based on the serial package MGridGen, + that implements (serial) algorithms for obtaining a sequence of successive coarse grids that are well-suited + for geometric multigrid methods.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'usempi': True, 'pic': True} + +source_urls = ['http://www-users.cs.umn.edu/~moulitsa/download/'] +sources = [SOURCE_TAR_GZ] + +patches = ['ParMGridGen-1.0_malloc_include.patch'] + +buildopts = 'parallel CC="$CC" PARCC="$CC" PARLD="$CC" COPTIONS="$CFLAGS" LDOPTIONS="$CFLAGS" BINDIR="."' + +files_to_copy = [ + (['MGridGen/Programs/mgridgen', 'ParMGridGen/Programs/parmgridgen'], 'bin'), + (['mgridgen.h', 'parmgridgen.h'], 'include'), + (['libmgrid.a', 'libparmgrid.a'], 'lib'), +] + +moduleclass = 'math' -- GitLab From 5c968a6a71bc84949e2fa413d5342d71a5651eb9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 21 Sep 2017 17:03:20 +0200 Subject: [PATCH 1589/1603] add checksums for OpenFOAM-Extend 4.0 + Mesquite & ParMGridGen deps --- .../easyconfigs/m/Mesquite/Mesquite-2.3.0-intel-2017a.eb | 1 + .../o/OpenFOAM-Extend/OpenFOAM-Extend-4.0-intel-2017a.eb | 9 ++++++++- .../p/ParMGridGen/ParMGridGen-1.0-intel-2017a.eb | 5 ++++- 3 files changed, 13 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/Mesquite/Mesquite-2.3.0-intel-2017a.eb b/easybuild/easyconfigs/m/Mesquite/Mesquite-2.3.0-intel-2017a.eb index dc505ca541..15596337b3 100644 --- a/easybuild/easyconfigs/m/Mesquite/Mesquite-2.3.0-intel-2017a.eb +++ b/easybuild/easyconfigs/m/Mesquite/Mesquite-2.3.0-intel-2017a.eb @@ -11,5 +11,6 @@ toolchainopts = {'pic': True} source_urls = ['https://software.sandia.gov/mesquite/'] sources = [SOURCELOWER_TAR_GZ] +checksums = ['4ab4ceadfa596e16c00dbb0e8b830a9112fa1b73291ca07633ec379a39b8bb28'] moduleclass = 'math' diff --git a/easybuild/easyconfigs/o/OpenFOAM-Extend/OpenFOAM-Extend-4.0-intel-2017a.eb b/easybuild/easyconfigs/o/OpenFOAM-Extend/OpenFOAM-Extend-4.0-intel-2017a.eb index b2fc23dde1..d591d79e9a 100644 --- a/easybuild/easyconfigs/o/OpenFOAM-Extend/OpenFOAM-Extend-4.0-intel-2017a.eb +++ b/easybuild/easyconfigs/o/OpenFOAM-Extend/OpenFOAM-Extend-4.0-intel-2017a.eb @@ -14,13 +14,20 @@ toolchainopts = {'usempi': True} source_urls = ['https://github.com/Unofficial-Extend-Project-Mirror/foam-extend-foam-extend-%(version)s/archive'] sources = ['v%(version)s.tar.gz'] - patches = [ 'OpenFOAM-Extend-3.2-ParMGridGen.patch', 'OpenFOAM-Extend-3.1_build-qa.patch', 'OpenFOAM-Extend-3.1_comp-mpi.patch', 'OpenFOAM-Extend-3.1_skip-ThirdParty-OpenMPI.patch', ] +checksums = [ + '5c64fcf443ae60760fcc13573ed7a8eddeddd0d511be7bc224f9eda5ab65c5da', # v4.0.tar.gz + 'f7676a7a12ced7c74caea64c62826a28449fdb2beb8b5be2c4ae7528ffece16e', # OpenFOAM-Extend-3.2-ParMGridGen.patch + '14dcc12ea7191ba42a9c297fcb2f4fbc2c55bf57226029489aa116e2d060b4bf', # OpenFOAM-Extend-3.1_build-qa.patch + '89fe47abec4cd9dbe863887140421e803e16801655bb2c7fb7bb1ac8532861ca', # OpenFOAM-Extend-3.1_comp-mpi.patch + # OpenFOAM-Extend-3.1_skip-ThirdParty-OpenMPI.patch + 'c88b23cd2f5dcf3bd86e02d7ea5dc6719c2049cf4b20e39f1b3262381dee3c50', +] dependencies = [ ('hwloc', '1.11.8'), diff --git a/easybuild/easyconfigs/p/ParMGridGen/ParMGridGen-1.0-intel-2017a.eb b/easybuild/easyconfigs/p/ParMGridGen/ParMGridGen-1.0-intel-2017a.eb index 2254b7c913..e697f5d9d6 100644 --- a/easybuild/easyconfigs/p/ParMGridGen/ParMGridGen-1.0-intel-2017a.eb +++ b/easybuild/easyconfigs/p/ParMGridGen/ParMGridGen-1.0-intel-2017a.eb @@ -13,8 +13,11 @@ toolchainopts = {'usempi': True, 'pic': True} source_urls = ['http://www-users.cs.umn.edu/~moulitsa/download/'] sources = [SOURCE_TAR_GZ] - patches = ['ParMGridGen-1.0_malloc_include.patch'] +checksums = [ + '62cdb6e48cfc59124e5d5d360c2841e0fc2feecafe65bda110b74e942740b395', # ParMGridGen-1.0.tar.gz + '3e0d72f82b3b56cbfcb1e3c9afc6594eb25316a0faeb49237faa8d969b4daeaa', # ParMGridGen-1.0_malloc_include.patch +] buildopts = 'parallel CC="$CC" PARCC="$CC" PARLD="$CC" COPTIONS="$CFLAGS" LDOPTIONS="$CFLAGS" BINDIR="."' -- GitLab From 8d05a0ec6b33c6c71258d42094cd8dcec075f309 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 21 Sep 2017 21:46:37 +0200 Subject: [PATCH 1590/1603] add additional patch for Boost 1.64.0 to fix issue with use of boost/serialization/detail/get_data.hpp --- .../b/Boost/Boost-1.64.0-intel-2017a.eb | 6 +- ...-boost-serialization-detail-get_data.patch | 123 ++++++++++++++++++ 2 files changed, 128 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.64.0_fix-boost-serialization-detail-get_data.patch diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.64.0-intel-2017a.eb b/easybuild/easyconfigs/b/Boost/Boost-1.64.0-intel-2017a.eb index 446a15ecf7..299cf50394 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.64.0-intel-2017a.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.64.0-intel-2017a.eb @@ -9,10 +9,14 @@ toolchainopts = {'pic': True, 'usempi': True} source_urls = [SOURCEFORGE_SOURCE] sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] -patches = ['Boost-%(version)s_fix-include-array_wrapper.patch'] +patches = [ + 'Boost-%(version)s_fix-include-array_wrapper.patch', + 'Boost-%(version)s_fix-boost-serialization-detail-get_data.patch', +] checksums = [ '0445c22a5ef3bd69f5dfb48354978421a85ab395254a26b1ffb0aa1bfd63a108', # boost_1_64_0.tar.gz 'aaf0657246d9cde4857954b6d1b9f9454370896b2077294461357d47951ca891', # Boost-1.64.0_fix-include-array_wrapper.patch + '5a569ac999bc3b6bf6386f2e37249f86137eec39a3649ab8a454479ca1ac7d9f', # Boost-1.64.0_fix-boost-serialization-detail-get_data.patch ] dependencies = [ diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.64.0_fix-boost-serialization-detail-get_data.patch b/easybuild/easyconfigs/b/Boost/Boost-1.64.0_fix-boost-serialization-detail-get_data.patch new file mode 100644 index 0000000000..2557991603 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.64.0_fix-boost-serialization-detail-get_data.patch @@ -0,0 +1,123 @@ +fix for: catastrophic error: cannot open source file "boost/serialization/detail/get_data.hpp" +see https://github.com/boostorg/mpi/pull/49 +--- /dev/null ++++ b/include/boost/mpi/detail/antiques.hpp +@@ -0,0 +1,29 @@ ++// Copyright Alain Miniussi 2014. ++// Distributed under the Boost Software License, Version 1.0. ++// (See accompanying file LICENSE_1_0.txt or copy at ++// http://www.boost.org/LICENSE_1_0.txt) ++ ++// Authors: Alain Miniussi ++ ++#ifndef BOOST_MPI_ANTIQUES_HPP ++#define BOOST_MPI_ANTIQUES_HPP ++ ++#include ++ ++// Support for some obsolette compilers ++ ++namespace boost { namespace mpi { ++ namespace detail { ++ // Some old gnu compiler have no support for vector<>::data ++ // Use this in the mean time, the cumbersome syntax should ++ // serve as an incentive to get rid of this when those compilers ++ // are dropped. ++ template ++ T* c_data(std::vector& v) { return &(v[0]); } ++ ++ template ++ T const* c_data(std::vector const& v) { return &(v[0]); } ++ ++} } } ++ ++#endif +diff --git a/include/boost/mpi/detail/mpi_datatype_primitive.hpp b/include/boost/mpi/detail/mpi_datatype_primitive.hpp +index c230055..b2263fa 100644 +--- a/include/boost/mpi/detail/mpi_datatype_primitive.hpp ++++ b/include/boost/mpi/detail/mpi_datatype_primitive.hpp +@@ -25,10 +25,10 @@ namespace std{ + #include + #include + #include +-#include + #include + #include + #include ++#include + + namespace boost { namespace mpi { namespace detail { + +@@ -80,18 +80,18 @@ class mpi_datatype_primitive + BOOST_MPI_CHECK_RESULT(MPI_Type_create_struct, + ( + addresses.size(), +- boost::serialization::detail::get_data(lengths), +- boost::serialization::detail::get_data(addresses), +- boost::serialization::detail::get_data(types), ++ c_data(lengths), ++ c_data(addresses), ++ c_data(types), + &datatype_ + )); + #else + BOOST_MPI_CHECK_RESULT(MPI_Type_struct, + ( + addresses.size(), +- boost::serialization::detail::get_data(lengths), +- boost::serialization::detail::get_data(addresses), +- boost::serialization::detail::get_data(types), ++ c_data(lengths), ++ c_data(addresses), ++ c_data(types), + &datatype_ + )); + #endif +diff --git a/include/boost/mpi/detail/packed_iprimitive.hpp b/include/boost/mpi/detail/packed_iprimitive.hpp +index 7080cbf..69d2c73 100644 +--- a/include/boost/mpi/detail/packed_iprimitive.hpp ++++ b/include/boost/mpi/detail/packed_iprimitive.hpp +@@ -16,8 +16,8 @@ + #include + #include + #include +-#include + #include ++#include + #include + + namespace boost { namespace mpi { +@@ -104,7 +104,7 @@ class BOOST_MPI_DECL packed_iprimitive + void load_impl(void * p, MPI_Datatype t, int l) + { + BOOST_MPI_CHECK_RESULT(MPI_Unpack, +- (const_cast(boost::serialization::detail::get_data(buffer_)), buffer_.size(), &position, p, l, t, comm)); ++ (const_cast(detail::c_data(buffer_)), buffer_.size(), &position, p, l, t, comm)); + } + + buffer_type & buffer_; +diff --git a/include/boost/mpi/detail/packed_oprimitive.hpp b/include/boost/mpi/detail/packed_oprimitive.hpp +index 5b6b3b2..1cb4ba0 100644 +--- a/include/boost/mpi/detail/packed_oprimitive.hpp ++++ b/include/boost/mpi/detail/packed_oprimitive.hpp +@@ -15,7 +15,7 @@ + + #include + #include +-#include ++#include + #include + #include + #include +@@ -98,7 +98,10 @@ class BOOST_MPI_DECL packed_oprimitive + + // pack the data into the buffer + BOOST_MPI_CHECK_RESULT(MPI_Pack, +- (const_cast(p), l, t, boost::serialization::detail::get_data(buffer_), buffer_.size(), &position, comm)); ++ (const_cast(p),l,t, ++ detail::c_data(buffer_), ++ buffer_.size(), ++ &position,comm)); + // reduce the buffer size if needed + BOOST_ASSERT(std::size_t(position) <= buffer_.size()); + if (std::size_t(position) < buffer_.size()) -- GitLab From 08f0ad986be135b067ab320e8b41fc84a811e2d9 Mon Sep 17 00:00:00 2001 From: John Donners Date: Fri, 22 Sep 2017 08:47:51 +0200 Subject: [PATCH 1591/1603] Fixed sanity check, changed class --- .../easyconfigs/n/NEST/NEST-2.12.0-foss-2015b-Python-2.7.9.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/n/NEST/NEST-2.12.0-foss-2015b-Python-2.7.9.eb b/easybuild/easyconfigs/n/NEST/NEST-2.12.0-foss-2015b-Python-2.7.9.eb index cc85bcdf97..91bde2ba50 100644 --- a/easybuild/easyconfigs/n/NEST/NEST-2.12.0-foss-2015b-Python-2.7.9.eb +++ b/easybuild/easyconfigs/n/NEST/NEST-2.12.0-foss-2015b-Python-2.7.9.eb @@ -37,8 +37,8 @@ modextrapaths = { } sanity_check_paths = { - 'files': ['bin/nest', 'lib/libnest.so', 'lib/libmodels.so'], + 'files': ['bin/nest', 'lib/libnest.%s' % SHLIB_EXT, 'lib/libmodels.%s' % SHLIB_EXT], 'dirs': ['lib/python%(pyshortver)s/site-packages'], } -moduleclass = 'math' +moduleclass = 'bio' -- GitLab From b492aae72818d2f9fd5502941bde40bc4582b436 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Fri, 22 Sep 2017 09:48:54 +0200 Subject: [PATCH 1592/1603] adding easyconfigs: REMORA-1.8.2-goolf-1.7.20.eb --- .../r/REMORA/REMORA-1.8.2-goolf-1.7.20.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/r/REMORA/REMORA-1.8.2-goolf-1.7.20.eb diff --git a/easybuild/easyconfigs/r/REMORA/REMORA-1.8.2-goolf-1.7.20.eb b/easybuild/easyconfigs/r/REMORA/REMORA-1.8.2-goolf-1.7.20.eb new file mode 100644 index 0000000000..cdf2dfc565 --- /dev/null +++ b/easybuild/easyconfigs/r/REMORA/REMORA-1.8.2-goolf-1.7.20.eb @@ -0,0 +1,32 @@ +# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'PackedBinary' + +name = "REMORA" +version = "1.8.2" + +homepage = 'https://github.com/TACC/remora' +description = """REsource MOnitoring for Remote Applications""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +source_urls = ['https://github.com/TACC/remora/archive/'] +sources = ['v%(version)s.tar.gz'] + +unpack_options = '--strip-components=1' + +install_cmd = 'REMORA_INSTALL_PREFIX=%(installdir)s ./install.sh' + +modextravars = { + 'REMORA_BIN': '%(installdir)s/bin', +} + +sanity_check_paths = { + 'files': ['bin/remora'], + 'dirs': [] +} + +moduleclass = 'tools' -- GitLab From b2f87bd773ab5addcb040d730bacdbddb56d7d2c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 22 Sep 2017 11:44:30 +0200 Subject: [PATCH 1593/1603] fix long line in Boost 1.64.0 easyconfig --- easybuild/easyconfigs/b/Boost/Boost-1.64.0-intel-2017a.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.64.0-intel-2017a.eb b/easybuild/easyconfigs/b/Boost/Boost-1.64.0-intel-2017a.eb index 299cf50394..bba859d9da 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.64.0-intel-2017a.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.64.0-intel-2017a.eb @@ -16,7 +16,8 @@ patches = [ checksums = [ '0445c22a5ef3bd69f5dfb48354978421a85ab395254a26b1ffb0aa1bfd63a108', # boost_1_64_0.tar.gz 'aaf0657246d9cde4857954b6d1b9f9454370896b2077294461357d47951ca891', # Boost-1.64.0_fix-include-array_wrapper.patch - '5a569ac999bc3b6bf6386f2e37249f86137eec39a3649ab8a454479ca1ac7d9f', # Boost-1.64.0_fix-boost-serialization-detail-get_data.patch + # Boost-1.64.0_fix-boost-serialization-detail-get_data.patch + '5a569ac999bc3b6bf6386f2e37249f86137eec39a3649ab8a454479ca1ac7d9f', ] dependencies = [ -- GitLab From 689a325a1a3734338516fc4923188ba7534dfb92 Mon Sep 17 00:00:00 2001 From: Joachim Hein Date: Fri, 22 Sep 2017 12:29:59 +0200 Subject: [PATCH 1594/1603] Boost 1.65.1 for latest foss and intel toolchains (no Python) --- .../b/Boost/Boost-1.65.1-foss-2017a.eb | 24 +++++++++++++++++++ .../b/Boost/Boost-1.65.1-foss-2017b.eb | 24 +++++++++++++++++++ .../b/Boost/Boost-1.65.1-intel-2017a.eb | 24 +++++++++++++++++++ .../b/Boost/Boost-1.65.1-intel-2017b.eb | 24 +++++++++++++++++++ 4 files changed, 96 insertions(+) create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.65.1-foss-2017a.eb create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.65.1-foss-2017b.eb create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.65.1-intel-2017a.eb create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.65.1-intel-2017b.eb diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.65.1-foss-2017a.eb b/easybuild/easyconfigs/b/Boost/Boost-1.65.1-foss-2017a.eb new file mode 100644 index 0000000000..c7a4b5126f --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.65.1-foss-2017a.eb @@ -0,0 +1,24 @@ +name = 'Boost' +version = '1.65.1' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'foss', 'version': '2017a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] +checksums = ['a13de2c8fbad635e6ba9c8f8714a0e6b4264b60a29b964b940a22554705b6b60'] + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.11'), +] + +configopts = '--without-libraries=python' + +# also build boost_mpi +boost_mpi = True + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.65.1-foss-2017b.eb b/easybuild/easyconfigs/b/Boost/Boost-1.65.1-foss-2017b.eb new file mode 100644 index 0000000000..a4f147a109 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.65.1-foss-2017b.eb @@ -0,0 +1,24 @@ +name = 'Boost' +version = '1.65.1' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'foss', 'version': '2017b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] +checksums = ['a13de2c8fbad635e6ba9c8f8714a0e6b4264b60a29b964b940a22554705b6b60'] + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.11'), +] + +configopts = '--without-libraries=python' + +# also build boost_mpi +boost_mpi = True + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.65.1-intel-2017a.eb b/easybuild/easyconfigs/b/Boost/Boost-1.65.1-intel-2017a.eb new file mode 100644 index 0000000000..b793a8e7ee --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.65.1-intel-2017a.eb @@ -0,0 +1,24 @@ +name = 'Boost' +version = '1.65.1' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] +checksums = ['a13de2c8fbad635e6ba9c8f8714a0e6b4264b60a29b964b940a22554705b6b60'] + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.11'), +] + +configopts = '--without-libraries=python' + +# also build boost_mpi +boost_mpi = True + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.65.1-intel-2017b.eb b/easybuild/easyconfigs/b/Boost/Boost-1.65.1-intel-2017b.eb new file mode 100644 index 0000000000..72f58c1d24 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.65.1-intel-2017b.eb @@ -0,0 +1,24 @@ +name = 'Boost' +version = '1.65.1' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'intel', 'version': '2017b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] +checksums = ['a13de2c8fbad635e6ba9c8f8714a0e6b4264b60a29b964b940a22554705b6b60'] + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.11'), +] + +configopts = '--without-libraries=python' + +# also build boost_mpi +boost_mpi = True + +moduleclass = 'devel' -- GitLab From e8f97f020cdb72da5b6e8ef46f1534a17cd78d19 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 22 Sep 2017 14:51:43 +0200 Subject: [PATCH 1595/1603] fix remarks in REMORA easyconfig --- .../r/REMORA/REMORA-1.8.2-goolf-1.7.20.eb | 21 ++++++++----------- 1 file changed, 9 insertions(+), 12 deletions(-) diff --git a/easybuild/easyconfigs/r/REMORA/REMORA-1.8.2-goolf-1.7.20.eb b/easybuild/easyconfigs/r/REMORA/REMORA-1.8.2-goolf-1.7.20.eb index cdf2dfc565..9ae5e9ebf1 100644 --- a/easybuild/easyconfigs/r/REMORA/REMORA-1.8.2-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/r/REMORA/REMORA-1.8.2-goolf-1.7.20.eb @@ -1,32 +1,29 @@ # This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ # Author: Pablo Escobar Lopez # sciCORE - University of Basel -# SIB Swiss Institute of Bioinformatics +# SIB Swiss Institute of Bioinformatics easyblock = 'PackedBinary' -name = "REMORA" -version = "1.8.2" +name = 'REMORA' +version = '1.8.2' homepage = 'https://github.com/TACC/remora' -description = """REsource MOnitoring for Remote Applications""" +description = "REsource MOnitoring for Remote Applications" toolchain = {'name': 'goolf', 'version': '1.7.20'} source_urls = ['https://github.com/TACC/remora/archive/'] sources = ['v%(version)s.tar.gz'] +checksums = ['140f71671787a49af822e97226c60db208b9ff6f3bf20556eac5b8c59e9fd42b'] -unpack_options = '--strip-components=1' - -install_cmd = 'REMORA_INSTALL_PREFIX=%(installdir)s ./install.sh' - -modextravars = { - 'REMORA_BIN': '%(installdir)s/bin', -} +install_cmd = 'cd remora-%(version)s && REMORA_INSTALL_PREFIX=%(installdir)s ./install.sh' sanity_check_paths = { - 'files': ['bin/remora'], + 'files': ['bin/mpstat', 'bin/remora', 'lib/libmpiP.a', 'lib/libmpiP.%s' % SHLIB_EXT], 'dirs': [] } +modextravars = {'REMORA_BIN': '%(installdir)s/bin'} + moduleclass = 'tools' -- GitLab From 8251ccb357ce22dc1631574b358d4a982730c9e0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 22 Sep 2017 14:56:53 +0200 Subject: [PATCH 1596/1603] add easyconfigs for REMORA with foss/2017a and intel/2017a --- .../r/REMORA/REMORA-1.8.2-foss-2017a.eb | 29 +++++++++++++++++++ .../r/REMORA/REMORA-1.8.2-intel-2017a.eb | 29 +++++++++++++++++++ 2 files changed, 58 insertions(+) create mode 100644 easybuild/easyconfigs/r/REMORA/REMORA-1.8.2-foss-2017a.eb create mode 100644 easybuild/easyconfigs/r/REMORA/REMORA-1.8.2-intel-2017a.eb diff --git a/easybuild/easyconfigs/r/REMORA/REMORA-1.8.2-foss-2017a.eb b/easybuild/easyconfigs/r/REMORA/REMORA-1.8.2-foss-2017a.eb new file mode 100644 index 0000000000..711bd6825e --- /dev/null +++ b/easybuild/easyconfigs/r/REMORA/REMORA-1.8.2-foss-2017a.eb @@ -0,0 +1,29 @@ +# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'PackedBinary' + +name = 'REMORA' +version = '1.8.2' + +homepage = 'https://github.com/TACC/remora' +description = "REsource MOnitoring for Remote Applications" + +toolchain = {'name': 'foss', 'version': '2017a'} + +source_urls = ['https://github.com/TACC/remora/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['140f71671787a49af822e97226c60db208b9ff6f3bf20556eac5b8c59e9fd42b'] + +install_cmd = 'cd remora-%(version)s && REMORA_INSTALL_PREFIX=%(installdir)s ./install.sh' + +sanity_check_paths = { + 'files': ['bin/mpstat', 'bin/remora', 'lib/libmpiP.a', 'lib/libmpiP.%s' % SHLIB_EXT], + 'dirs': [] +} + +modextravars = {'REMORA_BIN': '%(installdir)s/bin'} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/r/REMORA/REMORA-1.8.2-intel-2017a.eb b/easybuild/easyconfigs/r/REMORA/REMORA-1.8.2-intel-2017a.eb new file mode 100644 index 0000000000..6ac17a4b99 --- /dev/null +++ b/easybuild/easyconfigs/r/REMORA/REMORA-1.8.2-intel-2017a.eb @@ -0,0 +1,29 @@ +# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'PackedBinary' + +name = 'REMORA' +version = '1.8.2' + +homepage = 'https://github.com/TACC/remora' +description = "REsource MOnitoring for Remote Applications" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['https://github.com/TACC/remora/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['140f71671787a49af822e97226c60db208b9ff6f3bf20556eac5b8c59e9fd42b'] + +install_cmd = 'cd remora-%(version)s && REMORA_INSTALL_PREFIX=%(installdir)s ./install.sh' + +sanity_check_paths = { + 'files': ['bin/mpstat', 'bin/remora'], + 'dirs': [] +} + +modextravars = {'REMORA_BIN': '%(installdir)s/bin'} + +moduleclass = 'tools' -- GitLab From d98a208d742d3433e228622b73046456b9fcc385 Mon Sep 17 00:00:00 2001 From: Joachim Hein Date: Fri, 22 Sep 2017 16:06:24 +0200 Subject: [PATCH 1597/1603] Here is the actual file --- .../g/git/git-2.14.1-GCCcore-6.4.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/g/git/git-2.14.1-GCCcore-6.4.0.eb diff --git a/easybuild/easyconfigs/g/git/git-2.14.1-GCCcore-6.4.0.eb b/easybuild/easyconfigs/g/git/git-2.14.1-GCCcore-6.4.0.eb new file mode 100644 index 0000000000..2131b6050d --- /dev/null +++ b/easybuild/easyconfigs/g/git/git-2.14.1-GCCcore-6.4.0.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'git' +version = '2.14.1' + +homepage = 'http://git-scm.com/' +description = """Git is a free and open source distributed version control system designed +to handle everything from small to very large projects with speed and efficiency.""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} + +sources = ['v%(version)s.tar.gz'] +source_urls = ['https://github.com/git/git/archive'] +checksums = ['ccc366d5d674fb755fd98d219c23f2b4e5da8a49d8582a6314813b280d75536b'] + +dependencies = [ + ('cURL', '7.55.1'), + ('expat', '2.2.4'), + ('gettext', '0.19.8.1'), + ('Perl', '5.26.0'), +] + +preconfigopts = 'make configure && ' + +# Work around git build system bug. If LIBS contains -lpthread, then configure +# will not append -lpthread to LDFLAGS, but Makefile ignores LIBS. +configopts = "--with-perl=${EBROOTPERL}/bin/perl --enable-pthreads='-lpthread'" + +sanity_check_paths = { + 'files': ['bin/git'], + 'dirs': [], +} + +moduleclass = 'tools' -- GitLab From fd91e00a3d839815cf2ac5054522b605fd79bbd8 Mon Sep 17 00:00:00 2001 From: Joachim Hein Date: Fri, 22 Sep 2017 16:55:23 +0200 Subject: [PATCH 1598/1603] Added binutils as build dependency --- easybuild/easyconfigs/g/git/git-2.14.1-GCCcore-6.4.0.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/g/git/git-2.14.1-GCCcore-6.4.0.eb b/easybuild/easyconfigs/g/git/git-2.14.1-GCCcore-6.4.0.eb index 2131b6050d..6ddfd56f5a 100644 --- a/easybuild/easyconfigs/g/git/git-2.14.1-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/g/git/git-2.14.1-GCCcore-6.4.0.eb @@ -13,6 +13,10 @@ sources = ['v%(version)s.tar.gz'] source_urls = ['https://github.com/git/git/archive'] checksums = ['ccc366d5d674fb755fd98d219c23f2b4e5da8a49d8582a6314813b280d75536b'] +builddependencies = [ + ('binutils', '2.28'), +] + dependencies = [ ('cURL', '7.55.1'), ('expat', '2.2.4'), -- GitLab From c40d7069a3a3d4a3219cffc1d0f6f17260101b2b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 22 Sep 2017 19:48:52 +0200 Subject: [PATCH 1599/1603] fix checksums for packages that download from github.com/x/y/archive --- .../AdapterRemoval/AdapterRemoval-2.2.0-foss-2016b.eb | 2 +- .../a/arpack-ng/arpack-ng-3.1.3-ictce-5.3.0-mt.eb | 6 +++++- .../a/arpack-ng/arpack-ng-3.1.3-ictce-5.3.0.eb | 7 ++++++- .../a/arpack-ng/arpack-ng-3.1.3-ictce-5.5.0-mt.eb | 6 +++++- .../a/arpack-ng/arpack-ng-3.1.3-ictce-5.5.0.eb | 7 ++++++- .../a/arpack-ng/arpack-ng-3.1.5-ictce-7.1.2-mt.eb | 2 +- .../a/arpack-ng/arpack-ng-3.1.5-ictce-7.1.2.eb | 2 +- .../k/kallisto/kallisto-0.43.1-foss-2016b.eb | 2 +- .../Lucene-Geo-Gazetteer-20170718.eb | 2 +- .../MXNet-0.9.3-foss-2016b-Python-2.7.12-R-3.3.3.eb | 10 +++++----- .../o/OpenFOAM/OpenFOAM-3.0.1-intel-2016b.eb | 5 ++++- .../easyconfigs/o/OpenFOAM/OpenFOAM-4.0-foss-2016b.eb | 5 ++++- .../easyconfigs/o/OpenFOAM/OpenFOAM-4.0-intel-2016b.eb | 5 ++++- .../easyconfigs/o/OpenFOAM/OpenFOAM-4.1-foss-2016b.eb | 5 ++++- .../easyconfigs/o/OpenFOAM/OpenFOAM-4.1-intel-2017a.eb | 5 ++++- .../easyconfigs/t/Trinity/Trinity-2.4.0-foss-2017a.eb | 6 +++++- easybuild/easyconfigs/t/tbb/tbb-2017_U5-foss-2016b.eb | 2 +- .../easyconfigs/t/tbb/tbb-2017_U6-GCCcore-6.3.0.eb | 2 +- 18 files changed, 59 insertions(+), 22 deletions(-) diff --git a/easybuild/easyconfigs/a/AdapterRemoval/AdapterRemoval-2.2.0-foss-2016b.eb b/easybuild/easyconfigs/a/AdapterRemoval/AdapterRemoval-2.2.0-foss-2016b.eb index 50e7938a22..9089ed3e82 100644 --- a/easybuild/easyconfigs/a/AdapterRemoval/AdapterRemoval-2.2.0-foss-2016b.eb +++ b/easybuild/easyconfigs/a/AdapterRemoval/AdapterRemoval-2.2.0-foss-2016b.eb @@ -18,7 +18,7 @@ sources = ['v%(version)s.tar.gz'] files_to_copy = [(['build/%(name)s'], 'bin'), (['build/%(name)s.1'], 'share/man/man1')] -checksums = ['159e5c7c527dde70eac444a87bf5fbfc'] +checksums = ['20fdbdef2ecfd74af8d078f3f63e9444926dab1dd02b7dcef7c2aee77cb73b60'] dependencies = [ ('bzip2', '1.0.6'), diff --git a/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.1.3-ictce-5.3.0-mt.eb b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.1.3-ictce-5.3.0-mt.eb index 4562fea8de..66c7769216 100644 --- a/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.1.3-ictce-5.3.0-mt.eb +++ b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.1.3-ictce-5.3.0-mt.eb @@ -13,7 +13,11 @@ toolchainopts = {'opt': True, 'optarch': True, 'pic': True, 'usempi': False} source_urls = ['https://github.com/opencollab/arpack-ng/archive/'] sources = ['%(version)s.tar.gz'] -checksums = ['ae659c8c6f8857f4850a5bcd4f97b23f'] +checksums = [ + '13ac771c2a28cc4b7d770c85525894d230c705f151d90b42d3f4982ed1dfda53', # 3.1.3.tar.gz + '928b71003a99b04fb205edd59473dd2fd84f6581c3e79c49d915e78a2395d8d7', # arpack-ng-3.1.3-update-to-head.patch + 'd2b3885eccba3d0dd2272969b14baa2d22deaa830c21c508b12687fc7aaeca06', # arpack-ng-3.1.3-pkgconfig.patch +] # do not change the order of the patches or things will break patches = [ diff --git a/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.1.3-ictce-5.3.0.eb b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.1.3-ictce-5.3.0.eb index 36abbfba39..f319e77d02 100644 --- a/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.1.3-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.1.3-ictce-5.3.0.eb @@ -12,7 +12,12 @@ toolchainopts = {'opt': True, 'optarch': True, 'pic': True, 'usempi': True} source_urls = ['https://github.com/opencollab/arpack-ng/archive/'] sources = ['%(version)s.tar.gz'] -checksums = ['ae659c8c6f8857f4850a5bcd4f97b23f'] +checksums = [ + '13ac771c2a28cc4b7d770c85525894d230c705f151d90b42d3f4982ed1dfda53', # 3.1.3.tar.gz + '928b71003a99b04fb205edd59473dd2fd84f6581c3e79c49d915e78a2395d8d7', # arpack-ng-3.1.3-update-to-head.patch + 'd2b3885eccba3d0dd2272969b14baa2d22deaa830c21c508b12687fc7aaeca06', # arpack-ng-3.1.3-pkgconfig.patch + '6dc832bc4458c30a67f9d6348e60bee9ed9ddb413a54418e706661ef74695910', # arpack-ng-3.1.3-configure-mpi.patch +] # do not change the order of the patches or things will break patches = [ diff --git a/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.1.3-ictce-5.5.0-mt.eb b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.1.3-ictce-5.5.0-mt.eb index a63af2d197..18c202769e 100644 --- a/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.1.3-ictce-5.5.0-mt.eb +++ b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.1.3-ictce-5.5.0-mt.eb @@ -13,7 +13,11 @@ toolchainopts = {'opt': True, 'optarch': True, 'pic': True, 'usempi': False} source_urls = ['https://github.com/opencollab/arpack-ng/archive/'] sources = ['%(version)s.tar.gz'] -checksums = ['ae659c8c6f8857f4850a5bcd4f97b23f'] +checksums = [ + '13ac771c2a28cc4b7d770c85525894d230c705f151d90b42d3f4982ed1dfda53', # 3.1.3.tar.gz + '928b71003a99b04fb205edd59473dd2fd84f6581c3e79c49d915e78a2395d8d7', # arpack-ng-3.1.3-update-to-head.patch + 'd2b3885eccba3d0dd2272969b14baa2d22deaa830c21c508b12687fc7aaeca06', # arpack-ng-3.1.3-pkgconfig.patch +] # do not change the order of the patches or things will break patches = [ diff --git a/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.1.3-ictce-5.5.0.eb b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.1.3-ictce-5.5.0.eb index e390bd7768..a0635d43bd 100644 --- a/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.1.3-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.1.3-ictce-5.5.0.eb @@ -12,7 +12,12 @@ toolchainopts = {'opt': True, 'optarch': True, 'pic': True, 'usempi': True} source_urls = ['https://github.com/opencollab/arpack-ng/archive/'] sources = ['%(version)s.tar.gz'] -checksums = ['ae659c8c6f8857f4850a5bcd4f97b23f'] +checksums = [ + '13ac771c2a28cc4b7d770c85525894d230c705f151d90b42d3f4982ed1dfda53', # 3.1.3.tar.gz + '928b71003a99b04fb205edd59473dd2fd84f6581c3e79c49d915e78a2395d8d7', # arpack-ng-3.1.3-update-to-head.patch + 'd2b3885eccba3d0dd2272969b14baa2d22deaa830c21c508b12687fc7aaeca06', # arpack-ng-3.1.3-pkgconfig.patch + '6dc832bc4458c30a67f9d6348e60bee9ed9ddb413a54418e706661ef74695910', # arpack-ng-3.1.3-configure-mpi.patch +] # do not change the order of the patches or things will break patches = [ diff --git a/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.1.5-ictce-7.1.2-mt.eb b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.1.5-ictce-7.1.2-mt.eb index b22908df9d..a8e1f0cfdf 100644 --- a/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.1.5-ictce-7.1.2-mt.eb +++ b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.1.5-ictce-7.1.2-mt.eb @@ -13,7 +13,7 @@ toolchainopts = {'opt': True, 'optarch': True, 'pic': True, 'usempi': False} source_urls = ['https://github.com/opencollab/arpack-ng/archive/'] sources = ['%(version)s.tar.gz'] -checksums = ['d84e1b6108d9ee67c0d21aba7099e953'] +checksums = ['f609d001a247195c019626cb0f2144db7b08c83f53d875dcdeeee4cdb0609098'] configopts = '--with-pic --with-blas="$LIBBLAS_MT" --with-lapack="$LIBLAPACK_MT"' diff --git a/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.1.5-ictce-7.1.2.eb b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.1.5-ictce-7.1.2.eb index cdb3eae35c..c29fa0b72d 100644 --- a/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.1.5-ictce-7.1.2.eb +++ b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.1.5-ictce-7.1.2.eb @@ -12,7 +12,7 @@ toolchainopts = {'opt': True, 'optarch': True, 'pic': True, 'usempi': True} source_urls = ['https://github.com/opencollab/arpack-ng/archive/'] sources = ['%(version)s.tar.gz'] -checksums = ['d84e1b6108d9ee67c0d21aba7099e953'] +checksums = ['f609d001a247195c019626cb0f2144db7b08c83f53d875dcdeeee4cdb0609098'] configopts = '--with-pic --with-blas="$LIBBLAS_MT" --with-lapack="$LIBLAPACK_MT"' diff --git a/easybuild/easyconfigs/k/kallisto/kallisto-0.43.1-foss-2016b.eb b/easybuild/easyconfigs/k/kallisto/kallisto-0.43.1-foss-2016b.eb index 54e8f3a226..a67d509532 100644 --- a/easybuild/easyconfigs/k/kallisto/kallisto-0.43.1-foss-2016b.eb +++ b/easybuild/easyconfigs/k/kallisto/kallisto-0.43.1-foss-2016b.eb @@ -15,7 +15,7 @@ toolchainopts = {'pic': True, 'usempi': True} source_urls = ['https://github.com/pachterlab/kallisto/archive/'] sources = ['v%(version)s.tar.gz'] -checksums = ['7baef1b3b67bcf81dc7c604db2ef30f5520b48d532bf28ec26331cb60ce69400'] +checksums = ['2164938c2c61c04e338c4c132cf749f56d39e6f0b4c517121bca1fbc218e430e'] builddependencies = [('CMake', '3.7.2')] diff --git a/easybuild/easyconfigs/l/Lucene-Geo-Gazetteer/Lucene-Geo-Gazetteer-20170718.eb b/easybuild/easyconfigs/l/Lucene-Geo-Gazetteer/Lucene-Geo-Gazetteer-20170718.eb index c21c6baf85..6aab03ee44 100644 --- a/easybuild/easyconfigs/l/Lucene-Geo-Gazetteer/Lucene-Geo-Gazetteer-20170718.eb +++ b/easybuild/easyconfigs/l/Lucene-Geo-Gazetteer/Lucene-Geo-Gazetteer-20170718.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'dummy', 'version': ''} source_urls = ['https://github.com/chrismattmann/lucene-geo-gazetteer/archive/'] sources = [{'filename': SOURCE_TAR_GZ, 'download_filename': '6c38272.tar.gz'}] -checksums = ['2ed355bfdcf865d815df9dc52ee747eeb8a15d065ef159ebf933ad36e1555ad4'] +checksums = ['c9d1412ecef1f2c04937c2ee7acec325e5cbb1fb7fbe525bdd59c9109a790494'] builddependencies = [('Maven', '3.5.0')] dependencies = [('Java', '1.8.0_144')] diff --git a/easybuild/easyconfigs/m/MXNet/MXNet-0.9.3-foss-2016b-Python-2.7.12-R-3.3.3.eb b/easybuild/easyconfigs/m/MXNet/MXNet-0.9.3-foss-2016b-Python-2.7.12-R-3.3.3.eb index ba00fd6f18..b2b5f4620d 100644 --- a/easybuild/easyconfigs/m/MXNet/MXNet-0.9.3-foss-2016b-Python-2.7.12-R-3.3.3.eb +++ b/easybuild/easyconfigs/m/MXNet/MXNet-0.9.3-foss-2016b-Python-2.7.12-R-3.3.3.eb @@ -21,11 +21,11 @@ sources = [ ] checksums = [ - "84971e4a0e2e9db3757623657aa5b9ec", # v0.9.3.tar.gz - "12c96664978c545a7269b93635719b18", # 6856021ca925c7.tar.gz - "3dc48183e123c650707bcf26a9254941", # c29ac58320d7b0.tar.gz - "fb04cb1694f1e66591a31a18bc92b451", # 0d64855f741e04.tar.gz - "da873c881758c0e10ac0928f86568456", # b32ec4aee65a66.tar.gz + 'c8d1e6d8a178e475625e60a8fd71b49efbd7c8a2b222300858f50201d89127e3', # v0.9.3.tar.gz + '5a7aa092ae2cca51bf068b152908d0e4407daa3f5c281d56e3dbf2effeb0721a', # 6856021ca925c7.tar.gz + '53265bd2157258eac42d614f60f9987c66bc7017cb75cfbc7774f44bd7c4fb66', # c29ac58320d7b0.tar.gz + '7cabefb333acb77d81fdb747dbe911b13a6df1e093c7e3a804d9dca10341666d', # 0d64855f741e04.tar.gz + 'a825082d8d495ca5bc228277bc075c91d1cf0e255632ac7952564e53bf8f0d2f', # b32ec4aee65a66.tar.gz ] dependencies = [ diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-3.0.1-intel-2016b.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-3.0.1-intel-2016b.eb index 065d8bedfb..566f734948 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-3.0.1-intel-2016b.eb +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-3.0.1-intel-2016b.eb @@ -13,7 +13,10 @@ toolchainopts = {'cstd': 'c++11'} source_urls = ['https://github.com/OpenFOAM/OpenFOAM-%(version_major_minor)s.x/archive'] sources = ['version-%(version)s.tar.gz'] -checksums = ['a6ffe3edabdd23f9eff31be47a092b07'] +checksums = [ + '4b7d25a17f5fb075e206d7fbdf863253335f705538df6404c6ca44f6147953c3', # version-3.0.1.tar.gz + '251833f259d25f82808fe59869797c11a9a7d10d37f71d6a8cf92d108a35fd4c', # OpenFOAM-3.0.1_cleanup.patch +] patches = ['OpenFOAM-%(version)s_cleanup.patch'] diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.0-foss-2016b.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.0-foss-2016b.eb index 3db67b3e22..aca1f74b1d 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.0-foss-2016b.eb +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.0-foss-2016b.eb @@ -13,7 +13,10 @@ toolchainopts = {'cstd': 'c++11'} source_urls = ['https://github.com/OpenFOAM/OpenFOAM-%(version_major)s.x/archive'] sources = ['version-%(version)s.tar.gz'] -checksums = ['294b520811aae87241f3a78423f05952'] +checksums = [ + '73aebe35a1134b1b51dcacc23c097a38e492c3bdb1dcc5d1fb3ca81c4c61df49', # version-4.0.tar.gz + '7451b71741347f230689f18462824ebb9e42e80b1d0894d2a72af01a998d524c', # OpenFOAM-4.0-cleanup.patch +] patches = ['OpenFOAM-%(version)s-cleanup.patch'] diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.0-intel-2016b.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.0-intel-2016b.eb index 635072f873..581812bf13 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.0-intel-2016b.eb +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.0-intel-2016b.eb @@ -13,7 +13,10 @@ toolchainopts = {'cstd': 'c++11'} source_urls = ['https://github.com/OpenFOAM/OpenFOAM-%(version_major)s.x/archive'] sources = ['version-%(version)s.tar.gz'] -checksums = ['294b520811aae87241f3a78423f05952'] +checksums = [ + '73aebe35a1134b1b51dcacc23c097a38e492c3bdb1dcc5d1fb3ca81c4c61df49', # version-4.0.tar.gz + '7451b71741347f230689f18462824ebb9e42e80b1d0894d2a72af01a998d524c', # OpenFOAM-4.0-cleanup.patch +] patches = ['OpenFOAM-%(version)s-cleanup.patch'] diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.1-foss-2016b.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.1-foss-2016b.eb index eea7c1b416..0c1616045a 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.1-foss-2016b.eb +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.1-foss-2016b.eb @@ -13,7 +13,10 @@ toolchainopts = {'cstd': 'c++11'} source_urls = ['https://github.com/OpenFOAM/OpenFOAM-%(version_major)s.x/archive'] sources = ['version-%(version)s.tar.gz'] -checksums = ['318a446c4ae6366c7296b61184acd37c'] +checksums = [ + '2de18de64e7abdb1b649ad8e9d2d58b77a2b188fb5bcb6f7c2a038282081fd31', # version-4.1.tar.gz + '7a9d418f18c475fb48ddc427be7271b0fd759ad183f09a6bcafe4b76924b2a70', # OpenFOAM-4.1-cleanup.patch +] patches = ['OpenFOAM-%(version)s-cleanup.patch'] diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.1-intel-2017a.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.1-intel-2017a.eb index c3f3f806f9..e4305fdec8 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.1-intel-2017a.eb +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-4.1-intel-2017a.eb @@ -13,7 +13,10 @@ toolchainopts = {'cstd': 'c++11'} source_urls = ['https://github.com/OpenFOAM/OpenFOAM-%(version_major)s.x/archive'] sources = ['version-%(version)s.tar.gz'] -checksums = ['318a446c4ae6366c7296b61184acd37c'] +checksums = [ + '2de18de64e7abdb1b649ad8e9d2d58b77a2b188fb5bcb6f7c2a038282081fd31', # version-4.1.tar.gz + '7a9d418f18c475fb48ddc427be7271b0fd759ad183f09a6bcafe4b76924b2a70', # OpenFOAM-4.1-cleanup.patch +] patches = ['OpenFOAM-%(version)s-cleanup.patch'] diff --git a/easybuild/easyconfigs/t/Trinity/Trinity-2.4.0-foss-2017a.eb b/easybuild/easyconfigs/t/Trinity/Trinity-2.4.0-foss-2017a.eb index c700a10e06..98a63c78c7 100644 --- a/easybuild/easyconfigs/t/Trinity/Trinity-2.4.0-foss-2017a.eb +++ b/easybuild/easyconfigs/t/Trinity/Trinity-2.4.0-foss-2017a.eb @@ -10,7 +10,11 @@ toolchainopts = {'optarch': True} source_urls = ['https://github.com/trinityrnaseq/trinityrnaseq/archive/'] sources = ['%(name)s-v%(version)s.tar.gz'] -checksums = ['2e91ed242923205b060164398aa325e5fe824040732d86c74ece4f98d7a6f220'] +checksums = [ + '9f816fdc7870fb85af9a44249be05bf06f2a3f0b780275513eec9b0124fa9bda', # Trinity-v2.4.0.tar.gz + # chrysalis_commandline_noconsts_2012-10-05.patch + '3442803c357576557de843c80b73436e59e9a99027d60f5f63bb3368eceb4a5c', +] patches = [ 'chrysalis_commandline_noconsts_2012-10-05.patch', diff --git a/easybuild/easyconfigs/t/tbb/tbb-2017_U5-foss-2016b.eb b/easybuild/easyconfigs/t/tbb/tbb-2017_U5-foss-2016b.eb index c187512784..af70dc027a 100644 --- a/easybuild/easyconfigs/t/tbb/tbb-2017_U5-foss-2016b.eb +++ b/easybuild/easyconfigs/t/tbb/tbb-2017_U5-foss-2016b.eb @@ -12,6 +12,6 @@ toolchain = {'name': 'foss', 'version': '2016b'} source_urls = ['https://github.com/01org/tbb/archive/'] sources = ['%(version)s.tar.gz'] -checksums = ['780baf0ad520f23b54dd20dc97bf5aae4bc562019e0a70f53bfc4c1afec6e545'] +checksums = ['3122c87a35fde759567c8579ba36a36037c6df84c3f9c4df6c9e171f866f352f'] moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/tbb/tbb-2017_U6-GCCcore-6.3.0.eb b/easybuild/easyconfigs/t/tbb/tbb-2017_U6-GCCcore-6.3.0.eb index 1b8ceddb15..99471b647c 100644 --- a/easybuild/easyconfigs/t/tbb/tbb-2017_U6-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/t/tbb/tbb-2017_U6-GCCcore-6.3.0.eb @@ -9,7 +9,7 @@ toolchain = {'name': 'GCCcore', 'version': '6.3.0'} source_urls = ['https://github.com/01org/tbb/archive/'] sources = ['%(version)s.tar.gz'] -checksums = ['1f7df7af6045179a45eba9b5dfde74d185ee7f573328f103c137696f81e4ae5a'] +checksums = ['40d5409a6fd7e214a21fd1949df422ba113fa78fde42a6aac40a2fba36e9bcdb'] builddependencies = [ ('binutils', '2.27') -- GitLab From 3c93352d59459be0d92618ef376fd51406e1313f Mon Sep 17 00:00:00 2001 From: Joachim Hein Date: Fri, 22 Sep 2017 20:33:21 +0200 Subject: [PATCH 1600/1603] Deleted whitespace --- easybuild/easyconfigs/g/git/git-2.14.1-GCCcore-6.4.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/git/git-2.14.1-GCCcore-6.4.0.eb b/easybuild/easyconfigs/g/git/git-2.14.1-GCCcore-6.4.0.eb index 6ddfd56f5a..dc6cd8a86d 100644 --- a/easybuild/easyconfigs/g/git/git-2.14.1-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/g/git/git-2.14.1-GCCcore-6.4.0.eb @@ -13,7 +13,7 @@ sources = ['v%(version)s.tar.gz'] source_urls = ['https://github.com/git/git/archive'] checksums = ['ccc366d5d674fb755fd98d219c23f2b4e5da8a49d8582a6314813b280d75536b'] -builddependencies = [ +builddependencies = [ ('binutils', '2.28'), ] -- GitLab From 35580b6a1fe7b2877c61e26f356269c3062f80ac Mon Sep 17 00:00:00 2001 From: Joachim Hein Date: Mon, 25 Sep 2017 11:11:39 +0200 Subject: [PATCH 1601/1603] netCDF 4.4.1.1 configs for foss/2017a --- .../netCDF-4.4.1.1-foss-2017a-HDF5-1.10.1.eb | 36 +++++++++++++++++++ .../netCDF-4.4.1.1-foss-2017a-HDF5-1.8.19.eb | 36 +++++++++++++++++++ 2 files changed, 72 insertions(+) create mode 100644 easybuild/easyconfigs/n/netCDF/netCDF-4.4.1.1-foss-2017a-HDF5-1.10.1.eb create mode 100644 easybuild/easyconfigs/n/netCDF/netCDF-4.4.1.1-foss-2017a-HDF5-1.8.19.eb diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.4.1.1-foss-2017a-HDF5-1.10.1.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.4.1.1-foss-2017a-HDF5-1.10.1.eb new file mode 100644 index 0000000000..8e41b9784a --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.4.1.1-foss-2017a-HDF5-1.10.1.eb @@ -0,0 +1,36 @@ +name = 'netCDF' +version = '4.4.1.1' +hdf5_ver = '1.10.1' +versionsuffix = '-HDF5-%s' % hdf5_ver + +homepage = 'http://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'foss', 'version': '2017a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://github.com/Unidata/netcdf-c/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['7f040a0542ed3f6d27f3002b074e509614e18d6c515b2005d1537fec01b24909'] + +dependencies = [ + ('HDF5', hdf5_ver), + ('cURL', '7.54.0'), + ('Szip', '2.1.1'), +] + +builddependencies = [ + ('Autotools', '20150215'), + ('CMake', '3.9.1'), + ('Doxygen', '1.8.13'), +] + +# make sure both static and shared libs are built +configopts = [ + "-DBUILD_SHARED_LIBS=OFF ", + "-DBUILD_SHARED_LIBS=ON ", +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.4.1.1-foss-2017a-HDF5-1.8.19.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.4.1.1-foss-2017a-HDF5-1.8.19.eb new file mode 100644 index 0000000000..599e58b58f --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.4.1.1-foss-2017a-HDF5-1.8.19.eb @@ -0,0 +1,36 @@ +name = 'netCDF' +version = '4.4.1.1' +hdf5_ver = '1.8.19' +versionsuffix = '-HDF5-%s' % hdf5_ver + +homepage = 'http://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'foss', 'version': '2017a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://github.com/Unidata/netcdf-c/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['7f040a0542ed3f6d27f3002b074e509614e18d6c515b2005d1537fec01b24909'] + +dependencies = [ + ('HDF5', hdf5_ver), + ('cURL', '7.54.0'), + ('Szip', '2.1.1'), +] + +builddependencies = [ + ('Autotools', '20150215'), + ('CMake', '3.9.1'), + ('Doxygen', '1.8.13'), +] + +# make sure both static and shared libs are built +configopts = [ + "-DBUILD_SHARED_LIBS=OFF ", + "-DBUILD_SHARED_LIBS=ON ", +] + +moduleclass = 'data' -- GitLab From 89f39b0de84e7045c73189d0eabbaf3b6548dcb3 Mon Sep 17 00:00:00 2001 From: Joachim Hein Date: Mon, 25 Sep 2017 11:53:13 +0200 Subject: [PATCH 1602/1603] hdf5 configs for 2017b toolchains --- .../h/HDF5/HDF5-1.10.1-foss-2017b.eb | 20 +++++++++++++++++++ .../h/HDF5/HDF5-1.10.1-intel-2017b.eb | 20 +++++++++++++++++++ 2 files changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.10.1-foss-2017b.eb create mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.10.1-intel-2017b.eb diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.10.1-foss-2017b.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.1-foss-2017b.eb new file mode 100644 index 0000000000..c2424386eb --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.1-foss-2017b.eb @@ -0,0 +1,20 @@ +name = 'HDF5' +version = '1.10.1' + +homepage = 'https://support.hdfgroup.org/HDF5/' +description = """HDF5 is a unique technology suite that makes possible the management of + extremely large and complex data collections.""" + +toolchain = {'name': 'foss', 'version': '2017b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['048a9d149fb99aaa1680a712963f5a78e9c43b588d0e79d55e06760ec377c172'] + +dependencies = [ + ('zlib', '1.2.11'), + ('Szip', '2.1.1'), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.10.1-intel-2017b.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.1-intel-2017b.eb new file mode 100644 index 0000000000..6b287febe5 --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.1-intel-2017b.eb @@ -0,0 +1,20 @@ +name = 'HDF5' +version = '1.10.1' + +homepage = 'https://support.hdfgroup.org/HDF5/' +description = """HDF5 is a unique technology suite that makes possible the management of + extremely large and complex data collections.""" + +toolchain = {'name': 'intel', 'version': '2017b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['048a9d149fb99aaa1680a712963f5a78e9c43b588d0e79d55e06760ec377c172'] + +dependencies = [ + ('zlib', '1.2.11'), + ('Szip', '2.1.1'), +] + +moduleclass = 'data' -- GitLab From 6588c18afba064b6011c479edafbd1df209a78d4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 25 Sep 2017 12:53:21 +0200 Subject: [PATCH 1603/1603] move up checksums in AdapterRemoval easyconfig, right below sources --- .../a/AdapterRemoval/AdapterRemoval-2.2.0-foss-2016b.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/a/AdapterRemoval/AdapterRemoval-2.2.0-foss-2016b.eb b/easybuild/easyconfigs/a/AdapterRemoval/AdapterRemoval-2.2.0-foss-2016b.eb index 9089ed3e82..6cc4080cdd 100644 --- a/easybuild/easyconfigs/a/AdapterRemoval/AdapterRemoval-2.2.0-foss-2016b.eb +++ b/easybuild/easyconfigs/a/AdapterRemoval/AdapterRemoval-2.2.0-foss-2016b.eb @@ -15,11 +15,10 @@ toolchainopts = {'pic': True} source_urls = ['https://github.com/MikkelSchubert/%(namelower)s/archive/'] sources = ['v%(version)s.tar.gz'] +checksums = ['20fdbdef2ecfd74af8d078f3f63e9444926dab1dd02b7dcef7c2aee77cb73b60'] files_to_copy = [(['build/%(name)s'], 'bin'), (['build/%(name)s.1'], 'share/man/man1')] -checksums = ['20fdbdef2ecfd74af8d078f3f63e9444926dab1dd02b7dcef7c2aee77cb73b60'] - dependencies = [ ('bzip2', '1.0.6'), ('zlib', '1.2.8'), -- GitLab